Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008726.1 Hibiscus syriacus cultivar Beakdansim tig00111792_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: 1298898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1086521 original size:19 final size:20
Alignment explanation
Indices: 1086452--1086526 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1086442 GTTTTTTAGC
* * * *
1086452 ATCATTACTGTTCACACAAT
1 ATCAATACTATTCATACAGT
* *
1086472 ATCGATACTATTTATACAGT
1 ATCAATACTATTCATACAGT
* *
1086492 ATCAGTACTATTCATATAGT
1 ATCAATACTATTCATACAGT
1086512 A-CAATACTATTCATA
1 ATCAATACTATTCATA
1086527 AAATATTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
ATCAATACTATTCATACAGT
Found at i:1088530 original size:21 final size:21
Alignment explanation
Indices: 1088506--1088575 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
1088496 ACCACAGCTA
1088506 ACATAATTG-CACCGAAGTG-CC
1 ACATAATTGTC-CCGAAG-GACC
*
1088527 ACATATTTGTCCCGAAGGACC
1 ACATAATTGTCCCGAAGGACC
* *
1088548 ACATAGTTTTGTCCCGAAGAACC
1 ACATA--ATTGTCCCGAAGGACC
1088571 ACATA
1 ACATA
1088576 GAACCCTCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 21 0.49
22 1 0.02
23 20 0.47
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (21 bp):
ACATAATTGTCCCGAAGGACC
Found at i:1088562 original size:23 final size:22
Alignment explanation
Indices: 1088517--1088576 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
1088507 CATAATTGCA
1088517 CCGAAGTG-CCACATA-TTTGTC
1 CCGAAG-GACCACATAGTTTGTC
1088538 CCGAAGGACCACATAGTTTTGTC
1 CCGAAGGACCACATAG-TTTGTC
*
1088561 CCGAAGAACCACATAG
1 CCGAAGGACCACATAG
1088577 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 13 0.37
23 21 0.60
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (22 bp):
CCGAAGGACCACATAGTTTGTC
Found at i:1092580 original size:12 final size:11
Alignment explanation
Indices: 1092556--1092594 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1092546 ATCCATGAGG
1092556 AAAGAAAAAAA
1 AAAGAAAAAAA
*
1092567 AAAGAAACAAA
1 AAAGAAAAAAA
* *
1092578 AAAGGAAAAAC
1 AAAGAAAAAAA
1092589 AAAGAA
1 AAAGAA
1092595 GTCACAAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1109779 original size:2 final size:2
Alignment explanation
Indices: 1109772--1109807 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1109762 CATTTAACAA
1109772 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
1109808 TAGTGCGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1112269 original size:200 final size:199
Alignment explanation
Indices: 1111840--1112571 Score: 784
Period size: 200 Copynumber: 3.6 Consensus size: 199
1111830 TAGGTAGCTC
* ** * * * *
1111840 TTATATTGACCTATTTTCGAAGT-AAACCGATATATTTATACTGGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTCA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * * **
1111904 TTACATTATTATTATCGGTTACGATGTTTTTTA-GATTGATACAATTT-TAAATGTATCGACACT
65 TTACATTATAATTATCGGTTTCGATG-TTTTTAGGATCGATACTTTTTATAAATGTATCGACACT
** * * * *
1111967 TTATGCTTGCACCT-GATTGGGCATTTATATTTCATTCTGGAAAAAAGTATCGACACAAACTAAC
129 TTATGAGTGCACCTCGTTTGTGC------A-TTCATTCTGGACAAAAGTATCGACACAAATTAAC
1112031 AACGTGTCGATACA
187 AA-GTGTCGATACA
* * *
1112045 TTAT-TTAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTGAAAATTTACCTA
1 TTATGTT-GACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* **
1112109 TTACATTATACA-TATGGGTTTCGATGTTTCCAGGATCGATACTTTTTATAAATGTATCGACACT
65 TTACATTATA-ATTATCGGTTTCGATGTTTTTAGGATCGATACTTTTTATAAATGTATCGACACT
* * * *
1112173 TTATG-GTCTCACC-C-TTTTTGGTATTCATTCTGGACCAAAAGTATCGACACAAATTTATCAAG
129 TTATGAGT-GCACCTCGTTTGT-GCATTCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAG
*
1112235 TGTCGATACT
190 TGTCGATACA
* * * *
1112245 TTATGCTGACCTATTTTATCATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTAA
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* * * *
1112310 TACATTATAATTAACGGTTTCGATGTTTTTGGGATTGATACTTTTAATAAATGTATCGACACTTT
66 TACATTATAATTATCGGTTTCGATGTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTT
*
1112375 ATGAGTGCACCTCGTTTGTGCATTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTGTC
131 ATGAGTGCACCTCGTTTGTGCATTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTGTC
1112440 GATACA
194 GATACA
* * * * *
1112446 TTATGTTGACCTGTTTTCTAAT-TAACCGATATATTTATACCGGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* * * * *
1112510 TACATTATAATTATTGGTTTTGATGTTTTTTGGGTCGATAC-TTGTATAAAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATGTTTTTAGGATCGATACTTTTTAT-AAATGTATCGACAC
1112572 ATATTTAGGT
Statistics
Matches: 446, Mismatches: 63, Indels: 41
0.81 0.11 0.07
Matches are distributed among these distances:
199 16 0.04
200 239 0.54
201 67 0.15
202 4 0.01
204 7 0.02
205 86 0.19
206 27 0.06
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTT
ATGAGTGCACCTCGTTTGTGCATTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGA
TACA
Found at i:1114910 original size:199 final size:198
Alignment explanation
Indices: 1114521--1114879 Score: 551
Period size: 199 Copynumber: 1.8 Consensus size: 198
1114511 GTTTTCAACA
* * * * *
1114521 AAGTGTCGATACAGGTTGTATACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACAGATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTA
* * * *
1114586 TAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTTTGAAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAAT
*
1114651 GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACAAAAATTATCGACACAATA
131 GTATCGACACTTTATGCGTGCACCCTTTTTGGCATCCATTATGG--AAAAATTATCGACACAATA
1114716 TTAAT
194 TTAAT
* *
1114721 AAGTGTCGATACATATTATAGACCTATTCTCTCATAAAA-CGGTATATGTATACCGGTTATATTA
1 AAGTGTCGATACAGATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTA
1114785 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAC-TTTTAATAAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTTAA-AAA
*
1114849 TGTATCGACACTTTATGTGTGCAACCCTTTT
130 TGTATCGACACTTTATGCGTGC-ACCCTTTT
1114880 GGATCGACAC
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
198 5 0.03
199 96 0.67
200 43 0.30
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (198 bp):
AAGTGTCGATACAGATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTA
CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTTAAAAAT
GTATCGACACTTTATGCGTGCACCCTTTTTGGCATCCATTATGGAAAAATTATCGACACAATATT
AAT
Found at i:1115016 original size:250 final size:251
Alignment explanation
Indices: 1114625--1115115 Score: 713
Period size: 250 Copynumber: 2.0 Consensus size: 251
1114615 GTTTCGATGT
* * *
1114625 TTTTGGGATCGATACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
* * * *
1114690 TATGGACAAAAATTATCGACACAATATTAATAAGTGTCGATACATATTATAGACCTATTCTCTCA
66 TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTCA
* *
1114755 TAAAACGGTATATGTATACCGGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTC
131 TAAAACGGTATATGTATACCGATTATATTGA-AAAATTACCCATTACATTATAATTATGGGTTTC
*
1114819 GATG-TTTTTGGGATCGACACTTTTAATAAATGTATCGACACTTTATGTGTGCAACCC
195 GATGTTTTTTGGG-TCGACACTTTTAATAAATGGATCGACACTTTATGTGTGCAACCC
*
1114876 TTTT-GGATCGACACTCTATGAAAATGTATCGACACTTTGTAG-GTTCACCCTTTTTGGCATCCA
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTAT-GCGTTCACCCTTTTTGGCATCCA
* * * *
1114939 TTCTGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-TTTC
65 TTATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTC
* **
1115003 ATAAAACCGGTATATTTATATTGATTATATTGAAAAATTACCCATTACATTATAATTATGGGTTT
130 ATAAAA-CGGTATATGTATACCGATTATATTGAAAAATTACCCATTACATTATAATTATGGGTTT
** * *
1115068 CGATGTTTTTTGGGTCGTTACTTTTTATATATGGATCGACACTTTATG
194 CGATGTTTTTTGGGTCGACACTTTTAATAAATGGATCGACACTTTATG
1115116 GGAAACTTTA
Statistics
Matches: 214, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
249 9 0.04
250 191 0.89
251 14 0.07
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (251 bp):
TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCAT
TATGGACAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTCA
TAAAACGGTATATGTATACCGATTATATTGAAAAATTACCCATTACATTATAATTATGGGTTTCG
ATGTTTTTTGGGTCGACACTTTTAATAAATGGATCGACACTTTATGTGTGCAACCC
Found at i:1116410 original size:6 final size:6
Alignment explanation
Indices: 1116401--1116440 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
