Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1021558 original size:15 final size:16
Alignment explanation
Indices: 1021540--1021574 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1021530 AAATTATTAT
1021540 TTTTTATTTT-TTTCA
1 TTTTTATTTTATTTCA
*
1021555 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTCA
1021571 TTTT
1 TTTT
1021575 ATTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTATTTTATTTCA
Found at i:1030019 original size:23 final size:23
Alignment explanation
Indices: 1029972--1030022 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1029962 AATAACATAT
* **
1029972 TAGGCAGCGCTTAAATAATGTAA
1 TAGGTAGCGCTTAAATAATAAAA
*
1029995 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTAAATAATAAAA
1030018 TAGGT
1 TAGGT
1030023 TAATTACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (23 bp):
TAGGTAGCGCTTAAATAATAAAA
Found at i:1030147 original size:23 final size:23
Alignment explanation
Indices: 1030121--1030180 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1030111 ATCAAGCACA
*
1030121 ATAACATATTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
1030144 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
1030167 ATAATAAAATAGGT
1 ATAACATAATAGGT
1030181 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:1030153 original size:158 final size:158
Alignment explanation
Indices: 1029960--1030483 Score: 872
Period size: 158 Copynumber: 3.3 Consensus size: 158
1029950 ATTATTAAAT
* * * *
1029960 ACAATAACATATTAGGCAGCGCTTAAATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTAACGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
* *
1030025 ATTACTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAAGGATAACAAAAC
66 ATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGGATAACATAAC
*
1030090 CAGTTAATTACTCGAAACATTATCAAGC
131 CAGTTAATTACTAGAAACATTATCAAGC
1030118 ACAATAACATATTAGGTAACGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTAACGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
* *
1030183 ATTACTTAATTTGTTATTACAACATATTAGGTGAACGCCTAAAATGTTATCAAGGATAACATAAC
66 ATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGGATAACATAAC
* *
1030248 CGGTTATTTACTAGAAACATTATCAAGC
131 CAGTTAATTACTAGAAACATTATCAAGC
*
1030276 ACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATAT-ATAAAATAGGTTA
1 ACAATAACATATTAGGTAACGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
1030340 ATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATTGTTACCAAGGATAACATAA
66 ATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAA-TGTTACCAAGGATAACATAA
*
1030405 CCAGTTAATTACTGGAAACATTATCAAGC
130 CCAGTTAATTACTAGAAACATTATCAAGC
* *
1030434 ATAATAACATATTAGGTAGA-GCTTATATAACGTAATAGGTTGCGCATTAT
1 ACAATAACATATTAGGTA-ACGCTTATATAACGTAATAGGTAGCGC-TTAT
1030484 TAAATCTGAT
Statistics
Matches: 343, Mismatches: 20, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
157 56 0.16
158 283 0.83
159 4 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (158 bp):
ACAATAACATATTAGGTAACGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTA
ATTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACCAAGGATAACATAAC
CAGTTAATTACTAGAAACATTATCAAGC
Found at i:1030305 original size:23 final size:23
Alignment explanation
Indices: 1030279--1030327 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1030269 ATCAAGCACA
*
1030279 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
1030302 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1030325 ATA
1 ATA
1030328 TAAAATAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1030721 original size:18 final size:18
Alignment explanation
Indices: 1030698--1030737 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1030688 TTACTCCTAA
*
1030698 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTACTT
1030716 CTTCCTCCATCTTTACTT
1 CTTCCTCCATCTTTACTT
1030734 CTTC
1 CTTC
1030738 ATAATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTCCTCCATCTTTACTT
Found at i:1033490 original size:182 final size:180
Alignment explanation
Indices: 1033176--1033842 Score: 962
Period size: 182 Copynumber: 3.7 Consensus size: 180
1033166 TATTTTACGT
* *
1033176 ATACTT-TTTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTATCAT-TTC
1 ATACTTATTTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAAT-
*
1033239 GAGACCGGTTTTATCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTAT
65 GAGACC-GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTAT
1033304 CGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
129 CGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
*
1033356 ATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAAT
1 ATACTTAT-TTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAAT
* * * *
1033421 GATACTTGTTTTGTCTTATTTTTACCTATTATATTGTTATAGATCGATACATTTTTATAAAGTAT
65 GAGAC-CGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTAT
* * **
1033486 CGACATTTTATAGGCGCTATTACTGTTTCTCTTTTAAATTCCAAAAGTGTTT
129 CGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
* **
1033538 ATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTATCGGTTTTGTCATTTT
1 ATACTTAT-TTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAAT
* *
1033603 GAGACCGTTTTGTCATATTTTTACTTTTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
65 GAGACCGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATC
* * *
1033668 GACACTTTATAGACGCTATTATTGCTTCTCTTGTAAATTCCAAAAGTGTCG
130 GACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
* * * * ** *
1033719 ATATTTATTTCAATGAAATCGATACTTTCAACATATTAGGTAGCGCTTTACCGGTTTTGTTATAA
1 ATACTTATTT-AAAG-TATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAA
* * *
1033784 TGAAACCGGTTTGATCATATTTTTACC-AGTTATACTGTTATGGATCGATACATTTTTAT
64 TGAGACCGTTTTG-TCATATTTTTACCTA-TTATATTGTTATGGATCGATACATTTTTAT
1033843 TTGTATTGAT
Statistics
Matches: 435, Mismatches: 44, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
180 8 0.02
181 110 0.25
182 275 0.63
183 42 0.10
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (180 bp):
ATACTTATTTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATG
AGACCGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
ACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
Found at i:1037346 original size:2 final size:2
Alignment explanation
Indices: 1037339--1037454 Score: 59
Period size: 2 Copynumber: 62.0 Consensus size: 2
1037329 TAAAAATAAT
* * *
1037339 TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
1037377 AA TT TA -A AA TA TA TA TT TA -A TT TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1037417 TA TA TA -A TA TT TA TA TA TT TA -A TT TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1037455 CCCGGCCCGA
Statistics
Matches: 81, Mismatches: 25, Indels: 16
0.66 0.20 0.13
Matches are distributed among these distances:
1 8 0.10
2 73 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1038168 original size:39 final size:39
Alignment explanation
Indices: 1038113--1038223 Score: 143
Period size: 41 Copynumber: 2.8 Consensus size: 39
1038103 AATCATTTCT
*
1038113 AAAA-TTTAGTTTTTGTTTCATTTTAGTACCCACCGTTA
1 AAAACTTTAGTTTTTGTTTCATTTTAGTACCCACCATTA
** *
1038151 AAATTTTTAATTTTTGTTTCATTTTAGTATCCCCACCATTA
1 AAAACTTTAGTTTTTGTTTCATTTTAGTA--CCCACCATTA
* *
1038192 AAAACTTTAGCTTTTGTTTCATTTTAATACCC
1 AAAACTTTAGTTTTTGTTTCATTTTAGTACCC
1038224 CTTTTAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
38 3 0.05
39 26 0.42
41 33 0.53
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (39 bp):
AAAACTTTAGTTTTTGTTTCATTTTAGTACCCACCATTA
Found at i:1041974 original size:18 final size:18
Alignment explanation
Indices: 1041951--1041995 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1041941 AGAGAATGTT
1041951 TTATGATGTTAAATGATA
1 TTATGATGTTAAATGATA
1041969 TTATGATGTTAAATGATA
1 TTATGATGTTAAATGATA
1041987 TTATGATGT
1 TTATGATGT
1041996 GTTTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (18 bp):
TTATGATGTTAAATGATA
Found at i:1043938 original size:20 final size:20
Alignment explanation
Indices: 1043915--1043957 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1043905 AATCCACCAC
*
1043915 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
1043935 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
1043955 ATG
1 ATG
1043958 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:1054262 original size:20 final size:20
Alignment explanation
Indices: 1054239--1054281 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1054229 AATCCACCAC
*
1054239 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
1054259 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
