Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005725.1 Hibiscus syriacus cultivar Beakdansim tig00013380_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: 59557
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:565 original size:12 final size:12
Alignment explanation
Indices: 532--571 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
522 ATGTACAACA
532 TACATTTCTTCTT
1 TACATTT-TTCTT
545 ATACATTTTTCTT
1 -TACATTTTTCTT
*
558 TTCATTTTTCTT
1 TACATTTTTCTT
570 TA
1 TA
572 GTAATTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 12 0.50
13 5 0.21
14 7 0.29
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (12 bp):
TACATTTTTCTT
Found at i:749 original size:45 final size:45
Alignment explanation
Indices: 643--1345 Score: 977
Period size: 45 Copynumber: 16.0 Consensus size: 45
633 TTTTGAGTTA
*
643 TGGCATCCTTTCATGCCTATAATGCACCCATAAGCATTATTA-TT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
**
687 TGGCATCCTTTCATGCCTATAATGCACCCATACACATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
732 TGGCATCCTTTCATGCC--TAATGTACCCATATGC---ATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
772 TGGCATCCTTTCATGCATATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
817 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
862 TGGCATCTTTTCATGCCTATAATGCA-CC-TATGCATTATTA-TT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
* * *
904 TGGCATCCTTTCATACCTATAATGCACCCCTATGGA-TATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
* *
948 TGGCATCATTTCATGTCTATAATGCACCCATATGCATTAATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATT-ATTATTT
* *
994 TGGCATCCTTTTATGCCTATAATGCACCCATATACATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
* * ** *
1039 TGGCACCCTTTCATG--TCTAATGCATCCGTTCATGCAATT-TTAGTTA
1 TGGCATCCTTTCATGCCTATAATGCA-CCCAT-ATGC-ATTATTA-TTT
*
1085 TGACATCCTTTCATGCCTATAATGCACCCATAT--ATTA-T-TTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
1126 TGGTATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
1171 TGGCATCCTTTCATGCCAATAATGCACCCATATG-ATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
1215 TGGCATCCTTTCATGCCTATAATGCACCCATATACATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
1260 TGGCATCCTTTCATGCCTAT-ATGCA-CC-TAT--ATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
*
1300 TGGCATCC-TTCATGCCTATAATTCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
1344 TG
1 TG
1346 TTCATTCGTT
Statistics
Matches: 588, Mismatches: 43, Indels: 56
0.86 0.06 0.08
Matches are distributed among these distances:
39 11 0.02
40 45 0.08
41 35 0.06
42 47 0.08
43 50 0.09
44 143 0.24
45 185 0.31
46 61 0.10
47 3 0.01
48 8 0.01
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.40
Consensus pattern (45 bp):
TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTT
Found at i:996 original size:132 final size:135
Alignment explanation
Indices: 643--1345 Score: 977
Period size: 132 Copynumber: 5.3 Consensus size: 135
633 TTTTGAGTTA
*
643 TGGCATCCTTTCATGCCTATAATGCACCCATAAGCATTATTA-TTTGGCATCCTTTCATGCCTAT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTAT
* *
707 AATGCACCCATACACATTATTATTTTGGCATCCTTTCATGCC--TAATGTACCCATATGC---AT
66 AATGCACCCATATACATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCATATGCATTAT
767 TATTT
131 TATTT
* *
772 TGGCATCCTTTCATGCATATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCAAT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTAT
* *
837 AATGCACCCATATGCATTATTATTTTGGCATCTTTTCATGCCTATAATGCA-CC-TATGCATTAT
66 AATGCACCCATATACATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCATATGCATTAT
900 TA-TT
131 TATTT
* * * * *
904 TGGCATCCTTTCATACCTATAATGCACCCCTATGGA-TATTATTTTGGCATCATTTCATGTCTAT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTAT
* * *
968 AATGCACCCATATGCATTAATTATTTTGGCATCCTTTTATGCCTATAATGCACCCATATACATTA
66 AATGCACCCATATACATT-ATTATTTTGGCATCCTTTCATGCCTATAATGCACCCATATGCATTA
1033 TTATTT
130 TTATTT
* * ** * *
1039 TGGCACCCTTTCATG--TCTAATGCATCCGTTCATGCAATT-TTAGTTATGACATCCTTTCATGC
1 TGGCATCCTTTCATGCCTATAATGCA-CCCAT-ATGC-ATTATTA-TTTTGGCATCCTTTCATGC
*
1101 CTATAATGCACCCATAT--ATTA-T-TTTTGGTATCCTTTCATGCCTATAATGCACCCATATGCA
62 CTATAATGCACCCATATACATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCATATGCA
1162 TTATTATTT
127 TTATTATTT
*
1171 TGGCATCCTTTCATGCCAATAATGCACCCATATG-ATTATTATTTTGGCATCCTTTCATGCCTAT
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTAT
1235 AATGCACCCATATACATTATTATTTTGGCATCCTTTCATGCCTAT-ATGCA-CC-TAT--ATTAT
66 AATGCACCCATATACATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCATATGCATTAT
1295 TATTT
131 TATTT
*
1300 TGGCATCC-TTCATGCCTATAATTCACCCATATGCATTATTATTTTG
1 TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTTTG
1346 TTCATTCGTT
Statistics
Matches: 511, Mismatches: 40, Indels: 46
0.86 0.07 0.08
Matches are distributed among these distances:
128 23 0.05
129 70 0.14
130 102 0.20
131 51 0.10
132 139 0.27
133 24 0.05
134 44 0.09
135 21 0.04
136 4 0.01
137 33 0.06
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.40
Consensus pattern (135 bp):
TGGCATCCTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTAT
AATGCACCCATATACATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCATATGCATTAT
TATTT
Found at i:4159 original size:23 final size:24
Alignment explanation
Indices: 4135--4238 Score: 83
Period size: 23 Copynumber: 4.5 Consensus size: 24
4125 TAACGTAGAT
*
4135 ATCAAAAATCA-AACAGAATTCAT
1 ATCAAAAATCAGAACAGAATTCAG
* * * * *
4158 AT-ATATACCATAACAGAATCCAG
1 ATCAAAAATCAGAACAGAATTCAG
*
4181 ATCGAAAATCAGAAC--AATTCAG
1 ATCAAAAATCAGAACAGAATTCAG
* *
4203 ATCAGAAATCAGAATAGAATTCA-
1 ATCAAAAATCAGAACAGAATTCAG
*
4226 ATCAGAAATCAGA
1 ATCAAAAATCAGA
4239 TAAAATATTC
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
22 23 0.37
23 27 0.43
24 13 0.21
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAAAAATCAGAACAGAATTCAG
Found at i:11059 original size:31 final size:33
Alignment explanation
Indices: 11021--11083 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
11011 TTTGCAACAT
*
11021 AAATCATA-ACAAA-TCACTTTCCAGT-TCCAAA
1 AAATCATACAAAAACTC-CTTTCCAGTGTCCAAA
11052 AAATCATACAAAAACTCCTTTCCAGTGTCCAA
1 AAATCATACAAAAACTCCTTTCCAGTGTCCAA
11084 GTCCTTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
32 13 0.46
33 7 0.25
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (33 bp):
AAATCATACAAAAACTCCTTTCCAGTGTCCAAA
Found at i:19704 original size:18 final size:19
Alignment explanation
Indices: 19660--19707 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
19650 AATGTCGAGT
19660 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
19679 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
19698 T-ATTTTGTAT
1 TAATTTTGTAT
19708 GTGAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:20249 original size:198 final size:198
Alignment explanation
Indices: 19824--20964 Score: 1919
Period size: 198 Copynumber: 5.9 Consensus size: 198
19814 CAATATGGCC
* * *
19824 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG--A
*
19889 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAG
63 ACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
19953 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
128 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
20018 ATGGAA
193 ATGGAA
20024 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
20088 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
20153 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
20218 GAA
196 GAA
*
20221 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
20286 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
20351 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
20415 TAAA
195 GGAA
20419 AACAAGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
20482 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA-
66 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
20546 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGAA
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTT-CCAGAATGAA
20611 TGGAA
194 TGGAA
20616 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
20681 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
*
20746 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
20811 GAA
196 GAA
* *