1116391 GTCGTCGTCG
*
1116401 TCATCT TCATCG TCATCT TCATCGT T-ATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATC-T TCATCT TCATCT TCAT
1116441 TGACCGCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.17, C:0.30, G:0.05, T:0.47
Consensus pattern (6 bp):
TCATCT
Found at i:1116413 original size:12 final size:12
Alignment explanation
Indices: 1116377--1116440 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
1116367 GTTTGGATCA
*
1116377 TCATCATCATCG
1 TCATCTTCATCG
* * *
1116389 TCGTCGTCGTCG
1 TCATCTTCATCG
1116401 TCATCTTCATCG
1 TCATCTTCATCG
1116413 TCATCTTCATCG
1 TCATCTTCATCG
* *
1116425 TTATCTTCATCT
1 TCATCTTCATCG
1116437 TCAT
1 TCAT
1116441 TGACCGCTTG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.16, C:0.31, G:0.11, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1118261 original size:198 final size:201
Alignment explanation
Indices: 1117920--1118432 Score: 854
Period size: 198 Copynumber: 2.6 Consensus size: 201
1117910 TATTTAAATT
* * *
1117920 AGTATCGACACAATATTAAAAACGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
1 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTAGT
**
1117985 ATATTTATACTTGTTACATTGAAAATTTA-CTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
*
1118049 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTAACCCTTTTTGGCATCCATTCTGG
1118114 A-CAAA
196 ACCAAA
* * *
1118119 AGTATCGACACAAAATTAAAAACGTATCGATACATGTTGTAGACCTA-T-TCTCATAAAATTGGT
1 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTAGT
* *
1118182 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* *
1118247 GGATCTACACTTTTTGAAAATGTATCGACACTTTATGCGTTAACCCTTTTTGGCGTCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTAACCCTTTTTGGCATCCATTCTGG
1118312 ACCAAA
196 ACCAAA
**
1118318 AGTATCGACACAAAATTAAAAAATTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTAGT
1 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTAGT
*
1118383 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGG
1118433 ATGCATATGT
Statistics
Matches: 290, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
197 38 0.13
198 98 0.34
199 92 0.32
200 1 0.00
201 61 0.21
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTAGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTAACCCTTTTTGGCATCCATTCTGG
ACCAAA
Found at i:1122958 original size:19 final size:19
Alignment explanation
Indices: 1122934--1122985 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1122924 GAATGCCATC
1122934 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1122953 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1122972 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1122986 CCCCCTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:1123441 original size:31 final size:30
Alignment explanation
Indices: 1123392--1123451 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1123382 TTATATAAGC
*
1123392 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
1123423 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
1123452 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:1129897 original size:64 final size:63
Alignment explanation
Indices: 1129822--1129941 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
1129812 ATTGTTCAAG
* * * **
1129822 GTGTATCGATGCACATGAAGTGCATCGATTCACTCTTTTAAATTACAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAA-TACAAACATCGAATGCCATCA
* * *
1129886 GTGTATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAATATAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATACAAACATCGAAT
1129942 AGGATTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 13 0.27
64 35 0.73
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATGCCATCA
Found at i:1130276 original size:25 final size:25
Alignment explanation
Indices: 1130221--1130282 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
1130211 ATAAGTCTAG
*
1130221 ATTCAATATTTTGATACATGATCGCA
1 ATTC-ATATTATGATACATGATCGCA
* *
1130247 TTTCATATTATGATACATGA-CGTGA
1 ATTCATATTATGATACATGATCG-CA
1130272 ATTCATATTAT
1 ATTCATATTAT
1130283 ATGCATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCGCA
Found at i:1130374 original size:31 final size:30
Alignment explanation
Indices: 1130325--1130384 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1130315 TTATATAAGC
*
1130325 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
1130356 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
1130385 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:1130660 original size:23 final size:23
Alignment explanation
Indices: 1130607--1130667 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1130597 CAAGCTTATA
** *
1130607 TGGCACTACGGTGCAATTCTATG
1 TGGCACTTTGGTGCAATTCTACG
*
1130630 AGGCACTTTGGTGCAATTCTACG
1 TGGCACTTTGGTGCAATTCTACG
1130653 TGGCACTTTGGTGCA
1 TGGCACTTTGGTGCA
1130668 TTTATACAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTTGGTGCAATTCTACG
Found at i:1130885 original size:13 final size:13
Alignment explanation
Indices: 1130851--1130878 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1130841 ATTTCGTCTC
1130851 ATTCCATTTAATT
1 ATTCCATTTAATT
1130864 ATTCCATTTAATT
1 ATTCCATTTAATT
1130877 AT
1 AT
1130879 GTCATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTCCATTTAATT
Found at i:1132122 original size:20 final size:19
Alignment explanation
Indices: 1132068--1132113 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
1132058 CCGGTAGCGC
1132068 TTTACCGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
1132087 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCAT-TT
1132108 TTTACC
1 TTTACC
1132114 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:1133037 original size:20 final size:20
Alignment explanation
Indices: 1133012--1133056 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1133002 TTCCAATTTT
*
1133012 GCAACGCGAATCTGTAAATC
1 GCAACGCAAATCTGTAAATC
*
1133032 GCAACGCAAATTTGTAAATC
1 GCAACGCAAATCTGTAAATC
1133052 GCAAC
1 GCAAC
1133057 ACAGAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
GCAACGCAAATCTGTAAATC
Found at i:1133073 original size:20 final size:20
Alignment explanation
Indices: 1133050--1133116 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1133040 AATTTGTAAA
1133050 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
1133070 TCGCAAC-GTGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
1133090 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1133110 TCGCAAC
1 TCGCAAC
1133117 GCGAAATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 37 0.93
21 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1133074 original size:40 final size:42
Alignment explanation
Indices: 1133030--1133177 Score: 129
Period size: 40 Copynumber: 3.7 Consensus size: 42
1133020 AATCTGTAAA
*
1133030 TCGCAACGCAAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCAAATTTGTCAAATTCGCAACACAAAAGTCAAAT
** *
1133070 TCGCAACG-TGA-TAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCAAATTTGTCAAATTCGCAACACAAAAGTCAAAT
** **
1133110 TCGCAACGCGAAA-TT-TCAAATTCGCAAC-TGAATTTCAAAT
1 TCGCAACGC-AAATTTGTCAAATTCGCAACACAAAAGTCAAAT
1133150 TCGCAACTG--AA-TT-TCAAATTCGCAACAC
1 TCGCAAC-GCAAATTTGTCAAATTCGCAACAC
1133178 GAATTTAGTT
Statistics
Matches: 90, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
38 20 0.22
39 4 0.04
40 50 0.56
41 14 0.16
42 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.23
Consensus pattern (42 bp):
TCGCAACGCAAATTTGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:1133145 original size:19 final size:20
Alignment explanation
Indices: 1133064--1133175 Score: 122
Period size: 19 Copynumber: 5.7 Consensus size: 20
1133054 AACACAGAAG
*
1133064 TCAAATTCGCAACGTG-ATAG
1 TCAAATTCGCAACGTGAAT-T
*** **
1133084 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACGTGAATT
*
1133104 TCAAATTCGCAACGCGAAATT
1 TCAAATTCGCAACGTG-AATT
1133125 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACGTGAATT
1133144 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACGTGAATT
1133163 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1133176 ACGAATTTAG
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
19 36 0.44
20 29 0.36
21 16 0.20
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (20 bp):
