Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 91
Found at i:1245905 original size:53 final size:52
Alignment explanation
Indices: 1245765--1246416 Score: 296
Period size: 52 Copynumber: 13.1 Consensus size: 52
1245755 AGTGAAGCAA
* ** * *
1245765 AAGAAGATTTCGAGTTCCATACTCCCTAGAGAAAAAAGGGAGCGAACCCG-TTG
1 AAGAAGA-GTCGAGTTTTATACTCCCTAAAG-AAAGAGGGAGCGAACCCGTTTG
* * *
1245818 AAGATG-TTCGAGTTTTCATACT-CCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGAGTCGAGTTTT-ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * *
1245869 AAGAAGAGGTAGAGTTTTATACTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
1 AAGAAGA-GTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * *
1245922 AAGAAGA-TCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGAGT-CGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * ** *
1245974 AAGAAAATATCCGAGTTCCATACTCCCTAGAG-AA-A--GA--G-----GTTTG
1 AAGAAGA-GT-CGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
** ** ** * * * * ** *
1246017 AAGAA-ATACGAGTTCCATACTCCTAGAGAA-AGAG-GGAGCG-AACCCGTTTGAAG
1 AAGAAGAGTCGAGTTTTATACTCC-CTA-AAGAAAGAGG-GAGCGAACCCGTT--TG
* * *
1246070 AAG-A-TGTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTG
1 AAGAAGAGTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* *
1246119 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGA-GGAGCGAACCCGTTTG
1 AAGAAGA-GT-CGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * ** *
1246172 AAGAAGATTCCAGTTCCATACT-CCTAGAGAAAGA-GGAGCGAACCCG-TTG
1 AAGAAGAGTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* **
1246221 AAG-A-A-TCCAGTTCCATACT-CCT-AAG-AAGA-GGAGCGAACCCG-TTG
1 AAGAAGAGTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * **
1246265 AAGATG-TTTGAGTTCCATACT-CCT-AAGAAAGA-GGAGCGAACCCGTTTG
1 AAGAAGAGTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * ** * *
1246313 AA-AAGATTTTGAGTTCCATACT-CCTAGAGAAAGAGGGAGTGAACCCG--T-
1 AAGAAGA-GTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * *
1246361 AAGAAGATTTTCGAGTTCTATACTGCCT-GAGAAAGAGGGAGCGAACCCG-TTG
1 AAGAAGA--GTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
1246413 AAGA
1 AAGA
1246417 TTGTTCGAGT
Statistics
Matches: 495, Mismatches: 59, Indels: 91
0.77 0.09 0.14
Matches are distributed among these distances:
40 15 0.03
41 1 0.00
42 3 0.01
43 10 0.02
44 22 0.04
45 3 0.01
46 35 0.07
47 19 0.04
48 9 0.02
49 33 0.07
50 85 0.17
51 57 0.12
52 93 0.19
53 88 0.18
54 22 0.04
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (52 bp):
AAGAAGAGTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
Found at i:1246009 original size:54 final size:52
Alignment explanation
Indices: 1245765--1246416 Score: 625
Period size: 53 Copynumber: 13.1 Consensus size: 52
1245755 AGTGAAGCAA
* *
1245765 AAGAAGATTTCGAGTTCCATACTCCCTAGAGAAAAAAGGGAGCGAACCCG-TTG
1 AAGAAGA-TCCGAGTTCCATACTCCCTAGAG-AAAGAGGGAGCGAACCCGTTTG
* * *
1245818 AAGATG-TTCGAGTTTTCATACT-CCT-GAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATCCGAG-TTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTG
* ** * * *
1245869 AAGAAGAGGT-AGAGTTTTATACTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
1 AAGAAGA--TCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
1245922 AAGAAGATCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
1245974 AAGAAAATATCCGAGTTCCATACTCCCTAGAG-AA-A--GA--G-----GTTTG
1 AAG--AAGATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
1246017 AAGAA-ATACGAGTTCCATACT-CCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
1246067 AAGAAGATGTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTG
1 AAGAAGAT-CCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
1246119 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGA-GGAGCGAACCCGTTTG
1 AAGAAGA--TCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1246172 AAGAAGATTCC-AGTTCCATACT-CCTAGAGAAAGA-GGAGCGAACCCG-TTG
1 AAGAAGA-TCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1246221 AAG-A-ATCC-AGTTCCATACT-CCTA-AG-AAGA-GGAGCGAACCCG-TTG
1 AAGAAGATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* **
1246265 AAGATG-TTTGAGTTCCATACT-CCTA-AGAAAGA-GGAGCGAACCCGTTTG
1 AAGAAGATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
** *
1246313 AA-AAGATTTTGAGTTCCATACT-CCTAGAGAAAGAGGGAGTGAACCCG--T-
1 AAGAAGA-TCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
1246361 AAGAAGATTTTCGAGTTCTATACTGCCT-GAGAAAGAGGGAGCGAACCCG-TTG
1 AAGAAGA--TCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1246413 AAGA
1 AAGA
1246417 TTGTTCGAGT
Statistics
Matches: 525, Mismatches: 32, Indels: 85
0.82 0.05 0.13
Matches are distributed among these distances:
39 7 0.01
40 17 0.03
41 3 0.01
43 10 0.02
44 22 0.04
45 4 0.01
46 35 0.07
47 19 0.04
48 9 0.02
49 30 0.06
50 94 0.18
51 47 0.09
52 98 0.19
53 103 0.20
54 27 0.05
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (52 bp):
AAGAAGATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:1246035 original size:40 final size:41
Alignment explanation
Indices: 1245969--1246051 Score: 134
Period size: 39 Copynumber: 2.0 Consensus size: 41
1245959 AAGCGAACCC
1245969 GTTTGAAGAAAATATCCGAGTTCCATACTCCCTAGAGAAAGAG
1 GTTTGAAGAAAATA-CCGAGTTCCATACT-CCTAGAGAAAGAG
1246012 GTTTGAAG-AAATA-CGAGTTCCATACTCCTAGAGAAAGAG
1 GTTTGAAGAAAATACCGAGTTCCATACTCCTAGAGAAAGAG
1246051 G
1 G
1246052 GAGCGAACCC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
39 14 0.35
40 13 0.32
42 5 0.12
43 8 0.20
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (41 bp):
GTTTGAAGAAAATACCGAGTTCCATACTCCTAGAGAAAGAG
Found at i:1246136 original size:145 final size:149
Alignment explanation
Indices: 1245765--1246416 Score: 631
Period size: 145 Copynumber: 4.4 Consensus size: 149
1245755 AGTGAAGCAA
* * *
1245765 AAGAAGATTTCGAGTTCCATACTCCCTAGAGAAAAAAGGGAGCGAACCCGTT---GAAGATGTTC
1 AAGAAGA-TTCGAGTTCTATACTCCCTAGAG-AAAGAGGGAGCGAACCCGTTGAAGAAGATGTCC
* * * **
1245827 GAGTTTTCATACT-CCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAGGTAGAGTTTTATA
64 GAG-TTCCATACTCCCTAG-AGAAAGA-GGA-CG----CGTTTGAAGAAGA-TTCGAGTTCCATA
* *
1245890 CTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
120 CTCC-TAGAGAAAGAGGGAGCGAACCCG-TTG
* * * *
1245922 AAGAAGATCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTGAAGAAAATATCCG
1 AAGAAGATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTGAAGAAGATGTCCG
*
1245987 AGTTCCATACTCCCTAGAG-AA-A-GA-G-GTTTGAAGAA-ATACGAGTTCCATACTCCTAGAGA
65 AGTTCCATACTCCCTAGAGAAAGAGGACGCGTTTGAAGAAGATTCGAGTTCCATACTCCTAGAGA
1246046 AAGAGGGAGCGAACCCGTTTG
130 AAGAGGGAGCGAACCCG-TTG
1246067 AAGAAGATGTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTCCG
1 AAGAAGAT-TCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTCCG
* *
1246132 AGTTCTATACTCCCTAGAGAAAGAGGAGCGAACCCGTTTGAAGAAGATTCCAGTTCCATACTCCT
65 AGTTCCATACTCCCTAGAGAAAGAGGA-CG----CGTTTGAAGAAGATTCGAGTTCCATACTCCT
1246197 AGAGAAAGA-GGAGCGAACCCGTTG
125 AGAGAAAGAGGGAGCGAACCCGTTG
* * **
1246221 AAG-A-A-TCCAGTTCCATACT-CCTA-AG-AAGA-GGAGCGAACCCGTT---GAAGATGTTTGA
1 AAGAAGATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTCCGA
*
1246276 GTTCCATACT-CCTA-AGAAAGAGGAGCGAACCCGTTTGAA-AAGATTTTGAGTTCCATACTCCT
66 GTTCCATACTCCCTAGAGAAAGAGGA-CG----CGTTTGAAGAAGA-TTCGAGTTCCATACTCCT
*
1246338 AGAGAAAGAGGGAGTGAACCCG-T-
125 AGAGAAAGAGGGAGCGAACCCGTTG
*
1246361 AAGAAGATTTTCGAGTTCTATACTGCCT-GAGAAAGAGGGAGCGAACCCGTTGAAGA
1 AAGAAGA--TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGA
1246417 TTGTTCGAGT
Statistics
Matches: 431, Mismatches: 32, Indels: 70
0.81 0.06 0.13
Matches are distributed among these distances:
140 7 0.02
141 52 0.12
142 16 0.04
143 19 0.04
145 77 0.18
146 71 0.16
147 10 0.02
148 28 0.06
149 4 0.01
150 13 0.03
151 2 0.00
152 1 0.00
153 2 0.00
154 6 0.01
155 40 0.09
156 49 0.11
157 8 0.02
158 10 0.02
159 15 0.03
160 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (149 bp):
AAGAAGATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTCCGA
GTTCCATACTCCCTAGAGAAAGAGGACGCGTTTGAAGAAGATTCGAGTTCCATACTCCTAGAGAA
AGAGGGAGCGAACCCGTTG
Found at i:1246164 original size:198 final size:194
Alignment explanation
Indices: 1245834--1246398 Score: 664
Period size: 198 Copynumber: 2.9 Consensus size: 194
1245824 TTCGAGTTTT
* * *
1245834 CATACTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAGGTAGAGTTTTATACTCCTTAA
1 CATACTCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTAGAGTTCTATACTCCCT-A
*
1245898 AGAAAGAGGGAGCGAACCAGTTTGAAGAAGA-TCCGAGTTCTATACTCCCTAGAGAAAGAGGAAG
64 AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTCCGAGTTCTATACTCCCTAGAGAAAGAGG-AG
* *
1245962 CGAACCCGTTTGAAGAAAATATCCGAGTTCCATACTCCCTAGAGAAAGAGG-TTTGAAGAAATAC
128 CGAACCCGTTTGAAGAAGAT-TCCGAGTTCCATACT-CCTAGAGAAAGAGGCGTTGAAG-AAT-C
*
1246026 GAGTTC
189 CAGTTC
*
1246032 CATACTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTCCCTAGA
1 CATACTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTAGAGTTCTATACTCCCTA-A
1246097 GAAAGAGGGAGCGAACCCG-TTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGAGC
65 GAAAGAGGGAGCGAACCCGTTTGAAGAAGAT-TCCGAGTTCTATACTCCCTAGAGAAAGAGGAGC
1246161 GAACCCGTTTGAAGAAGATTCC-AGTTCCATACTCCTAGAGAAAGAGGAGCGAACCCGTTGAAGA
129 GAACCCGTTTGAAGAAGATTCCGAGTTCCATACTCCTAGAG-AA-A-GAG-G----CGTTGAAGA
1246225 ATCCAGTTC
186 ATCCAGTTC
* * *
1246234 CATACTCCTA-AG-AAGA-GGAGCGAACCCG-TTGAAGATG-T-TTGAGTTCCATACT-CCTAAG
1 CATACTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTAGAGTTCTATACTCCCTAAG
** * *
1246292 AAAGA-GGAGCGAACCCGTTTGAA-AAGATTTTGAGTTCCATACT-CCTAGAGAAAGAGGGAGTG
66 AAAGAGGGAGCGAACCCGTTTGAAGAAGATTCCGAGTTCTATACTCCCTAGAGAAAGA-GGAGCG
* *
1246354 AACCCG--T-AAGAAGATTTTCGAGTTCTATACTGCCT-GAGAAAGAGG
130 AACCCGTTTGAAGAAGA-TTCCGAGTTCCATACT-CCTAGAGAAAGAGG
1246399 GAGCGAACCC
Statistics
Matches: 332, Mismatches: 17, Indels: 47
0.84 0.04 0.12
Matches are distributed among these distances:
187 1 0.00
188 3 0.01
189 8 0.02
190 6 0.02
191 25 0.08
192 26 0.08
193 17 0.05
194 12 0.04
195 11 0.03
196 25 0.08
197 16 0.05
198 107 0.32
199 44 0.13
200 4 0.01
201 2 0.01
202 16 0.05
203 3 0.01
204 6 0.02
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (194 bp):
CATACTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTAGAGTTCTATACTCCCTAAG
AAAGAGGGAGCGAACCCGTTTGAAGAAGATTCCGAGTTCTATACTCCCTAGAGAAAGAGGAGCGA
ACCCGTTTGAAGAAGATTCCGAGTTCCATACTCCTAGAGAAAGAGGCGTTGAAGAATCCAGTTC
Found at i:1246444 original size:50 final size:49
Alignment explanation
Indices: 1246025--1246540 Score: 454
Period size: 50 Copynumber: 10.3 Consensus size: 49
1246015 TGAAGAAATA
* *
1246025 CGAGTTCCATACTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGA-AGATGT
1 CGAGTTCTATACTCCTA-AGAAAGAGGGAGCGAACCCG-TTGAAGATTG-T-T
* *
1246077 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTC
1 CGAGTTCTATACT-CCTA-AGAAAGAGGGAGCGAACCCGTTGAAG-A-TTGTT
*
1246130 CGAGTTCTATACTCCCTAGAGAAAGA-GGAGCGAACCCGTTTGAAGA-AGATT
1 CGAGTTCTATACT-CCTA-AGAAAGAGGGAGCGAACCCG-TTGAAGATTG-TT
* * *
1246181 CCAGTTCCATACTCCTAGAGAAAGA-GGAGCGAACCCGTTGAAGA---AT
1 CGAGTTCTATACTCCTA-AGAAAGAGGGAGCGAACCCGTTGAAGATTGTT
* *
1246227 CCAGTTCCATACTCCTAAG-AAGA-GGAGCGAACCCGTTGAAGA-TGTT
1 CGAGTTCTATACTCCTAAGAAAGAGGGAGCGAACCCGTTGAAGATTGTT
* *
1246273 TGAGTTCCATACTCCTAAGAAAGA-GGAGCGAACCCGTTTGAAAAGATT-TT
1 CGAGTTCTATACTCCTAAGAAAGAGGGAGCGAACCCG-TTG--AAGATTGTT
* * *
1246323 -GAGTTCCATACTCCTAGAGAAAGAGGGAGTGAACCCGTAAGAAGATT-TT
1 CGAGTTCTATACTCCTA-AGAAAGAGGGAGCGAACCCGT-TGAAGATTGTT
*
1246372 CGAGTTCTATACTGCCTGAGAAAGAGGGAGCGAACCCGTTGAAGATTGTT
1 CGAGTTCTATACT-CCTAAGAAAGAGGGAGCGAACCCGTTGAAGATTGTT
* * **
1246422 CGAGTTCTATACTCCTGAAGAAATA-GGAGTAGAACGATGTTGAAGATTGTT
1 CGAGTTCTATACTCCT-AAGAAAGAGGGAG-CGAAC-CCGTTGAAGATTGTT
* *
1246473 CGAG-TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGACGTTGAAGATTGTT
1 CGAGTTC-TATACTC-CT-AAGAAAGAGGGAGC-GA-AC-CCGTTGAAGATTGTT
1246527 CGAG-TCTTATACTC
1 CGAGTTC-TATACTC
1246541 TTGAAGAATA
Statistics
Matches: 413, Mismatches: 24, Indels: 52
0.84 0.05 0.11
Matches are distributed among these distances:
44 23 0.06
45 2 0.00
46 36 0.09
47 16 0.04
48 3 0.01
49 45 0.11
50 97 0.23
51 52 0.13
52 42 0.10
53 64 0.15
54 32 0.08
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (49 bp):
CGAGTTCTATACTCCTAAGAAAGAGGGAGCGAACCCGTTGAAGATTGTT
Found at i:1246484 original size:51 final size:53
Alignment explanation
Indices: 1246363--1246590 Score: 280
Period size: 51 Copynumber: 4.4 Consensus size: 53
1246353 GAACCCGTAA
* **
1246363 GAAGATT-TTCGAGT-TCTATACTGCCTG-AGAAAGAGGGAGC-GA-AC-CCGTT
1 GAAGATTGTTCGAGTCT-TATACT-CCTGAAGAAATAGGGAGCAGACACGATGTT
*
1246412 GAAGATTGTTCGAGT-TCTATACTCCTGAAGAAATA-GGAGTAGA-ACGATGTT
1 GAAGATTGTTCGAGTCT-TATACTCCTGAAGAAATAGGGAGCAGACACGATGTT
*
1246463 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGACGTT
1 GAAGATTGTTCGAGTCTTATACTC-CTGAAGAAATAGGGAGCAGACACGATGTT
*
1246517 GAAGATTGTTCGAGTCTTATACTCTTGAAG-AATAGGGAGCAGACACGAT-TT
1 GAAGATTGTTCGAGTCTTATACTCCTGAAGAAATAGGGAGCAGACACGATGTT
*
1246568 GAAGATTGTTTGAGTCTTATACT
1 GAAGATTGTTCGAGTCTTATACT
1246591 TATCTCTGAA
Statistics
Matches: 162, Mismatches: 9, Indels: 14
0.88 0.05 0.08
Matches are distributed among these distances:
49 15 0.09
50 25 0.15
51 49 0.30
52 30 0.19
53 12 0.07
54 31 0.19
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (53 bp):
GAAGATTGTTCGAGTCTTATACTCCTGAAGAAATAGGGAGCAGACACGATGTT
Found at i:1246538 original size:105 final size:101
Alignment explanation
Indices: 1246069--1246590 Score: 293
Period size: 105 Copynumber: 5.2 Consensus size: 101
1246059 CCCGTTTGAA
* * * *
1246069 GAAGA-TG-TCGAGT-TCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTGAAGAAGATGTCC
1 GAAGATTGTTCGAGTCT-TATACTGCCT-GAGAAAGAGGGAGCGAACACGTTGAAG-A-TTGTTC
*
1246131 GAGTTCTATACTCCCT-AGAGAA-AGAGGAGC-GAACCCG-TTT
62 GAGTTCTATACT-CCTGA-AGAATAG-GGAGCAG-ACACGATTT
* * * * * *
1246171 GAAGA-AGATTCCAGT-TCCATACT-CCTAGAGAAAGA-GGAGCGAACCCGTTGAAGA---ATCC
1 GAAGATTG-TTCGAGTCT-TATACTGCCT-GAGAAAGAGGGAGCGAACACGTTGAAGATTGTTCG
* * *
1246229 AGTTCCATACTCCT-AAGAAGA-GGAGC-GAACCCG--TT
63 AGTTCTATACTCCTGAAGAATAGGGAGCAG-ACACGATTT
* * * *