20814 AACAAGGTGCACCCATAAAGTGTCGATCC------CAAAA---TC-AT--C--GA--A-C---CC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
20859 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGA
66 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
20923 ATATGTCTAAATAATGTGTCGACAC---TATAGTTTGTGTCGATA
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
20965 CTAATTTAAA
Statistics
Matches: 919, Mismatches: 14, Indels: 42
0.94 0.01 0.04
Matches are distributed among these distances:
174 17 0.02
177 36 0.04
178 54 0.06
181 1 0.00
182 1 0.00
184 1 0.00
186 1 0.00
188 2 0.00
189 2 0.00
192 4 0.00
195 46 0.05
196 136 0.15
197 149 0.16
198 260 0.28
199 206 0.22
200 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
GAA
Found at i:20599 original size:395 final size:395
Alignment explanation
Indices: 19824--20964 Score: 1960
Period size: 395 Copynumber: 2.9 Consensus size: 395
19814 CAATATGGCC
* *
19824 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
19889 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
19953 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGA
20018 ATGGAAAAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
193 ATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCC-AAATCAT
20082 CGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
256 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
*
20146 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
321 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGA
20211 ATGAATGGAA
386 ATGAATGGAA
20221 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
20286 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
20351 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
*
20416 AAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAATCATCGAAC
196 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAATCATCGAAC
20481 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
261 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
20546 -AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGA
326 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGA
20610 ATGGAA
390 ATGGAA
*
20616 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
20681 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
20745 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
20810 GGAAAACAAGGTGCACCCATAAAGTGTCGATCC--------------C-A----AAATCATCGAA
195 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAATCATCGAA
20856 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAG
260 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
20920 AGAATATGTCTAAATAATGTGTCGACAC---TATAGTTTGTGTCGATA
325 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
20965 CTAATTTAAA
Statistics
Matches: 729, Mismatches: 9, Indels: 36
0.94 0.01 0.05
Matches are distributed among these distances:
373 17 0.02
375 9 0.01
376 93 0.13
380 1 0.00
381 1 0.00
394 176 0.24
395 283 0.39
396 114 0.16
397 35 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (395 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAATCATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
TGGAA
Found at i:22442 original size:18 final size:18
Alignment explanation
Indices: 22421--22488 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
22411 AGCGGTCGCA
22421 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
22439 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
22460 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
22481 GAAGATGA
1 GAAGATGA
22489 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:22445 original size:6 final size:6
Alignment explanation
Indices: 22421--22518 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
22411 AGCGGTCGCA
* * * * * *
22421 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
22469 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
22517 GA
1 GA
22519 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:22456 original size:3 final size:3
Alignment explanation
Indices: 22436--22522 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
22426 TGAAGCTGAC
* * * * * ** *
22436 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