TCAAATTCGCAACGTGAATT
Found at i:1133183 original size:20 final size:20
Alignment explanation
Indices: 1133084--1133196 Score: 124
Period size: 19 Copynumber: 5.8 Consensus size: 20
1133074 AACGTGATAG
* **
1133084 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACACGAATT
*
1133104 TCAAATTCGCAACGCGAAATT
1 TCAAATTCGCAACACG-AATT
*
1133125 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
*
1133144 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
1133163 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
**
1133183 T-AGTTTCGCAACAC
1 TCAAATTCGCAACAC
1133197 AAATGTTTTG
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
19 47 0.57
20 21 0.25
21 15 0.18
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:1134097 original size:24 final size:24
Alignment explanation
Indices: 1134070--1134123 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1134060 GTATTCGAAA
1134070 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1134094 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1134118 TTTGAT
1 TTTGAT
1134124 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1134316 original size:12 final size:12
Alignment explanation
Indices: 1134298--1134330 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1134288 ATATAACCCT
1134298 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
1134310 TAAGAAGAAAAA
1 GAAGAAGAAAAA
1134322 GAAGAAGAA
1 GAAGAAGAA
1134331 GAAGTCCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1136420 original size:18 final size:18
Alignment explanation
Indices: 1136394--1136429 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1136384 AAGCAAAAGG
*
1136394 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
*
1136412 AAATTAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1136430 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1136745 original size:20 final size:20
Alignment explanation
Indices: 1136720--1136765 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1136710 TGCGATCAAT
1136720 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
1136740 GCGAAAGTCAAATTCGCAAT
1 GCGAAAGTCAAATTCGCAAC
1136760 GCGAAA
1 GCGAAA
1136766 TAAGCGTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1136938 original size:25 final size:25
Alignment explanation
Indices: 1136903--1136957 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
1136893 TCAATTAAAT
*
1136903 ATTGTTGTGGGTACATTATTTGAAC
1 ATTGTTATGGGTACATTATTTGAAC
1136928 ATTGTTATGGGTACATTATTTGAAC
1 ATTGTTATGGGTACATTATTTGAAC
1136953 ATTGT
1 ATTGT
1136958 ATGTATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (25 bp):
ATTGTTATGGGTACATTATTTGAAC
Found at i:1137245 original size:39 final size:39
Alignment explanation
Indices: 1137202--1137288 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
1137192 TCCGATGCTC
* * *
1137202 ATCAAAATCCAAGGCTCATATGGTGCCAAGTAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
1137241 ATCAAAATCAAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
1137280 ATCAAAATC
1 ATCAAAATC
1137289 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (39 bp):
ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:1139068 original size:21 final size:21
Alignment explanation
Indices: 1139027--1139116 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
1139017 GCGGGCGGGA
*
1139027 CCTCTTGAACGATGACG-GGGG
1 CCTCTTGAACGATG-GGAGGGG
*
1139048 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGGGAGGGG
* * * *
1139069 CTTCTTCG-ATGATGAGAGAGG
1 CCTCTT-GAACGATGGGAGGGG
* *
1139090 CCTCTTGAACGATAGGAGGCG
1 CCTCTTGAACGATGGGAGGGG
1139111 CCTCTT
1 CCTCTT
1139117 AAATGATGAT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 2 0.04
21 50 0.94
22 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.36, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGGGAGGGG
Found at i:1139123 original size:42 final size:42
Alignment explanation
Indices: 1139046--1139125 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1139036 CGATGACGGG
* * * * **
1139046 GGCCTCTTGAACGGTGGGAGGGGCTTCTTCGATGATGAGAGA
1 GGCCTCTTGAACGATAGGAGGCGCCTCTTAAATGATGAGAGA
1139088 GGCCTCTTGAACGATAGGAGGCGCCTCTTAAATGATGA
1 GGCCTCTTGAACGATAGGAGGCGCCTCTTAAATGATGA
1139126 TAGGTGCATC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
GGCCTCTTGAACGATAGGAGGCGCCTCTTAAATGATGAGAGA
Found at i:1141340 original size:13 final size:13
Alignment explanation
Indices: 1141322--1141352 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1141312 GGGTTTCTTC
1141322 AACAAAAAGACAA
1 AACAAAAAGACAA
1141335 AAC-AAAAGACAA
1 AACAAAAAGACAA
1141347 AACAAA
1 AACAAA
1141353 GACAAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.77, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:1141355 original size:11 final size:12
Alignment explanation
Indices: 1141326--1141358 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1141316 TTCTTCAACA
1141326 AAAAGACAAAAC
1 AAAAGACAAAAC
1141338 AAAAGACAAAAC
1 AAAAGACAAAAC
1141350 -AAAGACAAA
1 AAAAGACAAA
1141359 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:1141597 original size:22 final size:22
Alignment explanation
Indices: 1141569--1141611 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1141559 GGAGATAGAC
1141569 GGATTTCGTCGGAAATGGGGAT
1 GGATTTCGTCGGAAATGGGGAT
*
1141591 GGATTTCGTCGGAGATGGGGA
1 GGATTTCGTCGGAAATGGGGA
1141612 CGAATGTCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.44, T:0.26
Consensus pattern (22 bp):
GGATTTCGTCGGAAATGGGGAT
Found at i:1141769 original size:20 final size:20
Alignment explanation
Indices: 1141744--1141792 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1141734 GCGTAAAAAC
*
1141744 ATTTGACTTTCGCTTTGCAA
1 ATTTGACTTTCGCGTTGCAA
* *
1141764 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCAA
1141784 ATTTGACTT
1 ATTTGACTT
1141793 CTGTGTTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCAA
Found at i:1141860 original size:20 final size:20
Alignment explanation
Indices: 1141811--1141864 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1141801 TGATTTACAT
1141811 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
1141831 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
1141851 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
1141865 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:1147302 original size:16 final size:18
Alignment explanation
Indices: 1147283--1147320 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1147273 ATATTATTTT
1147283 TATTTAA-T-AAAAATAA
1 TATTTAATTAAAAAATAA
1147299 TATTTAATTGAAAAAATAA
1 TATTTAATT-AAAAAATAA
1147318 TAT
1 TAT
1147321 AAAAAGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
19 11 0.58
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TATTTAATTAAAAAATAA
Found at i:1147867 original size:23 final size:21
Alignment explanation
Indices: 1147832--1147879 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
1147822 AATAAAGATA
1147832 AGAAAGTAAAGAAGATTAAAG
1 AGAAAGTAAAGAAGATTAAAG
*
1147853 AGAACAGTAAAAGAAGATTAAGG
1 AGAA-AGT-AAAGAAGATTAAAG
1147876 AGAA
1 AGAA
1147880 GATTTAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 3 0.12
23 17 0.71
ACGTcount: A:0.60, C:0.02, G:0.25, T:0.12
Consensus pattern (21 bp):
AGAAAGTAAAGAAGATTAAAG
Found at i:1147891 original size:12 final size:11
Alignment explanation
Indices: 1147839--1147891 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
1147829 ATAAGAAAGT
1147839 AAAGAAGATTA
1 AAAGAAGATTA
* *
1147850 AAGAGAACAGTA
1 AA-AGAAGATTA
1147862 AAAGAAGATTA
1 AAAGAAGATTA
*
1147873 AGGAGAAGATTTA
1 A-AAGAAGA-TTA
1147886 AAAGAA
1 AAAGAA
1147892 AAAAAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 10 0.30
12 19 0.58
13 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (11 bp):
AAAGAAGATTA
Found at i:1149137 original size:36 final size:36
Alignment explanation
Indices: 1149077--1149289 Score: 250
Period size: 36 Copynumber: 5.9 Consensus size: 36
1149067 AGATAAACAA
* * *
1149077 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1149113 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
* * *
1149149 TTGAATCGAAAGTGCTGATACTTCATTCCTTTCA-T
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
* ** * * *