1054279 ATG
1 ATG
1054282 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:1058058 original size:20 final size:21
Alignment explanation
Indices: 1058020--1058060 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1058010 CAGATTGTGC
1058020 AGGGGGTACAGATTCCCCCTG
1 AGGGGGTACAGATTCCCCCTG
1058041 AGGGGGTATC-GATTCCCCCT
1 AGGGGGTA-CAGATTCCCCCT
1058061 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.29, G:0.32, T:0.22
Consensus pattern (21 bp):
AGGGGGTACAGATTCCCCCTG
Found at i:1062635 original size:16 final size:16
Alignment explanation
Indices: 1062602--1062658 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
1062592 AAAAGTTAGT
* **
1062602 GGAAAAACTAAAGGAA
1 GGAAAAATTAAATAAA
1062618 GGAAAAATTAAATAAAGGAA
1 GGAAAAATTAAAT--A--AA
1062638 GGAAAAATTAAATAAA
1 GGAAAAATTAAATAAA
1062654 GGAAA
1 GGAAA
1062659 CAACATGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 18 0.53
18 1 0.03
20 15 0.44
ACGTcount: A:0.65, C:0.02, G:0.21, T:0.12
Consensus pattern (16 bp):
GGAAAAATTAAATAAA
Found at i:1062635 original size:20 final size:20
Alignment explanation
Indices: 1062610--1062657 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1062600 GTGGAAAAAC
1062610 TAAAGGAAGGAAAAATTAAA
1 TAAAGGAAGGAAAAATTAAA
1062630 TAAAGGAAGGAAAAATTAAA
1 TAAAGGAAGGAAAAATTAAA
1062650 TAAAGGAA
1 TAAAGGAA
1062658 ACAACATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (20 bp):
TAAAGGAAGGAAAAATTAAA
Found at i:1063441 original size:21 final size:22
Alignment explanation
Indices: 1063411--1063453 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1063401 AAGTTGATAT
1063411 AGTGAATTTTC-GGGCATGAAC
1 AGTGAATTTTCTGGGCATGAAC
* *
1063432 AGTGATTTTTCTGGGCTTGAAC
1 AGTGAATTTTCTGGGCATGAAC
1063454 GAAATTCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
AGTGAATTTTCTGGGCATGAAC
Found at i:1064281 original size:13 final size:14
Alignment explanation
Indices: 1064263--1064291 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1064253 TTTTAAACGT
1064263 ATAAATGTA-AATG
1 ATAAATGTATAATG
1064276 ATAAATGTATAATG
1 ATAAATGTATAATG
1064290 AT
1 AT
1064292 GAACGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
ATAAATGTATAATG
Found at i:1070394 original size:38 final size:35
Alignment explanation
Indices: 1070319--1070392 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 35
1070309 ACTATAAGAT
*
1070319 ATTTATATATTTTCTTTAAAAATTTAAATCCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAT-CATAAA
*
1070355 ATTTATATAATTTTTTTTACAAAATTGATAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGA-AATCATAAA
1070392 A
1 A
1070393 ATATTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 7 0.21
39 3 0.09
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (35 bp):
ATTTATATATTTTCTTTAAAAATTGAAATCATAAA
Found at i:1075432 original size:10 final size:10
Alignment explanation
Indices: 1075417--1075448 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1075407 TAATCTGATA
1075417 GGTGGCAGCG
1 GGTGGCAGCG
1075427 GGTGGCAGCG
1 GGTGGCAGCG
1075437 GGTGGCAGCG
1 GGTGGCAGCG
1075447 GG
1 GG
1075449 AGGAATGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.62, T:0.09
Consensus pattern (10 bp):
GGTGGCAGCG
Found at i:1091084 original size:11 final size:12
Alignment explanation
Indices: 1091052--1091076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1091042 ACCTCCCTAA
1091052 GCAAAATTTTCT
1 GCAAAATTTTCT
1091064 GCAAAATTTTCT
1 GCAAAATTTTCT
1091076 G
1 G
1091077 AGAATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (12 bp):
GCAAAATTTTCT
Found at i:1105200 original size:17 final size:17
Alignment explanation
Indices: 1105178--1105223 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1105168 ATTATATCAG
1105178 AATCAGAATCATTTCCA
1 AATCAGAATCATTTCCA
1105195 AATCAGAATCATTTCCA
1 AATCAGAATCATTTCCA
*
1105212 AATCATAATCAT
1 AATCAGAATCAT
1105224 AAAATATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.30
Consensus pattern (17 bp):
AATCAGAATCATTTCCA
Found at i:1107738 original size:15 final size:16
Alignment explanation
Indices: 1107718--1107750 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1107708 CAAAATACAA
1107718 TATTCCC-AGTAATCT
1 TATTCCCTAGTAATCT
*
1107733 TATTCCCTGGTAATCT
1 TATTCCCTAGTAATCT
1107749 TA
1 TA
1107751 CATTCCCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
TATTCCCTAGTAATCT
Found at i:1107747 original size:16 final size:18
Alignment explanation
Indices: 1107726--1107770 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1107716 AATATTCCCA
1107726 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
1107742 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
1107762 GTAATCTTA
1 GTAATCTTA
1107771 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:1107764 original size:20 final size:20
Alignment explanation
Indices: 1107739--1107776 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1107729 ATCTTATTCC
1107739 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1107759 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1107777 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1108277 original size:7 final size:7
Alignment explanation
Indices: 1108265--1108311 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
1108255 AATATTAATG
1108265 TATATGT
1 TATATGT
1108272 TATATGT
1 TATATGT
1108279 TAT-TG-
1 TATATGT
1108284 TATATGT
1 TATATGT
*
1108291 TACATGT
1 TATATGT
1108298 TAT-TG-
1 TATATGT
1108303 TATATGT
1 TATATGT
1108310 TA
1 TA
1108312 CATGATCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 6 0.18
6 8 0.24
7 20 0.59
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (7 bp):
TATATGT
Found at i:1108287 original size:19 final size:19
Alignment explanation
Indices: 1108263--1108315 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1108253 TGAATATTAA
*
1108263 TGTATATGTTATATGTTAT
1 TGTATATGTTACATGTTAT
1108282 TGTATATGTTACATGTTAT
1 TGTATATGTTACATGTTAT
1108301 TGTATATGTTACATG
1 TGTATATGTTACATG
1108316 ATCCATGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (19 bp):
TGTATATGTTACATGTTAT
Found at i:1112915 original size:21 final size:21
Alignment explanation
Indices: 1112889--1112984 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
1112879 TCGAGGGTTC
*
1112889 TATGTAGTCCTTCGGGACATA
1 TATGTAGTCCTTCGGAACATA
* *
1112910 TATGTAATCCTTTGGAACATA
1 TATGTAGTCCTTCGGAACATA
* * * *
1112931 TATGTTGTACTTCGGGACACA
1 TATGTAGTCCTTCGGAACATA
* * *
1112952 TATTTGGTCCATT-GGAATATA
1 TATGTAGTCC-TTCGGAACATA
1112973 TATGTAGTCCTT
1 TATGTAGTCCTT
1112985 AAGGAGAATT
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (21 bp):
TATGTAGTCCTTCGGAACATA
Found at i:1112948 original size:42 final size:42
Alignment explanation
Indices: 1112889--1112980 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
1112879 TCGAGGGTTC
* * *
1112889 TATGTAGTCCTTCGGGACATATATGTAATCCTTTGGAACATA
1 TATGTAGTACTTCGGGACACATATGTAATCCATTGGAACATA
* * ** *
1112931 TATGTTGTACTTCGGGACACATATTTGGTCCATTGGAATATA
1 TATGTAGTACTTCGGGACACATATGTAATCCATTGGAACATA
1112973 TATGTAGT
1 TATGTAGT
1112981 CCTTAAGGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (42 bp):
TATGTAGTACTTCGGGACACATATGTAATCCATTGGAACATA
Found at i:1120536 original size:20 final size:21
Alignment explanation
Indices: 1120511--1120557 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1120501 GGTTGTACTC
1120511 ATTTCTAGCC-GTTGGGGATG
1 ATTTCTAGCCTGTTGGGGATG
*
1120531 ATTTCTAGCCTTTTGGGGATG
1 ATTTCTAGCCTGTTGGGGATG
*
1120552 TTTTCT
1 ATTTCT
1120558 TTGCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (21 bp):
ATTTCTAGCCTGTTGGGGATG
Found at i:1122111 original size:24 final size:24
Alignment explanation
Indices: 1122052--1122115 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
1122042 ATTTGGGATA
*
1122052 GGTATCGGTACCTCTATATAAAGG
1 GGTATCGATACCTCTATATAAAGG
*
1122076 GGTAT-TAGTACCTCTATATAAAGG
1 GGTATCGA-TACCTCTATATAAAGG
*
1122100 GTTATCGATACC-CTAT
1 GGTATCGATACCTCTAT
1122116 GGGGTATCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.12
24 29 0.85
25 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (24 bp):
GGTATCGATACCTCTATATAAAGG
Found at i:1128446 original size:24 final size:24
Alignment explanation
Indices: 1128411--1128463 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1128401 TCTACTTTCA
*
1128411 AGATCATTATTGGTCTTGGATATG
1 AGATCATCATTGGTCTTGGATATG
1128435 AGATCATCATTGGTCTTGGATATG
1 AGATCATCATTGGTCTTGGATATG
1128459 AGATC
1 AGATC
1128464 TTTGTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (24 bp):
AGATCATCATTGGTCTTGGATATG
Found at i:1136530 original size:21 final size:20
Alignment explanation
