Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 5 of 120
Found at i:1179179 original size:24 final size:25
Alignment explanation
Indices: 1179152--1179205 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1179142 CTATATGAGA
*
1179152 ATTTTATCAAAC-AA-TTATATTTTT
1 ATTTTATAAAACAAAGTTA-ATTTTT
*
1179176 ATTTTTTAAAACAAAGTTAATTTTT
1 ATTTTATAAAACAAAGTTAATTTTT
1179201 ATTTT
1 ATTTT
1179206 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 10 0.38
25 13 0.50
26 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTTATAAAACAAAGTTAATTTTT
Found at i:1185395 original size:17 final size:19
Alignment explanation
Indices: 1185356--1185396 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1185346 TTTTATTTTT
*
1185356 TATTTTTTCATTGTGTACT
1 TATTTTTTCATTGTGTACA
*
1185375 TATTTTTT-ATT-TGTCCA
1 TATTTTTTCATTGTGTACA
1185392 TATTT
1 TATTT
1185397 ATTGTGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.45
18 3 0.15
19 8 0.40
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.66
Consensus pattern (19 bp):
TATTTTTTCATTGTGTACA
Found at i:1186403 original size:31 final size:31
Alignment explanation
Indices: 1186363--1186421 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1186353 TAACTTAAGA
*
1186363 AAAAATGTCAAATTTAG-GTGTCAAATTAGGG
1 AAAAATGTCAAA-TTAGAGTATCAAATTAGGG
*
1186394 AAAAGTGTCAAATTAGAGTATCAAATTA
1 AAAAATGTCAAATTAGAGTATCAAATTA
1186422 AACCAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.29
Consensus pattern (31 bp):
AAAAATGTCAAATTAGAGTATCAAATTAGGG
Found at i:1186457 original size:23 final size:24
Alignment explanation
Indices: 1186415--1186460 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1186405 ATTAGAGTAT
1186415 CAAATTAAACCAAAAAATTAAATAC
1 CAAATTAAA-CAAAAAATTAAATAC
*
1186440 CAAATTAAA-AAAATATTAAAT
1 CAAATTAAACAAAAAATTAAAT
1186461 TCAAAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (24 bp):
CAAATTAAACAAAAAATTAAATAC
Found at i:1187484 original size:31 final size:31
Alignment explanation
Indices: 1187446--1187509 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1187436 TTATAAAATT
* *
1187446 GTAACTAAATTATTCAAAAGTTTTTATTTAA
1 GTAACTAAACTATTCAAAAGTTTCTATTTAA
***
1187477 GTAACTAAACTATTTGGAAGTTTCTATTTAA
1 GTAACTAAACTATTCAAAAGTTTCTATTTAA
1187508 GT
1 GT
1187510 CATAAAGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.44
Consensus pattern (31 bp):
GTAACTAAACTATTCAAAAGTTTCTATTTAA
Found at i:1188892 original size:5 final size:5
Alignment explanation
Indices: 1188882--1188906 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1188872 ATTAGATAGG
1188882 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
1188907 ATTTATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:1192016 original size:213 final size:211
Alignment explanation
Indices: 1191671--1192062 Score: 581
Period size: 213 Copynumber: 1.8 Consensus size: 211
1191661 TCCTTCTGAA
* **
1191671 TTATGATCTTGATCATCATAATCATGAAGTGTTTTTGTTAATCTCTTTTTTATATTCTTTATTAA
1 TTATGATCTTGATCATCATAATCACGAAGTGTTTTTGTTAATCTCTTTTAAATATTCTTTATTAA
* * * *
1191736 TTTATTTCTGCAGGGAGAAGTGAACAGGTTGTCAGTTATGTTTTCATTTTAGCTAAATTCTCCTT
66 TTTATTTCTCCAGGGAGAAGAGAACAAGTTGTCAGTTATCTTTTCATTTTAGCTAAATTCTCCTT
*
1191801 AAATTAGTTACTAAATCTTTCTATAGATTTGAAAATTAGAGAAATTATTCTTTGTTAATCTTTAT
131 AAATTAGTTACTAAATATTTCTATAGATTTGAAAATTAGAGAAATTATTCTTTGTTAATCTTTAT
1191866 TATCAAATATTCTTTG
196 TATCAAATATTCTTTG
* *
1191882 TTATGATCTTGATCATCATAATTACGAAGTGTTTTTGTTAATCT-TTTTCAAAAATATTCTTTGT
1 TTATGATCTTGATCATCATAATCACGAAGTGTTTTTGTTAATCTCTTTT---AAATATTCTTTAT
* * * * *
1191946 TAATTTAATTT-TCCCGGGAGAAGAGAACAAGTTTTCAGTTATCTTTTCTTTTTAGCTACATTTT
63 TAATTT-ATTTCTCCAGGGAGAAGAGAACAAGTTGTCAGTTATCTTTTCATTTTAGCTAAATTCT
* *
1192010 CCTTAAATTAGTTCCTAAATATTTCTTTAGATTTGAAAATTAGAGAAATTATT
127 CCTTAAATTAGTTACTAAATATTTCTATAGATTTGAAAATTAGAGAAATTATT
1192063 ATGCCTCTTT
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
210 4 0.03
211 42 0.26
213 110 0.69
214 4 0.03
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (211 bp):
TTATGATCTTGATCATCATAATCACGAAGTGTTTTTGTTAATCTCTTTTAAATATTCTTTATTAA
TTTATTTCTCCAGGGAGAAGAGAACAAGTTGTCAGTTATCTTTTCATTTTAGCTAAATTCTCCTT
AAATTAGTTACTAAATATTTCTATAGATTTGAAAATTAGAGAAATTATTCTTTGTTAATCTTTAT
TATCAAATATTCTTTG
Found at i:1218842 original size:21 final size:21
Alignment explanation
Indices: 1218784--1218853 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
1218774 TTTGAGTAAG
* *
1218784 TTCTACCAATACAAGT-GTAAC
1 TTCTACCAATACAAGTCAT-GC
*
1218805 TTCTACCGATACAAGTCATGC
1 TTCTACCAATACAAGTCATGC
1218826 TTCTACCAATACAAGTCATGC
1 TTCTACCAATACAAGTCATGC
*
1218847 TTTTACC
1 TTCTACC
1218854 GATATTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (21 bp):
TTCTACCAATACAAGTCATGC
Found at i:1219604 original size:3 final size:3
Alignment explanation
Indices: 1219598--1219638 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1219588 AATAATATAA
* *
1219598 ATT ATT ATT -TA ATT AGT ATT A-T ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1219639 ACTAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1219653 original size:2 final size:2
Alignment explanation
Indices: 1219646--1219706 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1219636 TTAACTAATA
1219646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1219688 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1219707 AATAAAAGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1219749 original size:11 final size:12
Alignment explanation
Indices: 1219718--1219752 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1219708 ATAAAAGAAT
1219718 AAAGAAACAAAA
1 AAAGAAACAAAA
1219730 AAAGAAACAAAA
1 AAAGAAACAAAA
*
1219742 GAAG-AACAAAA
1 AAAGAAACAAAA
1219753 TAGAGAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAGAAACAAAA
Found at i:1221969 original size:60 final size:56
Alignment explanation
Indices: 1221861--1222204 Score: 257
Period size: 52 Copynumber: 6.4 Consensus size: 56
1221851 TTCGCATTTG
* * * ** **
1221861 ATACTCACGATGACACAAAGTCATCGGACCTC-TAATTTGTATTGGGATTCATTTCATTT
1 ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTA-AAGGATTCA-TTCA--T
**
1221920 AATACTCACGATGACACATAGTCATTGAACCTCATAATTTGTAAAGG----ATTCAT
1 -ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTAAAGGATTCATTCAT
*
1221973 ATACTCACGATGAGACATAGTCATTAGAA-CTCATAATCCGTAAAGGATTCA-T-AT
1 ATACTCACGATGACACATAGTCATT-GAACCTCATAATCCGTAAAGGATTCATTCAT
* * *
1222027 AT--TCACAACGACACATAGTCATTGGACCTCATAATCCGTAAAGG----ATTCAT
1 ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTAAAGGATTCATTCAT
* * * *
1222077 ATACTCACAATGACACATAGTTA-TCAGACCTCATAATCCATAAAGG----ATTCAT
1 ATACTCACGATGACACATAGTCATTGA-ACCTCATAATCCGTAAAGGATTCATTCAT
* * **
1222129 ATACTCACGATAACACATAGTCATCGGGCCTCATAATCCGTAAAGG----ATTCAT
1 ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTAAAGGATTCATTCAT
* *
1222181 ATACTCATGATGACACATTGTCAT
1 ATACTCACGATGACACATAGTCAT
1222205 CGGACCTTTC
Statistics
Matches: 243, Mismatches: 28, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
48 1 0.00
49 1 0.00
50 4 0.02
51 3 0.01
52 179 0.74
53 4 0.02
54 4 0.02
55 5 0.02
56 2 0.01
60 31 0.13
61 9 0.04
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (56 bp):
ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTAAAGGATTCATTCAT
Found at i:1222135 original size:26 final size:26
Alignment explanation
Indices: 1222054--1222135 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
1222044 GTCATTGGAC
*
1222054 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCATAAAGGATTCATATA
* * * * *
1222080 CTCACAATGACACATA-G-TT-ATCAGA
1 CTCATAAT-CCATAAAGGATTCAT-ATA
1222105 CCTCATAATCCATAAAGGATTCATATA
1 -CTCATAATCCATAAAGGATTCATATA
1222132 CTCA
1 CTCA
1222136 CGATAACACA
Statistics
Matches: 39, Mismatches: 11, Indels: 12
0.63 0.18 0.19
Matches are distributed among these distances:
24 2 0.05
25 8 0.21
26 20 0.51
27 7 0.18
28 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (26 bp):
CTCATAATCCATAAAGGATTCATATA
Found at i:1222205 original size:52 final size:52
Alignment explanation
Indices: 1221921--1222211 Score: 402
Period size: 52 Copynumber: 5.6 Consensus size: 52
1221911 ATTTCATTTA
* * **
1221921 ATACTCACGATGACACATAGTCATTGAACCTCATAATTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* ** *
1221973 ATACTCACGATGAGACATAGTCATTAGAACTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
1222025 ATATTCACAACGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
1222077 ATACTCACAATGACACATAGTTATCAGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
1222129 ATACTCACGATAACACATAGTCATCGGGCCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
1222181 ATACTCATGATGACACATTGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
1222212 TTCATTTACG
Statistics
Matches: 211, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 211 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:1238864 original size:312 final size:312
Alignment explanation
Indices: 1238299--1238928 Score: 947
