Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1244880 original size:35 final size:35
Alignment explanation
Indices: 1244834--1244900 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1244824 GGTGTCAAAG
*
1244834 TGCATCCATGCACTCTG-TAGTGCATCCATGCATTA
1 TGCATCCATGCACCCTGAT-GTGCATCCATGCATTA
*
1244869 TGCATCGATGCACCCTGATGTGCATCCATGCA
1 TGCATCCATGCACCCTGATGTGCATCCATGCA
1244901 CTCAAACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.28
Consensus pattern (35 bp):
TGCATCCATGCACCCTGATGTGCATCCATGCATTA
Found at i:1246384 original size:15 final size:15
Alignment explanation
Indices: 1246364--1246405 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1246354 GATGGTGAAA
1246364 GAAGATGAAGAAAGG
1 GAAGATGAAGAAAGG
1246379 GAAGATGAAGAAAGG
1 GAAGATGAAGAAAGG
1246394 GAAGA-GAAGAAA
1 GAAGATGAAGAAA
1246406 AACAAGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.05
Consensus pattern (15 bp):
GAAGATGAAGAAAGG
Found at i:1248105 original size:21 final size:21
Alignment explanation
Indices: 1248079--1248118 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1248069 CAACAATTGG
1248079 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1248100 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1248119 CATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1248365 original size:20 final size:20
Alignment explanation
Indices: 1248340--1248410 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1248330 AGGGTGTCAA
1248340 AGTGCATCCATGCACTATGT
1 AGTGCATCCATGCACTATGT
1248360 AGTGCATCCATG--C-AT-T
1 AGTGCATCCATGCACTATGT
* **
1248376 A-TGCATCGATGCACCCTGT
1 AGTGCATCCATGCACTATGT
*
1248395 TGTGCATCCATGCACT
1 AGTGCATCCATGCACT
1248411 CTGGCTGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 9 0.22
16 2 0.05
17 3 0.07
18 2 0.05
19 1 0.02
20 24 0.59
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (20 bp):
AGTGCATCCATGCACTATGT
Found at i:1248388 original size:35 final size:35
Alignment explanation
Indices: 1248342--1248408 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
1248332 GGTGTCAAAG
*
1248342 TGCATCCATGCACTATGTAGTGCATCCATGCATTA
1 TGCATCCATGCACCATGTAGTGCATCCATGCATTA
* * *
1248377 TGCATCGATGCACCCTGTTGTGCATCCATGCA
1 TGCATCCATGCACCATGTAGTGCATCCATGCA
1248409 CTCTGGCTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (35 bp):
TGCATCCATGCACCATGTAGTGCATCCATGCATTA
Found at i:1251539 original size:7 final size:7
Alignment explanation
Indices: 1251527--1251572 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
1251517 TTTTTCTTTA
1251527 CTTTTTT
1 CTTTTTT
1251534 CTTTTTT
1 CTTTTTT
1251541 CTTTTTT
1 CTTTTTT
1251548 CTTTTTT
1 CTTTTTT
1251555 C-TTTTT
1 CTTTTTT
*
1251561 CTTTTTG
1 CTTTTTT
1251568 CTTTT
1 CTTTT
1251573 ACTTGAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
6 6 0.16
7 31 0.84
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:1251545 original size:13 final size:13
Alignment explanation
Indices: 1251529--1251572 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
1251519 TTTCTTTACT
1251529 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
1251542 TTTTTTCTTTTTTC
1 -TTTTTCTTTTTTC
*
1251556 TTTTTCTTTTTGC
1 TTTTTCTTTTTTC
1251569 TTTT
1 TTTT
1251573 ACTTGAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:1252265 original size:132 final size:132
Alignment explanation
Indices: 1252028--1252274 Score: 311
Period size: 132 Copynumber: 1.9 Consensus size: 132
1252018 ATGACAATGT
1252028 TGATCCAACTCCGTATGCGATGGATTTGAGCGAAATAAAAATGTCGATCTACCTCATTCTGTGAT
1 TGATCCAACTCCGTATGCGATGGATTTGAGCGAAATAAAAATGTCGATCTACCTCATTCTGTGAT
*** *
1252093 GGAATCGAACGAGATGTCAGTGATGATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTTGAT
66 GGAATCGAACGAGATAAAAATGATGATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTTGAT
1252158 GC
131 GC
* * * * * *
1252160 TGATCCAACTCCTTCTGTGATGGATTTGAGCGAGATAAAAATGTCGATC-ATTCTCCTTCTGTGA
1 TGATCCAACTCCGTATGCGATGGATTTGAGCGAAATAAAAATGTCGATCTA-CCTCATTCTGTGA
* * * * *
1252224 TGGATTTGAGCTAGATAAAAATG-TCGATCCT-CCTCCTTCTGTGATGGAATC
65 TGGAATCGAACGAGATAAAAATGAT-GAT-CTACCTCCTTCTGTGATAGAATC
1252275 AAACGAGATG
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
131 2 0.02
132 93 0.96
133 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (132 bp):
TGATCCAACTCCGTATGCGATGGATTTGAGCGAAATAAAAATGTCGATCTACCTCATTCTGTGAT
GGAATCGAACGAGATAAAAATGATGATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTTGAT
GC
Found at i:1252304 original size:88 final size:85
Alignment explanation
Indices: 1252046--1252312 Score: 216
Period size: 88 Copynumber: 3.0 Consensus size: 85
1252036 CTCCGTATGC
*
1252046 GATGGATTTGAGCGAAATAAAAATGTCGAT-CTACCTCATTCTGTGATGGAATCGAACGAGATGT
1 GATGGATTTGAGC--AATAAAAATGTCGATCCT-CCTCCTTCTGTGATGGAATCGAACGAGATGT
*
1252110 CAGTGATGATCTACCTCCTTCTGT
63 AAGTG-TGATCTACCTCCTTCTGT
* * * * *** ** * * * **
1252134 GATAGAATCGATCAA-AACGTTGATGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAGATAA
1 GATGGATTTGAGCAATAAAAATG-T-C-GATCCTCCTCCTTCTGTGATGGAATCGAACGAGATGT
* *
1252198 AAATGTCGATC-ATTCTCCTTCTGT
63 AAGTGT-GATCTA-CCTCCTTCTGT
* *
1252222 GATGGATTTGAGCTAGATAAAAATGTCGATCCTCCTCCTTCTGTGATGGAATCAAACGAGATGTT
1 GATGGATTTGAGC-A-ATAAAAATGTCGATCCTCCTCCTTCTGTGATGGAATCGAACGAGATGTA
*
1252287 AGTGCTAATCTACCTCCTTCTGT
64 AGTG-TGATCTACCTCCTTCTGT
1252310 GAT
1 GAT
1252313 AGAATCGAGC
Statistics
Matches: 131, Mismatches: 37, Indels: 22
0.69 0.19 0.12
Matches are distributed among these distances:
85 4 0.03
86 3 0.02
87 3 0.02
88 110 0.84
89 5 0.04
90 2 0.02
91 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (85 bp):
GATGGATTTGAGCAATAAAAATGTCGATCCTCCTCCTTCTGTGATGGAATCGAACGAGATGTAAG
TGTGATCTACCTCCTTCTGT
Found at i:1252304 original size:132 final size:133
Alignment explanation
Indices: 1252117--1252591 Score: 480
Period size: 132 Copynumber: 3.6 Consensus size: 133
1252107 TGTCAGTGAT
* * * * * * * *
1252117 GATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTT-GATGCTGATCCAACTCCTTCTGTGAT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTAG-TGCTGATCTACCTCCTTCTGTGAT
* * * * *
1252181 GGATTTGAGCGAGATAAAAATG-T-C-GAT-CATTCTCCTTCTGTGATGGATTTGAGCTAGATAA
65 AGAATCGAGC-A-A-AAAAATGATGCTGATCCATTCTCATTCTGTGATGGATTTGAGCGAGATAA
1252242 AAATGTC
127 AAATGTC
* * *
1252249 GATCCTCCTCCTTCTGTGATGGAATCAAACGAGATGTTAGTGCTAATCTACCTCCTTCTGTGATA
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTAGTGCTGATCTACCTCCTTCTGTGATA
** * * * *
1252314 GAATCGAGCAAAAAGTTGATGCTGGTCCA-ACTCCTTCTGTGGTGGATTTGAGCGAGATAAAAAT
66 GAATCGAGCAAAAAAATGATGCTGATCCATTCTCATTCTGTGATGGATTTGAGCGAGATAAAAAT
* *
1252378 TTT
131 GTC
* * * **
1252381 GATCCACCTCCTTTTATGATGGAATCGAATGAGATGCCAGTGCTGATCTACCTCCTTCTGTGATA
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTAGTGCTGATCTACCTCCTTCTGTGATA
* ** * * * *
1252446 GAATCAAGCAAAAAGTTGATGCTGATCCAAT-TCATTCTGTGATGGATTTAAGAGAAATAAAAAT
66 GAATCGAGCAAAAAAATGATGCTGATCCATTCTCATTCTGTGATGGATTTGAGCGAGATAAAAAT
*
1252510 ATC
131 GTC
* * * *
1252513 GATCAACCTCCTTCTGTGATGGAATCGAACGAGAT-TTCGGTGTTGATCTACCTCATTCTGTGAT
1 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTT-AGTGCTGATCTACCTCCTTCTGTGAT
1252577 AGAATCGAGCAAAAA
65 AGAATCGAGCAAAAA
1252592 GTTGATGCAT
Statistics
Matches: 286, Mismatches: 50, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
129 5 0.02
130 2 0.01
131 2 0.01
132 274 0.96
133 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (133 bp):
GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTAGTGCTGATCTACCTCCTTCTGTGATA
GAATCGAGCAAAAAAATGATGCTGATCCATTCTCATTCTGTGATGGATTTGAGCGAGATAAAAAT
GTC
Found at i:1252345 original size:176 final size:176
Alignment explanation
Indices: 1252046--1252377 Score: 549
Period size: 176 Copynumber: 1.9 Consensus size: 176
1252036 CTCCGTATGC
*
1252046 GATGGATTTGAGCGAAATAAAAATGTCGATCTACCTCATTCTGTGATGGAATCGAACGAGATGTC
1 GATGGATTTGAGCGAAATAAAAATGTCGATCTACCTCATTCTGTGATGGAATCAAACGAGATGTC
* * *
1252111 AGTGATGATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTTGATGCTGATCCAACTCCTTCT
66 AGTGATAATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCT
1252176 GTGATGGATTTGAGCGAGATAAAAATGTCGATCATTCTCCTTCTGT
131 GTGATGGATTTGAGCGAGATAAAAATGTCGATCATTCTCCTTCTGT
* * *
1252222 GATGGATTTGAGCTAGATAAAAATGTCGATCCT-CCTCCTTCTGTGATGGAATCAAACGAGATGT
1 GATGGATTTGAGCGAAATAAAAATGTCGAT-CTACCTCATTCTGTGATGGAATCAAACGAGATGT
* * *
1252286 TAGTGCTAATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGGTCCAACTCCTTC
65 CAGTGATAATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTC
*
1252351 TGTGGTGGATTTGAGCGAGATAAAAAT
130 TGTGATGGATTTGAGCGAGATAAAAAT
1252378 TTTGATCCAC
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 142 0.99
177 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (176 bp):
GATGGATTTGAGCGAAATAAAAATGTCGATCTACCTCATTCTGTGATGGAATCAAACGAGATGTC
AGTGATAATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCT
GTGATGGATTTGAGCGAGATAAAAATGTCGATCATTCTCCTTCTGT
Found at i:1252371 original size:88 final size:87
Alignment explanation
Indices: 1252084--1252359 Score: 263
Period size: 88 Copynumber: 3.1 Consensus size: 87
1252074 ATCTACCTCA
* *
1252084 TTCTGTGATGGAATCGAACGAGATGTCAGTGATGATCTACCTCCTTCTGTGATAGAATCGATCAA
1 TTCTGTGATGGAATCGAACGAGATGTAAGTG-TGATCTACCTCCTTCTGTGATAGAATCGAGCAA
*
1252149 AACGTTGATGCTGATCCAACTCC
65 AAAGTTGATGCTGATCCAACTCC
* * * ** * * * * *
1252172 TTCTGTGATGGATTTGAGCGAGATAAAAATGTCGATC-ATTCTCCTTCTGTGATGGATTTGAGCT
1 TTCTGTGATGGAATCGAACGAGATGTAAGTGT-GATCTA-CCTCCTTCTGTGATAGAATCGAGC-
** **
1252236 AGATAAAAATG-T-C-GATCCTCCTCC
63 A-A-AAAGTTGATGCTGATCCAACTCC
* * *
1252260 TTCTGTGATGGAATCAAACGAGATGTTAGTGCTAATCTACCTCCTTCTGTGATAGAATCGAGCAA
1 TTCTGTGATGGAATCGAACGAGATGTAAGTG-TGATCTACCTCCTTCTGTGATAGAATCGAGCAA
*
1252325 AAAGTTGATGCTGGTCCAACTCC
65 AAAGTTGATGCTGATCCAACTCC
*
1252348 TTCTGTGGTGGA
1 TTCTGTGATGGA
1252360 TTTGAGCGAG
Statistics
Matches: 142, Mismatches: 36, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
85 5 0.04
86 2 0.01
87 4 0.03
88 121 0.85
89 4 0.03
90 2 0.01
91 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (87 bp):
TTCTGTGATGGAATCGAACGAGATGTAAGTGTGATCTACCTCCTTCTGTGATAGAATCGAGCAAA
AAGTTGATGCTGATCCAACTCC
Found at i:1252390 original size:88 final size:88
Alignment explanation
Indices: 1252116--1252408 Score: 261
Period size: 88 Copynumber: 3.3 Consensus size: 88
1252106 ATGTCAGTGA
* * *
1252116 TGATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTTGATGCTGATCCAACTCCTTCTGTGAT
1 TGATCCACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGAT
1252181 GGATTTGAGCGAGATAAAAATGT
66 GGATTTGAGCGAGATAAAAATGT
* * * * * ** **
1252204 CGAT-CATTCTCCTTCTGTGATGGATTTGAGCTAGATAAAAATG-T-C-GATCCTCCTCCTTCTG
1 TGATCCA-CCTCCTTCTGTGATAGAATCGAGC-A-A-AAAGTTGATGCTGATCCAACTCCTTCTG
* ** * *** * *
1252265 TGATGGAATCAAACGAGATGTTAGTGC
62 TGATGGATTTGAGCGAGATAAAAATGT
* * * *
1252292 TAATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGGTCCAACTCCTTCTGTGGT
1 TGATCCACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGAT
*
1252357 GGATTTGAGCGAGATAAAAATTT
66 GGATTTGAGCGAGATAAAAATGT
* * *
1252380 TGATCCACCTCCTTTTATGATGGAATCGA
1 TGATCCACCTCCTTCTGTGATAGAATCGA
1252409 ATGAGATGCC
Statistics
Matches: 148, Mismatches: 49, Indels: 16
0.69 0.23 0.08
Matches are distributed among these distances:
85 5 0.03
86 2 0.01
87 3 0.02
88 129 0.87
89 3 0.02
90 2 0.01
91 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (88 bp):
TGATCCACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGAT
GGATTTGAGCGAGATAAAAATGT
Found at i:1252392 original size:44 final size:44
Alignment explanation
Indices: 1252023--1252403 Score: 185
Period size: 44 Copynumber: 8.7 Consensus size: 44
1252013 CAAGAATGAC
* * * * *
1252023 AATGTTGATCCAACTCCGTATGCGATGGATTTGAGCGAAATAAA