1246264 GAAGA-TGTTTGAGT-TCCATACT-CCTAAGAAAGA-GGAGCGAACCCGTTTGAAAAGATT-TT-
1 GAAGATTGTTCGAGTCT-TATACTGCCTGAGAAAGAGGGAGCGAACACG-TTG--AAGATTGTTC
* * * * **
1246323 GAGTTCCATACTCCT-AGAGAAAGAGGGAG-TGAACCCG-TAA
62 GAGTTCTATACTCCTGA-AG-AATAGGGAGCAG-ACACGATTT
*
1246363 GAAGATT-TTCGAGT-TCTATACTGCCTGAGAAAGAGGGAGCGAACCCGTTGAAGATTGTTCGAG
1 GAAGATTGTTCGAGTCT-TATACTGCCTGAGAAAGAGGGAGCGAACACGTTGAAGATTGTTCGAG
*
1246426 TTCTATACTCCTGAAGAAATA-GGAGTAGA-ACGATGTT
65 TTCTATACTCCTGAAG-AATAGGGAGCAGACACGAT-TT
*
1246463 GAAGATTGTTCGAGTCTTATACT-CTCTGAAGAAATAGGGAGCAGACACGACGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTGC-CTG-AGAAAGAGGGAGC-GA-AC-ACGTTGAAGATTGTT
*
1246527 CGAG-TCTTATACTCTTGAAGAATAGGGAGCAGACACGATTT
61 CGAGTTC-TATACTCCTGAAGAATAGGGAGCAGACACGATTT
*
1246568 GAAGATTGTTTGAGTCTTATACT
1 GAAGATTGTTCGAGTCTTATACT
1246591 TATCTCTGAA
Statistics
Matches: 359, Mismatches: 29, Indels: 61
0.80 0.06 0.14
Matches are distributed among these distances:
91 19 0.05
92 19 0.05
93 8 0.02
94 16 0.04
95 19 0.05
96 8 0.02
97 15 0.04
98 19 0.05
99 26 0.07
100 43 0.12
101 30 0.08
102 37 0.10
103 14 0.04
104 20 0.06
105 61 0.17
106 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (101 bp):
GAAGATTGTTCGAGTCTTATACTGCCTGAGAAAGAGGGAGCGAACACGTTGAAGATTGTTCGAGT
TCTATACTCCTGAAGAATAGGGAGCAGACACGATTT
Found at i:1246621 original size:105 final size:102
Alignment explanation
Indices: 1246363--1246621 Score: 282
Period size: 105 Copynumber: 2.5 Consensus size: 102
1246353 GAACCCGTAA
* * *
1246363 GAAGATT-TTCGAGT-TCTATACTGC-CTG-AGAAAGAGGGAGCGAACCCGTTGAAGATTGTTCG
1 GAAGATTGTTCGAGTCT-TATACT-CTCTGAAGAAATAGAGAGCGAACACGTTGAAGATTGTTCG
*
1246424 AGTTCTATACTCCTGAAGAAATAGGAGTAGAACGATGTT
64 AGTTCTATACTCCTGAAGAAATAGGAGCAGAACGATGTT
*
1246463 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGACGTTGAAGATTGTTC
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGC-GA-AC-ACGTTGAAGATTGTTC
*
1246528 GAG-TCTTATACTCTTGAAG-AATAGGGAGCAGACACGAT-TT
63 GAGTTC-TATACTCCTGAAGAAATA-GGAGCAGA-ACGATGTT
* *
1246568 GAAGATTGTTTGAGTCTTATACTTATCTCTGAA-AGAATAGAGAGCGGACACGTT
1 GAAGATTGTTCGAGTCTTATAC---TCTCTGAAGA-AATAGAGAGCGAACACGTT
1246622 TTCCGAAGAT
Statistics
Matches: 138, Mismatches: 7, Indels: 23
0.82 0.04 0.14
Matches are distributed among these distances:
100 8 0.06
101 16 0.12
102 13 0.09
103 2 0.01
104 8 0.06
105 65 0.47
106 7 0.05
107 2 0.01
108 17 0.12
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (102 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCGAACACGTTGAAGATTGTTCGAG
TTCTATACTCCTGAAGAAATAGGAGCAGAACGATGTT
Found at i:1248856 original size:21 final size:23
Alignment explanation
Indices: 1248817--1248859 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1248807 TGCAGACCTA
1248817 AATTTGTTGTTTTAATTAAAATT
1 AATTTGTTGTTTTAATTAAAATT
*
1248840 AATTT-TT-TTTTATTTAAAAT
1 AATTTGTTGTTTTAATTAAAAT
1248860 GGCAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
AATTTGTTGTTTTAATTAAAATT
Found at i:1249612 original size:16 final size:16
Alignment explanation
Indices: 1249588--1249618 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1249578 TTAGATTTAT
1249588 ATAAATTATAATATAA
1 ATAAATTATAATATAA
*
1249604 ATAATTTATAATATA
1 ATAAATTATAATATA
1249619 TGTTAAGCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAATTATAATATAA
Found at i:1252685 original size:55 final size:55
Alignment explanation
Indices: 1252596--1252935 Score: 501
Period size: 55 Copynumber: 6.3 Consensus size: 55
1252586 GGAGAATAGA
* * * * *
1252596 ACTCGAAC-ATCTTCAAAAATCGCGTCAGCTCCCTAGTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1252650 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1252705 AC-C-CACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
1252758 ACTCGAACAATCTTTATCAATCGCGTCTGCCCCCTATTTTTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1252813 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
1252868 AC-C-CACAATCTTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1252921 ACTCGAACAATCTTC
1 ACTCGAACAATCTTC
1252936 TTTTGCTTCA
Statistics
Matches: 256, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
53 96 0.38
54 12 0.05
55 148 0.58
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:1252729 original size:108 final size:110
Alignment explanation
Indices: 1252596--1252935 Score: 510
Period size: 108 Copynumber: 3.1 Consensus size: 110
1252586 GGAGAATAGA
* * * *
1252596 ACTCGAAC-ATCTTCAAAAATCGCGTCAGCTCCCTAGTCCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAAAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
1252660 TCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1252705 AC-C-CACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAAAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* *
1252768 TCTTTATCAATCGCGTCTGCCCCCTATTTTTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** *
1252813 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 ACTCGAACAATCTTCAAAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
1252876 TCTTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1252921 ACTCGAACAATCTTC
1 ACTCGAACAATCTTC
1252936 TTTTGCTTCA
Statistics
Matches: 210, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
107 2 0.01
108 155 0.74
109 4 0.02
110 49 0.23
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (110 bp):
ACTCGAACAATCTTCAAAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:1252890 original size:163 final size:163
Alignment explanation
Indices: 1252635--1252934 Score: 566
Period size: 163 Copynumber: 1.8 Consensus size: 163
1252625 TCCCTAGTCC
*
1252635 TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGT
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
*
1252700 ATAAGACCCACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
66 ATAAGACCCACAATCTTCAATAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
1252765 CAATCTTTATCAATCGCGTCTGCCCCCTATTTT
131 CAATCTTTATCAATCGCGTCTGCCCCCTATTTT
1252798 TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
1252863 ATAAGACCCACAATCTTC-ATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGA
66 ATAAGACCCACAATCTTCAAT-AATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGA
1252927 ACAATCTT
130 ACAATCTT
1252935 CTTTTGCTTC
Statistics
Matches: 134, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
162 2 0.01
163 132 0.99
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (163 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
ATAAGACCCACAATCTTCAATAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
CAATCTTTATCAATCGCGTCTGCCCCCTATTTT
Found at i:1255420 original size:10 final size:9
Alignment explanation
Indices: 1255405--1255481 Score: 73
Period size: 10 Copynumber: 7.8 Consensus size: 9
1255395 TTTTTCCTTC
1255405 TTTCTTTTCT
1 TTTCTTTT-T
1255415 TTTCTTTTT
1 TTTCTTTTT
*
1255424 TTTTTATTTT
1 TTTCT-TTTT
*
1255434 TTTCTCATTT
1 TTTCT-TTTT
1255444 TTTCTTTTT
1 TTTCTTTTT
1255453 TCTTCTTTTT
1 T-TTCTTTTT
1255463 TCTATCTTTTTT
1 T-T-TC-TTTTT
1255475 TTTCTTT
1 TTTCTTT
1255482 CATTTTTTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
9 12 0.21
10 37 0.64
11 3 0.05
12 6 0.10
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1255437 original size:29 final size:30
Alignment explanation
Indices: 1255402--1255481 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 30
1255392 CGATTTTTCC
1255402 TTCTTTCTTTTCTTTTCTTTTTT-TT-TTATT
1 TTCTTTCTTTT-TTTTCTTTTTTCTTCTT-TT
*
1255432 TT-TTTCTCATTTTTTCTTTTTTCTTCTTTT
1 TTCTTTCT-TTTTTTTCTTTTTTCTTCTTTT
*
1255462 TTCTATCTTTTTTTTTCTTT
1 TTCTTTC-TTTTTTTTCTTT
1255482 CATTTTTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
29 16 0.38
30 10 0.24
31 15 0.36
32 1 0.02
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (30 bp):
TTCTTTCTTTTTTTTCTTTTTTCTTCTTTT
Found at i:1255449 original size:39 final size:42
Alignment explanation
Indices: 1255405--1255489 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 42
1255395 TTTTTCCTTC
1255405 TTTCTTTTCTT-TTCTTTTTT-T-T-TTATTTTTTTC-TCATTT
1 TTTCTTTT-TTCTTCTTTTTTCTATCTT-TTTTTTTCTTCATTT
1255444 TTTCTTTTTTCTTCTTTTTTCTATCTTTTTTTTTCTTTCATTT
1 TTTCTTTTTTCTTCTTTTTTCTATCTTTTTTTTTC-TTCATTT
1255487 TTT
1 TTT
1255490 GCTTATATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
38 2 0.05
39 17 0.43
40 1 0.03
41 9 0.22
42 2 0.05
43 9 0.22
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (42 bp):
TTTCTTTTTTCTTCTTTTTTCTATCTTTTTTTTTCTTCATTT
Found at i:1255461 original size:17 final size:17
Alignment explanation
Indices: 1255402--1255489 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
1255392 CGATTTTTCC
*
1255402 TTCTTTCTTTTC-TTTT
1 TTCTTTTTTTTCATTTT
1255418 CTT-TTTTTTTT-ATTTTT
1 -TTCTTTTTTTTCA-TTTT
*
1255435 TTCTCATTTTTTC-TTTT
1 TTCT-TTTTTTTCATTTT
1255452 TTCTTCTTTTTTCTATCTTT
1 TTCTT-TTTTTTC-AT-TTT
*
1255472 TT-TTTTCTTTCATTTT
1 TTCTTTTTTTTCATTTT
1255488 TT
1 TT
1255490 GCTTATATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
16 14 0.24
17 24 0.41
18 12 0.21
19 3 0.05
20 5 0.09
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTTTTTTTTCATTTT
Found at i:1257742 original size:6 final size:6
Alignment explanation
Indices: 1257727--1257760 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1257717 AAACAAATAC
1257727 ATGC-A ATGCAA ATGCAA ATGCAA ATGCAA ATGCA
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCA
1257761 CGAGGTGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:1264705 original size:19 final size:19
Alignment explanation
Indices: 1264683--1264722 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1264673 AATTACTGGA
1264683 TTGTTTTGGCCTTTTCTCT
1 TTGTTTTGGCCTTTTCTCT
* *
1264702 TTGTTTTTGCCTTTTTTCT
1 TTGTTTTGGCCTTTTCTCT
1264721 TT
1 TT
1264723 TCTTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.12, T:0.70
Consensus pattern (19 bp):
TTGTTTTGGCCTTTTCTCT
Found at i:1266116 original size:75 final size:75
Alignment explanation
Indices: 1266026--1266174 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 75
1266016 ATTTAAAACC
* * *
1266026 TTTAATAGATGAGTTGGAAGATTTATGGGAA-AATGATGTTGCAACATATGATGCATAT-AGTGA
1 TTTAATAGATGAGTTGAAAGATTTAT-GAAAGAACGATGTTGCAACATATGATGCAT-TCAGTGA
1266089 TGAAAAGTTTCT
64 TGAAAAGTTTCT
* * *
1266101 TTTAATAGATGAGTTGAAAGTTTTATGAAAGAACGGTGTTGTAACATATGATGCATTCAGTGATG
1 TTTAATAGATGAGTTGAAAGATTTATGAAAGAACGATGTTGCAACATATGATGCATTCAGTGATG
1266166 AAAAGTTTC
66 AAAAGTTTC
1266175 AATTGTACGT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
74 4 0.06
75 62 0.94
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (75 bp):
TTTAATAGATGAGTTGAAAGATTTATGAAAGAACGATGTTGCAACATATGATGCATTCAGTGATG
AAAAGTTTCT
Found at i:1268499 original size:21 final size:21
Alignment explanation
Indices: 1268475--1268518 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1268465 AATTTAATTG
1268475 ATGAAGATGATGGTAATGATT
1 ATGAAGATGATGGTAATGATT
* * * *
1268496 ATGATGATGGTGGTGATGGTT
1 ATGAAGATGATGGTAATGATT
1268517 AT
1 AT
1268519 AATACTATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (21 bp):
ATGAAGATGATGGTAATGATT
Found at i:1268881 original size:2 final size:2
Alignment explanation
Indices: 1268874--1268924 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1268864 TTTGTCCATT
1268874 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1268914 TA TA TA TA TA T
1 TA TA TA TA TA T
1268925 TATTATAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1268988 original size:36 final size:35
Alignment explanation
Indices: 1268917--1269246 Score: 192
Period size: 37 Copynumber: 8.9 Consensus size: 35
1268907 TATAATATAT
*
1268917 ATATATATTATTATAG--TTTG-AAATCATTTTGAAA
1 ATATATAATA-TATAGTTTTTGAAAAT-ATTTTGAAA
*
1268951 ATTATATAATATATGAGTTTTT-TAAATATTTTGAAA
1 A-TATATAATATAT-AGTTTTTGAAAATATTTTGAAA
*
1268987 ATATATAATATATAGTTTTTGAAAACATTTTTGAAA
1 ATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
* * * * *
1269023 ATATATATTATATTG-ATTTGAAAACTTTTTTTTAAAA
1 ATATATAATATATAGTTTTTGAAAA---TATTTTGAAA
* *
1269060 TATATATAATATATAGTTTTTAAAAACATTTTTGAAAAA
1 -ATATATAATATATAGTTTTTGAAAATA-TTTTG--AAA
* *
1269099 CATATATATTATATAG-TTTTGAAAATTAGTTTTTAAAA
1 -ATATATAATATATAGTTTTTGAAAA-TA--TTTTGAAA
* *
1269137 ATATATATTATATAG-TTTTGAAAATTAGTTTTTAATA
1 ATATATAATATATAGTTTTTGAAAA-TA-TTTTGAA-A
*
1269174 TATATATATATATTATA-TAGTTTTGAAAATTAGTTTTTAAAA
1 -ATATATA-ATA-TATAGT--TTTTGAAAA-TA--TTTTGAAA
* *
1269216 ATATATATTATATA-ATTTTGAAAATTATTTT
1 ATATATAATATATAGTTTTTGAAAA-TATTTT
1269247 TTTAAAAAAT
Statistics
Matches: 243, Mismatches: 28, Indels: 49
0.76 0.09 0.15
Matches are distributed among these distances:
34 11 0.05
35 38 0.16
36 37 0.15
37 58 0.24
38 31 0.13
39 31 0.13
40 11 0.05
41 7 0.03
42 13 0.05
43 6 0.02
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:1269104 original size:37 final size:37
Alignment explanation
Indices: 1268943--1269314 Score: 208
Period size: 39 Copynumber: 9.9 Consensus size: 37
1268933 TTTGAAATCA
* * *
1268943 TTTTGAAAATTATATAATATATGAGTTTTT-TAAATA-
1 TTTTGAAAAATATATAATATAT-AGTTTTTAAAAACAT
*
1268979 TTTTG-AAAATATATAATATATAGTTTTTGAAAACAT
1 TTTTGAAAAATATATAATATATAGTTTTTAAAAACAT
* * * * *
1269015 TTTTG-AAAATATATATTATATTG-ATTTGAAAACTTT
1 TTTTGAAAAATATATAATATATAGTTTTTAAAAAC-AT
*
1269051 TTTTTAAAATATATATAATATATAGTTTTTAAAAACAT
1 TTTTGAAAA-ATATATAATATATAGTTTTTAAAAACAT
* * **
1269089 TTTTGAAAAACATATATATTATATAGTTTTGAAAATTAGT
1 TTTTG-AAAA-ATATATAATATATAGTTTTTAAAAACA-T
* * **
1269129 TTTT-AAAAATATATATTATATAGTTTTGAAAATTAGT
1 TTTTGAAAAATATATAATATATAGTTTTTAAAAACA-T
* **
1269166 TTTT-AATATATATATATATATTATATAGTTTTGAAAATTAGT
1 TTTTGAA-A-A-ATATATA-A-TATATAGTTTTTAAAAACA-T
* * * **
1269208 TTTT-AAAAATATATATTATATAATTTTGAAAATTATTT
1 TTTTGAAAAATATATAATATATAGTTTTTAAAA--ACAT
* * * * * **
1269246 TTTTAAAAAATATGTATTATATGGTTTTGAAAATTAT
1 TTTTGAAAAATATATAATATATAGTTTTTAAAAACAT
* *
1269283 TTTTTAAAACATATAT--TGTATAG-TTTTAAAAA
1 TTTTGAAAA-ATATATAATATATAGTTTTTAAAAA
1269315 TGTTTTAATT
Statistics
Matches: 284, Mismatches: 35, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
34 7 0.02
35 35 0.12
36 36 0.13
37 63 0.22
38 33 0.12