1149184 TATGAATCGAAAGTGGCGACGCTTCCTTTCATTC-TT
1 T-TGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1149220 CTTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
** * *
1149257 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTC
1149290 TTCTTATTCA
Statistics
Matches: 150, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
35 2 0.01
36 146 0.97
37 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
Found at i:1149209 original size:72 final size:72
Alignment explanation
Indices: 1149077--1149294 Score: 278
Period size: 72 Copynumber: 3.0 Consensus size: 72
1149067 AGATAAACAA
* * * *
1149077 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATACTTCCTTCC
1 TTGAATCGAAAGTGCTGATACTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
1149142 GTTCACT-
66 GTTC-CTC
* * * *
1149149 TTGAATCGAAAGTGCTGATACTTCATTCCTTTCA-TTATGAATCGAAAGTGGCGACGCTTCCTTT
1 TTGAATCGAAAGTGCTGATACTTCCTTCCGTTCACTT-TGAATCGAAAGTGCCGATGCTTCCTTT
* *
1149213 CATTCTTC
65 CGTTCCTC
* **
1149221 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACTTTGAATCGAAAGTGTTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCTGATACTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
*
1149286 GTTCTTC
66 GTTCCTC
1149293 TT
1 TT
1149295 ATTCACCTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
71 3 0.02
72 121 0.96
73 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (72 bp):
TTGAATCGAAAGTGCTGATACTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
GTTCCTC
Found at i:1150763 original size:36 final size:36
Alignment explanation
Indices: 1150708--1150915 Score: 242
Period size: 36 Copynumber: 5.8 Consensus size: 36
1150698 AACAATTGAG
** *
1150708 TCGAAAGTGCTAATGCTTCCTTCCGTTCACTTAGAA
1 TCGAAAGTGCCGATACTTCCTTCCGTTCACTTAGAA
*
1150744 TCGAAAGTGCCGATACTTCCTTCCGTTCACTTTGAA
1 TCGAAAGTGCCGATACTTCCTTCCGTTCACTTAGAA
1150780 TCGAAAGTGCCGATACTTCCTTCCGTTCAC-TATGAA
1 TCGAAAGTGCCGATACTTCCTTCCGTTCACTTA-GAA
* * * *
1150816 TCGAAAGTGGCGACGA-TTCCTTTCGTTCTTCTT-GAA
1 TCGAAAGTGCCGA-TACTTCCTTCCGTTC-ACTTAGAA
* * *
1150852 TCGAAAGTGTCGATACTTCCTTCCATTCACTTTGAA
1 TCGAAAGTGCCGATACTTCCTTCCGTTCACTTAGAA
* * *
1150888 TCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TCGAAAGTGCCGATACTTCCTTCCGTTC
1150916 TTCTTATTCA
Statistics
Matches: 147, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
35 5 0.03
36 139 0.95
37 2 0.01
38 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (36 bp):
TCGAAAGTGCCGATACTTCCTTCCGTTCACTTAGAA
Found at i:1157319 original size:20 final size:21
Alignment explanation
Indices: 1157294--1157354 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
1157284 TTTTGGTGCA
*
1157294 GAGGGAATCGA-TCCCCCTAT
1 GAGGGAACCGATTCCCCCTAT
*
1157314 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTAT
*
1157335 GAAGGGGAACCAATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1157355 CATAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTAT
Found at i:1161927 original size:36 final size:36
Alignment explanation
Indices: 1161867--1162079 Score: 275
Period size: 36 Copynumber: 5.9 Consensus size: 36
1161857 AGATGAACAA
* *
1161867 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* * *
1161903 TTGAATCGAATGTGTCGATACTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* *
1161939 TTGAATCGAAAGTGCCGATACTTTCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* * * * *
1161975 ATGAATCGAAAGTGGCGACGCTTCCTTTCGTTC-TT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
*
1162010 CTTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
1 -TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* *
1162047 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
1162080 TTCTTATTCA
Statistics
Matches: 155, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
35 1 0.01
36 153 0.99
37 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
Found at i:1165992 original size:18 final size:17
Alignment explanation
Indices: 1165938--1165986 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1165928 TTGGACCCTT
* *
1165938 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1165956 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1165974 AGTGCATTCGATG
1 AGTGCA-TCGATG
1165987 TTTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1166007 original size:65 final size:63
Alignment explanation
Indices: 1165938--1166118 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 63
1165928 TTGGACCCTT
*
1165938 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAAATAGCCA
1 AGTGCATCGGTGCA-TAAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAT--CCA
1166002 G
63 G
* * * *
1166003 AGTGCATCGATGCATGACTG-GTGCATCGATGCATCAAATGCATTCGATATTTTCATAAAATCCT
1 AGTGCATCGGTGCAT-A-AGAGTGCATCGATGCATCAAATGCATTCGAT-GTTTCATAAAATCCA
*
1166067 T
63 G
* * *
1166068 AGTGCATCAGTGCAT-GGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATAAG-A-GTGCATCGATGCATCAAATGCATTCGATGTT
1166119 CAATTTAATT
Statistics
Matches: 98, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
64 3 0.03
65 83 0.85
66 6 0.06
67 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCAG
Found at i:1166157 original size:65 final size:65
Alignment explanation
Indices: 1165958--1166168 Score: 202
Period size: 65 Copynumber: 3.2 Consensus size: 65
1165948 TGCACTAAGA
* * *
1165958 GTGCATCGATGCATCAAGTGCATTCG-ATGTTTCA-AAAATAGCCAGAGTGCATCGATGCAT-GA
1 GTGCATCGATGCATCAAATGCATTCGAATG-TTCATAAAAT--CCATAGCGCATCGATGCATGGA
*
1166020 CTG
63 TTG
* * *
1166023 GTGCATCGATGCATCAAATGCATTCGATATTTTCATAAAATCCTTAGTGCATC-AGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGA-ATGTTCATAAAATCCATAGCGCATCGA-TGCATGGAT
1166086 AT-
64 -TG
* ** * *
1166088 GTGCATCGATGCATGAAATGCATTCG-ATGTTCAATTTAATTCATGGCGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGAATGTTC-ATAAAATCCATAGCGCATCGATGCATGGATT
1166152 G
65 G
1166153 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
1166169 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
63 5 0.04
64 22 0.18
65 82 0.67
66 6 0.05
67 7 0.06
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGAATGTTCATAAAATCCATAGCGCATCGATGCATGGATTG
Found at i:1174638 original size:64 final size:64
Alignment explanation
Indices: 1174569--1174727 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 64
1174559 GGACCCTTAA
* *
1174569 TGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAATGCATCGATGCATGGT-TG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCACAATGCATCGATGCATGGTAT-
1174632 G
64 G
* * * *
1174633 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATG
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAGCCACAATGCATCGATGCATGGTATG
* *
1174698 TACATCGATGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATCAAATGCATTCGATGTT
1174728 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
64 29 0.35
65 51 0.61
66 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCACAATGCATCGATGCATGGTATG
Found at i:1176013 original size:21 final size:22
Alignment explanation
Indices: 1175983--1176025 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1175973 AAGTTGACAT
1175983 AGTGAATTTTC-GGGCATGAAC
1 AGTGAATTTTCTGGGCATGAAC
* *
1176004 AGTGATTTTTCTGGGCTTGAAC
1 AGTGAATTTTCTGGGCATGAAC
1176026 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:1184417 original size:17 final size:16
Alignment explanation
Indices: 1184390--1184431 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1184380 TTTCCACCTC
*
1184390 ATTCTTTTTCTTATTT
1 ATTCTTCTTCTTATTT
*
1184406 ATCTCTTCTTCTTCTTT
1 AT-TCTTCTTCTTATTT
1184423 ATTCTTCTT
1 ATTCTTCTT
1184432 TGGAGCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTCTTCTTCTTATTT
Found at i:1189558 original size:20 final size:20
Alignment explanation
Indices: 1189521--1189559 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1189511 AGATTGAGTG
* * *
1189521 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1189541 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1189560 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1189745 original size:20 final size:20
Alignment explanation
Indices: 1189716--1189753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1189706 AGAACCCCAG
*
1189716 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
