Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 181 of 193
Found at i:56502707 original size:29 final size:30
Alignment explanation
Indices: 56502675--56502763 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 30
56502665 TTGATTTAAT
56502675 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTGTATACATGAAACTTTAATTTG
* * * *
56502704 GTGCAATTATACACGTGAAACTCTAATTGTG
1 GTGCAATTGTATACATGAAACTTTAATT-TG
** * *
56502735 GTTTAAATGTATACTTGAAACTTTAATTT
1 GTGCAATTGTATACATGAAACTTTAATTT
56502764 TGATTTAATC
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 14 0.30
30 10 0.21
31 23 0.49
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (30 bp):
GTGCAATTGTATACATGAAACTTTAATTTG
Found at i:56504339 original size:92 final size:90
Alignment explanation
Indices: 56504197--56504405 Score: 264
Period size: 92 Copynumber: 2.3 Consensus size: 90
56504187 TTAAGAATAT
* * * *
56504197 AAAAAGCTCTCAAAC--TTTC-TAAAAAAAAGCAATTAAGCTATTTTTTTTTGCATTCATTTGGG
1 AAAAAGCTCTCAAACTTTTTCAAAAAAAAAAGCAATTAAGCTATTTTTTTTTGCACTCAATTGAG
* *
56504259 TACTTGAACTTTCAAACTGCAT-AA
66 TACTTAAACTTTCAAAATGCATAAA
*
56504283 AAAAAGCCCTCAAACTTTTTCAAAAAAAAAAGCAATTAAGTCCCTATTTTTTTTTGCACTCAATT
1 AAAAAGCTCTCAAACTTTTTCAAAAAAAAAAGCAATTAAG---CTATTTTTTTTTGCACTCAATT
*
56504348 GAGTACTTAAACTTTTAAAATGCATAAA
63 GAGTACTTAAACTTTCAAAATGCATAAA
* *
56504376 AAAAATACTCTCAAAATTTTTCAAAAAAAA
1 AAAAA-GCTCTCAAACTTTTTCAAAAAAAA
56504406 CTTTTATTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
86 14 0.13
88 4 0.04
89 17 0.16
92 41 0.39
93 7 0.07
94 21 0.20
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (90 bp):
AAAAAGCTCTCAAACTTTTTCAAAAAAAAAAGCAATTAAGCTATTTTTTTTTGCACTCAATTGAG
TACTTAAACTTTCAAAATGCATAAA
Found at i:56504480 original size:21 final size:20
Alignment explanation
Indices: 56504455--56504498 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
56504445 AGTTATAAAT
**
56504455 ATTATTAAATTTTAATAAAAA
1 ATTATTAAAAATTAA-AAAAA
56504476 ATTATTAAAAATTAAAAAAA
1 ATTATTAAAAATTAAAAAAA
56504496 ATT
1 ATT
56504499 GTAAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATTAAAAATTAAAAAAA
Found at i:56504843 original size:20 final size:20
Alignment explanation
Indices: 56504818--56504856 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
56504808 GTTAAAGATA
56504818 TTTTTTGATGCATTT-TATAT
1 TTTTTTGATG-ATTTCTATAT
*
56504838 TTTTTTTATGATTTCTATA
1 TTTTTTGATGATTTCTATA
56504857 AAATTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTTTGATGATTTCTATAT
Found at i:56504937 original size:10 final size:10
Alignment explanation
Indices: 56504917--56504986 Score: 65
Period size: 10 Copynumber: 7.2 Consensus size: 10
56504907 GTTTAATAAA
56504917 TTTTAAA-TT
1 TTTTAAATTT
*
56504926 TTTTATATTT
1 TTTTAAATTT
*
56504936 TTATTAAAATT
1 TT-TTAAATTT
**
56504947 TAAT-AATTT
1 TTTTAAATTT
*
56504956 TTCTAAA-TT
1 TTTTAAATTT
56504965 TTTTAAATTT
1 TTTTAAATTT
56504975 TTTTAAATTT
1 TTTTAAATTT
56504985 TT
1 TT
56504987 AATAAGAGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 20 0.42
10 21 0.44
11 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:56504973 original size:19 final size:19
Alignment explanation
Indices: 56504917--56504986 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
56504907 GTTTAATAAA
*
56504917 TTTTAAATTTTTTATATTT
1 TTTTAAATTTTTTAAATTT
* *
56504936 TTATTAAA-ATTTAATAATTT
1 TT-TTAAATTTTTTA-AATTT
*
56504956 TTCTAAATTTTTTAAATTT
1 TTTTAAATTTTTTAAATTT
56504975 TTTTAAATTTTT
1 TTTTAAATTTTT
56504987 AATAAGAGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAAATTTTTTAAATTT
Found at i:56505501 original size:30 final size:30
Alignment explanation
Indices: 56505467--56505524 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56505457 TTAGTAAAAG
*
56505467 TAAAATTACATTTTAACCCTTTAAAAATGA
1 TAAAATTACAATTTAACCCTTTAAAAATGA
* * *
56505497 TAAAATTTCAATTTAATCTTTTAAAAAT
1 TAAAATTACAATTTAACCCTTTAAAAAT
56505525 TATATTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (30 bp):
TAAAATTACAATTTAACCCTTTAAAAATGA
Found at i:56505523 original size:22 final size:22
Alignment explanation
Indices: 56505498--56505556 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
56505488 TAAAAATGAT
* *
56505498 AAAATTTCAATTTAATCTTTTA
1 AAAATTTCAATTTAATATTATA
* *
56505520 AAAATTAT-ATTTTACTATTATA
1 AAAATT-TCAATTTAATATTATA
*
56505542 AAAATTACAATTTAA
1 AAAATTTCAATTTAA
56505557 CTCCGATCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATTTCAATTTAATATTATA
Found at i:56506122 original size:18 final size:18
Alignment explanation
Indices: 56506099--56506162 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
56506089 TTTTGGTACT
*
56506099 TTTTTTACTGTTTTGTTG
1 TTTTTTACTGTTTTGTTA
**
56506117 TTTTTTGTTGTTTTGATGTTA
1 TTTTTTACTG-TTT--TGTTA
*
56506138 TTTTTTACTGTTTTGATA
1 TTTTTTACTGTTTTGTTA
56506156 CTTTTTT
1 -TTTTTT
56506163 TTAATGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 12 0.33
19 9 0.25
20 3 0.08
21 12 0.33
ACGTcount: A:0.09, C:0.05, G:0.14, T:0.72
Consensus pattern (18 bp):
TTTTTTACTGTTTTGTTA
Found at i:56506136 original size:21 final size:21
Alignment explanation
Indices: 56506112--56506227 Score: 76
Period size: 21 Copynumber: 5.4 Consensus size: 21
56506102 TTTACTGTTT
*
56506112 TGTTGTTTTTTGTTGTTTTGA
1 TGTTGTTTTTTATTGTTTTGA
* *
56506133 TGTTATTTTTTACTGTTTTGA
1 TGTTGTTTTTTATTGTTTTGA
* *
56506154 TACTT-TTTTTTAATGTTTTGA
1 T-GTTGTTTTTTATTGTTTTGA
* *
56506175 TGCTGTTTTTACTATTATTTT--
1 TGTTGTTTTT--TATTGTTTTGA
* * *
56506196 TGTTACTTTTTTGTTGTTTTTGT
1 TGTT-GTTTTTTATTG-TTTTGA
56506219 TGTTGTTTT
1 TGTTGTTTT
56506228 ACTGTTATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
20 4 0.05
21 47 0.64
22 11 0.15
23 11 0.15
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.70
Consensus pattern (21 bp):
TGTTGTTTTTTATTGTTTTGA
Found at i:56506206 original size:23 final size:23
Alignment explanation
Indices: 56506180--56506327 Score: 62
Period size: 23 Copynumber: 6.7 Consensus size: 23
56506170 TTTGATGCTG
56506180 TTTTTACTATTATTTTTGTTAC-
1 TTTTTACTATTATTTTTGTTACT
* * *
56506202 TTTTT--TGTTGTTTTTGTT-GT
1 TTTTTACTATTATTTTTGTTACT
* * *
56506222 TGTTTTACTGTTATTTTTGCTGCT
1 T-TTTTACTATTATTTTTGTTACT
* * *
56506246 GTTTTGATTGTTATTTTTGTTA-T
1 -TTTTTACTATTATTTTTGTTACT
** *
56506269 TTGGT--TATTATTTTT-TATACG
1 TTTTTACTATTATTTTTGT-TACT
*
56506290 TTTTTACTATTA-TTTCGTTATCT
1 TTTTTACTATTATTTTTGTTA-CT
* *
56506313 TTTTTAATATCATTT
1 TTTTTACTATTATTT
56506328 GAATATTGTA
Statistics
Matches: 92, Mismatches: 21, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
19 1 0.01
20 23 0.25
21 7 0.08
22 12 0.13
23 29 0.32
24 19 0.21
25 1 0.01
ACGTcount: A:0.14, C:0.07, G:0.11, T:0.68
Consensus pattern (23 bp):
TTTTTACTATTATTTTTGTTACT
Found at i:56506228 original size:43 final size:44
Alignment explanation
Indices: 56506181--56506266 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
56506171 TTGATGCTGT
* *
56506181 TTTTACTATTATTTTTGTTACTTTTTTG-TTGTT-TTTGTTGTTG
1 TTTTACTATTATTTTTGCTACTGTTTTGATTGTTATTT-TTGTTG
* *
56506224 TTTTACTGTTATTTTTGCTGCTGTTTTGATTGTTATTTTTGTT
1 TTTTACTATTATTTTTGCTACTGTTTTGATTGTTATTTTTGTT
56506267 ATTTGGTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 24 0.65
44 10 0.27
45 3 0.08
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (44 bp):
TTTTACTATTATTTTTGCTACTGTTTTGATTGTTATTTTTGTTG
Found at i:56506450 original size:27 final size:27
Alignment explanation
Indices: 56506396--56506450 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
56506386 CTTAATATAA
*
56506396 ATTTTTTAATGTTTTTTAAATTTGTTT
1 ATTTTTTAATGTTTTTTAAATGTGTTT
*
56506423 ATTTTTTAATGTTTGTTTTAATGT-TTT
1 ATTTTTTAATGTTT-TTTAAATGTGTTT
56506450 A
1 A
56506451 AGTGTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (27 bp):
ATTTTTTAATGTTTTTTAAATGTGTTT
Found at i:56507720 original size:16 final size:17
Alignment explanation
Indices: 56507696--56507736 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
56507686 TTACAATTTA
56507696 TTAAATAAAA-ATTATC
1 TTAAATAAAATATTATC
*
56507712 TTAATTAAAATATTAT-
1 TTAAATAAAATATTATC
*
56507728 TTCAATAAA
1 TTAAATAAA
56507737 GTGCTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAAAATATTATC
Found at i:56510716 original size:6 final size:6
Alignment explanation
Indices: 56510705--56510729 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56510695 CTCTTCAGCC
56510705 CTGCAT CTGCAT CTGCAT CTGCAT C
1 CTGCAT CTGCAT CTGCAT CTGCAT C
56510730 GTAACAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CTGCAT
Found at i:56512495 original size:106 final size:106
Alignment explanation
Indices: 56512372--56512563 Score: 235
Period size: 106 Copynumber: 1.8 Consensus size: 106
56512362 AAAAATATCC
* ** * * * * *
56512372 TTAAAATAAAGATATTTTGGTAATTTAACAATTTAGTTGGGAGCCGGTTATGGGTGACATC-AAT
1 TTAAAATAAAGACATTTTAATAATTTAACAACTGAATTGAGAGCCGGTTATGAGTGACA-CAAAT
**
56512436 TCAATTTGAATCTTTATATATAGTATAAGATTTATTGCTATG
65 TCAATAAGAATCTTTATATATAGTATAAGATTTATTGCTATG
* *
56512478 TTAAAATAAATG-CATTTTAATAATTTAATAACTGAATTGAGATCCGGTTATGAGTGACACAAAT
1 TTAAAATAAA-GACATTTTAATAATTTAACAACTGAATTGAGAGCCGGTTATGAGTGACACAAAT
*
56512542 TCAATAAGAATCTTTGTATATA
65 TCAATAAGAATCTTTATATATA
56512564 TAGATATACA
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
105 1 0.01
106 69 0.97
107 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (106 bp):
TTAAAATAAAGACATTTTAATAATTTAACAACTGAATTGAGAGCCGGTTATGAGTGACACAAATT
CAATAAGAATCTTTATATATAGTATAAGATTTATTGCTATG
Found at i:56513429 original size:13 final size:12
Alignment explanation
Indices: 56513398--56513425 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
56513388 GAGATATAGT
56513398 AAAATATTTTAA
1 AAAATATTTTAA
56513410 AAAATATTTTAA
1 AAAATATTTTAA
56513422 AAAA
1 AAAA
56513426 ATATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:56518017 original size:152 final size:152
Alignment explanation
Indices: 56517741--56518044 Score: 527
Period size: 152 Copynumber: 2.0 Consensus size: 152
56517731 AATAGACTAC
* * * *
56517741 ATATGTGTCACTTGTGTACTTTGAAGTAAGTAAAAGCTTGAGTCCAAGTAGATAAGGAATCGAAA
1 ATATGTGTCACTCGTATACTTTGAAGTAAGTAAAAGCTTGAGTCCAAATAAATAAGGAATCGAAA
*
56517806 GTTGTTGCGTTGAGTATATGACTTCTGCAGTATGTAGCATCATTAATAATAGTGGAATTCATAGC
66 GTTGTTGCGTTGAGTATATGACTTCTACAGTATGTAGCATCATTAATAATAGTGGAATTCATAGC
56517871 CTAAGAAATGGATAAATGATAT
131 CTAAGAAATGGATAAATGATAT
* *
56517893 ATATGTGTCACTCGTATACTTTGATGTAAGTAAAAGCTTGAGTTCAAATAAATAAGGAATCGAAA
1 ATATGTGTCACTCGTATACTTTGAAGTAAGTAAAAGCTTGAGTCCAAATAAATAAGGAATCGAAA
*
56517958 GTTGTTGCGTTGGGTATATGACTTCTACAGTATGTAGCATCATTAATAATAGTGGAATTCATAGC
66 GTTGTTGCGTTGAGTATATGACTTCTACAGTATGTAGCATCATTAATAATAGTGGAATTCATAGC
*
56518023 CTAAGAAATGGGTAAATGATAT
131 CTAAGAAATGGATAAATGATAT
56518045 CCTCTCATTG
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 143 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (152 bp):