Indices: 1136492--1136535 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1136482 TAAGCCTAAA
*
1136492 AAAGAAAAAAATATAAAATAT
1 AAAGAAAAAAATACAAAA-AT
**
1136513 AAAGAAAATTATACAAAAAT
1 AAAGAAAAAAATACAAAAAT
1136533 AAA
1 AAA
1136536 TAAGCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAGAAAAAAATACAAAAAT
Found at i:1144152 original size:22 final size:22
Alignment explanation
Indices: 1144127--1144176 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1144117 ATTAGATATT
*
1144127 ATTTTAATAAAA-ATAGTTTAAA
1 ATTTTAA-AAAATATAATTTAAA
1144149 ATTTTAAAAAATATAATTTAAA
1 ATTTTAAAAAATATAATTTAAA
*
1144171 AATTTA
1 ATTTTA
1144177 TCTTAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTTTAAAAAATATAATTTAAA
Found at i:1144556 original size:60 final size:58
Alignment explanation
Indices: 1144443--1144592 Score: 146
Period size: 60 Copynumber: 2.5 Consensus size: 58
1144433 TCTACGGTAT
* * **
1144443 TTAAACTTTTAAATATTTTAATTTCATCTATAAACTATGATTATCATATTAAATT-AGTCC
1 TTAAACTTTTGAATA-TTTCATTTCATCCCTAAACTATGATTATCATATTAAATTGA-T-C
1144503 TTAAACTTTTGAATATTTCATTTTCATCCCTAAACTA-GTATCT-TCA-ATCTAAATTGATC
1 TTAAACTTTTGAATATTTCA-TTTCATCCCTAAACTATG-AT-TATCATAT-TAAATTGATC
*
1144562 TCAAACTTTTTGAATATTTTCATTTCATCCC
1 TTAAAC-TTTTGAATA-TTTCATTTCATCCC
1144593 AAATTATACA
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
59 13 0.17
60 58 0.74
61 7 0.09
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (58 bp):
TTAAACTTTTGAATATTTCATTTCATCCCTAAACTATGATTATCATATTAAATTGATC
Found at i:1144845 original size:58 final size:60
Alignment explanation
Indices: 1144744--1144871 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 60
1144734 TTGAAGACTC
* * ** *
1144744 AAAATTTTGAGGATCAATTTAGAATGAGAGCCCTAGTTTAAGGATGAAATTGAAAT-TTT
1 AAAATTTTAAGGATCAATTTAGAATGAGAGCCATAGTAAAAGGATGAAATTAAAATGTTT
* ** *
1144803 -CAATTTTAAGGA-CTAATTTAGAATGAGAGTTATAGTAAAAGGATTAAATTAAAATGTTT
1 AAAATTTTAAGGATC-AATTTAGAATGAGAGCCATAGTAAAAGGATGAAATTAAAATGTTT
1144862 AAAATTTTAA
1 AAAATTTTAA
1144872 ATACAACATT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.02
58 44 0.79
59 3 0.05
60 8 0.14
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (60 bp):
AAAATTTTAAGGATCAATTTAGAATGAGAGCCATAGTAAAAGGATGAAATTAAAATGTTT
Found at i:1148919 original size:32 final size:32
Alignment explanation
Indices: 1148876--1148951 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
1148866 TTAAACTTTG
1148876 TTTCAATTATCGAACTTGGAAGT-TTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTATTTAAGTA
*
1148907 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGGAAGTATTTAAGTA
1148940 TTTCAATTATCG
1 TTTCAATTATCG
1148952 TAAACTTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 5 0.12
32 23 0.56
33 13 0.32
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTATTTAAGTA
Found at i:1150260 original size:64 final size:64
Alignment explanation
Indices: 1150141--1150284 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
1150131 ATTGTTCAAG
* * *
1150141 GTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTATATCGATGCACAAG-TA
1 GTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGTATACCGATGCA-AAGATA
* ** * * *
1150205 GTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGGGATTTA-TGTACCGATGCATAGATA
1 GTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TCAGTATACCGATGCAAAGATA
1150269 GTGCATCGATGCACCC
1 GTGCATCGATGCACCC
1150285 GTCAAGGGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 65 0.94
65 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (64 bp):
GTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGTATACCGATGCAAAGATA
Found at i:1150960 original size:23 final size:23
Alignment explanation
Indices: 1150934--1150978 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1150924 TAGCACTACA
1150934 GTGCAATTCTACGCGGCACTTCG
1 GTGCAATTCTACGCGGCACTTCG
*
1150957 GTGCAATTCTACGTGGCACTTC
1 GTGCAATTCTACGCGGCACTTC
1150979 TATGCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTTCG
Found at i:1150984 original size:23 final size:23
Alignment explanation
Indices: 1150935--1150984 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1150925 AGCACTACAG
*
1150935 TGCAATTCTACGCGGCACTTCGG
1 TGCAATTCTACGCGGCACTTCGA
* *
1150958 TGCAATTCTACGTGGCACTTCTA
1 TGCAATTCTACGCGGCACTTCGA
1150981 TGCA
1 TGCA
1150985 TTTATACGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (23 bp):
TGCAATTCTACGCGGCACTTCGA
Found at i:1150992 original size:23 final size:23
Alignment explanation
Indices: 1150935--1150992 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1150925 AGCACTACAG
* *
1150935 TGCAATTCTACGCGGCACTTCGG
1 TGCAATTATACGCGGCACTTCGA
* * *
1150958 TGCAATTCTACGTGGCACTTCTA
1 TGCAATTATACGCGGCACTTCGA
*
1150981 TGCATTTATACG
1 TGCAATTATACG
1150993 AGTTGTGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (23 bp):
TGCAATTATACGCGGCACTTCGA
Found at i:1157111 original size:63 final size:64
Alignment explanation
Indices: 1157037--1157157 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 64
1157027 ATTGTTCAAG
* * *
1157037 GTGTATCGATGCACATGAAGTGTATCGATGCA-CTCCTCT-AAATAAAAACATCGAATGCCATCC
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCT-TAAAATAAAAACATCGAATGCCATCC
* * *
1157100 GTGTATCGATGCACAAGTAGTGCATTGATGCACCCCCTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
1157158 GGATTTATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 29 0.58
64 21 0.42
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCC
Found at i:1157906 original size:23 final size:23
Alignment explanation
Indices: 1157840--1157898 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1157830 ATCTTATATA
*
1157840 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
*
1157863 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
1157886 GCACTTCGGTGCA
1 GCACTTCGGTGCA
1157899 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:1159410 original size:258 final size:258
Alignment explanation
Indices: 1158945--1159465 Score: 988
Period size: 258 Copynumber: 2.0 Consensus size: 258
1158935 AAATCAATTT
1158945 ATGTGTTATATAAAAAACATATTAAAGGGTAAAGTATACAAAACGTCTTCCGCCCCGATTATAAG
1 ATGTGTTATATAAAAAACATATTAAAGGGTAAAGTATACAAAACGTCTTCCGCCCCGATTATAAG
*
1159010 ATATTATTTTATTAAATTCATCAATTATTAGAAGTTATAAAATGATAATTTGACTATCGAGTGTT
66 ATATTATTTTATTAAATTCATCAATTATTAGAAGTTATAAAATGATAATCTGACTATCGAGTGTT
1159075 GTTTTGTTGAGTCCCTCGACTATTAAAAGTTATAAAATGATCATTTGACTTTTCATTATGTTCCA
131 GTTTTGTTGAGTCCCTCGACTATTAAAAGTTATAAAATGATCATTTGACTTTTCATTATGTTCCA
* *
1159140 AAAGTATTCTTTTTGGTTAAAAATCAATTATTGTATGAGCTGGATGTTAACATGATGACTGAA
196 AAAGTATTCTTTTCGGTTAAAAATCAATTATTGTATGAGCTGGACGTTAACATGATGACTGAA
* *
1159203 ATGTTTTATATAAAAAACATATTAAAGGGTAAAGTATACAAAACGTCTTCTGCCCCGATTATAAG
1 ATGTGTTATATAAAAAACATATTAAAGGGTAAAGTATACAAAACGTCTTCCGCCCCGATTATAAG
1159268 ATATTATTTTATTAAATTCATCAATTATTAGAAGTTATAAAATGATAATCTGACTATCGAGTGTT
66 ATATTATTTTATTAAATTCATCAATTATTAGAAGTTATAAAATGATAATCTGACTATCGAGTGTT
1159333 GTTTTGTTGAGTCCCTCGACTATTAAAAGTTATAAAATGATCATTTGACTTTTCATTATGTTCCA
131 GTTTTGTTGAGTCCCTCGACTATTAAAAGTTATAAAATGATCATTTGACTTTTCATTATGTTCCA
*
1159398 AAAGTGTTCTTTTCGGTTAAAAATCAATTATTGTATGAGCTGGACGTTAACATGATGACTGAA
196 AAAGTATTCTTTTCGGTTAAAAATCAATTATTGTATGAGCTGGACGTTAACATGATGACTGAA
1159461 ATGTG
1 ATGTG
1159466 ATAGTTGTTT
Statistics
Matches: 256, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
258 256 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (258 bp):
ATGTGTTATATAAAAAACATATTAAAGGGTAAAGTATACAAAACGTCTTCCGCCCCGATTATAAG
ATATTATTTTATTAAATTCATCAATTATTAGAAGTTATAAAATGATAATCTGACTATCGAGTGTT
GTTTTGTTGAGTCCCTCGACTATTAAAAGTTATAAAATGATCATTTGACTTTTCATTATGTTCCA
AAAGTATTCTTTTCGGTTAAAAATCAATTATTGTATGAGCTGGACGTTAACATGATGACTGAA
Found at i:1160005 original size:26 final size:26
Alignment explanation
Indices: 1159976--1160055 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
1159966 GATAAAATCG
1159976 ATCTCATAATCTCAAATGACTATCAT
1 ATCTCATAATCTCAAATGACTATCAT
*
1160002 ATCTC--AA--TCAACATGTTAAC-GTC-T
1 ATCTCATAATCTCAA-ATG---ACTATCAT
*
1160026 AACTCATAATCTCAAATGACTATCAT
1 ATCTCATAATCTCAAATGACTATCAT
1160052 ATCT
1 ATCT
1160056 GAGTCAACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 20
0.62 0.06 0.31
Matches are distributed among these distances:
22 4 0.10
23 3 0.08
24 9 0.22
25 4 0.10
26 13 0.32
27 3 0.08
28 4 0.10
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
ATCTCATAATCTCAAATGACTATCAT
Found at i:1160033 original size:50 final size:50
Alignment explanation
Indices: 1159978--1160082 Score: 174
Period size: 50 Copynumber: 2.1 Consensus size: 50
1159968 TAAAATCGAT
* *
