Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1313518 original size:19 final size:20
Alignment explanation
Indices: 1313475--1313529 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1313465 CGCAACACGA
1313475 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
1313495 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
**
1313514 AAATGAAAATCGCAAC
1 AAATGACTATCGCAAC
1313530 AACAAAATCG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:1313545 original size:33 final size:33
Alignment explanation
Indices: 1313503--1313589 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
1313493 AGAAATGGCT
1313503 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1313536 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1313568 ATCGCAACGCGAAATGAAAATC
1 ATCGCAATGCGAAATGAAAATC
1313590 ACAATGCGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:1313576 original size:14 final size:14
Alignment explanation
Indices: 1313519--1313576 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1313509 ATGCGAAATG
*
1313519 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
1313533 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1313549 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1313565 AAAATCGCAACG
1 AAAATCGCAACG
1313577 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1313629 original size:14 final size:14
Alignment explanation
Indices: 1313610--1313700 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
1313600 TTGTATTTCG
1313610 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1313624 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1313640 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1313656 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1313673 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1313689 CGTTGCGATTTT
1 CGTTGCGATTTT
1313701 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1313673 original size:65 final size:66
Alignment explanation
Indices: 1313594--1313716 Score: 214
Period size: 65 Copynumber: 1.9 Consensus size: 66
1313584 AAAATCACAA
*
1313594 TGCGATTTGTATTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TGCGATTTGTATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1313658 T
66 T
1313659 TGCGATTT-TCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTGT-ATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1313717 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 1 0.02
65 35 0.64
66 19 0.35
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (66 bp):
TGCGATTTGTATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCG
T
Found at i:1313674 original size:33 final size:33
Alignment explanation
Indices: 1313594--1313716 Score: 214
Period size: 33 Copynumber: 3.8 Consensus size: 33
1313584 AAAATCACAA
*
1313594 TGCGATTTGT-ATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTT-TCATTTCGCATTGCGATTTTGTCGT
1313627 TGCGA-TTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
1313659 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
1313692 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
1313717 AGCCATTTCC
Statistics
Matches: 87, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
31 1 0.01
32 29 0.33
33 57 0.66
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
Found at i:1313735 original size:20 final size:19
Alignment explanation
Indices: 1313701--1313756 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1313691 TTGCGATTTT
*
1313701 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1313720 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1313740 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1313757 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1314182 original size:21 final size:20
Alignment explanation
Indices: 1314123--1314182 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
1314113 ACTCACCTGT
1314123 CATCCCTCAAGAGTCCCCTC
1 CATCCCTCAAGAGTCCCCTC
**
1314143 CAATCGTTCAAGA-TGCCCCTATC
1 C-ATCCCTCAAGAGT-CCCC--TC
1314166 C-TCCCTCAAGAGTCCCC
1 CATCCCTCAAGAGTCCCC
1314183 CCACCGTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
20 2 0.06
21 25 0.81
22 1 0.03
23 3 0.10
ACGTcount: A:0.22, C:0.45, G:0.12, T:0.22
Consensus pattern (20 bp):
CATCCCTCAAGAGTCCCCTC
Found at i:1315821 original size:19 final size:19
Alignment explanation
Indices: 1315797--1315845 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1315787 ATCGCAACGA
1315797 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1315816 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1315835 GAAAATCGCAA
1 GAAAATCGCAA
1315846 CGACAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1315914 original size:20 final size:20
Alignment explanation
Indices: 1315891--1315978 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
1315881 CGATTTTTTA
1315891 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
1315911 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
1315931 ATGGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1315951 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1315971 GTTGCGAT
1 GTTGCGAT
1315979 TTCCCCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 48 0.89
21 3 0.06
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1315916 original size:34 final size:36
Alignment explanation
Indices: 1315871--1315958 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
1315861 GCGATTTTCA
* * *
1315871 TTTCGCATTGCGATTT-TTT-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTATTTCAATGGCGATAGCCAT
1315905 TTTCGCGTTGCGATTTTTCATTTCGAATGGCGATAGCCAT
1 TTTCGCGTTGCGA--TTT-ATTTC-AATGGCGATAGCCAT
1315945 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1315959 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
34 12 0.27
36 3 0.07
38 4 0.09
40 26 0.58
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTATTTCAATGGCGATAGCCAT
Found at i:1316312 original size:20 final size:21
Alignment explanation
Indices: 1316268--1316319 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1316258 ATAGTCAGTA
*
1316268 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1316289 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1316309 TCGCATTGCGA
1 TCGCATTGCGA
1316320 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1316535 original size:12 final size:12
Alignment explanation
Indices: 1316516--1316549 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1316506 CTCTCCGGTG
1316516 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1316528 ATATCCGTTCCT
1 ACATCCGTTCCT
1316540 ACATCC-TTCC
1 ACATCCGTTCC
1316550 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1317157 original size:24 final size:24
Alignment explanation
Indices: 1317099--1317145 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1317089 AGTCAGTATT
* *
1317099 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTGGTCAATACC
1317123 CGAACTTTGATATTGGTCAATAC
1 CGAACTTTGATATTGGTCAATAC
1317146 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACC
Found at i:1317349 original size:12 final size:12
Alignment explanation
Indices: 1317332--1317356 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1317322 ATATAATCCT
1317332 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1317344 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1317356 G
1 G
1317357 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:1318989 original size:597 final size:597
Alignment explanation
Indices: 1317850--1319050 Score: 2375
Period size: 597 Copynumber: 2.0 Consensus size: 597
1317840 TATCATATTC
*
1317850 TCAAGCTTGGAGAGCCAAATGTTATGCCTTGGAATTGTTGAGGGGGTCGCCAGAAGCATCGTTTG
1 TCAAGGTTGGAGAGCCAAATGTTATGCCTTGGAATTGTTGAGGGGGTCGCCAGAAGCATCGTTTG
1317915 CCCAACTGCCGACTTATTGTCACAATTTAAAGCTGAAAAATCCTGGGTCGGTAACTCATATCAAA
66 CCCAACTGCCGACTTATTGTCACAATTTAAAGCTGAAAAATCCTGGGTCGGTAACTCATATCAAA
1317980 ACAGATAGAGATGGACGCTTTGAGTTGCTGTTTATCGCCATTGGTGCTGCGGTTAGTAAATCAAT
131 ACAGATAGAGATGGACGCTTTGAGTTGCTGTTTATCGCCATTGGTGCTGCGGTTAGTAAATCAAT
1318045 ATAATTATGTTGACTCATTTCTGTTAGTTATATGCATTTCACATTTAAATGATTATATTTCTTGT
196 ATAATTATGTTGACTCATTTCTGTTAGTTATATGCATTTCACATTTAAATGATTATATTTCTTGT
*
1318110 GTATATTATTTTGTAGATTCGTTCGTTTATTACTTGCATGCGCCCAGTTATTATAGTTGACGGAG
261 GTATATTATTTTGTAGATTCGTTCGTTTATTACTTGCATGCACCCAGTTATTATAGTTGACGGAG
1318175 CACATTTGAAAGGTCGATACCTTGGAGTAAACTTATGAGCAGTAGCCATGGATGCTAACAATGGG
326 CACATTTGAAAGGTCGATACCTTGGAGTAAACTTATGAGCAGTAGCCATGGATGCTAACAATGGG
1318240 ATATTGCCAATAGCTTACGGGGTTGGAAAATCTGAAACCTCTGATTCATGGACATGGTTTATGGG
391 ATATTGCCAATAGCTTACGGGGTTGGAAAATCTGAAACCTCTGATTCATGGACATGGTTTATGGG
1318305 GCATCTTAGGGATTGCATAGGTCCTATTAGCAATCTGACAATCATATCCGATAGGGCAAACTCAA
456 GCATCTTAGGGATTGCATAGGTCCTATTAGCAATCTGACAATCATATCCGATAGGGCAAACTCAA
*
1318370 TTGACAACGCTGTTAGAAGGTGTTTCCCAGATGCTTTTCATGGACTTTGTGGTGTTCATTTGTAT
521 TTGACAACACTGTTAGAAGGTGTTTCCCAGATGCTTTTCATGGACTTTGTGGTGTTCATTTGTAT
1318435 AGAAATCTAAAA
586 AGAAATCTAAAA
1318447 TCAAGGTTGGAGAGCCAAATGTTATGCCTTGGAATTGTTGAGGGGGTCGCCAGAAGCATCGTTTG
1 TCAAGGTTGGAGAGCCAAATGTTATGCCTTGGAATTGTTGAGGGGGTCGCCAGAAGCATCGTTTG
1318512 CCCAACTGCCGACTTATTGTCACAATTTAAAGCTGAAAAATCCTGGGTCGGTAACTCATATCAAA
66 CCCAACTGCCGACTTATTGTCACAATTTAAAGCTGAAAAATCCTGGGTCGGTAACTCATATCAAA
1318577 ACAGATAGAGATGGACGCTTTGAGTTGCTGTTTATCGCCATTGGTGCTGCGGTTAGTAAATCAAT
131 ACAGATAGAGATGGACGCTTTGAGTTGCTGTTTATCGCCATTGGTGCTGCGGTTAGTAAATCAAT
1318642 ATAATTATGTTGACTCATTTCTGTTAGTTATATGCATTTCACATTTAAATGATTATATTTCTTGT
196 ATAATTATGTTGACTCATTTCTGTTAGTTATATGCATTTCACATTTAAATGATTATATTTCTTGT
1318707 GTATATTATTTTGTAGATTCGTTCGTTTATTACTTGCATGCACCCAGTTATTATAGTTGACGGAG
261 GTATATTATTTTGTAGATTCGTTCGTTTATTACTTGCATGCACCCAGTTATTATAGTTGACGGAG
1318772 CACATTTGAAAGGTCGATACCTTGGAGTAAACTTATGAGCAGTAGCCATGGATGCTAACAATGGG
326 CACATTTGAAAGGTCGATACCTTGGAGTAAACTTATGAGCAGTAGCCATGGATGCTAACAATGGG
1318837 ATATTGCCAATAGCTTACGGGGTTGGAAAATCTGAAACCTCTGATTCATGGACATGGTTTATGGG
391 ATATTGCCAATAGCTTACGGGGTTGGAAAATCTGAAACCTCTGATTCATGGACATGGTTTATGGG
1318902 GCATCTTAGGGATTGCATAGGTCCTATTAGCAATCTGACAATCATATCCGATAGGGCAAACTCAA