1 AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * * * * * ***
1252067 AATGTCGATCTACCTCATTCTGTGATGGAATCGAACGAGATGTC
1 AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * * * * * * * * ****
1252111 AGTGATGATCTACCTCCTTCTGTGATAGAATCGATCAAAACGTT
1 AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * *
1252155 GATGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAGATAAA
1 AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * *
1252199 AATGTCGAT-CATTCTCCTTCTGTGATGGATTTGAGCTAGATAAA
1 AATGTTGATCCA-CCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * * ** * ***
1252243 AATGTCGATCCTCCTCCTTCTGTGATGGAATCAAACGAGATGTT
1 AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * * * * * *
1252287 AGTGCTAATCTACCTCCTTCTGTGATAGAATCGAGC-A-A-AAA
1 AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * * * *
1252328 GTTGATGCTGGTCCAACTCCTTCTGTGGTGGATTTGAGCGAGATAAA
1 ---AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
* * *
1252375 AATTTTGATCCACCTCCTTTTATGATGGA
1 AATGTTGATCCACCTCCTTCTGTGATGGA
1252404 ATCGAATGAG
Statistics
Matches: 245, Mismatches: 84, Indels: 16
0.71 0.24 0.05
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 235 0.96
45 2 0.01
46 1 0.00
47 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (44 bp):
AATGTTGATCCACCTCCTTCTGTGATGGATTTGAGCGAGATAAA
Found at i:1252437 original size:176 final size:176
Alignment explanation
Indices: 1252062--1252452 Score: 520
Period size: 176 Copynumber: 2.2 Consensus size: 176
1252052 TTTGAGCGAA
* * *
1252062 ATAAAAATGTCGATCTACCTCATTCTGTGATGGAATCGAACGAGATGTCAGTGATGATCTACCTC
1 ATAAAAATGTCGATCTACCTCCTTCTGTGATGGAATCAAACGAGATGTCAGTGATAATCTACCTC
* *
1252127 CTTCTGTGATAGAATCGATCAAAACGTTGATGCTGATCCAACTCCTTCTGTGATGGATTTGAGCG
66 CTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGATGGATTTGAGCG
* * * * *
1252192 AGATAAAAATGTCGATCATTCTCCTTCTGTGATGGATTTGAGCTAG
131 AGATAAAAATGTCGATCATCCTCCTTCTATGATGGAATCGAGATAG
* *
1252238 ATAAAAATGTCGATCCT-CCTCCTTCTGTGATGGAATCAAACGAGATGTTAGTGCTAATCTACCT
1 ATAAAAATGTCGAT-CTACCTCCTTCTGTGATGGAATCAAACGAGATGTCAGTGATAATCTACCT
* *
1252302 CCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGGTCCAACTCCTTCTGTGGTGGATTTGAGC
65 CCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGATGGATTTGAGC
* * *
1252367 GAGATAAAAATTTTGATCCA-CCTCCTTTTATGATGGAATCGA-ATGAG
130 GAGATAAAAATGTCGAT-CATCCTCCTTCTATGATGGAATCGAGAT-AG
*** * *
1252414 ATGCCAGTG-CTGATCTACCTCCTTCTGTGATAGAATCAA
1 ATAAAAATGTC-GATCTACCTCCTTCTGTGATGGAATCAA
1252453 GCAAAAAGTT
Statistics
Matches: 188, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
175 4 0.02
176 180 0.96
177 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (176 bp):
ATAAAAATGTCGATCTACCTCCTTCTGTGATGGAATCAAACGAGATGTCAGTGATAATCTACCTC
CTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGATGGATTTGAGCG
AGATAAAAATGTCGATCATCCTCCTTCTATGATGGAATCGAGATAG
Found at i:1252469 original size:44 final size:44
Alignment explanation
Indices: 1252421--1252599 Score: 107
Period size: 44 Copynumber: 4.1 Consensus size: 44
1252411 GAGATGCCAG
*
1252421 TGCTGATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGA
1 TGCTGATCTACCTCATTCTGTGATAGAATCAAGCAAAAAGTTGA
* ** * * * * **
1252465 TGCTGATCCAATTCATTCTGTGATGGATTTAAGAGAAATAAAAAT-A
1 TGCTGATCTACCTCATTCTGTGATAGA-ATCA-AGCAA-AAAGTTGA
* * * * * * *
1252511 T-C-GATCAACCTCCTTCTGTGATGGAATCGAA-C-GAGATTTCGG
1 TGCTGATCTACCTCATTCTGTGATAGAATC-AAGCAAAAAGTT-GA
* *
1252553 TGTTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
1 TGCTGATCTACCTCATTCTGTGATAGAATCAAGCAAAAAGTTGA
1252597 TGC
1 TGC
1252600 ATGGTTGAAC
Statistics
Matches: 93, Mismatches: 32, Indels: 20
0.64 0.22 0.14
Matches are distributed among these distances:
40 3 0.03
42 1 0.01
43 3 0.03
44 69 0.74
45 7 0.08
46 6 0.06
47 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
TGCTGATCTACCTCATTCTGTGATAGAATCAAGCAAAAAGTTGA
Found at i:1252592 original size:132 final size:132
Alignment explanation
Indices: 1252216--1252599 Score: 536
Period size: 132 Copynumber: 2.9 Consensus size: 132
1252206 ATCATTCTCC
* * * *
1252216 TTCTGTGATGGATTTGAGCTAGATAAAAATGTCGATCCTCCTCCTTCTGTGATGGAATCAAACGA
1 TTCTGTGATGGATTTGAGCGAGATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGA
* *
1252281 GATGTT-AGTGCTAATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGGTCCAAC
66 GAT-TTCAGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAAC
*
1252345 TCC
130 TCA
* * * * * *
1252348 TTCTGTGGTGGATTTGAGCGAGATAAAAATTTTGATCCACCTCCTTTTATGATGGAATCGAATGA
1 TTCTGTGATGGATTTGAGCGAGATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGA
** * *
1252413 GATGCCAGTGCTGATCTACCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGATGCTGATCCAATT
66 GATTTCAGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACT
1252478 CA
131 CA
* * * *
1252480 TTCTGTGATGGATTTAAGAGAAATAAAAATATCGATCAACCTCCTTCTGTGATGGAATCGAACGA
1 TTCTGTGATGGATTTGAGCGAGATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGA
* * *
1252545 GATTTCGGTGTTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGATGC
66 GATTTCAGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGC
1252600 ATGGTTGAAC
Statistics
Matches: 219, Mismatches: 32, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
132 219 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (132 bp):
TTCTGTGATGGATTTGAGCGAGATAAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGA
GATTTCAGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACT
CA
Found at i:1253431 original size:24 final size:24
Alignment explanation
Indices: 1253387--1253436 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1253377 ATAAAGAACC
*
1253387 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
1253411 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
1253435 AA
1 AA
1253437 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:1254362 original size:18 final size:19
Alignment explanation
Indices: 1254339--1254375 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1254329 ATTTTACAAT
1254339 TAGGGA-ACCGATTCCCCA
1 TAGGGAGACCGATTCCCCA
1254357 TAGGGAGTACCGATTCCCC
1 TAGGGAG-ACCGATTCCCC
1254376 CCACGCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (19 bp):
TAGGGAGACCGATTCCCCA
Found at i:1260076 original size:20 final size:21
Alignment explanation
Indices: 1260051--1260132 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
1260041 TTTTGGTGCA
1260051 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
**
1260071 GAGGGAA-CGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCAT
*
1260091 GAAAGGGAACCGATTCCCCCCA-
1 G--AGGGAATCGATTCCCCCCAT
* *
1260113 CAGGGGAATCGATACCCCCC
1 GA-GGGAATCGATTCCCCCC
1260133 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
19 3 0.06
20 16 0.32
21 15 0.30
22 6 0.12
23 10 0.20
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:1262807 original size:23 final size:23
Alignment explanation
Indices: 1262770--1262825 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1262760 CTCAGAGGGA
1262770 ACCGATT--CCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGGGT
1262791 ACCGATTCCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGGGT
1262814 ACCGATTCCCCC
1 ACCGATTCCCCC
1262826 TGAATGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 7 0.21
23 26 0.79
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (23 bp):
ACCGATTCCCCCCCCAAGGGGGT
Found at i:1262957 original size:18 final size:19
Alignment explanation
Indices: 1262934--1262970 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1262924 ATTTTACACT
1262934 TAGGGA-ACCGATTCCCCA
1 TAGGGAGACCGATTCCCCA
1262952 TAGGGAGTACCGATTCCCC
1 TAGGGAG-ACCGATTCCCC
1262971 CACGCTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (19 bp):
TAGGGAGACCGATTCCCCA
Found at i:1274402 original size:90 final size:91
Alignment explanation
Indices: 1274145--1274501 Score: 450
Period size: 91 Copynumber: 3.9 Consensus size: 91
1274135 AAAGTTGATG
* * * *
1274145 CAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTCCCTC-TTCGGATGAGCTCTTCTTATT
1 CAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCGTT-GGATGAGTTCTTCTCATT
* * * *
1274209 ATGAACACCCCGCTTGAAATGTTGATG-
65 ATGAACTCTCCACTGGAAATGTTGA-GC
* * * *
1274236 CAAGGTTGAACAAGTTCTTCTCATTATGAAATTTTTCTCCCTTGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* * *
1274301 TAAACTCTCCACTGGGAATTTTGAGC
66 TGAACTCTCCACTGGAAATGTTGAGC
* * *
1274327 CAAGGTTGAACAATTTCTTCTCATTGTGAACTT-TTGTCCCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* * * *
1274391 TGAACTTTCCACTGGAAACGCTGATC
66 TGAACTCTCCACTGGAAATGTTGAGC
* *
1274417 AAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTTGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATTA
*
1274482 TGAACTCTCCATTGGAAATG
66 TGAACTCTCCACTGGAAATG
1274502 ACAATCCCTC
Statistics
Matches: 229, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
90 79 0.34
91 148 0.65
92 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (91 bp):
CAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGGAAATGTTGAGC
Found at i:1274457 original size:181 final size:182
Alignment explanation
Indices: 1274145--1274492 Score: 506
Period size: 181 Copynumber: 1.9 Consensus size: 182
1274135 AAAGTTGATG
*
1274145 CAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTCCCTCTTCGGATGAGCTCTTCTTATTA
1 CAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTCCCTCTTCGGATGAGCTCTTCTCATTA
* * * * * *
1274210 TGAACACCCCGCTTGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAAATTTTTCTC
66 TGAACACCCCACTGGAAACGCTGATGCAAGGTTGAACAAATTCTTCTCATTATGAAATTATTCTC
1274275 CCTTGTTGGATGAGTTCTTCTCATTATAAACTCTCCACTGGGAATTTTGAGC
131 CCTTGTTGGATGAGTTCTTCTCATTATAAACTCTCCACTGGGAATTTTGAGC
* * *
1274327 CAAGGTTGAACAATTTCTTCTCATTG-TGAACTT-TTGTCCCTCGTT-GGATGAGTTCTTCTCAT
1 CAAGGTTGAACAAATTCTTCTCA-TGATGAACTTCTTCTCCCTC-TTCGGATGAGCTCTTCTCAT
*** *
1274389 TATGAACTTTCCACTGGAAACGCTGAT-CAAAGGTTGAACAAATTCTTCTCATTATGAACTTATT
64 TATGAACACCCCACTGGAAACGCTGATGC-AAGGTTGAACAAATTCTTCTCATTATGAAATTATT
*
1274453 CTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
128 CTCCCTTGTTGGATGAGTTCTTCTCATTATAAACTCTCCA
1274493 TTGGAAATGA
Statistics
Matches: 148, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
180 1 0.01
181 114 0.77
182 31 0.21
183 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (182 bp):
CAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTCCCTCTTCGGATGAGCTCTTCTCATTA
TGAACACCCCACTGGAAACGCTGATGCAAGGTTGAACAAATTCTTCTCATTATGAAATTATTCTC
CCTTGTTGGATGAGTTCTTCTCATTATAAACTCTCCACTGGGAATTTTGAGC
Found at i:1275027 original size:75 final size:75
Alignment explanation
Indices: 1274895--1275078 Score: 221
Period size: 75 Copynumber: 2.5 Consensus size: 75
1274885 AGAAGAGTTC
* * * *
1274895 TCTCGAGTGAGATAAAATTTATTGTTTCAAGGGAAAATTATCTCAAGAGAGACGAAGTTGGTTTT
1 TCTCAAGTGAGAT-AAATTTTTTGTTTCAAGGGAAAACTATCTCAAGAGAGACGAAGTTAGTTTT
*
1274960 AAGAAAAACCA
65 AAGAAAAAACA
* * * *
1274971 TCTCAAGTGAGATATATTTTTTGTTTCAAGGTAAAACTGTCTCAAGCA-AGATGAAGTTAGTTTT
1 TCTCAAGTGAGATAAATTTTTTGTTTCAAGGGAAAACTATCTCAAG-AGAGACGAAGTTAGTTTT
*
1275035 AAGAAAAAACG
65 AAGAAAAAACA
* *
1275046 TCTCAAGTGAGATACA--TTTTATTTCAAGGGAAA
1 TCTCAAGTGAGATAAATTTTTTGTTTCAAGGGAAA
1275079 CGGGTTCAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
73 15 0.16
75 66 0.70
76 13 0.14
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (75 bp):
TCTCAAGTGAGATAAATTTTTTGTTTCAAGGGAAAACTATCTCAAGAGAGACGAAGTTAGTTTTA
AGAAAAAACA
Found at i:1275177 original size:36 final size:36
Alignment explanation
Indices: 1275098--1275356 Score: 225
Period size: 36 Copynumber: 7.4 Consensus size: 36
1275088 AGATTTTGCA
* *
1275098 TTTC-AGGAGAAACTGTCTC-AGGAAGACAAAACTTA
1 TTTCAAGG-GAAACTGTCTCAAGGGAGACAAAACTTG