1189736 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1189754 TCAAAGGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:1198183 original size:18 final size:18
Alignment explanation
Indices: 1198160--1198205 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1198150 CATTGGAAGG
1198160 CTTTAATTTTCTTAGTAT
1 CTTTAATTTTCTTAGTAT
1198178 CTTTAATTTTCTTAGTAT
1 CTTTAATTTTCTTAGTAT
1198196 CTTTAATTTT
1 CTTTAATTTT
1198206 AATTTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (18 bp):
CTTTAATTTTCTTAGTAT
Found at i:1199776 original size:23 final size:23
Alignment explanation
Indices: 1199750--1199797 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1199740 ATAAAGTACA
*
1199750 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1199773 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1199796 AT
1 AT
1199798 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1201065 original size:24 final size:24
Alignment explanation
Indices: 1201028--1201080 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1201018 CCGTTCTATC
1201028 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1201052 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1201076 TATTT
1 TATTT
1201081 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1201273 original size:21 final size:20
Alignment explanation
Indices: 1201225--1201273 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1201215 TCCGGTATCA
*
1201225 TTTTACCGTTTTTTATCATT
1 TTTTACCGGTTTTTATCATT
*
1201245 TTGATACCGGTTTTTATCATAT
1 TT-TTACCGGTTTTTATCAT-T
1201267 TTTTACC
1 TTTTACC
1201274 TGTTATATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.79
22 3 0.12
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTTACCGGTTTTTATCATT
Found at i:1201436 original size:20 final size:19
Alignment explanation
Indices: 1201390--1201437 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
1201380 GACACTTTTA
1201390 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
*
1201409 TTTGTTACCGGTTTTTATCAT
1 ATT-TTACCGG-TTTTATCAT
1201430 ATTTTACC
1 ATTTTACC
1201438 TGGTATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 12 0.48
21 11 0.44
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:1201893 original size:222 final size:223
Alignment explanation
Indices: 1201503--1201944 Score: 721
Period size: 224 Copynumber: 2.0 Consensus size: 223
1201493 TTAAAACTGC
*
1201503 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
1201568 TTAATAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATTT
66 TTAATAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
*
1201633 AGAATTTAAATTTAACAATTTAACCAAATAT-AATAAT-AA-ATGTTTTCAACAGTGAAATAAGT
131 AGAATTTAAATTTAACAATTTAACCAAATATAAATAATAAATATATTTTC-ACAGTGAAATAAGT
*
1201695 ATGGACACTTTTATAAAAATGATATACTT
195 ATGGACACTTTTATAAAAAGGATATACTT
*
1201724 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
1201789 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAA--TAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* * *
1201854 TTTAGATTTTAAATTTAACAATATTAACTAAAGAT-AATAATAAATATATTTTCACAGTGAAATA
128 TTTAGAATTTAAATTTAACAAT-TTAACCAAATATAAATAATAAATATATTTTCACAGTGAAATA
1201918 AGTATGGACACTTTTATAAAAAGGATA
192 AGTATGGACACTTTTATAAAAAGGATA
1201945 GATAATTTAC
Statistics
Matches: 205, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
221 4 0.02
222 63 0.31
224 76 0.37
225 16 0.08
226 39 0.19
227 7 0.03
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (223 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTT
AGAATTTAAATTTAACAATTTAACCAAATATAAATAATAAATATATTTTCACAGTGAAATAAGTA
TGGACACTTTTATAAAAAGGATATACTT
Found at i:1203262 original size:157 final size:158
Alignment explanation
Indices: 1202919--1203291 Score: 491
Period size: 158 Copynumber: 2.4 Consensus size: 158
1202909 TCTGATTTCA
* ** * * * * *
1202919 TTATTTCTTCAATTCATCCTTTATTTTAAGT-TCATTTTTTACCAAATTTGAACCGCATGCTCTT
1 TTATTCCTTCAATTTGTCATTTATTTTAAGTCT-ATTTTTTATCAAATTTGAACCACACGCTCCT
* * * *
1202983 AAACTATAGTAGAATACATGTGTACTTCCAATTCTTCTTTTTGATAACGAATTTTATATTTTTTA
65 AAACCATAGTAGAATACATGTGTACTTCCAAATCCTCTTTTTGATAACGAATTTTATATTTTTCA
* * *
1203048 ATTTTGTTATTTAATTTTTCATAATCTCC
130 ATTTAGTCATTCAATTTTTCATAATCTCC
* *
1203077 TTATTTCTTCAATTTGTCATTTATTTTAAGTCTATTTTTTATCAAAATTGAACCACACGCTCCTA
1 TTATTCCTTCAATTTGTCATTTATTTTAAGTCTATTTTTTATCAAATTTGAACCACACGCTCCTA
* * *
1203142 AACCATAGTAGAATACATTTGTACTTTCAAATCCTCTTTTTGATAAC-ATTTTTATATTTTTCAA
66 AACCATAGTAGAATACATGTGTACTTCCAAATCCTCTTTTTGATAACGAATTTTATATTTTTCAA
*
1203206 TTTAGTCCTTCAATTTTTCATAATCTCC
131 TTTAGTCATTCAATTTTTCATAATCTCC
* *
1203234 TTATTCCTTCAATTTGTGATTTATTTTAAGTC-ATTTTTTTTACTAAATTTGAACCACA
1 TTATTCCTTCAATTTGTCATTTATTTTAAGTCTATTTTTTAT-C-AAATTTGAACCACA
1203292 TACTCATATA
Statistics
Matches: 189, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
156 8 0.04
157 70 0.37
158 110 0.58
159 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (158 bp):
TTATTCCTTCAATTTGTCATTTATTTTAAGTCTATTTTTTATCAAATTTGAACCACACGCTCCTA
AACCATAGTAGAATACATGTGTACTTCCAAATCCTCTTTTTGATAACGAATTTTATATTTTTCAA
TTTAGTCATTCAATTTTTCATAATCTCC
Found at i:1205095 original size:21 final size:20
Alignment explanation
Indices: 1205055--1205097 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1205045 CCAACTTACA
*
1205055 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
1205075 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
1205096 AT
1 AT
1205098 TAGTTGTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:1209749 original size:20 final size:21
Alignment explanation
Indices: 1209724--1209765 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1209714 TCAACTTACA
*
1209724 ATGCATTAT-GAACTATTATT
1 ATGCATTATACAACTATTATT
1209744 ATGCATTATACAACTATTATT
1 ATGCATTATACAACTATTATT
1209765 A
1 A
1209766 GTTGTATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (21 bp):
ATGCATTATACAACTATTATT
Found at i:1216059 original size:22 final size:22
Alignment explanation
Indices: 1216025--1216068 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1216015 CACAATTTGG
*
1216025 TATTTTGAAATTTATAAAAAAA
1 TATTATGAAATTTATAAAAAAA
*
1216047 TATTATGATATTTATAAAAAAA
1 TATTATGAAATTTATAAAAAAA
1216069 ACACTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTATGAAATTTATAAAAAAA
Found at i:1221820 original size:23 final size:23
Alignment explanation
Indices: 1221792--1221842 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1221782 GAAAAAAAAT
* *
1221792 AAGAAGATGAGGTTGGGTTGAGG
1 AAGAAGATCAGGTTGGGTTGAAG
1221815 AAGAAGATCAGGTTGGGTTGAAG
1 AAGAAGATCAGGTTGGGTTGAAG
1221838 AAGAA
1 AAGAA
1221843 AAAAAGCCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.41, T:0.20
Consensus pattern (23 bp):
AAGAAGATCAGGTTGGGTTGAAG
Found at i:1222130 original size:27 final size:26
Alignment explanation
Indices: 1222100--1222157 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1222090 ATAATAAACT
1222100 AATTACTAACGTTATCGATTTATAACA
1 AATTACTAACGTTATCGATTTATAA-A
** * *
1222127 AATTGTTCATGTTATCGATTTATAAA
1 AATTACTAACGTTATCGATTTATAAA
1222153 AATTA
1 AATTA
1222158 TGTCACCCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (26 bp):
AATTACTAACGTTATCGATTTATAAA
Found at i:1223946 original size:31 final size:31
Alignment explanation
Indices: 1223911--1223989 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1223901 GTTAGTAATG
*
1223911 AGTGACCAATTTGTTACAAATTGATAACATT
1 AGTGACCAATTTGTTACAAATCGATAACATT
* * **
1223942 AGTGACAAATTTGTTATAAATCGATAATGTT
1 AGTGACCAATTTGTTACAAATCGATAACATT
*
1223973 AGTAACCAATTTGTTAC
1 AGTGACCAATTTGTTAC
1223990 TTTTAAAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (31 bp):
AGTGACCAATTTGTTACAAATCGATAACATT
Found at i:1225782 original size:21 final size:21
Alignment explanation
Indices: 1225756--1225813 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1225746 GTCGAGGGTT
* * *
1225756 TTATGTGGTTCTTTGGGATAA
1 TTATGTGGTCCTTCGGGACAA
1225777 TTATGTGGTCCTTCGGGACAA
1 TTATGTGGTCCTTCGGGACAA
1225798 TTATGTGG-CACTTCGG
1 TTATGTGGTC-CTTCGG
1225814 TGCAAACCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (21 bp):
TTATGTGGTCCTTCGGGACAA
Found at i:1225840 original size:44 final size:44
Alignment explanation
Indices: 1225778--1225863 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