456 GCATCTTAGGGATTGCATAGGTCCTATTAGCAATCTGACAATCATATCCGATAGGGCAAACTCAA
1318967 TTGACAACACTGTTAGAAGGTGTTTCCCAGATGCTTTTCATGGACTTTGTGGTGTTCATTTGTAT
521 TTGACAACACTGTTAGAAGGTGTTTCCCAGATGCTTTTCATGGACTTTGTGGTGTTCATTTGTAT
1319032 AGAAATCTAAAA
586 AGAAATCTAAAA
1319044 TCAAGGT
1 TCAAGGT
1319051 CTGCTGGTAT
Statistics
Matches: 601, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
597 601 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (597 bp):
TCAAGGTTGGAGAGCCAAATGTTATGCCTTGGAATTGTTGAGGGGGTCGCCAGAAGCATCGTTTG
CCCAACTGCCGACTTATTGTCACAATTTAAAGCTGAAAAATCCTGGGTCGGTAACTCATATCAAA
ACAGATAGAGATGGACGCTTTGAGTTGCTGTTTATCGCCATTGGTGCTGCGGTTAGTAAATCAAT
ATAATTATGTTGACTCATTTCTGTTAGTTATATGCATTTCACATTTAAATGATTATATTTCTTGT
GTATATTATTTTGTAGATTCGTTCGTTTATTACTTGCATGCACCCAGTTATTATAGTTGACGGAG
CACATTTGAAAGGTCGATACCTTGGAGTAAACTTATGAGCAGTAGCCATGGATGCTAACAATGGG
ATATTGCCAATAGCTTACGGGGTTGGAAAATCTGAAACCTCTGATTCATGGACATGGTTTATGGG
GCATCTTAGGGATTGCATAGGTCCTATTAGCAATCTGACAATCATATCCGATAGGGCAAACTCAA
TTGACAACACTGTTAGAAGGTGTTTCCCAGATGCTTTTCATGGACTTTGTGGTGTTCATTTGTAT
AGAAATCTAAAA
Found at i:1322739 original size:8 final size:8
Alignment explanation
Indices: 1322728--1322761 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1322718 ATATTTTATA
1322728 TATTTAAT
1 TATTTAAT
*
1322736 TATTCAAT
1 TATTTAAT
*
1322744 TATTTAAC
1 TATTTAAT
1322752 TATTTAAT
1 TATTTAAT
1322760 TA
1 TA
1322762 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:1323179 original size:54 final size:54
Alignment explanation
Indices: 1323047--1323196 Score: 198
Period size: 54 Copynumber: 2.7 Consensus size: 54
1323037 TTTTCAACAT
* *
1323047 CGGGTTCGCTCCCTATCGTTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCTAC
1 CGGGTTCGCTCCCTAT-TTTTCAGGGAGA-ATAGAACTCGAAGAATCTTCTGCTAC
*
1323102 CGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTC-AAGAATCTTCTGCTAAC
1 CGGGTTCGCTCCCTATT-TTTCAGGGAGAATAGAACTCGAAGAATCTTCTGCT-AC
*
1323157 C-GGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAA
1 CGGGTTCGCTCCCTATTT-TTCAGGGAGAATAGAACTCGAA
1323197 TATCTTCAAC
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
53 1 0.01
54 45 0.53
55 39 0.46
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (54 bp):
CGGGTTCGCTCCCTATTTTTCAGGGAGAATAGAACTCGAAGAATCTTCTGCTAC
Found at i:1323353 original size:55 final size:55
Alignment explanation
Indices: 1323166--1323487 Score: 441
Period size: 55 Copynumber: 5.9 Consensus size: 55
1323156 CCGGTTCGCT
* * * * * * *
1323166 CCCTCTTTCTTCAGGGAGAAT-AGAACTCGAA-TATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACGATCGCGTCTGCC
* * * ** *
1323220 CCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCTTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-GATCGCGTCTGCC
* * *
1323276 CCCTATTCCCTCAGAGAGTATAAGACTCGAACAATCTTCAATGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1323331 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
* * *
1323386 CCCTATTTCTTCAGGGAGTATAAGACTCGAACAATCTTCAACGATCGCCTCTTCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1323441 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
1323488 TTGGGAAACC
Statistics
Matches: 242, Mismatches: 23, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
54 23 0.10
55 170 0.70
56 49 0.20
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
Found at i:1324509 original size:21 final size:22
Alignment explanation
Indices: 1324485--1324541 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
1324475 TCTTGAACCC
1324485 TCATTTTTTCATTTTTT-TCAT
1 TCATTTTTTCATTTTTTATCAT
* **
1324506 TCATTTTTT-GTTTTTTATTTT
1 TCATTTTTTCATTTTTTATCAT
1324527 TCATTTTTTCATTTT
1 TCATTTTTTCATTTT
1324542 CACTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.20
21 20 0.67
22 4 0.13
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.75
Consensus pattern (22 bp):
TCATTTTTTCATTTTTTATCAT
Found at i:1324525 original size:14 final size:15
Alignment explanation
Indices: 1324485--1324541 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 15
1324475 TCTTGAACCC
1324485 TCATTTTTTCATTTT
1 TCATTTTTTCATTTT
**
1324500 T--TTCATTCATTTT
1 TCATTTTTTCATTTT
**
1324513 TTGTTTTTT-ATTTT
1 TCATTTTTTCATTTT
1324527 TCATTTTTTCATTTT
1 TCATTTTTTCATTTT
1324542 CACTCATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 11 0.33
14 12 0.36
15 10 0.30
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.75
Consensus pattern (15 bp):
TCATTTTTTCATTTT
Found at i:1324562 original size:42 final size:41
Alignment explanation
Indices: 1324485--1324569 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
1324475 TCTTGAACCC
** *
1324485 TCATTTTTTCATTTTTTTCATTCATTTTTTGTTTTTTATTTT
1 TCATTTTTTCATTTTACTCATT-ATTTTTTCTTTTTTATTTT
*
1324527 TCATTTTTTCATTTTCACTCATT-TTTTCTTCTTTTTTTTTTT
1 TCATTTTTTCATTTT-ACTCATTATTTT-TTCTTTTTTATTTT
1324569 T
1 T
1324570 TTCTTCAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.11
42 28 0.76
43 5 0.14
ACGTcount: A:0.11, C:0.13, G:0.01, T:0.75
Consensus pattern (41 bp):
TCATTTTTTCATTTTACTCATTATTTTTTCTTTTTTATTTT
Found at i:1334542 original size:16 final size:16
Alignment explanation
Indices: 1334521--1334558 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
1334511 AACCTTATTC
1334521 ACATGATATCTACCCA
1 ACATGATATCTACCCA
1334537 ACATGATATCTACCCA
1 ACATGATATCTACCCA
1334553 ATCATG
1 A-CATG
1334559 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:1338010 original size:8 final size:8
Alignment explanation
Indices: 1337999--1338032 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1337989 ATATTTTATA
1337999 TATTTAAT
1 TATTTAAT
*
1338007 TATTCAAT
1 TATTTAAT
*
1338015 TATTTAAC
1 TATTTAAT
1338023 TATTTAAT
1 TATTTAAT
1338031 TA
1 TA
1338033 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:1338359 original size:19 final size:19
Alignment explanation
Indices: 1338337--1338467 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1338327 GGAAATTACT
1338337 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1338356 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1338370 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1338389 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1338403 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1338422 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1338436 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1338455 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1338468 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1338379 original size:33 final size:33
Alignment explanation
Indices: 1338337--1338463 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1338327 GGAAATTACT
1338337 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1338370 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1338402 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1338436 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1338464 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1338444 original size:66 final size:66
Alignment explanation
Indices: 1338338--1338470 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1338328 GAAATTACTA
*
1338338 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1338403 T
66 T
*
1338404 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1338469 T
66 T
1338470 T
1 T
1338471 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1338485 original size:19 final size:19
Alignment explanation
Indices: 1338463--1338504 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1338453 AAATCGCAAC
*
1338463 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
1338482 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
1338501 GCGA
1 GCGA
1338505 TAGTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:1338631 original size:14 final size:14
Alignment explanation
Indices: 1338612--1338648 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1338602 CATCAATTAA
1338612 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1338626 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1338640 ACAAATCAA
1 ACAAATCAA
1338649 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1340064 original size:42 final size:41
Alignment explanation
Indices: 1340005--1340207 Score: 176
Period size: 42 Copynumber: 4.8 Consensus size: 41
1339995 GTGAATCGGG
* ** *
1340005 CTCTTGAATGGTGGGAGGGACCTCTTCAACAATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAGGAATGATAGTGGC
*
1340047 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTC-AGGAATGATAGTGGC
* * * * * *
1340089 CTCTTCAACGATAGAAGTGGACTCTTGAGGGATGATAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAGGAATGATAGTGGC
*
1340131 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTC-AGGAATGATAGTGGC
* * * * *
1340173 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAG-GGACTCTTCAGGAATGA
1340208 CAGGCGAGTC
Statistics
Matches: 129, Mismatches: 24, Indels: 16
0.76 0.14 0.09
Matches are distributed among these distances:
41 5 0.04
42 117 0.91
43 7 0.05
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAGGAATGATAGTGGC
Found at i:1340086 original size:21 final size:20
Alignment explanation
Indices: 1340062--1340176 Score: 54
Period size: 21 Copynumber: 5.5 Consensus size: 20
1340052 GAACGGTGGG
1340062 AGGGGACTCTCGAGGAATGAT
1 AGGGGACTCTCGAGG-ATGAT
* * *
1340083 AGGGGCCTCTTCAACGATAGA-
1 AGGGGACTC-TCGAGGAT-GAT
* *
1340104 AGTGGACTCTTGAGGGATGAT
1 AGGGGACTCTCGA-GGATGAT
* * * **
1340125 AGTGGCCTCTTGAACGG-TGGG
1 AGGGGACTCTCG-A-GGATGAT
1340146 AGGGGACTCTCGAGGAATGAT
1 AGGGGACTCTCGAGG-ATGAT
*
1340167 AGGGGCCTCT
1 AGGGGACTCT
1340177 TCAACGATAG
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 53 0.77
22 9 0.13
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (20 bp):
AGGGGACTCTCGAGGATGAT
Found at i:1340146 original size:84 final size:84
Alignment explanation
Indices: 1340036--1340210 Score: 332
Period size: 84 Copynumber: 2.1 Consensus size: 84
1340026 CTCTTCAACA
1340036 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
1 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