*
1275133 TTTCAAGGGAAAATGTCTCAAGGGAGACAAAACTTG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTG
* * ***
1275169 TTTGAAGGGAAAC-GTTTTCAA---AG--TTTA--TG
1 TTTCAAGGGAAACTG-TCTCAAGGGAGACAAAACTTG
* * *
1275198 TTTCAAGGGAAACTGTCTTAAGAGAGACAAAACTTA
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTG
* * *
1275234 TTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTTTG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAAC-TTG
* *
1275271 TTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTTG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAAC-TTG
* * *
1275308 TTTCAAGGTAAACTTTCTCAAGGGAGACGAAA-TTCG
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTT-G
1275344 TTTCAAGGGAAAC
1 TTTCAAGGGAAAC
1275357 ATTTTTAAAG
Statistics
Matches: 182, Mismatches: 29, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
29 18 0.10
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 17 0.09
36 78 0.43
37 62 0.34
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGGGAGACAAAACTTG
Found at i:1275251 original size:101 final size:102
Alignment explanation
Indices: 1275067--1275283 Score: 280
Period size: 101 Copynumber: 2.1 Consensus size: 102
1275057 ATACATTTTA
*
1275067 TTTCAAGGGAAACGGGTTCAAAGATTTTGCATTTCAGGAGAAACTGTCTCAGGAAGACAAAACTT
1 TTTCAAGGGAAACGGGTTCAAAGATTTTG-ATTTCAGGAGAAACTGTCTCAAGAAGACAAAACTT
* * *
1275132 ATTTCAAGGGAAAATGTCTCAAGGGAGACAAAAC-TTG
65 ATTTCAAGGGAAAATGTCTAAAGAGAGAAAAAACTTTG
* ** *
1275169 TTTGAAGGGAAACGTTTTCAAAG-TTTATG-TTTCAAGG-GAAACTGTCTTAAGAGAGACAAAAC
1 TTTCAAGGGAAACGGGTTCAAAGATTT-TGATTTC-AGGAGAAACTGTCTCAAGA-AGACAAAAC
*
1275231 TTATTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTTTG
63 TTATTTCAAGGGAAAATGTCTAAAGAGAGAAAAAACTTTG
*
1275271 TTTCAAGAGAAAC
1 TTTCAAGGGAAAC
1275284 TGTCTCAAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
100 17 0.17
101 47 0.47
102 36 0.36
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (102 bp):
TTTCAAGGGAAACGGGTTCAAAGATTTTGATTTCAGGAGAAACTGTCTCAAGAAGACAAAACTTA
TTTCAAGGGAAAATGTCTAAAGAGAGAAAAAACTTTG
Found at i:1275284 original size:37 final size:37
Alignment explanation
Indices: 1275196--1275356 Score: 182
Period size: 37 Copynumber: 4.4 Consensus size: 37
1275186 TCAAAGTTTA
* *
1275196 TGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAAC-T
1 TGTTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTT
*
1275232 TATTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTT
1 TGTTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTT
* * * *
1275269 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTT
1 TGTTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTT
* * * * **
1275306 TGTTTCAAGGTAAACTTTCTCAAGGGAGACGAAA-TT
1 TGTTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTT
*
1275342 CGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
1275357 ATTTTTAAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
36 47 0.43
37 62 0.57
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTT
Found at i:1275347 original size:73 final size:73
Alignment explanation
Indices: 1275197--1275356 Score: 196
Period size: 73 Copynumber: 2.2 Consensus size: 73
1275187 CAAAGTTTAT
*
1275197 GTTTCAAGGGAAACTGTCTTAAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTAAAGAGAGAA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTAAAGAGAGAA
*
1275262 AAAACTTT
66 AAAACTTC
* * * * * * * *
1275270 GTTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTTGTTTCAAGGTAAACTTTCTCAAGGGAGA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-TTATTTCAAGGGAAACTGTCTAAAGAGAGA
**
1275335 CGAAA-TTC
65 AAAAACTTC
1275343 GTTTCAAGGGAAAC
1 GTTTCAAGGGAAAC
1275357 ATTTTTAAAG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 45 0.62
74 28 0.38
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (73 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTAAAGAGAGAA
AAAACTTC
Found at i:1275354 original size:175 final size:173
Alignment explanation
Indices: 1275098--1275421 Score: 454
Period size: 175 Copynumber: 1.9 Consensus size: 173
1275088 AGATTTTGCA
*
1275098 TTTCAGGAGAAACTGTCTCAGGAAGACAAAACTTATTTCAAGGGAAAATGTCTCAAGGGAGACAA
1 TTTCAAGAGAAACTGTCTCAGGAAGACAAAACTTATTTCAAGGGAAAATGTCTCAAGGGAGACAA
* * * * *
1275163 AACTTGTTTGAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGGGAAACTGTCTTAAGAGAGACAA
66 AACTTGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGACAA
1275228 AACTT-ATTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTTTG
131 AA-TTCATTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTTTG
* * * * * *
1275271 TTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTTGTTTCAAGGTAAACTTTCTCAAGGGAGAC
1 TTTCAAGAGAAACTGTCTC-AGGAAGACAAAAC-TTATTTCAAGGGAAAATGTCTCAAGGGAGAC
* *
1275336 GAAA-TTCGTTTCAAGGGAAACATTTTTAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGA
64 AAAACTT-GTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGA
* *
1275400 CAAAATTCATTTTAAGTGAAAC
128 CAAAATTCATTTCAAGGGAAAC
1275422 ATTTTCAAAG
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
173 18 0.14
174 15 0.11
175 98 0.75
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (173 bp):
TTTCAAGAGAAACTGTCTCAGGAAGACAAAACTTATTTCAAGGGAAAATGTCTCAAGGGAGACAA
AACTTGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGACAA
AATTCATTTCAAGGGAAACTGTCTAAAGAGAGAAAAAACTTTG
Found at i:1275421 original size:65 final size:65
Alignment explanation
Indices: 1275308--1275431 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 65
1275298 TAAAACTTTG
* * * * *
1275308 TTTCAAGGTAAACTTTCTCAAGGGAGACGAAATTCGTTTCAAGGGAAACATTTTTAAAGTTTATA
1 TTTCAAGGTAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATTTTCAAAGTTTATA
* *
1275373 TTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTCATTTTAAGTGAAACATTTTCAAAG
1 TTTCAAG-GTAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATTTTCAAAG
1275432 AAACTATCTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 50 0.98
66 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (65 bp):
TTTCAAGGTAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATTTTCAAAGTTTATA
Found at i:1275444 original size:65 final size:65
Alignment explanation
Indices: 1275317--1275444 Score: 150
Period size: 65 Copynumber: 2.0 Consensus size: 65
1275307 GTTTCAAGGT
* * * * * ** *
1275317 AAACTTTCTCAAGGGAGACGAAATTCGTTTCAAGGGAAACATTTTTAAAGTTTATATTTCAAGAG
1 AAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATTTTCAAAGTAAATATCTCAAGAG
* *
1275382 AAACTGTCTCAAGAGAGACAAAATTCATTTTAAGTGAAACATTTTCAAAG-AAACTATCTCAAG
1 AAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATTTTCAAAGTAAA-TATCTCAAG
1275445 GGAGACAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
64 1 0.02
65 51 0.98
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (65 bp):
AAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATTTTCAAAGTAAATATCTCAAGAG
Found at i:1275471 original size:36 final size:36
Alignment explanation
Indices: 1275424--1275581 Score: 134
Period size: 36 Copynumber: 4.6 Consensus size: 36
1275414 AGTGAAACAT
*
1275424 TTTCAA-AGAAACTATCTCAAGGGAGACAAATTTTG
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTG
* *
1275459 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTG
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTG
* * * *
1275495 TTTCAAGGGAAACGATTTCAA---AG----ATTTATG
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATT-TG
* * *
1275525 TTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTCG
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTG
* * *
1275561 TTTAAAGGGAAACGATCTCAA
1 TTTCAAGAGAAACTATCTCAA
1275582 AGATTGGTGT
Statistics
Matches: 93, Mismatches: 21, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
29 2 0.02
30 18 0.19
33 4 0.04
35 6 0.06
36 60 0.65
37 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTG
Found at i:1275471 original size:50 final size:51
Alignment explanation
Indices: 1275373--1275471 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 51
1275363 AAAGTTTATA
* * *
1275373 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGTGAAACAT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAACAT
* * **
1275424 TTTCAA-AGAAACTATCTCAAGGGAGACAAATTTTGTTTCAAGAGAAAC
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAAC
1275472 TGTCTCAAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 35 0.85
51 6 0.15
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (51 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAACAT
Found at i:1275536 original size:66 final size:64
Alignment explanation
Indices: 1275453--1275629 Score: 255
Period size: 66 Copynumber: 2.7 Consensus size: 64
1275443 AGGGAGACAA
* *
1275453 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACGATTTCAAAG
1 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTGTTTAAAGGGAAACGATCTCAAAG
*
1275518 ATTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAA
1 ATTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-GTTTAAAGGGAAACGATCTCAAA
1275583 G
64 G
* * *
1275584 ATTGGTGTTTCAAGGGAAACTGTCTCAAGGGAGAAAAAAATTGTTT
1 ATT-TTGTTTCAAGAGAAACTGTCTCAAGGGAG-ACAAAATTGTTT
1275630 TAAGAAAAAC
Statistics
Matches: 101, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
65 6 0.06
66 88 0.87
67 7 0.07
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (64 bp):
ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGTTTAAAGGGAAACGATCTCAAAG
Found at i:1275554 original size:152 final size:153
Alignment explanation
Indices: 1275271--1275573 Score: 427
Period size: 152 Copynumber: 2.0 Consensus size: 153
1275261 AAAAACTTTG
* *
1275271 TTTCAAGAGAAACTGTCTCAAGGGAGATAAAACTTTGTTTCAAGGTAAACTTTCTCAAGGGAGAC
1 TTTCAAGAGAAACTATCTCAAGGGAGATAAAACTTTGTTTCAAGGTAAACTGTCTCAAGGGAGAC
* *
1275336 GAAATTCGTTTCAAGGGAAACATTTTTAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGAC
66 AAAATTCGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGAC
* *
1275401 AAAATTCATTTTAAGTGAAACAT
131 AAAATTCATTTAAAGGGAAACAT
* *
1275424 TTTCAA-AGAAACTATCTCAAGGGAGA-CAAATTTTGTTTCAAGAG-AAACTGTCTCAAGGGAGA
1 TTTCAAGAGAAACTATCTCAAGGGAGATAAAACTTTGTTTCAAG-GTAAACTGTCTCAAGGGAGA
* * *
1275486 CAAAACTT-GTTTCAAGGGAAACGA-TTTCAAAGATTTATGTTTCAAGAGAAATTGTCTCAAGGG
65 CAAAA-TTCGTTTCAAGGGAAAC-ATTTTCAAAG-TTTATATTTCAAGAGAAACTGTCTCAAGAG
*
1275549 AGACAAAATTCGTTTAAAGGGAAAC
127 AGACAAAATTCATTTAAAGGGAAAC
1275574 GATCTCAAAG
Statistics
Matches: 134, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
151 56 0.42
152 72 0.54
153 6 0.04
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (153 bp):
TTTCAAGAGAAACTATCTCAAGGGAGATAAAACTTTGTTTCAAGGTAAACTGTCTCAAGGGAGAC
AAAATTCGTTTCAAGGGAAACATTTTCAAAGTTTATATTTCAAGAGAAACTGTCTCAAGAGAGAC
AAAATTCATTTAAAGGGAAACAT
Found at i:1275865 original size:75 final size:75
Alignment explanation
Indices: 1275600--1275946 Score: 344
Period size: 76 Copynumber: 4.6 Consensus size: 75
1275590 GTTTCAAGGG
* * * * * * *
1275600 AAACTGTCTCAAGGGAGA-AAAAAATTGTTTTAAGAAAAACCATCTCGAGTGAGATAAAATTTCT
1 AAACTGTCTCAAGCGAGACAAAATA-TGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
1275664 TATTTC-AGGTA
65 TATTTCGA-GTA
* * *
1275675 AAATCTGTCTCAAGCGAGAC-AAATCTAGTTTTAAGAAAACCAATC-TGTTGTGAAATGAAATGT
1 AAA-CTGTCTCAAGCGAGACAAAATAT-GTTTTAAGAAAAACAATCTTG-AGTGAAATGAAATGT
*
1275738 CTTGTTTCGAGTAA
63 CTTATTTCGAGT-A
*
1275752 AAACTGTCTCAAGCGAGACAAAATATATTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT
1 AAACTGTCTCAAGCGAGACAAAATATGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT
*
1275817 CTTTCGAGTA
66 ATTTCGAGTA
* ** * * *
1275827 AAACTGTCTCAAGCGAGACAAAGTATGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATAT-TC
1 AAACTGTCTCAAGCGAGACAAAATATGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT-