1159978 CTCATAATCTCAAATGACTATCATATCTCAATCAACATGTTAACGTCTAA
1 CTCATAATCTCAAATGACTATCATATCTCAATCAACATGTTAACATCAAA
* *
1160028 CTCATAATCTCAAATGACTATCATATCTGAGTCAACATGTTAACATCAAA
1 CTCATAATCTCAAATGACTATCATATCTCAATCAACATGTTAACATCAAA
1160078 CTCAT
1 CTCAT
1160083 GTGATCGTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (50 bp):
CTCATAATCTCAAATGACTATCATATCTCAATCAACATGTTAACATCAAA
Found at i:1161471 original size:20 final size:20
Alignment explanation
Indices: 1161446--1161489 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1161436 GTTCACCCTA
*
1161446 ATTCTACCGATTTTCAATCG
1 ATTCTACCGATTTTCAACCG
* *
1161466 ATTCTATCGGTTTTCAACCG
1 ATTCTACCGATTTTCAACCG
1161486 ATTC
1 ATTC
1161490 ATTACAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (20 bp):
ATTCTACCGATTTTCAACCG
Found at i:1163038 original size:17 final size:17
Alignment explanation
Indices: 1162998--1163042 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1162988 GACTAAAATG
*
1162998 TTTAAAAAAAATTTCTT
1 TTTAAAAAAATTTTCTT
**
1163015 TCAAAAAAAATTTTCTT
1 TTTAAAAAAATTTTCTT
1163032 TTTAAAAAAAT
1 TTTAAAAAAAT
1163043 CCTTATTCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAAAAATTTTCTT
Found at i:1166836 original size:31 final size:29
Alignment explanation
Indices: 1166783--1166879 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 29
1166773 TTTTAAGCAT
*
1166783 CTAAAGTATATTTTAGTCAAAATAAGTAC
1 CTAAAGTATTTTTTAGTCAAAATAAGTAC
*
1166812 CTAAAGTTATTTTTTTAGTTAAAAT-AGTTAC
1 CTAAAG-TA-TTTTTTAGTCAAAATAAG-TAC
* *
1166843 CT-AAGTATTTTGT-GTCAAAATAGGTAC
1 CTAAAGTATTTTTTAGTCAAAATAAGTAC
*
1166870 CTAAACTATT
1 CTAAAGTATT
1166880 CAAATTTTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
27 12 0.21
28 12 0.21
29 8 0.14
30 7 0.12
31 18 0.32
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.40
Consensus pattern (29 bp):
CTAAAGTATTTTTTAGTCAAAATAAGTAC
Found at i:1167307 original size:30 final size:30
Alignment explanation
Indices: 1167273--1167345 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1167263 AAATTATGTA
* *
1167273 TTTAGTATCTAAACTATTAATTTTAATTTT
1 TTTAGTATCTAAACTATCAATTTTAATTCT
*
1167303 TTTAGTATCTAAACTATCAATTTTAGTTCT
1 TTTAGTATCTAAACTATCAATTTTAATTCT
1167333 TTTAGTATCTAAA
1 TTTAGTATCTAAA
1167346 TTTTCATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTAGTATCTAAACTATCAATTTTAATTCT
Found at i:1168188 original size:26 final size:26
Alignment explanation
Indices: 1168159--1168212 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1168149 GTGGATTGCA
1168159 CCTCCAAAAATTACAAGTGACGGTCT
1 CCTCCAAAAATTACAAGTGACGGTCT
1168185 CCTCCAAAAATTACAAGTGACGGTCT
1 CCTCCAAAAATTACAAGTGACGGTCT
1168211 CC
1 CC
1168213 AAAAATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (26 bp):
CCTCCAAAAATTACAAGTGACGGTCT
Found at i:1168216 original size:23 final size:25
Alignment explanation
Indices: 1168159--1168220 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 25
1168149 GTGGATTGCA
1168159 CCTCCAAAAATTACAAGTGACGGTCT
1 CCTCCAAAAATTACAAGTGACGG-CT
1168185 CCTCCAAAAATTACAAGTGACGG-T
1 CCTCCAAAAATTACAAGTGACGGCT
1168209 -CTCCAAAAATTA
1 CCTCCAAAAATTA
1168221 TGTTGCTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.33
24 1 0.03
26 23 0.64
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (25 bp):
CCTCCAAAAATTACAAGTGACGGCT
Found at i:1171523 original size:23 final size:25
Alignment explanation
Indices: 1171480--1171525 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1171470 GTGATTTACC
*
1171480 CTTACTTTTAAAATTAGTTTTTGGT
1 CTTACTTTTAAAATTAATTTTTGGT
1171505 CTTA-TTTT-AAATTAATTTTTG
1 CTTACTTTTAAAATTAATTTTTG
1171526 ACAATTAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.59
Consensus pattern (25 bp):
CTTACTTTTAAAATTAATTTTTGGT
Found at i:1172944 original size:2 final size:2
Alignment explanation
Indices: 1172937--1172967 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1172927 GAAGCTAAGC
1172937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1172968 AGAGAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1174000 original size:22 final size:22
Alignment explanation
Indices: 1173972--1174022 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1173962 TACAATTATG
1173972 AATACATGAGTAAGGTTCTATA
1 AATACATGAGTAAGGTTCTATA
*
1173994 AATACATGAGTAAGGTTCTATG
1 AATACATGAGTAAGGTTCTATA
1174016 AATACAT
1 AATACAT
1174023 ATGCCCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (22 bp):
AATACATGAGTAAGGTTCTATA
Found at i:1177670 original size:19 final size:19
Alignment explanation
Indices: 1177646--1177685 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1177636 TCTTTTCAGG
1177646 TTTCTGATAAAGAAACAAC
1 TTTCTGATAAAGAAACAAC
1177665 TTTCTGATAAAGAAACAAC
1 TTTCTGATAAAGAAACAAC
1177684 TT
1 TT
1177686 GAGATATCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (19 bp):
TTTCTGATAAAGAAACAAC
Found at i:1179126 original size:20 final size:19
Alignment explanation
Indices: 1179101--1179150 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1179091 TCATCGACAA
1179101 ATACATAAAAGATATATAAC
1 ATACATAAAAG-TATATAAC
* *
1179121 ATACATAGAAAGTATTTAAT
1 ATACATA-AAAGTATATAAC
*
1179141 ATGCATAAAA
1 ATACATAAAA
1179151 TACATACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (19 bp):
ATACATAAAAGTATATAAC
Found at i:1179633 original size:40 final size:40
Alignment explanation
Indices: 1179584--1179813 Score: 256
Period size: 40 Copynumber: 5.8 Consensus size: 40
1179574 AGTTTCCAAT
1179584 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-ATA-GTCAAATTCGCAACACAGAAGTCAAA
* * *
1179624 TTCGTAACGCGATAGTCAAATCCAG-AACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTC-GCAACACAGAAGTCAAA
* * * * *
1179664 TTCTCAACACAAAAGTCAAATTCGCAACGC-GATAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAGA-AGTCAAA
*
1179704 TTCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-A-TAGTCAAATTCGCAACACAGAAGTCAAA
* * *
1179744 TTTGCAACGCGATAGCCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAA
1179784 TTCGCAACGCGATAGTCAAATTCGCAACAC
1 TTCGCAACGCGATAGTCAAATTCGCAACAC
1179814 GAAACACATA
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
38 4 0.03
39 12 0.08
40 132 0.84
41 7 0.04
42 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:1179642 original size:20 final size:20
Alignment explanation
Indices: 1179584--1179811 Score: 191
Period size: 20 Copynumber: 11.4 Consensus size: 20
1179574 AGTTTCCAAT
1179584 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCG-ATA-GTCAAA
*
1179605 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
*
1179624 TTCGTAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * * *
1179644 TCCAG-AACACAAAAGTCAAA
1 TTC-GCAACGCGATAGTCAAA
* * * *
1179664 TTCTCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
1179684 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*
1179704 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCG-A-TAGTCAAA
*
1179725 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
* *
1179744 TTTGCAACGCGATAGCCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
1179764 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
1179784 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
1179804 TTCGCAAC
1 TTCGCAAC
1179812 ACGAAACACA
Statistics
Matches: 168, Mismatches: 27, Indels: 25
0.76 0.12 0.11
Matches are distributed among these distances:
18 4 0.02
19 11 0.07
20 143 0.85
21 7 0.04
22 3 0.02
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:1179701 original size:60 final size:60
Alignment explanation
Indices: 1179605--1179811 Score: 249
Period size: 60 Copynumber: 3.5 Consensus size: 60
1179595 AATATGTAAA
* * *
1179605 TCGCAACACAGAAGTCAAATTCGTAACGCGATAGTCAAATCCAG-AACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTC-GCAACACAAAAGTCAAAT
* * **
1179665 TCTCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATTTGT-AAA-
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACAC-AA-AAGTCAAAT
* * *
1179725 TCGCAACACAGAAGTCAAATTTGCAACGCGATAGCCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
* * *
1179785 TCGCAACGCGATAGTCAAATTCGCAAC
1 TCGCAACACAAAAGTCAAATTCGCAAC
1179812 ACGAAACACA
Statistics
Matches: 123, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 6 0.05
60 108 0.88
61 5 0.04
62 2 0.02
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (60 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:1180361 original size:19 final size:20
Alignment explanation
Indices: 1180337--1180376 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1180327 AAATCGCAAC
1180337 GCGATTTT-AGTTTT-GCGTT
1 GCGATTTTCA-TTTTCGCGTT
1180356 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