ATATGTGTCACTCGTATACTTTGAAGTAAGTAAAAGCTTGAGTCCAAATAAATAAGGAATCGAAA
GTTGTTGCGTTGAGTATATGACTTCTACAGTATGTAGCATCATTAATAATAGTGGAATTCATAGC
CTAAGAAATGGATAAATGATAT
Found at i:56520610 original size:216 final size:216
Alignment explanation
Indices: 56520229--56521617 Score: 2041
Period size: 216 Copynumber: 6.4 Consensus size: 216
56520219 TTTTACTTTT
* * * *
56520229 TTTCTCGCTTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTAAAACTT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
* * * *
56520294 CCATTCCTTAAAGTATTCAATACGATCCATTCCTTCGTGCAATTTTTCAAACATTCCATGCTCGA
66 CCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGG
* * *
56520359 GAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTGTAGGTCTTTGAATTAAA
131 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
*
56520424 AATTTATTTATGTGAGAATTG
196 AACTTATTTATGTGAGAATTG
** *
56520445 TTTCTCTCTTGGTTCTTGGCTAAACTTCCAAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
* * *
56520510 CGGTTCCTTAAAGTATTCAAGACGATCCATTCATTCGAGCAATTTTTCGAACATTCCATGCTCGG
66 CCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGG
* * * * *
56520575 GAAATTGCATCATTTGGTCTAAATAATTTGTCATTTTGTAAAAAACTTTTGATCTTTGAATTATA
131 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
56520640 AACTTATTTATGTGAGAATTG
196 AACTTATTTATGTGAGAATTG
*
56520661 TTTCTCTCTTGGTTCTCGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
** * *
56520726 CAATTCCTTAAAGTATTCAAGACGATTCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGG
66 CCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGG
* * *
56520791 GAAATTGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAAACTTTTGATCTTTGAATTAA
131 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGT-AAACAACTTTTGGTCTTTGAATTAA
*
56520856 AAACTTATTTAGGTGAGAATTG
195 AAACTTATTTATGTGAGAATTG
* **
56520878 TTTCTTTCTTGGTT-TTCGGCCGAACTTCTAAACTTGACAAACTTTTACGAGTTCTTTTATAACT
1 TTTCTCTCTTGGTTCTT-GGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
** *
56520942 TTGGTTCCTTAAAGTATTCAAGACGA-CTAGTTCCTTCGAGCAATTTTTCAAACATTCCATGCTC
65 TCCGTTCCTTAAAGTATTCAAGACGATCCA-TTCCTTCGAGCAATTTTTCAAACATTCCATGCTC
* * *
56521006 GGGAAATCGCATCATTTGATCTAAATAGTTTGCCATTTTGTAAACAACTTTTGGTATTTGAATTA
129 GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* * *
56521071 TAAATTTATTTATATGAGAATTG
194 AAAACTTATTTATGTGAGAATTG
* * *
56521094 TTTCTCTCTTGGTTCTTTGCCGAACTCCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
* * *
56521159 CCGTTCCTTAAAGTATTCAATACGATCCATTCCTTCGTGCAATTTTTCAAACATTCCATGCTCGA
66 CCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGG
* * *
56521224 AAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTATA
131 GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
** *
56521289 AACTTATTTACATGAGGATTG
196 AACTTATTTATGTGAGAATTG
* * * * * * *
56521310 TGTCTCTTTTGGTTCTTTGCCGAACTCCCGAACTTGTCAAACTTTTA-GAAATTATTTTATAACT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACG-AGTTCTTTTATAACT
* * *
56521374 TCCGTTCCTTAAAGTATTCAATATGATCCATTCCTTCGTGCAATTTTTCAAACATTCCATGCTCG
65 TCCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCG
*
56521439 GGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTATTTGAATTAA
130 GGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAA
*
56521504 AAACTTATTTA-GATGAAAATTG
195 AAACTTATTTATG-TGAGAATTG
* * *
56521526 TTTCTCTCTTGGTTCTTGGCCAAAGTTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
*
56521591 -CGATTCTTTAAAGTATTCAAGACGATC
66 CCG-TTCCTTAAAGTATTCAAGACGATC
56521618 ATCCCATTGA
Statistics
Matches: 1064, Mismatches: 100, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
215 3 0.00
216 859 0.81
217 202 0.19
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (216 bp):
TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
CCGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGG
GAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAA
AACTTATTTATGTGAGAATTG
Found at i:56521473 original size:649 final size:648
Alignment explanation
Indices: 56520229--56521617 Score: 2104
Period size: 649 Copynumber: 2.1 Consensus size: 648
56520219 TTTTACTTTT
* * * * *
56520229 TTTCTCGCTTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTAAAACTT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
* * *
56520294 CCATTCCTTAAAGTATTCAATACGATCCATTCCTTCGTGCAATTTTTCAAACATTCCATGCTCGA
66 CGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGA
* *
56520359 GAAATCGCATCATTTAGTCTAAATAGTTTGTCATTTTGTAAACAACTGTAGGTCTTTGAATTAAA
131 GAAATCGCATCATTTAGTCTAAATAGTTTGCCATTTTGTAAACAACTGTAGGTATTTGAATTAAA
* * *
56520424 AATTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCTAAACTTCCAAACTTGACAAACTT
196 AATTTATTTATATGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTCCCAAACTTGACAAACTT
*
56520489 TTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCATTCGAGCAATT
261 TTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCATTCGAGCAATT
* ** *
56520554 TTTCGAACATTCCATGCTCGGGAAATTGCATCATTTGGTCTAAATAATTTGTCATTTTGTAAAAA
326 TTTCAAACATTCCATGCTCGAAAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTAAAAA
** *
56520619 ACTTTTGATCTTTGAATTATAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTCGGCCGA
391 ACTTTTGATCTTTGAATTATAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTCGGCCGA
* * *
56520684 ACTTCCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTCAATTCCTTAAAGTATTCAAGAC
456 ACTCCCGAACTTGACAAACTTTTACGAATTATTTTATAACTTCAATTCCTTAAAGTATTCAAGAC
* * *
56520749 GATTCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATTGCATCATTTGGTCTAAA
521 GATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
* * *
56520814 TAGTTTGTCATTTTGTAAAAAAACTTTTGATCTTTGAATTAAAAACTTATTTAGGTGAGAATTG
586 TAGTTTGTCATTTTGT-AAAAAACTTTTGATATTTGAATTAAAAACTTATTTAGATGAAAATTG
* *
56520878 TTTCTTTCTTGGTT-TTCGGCCGAACTTCTAAACTTGACAAACTTTTACGAGTTCTTTTATAACT
1 TTTCTCTCTTGGTTCTT-GGCCGAACTTCTGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
* * *
56520942 TTGGTTCCTTAAAGTATTCAAGACGA-CTAGTTCCTTCGAGCAATTTTTCAAACATTCCATGCTC
65 TCGATTCCTTAAAGTATTCAAGACGATCCA-TTCCTTCGAGCAATTTTTCAAACATTCCATGCTC
* * *
56521006 GGGAAATCGCATCATTT-GATCTAAATAGTTTGCCATTTTGTAAACAACTTTTGGTATTTGAATT
129 GAGAAATCGCATCATTTAG-TCTAAATAGTTTGCCATTTTGTAAACAACTGTAGGTATTTGAATT
* * * * *
56521070 ATAAATTTATTTATATGAGAATTGTTTCTCTCTTGGTTCTTTGCCGAACTCCCGAACTTGTCAAA
193 AAAAATTTATTTATATGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTCCCAAACTTGACAAA
* * *
56521135 CTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAATACGATCCATTCCTTCGTGCA
258 CTTTTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCATTCGAGCA
* *
56521200 ATTTTTCAAACATTCCATGCTCGAAAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAA
323 ATTTTTCAAACATTCCATGCTCGAAAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTAA
* * * * **
56521265 ACAACTTTTGGTCTTTGAATTATAAACTTATTTACATGAGGATTGTGTCTCTTTTGGTTCTTTGC
388 AAAACTTTTGATCTTTGAATTATAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTCGGC
* **
56521330 CGAACTCCCGAACTTGTCAAACTTTTA-GAAATTATTTTATAACTTCCGTTCCTTAAAGTATTCA
453 CGAACTCCCGAACTTGACAAACTTTTACG-AATTATTTTATAACTTCAATTCCTTAAAGTATTCA
* * *
56521394 ATATGATCCATTCCTTCGTGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
517 AGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTC
* *
56521459 TAAATAGTTTGTCATTTTGTAAACAACTTTTGGTATTTGAATTAAAAACTTATTTAGATGAAAAT
582 TAAATAGTTTGTCATTTTGTAAAAAACTTTTGATATTTGAATTAAAAACTTATTTAGATGAAAAT
56521524 TG
647 TG
* *
56521526 TTTCTCTCTTGGTTCTTGGCCAAAGTT-TCGAACTTGACAAACTTTTACGAGTTCTTTTATAACT
1 TTTCTCTCTTGGTTCTTGGCCGAACTTCT-GAACTTGACAAACTTTTACGAGTTCTTTTATAACT
*
56521590 TCGATTCTTTAAAGTATTCAAGACGATC
65 TCGATTCCTTAAAGTATTCAAGACGATC
56521618 ATCCCATTGA
Statistics
Matches: 664, Mismatches: 69, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
647 1 0.00
648 126 0.19
649 537 0.81
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (648 bp):
TTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGACAAACTTTTACGAGTTCTTTTATAACTT
CGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGA
GAAATCGCATCATTTAGTCTAAATAGTTTGCCATTTTGTAAACAACTGTAGGTATTTGAATTAAA
AATTTATTTATATGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTCCCAAACTTGACAAACTT
TTACGAGTTCTTTTATAACTTCCGTTCCTTAAAGTATTCAAGACGATCCATTCATTCGAGCAATT
TTTCAAACATTCCATGCTCGAAAAATCGCATCATTTGGTCTAAATAATTTGTCATTTTGTAAAAA
ACTTTTGATCTTTGAATTATAAACTTATTTACATGAGAATTGTGTCTCTCTTGGTTCTCGGCCGA
ACTCCCGAACTTGACAAACTTTTACGAATTATTTTATAACTTCAATTCCTTAAAGTATTCAAGAC
GATCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAA
TAGTTTGTCATTTTGTAAAAAACTTTTGATATTTGAATTAAAAACTTATTTAGATGAAAATTG
Found at i:56524866 original size:6 final size:6
Alignment explanation
Indices: 56524832--56524905 Score: 53
Period size: 6 Copynumber: 12.5 Consensus size: 6
56524822 TAATAGGGAT
* * * * *
56524832 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA CTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * *
56524879 TTTCAC TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTTCAA TTT
56524906 TGATCACAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
4 1 0.02
5 3 0.05
6 50 0.88
7 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Found at i:56524874 original size:18 final size:19
Alignment explanation
Indices: 56524851--56524902 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
56524841 ACAATTCATA
*
56524851 TCACTTTCAATTTCAAC-T
1 TCACTTTCACTTTCAACTT
56524869 TCACTTTCACTTTC-ACTT
1 TCACTTTCACTTTCAACTT
56524887 TCACTTTCACTTTCAA
1 TCACTTTCACTTTCAA
56524903 TTTTGATCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 2 0.06
18 28 0.90
19 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (19 bp):
TCACTTTCACTTTCAACTT
Found at i:56524876 original size:12 final size:12
Alignment explanation
Indices: 56524851--56524901 Score: 77
Period size: 12 Copynumber: 4.2 Consensus size: 12
56524841 ACAATTCATA
*
56524851 TCACTTTCAATT
1 TCACTTTCACTT
56524863 TCAAC-TTCACTT
1 TC-ACTTTCACTT
56524875 TCACTTTCACTT
1 TCACTTTCACTT
56524887 TCACTTTCACTT
1 TCACTTTCACTT
56524899 TCA
1 TCA
56524902 ATTTTGATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (12 bp):
TCACTTTCACTT
Found at i:56533220 original size:17 final size:17
Alignment explanation
Indices: 56533198--56533258 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
56533188 TTTTATTATT
56533198 AATTTAAATTTTAATTA
1 AATTTAAATTTTAATTA
* **
56533215 AATTTAAATTTAAAGCA
1 AATTTAAATTTTAATTA
56533232 AATTTAAATTTTTACATTTA
1 AATTTAAA-TTTTA-A-TTA
56533252 AATTTAA
1 AATTTAA
56533259 TCATAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 22 0.63
18 4 0.11
19 1 0.03
20 8 0.23
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTTAATTA
Found at i:56533221 original size:6 final size:6
Alignment explanation
Indices: 56533198--56533272 Score: 57
Period size: 6 Copynumber: 12.5 Consensus size: 6
56533188 TTTTATTATT
* **