* *
1275891 TGTTTCGAGTG
65 TATTTCGAGTA
* * * * * * *
1275902 AAACTATCTCAATCGAGATAAAACATGTTTCAGGAGAAACAATCT
1 AAACTGTCTCAAGCGAGACAAAATATGTTTTAAGAAAAACAATCT
1275947 CAAAGTTTAT
Statistics
Matches: 230, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
74 1 0.00
75 107 0.47
76 110 0.48
77 12 0.05
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (75 bp):
AAACTGTCTCAAGCGAGACAAAATATGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT
ATTTCGAGTA
Found at i:1275866 original size:36 final size:35
Alignment explanation
Indices: 1275758--1275889 Score: 84
Period size: 36 Copynumber: 3.6 Consensus size: 35
1275748 GTAAAAACTG
*
1275758 TCTCAAGCGAGACAAAATATATTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAAGTAT-TTTTAAGAAAAACAA
** * * * * * * **
1275794 TCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAACTG
1 TCTCAAGCGAGA-CAAA-GTATT-TTT-AAGAAAAACAA
1275833 TCTCAAGCGAGACAAAGTATGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAAGTAT-TTTTAAGAAAAACAA
* * *
1275869 TCTCAAGTGAGATAAAATATT
1 TCTCAAGCGAGACAAAGTATT
1275890 CTGTTTCGAG
Statistics
Matches: 67, Mismatches: 24, Indels: 11
0.66 0.24 0.11
Matches are distributed among these distances:
35 1 0.01
36 32 0.48
37 10 0.15
38 9 0.13
39 15 0.22
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (35 bp):
TCTCAAGCGAGACAAAGTATTTTTAAGAAAAACAA
Found at i:1275895 original size:151 final size:151
Alignment explanation
Indices: 1275600--1275924 Score: 381
Period size: 151 Copynumber: 2.2 Consensus size: 151
1275590 GTTTCAAGGG
* * * * *
1275600 AAACTGTCTCAAGGGAGAAAAAAATTGTTTTAAGAAAAACCATCTCGAGTGAGATAAAATTTCTT
1 AAACTGTCTCAAGCGAGAAAAAAATTATTTTAAGAAAAACAATCTCGAGTGAAATAAAATGTCTT
* * ***
1275665 ATTTCAGGTAAAATCTGTCTCAAGCGAGACAAATCTAGTTTTAAGAAAACCAATCTGTTGTGAAA
66 ATTTCAGGTAAAATCTGTCTCAAGCGAGACAAATATAGTTTTAAGAAAAACAATCTCAAGTGAAA
*
1275730 TGAAATGTCTTGTTTCGAGTAA
131 TAAAATGTCTTGTTTCGAGT-A
* * *
1275752 AAACTGTCTCAAGCGAG-ACAAAATATATTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
1 AAACTGTCTCAAGCGAGAAAAAAAT-TATTTTAAGAAAAACAATCTCGAGTGAAATAAAATGTCT
*
1275816 TCTTTC-GAGTAAAA-CTGTCTCAAGCGAGACAAAGTAT-GTTTTAAGAAAAACAATCTCAAGTG
65 TATTTCAG-GTAAAATCTGTCTCAAGCGAGACAAA-TATAGTTTTAAGAAAAACAATCTCAAGTG
* * *
1275878 AGATAAAATAT-TCTGTTTCGAGTG
128 AAATAAAATGTCT-TGTTTCGAGTA
* * *
1275902 AAACTATCTCAATCGAGATAAAA
1 AAACTGTCTCAAGCGAGAAAAAA
1275925 CATGTTTCAG
Statistics
Matches: 146, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
150 16 0.11
151 68 0.47
152 62 0.42
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (151 bp):
AAACTGTCTCAAGCGAGAAAAAAATTATTTTAAGAAAAACAATCTCGAGTGAAATAAAATGTCTT
ATTTCAGGTAAAATCTGTCTCAAGCGAGACAAATATAGTTTTAAGAAAAACAATCTCAAGTGAAA
TAAAATGTCTTGTTTCGAGTA
Found at i:1276042 original size:36 final size:36
Alignment explanation
Indices: 1275994--1276188 Score: 160
Period size: 36 Copynumber: 5.3 Consensus size: 36
1275984 AGAATTTGTA
*
1275994 TTTTAAAGAAAAACTGTCTCTAGTGAGACGAAATTTG
1 TTTT-AAGAAAAACTGTCTCAAGTGAGACGAAATTTG
* * *
1276031 TTTTGAGAAAAAGATGTCTCAAGTAAGAC-AAATTTG
1 TTTTAAGAAAAA-CTGTCTCAAGTGAGACGAAATTTG
* ** ** *
1276067 TTTTTTAGAGAAAACAATCTCAAGTGAGATTAATTTTG
1 -TTTTAAGA-AAAACTGTCTCAAGTGAGACGAAATTTG
* * * * *
1276105 TTTTAAGGAAAATTATCTCTAGCGAGACGAAATTTG
1 TTTTAAGAAAAACTGTCTCAAGTGAGACGAAATTTG
* * *
1276141 TTTTTAAG-AAAACTGTCTCGAGCGAGACAAAATTTG
1 -TTTTAAGAAAAACTGTCTCAAGTGAGACGAAATTTG
1276177 TTCTTAAGAAAA
1 TT-TTAAGAAAA
1276189 CTCGTCTTTA
Statistics
Matches: 127, Mismatches: 24, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
35 2 0.02
36 64 0.50
37 51 0.40
38 10 0.08
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTTAAGAAAAACTGTCTCAAGTGAGACGAAATTTG
Found at i:1278679 original size:14 final size:15
Alignment explanation
Indices: 1278659--1278695 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1278649 GCAAATGCAA
1278659 AGATGCAAAAATATG
1 AGATGCAAAAATATG
*
1278674 AG-TGC-AAAATGTG
1 AGATGCAAAAATATG
1278687 AGATGCAAA
1 AGATGCAAA
1278696 TGCAACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.19
Consensus pattern (15 bp):
AGATGCAAAAATATG
Found at i:1279150 original size:149 final size:149
Alignment explanation
Indices: 1278848--1279140 Score: 390
Period size: 149 Copynumber: 2.0 Consensus size: 149
1278838 TTCAATACTT
* ** * * *
1278848 CTACTTCATCTCCTACTTTCAGATGTCTTTCATGCTGGTTCGTGATCTTCAATTGCTGGTTTCGA
1 CTACTTCATCTCCTAATTTCAGAAATATTTCAGGCTGGTTCGTGATCTTCAATTGCTGGCTTCGA
* * * *
1278913 CGTCGAATCGTCTCGAGTCCAACTTGTCACCTCGGCATGCAGATATCTAGCTCATCTCCTTAGTG
66 CGTCGAATCGTCTCGAGTCCAACTTGTCACCTCAGCAGGCAAATATCTAGCTCATCTCCTTAGTA
1278978 GGTAGACTCCCTCTAGCTC
131 GGTAGACTCCCTCTAGCTC
* *
1278997 CTACTTCATCTCCTAATTTCAGAAATATTTCGGGCTGGTTCGTGATCTTCAATTGTTGGCTTC-A
1 CTACTTCATCTCCTAATTTCAGAAATATTTCAGGCTGGTTCGTGATCTTCAATTGCTGGCTTCGA
* * * * * * *
1279061 GCGTCGAATCGTCTCGAGTCTAACTTGTTACCTCAGTAGGTAAATGTCTGGCTCGTCTCCTTAGT
66 -CGTCGAATCGTCTCGAGTCCAACTTGTCACCTCAGCAGGCAAATATCTAGCTCATCTCCTTAGT
*
1279126 AGGTAGGCTCCCTCT
130 AGGTAGACTCCCTCT
1279141 TGACGCTACT
Statistics
Matches: 123, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
148 1 0.01
149 122 0.99
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (149 bp):
CTACTTCATCTCCTAATTTCAGAAATATTTCAGGCTGGTTCGTGATCTTCAATTGCTGGCTTCGA
CGTCGAATCGTCTCGAGTCCAACTTGTCACCTCAGCAGGCAAATATCTAGCTCATCTCCTTAGTA
GGTAGACTCCCTCTAGCTC
Found at i:1280165 original size:18 final size:18
Alignment explanation
Indices: 1280124--1280166 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1280114 AAAACCGGGC
*
1280124 GATTTTAATAAAATATTT
1 GATTTTAATAAAATATAT
*
1280142 TATTTTAATAAAATA-AT
1 GATTTTAATAAAATATAT
1280159 GAGTTTTA
1 GA-TTTTA
1280167 GGGTTTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (18 bp):
GATTTTAATAAAATATAT
Found at i:1281215 original size:15 final size:17
Alignment explanation
Indices: 1281185--1281216 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1281175 GTTTGGGGGA
1281185 CTAAAAATGATAATAAC
1 CTAAAAATGATAATAAC
1281202 CTAAAAA-G-TAATAAC
1 CTAAAAATGATAATAAC
1281217 ACATACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.22
Consensus pattern (17 bp):
CTAAAAATGATAATAAC
Found at i:1282329 original size:13 final size:13
Alignment explanation
Indices: 1282313--1282343 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1282303 TTTCTTTACT
1282313 TTTTTTATTTTTC
1 TTTTTTATTTTTC
1282326 TTTTTTATTTTTC
1 TTTTTTATTTTTC
1282339 TTTTT
1 TTTTT
1282344 GCTTTTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTATTTTTC
Found at i:1282336 original size:19 final size:18
Alignment explanation
Indices: 1282301--1282349 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1282291 CTTATTACTT
*
1282301 TTTTTCTTTACTTTTTTTA
1 TTTTTCTTT-TTTTTTTTA
*
1282320 TTTTTCTTTTTTATTTTTC
1 TTTTTCTTTTTT-TTTTTA
1282339 TTTTTGCTTTT
1 TTTTT-CTTTT
1282350 ACTTGAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 19 0.73
20 5 0.19
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTTTA
Found at i:1286011 original size:21 final size:21
Alignment explanation
Indices: 1285987--1286047 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1285977 CCAACTTTGA
1285987 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1286008 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
1286022 AAATGGTTTTTAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1286043 AAATG
1 AAATG
1286048 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 3 0.10
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1286068 original size:36 final size:35
Alignment explanation
Indices: 1285981--1286096 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
1285971 TGGCAACCAA
*
1285981 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
1286016 CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
* *
1286051 CTTTGAAAAATGTTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTT-AAAGTTTGGTAAATGTTT
*
1286088 -GTTGAAAAT
1 CTTTGAAAAT
1286097 AGGAATGGGT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 44 0.59
36 14 0.19
37 17 0.23
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTTAAAGTTTGGTAAATGTTT
Found at i:1290015 original size:10 final size:10
Alignment explanation
Indices: 1290000--1290025 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1289990 ATCTTATTTG
1290000 CTATCCTCTC
1 CTATCCTCTC
1290010 CTATCCTCTC
1 CTATCCTCTC
1290020 CTATCC
1 CTATCC
1290026 CAGTATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (10 bp):
CTATCCTCTC
Found at i:1291979 original size:15 final size:15
Alignment explanation
Indices: 1291959--1291987 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1291949 TTAATATTAT
1291959 ATAAAATAAACCTAC
1 ATAAAATAAACCTAC
1291974 ATAAAATAAACCTA
1 ATAAAATAAACCTA
1291988 AAATAGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAATAAACCTAC
Found at i:1292871 original size:13 final size:13
Alignment explanation
Indices: 1292853--1292894 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1292843 TAAAATGAAA
*
1292853 ATAAATAAATAGT
1 ATAAATAAATAAT
1292866 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
1292880 A-AAATAAAGAAT
1 ATAAATAAATAAT
1292892 ATA
1 ATA
1292895 TACAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1293031 original size:12 final size:12
Alignment explanation
Indices: 1293014--1293071 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
1293004 CATAATAATT
1293014 ATAAAATAAATA
1 ATAAAATAAATA
*
1293026 AT-AAA-ACATA
1 ATAAAATAAATA
* *
1293036 ATATATTAAATA
1 ATAAAATAAATA
*
1293048 ATAAACTAAATA
1 ATAAAATAAATA
1293060 A-ATAAATAAATA
1 ATA-AAATAAATA
1293072 GATGAAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 6 0.17
11 5 0.14
12 25 0.69
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAAAATAAATA
Found at i:1294510 original size:36 final size:36
Alignment explanation
Indices: 1294461--1294591 Score: 155
Period size: 36 Copynumber: 3.7 Consensus size: 36
1294451 AAAGCTTTGG
*
1294461 TGTTTCAATAGAAAC-ATGTTCAAAGGTTTTCTTTTT
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTTTTCTTTTT
1294497 TGTTTCAAGAGAAACAATTTCAAAGGTTTTC-TTTT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
* *
1294532 TGTGTTCTAAGAGAAACGATTTCAAAGG--TT-TTTTG
1 TGT-TTC-AAGAGAAACAATTTCAAAGGTTTTCTTTTT
*
1294567 TGTTTCAAGAGAAAACGATTTCAAA
1 TGTTTCAAGAG-AAACAATTTCAAA
1294592 TTTTTTTTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
33 5 0.06
34 16 0.18
35 15 0.17
36 30 0.34
37 21 0.24
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
Found at i:1294676 original size:29 final size:29
Alignment explanation
Indices: 1294631--1294705 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1294621 GGAGGAAAAA
1294631 TTTTGTTTCAAGAGAAAC-ATATTCAAAGG
1 TTTTGTTTCAAGAGAAACTATATTCAAA-G
* * *
1294660 TTTTGTTTCAAGGGAAACTGTTTTCAAAG
1 TTTTGTTTCAAGAGAAACTATATTCAAAG
1294689 TTTATGTTTCAAGAGAA
1 TTT-TGTTTCAAGAGAA
1294706 GCTGTCTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (29 bp):
TTTTGTTTCAAGAGAAACTATATTCAAAG
Found at i:1294688 original size:30 final size:29
Alignment explanation
Indices: 1294631--1294710 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
1294621 GGAGGAAAAA
*
1294631 TTTTGTTTCAAGAGAAAC-ATATTCAAAGG
1 TTTTGTTTCAAGAGAAACTGTATTCAAA-G
* *
1294660 TTTTGTTTCAAGGGAAACTGTTTTCAAAG
1 TTTTGTTTCAAGAGAAACTGTATTCAAAG
*
1294689 TTTATGTTTCAAGAGAAGCTGT
1 TTT-TGTTTCAAGAGAAACTGT
1294711 CTCAAGGGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTGTTTCAAGAGAAACTGTATTCAAAG
Found at i:1294750 original size:36 final size:36
Alignment explanation
Indices: 1294693--1294876 Score: 104
Period size: 36 Copynumber: 5.3 Consensus size: 36
1294683 TCAAAGTTTA
* * *