39 69 0.24
40 13 0.05
41 1 0.00
42 27 0.10
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTTGAAAAATATATAATATATAGTTTTTAAAAACAT
Found at i:1270614 original size:32 final size:32
Alignment explanation
Indices: 1270535--1270602 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
1270525 AAAATTATTT
* * *
1270535 TTTTAATGTTTTTATTTCTCATTTTCTTCCTTAC
1 TTTTAATATTTTT-TAT-TCATTTTCTTCCTTAA
1270569 TTTTAATATTTTTTATTCATTTTC-TCCTTAA
1 TTTTAATATTTTTTATTCATTTTCTTCCTTAA
1270600 TTT
1 TTT
1270603 ATTTATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 9 0.29
32 8 0.26
33 2 0.06
34 12 0.39
ACGTcount: A:0.18, C:0.15, G:0.01, T:0.66
Consensus pattern (32 bp):
TTTTAATATTTTTTATTCATTTTCTTCCTTAA
Found at i:1271724 original size:15 final size:16
Alignment explanation
Indices: 1271697--1271726 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1271687 CCTCACTAAT
1271697 TCTTTTAATTTTGTTC
1 TCTTTTAATTTTGTTC
1271713 TCTTTT-ATTTTGTT
1 TCTTTTAATTTTGTT
1271727 TTCATCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (16 bp):
TCTTTTAATTTTGTTC
Found at i:1274261 original size:95 final size:94
Alignment explanation
Indices: 1274069--1274312 Score: 278
Period size: 95 Copynumber: 2.7 Consensus size: 94
1274059 TATAATATTA
* *
1274069 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCAGACTTTATGGA
1 TATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGAAATTGGTTAAACACCCAGACTTTATGGA
* * *
1274134 TAATATTCAGCTAGCATGATAAATGTACT
66 TAAGATTCAGCTAACATGATAAAGGTACT
* * *
1274163 TATACTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGAAATTGGTTAAACGCCCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GAAATTGGTTAAACACCCAGACTTTATG
* *
1274227 GATAAGATTCAGCTAACGTGATAAAGGT-GT
64 GATAAGATTCAGCTAACATGATAAAGGTACT
* *
1274257 T-TATAT---ATTAAG--T----TGTCCCTCTAGAGAAATTGGTTAAACTCCCAGACTTTATGGA
1 TATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGAAATTGGTTAAACACCCAGACTTTATGGA
1274312 T
66 T
1274313 CCAGCTAGCC
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
83 38 0.29
84 1 0.01
87 1 0.01
89 5 0.04
92 3 0.02
93 2 0.02
94 7 0.05
95 76 0.57
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGAAATTGGTTAAACACCCAGACTTTATGGA
TAAGATTCAGCTAACATGATAAAGGTACT
Found at i:1275883 original size:248 final size:248
Alignment explanation
Indices: 1275442--1276922 Score: 1851
Period size: 248 Copynumber: 6.0 Consensus size: 248
1275432 TTTAAGACAA
* * * * * *
1275442 CATTTGCAGCATAACTCAAGACTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCTTCGAGTTCGACTACA
* * * * * * *
1275507 CTCAGC-TCCAAGGCGCATCATTTGA-AGCATAGCTTAAGTCGAGAAGGGCTATATGCTTACCAA
63 CTCAGCTTCGAAGGCACATCATTT-ACAGCATAACTCAAGGCGAGAAGGGTTATCT-CTTACCAA
* *
1275570 AGACCTTCT-AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGTATAACTTAAGTCGAG
126 AGACCTT-TGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
* * *
1275634 AAGGGTTATCTGTCAACCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAAGCGTAT
190 AAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCAT
* *
1275693 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * * * *
1275758 AGCTTTGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTTACCAAAGACC
66 AGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTCTTACCAAAGACC
1275823 TTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
131 TTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
* * * *
1275888 TATCTGTCAACCAAAGACCTTCGAGTTTGACTACGGTCAGCTCCAAGACGTAT
196 TATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCAT
* *
1275941 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * * *
1276006 AGCTTTGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTCTTACCAAAGACC
66 AGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTCTTACCAAAGACC
* *
1276071 TTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGTATAACTTAAGTCGAGAAGGGT
131 TTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
* * *
1276136 TATCTGTCAACCAAAGACCTTCGTGTTCGACTACGCTCAGCTCCAAGGTGAAT
196 TATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCAT
*
1276189 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * *
1276254 AGCTTCGAGGGCACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT-TTCACCAAAGAC
66 AGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTCTT-ACCAAAGAC
* *
1276318 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGG
130 CTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* *
1276383 TTATCTG----CCAAAGACCCTCAAGTTCGACTACGCTCAGCTCCAAGGCGCAT
195 TTATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCAT
*
1276433 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCTGCCAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA--T--CTGCCAAAGACCTTCGAGTTCGACTAC
* * * * * * * **
1276498 GCTCAGC-TCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTCCCAACCAA
62 ACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCT-CTTACCAA
* *
1276562 AGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCGTATCATTTGCAGCATAACTTAAGTCGAGA
126 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGA
* * * * * * * *
1276627 AGGGCTATC--T--ACCAAAGACCCTCGAGTTCAATTACACTCAGCTTCGAGGGCACAT
191 AGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCGCAT
** * * * * * * * *
1276682 CATTTATAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCTTCGAGTTCGACTACA
* * * * * **
1276747 CTCAGC-TCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAA
63 CTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCT-CTTACCAAA
* * *
1276811 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
127 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAA
* * * *
1276876 AGGCTATCT-TCCTACCAAAGACCTTCGCGTTCGA-TGACGCTCAGCTC
192 GGGTTATCTGT-CAACCAAAGACCTTCGAGTTCGACT-ACGCTCAGCTC
1276923 AGAGGCAAAC
Statistics
Matches: 1111, Mismatches: 98, Indels: 42
0.89 0.08 0.03
Matches are distributed among these distances:
244 71 0.06
245 3 0.00
246 1 0.00
247 43 0.04
248 861 0.77
249 70 0.06
250 1 0.00
251 35 0.03
252 26 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (248 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
AGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTCTTACCAAAGACC
TTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
TATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCAT
Found at i:1276929 original size:84 final size:83
Alignment explanation
Indices: 1275442--1276922 Score: 1618
Period size: 84 Copynumber: 17.9 Consensus size: 83
1275432 TTTAAGACAA
* * * * * *
1275442 CATTTGCAGCATAACTCAAGACTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
**
1275507 CTCAGCTCCAAGGCGCAT
66 CTCAGCTCCAAGGCATAT
* * * * * *
1275525 CATTTGAAGCATAGCTTAAGTCGAGAAGGGCTATATGCTTACCAAAGACCTTCTAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTC-TACCAAAGACCTTCGAGTTCGACTAC
1275590 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCATAT
* * * *
1275609 CATTTGTAGTATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACATTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
* *
1275674 GCTCAGCTCCAAAGCGTAT
65 GCTCAGCTCCAAGGCATAT
* * * * * *
1275693 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA---TCTGCCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
** * *
1275755 CTCAGCTTTGAGGGCACAT
66 CTCAGC-TCCAAGGCATAT
* * * * * *
1275774 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGT-TACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
1275838 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCATAT
* *
1275857 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
* * *
1275922 GGTCAGCTCCAAGACGTAT
65 GCTCAGCTCCAAGGCATAT
* * * * * *
1275941 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA---TCTGCCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
** * *
1276003 CTCAGCTTTGAGGGCACAT
66 CTCAGC-TCCAAGGCATAT
* * * * * *
1276022 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATC-TCTTACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTC-TACCAAAGACCTTCGAGTTCGACTAC
1276086 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCATAT
* * * *
1276105 CATTTACAGTATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGTGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
*
1276170 GCTCAGCTCCAAGGTGA-AT
65 GCTCAGCTCCAAGG-CATAT
* * * * *
1276189 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA---TCTGCCAAAGACCTTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
* * *
1276251 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCATAT
* * * * *
1276270 TATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTT-TCACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCT-ACCAAAGACCTTCGAGTTCGACTAC
1276334 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCATAT
* * * *
1276353 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTA---TCTGCCAAAGACCCTCAAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
**
1276415 CTCAGCTCCAAGGCGCAT
66 CTCAGCTCCAAGGCATAT
* * * * *
1276433 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCTGCCAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
1276498 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCATAT
* * * * *
1276517 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTCCCAACCAAAGACCTTTGAGTTCAACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
*
1276582 GCTCAGCTCCAAGGCGTAT
65 GCTCAGCTCCAAGGCATAT
* * * * *
1276601 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTA---TCTACCAAAGACCCTCGAGTTCAATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
* * *
1276663 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCATAT
** * * * * *
1276682 CATTTATAGTATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
*
1276746 GCTCAGCTCTAAGGCATAT
65 GCTCAGCTCCAAGGCATAT
* *
1276765 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCTACCAAAGACCTTCGAGTTCGACTAC
*
1276830 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCATAT
* * * *
1276849 CATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTTCCTACCAAAGACCTTCGCGTTCGA-TGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT-CTACCAAAGACCTTCGAGTTCGACT-A
1276913 CGCTCAGCTC
64 CGCTCAGCTC
1276923 AGAGGCAAAC
Statistics
Matches: 1163, Mismatches: 201, Indels: 67
0.81 0.14 0.05
Matches are distributed among these distances:
80 187 0.16
81 132 0.11
83 192 0.17
84 645 0.55
85 7 0.01
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCTACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCATAT
Found at i:1277366 original size:21 final size:20
Alignment explanation
Indices: 1277342--1277387 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1277332 TTTTATTCAC
*
1277342 TTTTTTCAATT-TATTTTTAA
1 TTTTTTAAATTCTATTTTT-A
1277362 TTTTTTAAATTCTATTTTTA
1 TTTTTTAAATTCTATTTTTA
1277382 TTTTTT
1 TTTTTT
1277388 TATCTAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTAAATTCTATTTTTA
Found at i:1277388 original size:21 final size:20
Alignment explanation
Indices: 1277342--1277389 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1277332 TTTTATTCAC
*
1277342 TTTTTTCAATTTATTTTTAA
1 TTTTTTAAATTTATTTTTAA
*
1277362 TTTTTTAAATTCTATTTTTAT
1 TTTTTTAAATT-TATTTTTAA
1277383 TTTTTTA
1 TTTTTTA
1277390 TCTAACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTAAATTTATTTTTAA
Found at i:1277520 original size:12 final size:13
Alignment explanation
Indices: 1277498--1277526 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1277488 CAAATCGATG
1277498 TTTTAAATTTTAA
1 TTTTAAATTTTAA
1277511 TTTT-AATTTTAA
1 TTTTAAATTTTAA
1277523 TTTT
1 TTTT
1277527 CACAACTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1280579 original size:38 final size:40
Alignment explanation
Indices: 1280499--1280581 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 40
1280489 TAACAAGTTG
* *
1280499 AAAAATATTTATATATTTTCTTTTAAAAATTTAAATTCAT
1 AAAAATATTTATATATTTTCTTTTAAAAATTGAAAATCAT
1280539 AAAAAT-TTTATA-ATTTT-TATTTACAAAATTGAAAAT-AT
1 AAAAATATTTATATATTTTCT-TTTA-AAAATTGAAAATCAT
1280577 AAAAA
1 AAAAA
1280582 GGTTTAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 1 0.03
38 16 0.41
39 16 0.41
40 6 0.15
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (40 bp):
AAAAATATTTATATATTTTCTTTTAAAAATTGAAAATCAT
Found at i:1282495 original size:182 final size:182
Alignment explanation
Indices: 1282168--1282852 Score: 968
Period size: 182 Copynumber: 3.8 Consensus size: 182
1282158 ACTTTATGTT
* * * * *
1282168 GACCTATTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTCATAAAGTGTCG
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCG
*
1282233 ACAC-TTTTAGGCGCTATAACTTC-T-TCTTTTAAATTCAAAAAGTGTCAATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAAT
* *
1282295 TATCGACACTTTCAACATATCCGATATCCTTTTACCGGTTTTGTCATTTTGA
131 TATCGACACTTGCAACATATCCGATATCGTTTTACCGGTTTTGTCATTTTGA
* *
1282347 GACCGATTTTGTCATATTTTTAACTGTTATATTGTTAT-GTATCGATACATTTT-TTAAAAGTAT
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAG-ATCGATACATTTTCAT-AAAGTAT
* * *
1282410 AGACACTTTTTAGGCGCTATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAA
64 CGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAA
* * * *
1282475 ATTATCGACACTTGCAACATATCAGGTAGCGTTTTACCGGTATTGTCATTTTGA
129 ATTATCGACACTTGCAACATATCCGATATCGTTTTACCGGTTTTGTCATTTTGA
* *
1282529 GACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCG
1282594 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAAT
* * *
1282659 TATCGACACTTGCAACGTATCC-ACAATCGTTTTACCCGTTTTGTCATTTTGA
131 TATCGACACTTGCAACATATCCGA-TATCGTTTTACCGGTTTTGTCATTTTGA
** ** * * * **
1282711 GATTGGCTTTGTCATATTTTTACCTGTAATATTTTTATGGATCGATACATTTTTTTTAAAAGTAT
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACA-TTTTCAT-AAAGTAT
* * *
1282776 CGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTTATTTCCAAAAGTGTCGATACTTATATTAA
64 CGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAA
*
1282841 AGTATCGACACT
129 ATTATCGACACT
1282853 GTTAATTTAC
Statistics
Matches: 454, Mismatches: 42, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
178 2 0.00
179 59 0.13
180 18 0.04
181 1 0.00
182 288 0.63
183 7 0.02
184 79 0.17
