Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 131 of 185
Found at i:40756305 original size:34 final size:34
Alignment explanation
Indices: 40756267--40756412 Score: 150
Period size: 34 Copynumber: 4.3 Consensus size: 34
40756257 AATTGATTGA
* * *
40756267 TTATAAGTATATTATTTGTTACCGTATCGATCTG
1 TTATAAGCATATTAATTGCTACCGTATCGATCTG
* * *
40756301 TTATAAGCATATTAATTACTACTGTA-CTGATTTG
1 TTATAAGCATATTAATTGCTACCGTATC-GATCTG
* * * *
40756335 TTATAAGCATATTAATTGCGATCGTATTGATCTA
1 TTATAAGCATATTAATTGCTACCGTATCGATCTG
* * *
40756369 TTATACGCATATAAATTGCTACCGTATTGATCTG
1 TTATAAGCATATTAATTGCTACCGTATCGATCTG
*
40756403 TAATAAGCAT
1 TTATAAGCAT
40756413 GTCATATTGC
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
33 1 0.01
34 89 0.99
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.42
Consensus pattern (34 bp):
TTATAAGCATATTAATTGCTACCGTATCGATCTG
Found at i:40756630 original size:44 final size:45
Alignment explanation
Indices: 40756519--40756711 Score: 156
Period size: 45 Copynumber: 4.3 Consensus size: 45
40756509 TATCTGCAAA
* * * * * * *
40756519 TTTGGTGTGCATCCACAGCCAAAGGTAGATTCTATCTACGGGATT
1 TTTGCTGTGTATCCATAGCCAGAGATAAATTCTATCTACGAGATT
* * * * *
40756564 TTTGTTGTGCATCCACAGCCAGAGGTAAATTCTATCTGCGAGA-T
1 TTTGCTGTGTATCCATAGCCAGAGATAAATTCTATCTACGAGATT
* * * * * *
40756608 TTTGCTGCGTATTCATAGCCAGAGACAAATTTTATTTGCGAGATT
1 TTTGCTGTGTATCCATAGCCAGAGATAAATTCTATCTACGAGATT
* * * * *
40756653 TTTTCTATGTACCCATAGCCAGAGATAGATTCTATCTACGGGA-T
1 TTTGCTGTGTATCCATAGCCAGAGATAAATTCTATCTACGAGATT
*
40756697 TTTGTTGTGTATCCA
1 TTTGCTGTGTATCCA
40756712 CAGTCATTGA
Statistics
Matches: 118, Mismatches: 29, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
44 47 0.40
45 71 0.60
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (45 bp):
TTTGCTGTGTATCCATAGCCAGAGATAAATTCTATCTACGAGATT
Found at i:40764133 original size:96 final size:96
Alignment explanation
Indices: 40764014--40764234 Score: 282
Period size: 96 Copynumber: 2.3 Consensus size: 96
40764004 TGTTTATTAT
* * *
40764014 TTTTTAATAAAAAATTAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTAAAAATTATT
1 TTTTTAAGAAAAAATTAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTAAAAATT-TT
*
40764079 TA-AAAGTCAGATAAGGGTTTAGAGTTAAGGG
65 TATAAAATCAGATAAGGGTTTAGAGTTAAGGG
* * **
40764110 TTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTGTAAATTTTT
1 TTTTTAAGAAAAAATTAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTAAAAATTTTT
** * * *
40764175 ATAAAATTTGATTAGGGTTTAGTGTTTAGGG
66 ATAAAATCAGATAAGGGTTTAGAGTTAAGGG
* *
40764206 TTTTTAAGTAAAAACTCAAATAAATTAGG
1 TTTTTAAG-AAAAAATTAAATAAATTAGG
40764235 ATTTGGGGTT
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
95 4 0.04
96 86 0.80
97 17 0.16
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (96 bp):
TTTTTAAGAAAAAATTAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTAAAAATTTTT
ATAAAATCAGATAAGGGTTTAGAGTTAAGGG
Found at i:40764502 original size:126 final size:126
Alignment explanation
Indices: 40764277--40764564 Score: 450
Period size: 126 Copynumber: 2.3 Consensus size: 126
40764267 TTGTTAATTT
* *
40764277 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
* * * * * *
40764342 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAACAGAAGTCCTG
66 GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAAGATACTTTGTCAACAAAAGTACTG
*
40764403 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
1 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
* * *
40764468 GTTTCTAAGAAAATAGTGTCAAAAATGCTTTAAGCAAGATATTTTGTCAGCAAAAGTACTG
66 GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAAGATACTTTGTCAACAAAAGTACTG
* *
40764529 AAAGAAGCTCCCACGTGGACACGCTTTTGCTACAGT
1 AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGT
40764565 GGCGCATGTT
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 148 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (126 bp):
AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTAAGAAAATAGTGTCAAAAACGCTTTAAGCAAGATACTTTGTCAACAAAAGTACTG
Found at i:40768281 original size:18 final size:18
Alignment explanation
Indices: 40768255--40768297 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40768245 GACTAGAAAA
* * *
40768255 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
40768273 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
40768291 AGGATAC
1 AGGATAC
40768298 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40770149 original size:33 final size:33
Alignment explanation
Indices: 40770105--40770182 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 33
40770095 TCTTTTAAAT
*
40770105 AGAAATCTGAGAGGAATTTGAGAGGAAT-TT-GAG
1 AGAAAT-TGAGAGAAATTTGAGA-GAATATTAGAG
40770138 AGAAAATTGAGAGAAATTTGAGAGAATATTAGAG