1294693 TGTTTCAA-GAGAAGCTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGA-AAACTATCTCAAGAGAGACAAAATT
*
1294729 TGTTTCAAGGAAAACTATCTCAAGAAAGACAAAATT
1 TGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATT
** * * * *
1294765 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-C----TT
1 TGTTTCAAGGAAAACT-ATCTCAAGAGAGACAAAATT
* *
1294793 ATGTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGA-AAACTATCTCAAGAGAGACAAAA-TT
1294831 TGTTTCAAAGG-AAACTATCTCAAGAGAGACAAAATT
1 TGTTTC-AAGGAAAACTATCTCAAGAGAGACAAAATT
**
1294867 CATTTCAAGG
1 TGTTTCAAGG
1294877 GAAATGTTTT
Statistics
Matches: 111, Mismatches: 21, Indels: 33
0.67 0.13 0.20
Matches are distributed among these distances:
28 3 0.03
29 12 0.11
30 2 0.02
32 2 0.02
33 2 0.02
34 1 0.01
35 6 0.05
36 49 0.44
37 29 0.26
38 4 0.04
39 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATT
Found at i:1294801 original size:101 final size:102
Alignment explanation
Indices: 1294665--1294919 Score: 424
Period size: 102 Copynumber: 2.5 Consensus size: 102
1294655 AAAGGTTTTG
* *
1294665 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAGCTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1294729 TGTTTC-AAGGAAAACTATCTCAAGAAAGACAAAATTCA
65 TGTTTCAAAGG-AAACTATCTCAAGAAAGACAAAATTCA
*
1294767 TTTCAAGGGAAATGTTTTCAATGCTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
1294832 GTTTCAAAGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAAGGAAACTATCTCAAGAAAGACAAAATTCA
* *
1294869 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAG
1294920 ATAAATTGTC
Statistics
Matches: 144, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
101 46 0.32
102 94 0.65
103 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAAGGAAACTATCTCAAGAAAGACAAAATTCA
Found at i:1294845 original size:37 final size:37
Alignment explanation
Indices: 1294794--1294866 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1294784 TCAATGCTTA
* *
1294794 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
1294831 TGTTTCAA-AGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-GAAACTATCTCAAGAGAGACAAAATT
1294867 CATTTCAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1294880 original size:36 final size:37
Alignment explanation
Indices: 1294796--1294880 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
1294786 AATGCTTATG
* * * **
1294796 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTCA
*
1294833 TTTCAAAGGAAACTATCTCAAGAGAGACAAAA-TTCA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTCA
1294869 TTTCAAGGGAAA
1 TTTCAAGGGAAA
1294881 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 13 0.32
37 28 0.68
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (37 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTCA
Found at i:1294914 original size:15 final size:15
Alignment explanation
Indices: 1294896--1294934 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1294886 TCAATGTTTA
1294896 TGTTTCAAGAGAAAT
1 TGTTTCAAGAGAAAT
*
1294911 TGTTTCAAGATAAAT
1 TGTTTCAAGAGAAAT
*
1294926 TGTCTCAAG
1 TGTTTCAAG
1294935 GGAGACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (15 bp):
TGTTTCAAGAGAAAT
Found at i:1294971 original size:39 final size:39
Alignment explanation
Indices: 1294928--1295055 Score: 157
Period size: 39 Copynumber: 3.2 Consensus size: 39
1294918 AGATAAATTG
1294928 TCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAAACTA
1 TCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAAACTA
* * * **
1294967 TCTCAAGCGAGATAAAATCTTGTTTATGTTTCAATAGAAACTA
1 TCTCAAGGGAGACAAAA--TT-TTT-TGTTTCGAGGGAAACTA
* *
1295010 TCTCAAGGGAGACAAAATTTTCTATTTCGAGGGAAACTA
1 TCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAAACTA
1295049 TCTCAAG
1 TCTCAAG
1295056 TGATATAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
39 35 0.48
40 2 0.03
41 4 0.05
42 3 0.04
43 29 0.40
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (39 bp):
TCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAAACTA
Found at i:1295008 original size:43 final size:41
Alignment explanation
Indices: 1294913--1295073 Score: 132
Period size: 39 Copynumber: 4.0 Consensus size: 41
1294903 AGAGAAATTG
* * * * * *
1294913 TTTCAAGATAAATTGTCTCAAGGGAGACAAAAT-TT-TTTG
1 TTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
* *
1294952 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
1 TTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
* * * *
1294993 TGTTTCAATAGAAACTATCTCAAGGGAGACAAAAT-TT-TCTA
1 --TTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
* * * *
1295034 TTTCGAGGGAAACTATCTCAAGTGATATAAAATCTTGTTT
1 TTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTGTTT
1295074 TAATAAAAAC
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
39 53 0.56
40 4 0.04
41 8 0.08
42 2 0.02
43 28 0.29
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (41 bp):
TTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
Found at i:1295103 original size:36 final size:36
Alignment explanation
Indices: 1295063--1295177 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 36
1295053 AAGTGATATA
1295063 AAATCTTGTTTTAATAAAAACAATCTTGAGGGAAAT
1 AAATCTTGTTTTAATAAAAACAATCTTGAGGGAAAT
* * ** * * *
1295099 AAATCTT-TTTTCGAGT-AAAACAGTCTCAAGTGAGAC
1 AAATCTTGTTTT--AATAAAAACAATCTTGAGGGAAAT
*
1295135 AAAGTC-TGTTTTAAGAAAAACAATCTTGAGGGAAAT
1 AAA-TCTTGTTTTAATAAAAACAATCTTGAGGGAAAT
1295171 AAATCTT
1 AAATCTT
1295178 CTTTCAAGTA
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
35 7 0.12
36 43 0.74
37 8 0.14
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (36 bp):
AAATCTTGTTTTAATAAAAACAATCTTGAGGGAAAT
Found at i:1295158 original size:72 final size:72
Alignment explanation
Indices: 1295049--1295352 Score: 428
Period size: 72 Copynumber: 4.2 Consensus size: 72
1295039 AGGGAAACTA
* * * * ** * *
1295049 TCTCAAGTGATATAAAATCTTGTTTTAATAAAAACAATCTTGAGGGAAATAAATCTTTTTTCGAG
1 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAG
1295114 TAAAACAG
65 TAAAACAG
**
1295122 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1295187 AAAACAG
66 AAAACAG
* ** **
1295194 TCTCAAGTGAGACAAGGTCAATTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1295259 AAAACAG
66 AAAACAG
* * **
1295266 ACTCAAGTGAGACAAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1295331 AAAACAG
66 AAAACAG
1295338 TCTCAAGTGAGACAA
1 TCTCAAGTGAGACAA
1295353 GTCATCTATA
Statistics
Matches: 214, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
72 198 0.93
73 16 0.07
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (72 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
AAAACAG
Found at i:1295191 original size:36 final size:35
Alignment explanation
Indices: 1295079--1295192 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 35
1295069 TGTTTTAATA
*
1295079 AAAACAATCTTGAGGGAAATAAATCTTTTTTCGAGT
1 AAAACAATCTTGAGGGAAATAAATC-TTTTTCAAGT
* ** * * * *
1295115 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTT-AAGA
1 AAAACAATCTTGAGGGAAATAAA-TCT-TTTTCAAGT
1295151 AAAACAATCTTGAGGGAAATAAATCTTCTTTCAAGT
1 AAAACAATCTTGAGGGAAATAAATCTT-TTTCAAGT
1295187 AAAACA
1 AAAACA
1295193 GTCTCAAGTG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 46 0.78
37 6 0.10
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (35 bp):
AAAACAATCTTGAGGGAAATAAATCTTTTTCAAGT
Found at i:1295271 original size:36 final size:35
Alignment explanation
Indices: 1295091--1295344 Score: 128
Period size: 36 Copynumber: 7.1 Consensus size: 35
1295081 AACAATCTTG
* *
1295091 AGGGAAATAAATCTTTTTTCGAGTAAAACAGTCTCA
1 AGGGAAATAAATC-TTTTTCAAGTAAAACAGACTCA
* * * * **
1295127 AGTGAGACAAAGTCTGTTTT-AAGAAAAACA-ATCTTG
1 AGGGAAATAAA-TCT-TTTTCAAGTAAAACAGA-CTCA
*
1295163 AGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAGACTCA
* * * * * *
1295199 AGTGAGACAAGGTCAATTTT-AAG-AATGACA-ATCTCA
1 AGGGAAATAA-ATC-TTTTTCAAGTAA-AACAGA-CTCA
1295235 AGGGAAATAAATCTTCTTTCAAGTAAAACAGACTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAGACTCA
* * * * *
1295271 AGTGAGACAAGGTCTGTTTT-AAG-AATGACA-ATCTCA
1 AGGGAAATAA-ATCT-TTTTCAAGTAA-AACAGA-CTCA
*
1295307 AGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAGACTCA
1295343 AG
1 AG
1295345 TGAGACAAGT
Statistics
Matches: 157, Mismatches: 39, Indels: 44
0.65 0.16 0.18
Matches are distributed among these distances:
34 3 0.02
35 22 0.14
36 108 0.69
37 22 0.14
38 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (35 bp):
AGGGAAATAAATCTTTTTCAAGTAAAACAGACTCA
Found at i:1295370 original size:72 final size:72
Alignment explanation
Indices: 1295082--1295353 Score: 436
Period size: 72 Copynumber: 3.8 Consensus size: 72
1295072 TTTAATAAAA
** * * *
1295082 ACAATCTTGAGGGAAATAAATCTTTTTTCGAGTAAAACAGTCTCAAGTGAGACAAAGTCTGTTTT
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
**
1295147 AAGAAAA
66 AAGAATG
** **
1295154 ACAATCTTGAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCAATTTT
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
1295219 AAGAATG
66 AAGAATG
*
1295226 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGACTCAAGTGAGACAAGGTCTGTTTT
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
1295291 AAGAATG
66 AAGAATG
1295298 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAG
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAG
1295354 TCATCTATAT
Statistics
Matches: 187, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 187 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (72 bp):
ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
AAGAATG
Found at i:1295650 original size:28 final size:27
Alignment explanation
Indices: 1295611--1295663 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
1295601 AATATGCGTG
*
1295611 TGTTGATGCAACTATCATGATGATGGA
1 TGTTGATGCAACTAACATGATGATGGA
1295638 TGTTGGATGCAACTAACATGATGATG
1 TGTT-GATGCAACTAACATGATGATG
1295664 AATGCAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (27 bp):
TGTTGATGCAACTAACATGATGATGGA
Found at i:1299549 original size:13 final size:13
Alignment explanation
Indices: 1299531--1299572 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1299521 CACAATGAAA
*
1299531 ATAAATAAATAGT
1 ATAAATAAATAAT
1299544 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
1299558 A-AAATAAAGAAT
1 ATAAATAAATAAT
1299570 ATA
1 ATA
1299573 TACAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1299562 original size:22 final size:22
Alignment explanation
Indices: 1299528--1299628 Score: 57
Period size: 22 Copynumber: 4.5 Consensus size: 22
1299518 AAACACAATG
1299528 AAAATAA-ATAAATAGTATAAAT
1 AAAATAATA-AAATAGTATAAAT
* *
1299550 AAAATAATAAAATAAAGAATATAT
1 AAAATAATAAAAT--AGTATAAAT
**
1299574 ACAAAT-ATAAAA-ATGTATGTAT
1 A-AAATAATAAAATA-GTATAAAT
* * *
1299596 AATAGAATAAAATATTA-AAAT
1 AAAATAATAAAATAGTATAAAT
1299617 AATAATAATAAA
1 AA-AATAATAAA
1299629 TAAACGAGAA
Statistics
Matches: 60, Mismatches: 11, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
21 7 0.12
22 33 0.55
23 2 0.03
24 14 0.23
25 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAATAATAAAATAGTATAAAT
Found at i:1299664 original size:3 final size:3
Alignment explanation
Indices: 1299656--1299735 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
1299646 GGAAAAACCC
* * *
1299656 AAT AAT AAT AAT AAT -AG AAT AAT ATT CCAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
1299700 AAAT AAT AAA ACAT AAT -AT ATT AAAT AAT AA- AAT AA
1 -AAT AAT AAT A-AT AAT AAT AAT -AAT AAT AAT AAT AA
1299736 ATAAATGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
2 7 0.12
3 44 0.75
4 8 0.14
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1299706 original size:12 final size:12
Alignment explanation
Indices: 1299689--1299739 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