Period size: 312 Copynumber: 2.0 Consensus size: 312
1238289 AAAGTTGCTT
* * *
1238299 TTCTGAGGAAGACTGACCAGAAGCAATTTCTTCTTTTGTAACTAATTGAAGCTCATTTAGCTCTT
1 TTCTGAGGAAGACTGACCAGAAGAAAGTTCTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTT
* ** * *
1238364 CTGTTTCTCCAGCTGATGAGTCTTCATGGTTCCCATCATGAAGCTTTTCAGTTTCTTTCCTTTTT
66 CTGTTTCTCCAGCTGACGAGTCTTCACAGTTCCCATCATCAAGCTTTTCAGCTTCTTTCCTTTTT
* * * * *
1238429 CCTTCGTTTGCTTCAACCTCTTGTGATTCCTCTGTTATGGAAGCCTGAGCAATAATGGTTTCTTG
131 CCTTCGTTTGCTTCAACATCTTGAGACTCCACTGTTATGGAAGCCTGAACAATAATGGTTTCTTG
*
1238494 ATCGATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTTT
196 ATCCATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTTT
* ** *
1238559 CCCCCTCTTCTTCATTGGCATCAGCTCCATGCTTTAGGTTCTCTTCGGTCAA
261 CCCCCTCTTCTTCATTGGCATCAGCGCCATGCTTTAGGTTCTCAACAGTCAA
1238611 TTCTGAGGAAGACTGACCAGAAGAAAGTTCTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTT
1 TTCTGAGGAAGACTGACCAGAAGAAAGTTCTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTT
* * * * **
1238676 CTGTTTCTCCAGCTGACGAGTCTTTACAGTTCCTATCGTCCAGCTTTTTGGCTTCTTTCC-TTTT
66 CTGTTTCTCCAGCTGACGAGTCTTCACAGTTCCCATCATCAAGCTTTTCAGCTTCTTTCCTTTTT
* * *
1238740 CTCTTCGTTTGCTTCAATATCTTGAGACTCCACTGTTATTGAAGCCTGAACTATAATGGTTTCTT
131 C-CTTCGTTTGCTTCAACATCTTGAGACTCCACTGTTATGGAAGCCTGAACAATAATGGTTTCTT
* * *
1238805 GATCCATAACAGTTTTAGGCTCCTGAGGTCGTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTT
195 GATCCATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTT
** *
1238870 TCTTCCTCTTCTTCATTGGCCTCAGCGCCATGCTTTAGGTTCTCAACAGTCAA
260 TCCCCCTCTTCTTCATTGGCATCAGCGCCATGCTTTAGGTTCTCAACAGTCAA
1238923 TTCTGA
1 TTCTGA
1238929 AGGCAAAGAT
Statistics
Matches: 284, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
311 5 0.02
312 279 0.98
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (312 bp):
TTCTGAGGAAGACTGACCAGAAGAAAGTTCTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTT
CTGTTTCTCCAGCTGACGAGTCTTCACAGTTCCCATCATCAAGCTTTTCAGCTTCTTTCCTTTTT
CCTTCGTTTGCTTCAACATCTTGAGACTCCACTGTTATGGAAGCCTGAACAATAATGGTTTCTTG
ATCCATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTTT
CCCCCTCTTCTTCATTGGCATCAGCGCCATGCTTTAGGTTCTCAACAGTCAA
Found at i:1247789 original size:20 final size:20
Alignment explanation
Indices: 1247764--1247812 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1247754 TCAGCAACTT
1247764 ATATCCCTAATCAACAAATC
1 ATATCCCTAATCAACAAATC
*
1247784 ATATCCCTAATCAGCAAATC
1 ATATCCCTAATCAACAAATC
1247804 ATATCCCTA
1 ATATCCCTA
1247813 TCACATCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.31, G:0.02, T:0.27
Consensus pattern (20 bp):
ATATCCCTAATCAACAAATC
Found at i:1253727 original size:21 final size:19
Alignment explanation
Indices: 1253703--1253742 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1253693 CATCTCCAAT
1253703 TGATCTTCACTTCCTGCATTG
1 TGATCTTCA--TCCTGCATTG
*
1253724 TGATCTTTATCCTGCATTG
1 TGATCTTCATCCTGCATTG
1253743 CATCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (19 bp):
TGATCTTCATCCTGCATTG
Found at i:1260674 original size:137 final size:136
Alignment explanation
Indices: 1260428--1261054 Score: 952
Period size: 137 Copynumber: 4.6 Consensus size: 136
1260418 GCACAATACG
* *
1260428 TGTAAGATGAAAGAACTTTACCACTACAGAAATGGGTTCTTGGATGATCACTGCTTCAGTTGCCA
1 TGTAAGATGAAAGAACTTTACCACTA-TGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
* * *
1260493 TTTTTTCCTGCACAAGTTATCGAATTCGAGTTAGAGAGCTTATCATTTCAAACATTCATAAACTG
65 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
1260558 TGAATCA
130 TGAATCA
*
1260565 TGTAAGATGAAAGAACTTTACCACTATGAAAATGGGTTCTTGAATGATCACTGATTCAGTTGCCA
1 TGTAAGATGAAAGAACTTTACCACTATG-AAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
*
1260630 TTTTTTCCTGCACAAGTGGTCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
65 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
1260695 TGAATCA
130 TGAATCA
* * *
1260702 TGTAGGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGATTCAGATGCCA
1 TGTAAGATGAAAGAACTTTACCACTA-TGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
*
1260767 TTTTTTCCTGCACAAGTGATCGAGTTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
65 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
1260832 TGAATCA
130 TGAATCA
* * *
1260839 GGTAGGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCTA
1 TGTAAGATGAAAGAACTTTACCACTA-TGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
* * * * *
1260904 TTTCTTCCTGCACAAGTTATAGAATTCGAGTTTGAGAGCCTATCATTTCGAACATTCATAAATTG
65 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
1260969 TGAAT--
130 TGAATCA
* * **
1260974 TTTAAAGATGAAAGAACTTCACCACTATGGAAACAGGTTCTTGAATGATCACTGCTTCAGTTGCC
1 TGT-AAGATGAAAGAACTTTACCACTAT-GAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCC
1261039 ATCTACTTTTCCTGCA
64 AT-T--TTTTCCTGCA
1261055 GAAATAATAG
Statistics
Matches: 454, Mismatches: 29, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
135 2 0.00
136 57 0.13
137 384 0.85
138 2 0.00
139 9 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (136 bp):
TGTAAGATGAAAGAACTTTACCACTATGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCAT
TTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTGT
GAATCA
Found at i:1273599 original size:42 final size:42
Alignment explanation
Indices: 1273537--1273639 Score: 197
Period size: 42 Copynumber: 2.5 Consensus size: 42
1273527 CGATCCCTCC
1273537 TTTTAAGGGATCGATCCCCACTAAGTTAGTAGCTAAAAGAAA
1 TTTTAAGGGATCGATCCCCACTAAGTTAGTAGCTAAAAGAAA
*
1273579 TTTTAAGGGATCGATTCCCACTAAGTTAGTAGCTAAAAGAAA
1 TTTTAAGGGATCGATCCCCACTAAGTTAGTAGCTAAAAGAAA
1273621 TTTTAAGGGATCGATCCCC
1 TTTTAAGGGATCGATCCCC
1273640 CTTTTAAAGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (42 bp):
TTTTAAGGGATCGATCCCCACTAAGTTAGTAGCTAAAAGAAA
Found at i:1276149 original size:69 final size:69
Alignment explanation
Indices: 1276071--1276209 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
1276061 TCGATACTTG
1276071 CAACTTTTGGAGTTGAAAATTGATTAGTCTAGTAGGTCTCGAAACTTAACCTTTCATATGTTAAT
1 CAACTTTTGGAGTTGAAAATTGATTAGTCTAGTAGGTCTCGAAACTTAACCTTTCATATGTTAAT
1276136 ATGT
66 ATGT
1276140 CAACTTTTGGAGTTGAAAATTGATTAGTCTAGTAGGTCTCGAAACTTAACCTTTCATATGTTAAT
1 CAACTTTTGGAGTTGAAAATTGATTAGTCTAGTAGGTCTCGAAACTTAACCTTTCATATGTTAAT
1276205 ATGT
66 ATGT
1276209 C
1 C
1276210 TTGTACAACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (69 bp):
CAACTTTTGGAGTTGAAAATTGATTAGTCTAGTAGGTCTCGAAACTTAACCTTTCATATGTTAAT
ATGT
Found at i:1277919 original size:20 final size:19
Alignment explanation
Indices: 1277891--1277928 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1277881 AAAATTAATT
*
1277891 TACTTTAAAATTATATAAAA
1 TACTATAAAATTAT-TAAAA
1277911 TACTATAAAATTATTAAA
1 TACTATAAAATTATTAAA
1277929 TCATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TACTATAAAATTATTAAAA
Found at i:1277939 original size:20 final size:19
Alignment explanation
Indices: 1277895--1277941 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1277885 TTAATTTACT
*
1277895 TTAAAATTATATAAAATAC
1 TTAAAATTATATAAAATAA
1277914 TATAAAATTAT-TAAATCATAA
1 T-TAAAATTATATAAA--ATAA
1277935 TTAAAAT
1 TTAAAAT
1277942 ATAGTTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAATTATATAAAATAA
Found at i:1279467 original size:29 final size:30
Alignment explanation
Indices: 1279412--1279470 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1279402 ATCTCAAAAT
*
1279412 TATACATGAACTTTAATTTAATGTGCAATTG
1 TATACATGAACTTTAATTT-AGGTGCAATTG
*
1279443 TATACATGAATTTTAATTT-GGTGCAATT
1 TATACATGAACTTTAATTTAGGTGCAATT
1279471 ATACAGGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGGTGCAATTG
Found at i:1280662 original size:3 final size:3
Alignment explanation
Indices: 1280656--1280693 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1280646 TTGGGAATGA
1280656 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1280694 CGGGTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1282189 original size:17 final size:17
Alignment explanation
Indices: 1282115--1282190 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
1282105 ATTTTATTTT
* *
1282115 AATTAAAAATAAATTTA
1 AATTTAAAATAAATTCA
*
1282132 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATTCA
** * *
1282149 AACTCAAAAAATGAATTTA
1 AA-T-TTAAAATAAATTCA
1282168 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
1282185 AATTTA
1 AATTTA
1282191 TTTAAAATTA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
17 32 0.71
18 2 0.04
19 11 0.24
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:1291083 original size:40 final size:40
Alignment explanation
Indices: 1291023--1291104 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1291013 AGCATAGATT
1291023 TCATCTGTCAATATCAATCTAAATTACGCAATTTCTTTAC
1 TCATCTGTCAATATCAATCTAAATTACGCAATTTCTTTAC
*
1291063 TCATCTGTCAATATCTATCTAAATTACGCAATTTCTTTAC
1 TCATCTGTCAATATCAATCTAAATTACGCAATTTCTTTAC
1291103 TC
1 TC
1291105 GTCACCTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.41
Consensus pattern (40 bp):
TCATCTGTCAATATCAATCTAAATTACGCAATTTCTTTAC