1 AG-AAATTGAGAGAAATTTGAGAGAATATTAGAG
40770172 AGAAATTGAGA
1 AGAAATTGAGA
40770183 AAAAGGATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
32 4 0.10
33 28 0.68
34 9 0.22
ACGTcount: A:0.46, C:0.01, G:0.29, T:0.23
Consensus pattern (33 bp):
AGAAATTGAGAGAAATTTGAGAGAATATTAGAG
Found at i:40770171 original size:10 final size:10
Alignment explanation
Indices: 40770105--40770182 Score: 75
Period size: 11 Copynumber: 7.1 Consensus size: 10
40770095 TCTTTTAAAT
40770105 AGAAATCTGAG
1 AGAAAT-TGAG
*
40770116 AGGAATTTGAG
1 A-GAAATTGAG
*
40770127 AGGAATTTGAG
1 A-GAAATTGAG
40770138 AGAAAATTGAG
1 AG-AAATTGAG
40770149 AGAAATTTGAG
1 AGAAA-TTGAG
40770160 AGAATATTAGAG
1 AGAA-ATT-GAG
40770172 AGAAATTGAG
1 AGAAATTGAG
40770182 A
1 A
40770183 AAAAGGATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
10 8 0.13
11 40 0.67
12 12 0.20
ACGTcount: A:0.46, C:0.01, G:0.29, T:0.23
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:40775572 original size:3 final size:3
Alignment explanation
Indices: 40775564--40775589 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40775554 CAAAACCCAA
40775564 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
40775590 CCTTAGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40778941 original size:19 final size:19
Alignment explanation
Indices: 40778917--40778954 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40778907 ATTTATGAAG
40778917 TGTCATTAAAGTGGTATTA
1 TGTCATTAAAGTGGTATTA
40778936 TGTCATTAAAGTGGTATTA
1 TGTCATTAAAGTGGTATTA
40778955 AAGTTCCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TGTCATTAAAGTGGTATTA
Found at i:40786595 original size:25 final size:25
Alignment explanation
Indices: 40786567--40786615 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40786557 TACAATCTAT
* *
40786567 CTATAGTAGTCTCAGTATATACTAC
1 CTATAGCAGTCTCAATATATACTAC
*
40786592 CTATAGCAGTTTCAATATATACTA
1 CTATAGCAGTCTCAATATATACTA
40786616 TCAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (25 bp):
CTATAGCAGTCTCAATATATACTAC
Found at i:40787506 original size:97 final size:96
Alignment explanation
Indices: 40787390--40787709 Score: 412
Period size: 97 Copynumber: 3.3 Consensus size: 96
40787380 GTTTTTAAAT
* * * * *
40787390 TTTAGGG-TTTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
40787454 AAATTTTAAAAAATTAGATTAGGGTTTAGCG
66 AAATTTTAAAAAATTAGATTAGGGTTTAGTG
* * * * *
40787485 TTTATGGTTTTTAAAGAAAAAATCAAATAAATTAGGGTTTAAGGCTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
40787550 AAATTTTAAAAAAATTAGATTAGGATTTAGTG
66 AAATTTT-AAAAAATTAGATTAGGGTTTAGTG
* * *
40787582 TTTAGGGTTTTTAAGGAAAGAATAAAATAAATTAGGGATCAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
* * *
40787647 AAATTTAAAAAAAAAGTAGATT-GAGGTTTAGTA
66 AAATTT--TAAAAAATTAGATTAG-GGTTTAGTG
*
40787680 TTTAGGGTTTTTAAGG-AAAAATCAAATAAA
1 TTTAGGGTTTTTAAGGAAAAAATAAAATAAA
40787710 GATAGTTGTT
Statistics
Matches: 195, Mismatches: 25, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
95 6 0.03
96 56 0.29
97 98 0.50
98 35 0.18
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.37
Consensus pattern (96 bp):
TTTAGGGTTTTTAAGGAAAAAATAAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
AAATTTTAAAAAATTAGATTAGGGTTTAGTG
Found at i:40787783 original size:34 final size:33
Alignment explanation
Indices: 40787745--40787832 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 33
40787735 TAAACTCCTC
40787745 TAAAAAATAAAATAATAAAATTAAATGTTTTTAA
1 TAAAAAATAAAATAATAAAA-TAAATGTTTTTAA
* * * * *
40787779 TAAAAATTAAATTTATTAAAA-GAATTTTTTTAA
1 TAAAAAATAAA-ATAATAAAATAAATGTTTTTAA
* *
40787812 TAATAAATTAAAT-ATAAAATA
1 TAAAAAATAAAATAATAAAATA
40787833 TATAATCAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
31 5 0.12
32 1 0.02
33 18 0.44
34 10 0.24
35 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
TAAAAAATAAAATAATAAAATAAATGTTTTTAA
Found at i:40788277 original size:11 final size:11
Alignment explanation
Indices: 40788261--40788286 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40788251 GTTAGACTTG
40788261 ATAAATAATTT
1 ATAAATAATTT
40788272 ATAAATAATTT
1 ATAAATAATTT
40788283 ATAA
1 ATAA
40788287 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:40788288 original size:18 final size:17
Alignment explanation
Indices: 40788265--40788305 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
40788255 GACTTGATAA
*
40788265 ATAATTTATAAATAATTT
1 ATAATTTATAAA-AAATT
*
40788283 ATAATTTTTAAAAAATT
1 ATAATTTATAAAAAATT
40788300 ATAATT
1 ATAATT
40788306 AATTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTATAAAAAATT
Found at i:40788535 original size:39 final size:40
Alignment explanation
Indices: 40788463--40788541 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