1299679 ATTCCATAAT
1299689 AATAATAAAATA
1 AATAATAAAATA
1299701 AATAAT-AAA-A
1 AATAATAAAATA
* * *
1299711 CATAATATATTA
1 AATAATAAAATA
1299723 AATAATAAAATA
1 AATAATAAAATA
1299735 AATAA
1 AATAA
1299740 ATGAAATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 6 0.19
11 4 0.13
12 21 0.68
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:1299724 original size:22 final size:22
Alignment explanation
Indices: 1299690--1299740 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1299680 TTCCATAATA
1299690 ATAATAAAATAAATAATAAAAC
1 ATAATAAAATAAATAATAAAAC
* * *
1299712 ATAATATATTAAATAATAAAAT
1 ATAATAAAATAAATAATAAAAC
1299734 A-AATAAA
1 ATAATAAA
1299741 TGAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAATAAAATAAATAATAAAAC
Found at i:1301244 original size:37 final size:37
Alignment explanation
Indices: 1301150--1301287 Score: 180
Period size: 36 Copynumber: 3.8 Consensus size: 37
1301140 CAAATCTTTG
1301150 GTGTTTCAAGAGAAAC-ATGTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAACGAT-TTCAAAGGTTTTCTTTTT
**
1301187 -TGTTTCAAGAGAAATAATTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTCTTTTT
* *
1301223 GTGTTCCAAGAGAAACGATTTCAAAGG----GTTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTCTTTTT
1301256 GTGTTTCAAGAGAAAACGATTTCAAAGGTTTT
1 GTGTTTCAAGAG-AAACGATTTCAAAGGTTTT
1301288 TTTCAAGAGA
Statistics
Matches: 88, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
33 16 0.18
34 15 0.17
36 32 0.36
37 25 0.28
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (37 bp):
GTGTTTCAAGAGAAACGATTTCAAAGGTTTTCTTTTT
Found at i:1301260 original size:33 final size:34
Alignment explanation
Indices: 1301218--1301289 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1301208 AAAGGTTTTC
1301218 TTTTTGTGTTCCAAGAG-AAACGATTTCAAAGGG
1 TTTTTGTGTTCCAAGAGAAAACGATTTCAAAGGG
* *
1301251 TTTTTGTGTTTCAAGAGAAAACGATTTCAAAGGT
1 TTTTTGTGTTCCAAGAGAAAACGATTTCAAAGGG
1301285 TTTTT
1 TTTTT
1301290 TCAAGAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 16 0.44
34 20 0.56
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (34 bp):
TTTTTGTGTTCCAAGAGAAAACGATTTCAAAGGG
Found at i:1301278 original size:34 final size:33
Alignment explanation
Indices: 1301150--1301290 Score: 149
Period size: 37 Copynumber: 4.0 Consensus size: 33
1301140 CAAATCTTTG
1301150 GTGTTTCAAGAGAAACATGTTCAAAGGTTTTCTTTT
1 GTGTTTCAAGAGAAACAT-TTCAAAGG-TTT-TTTT
* *
1301186 TTGTTTCAAGAGAAATAATTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAA-CATTTCAAAGG--TT-TTTTT
* *
1301223 GTGTTCCAAGAGAAACGATTTCAAAGG-GTTTTT
1 GTGTTTCAAGAGAAAC-ATTTCAAAGGTTTTTTT
1301256 GTGTTTCAAGAGAAAACGATTTCAAAGGTTTTTTT
1 GTGTTTCAAGAG-AAAC-ATTTCAAAGGTTTTTTT
1301291 CAAGAGAAAC
Statistics
Matches: 91, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
33 16 0.18
34 15 0.16
35 5 0.05
36 22 0.24
37 32 0.35
38 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACATTTCAAAGGTTTTTTT
Found at i:1301356 original size:29 final size:29
Alignment explanation
Indices: 1301315--1301396 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
1301305 TCCAGGGAGG
*
1301315 CAAAATTTTGTTTCAAGAGAAAC-ATATT
1 CAAAGTTTTGTTTCAAGAGAAACTATATT
* * *
1301343 CAAAGGTTTTGTTTCAAGGGAAACTGTTTT
1 CAAA-GTTTTGTTTCAAGAGAAACTATATT
1301373 CAAAGTTTATGTTTCAAGA-AAACT
1 CAAAGTTT-TGTTTCAAGAGAAACT
1301397 GTCTCAAGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.09
29 26 0.57
30 16 0.35
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (29 bp):
CAAAGTTTTGTTTCAAGAGAAACTATATT
Found at i:1301438 original size:36 final size:36
Alignment explanation
Indices: 1301382--1301568 Score: 133
Period size: 36 Copynumber: 5.4 Consensus size: 36
1301372 TCAAAGTTTA
* * *
1301382 TGTTTCAA-GAAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1301417 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
** * * * *
1301453 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATT
* * **
1301481 ATGTTTCAAGAGAAACTATCTCAAGGGAGGTAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
*
1301519 TGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
1301555 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1301569 TGTTTTCAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
28 2 0.02
29 14 0.12
30 2 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 10 0.09
36 52 0.46
37 29 0.25
38 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:1301552 original size:102 final size:102
Alignment explanation
Indices: 1301288--1301657 Score: 490
Period size: 102 Copynumber: 3.7 Consensus size: 102
1301278 CAAAGGTTTT
* * *
1301288 TTTCAAGAGAAACTGTCTCCAGGGAGGCAAAATTTTGTTTCAAGAGAAACATAT-TCAA-AG-G-
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC-TATCTCAAGAGAGA
* ** *
1301349 ----TTTTGTTTCAAGGGAAACTGTTTTCAAAGTTTATG
65 CAAAATTCATTTCAAGGGAAA-TGTTTTCAATGTTTATG
1301384 TTTCAAGA-AAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1301447 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* ** *
1301484 TTTCAAGAGAAACTATCTCAAGGGAGGTAAAATTTTGTTTCAAGGAAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1301549 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* * * *
1301586 TTTCAAGAGAAATTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-TGTTTCAAGGGAAACTATCTCAAGAGAG
*
1301651 ATAAAAT
64 ACAAAAT
1301658 CTTGTTTATG
Statistics
Matches: 242, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
93 3 0.01
94 20 0.08
95 23 0.10
96 9 0.04
100 24 0.10
101 34 0.14
102 95 0.39
103 3 0.01
104 31 0.13
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
Found at i:1301553 original size:37 final size:37
Alignment explanation
Indices: 1301482--1301554 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
1301472 TCAATGTTTA
* **
1301482 TGTTTCAAGAGAAACTATCTCAAGGGAGGTAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
1301519 TGTTTCAAG-GAAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAG-AAACTATCTCAAGAGAGACAAAATT
1301555 CATTTCAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1301568 original size:37 final size:38
Alignment explanation
Indices: 1301484--1301568 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 38
1301474 AATGTTTATG
* * ** **
1301484 TTTCAAGAG-AAACTATCTCAAGGGAGGTAAAATTTTG
1 TTTCAAGGGAAAACTATCTCAAGAGAGACAAAATTTCA
1301521 TTTCAA-GGAAAACTATCTCAAGAGAGACAAAA-TTCA
1 TTTCAAGGGAAAACTATCTCAAGAGAGACAAAATTTCA
1301557 TTTCAAGGGAAA
1 TTTCAAGGGAAA
1301569 TGTTTTCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 9 0.22
37 31 0.77
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (38 bp):
TTTCAAGGGAAAACTATCTCAAGAGAGACAAAATTTCA
Found at i:1301657 original size:39 final size:39
Alignment explanation
Indices: 1301609--1301739 Score: 154
Period size: 39 Copynumber: 3.3 Consensus size: 39
1301599 TGTCTTAAGG
*
1301609 GAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGC
1 GAGATAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGC
* * * * *
1301648 GAGATAAAATCTTGTTTATGTTTCAAGAGAAACTGTCTCAAGG
1 GAGATAAAA---T-TTTCTGTTTCGAGGGAAACTATCTCAAGC
*
1301691 GAGATAAAATTTTCTGTTTCGAGGGAAACTATTTCAAGC
1 GAGATAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGC
*
1301730 GATATAAAAT
1 GAGATAAAAT
1301740 CTTATTTTCA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
39 40 0.53
40 1 0.01
42 1 0.01
43 33 0.44
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (39 bp):
GAGATAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGC
Found at i:1301670 original size:82 final size:82
Alignment explanation
Indices: 1301578--1301742 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 82
1301568 ATGTTTTCAA
* *
1301578 TGTTTATGTTTCAAGAGAAATTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCT
1 TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCT
1301643 CAAGCGAGATAAAATCT
66 CAAGCGAGATAAAATCT
* *
1301660 TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTCTGTTTCGAGGGAAACTATTT
1 TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCT
*
1301725 CAAGCGATATAAAATCT
66 CAAGCGAGATAAAATCT
1301742 T
1 T
1301743 ATTTTCAGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (82 bp):
TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCT
CAAGCGAGATAAAATCT
Found at i:1301671 original size:43 final size:42
Alignment explanation
Indices: 1301618--1301742 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 42
1301608 GGAGACAAAA
*
1301618 TTTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCT
1 TTTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCT
* * * *
1301660 TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA---
1 T-TTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCT
* * *
1301700 TTTTCTGTTTCGAGGGAAACTATTTCAAGCGATATAAAATCT
1 TTTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCT
1301742 T
1 T
1301743 ATTTTCAGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
39 31 0.46
40 1 0.01
42 2 0.03
43 33 0.49
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (42 bp):
TTTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCT
Found at i:1301956 original size:36 final size:36
Alignment explanation
Indices: 1301772--1301956 Score: 132
Period size: 36 Copynumber: 5.1 Consensus size: 36
1301762 TGAGGGAAAT
* * *
1301772 AAATCTTCTTTCAAGTAAAATAATCTCAAGTAAGGC
1 AAATCTTCTTTCAAGTAAAACAATCTCAAGTGAGAC
* * * * *
1301808 AAGGTCTGT-TTT-AAG-AATGACAATCTCAAGGGAAAT
1 AA-ATCT-TCTTTCAAGTAA-AACAATCTCAAGTGAGAC
1301844 AAATCTTCTTTCAAGTAAAACAGA-CTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACA-ATCTCAAGTGAGAC
* * * * *
1301880 AAGGTCTGT-TTT-AAG-AATGACAATCTCAAGGGAAAT
1 AA-ATCT-TCTTTCAAGTAA-AACAATCTCAAGTGAGAC
*
1301916 AAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTCAAGTGAGAC
1301952 AAATC
1 AAATC
1301957 ATCTATATTA
Statistics
Matches: 111, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
34 2 0.02
35 17 0.15
36 73 0.66
37 17 0.15
38 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (36 bp):
AAATCTTCTTTCAAGTAAAACAATCTCAAGTGAGAC
Found at i:1301971 original size:72 final size:72
Alignment explanation
Indices: 1301755--1301953 Score: 335
Period size: 72 Copynumber: 2.8 Consensus size: 72
1301745 TTTCAGAAAA
** * * * *
1301755 ACAATCTTGAGGGAAATAAATCTTCTTTCAAGTAAAATAATCTCAAGTAAGGCAAGGTCTGTTTT
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
1301820 AAGAATG
66 AAGAATG
*
1301827 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGACTCAAGTGAGACAAGGTCTGTTTT
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
1301892 AAGAATG
66 AAGAATG
1301899 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
1 ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAA
1301954 ATCATCTATA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 119 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (72 bp):
ACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGACAAGGTCTGTTTT
AAGAATG
Found at i:1307133 original size:3 final size:3
Alignment explanation
Indices: 1307125--1307149 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1307115 GTTAAAAGAA
1307125 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1307150 GAAGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1307385 original size:13 final size:13
Alignment explanation
Indices: 1307367--1307408 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1307357 CACAATGAAA
*
1307367 ATAAATAAATAGT
1 ATAAATAAATAAT
1307380 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
1307394 A-AAATAAAGAAT
1 ATAAATAAATAAT
1307406 ATA
1 ATA
1307409 TACAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1307542 original size:12 final size:12
Alignment explanation
Indices: 1307525--1307575 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
1307515 ATACCATGAT