Found at i:1293556 original size:22 final size:22
Alignment explanation
Indices: 1293508--1293549 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1293498 TAACAAGTAT
1293508 ATCTTCAATAATACCCATAAAA
1 ATCTTCAATAATACCCATAAAA
*
1293530 ATCTTCAATAATGCCCATAA
1 ATCTTCAATAATACCCATAA
1293550 GATTCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (22 bp):
ATCTTCAATAATACCCATAAAA
Found at i:1295432 original size:17 final size:17
Alignment explanation
Indices: 1295410--1295442 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1295400 ATTCTGATAA
1295410 AAAGTGATATCTAAATG
1 AAAGTGATATCTAAATG
*
1295427 AAAGTGATATTTAAAT
1 AAAGTGATATCTAAAT
1295443 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
AAAGTGATATCTAAATG
Found at i:1296861 original size:18 final size:20
Alignment explanation
Indices: 1296817--1296864 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
1296807 TTATGTCATT
*
1296817 TTTTTAATTTAAATAAATTA
1 TTTTTAAATTAAATAAATTA
*
1296837 TTGTTAAATT-AATAAA-TA
1 TTTTTAAATTAAATAAATTA
1296855 TTTTTAAATT
1 TTTTTAAATT
1296865 TAACATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
19 6 0.24
20 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTAAATTAAATAAATTA
Found at i:1296867 original size:19 final size:20
Alignment explanation
Indices: 1296816--1296867 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1296806 ATTATGTCAT
*
1296816 TTTTTTAATTTAAATAAATTA
1 TTTTTAAATTT-AATAAATTA
*
1296837 TTGTTAAA-TTAATAAA-TA
1 TTTTTAAATTTAATAAATTA
1296855 TTTTTAAATTTAA
1 TTTTTAAATTTAA
1296868 CATTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.33
19 10 0.37
20 2 0.07
21 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTAAATTTAATAAATTA
Found at i:1297845 original size:18 final size:17
Alignment explanation
Indices: 1297822--1297858 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1297812 TTATAGTTTG
*
1297822 ATATTCGATTTATTCGAA
1 ATATTCGAGTTATTC-AA
1297840 ATATTCGAGTTATTCAA
1 ATATTCGAGTTATTCAA
1297857 AT
1 AT
1297859 TCGAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (17 bp):
ATATTCGAGTTATTCAA
Found at i:1300057 original size:27 final size:27
Alignment explanation
Indices: 1300030--1300080 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1300020 TAAAAAATCA
1300030 AATAATTT-AATAATTATTTGTAATTC
1 AATAATTTAAATAATTATTTGTAATTC
* *
1300056 AATTATTTAAATAATTATTTTTAAT
1 AATAATTTAAATAATTATTTGTAAT
1300081 AATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
AATAATTTAAATAATTATTTGTAATTC
Found at i:1300083 original size:13 final size:13
Alignment explanation
Indices: 1300035--1300089 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
1300025 AATCAAATAA
1300035 TTTAATAATTATT
1 TTTAATAATTATT
*
1300048 TGTAATTCAATTA-T
1 TTTAA-T-AATTATT
*
1300062 TTAAATAATTATT
1 TTTAATAATTATT
1300075 TTTAATAATTTATT
1 TTTAATAA-TTATT
1300089 T
1 T
1300090 ACTATTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
12 5 0.15
13 13 0.38
14 11 0.32
15 5 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
TTTAATAATTATT
Found at i:1306194 original size:31 final size:30
Alignment explanation
Indices: 1306127--1306195 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
1306117 GATGATTTGT
* * *
1306127 AAAATTTTGAGAGGCCTAATTAAAATTTTT
1 AAAATTTTGAAAGGCCTAATCAAAATTTTC
1306157 ATAAATTTTGAAAGGCCTAA-CAACAATATTTC
1 A-AAATTTTGAAAGGCCTAATCAA-AAT-TTTC
1306189 AAAATTT
1 AAAATTT
1306196 GGGGGGCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
AAAATTTTGAAAGGCCTAATCAAAATTTTC
Found at i:1311276 original size:17 final size:19
Alignment explanation
Indices: 1311254--1311291 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1311244 AACACATTAA
1311254 AAATATA-AAT-TTATATT
1 AAATATATAATATTATATT
*
1311271 AAATATATAATATTATTTT
1 AAATATATAATATTATATT
1311290 AA
1 AA
1311292 TACAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATATAATATTATATT
Found at i:1316029 original size:96 final size:95
Alignment explanation
Indices: 1315949--1316126 Score: 227
Period size: 95 Copynumber: 1.9 Consensus size: 95
1315939 TTTTTTGTAC
* * *
1315949 TTTTTTTAAAATAAAATATTATTTATTTGGTGATGCTATA-AAAA-AACGT-CACCACCATGGTT
1 TTTTTTTAAAATAAAAT-TT-TTAATTTGATGATGCCATAGAAAATAACGTGCACCACCATGGTT
1316011 TTTTTTTCCAACCCTTTTTTTAATGTGTTTTTA
64 TTTTTTTCCAA-CCTTTTTTTAATGTGTTTTTA
* * * * *
1316044 TTTTTTTTAAATATAATTTTTAATTTGATGGTGCCATAGAAAATGACGTGCACCATCATGGTTTT
1 TTTTTTTAAAATAAAATTTTTAATTTGATGATGCCATAGAAAATAACGTGCACCACCATGGTTTT
*
1316109 TTTTTCCAACTTTTTTTT
66 TTTTTCCAACCTTTTTTT
1316127 GTGCATCATA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 15 0.21
94 6 0.08
95 27 0.38
96 23 0.32
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (95 bp):
TTTTTTTAAAATAAAATTTTTAATTTGATGATGCCATAGAAAATAACGTGCACCACCATGGTTTT
TTTTTCCAACCTTTTTTTAATGTGTTTTTA
Found at i:1317418 original size:19 final size:18
Alignment explanation
Indices: 1317387--1317424 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1317377 AAACATTATT
1317387 TTTAAAAAATTAAAAATA
1 TTTAAAAAATTAAAAATA
*
1317405 TTTAAAAAGTTTAAAAATA
1 TTTAAAAA-ATTAAAAATA
1317424 T
1 T
1317425 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTTAAAAAATTAAAAATA
Found at i:1321837 original size:39 final size:39
Alignment explanation
Indices: 1321761--1321837 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
1321751 TAAGGAAGAA
* * **
1321761 AATATGTATTTGAATATGAATAACTCGTATTGTTTATTGT
1 AATATGTATTTGAAAAT-AATAACTCATATTAATTATTGT
1321801 AATATGTAATTTGAAAAT-ATAACTCATATTAATTATT
1 AATATGT-ATTTGAAAATAATAACTCATATTAATTATT
1321838 AACATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.50
40 7 0.22
41 9 0.28
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.45
Consensus pattern (39 bp):
AATATGTATTTGAAAATAATAACTCATATTAATTATTGT
Found at i:1324433 original size:158 final size:158
Alignment explanation
Indices: 1324145--1324435 Score: 413
Period size: 158 Copynumber: 1.8 Consensus size: 158
1324135 TATCATGTAA
* ** *
1324145 TGCTCACACGAGCTGTAGGTCGAGATGTTAAACTACTTGATGTTGCTCACATGAACTGTAGAGAA
1 TGCTCACACGAGCTGTAGGTCGAGATATTAAACTACTCAATGCTGCTCACATGAACTGTAGAGAA
* * * *
1324210 TCCGCAAATATTGTCAAATCTCAGCCATCGGTAGGACATCTAGGACCAACACTCATATAACCTGT
66 TCCACAAATATTATCAAATCTCAGCCATCGATAGGACATCTAGGACCAACACCCATATAACCTGT
1324275 AATGCTCACCTGAGCTGTGAAATGGGCC
131 AATGCTCACCTGAGCTGTGAAATGGGCC
* * * **
1324303 TGCTCACACGAGCTGTTGGTCGAGATATTGAGCTACTCAATGCTGCTCACATGAGTTGT-GAAGA
1 TGCTCACACGAGCTGTAGGTCGAGATATTAAACTACTCAATGCTGCTCACATGAACTGTAG-AGA
* * * *
1324367 ATCTACAAATATTATCAGATCTCAGCCATCGATAGGACATGTAGGACCAGCACCCATATAACCTG
65 ATCCACAAATATTATCAAATCTCAGCCATCGATAGGACATCTAGGACCAACACCCATATAACCTG
1324432 TAAT
130 TAAT
1324436 CCCGATGACG
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
157 1 0.01
158 114 0.99
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (158 bp):
TGCTCACACGAGCTGTAGGTCGAGATATTAAACTACTCAATGCTGCTCACATGAACTGTAGAGAA
TCCACAAATATTATCAAATCTCAGCCATCGATAGGACATCTAGGACCAACACCCATATAACCTGT
AATGCTCACCTGAGCTGTGAAATGGGCC
Found at i:1326731 original size:19 final size:18
Alignment explanation
Indices: 1326700--1326737 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1326690 AAACATTATT
1326700 TTTAAAAAATTAAAAATA
1 TTTAAAAAATTAAAAATA
*
1326718 TTTAAAAAGTTTAAAAATA
1 TTTAAAAA-ATTAAAAATA
1326737 T
1 T
1326738 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTTAAAAAATTAAAAATA
Found at i:1328480 original size:15 final size:15
Alignment explanation
Indices: 1328457--1328492 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1328447 ACTCTGAGCG
*
1328457 GGACTCGGGCATGCT
1 GGACACGGGCATGCT
1328472 GGACACGGGCATGCT
1 GGACACGGGCATGCT
1328487 GGACAC
1 GGACAC
1328493 TTGTATCGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.28, G:0.39, T:0.14
Consensus pattern (15 bp):
GGACACGGGCATGCT
Found at i:1328907 original size:19 final size:18
Alignment explanation
Indices: 1328876--1328913 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1328866 AAACATTATT
1328876 TTTAAAAAATTAAAAATA
1 TTTAAAAAATTAAAAATA
*
1328894 TTTAAAAAGTTTAAAAATA
1 TTTAAAAA-ATTAAAAATA
1328913 T
1 T
1328914 AAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTTAAAAAATTAAAAATA
Found at i:1332600 original size:24 final size:25
Alignment explanation
Indices: 1332566--1332614 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1332556 AATTGAAAAG
* *
1332566 AAAAATTA-TTTTTTATAAATAATA
1 AAAAATGATTTTTTTATAAAAAATA
1332590 AAAAATGATTTTTTTATAAAAAATA
1 AAAAATGATTTTTTTATAAAAAATA
1332615 TCAAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAAATGATTTTTTTATAAAAAATA
Found at i:1333189 original size:19 final size:18
Alignment explanation
Indices: 1333158--1333195 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1333148 AAACATTATT
1333158 TTTAAAAAATTAAAAATA
1 TTTAAAAAATTAAAAATA
*
1333176 TTTAAAAAGTTTAAAAATA
1 TTTAAAAA-ATTAAAAATA
1333195 T
1 T
1333196 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTTAAAAAATTAAAAATA
Found at i:1336173 original size:39 final size:39