22484 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
22523 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:22471 original size:42 final size:42
Alignment explanation
Indices: 22424--22514 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
22414 GGTCGCAGAA
*
22424 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
22466 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
22508 GATGAAG
1 GATGAAG
22515 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:22522 original size:18 final size:18
Alignment explanation
Indices: 22421--22518 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
22411 AGCGGTCGCA
* *
22421 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
22439 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
22457 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
22475 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
22493 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
22511 GAAGATGA
1 GAAGATGA
22519 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:24291 original size:184 final size:184
Alignment explanation
Indices: 23982--24693 Score: 1316
Period size: 184 Copynumber: 3.9 Consensus size: 184
23972 CTTTCAACAT
** * * * * * *
23982 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATCTACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
* * *
24047 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
24112 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24166 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
24231 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
24296 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24350 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
24415 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
24480 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24534 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
24599 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
*
24664 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
24694 GTAATTTGAA
Statistics
Matches: 516, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 516 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:27189 original size:25 final size:25
Alignment explanation
Indices: 27155--27219 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
27145 TTATCATTAA
27155 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
27180 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
27205 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
27220 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:27537 original size:23 final size:23
Alignment explanation
Indices: 27506--27569 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
27496 ATAGGTAAAC
*
27506 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
27529 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
27552 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
27570 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:27576 original size:23 final size:23
Alignment explanation
Indices: 27506--27578 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
27496 ATAGGTAAAC
* **
27506 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
27529 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
27552 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
27575 ATAT
1 ATAT
27579 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:27877 original size:25 final size:25
Alignment explanation
Indices: 27843--27893 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
27833 ACAACAAATC
*
27843 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
27868 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
27893 A
1 A
27894 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:28208 original size:18 final size:18
Alignment explanation
Indices: 28187--28223 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28177 GTAATTGGAG
28187 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
28205 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
28223 T
1 T
28224 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:28231 original size:24 final size:24