1340101 AGAAGTGGACTCTTGAGGG
66 AGAAGTGGACTCTTGAGGG
*
1340120 ATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
1 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
*
1340185 AGGAGTGGACTCTTGAGGG
66 AGAAGTGGACTCTTGAGGG
1340204 ATGACAG
1 ATGACAG
1340211 GCGAGTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (84 bp):
ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
AGAAGTGGACTCTTGAGGG
Found at i:1340607 original size:91 final size:90
Alignment explanation
Indices: 1340429--1340613 Score: 284
Period size: 91 Copynumber: 2.0 Consensus size: 90
1340419 ATTTCAAACT
1340429 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGC
*
1340494 AGAATTGGCAGCAATCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1340522 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGC
*
1340585 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1340613 T
1 T
1340614 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
91 35 0.40
93 19 0.22
95 32 0.37
96 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1342345 original size:20 final size:19
Alignment explanation
Indices: 1342300--1342440 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
1342290 TCTTTTGGTT
1342300 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1342319 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1342340 GAAATGACTATTGCAACGA
1 GAAATGAAAATCGCAACGA
*
1342359 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** * *
1342373 GAAATGACTATTGCGACGA
1 GAAATGAAAATCGCAACGA
*
1342392 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1342406 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1342425 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1342441 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 17 0.18
16 4 0.04
17 4 0.04
19 38 0.41
20 28 0.30
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1342382 original size:33 final size:33
Alignment explanation
Indices: 1342325--1342412 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
1342315 ACGAGATAAT
1342325 GAGAATCGCAACGCGGAAATGACTATTGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATTGCAACGA
*
1342359 GAGAATCGCAACGCGAAATGACTATTGCGACGA
1 GAGAATCGCAACGCGAAATGACTATTGCAACGA
1342392 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
1342413 AAATCGCAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATTGCAACGA
Found at i:1342417 original size:19 final size:19
Alignment explanation
Indices: 1342395--1342445 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1342385 GCGACGAGAG
1342395 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1342414 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1342433 AATCGCAATGCGA
1 AATCGCAACGCGA
1342446 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1342468 original size:19 final size:19
Alignment explanation
Indices: 1342441--1342506 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
1342431 AAAATCGCAA
**
1342441 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
1342459 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1342478 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1342498 TGCGATTTT
1 TGCGATTTT
1342507 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.40
19 12 0.30
20 12 0.30
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1342498 original size:20 final size:19
Alignment explanation
Indices: 1342452--1342503 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1342442 GCGATTTTGG
**
1342452 TTTCGCG-TGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
1342470 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
1342489 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
1342504 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 11 0.37
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:1343049 original size:20 final size:20
Alignment explanation
Indices: 1343024--1343076 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1343014 GCGCTATGTA
1343024 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1343044 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1343064 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1343077 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1343110 original size:20 final size:20
Alignment explanation
Indices: 1343085--1343138 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1343075 GATTTTGTAT
1343085 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1343105 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1343125 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1343139 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1343123 original size:61 final size:61
Alignment explanation
Indices: 1343025--1343141 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1343015 CGCTATGTAA
* * * * *
1343025 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1343086 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1343142 CCCAATTCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1343778 original size:183 final size:183
Alignment explanation
Indices: 1343460--1343832 Score: 631
Period size: 183 Copynumber: 2.0 Consensus size: 183
1343450 GACGAATATC
* * *
1343460 CATAATACACCAAACGCTACATAATGCACCAAAGTATCACAACACACCTAAGTGTTACAGAATGC
1 CATAATGCACCAAAAGCTACATAATGCACAAAAGTATCACAACACACCTAAGTGTTACAGAATGC
* *
1343525 ACTGAAGGTCATAATATAGCTGTTATATTTTATGACATGTCTACTATATCCTAATGCTCTTACAA
66 ACTGAAGGTCATAATATAGCTGTTATACTCTATGACATGTCTACTATATCCTAATGCTCTTACAA
*
1343590 AATTACTTGGACAATTTATATCACAATATATACATATATCAGTCCACATAATA
131 AATTACTTGGACAATTTATATCACAATATATACATATATCAATCCACATAATA
* *
1343643 CATAATGCACCAAAATCTACATAATGCACAAAAGTATCACAATACACCTAAGTGTTACAGAATGC
1 CATAATGCACCAAAAGCTACATAATGCACAAAAGTATCACAACACACCTAAGTGTTACAGAATGC
* *
1343708 ACTGAAGCTTCATAATATAGTTGTTATACTCTATGACATGTCTACTATATCCTAATGCTCTTAC-
66 ACTGAAG-GTCATAATATAGCTGTTATACTCTATGACATGTCTACTATATCCTAATGCTCTTACA
*
1343772 AAATTACTTGGACAATTTATATCACAATATATATATATATCAATCCACATAATA
130 AAATTACTTGGACAATTTATATCACAATATATACATATATCAATCCACATAATA
1343826 CATAATG
1 CATAATG
1343833 TCACAATAAC
Statistics
Matches: 178, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 126 0.71
184 52 0.29
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (183 bp):
CATAATGCACCAAAAGCTACATAATGCACAAAAGTATCACAACACACCTAAGTGTTACAGAATGC
ACTGAAGGTCATAATATAGCTGTTATACTCTATGACATGTCTACTATATCCTAATGCTCTTACAA
AATTACTTGGACAATTTATATCACAATATATACATATATCAATCCACATAATA
Found at i:1344546 original size:3 final size:3
Alignment explanation
Indices: 1344540--1344593 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1344530 TTAATTTTTT
1344540 TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1344585 TTA TTA TTA
1 TTA TTA TTA
1344594 ATTACAAGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1344557 original size:14 final size:14
Alignment explanation
Indices: 1344540--1344593 Score: 99
Period size: 14 Copynumber: 3.8 Consensus size: 14
1344530 TTAATTTTTT
1344540 TTATTATATTATTA
1 TTATTATATTATTA
1344554 TTATTATATTATTA
1 TTATTATATTATTA
1344568 TTATTATATTATTA
1 TTATTATATTATTA
1344582 TTATTATTATTA
1 TTATTA-TATTA
1344594 ATTACAAGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
14 34 0.87
15 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:1346445 original size:137 final size:135
Alignment explanation
Indices: 1346216--1346467 Score: 319
Period size: 137 Copynumber: 1.9 Consensus size: 135
1346206 TTAATAATAG
* * * *
1346216 TATTTACTTATTTCAATATTAAGAAAGGGCAGTCTTAACCTAACTAGATGTCATTTTCTGATATT
1 TATTTACTTATTTCAATATTAAGAAAGGACAGTCATAAACTAACTAGATGTCATATTCTGATATT
* * * * * *
1346281 TTTAAATAAATAAATATCATATTTTTATAAATTATATATATTAATCTATTGTTTTAGAAAAATGT
66 TTAAAATAAATAAATATCATATATTTATAAAATATAAAAATTAATATATTGTTTTAGAAAAATGT
1346346 TTTAA
131 TTTAA
* * * * *
1346351 TATTTATTTATTTTTAATATTAAGAAAAGGACAGTCATAAAGTAACTAGATGTCCTATTCTGGTA
1 TATTTACTTA-TTTCAATATTAAG-AAAGGACAGTCATAAACTAACTAGATGTCATATTCTGATA
1346416 TTTTAAAAAATAAATAAATATC-T-TATTTATAAAATATAAAAATTAATATATT
64 TTTT--AAAATAAATAAATATCATATATTTATAAAATATAAAAATTAATATATT
1346468 TTCTTAAAGT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
135 9 0.09
136 12 0.12
137 61 0.62
138 1 0.01
139 15 0.15
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (135 bp):
TATTTACTTATTTCAATATTAAGAAAGGACAGTCATAAACTAACTAGATGTCATATTCTGATATT
TTAAAATAAATAAATATCATATATTTATAAAATATAAAAATTAATATATTGTTTTAGAAAAATGT
TTTAA
Found at i:1347572 original size:46 final size:49
Alignment explanation
Indices: 1347495--1347586 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 49
1347485 AATTTATTCC
* * *
1347495 ATTTTTCCTAAATAAATGCATGTGAACTAGAAATCATGCA-GTTAGGTTA
1 ATTTTTCCTAAACAAATGCATGTAAACTAGAAAGCATG-AGGTTAGGTTA
1347544 ATTTTTCC-AAACAAA-GCATG-AAACTAGAAAGCATGAGGTTAGG
1 ATTTTTCCTAAACAAATGCATGTAAACTAGAAAGCATGAGGTTAGG
1347587 ATTTATACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
45 1 0.03
46 19 0.49
47 5 0.13
48 6 0.15
49 8 0.21
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (49 bp):
ATTTTTCCTAAACAAATGCATGTAAACTAGAAAGCATGAGGTTAGGTTA
Found at i:1351838 original size:8 final size:8
Alignment explanation
Indices: 1351825--1351869 Score: 90
Period size: 8 Copynumber: 5.6 Consensus size: 8
1351815 CTATACTTAA
1351825 AAAAAAGG
1 AAAAAAGG
1351833 AAAAAAGG
1 AAAAAAGG
1351841 AAAAAAGG
1 AAAAAAGG
1351849 AAAAAAGG
1 AAAAAAGG
1351857 AAAAAAGG
1 AAAAAAGG
1351865 AAAAA
1 AAAAA
1351870 TTGAATCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1354475 original size:54 final size:54
Alignment explanation
Indices: 1354411--1354517 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
1354401 CGATGAAAAC
* * *
1354411 TCTGGGCAGAAGGCACAAGAAATAATGAATGTGTTGTCAAATGTTTTATGAACA
1 TCTGGACAGAAGCCACAAGAAAGAATGAATGTGTTGTCAAATGTTTTATGAACA
* *
1354465 TCTGGACAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTCTGAAC
1 TCTGGACAGAAGCCACAAGAAAGAATGAATGTGTTGTCAAATGTTTTATGAAC
1354518 CAGTGATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (54 bp):
TCTGGACAGAAGCCACAAGAAAGAATGAATGTGTTGTCAAATGTTTTATGAACA