1180376 G
1 G
1180377 TGAATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.50
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:1182162 original size:63 final size:63
Alignment explanation
Indices: 1182077--1182197 Score: 138
Period size: 63 Copynumber: 1.9 Consensus size: 63
1182067 AAGGTCGGTA
* * * * *
1182077 TTTTACGTGAAGATAATAGTGCA-TGGCGTGATGAGGT-TCGTTCTTTACGTGGTGAGGTGGATT
1 TTTTACGCGAAGACAATAGTGCACT-ACGTGATGAGGTATC-TACTTTACGTGATGAGGTGGATT
* * *
1182140 TTTTACGCGATGACAATGGTGCACTACGTGGTGAGGTATCTACTTTACGTGATGAGGT
1 TTTTACGCGAAGACAATAGTGCACTACGTGATGAGGTATCTACTTTACGTGATGAGGT
1182198 TGCCGCTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
63 45 0.94
64 3 0.06
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.35
Consensus pattern (63 bp):
TTTTACGCGAAGACAATAGTGCACTACGTGATGAGGTATCTACTTTACGTGATGAGGTGGATT
Found at i:1182318 original size:4 final size:4
Alignment explanation
Indices: 1182309--1182346 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
1182299 TTTTTCGGCA
* *
1182309 TTAT TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1182347 TCAGCGGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1182570 original size:21 final size:21
Alignment explanation
Indices: 1182546--1182608 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1182536 TATCGTAAAA
*
1182546 GCCCCTCCCACCGTTTAAGAG
1 GCCCCTCCCACCGTTCAAGAG
** *
1182567 GCCCCTGTCATCGTTCAAGAG
1 GCCCCTCCCACCGTTCAAGAG
* * *
1182588 GTCCCGCCCGCCGTTCAAGAG
1 GCCCCTCCCACCGTTCAAGAG
1182609 TCTGATTCAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.40, G:0.24, T:0.19
Consensus pattern (21 bp):
GCCCCTCCCACCGTTCAAGAG
Found at i:1184004 original size:69 final size:67
Alignment explanation
Indices: 1183931--1184107 Score: 218
Period size: 68 Copynumber: 2.6 Consensus size: 67
1183921 GAGGTACACT
*
1183931 TTTTTTGCTTGTTTAATTAAATTT-TACATTGAAAGTTGTTTTGTTTAA-TTGATGAGGAAATAA
1 TTTTTTGCTTGTTTAATT-AATTTGT--A---AAAGTTGATTTGTTTAAGTTGATGAGGAAATAA
1183994 G-A-ATTA
60 GAATATTA
* * *
1184000 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAAGTTGATGTGTAAATAAGAATTA
1 TTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTTTAAGTTGATGAGGAAATAAGAA-TA
1184065 TTA
65 TTA
*
1184068 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTT
1184108 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
64 16 0.16
65 14 0.14
66 1 0.01
67 1 0.01
68 48 0.48
69 19 0.19
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (67 bp):
TTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTTTAAGTTGATGAGGAAATAAGAATAT
TA
Found at i:1184035 original size:14 final size:14
Alignment explanation
Indices: 1184016--1184055 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1184006 GCTTGTTTAA
1184016 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
1184030 TTGATTTGTTTAAG
1 TTGATTTGTAAAAG
*
1184044 TTGATGTGTAAA
1 TTGATTTGTAAA
1184056 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1184086 original size:68 final size:64
Alignment explanation
Indices: 1183962--1184107 Score: 229
Period size: 68 Copynumber: 2.2 Consensus size: 64
1183952 TTTTACATTG
*
1183962 AAAGTTGTTTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
* *
1184026 AAAGTTGATTTGTTTAAGTTGATGTGTAAATAAGAATTATTATTTTTTGCTTGTTTAATTGATTT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAG-A--ATTATTTTTTGCTTGTTTAATTGATTT
1184091 GTA
62 GTA
1184094 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1184108 GTTTTAAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
64 16 0.21
65 14 0.19
66 1 0.01
68 44 0.59
ACGTcount: A:0.29, C:0.01, G:0.18, T:0.51
Consensus pattern (64 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
Found at i:1184186 original size:20 final size:20
Alignment explanation
Indices: 1184161--1184209 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1184151 GTTGAAGGTA
*
1184161 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1184181 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
1184201 CAAATTCGC
1 CAAATTCGC
1184210 GTTGCGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1184596 original size:6 final size:6
Alignment explanation
Indices: 1184587--1184621 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1184577 TTGTGATTGG
**
1184587 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
1184622 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:1184603 original size:18 final size:18
Alignment explanation
Indices: 1184580--1184620 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1184570 AAGCCTGTTG
*
1184580 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1184598 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1184616 TGATT
1 TGATT
1184621 TCCTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1186690 original size:23 final size:24
Alignment explanation
Indices: 1186660--1186705 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1186650 GTGGCATTTT
1186660 CTTCTTTTTCTT-TTCTTCAGGGA
1 CTTCTTTTTCTTCTTCTTCAGGGA
*
1186683 CTTCTTTTTCTTCTTCTTTAGGG
1 CTTCTTTTTCTTCTTCTTCAGGG
1186706 TTATATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.07, C:0.22, G:0.13, T:0.59
Consensus pattern (24 bp):
CTTCTTTTTCTTCTTCTTCAGGGA
Found at i:1186940 original size:24 final size:24
Alignment explanation
Indices: 1186889--1186943 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1186879 AAAATCCGAG
**
1186889 TATTGACCAAGATCAAAGTCTGGG
1 TATTGACCAAGATCAAAGTCTGAA
* *
1186913 TATTGACCAAGATCAAATTTTGAA
1 TATTGACCAAGATCAAAGTCTGAA
1186937 TATTGAC
1 TATTGAC
1186944 TAGTACTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCTGAA
Found at i:1187076 original size:12 final size:12
Alignment explanation
Indices: 1187055--1187088 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1187045 GGTTGTGGGT
*
1187055 TTTGAGATTGTG
1 TTTGATATTGTG
1187067 TTTGATATTGTG
1 TTTGATATTGTG
*
1187079 TTTGGTATTG
1 TTTGATATTG
1187089 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1187705 original size:16 final size:15
Alignment explanation
Indices: 1187683--1187721 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1187673 GAAATCATTG
1187683 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
1187699 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
1187714 AAAAATTA
1 AAAAATTA
1187722 GAGATGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:1187904 original size:19 final size:18
Alignment explanation
Indices: 1187861--1187907 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1187851 CAAAACATTT
1187861 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
1187879 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
1187898 GTGTTGCGAA
1 GTGTTGCGAA
1187908 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:1187941 original size:19 final size:20
Alignment explanation
Indices: 1187881--1187991 Score: 120
Period size: 19 Copynumber: 5.7 Consensus size: 20
1187871 ACTAAAACCT
* *
1187881 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
1187900 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
1187920 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
1187939 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
* *
1187958 ATTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CGA
*
1187979 GTTGTGAATTTGA
1 GTTGCGAATTTGA
1187992 CTTTTGTGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 45 0.58
20 22 0.28
21 11 0.14
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:1187968 original size:38 final size:40
Alignment explanation
Indices: 1187882--1187975 Score: 122
Period size: 39 Copynumber: 2.4 Consensus size: 40
1187872 CTAAAACCTG
* * *
1187882 TTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATCTAG
1 TTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCTAA
* *
1187921 TTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTC-AA
1 TTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCTAA
1187959 TTGCGAATTTGAAATTC
1 TTGCGAATTTGAAATTC
1187976 CGCGTTGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 18 0.37
39 25 0.51
40 6 0.12
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (40 bp):
TTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCTAA
Found at i:1188009 original size:20 final size:20
Alignment explanation
Indices: 1187976--1188053 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1187966 TTTGAAATTC
* * *
1187976 CGCGTTGTGAATTTGACTTT
1 CGCGTTGCGGATTTGACTAT
* *
1187996 TGTGTTGCGGATTTGACTAT
1 CGCGTTGCGGATTTGACTAT
1188016 CGCGTTGCGGATTTGACTAT
1 CGCGTTGCGGATTTGACTAT
*
1188036 CGCGTTGCGAATTTGACT
1 CGCGTTGCGGATTTGACT