Alignment explanation
Indices: 28179--28225 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
28169 TTTCATATGT
* *
28179 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
28203 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
28226 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:28525 original size:39 final size:39
Alignment explanation
Indices: 28482--28568 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
28472 TCCGATGCTC
*
28482 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
28521 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
28560 ATCAAAATC
1 ATCAAAATC
28569 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:29000 original size:23 final size:23
Alignment explanation
Indices: 28969--29032 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
28959 ATAGGTAAAC
*
28969 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
28992 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
29015 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
29033 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:29039 original size:23 final size:23
Alignment explanation
Indices: 28969--29041 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
28959 ATAGGTAAAC
* **
28969 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
28992 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
29015 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
29038 ATAT
1 ATAT
29042 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:31926 original size:42 final size:42
Alignment explanation
Indices: 31877--31973 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
31867 ACTAAAACTC
*
31877 GTACTTTAGTGGTGTTTATTTGACAAACGCCGCTAAATATAA
1 GTACTTTAGTGGCGTTTATTTGACAAACGCCGCTAAATATAA
*
31919 GTACTTTAGTGGCGTTTATTTGACAAACGCCGCTAAATATCA
1 GTACTTTAGTGGCGTTTATTTGACAAACGCCGCTAAATATAA
31961 GTACTTTAGTGGC
1 GTACTTTAGTGGC
31974 ATTTGTAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (42 bp):
GTACTTTAGTGGCGTTTATTTGACAAACGCCGCTAAATATAA
Found at i:32050 original size:41 final size:41
Alignment explanation
Indices: 31847--32146 Score: 144
Period size: 41 Copynumber: 7.2 Consensus size: 41
31837 TAACATTAAC
* * * * **
31847 GGCGTTTCTCAACAAGCGCCACTAAAAC-TCGTACTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAGT
* ** *
31887 GGTGTTTATTTGACAAACGCCGCT-AAATATAAGTACTTTAGT
1 GGCGTTT-TTAAACAAACGCCGCTAAAACATAA-TACTTTAGT
** * *
31929 GGCGTTTATTTGACAAACGCCGCT-AAATATCAGTACTTTAGT
1 GGCGTTT-TTAAACAAACGCCGCTAAAACAT-AATACTTTAGT
* * * * * * ** *
31971 GGCATTTGTAAACAAATGCCG-TCATATAGTCGTTCTTTAGT
1 GGCGTTTTTAAACAAACGCCGCTAAAACA-TAATACTTTAGT
* *
32012 GGTGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAAT
1 GGCGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAGT
* * * * **
32053 GGCATTTTAAGCAAAAAAATGCCGCTAAATAC-TCGTACTTTAGT
1 GGCGTTTT---TAAACAAACGCCGCTAAA-ACATAATACTTTAGT
** * *
32097 GGCGTTTTCCAACAAACGCCGCTAAATAC-TCATACTATAGT
1 GGCGTTTTTAAACAAACGCCGCTAAA-ACATAATACTTTAGT
*
32138 GGCATTTTT
1 GGCGTTTTT
32147 TGAATAAATG
Statistics
Matches: 203, Mismatches: 46, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
40 10 0.05
41 101 0.50
42 58 0.29
43 1 0.00
44 31 0.15
45 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (41 bp):
GGCGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAGT
Found at i:32092 original size:44 final size:41
Alignment explanation
Indices: 31901--32145 Score: 158
Period size: 41 Copynumber: 5.9 Consensus size: 41
31891 TTTATTTGAC
* * *** *
31901 AAACGCCGCTAAATA-TAAGTACTTTAGTGGCGTTTATTTGAC
1 AAACGCCGCTAAATACTCA-TACTTTAGTGGCATTT-TCAAAA
*
31943 AAACGCCGCTAAATA-TCAGTACTTTAGTGGCATTTGT-AAAC
1 AAACGCCGCTAAATACTCA-TACTTTAGTGGCATTT-TCAAAA
* * * * * ** * *
31984 AAATGCCG-TCATATAGTCGTTCTTTAGTGGTGTTTTTAAAC
1 AAACGCCGCT-AAATACTCATACTTTAGTGGCATTTTCAAAA
* *
32025 AAACGCCGCTAAA-ACATAATACTTTAATGGCATTTTAAGCAAAA
1 AAACGCCGCTAAATAC-TCATACTTTAGTGGCATTTT---CAAAA
* * * * *
32069 AAATGCCGCTAAATACTCGTACTTTAGTGGCGTTTTCCAAC
1 AAACGCCGCTAAATACTCATACTTTAGTGGCATTTTCAAAA
*
32110 AAACGCCGCTAAATACTCATACTATAGTGGCATTTT
1 AAACGCCGCTAAATACTCATACTTTAGTGGCATTTT
32146 TTGAATAAAT
Statistics