Alignment explanation
Indices: 1336097--1336173 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
1336087 TAAGGAAGAA
* * **
1336097 AATATGTATTTGAATATGAATAACTCGTATTGTTTATTGT
1 AATATGTATTTGAAAAT-AATAACTCATATTAATTATTGT
1336137 AATATGTAATTTGAAAAT-ATAACTCATATTAATTATT
1 AATATGT-ATTTGAAAATAATAACTCATATTAATTATT
1336174 AACATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.50
40 7 0.22
41 9 0.28
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.45
Consensus pattern (39 bp):
AATATGTATTTGAAAATAATAACTCATATTAATTATTGT
Found at i:1338774 original size:158 final size:158
Alignment explanation
Indices: 1338486--1338776 Score: 406
Period size: 158 Copynumber: 1.8 Consensus size: 158
1338476 TATCATGTAA
* ** *
1338486 TGCTCACACGAGCTGTAGGTCGAGATGTTAAACTACTTGATGTTGCTCACATGAACTGTAGAGAA
1 TGCTCACACGAGCTGTAGGTCGAGAGGTTAAACTACTCAATGCTGCTCACATGAACTGTAGAGAA
* * * *
1338551 TTCGCAAATATTGTCAAATCTCAGCCATCGGTAGGACATCTAGGACCAACACTCATATAACCTGT
66 TTCACAAATATTATCAAATCTCAGCCATCGATAGGACATCTAGGACCAACACCCATATAACCTGT
1338616 AATGCTCACCTGAGCTGTGAAATGGGCC
131 AATGCTCACCTGAGCTGTGAAATGGGCC
* * * **
1338644 TGCTCACACGAGCTGTTGGTCGAGAGGTTGAGCTACTCAATGCTGCTCACATGAGTTGT-GAAGA
1 TGCTCACACGAGCTGTAGGTCGAGAGGTTAAACTACTCAATGCTGCTCACATGAACTGTAG-AGA
* * *
1338708 A-TCTACAAATATTATCAGATCTCAGCCATCGATAGGACATGTAGGACCAGCACCCATATAACCT
65 ATTC-ACAAATATTATCAAATCTCAGCCATCGATAGGACATCTAGGACCAACACCCATATAACCT
1338772 GTAAT
129 GTAAT
1338777 CCCAATGACG
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
157 3 0.03
158 112 0.97
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (158 bp):
TGCTCACACGAGCTGTAGGTCGAGAGGTTAAACTACTCAATGCTGCTCACATGAACTGTAGAGAA
TTCACAAATATTATCAAATCTCAGCCATCGATAGGACATCTAGGACCAACACCCATATAACCTGT
AATGCTCACCTGAGCTGTGAAATGGGCC
Found at i:1339877 original size:21 final size:20
Alignment explanation
Indices: 1339849--1339888 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1339839 TCTCTGCTTC
*
1339849 CCTCGCTTGCCTCGCTGTTG
1 CCTCGCTTCCCTCGCTGTTG
1339869 CCTCTGCTTCCCTCGCTGTT
1 CCTC-GCTTCCCTCGCTGTT
1339889 ACTTCCGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.42, G:0.20, T:0.38
Consensus pattern (20 bp):
CCTCGCTTCCCTCGCTGTTG
Found at i:1339898 original size:21 final size:21
Alignment explanation
Indices: 1339852--1339898 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1339842 CTGCTTCCCT
* *
1339852 CGCTTGCCTCGCTGTTGCCTC
1 CGCTTCCCTCGCTGTTACCTC
* *
1339873 TGCTTCCCTCGCTGTTACTTC
1 CGCTTCCCTCGCTGTTACCTC
1339894 CGCTT
1 CGCTT
1339899 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.40, G:0.19, T:0.38
Consensus pattern (21 bp):
CGCTTCCCTCGCTGTTACCTC
Found at i:1342703 original size:30 final size:30
Alignment explanation
Indices: 1342601--1342898 Score: 377
Period size: 30 Copynumber: 10.0 Consensus size: 30
1342591 GGATTTAGGG
* * *
1342601 AAGTTTGGGGGT-AAAATGATAATTTT-TAG
1 AAGTTTTGGGGTCAAAATG-TAATTTTGGAA
* * * *
1342630 AAGTTTCGAGGTCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1342660 AA-TTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
** * *
1342689 AAGTTTCAGGGTCAAAATATAAATTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * * *
1342719 AAGTTTCGAGGTTAAAATGTAATTATGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
1342749 AAGTTTTGGGGTCAAAATGTAATTATGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
1342779 AAGTTTTGGGGTCAAAATGTAATTTTGGTA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
1342809 AAGTTTTGGGGTCGAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
1342839 AAGTTTTGGGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1342869 AAGTTTTGGGGTCAAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
1342899 TAATTTAGGG
Statistics
Matches: 234, Mismatches: 31, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
29 42 0.18
30 188 0.80
31 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:1344661 original size:18 final size:18
Alignment explanation
Indices: 1344640--1344688 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1344630 AAAATTGATT
1344640 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
1344658 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
1344676 TAAATTTAGAATT
1 TAAATTTA-AATT
1344689 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:1345343 original size:76 final size:76
Alignment explanation
Indices: 1345215--1345749 Score: 872
Period size: 76 Copynumber: 7.0 Consensus size: 76
1345205 TTGGTGCTTT
* * * *
1345215 ATCTTACTCTTACTTCAATTTCAGAGATAAATACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
*
1345280 GATAGGAAACG
66 GATAGGAAATG
* *
1345291 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1345356 GATAGGAAATG
66 GATAGGAAATG
* * * * *
1345367 ATCTTTCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1345432 GATAGGAAATG
66 GATAGGAAATG
* * * *
1345443 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGCTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
*
1345508 GATAGGAAATA
66 GATAGGAAATG
1345519 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
*
1345584 GATAGGAATTG
66 GATAGGAAATG
1345595 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1345660 GATAGGAAATG
66 GATAGGAAATG
* *
1345671 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCTGCTTTGCTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
*
1345736 GATAAGAAAATG
66 GAT-AGGAAATG
1345748 AT
1 AT
1345750 GTTGGTGCTT
Statistics
Matches: 434, Mismatches: 24, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
76 425 0.98
77 9 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:1353276 original size:30 final size:30
Alignment explanation
Indices: 1353174--1353471 Score: 377
Period size: 30 Copynumber: 10.0 Consensus size: 30
1353164 GGATTTAGGG
* * *
1353174 AAGTTTGGGGGT-AAAATGATAATTTT-TAG
1 AAGTTTTGGGGTCAAAATG-TAATTTTGGAA
* * * *
1353203 AAGTTTCGAGGTCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1353233 AA-TTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
** * *
1353262 AAGTTTCAGGGTCAAAATATAAATTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * * *
1353292 AAGTTTCGAGGTTAAAATGTAATTATGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
1353322 AAGTTTTGGGGTCAAAATGTAATTATGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
1353352 AAGTTTTGGGGTCAAAATGTAATTTTGGTA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
1353382 AAGTTTTGGGGTCGAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
1353412 AAGTTTTGGGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1353442 AAGTTTTGGGGTCAAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
1353472 TAATTTAGGG
Statistics
Matches: 234, Mismatches: 31, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
29 42 0.18
30 188 0.80
31 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:1355233 original size:18 final size:18
Alignment explanation
Indices: 1355212--1355260 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1355202 AAAATTGATT
1355212 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
1355230 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
1355248 TAAATTTAGAATT
1 TAAATTTA-AATT
1355261 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:1358210 original size:41 final size:41
Alignment explanation
Indices: 1358135--1358919 Score: 824
Period size: 41 Copynumber: 19.2 Consensus size: 41
1358125 TTTAAATAAA
* * * * *
1358135 TTAGCGGGGTTTTCACATAAGCGCCGCTAATGCTCTGAGCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
1358176 TTAGTGGCGCTTACCCATAAGCGTCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* ** * *
1358217 TTAGCGGTGCTTTTACATAAGTGCCGCTATTGCTCTTACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
1358258 TTAGAGGCGCTTTACCGA-AAGCGCCGCTATTGCTTTGACCT
1 TTAGCGGCGCTTT-CCCATAAGCGCCGCTATTGCTCTGACCT
* * * * *
1358299 TTAGTGGCGCTTTCCTATAAGCGTCGCTATTGATTTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
1358340 TTAGCGGCGTTTTCCCATAAGCGCCGCTATTGCTCTGA-CT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * *
1358380 TTAGCGGCGCTTACCCATAAGCGTCGCTATTGATCTAACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
1358421 TTAGCGGCGCTTGCCCATAAGCGCCGCTATTGATCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
1358462 TTAGCGGCACTTT-CCATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*** * * *
1358502 TTAGTAACGCTTTCCCATAAGCACCTCTAGTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
1358543 TTAGCAGCGCTTTCCCATAAGCGCCACTATTGTTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
** * ** * * *
1358584 TTAGCGATGCGTTCTGATAAGCGCCACTATTGATCTCACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * *
1358625 TTTGCGGCGCTTGCCAATAAGCGCTGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * * *
1358666 TTAGCGGCGCTTGCCAATAAGCGCCGTTATTGATCTCACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* ** * *
1358707 TTCGCGGCG-TTTGCTAATAAGCGCCGCTATTGATCTCACCT
1 TTAGCGGCGCTTT-CCCATAAGCGCCGCTATTGCTCTGACCT
* * **
1358748 TTCGCGGCGCTTGCTAATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * * *
1358789 TTAGCGGCGCTTGCCAATAAGCGCCACTGTTGATCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * * *
1358830 TTAGCGGCGCTTTCCCATAAGCGCCACTGTTGGTTTTACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
1358871 TTAGCGACGCTTTCCCATAAGCGCTGCTATTGCTCT-ACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
1358911 TTTGCGGCG
1 TTAGCGGCG
1358920 TTTATGTAAA
Statistics
Matches: 631, Mismatches: 107, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
40 86 0.14
41 542 0.86
42 3 0.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
Found at i:1362823 original size:20 final size:20
Alignment explanation
Indices: 1362753--1362830 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 20
1362743 ACTTTTTGAA
1362753 AATTTTTATGTATATATA-T
1 AATTTTTATGTATATATATT
* * * *
1362772 CATTTTAATCTAT-TGTTATGT
1 AATTTTTATGTATAT-ATAT-T
* *
1362793 -ATTTATGTGTATATATATT
1 AATTTTTATGTATATATATT
*
1362812 AATTTTTATGTATTTATAT
1 AATTTTTATGTATATATAT
1362831 ATTTTTTAGA
Statistics
Matches: 42, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
18 1 0.02
19 13 0.31
20 26 0.62
21 2 0.05
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (20 bp):
AATTTTTATGTATATATATT
Found at i:1362837 original size:20 final size:21
Alignment explanation
Indices: 1362794--1362837 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1362784 TTGTTATGTA
*
1362794 TTTATGTGTATATATATTAATT
1 TTTATGTATATATATATT-ATT
*
1362816 TTTATGTATTTATATATT-TT
1 TTTATGTATATATATATTATT
1362836 TT
1 TT
1362838 AGAATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (21 bp):
TTTATGTATATATATATTATT
Found at i:1372119 original size:18 final size:18
Alignment explanation
Indices: 1372096--1372138 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1372086 TTTTCAATTG
1372096 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
1372114 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
1372132 TAATTAA
1 TAATTAA
1372139 AATTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:1374348 original size:38 final size:38
Alignment explanation
Indices: 1374297--1374373 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1374287 TTTGACACCA
1374297 ATTGATCATGCAAAGTGGGCTACGAACGAGGTTCAGCC
1 ATTGATCATGCAAAGTGGGCTACGAACGAGGTTCAGCC
1374335 ATTGATCATGCAAAGTGGGCTACGAACGAGGTTCAGCC
1 ATTGATCATGCAAAGTGGGCTACGAACGAGGTTCAGCC
1374373 A
1 A
1374374 GCTTTAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (38 bp):
ATTGATCATGCAAAGTGGGCTACGAACGAGGTTCAGCC
Found at i:1377288 original size:18 final size:18
Alignment explanation
Indices: 1377265--1377300 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1377255 ACGACCCTCG
1377265 CTTATATCGATAGAGATA
1 CTTATATCGATAGAGATA
1377283 CTTATATCGATAGAGATA
1 CTTATATCGATAGAGATA
1377301 GCAATAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
CTTATATCGATAGAGATA
Found at i:1388561 original size:82 final size:81
Alignment explanation
Indices: 1388434--1388586 Score: 254
Period size: 82 Copynumber: 1.9 Consensus size: 81
1388424 AAAAATGAAG
* *
1388434 GTACTCATTTGCAAATTATGACATTCCACTCAAGCTTCAATATTTTCTATTGGTTCCCAAAATTA
1 GTACTCATTTGCAAATGATGACATTCCACTCAAGCTTCAATATTTTCTATTGGTCCCCAAAATTA
1388499 TTGAAAATATGAAAAAT
66 TT-AAAATATGAAAAAT
*
1388516 GTACTCATTTGCAAATGATGACATTCCACGT-AAGCTTCAATATTTTCTATTGGTCCCCAACATT
1 GTACTCATTTGCAAATGATGACATTCCAC-TCAAGCTTCAATATTTTCTATTGGTCCCCAAAATT
1388580 ATTAAAA
65 ATTAAAA
1388587 CTTCTCATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 4 0.06
82 62 0.93
83 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (81 bp):
GTACTCATTTGCAAATGATGACATTCCACTCAAGCTTCAATATTTTCTATTGGTCCCCAAAATTA
TTAAAATATGAAAAAT
Found at i:1391722 original size:31 final size:29
Alignment explanation
Indices: 1391651--1391726 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 29
1391641 TTTAATAATT
*
1391651 TATATTTTTATAATTTTTAAAAAATTAAA
1 TATATTTTTATTATTTTTAAAAAATTAAA
* *
1391680 TCAAATTTTTATTATTTTTAAAAGATTCAAA
1 T-ATATTTTTATTATTTTTAAAAAATT-AAA
1391711 CTATATTTTTATTATT
1 -TATATTTTTATTATT
1391727 ACTATTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 22 0.55
31 16 0.40
32 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (29 bp):
TATATTTTTATTATTTTTAAAAAATTAAA
Found at i:1392057 original size:15 final size:15
Alignment explanation
Indices: 1392018--1392060 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1392008 TAAATTCAGT
*
1392018 ATTTAAATTTTCAAC
1 ATTTAATTTTTCAAC
*
1392033 ACTT-ATTTTTCAAC
1 ATTTAATTTTTCAAC
1392047 ATTTAATTTTTCAA
1 ATTTAATTTTTCAA
1392061 TCTATCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTAATTTTTCAAC
Found at i:1394389 original size:12 final size:13
Alignment explanation
Indices: 1394364--1394389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1394354 TTTTTCCATC
1394364 ATACTTTTTAAAA
1 ATACTTTTTAAAA
1394377 ATACTTTTTAAAA
1 ATACTTTTTAAAA
1394390 GTAATGCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATACTTTTTAAAA
Found at i:1394530 original size:29 final size:29
Alignment explanation
Indices: 1394498--1394564 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
1394488 TCAAGTTACA
*
1394498 TTTTAGTCACTTATATTTGAAATGTTATC
1 TTTTAGTCACTTATATTTAAAATGTTATC
* *
1394527 TTTTAGTCACTTATGTTTAAAATTTTATC
1 TTTTAGTCACTTATATTTAAAATGTTATC
1394556 TTTTAGTCA
1 TTTTAGTCA
1394565 ACTGACTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (29 bp):
TTTTAGTCACTTATATTTAAAATGTTATC
Found at i:1395576 original size:38 final size:38
Alignment explanation
Indices: 1395534--1395609 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1395524 TTGAATTGAT
*
1395534 TGACTCAGAAACTACTTGAAATTGATAAAAATAAAAAA
1 TGACTCAGAAACTACTTGAAATCGATAAAAATAAAAAA
**
1395572 TGACTTGGAAACTACTTGAAATCGATAAAAATAAAAAA
1 TGACTCAGAAACTACTTGAAATCGATAAAAATAAAAAA
1395610 AAAATTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.24
Consensus pattern (38 bp):
TGACTCAGAAACTACTTGAAATCGATAAAAATAAAAAA
Found at i:1397731 original size:21 final size:21
Alignment explanation
Indices: 1397685--1397731 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1397675 TGAATTTTCA
*
1397685 GATTTTTTAAGAATTTTTTTT
1 GATTTTTTAAGAATTTTTTTG
* *
1397706 AATTTTTTTAG-ATTTCTTTTG
1 GATTTTTTAAGAATTT-TTTTG
1397727 GATTT
1 GATTT
1397732 AACAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (21 bp):
GATTTTTTAAGAATTTTTTTG
Found at i:1398691 original size:9 final size:9
Alignment explanation
Indices: 1398653--1398699 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1398643 AATAATTTCT
*
1398653 TAATTTTTA
1 TAATTTTAA
*
1398662 TGATTTTAA
1 TAATTTTAA
1398671 TAATTATTTAA
1 TAA-T-TTTAA
1398682 TAATTTTAA
1 TAATTTTAA
1398691 T-ATTTTAA
1 TAATTTTAA
1398699 T
1 T
1398700 TTTAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
8 8 0.24
9 15 0.45
10 2 0.06
11 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
TAATTTTAA
Found at i:1398749 original size:19 final size:18
Alignment explanation
Indices: 1398727--1398774 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1398717 TTGTTTACCA
*
1398727 TTTTTATAATTTCATTACT
1 TTTTTATAATTTCAATA-T
*
1398746 TTTTTAT-ATTTTAATAT
1 TTTTTATAATTTCAATAT
1398763 TTTTTATAATTT
1 TTTTTATAATTT
1398775 TAAATGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 8 0.31
18 11 0.42
19 7 0.27
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTATAATTTCAATAT
Found at i:1400222 original size:39 final size:39
Alignment explanation
Indices: 1400178--1400256 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
1400168 GCAATATTAT
* * *
1400178 CCGCATTCTCAACACGAGCCGACGTATTATCCGCCTACA
1 CCGCATTCGCAACACGAGCCGACATATTATCCGCATACA
* *
1400217 CCGCATTCGCAACACGAGCCGCCATATTATCTGCATACA
1 CCGCATTCGCAACACGAGCCGACATATTATCCGCATACA
1400256 C
1 C
1400257 GAGACCATGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.38, G:0.15, T:0.20
Consensus pattern (39 bp):
CCGCATTCGCAACACGAGCCGACATATTATCCGCATACA
Found at i:1402778 original size:12 final size:12
Alignment explanation
Indices: 1402761--1402787 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1402751 TAAATCTTAA
1402761 TTTTTGAATTTT
1 TTTTTGAATTTT
1402773 TTTTTGAATTTT
1 TTTTTGAATTTT
1402785 TTT
1 TTT
1402788 GAATGCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTGAATTTT
Found at i:1410516 original size:29 final size:29
Alignment explanation
Indices: 1410476--1410546 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
1410466 TTTTTTATAA
1410476 ATTT-AAAATTTAATATTTGTAATTTTAT
1 ATTTCAAAATTTAATATTTGTAATTTTAT
* * *
1410504 -TTTCAAGAATTTAATCTTTTTACTTTTAT
1 ATTTCAA-AATTTAATATTTGTAATTTTAT
*
1410533 ATTTTAAAATTTAA
1 ATTTCAAAATTTAA
1410547 GTCTTATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.08
28 2 0.06
29 26 0.72
30 5 0.14
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTTCAAAATTTAATATTTGTAATTTTAT
Found at i:1410742 original size:30 final size:28
Alignment explanation
Indices: 1410706--1410772 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
1410696 ATTGTTGAAC
1410706 TTAAATTTTA-AAATCTAAAAAGTATAG-GAA
1 TTAAATTTTAGAAA--T-AAAAGTATAGAG-A