56533198 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
* *
56533246 CATTTA AATTT- AATCATA AATTTA AAT
1 AATTTA AATTTA AAT-TTA AATTTA AAT
56533273 CTTGTTCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
5 10 0.19
6 35 0.66
7 3 0.06
8 5 0.09
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:56534075 original size:6 final size:6
Alignment explanation
Indices: 56534041--56534108 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
56534031 TAATAGGGAT
* * * * *
56534041 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA CTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
56534088 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
56534109 TGATCACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 44 0.86
7 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Found at i:56534083 original size:18 final size:18
Alignment explanation
Indices: 56534060--56534108 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
56534050 ACAATTCATA
56534060 TCACTTTCAATTTCAAC-T
1 TCACTTTCAATTTC-ACTT
*
56534078 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCACTT
56534096 TCACTTTCAATTT
1 TCACTTTCAATTT
56534109 TGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCACTT
Found at i:56534085 original size:12 final size:13
Alignment explanation
Indices: 56534062--56534104 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
56534052 AATTCATATC
*
56534062 ACTTTCAATTTCA
1 ACTTTCACTTTCA
56534075 AC-TTCACTTTC-
1 ACTTTCACTTTCA
56534086 ACTTTCACTTTC-
1 ACTTTCACTTTCA
56534098 ACTTTCA
1 ACTTTCA
56534105 ATTTTGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:56536225 original size:20 final size:19
Alignment explanation
Indices: 56536190--56536239 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
56536180 CCATTCAATT
*
56536190 ATTTTGTTTTC-T-TTTCA
1 ATTTTCTTTTCTTATTTCA
56536207 ATTTTCTTATTCTTATTTCA
1 ATTTTCTT-TTCTTATTTCA
56536227 ATTTTCTTTTCTT
1 ATTTTCTTTTCTT
56536240 TCTCGAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.24
18 3 0.10
19 6 0.21
20 13 0.45
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTCTTTTCTTATTTCA
Found at i:56538620 original size:17 final size:16
Alignment explanation
Indices: 56538598--56538639 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
56538588 TAATAAAAAT
56538598 ATAATTTTATTATTTTA
1 ATAATTTTA-TATTTTA
*
56538615 ATAA-TTTATATTTTT
1 ATAATTTTATATTTTA
56538630 ATAATGTTTA
1 ATAAT-TTTA
56538640 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
17 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
ATAATTTTATATTTTA
Found at i:56538624 original size:24 final size:25
Alignment explanation
Indices: 56538597--56538645 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
56538587 ATAATAAAAA
* *
56538597 TATAATTTTATTAT-TTTAATAATT
1 TATAATTTTATAATGTTTAAAAATT
*
56538621 TATATTTTTATAATGTTTAAAAATT
1 TATAATTTTATAATGTTTAAAAATT
56538646 AAATTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TATAATTTTATAATGTTTAAAAATT
Found at i:56541063 original size:5 final size:5
Alignment explanation
Indices: 56541049--56541098 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
56541039 TAAATAATAT
* *
56541049 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TTTAA TTTTA TTTAA TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
56541099 CATATGATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:56543810 original size:3 final size:3
Alignment explanation
Indices: 56543802--56543834 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
56543792 TCTTCAGATT
*
56543802 ATG ATG ATG ATG ATG ATG CTG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
56543835 GCGCTGAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:56548031 original size:17 final size:19
Alignment explanation
Indices: 56548009--56548044 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
56547999 GTTTGTAGGA
56548009 AGATGTTG-A-TTTGATGC
1 AGATGTTGAATTTTGATGC
56548026 AGATGTTGAATTTTGATGC
1 AGATGTTGAATTTTGATGC
56548045 CTATCGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.42
Consensus pattern (19 bp):
AGATGTTGAATTTTGATGC
Found at i:56550493 original size:15 final size:16
Alignment explanation
Indices: 56550475--56550508 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56550465 TCATTTAGAG
*
56550475 ATTTTGT-AATAAACT
1 ATTTTGTGAATAAAAT
56550490 ATTTTGTGAATAAAAT
1 ATTTTGTGAATAAAAT
56550506 ATT
1 ATT
56550509 CTTTAGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (16 bp):
ATTTTGTGAATAAAAT
Found at i:56555756 original size:105 final size:105
Alignment explanation
Indices: 56555574--56555762 Score: 360
Period size: 105 Copynumber: 1.8 Consensus size: 105
56555564 TTATCAAGGC
* *
56555574 CACCATCTAATTTTATAAAGAGGTCGCCAATACCACACCCAACAGCACCTAGAACAAAGACCCCT
1 CACCATATAATTTTATAAAGAGGTCGCCAATACCACACCCAACAGCACCCAGAACAAAGACCCCT
56555639 GAGAGGAACAATGAAGTGGTGTCCACCGTTGGGAAGGGCT
66 GAGAGGAACAATGAAGTGGTGTCCACCGTTGGGAAGGGCT
56555679 CACCATATAATTTTATAAAGAGGTCGCCAATACCACACCCAACAGCACCCAGAACAAAGACCCCT
1 CACCATATAATTTTATAAAGAGGTCGCCAATACCACACCCAACAGCACCCAGAACAAAGACCCCT
56555744 GAGAGGAACAATGAAGTGG
66 GAGAGGAACAATGAAGTGG
56555763 GGAAGGACTC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 82 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (105 bp):
CACCATATAATTTTATAAAGAGGTCGCCAATACCACACCCAACAGCACCCAGAACAAAGACCCCT
GAGAGGAACAATGAAGTGGTGTCCACCGTTGGGAAGGGCT
Found at i:56560635 original size:99 final size:99
Alignment explanation
Indices: 56560460--56560652 Score: 305
Period size: 99 Copynumber: 1.9 Consensus size: 99
56560450 AATCGAATCA
* * *
56560460 GATTTTGCTCACCCCTACTCTCAAATGATATCATACCCCACGATTTAATGCAAGAAACTTTTTGT
1 GATTTTGCTCACCCCTACGCTCAAATGATATCATACCCCACGATATAATGCAAGAAACCTTTTGT
**
56560525 ATTTGCATAACTCTCAAATTATATCATACGTTAC
66 ATTTGCATAACTCTCAAAAAATATCATACGTTAC
* * *
56560559 GATTTTGCTTACCCCTACGCTCAAATGATTTCGTACCCCACGATATAATGCAAGAAACCTTTTGT
1 GATTTTGCTCACCCCTACGCTCAAATGATATCATACCCCACGATATAATGCAAGAAACCTTTTGT
*
56560624 ATTTGCGTAACTCTCAAAAAATATCATAC
66 ATTTGCATAACTCTCAAAAAATATCATAC
56560653 CCCACGATAT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (99 bp):
GATTTTGCTCACCCCTACGCTCAAATGATATCATACCCCACGATATAATGCAAGAAACCTTTTGT
ATTTGCATAACTCTCAAAAAATATCATACGTTAC
Found at i:56562186 original size:7 final size:7
Alignment explanation
Indices: 56562174--56562210 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
56562164 TGAAGCTTCC
56562174 TTTGCTT
1 TTTGCTT
56562181 TTTGCTT
1 TTTGCTT
56562188 TTTGCTT
1 TTTGCTT
56562195 TTTGCTT
1 TTTGCTT
*
56562202 TCTGCTT
1 TTTGCTT
56562209 TT
1 TT
56562211 ACATATCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.16, G:0.14, T:0.70
Consensus pattern (7 bp):
TTTGCTT
Found at i:56566127 original size:11 final size:11
Alignment explanation
Indices: 56566095--56566127 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
56566085 CCATATTAAT
*
56566095 ATTTTTATATT
1 ATTTTTATATA
56566106 ATTTTTATATA
1 ATTTTTATATA
56566117 ATTTTTATATA
1 ATTTTTATATA
56566128 TATAATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:56566162 original size:8 final size:9
Alignment explanation
Indices: 56566136--56566160 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
56566126 TATATAATGC
56566136 ATTAAAAAT
1 ATTAAAAAT
56566145 ATTAAAAAT
1 ATTAAAAAT
56566154 ATTAAAA
1 ATTAAAA
56566161 TAAATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:56566281 original size:30 final size:30
Alignment explanation
Indices: 56566238--56566302 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
56566228 TAACTTAATA
*
56566238 AACAAATAACTCTAAAATAATAACAAAATT
1 AACAAACAACTCTAAAATAATAACAAAATT
*
56566268 AACAAACACCTCTAAAATAATAACAAAATT
1 AACAAACAACTCTAAAATAATAACAAAATT
56566298 AACAA
1 AACAA
56566303 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (30 bp):
AACAAACAACTCTAAAATAATAACAAAATT
Found at i:56566831 original size:62 final size:62
Alignment explanation
Indices: 56566755--56566878 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
56566745 TGCTTAACAT
56566755 CACATCAATTCACATTAACGATAAAATGAGGATACATTACCAGCGTAATCACAAGCTTTACC
1 CACATCAATTCACATTAACGATAAAATGAGGATACATTACCAGCGTAATCACAAGCTTTACC
56566817 CACATCAATTCACATTAACGATAAAATGAGGATACATTACCAGCGTAATCACAAGCTTTACC
1 CACATCAATTCACATTAACGATAAAATGAGGATACATTACCAGCGTAATCACAAGCTTTACC
56566879 TTGACCCTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24
Consensus pattern (62 bp):
CACATCAATTCACATTAACGATAAAATGAGGATACATTACCAGCGTAATCACAAGCTTTACC
Found at i:56575181 original size:15 final size:14
Alignment explanation
Indices: 56575151--56575194 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
56575141 TTAACTCGAA
*
56575151 TAATTTAAATTATT
1 TAATTTAAATTTTT
56575165 TAATTTAAAATTTTT
1 TAATTT-AAATTTTT
56575180 T-ATATTAAATTTTT
1 TAAT-TTAAATTTTT
56575194 T
1 T
56575195 GAGTCGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAATTTAAATTTTT
Found at i:56582415 original size:2 final size:2
Alignment explanation
Indices: 56582410--56582457 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
56582400 ATTTTTTTTA
56582410 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
56582452 AT AT AT
1 AT AT AT
56582458 TTACTTGTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56585048 original size:51 final size:51
Alignment explanation
Indices: 56584989--56585128 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 51
56584979 CTATAAACGA
* * * *
56584989 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAAAT
* *
56585040 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCATGATGAAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAAAT
* * * *
56585091 ATAGGTCCAATGACTCAGTGTCATCGTGAGTATATGAA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA
56585129 CTTCTATACA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 78 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAAAT
Found at i:56587124 original size:23 final size:23
Alignment explanation
Indices: 56587079--56587131 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
56587069 ATGCTAGCGC
** *
56587079 GCTTACTGTTTCGCATTTTGTGT
1 GCTTACTGTTTCGCACCTCGTGT
56587102 GCTTACTGTTTCGCACCTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
*
56587125 GCCTACT
1 GCTTACT
56587132 AATTTGTGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTCGTGT
Found at i:56587185 original size:23 final size:23
Alignment explanation
Indices: 56587143--56587200 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
56587133 ATTTGTGCTA
*
56587143 TGTGCGCCTACT-GATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
56587165 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACTGGATTGCACTG
*
56587188 TGTGTGCTTACTG
1 TGTGTGCCTACTG
56587201 TTTCTCCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.12, C:0.22, G:0.29, T:0.36
Consensus pattern (23 bp):
TGTGTGCCTACTGGATTGCACTG