40788453 TGAAGCGCTT
*
40788463 TGTCCACGTGGACACAAAGCGCTCCCTCAAGGAAGCTTTTC
1 TGTCCACGTGGA-ACAAAGCGCTCCCTCAAGGAAGATTTTC
* **
40788504 TGTCCACGTGG-ACAAAGCGCTTCCTTGAGGAAGATTTT
1 TGTCCACGTGGAACAAAGCGCTCCCTCAAGGAAGATTTT
40788542 TTACTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 23 0.68
41 11 0.32
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
TGTCCACGTGGAACAAAGCGCTCCCTCAAGGAAGATTTTC
Found at i:40789562 original size:18 final size:18
Alignment explanation
Indices: 40789523--40789558 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40789513 CATGATGTTC
*
40789523 GCCCGTGTAGGTCCACAT
1 GCCCGTGTAGGCCCACAT
40789541 GCCCGTGT-GGCCCACAT
1 GCCCGTGTAGGCCCACAT
40789558 G
1 G
40789559 GCCCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.36, G:0.31, T:0.19
Consensus pattern (18 bp):
GCCCGTGTAGGCCCACAT
Found at i:40793706 original size:17 final size:17
Alignment explanation
Indices: 40793686--40793724 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40793676 GTCTCAGCCA
*
40793686 TGTGAATCACACGGTCG
1 TGTGAATCACACGGCCG
*
40793703 TGTGAATCACACTGCCG
1 TGTGAATCACACGGCCG
40793720 TGTGA
1 TGTGA
40793725 CCCCTGCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (17 bp):
TGTGAATCACACGGCCG
Found at i:40800825 original size:47 final size:47
Alignment explanation
Indices: 40800756--40800851 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
40800746 TTTGGTCTTC
*
40800756 AAACAATGTTTTATATTACTTATATTGTTTCATTAAAAATTATAATT
1 AAACAATGTTTTATATTACTTATATTATTTCATTAAAAATTATAATT
* *
40800803 AAACAATGTTTTATATTACTTATATTATTTGATTAGAAATTATAATT
1 AAACAATGTTTTATATTACTTATATTATTTCATTAAAAATTATAATT
40800850 AA
1 AA
40800852 CACTACAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (47 bp):
AAACAATGTTTTATATTACTTATATTATTTCATTAAAAATTATAATT
Found at i:40804095 original size:43 final size:43
Alignment explanation
Indices: 40804034--40804141 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
40804024 TGTCCTAGAC
* **
40804034 ATGGTCTTACATGGAAATCTCGTATCGATGCCAATAGCACAACT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCACAACT
* * *
40804078 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCATCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCACAACT
*
40804121 ATGGTCTTACATGAAATCTCA
1 ATGGTCTTACACGAAATCTCA
40804142 CCTCAGAAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 45 0.80
44 11 0.20
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCACAACT
Found at i:40804335 original size:30 final size:30
Alignment explanation
Indices: 40804256--40804338 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
40804246 ATTCAATGCT
* * *
40804256 CAAATCAATTCGACAATATATATACATATA
1 CAAATCAATTCGGCAATGTATATACACATA
* **
40804286 CGAATCAAATTTAGCAATGTATAT-CTACATA
1 CAAATC-AATTCGGCAATGTATATAC-ACATA
40804317 CAAATCAATTCGGCAATGTATA
1 CAAATCAATTCGGCAATGTATA
40804339 AAACATATAC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
30 20 0.48
31 22 0.52
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATATACACATA
Found at i:40804349 original size:31 final size:30
Alignment explanation
Indices: 40804256--40804349 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
40804246 ATTCAATGCT
* * *
40804256 CAAATCAATTCGACAATATATATACATATA
1 CAAATCAATTCGGCAATGTATAAACATATA
* ** * *
40804286 CGAATCAAATTTAGCAATGTAT-ATCTACATA
1 CAAATC-AATTCGGCAATGTATAAAC-ATATA
40804317 CAAATCAATTCGGCAATGTATAAAACATATA
1 CAAATCAATTCGGCAATGTAT-AAACATATA
40804348 CA
1 CA
40804350 TTTAAATTCA
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
30 19 0.40
31 26 0.55
32 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATAAACATATA
Found at i:40806928 original size:190 final size:190
Alignment explanation
Indices: 40806690--40807068 Score: 695
Period size: 190 Copynumber: 2.0 Consensus size: 190
40806680 TGGTTGGGAT
* * *
40806690 GAGCATAGGCAGCTTGTTGTTGTTGAAGATGTTGTGTGGAACTCATATATAAATGTAAGAATTAT
1 GAGCATAGGCAGCTTGTTGTTGTTGAAGATGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
* *
40806755 TTCAAGTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCCTCATTTTTATAGAG
66 TTCAACTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
40806820 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTGA
131 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTGA
*
40806880 GAGCATAGGCAGCTTGTTGTTGTTGAAGGTGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
1 GAGCATAGGCAGCTTGTTGTTGTTGAAGATGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
*
40806945 TTCAACTCTTTATTATTTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
66 TTCAACTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
40807010 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTG
131 TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTG
40807069 CCATCTACGC
Statistics
Matches: 182, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 182 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (190 bp):
GAGCATAGGCAGCTTGTTGTTGTTGAAGATGCTGTGTAGAAATCATATATAAATGTAAGAATTAT
TTCAACTCTTTATTATCTTATTTGACCAAACTTATATCTAAGATGAATTCATCATTTTTATAGAG
TCATAAAGAAACTGGTCAATTCAAACATCGTAGTTTCCCTTATTATGACCAACTTACTGA
Found at i:40808015 original size:12 final size:12
Alignment explanation
Indices: 40808000--40808044 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
40807990 TTCATATAAT
40808000 AATTATATTAAG
1 AATTATATTAAG
*
40808012 AATTTTATT-A-
1 AATTATATTAAG
40808022 AATTATATTAAG
1 AATTATATTAAG
*
40808034 AATTTTATTAA
1 AATTATATTAA
40808045 ATCATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (12 bp):
AATTATATTAAG
Found at i:40808025 original size:22 final size:22
Alignment explanation
Indices: 40808000--40808052 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
40807990 TTCATATAAT
40808000 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATTTTATTA
40808022 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATTTTATTA
*
40808044 AATCATATT
1 AATTATATT
40808053 TAATAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTATATTAAGAATTTTATTA
Found at i:40808113 original size:58 final size:60
Alignment explanation
Indices: 40807995--40808120 Score: 157
Period size: 58 Copynumber: 2.1 Consensus size: 60
40807985 TTTAATTCAT
* *
40807995 ATAATAATTATATTAAGAATTTTATTAAATTATATTAAGAATTTTATTAAATCATATTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATTAAGAATTTTATTAAATCATATTTA
* * ** * * *
40808055 ATAATAATTATGTTAA-AATATGGTTAAATTAT-TTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATTAAGAATTTTATTAAATCATATTTA
40808113 ATAATAAT
1 ATAATAAT
40808121 CGTATTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 29 0.51
59 13 0.23
60 15 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (60 bp):
ATAATAATTATATTAAGAATATGATTAAATTATATTAAGAATTTTATTAAATCATATTTA
Found at i:40808319 original size:16 final size:16
Alignment explanation
Indices: 40808298--40808349 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
40808288 TAAATTACTG
40808298 ATTACAACTTTATTCC
1 ATTACAACTTTATTCC
* * *
40808314 ATTACAGCTCTATTCA
1 ATTACAACTTTATTCC
40808330 ATTACAA-TTCTATTCC
1 ATTACAACTT-TATTCC
40808346 ATTA
1 ATTA
40808350 TAGTGAACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTACAACTTTATTCC
Found at i:40809544 original size:14 final size:14
Alignment explanation
Indices: 40809503--40809610 Score: 81
Period size: 14 Copynumber: 7.7 Consensus size: 14
40809493 GTTTGTATAT
*
40809503 ATGCGACTCAATAC
1 ATGCGAGTCAATAC
* *
40809517 ATGCAAGTCTATAC
1 ATGCGAGTCAATAC
*
40809531 ATGCGAGCCAATAC
1 ATGCGAGTCAATAC
* * *
40809545 TTGTGAGTCAATAT
1 ATGCGAGTCAATAC
* * *
40809559 ATGTGAGACAACAC
1 ATGCGAGTCAATAC
* * *
40809573 CTACGATTCAATAC
1 ATGCGAGTCAATAC
*
40809587 ATGCGAGTCAATAT
1 ATGCGAGTCAATAC
*
40809601 ATGCAAGTCA
1 ATGCGAGTCA
40809611 TAAATCACAT
Statistics
Matches: 69, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (14 bp):
ATGCGAGTCAATAC
Found at i:40809668 original size:27 final size:26
Alignment explanation
Indices: 40809648--40809702 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
40809638 ACCCCTGCTT
40809648 GTGCGAACCTATGTGCAACCCCCTTA
1 GTGCGAACCTATGTGCAACCCCCTTA
* *
40809674 GGTGTGAACCTATGTGCGACCCCCCTTA
1 -GTGCGAACCTATGTGC-AACCCCCTTA
40809702 G
1 G
40809703 GTGTAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCGAACCTATGTGCAACCCCCTTA
Found at i:40809697 original size:28 final size:27
Alignment explanation
Indices: 40809652--40809711 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
40809642 CTGCTTGTGC
40809652 GAACCTATGTGCAACCCCCTTAGGTGT
1 GAACCTATGTGCAACCCCCTTAGGTGT
*
40809679 GAACCTATGTGCGACCCCCCTTAGGTGT
1 GAACCTATGTGC-AACCCCCTTAGGTGT
*
40809707 AAACC
1 GAACC
40809712 CCTAACTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (27 bp):
GAACCTATGTGCAACCCCCTTAGGTGT
Found at i:40809816 original size:33 final size:34
Alignment explanation
Indices: 40809720--40809830 Score: 152
Period size: 34 Copynumber: 3.3 Consensus size: 34
40809710 CCCCTAACTA
* * *
40809720 TGCGAGCTTATATGTTATACGAACTCTAGGAATG
1 TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
* *
40809754 TGCGACCCTATATGTTATGCGAACCCTAGGAATA
1 TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
* *
40809788 TGTGAGCCTATATG-TATGTGAACCCTAGGAATG
1 TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
40809821 TGCGAGCCTA
1 TGCGAGCCTA
40809831 CATGCGAACC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 26 0.39
34 41 0.61
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (34 bp):