1410736 TTAAATTCTTAGAAATAAAAGTATAGAGA
1 TTAAATT-TTAGAAATAAAAGTATAGAGA
1410765 TTAAATTT
1 TTAAATTT
1410773 AAATTTATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 1 0.03
29 18 0.53
30 9 0.26
31 3 0.09
32 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (28 bp):
TTAAATTTTAGAAATAAAAGTATAGAGA
Found at i:1416569 original size:17 final size:17
Alignment explanation
Indices: 1416547--1416582 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1416537 TGTCGGCCAT
1416547 TGCATGGTCGACACCTG
1 TGCATGGTCGACACCTG
*
1416564 TGCATGGTCGACACTTG
1 TGCATGGTCGACACCTG
1416581 TG
1 TG
1416583 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (17 bp):
TGCATGGTCGACACCTG
Found at i:1416730 original size:59 final size:58
Alignment explanation
Indices: 1416646--1416835 Score: 228
Period size: 59 Copynumber: 3.3 Consensus size: 58
1416636 AAATTTTGAA
* *
1416646 GTGTTGGCCATGC-AATGGCCGACACCTCCTTTTTGTCAAAAAAAATTCAAAATTTTTTG
1 GTGTTGGCCAT-CAAATGGTCAACACCTCCTTTTT-TCAAAAAAAATTCAAAATTTTTTG
**
1416705 GTGTTAACCATCAAATGGTCAACACCT-CTTTTTTCGAGAAAAAAATTCAAAATTTTTTG
1 GTGTTGGCCATCAAATGGTCAACACCTCCTTTTTTC-A-AAAAAAATTCAAAATTTTTTG
* * * * *
1416764 GTGTTGGCCATCAAATGGTCGACACC-CCCTATTTCAAAAAAAATT--ATATTTTTGG
1 GTGTTGGCCATCAAATGGTCAACACCTCCTTTTTTCAAAAAAAATTCAAAATTTTTTG
1416819 GTGTTGGCCATCAAATG
1 GTGTTGGCCATCAAATG
1416836 ATTGACACCC
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
55 25 0.22
57 11 0.09
58 9 0.08
59 71 0.61
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (58 bp):
GTGTTGGCCATCAAATGGTCAACACCTCCTTTTTTCAAAAAAAATTCAAAATTTTTTG
Found at i:1416860 original size:114 final size:117
Alignment explanation
Indices: 1416646--1416876 Score: 256
Period size: 114 Copynumber: 2.0 Consensus size: 117
1416636 AAATTTTGAA
* * *
1416646 GTGTTGGCCATGCAATGGCCGACACCTCCTTTTTGTCAAAAAAAATTCAAAATTTTTTGGTGTTA
1 GTGTTGGCCATGCAATGGCCGACACCTCCCTATTGTCAAAAAAAATT-AAAATTTTTGGGTGTTA
* * * *
1416711 ACCATCAAATGGTCAACACCTCTTTTTTCGAG-AAAAAAATTCAAAATTTTTTG
65 ACCATCAAATGATCAACACCCCTTATTACGAGAAAAAAAATT-AAAATTTTTTG
* * *
1416764 GTGTTGGCCAT-CAAATGGTCGACACC-CCCTATT-TCAAAAAAAATT-ATATTTTTGGGTGTTG
1 GTGTTGGCCATGC-AATGGCCGACACCTCCCTATTGTCAAAAAAAATTAAAATTTTTGGGTGTTA
* ** ** *
1416825 GCCATCAAATGATTGACACCCCTTATTACTCGAAAAAAAATTTAAATTTTTT
65 ACCATCAAATGATCAACACCCCTTATTACGAGAAAAAAAATTAAAATTTTTT
1416877 CTCGAGAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
114 45 0.47
115 9 0.09
116 12 0.13
117 6 0.06
118 23 0.24
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (117 bp):
GTGTTGGCCATGCAATGGCCGACACCTCCCTATTGTCAAAAAAAATTAAAATTTTTGGGTGTTAA
CCATCAAATGATCAACACCCCTTATTACGAGAAAAAAAATTAAAATTTTTTG
Found at i:1422699 original size:18 final size:18
Alignment explanation
Indices: 1422676--1422715 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1422666 TCTATCAATA
1422676 ATCATATTGCATTAACCC
1 ATCATATTGCATTAACCC
1422694 ATCATATTGCATTAACCC
1 ATCATATTGCATTAACCC
1422712 ATCA
1 ATCA
1422716 AGAAACTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (18 bp):
ATCATATTGCATTAACCC
Found at i:1438884 original size:12 final size:13
Alignment explanation
Indices: 1438857--1438898 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1438847 TTTTTAATGG
1438857 AATTTTAATTAATT
1 AATTTTAA-TAATT
1438871 AATTTTAA-AATT
1 AATTTTAATAATT
* *
1438883 AAATTTATTAATT
1 AATTTTAATAATT
1438896 AAT
1 AAT
1438899 AATTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 6 0.25
14 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:1439543 original size:18 final size:18
Alignment explanation
Indices: 1439520--1439554 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1439510 GAGTTAAACG
* *
1439520 AATCGAGTTATTTGAGTT
1 AATCGAATTATTAGAGTT
1439538 AATCGAATTATTAGAGT
1 AATCGAATTATTAGAGT
1439555 CACCTCGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (18 bp):
AATCGAATTATTAGAGTT
Found at i:1447222 original size:30 final size:30
Alignment explanation
Indices: 1447178--1447274 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
1447168 CTTTTGGGGG
1447178 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
* *
1447208 TAAAAATGG-GA-TTTT-G-GAAAGTTC-AGGGG
1 T-AAAATGGTAATTTTTGGTGAAA--TCGA-GGT
* *
1447237 TAAAATGGTAATTTTTGGTGAAGTCGGGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1447267 TAAAATGG
1 TAAAATGG
1447275 GATTTTGGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
27 4 0.08
28 9 0.17
29 10 0.19
30 18 0.35
31 8 0.15
32 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTGAAATCGAGGT
Found at i:1447240 original size:29 final size:27
Alignment explanation
Indices: 1447210--1447319 Score: 96
Period size: 30 Copynumber: 3.8 Consensus size: 27
1447200 ATCGAGGTTA
*
1447210 AAAATGGGATTTTGGAAAGTTCAGGGGT
1 AAAATGGAATTTTGGAAAGTTC-GGGGT
*
1447238 AAAATGGTAATTTTTGGTGAAG-TCGGGGTT
1 AAAATGG-AA-TTTTGG-AAAGTTCGGGG-T
*
1447268 AAAATGGGATTTTGGAAAGTTCGAGGGT
1 AAAATGGAATTTTGGAAAGTTCG-GGGT
* *
1447296 CAAAATGTAATTTATGGACAGTTC
1 -AAAATGGAATTT-TGGAAAGTTC
1447320 AAGGACCTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.04
28 17 0.25
29 19 0.28
30 25 0.37
31 3 0.04
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAAGTTCGGGGT
Found at i:1447306 original size:58 final size:59
Alignment explanation
Indices: 1447174--1447308 Score: 213
Period size: 59 Copynumber: 2.3 Consensus size: 59
1447164 TTGACTTTTG
1447174 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCA
* *
1447233 GGGGTAAAATGGTAATTTTTGGTGAAGTCGGGGTT-AAAATGGGATTTTGGAAAGTTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCA
1447290 GAGGGTCAAAAT-GTAATTT
1 G-GGGT-AAAATGGTAATTT
1447309 ATGGACAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
57 1 0.01
58 33 0.46
59 38 0.53
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCA
Found at i:1447827 original size:6 final size:6
Alignment explanation
Indices: 1447818--1447913 Score: 60
Period size: 6 Copynumber: 16.0 Consensus size: 6
1447808 TAAATTCATT
*
1447818 TTTAAA TTT--A TCTTAAA TTTAAA TTTACTTA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA T-TTAAA
* * *
1447866 TTTAAA TTTACTTA TTTAAA TTT-AT TTTAAA TTTAAA CTT-AA TTTAAA
1 TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1447914 ATAATATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
4 4 0.06
5 12 0.17
6 40 0.57
7 4 0.06
8 10 0.14
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:1447851 original size:25 final size:27
Alignment explanation
Indices: 1447822--1447912 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 27
1447812 TTCATTTTTA
1447822 AATTTATCTTAAATTTAAATTTACTTATTT
1 AATTTATCTTAAATTTAAATTTAC---TTT
1447852 AAATTTATCTTAAATTTAAATTTACTTATTT
1 -AATTTATCTTAAATTTAAATTTAC---TTT
* * *
1447883 AAATTTATTTTAAATTTAAACTTAATTT
1 -AATTTATCTTAAATTTAAATTTACTTT
1447911 AA
1 AA
1447913 AATAATATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
27 2 0.04
28 3 0.05
31 52 0.91
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTTATCTTAAATTTAAATTTACTTT
Found at i:1447871 original size:37 final size:31
Alignment explanation
Indices: 1447801--1447902 Score: 163
Period size: 31 Copynumber: 3.4 Consensus size: 31
1447791 AAAGTTTGAA
* *
1447801 TTAATTTTAAATTCA-TT-TTTAAATTTATC
1 TTAAATTTAAATTTACTTATTTAAATTTATC
1447830 TTAAATTTAAATTTACTTATTTAAATTTATC
1 TTAAATTTAAATTTACTTATTTAAATTTATC
*
1447861 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTTACTTATTTAAATTTATC
1447892 TTAAATTTAAA
1 TTAAATTTAAA
1447903 CTTAATTTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 13 0.19
30 2 0.03
31 53 0.78
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAAATTTAAATTTACTTATTTAAATTTATC
Found at i:1447899 original size:11 final size:11
Alignment explanation
Indices: 1447799--1447900 Score: 63
Period size: 11 Copynumber: 9.5 Consensus size: 11
1447789 TTAAAGTTTG
*
1447799 AATTAATTTTA
1 AATTTATTTTA
*
1447810 AATTCATTTTTA
1 AATTTA-TTTTA
*
1447822 AATTTATCTTA
1 AATTTATTTTA
*
1447833 AATTTAAATTT-
1 AATTT-ATTTTA
*
1447844 -ACTTA-TTTA
1 AATTTATTTTA
*
1447853 AATTTATCTTA
1 AATTTATTTTA
*
1447864 AATTTAAATTT-
1 AATTT-ATTTTA
*
1447875 -ACTTA-TTTA
1 AATTTATTTTA
1447884 AATTTATTTTA
1 AATTTATTTTA
1447895 AATTTA
1 AATTTA
1447901 AACTTAATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.09
9 2 0.03
10 14 0.20
11 32 0.46
12 16 0.23
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:1448539 original size:16 final size:16
Alignment explanation
Indices: 1448518--1448548 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1448508 TAAAAATATT
1448518 ATTAATAATCATAATA
1 ATTAATAATCATAATA
*
1448534 ATTAATAATTATAAT
1 ATTAATAATCATAAT
1448549 TAATATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATAATCATAATA
Found at i:1448541 original size:7 final size:7
Alignment explanation
Indices: 1448518--1448587 Score: 67
Period size: 7 Copynumber: 10.3 Consensus size: 7
1448508 TAAAAATATT
1448518 ATTAATA
1 ATTAATA
1448525 ATCATAATA
1 AT--TAATA
1448534 ATTAATA
1 ATTAATA
1448541 ATT-ATA
1 ATTAATA
1448547 ATTAAT-
1 ATTAATA
* *
1448553 ATTTATG
1 ATTAATA