Found at i:56591397 original size:94 final size:94
Alignment explanation
Indices: 56591239--56591667 Score: 616
Period size: 94 Copynumber: 4.6 Consensus size: 94
56591229 TTTAAAATTA
* * * *
56591239 ATTTAACATTATTTAAATAAAAAA-GATTAGTATAATATTTCAATTTATATCAAATAATGTGTTG
1 ATTTAACTTTATTTAAATAAAAAACTATTA-T-T-ATATTACAATTTTTATCAAATAATGTGTTG
* *
56591303 ATTTGAGAATATATTATTTA-TCAAATTTTAAT
63 ATTTGACAATACATTATTTACT-AAATTTTAAT
* *
56591335 ATTTAACTTTATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
* *
56591400 TAACAATATATTATTTACTAAATTTTAAT
66 TGACAATACATTATTTACTAAATTTTAAT
* *
56591429 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATATGTTAATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
56591494 TGACAATACATTATTTA-TCAAATTTTAAT
66 TGACAATACATTATTTACT-AAATTTTAAT
* * * *
56591523 ATTTAACTTTATTTAAATCAAAAACTATTTTTATATTAAAATTTTTATCAAATAA--TATTGATT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
*
56591586 TGATAATACATTATTTACTAAATTTTAAT
66 TGACAATACATTATTTACTAAATTTTAAT
*
56591615 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTCTTATCAAAT
1 ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAAT
56591668 TTTAAATTTA
Statistics
Matches: 306, Mismatches: 23, Indels: 12
0.90 0.07 0.04
Matches are distributed among these distances:
92 81 0.26
93 2 0.01
94 193 0.63
95 2 0.01
96 24 0.08
97 4 0.01
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (94 bp):
ATTTAACTTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTACTAAATTTTAAT
Found at i:56591412 original size:48 final size:47
Alignment explanation
Indices: 56591360--56591519 Score: 125
Period size: 46 Copynumber: 3.4 Consensus size: 47
56591350 AATAAAAAAT
* *
56591360 TATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTAACAATA
1 TATTATTATATTA-AATTTTTATCAAATAATATGTTAATTTAACAATA
* * * * * *
56591408 TATTATT-TACTAAATTTTAATATTTAACT-TTAT-TTAA-ATAA-AAAA
1 TATTATTATATTAAATTTT--TA-TCAAATAATATGTTAATTTAACAATA
*
56591453 CTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTGACAATA
1 -TATTATTATATTA-AATTTTTATCAAATAATATGTTAATTTAACAATA
* *
56591502 CATTATT-TATCAAATTTT
1 TATTATTATATTAAATTTT
56591520 AATATTTAAC
Statistics
Matches: 85, Mismatches: 17, Indels: 22
0.69 0.14 0.18
Matches are distributed among these distances:
45 7 0.08
46 27 0.32
47 19 0.22
48 25 0.29
49 7 0.08
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (47 bp):
TATTATTATATTAAATTTTTATCAAATAATATGTTAATTTAACAATA
Found at i:56591796 original size:22 final size:22
Alignment explanation
Indices: 56591761--56591819 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
56591751 AGACCACTCA
*
56591761 AAATT-CAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCG
* *
56591782 AAATTCCACCTCACCAAAATCG
1 AAATTCCAGCTCACCAAAACCG
56591804 AAATTCCAGCTCACCA
1 AAATTCCAGCTCACCA
56591820 CCACCCAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.39, C:0.36, G:0.07, T:0.19
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCG
Found at i:56591860 original size:10 final size:10
Alignment explanation
Indices: 56591837--56591885 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
56591827 ACTTTCGTCG
*
56591837 TTGACCGCCA
1 TTGATCGCCA
* *
56591847 TTGATCGACT
1 TTGATCGCCA
56591857 TTGATCGCCA
1 TTGATCGCCA
56591867 TTGATCGCCA
1 TTGATCGCCA
56591877 TTGATCGCC
1 TTGATCGCC
56591886 GTTGTCCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (10 bp):
TTGATCGCCA
Found at i:56592901 original size:22 final size:22
Alignment explanation
Indices: 56592863--56592924 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
56592853 ATGATGTAAG
* *
56592863 ATATTTTTTTCGAATTTTTTATA
1 ATATTTTTTTC-TATTTTTTAAA
56592886 ATATTTTTTTCTATTTTTTAAA
1 ATATTTTTTTCTATTTTTTAAA
* *
56592908 ATGTTTTTTTATATTTT
1 ATATTTTTTTCTATTTT
56592925 CGAAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (22 bp):
ATATTTTTTTCTATTTTTTAAA
Found at i:56592933 original size:31 final size:30
Alignment explanation
Indices: 56592898--56592994 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
56592888 ATTTTTTTCT
56592898 ATTTTTTAAAATGTTTTTTTATATTTTCGAA
1 ATTTTTTAAAAT-TTTTTTTATATTTTCGAA
* * *
56592929 ATTTTTAAAAATAAAATTTTATATATTTTCGAA
1 ATTTTTTAAAAT---TTTTTTTATATTTTCGAA
* *
56592962 ATATTTTT-AAATTATTTTTTATATCTTCAAA
1 AT-TTTTTAAAATT-TTTTTTATATTTTCGAA
56592993 AT
1 AT
56592995 GAAATTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
31 27 0.51
33 22 0.42
34 4 0.08
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (30 bp):
ATTTTTTAAAATTTTTTTTATATTTTCGAA
Found at i:56592982 original size:33 final size:32
Alignment explanation
Indices: 56592898--56592985 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
56592888 ATTTTTTTCT
* *
56592898 ATTTTTTAAAATGTTTTTT-TATATTTTCGAA
1 ATTTTTTAAATTATTTTTTATATATTTTCGAA
* * **
56592929 ATTTTTAAAAATAAAATTTTATATATTTTCGAA
1 ATTTTT-TAAATTATTTTTTATATATTTTCGAA
56592962 ATATTTTTAAATTATTTTTTATAT
1 AT-TTTTTAAATTATTTTTTATAT
56592986 CTTCAAAATG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
31 6 0.14
32 7 0.16
33 27 0.61
34 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (32 bp):
ATTTTTTAAATTATTTTTTATATATTTTCGAA
Found at i:56594187 original size:30 final size:30
Alignment explanation
Indices: 56594153--56594270 Score: 166
Period size: 30 Copynumber: 4.0 Consensus size: 30
56594143 TGATTTTTTC
* *
56594153 CGTTTATTTTTTAAATTTAATTTGTAATTT
1 CGTTTATATTTTAAATTTAATTTCTAATTT
56594183 CGTTTATATTTTAAATTTAATTTCTAATTT
1 CGTTTATATTTTAAATTTAATTTCTAATTT
* * *
56594213 CCTGTATATTTTAATTTTAATTTCTAATTT
1 CGTTTATATTTTAAATTTAATTTCTAATTT
* *
56594243 -TTTTATATTTTAAATTTCATTTCTAATT
1 CGTTTATATTTTAAATTTAATTTCTAATT
56594271 ATTAATTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 24 0.30
30 55 0.70
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (30 bp):
CGTTTATATTTTAAATTTAATTTCTAATTT
Found at i:56594188 original size:23 final size:23
Alignment explanation
Indices: 56594162--56594206 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
56594152 CCGTTTATTT
*
56594162 TTTA-AATTTAATTTGTAATTTCG
1 TTTATAATTTAAATT-TAATTTCG
*
56594185 TTTATATTTTAAATTTAATTTC
1 TTTATAATTTAAATTTAATTTC
56594207 TAATTTCCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTATAATTTAAATTTAATTTCG
Found at i:56595142 original size:59 final size:59
Alignment explanation
Indices: 56595074--56595580 Score: 208
Period size: 59 Copynumber: 8.7 Consensus size: 59
56595064 GAAATGAAAG
* * *
56595074 AAAGTTGGTGTCAGTCAATGCATGGCCAATACAAAAAATTTGA-AATTTTCTCAGATAAAA
1 AAAG-TGGTGTCAGTCAATGCATGGCCAACACAAAAAAATTGATAATTTTATCAGAT-AAA
* **
56595134 AAAGTGGTGTCAG-CCATGCAATGGCCAACACAAAAAAATTGATTTTTTTATCAGATAAA
1 AAAGTGGTGTCAGTCAATGC-ATGGCCAACACAAAAAAATTGATAATTTTATCAGATAAA
* * * * **
56595193 AAGGGGGTGTCGGTCAATGCATGGCCAACACAAAAAAAGTTAAATTTTTTTATCAGA-AAA
1 AAAGTGGTGTCAGTCAATGCATGGCCAACACAAAAAAA-TT-GATAATTTTATCAGATAAA
** * ** *
56595253 AAAGTCATG---G-C-CTGCA---CCAA-A-AAATTTGAATT--T--TTTTATCTGATAAA
1 AAAGTGGTGTCAGTCAATGCATGGCCAACACAAA--AAAATTGATAATTTTATCAGATAAA
* * * * *
56595300 AAGGTGTTGTC-GACCAATGCATGGCCAACACAAAAAAATTTA-AATTTTTTTATTAGATAAA
1 AAAGTGGTGTCAG-TCAATGCATGGCCAACACAAAAAAATTGATAA---TTTTATCAGATAAA
* * * * **
56595361 AAGGTGATGTC-GACAATGCAATGACCAACACAAAAAAAATTGATTTTTTTATCAGAT-AA
1 AAAGTGGTGTCAGTCAATGC-ATGGCCAACAC-AAAAAAATTGATAATTTTATCAGATAAA
* * * *
56595420 AAAG-GGAATGTC-GACCAATGCATGACCAACTCAAAAAAAATTTGA-ATTTTTTATCAGAT-AA
1 AAAGTGG--TGTCAG-TCAATGCATGGCCAACAC-AAAAAAA-TTGATA-ATTTTATCAGATAAA
* * * * * * *
56595481 AAAGGGGATGTC-GGCCATGCAATGGTCAACATC-AAAAATTTGA-ATTTTTTATCTGATAAA
1 AAAGTGG-TGTCAGTCAATGC-ATGGCCAACA-CAAAAAAATTGATA-ATTTTATCAGATAAA
* * *
56595541 AAGGTGGTGTCGAG-CAATGCATGACCAACACCAAAAAATT
1 AAAGTGGTGTC-AGTCAATGCATGGCCAACACAAAAAAATT
56595581 TTGAATTTTT
Statistics
Matches: 355, Mismatches: 52, Indels: 81
0.73 0.11 0.17
Matches are distributed among these distances:
46 9 0.03
47 9 0.03
48 1 0.00
49 1 0.00
50 3 0.01
51 4 0.01
52 10 0.03
55 12 0.03
56 2 0.01
57 4 0.01
58 7 0.02
59 101 0.28
60 90 0.25
61 89 0.25
62 13 0.04
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (59 bp):
AAAGTGGTGTCAGTCAATGCATGGCCAACACAAAAAAATTGATAATTTTATCAGATAAA
Found at i:56595189 original size:60 final size:58
Alignment explanation
Indices: 56595091--56595887 Score: 412
Period size: 60 Copynumber: 13.3 Consensus size: 58
56595081 GTGTCAGTCA
* * ** *
56595091 ATGCATGGCCAATACAAAAAATTTGA-AATTTTCTCAGATAAAAAAAGTGGTGTC-AGCC
1 ATGCATGGCCAACACAAAAAAATTGATTTTTTTATCAGAT-AAAAAAGTGGTGTCGA-CC
* * * *
56595149 ATGCAATGGCCAACACAAAAAAATTGATTTTTTTATCAGATAAAAAGGGGGTGTCGGTCA
1 ATGC-ATGGCCAACACAAAAAAATTGATTTTTTTATCAGATAAAAAAGTGGTGTC-GACC
* **
56595209 ATGCATGGCCAACACAAAAAAAGTTAAATTTTTTTATCAGA-AAAAAAGTCATG--G--C
1 ATGCATGGCCAACACAAAAAAA-TT-GATTTTTTTATCAGATAAAAAAGTGGTGTCGACC
* * * *
56595264 ---C-T-G-C-AC-CAAAAAATTTGAATTTTTTTATCTGATAAAAAGGTGTTGTCGACC
1 ATGCATGGCCAACACAAAAAAATTG-ATTTTTTTATCAGATAAAAAAGTGGTGTCGACC
* * * * *
56595315 AATGCATGGCCAACACAAAAAAATTTAAATTTTTTTATTAGATAAAAAGGTGATGTCGACA
1 -ATGCATGGCCAACACAAAAAAA-TT-GATTTTTTTATCAGATAAAAAAGTGGTGTCGACC
*
56595376 ATGCAATGACCAACACAAAAAAAATTGATTTTTTTATCAGAT-AAAAAG-GGAATGTCGACC
1 ATGC-ATGGCCAACAC-AAAAAAATTGATTTTTTTATCAGATAAAAAAGTGG--TGTCGACC
* * * * *
56595436 AATGCATGACCAACTCAAAAAAAATTTGAATTTTTTATCAGAT-AAAAAGGGGATGTCGGCC
1 -ATGCATGGCCAACAC-AAAAAAA-TTGATTTTTTTATCAGATAAAAAAGTGG-TGTCGACC
* * * * * *
56595497 ATGCAATGGTCAACATC-AAAAATTTGAATTTTTTATCTGATAAAAAGGTGGTGTCGAGCA
1 ATGC-ATGGCCAACA-CAAAAAAATTGATTTTTTTATCAGATAAAAAAGTGGTGTCGA-CC
* * * * * * * **
56595557 ATGCATGACCAACACCAAAAAATTTTGAATTTTTTTATTTGATGCACAAAAAATTTGATTTTTTA
1 ATGCATGGCCAACA-CAAAAAA-ATTG-ATTTTTTTA--TCA-G-ATAAAAAA-GTG-GTGTCGA
*
56595622 TCAA
57 -C-C
* * *
56595626 ATAAAAAG-AGGGTGGCCAACACCAAAAAAATTTGAATTTTTTTATCAGATAAAAATGGGGTGTT
1 AT-----GCA---TGGCCAACA-CAAAAAAA-TTG-ATTTTTTTATCAGATAAAAAAGTGGTGTC
56595690 GACC
55 GACC
* * * * * **
56595694 ATGCAATGACCAACACAAAAAACTTGAATTTTTTATCTGATAAAAAAATAATGTC-AGCC
1 ATGC-ATGGCCAACACAAAAAAATTGATTTTTTTATCAGATAAAAAAGTGGTGTCGA-CC
* * * * * * * * *
56595753 AATGCATGACTAACACAAAAAAATTTAAATTTTTTGTCAAACAAAAAGGTGGTGTCGGCC
1 -ATGCATGGCCAACACAAAAAAA-TTGATTTTTTTATCAGATAAAAAAGTGGTGTCGACC
* * * *
56595813 AATGCATGGCCAACACAAAAAAAATTTAATTTTTTATCAGATAGAAAGGTGGTGTCGACC
1 -ATGCATGGCCAACAC-AAAAAAATTGATTTTTTTATCAGATAAAAAAGTGGTGTCGACC
56595873 ATGCATGGCCAACAC
1 ATGCATGGCCAACAC
56595888 CAATTTTTTT
Statistics
Matches: 579, Mismatches: 100, Indels: 119
0.73 0.13 0.15
Matches are distributed among these distances:
46 15 0.03
47 16 0.03
48 2 0.00
49 2 0.00
50 1 0.00
51 2 0.00
52 1 0.00
55 1 0.00
56 1 0.00
57 2 0.00
58 7 0.01
59 142 0.25
60 177 0.31
61 117 0.20
62 26 0.04
63 1 0.00
64 1 0.00
65 2 0.00
66 6 0.01
67 2 0.00
68 6 0.01
69 4 0.01
70 4 0.01
71 1 0.00
72 6 0.01
73 2 0.00
74 3 0.01
76 29 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (58 bp):