1188054 TCTGTGTTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGGATTTGACTAT
Found at i:1188062 original size:20 final size:19
Alignment explanation
Indices: 1187920--1188065 Score: 98
Period size: 20 Copynumber: 7.4 Consensus size: 19
1187910 CGAAAATCTA
* *
1187920 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
* *
1187939 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
* *
1187958 ATTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTG-ACTT-CGC
* * *
1187979 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGAC-TTCGC
*
1187999 GTTGCGGATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
1188019 GTTGCGGATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
1188039 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
1188059 GTTGCGA
1 GTTGCGA
1188066 TTTACAAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
19 38 0.35
20 59 0.54
21 12 0.11
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:1188063 original size:40 final size:40
Alignment explanation
Indices: 1187999--1188172 Score: 142
Period size: 40 Copynumber: 4.3 Consensus size: 40
1187989 TGACTTTTGT
* *
1187999 GTTGCGGATTTGACTATCGCGTTGCGGATTTGAC-TA-TCGC
1 GTTGCGAATTTGACTATCGCGTTGC-GATTT-ACAAATTCGC
*
1188039 GTTGCGAATTTGACT-TCTGTGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGACTATC-GCGTTGCGATTTACAAATTCGC
** *
1188079 GTTGCG-ATTT-ACATATTCATGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGATTTACAAATTCGC
** ** * *
1188119 GTTGCGAATTTGGAAAATCGCAATGCGATTTACATATTCGT
1 GTTGCGAATTT-GACTATCGCGTTGCGATTTACAAATTCGC
*
1188160 GTTGCGAAATTGA
1 GTTGCGAATTTGA
1188173 AAACTGGGTT
Statistics
Matches: 111, Mismatches: 14, Indels: 18
0.78 0.10 0.13
Matches are distributed among these distances:
38 4 0.04
39 13 0.12
40 58 0.52
41 34 0.31
42 1 0.01
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGATTTACAAATTCGC
Found at i:1188082 original size:20 final size:20
Alignment explanation
Indices: 1188059--1188166 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
1188049 TGACTTCTGT
1188059 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* **
1188079 GTTGCGATTTACATATTCAT
1 GTTGCGATTTACAAATTCGC
*
1188099 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
** *
1188119 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** * *
1188140 AATGCGATTTACATATTCGT
1 GTTGCGATTTACAAATTCGC
1188160 GTTGCGA
1 GTTGCGA
1188167 AATTGAAAAC
Statistics
Matches: 68, Mismatches: 19, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
20 54 0.79
21 14 0.21
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1188103 original size:60 final size:59
Alignment explanation
Indices: 1187979--1188172 Score: 159
Period size: 60 Copynumber: 3.2 Consensus size: 59
1187969 GAAATTCCGC
* * * *
1187979 GTTGTGAATTTGACTTTTGTGTTGCGGATTTGAC-TATCGCGTTGCGGATTTGAC-TA-TCGC
1 GTTGCGAATTTGACTTCTGTGTTGC-GATTT-ACAAATCGCGTTGC-GATTT-ACATATTCGT
*
1188039 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATATTCAT
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAA-TCGCGTTGCGATTTACATATTCGT
* **
1188099 GTTGCG-ATTT-ACAGATTC-GCGTTGCGAATTTGGA-AAATCGCAATGCGATTTACATATTCGT
1 GTTGCGAATTTGAC---TTCTGTGTTGCG-ATTT--ACAAATCGCGTTGCGATTTACATATTCGT
*
1188160 GTTGCGAAATTGA
1 GTTGCGAATTTGA
1188173 AAACTGGGTT
Statistics
Matches: 112, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
58 6 0.05
59 17 0.15
60 47 0.42
61 34 0.30
62 6 0.05
63 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (59 bp):
GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATCGCGTTGCGATTTACATATTCGT
Found at i:1192745 original size:4 final size:4
Alignment explanation
Indices: 1192736--1192763 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1192726 GCATTATCTT
1192736 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1192764 TTATTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:1195697 original size:19 final size:19
Alignment explanation
Indices: 1195663--1195703 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1195653 GTAGAGGTAT
1195663 TATTTGGATAAATTATT-G
1 TATTTGGATAAATTATTAG
1195681 TATTCTGGA-AAATTTATTAG
1 TATT-TGGATAAA-TTATTAG
1195701 TAT
1 TAT
1195704 GCTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (19 bp):
TATTTGGATAAATTATTAG
Found at i:1197217 original size:14 final size:15
Alignment explanation
Indices: 1197198--1197226 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1197188 TAGAACTACT
1197198 TTAGTTTA-TTTTAC
1 TTAGTTTAGTTTTAC
1197212 TTAGTTTAGTTTTAC
1 TTAGTTTAGTTTTAC
1197227 AGTATTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (15 bp):
TTAGTTTAGTTTTAC
Found at i:1197412 original size:15 final size:16
Alignment explanation
Indices: 1197385--1197414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1197375 AATTTTTAAA
1197385 TTTAAAATAGAAACAT
1 TTTAAAATAGAAACAT
1197401 TTTAAAAT-GAAACA
1 TTTAAAATAGAAACA
1197415 AAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (16 bp):
TTTAAAATAGAAACAT
Found at i:1197914 original size:21 final size:21
Alignment explanation
Indices: 1197880--1197923 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1197870 CCTGTCGCAA
* *
1197880 CACCTCCCCTTCCT-CTACCTC
1 CACCTCCACATCCTGCT-CCTC
1197901 CACCTCCACATCCTGCTCCTC
1 CACCTCCACATCCTGCTCCTC
1197922 CA
1 CA
1197924 GTTCTGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.14, C:0.59, G:0.02, T:0.25
Consensus pattern (21 bp):
CACCTCCACATCCTGCTCCTC
Found at i:1204737 original size:12 final size:14
Alignment explanation
Indices: 1204719--1204759 Score: 59
Period size: 12 Copynumber: 3.0 Consensus size: 14
1204709 TAGAACTACT
1204719 TTAGTTTATTTT-C
1 TTAGTTTATTTTAC
1204732 -TAGTTTATTTTAC
1 TTAGTTTATTTTAC
1204745 TTAGTTTAGTTTTAC
1 TTAGTTTA-TTTTAC
1204760 CATTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
14 7 0.28
15 6 0.24
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (14 bp):
TTAGTTTATTTTAC
Found at i:1205352 original size:3 final size:3
Alignment explanation
Indices: 1205344--1205385 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1205334 TTGTAACTTG
1205344 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1205386 AGTAAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1206605 original size:20 final size:21
Alignment explanation
Indices: 1206580--1206619 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1206570 TTTACCTGAA
*
1206580 TTCAT-CTAGTATCGGTACTG
1 TTCATCCTAGTATCGATACTG
1206600 TTCATCCTAGTATCGATACT
1 TTCATCCTAGTATCGATACT
1206620 CGACCCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCATCCTAGTATCGATACTG
Found at i:1210538 original size:53 final size:54
Alignment explanation
Indices: 1210479--1210586 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
1210469 TTAAACAACC
*
1210479 ACCAA-TTTTTTAACGAAAAATGACAAGTCTAGAACATAATAAATAGTTTGATG
1 ACCAATTTTTTTAACGAAAAATGACAAGTCTAGAACATAATAAATAGTTAGATG
**
1210532 ACCAATTTTTTTAACGAAAAATGATGAGTCTAGAACATAATAAATAGTTAGATG
1 ACCAATTTTTTTAACGAAAAATGACAAGTCTAGAACATAATAAATAGTTAGATG
1210586 A
1 A
1210587 TCATTTTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 5 0.10
54 46 0.90
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (54 bp):
ACCAATTTTTTTAACGAAAAATGACAAGTCTAGAACATAATAAATAGTTAGATG
Found at i:1211502 original size:31 final size:31
Alignment explanation
Indices: 1211450--1211549 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 31
1211440 TGAAAATTAT
1211450 AATATTT--TAACAGTTTTGGTTG-AACCGAA
1 AATATTTCATAACA-TTTTGGTTGCAACCGAA
* *
1211479 AATGTTTCATAACATTTTCGGTTGCCAACTGAA
1 AATATTTCATAACATTTT-GGTTG-CAACCGAA
* * *
1211512 AATATTTCATAATATTTTTAGTTGCCAACTGAA
1 AATATTTCATAACA-TTTTGGTTG-CAACCGAA
1211545 AATAT
1 AATAT
1211550 CTAAATAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
29 6 0.10
30 4 0.07
31 10 0.17
33 36 0.60
34 4 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (31 bp):
AATATTTCATAACATTTTGGTTGCAACCGAA
Found at i:1211520 original size:33 final size:33
Alignment explanation
Indices: 1211476--1211549 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
1211466 TGGTTGAACC
* *
1211476 GAAAATGTTTCATAACATTTTCGGTTGCCAACT
1 GAAAATATTTCATAACATTTTCAGTTGCCAACT
* *
1211509 GAAAATATTTCATAATATTTTTAGTTGCCAACT
1 GAAAATATTTCATAACATTTTCAGTTGCCAACT
1211542 GAAAATAT
1 GAAAATAT
1211550 CTAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
GAAAATATTTCATAACATTTTCAGTTGCCAACT
Found at i:1214905 original size:2 final size:2
Alignment explanation
Indices: 1214893--1214932 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1214883 AGCAACTTTA
1214893 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1214933 CACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1217736 original size:23 final size:23