Matches: 161, Mismatches: 33, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
40 3 0.02
41 88 0.55
42 37 0.23
44 31 0.19
45 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAAATACTCATACTTTAGTGGCATTTTCAAAA
Found at i:32114 original size:85 final size:82
Alignment explanation
Indices: 31905--32145 Score: 238
Period size: 85 Copynumber: 2.9 Consensus size: 82
31895 TTTGACAAAC
* ** * *
31905 GCCGCTAAATATAAGTACTTTAGTGGCGTTTATTTGACAAACGCCGCT-AAATATCAGTACTTTA
1 GCCGCTAAATAT-CGTACTTTAGTGGCGTTT-TTAAACAAACGCCGCTAAAACAT-AATACTTTA
* *
31969 GTGGCA-TTTGTAAACAAAT
63 GTGGCATTTTGCAAAAAAAT
* * * *
31988 GCCG-TCATATAGTCGTTCTTTAGTGGTGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAA
1 GCCGCT-AAATA-TCGTACTTTAGTGGCGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAG
32052 TGGCATTTTAAGCAAAAAAAT
64 TGGCATTTT--GCAAAAAAAT
** * *
32073 GCCGCTAAATACTCGTACTTTAGTGGCGTTTTCCAACAAACGCCGCTAAATAC-TCATACTATAG
1 GCCGCTAAATA-TCGTACTTTAGTGGCGTTTTTAAACAAACGCCGCTAAA-ACATAATACTTTAG
32137 TGGCATTTT
64 TGGCATTTT
32146 TTGAATAAAT
Statistics
Matches: 130, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
82 28 0.22
83 31 0.24
84 1 0.01
85 67 0.52
86 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (82 bp):
GCCGCTAAATATCGTACTTTAGTGGCGTTTTTAAACAAACGCCGCTAAAACATAATACTTTAGTG
GCATTTTGCAAAAAAAT
Found at i:35354 original size:43 final size:42
Alignment explanation
Indices: 35105--35462 Score: 491
Period size: 42 Copynumber: 8.4 Consensus size: 42
35095 TTTGTATAAA
* **
35105 AAAAACGCCGCTATAGATATGACTTTTTGCGGCGTTTGTTAT
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* * *
35147 AAAAACGCCGCTATAGATCTGACCTTTTGCGGTGTTTGTTAC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* *
35189 AAAAACGCCGCTATAGATTTGACCTTTTGCGGTGTTTGTTCC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* *
35231 AAAAACGCCGCTATAGATATGACCTTTTGCGACATTTGTTCC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* * * *
35273 AAAAATGACGCTATAAATATGACCTTTTGCGACGTTTGTTCC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
** *
35315 AAAAACGCCGCTATAGATATCGACCTTTTGCGAAGTTTGTTCT
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCC
35358 AAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCC
* * * *
35401 AAAAATGCCACTATATATATCGACCTTTTGCGGCGTTTGTTTCA
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGGCGTTTG-TTCC
35445 AAAAACGCCGCTATAGAT
1 AAAAACGCCGCTATAGAT
35463 CTTGACTTAT
Statistics
Matches: 285, Mismatches: 29, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 171 0.60
43 96 0.34
44 18 0.06
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
Found at i:36074 original size:16 final size:15
Alignment explanation
Indices: 36053--36109 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
36043 GCTATTTTTT
36053 CAAAAAAGAAAAAGGC
1 CAAAAAA-AAAAAGGC
**
36069 CAAAAAATCAAAGGC
1 CAAAAAAAAAAAGGC
*
36084 CAAAAAAATCAAAAAGC
1 CAAAAAAA--AAAAGGC
36101 CAAAAAAAA
1 CAAAAAAAA
36110 GTCACAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 14 0.41
16 7 0.21
17 13 0.38
ACGTcount: A:0.70, C:0.16, G:0.11, T:0.04
Consensus pattern (15 bp):
CAAAAAAAAAAAGGC
Found at i:36081 original size:15 final size:16
Alignment explanation
Indices: 36062--36107 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
36052 TCAAAAAAGA
36062 AAAAGGCCAAAAAATC
1 AAAAGGCCAAAAAATC
36078 -AAAGGCCAAAAAAATC
1 AAAAGGCC-AAAAAATC
*
36094 AAAAAGCCAAAAAA
1 AAAAGGCCAAAAAA
36108 AAGTCACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 7 0.26
16 14 0.52
17 6 0.22
ACGTcount: A:0.67, C:0.17, G:0.11, T:0.04
Consensus pattern (16 bp):
AAAAGGCCAAAAAATC
Found at i:36090 original size:17 final size:17
Alignment explanation
Indices: 36061--36108 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
36051 TTCAAAAAAG
36061 AAAAAGGCC-AAAAAATC
1 AAAAA-GCCAAAAAAATC
*
36078 -AAAGGCCAAAAAAATC
1 AAAAAGCCAAAAAAATC
36094 AAAAAGCCAAAAAAA
1 AAAAAGCCAAAAAAA
36109 AGTCACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 13 0.48
ACGTcount: A:0.69, C:0.17, G:0.10, T:0.04
Consensus pattern (17 bp):
AAAAAGCCAAAAAAATC
Found at i:45425 original size:183 final size:183
Alignment explanation