ATGCATGGCCAACACAAAAAAATTGATTTTTTTATCAGATAAAAAAGTGGTGTCGACC
Found at i:56595359 original size:61 final size:60
Alignment explanation
Indices: 56595271--56595887 Score: 493
Period size: 60 Copynumber: 10.0 Consensus size: 60
56595261 GGCCTGCACC
* * *
56595271 AAAAAATTTGAATTTTTTTATCTGATAAAAAGGTGTTGTCGACCAATGCATGGCCAACACA
1 AAAAAATTTGAA-TTTTTTATCAGATAAAAAGGTGATGTCGACCAATGCATGACCAACACA
* *
56595332 AAAAAATTTAAATTTTTTTATTAGATAAAAAGGTGATGTCGA-CAATGCAATGACCAACACA
1 AAAAAATTTGAA-TTTTTTATCAGATAAAAAGGTGATGTCGACCAATGC-ATGACCAACACA
* * *
56595393 AAAAAAATTGATTTTTTTATCAGATAAAAAGG-GAATGTCGACCAATGCATGACCAACTCAA
1 AAAAAATTTGAATTTTTTATCAGATAAAAAGGTG-ATGTCGACCAATGCATGACCAACAC-A
* * **
56595454 AAAAAATTTGAATTTTTTATCAGATAAAAAGGGGATGTCGGCC-ATGCAATGGTCAACATC-
1 AAAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACCAATGC-ATGACCAACA-CA
* * *
56595514 -AAAAATTTGAATTTTTTATCTGATAAAAAGGTGGTGTCGAGCAATGCATGACCAACACCA
1 AAAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACCAATGCATGACCAACA-CA
* * * ** * ** *
56595574 AAAAATTTTGAATTTTTTTATTTGATGCACAAAAAATTTGATTTTTTATCAAATAAAAAG-AGGG
1 AAAAAATTTGAA-TTTTTTA--TCA-G-A-TAAAAAGGTGA-TGTCGA-CCAAT-----GCA---
*
56595638 TGGCCAACACCA
50 TGACCAACA-CA
* *
56595650 AAAAAATTTGAATTTTTTTATCAGATAAAAATGG-GGTGTTGACC-ATGCAATGACCAACAC-
1 AAAAAATTTGAA-TTTTTTATCAGATAAAAA-GGTGATGTCGACCAATGC-ATGACCAACACA
* * ** * *
56595710 AAAAAACTTGAATTTTTTATCTGATAAAAAAATAATGTC-AGCCAATGCATGACTAACACA
1 AAAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGA-CCAATGCATGACCAACACA
* * * * * * *
56595770 AAAAAATTTAAATTTTTTGTCAAACAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACAA
1 AAAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACCAATGCATGACCAACAC-A
* * *
56595831 AAAAAATTT-AATTTTTTATCAGATAGAAAGGTGGTGTCGACC-ATGCATGGCCAACAC
1 AAAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACCAATGCATGACCAACAC
56595888 CAATTTTTTT
Statistics
Matches: 448, Mismatches: 73, Indels: 72
0.76 0.12 0.12
Matches are distributed among these distances:
58 1 0.00
59 94 0.21
60 138 0.31
61 131 0.29
62 17 0.04
63 1 0.00
64 1 0.00
65 2 0.00
66 1 0.00
67 7 0.02
68 5 0.01
69 4 0.01
70 4 0.01
71 6 0.01
72 1 0.00
73 2 0.00
74 3 0.01
76 30 0.07
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (60 bp):
AAAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACCAATGCATGACCAACACA
Found at i:56595484 original size:121 final size:121
Alignment explanation
Indices: 56595271--56595887 Score: 527
Period size: 121 Copynumber: 5.0 Consensus size: 121
56595261 GGCCTGCACC
* * *
56595271 AAAAAATTTGAATTTTTTTATCTGATAAAAAGGTGTTGTCGACCAATGCATGGCCAACAC-AAAA
1 AAAAAATTTG-ATTTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAAA
* * *
56595335 AAATTTAAATTTTTTTATTAGATAAAAAGGTGATGTCGACAATGCAATGACCAACACA
65 AAATTTGAA-TTTTTTATCAGATAAAAAGGTGATGTCGACAATGCAATGGCCAACACA
* * *
56595393 AAAAAAATTGATTTTTTTATCAGATAAAAAGG-GAATGTCGACCAATGCATGACCAACTCAAAAA
1 AAAAAATTTGATTTTTTTATCAGATAAAAAGGTG-GTGTCGACCAATGCATGACCAACACAAAAA
* * * *
56595457 AAATTTGAATTTTTTATCAGATAAAAAGGGGATGTCGGCCATGCAATGGTCAACATC-
65 AAATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACAATGCAATGGCCAACA-CA
* * * *
56595514 -AAAAATTTGAATTTTTTATCTGATAAAAAGGTGGTGTCGAGCAATGCATGACCAACACCAAAAA
1 AAAAAATTTGATTTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAAAA
* * * ** * ** **
56595578 ATTTTGAATTTTTTTATTTGATGCACAAAAAATTTGATTTTTTATCAAATAAAAAGAGGGTGGCC
66 AATTTGAA-TTTTTTA--TCA-G-A-TAAAAAGGTGA-TGTCGA-C-AAT--GCA-A---TGGCC
56595643 AACACCA
116 AACA-CA
*
56595650 AAAAAATTTGAATTTTTTTATCAGATAAAAATGG-GGTGTTGACC-ATGCAATGACCAACAC--A
1 AAAAAATTTG-ATTTTTTTATCAGATAAAAA-GGTGGTGTCGACCAATGC-ATGACCAACACAAA
* * ** * * * *
56595711 AAAAACTTGAATTTTTTATCTGATAAAAAAATAATGTCAGCCAATGC-ATGACTAACACA
63 AAAAATTTGAATTTTTTATCAGATAAAAAGGTGATGTC-GACAATGCAATGGCCAACACA
* * * * * * *
56595770 AAAAAATTTAAATTTTTTGTCAAACAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACAAAAAA
1 AAAAAATTTGATTTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAAAA
* * *
56595835 AATTT-AATTTTTTATCAGATAGAAAGGTGGTGTCGACCATGC-ATGGCCAACAC
66 AATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACAATGCAATGGCCAACAC
56595888 CAATTTTTTT
Statistics
Matches: 393, Mismatches: 73, Indels: 61
0.75 0.14 0.12
Matches are distributed among these distances:
118 2 0.01
119 49 0.12
120 101 0.26
121 106 0.27
122 22 0.06
123 2 0.01
124 2 0.01
125 1 0.00
126 7 0.02
127 2 0.01
128 4 0.01
129 5 0.01
130 7 0.02
131 2 0.01
132 2 0.01
133 1 0.00
135 16 0.04
136 10 0.03
137 13 0.03
138 37 0.09
139 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (121 bp):
AAAAAATTTGATTTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAAAA
AATTTGAATTTTTTATCAGATAAAAAGGTGATGTCGACAATGCAATGGCCAACACA
Found at i:56595944 original size:55 final size:55
Alignment explanation
Indices: 56595849--56596010 Score: 184
Period size: 55 Copynumber: 3.0 Consensus size: 55
56595839 TAATTTTTTA
* * *
56595849 TCAGA-TAGAAAGGTGGTGTCGACCATGC-ATGGCCAACACCAATTTTTTTTTCTG
1 TCAGATTAAAAAGG-GGTGTCGACTATGCAATGGCCAACACCAAATTTTTTTTCTG
* *
56595903 TCAGATTAAAAAGGGGTGTCGACTATGCAATGGCTAACACCAAATTTTTTTCCTG
1 TCAGATTAAAAAGGGGTGTCGACTATGCAATGGCCAACACCAAATTTTTTTTCTG
* * ** * * * *
56595958 TTAGATAAAAAAAAGGTGCCGGCTATACAATGGCCAACACCAAATTTCTTTTC
1 TCAGATTAAAAAGGGGTGTCGACTATGCAATGGCCAACACCAAATTTTTTTTC
56596011 AAAATCTCGT
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
54 18 0.20
55 73 0.80
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (55 bp):
TCAGATTAAAAAGGGGTGTCGACTATGCAATGGCCAACACCAAATTTTTTTTCTG
Found at i:56596412 original size:18 final size:20
Alignment explanation
Indices: 56596391--56596445 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
56596381 TTTACAAAAT
*
56596391 AAATAAAATGG-AT-ATGGA
1 AAATAAAATGGAATGAAGGA
*
56596409 AAATAATATGGAAATGAAGGA
1 AAATAAAATGG-AATGAAGGA
56596430 AAATAAAAT-GAATGAA
1 AAATAAAATGGAATGAA
56596446 AACCAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
20 3 0.10
21 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATAAAATGGAATGAAGGA
Found at i:56603546 original size:5 final size:5
Alignment explanation
Indices: 56603526--56603559 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
56603516 TTTTAAAATC
*
56603526 TATAA TATCA -ATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
56603560 AAATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:56606494 original size:15 final size:14
Alignment explanation
Indices: 56606465--56606512 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
56606455 TCCATTAAGC
*
56606465 CCAAACCAAGGTGAA
1 CCAAACCAA-TTGAA
*
56606480 CCAAACCCATTTGAA
1 CCAAA-CCAATTGAA
*
56606495 CCAAATCAATTGAA
1 CCAAACCAATTGAA
56606509 CCAA
1 CCAA
56606513 GTCCAACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 11 0.39
15 14 0.50
16 3 0.11
ACGTcount: A:0.46, C:0.29, G:0.10, T:0.15
Consensus pattern (14 bp):
CCAAACCAATTGAA
Found at i:56606573 original size:20 final size:20
Alignment explanation
Indices: 56606548--56606638 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
56606538 TTGACCGGCG
* * *
56606548 TTGACCGCTGATCGTTGATT
1 TTGACCGTTGACCGTTGACT
56606568 TTGACCGTTGACCGTTGA-T
1 TTGACCGTTGACCGTTGACT
* *
56606587 AGTTGACCGTTGA-CTTTGACCA
1 --TTGACCGTTGACCGTTGA-CT
56606609 TTGACCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGACT
56606629 TTGACCGTTG
1 TTGACCGTTG
56606639 CCTTTTTTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 43 0.72
21 16 0.27
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:56606578 original size:7 final size:7
Alignment explanation
Indices: 56606546--56606638 Score: 84
Period size: 7 Copynumber: 13.7 Consensus size: 7
56606536 CGTTGACCGG
56606546 CGTTGAC
1 CGTTGAC
* *
56606553 CGCTGAT
1 CGTTGAC
56606560 CGTTGA-
1 CGTTGAC
**
56606566 TTTTGAC
1 CGTTGAC
56606573 CGTTGAC
1 CGTTGAC
*
56606580 CGTTGAT
1 CGTTGAC
*
56606587 AGTTGAC
1 CGTTGAC
56606594 CGTTGA-
1 CGTTGAC
*
56606600 CTTTGAC
1 CGTTGAC
*
56606607 CATTGAC
1 CGTTGAC
56606614 CGTTGAC
1 CGTTGAC
56606621 CGTTGA-
1 CGTTGAC
*
56606627 CTTTGAC
1 CGTTGAC
56606634 CGTTG
1 CGTTG
56606639 CCTTTTTTCG
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
6 14 0.21
7 53 0.79
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (7 bp):
CGTTGAC
Found at i:56606605 original size:27 final size:27
Alignment explanation
Indices: 56606575--56606638 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
56606565 ATTTTGACCG
*
56606575 TTGACCGTTGATAGTTGACCGTTGACT
1 TTGACCGTTGACAGTTGACCGTTGACT
* *
56606602 TTGACCATTGACCGTTGACCGTTGACT
1 TTGACCGTTGACAGTTGACCGTTGACT
56606629 TTGACCGTTG
1 TTGACCGTTG
56606639 CCTTTTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (27 bp):
TTGACCGTTGACAGTTGACCGTTGACT
Found at i:56606626 original size:34 final size:34
Alignment explanation
Indices: 56606546--56606627 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
56606536 CGTTGACCGG
* * * *
56606546 CGTTGACCGCTGATCGTTGATTTTGACCGTTGAC
1 CGTTGACCGTTGACCGTTGACTTTGACCATTGAC
**
56606580 CGTTGATAGTTGACCGTTGACTTTGACCATTGAC
1 CGTTGACCGTTGACCGTTGACTTTGACCATTGAC
56606614 CGTTGACCGTTGAC
1 CGTTGACCGTTGAC
56606628 TTTGACCGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (34 bp):
CGTTGACCGTTGACCGTTGACTTTGACCATTGAC
Found at i:56606643 original size:13 final size:13
Alignment explanation
Indices: 56606575--56606643 Score: 77
Period size: 13 Copynumber: 5.2 Consensus size: 13
56606565 ATTTTGACCG
56606575 TTGACCGTTGA-T
1 TTGACCGTTGACT
56606587 AGTTGACCGTTGACT
1 --TTGACCGTTGACT
* *
56606602 TTGACCATTGACCG
1 TTGACCGTTGA-CT
56606616 TTGACCGTTGACT
1 TTGACCGTTGACT
*
56606629 TTGACCGTTGCCT
1 TTGACCGTTGACT
56606642 TT
1 TT
56606644 TTTCGAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
13 25 0.52
14 22 0.46
15 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:56607689 original size:3 final size:3
Alignment explanation
Indices: 56607677--56607718 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
56607667 TATTCTATTC
56607677 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
56607719 TTGGGATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:56617920 original size:31 final size:29
Alignment explanation
Indices: 56617879--56617939 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
56617869 GAGCAGTTTT
* *
56617879 ATACTTAAAATCATTAAAAAAGTATAAAAAA
1 ATACTGAAAATC-GTAAAAAA-TATAAAAAA
*
56617910 ATACTGAAAATCGTAAAAAATATTAAAAA
1 ATACTGAAAATCGTAAAAAATATAAAAAA
56617939 A
1 A
56617940 CTAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 7 0.26
31 11 0.41
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (29 bp):
ATACTGAAAATCGTAAAAAATATAAAAAA
Found at i:56618154 original size:19 final size:18
Alignment explanation
Indices: 56618094--56618156 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 18
56618084 GGAAAATTTT