Alignment explanation
Indices: 1217706--1217768 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1217696 AATGATTCAG
1217706 TGCTGACTGATTCAACAAAACAA
1 TGCTGACTGATTCAACAAAACAA
* *
1217729 TGCTGACTGATTCAGCAAAATAA
1 TGCTGACTGATTCAACAAAACAA
*
1217752 TGCTAAAC-GATTCAACA
1 TGCT-GACTGATTCAACA
1217769 CAGAAGTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (23 bp):
TGCTGACTGATTCAACAAAACAA
Found at i:1217883 original size:15 final size:16
Alignment explanation
Indices: 1217845--1217885 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1217835 ACAGAGCCTC
*
1217845 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
1217861 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
1217877 T-AATCATTC
1 TGAATCATTC
1217886 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:1219347 original size:20 final size:21
Alignment explanation
Indices: 1219309--1219349 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1219299 TTCCACATTT
*
1219309 CATTTCATAATCAATACTTTCA
1 CATTTCATAATC-ACACTTTCA
1219331 CATTTCATAATC-CACTTTC
1 CATTTCATAATCACACTTTC
1219350 TGATTCAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (21 bp):
CATTTCATAATCACACTTTCA
Found at i:1221305 original size:18 final size:17
Alignment explanation
Indices: 1221265--1221313 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1221255 TGATTAAAAA
1221265 TAAAATTTT-TAATTAT
1 TAAAATTTTATAATTAT
* *
1221281 AAAAATTTTATTATCTAT
1 TAAAATTTTATAAT-TAT
1221299 TAAAATTTTA-AATTA
1 TAAAATTTTATAATTA
1221314 GATGCTTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 10 0.37
17 5 0.19
18 12 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAATTTTATAATTAT
Found at i:1222584 original size:12 final size:12
Alignment explanation
Indices: 1222567--1222618 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
1222557 CTTCAAAGAG
1222567 ATTTTATATTTA
1 ATTTTATATTTA
1222579 ATTTTATA-TTA
1 ATTTTATATTTA
*
1222590 TATTTGAT-TTTA
1 -ATTTTATATTTA
1222602 ATTTTA-ATATTA
1 ATTTTATAT-TTA
1222614 ATTTT
1 ATTTT
1222619 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
ATTTTATATTTA
Found at i:1222675 original size:64 final size:65
Alignment explanation
Indices: 1222580--1222736 Score: 270
Period size: 64 Copynumber: 2.5 Consensus size: 65
1222570 TTATATTTAA
1222580 TTTT-ATATTATATT-T-GAT-TTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
*
1222641 TTTTAATATTCTATTATAGATA-TTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1222705 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATATTTAATTTTA
1222737 TACCATATAA
Statistics
Matches: 89, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
61 4 0.04
62 9 0.10
63 1 0.01
64 66 0.74
65 9 0.10
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (65 bp):
TTTTAATATTATATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
Found at i:1223865 original size:16 final size:17
Alignment explanation
Indices: 1223834--1223872 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1223824 AAAAAAATCG
* *
1223834 ATATATTTTTATTATAT
1 ATATAATTTTAATATAT
1223851 A-ATAATTTTAATATAT
1 ATATAATTTTAATATAT
1223867 ATATAA
1 ATATAA
1223873 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATAATTTTAATATAT
Found at i:1224072 original size:21 final size:20
Alignment explanation
Indices: 1223986--1224143 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1223976 AAATGACCAA
**
1223986 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1224005 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1224025 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1224045 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1224066 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1224087 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1224107 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1224128 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1224144 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1224172 original size:20 final size:20
Alignment explanation
Indices: 1224111--1224339 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
1224101 GATTTTCAAG
* ** *
1224111 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1224131 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1224151 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1224171 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224191 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224211 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224231 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1224251 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * * *
1224271 AATCGAAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1224291 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1224311 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1224331 AATCACAAC
1 AATCGCAAC
1224340 ACTGAAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 169 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1225078 original size:24 final size:24
Alignment explanation
Indices: 1225039--1225085 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1225029 AAATTTGGTC
1225039 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1225063 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1225086 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1225277 original size:12 final size:12
Alignment explanation
Indices: 1225260--1225284 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1225250 ATATAATCCT
1225260 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1225272 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1225284 G
1 G
1225285 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1227655 original size:72 final size:72
Alignment explanation
Indices: 1227562--1227795 Score: 288
Period size: 72 Copynumber: 3.3 Consensus size: 72
1227552 GCAACGAGAG
*
1227562 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCACAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1227627 AAATGAA
66 AAATGAA
* *
1227634 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCACAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
1227698 GAAATGAA
65 GAAATGAA
* * * * *
1227706 AATCGCAACGAGAGAATCG-CAATGAGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCACAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
1227766 CG--A-GAG
64 CGAAATGAA
1227772 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
1227796 GCAATGCGAA
Statistics
Matches: 142, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 17 0.12
72 92 0.65
73 9 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCACAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:1227676 original size:105 final size:102
Alignment explanation
Indices: 1227548--1227817 Score: 375
Period size: 105 Copynumber: 2.6 Consensus size: 102
1227538 CGGAAATTAC
1227548 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAATGAAAATCGCAA--C-G--
*
1227610 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
61 A-GAAAATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
*
1227653 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC--AATGAAAATCGCAACGAG
*
1227718 AGAATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
63 AAAATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
*
1227758 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC--AATGAAAATCGCA
1227818 TTGCGATTCT
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 124 0.79
106 16 0.10
108 2 0.01
109 1 0.01
111 13 0.08
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (102 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAATGAAAATCGCAACGAGAAA
ATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1227683 original size:53 final size:52
Alignment explanation
Indices: 1227548--1227817 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
1227538 CGGAAATTAC
*
1227548 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1227595 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1227653 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
1227706 AATCGCAACGAGAGAATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1227758 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1227811 AATCGCA
1 AATCGCA
1227818 TTGCGATTCT
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 65 0.32
53 114 0.56
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1227796 original size:72 final size:72
Alignment explanation
Indices: 1227529--1227822 Score: 274
Period size: 72 Copynumber: 4.2 Consensus size: 72
1227519 GCATTTGACT