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCG
ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAAT
TATCGACACTTGCAACATATCCGATATCGTTTTACCGGTTTTGTCATTTTGA
Found at i:1286778 original size:199 final size:199
Alignment explanation
Indices: 1286542--1287528 Score: 1541
Period size: 199 Copynumber: 5.0 Consensus size: 199
1286532 GTAAAAAGTA
* * * * * *
1286542 TCGATACATTATGTAGACCTATTTGCTCATAAAATCGGTATATTTAGACCGGTTACATTGTTAAT
1 TCGATACTTTTTGTACACCTGTTTTCTCA-AAAACCGGTATATTTAGACCGGTTACATTGTTAAT
* ** * *
1286607 TTACCTATTACACTAT-ATCTATGTATTTCGATGTTTTTAGTATCGACACTTCTTATAAATGTAT
65 TTACCTATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTAT
* * * *
1286671 CGACACGTTTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGAATCGAAACTTGTTTTA
129 CGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTA
1286736 TTTGTG
194 TTTGTG
* * * *
1286742 TCGATACTTTTTGTACACATGTTTTCTCATAAATCGGTATATTTAGACCGTTTACATTGTTAATT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATT
*
1286807 TACCTATTAC-TTCATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATGTATC
66 TACCTATTACATT-ATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATC
* * *
1286871 GACAC-GTTTAGTGCATTTGGTTTTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTTTAT
130 GACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTAT
1286935 TTGTG
195 TTGTG
* *
1286940 TCGATAC-TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCAGTTAAATTGTTAATT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATT
* *
1287004 TACCTAGTAGATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
*
1287069 ACACTTTTTAGTGCACCTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
1287134 TGTG
196 TGTG
* * *
1287138 TTGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTTTTAATT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATT
* *
1287203 TACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTCTTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
*
1287268 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACCCTTGTTTTATT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
1287333 TGTG
196 TGTG
** * * *
1287337 TCGATACTTTTTGTACAGTTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTTTTAATT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATT
* *
1287402 TACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
*
1287467 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTTT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTT
1287529 CTCAAAAACT
Statistics
Matches: 731, Mismatches: 51, Indels: 11
0.92 0.06 0.01
Matches are distributed among these distances:
197 114 0.16
198 135 0.18
199 457 0.63
200 25 0.03
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (199 bp):
TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATT
TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
TGTG
Found at i:1287129 original size:396 final size:398
Alignment explanation
Indices: 1286542--1287528 Score: 1550
Period size: 396 Copynumber: 2.5 Consensus size: 398
1286532 GTAAAAAGTA
* * * * * *
1286542 TCGATACATTATGTAGACCTATTTGCTCATAAAATCGGTATATTTAGACCGGTTACATTGTTAAT
1 TCGATACATTTTGTACACCTGTTTTCTCA-AAAACCGGTATATTTAGACCGGTTAAATTGTTAAT
* ** * *
1286607 TTACCTATTACACTAT-ATCTATGTATTTCGATGTTTTTAGTATCGACACTTCTTATAAATGTAT
65 TTACCTATTACATTATAAT-TATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTAT
* * * *
1286671 CGACACGTTTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGAATCGAAACTTGTTTTA
129 CGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTA
* * * *
1286736 TTTGTGTCGATACTTTTTGTACACATGTTTTCTCATAAATCGGTATATTTAGACCGTTTACATTG
194 TTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTG
* *
1286801 TTAATTTACCTATTAC-TTCATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAA
259 TTAATTTACCTAGTACATT-ATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAA
*
1286865 TGTATCGACAC-GTTTAGTGCATTTGGTTTTGAAATACATTCTGAACCAAAAGTATCGACACTTG
323 TGTATCGACACTGTTTAGTGCACTTGGTTTTGAAATACATTCTGAACCAAAAGTATCGACACTTG
1286929 TTTTATTTGTG
388 TTTTATTTGTG
*
1286940 TCGATAC-TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCAGTTAAATTGTTAATT
1 TCGATACATTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTAAATTGTTAATT
* *
1287004 TACCTAGTAGATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
*
1287069 ACACTTTTTAGTGCACCTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
* * *
1287134 TGTGTTGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTTTT
196 TGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTT
*
1287199 AATTTACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTCTTATAAATGT
261 AATTTACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGT
* * *
1287264 ATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACCCTTGTTT
326 ATCGACACTGTTTAGTGCACTTGGTTTTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTT
1287329 TATTTGTG
391 TATTTGTG
* ** * *
1287337 TCGATACTTTTTGTACAGTTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTTTTAATT
1 TCGATACATTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTAAATTGTTAATT
* *
1287402 TACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
66 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
*
1287467 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTTT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTT
1287529 CTCAAAAACT
Statistics
Matches: 541, Mismatches: 44, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
396 273 0.50
397 88 0.16
398 180 0.33
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (398 bp):
TCGATACATTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTAAATTGTTAATT
TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
TGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTT
AATTTACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGT
ATCGACACTGTTTAGTGCACTTGGTTTTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTT
TATTTGTG
Found at i:1287631 original size:167 final size:167
Alignment explanation
Indices: 1287355--1287695 Score: 610
Period size: 167 Copynumber: 2.0 Consensus size: 167
1287345 TTTTGTACAG
* *
1287355 TTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTTTTAATTTACCTATTACATCATAAT
1 TTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTAGTACATCATAAT
*
1287420 TATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTT
66 TATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTT
*
1287485 GGTTTTGAAATACATTTTGGACCAAAAGTATCGACAC
131 GGTTTTGAAATACATTCTGGACCAAAAGTATCGACAC
* * * *
1287522 TTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTAGTACATTATAAT
1 TTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTAGTACATCATAAT
1287587 TATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTT
66 TATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTT
1287652 GGTTTTGAAATACATTCTGGACCAAAAGTATCGACAC
131 GGTTTTGAAATACATTCTGGACCAAAAGTATCGACAC
1287689 TTGTTTT
1 TTGTTTT
1287696 ATTTGTGTCG
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (167 bp):
TTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTAGTACATCATAAT
TATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTT
GGTTTTGAAATACATTCTGGACCAAAAGTATCGACAC
Found at i:1287829 original size:366 final size:366
Alignment explanation
Indices: 1287152--1287836 Score: 1208
Period size: 366 Copynumber: 1.9 Consensus size: 366
1287142 TACTTTTTGT
*
1287152 ACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTTTTAATTTACCTAGTACATTA
1 ACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTACCTAGTACATTA
* * *
1287217 TAATTATGGGTTTCGATGTTTTTGGGATCGATACTTCTTATAAATGTATCGACACTTTTTAGTGC
66 TAATTATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGC
* *
1287282 ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACCCTTGTTTTATTTGTGTCGATACTTT
131 ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACGTT
** * *
1287347 TTGTACAGTTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTTTTAATTTACCTATTAC
196 TTGTACACCTATTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTATTAC
*
1287412 ATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTA
261 ATCATAATAATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTA
1287477 GTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCG
326 GTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCG
* * *
1287518 ACACTTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTAGTACATTA
1 ACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTACCTAGTACATTA
1287583 TAATTATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGC
66 TAATTATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGC
1287648 ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACGTT
131 ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACGTT
* *
1287713 TTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTAC
196 TTGTACACCTATTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTATTAC
* *
1287778 ATTATAATAATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCGACAC
261 ATCATAATAATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACAC
1287837 ATAAGTTTAC
Statistics
Matches: 301, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
366 301 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (366 bp):
ACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATTTACCTAGTACATTA
TAATTATAGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGC
ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACGTT
TTGTACACCTATTTTCTCAAAAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTATTAC
ATCATAATAATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTA
GTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCG
Found at i:1288221 original size:19 final size:18
Alignment explanation
Indices: 1288193--1288240 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1288183 ATACATTCAC
1288193 ATAC-AAATTATAAATCGT
1 ATACAAAATTA-AAATCGT
*
1288211 ATACAAAATTAAAATCTT
1 ATACAAAATTAAAATCGT
1288229 ATACAAAATTAA
1 ATACAAAATTAA
1288241 CCCTACATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTAAAATCGT
Found at i:1290384 original size:22 final size:21
Alignment explanation
Indices: 1290356--1290411 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
1290346 AACCTGCATT
*
1290356 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
1290378 TATAATAACTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
1290402 TATAAAAAAA
1 TATAATAAAA
1290412 ACAAAGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:1291711 original size:18 final size:18
Alignment explanation
Indices: 1291670--1291736 Score: 89
Period size: 19 Copynumber: 3.6 Consensus size: 18
1291660 CATTTATACA
* *
1291670 ACCTAAAATATTATTTTCT
1 ACCTATAATATCATTTT-T
1291689 ACCTATAATATCATTTTT
1 ACCTATAATATCATTTTT
1291707 ACCTATAATATCATTTTTT
1 ACCTATAATATCA-TTTTT
*
1291726 ACATATAATAT
1 ACCTATAATAT
1291737 TAAATAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 14 0.32
19 30 0.68
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (18 bp):
ACCTATAATATCATTTTT
Found at i:1292187 original size:20 final size:18
Alignment explanation
Indices: 1292141--1292190 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
1292131 CCGGTAGCGC
*
1292141 TTTACCGGTTTTTTCATT
1 TTTACCTGTTTTTTCATT
1292159 TTTAGACCTGTTTTGTTCTATT
1 TTT--ACCTGTTTT-TTC-ATT
1292181 TTTACCTGTT
1 TTTACCTGTT
1292191 ATATTGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.11
20 15 0.56
21 3 0.11
22 6 0.22
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (18 bp):
TTTACCTGTTTTTTCATT
Found at i:1292314 original size:182 final size:180
Alignment explanation
Indices: 1292103--1293665 Score: 2009
Period size: 182 Copynumber: 8.6 Consensus size: 180
1292093 TACGCGTACT
* * * *
1292103 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTTTCATTTTTAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
*
1292168 GTTTTGTTCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGCATCGACACT
66 GTTTTG-TCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
1292233 TTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
130 TT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* ** * *
1292285 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
* *** *
1292350 GTTTTGTC-ATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTCGACAC
66 GTTTTGTCTAT-TTTTA-CCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
* *
1292414 GTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTA
129 -TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
1292467 TATTAAATTATCGATACTTTCAACATATCCGGTAGC-AGTTTACCGGTTTTGTCATTTTTAGA-T
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGA-TTTACCTGTTTTGTCATTTTTAGACC
* *
1292530 TGGTTTTGTCCTATTTTTACCTGTCATATT-TCTATAGATCGATACA-TTTTTTAAAGTATCGAC
65 T-GTTTTGT-CTATTTTTACCTGTTATATTGT-TATGGATCGATACATTTTTTTAAAGTATCGAC
*
1292593 ACTTTGTAGGCGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
127 ACTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * ** * * *
1292648 TATTAAAGTATCGACACTTTCAATATATCCGGTAGTTATTTACCTATTTTATCATTTTGAGACC-
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
* *
1292712 GATTTTGTC-ATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTGTCGACA
66 G-TTTTGTCTAT-TTTTA-CCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACA
* * *
1292776 CGCTTTAGGCGCTATAACTTCTTCTTTTTTAAATT-TAGAAAGTGTCGATACTTA
128 C-TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* * **
1292830 TATTAAATTATCGACACTTTCAATATATCCGGTATC-ATTTTACAGGTTTTGTCATTTTTAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGA-TTTACCTGTTTTGTCATTTTTAGACC
1292894 TGTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
65 TGTTTTGT-CTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
1292959 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
129 TTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * *
1293012 TATTAAATTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
* * * *** *
1293077 GTTTTGTC-ATAGTTTAGGCTGTTATATTGTTATGGATTGATACATTTGCATAAAGTGTCGACAC
66 GTTTTGTCTAT-TTTTA-CCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