Indices: 45115--45470 Score: 538
Period size: 183 Copynumber: 1.9 Consensus size: 183
45105 TCATTCAAAT
* *
45115 ATGTATCGATACATAACAATATAACAGGTAAAAATATGATAAAATCAGGTTCAATATGACAAAAC
1 ATGTATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCAGGTTCAATATGACAAAAC
45180 CGATAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTA-TG
66 CGATAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATTG
*
45244 AAATTTAAAAAAATAATAATAATAGTGCCTATAAAGTATCGATATTTTATAAAC
131 AAATTTAAAAAAA-AATAATAATAGCGCCTATAAAGTATCGATATTTTATAAAC
** * * *
45298 ATGTATCGATATGTAACAATATAAAATGTAAAAATATGACAAAA-CCGGTTTCATTATGACAAAA
1 ATGTATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCAGG-TTCAATATGACAAAA
* *
45362 CCGGTAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTTAAATAAGTATC-AGTACTTAT
65 CCGATAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGA-TACTTAT
* * * *
45426 TGAATTTTAAAGAAAAGTGATAATAGCGCCTATAAAGTATCGATA
129 TGAAATTTAAAAAAAAATAATAATAGCGCCTATAAAGTATCGATA
45471 CGTAACAATA
Statistics
Matches: 156, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
182 4 0.03
183 139 0.89
184 13 0.08
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (183 bp):
ATGTATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCAGGTTCAATATGACAAAAC
CGATAAAGCGCTACCAGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATTG
AAATTTAAAAAAAAATAATAATAGCGCCTATAAAGTATCGATATTTTATAAAC
Found at i:45468 original size:162 final size:162
Alignment explanation
Indices: 45300--45814 Score: 638
Period size: 162 Copynumber: 3.1 Consensus size: 162
45290 TTATAAACAT
* *
45300 GTATCGATATGTAACAATATAAAATGTAAAAATATGACAAAACCGGTTTCATTATGACAAAACCG
1 GTATCGATATGTAACAATATAAAAGGTAAAAATATGACAAAACCGATTTCATTATGACAAAACCG
* * *
45365 GTAAAGCGCTACC-AGATATGTTGAAGGTATCGATTCCATTTAAATAAGTATC-AGTACTTATTG
66 GTAAAACGCTACCGA-ATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGA-TACTTATGG
**
45428 AATTTTAAAGAAAAGTGATAATAGCGCCTATAAA
129 AATTTTAAAGAAAAGCAATAATAGCGCCTATAAA
* * * *
45462 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGATTTCATTATGACAAAATCG
1 GTATCGATATGTAACAATATAAAAGGTAAAAATATGACAAAACCGATTTCATTATGACAAAACCG
* *
45527 GTAAAACGCTACCGAATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATGGAA
66 GTAAAACGCTACCGAATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATGGAA
45592 TTTTAAAGAAAAGCAATAATAGCGCCTATAAA
131 TTTTAAAGAAAAGCAATAATAGCGCCTATAAA
* *
45624 GTATCGATATTTTACAAACATGTATCGGTACGTAACAATAAACAGGTAAAAATATGACAAAGCCG
1 GTATCG--A---T------ATGTA-----AC--AA-TATAAA-AGGTAAAAATATGACAAAACCG
* * *
45689 GTTTCATTATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAGGTATCGATTCCATTCAAAT
46 ATTTCATTATGACAAAACCGGTAAAACGCTACCGAATATGTTGAAGGTATCGATTCCATTCAAAT
* *
45754 AAGTATCGATACTTATGGAATTTTAAAGAAAAACAATAATAGCTCCTATAAA
111 AAGTATCGATACTTATGGAATTTTAAAGAAAAGCAATAATAGCGCCTATAAA
45806 GTATCGATA
1 GTATCGATA
45815 CTTTATAAAC
Statistics
Matches: 305, Mismatches: 26, Indels: 35
0.83 0.07 0.10
Matches are distributed among these distances:
162 151 0.50
163 2 0.01
164 1 0.00
167 1 0.00
171 1 0.00
173 4 0.01
177 1 0.00
178 2 0.01
180 3 0.01
181 4 0.01
182 135 0.44
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (162 bp):
GTATCGATATGTAACAATATAAAAGGTAAAAATATGACAAAACCGATTTCATTATGACAAAACCG
GTAAAACGCTACCGAATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATGGAA
TTTTAAAGAAAAGCAATAATAGCGCCTATAAA
Found at i:45967 original size:183 final size:183
Alignment explanation
Indices: 45462--46108 Score: 1019
Period size: 183 Copynumber: 3.5 Consensus size: 183
45452 CGCCTATAAA
* *
45462 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGATTTCATTATGACAAAATCG
1 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATTATGACAAAACCG
* * *
45527 GTAAAACGCTACCGAATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATGGAA
66 ATAAAGCGCTACCGGATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATGGAA
* *
45592 TTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATATTTTACAAACAT
131 TTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACAT
* **
45645 GTATCGGTACGTAACAATA-AACAGGTAAAAATATGACAAAGCCGGTTTCATTATGACAAAACCG