Found at i:1354927 original size:20 final size:22
Alignment explanation
Indices: 1354881--1354938 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1354871 TACATCTACA
1354881 CTCTTCAAAGATGATAGATTAT
1 CTCTTCAAAGATGATAGATTAT
*
1354903 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTAT
* *
1354925 CTTTTTAAAGATGA
1 CTCTTCAAAGATGA
1354939 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTAT
Found at i:1355925 original size:116 final size:116
Alignment explanation
Indices: 1355606--1356213 Score: 984
Period size: 116 Copynumber: 5.2 Consensus size: 116
1355596 CCCACATCTG
* * * * * *
1355606 TAAGACCTACAGTGCATGATGTTTCCAAAAAGGCTACAGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
* * *
1355671 GGTCATCTGTAAGACCTATAGTGCAAGATGATAAGATCTCAGAGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* * *
1355722 TAAGACCTACAGTGCAGGATGTTTTCCAAAAAACCTTCGGGAGCTTTTTGATATTTAAAACCTCC
1 TAAGACCTATAGTGCAGGATGTTTT-CAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCC
1355787 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
65 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
*
1355839 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1355904 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* * *
1355955 TAAGACCTATAATGCAGGATGTTTTCAAAATGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCA
1 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
* * *
1356020 GGTCATCTGTAAGACCTATAGTGCCAGATGATAAGACCTCATGGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
1356071 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
* * *
1356136 GGTCATCTGTAAAACCTACAATGCAAGATGATAAGACCTCAGGGCCATTCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* *
1356187 TAAGACCTCTAG-GCAGAATGTTTTCAA
1 TAAGACCTATAGTGCAGGATGTTTTCAA
1356214 CATTTCCGTC
Statistics
Matches: 459, Mismatches: 32, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
115 14 0.03
116 338 0.74
117 107 0.23
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (116 bp):
TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
Found at i:1357164 original size:14 final size:15
Alignment explanation
Indices: 1357142--1357195 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
1357132 CTAGAGAAAG
1357142 AATGAAAAATGAAGA
1 AATGAAAAATGAAGA
*
1357157 AATG-AAAATGGAAAA
1 AATGAAAAAT-GAAGA
*
1357172 GAATGAAAAATAAAGA
1 -AATGAAAAATGAAGA
1357188 AATGAAAA
1 AATGAAAA
1357196 TGGCCCTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.15
15 16 0.48
16 7 0.21
17 5 0.15
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.13
Consensus pattern (15 bp):
AATGAAAAATGAAGA
Found at i:1357176 original size:31 final size:31
Alignment explanation
Indices: 1357138--1357198 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
1357128 TCTTCTAGAG
*
1357138 AAAGAATGAAAAATGAAGAAATGAAAATGGA
1 AAAGAATGAAAAATAAAGAAATGAAAATGGA
1357169 AAAGAATGAAAAATAAAGAAATGAAAATGG
1 AAAGAATGAAAAATAAAGAAATGAAAATGG
1357199 CCCTTAGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAGAATGAAAAATAAAGAAATGAAAATGGA
Found at i:1359729 original size:2 final size:2
Alignment explanation
Indices: 1359722--1359778 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1359712 GTTCCTGTAA
1359722 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
1359764 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1359779 ATTAGGCCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1368462 original size:17 final size:17
Alignment explanation
Indices: 1368440--1368483 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1368430 AGGCACGTTA
1368440 GAGAAGAGAAGAAGATG
1 GAGAAGAGAAGAAGATG
1368457 GAGAAGAGAAGAAGATG
1 GAGAAGAGAAGAAGATG
*
1368474 AAGAAGAGAA
1 GAGAAGAGAA
1368484 TTGTCTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.05
Consensus pattern (17 bp):
GAGAAGAGAAGAAGATG
Found at i:1371152 original size:41 final size:41
Alignment explanation
Indices: 1371048--1371157 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 41
1371038 TTTCCAAAAT
* * * ** *
1371048 TGATAAGTCCTTCGAGCCACCAGTAAGTCTTTTGAGCATGA
1 TGATAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGA
* * * *
1371089 TGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCAAGTAAGA
1 TGA-TAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGA
*
1371131 TGATAAGTCCTTCGGGCCATCTATAAG
1 TGATAAGTCCTTCGGGCCATCTGTAAG
1371158 ACCTTTGGGA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 23 0.43
42 31 0.57
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (41 bp):
TGATAAGTCCTTCGGGCCATCTGTAAGTCTTTCAAGCAAGA
Found at i:1371260 original size:19 final size:18
Alignment explanation
Indices: 1371232--1371292 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1371222 AATATTGATT
*
1371232 AAAATAAGAAGAAGAAGAG
1 AAAAAAAGAAGAAGAA-AG
* * *
1371251 AAAAAGAGAAAAAAAAAAG
1 AAAAAAAG-AAGAAGAAAG
1371270 AAAAAAAGAAGGAAGAAAG
1 AAAAAAAGAA-GAAGAAAG
1371289 AAAA
1 AAAA
1371293 GGAAATTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.06
19 25 0.76
20 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAGAAGAAAG
Found at i:1372118 original size:32 final size:32
Alignment explanation
Indices: 1372067--1372232 Score: 133
Period size: 32 Copynumber: 5.2 Consensus size: 32
1372057 ATTTCGTCAC
* *
1372067 TAAAT-ATTTTTTTATAATTTTTTATTGTGAT
1 TAAATAATTTTGTTACAATTTTTTATTGTGAT
*
1372098 TAAATAATTTTGTTACAATTTGTTATTGTGA-
1 TAAATAATTTTGTTACAATTTTTTATTGTGAT
* * * **
1372129 AATAATATTATTTGTCACAATTTTTTATAATGA-
1 TA-AATAAT-TTTGTTACAATTTTTTATTGTGAT
* *
1372162 TAAATTAATATTT-TTATAATTTTTTATTTTGAT
1 TAAA-TAAT-TTTGTTACAATTTTTTATTGTGAT
* * * *
1372195 TAAATAAATTTGTCACAATTTTTCATTTTGAT
1 TAAATAATTTTGTTACAATTTTTTATTGTGAT
*
1372227 AAAATA
1 TAAATA
1372233 TTGTGACGAA
Statistics
Matches: 109, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
31 9 0.08
32 69 0.63
33 31 0.28
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (32 bp):
TAAATAATTTTGTTACAATTTTTTATTGTGAT
Found at i:1372151 original size:65 final size:64
Alignment explanation
Indices: 1372082--1372232 Score: 155
Period size: 65 Copynumber: 2.3 Consensus size: 64
1372072 ATTTTTTTAT
* *
1372082 AATTTTTTATTGTGATTAAATAAT-TTTGTTACAATTTGTTATTGTGAA-ATAATATTATTTGTC
1 AATTTTTTATTATGATTAAATAATATTT-TTACAATTTGTTATTGTGAATA-AATA-AATTTGTC
1372145 AC
63 AC
* * * * *
1372147 AATTTTTTATAATGA-TAAATTAATATTTTTATAATTTTTTATTTTGATTAAATAAATTTGTCAC
1 AATTTTTTATTATGATTAAA-TAATATTTTTACAATTTGTTATTGTGAATAAATAAATTTGTCAC
* * *
1372211 AATTTTTCATTTTGATAAAATA
1 AATTTTTTATTATGATTAAATA
1372233 TTGTGACGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
64 27 0.38
65 40 0.56
66 4 0.06
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (64 bp):
AATTTTTTATTATGATTAAATAATATTTTTACAATTTGTTATTGTGAATAAATAAATTTGTCAC
Found at i:1372292 original size:35 final size:37
Alignment explanation
Indices: 1372231--1372326 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 37
1372221 TTTGATAAAA
* * * * *
1372231 TATTGTGACGAAATAAATTTGACAT-AACTT-TTTAC
1 TATTGTGACTAAATCATTTTGTCATAAACTTATGTAC
**
1372266 TATTGTGACTAAATCATTTTGTCATAAAACTTAATGTGT
1 TATTGTGACTAAATCATTTTGTCAT-AAACTT-ATGTAC
1372305 TATTGTGACTAAATCATTTTGT
1 TATTGTGACTAAATCATTTTGT
1372327 TACAATTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 21 0.42
37 5 0.10
39 24 0.48
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (37 bp):
TATTGTGACTAAATCATTTTGTCATAAACTTATGTAC
Found at i:1372634 original size:22 final size:23
Alignment explanation
Indices: 1372609--1372660 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1372599 TTATAATTTA
*
1372609 AATTTTTTATTATAACT-AAAAT
1 AATTTTTTATGATAACTAAAAAT
**
1372631 AATTGGTTATGATAACTAAAAAT
1 AATTTTTTATGATAACTAAAAAT
1372654 ATATTTT
1 A-ATTTT
1372661 AAAATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 14 0.61
23 6 0.26
24 3 0.13
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (23 bp):
AATTTTTTATGATAACTAAAAAT
Found at i:1373735 original size:17 final size:17
Alignment explanation
Indices: 1373709--1373749 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1373699 TGATTTATTC
* *
1373709 AAATTCTTTACTTAATT
1 AAATTATTTACATAATT
1373726 AAATTATTTACATAATT
1 AAATTATTTACATAATT
1373743 ATAATTA
1 A-AATTA
1373750 AGAGAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTATTTACATAATT
Found at i:1375175 original size:177 final size:179
Alignment explanation
Indices: 1374707--1375193 Score: 547
Period size: 182 Copynumber: 2.7 Consensus size: 179
1374697 ATATATGCTA
* * * * *
1374707 TCACTATAGTTAACATTTATAACTACAAATATAATTTGTCACAAAAAACTTGAATATCATTATTT
1 TCACTATAATTAAAATATATAACTACAAATATAATTTTTCAC-AAAAACTTGAATCTCATTATTT
* * * * *
1374772 TTTGTGAC-AATGTTTTTTGTAATAATTATTAACACTTATATTTACAAAATTTGTCACTATATGA
65 GTTGTGACAAAT-TTTTTTGTAACAATTATTAAAACTTATAGTTACAAAACTTGTCACTATATGA
* *
1374836 CTTTTTTTGCGCAAAACAATATGGAGGGAAATCTTTGTGACAATATATTTTG
129 CTTTTTTTACGCAAAACAATATGGA-GGAAATCTTTGTGACAATACATTTTG
* * * *
1374888 TCACTATAATTAAAACATATAACGACAAATATTATTTTTTTACTAAAAACTTGAATCTCATTATT
1 TCACTATAATTAAAATATATAACTACAAATA-TAATTTTTCAC-AAAAACTTGAATCTCATTATT
* * * * * *
1374953 TGTTGTGACAATTTTTTTTGTAACAATAATTATAGCTTATAGTTACAAAACATGTCAATATATGA
64 TGTTGTGACAAATTTTTTTGTAACAATTATTAAAACTTATAGTTACAAAACTTGTCACTATATGA
* * *
1375018 TTTTTTTTAC-C-AAA-AAT-TTGA-GATAATCATTTGTGACTATACATTTTG
129 CTTTTTTTACGCAAAACAATATGGAGGA-AATC-TTTGTGACAATACATTTTG
* * * *
1375066 TCACTATAATTAAAATATATAATTACAAACAAAATTTTTCACAACAAA-TCTAAATCTCATTATT
1 TCACTATAATTAAAATATATAACTACAAATATAATTTTTCACAA-AAACT-TGAATCTCATTATT
* * * *
1375130 TGTTGTGACAAATTTTTTTGTCACAATTACTAAAACTTTTAGTTACAAAAGTTGTCACTATATG
64 TGTTGTGACAAATTTTTTTGTAACAATTATTAAAACTTATAGTTACAAAACTTGTCACTATATG
1375194 CATTCAATTT
Statistics
Matches: 256, Mismatches: 44, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
176 5 0.02
177 82 0.32
178 47 0.18
179 3 0.01
180 3 0.01
181 27 0.11
182 87 0.34
183 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (179 bp):
TCACTATAATTAAAATATATAACTACAAATATAATTTTTCACAAAAACTTGAATCTCATTATTTG
TTGTGACAAATTTTTTTGTAACAATTATTAAAACTTATAGTTACAAAACTTGTCACTATATGACT