1225768 TTGGGATAAT
* *
1225778 TATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCCTTCAGGACAATTATATGGCACTTCGGTGCAAACC
* *
1225822 TATGTTGTCTTTCAGGACAATTATATGGCACTTCGGTGCAAA
1 TATGTGGTCCTTCAGGACAATTATATGGCACTTCGGTGCAAA
1225864 TTACGAGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (44 bp):
TATGTGGTCCTTCAGGACAATTATATGGCACTTCGGTGCAAACC
Found at i:1227878 original size:32 final size:31
Alignment explanation
Indices: 1227797--1227916 Score: 118
Period size: 32 Copynumber: 3.9 Consensus size: 31
1227787 GAGTCGAGGG
* * * *
1227797 TTACTTATGCCTTTCGAGACATATGGATAGT
1 TTACTTATGTCTTTCGGGACATATGGACAGA
* * * *
1227828 TTACCTATATCCTTCGGGATATATGGACATGA
1 TTACTTATGTCTTTCGGGACATATGGACA-GA
1227860 TTACTTATGTCTTTCGGGACATATGGACAG-
1 TTACTTATGTCTTTCGGGACATATGGACAGA
* *
1227890 TTACCTATGT-TCTTCGGAACATATGGA
1 TTACTTATGTCT-TTCGGGACATATGGA
1227917 TAGGTCCTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
29 1 0.01
30 23 0.32
31 23 0.32
32 26 0.36
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (31 bp):
TTACTTATGTCTTTCGGGACATATGGACAGA
Found at i:1228944 original size:2 final size:2
Alignment explanation
Indices: 1228937--1228975 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1228927 GATATGTTGT
1228937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1228976 GAGTAAATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1230823 original size:21 final size:21
Alignment explanation
Indices: 1230797--1230846 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1230787 AAGGGGTATT
1230797 GATGCACCTAT-ATAGTGCACC
1 GATGCACCT-TGATAGTGCACC
1230818 GATGCACCTTGATAGTGCACC
1 GATGCACCTTGATAGTGCACC
1230839 GATGCACC
1 GATGCACC
1230847 ATGTTATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (21 bp):
GATGCACCTTGATAGTGCACC
Found at i:1233872 original size:18 final size:18
Alignment explanation
Indices: 1233849--1233906 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
1233839 CAACAATTGG
1233849 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
*
1233867 TAACAATTGATATCATTCTGC
1 TAACAATTGATATC-TT-T-T
*
1233888 TAACAATTGGTATCTTTT
1 TAACAATTGATATCTTTT
1233906 T
1 T
1233907 CATTAAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.44
19 3 0.09
20 3 0.09
21 13 0.38
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:1234181 original size:23 final size:20
Alignment explanation
Indices: 1234130--1234208 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
1234120 AGGGTGTCAA
* * *
1234130 AGTGCATCCATACACCCCTGC
1 AGTGCATCCATGCA-CCATGT
1234151 AGTGCATCCATGCACC-TGGCACT
1 AGTGCATCCATGCACCAT-G---T
*
1234174 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
1234194 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1234209 TCCATTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.02
20 18 0.37
21 13 0.27
23 16 0.33
24 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:1236359 original size:23 final size:23
Alignment explanation
Indices: 1236315--1236368 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1236305 TATATGATGG
1236315 TATAAGAAATTATATGAATTAT-A
1 TATAAGAAATTATATG-ATTATGA
1236338 TATAAGAACATGTATATG-TTATGA
1 TATAAGAA-AT-TATATGATTATGA
*
1236362 GATAAGA
1 TATAAGA
1236369 CCTATGACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 12 0.44
24 9 0.33
25 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (23 bp):
TATAAGAAATTATATGATTATGA
Found at i:1236623 original size:30 final size:31
Alignment explanation
Indices: 1236528--1236646 Score: 136
Period size: 30 Copynumber: 3.8 Consensus size: 31
1236518 CGAGGGTTAT
* * *
1236528 CTATGTCTTTCGAGATATATGGATAGTTTAC
1 CTATGTCTTTCGGGACATATGGATAGATTAC
*
1236559 CTATGTCTTTCGGGACATATGGACAAGATTAC
1 CTATGTCTTTCGGGACATATGGA-TAGATTAC
*
1236591 CTATGT-TCTTCGGGATATATGGATAG-TTAC
1 CTATGTCT-TTCGGGACATATGGATAGATTAC
*
1236621 CTATGT-TCTTCGGAACATATGGATAG
1 CTATGTCT-TTCGGGACATATGGATAG
1236647 GTCCTTCGGG
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
30 28 0.36
31 24 0.31
32 26 0.33
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (31 bp):
CTATGTCTTTCGGGACATATGGATAGATTAC
Found at i:1239174 original size:23 final size:23
Alignment explanation
Indices: 1239144--1239196 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1239134 TAAACTACCA
1239144 AAAGGCAGAGAAAAATGTGCCAC
1 AAAGGCAGAGAAAAATGTGCCAC
* *
1239167 AAAGGCAGAGATAAATGTGCCAT
1 AAAGGCAGAGAAAAATGTGCCAC
1239190 AAAGGCA
1 AAAGGCA
1239197 TATAATGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.11
Consensus pattern (23 bp):
AAAGGCAGAGAAAAATGTGCCAC
Found at i:1240222 original size:21 final size:22
Alignment explanation
Indices: 1240185--1240225 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1240175 TATTCATCAT
1240185 TTCTCTTATGATCACATATCTC
1 TTCTCTTATGATCACATATCTC
*
1240207 TTCTCTTTTG-TCACATATC
1 TTCTCTTATGATCACATATC
1240226 ACATGTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.49
Consensus pattern (22 bp):
TTCTCTTATGATCACATATCTC
Found at i:1247325 original size:2 final size:2
Alignment explanation
Indices: 1247318--1247365 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1247308 TCAAAAATTG
1247318 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
1247360 AT AT AT
1 AT AT AT
1247366 CAATGGATCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1255802 original size:15 final size:15
Alignment explanation
Indices: 1255782--1255812 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1255772 TAACAAAACA
1255782 ATAATAATAATAAAT
1 ATAATAATAATAAAT
1255797 ATAATAATAATAAAT
1 ATAATAATAATAAAT
1255812 A
1 A
1255813 ATATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:1256064 original size:40 final size:42
Alignment explanation
Indices: 1255962--1256073 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 42
1255952 TTGTTGGTGG
* * *
1255962 GGATGACATGACTCATACGTGATGAAGAGGTCTGGTCGTTTAAA
1 GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGT--A
* * *
1256006 GG-TGACACAACTCCTACGTGATGAGGAGATCTGGTCG-GT-
1 GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGTA
* *
1256045 GGATGACACGGCTCATACGTGGTGAAGAG
1 GGATGACACGACTCATACGTGATGAAGAG
1256074 TTATGGCCAT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
39 2 0.04
40 21 0.38
42 1 0.02
43 30 0.54
44 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (42 bp):
GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGTA
Found at i:1256222 original size:134 final size:134
Alignment explanation
Indices: 1256006--1256484 Score: 500
Period size: 134 Copynumber: 3.6 Consensus size: 134
1255996 GTCGTTTAAA
* * * *
1256006 GGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGGTGAA
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
*
1256071 GAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGCGATGATGAAGGCTGGTTATC
66 GAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGAGATGATGAAGGCTGGTTATC
1256136 TAAG
131 TAAG
* * * **
1256140 GGTGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTTGTACGTGATGAG
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGA-
* ** * * * * ** *
1256205 GACAG-TAT-GCCATCTTTA-G--GGATGATAACATGATTCCTACGTA-ATGAGGTTGGCTCGTT
65 -AGAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACG-AGATGATGAAGGCTGGTT
**
1256264 AT-TCGG
128 ATCTAAG
* * *
1256270 GGTAACAC-GACTCCTACGTGATAAGGAGGTCTGATC-G-GG-T-ACATGGCTCATACGTGATGA
1 GGTGACACAG-CTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGA
* * *
1256330 AGAGTTATGGTCATCTTTAGGAAGGGCGATAACAAGGTTTCTACAAGATGATGAAGGTTGGTTAT
65 AGAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGAGATGATGAAGGCTGGTTAT
1256395 CTAAG
130 CTAAG
* * * * * *
1256400 GGTGACACGGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAG
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
1256465 GA-TAGTAT-GCCATCTTTAGG
66 GAGT--TATGGCCATCTTTAGG
1256485 GATGATAACA
Statistics
Matches: 273, Mismatches: 54, Indels: 36
0.75 0.15 0.10
Matches are distributed among these distances:
124 3 0.01
125 3 0.01
126 25 0.09
127 2 0.01
128 3 0.01
129 31 0.11
130 64 0.23
131 33 0.12
132 2 0.01
133 3 0.01
134 95 0.35
135 6 0.02
136 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (134 bp):
GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
GAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGAGATGATGAAGGCTGGTTATC
TAAG
Found at i:1256528 original size:260 final size:262
Alignment explanation
Indices: 1256010--1256578 Score: 926
Period size: 260 Copynumber: 2.2 Consensus size: 262
1256000 TTTAAAGGTG
* * * * *
1256010 ACACAACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGGTGAAGAGT
1 ACACGACTCCTACGTGATAAGGAGGTCTGATC-G-GGATGACACGGCTCATACGTGATGAAGAGT
**
1256075 TATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGCGATGATGAAGGCTGGTTATCTAAG
64 TATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAG
*
1256140 GGTGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTTGTACGTGATGAG
129 GGTGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAG
* * * *
1256205 GACAGTATGCCATCTTTAGGGATGATAACATGATTCCTACGTAATGAGGTTGGCTCGTTATTCGG
194 GACAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATAAGGTCGGCTCATTATTCGG
1256270 GGTA
259 GGTA
*
1256274 ACACGACTCCTACGTGATAAGGAGGTCTGATCGGG-T-ACATGGCTCATACGTGATGAAGAGTTA
1 ACACGACTCCTACGTGATAAGGAGGTCTGATCGGGATGACACGGCTCATACGTGATGAAGAGTTA
* *
1256337 TGGTCATCTTTAGGAAGGGCGATAACAAGGTTTCTACAAGATGATGAAGGTTGGTTATCTAAGGG
66 TGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGG
*
1256402 TGACACGGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA
131 TGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA
*
1256467 TAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATAAGGTCGGCTCATTATTCGGGG
196 CAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATAAGGTCGGCTCATTATTCGGGG
1256532 TA
261 TA
*
1256534 ACACGGCTCCTACGTGATAAGGAGGTCTGATCGGGGGATGACACG
1 ACACGACTCCTACGTGATAAGGAGGTCTGATC--GGGATGACACG
1256579 ATTCCTACGC
Statistics
Matches: 282, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
260 242 0.86
261 1 0.00
262 5 0.02
263 2 0.01
264 32 0.11
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (262 bp):
ACACGACTCCTACGTGATAAGGAGGTCTGATCGGGATGACACGGCTCATACGTGATGAAGAGTTA
TGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGG
TGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA
CAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATAAGGTCGGCTCATTATTCGGGG
TA
Found at i:1256875 original size:68 final size:63
Alignment explanation
Indices: 1256715--1256935 Score: 236
Period size: 66 Copynumber: 3.4 Consensus size: 63
1256705 TCAAAGATGT
* * *
1256715 TTTGTTTCAAGGGAAACAAACTCAAAGATAGGTGTTTGTAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTGTTTCAAAGGAAACAAACTCAAAGAT---TTTTTTTAAAAGAAACTGTCTCGAGAGACAAAA
*
1256780 T
63 A
*
1256781 TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCCTCAAAAGAAATTGTCTCAAGAGAGACAA
1 TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT--T-AAAAGAAACTGTCTC--GAGAGACAA
1256846 AAA
61 AAA
* ***
1256849 TTTGTTTC-TAGAGAAATGGACTCAAAGATTTTTTTTAAAAGAAACTGTCTCGAGAGAC-AAAA
1 TTTGTTTCAAAG-GAAACAAACTCAAAGATTTTTTTTAAAAGAAACTGTCTCGAGAGACAAAAA
1256911 -TTGTTTCAATA-GAAAC-AACTCAAAG
1 TTTGTTTCAA-AGGAAACAAACTCAAAG
1256936 GATACTGATA
Statistics
Matches: 134, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
60 8 0.06
61 11 0.08
62 4 0.03
63 12 0.09
65 15 0.11
66 43 0.32
67 2 0.01
68 39 0.29
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (63 bp):
TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTTAAAAGAAACTGTCTCGAGAGACAAAAA
Found at i:1258138 original size:11 final size:11
Alignment explanation
Indices: 1258124--1258188 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
1258114 GTCTTCTTTC
1258124 TCTTTGTTTTT
1 TCTTTGTTTTT
1258135 TCTTTGTTTTCT
1 TCTTTGTTTT-T
*
1258147 TCTTTTTTTCTT
1 TCTTTGTTT-TT
*
1258159 TC-TT-TTTTC
1 TCTTTGTTTTT
1258168 TCTTTGTTTTT
1 TCTTTGTTTTT
1258179 TCTTT-TTTTT
1 TCTTTGTTTTT
1258189 CTCTCTCTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
9 3 0.06
10 10 0.21
11 21 0.45
12 12 0.26
13 1 0.02
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (11 bp):
TCTTTGTTTTT
Found at i:1258147 original size:20 final size:20
Alignment explanation
Indices: 1258124--1258190 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 20
1258114 GTCTTCTTTC
1258124 TCTTTGTTTTTTCTTTGTTTTCT
1 TCTTTGTTTTTTC-TT-TTTT-T
* *
1258147 TCTTTTTTTCTTTCTTTTTTC
1 TCTTTGTTT-TTTCTTTTTTT
1258168 TCTTTGTTTTTTCTTTTTTT
1 TCTTTGTTTTTTCTTTTTTT
1258188 TCT
1 TCT
1258191 CTCTCTGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 13 0.33
21 8 0.21
22 4 0.10
23 10 0.26
24 4 0.10
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (20 bp):
TCTTTGTTTTTTCTTTTTTT
Found at i:1258171 original size:13 final size:13
Alignment explanation
Indices: 1258133--1258211 Score: 69
Period size: 12 Copynumber: 6.2 Consensus size: 13
1258123 CTCTTTGTTT
1258133 TTTCTTTGTTT-TC
1 TTTCTTT-TTTCTC
1258146 -TTCTTTTTT-TC
1 TTTCTTTTTTCTC
1258157 TTTCTTTTTTCTC
1 TTTCTTTTTTCTC
*
1258170 TTTGTTTTTTCT-
1 TTTCTTTTTTCTC
*
1258182 TTT-TTTTCTCTC
1 TTTCTTTTTTCTC
*
1258194 TCTGCTTTGTTTCTC
1 T-TTCTTT-TTTCTC
1258209 TTT
1 TTT
1258212 GCTCTTTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
11 12 0.22
12 19 0.35
13 14 0.25
14 4 0.07
15 6 0.11
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTCTTTTTTCTC
Found at i:1258171 original size:24 final size:24
Alignment explanation
Indices: 1258124--1258194 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
1258114 GTCTTCTTTC
*
1258124 TCTTTGTTT-TTTCTTTGTTT-TCT
1 TCTTTTTTTCTTTCTTT-TTTCTCT
1258147 TCTTTTTTTCTTTCTTTTTTCTCT
1 TCTTTTTTTCTTTCTTTTTTCTCT
1258171 T-TGTTTTTTCTTT-TTTTTCTCTCT
1 TCT-TTTTTTCTTTCTTTTT-TCTCT
1258195 CTGCTTTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
23 17 0.40
24 26 0.60
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TCTTTTTTTCTTTCTTTTTTCTCT
Found at i:1258173 original size:44 final size:46
Alignment explanation
Indices: 1258109--1258224 Score: 146
Period size: 44 Copynumber: 2.5 Consensus size: 46
1258099 TTGCATGTTC
* **
1258109 TTCTTGTCTTCTTTCTCTTTGTTTTTTCTTTGTTTTCT-TCT-TTTT
1 TTCTT-TCTTTTTTCTCTTTGTTTTTTCTTTGTTTTCTCTCTCTGCT
*
1258154 TTCTTTCTTTTTTCTCTTTGTTTTTTCTTTTTTTTCTCTCTCTGCT
1 TTCTTTCTTTTTTCTCTTTGTTTTTTCTTTGTTTTCTCTCTCTGCT
* * *
1258200 TTGTTTCTCTTTGCTCTTTGTTTTT
1 TTCTTTCTTTTTTCTCTTTGTTTTT
1258225 CCCTTTTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 30 0.48
45 8 0.13
46 24 0.39
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (46 bp):
TTCTTTCTTTTTTCTCTTTGTTTTTTCTTTGTTTTCTCTCTCTGCT
Found at i:1267391 original size:229 final size:227
Alignment explanation
Indices: 1266981--1267429 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
1266971 GTAAATTATC
* * *
1266981 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1267046 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
1267111 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
1267176 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
1267209 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1267274 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1267339 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
1267404 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1267430 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1267683 original size:19 final size:19
Alignment explanation
Indices: 1267650--1267707 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
1267640 TCGATCCACA
* *
1267650 ATGATATAACAGGTAAAAT
1 ATGATAAAACCGGTAAAAT
1267669 ATGATAAAACCGGTATCAAA-
1 ATGATAAAACCGGTA--AAAT
*
1267689 ATGATAAAAACGGTAAAAT
1 ATGATAAAACCGGTAAAAT
1267708 GATACCGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
20 14 0.42
21 3 0.09
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (19 bp):
ATGATAAAACCGGTAAAAT
Found at i:1270046 original size:33 final size:33
Alignment explanation
Indices: 1270004--1270069 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1269994 AAATAGATGG
*
1270004 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1270037 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1270070 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1271926 original size:19 final size:19
Alignment explanation
Indices: 1271863--1271925 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
1271853 AATGTCGAGT
*
1271863 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