1307525 AATAATAAAATA
1 AATAATAAAATA
1307537 AATAAT-AAA-A
1 AATAATAAAATA
* * *
1307547 CATAATATATTA
1 AATAATAAAATA
1307559 AATAATAAAATA
1 AATAATAAAATA
1307571 AATAA
1 AATAA
1307576 ATGAAATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 6 0.19
11 4 0.13
12 21 0.68
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:1307560 original size:22 final size:22
Alignment explanation
Indices: 1307526--1307576 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1307516 TACCATGATA
1307526 ATAATAAAATAAATAATAAAAC
1 ATAATAAAATAAATAATAAAAC
* * *
1307548 ATAATATATTAAATAATAAAAT
1 ATAATAAAATAAATAATAAAAC
1307570 A-AATAAA
1 ATAATAAA
1307577 TGAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAATAAAATAAATAATAAAAC
Found at i:1309023 original size:36 final size:36
Alignment explanation
Indices: 1308976--1309111 Score: 165
Period size: 36 Copynumber: 3.8 Consensus size: 36
1308966 AAAGCTTTGG
1308976 TGTTTCAAGAGAAAC-ATGTTCAAAGGTTTTCTTTTT
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTTTTCTTTTT
*
1309012 TGTTTCAAGAGAAACTATTTCAAAGGTTTTCTTTTT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
* * *
1309048 GTGTTCCAAGAGAAA-GATTTCAAAGG--TT-TTTTG
1 -TGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
*
1309081 TGTTTAAAGAGAAAACAATTTCAAAGGTTTT
1 TGTTTCAAGAG-AAACAATTTCAAAGGTTTT
1309112 TTTCAAGAGA
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
32 9 0.10
33 7 0.08
34 12 0.14
36 45 0.51
37 15 0.17
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
Found at i:1309212 original size:30 final size:29
Alignment explanation
Indices: 1309139--1309223 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
1309129 TCCAGGGAGG
* *
1309139 CAAAATTTTGTTTCAAGAGAAACAT-ATTT
1 CAAAGTTTTGTTTCAAGAGAAAC-TGTTTT
*
1309168 -AAAGGTTTTGTTTCAAGGGAAACTGTTTT
1 CAAA-GTTTTGTTTCAAGAGAAACTGTTTT
1309197 CAAAGTTTATGTTTCAAGAGAAACTGT
1 CAAAGTTT-TGTTTCAAGAGAAACTGT
1309224 CTCAAGGGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 4 0.08
29 24 0.50
30 20 0.42
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (29 bp):
CAAAGTTTTGTTTCAAGAGAAACTGTTTT
Found at i:1309256 original size:36 final size:36
Alignment explanation
Indices: 1309206--1309291 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
1309196 TCAAAGTTTA
* * *
1309206 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
1309242 TGTTTTAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
1309278 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1309292 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:1309322 original size:101 final size:102
Alignment explanation
Indices: 1309178--1309482 Score: 459
Period size: 102 Copynumber: 3.0 Consensus size: 102
1309168 AAAGGTTTTG
*
1309178 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1309242 TGTTTTAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
1309280 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* * *
1309345 GTTTCAAGGGAAATTATCTCAAGAGAGGCAAAATTCT
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * *
1309382 TTTTAAGGGAAATGTTTTCAATGTTTATGTTTCAATAGAAATTGTCTTAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
1309447 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
65 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1309483 CTTGTTTATG
Statistics
Matches: 184, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
101 47 0.26
102 104 0.57
103 3 0.02
104 30 0.16
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:1309365 original size:37 final size:38
Alignment explanation
Indices: 1309307--1309394 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 38
1309297 TCAATGTTTA
* * * *
1309307 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATT-T
1 TGTTTCAAGGGAAATTATCTCAAGAGAGAAAAAATTCT
**
1309344 TGTTTCAAGGGAAATTATCTCAAGAGAGGCAAAATTCT
1 TGTTTCAAGGGAAATTATCTCAAGAGAGAAAAAATTCT
1309382 T-TTT-AAGGGAAAT
1 TGTTTCAAGGGAAAT
1309395 GTTTTCAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 9 0.20
37 33 0.75
38 2 0.05
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.30
Consensus pattern (38 bp):
TGTTTCAAGGGAAATTATCTCAAGAGAGAAAAAATTCT
Found at i:1309482 original size:39 final size:39
Alignment explanation
Indices: 1309434--1309556 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 39
1309424 TGTCTTAAGG
* *
1309434 GAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGC
1 GAGACAAAATTTTCTGTTTCAAAGGAAACTATCTCAAGC
* * * ** *
1309473 GAGATAAAATCTTGTTTATGTTTCAATA-AAAACTGCCTCAAGG
1 GAGACAAAA---T-TTTCTGTTTCAA-AGGAAACTATCTCAAGC
*
1309516 GAGACAAAATTTTCTGTTTCCAAGGAAACTATCTCAAGC
1 GAGACAAAATTTTCTGTTTCAAAGGAAACTATCTCAAGC
1309555 GA
1 GA
1309557 TATAAAATCT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
38 1 0.02
39 31 0.49
40 1 0.02
42 1 0.02
43 29 0.46
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
GAGACAAAATTTTCTGTTTCAAAGGAAACTATCTCAAGC
Found at i:1309493 original size:82 final size:82
Alignment explanation
Indices: 1309403--1309571 Score: 275
Period size: 82 Copynumber: 2.1 Consensus size: 82
1309393 ATGTTTTCAA
* * * * * *
1309403 TGTTTATGTTTCAATAGAAATTGTCTTAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCT
1 TGTTTATGTTTCAATAAAAACTGCCTCAAGGGAGACAAAATTTTCTGTTTCCAAGGAAACTATCT
1309468 CAAGCGAGATAAAATCT
66 CAAGCGAGATAAAATCT
1309485 TGTTTATGTTTCAATAAAAACTGCCTCAAGGGAGACAAAATTTTCTGTTTCCAAGGAAACTATCT
1 TGTTTATGTTTCAATAAAAACTGCCTCAAGGGAGACAAAATTTTCTGTTTCCAAGGAAACTATCT
*
1309550 CAAGCGATATAAAATCT
66 CAAGCGAGATAAAATCT
1309567 TGTTT
1 TGTTT
1309572 TAAGAAAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (82 bp):
TGTTTATGTTTCAATAAAAACTGCCTCAAGGGAGACAAAATTTTCTGTTTCCAAGGAAACTATCT
CAAGCGAGATAAAATCT
Found at i:1309496 original size:43 final size:43
Alignment explanation
Indices: 1309448--1309571 Score: 114
Period size: 43 Copynumber: 3.0 Consensus size: 43
1309438 CAAAATTTTC
* *
1309448 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
1 TGTTTCAAAGGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
* ** * * *
1309491 TGTTTCAATA-AAAACTGCCTCAAGGGAGACAAAA---T-TTTC
1 TGTTTCAA-AGGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
* *
1309530 TGTTTCCAAGGAAACTATCTCAAGCGATATAAAATCTTGTTT
1 TGTTTCAAAGGAAACTATCTCAAGCGAGATAAAATCTTGTTT
1309572 TAAGAAAAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
38 1 0.02
39 28 0.47
40 1 0.02
42 1 0.02
43 29 0.48
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (43 bp):
TGTTTCAAAGGAAACTATCTCAAGCGAGATAAAATCTTGTTTA
Found at i:1309769 original size:36 final size:35
Alignment explanation
Indices: 1309589--1309842 Score: 101
Period size: 36 Copynumber: 7.1 Consensus size: 35
1309579 AAAAATCTTG
* *
1309589 AGGGAAATAAATCTTTTTTCGAGTAAAACAGTCTCA
1 AGGGAAATAAATC-TTTTTCAAGTAAAACAGACTCA
* * * * * **
1309625 AGTGAGACAAAGTCTGTTTT-AAGAAAAATA-ATCTTG
1 AGGGAAATAAA-TCT-TTTTCAAGTAAAACAGA-CTCA
* *
1309661 AGGGAAATAAATTTTCTTTCAAGTAAAACAGTCTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAGACTCA
* * * * *
1309697 AGTGAGACAAGGTCTGTTTT-AAG-AATGACA-ATCTCA
1 AGGGAAATAA-ATCT-TTTTCAAGTAA-AACAGA-CTCA
1309733 AGGGAAATAAATCTTCTTTCAAGTAAAACAGACTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAGACTCA
* * * * * *
1309769 AGTGAGACAAGGTCTGTTTT-AAG-AATGACA-ATCTTA
1 AGGGAAATAA-ATCT-TTTTCAAGTAA-AACAGA-CTCA
* *
1309805 AGGGAAATAAATATTCTTTCAAGTAAAACAGTCTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAGACTCA
1309841 AG
1 AG
1309843 TGAGACAAAT
Statistics
Matches: 152, Mismatches: 44, Indels: 44
0.63 0.18 0.18
Matches are distributed among these distances:
34 3 0.02
35 21 0.14
36 104 0.68
37 22 0.14
38 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (35 bp):
AGGGAAATAAATCTTTTTCAAGTAAAACAGACTCA
Found at i:1309868 original size:72 final size:72
Alignment explanation
Indices: 1309567--1309850 Score: 433
Period size: 72 Copynumber: 3.9 Consensus size: 72
1309557 TATAAAATCT
** * * * *
1309567 TGTTTTAAGAAAAAAAATCTTGAGGGAAATAAATCTTTTTTCGAGTAAAACAGTCTCAAGTGAGA
1 TGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGA
*
1309632 CAAAGTC
66 CAAGGTC
** * * *
1309639 TGTTTTAAGAAAAATAATCTTGAGGGAAATAAATTTTCTTTCAAGTAAAACAGTCTCAAGTGAGA
1 TGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGA
1309704 CAAGGTC
66 CAAGGTC
* *
1309711 TGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGACTCAAGTGAGA
1 TGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGA
1309776 CAAGGTC
66 CAAGGTC
*
1309783 TGTTTTAAGAATGACAATCTTAAGGGAAATAAATATTCTTTCAAGTAAAACAGTCTCAAGTGAGA
1 TGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGA
1309848 CAA
66 CAA
1309851 ATCATCTGTA
Statistics
Matches: 197, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 197 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (72 bp):
TGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAAGTGAGA
CAAGGTC
Found at i:1311269 original size:95 final size:95
Alignment explanation
Indices: 1311105--1311286 Score: 276
Period size: 95 Copynumber: 1.9 Consensus size: 95
1311095 ATATGTAAAT
* * * * * *
1311105 ACCTTTATAAGGTTAGCTGAATCTTATCCATAAAGCCAGGGTGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATAAGGCTAGCTAAATATTATCCATAAAGCCAGGGCGTTTAACCAATTACCTTAGAGGA
1311170 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
* *
1311200 ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCC-GTGGCGTTTAACCAATTACTTTAGAGG
1 ACCTTTATAAGGCTAGCTAAATATTATCCATAAAGCCAG-GGCGTTTAACCAATTACCTTAGAGG
1311264 AACAACTCAAGCTTTATTGTATA
65 AACAACTCAAGCTTTATTGTATA
1311287 TAAATAATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 77 0.99
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (95 bp):
ACCTTTATAAGGCTAGCTAAATATTATCCATAAAGCCAGGGCGTTTAACCAATTACCTTAGAGGA
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:1315238 original size:13 final size:13
Alignment explanation
Indices: 1315220--1315261 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1315210 CACAATGAAA
*
1315220 ATAAATAAATAGT
1 ATAAATAAATAAT
1315233 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
1315247 A-AAATAAAGAAT
1 ATAAATAAATAAT
1315259 ATA
1 ATA
1315262 TACAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1315351 original size:3 final size:3
Alignment explanation
Indices: 1315345--1315445 Score: 88
Period size: 3 Copynumber: 33.7 Consensus size: 3
1315335 GGAAAAAAAC
1315345 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGA- AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
1315389 -AT ACCAT AAT AAT AAT AA- AAT AAAT AAT AAA ACAT AAT -AT ATT AAAT
1 AAT A--AT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT -AAT
1315436 AAT AA- AAT AA
1 AAT AAT AAT AA
1315446 ATAAATGAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
2 11 0.13
3 61 0.73
4 8 0.10
5 3 0.04
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1316883 original size:36 final size:35
Alignment explanation
Indices: 1316843--1316982 Score: 162
Period size: 36 Copynumber: 4.0 Consensus size: 35
1316833 AAAGCTTTGG
1316843 TGTTTCAAGAGAAAC-ATGTTCAAAGGTATTCTTTTT
1 TGTTTCAAGAGAAACGAT-TTCAAAGGT-TTCTTTTT
* * *
1316879 TGTTTTAAGAGAAACAATTTCAAAAGTTTTCTTTTT
1 TGTTTCAAGAGAAACGATTTC-AAAGGTTTCTTTTT
* *
1316915 GTGTTCCAAGAGAAACGATTTCAAAGG-TT-TTTTG
1 -TGTTTCAAGAGAAACGATTTCAAAGGTTTCTTTTT
1316949 TGTTTCAAGAGAAAACGATTTCAAAGGTTT-TTTT
1 TGTTTCAAGAG-AAACGATTTCAAAGGTTTCTTTT
1316983 CAAGAGAAAC
Statistics
Matches: 91, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
33 10 0.11
34 19 0.21
35 8 0.09
36 29 0.32
37 25 0.27
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTTCAAGAGAAACGATTTCAAAGGTTTCTTTTT
Found at i:1316970 original size:34 final size:33
Alignment explanation
Indices: 1316842--1316981 Score: 147
Period size: 37 Copynumber: 4.0 Consensus size: 33