TTTTTTACGCAAAACAATATGGAGGAAATCTTTGTGACAATACATTTTG
Found at i:1375516 original size:45 final size:44
Alignment explanation
Indices: 1375459--1375773 Score: 267
Period size: 45 Copynumber: 7.1 Consensus size: 44
1375449 TAGTGTGTTG
* *
1375459 TTCTTGACTTTCTCATGAAGAGGAGTCAATCTTTTAGGGTTGTC
1 TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTC
* * * * *
1375503 TTCCTTGACTTTCTCGTGAAGAGAAATCAATATTTCAATGTTGTC
1 TT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTC
* * * * * *
1375548 ATTCTTGACTTTTTTGTGAAGATGAGTCAATCTTTAAAGT-TTTTA
1 -TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTT-TAGTGTTGTC
* *
1375593 TTCTTGACTTTCTCGTGAAGAGGAGTCAA-CTTTTAGTATTCTC
1 TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTC
* ** * *
1375636 ATTCTTGACTTTTTCGTGAAGAAAAGTCAATATTTTAGTGTTGGCC
1 -TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTT-GTC
* * ** *
1375682 TAT-TTGACTTTCTTGTGAAGAGAAGTCGCTCTTTAAGTGTTGTCC
1 T-TCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGT-C
*** * * *
1375727 TTCTTGACTTTCTCACAAAGATGAGTCAACCTTTTAGTGATGTC
1 TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTC
1375771 TTC
1 TTC
1375774 CTCAACTTGA
Statistics
Matches: 212, Mismatches: 49, Indels: 20
0.75 0.17 0.07
Matches are distributed among these distances:
42 3 0.01
43 7 0.03
44 60 0.28
45 136 0.64
46 6 0.03
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (44 bp):
TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTC
Found at i:1376576 original size:136 final size:134
Alignment explanation
Indices: 1376331--1376870 Score: 724
Period size: 136 Copynumber: 4.0 Consensus size: 134
1376321 ATCTTTAAAA
* * *
1376331 CAAATCATATTCGATTCAATATTCCCTGAAGAGCAGCGAAGTGAATCAAATATTTCTCGAGTCTG
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATCAAATTTTTCTCGAGTCTG
* * * ** * *
1376396 ACCTCTCCTAACGAGCAGTGGAGCAGATTCTTCTTATTTCAAGATTTGGTCTTCATGAAAAGCAG
66 ACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTTC-AGATTTGGTCTTCCTGAAAAGCAG
1376461 CGAAG
130 CGAAG
* * * *
1376466 CTAATCACATTCGATTCAATCTTCCCTGAATAGCAGTGAAGTGAATGAAAGTTTTTCTCGAGTCT
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATCAAA-TTTTTCTCGAGTCT
* *
1376531 GACCTCCCCTAAAGAGTACCAGAGCAGATTCTTCTTCTTTCAAGATTTGGTCTTCCTGAAAAGTA
65 GACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTTC-AGATTTGGTCTTCCTGAAAAGCA
1376596 GCGAAG
129 GCGAAG
* * *
1376602 CAAATCACATTCGATTCAGTCTTCCCTGAAGAGCAGTGAAGTGAATCAATTTTTTTCTCGAGTCT
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATCAA-ATTTTTCTCGAGTCT
* *
1376667 GACCTCCCCTAAAGAGTAGTAGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAG
65 GACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAAAGCAG
*
1376732 TGAAG
130 CGAAG
* * * * *
1376737 CAAATCACATTTGATTCAATCTTTCCTAAAGATCAGCGAAATGAATCAAAATTTTT-TCGAGTCT
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATC-AAATTTTTCTCGAGTCT
** * * *
1376801 GAATTCCCCTAAAGAGTAGCGGAGTAGATTATTCTTCTTTCAGATTTGGTCTTCCTGAAGAA-CA
65 GACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAA-AAGCA
1376865 GCGAAG
129 GCGAAG
1376871 TGGATCAAAA
Statistics
Matches: 359, Mismatches: 42, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
134 68 0.19
135 116 0.32
136 175 0.49
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (134 bp):
CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATCAAATTTTTCTCGAGTCTG
ACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAAAGCAGC
GAAG
Found at i:1376968 original size:90 final size:89
Alignment explanation
Indices: 1376805--1376968 Score: 213
Period size: 90 Copynumber: 1.8 Consensus size: 89
1376795 GAGTCTGAAT
* *
1376805 TCCCCTAAAGAGTAGCGGAGTAGATTATTCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGCGAA
1 TCCCCTAAAGAGTAGCGGAGCAGATCA-TCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGCGAA
***
1376870 GTGGATCAAAATTACATGTATGATC
65 GAAAATCAAAATTACATGTATGATC
* * * *
1376895 TCCCCTAAAGAGTAGTGGAGCAGACTCA-CTATCTTTCATATTTGGTCTTCTTGAAGAACAGTGA
1 TCCCCTAAAGAGTAGCGGAGCAGA-TCATCT-TCTTTCAGATTTGGTCTTCCTGAAGAACAGCGA
1376959 AGAAAATCAA
64 AGAAAATCAA
1376969 GTTCGGTTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 2 0.03
90 59 0.94
91 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (89 bp):
TCCCCTAAAGAGTAGCGGAGCAGATCATCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGCGAAG
AAAATCAAAATTACATGTATGATC
Found at i:1378362 original size:2 final size:2
Alignment explanation
Indices: 1378355--1378384 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1378345 GCTCCTGTAA
*
1378355 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1378385 GTATTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1380168 original size:7 final size:7
Alignment explanation
Indices: 1380156--1380181 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1380146 TGGATCTCAA
1380156 AAATTAT
1 AAATTAT
1380163 AAATTAT
1 AAATTAT
1380170 AAATTAT
1 AAATTAT
1380177 AAATT
1 AAATT
1380182 TTTAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTAT
Found at i:1380299 original size:27 final size:27
Alignment explanation
Indices: 1380244--1380299 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
1380234 TCATATTTGT
**
1380244 TTAAAAAAGTAATTATAATTTTATGAC
1 TTAAAAAAGTAATTATAAAGTTATGAC
*
1380271 TTAAAAAGATTAATTATAAAGTTAT-AC
1 TTAAAAA-AGTAATTATAAAGTTATGAC
1380298 TT
1 TT
1380300 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
TTAAAAAAGTAATTATAAAGTTATGAC
Found at i:1384264 original size:22 final size:21
Alignment explanation
Indices: 1384236--1384295 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
1384226 ATACATTAAT
* *
1384236 GGGTATCGATACCCTAA-TAG
1 GGGTATCGATACCATAAGCAG
1384256 GGTGATATCGATACCATAAGCAG
1 GG-G-TATCGATACCATAAGCAG
1384279 GGGTATCGATACC-TAAG
1 GGGTATCGATACCATAAG
1384296 GGATAGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.17
21 11 0.31
22 14 0.40
23 4 0.11
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (21 bp):
GGGTATCGATACCATAAGCAG
Found at i:1384270 original size:95 final size:94
Alignment explanation
Indices: 1384070--1384290 Score: 207
Period size: 95 Copynumber: 2.3 Consensus size: 94
1384060 TACCCAAGCC
* *
1384070 GTATCGATACCATGGTAAGGGTATCGATACCAGTAAACATCGAATCTAAATTAGGTATCGATACT
1 GTATCGATACCATGGTAAGGGTATCGATACAAGTAAACATCGAAGCTAAATTAGGTATCGATACT
*
1384135 TATAGGGGGTATCGGTACCATAGGATAGGG
66 TATAGGGGGTATCGATACCATA-GATAGGG
* * * * * * * *
1384165 GTATCAATACCATGGTGAGGGTATCTATACAAGGCTATA-TTCGAAGCTAATTTTGGTATTGATA
1 GTATCGATACCATGGTAAGGGTATCGATACAA-G-TAAACATCGAAGCTAAATTAGGTATCGATA
* *
1384229 CATTA-A-TGGGTATCGATACCCTA-ATAGGG
64 C-TTATAGGGGGTATCGATACCATAGATAGGG
* * *
1384258 TGATATCGATACCATAAGCAGGGGTATCGATAC
1 -G-TATCGATACCAT-GGTAAGGGTATCGATAC
1384291 CTAAGGGATA
Statistics
Matches: 101, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
93 6 0.06
94 1 0.01
95 53 0.52
96 35 0.35
97 6 0.06
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (94 bp):
GTATCGATACCATGGTAAGGGTATCGATACAAGTAAACATCGAAGCTAAATTAGGTATCGATACT
TATAGGGGGTATCGATACCATAGATAGGG
Found at i:1384287 original size:21 final size:20
Alignment explanation
Indices: 1384236--1384295 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
1384226 ATACATTAAT
*
1384236 GGGTATCGATACCCTAA-TAG
1 GGGTATCGATA-CCTAAGCAG
1384256 GGTGATATCGATACCATAAGCAG
1 GG-G-TATCGATACC-TAAGCAG
1384279 GGGTATCGATACCTAAG
1 GGGTATCGATACCTAAG
1384296 GGATAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 6 0.17
21 13 0.37
22 12 0.34
23 4 0.11
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (20 bp):
GGGTATCGATACCTAAGCAG
Found at i:1384858 original size:79 final size:79
Alignment explanation
Indices: 1384696--1384858 Score: 211
Period size: 79 Copynumber: 2.1 Consensus size: 79
1384686 AAATGAATGT
* * *
1384696 AAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGCATGCCATAGCTGAAATGCATATGAG
* * *
1384761 TACATTGTCAGCAT
66 TACATTATAAGCAA
* * * *
1384775 AAAAGAATAATGCATATGGGTGCATTGTTGGCATGAATGCATGCCATAGTTGAAATGCATATGAG
1 AAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGCATGCCATAGCTGAAATGCATATGAG
*
1384840 TGCATTAATAAG-AA
66 TACATT-ATAAGCAA
1384854 AAAAG
1 AAAAG
1384859 TATGCTAAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
79 69 0.96
80 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.26
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGCATGCCATAGCTGAAATGCATATGAG
TACATTATAAGCAA
Found at i:1384871 original size:45 final size:45
Alignment explanation
Indices: 1384820--1385037 Score: 287
Period size: 45 Copynumber: 4.9 Consensus size: 45
1384810 AATGCATGCC
* * * *
1384820 ATAGTTGAAATGCATATGAGTGCATTAAT-AAGAAAAAAGTATGCT
1 ATAGTTGAAATGCATATGGGTACATT-ATCAACAAAAAAGTATACT
* * *
1384865 AAAGTTGAAATGCATATGGGTTCATTATCAAC-AGAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAAAAAAGTATACT
* *
1384909 AGAGTTGAAATGTATATGGGTACATTATCAACAAAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAAAAAAGTATACT
* * *
1384954 ATGGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAAAAAAGTATACT
* *
1384999 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 ATAGTTGAAATGCATATGGGTACATTATCAACAAAAAAG
1385038 ATGTTAGAAT
Statistics
Matches: 154, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
44 41 0.27
45 113 0.73
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (45 bp):
ATAGTTGAAATGCATATGGGTACATTATCAACAAAAAAGTATACT
Found at i:1384935 original size:89 final size:91
Alignment explanation
Indices: 1384822--1385037 Score: 296
Period size: 89 Copynumber: 2.4 Consensus size: 91
1384812 TGCATGCCAT
* * *
1384822 AGTTGAAATGCATATGAGTGCATTAAT-AAGAAAAAAGTATGCTAAAGTTGAAATGCATATGGGT
1 AGTTGAAATGCATATGGGTGCATTAATCAACAAAAAAGTATACTAAAGTTGAAATGCATATGGGT
* *
1384886 TCATTATCAACA-GAAAGTATACTAG
66 ACATTATCAACATAAAAGTATACTAG
* * ** *
1384911 AGTTGAAATGTATATGGGTACATT-ATCAACAAAAAAGTATACTATGGTTGAAATGTATATGGGT
1 AGTTGAAATGCATATGGGTGCATTAATCAACAAAAAAGTATACTAAAGTTGAAATGCATATGGGT
*
1384975 ACATTATCAACATAAAAGTATACTAT
66 ACATTATCAACATAAAAGTATACTAG
*
1385001 AGTTGAAATGCATATGGGTGCATT-ATCAACAGAAAAG