56618094 AAAATATAATAAATTATTATA
1 AAAATATAA-AAATTA-TA-A
*
56618115 AAAATATAGAAAAGTGA-AA
1 AAAATATA-AAAA-TTATAA
56618134 AAAATATTAAAAATTATAA
1 AAAATA-TAAAAATTATAA
56618153 AAAA
1 AAAA
56618157 GATACAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 2 0.06
19 17 0.47
20 3 0.08
21 11 0.31
22 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATATAAAAATTATAA
Found at i:56622642 original size:16 final size:16
Alignment explanation
Indices: 56622621--56622651 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56622611 ATTTATTCAT
56622621 TTATCTAAATAAAATA
1 TTATCTAAATAAAATA
*
56622637 TTATCTAACTAAAAT
1 TTATCTAAATAAAAT
56622652 TTAAAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATCTAAATAAAATA
Found at i:56631682 original size:5 final size:5
Alignment explanation
Indices: 56631674--56631712 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
56631664 TGCCCTATTC
56631674 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
56631713 GGGTTGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:56633063 original size:21 final size:21
Alignment explanation
Indices: 56633037--56633112 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
56633027 TTCAAGTTTT
*
56633037 ATTTTATAAAAGTATTTTTAA
1 ATTTTATAAAATTATTTTTAA
* *
56633058 ATTTTAAAAAATTATTTTT-T
1 ATTTTATAAAATTATTTTTAA
*
56633078 ATTTTATGAGAAATTTTTTTTAA
1 ATTTTAT-A-AAATTATTTTTAA
*
56633101 TTTTTTATAAAA
1 -ATTTTATAAAA
56633113 AATTACGATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 6 0.14
21 18 0.41
22 13 0.30
23 1 0.02
24 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTTATAAAATTATTTTTAA
Found at i:56633091 original size:22 final size:20
Alignment explanation
Indices: 56633033--56633104 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
56633023 TATTTTCAAG
*
56633033 TTTTATTTTATAAAAGTATT
1 TTTTATTTTATAAAATTATT
* *
56633053 TTTAAATTTTAAAAAATTATT
1 TTT-TATTTTATAAAATTATT
56633074 TTTTATTTTATGAGAAATT-TT
1 TTTTATTTTAT-A-AAATTATT
56633095 TTTTAATTTT
1 TTTT-ATTTT
56633105 TTATAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.21
21 24 0.56
22 10 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTATTTTATAAAATTATT
Found at i:56639584 original size:29 final size:30
Alignment explanation
Indices: 56639536--56639600 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
56639526 AAATACCAAT
* *
56639536 TTTTAAGGAGTTTCAATTTTTTTTTTTAAC
1 TTTTAAGGAGTTTAAATTTTTTTTATTAAC
*
56639566 TTTTAATGA-TTTAAATTTTTTTTATTAAC
1 TTTTAAGGAGTTTAAATTTTTTTTATTAAC
56639595 TTTTAA
1 TTTTAA
56639601 AAAATCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.62
Consensus pattern (30 bp):
TTTTAAGGAGTTTAAATTTTTTTTATTAAC
Found at i:56639614 original size:29 final size:29
Alignment explanation
Indices: 56639550--56639624 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
56639540 AAGGAGTTTC
* ** *
56639550 AATTTTTTTTTTTAACTTTTAATGATTTA
1 AATTTTTTTTATTAACTTTTAAAAATCTA
56639579 AATTTTTTTTATTAACTTTTAAAAAATCTA
1 AATTTTTTTTATTAACTTTT-AAAAATCTA
56639609 AATTTTTATTTTATTA
1 AA-TTTT-TTTTATTA
56639625 TTTTATTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 19 0.49
30 8 0.21
31 4 0.10
32 8 0.21
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (29 bp):
AATTTTTTTTATTAACTTTTAAAAATCTA
Found at i:56645377 original size:19 final size:20
Alignment explanation
Indices: 56645348--56645388 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
56645338 TGTATTTTAT
*
56645348 TTTTTTAATATTTTAATCAA
1 TTTTTTAATATTATAATCAA
*
56645368 TTTTTT-ATATTATAATTAA
1 TTTTTTAATATTATAATCAA
56645387 TT
1 TT
56645389 ATAATATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTTAATATTATAATCAA
Found at i:56654906 original size:23 final size:23
Alignment explanation
Indices: 56654880--56655000 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
56654870 ACACTAGCGC
56654880 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
56654903 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
56654926 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
56654951 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
56654974 GCTCTCTGATTAGCACTTTCTGT
1 GCTCTCTGATTAGCACTGTGTGT
56654997 GCTC
1 GCTC
56655001 AGTACTTTGT
Statistics
Matches: 87, Mismatches: 5, Indels: 12
0.84 0.05 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.71
24 1 0.01
25 17 0.20
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:56654949 original size:48 final size:46
Alignment explanation
Indices: 56654880--56655000 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
56654870 ACACTAGCGC
*
56654880 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGT-GT
*
56654926 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGT
* *
56654974 GCTCTCTGATTAGCACTTTCTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
56655001 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 25 0.37
48 42 0.62
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGT
Found at i:56655029 original size:39 final size:39
Alignment explanation
Indices: 56654965--56655039 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
56654955 TCTGATTAGC
*
56654965 ACTTCGTGTGCTCTCTGATTAGCACTTTCTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTCTGTGCTCAGT
* * *
56655004 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTCTGTGCTC
56655040 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTCTGTGCTCAGT
Found at i:56655031 original size:23 final size:23
Alignment explanation
Indices: 56654999--56655092 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
56654989 CTTTCTGTGC
*
56654999 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
56655022 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
56655045 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
56655070 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
56655092 T
1 T
56655093 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:56671747 original size:29 final size:30
Alignment explanation
Indices: 56671714--56671770 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
56671704 TGGTTTAATG
56671714 TGCAACTGTATACATG-AATTTTGATTTTA
1 TGCAACTGTATACATGAAATTTTGATTTTA
* *
56671743 TGCAATTTTATACATGAAATTTTGATTT
1 TGCAACTGTATACATGAAATTTTGATTT
56671771 GATCCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (30 bp):
TGCAACTGTATACATGAAATTTTGATTTTA
Found at i:56671766 original size:30 final size:29
Alignment explanation
Indices: 56671722--56671779 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
56671712 TGTGCAACTG
* *
56671722 TATACATGAATTTTGATTTTATGCAATTT
1 TATACATGAATTTTGATTTGATCCAATTT
56671751 TATACATGAAATTTTGATTTGATCCAATT
1 TATACATG-AATTTTGATTTGATCCAATT
56671780 ATTGTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (29 bp):
TATACATGAATTTTGATTTGATCCAATTT
Found at i:56672156 original size:90 final size:91
Alignment explanation
Indices: 56672059--56672238 Score: 290
Period size: 91 Copynumber: 2.0 Consensus size: 91
56672049 ATTATATATA
* * *
56672059 AACTAATTATGGTGAATTTATATTA-TAAAATTAATTACAATAAATATAATAACTAATTAGAGTG
1 AACTAATTATGGTGAATTTATACTAGGAAAATTAATTACAATAAATATAATAACTAATTAGAATG
56672123 AATTCACATTAATTATGATAAATGTT
66 AATTCACATTAATTATGATAAATGTT
* *
56672149 AACTAATTGTGGTGAATTTATACTAGGAAAATTAATTACAATAAATATAATAACTAATTATAATG
1 AACTAATTATGGTGAATTTATACTAGGAAAATTAATTACAATAAATATAATAACTAATTAGAATG
* *
56672214 ATTTTACATTAATTATGATAAATGT
66 AATTCACATTAATTATGATAAATGT
56672239 ATTAATTATT
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 23 0.28
91 59 0.72
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (91 bp):
AACTAATTATGGTGAATTTATACTAGGAAAATTAATTACAATAAATATAATAACTAATTAGAATG
AATTCACATTAATTATGATAAATGTT
Found at i:56672651 original size:24 final size:22
Alignment explanation
Indices: 56672610--56672653 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
56672600 TTATTAAATA
*
56672610 TAAAAAAATAATAATAATATTT
1 TAAAAAAATAAAAATAATATTT
56672632 TAAAAAAATAGAAAATTAATAT
1 TAAAAAAATA-AAAA-TAATAT
56672654 GAGCGGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
TAAAAAAATAAAAATAATATTT
Found at i:56673032 original size:18 final size:18
Alignment explanation
Indices: 56673009--56673087 Score: 65
Period size: 18 Copynumber: 4.3 Consensus size: 18
56672999 GCAGTATTCC
56673009 AACATAACAATCGATTTA
1 AACATAACAATCGATTTA
* *
56673027 AACATATAAACAATTGATTCA
1 AAC--AT-AACAATCGATTTA
* *
56673048 AA-AGAAGCAAT--ATTTC
1 AACATAA-CAATCGATTTA
56673064 AACATAACAATCGATTTA
1 AACATAACAATCGATTTA
56673082 AACATA
1 AACATA
56673088 TAAAAAATCG
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
16 9 0.19
17 5 0.11
18 18 0.38
20 2 0.04
21 13 0.28
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (18 bp):
AACATAACAATCGATTTA
Found at i:56673040 original size:21 final size:20
Alignment explanation
Indices: 56673014--56673100 Score: 60
Period size: 21 Copynumber: 4.5 Consensus size: 20
56673004 ATTCCAACAT
56673014 AACAATCGATTTAAACATATA
1 AACAATCGATTTAAACA-ATA
* * *
56673035 AACAATTGA-TTCAA-AAGA
1 AACAATCGATTTAAACAATA
* *
56673053 AGCAAT--ATTTCAAC-AT-
1 AACAATCGATTTAAACAATA
56673069 AACAATCGATTTAAACATATA
1 AACAATCGATTTAAACA-ATA
*
56673090 AAAAATCGATT
1 AACAATCGATT
56673101 CAAAAGAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
16 6 0.12
17 6 0.12
18 14 0.27
19 1 0.02
20 6 0.12
21 18 0.35
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (20 bp):
AACAATCGATTTAAACAATA
Found at i:56673081 original size:55 final size:55
Alignment explanation
Indices: 56672957--56673218 Score: 330
Period size: 55 Copynumber: 4.7 Consensus size: 55
56672947 ATGTGCTACG
* * * *
56672957 TAACAATTGATTTAAATATATAAACAATTGATTCAAAAAAAAGCAGTATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATTGATTC-AAAAGAAGCAATATTCCAACA
*
56673013 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTTCAACA
1 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTCCAACA
* * * *
56673068 TAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAATAAGTAGTATTCC-ACTA
1 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAG---AAGCAATATTCCAAC-A
* *
56673126 TAACAATTGATTTAAACATATAAACAATTGATTCAAAA-TAGCAATATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTCCAACA
*** *
56673180 TGGTAATCGATTTAAACATATAAACAATCGATTCAAAAG
1 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAG
56673219 CATTTCGACC
Statistics
Matches: 179, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
54 43 0.24
55 57 0.32
56 32 0.18
57 2 0.01
58 45 0.25
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (55 bp):
TAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTCCAACA
Found at i:56673216 original size:112 final size:112
Alignment explanation
Indices: 56672957--56673218 Score: 386
Period size: 112 Copynumber: 2.3 Consensus size: 112
56672947 ATGTGCTACG
* * *
56672957 TAACAATTGATTTAAATATATAAACAATTGATTCAAAA-AAAAGCAGTATTCCAACATAACAATC