*
1293141 GTTTTAGGCG-------TTCTTCTCTTTTAAATT-CAGAAAATGTCGATACTTA
129 -TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
** * * * *
1293187 TATTAAATTATCGACACTTTCAACATATTTGGTACCGCTTTACCGGTTTTGTCATTTTTAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
1293252 GTTTTGTCCTATTTTTACCTGTTATATT-TCTATGGATCGATACATTTTTTTAAAGTATCGACAC
66 GTTTTGT-CTATTTTTACCTGTTATATTGT-TATGGATCGATACATTTTTTTAAAGTATCGACAC
*
1293316 TTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTA
129 TTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* ** *
1293369 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACC-
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
* * * **
1293433 GATTTTATC-ATATTTTAGGCTGTTATATTGTTATGGATCGATATATTTTTTTAAAAACATCGAC
66 G-TTTTGTCTAT-TTTTA-CCTGTTATATTGTTATGGATCGATACATTTTTTT-AAAGTATCGAC
* *
1293497 ACTTTTTAGGCGCTGTAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATATTTA
127 AC-TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* * *
1293552 TATTAAATTATCGACACTTTCAACATATCTGATAGCGCTTTACCTGTTTTGTCATTTTTAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
* *
1293617 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATAGATACATTTTT
66 GTTTTGTC-TATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1293666 CATTTGTATC
Statistics
Matches: 1206, Mismatches: 124, Indels: 101
0.84 0.09 0.07
Matches are distributed among these distances:
174 6 0.00
175 141 0.12
176 5 0.00
177 2 0.00
179 2 0.00
180 16 0.01
181 166 0.14
182 682 0.57
183 171 0.14
184 13 0.01
185 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (180 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTTAGACCT
GTTTTGTCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTT
TTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:1292769 original size:363 final size:364
Alignment explanation
Indices: 1292103--1293665 Score: 2477
Period size: 363 Copynumber: 4.3 Consensus size: 364
1292093 TACGCGTACT
* *
1292103 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTTTCATTTTTAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTTAGACCT
* *
1292168 GTTTTGTTCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGCATCGACACT
66 GTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
1292233 TTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
*
1292298 ACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATATT
196 ACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGATTTTGTCATATT
1292363 TTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTCGACACGTTTTAGGCGCTAT
261 TTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTCGACACGTTTTAGGCGCTAT
*
1292428 AACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTA
326 AACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
* *
1292467 TATTAAATTATCGATACTTTCAACATATCCGGTAGCAG-TTTACCGGTTTTGTCATTTTTAGA-T
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGC-GCTTTACCGGTTTTGTCATTTTTAGACC
* *
1292530 TGGTTTTGTCCTATTTTTACCTGTCATATT-TCTATAGATCGATACA-TTTTTTAAAGTATCGAC
65 T-GTTTTGTCCTATTTTTACCTGTTATATTGT-TATGGATCGATACATTTTTTTAAAGTATCGAC
* *
1292593 ACTTTGTAGGCGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTA
128 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTA
* * *
1292658 TCGACACTTTCAATATATCCGGTAGTTATTTACCTATTTTATCATTTTGAGACCGATTTTGTCAT
193 TCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGATTTTGTCAT
*** *
1292723 ATTTTAGGCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTGTCGACACGCTTTAGGCGC
258 ATTTTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTCGACACGTTTTAGGCGC
* * *
1292788 TATAACTTCTTCTTTTTTAAATTTAGAAAGTGTCGATACTTA
323 TATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
* * ** *
1292830 TATTAAATTATCGACACTTTCAATATATCCGGTATCATTTTACAGGTTTTGTCATTTTTAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTTAGACCT
1292895 GTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
66 GTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
1292960 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
* *
1293025 ACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATAGT
196 ACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGATTTTGTCATATT
*
1293090 TTAGGCTGTTATATTGTTATGGATTGATACATTTGCATAAAGTGTCGACACGTTTTAGGCG----
261 TTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTCGACACGTTTTAGGCGCTAT
1293151 ---TTCTTCTCTTTTAAATTCAGAAAA-TGTCGATACTTA
326 AACTTCTTCTCTTTTAAATTCA-AAAAGTGTCGATACTTA
** * *
1293187 TATTAAATTATCGACACTTTCAACATATTTGGTACCGCTTTACCGGTTTTGTCATTTTTAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTTAGACCT
1293252 GTTTTGTCCTATTTTTACCTGTTATATT-TCTATGGATCGATACATTTTTTTAAAGTATCGACAC
66 GTTTTGTCCTATTTTTACCTGTTATATTGT-TATGGATCGATACATTTTTTTAAAGTATCGACAC
* *
1293316 TTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAAGTATC
130 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATC
*
1293381 GACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGATTTTATCATAT
195 GACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGATTTTGTCATAT
* *** *** *
1293446 TTTAGGCTGTTATATTGTTATGGATCGATATATTTTTTTAAAAACATCGACACTTTTTAGGCGCT
260 TTTAGGCTGTTATATTGTTATGGATCGATACATTTGCAT-AAAGTGTCGACACGTTTTAGGCGCT
* * *
1293511 GTAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATATTTA
324 ATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
* * *
1293552 TATTAAATTATCGACACTTTCAACATATCTGATAGCGCTTTACCTGTTTTGTCATTTTTAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTTAGACCT
* * *
1293617 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATAGATACATTTTT
66 GTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1293666 CATTTGTATC
Statistics
Matches: 1100, Mismatches: 80, Indels: 37
0.90 0.07 0.03
Matches are distributed among these distances:
356 1 0.00
357 306 0.28
358 22 0.02
363 336 0.31
364 299 0.27
365 135 0.12
366 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (364 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTTAGACCT
GTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
ACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGATTTTGTCATATT
TTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTCGACACGTTTTAGGCGCTAT
AACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTA
Found at i:1293618 original size:20 final size:21
Alignment explanation
Indices: 1293593--1293631 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1293583 ATAGCGCTTT
1293593 ACCTGTTTTGTCAT-TTTTAG
1 ACCTGTTTTGTCATATTTTAG
1293613 ACCTGTTTTGTCATATTTT
1 ACCTGTTTTGTCATATTTT
1293632 TACCTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.56
Consensus pattern (21 bp):
ACCTGTTTTGTCATATTTTAG
Found at i:1293636 original size:20 final size:19
Alignment explanation
Indices: 1293590--1293636 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1293580 CTGATAGCGC
1293590 TTTACCTGTTTTGTCATTT
1 TTTACCTGTTTTGTCATTT
*
1293609 TTAGACCTGTTTTGTCATATT
1 TT-TACCTGTTTTGTCAT-TT
1293630 TTTACCT
1 TTTACCT
1293637 ATTATATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 4 0.17
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTACCTGTTTTGTCATTT
Found at i:1296919 original size:44 final size:44
Alignment explanation
Indices: 1296851--1296947 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
1296841 CCATGATCGA
** ** *
1296851 TATCGATACTACTTTACATTGTAGTATCAATACTCCCTGGACGG
1 TATCGATACTACACTACAAAGTAGTATCAATACTCCCTGGACAG
* * *
1296895 TATCGATACTACACTACAAAGTAGTATCGATATTCCCTGGCCAG
1 TATCGATACTACACTACAAAGTAGTATCAATACTCCCTGGACAG
1296939 TATCGATAC
1 TATCGATAC
1296948 CGTTAGATTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
TATCGATACTACACTACAAAGTAGTATCAATACTCCCTGGACAG
Found at i:1302761 original size:21 final size:21
Alignment explanation
Indices: 1302736--1302807 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
1302726 TACTAGTATA
1302736 GTATCGATACTGCTTCAATGG
1 GTATCGATACTGCTTCAATGG
* **
1302757 GTATCGATATTG-TTCTTAA-CA
1 GTATCGATACTGCTTC--AATGG
* *
1302778 GTACCAATACTGCTTCAATGG
1 GTATCGATACTGCTTCAATGG
1302799 GTATCGATA
1 GTATCGATA
1302808 TGCGAAAATG
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
20 5 0.14
21 27 0.73
22 5 0.14
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (21 bp):
GTATCGATACTGCTTCAATGG
Found at i:1303356 original size:12 final size:13
Alignment explanation
Indices: 1303329--1303361 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1303319 ATATTATAAA
*
1303329 TTTTCAAACTTAG
1 TTTTCAAACATAG
1303342 TTTTCAAA-ATAG
1 TTTTCAAACATAG
1303354 TTTTCAAA
1 TTTTCAAA
1303362 TTTGTCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:1304997 original size:43 final size:42
Alignment explanation
Indices: 1304949--1305033 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
1304939 TTTGATAACA
* *
1304949 AAAAATGCCACAATTGGTGAAGAGATATAGCGGCATTTCTATG
1 AAAAATGCCACAATAGGTGAAGAGATATAACGGCATTT-TATG
* *
1304992 AAAAATGCCGCAATAGGTGAAGAGATATAACGGCGTTTTATG
1 AAAAATGCCACAATAGGTGAAGAGATATAACGGCATTTTATG
1305034 GATACAAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 4 0.11
43 34 0.89
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (42 bp):
AAAAATGCCACAATAGGTGAAGAGATATAACGGCATTTTATG
Found at i:1305122 original size:85 final size:87
Alignment explanation
Indices: 1304974--1305136 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 87
1304964 GGTGAAGAGA
*
1304974 TATAGCGGCATTTCTATGAAAAATGCCGCAATAGGTGAAGAGATATAACGGCGTTTTATGGATAC
1 TATAGCGGCATTTCTATGAAAAA-GCCGCAAAAGGTGAAGAGATATAACGGCGTTTTATGGATAC
*
1305039 AAACGCCACAAAATGTCTATATC
65 AAAAGCCACAAAATGTCTATATC
* * * * * *
1305062 TATAGCGGCATTTTTAT-AAACA-CCGCAAAAGGTTAAGATATTTAGCGGCGTTTT-TAGGATAC
1 TATAGCGGCATTTCTATGAAAAAGCCGCAAAAGGTGAAGAGATATAACGGCGTTTTAT-GGATAC
*
1305124 AAAAGCCGCAAAA
65 AAAAGCCACAAAA
1305137 GTTCTGGTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
84 1 0.02
85 44 0.68
87 4 0.06
88 16 0.25
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (87 bp):
TATAGCGGCATTTCTATGAAAAAGCCGCAAAAGGTGAAGAGATATAACGGCGTTTTATGGATACA
AAAGCCACAAAATGTCTATATC
Found at i:1307922 original size:46 final size:46
Alignment explanation
Indices: 1307855--1307943 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
1307845 AAAGTGGTTC
*
1307855 CAATTATACACAAGCTTAAAACGAATGCTAAGGACGAATTTAATAA
1 CAATTATACACAAGCTTAAAACGAATGCTAAGGAAGAATTTAATAA
* *
1307901 CAATTATACACAAGGTTAAAACGAATGCTAATGAAGAATTTAA
1 CAATTATACACAAGCTTAAAACGAATGCTAAGGAAGAATTTAA
1307944 AAGAAGTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (46 bp):
CAATTATACACAAGCTTAAAACGAATGCTAAGGAAGAATTTAATAA
Found at i:1307984 original size:13 final size:13
Alignment explanation
Indices: 1307966--1307992 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1307956 AATTCATATG
1307966 GACTCACTGTGAT
1 GACTCACTGTGAT
1307979 GACTCACTGTGAT
1 GACTCACTGTGAT
1307992 G
1 G
1307993 TTATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (13 bp):
GACTCACTGTGAT
Found at i:1310024 original size:18 final size:19
Alignment explanation
Indices: 1309997--1310032 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1309987 ATGCAAAAAG
*
1309997 GGTACGGATA-CCCTATAA
1 GGTACCGATACCCCTATAA
1310015 GGTACCGATACCCCTATA
1 GGTACCGATACCCCTATA
1310033 CAAAGAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (19 bp):
GGTACCGATACCCCTATAA
Found at i:1310041 original size:24 final size:23
Alignment explanation
Indices: 1310013--1310074 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
1310003 GATACCCTAT
*
1310013 AAGGTACCGATACCCCTATACAA
1 AAGGTACTGATACCCCTATACAA
* *
1310036 AGAGGTACTGATA--CCTATCCCA
1 A-AGGTACTGATACCCCTATACAA
1310058 AAGGTACTGATACCCCT
1 AAGGTACTGATACCCCT
1310075 TGTGTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.33
22 8 0.24
23 4 0.12
24 10 0.30
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (23 bp):
AAGGTACTGATACCCCTATACAA
Found at i:1311715 original size:65 final size:63
Alignment explanation
Indices: 1311643--1311832 Score: 236
Period size: 65 Copynumber: 2.9 Consensus size: 63
1311633 TACACTTGGG
* * * *
1311643 GTGCATCGGTACACTAATTACATTTGATGTTTCAAAAGAGCCAGGAGTGTATCGATGCATTGTCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAA-A-CCAGGAGTGTATCGATGCATTGTCT
* *
1311708 GTGCATCGGTACACAAAATGCATTCCATGTTTCATTAAAACCAGGAGTGTATCGATGCATTGTTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCA--AAAACCAGGAGTGTATCGATGCATTGTCT
* * **
1311773 ATGCATCGGTACACAAAATGCATTCGATGTTTTAATAAAATAAGGAGTGTATCGATGCAT
1 GTGCATCGGTACACAAAATGCATTCGATG-TTTCA-AAAACCAGGAGTGTATCGATGCAT
1311833 CAAGAGTGTA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
65 103 0.93
66 5 0.05
67 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (63 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAACCAGGAGTGTATCGATGCATTGTCT
Found at i:1312167 original size:12 final size:13
Alignment explanation
Indices: 1312150--1312181 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1312140 TAAGATTTTC
1312150 TTTGAAAATC-AT
1 TTTGAAAATCAAT
1312162 TTTG-AAATCAAT
1 TTTGAAAATCAAT
1312174 TTTGAAAA
1 TTTGAAAA
1312182 GTACACTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 10 0.56
13 3 0.17
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:1313997 original size:18 final size:17
Alignment explanation
Indices: 1313951--1313997 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1313941 AGTTTTCATG
1313951 AAAACAACATAATTAAAT
1 AAAACAA-ATAATTAAAT
*
1313969 AAAAAACAATAATTAAAT
1 AAAACA-AATAATTAAAT
1313987 CAAAACAAATA
1 -AAAACAAATA
1313998 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAACAAATAATTAAAT
Found at i:1320161 original size:65 final size:64
Alignment explanation
Indices: 1320067--1320256 Score: 238
Period size: 65 Copynumber: 2.9 Consensus size: 64
1320057 TACACTTGGG
* * * * *
1320067 GTGCATCGGTACACTAATTACATTTGATGTTTCA-AAAGAGCCATGAGTGTATCGATGCATTGTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCATAAA-A-CCAGGAGTGTATCGATGCATTGTT
1320131 T
64 T
1320132 GTGCATCGGTACACAAAATGCATTCGATGTTTCATTAAAACCAGGAGTGTATCGATGCATTGTTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCA-TAAAACCAGGAGTGTATCGATGCATTGTTT