1 AGTTGAAATGCATATGGGTGCATTAATCAACAAAAAAG
1385038 ATGTTAGAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
88 2 0.02
89 64 0.58
90 45 0.41
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (91 bp):
AGTTGAAATGCATATGGGTGCATTAATCAACAAAAAAGTATACTAAAGTTGAAATGCATATGGGT
ACATTATCAACATAAAAGTATACTAG
Found at i:1389810 original size:18 final size:17
Alignment explanation
Indices: 1389789--1389824 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1389779 AATCTAAATT
1389789 GGGTATCGATACCTATAG
1 GGGTATCGATACC-ATAG
*
1389807 GGGTATCGGTACCATAG
1 GGGTATCGATACCATAG
1389824 G
1 G
1389825 ATATAGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (17 bp):
GGGTATCGATACCATAG
Found at i:1390496 original size:79 final size:79
Alignment explanation
Indices: 1390362--1390512 Score: 239
Period size: 79 Copynumber: 1.9 Consensus size: 79
1390352 AAAACGAATG
*
1390362 TAAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
1390427 GTACATTGTCAGCA
66 GTACATTGTCAGCA
* * * * *
1390441 TAAAAGAATAATGCATATGGGTTCATTGTTGGCATGAATGGATGCCATAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
*
1390506 GTGCATT
66 GTACATT
1390513 ATCAATAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATGGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
GTACATTGTCAGCA
Found at i:1390540 original size:45 final size:45
Alignment explanation
Indices: 1390482--1390704 Score: 297
Period size: 45 Copynumber: 5.0 Consensus size: 45
1390472 GCATGAATGG
* *
1390482 ATGCCATAGTTGAAATGCATATGGGTGCATTATCAATAGAAAAGT
1 ATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGT
* *
1390527 ATGCTAAAATTGAAATGCATATGGGTGCATTATCAACAGAAAAGT
1 ATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGT
* * *
1390572 ATAG-TAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT
1 AT-GCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGT
* * * * *
1390617 AT-ATATGGTTGAAATGTATATGGGTACATTATTAACAGAAAAGT
1 ATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGT
* *
1390661 ATACTATAGTTGGAATGCATATGGGTGCATTATCAACAGAAAAG
1 ATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1390705 ATGTTAGAAT
Statistics
Matches: 158, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
44 40 0.25
45 117 0.74
46 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (45 bp):
ATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGT
Found at i:1390672 original size:89 final size:90
Alignment explanation
Indices: 1390487--1390704 Score: 312
Period size: 89 Copynumber: 2.4 Consensus size: 90
1390477 AATGGATGCC
* *
1390487 ATAGTTGAAATGCATATGGGTGCATTATCAATAGAAAAGTATGCTAAAATTGAAATGCATATGGG
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGATAAAATTGAAATGCATATGGG
* *
1390552 TGCATTATCAACAGAAAAGTATAGT
66 TACATTATCAACAGAAAAGTATACT
* * * *** *
1390577 AGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTAT-ATATGGTTGAAATGTATATGGG
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGATAAAATTGAAATGCATATGGG
*
1390641 TACATTATTAACAGAAAAGTATACT
66 TACATTATCAACAGAAAAGTATACT
*
1390666 ATAGTTGGAATGCATATGGGTGCATTATCAACAGAAAAG
1 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1390705 ATGTTAGAAT
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 74 0.66
90 38 0.34
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (90 bp):
ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGATAAAATTGAAATGCATATGGG
TACATTATCAACAGAAAAGTATACT
Found at i:1390738 original size:134 final size:133
Alignment explanation
Indices: 1390490--1390743 Score: 334
Period size: 134 Copynumber: 1.9 Consensus size: 133
1390480 GGATGCCATA
* * *
1390490 GTTGAAATGCATATGGGTGCATTATCAATAGAAAAGTATGCTAAAATTGAAATGCATATGGGTGC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAATTGAAATGCATATGGGTGC
* * *
1390555 ATTATCAACAGAAAAGTATAGTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATA
66 ATTATCAACAGAAAAGTATAGTAGAGTTAAAATGTATATGAGTA-ATTATAAACAGAAAAGTATA
1390620 TATG
130 TATG
* * * * *
1390624 GTTGAAATGTATATGGGTACATTATTAACAGAAAAGTATACTATAGTTGGAATGCATATGGGTGC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAATTGAAATGCATATGGGTGC
*
1390689 ATTATCAACAGAAAAG-AT-GTTAGAATTTAAAATGTATAATGAAGT-ATTATAAACA
66 ATTATCAACAGAAAAGTATAG-TAG-AGTTAAAATGTAT-ATG-AGTAATTATAAACA
1390744 TAAATGGAGG
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
132 1 0.01
133 5 0.05
134 93 0.89
135 3 0.03
136 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (133 bp):
GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAATTGAAATGCATATGGGTGC
ATTATCAACAGAAAAGTATAGTAGAGTTAAAATGTATATGAGTAATTATAAACAGAAAAGTATAT
ATG
Found at i:1392868 original size:19 final size:19
Alignment explanation
Indices: 1392844--1392892 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1392834 TATTTGTTCA
1392844 AGAGTGCATCGATGCATAG
1 AGAGTGCATCGATGCATAG
1392863 AGAGTGCATCGATGCATAG
1 AGAGTGCATCGATGCATAG
1392882 AGAGTGCATCG
1 AGAGTGCATCG
1392893 GTACATCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (19 bp):
AGAGTGCATCGATGCATAG
Found at i:1399284 original size:117 final size:117
Alignment explanation
Indices: 1399064--1399285 Score: 261
Period size: 117 Copynumber: 1.9 Consensus size: 117
1399054 CTTTCAAATC
* *
1399064 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* * *
1399129 CATTTTGATTTTTAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * * *
1399181 GAAAATTTCTTTTTCAA-AGTTTTTAGATTTTATTTTTGAAAGCTCTAACT-CTTTTCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
1399244 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
1399286 ATAATTTCTA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
116 5 0.06
117 78 0.90
118 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:1401285 original size:18 final size:18
Alignment explanation
Indices: 1401264--1401338 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
1401254 AAATTATTTT
*
1401264 TAAAATAAAAGAT-TAGAA
1 TAAAATAAAAGATAAAG-A
1401282 TAAAATAAAAGATAAAGA
1 TAAAATAAAAGATAAAGA
*
1401300 TAAAATAAATAAAT-AA-A
1 TAAAATAAA-AGATAAAGA
*
1401317 TAAAATATAAGGATAAA-A
1 TAAAATA-AAAGATAAAGA
1401335 TAAA
1 TAAA
1401339 TAATTAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
17 10 0.20
18 34 0.69
19 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (18 bp):
TAAAATAAAAGATAAAGA
Found at i:1401302 original size:13 final size:12
Alignment explanation
Indices: 1401281--1401338 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
1401271 AAAGATTAGA
1401281 ATAAAATAAAAG
1 ATAAAATAAAAG
1401293 ATAAAGAT-AAA-
1 ATAAA-ATAAAAG
*
1401304 AT-AAATAAATAA
1 ATAAAATAAA-AG
*
1401316 ATAAAATATAAGG
1 ATAAAATA-AAAG
1401329 ATAAAATAAA
1 ATAAAATAAA
1401339 TAATTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
9 2 0.05
10 4 0.11
11 3 0.08
12 12 0.32
13 15 0.39
14 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:1401320 original size:30 final size:30
Alignment explanation
Indices: 1401284--1401350 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1401274 GATTAGAATA
1401284 AAATAAAAGATAAAGATAAAATAAATAAAT
1 AAATAAAAGATAAAGATAAAATAAATAAAT
* * *
1401314 AAATAAAATATAAGGATAAAATAAATAATT
1 AAATAAAAGATAAAGATAAAATAAATAAAT
*
1401344 AATTAAA
1 AAATAAA
1401351 TTTATAGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (30 bp):
AAATAAAAGATAAAGATAAAATAAATAAAT
Found at i:1411868 original size:28 final size:28
Alignment explanation
Indices: 1411832--1411886 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1411822 AATAAAAGAT
* * *
1411832 AAAGATAAAATGATTAATTAATTAAATA
1 AAAGATAAAATAAATAAATAATTAAATA
1411860 AAAGATAAAATAAATAAATAATTAAAT
1 AAAGATAAAATAAATAAATAATTAAAT
1411887 TTAAAGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAGATAAAATAAATAAATAATTAAATA
Found at i:1411891 original size:34 final size:34
Alignment explanation
Indices: 1411821--1411907 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
1411811 ATTATTTTTA
* *
1411821 AAATAAAAGATAAAGATAAAATGATTAATTAATT
1 AAATAAAAGATAAAGATAAAATAAATAATTAATT
1411855 AAATAAAAGATAAA-AT-AAATAAATAATTAAATTT
1 AAATAAAAGATAAAGATAAAATAAATAATT-AA-TT
1411889 AAAGTAATTAAGATAAAGA
1 AAA-TAA--AAGATAAAGA
1411908 GAAACTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 10 0.22
33 4 0.09
34 19 0.42
35 3 0.07
37 8 0.18
38 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (34 bp):
AAATAAAAGATAAAGATAAAATAAATAATTAATT
Found at i:1419356 original size:41 final size:40
Alignment explanation
Indices: 1419309--1419388 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
1419299 CCTTGATTTA
* *
1419309 AATTGAATTGGTTTGTGAATTAATACATGTTATCATGATCT
1 AATTGAATTGGTTTGTGAATAAATACATG-TACCATGATCT
*
1419350 AATTGAATTGGTTTGTGAATAAATGCATGTACCATGATC
1 AATTGAATTGGTTTGTGAATAAATACATGTACCATGATC
1419389 GAATCAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 9 0.25
41 27 0.75
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (40 bp):
AATTGAATTGGTTTGTGAATAAATACATGTACCATGATCT
Found at i:1419707 original size:41 final size:41
Alignment explanation
Indices: 1419379--1419695 Score: 388
Period size: 41 Copynumber: 7.7 Consensus size: 41
1419369 TAAATGCATG
*
1419379 TACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGT
1 TACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGC
*
1419420 TACCATGATCGAATCAAGTTGAACGGTGAATTATTGTATGC
1 TACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGC
* * * *
1419461 TTCCATGATAGAATCAAGTTGAACGGTGAATTATTTTATGC
1 TACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGC
*
1419502 TACCATGATCGAATCAAGTTGAATGGTGAAGTAATT-TATGC
1 TACCATGATCGAATCAAGTTGAATGGTGAA-TTATTGTATGC
* * * *
1419543 TGCCATGATTGAATTGAA-TTGAATGGTGAATTATTGCATGC
1 TACCATGATCGAA-TCAAGTTGAATGGTGAATTATTGTATGC
** * *
1419584 TACCATGATCGAATCAAGTTGAATTATGAACTATTGTATTC
1 TACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGC
* * * * *
1419625 TGCCATGATTGAATTGAA-TCGAATGGTGAATTATTGCATGC
1 TACCATGATCGAA-TCAAGTTGAATGGTGAATTATTGTATGC
* *
1419666 TACCATGATCGAATTAAGTTGAATGATGAA
1 TACCATGATCGAATCAAGTTGAATGGTGAA
1419696 CAATTGCATG
Statistics
Matches: 234, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
40 10 0.04
41 214 0.91
42 10 0.04