TGCGAGCCTATATGTTATGCGAACCCTAGGAATG
Found at i:40809840 original size:29 final size:31
Alignment explanation
Indices: 40809770--40809845 Score: 75
Period size: 33 Copynumber: 2.5 Consensus size: 31
40809760 CCTATATGTT
* *
40809770 ATGCGAACCCTAGGAATATGTGAGCCTATATGT
1 ATGCGAACCCTAGGAATATGCGAGCC-ATA-GC
* *
40809803 ATGTGAACCCTAGGAATGTGCGAGCC-TA-C
1 ATGCGAACCCTAGGAATATGCGAGCCATAGC
*
40809832 ATGCGAACCTTAGG
1 ATGCGAACCCTAGG
40809846 TACATGTGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 12 0.32
31 2 0.05
33 23 0.62
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (31 bp):
ATGCGAACCCTAGGAATATGCGAGCCATAGC
Found at i:40811075 original size:21 final size:21
Alignment explanation
Indices: 40811049--40811095 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
40811039 AATACTAGTG
40811049 ATGTTACTAAAATGAAATATA
1 ATGTTACTAAAATGAAATATA
* *
40811070 ATGTTACTATAATGGAATATA
1 ATGTTACTAAAATGAAATATA
40811091 ATGTT
1 ATGTT
40811096 GGATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
ATGTTACTAAAATGAAATATA
Found at i:40815510 original size:69 final size:69
Alignment explanation
Indices: 40815410--40815545 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
40815400 TATACACTGC
*
40815410 CATGGTCCAACCATAGTATTACGTCTAAAAAACTATCATAGCCTCGCTATGGTCTTACATAAACA
1 CATGGTCCAACCATAGTATTACGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAAACA
40815475 TTTT
66 TTTT
* * * * * *
40815479 CATGGTCCAGCCATGGTCTTGCGTCTGAAAAACTGCCATAGCCTCGCTATGGTCTTACATAAACA
1 CATGGTCCAACCATAGTATTACGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAAACA
40815544 TT
66 TT
40815546 GCCGTAGTCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (69 bp):
CATGGTCCAACCATAGTATTACGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAAACA
TTTT
Found at i:40815556 original size:69 final size:69
Alignment explanation
Indices: 40815407--40815564 Score: 208
Period size: 69 Copynumber: 2.3 Consensus size: 69
40815397 ATATATACAC
* * * * *
40815407 TGCCATGGTCCAACCATAGTATTACGTCTAAAAAACTATCATAGCCTCGCTATGGTCTTACATAA
1 TGCCATAGTCCAACCATGGTCTTGCGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAA
40815472 ACAT
66 ACAT
** * * * *
40815476 TTTCATGGTCCAGCCATGGTCTTGCGTCTGAAAAACTGCCATAGCCTCGCTATGGTCTTACATAA
1 TGCCATAGTCCAACCATGGTCTTGCGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAA
40815541 ACAT
66 ACAT
*
40815545 TGCCGTAGTCCAACCATGGT
1 TGCCATAGTCCAACCATGGT
40815565 TTTGTACATT
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (69 bp):
TGCCATAGTCCAACCATGGTCTTGCGTCTAAAAAACTACCATAGCCTCGCTATGGTCTTACATAA
ACAT
Found at i:40825884 original size:110 final size:111
Alignment explanation
Indices: 40825664--40825886 Score: 403
Period size: 111 Copynumber: 2.0 Consensus size: 111
40825654 ATGTTTAGCC
40825664 CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
1 CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
*
40825729 AATTTAATGTTTACTAAACTTATATATTTTCCCTTTATCAAAATTG
66 AATTTAATGTTGACTAAACTTATATATTTTCCCTTTATCAAAATTG
* *
40825775 CAAACCTATTTTAAGTCTACCCATTTTATTTTTTTATTTTTTTGAAAAATATTTATA-TTTTTTT
1 CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
*
40825839 AATTTAATGTTGACTAAATTTATATATTTTCCCTTTATCAAAATTG
66 AATTTAATGTTGACTAAACTTATATATTTTCCCTTTATCAAAATTG
40825885 CA
1 CA
40825887 TATATGCAAC
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
110 53 0.49
111 55 0.51
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (111 bp):
CAAACCCATTTTAAGTCTACCCATTTTATTTTTTCATTTTTTTGAAAAATATTTATATTTTTTTT
AATTTAATGTTGACTAAACTTATATATTTTCCCTTTATCAAAATTG
Found at i:40828102 original size:18 final size:18
Alignment explanation
Indices: 40828079--40828114 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40828069 AGCCTCGTCT
* *
40828079 ATCACACGCCCGTGTTCG
1 ATCACAAGCCCATGTTCG
40828097 ATCACAAGCCCATGTTCG
1 ATCACAAGCCCATGTTCG
40828115 GTCATATGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (18 bp):
ATCACAAGCCCATGTTCG
Found at i:40829746 original size:45 final size:45
Alignment explanation
Indices: 40829695--40829785 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
40829685 GGTGTTTAGT
40829695 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
1 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
40829740 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
1 TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
40829785 T
1 T
40829786 CCTTATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (45 bp):
TAAAGCATTGTAGCATTTGGTGTTTAACGTCAAACATGTTAACTA
Found at i:40833233 original size:5 final size:5
Alignment explanation
Indices: 40833223--40833247 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40833213 TTTGGTATAT
40833223 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