1271882 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1271901 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1271920 T-ATTTT
1 TAATTTT
1271926 TTTATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:1272624 original size:199 final size:199
Alignment explanation
Indices: 1272009--1273424 Score: 2535
Period size: 199 Copynumber: 7.1 Consensus size: 199
1271999 TTAAGGGTCA
* * * *** *
1272009 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCTAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1272073 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1272138 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1272203 TAATG
195 TAATG
* *
1272208 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
1272273 AATAAAGTGTCGATCC--ATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1272336 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1272401 AATG
196 AATG
1272405 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1272470 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1272535 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1272600 AATG
196 AATG
1272604 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1272668 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1272733 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1272798 TAATG
195 TAATG
1272803 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1272868 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1272933 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1272998 TAATG
195 TAATG
* *** *
1273003 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1273067 AATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1273130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1273195 AATG
196 AATG
1273199 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1273263 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
1273328 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1273393 AATG
196 AATG
1273397 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1273425 CTAATTTAAA
Statistics
Matches: 1182, Mismatches: 27, Indels: 18
0.96 0.02 0.01
Matches are distributed among these distances:
195 18 0.02
196 166 0.14
197 204 0.17
198 171 0.14
199 397 0.34
200 226 0.19
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1273152 original size:595 final size:594
Alignment explanation
Indices: 1272009--1273424 Score: 2545
Period size: 595 Copynumber: 2.4 Consensus size: 594
1271999 TTAAGGGTCA
* * * *** * *
1272009 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCTAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
1272074 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1272139 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
1272204 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
* *
1272269 CATCAATAAAGTGTCGATCCATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
261 CACCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1272334 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
326 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
1272399 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGG
391 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGG
*
1272464 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
456 TGCACCAATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
1272529 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
520 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
1272594 CTAAATAATG
585 CTAAATAATG
1272604 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
1272669 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1272734 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1272799 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
1272864 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCAATAAAGTGTCGATCC--ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
*
1272929 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
323 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
* ***
1272994 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACA
388 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACA
*
1273058 AGGTGCATCAATAAAGTGTCGATCC-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
453 AGGTGCACCAATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1273122 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAA
518 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAA
1273187 GTCTAAATAATG
583 GTCTAAATAATG
1273199 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1273263 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
1273327 GTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1273392 TAATGTGTCGACACTAATATA-TTTGTGTCGATA
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
1273425 CTAATTTAAA
Statistics
Matches: 794, Mismatches: 23, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
593 12 0.02
594 144 0.18
595 450 0.57
597 30 0.04
598 158 0.20
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (594 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGG
TGCACCAATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
TAAATAATG
Found at i:1274911 original size:18 final size:18
Alignment explanation
Indices: 1274888--1274949 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1274878 ATCGGTCGCA
* * *
1274888 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
1274906 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
1274924 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
1274942 GAAGATGA
1 GAAGATGA
1274950 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:1274912 original size:6 final size:6
Alignment explanation
Indices: 1274888--1274949 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
1274878 ATCGGTCGCA
* * * * * *
1274888 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
1274936 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
1274950 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1274923 original size:3 final size:3
Alignment explanation
Indices: 1274903--1274953 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1274893 TGAAGCTGAC
* * * *
1274903 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1274951 GAT
1 GAT
1274954 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1274950 original size:12 final size:12
Alignment explanation
Indices: 1274891--1274953 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
1274881 GGTCGCAGAA
* *
1274891 GATGAAGCTGAC
1 GATGAAGATGAT
*
1274903 GATGAAGATGAC
1 GATGAAGATGAT
*
1274915 GATGATGATGAT
1 GATGAAGATGAT
*
1274927 GATGACGATGAT
1 GATGAAGATGAT
1274939 GATGAAGATGAT
1 GATGAAGATGAT
1274951 GAT
1 GAT
1274954 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:1276157 original size:23 final size:23
Alignment explanation
Indices: 1276126--1276188 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1276116 ATAGGTAAAC
*
1276126 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1276149 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1276172 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1276189 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1276196 original size:23 final size:23
Alignment explanation
Indices: 1276126--1276198 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1276116 ATAGGTAAAC
* * **
1276126 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1276149 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1276172 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1276195 ATAT
1 ATAT
1276199 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1294994 original size:47 final size:48
Alignment explanation
Indices: 1294927--1295028 Score: 143
Period size: 47 Copynumber: 2.1 Consensus size: 48
1294917 TTCAAATCAT
* * *
1294927 CCCCTGTGATTATAATGTCATCTACATACACTAATAAGGCAAT-ACTC
1 CCCCTGTGACTATAATGTCATCTACATAAACCAATAAGGCAATAACTC
* *
1294974 CCCCTTTGACTATAATGTCATCTACATAAACCAATAAGGCAGTAACTC
1 CCCCTGTGACTATAATGTCATCTACATAAACCAATAAGGCAATAACTC
*
1295022 CCACTGT
1 CCCCTGT
1295029 AGCAGGATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 38 0.81
48 9 0.19
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (48 bp):
CCCCTGTGACTATAATGTCATCTACATAAACCAATAAGGCAATAACTC
Done.