1 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATTATGACAAAACCG
* * *
45709 GTAAAGCGCTACCGGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTATGGAA
66 ATAAAGCGCTACCGGATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATGGAA
* *
45774 TTTTAAAGAAAAACAATAATAGCTCCTATAAAGTATCGATACTTTATAAACAT
131 TTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACAT
* * *
45827 GTATCGATACATAACAATATAACATGTAAAAATATGAAAAAATCGGTTTCATTATGACAAAACCG
1 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATTATGACAAAACCG
* * * * *
45892 ATAAATCGTTACCAGATATGTTGAAGGTGTCAATTTCATTCAAATAAGTATCGATACTTTTGGAA
66 ATAAAGCGCTACCGGATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATGGAA
*
45957 TTTAAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACAT
131 TTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACAT
*
46010 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAA-CTGGTTTCATTATGACGAAACC
1 GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATC-GGTTTCATTATGACAAAACC
* * *
46074 GATAAAGCGTTATCGGATATGTTGAAGGTATCGAT
65 GATAAAGCGCTACCGGATATGTTGAAGGTGTCGAT
46109 ACTTTAATAA
Statistics
Matches: 423, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
182 169 0.40
183 254 0.60
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (183 bp):
GTATCGATACGTAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATTATGACAAAACCG
ATAAAGCGCTACCGGATATGTTGAAGGTGTCGATTTCATTCAAATAAGTATCGATACTTATGGAA
TTTTAAAGAAAAGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACAT
Found at i:47622 original size:20 final size:20
Alignment explanation
Indices: 47577--47622 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
47567 GTTTACATAA
*
47577 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTTGTAC
*
47597 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACTTTTTGTAC
47618 AGTAT
1 AGTAT
47623 GCTTCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAC
Found at i:47970 original size:20 final size:20
Alignment explanation
Indices: 47925--47970 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
47915 TTTTACATAA
* *
47925 AGTATCGATACTTTTTGTAT
1 AGTATCAATACTTTTTGTAC
47945 ATGTATCAATACTTTTTGTAC
1 A-GTATCAATACTTTTTGTAC
47966 AGTAT
1 AGTAT
47971 ACTTCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (20 bp):
AGTATCAATACTTTTTGTAC
Found at i:48269 original size:118 final size:116
Alignment explanation
Indices: 48059--48317 Score: 333
Period size: 118 Copynumber: 2.2 Consensus size: 116
48049 AACAAATTCG
* * *
48059 GTAATTAACCTA-TTTTGTTATCGTCGGATTTCCAAAAGCTCTATCGCTTAAAAAGGACTACCTA
1 GTAATTAA-CTAGTTATGTTATCGTCAGATTTCCAAAAGCTCCATCGCTTAAAAAGGACTACCTA
* * * *
48123 TTACGTTATATAAGTGCTATCTAATATGTTATTATGTTTGATAATGTTTCCA
65 TTACGTTATATAAATGCTACCTAATATGTTATCATGCTTGATAATGTTTCCA
* *
48175 GTAATTAACTAGTTATGTTATCGTCAGATTTCC-AAAGCTCCATCAGCTTTAACAAGGCGCTACC
1 GTAATTAACTAGTTATGTTATCGTCAGATTTCCAAAAGCTCCATC-GC-TTAAAAAGG-ACTACC
* * *
48239 TATTACGTTATATAAATGTTACCTAATATGTTATCGTGCTTGATAATGTTTCGA
63 TATTACGTTATATAAATGCTACCTAATATGTTATCATGCTTGATAATGTTTCCA
* **
48293 ATAATTAACCGGTTATGTTATCGTC
1 GTAATTAACTAGTTATGTTATCGTC
48318 TATATATTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
115 13 0.10
116 29 0.23
117 8 0.06
118 74 0.60
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (116 bp):
GTAATTAACTAGTTATGTTATCGTCAGATTTCCAAAAGCTCCATCGCTTAAAAAGGACTACCTAT
TACGTTATATAAATGCTACCTAATATGTTATCATGCTTGATAATGTTTCCA
Found at i:56473 original size:8 final size:7
Alignment explanation
Indices: 56460--56500 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
56450 AAACTCTAAG
56460 TTTAAAT
1 TTTAAAT
*
56467 CTTTAAAA
1 -TTTAAAT
56475 TTTAAAT
1 TTTAAAT
*
56482 TTTAAAA
1 TTTAAAT
56489 TTTAAAT
1 TTTAAAT
56496 TTTAA
1 TTTAA
56501 TTTATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (7 bp):
TTTAAAT
Found at i:56487 original size:14 final size:14
Alignment explanation
Indices: 56460--56500 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
56450 AAACTCTAAG
56460 TTTAAATCTTTAAAA
1 TTTAAAT-TTTAAAA
56475 TTTAAATTTTAAAA
1 TTTAAATTTTAAAA
56489 TTTAAATTTTAA
1 TTTAAATTTTAA
56501 TTTATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTAAATTTTAAAA
Done.