* * * * **
1320197 ATGCATTGGTACATAAAATGCATTCGATGTTTTAATAAAATAAGGAGTGTATCGATGCAT
1 GTGCATCGGTACACAAAATGCATTCGATG-TTTCATAAAACCAGGAGTGTATCGATGCAT
1320257 CAAGAGTGTA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
65 103 0.93
66 5 0.05
67 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCATAAAACCAGGAGTGTATCGATGCATTGTTT
Found at i:1320275 original size:65 final size:65
Alignment explanation
Indices: 1320141--1320275 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 65
1320131 TGTGCATCGG
* * * **** *
1320141 TACACAAAATGCATTCGATGTTTCATTAAAACCAGGAGTGTATCGATGCATTGTTTATGCATTGG
1 TACATAAAATGCATTCGATGTTTCAATAAAACAAGGAGTGTATCGATGCATTCAAGATGCATTGA
* * *
1320206 TACATAAAATGCATTCGATGTTTTAATAAAATAAGGAGTGTATCGATGCA-TCAAGAGTGTATTG
1 TACATAAAATGCATTCGATGTTTCAATAAAACAAGGAGTGTATCGATGCATTCAAGA-TGCATTG
1320270 A
65 A
1320271 TACAT
1 TACAT
1320276 CCCTTTGTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 2 0.03
65 56 0.97
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (65 bp):
TACATAAAATGCATTCGATGTTTCAATAAAACAAGGAGTGTATCGATGCATTCAAGATGCATTGA
Found at i:1321600 original size:22 final size:22
Alignment explanation
Indices: 1321572--1321620 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1321562 CAGGTTTTCA
1321572 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTCCTATTCG
*
1321594 AAAGCTATTATTTTTCTATTCG
1 AAAGCTATTATTTTCCTATTCG
1321616 AAAGC
1 AAAGC
1321621 AGTAAAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (22 bp):
AAAGCTATTATTTTCCTATTCG
Found at i:1322621 original size:18 final size:18
Alignment explanation
Indices: 1322598--1322633 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1322588 GAATTTTAAG
1322598 ATTTTATATTCGATTCAA
1 ATTTTATATTCGATTCAA
1322616 ATTTTATATTCGATTCAA
1 ATTTTATATTCGATTCAA
1322634 TTATTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTTATATTCGATTCAA
Found at i:1323037 original size:44 final size:44
Alignment explanation
Indices: 1322988--1323080 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
1322978 ATCGGTATTG
** * *
1322988 ATACTACTTTACATAGTACTATCGATACTGCCTGGACAGTATCA
1 ATACTACACTACAAAGTACTATCGATACTCCCTGGACAGTATCA
* * * *
1323032 ATACTACACTATAAAGTAGTATCGATACTCCCTGGCCAGTATCG
1 ATACTACACTACAAAGTACTATCGATACTCCCTGGACAGTATCA
1323076 ATACT
1 ATACT
1323081 GTTGGATTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (44 bp):
ATACTACACTACAAAGTACTATCGATACTCCCTGGACAGTATCA
Found at i:1323153 original size:22 final size:22
Alignment explanation
Indices: 1323122--1323205 Score: 141
Period size: 22 Copynumber: 3.8 Consensus size: 22
1323112 TATAACATGT
*
1323122 AGTATCGATACCCCTATGAAGG
1 AGTACCGATACCCCTATGAAGG
*
1323144 AGTACTGATACCCCTATGAAGG
1 AGTACCGATACCCCTATGAAGG
1323166 AGTACCGATACCCCTATGAAGG
1 AGTACCGATACCCCTATGAAGG
*
1323188 AGTACCGATACCCATATG
1 AGTACCGATACCCCTATG
1323206 CTCCTAGTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (22 bp):
AGTACCGATACCCCTATGAAGG
Found at i:1325685 original size:18 final size:18
Alignment explanation
Indices: 1325662--1325704 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1325652 TATGACTACA
*
1325662 TAATAATA-ATAATAACAT
1 TAATAATACAT-ATAAAAT
1325680 TAATAATACATATAAAAT
1 TAATAATACATATAAAAT
1325698 TAA-AATA
1 TAATAATA
1325705 TAAACAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 17 0.74
19 2 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAATACATATAAAAT
Found at i:1327100 original size:3 final size:3
Alignment explanation
Indices: 1327081--1327128 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
1327071 TATTTAGTAG
* * * *
1327081 TAA TAA CAA AAA T-A TAA TAA TAA TTA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1327128 T
1 T
1327129 CAAACGGACC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1329639 original size:2 final size:2
Alignment explanation
Indices: 1329632--1329658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1329622 TACCCTAAAT
1329632 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1329659 GAGATAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1331494 original size:24 final size:22
Alignment explanation
Indices: 1331450--1331494 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
1331440 TATTAAGTTA
*
1331450 ATATTTTTTTAAAATAGTTATT
1 ATATTTTTTTAAAATAATTATT
*
1331472 ATATTTTATATTAATATAATTAT
1 ATATTTT-T-TTAAAATAATTAT
1331495 ATAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATTTTTTTAAAATAATTATT
Found at i:1331506 original size:35 final size:35
Alignment explanation
Indices: 1331461--1331546 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 35
1331451 TATTTTTTTA
1331461 AAATAGTTATTATATTTTATATT-AAT-ATAATTATAT
1 AAATA-TTATT-TATTTT-TATTAAATAATAATTATAT
*
1331497 AAATATTATTT-TTTTTATTAAAATAATATTTATAT
1 AAATATTATTTATTTTTATT-AAATAATAATTATAT
*
1331532 AATTATTATTTATTT
1 AAATATTATTTATTT
1331547 AAATTTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
34 4 0.09
35 24 0.55
36 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (35 bp):
AAATATTATTTATTTTTATTAAATAATAATTATAT
Found at i:1331516 original size:32 final size:34
Alignment explanation
Indices: 1331468--1331565 Score: 92
Period size: 35 Copynumber: 2.9 Consensus size: 34
1331458 TTAAAATAGT
*
1331468 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTATTTTTTATATTAAATAATAATTATATAAA
* * *
1331500 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATAATTATATAAA
* * *
1331535 TATTATTTATTTAAATTTATTAATTAATTAT
1 TATTATTT-TTTATATTAAATAA-TAATTAT
1331566 TTTTTGAGCT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
32 14 0.27
34 3 0.06
35 23 0.44
36 12 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATAATTATATAAA
Found at i:1333298 original size:21 final size:21
Alignment explanation
Indices: 1333272--1333337 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1333262 TCTCCGCAGA
*
1333272 GTTACATTCCTAGCCCTCAGG
1 GTTACATTCCTAGCCCACAGG
1333293 GTTACATTCCTAGCCCACTA-G
1 GTTACATTCCTAGCCCAC-AGG
* * *
1333314 GTTATATGCCTAGCCCGCAGG
1 GTTACATTCCTAGCCCACAGG
1333335 GTT
1 GTT
1333338 TTATGACACC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (21 bp):
GTTACATTCCTAGCCCACAGG
Found at i:1334012 original size:14 final size:14
Alignment explanation
Indices: 1333993--1334023 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1333983 TTTTATCCTT
1333993 AACATATACATTAA
1 AACATATACATTAA
1334007 AACATATACATTAA
1 AACATATACATTAA
1334021 AAC
1 AAC
1334024 CAACTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1334172 original size:63 final size:63
Alignment explanation
Indices: 1334091--1334213 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 63
1334081 TCATGCTCAC
* *
1334091 AACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAAA
1 AACCAAATGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAAA
* *
1334154 AACCAAATGATCACTTCACATTTATTTAATTTATCCATAACATTTTATCCAATTTATTCA
1 AACCAAATGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCA
1334214 TAACATTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (63 bp):
AACCAAATGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAAAA
Found at i:1334234 original size:23 final size:23
Alignment explanation
Indices: 1334181--1334236 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1334171 ACATTTATTT
*
1334181 AATTTATCCATAACATTTTATCC
1 AATTTATTCATAACATTTTATCC
1334204 AATTTATTCATAACATTTTATCC
1 AATTTATTCATAACATTTTATCC
1334227 AATTTATTCA
1 AATTTATTCA
1334237 AACTTCACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTATTCATAACATTTTATCC
Found at i:1334750 original size:117 final size:117
Alignment explanation
Indices: 1334391--1334844 Score: 678
Period size: 117 Copynumber: 3.9 Consensus size: 117
1334381 ATAAATAATA
* ** *
1334391 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATCTGAC-ATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
1334455 TCTGATAAAATAATGGAAGGCGCGCCCCCGGGAACACGCTTTCACCACTTTG
66 TCTGACAAAATAATCGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTG
* * **
1334507 GGTACTGATATGAATAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATACAC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * *
1334572 TTATCACAAAATAATCGAAGGCGCGCCCCCGGGAACGC-TCTTTCACTACTTTG
66 -TCTGACAAAATAATCGAAGGCGCGCCCCCGGGAACGCGT-TTTCACCACTTTG
* * * *
1334625 GGTACTGACATGAATAATGACCCCGAGTGACATGAGTGACATAATAGGGTAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
1334690 TCTGACAAAATAATCGAAGGCGTGCCCCCGGGAACGCGTTTTCACCACTTTG
66 TCTGACAAAATAATCGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTG
*
1334742 GGTACTGACATGAATAGTGCCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
1334807 TCTGACAAAATAATCGAAGGCGCGCCCCTGGGAACGCG
66 TCTGACAAAATAATCGAAGGCGCGCCCCCGGGAACGCG
1334845 CCTTCATATG
Statistics
Matches: 300, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
116 44 0.15
117 154 0.51
118 102 0.34
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (117 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATCGAAGGCGCGCCCCCGGGAACGCGTTTTCACCACTTTG
Found at i:1334801 original size:235 final size:233
Alignment explanation
Indices: 1334391--1334843 Score: 701
Period size: 235 Copynumber: 1.9 Consensus size: 233
1334381 ATAAATAATA
* * *
1334391 GGTACTGACATAAATAGTGCCCCCGAGGGACATGAGTGACATAATCTGACATGATAACATATTCT
1 GGTACTGACATAAATAATGACCCCGAGGGACATGAGTGACATAATCGGACATGATAACATATTCT
* * *
1334456 CTGATAAAATAATGGAAGGCGCGCCCCCGGGAACACGCTTTCACCACTTTGGGTACTGATATGAA
66 CTGACAAAATAATCGAAGGCGCGCCCCCGGGAACACGCTTTCACCACTTTGGGTACTGACATGAA
1334521 TAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATACACTTATCACAAAATAA
131 TAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATACAC-TATCACAAAATAA
1334586 TCGAAGGCGCGCCCCCGGGAACGCTCTTTCACTACTTTG
195 TCGAAGGCGCGCCCCCGGGAACGCTCTTTCACTACTTTG
* * *
1334625 GGTACTGACATGAATAATGACCCCGAGTGACATGAGTGACATAATAGGGTA-ATGATAACATATT
1 GGTACTGACATAAATAATGACCCCGAGGGACATGAGTGACATAAT-CGG-ACATGATAACATATT
* * *
1334689 CTCTGACAAAATAATCGAAGGCGTGCCCCCGGGAACGCGTTTTCACCACTTTGGGTACTGACATG
64 CTCTGACAAAATAATCGAAGGCGCGCCCCCGGGAACACGCTTTCACCACTTTGGGTACTGACATG
* * ** * *
1334754 AATAGTGCCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATA
129 AATAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATACACTATCACAAAATA
*
1334819 ATCGAAGGCGCGCCCCTGGGAACGC
194 ATCGAAGGCGCGCCCCCGGGAACGC
1334844 GCCTTCATAT
Statistics
Matches: 198, Mismatches: 19, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
234 75 0.38
235 122 0.62
236 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (233 bp):
GGTACTGACATAAATAATGACCCCGAGGGACATGAGTGACATAATCGGACATGATAACATATTCT
CTGACAAAATAATCGAAGGCGCGCCCCCGGGAACACGCTTTCACCACTTTGGGTACTGACATGAA
TAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATACACTATCACAAAATAAT
CGAAGGCGCGCCCCCGGGAACGCTCTTTCACTACTTTG
Found at i:1339690 original size:42 final size:42
Alignment explanation
Indices: 1339596--1339848 Score: 310
Period size: 42 Copynumber: 5.9 Consensus size: 42
1339586 CAAAATGTTA
* * *
1339596 CAAAAGGACAGATCTATAGCGGCGTTTTTTGGAACAAACGTAG
1 CAAAAGGTCAGATCTATAGCGGCG-TTTTTGAAACAAACGTCG
** *
1339639 CAAAAGGTCAGATCTATAGCGGCGTTTGTTCCAA-AAACGCCG
1 CAAAAGGTCAGATCTATAGCGGCGTTT-TTGAAACAAACGTCG
* *
1339681 CAAAAGGTCAGATCTATAGCGGCGCTTTTTGGAACAAAAGTCG
1 CAAAAGGTCAGATCTATAGCGGCG-TTTTTGAAACAAACGTCG
* * *
1339724 CAAAAGGTTGAGATCTATAGCGACGTTTTTGAAATAAACGTCG
1 CAAAAGG-TCAGATCTATAGCGGCGTTTTTGAAACAAACGTCG
* **
1339767 CGAAAGGTCAGATCTATAGCTACGTTTTTGAAACAAACGTCG
1 CAAAAGGTCAGATCTATAGCGGCGTTTTTGAAACAAACGTCG
* *
1339809 CAAAAGGTCAGATCTATAGCGGTGTTTTTGGATACAAACG
1 CAAAAGGTCAGATCTATAGCGGCGTTTTT-GAAACAAACG
1339849 CCGCTAATTA
Statistics
Matches: 182, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
42 94 0.52
43 73 0.40
44 15 0.08
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (42 bp):
CAAAAGGTCAGATCTATAGCGGCGTTTTTGAAACAAACGTCG
Found at i:1339698 original size:85 final size:84
Alignment explanation
Indices: 1339596--1339837 Score: 324
Period size: 85 Copynumber: 2.8 Consensus size: 84
1339586 CAAAATGTTA
* *
1339596 CAAAAGGACAGATCTATAGCGGCGTTTTTTGGAACAAACGTAGCAAAAGGTCAGATCTATAGCGG
1 CAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCGG
*
1339661 CGTTTGTTCCAA-AAACGCCG
65 CGTTT-TTCAAATAAACGCCG
* *
1339681 CAAAAGGTCAGATCTATAGCGGCGCTTTTTGGAACAAAAGTCGCAAAAGGTTGAGATCTATAGCG
1 CAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAACGTCGCAAAAGG-TCAGATCTATAGCG
* * *
1339746 ACGTTTTTGAAATAAACGTCG
64 GCGTTTTTCAAATAAACGCCG
* ** * *
1339767 CGAAAGGTCAGATCTATAGCTACGTTTTTGAAACAAACGTCGCAAAAGGTCAGATCTATAGCGGT
1 CAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCGGC
1339832 GTTTTT
66 GTTTTT
1339838 GGATACAAAC
Statistics
Matches: 138, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
84 19 0.14
85 73 0.53
86 46 0.33
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (84 bp):
CAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCGGC
GTTTTTCAAATAAACGCCG
Found at i:1339815 original size:128 final size:129
Alignment explanation
Indices: 1339605--1339846 Score: 346
Period size: 128 Copynumber: 1.9 Consensus size: 129
1339595 ACAAAAGGAC
* * *
1339605 AGATCTATAGCGGCGTTTTTTGGAACAAACGTAGCAAAAGGTCAGATCTATAGCGGCGTTTGTTC
1 AGATCTATAGCGACGTTTTTTGAAACAAACGTAGCAAAAGGTCAGATCTATAGCGACGTTTGTTC
*
1339670 CAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGCTTTTTGGA-ACAAAAGTCGCAAAAGGTTG
66 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGATACAAAAGTCGCAAAAGGTTG
* * * * *
1339734 AGATCTATAGCGACG-TTTTTGAAATAAACGTCGCGAAAGGTCAGATCTATAGCTACGTTT-TTG
1 AGATCTATAGCGACGTTTTTTGAAACAAACGTAGCAAAAGGTCAGATCTATAGCGACGTTTGTTC
* *
1339797 AAACAAACGTCGCAAAAGGTCAGATCTATAGCGGTGTTTTTGGATACAAA
66 AAA-AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAA
1339847 CGCCGCTAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
127 12 0.12
128 74 0.74
129 14 0.14
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (129 bp):
AGATCTATAGCGACGTTTTTTGAAACAAACGTAGCAAAAGGTCAGATCTATAGCGACGTTTGTTC
AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAAAGTCGCAAAAGGTTG
Found at i:1341289 original size:10 final size:10
Alignment explanation
Indices: 1341274--1341332 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
1341264 CATTTAATAA
1341274 ATAAACGAAC
1 ATAAACGAAC
1341284 ATAAACGAAC
1 ATAAACGAAC
** *
1341294 ACGAAC-ATAA
1 ATAAACGA-AC
1341304 ATGAACACGAAC
1 AT-AA-ACGAAC
1341316 ATAAACGAAC
1 ATAAACGAAC
1341326 ATAAACG
1 ATAAACG
1341333 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1341299 original size:16 final size:16
Alignment explanation
Indices: 1341278--1341326 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1341268 TAATAAATAA
1341278 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1341294 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1341310 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1341326 A
1 A
1341327 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1342443 original size:14 final size:14
Alignment explanation
Indices: 1342426--1342457 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1342416 AGCGAACATA
1342426 AACGAACATAACCG
1 AACGAACATAACCG
1342440 AACGAACATAACCG
1 AACGAACATAACCG
1342454 AACG
1 AACG
1342458 TTCACTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1344794 original size:15 final size:15
Alignment explanation
Indices: 1344774--1344921 Score: 172
Period size: 15 Copynumber: 9.5 Consensus size: 15
1344764 TAATAAGGTT
1344774 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1344789 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1344804 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1344819 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1344834 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1344849 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1344864 AATTATTATAAAATATAGATTA
1 ATTTATT-T----TA-A-AATA
*
1344886 ATTTATTTTTAAATA
1 ATTTATTTTAAAATA
1344901 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1344915 ATTTATT
1 ATTTATT
1344922 AGTATGGATT
Statistics
Matches: 117, Mismatches: 9, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.10
15 89 0.76
16 2 0.02
17 1 0.01
20 2 0.02
21 2 0.02
22 9 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1344831 original size:45 final size:45
Alignment explanation
Indices: 1344774--1344878 Score: 192
Period size: 45 Copynumber: 2.3 Consensus size: 45
1344764 TAATAAGGTT
*
1344774 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
1344819 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
*
1344864 AATTATTATAAAATA
1 ATTTATTATAAAATA
1344879 TAGATTAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (45 bp):
ATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATA
Found at i:1344940 original size:22 final size:23
Alignment explanation
Indices: 1344915--1344988 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
1344905 ATTTTAAATA
1344915 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
1344937 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
1344959 ATTATTGTAGTTGTATGGATTGATTT
1 A-T-TTATA-TAGTATGGATTGATTT
1344985 ATTT
1 ATTT
1344989 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 3 0.07
26 14 0.33
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:1344995 original size:80 final size:80
Alignment explanation
Indices: 1344901--1345619 Score: 661
Period size: 80 Copynumber: 8.8 Consensus size: 80
1344891 TTTTTAAATA
1344901 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1344966 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
*
1344981 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* *
1345046 ATAATTTATTTGTATGGATTG
62 AT--TGTAGTTGTATGGATTG
* * ***
1345067 ATTTA-TTT--AT--TTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATT
* * *
1345126 -TTAAATAATT-TATTAGTATTG
62 ATT--GTAGTTGTA-T-GGATTG
* * * * * *
1345147 ATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA
* ***
1345206 TTTATTTTA-AAATATGGATTG
60 -TTATTGTAGTTGTATGGATTG
1345227 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG----ATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
1345288 TAGTTGTATGAATTG
66 TAGTTGTATGGATTG
*
1345303 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTGA
* * * *
1345368 TTTATT-TTAAATAATT-TATTAGTATGG
56 TTTATTATT--GTAGTTGTA-T-GGATTG
* *
1345395 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
1 ATT----TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1345460 ATTGTAGTTGTATGGATTG
62 ATTGTAGTTGTATGGATTG
1345479 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
1345544 TAGTTGTTTGGATTG
66 TAGTTGTATGGATTG
*
1345559 ATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1345620 TTAAATCTCA
Statistics
Matches: 536, Mismatches: 49, Indels: 108
0.77 0.07 0.16
Matches are distributed among these distances:
75 7 0.01
76 49 0.09
77 4 0.01
78 7 0.01
79 7 0.01
80 258 0.48
81 12 0.02
82 21 0.04
83 8 0.01
84 27 0.05
85 15 0.03
86 56 0.10
87 2 0.00
89 2 0.00
90 6 0.01
91 6 0.01
92 9 0.02
94 2 0.00
95 2 0.00
96 36 0.07
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATGGATTG
Found at i:1345013 original size:32 final size:32
Alignment explanation
Indices: 1344971--1345442 Score: 402
Period size: 32 Copynumber: 15.7 Consensus size: 32
1344961 TATTGTAGTT
1344971 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345003 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345026 -TATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345057 GTATGGATTGATTTA-TTT--AT--TTTA-AA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
1345083 ATATGGATTGATTTA--TT--AT--TGTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
1345109 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345141 GTATTGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1345164 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1345195 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1345218 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345249 GTATGGATTGATTTATTTTAAAATATGGATTGATTA
1 GTATGGATTGATTTATTTT-AAATA---ATTTATTA
* *
1345285 TTGTAGTTG-TATGAATTGATTTATTTTAAATAATTTATTA
1 --GTA-TGGAT-TG-ATT--TAT--TTTAAATAATTTATTA
*
1345325 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345357 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1345389 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1345421 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1345443 ATATGAATTG
Statistics
Matches: 366, Mismatches: 21, Indels: 106
0.74 0.04 0.22
Matches are distributed among these distances:
22 40 0.11
23 12 0.03
25 10 0.03
26 37 0.10
27 4 0.01
28 11 0.03
29 5 0.01
30 2 0.01
31 16 0.04
32 177 0.48
33 5 0.01
34 2 0.01
36 10 0.03
37 3 0.01
38 8 0.02
39 4 0.01
40 10 0.03
42 2 0.01
43 5 0.01
44 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1345015 original size:58 final size:56
Alignment explanation
Indices: 1344946--1345099 Score: 213
Period size: 54 Copynumber: 2.7 Consensus size: 56
1344936 TATTTTAAAA
***
1344946 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTATT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
1345004 TATGAATTGATTTA-T-TTTAAAATATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
1345058 TATGGATTGATTTATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTA-TTA-TTTAAAATATGGATTGATTTATT
1345100 ATTGTAGTTG
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
54 44 0.51
55 2 0.02
56 3 0.03
57 1 0.01
58 36 0.42
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (56 bp):
TATGGATTGATTTATTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1345029 original size:22 final size:22
Alignment explanation
Indices: 1345004--1345046 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1344994 AATTTATTAG
1345004 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1345026 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1345047 TAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1345172 original size:54 final size:54
Alignment explanation
Indices: 1345110--1345625 Score: 438
Period size: 54 Copynumber: 9.4 Consensus size: 54
1345100 ATTGTAGTTG
1345110 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
*
1345164 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
*
1345218 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
* * * * * * *
1345272 TATGGATTGA-TTATTGT-AGT--TGTA-T-GAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGA-TTT--AT--TTTA-AAA
*
1345326 TATGAATTGATTTATTTTAAATAATTTATTAGTA-TGAATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGATTTA-TTT---TAA---A--A
* *
1345389 GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
* * * * * * *
1345444 TATGAATTGATTTATTATT--GTAGTTGTA-T-GGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATT-TTAAATAATT-TATTAGTATTGATTGA-TTT--AT--TTTA-AAA
* * * ***
1345502 TATGGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTA-AAA
*
1345550 TTTGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
1345604 TATGGATTGATTTATTTTAAAT
1 TATGGATTGATTTATTTTAAAT
1345626 CTCAGTATTG
Statistics
Matches: 380, Mismatches: 42, Indels: 80
0.76 0.08 0.16
Matches are distributed among these distances:
48 30 0.08
49 6 0.02
50 7 0.02
51 2 0.01
52 14 0.04
53 19 0.05
54 188 0.49
55 18 0.05
56 4 0.01
57 9 0.02
58 20 0.05
59 8 0.02
60 9 0.02
61 1 0.00
63 3 0.01
64 41 0.11
65 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
Found at i:1345221 original size:22 final size:22
Alignment explanation
Indices: 1345196--1345238 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1345186 AATTTATTAG
1345196 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1345218 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1345239 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1345275 original size:22 final size:22
Alignment explanation
Indices: 1345250--1345314 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1345240 AATTTATTAG
1345250 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
* ***
1345272 TATGGATTGA-TTATTGTAGTTG
1 TATGGATTGATTTATTTTA-AAA
*
1345294 TATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1345315 TAATTTATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 7 0.21
22 19 0.58
23 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1345322 original size:14 final size:14
Alignment explanation
Indices: 1345303--1345420 Score: 65
Period size: 14 Copynumber: 7.6 Consensus size: 14
1345293 GTATGAATTG
1345303 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1345317 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1345335 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1345349 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1345367 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
1345381 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
1345399 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1345413 ATTTATTT
1 ATTTATTT
1345421 GTATGGATTG
Statistics
Matches: 78, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
14 37 0.47
15 3 0.04
16 6 0.08
17 3 0.04
18 29 0.37
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.55
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1345516 original size:18 final size:18
Alignment explanation
Indices: 1345493--1345540 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1345483 ATTTTAAATA
*
1345493 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1345511 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1345533 ATTTATTA
1 ATTTATTA
1345541 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1345590 original size:112 final size:112
Alignment explanation
Indices: 1345330--1345602 Score: 312
Period size: 112 Copynumber: 2.4 Consensus size: 112
1345320 TATTAGTATG
1345330 AATTGATTTATTTTAAATAATTTATTAGTA-TGAATTGATTTATTTTAAATAATTTATTAGTATG
1 AATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGATTTATTTTAAATAATTTATTAGTATG
**
1345394 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAA
65 GATTGATTTATTTTAAATAATGGATTTGTATGGATTGATTTATTTTAA
* * *
1345442 AATATGAATTGA-TTT--ATTATTGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGT
1 AAT-TG-ATTTATTTTAAATAATT-TA-TTAGTATTGATTGATTTATTTTAAATAATTTATTAGT
** **
1345503 ATGGATTGATTTATTTTAAA-ATATGGA-TTG-ATTTATT-ATTGTAGTTGTTTG
62 ATGGATTGATTTATTTTAAATA-ATGGATTTGTATGGATTGATT-TA-TT-TTAA
*
1345554 GATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAA
1 AATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAA
1345603 ATATGGATTG
Statistics
Matches: 135, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
109 3 0.02
110 11 0.08
111 18 0.13
112 86 0.64
113 13 0.10
114 4 0.03
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (112 bp):
AATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAATAATTTATTAGTATGG
ATTGATTTATTTTAAATAATGGATTTGTATGGATTGATTTATTTTAA
Found at i:1346779 original size:41 final size:41
Alignment explanation
Indices: 1346678--1346792 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
1346668 ATTGAACAAA
* *
1346678 CTATAGCGGTGTTTGA-ACAAAAATGCCACTAAAGTACAAGT
1 CTATAGCGGTGTTT-ATATAAAAACGCCACTAAAGTACAAGT
** * * *
1346719 CTATAATGGCGTTTGTATAAAAACGCCACTAAAGTACGAGT
1 CTATAGCGGTGTTTATATAAAAACGCCACTAAAGTACAAGT
* * *
1346760 CTATAGCGATGTTTATATAAAAACTCCGCTAAA
1 CTATAGCGGTGTTTATATAAAAACGCCACTAAA
1346793 ATACTACTCT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (41 bp):
CTATAGCGGTGTTTATATAAAAACGCCACTAAAGTACAAGT
Found at i:1346847 original size:42 final size:41
Alignment explanation
Indices: 1346801--1346890 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
1346791 AAATACTACT
* * *
1346801 CTATTGCCGCGTTTGTTGAAAAAACACCACTATAGATTAACC
1 CTATTACCGCGTTTATTG-AAAAACACCACTATAGATGAACC
* ** *
1346843 CTATTACGGCGTTTATTGAAAAACAGTATTATAGATGAACC
1 CTATTACCGCGTTTATTGAAAAACACCACTATAGATGAACC
1346884 CTATTAC
1 CTATTAC
1346891 GGCATTTGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 26 0.63
42 15 0.37
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (41 bp):
CTATTACCGCGTTTATTGAAAAACACCACTATAGATGAACC
Found at i:1355965 original size:25 final size:24
Alignment explanation