1448560 ATT-ATA
1 ATTAATA
*
1448566 GTTAAT-
1 ATTAATA
1448572 ATTAATA
1 ATTAATA
1448579 ATTAATA
1 ATTAATA
1448586 AT
1 AT
1448588 ATTAAAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 20 0.38
7 26 0.49
9 7 0.13
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (7 bp):
ATTAATA
Found at i:1448547 original size:13 final size:13
Alignment explanation
Indices: 1448531--1448587 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
1448521 AATAATCATA
1448531 ATAATTAATAATT
1 ATAATTAATAATT
*
1448544 ATAATTAATATTT
1 ATAATTAATAATT
* *
1448557 ATGATT-ATAGTT
1 ATAATTAATAATT
1448569 A-ATATTAATAATT
1 ATA-ATTAATAATT
1448582 AATAAT
1 -ATAAT
1448588 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 9 0.26
13 22 0.63
14 3 0.09
15 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:1448582 original size:19 final size:19
Alignment explanation
Indices: 1448517--1448587 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1448507 ATAAAAATAT
*
1448517 TATTAATAATCATAA-T-A
1 TATTAATAATTATAATTAA
1448534 -ATTAATAATTATAATTAA
1 TATTAATAATTATAATTAA
* * *
1448552 TATTTATGATTATAGTTAA
1 TATTAATAATTATAATTAA
1448571 TATTAATAATTAATAAT
1 TATTAATAATT-ATAAT
1448588 ATTAAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 13 0.30
17 1 0.02
18 1 0.02
19 24 0.56
20 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTAATAATTATAATTAA
Found at i:1449774 original size:32 final size:30
Alignment explanation
Indices: 1449700--1449850 Score: 146
Period size: 30 Copynumber: 5.0 Consensus size: 30
1449690 CCCTAAATTG
* *
1449700 TCCAAAAATTACATTTCGACCCTAAAACTT
1 TCCAAAAATTACATTTTGACCCCAAAACTT
* *
1449730 TCTAAAAATTACATTTTGACCCCAAAATTTT
1 TCCAAAAATTACATTTTGACCCCAAAA-CTT
*
1449761 TCCCAAAAATTACATTTTGACTCCAAAACTT
1 T-CCAAAAATTACATTTTGACCCCAAAACTT
* * * *
1449792 GTCC-AAAATTATACTTTAACCCTAAAAC-T
1 -TCCAAAAATTACATTTTGACCCCAAAACTT
* *
1449821 TCCAAAATTTACCATTTT-ACCCCCAAACTT
1 TCCAAAAATTA-CATTTTGACCCCAAAACTT
1449851 CCCTAAATCC
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
28 3 0.03
29 15 0.15
30 48 0.49
31 7 0.07
32 25 0.26
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTACATTTTGACCCCAAAACTT
Found at i:1449885 original size:59 final size:58
Alignment explanation
Indices: 1449822--1450020 Score: 184
Period size: 59 Copynumber: 3.4 Consensus size: 58
1449812 CCTAAAACTT
* *
1449822 CCAAAATTTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAATTTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCA
* * * * ** ** * ** * **
1449881 CCAAAACTTACCGTTTTGCCTCTGAACTTTCCAAAATTTTATTTTTGACCTTGTTTTTTG
1 CCAAAATTTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCG-ATTTCA
* *
1449941 CCAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA
1 CCAAAATTTACCATTTTA-CCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCA
*
1450000 -CAAAAATTACCATTTTACCCC
1 CCAAAATTTACCATTTTACCCC
1450021 TAAAAACCCA
Statistics
Matches: 103, Mismatches: 35, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
57 3 0.03
58 16 0.16
59 42 0.41
60 32 0.31
61 10 0.10
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.38
Consensus pattern (58 bp):
CCAAAATTTACCATTTTACCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCA
Found at i:1451498 original size:23 final size:21
Alignment explanation
Indices: 1451452--1451499 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
1451442 TTCTTTTTTA
*
1451452 ATTA-TTATTAAATTAATAAT
1 ATTATTTATTAAATTAATAAC
*
1451472 ATTATTTATTAATACTTAATACC
1 ATTATTTATTAA-A-TTAATAAC
1451495 ATTAT
1 ATTAT
1451500 CACTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 1 0.04
23 11 0.48
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTTATTAAATTAATAAC
Found at i:1452371 original size:17 final size:17
Alignment explanation
Indices: 1452351--1452395 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
1452341 TTTCAACTGT
1452351 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
1452368 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
*
1452384 ATTTAAAATTAA
1 ATTTAAATTTAA
1452396 TTTCAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:1452392 original size:23 final size:24
Alignment explanation
Indices: 1452366--1452415 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1452356 AATTTAAAAC
1452366 AAATTTAAATTT-AAA-TAAATTTA
1 AAATTT-AATTTCAAACTAAATTTA
*
1452389 AAA-TTAATTTCAAACTTAATTTA
1 AAATTTAATTTCAAACTAAATTTA
1452412 AAAT
1 AAAT
1452416 CCAAGTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTAATTTCAAACTAAATTTA
Found at i:1452397 original size:27 final size:28
Alignment explanation
Indices: 1452354--1452407 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1452344 CAACTGTATT
*
1452354 TAAATTTAAAACAAATTT-AAATTTAAA
1 TAAATTTAAAACAAATTTCAAACTTAAA
**
1452381 TAAATTTAAAATTAATTTCAAACTTAA
1 TAAATTTAAAACAAATTTCAAACTTAA
1452408 TTTAAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATTTAAAACAAATTTCAAACTTAAA
Found at i:1452409 original size:12 final size:11
Alignment explanation
Indices: 1452373--1452415 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1452363 AACAAATTTA
*
1452373 AATTT-AAATA
1 AATTTAAAATT
1452383 AATTTAAAATT
1 AATTTAAAATT
*
1452394 AATTTCAAACTT
1 AATTT-AAAATT
1452406 AATTTAAAAT
1 AATTTAAAAT
1452416 CCAAGTTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:1454309 original size:27 final size:27
Alignment explanation
Indices: 1454274--1454333 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
1454264 AAAATATATT
1454274 TTTTA-TTATTAATTT-AATATTAATAA
1 TTTTATTTATTAATTTAAATATTAA-AA
**
1454300 TTTTATTTATTTTTTTCAAATATTAAAA
1 TTTTATTTATTAATTT-AAATATTAAAA
1454328 TTTTAT
1 TTTTAT
1454334 ATATAGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.17
27 8 0.28
28 8 0.28
29 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTATTTATTAATTTAAATATTAAAA
Found at i:1469774 original size:97 final size:97
Alignment explanation
Indices: 1469586--1469805 Score: 237
Period size: 97 Copynumber: 2.2 Consensus size: 97
1469576 CATCAAGTTT
* * * * *
1469586 CAAACCTTACACAATAAGATACTCATTTAGCGAGGCTTACACCAAGTTCGATCAAGTGGCATCTT
1 CAAACCTAACACAATAAAATA--C-TTTAGCGAGGCATACACCAACTTCGATCAAGTGACATCTT
*
1469651 ATTACATCCCAACAAAGTTCCCCATGACCTTACTA
63 ATCACATCCCAACAAAGTTCCCCATGACCTTACTA
* ** *
1469686 TAGTCCTCACACAATAAAATACTTTAGCGAGGCATACACCAAACTTC-ATCAAGTGACATCTTAT
1 CAAACCTAACACAATAAAATACTTTAGCGAGGCATACACC-AACTTCGATCAAGTGACATCTTAT
* * ** * *
1469750 CACATCTCAATAGAA-TTCTTCATGATCTTATTA
65 CACATCCCAACA-AAGTTCCCCATGACCTTACTA
1469783 CAAACCTAACACAATAAAATACT
1 CAAACCTAACACAATAAAATACT
1469806 CATTTAATGG
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
97 75 0.76
98 8 0.08
100 16 0.16
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.27
Consensus pattern (97 bp):
CAAACCTAACACAATAAAATACTTTAGCGAGGCATACACCAACTTCGATCAAGTGACATCTTATC
ACATCCCAACAAAGTTCCCCATGACCTTACTA
Found at i:1471670 original size:17 final size:16
Alignment explanation
Indices: 1471648--1471683 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1471638 TCGAAGGTTT
1471648 TCATATCAAACACATAC
1 TCATATC-AACACATAC
*
1471665 TCATATCCACACATAC
1 TCATATCAACACATAC
1471681 TCA
1 TCA
1471684 AATTGACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (16 bp):
TCATATCAACACATAC
Found at i:1474831 original size:15 final size:15
Alignment explanation
Indices: 1474811--1474843 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1474801 TGATCTCCCA
1474811 TTTTTTTCTCTGATT
1 TTTTTTTCTCTGATT
*
1474826 TTTTTTTCTTTGATT
1 TTTTTTTCTCTGATT
1474841 TTT
1 TTT
1474844 GATAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTCTGATT
Found at i:1475829 original size:18 final size:17
Alignment explanation
Indices: 1475790--1475829 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
1475780 TGTCTTTTCT
1475790 TTTTTGAATTTTTCTAA
1 TTTTTGAATTTTTCTAA
*
1475807 GTTTTGAATTTTTCTTAA
1 TTTTTGAATTTTTC-TAA
1475825 TTTTT
1 TTTTT
1475830 TTTTAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTTTGAATTTTTCTAA
Found at i:1476264 original size:19 final size:18
Alignment explanation
Indices: 1476227--1476261 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1476217 CTGTTTATCG
*
1476227 ATTAAATTTAATAAAAAT
1 ATTAAATTTAAAAAAAAT
1476245 ATTAAATTTAAAAAAAA
1 ATTAAATTTAAAAAAAA
1476262 ATAGGTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAAATTTAAAAAAAAT
Found at i:1482523 original size:20 final size:19
Alignment explanation
Indices: 1482494--1482536 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1482484 ATTAGTCCAT
*
1482494 TTAATAATAAAAAAATTAA
1 TTAATAATAAAAAAATCAA
*
1482513 TTAATTAATAAATAAATCAA
1 TTAA-TAATAAAAAAATCAA
1482533 TTAA
1 TTAA
1482537 AGGATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAATAATAAAAAAATCAA
Found at i:1488871 original size:10 final size:10
Alignment explanation
Indices: 1488856--1488894 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1488846 ACTTCATGAT
*
1488856 ATTTTTATGA
1 ATTTTTATAA
1488866 ATTTTTATAA
1 ATTTTTATAA
*
1488876 ACTTTCTATAA
1 A-TTTTTATAA