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (41 bp):
TACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGC
Found at i:1419721 original size:82 final size:82
Alignment explanation
Indices: 1419397--1419730 Score: 406
Period size: 82 Copynumber: 4.1 Consensus size: 82
1419387 TCGAATCAAG
* * * * **
1419397 TTGAATGGTGAATTATTGTATGTTACCATGATCGAATCAAGTTGAACGGTGAATTATTGTATGCT
1 TTGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAATGATGAACAATTGTATGCT
* *
1419462 TCCATGATAGAA-TCAA
66 GCCATGATAGAATTGAA
* ** * *
1419478 GTTGAACGGTGAATTATTTTATGCTACCATGATCGAATCAAGTTGAATGGTGAAGTAATT-TATG
1 -TTGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAATGATGAA-CAATTGTATG
*
1419542 CTGCCATGATTGAATTGAA
64 CTGCCATGATAGAATTGAA
* * *
1419561 TTGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAATTATGAACTATTGTATTCT
1 TTGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAATGATGAACAATTGTATGCT
*
1419626 GCCATGATTGAATTGAA
66 GCCATGATAGAATTGAA
* * *
1419643 TCGAATGGTGAATTATTGCATGCTACCATGATCGAATTAAGTTGAATGATGAACAATTGCATGCT
1 TTGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAATGATGAACAATTGTATGCT
*
1419708 GTCAAT-ATAGAATTTG-A
66 G-CCATGATAGAA-TTGAA
1419725 TTGAAT
1 TTGAAT
1419731 TGAAACCTTG
Statistics
Matches: 222, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
81 3 0.01
82 206 0.93
83 13 0.06
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (82 bp):
TTGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAATGATGAACAATTGTATGCT
GCCATGATAGAATTGAA
Found at i:1419873 original size:24 final size:24
Alignment explanation
Indices: 1419846--1419898 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1419836 AATAATGATT
*
1419846 TCTTGGCAAATATGATTCAATGTC
1 TCTTGGCAAATAAGATTCAATGTC
1419870 TCTTGGCAAATAAGATTCAATGTC
1 TCTTGGCAAATAAGATTCAATGTC
1419894 -CTTGG
1 TCTTGG
1419899 TTAACAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
TCTTGGCAAATAAGATTCAATGTC
Found at i:1424027 original size:25 final size:25
Alignment explanation
Indices: 1423999--1424053 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1423989 TTAGCTCATA
*
1423999 GATGTAGAACTCTCATCCACACCAT
1 GATGTAGAACTCTCAGCCACACCAT
*
1424024 GATGTAGAACTCTTAGCCACACCAT
1 GATGTAGAACTCTCAGCCACACCAT
1424049 GATGT
1 GATGT
1424054 CTACTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (25 bp):
GATGTAGAACTCTCAGCCACACCAT
Found at i:1425281 original size:21 final size:21
Alignment explanation
Indices: 1425243--1425304 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
1425233 TCATAAAAGG
1425243 ATTTTATATTATATTTTTAAT
1 ATTTTATATTATATTTTTAAT
*
1425264 ATTTTCTATTA-ATTTTTTCATAT
1 ATTTTATATTATA-TTTTT-A-AT
*
1425287 AATTTGATATTATATTTT
1 -ATTTTATATTATATTTT
1425305 ATTGTACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.03
21 15 0.45
22 1 0.03
23 2 0.06
24 13 0.39
25 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTATATTATATTTTTAAT
Found at i:1425464 original size:50 final size:48
Alignment explanation
Indices: 1425354--1425487 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 48
1425344 ACCAATTAAC
*
1425354 ACATATTTACACCAGTGTAAGTATGTAAATCTCCCAACTTAAAAATAA
1 ACATAATTACACCAGTGTAAGTATGTAAATCTCCCAACTTAAAAATAA
* * * *
1425402 ACATGTACTTACATCAGTGTAAGTATGTATATCTCCCAACTTGAAAATAAGA
1 ACA--TAATTACACCAGTGTAAGTATGTAAATCTCCCAACTTAAAAAT-A-A
* * * *
1425454 ACATAATTACACCGGTATAAGTTTGTACATCTCC
1 ACATAATTACACCAGTGTAAGTATGTAAATCTCC
1425488 TATATTATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 3 0.04
50 64 0.89
51 1 0.01
52 4 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (48 bp):
ACATAATTACACCAGTGTAAGTATGTAAATCTCCCAACTTAAAAATAA
Found at i:1437285 original size:2 final size:2
Alignment explanation
Indices: 1437278--1437311 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1437268 AGATCCTCCC
*
1437278 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1437312 CTTCTCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1440843 original size:32 final size:34
Alignment explanation
Indices: 1440800--1440878 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 34
1440790 AGAAGAAATA
1440800 AAAAAAT--GAAAAAAATGGAAAAAGG-AAAAGG
1 AAAAAATGAGAAAAAAATGGAAAAAGGTAAAAGG
* * *
1440831 -AAAAATGAGAAAAAAATTGAAAATGGTTAAAGG
1 AAAAAATGAGAAAAAAATGGAAAAAGGTAAAAGG
1440864 AAAAAATGA-AAAAAA
1 AAAAAATGAGAAAAAA
1440879 GAAGAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
32 16 0.39
33 11 0.27
34 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (34 bp):
AAAAAATGAGAAAAAAATGGAAAAAGGTAAAAGG
Found at i:1440886 original size:33 final size:31
Alignment explanation
Indices: 1440800--1440887 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 31
1440790 AGAAGAAATA
1440800 AAAAAATGAAAAAAATG-GAAAAAGGAAAAGG
1 AAAAAATGAAAAAAA-GAGAAAAAGGAAAAGG
* *
1440831 -AAAAATGAGAAAAAA-ATTGAAAATGGTTAAAGG
1 AAAAAATGA-AAAAAAGA--GAAAAAGG-AAAAGG
1440864 AAAAAATGAAAAAAAGAAGAAAAA
1 AAAAAATGAAAAAAAG-AGAAAAA
1440888 ATGAAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
30 8 0.17
31 6 0.13
32 7 0.15
33 16 0.35
34 8 0.17
35 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.10
Consensus pattern (31 bp):
AAAAAATGAAAAAAAGAGAAAAAGGAAAAGG
Found at i:1440887 original size:19 final size:19
Alignment explanation
Indices: 1440863--1440963 Score: 72
Period size: 19 Copynumber: 5.3 Consensus size: 19
1440853 ATGGTTAAAG
1440863 GAAAAAATGAAAAAAAGAA
1 GAAAAAATGAAAAAAAGAA
*
1440882 GAAAAAATGAAAAAATGAA
1 GAAAAAATGAAAAAAAGAA
1440901 -AAAACAA-GAAAACAAA-AA
1 GAAAA-AATGAAAA-AAAGAA
1440919 -AAAAAGA-GAAAAACAA-AA
1 GAAAAA-ATGAAAAA-AAGAA
*
1440937 AATGAAAAATGAAAAAATAG-A
1 GA--AAAAATGAAAAAA-AGAA
1440958 GAAAAA
1 GAAAAA
1440964 TAAAAGGGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
17 2 0.03
18 25 0.36
19 27 0.39
20 2 0.03
21 13 0.19
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.06
Consensus pattern (19 bp):
GAAAAAATGAAAAAAAGAA
Found at i:1440894 original size:7 final size:8
Alignment explanation
Indices: 1440863--1440968 Score: 58
Period size: 8 Copynumber: 12.6 Consensus size: 8
1440853 ATGGTTAAAG
1440863 GAAAAAAT
1 GAAAAAAT
*
1440871 GAAAAAAAGAA
1 G--AAAAA-AT
1440882 GAAAAAAT
1 GAAAAAAT
1440890 GAAAAAAT
1 GAAAAAAT
*
1440898 GAAAAAACAA
1 G-AAAAA-AT
1440908 GAAAACAA-
1 GAAAA-AAT
* *
1440916 AAAAAAAA
1 GAAAAAAT
1440924 GAGAAAAA-
1 GA-AAAAAT
*
1440932 CAAAAAAT
1 GAAAAAAT
1440940 G-AAAAAT
1 GAAAAAAT
1440947 GAAAAAAT
1 GAAAAAAT
1440955 AGAGAAAAAT
1 -GA-AAAAAT
1440965 -AAAA
1 GAAAA
1440969 GGGGATTCAA
Statistics
Matches: 79, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
7 17 0.22
8 24 0.30
9 22 0.28
10 14 0.18
11 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (8 bp):
GAAAAAAT
Found at i:1440963 original size:42 final size:43
Alignment explanation
Indices: 1440863--1440963 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 43
1440853 ATGGTTAAAG
*
1440863 GAAAAAAT-GAAAAAAAGAAGAAAAAATGAAAAAATGAAAAAA
1 GAAAAAATAGAAAAAAAGAAGAAAAAATCAAAAAATGAAAAAA
* * *
1440905 CAAGAAAACA-AAAAAAA-AAGAGAAAAA-CAAAAAATGAAAAAT
1 GAA-AAAATAGAAAAAAAGAAGA-AAAAATCAAAAAATGAAAAAA
*
1440947 GAAAAAATAGAGAAAAA
1 GAAAAAATAGAAAAAAA
1440964 TAAAAGGGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
41 5 0.10
42 27 0.56
43 16 0.33
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.06
Consensus pattern (43 bp):
GAAAAAATAGAAAAAAAGAAGAAAAAATCAAAAAATGAAAAAA
Found at i:1442244 original size:37 final size:36
Alignment explanation
Indices: 1442180--1442254 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
1442170 AAACAAGTCA
*
1442180 ATCTTAAACCTTCACGAAGAGTGGTGAAGCAAA-TC
1 ATCTTAAACCTTCACGAAGAGTAGTGAAGCAAACTC
*
1442215 ATCTATAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAACCTTCAC-GAAGAGTAGTGAAGCAAACTC
1442253 AT
1 AT
1442255 TTTATGAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 4 0.11
36 10 0.29
37 17 0.49
38 4 0.11
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (36 bp):
ATCTTAAACCTTCACGAAGAGTAGTGAAGCAAACTC
Found at i:1442552 original size:55 final size:51
Alignment explanation
Indices: 1442259--1442610 Score: 382
Period size: 51 Copynumber: 6.7 Consensus size: 51
1442249 ACTCATTTTA
* * * *
1442259 TGAAGATCAAGTCCTATACTCTCT-AAAGAAATAGGGAGCGGACACGCTTGT
1 TGAAGATCGAGTCTTATACTCTCTGAAAG-AATAGGGAGCAGACACGTTTGT
* * *
1442310 TGAATATCGAGTCTTATACTCTCTAAAAGAATAGGGAGCAGACATGTTTGT
1 TGAAGATCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
* ***
1442361 TGAAGATCGAGTCTTATACTCTCTGAATGAATAGGGAATGGACACGTTTGT
1 TGAAGATCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
* * *
1442412 TGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACATGTTTGT
1 TGAAGATCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
* * * * *
1442463 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCATACCCGTTTAT
1 TGAAGATCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
* * * * *
1442514 TGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACATTTAT
1 TGAAGA----TCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
* *
1442569 CGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAG
1 TGAAGA----TCGAGTCTTATACTCTCTGAAAGAATAGGGAG
1442611 TGGACCCGTC
Statistics
Matches: 263, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
51 182 0.69
52 4 0.02
55 77 0.29
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
TGAAGATCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
Found at i:1447913 original size:20 final size:20
Alignment explanation
Indices: 1447888--1447930 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1447878 TCTGAGATCC
*
1447888 CATTTAGGACCATATAGATG
1 CATTTAGAACCATATAGATG
* *
1447908 CATTTAGAAGCATATAGCTG
1 CATTTAGAACCATATAGATG
1447928 CAT
1 CAT
1447931 GTGGTGGAAT
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:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1448597 original size:20 final size:20
Alignment explanation
Indices: 1448574--1448615 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1448564 TGCTGGGGGC
1448574 AGTTCGTGGTGGCTGAGGGA
1 AGTTCGTGGTGGCTGAGGGA
1448594 AGTTCGTGGTGGCTGAGGGA