Indices: 1355911--1355967 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1355901 AAAGTTATAA
**
1355911 AATAAAAATTAAACTTTAGATTTT
1 AATAAAAATTAAACTTTAGAAATT
*
1355935 ATTAAAAATATAAACATTT-GAAATT
1 AATAAAAAT-TAAAC-TTTAGAAATT
1355960 AATAAAAA
1 AATAAAAA
1355968 AAAAACGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 8 0.30
25 16 0.59
26 3 0.11
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
AATAAAAATTAAACTTTAGAAATT
Found at i:1356059 original size:15 final size:15
Alignment explanation
Indices: 1356034--1356070 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1356024 TATTTTAACT
1356034 AATAT-TTTTTAAAA
1 AATATATTTTTAAAA
*
1356048 AATATATTTTTAGAA
1 AATATATTTTTAAAA
1356063 AATATATT
1 AATATATT
1356071 GAATTTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
AATATATTTTTAAAA
Found at i:1356733 original size:13 final size:13
Alignment explanation
Indices: 1356715--1356740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1356705 CATAGTTGAA
1356715 CAGTCTTCATATG
1 CAGTCTTCATATG
1356728 CAGTCTTCATATG
1 CAGTCTTCATATG
1356741 AGCGTCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1361758 original size:23 final size:22
Alignment explanation
Indices: 1361722--1361776 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1361712 AAAAAATTAC
*
1361722 TGCTGAGAAATTTTCGTTTTGAT
1 TGCTGATAAATTTT-GTTTTGAT
* *
1361745 TGCTGATAATTTTTTTTTTGAT
1 TGCTGATAAATTTTGTTTTGAT
*
1361767 TTCTGATAAA
1 TGCTGATAAA
1361777 AAAATGTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (22 bp):
TGCTGATAAATTTTGTTTTGAT
Found at i:1362698 original size:130 final size:133
Alignment explanation
Indices: 1362395--1362698 Score: 393
Period size: 135 Copynumber: 2.3 Consensus size: 133
1362385 AGTTTGGGTC
* ** *
1362395 ATCTAAGGGTGACATGGTTCCTACGTGATGAGGATATCTAAACAGGGGATGACACTGCTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGACACTGCTCATACG
* * * *
1362460 TGATGAAGAGTTCTTGGCCATCTTTAGGAAAGGTGATAACTTGGTTCCTACGCGATGAGGACAGC
66 TGATGAAGAGTTCTTGGCCATCTTT--GAAAGGCGATAACATAGTTCCTACGCAATGAGGACAGC
1362525 TGGTT
129 TGGTT
* *
1362530 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACACTGCTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGACACTGCTCATACG
* * *
1362595 TGATGAAGAGTTCTTGGCCAT-TTT-ATA-GCGATAACATAGTTCCTACGTAATGAGGACGGCTG
66 TGATGAAGAGTTCTTGGCCATCTTTGAAAGGCGATAACATAGTTCCTACGCAATGAGGACAGCTG
1362657 GTT
131 GTT
* * *
1362660 ATCTAATGTTGAC-CTTG-CTCCTACATGATGAGGAGATCT
1 ATCTAAGGGTGACAC--GACTCCTACGTGATGAGGAGATCT
1362699 GGTCAGCTGA
Statistics
Matches: 150, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
129 1 0.01
130 63 0.42
131 3 0.02
134 3 0.02
135 80 0.53
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (133 bp):
ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGACACTGCTCATACG
TGATGAAGAGTTCTTGGCCATCTTTGAAAGGCGATAACATAGTTCCTACGCAATGAGGACAGCTG
GTT
Found at i:1363661 original size:10 final size:10
Alignment explanation
Indices: 1363646--1363680 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1363636 CCTTTATTTA
1363646 TTTTTTCTTT
1 TTTTTTCTTT
*
1363656 TTTTTTCATT
1 TTTTTTCTTT
*
1363666 TTTTTCCTTT
1 TTTTTTCTTT
1363676 TTTTT
1 TTTTT
1363681 AAGTGTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1370812 original size:30 final size:30
Alignment explanation
Indices: 1370777--1370839 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1370767 TTAAATTCGA
**
1370777 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
1370807 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
1370837 ATG
1 ATG
1370840 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:1373706 original size:4 final size:4
Alignment explanation
Indices: 1373697--1373723 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1373687 ATTCTACCAA
1373697 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1373724 ATGTTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1375062 original size:15 final size:16
Alignment explanation
Indices: 1375044--1375077 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1375034 TATGAACATC
1375044 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
1375059 AAATAGAATAACAATA
1 AAATAAAATAACAATA
1375075 AAA
1 AAA
1375078 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:1380955 original size:16 final size:14
Alignment explanation
Indices: 1380922--1380956 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1380912 GTAGGGTAAG
1380922 GCGCGCCCCCTGAA
1 GCGCGCCCCCTGAA
1380936 GCGCGCCCCCTGAA
1 GCGCGCCCCCTGAA
1380950 GCGCGCC
1 GCGCGCC
1380957 TTATGTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.51, G:0.31, T:0.06
Consensus pattern (14 bp):
GCGCGCCCCCTGAA
Found at i:1385387 original size:27 final size:27
Alignment explanation
Indices: 1385357--1385426 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
1385347 TCTGTGACGG
*
1385357 TGGCGGCGGCGGCATCGGGTAAGGGAA
1 TGGCGGCGGCGACATCGGGTAAGGGAA
* * *
1385384 TGGCGGCGGCAACATCTGGTAATGGAA
1 TGGCGGCGGCGACATCGGGTAAGGGAA
* * *
1385411 AGGCGGTGGCGTCATC
1 TGGCGGCGGCGACATC
1385427 ATATATGGCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.44, T:0.16
Consensus pattern (27 bp):
TGGCGGCGGCGACATCGGGTAAGGGAA
Found at i:1398417 original size:21 final size:21
Alignment explanation
Indices: 1398395--1398435 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1398385 CCTCGTGCTA
1398395 TTTGTGATGACTTCAATCCTAT
1 TTTG-GATGACTTCAATCCTAT
*
1398417 TTTGGATGACTTGAATCCT
1 TTTGGATGACTTCAATCCT
1398436 GGGATTGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (21 bp):
TTTGGATGACTTCAATCCTAT
Found at i:1410001 original size:99 final size:98
Alignment explanation
Indices: 1409813--1410000 Score: 265
Period size: 98 Copynumber: 1.9 Consensus size: 98
1409803 GTAGGGAACT
* *
1409813 TATTTATTGCTGTAAATTTCACATATACAATAACTAAACAAGCTAATGATTTTCTATGAAATTGA
1 TATTTATTGCTGCAAATTTCACATATACAATAACTAAACAAGCTAATGATTTTCGATGAAATTGA
**
1409878 AACCTAATAAAGGGTTGGGTAAAAACTTATTTA
66 AACCTAATAAAGGGTTGAATAAAAACTTATTTA
* * *
1409911 TATTCTATTGTTGCAAATTTCACATATACAATCACTAAA-AAGCTACTGAATTTT-GATGAAATT
1 TATT-TATTGCTGCAAATTTCACATATACAATAACTAAACAAGCTAATG-ATTTTCGATGAAATT
1409974 GAAACCTAAT-AAGGGATTGAATAAAAA
64 GAAACCTAATAAAGGG-TTGAATAAAAA
1410001 AATATAGTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
97 5 0.06
98 39 0.49
99 36 0.45
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (98 bp):
TATTTATTGCTGCAAATTTCACATATACAATAACTAAACAAGCTAATGATTTTCGATGAAATTGA
AACCTAATAAAGGGTTGAATAAAAACTTATTTA
Found at i:1412632 original size:68 final size:69
Alignment explanation
Indices: 1412502--1412744 Score: 183
Period size: 68 Copynumber: 3.5 Consensus size: 69
1412492 AAAAGCGAGG
* * * * * *
1412502 GATTCATTCGAAGTCTTATTACCTCAAGTTGAAGAGGTACGAGACATC-TT-ATCACTTAAATTT
1 GATTCATTCAAAGTCTCATTACCTCAAGTTGGAGAGG--CAAAACATCTTTCATCGCTTAAATTT
1412565 G-GAGT
64 GAGAGT
* * *
1412570 GATTCATTCAAAGTCTCATTGCCTCAAGTTGGAGAGGCAATACATCTTTCATCGCTTTAATTTGA
1 GATTCATTCAAAGTCTCATTACCTCAAGTTGGAGAGGCAAAACATCTTTCATCGCTTAAATTTG-
*
1412635 ATGAAT
65 A-GAGT
* * * * * * * * *
1412641 GGTTTACTCAAAGTCTCATTACCTCAATTTGGAGGGGAAAAACAT-TTCTCACCG-TTGAAGTTG
1 GATTCATTCAAAGTCTCATTACCTCAAGTTGGAGAGGCAAAACATCTT-TCATCGCTTAAATTTG
1412704 AAGAGAT
65 -AGAG-T
* *
1412711 GATTCATTTAAAGTC-CTATTGCCTCAAGTTGGAG
1 GATTCATTCAAAGTCTC-ATTACCTCAAGTTGGAG
1412745 GTATAAGACA
Statistics
Matches: 140, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
66 7 0.05
67 2 0.01
68 45 0.32
69 3 0.02
70 38 0.27
71 45 0.32
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (69 bp):
GATTCATTCAAAGTCTCATTACCTCAAGTTGGAGAGGCAAAACATCTTTCATCGCTTAAATTTGA
GAGT
Found at i:1417180 original size:13 final size:13
Alignment explanation
Indices: 1417162--1417201 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1417152 ATGTATAGCA
1417162 AATTTTTTTATAT
1 AATTTTTTTATAT
1417175 AATTTTTTTAT-T
1 AATTTTTTTATAT
*
1417187 --TTGTTTTATAT
1 AATTTTTTTATAT
1417198 AATT
1 AATT
1417202 GTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
10 8 0.35
11 1 0.04
12 1 0.04
13 13 0.57
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
AATTTTTTTATAT
Found at i:1417582 original size:13 final size:13
Alignment explanation
Indices: 1417564--1417591 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1417554 TGACATATTT
1417564 TTATTTTTTAATA
1 TTATTTTTTAATA
1417577 TTATTTTTTAATA
1 TTATTTTTTAATA
1417590 TT
1 TT
1417592 TCATATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTTAATA
Found at i:1419418 original size:31 final size:31
Alignment explanation
Indices: 1419356--1419451 Score: 147
Period size: 31 Copynumber: 3.1 Consensus size: 31
1419346 TGAAGAAATA
* * *
1419356 AATGAAAAATACTTTAATAAAAAAACCTTAAT
1 AATGAAAAATACATTAAT-AGAAAACTTTAAT
1419388 AATGAAAAATACATTAATAGAAAACTTTAAT
1 AATGAAAAATACATTAATAGAAAACTTTAAT
*
1419419 AATGAAAAAGACATTAATAGAAAACTTTAAT
1 AATGAAAAATACATTAATAGAAAACTTTAAT
1419450 AA
1 AA
1419452 AAAATAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 43 0.72
32 17 0.28
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.27
Consensus pattern (31 bp):
AATGAAAAATACATTAATAGAAAACTTTAAT
Found at i:1421581 original size:30 final size:30
Alignment explanation
Indices: 1421523--1421582 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1421513 AGATTAGTTG
* *
1421523 ATTTTTGAGTCGAGTTAATATTATATCGGT
1 ATTTTTGAGTCGAATTAATATTAGATCGGT
*
1421553 ATTTTT-AGATCGAATTAATATTGGATCGGT
1 ATTTTTGAG-TCGAATTAATATTAGATCGGT
1421583 TGATTTTCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (30 bp):
ATTTTTGAGTCGAATTAATATTAGATCGGT
Found at i:1423357 original size:2 final size:2
Alignment explanation
Indices: 1423352--1423381 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1423342 TAAAAAAGAA
1423352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423382 TAATATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1424929 original size:73 final size:73
Alignment explanation
Indices: 1424822--1425073 Score: 371
Period size: 73 Copynumber: 3.4 Consensus size: 73
1424812 TGATATAATA
* * * * *
1424822 TATTTTCAAAAATATTTT-AAAACTATATAGTATATATGTTTTCAAAAATGTTTTAAAATTTATA
1 TATTTTC-AAAATGTTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAATCTATA
1424886 TATTATATT
65 TATTATATT
* *
1424895 TATTTTTAAAATGTTTTAAAAATTATATAATATATATATTTTTAAAAATGTTTTAAAATCTATAT
1 TATTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAATCTATAT
1424960 ATTATATT
66 ATTATATT
* *
1424968 TATTTTCAAAAAGTTTTAAAAACTATATAATATATATATTTTTTTAAAAATGTTTTAAAAACTAT
1 TATTTTCAAAATGTTTTAAAAACTATATAATATATATA--TTTTTAAAAATGTTTTAAAATCTAT
1425033 ATATTATATT
64 ATATTATATT
1425043 TATTTTCAAAATGTTTTAAAAAAACTATATA
1 TATTTTCAAAATGTTTT--AAAAACTATATA
1425074 TAAAAAAAAG
Statistics
Matches: 162, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 9 0.06
73 91 0.56
75 50 0.31
77 12 0.07
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (73 bp):
TATTTTCAAAATGTTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAATCTATAT
ATTATATT
Found at i:1425064 original size:36 final size:36
Alignment explanation
Indices: 1424822--1425074 Score: 292
Period size: 36 Copynumber: 6.8 Consensus size: 36
1424812 TGATATAATA
* * *
1424822 TATTTTCAAAAATATTTT-AAAACTATATAGTATATA
1 TATTTTC-AAAATGTTTTAAAAACTATATATTATATT
* **
1424858 TGTTTTCAAAAATGTTTTAAAATTTATATATTATATT
1 TATTTTC-AAAATGTTTTAAAAACTATATATTATATT
* * * *
1424895 TATTTTTAAAATGTTTTAAAAATTATATAATATATA
1 TATTTTCAAAATGTTTTAAAAACTATATATTATATT
* *
1424931 TATTTTTAAAAATGTTTTAAAATCTATATATTATATT
1 TA-TTTTCAAAATGTTTTAAAAACTATATATTATATT
*
1424968 TATTTTCAAAAAGTTTTAAAAACTATATAATATATATAT
1 TATTTTCAAAATGTTTTAAAAACTATAT-AT-TATAT-T
* *
1425007 TTTTTTAAAAATGTTTTAAAAACTATATATTATATT
1 TATTTTCAAAATGTTTTAAAAACTATATATTATATT
1425043 TATTTTCAAAATGTTTTAAAAAAACTATATAT
1 TATTTTCAAAATGTTTT--AAAAACTATATAT
1425075 AAAAAAAAGA
Statistics
Matches: 186, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
36 83 0.45
37 57 0.31
38 20 0.11
39 26 0.14
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
TATTTTCAAAATGTTTTAAAAACTATATATTATATT
Found at i:1425761 original size:84 final size:84
Alignment explanation
Indices: 1425680--1426337 Score: 669
Period size: 84 Copynumber: 7.9 Consensus size: 84
1425670 GTTTGCCTCT
* * * * * *
1425680 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGATAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
1425745 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* *
1425764 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGCTTGGA-AGATAACCCTTCTCGACTTAAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-GACAGATAACCCTTCTCGACTTAAGTTAT
*
1425828 GCTGCAAATGATATGCCTTG
65 GCTGCAAATGATGTGCCTTG
* * * * * *
1425848 GAGCCGAGTGTAGTCAAACTCGAAGG--TTT--TTGGCAGATAGCCCTTCTCGACTTATGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
*
1425909 CTGCAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * *
1425928 GAGCTGAGCATAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
* *
1425993 CTGCAAATGATATGCCTTA
66 CTGCAAATGATGTGCCTTG
* * * * * * *
1426012 GAGCAT-AGCATAGTCAAACTCGAAGGTCTTTTGG-AGACAAATAACCCTTCTAGCCTTGAGTTA
1 GAGC-TGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTCGACTTAAGTTA
* *
1426075 TGTTGTAAATGATGTGCCCTTG
64 TGCTGCAAATGATGTG-CCTTG
* * * * * ** * *
1426097 AAGCTGAGTGTAATCTAACTCGAGGGTCTTT-G--G-CAGATAGTCCTTCTCGACTTAAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
*
1426158 CTGCAAATGATGAGCCTTG
66 CTGCAAATGATGTGCCTTG
** * * * *
1426177 GAGCTGAGCGTAGTTAAACTCAAAGGTCTTTGGTTGGA-AAATAACGCTTCTCGATTTAAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-GACAGATAACCCTTCTCGACTTAAGTTAT
*
1426241 GCTGCAAAT-ATTGGTGCCTTT
65 GCTGCAAATGA-T-GTGCCTTG
* * * *
1426262 GAGCTGAGCGTAGTCGAACTCGAAGGTCCTTT-ATTGGCAAATAACCCTTCTCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTAT
* *
1426326 GTTGCAACTGAT
65 GCTGCAAATGAT
1426338 TTCTAAAAAA
Statistics
Matches: 480, Mismatches: 74, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.00
80 96 0.20
81 32 0.07
82 7 0.01
83 2 0.00
84 242 0.50
85 95 0.20
86 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Done.