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAAAGCAGTATTCCAACATAACAATC
*
56673021 GATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTTCAACA
66 GATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTCCAACA
* *
56673068 TAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAATAAGTAGTATTCC-ACTATAACAA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAA-AAGCAGTATTCCAAC-ATAACAA
* *
56673132 TTGATTTAAACATATAAACAATTGATTCAAAA-TAGCAATATTCCAACA
64 TCGATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTCCAACA
***
56673180 TGGTAATCGATTTAAACATATAAACAATCGATTCAAAAG
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAG
56673219 CATTTCGACC
Statistics
Matches: 136, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
111 34 0.25
112 53 0.39
113 49 0.36
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (112 bp):
TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAAAGCAGTATTCCAACATAACAATC
GATTTAAACATATAAACAATTGATTCAAAAGAAGCAATATTCCAACA
Found at i:56674534 original size:26 final size:25
Alignment explanation
Indices: 56674472--56674537 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
56674462 CAGATTCTAT
* *
56674472 GAAGCTAGTGTTAGCAGCATTGAAC
1 GAAGCTAGTGTTAGCAACACTGAAC
* * *
56674497 CAAGCTAGTGTTAGCAACCCTGATC
1 GAAGCTAGTGTTAGCAACACTGAAC
56674522 AGAAGCTAGTGTTAGC
1 -GAAGCTAGTGTTAGC
56674538 CGCCCGATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 20 0.59
26 14 0.41
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (25 bp):
GAAGCTAGTGTTAGCAACACTGAAC
Found at i:56682917 original size:60 final size:60
Alignment explanation
Indices: 56682827--56683036 Score: 223
Period size: 59 Copynumber: 3.5 Consensus size: 60
56682817 ATTTAGGGTT
* * * * **
56682827 AAAAATA-AAATTTTAGA-AGTTCGAGAGTAAAACGATAATTTTTAGAAAAAATCACGATC
1 AAAAATAGAATTTTTAGACA-TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGGATC
* ** *
56682886 AAAAATAGAATTTTTAGACATTCGGGGGTAAAATGGT-ATTTTTTTAAAAAATGGGGATC
1 AAAAATAGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGGATC
* *
56682945 AAAAATAGAATTTTTGGACATCCG-GTGGTAAAATGGTAATTTTTAG-AAAAATCGGGATC
1 AAAAATAGAATTTTTAGACATTCGAG-GGTAAAATGGTAATTTTTAGAAAAAATCGGGATC
** * *
56683004 AAAAACGGAATTTTTGGATATTCGAGGGTAAAA
1 AAAAATAGAATTTTTAGACATTCGAGGGTAAAA
56683037 ATGAAATTTT
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
58 1 0.01
59 96 0.76
60 29 0.23
61 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (60 bp):
AAAAATAGAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGGATC
Found at i:56682927 original size:59 final size:60
Alignment explanation
Indices: 56682853--56683036 Score: 228
Period size: 59 Copynumber: 3.1 Consensus size: 60
56682843 AAGTTCGAGA
* * ** *
56682853 GTAAAACGATAATTTTTAGAAAAAATCACGATCAAAAATAGAATTTTTAGACATTCGGGG
1 GTAAAATGGTAATTTTTAGAAAAAATCGGGATCAAAAATAGAATTTTTGGACATTCGGGG
** * * *
56682913 GTAAAATGGT-ATTTTTTTAAAAAATGGGGATCAAAAATAGAATTTTTGGACATCCGGTG
1 GTAAAATGGTAATTTTTAGAAAAAATCGGGATCAAAAATAGAATTTTTGGACATTCGGGG
** * *
56682972 GTAAAATGGTAATTTTTAG-AAAAATCGGGATCAAAAACGGAATTTTTGGATATTCGAGG
1 GTAAAATGGTAATTTTTAGAAAAAATCGGGATCAAAAATAGAATTTTTGGACATTCGGGG
56683031 GTAAAA
1 GTAAAA
56683037 ATGAAATTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 90 0.87
60 14 0.13
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (60 bp):
GTAAAATGGTAATTTTTAGAAAAAATCGGGATCAAAAATAGAATTTTTGGACATTCGGGG
Found at i:56683036 original size:29 final size:29
Alignment explanation
Indices: 56683004--56683142 Score: 120
Period size: 29 Copynumber: 4.8 Consensus size: 29
56682994 AATCGGGATC
*
56683004 AAAAACGGAATTTTTGGATA-TTCGAGGGT
1 AAAAACGGAATTTTTGGA-AGTTTGAGGGT
* * *
56683033 AAAAATGAAATTTTGGGAAGTTTTG-GGGT
1 AAAAACGGAATTTTTGGAAG-TTTGAGGGT
* *
56683062 CAAAAATGGAATTTTTGGAAGTTTTAGGGT
1 -AAAAACGGAATTTTTGGAAGTTTGAGGGT
** *
56683092 AAAAACATAATTTTTGGAAGTTTTAGGGT
1 AAAAACGGAATTTTTGGAAGTTTGAGGGT
* ** *
56683121 CAAAATAGAATTTTTGAAAGTT
1 AAAAACGGAATTTTTGGAAGTT
56683143 CGGGGGCAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.01
29 66 0.72
30 25 0.27
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAAACGGAATTTTTGGAAGTTTGAGGGT
Found at i:56683065 original size:59 final size:59
Alignment explanation
Indices: 56683002--56683154 Score: 170
Period size: 59 Copynumber: 2.6 Consensus size: 59
56682992 AAAATCGGGA
* *
56683002 TCAAAAACGGAATTTTTGGATA-TTCGAGGGTAAAAATGA-AATTTTGGGAAGTTTTGGGG
1 TCAAAAACGGAATTTTTGGA-AGTTCGAGGGTAAAAA-CATAATTTTGGGAAGTTTTAGGG
* ** *
56683061 TCAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAACATAATTTTTGGAAGTTTTAGGG
1 TCAAAAACGGAATTTTTGGAAGTTCGAGGGTAAAAACATAATTTTGGGAAGTTTTAGGG
* * *
56683120 TCAAAATA--GAATTTTTGAAAGTTCGGGGGCAAAAA
1 TCAAAA-ACGGAATTTTTGGAAGTTCGAGGGTAAAAA
56683155 TGTAATTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
58 24 0.30
59 55 0.69
60 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (59 bp):
TCAAAAACGGAATTTTTGGAAGTTCGAGGGTAAAAACATAATTTTGGGAAGTTTTAGGG
Found at i:56683069 original size:30 final size:29
Alignment explanation
Indices: 56683028--56683142 Score: 135
Period size: 29 Copynumber: 3.9 Consensus size: 29
56683018 TGGATATTCG
*
56683028 AGGGTAAAAATGAAATTTTGGGAAGTTTT
1 AGGGTAAAAATGAAATTTTTGGAAGTTTT
* *
56683057 GGGGTCAAAAATGGAATTTTTGGAAGTTTT
1 AGGGT-AAAAATGAAATTTTTGGAAGTTTT
*
56683087 AGGGTAAAAA-CATAATTTTTGGAAGTTTT
1 AGGGTAAAAATGA-AATTTTTGGAAGTTTT
* *
56683116 AGGGTCAAAAT-AGAATTTTTGAAAGTT
1 AGGGTAAAAATGA-AATTTTTGGAAGTT
56683143 CGGGGGCAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
29 48 0.65
30 26 0.35
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AGGGTAAAAATGAAATTTTTGGAAGTTTT
Found at i:56683933 original size:16 final size:17
Alignment explanation
Indices: 56683905--56683937 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
56683895 ACAGTTCTTT
56683905 CCTTTTTTCTTTTTTTA
1 CCTTTTTTCTTTTTTTA
56683922 CCTTTTTT-TTTTTTTA
1 CCTTTTTTCTTTTTTTA
56683938 AAGGTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (17 bp):
CCTTTTTTCTTTTTTTA
Found at i:56685068 original size:17 final size:17
Alignment explanation
Indices: 56685031--56685069 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
56685021 AAATTTAATT
*
56685031 AAATTTAAATTTAAAGC
1 AAATTTAAATTTAAAGA
56685048 AAATTTAAATTTTAAA-A
1 AAATTTAAA-TTTAAAGA
56685065 AAATT
1 AAATT
56685070 AAAGCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAGA
Found at i:56689227 original size:18 final size:16
Alignment explanation
Indices: 56689197--56689241 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 16
56689187 AACATTATTT
56689197 TAATGTTTATATTAGAG
1 TAATGTTTATATTA-AG
56689214 TAATGTTGTATATTAAG
1 TAATGTT-TATATTAAG
56689231 TATATGTTTAT
1 TA-ATGTTTAT
56689242 TTTTTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (16 bp):
TAATGTTTATATTAAG
Found at i:56689294 original size:17 final size:18
Alignment explanation
Indices: 56689256--56689294 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
56689246 TATGTATTTT
*
56689256 AAATTACATAATATATAA
1 AAATAACATAATATATAA
56689274 AAATAACATAATATA-AA
1 AAATAACATAATATATAA
56689291 AAAT
1 AAAT
56689295 TATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAACATAATATATAA
Found at i:56694224 original size:35 final size:35
Alignment explanation
Indices: 56694178--56694247 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
56694168 CGAAGCAAAA
56694178 ACTTCCAATGCTTTTGACTGCTACACCACAATTTT
1 ACTTCCAATGCTTTTGACTGCTACACCACAATTTT
56694213 ACTTCCAATGCTTTTGACTGCTACACCACAATTTT
1 ACTTCCAATGCTTTTGACTGCTACACCACAATTTT
56694248 GGGGACTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (35 bp):
ACTTCCAATGCTTTTGACTGCTACACCACAATTTT
Found at i:56696204 original size:57 final size:59
Alignment explanation
Indices: 56696141--56696606 Score: 493
Period size: 61 Copynumber: 7.8 Consensus size: 59
56696131 CCTATTTCAA
* * *
56696141 AAAAAAAATTCAAAATTTTTTGGTGTTGGCCATCAAATGACCGACACCCTCTTTTCTCG
1 AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCG
* ** *** * * *
56696200 AAAAAAATTTGC--A-TTTTTGGGTGTTAACCATTGCATGACCGACACCCCCTGTTTC-AG
1 AAAAAAATTT-CAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCT-TTTCTCG
* * * *
56696257 AAAAAAAATT-AAATTTTTTTTGTGTTGGTCATCAAATGGTCGACACCCTCTTTTCTCG
1 AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCG
*
56696315 AAAAAAAATTGC--A-TTTTTTGGTGTTGGCCATCAAATGGCCGACACCC-CTTATTCTCG
1 -AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTT-TTCTCG
* * * *
56696372 AGAAAAAATTTTCAATTTTTTTTGGTGTTGGCCATCAAATGGCTGACACCCCCTATTCTCGAG
1 A-AAAAAA-TTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTC--G
56696435 AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCTCG
1 AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCTCTTTTCTCG
* * *
56696495 AGAAAAAATTTTTAAATTTTTTTTGGTGTTGGCCATCAAATAGCCGACA-CCTCCTTTCTCG
1 A-AAAAAA-TTTCAAA-TTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCG
* *
56696556 AATAAAAAAATTTCAAATTTTTTTGGTGTTGACCATCAAACGGCCGACACC
1 ---AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
56696607 AACTTCTCAT
Statistics
Matches: 340, Mismatches: 42, Indels: 47
0.79 0.10 0.11
Matches are distributed among these distances:
56 4 0.01
57 88 0.26
58 36 0.11
59 17 0.05
60 3 0.01
61 121 0.36
62 31 0.09
63 39 0.11
64 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34
Consensus pattern (59 bp):
AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCG
Found at i:56696331 original size:115 final size:118
Alignment explanation
Indices: 56696099--56696606 Score: 508
Period size: 124 Copynumber: 4.3 Consensus size: 118
56696089 AAAAAAAAAA
* *** * * *
56696099 TTTGGGAGTTAACCATTGCATGGTCGACACCCCCTATT-TC-AAAAAAAAAATTCAAA-ATTTTT
1 TTTGGGTGTTAACCATCAAATGGCCGACACCCCCTATTCTCGAGAAAAAAAATT-AAATTTTTTT
* *
56696161 TGGTGTTGGCCATCAAATGACCGACACCCTCTTTTCTCGAAAAAAATTTGCATT
65 TGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
*** * *
56696215 TTTGGGTGTTAACCATTGCATGACCGACACCCCCTGTT-TC-AGAAAAAAAATTAAATTTTTTTT
1 TTTGGGTGTTAACCATCAAATGGCCGACACCCCCTATTCTCGAGAAAAAAAATTAAATTTTTTTT
* *
56696278 -GTGTTGGTCATCAAATGGTCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
66 GGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
* ** * ** *
56696330 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTATTCTCGAGAAAAAATTTTCAATTTTTTTT
1 TTTGGGTGTTAACCATCAAATGGCCGACACCCCCTATTCTCGAGAAAAAAAATTAAATTTTTTTT
* * * *
56696395 GGTGTTGGCCATCAAATGGCTGACACCCCCTATTCTCGAGAAAAAAATTTCAAATTT
66 GGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGA-AAAAAAATTGC--A-TT
* ** * **
56696452 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCTCGAGAAAAAATTTTTAAATTTTTT
1 TTTGGGTGTTAACCATCAAATGGCCGACACCCC-CTATTCTCGAGAAAAAA-AATTAAATTTTTT
* * *
56696517 TTGGTGTTGGCCATCAAATAGCCGACA-CCTCCTTTCTCGAATAAAAAAATTTCAAATTT
64 TTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCG-A-AAAAAAATTGC--A-TT