40833248 AGGTAATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:40834267 original size:20 final size:20
Alignment explanation
Indices: 40834238--40834275 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40834228 CTTGTACGAG
* *
40834238 ATTTGTACTTCGATGCCCTT
1 ATTTGCACTTCAATGCCCTT
40834258 ATTTGCACTTCAATGCCC
1 ATTTGCACTTCAATGCCC
40834276 CTGTATACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.39
Consensus pattern (20 bp):
ATTTGCACTTCAATGCCCTT
Found at i:40834344 original size:20 final size:20
Alignment explanation
Indices: 40834309--40834359 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
40834299 TTCGCACTAC
* *
40834309 GGTGCCCATGTTTGCACATTT
1 GGTGCCCCTGTCTGCA-ATTT
*
40834330 -GTGCCCCTGTCTGCATTTT
1 GGTGCCCCTGTCTGCAATTT
40834349 GGTGCCCCTGT
1 GGTGCCCCTGT
40834360 TATGCATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.08, C:0.29, G:0.25, T:0.37
Consensus pattern (20 bp):
GGTGCCCCTGTCTGCAATTT
Found at i:40837195 original size:32 final size:32
Alignment explanation
Indices: 40837151--40837214 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
40837141 ATATATTCCT
*
40837151 AGTTCTATATGTCGATGACATTTTGCTTGCCA
1 AGTTCTAGATGTCGATGACATTTTGCTTGCCA
* *
40837183 AGTTCTAGATGTCGTTGATATTTTGCTTGCCA
1 AGTTCTAGATGTCGATGACATTTTGCTTGCCA
40837215 CTAATGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (32 bp):
AGTTCTAGATGTCGATGACATTTTGCTTGCCA
Found at i:40840526 original size:29 final size:27
Alignment explanation
Indices: 40840480--40840534 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
40840470 ATATAGATAT
40840480 GAAAATATTCATTAAAAATATAAATATAG
1 GAAAATATTCATTAAAAA-A-AAATATAG
** *
40840509 GAAAATATTTGTTGAAAAAAAATATA
1 GAAAATATTCATTAAAAAAAAATATA
40840535 AATTTATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 1 0.04
29 15 0.65
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (27 bp):
GAAAATATTCATTAAAAAAAAATATAG
Found at i:40841741 original size:18 final size:18
Alignment explanation
Indices: 40841718--40841752 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40841708 TTTTGGGTCG
* *
40841718 CGTTTGTAATTGGGCCAC
1 CGTTTGAAATCGGGCCAC
40841736 CGTTTGAAATCGGGCCA
1 CGTTTGAAATCGGGCCA
40841753 TGTATTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTTTGAAATCGGGCCAC
Found at i:40842202 original size:44 final size:44
Alignment explanation
Indices: 40842138--40842249 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
40842128 GATCTACTCT
* * **
40842138 ACTGTGACTTCAGCGAGATAAGATCCA-TGATTTTAATCCGCTCC
1 ACTGTAACTTCAGGGAGATAAGAT-CATTGACCTTAATCCGCTCC
* * * *
40842182 ACTGTAACTTTAGGGAGATAAGATTATTGGCCTTAATCTGCTCC
1 ACTGTAACTTCAGGGAGATAAGATCATTGACCTTAATCCGCTCC
*
40842226 ACTGCAACTTCAGGGAGATAAGAT
1 ACTGTAACTTCAGGGAGATAAGAT
40842250 TCGCCCACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 56 0.98
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
ACTGTAACTTCAGGGAGATAAGATCATTGACCTTAATCCGCTCC
Found at i:40842471 original size:42 final size:42
Alignment explanation
Indices: 40842276--40843299 Score: 355
Period size: 44 Copynumber: 23.5 Consensus size: 42
40842266 GCCTCACTGC
* * * *
40842276 CAATATAAGAAGACAAGATCTGCTATTTTCAATCCACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * *
40842320 CAATACATGAAGACAAGATCTGCTTTCCTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * *
40842365 CAATAT-GGAAACACAAGATCTGCATCTTCGATCTACTTCGCCAC
1 CAATATAGG-AAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* *
40842409 CAATATGGGAAGACAAGATCTAGTCTTCGATCCACTTC-CTAA
1 CAATATAGGAAGACAAGATCT-GTCTTCGATCCACTTCGCCAA
* *
40842451 TAATATAGGAAGACAGGATCTG-C-T--AT---CTTCG-C--
1 CAATATAGGAAGACAAGATCTGTCTTCGATCCACTTCGCCAA
* * * *
40842483 CAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * *
40842528 CAATATGGGAAGACAAGATCTAGTCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCT-GTCTTCGATCCACTTCGCCAA
* * *
40842570 CAATATAGGAAGACAGGATCTGCTATCTTCAATCTACTTCATG-C--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTC--GCCAA
* * * **
40842614 CAATATATGAGGACAAGATCTGTTTTCTTCGATCTACTTCGCCGC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * * *
40842659 CAGTATGGGAAGACAAGATCTACATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCT--GTCTTCGATCCACTTCGCCAA
* * *
40842703 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * * *
40842747 CAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * *
40842792 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
40842836 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * ** * * *
40842880 CAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCACTAC
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * * * * * *
40842925 CAGTATGGGAAGTCAAAATCTGCATCTTTGATCCACTTCACTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
40842969 CAATATAGGAAGACAAGATCTATTATCTTTGATCTACTTCACGCCAA
1 CAATATAGGAAGACAAGATC---TGTCTTCGATCCACTT--CGCCAA
* * *
40843016 -TATATA--AATG-CAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 CAATATAGGAA-GACAAGATCTG---TCTTCGATCCACTTCGCCAA
* * * * *
40843058 CAGTATGGGAAGACAAGATCTGTATCTTCGATCCAATTC-CTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
40843101 CAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* * * * * * *
40843145 CAATACATGAAGACAACATATGCTTTCTTCGATCTACTTCACCAC
1 CAATATAGGAAGAC-A-AGAT-CTGTCTTCGATCCACTTCGCCAA
* * * *
40843190 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTAC
1 CAATATAGGAAGACAAGATCTG--TCTTCGATCCACTTCGCCAA
* * *
40843234 CAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGC--
1 CAATATAGGAAGACAAGATCTG---TCTTCGATCCACTTCGC-CAA
* *
40843278 CAATACATGAAGACAAGATCTG
1 CAATATAGGAAGACAAGATCTG
40843300 CTGCTTTTTA
Statistics
Matches: 764, Mismatches: 150, Indels: 132
0.73 0.14 0.13
Matches are distributed among these distances:
32 18 0.02
34 4 0.01
36 1 0.00
37 3 0.00
39 3 0.00
40 1 0.00
41 3 0.00
42 55 0.07
43 61 0.08
44 429 0.56
45 172 0.23
46 8 0.01
47 6 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
CAATATAGGAAGACAAGATCTGTCTTCGATCCACTTCGCCAA
Found at i:40842617 original size:44 final size:44
Alignment explanation
Indices: 40842480--40843301 Score: 730
Period size: 44 Copynumber: 18.6 Consensus size: 44
40842470 CTGCTATCTT
* * * *
40842480 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGC
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-A
* * *
40842525 CACCAATATGGGAAGACAAGA--T-CTAGTCTTCGATCCACTTC-
1 CGCCAATATAGGAAGACAAGATCTGCTA-TCTTCGATCTACTTCA
* * *
40842566 CTACCAATATAGGAAGACAGGATCTGCTATCTTCAATCTACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * * * * *
40842611 TGCCAATATATGAGGACAAGATCTGTTTTCTTCGATCTACTTCGC
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-A
* * * * *
40842656 CGCCAGTATGGGAAGACAAGATCTAC-ATCTTCGATCCACTTCG
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * *
40842699 CTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * * * * *
40842744 CGCCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGC
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-A
* * * * *
40842789 CACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCG
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * *
40842832 CTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * * *
40842877 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCA
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * * * * * *
40842921 CTACCAGTATGGGAAGTCAAAATCTGC-ATCTTTGATCCACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* ** *
40842965 CTACCAATATAGGAAGACAAGATCTATTATCTTTGATCTACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
** * *
40843010 CGCCAATATATAAATG-CAAGATCTGCTTTCTTCGATCTACTTCGC
1 CGCCAATATAGGAA-GACAAGATCTGCTATCTTCGATCTACTTC-A
* * * * *
40843055 CACCAGTATGGGAAGACAAGATCTG-TATCTTCGATCCAATTC-
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* *
40843097 CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * * * *
40843142 CGCCAATACATGAAGACAACATATGCTTTCTTCGATCTACTTCA
1 CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * * * *
40843186 CCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCG
1 -CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* * *
40843230 CTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCA
1 C-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
* *
40843275 CGCCAATACATGAAGACAAGATCTGCT
1 CGCCAATATAGGAAGACAAGATCTGCT
40843302 GCTTTTTAGC
Statistics
Matches: 618, Mismatches: 136, Indels: 47
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.00
42 21 0.03
43 39 0.06
44 376 0.61
45 181 0.29
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
Found at i:40842723 original size:89 final size:89
Alignment explanation
Indices: 40842482--40843301 Score: 786
Period size: 89 Copynumber: 9.3 Consensus size: 89
40842472 GCTATCTTCG
* * * * *
40842482 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* *
40842547 C---TAGTCTTCGATCCACTTCCTA
66 CTGTTA-TCTTCGATCTACTTCCCA
* * * * * *
40842569 CCAATATAGGAAGACAGGATCTGCTATCTTCAATCTACTTC-ATGCCAATATATGAGGACAAGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* *
40842633 CTGTTTTCTTCGATCTACTTCGCCG
66 CTGTTATCTTCGATCTACTTC-CCA
* * * * *
40842658 CCAGTATGGGAAGACAAGATCTAC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* *
40842722 CTGTTATCTTCGATCTACTTCACG
66 CTGTTATCTTCGATCTACTTCCCA
* * * * * * * *
40842746 CCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* * *
40842811 CTG-CATCTTCGATCCACTTCGCTA