1316832 CAAAGCTTTG
1316842 GTGTTTCAAGAGAAAC-ATGTTCAAAGGTATTCTTTT
1 GTGTTTCAAGAGAAACGAT-TTCAAAGG--TT-TTTT
* * * *
1316878 TTGTTTTAAGAGAAACAATTTCAAAAGTTTTCTTTTT
1 GTGTTTCAAGAGAAACGATTTC-AAAG--GT-TTTTT
*
1316915 GTGTTCCAAGAGAAACGATTTCAAAGGTTTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
1316948 GTGTTTCAAGAGAAAACGATTTCAAAGGTTTTTT
1 GTGTTTCAAGAG-AAACGATTTCAAAGGTTTTTT
1316982 TCAAGAGAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
33 16 0.18
34 22 0.25
36 21 0.24
37 29 0.33
38 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
Found at i:1317048 original size:29 final size:30
Alignment explanation
Indices: 1317007--1317087 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
1316997 TCCAGGGAGG
1317007 CAAAA-TTTTGTTTCAAGAGAAA-AATATT
1 CAAAAGTTTTGTTTCAAGAGAAATAATATT
* ** *
1317035 CAAAAGTTTTGTTTCAAGGGAAATTGTTTT
1 CAAAAGTTTTGTTTCAAGAGAAATAATATT
1317065 C-AAAGTTTATGTTTCAAGAGAAA
1 CAAAAGTTT-TGTTTCAAGAGAAA
1317088 CTGTCTCAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 5 0.11
29 23 0.51
30 17 0.38
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (30 bp):
CAAAAGTTTTGTTTCAAGAGAAATAATATT
Found at i:1317124 original size:36 final size:36
Alignment explanation
Indices: 1317074--1317261 Score: 160
Period size: 36 Copynumber: 5.4 Consensus size: 36
1317064 TCAAAGTTTA
* *
1317074 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
1317110 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
1317146 CATTTCAAAGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* *
1317174 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
1317212 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
**
1317248 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1317262 TGTTTTCAAT
Statistics
Matches: 117, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.02
29 13 0.11
30 3 0.03
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.02
36 61 0.52
37 31 0.26
38 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1317226 original size:37 final size:36
Alignment explanation
Indices: 1317175--1317261 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
1317165 TCAATGTTTA
* * *
1317175 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1317212 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
1317248 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1317262 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 14 0.31
37 31 0.69
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:1317237 original size:102 final size:102
Alignment explanation
Indices: 1317046--1317350 Score: 486
Period size: 102 Copynumber: 3.0 Consensus size: 102
1317036 AAAAGTTTTG
*
1317046 TTTCAAGGGAAATTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1317110 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
1317148 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1317213 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * *
1317250 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAATTATCTTAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * * *
1317315 CTGTTTCGAGGAAAACTATCTCAAGCGAGATAAAAT
65 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1317351 CTTGTTTATG
Statistics
Matches: 189, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
101 48 0.25
102 107 0.57
103 3 0.02
104 31 0.16
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:1317335 original size:39 final size:39
Alignment explanation
Indices: 1317292--1317421 Score: 118
Period size: 39 Copynumber: 3.2 Consensus size: 39
1317282 AAAGAGAAAT
*
1317292 TATCTTAAGGGAGACAAAATTTTCTGTTTCGAGGAAAAC
1 TATCTCAAGGGAGACAAAATTTTCTGTTTCGAGGAAAAC
* * * *
1317331 TATCTCAAGCGAGATAAAATCTTGTTTATGTTTC-AAGAGAAAC
1 TATCTCAAGGGAGACAAAA---T-TTTCTGTTTCGAGGA-AAAC
* * * *
1317374 TGTCTCAAAGGAGACAAAATTTTCTATTTCGAGGGAAAC
1 TATCTCAAGGGAGACAAAATTTTCTGTTTCGAGGAAAAC
*
1317413 TATATCAAG
1 TATCTCAAG
1317422 CGATATAAAG
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
39 34 0.49
40 3 0.04
42 4 0.06
43 28 0.41
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (39 bp):
TATCTCAAGGGAGACAAAATTTTCTGTTTCGAGGAAAAC
Found at i:1317369 original size:82 final size:82
Alignment explanation
Indices: 1317271--1317439 Score: 248
Period size: 82 Copynumber: 2.1 Consensus size: 82
1317261 ATGTTTTCAA
* * * * *
1317271 TGTTTATGTTTAAAGAGAAATTATCTTAAGGGAGACAAAATTTTCTGTTTCGAGGAAAACTATCT
1 TGTTTATGTTTAAAGAGAAACTATCTCAAAGGAGACAAAATTTTCTATTTCGAGGAAAACTATAT
1317336 CAAGCGAGATAAAATCT
66 CAAGCGAGATAAAATCT
* * *
1317353 TGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTCTATTTCGAGGGAAACTATAT
1 TGTTTATGTTTAAAGAGAAACTATCTCAAAGGAGACAAAATTTTCTATTTCGAGGAAAACTATAT
* *
1317418 CAAGCGATATAAAGTCT
66 CAAGCGAGATAAAATCT
1317435 TGTTT
1 TGTTT
1317440 TAAGAAAAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (82 bp):
TGTTTATGTTTAAAGAGAAACTATCTCAAAGGAGACAAAATTTTCTATTTCGAGGAAAACTATAT
CAAGCGAGATAAAATCT
Found at i:1317374 original size:43 final size:42
Alignment explanation
Indices: 1317271--1317424 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 42
1317261 ATGTTTTCAA
* * * *
1317271 TGTTTATGTTTAAAGAGAAATTATCTTAAGGGAGACAAAA--
1 TGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
* * *
1317311 T-TTTCTGTTTCGAG-GAAAACTATCTCAAGCGAGATAAAATCT
1 TGTTTATGTTTCAAGAG-AAACTATCTCAAGCGAGACAAAAT-T
*
1317353 TGTTTATGTTTCAAGAGAAACTGTCTCAAAG-GAGACAAAATT
1 TGTTTATGTTTCAAGAGAAACTATCTC-AAGCGAGACAAAATT
* * * *
1317395 T-TCTA--TTTCGAGGGAAACTATATCAAGCGA
1 TGTTTATGTTTCAAGAGAAACTATCTCAAGCGA
1317425 TATAAAGTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
38 4 0.04
39 46 0.51
40 1 0.01
41 3 0.03
42 3 0.03
43 29 0.32
44 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (42 bp):
TGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
Found at i:1317485 original size:36 final size:36
Alignment explanation
Indices: 1317426--1317630 Score: 125
Period size: 36 Copynumber: 5.7 Consensus size: 36
1317416 ATCAAGCGAT
* *
1317426 ATAAAGTCTTGTTTT-AAGAAAAACAATATTGAGGGAA
1 ATAAA-TCTT-TTTTCAAGTAAAACAATCTTGAGGGAA
* * ** *
1317463 ATAAATCTTTTTTCGAGTAAAACAGTCTCAAGTGAGAC
1 ATAAATCTTTTTTCAAGTAAAACAATCTTGAG-G-GAA
* * *
1317501 A-AAATATGTTTT-AAGAAAAACAATCTTGAGGGAA
1 ATAAATCTTTTTTCAAGTAAAACAATCTTGAGGGAA
* * *
1317535 ATAAATCTTCTTTCAAGTAAAACAATCTCT-AGTGAG
1 ATAAATCTTTTTTCAAGTAAAACAATCT-TGAGGGAA
* * * **
1317571 ATAAGGTCTGTTTT-AAG-AATGACAATCTCAAGGGAA
1 ATAA-ATCTTTTTTCAAGTAA-AACAATCTTGAGGGAA
* *
1317607 ATAAATATTCTTTCAAGTAAAACA
1 ATAAATCTTTTTTCAAGTAAAACA
1317631 GACTCAAGTG
Statistics
Matches: 124, Mismatches: 33, Indels: 23
0.69 0.18 0.13
Matches are distributed among these distances:
34 3 0.02
35 20 0.16
36 74 0.60
37 24 0.19
38 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (36 bp):
ATAAATCTTTTTTCAAGTAAAACAATCTTGAGGGAA
Found at i:1317518 original size:72 final size:72
Alignment explanation
Indices: 1317428--1317719 Score: 386
Period size: 72 Copynumber: 4.0 Consensus size: 72
1317418 CAAGCGATAT
* ** * *
1317428 AAAGTCTTGTTTTAAGAAAAACAATATTGAGGGAAATAAATCTTTTTTCGAGTAAAACAGTCTCA
1 AAAGTC-TGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCA
1317493 AGTGAGAC
65 AGTGAGAC
* * ** * *
1317501 AAAATATGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCAAGTAAAACAATCTCTA
1 AAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAA
*
1317566 GTGAGAT
66 GTGAGAC
* ** * *
1317573 AAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATATTCTTTCAAGTAAAACAGACTCAA
1 AAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAA
1317638 GTGAGAC
66 GTGAGAC
* ** *
1317645 AAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAATAGTCTCAA
1 AAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAA
1317710 GTGAGAC
66 GTGAGAC
1317717 AAA
1 AAA
1317720 TCATCTGTAT
Statistics
Matches: 195, Mismatches: 24, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
72 191 0.98
73 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (72 bp):
AAAGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCAAGTAAAACAGTCTCAA
GTGAGAC
Found at i:1317708 original size:36 final size:35
Alignment explanation
Indices: 1317457--1317710 Score: 153
Period size: 36 Copynumber: 7.1 Consensus size: 35
1317447 AACAATATTG
* *
1317457 AGGGAAATAAATCTTTTTTCGAGTAAAACAGTCTCA
1 AGGGAAATAAATC-TTTTTCAAGTAAAACAATCTCA
* * * **
1317493 AGTGAGACA-AAATATGTTTT-AAGAAAAACAATCTTG
1 AG-G-GAAATAAATCT-TTTTCAAGTAAAACAATCTCA
*
1317529 AGGGAAATAAATCTTCTTTCAAGTAAAACAATCTCT
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAATCTCA
* * * *
1317565 AGTGAGATAAGGTCTGTTTT-AAG-AATGACAATCTCA
1 AGGGAAATAA-ATCT-TTTTCAAGTAA-AACAATCTCA
*
1317601 AGGGAAATAAATATTCTTTCAAGTAAAACAGA-CTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACA-ATCTCA
* * * * *
1317637 AGTGAGACAAGGTCTGTTTT-AAG-AATGACAATCTCA
1 AGGGAAATAA-ATCT-TTTTCAAGTAA-AACAATCTCA
* *
1317673 AGGGAAATAAATCTTCTTTCAAGTAAAATAGTCTCA
1 AGGGAAATAAATCTT-TTTCAAGTAAAACAATCTCA
1317709 AG
1 AG
1317711 TGAGACAAAT
Statistics
Matches: 163, Mismatches: 35, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
34 6 0.04
35 25 0.15
36 102 0.63
37 25 0.15
38 5 0.03
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (35 bp):
AGGGAAATAAATCTTTTTCAAGTAAAACAATCTCA
Found at i:1318400 original size:95 final size:94
Alignment explanation
Indices: 1318231--1318411 Score: 263
Period size: 95 Copynumber: 1.9 Consensus size: 94
1318221 ATATGTAAAT
* * * *
1318231 ACCTTTATAAGGTTAGCTGAATCTTATCCATAAAGCCGGGCGTTTAACCAATTGCCTTATAGGGA
1 ACCTTTATAAGGCTAGCTAAATATTATCCATAAAGCCGGGCGTTTAACCAATTGCCTTAGAGGGA
*
1318296 CAGCTCAAGCTTTATTGTATAGTATAATC
66 CAACTCAAGCTTTATTGTATAGTATAATC
* * * *
1318325 ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCGGTGGTGTTTAACCAATTGCTTTAGAGGG
1 ACCTTTATAAGGCTAGCTAAATATTATCCATAAAGCCG-GGCGTTTAACCAATTGCCTTAGAGGG
*
1318390 ATAACTCAAGCTTTATTGTATA
65 ACAACTCAAGCTTTATTGTATA
1318412 TAAATAATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
94 33 0.43
95 43 0.57
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (94 bp):
ACCTTTATAAGGCTAGCTAAATATTATCCATAAAGCCGGGCGTTTAACCAATTGCCTTAGAGGGA
CAACTCAAGCTTTATTGTATAGTATAATC
Found at i:1322397 original size:13 final size:13
Alignment explanation
Indices: 1322379--1322420 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1322369 CACAATGAAA
*
1322379 ATAAATAAATAGT
1 ATAAATAAATAAT
1322392 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
1322406 A-AAATAAAGAAT
1 ATAAATAAATAAT
1322418 ATA
1 ATA
1322421 TACAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1322428 original size:30 final size:30
Alignment explanation
Indices: 1322376--1322436 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
1322366 AAACACAATG
* *
1322376 AAAATAAATAAATAGTATAAATA-AAATAAT
1 AAAATAAAGAAATAGTACAAATATAAA-AAT
1322406 AAAATAAAGAATATA-TACAAATATAAAAAT
1 AAAATAAAGAA-ATAGTACAAATATAAAAAT
1322436 A
1 A
1322437 TATGTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAATAAAGAAATAGTACAAATATAAAAAT
Found at i:1322570 original size:22 final size:22
Alignment explanation
Indices: 1322536--1322577 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1322526 TACCATAATA
1322536 ATAATAAAATAAATAATAAATC
1 ATAATAAAATAAATAATAAATC
* *
1322558 ATAATATACTAAATAATAAA
1 ATAATAAAATAAATAATAAA
1322578 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAATAAAATAAATAATAAATC
Found at i:1322598 original size:19 final size:19
Alignment explanation
Indices: 1322574--1322610 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1322564 TACTAAATAA
1322574 TAAAAT-AAATAAATGAAAT
1 TAAAATAAAAT-AATGAAAT
1322593 TAAAATAAAATAATGAAA
1 TAAAATAAAATAATGAAA
1322611 CACGAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
TAAAATAAAATAATGAAAT
Done.