** * * *
1227529 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATC-C---CA-A
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGAGA
*
1227589 CATGAAA
66 AATGAAA
*
1227596 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
1227661 CGAG--A-G--A
61 TGAGAAATGAAA
* * * * *
1227668 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATG
1227730 AGAAATGAAA
63 AGAAATGAAA
*
1227740 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGAG
1227804 AAATGAAA
65 AAATGAAA
*
1227812 ATCGCATTGCG
1 ATCGCAATGCG
1227823 ATTCTCTCGT
Statistics
Matches: 185, Mismatches: 19, Indels: 40
0.76 0.08 0.16
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 36 0.19
69 3 0.02
70 2 0.01
71 20 0.11
72 98 0.53
73 4 0.02
74 6 0.03
75 1 0.01
76 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGAGA
AATGAAA
Found at i:1227857 original size:53 final size:52
Alignment explanation
Indices: 1227794--1227909 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
1227784 GAAATGAAAA
* *
1227794 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTACGATTTTCATT
** ** **
1227846 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTACGATTTTCATT
1227899 TCGCATTGCGA
1 TCGCATTGCGA
1227910 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTACGATTTTCATT
Found at i:1227926 original size:52 final size:53
Alignment explanation
Indices: 1227813--1227929 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1227803 GAAATGAAAA
*
1227813 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTACGATTTTCATTTCCGCATTGCGATTTTCATT
1227866 TCGCATTGCGATTCTCTCGTTACGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTACGATTTTCATTTCCGCATTGCGATTTTCATT
1227918 TCGCATTGCGAT
1 TCGCATTGCGAT
1227930 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTACGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1227937 original size:19 final size:19
Alignment explanation
Indices: 1227832--1227929 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1227822 GATTCTCTCG
1227832 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1227852 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1227871 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1227885 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1227904 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1227923 TTGCGAT
1 TTGCGAT
1227930 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 35 0.51
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1228055 original size:14 final size:14
Alignment explanation
Indices: 1228036--1228072 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1228026 CATCAATTAC
1228036 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1228050 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1228064 ACAAATCAA
1 ACAAATCAA
1228073 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1230040 original size:19 final size:18
Alignment explanation
Indices: 1229998--1230156 Score: 146
Period size: 19 Copynumber: 8.6 Consensus size: 18
1229988 TAGTTTATTT
*
1229998 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA--TAAAA
1230018 TCGCAACGCGAAATAAGAA
1 TCGCAACGCGAAATAA-AA
* *
1230037 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAA-TAAAA
*
1230056 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-TAAAA
1230075 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAAT-AAAA
* *
1230094 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAATAAAA
*
1230108 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAT-AAAA
1230127 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAAT-AAAA
*
1230146 TCGCAATGCGA
1 TCGCAACGCGA
1230157 TTTGGTTTCG
Statistics
Matches: 120, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 2 0.02
17 2 0.02
18 4 0.03
19 88 0.73
20 14 0.12
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (18 bp):
TCGCAACGCGAAATAAAA
Found at i:1230063 original size:38 final size:37
Alignment explanation
Indices: 1229998--1230156 Score: 164
Period size: 38 Copynumber: 4.3 Consensus size: 37
1229988 TAGTTTATTT
* *
1229998 TCGCAACACGAAACTTAAAATCGCAACGCGAAATAAGAA
1 TCGCAACGCGAAA-TGAAAATCGCAACGCGAAATAA-AA
* ** *
1230037 TCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGCGAAA-TAAAA
* *
1230075 TCGCAACGCGAAATGAAAATCGCAA--CG--ACAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGCGAAATAAAA
*
1230108 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGCGAAAT-AAAA
*
1230146 TCGCAATGCGA
1 TCGCAACGCGA
1230157 TTTGGTTTCG
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
33 28 0.27
34 1 0.01
35 2 0.02
36 2 0.02
37 1 0.01
38 55 0.54
39 13 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (37 bp):
TCGCAACGCGAAATGAAAATCGCAACGCGAAATAAAA
Found at i:1230132 original size:52 final size:55
Alignment explanation
Indices: 1229998--1230151 Score: 190
Period size: 52 Copynumber: 2.8 Consensus size: 55
1229988 TAGTTTATTT
* *
1229998 TCGCAACACGAAACTTAAAATCGCAACGCGAAAT-AAGAATCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAA-AATCGCAAC-AG-AACCAAAA
*
1230056 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
* **
1230108 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA
1230152 TGCGATTTGG
Statistics
Matches: 89, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
52 45 0.51
53 1 0.01
55 1 0.01
57 27 0.30
58 15 0.17
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.10
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
Found at i:1230197 original size:33 final size:33
Alignment explanation
Indices: 1230152--1230274 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1230142 AAAATCGCAA
*
1230152 TGCGA-TTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1230184 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1230217 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1230250 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1230275 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 5 0.06
33 65 0.79
34 12 0.15
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1230205 original size:19 final size:18
Alignment explanation
Indices: 1230152--1230242 Score: 81
Period size: 14 Copynumber: 5.4 Consensus size: 18
1230142 AAAATCGCAA
*
1230152 TGCGATTTGGTTTCGCGT
1 TGCGATTTTGTTTCGCGT
1230170 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1230184 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1230203 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1230217 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1230236 TGCGATT
1 TGCGATT
1230243 CTCTCGTTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
14 23 0.39
15 1 0.02
16 2 0.03
17 2 0.03
18 10 0.17
19 21 0.36
ACGTcount: A:0.08, C:0.18, G:0.29, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1230252 original size:14 final size:14
Alignment explanation
Indices: 1230200--1230256 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1230190 TTTGGTTTCG
*
1230200 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1230214 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1230233 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1230247 CGTTGCGATT
1 CGTTGCGATT
1230257 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1230669 original size:90 final size:92
Alignment explanation
Indices: 1230371--1230681 Score: 567
Period size: 91 Copynumber: 3.4 Consensus size: 92
1230361 TCAGGGTATT
1230371 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230436 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTT-ACAGTGTTAAAGAATACAC
1230464 AGTTTAGC--AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230527 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTT-ACAGTGTTAAAGAATACAC
1230555 AGTTTAGCAGAATTGGCAGCAACCGAACAAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1230619 TACTATTT-CAGTGTTAAAGAATACAC
66 TACTATTTACAGTGTTAAAGAATACAC
*
1230645 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1230682 AAGCAATCTA
Statistics
Matches: 214, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
90 48 0.22
91 96 0.45
92 41 0.19
93 29 0.14
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (92 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTACAGTGTTAAAGAATACAC
Found at i:1232379 original size:20 final size:20
Alignment explanation
Indices: 1232348--1232411 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1232338 CTTTGGTTGA
1232348 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1232368 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1232388 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1232409 AAT
1 AAT
1232412 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Done.