1488887 ATTTTTAT
1 ATTTTTAT
1488895 TTTGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:1494675 original size:2 final size:2
Alignment explanation
Indices: 1494663--1494698 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
1494653 GCCGACTTTA
1494663 TC TC ATC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1494699 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1497956 original size:23 final size:23
Alignment explanation
Indices: 1497878--1497956 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
1497868 TCATCAACAT
* *
1497878 TGTTCATGAACATGTTTAATTATA
1 TGTTAATGAACATGTTTGATTA-A
* *
1497902 TGTTCAT-AACATGTTTGTTTAA
1 TGTTAATGAACATGTTTGATTAA
**
1497924 TGTTTGTGAACATGTTTGATTAA
1 TGTTAATGAACATGTTTGATTAA
1497947 -GTTAAATGAA
1 TGTT-AATGAA
1497957 TATATTCGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.20
23 30 0.65
24 7 0.15
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (23 bp):
TGTTAATGAACATGTTTGATTAA
Found at i:1503604 original size:2 final size:2
Alignment explanation
Indices: 1503599--1503627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1503589 GCGTCATATA
1503599 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1503628 TGAAAATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1503849 original size:158 final size:156
Alignment explanation
Indices: 1503623--1503936 Score: 384
Period size: 161 Copynumber: 2.0 Consensus size: 156
1503613 TGTGTGTGTG
1503623 TGTGTTGAAAATATCTAAAACACACAAATACAGCCCAAGAGTATACCAAACTATAACAAAAACCC
1 TGTGTTGAAAATATCTAAAACACACAAATACAGCCCAAGAGTATACCAAACTATAACAAAAACCC
* * * * * *
1503688 CAATTAG-T-ACAACTAATTTGATTTACGTTCATCATCTTTTCTCCATTTTACAGGCAAAGCATT
66 CAATTAGATAACAACTAATCTAATTTAAGTTCACCATCTTTTCTCCACTTTACAGGCAAAGCATG
1503751 CAGCATATTATATATATAGATATGTT
131 CAGCATATTATATATATAGATATGTT
* * * *
1503777 TGTGTTGCAAATATCTAACACACACAAA-ACCAGCCCAGTCTAGAGTATATCGAACTATAATC-A
1 TGTGTTGAAAATATCTAAAACACACAAATA-CAGCCCA----AGAGTATACCAAACTATAA-CAA
* * * * **
1503840 AAGCCCCAATTAGTATAACTACTAATCTAATTTAAGTTCACCTTCTTTTCTCCGCTTTAGGGGCA
60 AAACCCCAATTAG-ATAACAACTAATCTAATTTAAGTTCACCATCTTTTCTCCACTTTACAGGCA
*
1503905 AAGCATGCAGCATATTATATATATATATATGT
124 AAGCATGCAGCATATTATATATATAGATATGT
1503937 ATGTATGTAT
Statistics
Matches: 134, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
153 1 0.01
154 33 0.25
158 30 0.22
159 1 0.01
160 1 0.01
161 68 0.51
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (156 bp):
TGTGTTGAAAATATCTAAAACACACAAATACAGCCCAAGAGTATACCAAACTATAACAAAAACCC
CAATTAGATAACAACTAATCTAATTTAAGTTCACCATCTTTTCTCCACTTTACAGGCAAAGCATG
CAGCATATTATATATATAGATATGTT
Found at i:1504112 original size:4 final size:4
Alignment explanation
Indices: 1504103--1504149 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
1504093 ATAATACATA
1504103 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1504150 TATCTGTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1504967 original size:15 final size:15
Alignment explanation
Indices: 1504947--1504975 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1504937 AAGGTAAATA
1504947 ATTGTCTAATTAATT
1 ATTGTCTAATTAATT
1504962 ATTGTCTAATTAAT
1 ATTGTCTAATTAAT
1504976 CATTTAAAAG
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:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTGTCTAATTAATT
Found at i:1504996 original size:6 final size:7
Alignment explanation
Indices: 1504981--1505005 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1504971 TTAATCATTT
1504981 AAAAGAA
1 AAAAGAA
1504988 AAAAGAA
1 AAAAGAA
1504995 AAAAGAA
1 AAAAGAA
1505002 AAAA
1 AAAA
1505006 AATTATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1507328 original size:12 final size:13
Alignment explanation
Indices: 1507277--1507335 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
1507267 TAAATGGAAA
1507277 AATAAATTAATTT
1 AATAAATTAATTT
*
1507290 CATAAAATTAATATT
1 AAT-AAATTAAT-TT
*
1507305 AATGAA-TATATTT
1 AATAAATTA-ATTT
1507318 AATAAATT-ATTT
1 AATAAATTAATTT
*
1507330 ATTAAA
1 AATAAA
1507336 GGTTAATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
12 9 0.24
13 11 0.30
14 13 0.35
15 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
AATAAATTAATTT
Found at i:1507682 original size:31 final size:31
Alignment explanation
Indices: 1507641--1507704 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1507631 TGTATTTTAT
* ** *
1507641 TTGATCATTTTTAGTCTTTGTACTTTTCGAA
1 TTGATAATTTTTAGTCCCTGTACTTTTCAAA
1507672 TTGATAATTTTTAGTCCCTGTACTTTTCAAA
1 TTGATAATTTTTAGTCCCTGTACTTTTCAAA
1507703 TT
1 TT
1507705 TTGAGATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (31 bp):
TTGATAATTTTTAGTCCCTGTACTTTTCAAA
Found at i:1508273 original size:44 final size:44
Alignment explanation
Indices: 1508213--1508301 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1508203 AATTTGACCC
* *
1508213 ATAGTTTGGGGACGTTTGGTGCAATTAACTCTTAAATTTTTTTT
1 ATAGCTTGGGGACGTTTGGAGCAATTAACTCTTAAATTTTTTTT
* *
1508257 ATAGCTTGGGGGCGTTTTGAGCAATTAACTCTTAAATTTTTTTT
1 ATAGCTTGGGGACGTTTGGAGCAATTAACTCTTAAATTTTTTTT
1508301 A
1 A
1508302 CAATTTACAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (44 bp):
ATAGCTTGGGGACGTTTGGAGCAATTAACTCTTAAATTTTTTTT
Found at i:1508764 original size:19 final size:19
Alignment explanation
Indices: 1508740--1508777 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1508730 ATTACATGGT
1508740 TATACATAATTTGAATTAC
1 TATACATAATTTGAATTAC
1508759 TATACATAATTTGAATTAC
1 TATACATAATTTGAATTAC
1508778 CTAAAGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (19 bp):
TATACATAATTTGAATTAC
Found at i:1511168 original size:16 final size:16
Alignment explanation
Indices: 1511149--1511179 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1511139 TAAAATTTTA
*
1511149 TAAATTATAAAAAATC
1 TAAATTAAAAAAAATC
1511165 TAAATTAAAAAAAAT
1 TAAATTAAAAAAAAT
1511180 TATCATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAATTAAAAAAAATC
Found at i:1511944 original size:91 final size:91
Alignment explanation
Indices: 1511830--1512012 Score: 312
Period size: 91 Copynumber: 2.0 Consensus size: 91
1511820 TGTATAGTTA
*
1511830 AATTGGCCTTCGTGAGGAAGGAAGATCTACTAATGATTGAAAACCCTTCGAAAGAGGTCTTAGCT
1 AATTGGCCTTCATGAGGAAGGAAGATCTACTAATGATTGAAAACCCTTCGAAAGAGGTCTTAGCT
* *
1511895 TTTACCAAAGCAGACAAAGAAAGGAT
66 TTCACCAAAGCAGACAAAAAAAGGAT
*
1511921 AATTGGCCTTCATGAGGAAGGAAGATCTATTAATGATTGAAAACCCTTCGAAAGAGGTCTTAGCT
1 AATTGGCCTTCATGAGGAAGGAAGATCTACTAATGATTGAAAACCCTTCGAAAGAGGTCTTAGCT
* *
1511986 TTCATCAAAGCAGATAAAAAAAGGAT
66 TTCACCAAAGCAGACAAAAAAAGGAT
1512012 A
1 A
1512013 TTTTGTATTT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (91 bp):
AATTGGCCTTCATGAGGAAGGAAGATCTACTAATGATTGAAAACCCTTCGAAAGAGGTCTTAGCT
TTCACCAAAGCAGACAAAAAAAGGAT
Found at i:1512554 original size:17 final size:18
Alignment explanation
Indices: 1512523--1512560 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1512513 TCCAAACATT
* *
1512523 AAAAAATATTAATTTTTA
1 AAAAAAAATTAATTTTCA
1512541 AAAAAAAATT-ATTTTCA
1 AAAAAAAATTAATTTTCA
1512558 AAA
1 AAA
1512561 CTCATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAAAAATTAATTTTCA
Found at i:1514404 original size:28 final size:28
Alignment explanation
Indices: 1514340--1514414 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1514330 TAAGATTTAA
*
1514340 AAATATAAAATAGTAATTTTCAAAAAAAT
1 AAATATAAAATAGT-ATTATCAAAAAAAT
* *
1514369 AAAAATAAAATAGTATTATCTTAAAAAAT
1 AAATATAAAATAGTATTATC-AAAAAAAT
*
1514398 -TATATAAAATAGTATTA
1 AAATATAAAATAGTATTA
1514415 CTTTGCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 20 0.50
29 20 0.50
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATATAAAATAGTATTATCAAAAAAAT
Found at i:1531969 original size:106 final size:105
Alignment explanation
Indices: 1531646--1531995 Score: 531
Period size: 105 Copynumber: 3.3 Consensus size: 105
1531636 CAAGGTTTCG
* *
1531646 GGTTCAAGTATTTGTGAGATGGTGAGGAGTTTGGTTCCTTTAAGCAAGGTTTCGGGTTCAGGTTC
1 GGTTCGAGTATTTGTGAGATGGTGAGGAGTTTGGTACCTTTAAGCAAGGTTTCGGGTTC---TT-
1531711 GAGTGTTCTATTGATGCATGTTTAGTTGAGTGGTGAAGGAAGGTTA
62 --GTGTTCTATTGATGCATGTTTAGTTGAGTGGTGAAGGAAGGTTA
* **
1531757 GGTTTGAGTATTTGTGAGATGGTGAGGAGTTTGGTACCTTTAAGCAAGGTTTCGGGTTCGAGTGT
1 GGTTCGAGTATTTGTGAGATGGTGAGGAGTTTGGTACCTTTAAGCAAGGTTTCGGGTTCTTGTGT
* *
1531822 TCTATTGATTCATGTTTAGTCGAGTGGTGAAGGAAGGTTA
66 TCTATTGATGCATGTTTAGTTGAGTGGTGAAGGAAGGTTA
* * * *
1531862 GGTTCGAGTGTTTGTGAGATGGTGAGGAGTTTAGTACCTTTAAGGCAAGGGTTCGGGCTCTTGTG
1 GGTTCGAGTATTTGTGAGATGGTGAGGAGTTTGGTACCTTTAA-GCAAGGTTTCGGGTTCTTGTG
1531927 TTCTATTGATGCATGTTTAGTTGAGTGGTGAAGGAAGGTTA
65 TTCTATTGATGCATGTTTAGTTGAGTGGTGAAGGAAGGTTA
1531968 GGTTCGAGTATTTGTGAGATGGTG-GGAG
1 GGTTCGAGTATTTGTGAGATGGTGAGGAG
1531996 AGTTGTTTCC
Statistics
Matches: 221, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
105 86 0.39
106 79 0.36
111 56 0.25
ACGTcount: A:0.20, C:0.08, G:0.36, T:0.36
Consensus pattern (105 bp):
GGTTCGAGTATTTGTGAGATGGTGAGGAGTTTGGTACCTTTAAGCAAGGTTTCGGGTTCTTGTGT
TCTATTGATGCATGTTTAGTTGAGTGGTGAAGGAAGGTTA
Done.