1 AGTTCGTGGTGGCTGAGGGA
1448614 AG
1 AG
1448616 CTCCGGCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.10, G:0.50, T:0.24
Consensus pattern (20 bp):
AGTTCGTGGTGGCTGAGGGA
Found at i:1461890 original size:30 final size:30
Alignment explanation
Indices: 1461820--1461890 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
1461810 ATTGACCTCA
* * *
1461820 ACTCAACTCGAAAAGTTTAAACTGAGCTCG
1 ACTCAACTCGAAAAGTTTAAAATGAGATAG
** *
1461850 ACTCGGCTCGAAATGTTTAAAGATGAGATAG
1 ACTCAACTCGAAAAGTTTAAA-ATGAGATAG
1461881 ACTC-ACTCGA
1 ACTCAACTCGA
1461891 CTTGAAAGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (30 bp):
ACTCAACTCGAAAAGTTTAAAATGAGATAG
Found at i:1465817 original size:17 final size:18
Alignment explanation
Indices: 1465787--1465823 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1465777 AATTAAATTA
1465787 TTAAATTTTGTTA-TATT
1 TTAAATTTTGTTATTATT
1465804 TTAATATTTT-TTATTATT
1 TTAA-ATTTTGTTATTATT
1465822 TT
1 TT
1465824 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTAAATTTTGTTATTATT
Found at i:1468244 original size:2 final size:2
Alignment explanation
Indices: 1468232--1468266 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1468222 TTATTTAACC
1468232 AT AT A- 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
1468267 TTTATATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1470518 original size:2 final size:2
Alignment explanation
Indices: 1470511--1470543 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1470501 TATTTGTGTT
1470511 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 T
1470544 TCTTTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1472320 original size:26 final size:25
Alignment explanation
Indices: 1472285--1472340 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
1472275 TTAGCATATT
* *
1472285 TAAAAAC-AAAACTTTAAAAATAAAG
1 TAAAAACAAAAACTTGAAAAA-AAAA
1472310 TAAAAATCAAAAACTTGAAAAAAAAA
1 TAAAAA-CAAAAACTTGAAAAAAAAA
1472336 TAAAA
1 TAAAA
1472341 GAGAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.22
26 9 0.33
27 12 0.44
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (25 bp):
TAAAAACAAAAACTTGAAAAAAAAA
Found at i:1476086 original size:40 final size:40
Alignment explanation
Indices: 1476040--1476150 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
1476030 AAGGACACTA
*
1476040 AGTGTATATGGTGGGCACGACCTTATGTGTAATACATTTC
1 AGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTC
* *
1476080 -GATGTATATGGTGGGCACAACCTTATTTGTAATACACTTC
1 AG-TGTATATGGTGGGCACGACCTTATGTGTAATACACTTC
1476120 AGTGTATATGGTGGGCACGACCTTATGTGTA
1 AGTGTATATGGTGGGCACGACCTTATGTGTA
1476151 GCACTATGCT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.02
40 62 0.97
41 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (40 bp):
AGTGTATATGGTGGGCACGACCTTATGTGTAATACACTTC
Found at i:1484783 original size:28 final size:28
Alignment explanation
Indices: 1484751--1484811 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1484741 ATATTCCCTC
1484751 TCTTTGAGAAC-TTGAAACATTGCATTTA
1 TCTTTGAG-ACTTTGAAACATTGCATTTA
**
1484779 TCTTTTTGACTTTGAAACATTGCATTTA
1 TCTTTGAGACTTTGAAACATTGCATTTA
1484807 TCTTT
1 TCTTT
1484812 TTCGATTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (28 bp):
TCTTTGAGACTTTGAAACATTGCATTTA
Found at i:1485440 original size:18 final size:17
Alignment explanation
Indices: 1485419--1485489 Score: 52
Period size: 19 Copynumber: 3.9 Consensus size: 17
1485409 AAAACCAAAT
1485419 AAGAGAAAAAAAAAAGCA
1 AAGA-AAAAAAAAAAGCA
*
1485437 AAGAAAGAAAAATAAAGAA
1 AAGAAA-AAAAA-AAAGCA
* **
1485456 AAAATAAAAATAAAAAATA
1 AAGA-AAAAA-AAAAAGCA
*
1485475 AAGAAAAAAACAAAG
1 AAGAAAAAAAAAAAG
1485490 GAAAAAAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 6 0.14
18 14 0.33
19 18 0.43
20 4 0.10
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (17 bp):
AAGAAAAAAAAAAAGCA
Found at i:1485445 original size:20 final size:20
Alignment explanation
Indices: 1485392--1485448 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1485382 AAGATCAAAT
*
1485392 CAAAGCAAAGAGAGAAAAAAAC
1 CAAAG-AAAGA-AAAAAAAAAC
* *
1485414 CAAATAAGAGAAAAAAAAAAG
1 CAAAGAA-AGAAAAAAAAAAC
1485435 CAAAGAAAGAAAAA
1 CAAAGAAAGAAAAA
1485449 TAAAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.23
21 16 0.53
22 7 0.23
ACGTcount: A:0.74, C:0.09, G:0.16, T:0.02
Consensus pattern (20 bp):
CAAAGAAAGAAAAAAAAAAC
Found at i:1485460 original size:11 final size:11
Alignment explanation
Indices: 1485440--1485483 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
1485430 AAAAGCAAAG
1485440 AAAG-AAAAAT
1 AAAGAAAAAAT
1485450 AAAGAAAAAAT
1 AAAGAAAAAAT
*
1485461 AAAAATAAAAAAT
1 --AAAGAAAAAAT
1485474 AAAGAAAAAA
1 AAAGAAAAAA
1485484 ACAAAGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 4 0.14
11 15 0.52
13 10 0.34
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (11 bp):
AAAGAAAAAAT
Found at i:1485483 original size:13 final size:13
Alignment explanation
Indices: 1485426--1485510 Score: 70
Period size: 13 Copynumber: 6.4 Consensus size: 13
1485416 AATAAGAGAA
*
1485426 AAAAAAAAGCAAAG
1 AAAAAAAA-TAAAG
1485440 AAAGAAAAATAAAG
1 AAA-AAAAATAAAG
1485454 --AAAAAATAAA-
1 AAAAAAAATAAAG
1485464 AATAAAAAATAAAG
1 AA-AAAAAATAAAG
*
1485478 AAAAAAACA-AAGG
1 AAAAAAA-ATAAAG
1485491 AAAAAAAGAGTAAAG
1 AAAAAAA-A-TAAAG
1485506 AAAAA
1 AAAAA
1485511 CGAAGAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 26 0.44
14 10 0.17
15 13 0.22
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (13 bp):
AAAAAAAATAAAG
Found at i:1485494 original size:24 final size:24
Alignment explanation
Indices: 1485440--1485496 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1485430 AAAAGCAAAG
1485440 AAAG-AAAAATAAAGAAAAAATAA
1 AAAGAAAAAATAAAGAAAAAATAA
*
1485463 AAATAAAAAATAAAGAAAAAA-ACA
1 AAAGAAAAAATAAAGAAAAAATA-A
*
1485487 AAGGAAAAAA
1 AAAGAAAAAA
1485497 AGAGTAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.82, C:0.02, G:0.09, T:0.07
Consensus pattern (24 bp):
AAAGAAAAAATAAAGAAAAAATAA
Found at i:1485533 original size:17 final size:17
Alignment explanation
Indices: 1485442--1485536 Score: 53
Period size: 17 Copynumber: 5.9 Consensus size: 17
1485432 AAGCAAAGAA
1485442 AGAAAAATAAAGAAAAA-
1 AGAAAAAT-AAGAAAAAG
* *
1485459 ATAAAAATAA-AAAATAA
1 AGAAAAATAAGAAAA-AG
*
1485476 AG-AAAA-AA-ACAAAG
1 AGAAAAATAAGAAAAAG
*
1485490 -GAAAAA-AAGAGTAAAG
1 AGAAAAATAAGA-AAAAG
**
1485506 A-AAAACGAAGAAAAAG
1 AGAAAAATAAGAAAAAG
1485522 AGAAAAATAAGAAAA
1 AGAAAAATAAGAAAA
1485537 GAAGCACATG
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
13 1 0.02
14 7 0.11
15 10 0.16
16 20 0.33
17 23 0.38
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (17 bp):
AGAAAAATAAGAAAAAG
Found at i:1487078 original size:36 final size:37
Alignment explanation
Indices: 1486981--1487081 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 37
1486971 GTTATTTTCA
* *
1486981 TAAAAACAAATTTTGTCTCGCTTGAGATAGTTTTATC
1 TAAAAACAAATTTTGTCTCGCTTGAGACAGATTTATC
* * *
1487018 TAAAAACAAATTTTGTCTTGCTTGATACA-ATTTCTC
1 TAAAAACAAATTTTGTCTCGCTTGAGACAGATTTATC
* * *
1487054 TTAAAACAAATTTCGTCTCACTTGAGAC
1 TAAAAACAAATTTTGTCTCGCTTGAGAC
1487082 CTTATTCCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 28 0.52
37 26 0.48
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (37 bp):
TAAAAACAAATTTTGTCTCGCTTGAGACAGATTTATC
Found at i:1487258 original size:36 final size:35
Alignment explanation
Indices: 1487212--1487327 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 35
1487202 ATTTGAGATT
*
1487212 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTT-TCTCTCTTGAGACA
* * * *
1487248 ATTTCTCTTGAAAC--A---TCCTCT-TTGAGTCT
1 GTTTCTCTTGAAACAAATTTTTCTCTCTTGAGACA
*
1487277 GTTTCTCTTGAAA-AACATTTTTTCTCCCTTGAGACA
1 GTTTCTCTTGAAACAA-A-TTTTTCTCTCTTGAGACA
1487313 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1487328 CAAGATCTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
29 18 0.30
30 4 0.07
31 2 0.03
34 1 0.02
35 4 0.07
36 31 0.51
37 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (35 bp):
GTTTCTCTTGAAACAAATTTTTCTCTCTTGAGACA
Found at i:1487297 original size:65 final size:64
Alignment explanation
Indices: 1487159--1487393 Score: 264
Period size: 65 Copynumber: 3.6 Consensus size: 64
1487149 GTTTTTCTCA
* * * *
1487159 AAACAAACTTTGTCTCACTTGAGACAATTT-TCCTT-AAGC-CAATATTTGAGATTGTTTCCCTT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCT-CTTGAAACACAATCTTTGAG-TTGTTTCCCTT
1487221 G
64 G
* * *
1487222 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATC-CTCTTTGAGTCTGTTTCTCTT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACA-CAATCTTTGAGT-TGTTTCCCTT
1487286 G
64 G
* * *
1487287 AAA-AACATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACACAAGATCTTTGAGTGTGTATCCC
1 AAACAA-ATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAC-A-ATCTTTGAGT-TGTTTCCC
1487351 TTG
62 TTG
1487354 AAACAAAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAA
1 AAACAAA-TTTTGTCTCCCTTGAGACAATTTCTCTTGAAA
1487394 TAAATCCCTA
Statistics
Matches: 146, Mismatches: 15, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
63 31 0.21
64 8 0.05
65 52 0.36
66 1 0.01
67 22 0.15
68 32 0.22
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (64 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAATCTTTGAGTTGTTTCCCTTG
Found at i:1487550 original size:40 final size:40
Alignment explanation
Indices: 1487418--1487556 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 40
1487408 CGGTCAGCCA
**
1487418 TCCTCATCACGTAGGAA-TCGTGTCATCCACCGACCAGATC
1 TCCTCATCACGTAGGAACT-GTGTCATCCACAAACCAGATC
* * * * *
1487458 TCCTCATCACGTAGGAGCTGCGTGAACCTTAGATAACCAG-TC
1 TCCTCATCACGTAGGAACTGTGTCATCC--ACA-AACCAGATC
1487500 GTCCTCATCACGTAGGAACTGTGTCATCCACAAACCAGATC
1 -TCCTCATCACGTAGGAACTGTGTCATCCACAAACCAGATC
* *
1487541 TCTTTATCACGTAGGA
1 TCCTCATCACGTAGGA
1487557 GCCGCGTCAC
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
40 42 0.53
41 5 0.06
42 3 0.04
43 29 0.37
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACTGTGTCATCCACAAACCAGATC
Done.