* * *
56696576 TTTTGGTGTTGACCATCAAACGGCCGACACC
1 TTTGGGTGTTAACCATCAAATGGCCGACACC
56696607 AACTTCTCAT
Statistics
Matches: 342, Mismatches: 39, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
115 80 0.23
116 55 0.16
117 20 0.06
118 33 0.10
119 10 0.03
121 1 0.00
122 35 0.10
123 24 0.07
124 84 0.25
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (118 bp):
TTTGGGTGTTAACCATCAAATGGCCGACACCCCCTATTCTCGAGAAAAAAAATTAAATTTTTTTT
GGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAATTGCATT
Found at i:56699314 original size:13 final size:13
Alignment explanation
Indices: 56699296--56699320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56699286 TAAATATCTG
56699296 ATATTTTTTACAA
1 ATATTTTTTACAA
56699309 ATATTTTTTACA
1 ATATTTTTTACA
56699321 TTTTCGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTTTTACAA
Found at i:56700479 original size:30 final size:30
Alignment explanation
Indices: 56700445--56700536 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
56700435 TCCCTTTACT
*
56700445 TTTTAAATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
56700475 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** * *
56700505 TTTTAATTTTTCTTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
56700535 TT
1 TT
56700537 CTAATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.04
30 51 0.94
31 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:56701494 original size:61 final size:62
Alignment explanation
Indices: 56701358--56701505 Score: 183
Period size: 62 Copynumber: 2.4 Consensus size: 62
56701348 AGGAGAAGTT
* * * * *
56701358 GGTGTCGGTCATTTGATGGCCAGCACCAAAAAAATTTGGAATTTTTTTATTCTAGAAAAGGG
1 GGTGTCGGTCATTTGATGGCCAACAACAAAAAAATTTGAAATTTTTTTACTCGAGAAAAGGG
* * *
56701420 AGTATCGGTCATTTGATGGCCAACAAGAAAAAAATTT-AAAGTTTTTTT-CTCGAGAAAAGGG
1 GGTGTCGGTCATTTGATGGCCAACAACAAAAAAATTTGAAA-TTTTTTTACTCGAGAAAAGGG
* *
56701481 GGTGTCGGCCATTTGATGGCTAACA
1 GGTGTCGGTCATTTGATGGCCAACA
56701506 CCTAAAAATG
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
61 34 0.47
62 39 0.53
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (62 bp):
GGTGTCGGTCATTTGATGGCCAACAACAAAAAAATTTGAAATTTTTTTACTCGAGAAAAGGG
Found at i:56701513 original size:62 final size:62
Alignment explanation
Indices: 56701358--56701513 Score: 190
Period size: 61 Copynumber: 2.5 Consensus size: 62
56701348 AGGAGAAGTT
* * * *
56701358 GGTGTCGGTCATTTGATGGCCAGCACCAAAAAAATTTGGAATTTTTTTATTCTAGAAAAGGG
1 GGTGTCGGTCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTACTCGAGAAAAGGG
* * **
56701420 AGTATCGGTCATTTGATGGCCAACAAGAAAAAAATTT-AAAGTTTTTTT-CTCGAGAAAAGGG
1 GGTGTCGGTCATTTGATGGCCAACACCAAAAAAATTTGAAA-TTTTTTTACTCGAGAAAAGGG
* * *
56701481 GGTGTCGGCCATTTGATGGCTAACACCTAAAAA
1 GGTGTCGGTCATTTGATGGCCAACACCAAAAAA
56701514 TGTAATTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
61 39 0.50
62 39 0.50
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (62 bp):
GGTGTCGGTCATTTGATGGCCAACACCAAAAAAATTTGAAATTTTTTTACTCGAGAAAAGGG
Found at i:56701587 original size:154 final size:155
Alignment explanation
Indices: 56701381--56701679 Score: 435
Period size: 154 Copynumber: 1.9 Consensus size: 155
56701371 TGATGGCCAG
* * * *
56701381 CACCAAAAAAATTTGGAATTTTTTTATTCTAGAAAAGGGAGTATCGGTCATTTGATGGCCAACA-
1 CACCAAAAAAATTTGGAATTTTTTTACTCAAGAAAAGGGAGTATCGGCCATTTGATGACCAACAC
* * *
56701445 AGAAAAAAATTTAAAGTTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCTAACACCTA
66 A-AAAAAAATTTAAAGTTTTTTTCTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACACCCA
56701510 AAAATGTAATTTTTTTGAAAGGCCGA
130 AAAATGTAATTTTTTTGAAAGGCCGA
* *
56701536 CACC-AAAAAATTTTGAATTTTTTT-CTCAAGAAAACAGGG-GTGTCGGCCATTTGATGACCAAC
1 CACCAAAAAAATTTGGAATTTTTTTACTCAAG-AAA-AGGGAGTATCGGCCATTTGATGACCAAC
* * *
56701598 ACAAAAAAAATTTAAATTTTTTTTCTCGAGAATAGGGGGTGTTGACCATTTGATGGCCAACACCC
64 ACAAAAAAAATTTAAAGTTTTTTTCTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACACCC
56701663 AAAAATGTAATTTTTTT
129 AAAAATGTAATTTTTTT
56701680 TCGAGAAAAG
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
153 4 0.03
154 116 0.90
155 9 0.07
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (155 bp):
CACCAAAAAAATTTGGAATTTTTTTACTCAAGAAAAGGGAGTATCGGCCATTTGATGACCAACAC
AAAAAAAATTTAAAGTTTTTTTCTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACACCCAA
AAATGTAATTTTTTTGAAAGGCCGA
Found at i:56701606 original size:93 final size:95
Alignment explanation
Indices: 56701447--56701620 Score: 237
Period size: 93 Copynumber: 1.9 Consensus size: 95
56701437 GGCCAACAAG
* * * * **
56701447 AAAAAAATTTAAAGTTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCTAACAC-CTAA
1 AAAAAAATTTAAAGTTTTTTTCTCAAGAAAAAGGGGTGTCGGCCATTTGATGACCAACACAAAAA
56701511 AAATGT-AATTTTTTTGAAAGGCCGACACC
66 AAATGTAAATTTTTTTGAAAGGCCGACACC
* *
56701540 AAAAAATTTTGAA-TTTTTTTCTCAAGAAAACAGGGGTGTCGGCCATTTGATGACCAACACAAAA
1 AAAAAAATTTAAAGTTTTTTTCTCAAGAAAA-AGGGGTGTCGGCCATTTGATGACCAACACAAAA
*
56701604 AAAATTTAAATTTTTTT
65 AAAATGTAAATTTTTTT
56701621 TCTCGAGAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
92 16 0.23
93 37 0.54
94 7 0.10
95 9 0.13
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (95 bp):
AAAAAAATTTAAAGTTTTTTTCTCAAGAAAAAGGGGTGTCGGCCATTTGATGACCAACACAAAAA
AAATGTAAATTTTTTTGAAAGGCCGACACC
Found at i:56701834 original size:59 final size:59
Alignment explanation
Indices: 56701530--56701819 Score: 322
Period size: 57 Copynumber: 4.9 Consensus size: 59
56701520 TTTTTTGAAA
* *
56701530 GGCCGACACCAAAAAATTTTGAATTTTTTTCTCAAGAAAACA-GGGGTGTCGGCCATTTGAT
1 GGCCAACACCAAAAAATTTTGAATTTTTTTTTC--G-AAACAGGGGGTGTCGGCCATTTGAT
* * * * * * *
56701591 GACCAACACAAAAAAAATTTAAATTTTTTTTCTCGAGAATAGGGGGTGTTGACCATTTGAT
1 GGCCAACACCAAAAAATTTTGAATTTTTTTT-TCGA-AACAGGGGGTGTCGGCCATTTGAT
* * * *
56701652 GGCCAACACCCAAAAA-TGT-AA-TTTTTTTTCGAGAAAAGGGGATGTCGGCCATTTGAT
1 GGCCAACACCAAAAAATTTTGAATTTTTTTTTCGA-AACAGGGGGTGTCGGCCATTTGAT
** * *
56701709 GGCCAACATTAAAAAATTTTGAA-TTTTTTTT-GAAACAGGGGATGTCGACCATTTGAT
1 GGCCAACACCAAAAAATTTTGAATTTTTTTTTCGAAACAGGGGGTGTCGGCCATTTGAT
*
56701766 GGCCAACACCAAAAAATTTTGAATTTTTTTTTTGAAACAGGGGGTGTCGGCCAT
1 GGCCAACACCAAAAAATTTTGAATTTTTTTTTCGAAACAGGGGGTGTCGGCCAT
56701820 GCAATAGCCA
Statistics
Matches: 195, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
57 81 0.42
58 19 0.10
59 32 0.16
60 6 0.03
61 55 0.28
62 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (59 bp):
GGCCAACACCAAAAAATTTTGAATTTTTTTTTCGAAACAGGGGGTGTCGGCCATTTGAT
Found at i:56706997 original size:7 final size:7
Alignment explanation
Indices: 56706957--56706981 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56706947 CTTGTGCCAA
56706957 AAAAAAG
1 AAAAAAG
56706964 AAAAAAG
1 AAAAAAG
56706971 AAAAAAG
1 AAAAAAG
56706978 AAAA
1 AAAA
56706982 GAAAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:56706998 original size:16 final size:15
Alignment explanation
Indices: 56706957--56707000 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
56706947 CTTGTGCCAA
56706957 AAAAAAGAAA-AAAG
1 AAAAAAGAAAGAAAG
56706971 AAAAAAGAAAAGAAAGG
1 AAAAAAG-AAAGAAA-G
*
56706988 AAAACAGAAAGAA
1 AAAAAAGAAAGAA
56707001 GATAATCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 3 0.12
16 9 0.35
17 7 0.27
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAAAG
Found at i:56708513 original size:65 final size:63
Alignment explanation
Indices: 56708407--56708527 Score: 147
Period size: 65 Copynumber: 1.9 Consensus size: 63
56708397 GGCTTGAATC
* *
56708407 TTTTTTTTTTCAAGTTAAGTTTTGAAATTGGCAATCTTTTTTATA-TAGGGGTTTGAATTGTTT
1 TTTTTTTTTTCAAGTTAAGTTTTGAAATTGACAATCTTTTTTAAATTA-GGGTTTGAATTGTTT
* * *
56708470 TTTTTTTTTGTCTAAGTTAGGTTTTGAACTTGATAAT-TATTTTTAAATTAGGGTTTGA
1 TTTTTTTTT-TC-AAGTTAAGTTTTGAAATTGACAATCT-TTTTTAAATTAGGGTTTGA
56708528 TTTTTTATCC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 9 0.18
64 3 0.06
65 35 0.71
66 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.17, T:0.55
Consensus pattern (63 bp):
TTTTTTTTTTCAAGTTAAGTTTTGAAATTGACAATCTTTTTTAAATTAGGGTTTGAATTGTTT
Found at i:56709127 original size:23 final size:23
Alignment explanation
Indices: 56709100--56709143 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56709090 TTATTTAAAC
56709100 AAATACACATATTTATATAATTA
1 AAATACACATATTTATATAATTA
** *
56709123 AAATATTCATATTTTTATAAT
1 AAATACACATATTTATATAAT
56709144 AGGTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATACACATATTTATATAATTA
Found at i:56709638 original size:16 final size:16
Alignment explanation
Indices: 56709607--56709643 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
56709597 ATATGAAGAA
56709607 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
56709623 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
56709639 TATTA
1 TATTA
56709644 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:56711935 original size:19 final size:20
Alignment explanation
Indices: 56711897--56711946 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
56711887 AACAAAAATT
*
56711897 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTATAAA
56711917 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTTATAAA
56711936 AATTTCAAAAT
1 AA-TTCAAAAT
56711947 TTATATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTCAAAATAATTTATAAA
Found at i:56720001 original size:2 final size:2
Alignment explanation
Indices: 56719955--56719983 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56719945 TGTTGTTTCC
56719955 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 T
56719984 TGTGTGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56725190 original size:18 final size:18
Alignment explanation
Indices: 56725167--56725223 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
56725157 AAAAAATTTT
56725167 AAAATAATTTTTTAATTC
1 AAAATAATTTTTTAATTC
* **
56725185 AAAATACTTTTAAAAGTTC
1 AAAATAATTTTTTAA-TTC
*
56725204 AGAAT-ATTTTTTAATGTC
1 AAAATAATTTTTTAAT-TC
56725222 AA
1 AA
56725224 GATCAAGGGT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
17 1 0.03
18 21 0.72
19 7 0.24
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (18 bp):
AAAATAATTTTTTAATTC
Found at i:56726003 original size:69 final size:68
Alignment explanation
Indices: 56725919--56726047 Score: 222
Period size: 68 Copynumber: 1.9 Consensus size: 68
56725909 CTCAAATAAT
* *
56725919 AAAAATAAAATATTAAAATAAGTAAAAAATGAAATAAAATGAAAATAATCTTTTTGACTTTGAAT
1 AAAAATAAAACATTAAAATAAGT-AAAAATGAAATAAAATGAAAACAATCTTTTTGACTTTGAAT
56725984 AGTA
65 AGTA
*
56725988 AAAAATAAAACATTAAAATAAGTAATAATGAAATAAAATGAAAACAATCTTTTTGACTTT
1 AAAAATAAAACATTAAAATAAGTAAAAATGAAATAAAATGAAAACAATCTTTTTGACTTT
56726048 TTAAATAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
68 35 0.61
69 22 0.39
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (68 bp):
AAAAATAAAACATTAAAATAAGTAAAAATGAAATAAAATGAAAACAATCTTTTTGACTTTGAATA
GTA
Done.