66 CTGTTATCTTCGATCTACTTC-CCA
* * * * * *
40842835 CCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* *
40842899 CTGCTT-TCTTCGATTTACTTCACTA
66 CTG-TTATCTTCGATCTACTTC-CCA
* * * * * * *
40842924 CCAGTATGGGAAGTCAAAATCTGC-ATCTTTGATCCACTTCACTACCAATATAGGAAGACAAGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* * * *
40842988 CTATTATCTTTGATCTACTTCACG
66 CTGTTATCTTCGATCTACTTCCCA
** * * * *
40843012 CCAATATATAAATG-CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
1 CCAATATAGGAA-GACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGA
* * *
40843076 TCTG-TATCTTCGATCCAATTCCTA
65 TCTGTTATCTTCGATCTACTTCCCA
* * * * * *
40843100 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAACAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
*
40843164 ATGCTT-TCTTCGATCTACTTCACCA
66 CTG-TTATCTTCGATCTACTTC-CCA
* * * *
40843189 CCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGAT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
* *
40843253 CTGTTATCTTCGATCTACTTCACG
66 CTGTTATCTTCGATCTACTTCCCA
* *
40843277 CCAATACATGAAGACAAGATCTGCT
1 CCAATATAGGAAGACAAGATCTGCT
40843302 GCTTTTTAGC
Statistics
Matches: 582, Mismatches: 131, Indels: 38
0.77 0.17 0.05
Matches are distributed among these distances:
86 18 0.03
87 54 0.09
88 219 0.38
89 291 0.50
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (89 bp):
CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGAT
CTGTTATCTTCGATCTACTTCCCA
Found at i:40842751 original size:133 final size:133
Alignment explanation
Indices: 40842480--40843301 Score: 1330
Period size: 133 Copynumber: 6.2 Consensus size: 133
40842470 CTGCTATCTT
*
40842480 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
* *
40842545 ATCT--AGTCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCAATCTAC
66 ATCTGCA-TCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTAC
40842607 TTCA
130 TTCA
* * * * *
40842611 TGCCAATATATGAGGACAAGATCTGTTTTCTTCGATCTACTTCGCCGCCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
*
40842676 ATCTACATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
40842741 TCA
131 TCA
* *
40842744 CGCCAATACATGAAGACAAAATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
40842809 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
40842874 TCA
131 TCA
* * * * *
40842877 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATTTACTTCACTACCAGTATGGGAAGTCAAA
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
* * * * *
40842942 ATCTGCATCTTTGATCCACTTCACTACCAATATAGGAAGACAAGATCTATTATCTTTGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
40843007 TCA
131 TCA
* *
40843010 CGCCAATATATAAATG-CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 CGCCAATACATGAA-GACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
* * *
40843074 GATCTGTATCTTCGATCCAATTC-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTAC
65 GATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTAC
40843138 TTCA
130 TTCA
* * *
40843142 CGCCAATACATGAAGACAACATATGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAG
1 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
40843207 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
66 ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
40843272 TCA
131 TCA
40843275 CGCCAATACATGAAGACAAGATCTGCT
1 CGCCAATACATGAAGACAAGATCTGCT
40843302 GCTTTTTAGC
Statistics
Matches: 633, Mismatches: 52, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
131 64 0.10
132 134 0.21
133 434 0.69
134 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (133 bp):
CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
ATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACT
TCA
Found at i:40853874 original size:23 final size:23
Alignment explanation
Indices: 40853844--40853889 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40853834 GGTACCCGAA
40853844 CCAGCAGATTCCTCGATCTTCAC
1 CCAGCAGATTCCTCGATCTTCAC
40853867 CCAGCAGATTCCTCGATCTTCAC
1 CCAGCAGATTCCTCGATCTTCAC
40853890 AACAAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.39, G:0.13, T:0.26
Consensus pattern (23 bp):
CCAGCAGATTCCTCGATCTTCAC
Found at i:40855175 original size:19 final size:19
Alignment explanation
Indices: 40855151--40855225 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
40855141 AATCATATTT
40855151 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
* *
40855170 TCTAAGATTGCATATATCAAA
1 TCTAAGATT--ACATATCATA
*
40855191 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
40855210 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
40855226 CTTGAAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 32 0.65
21 17 0.35
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:40855188 original size:21 final size:21
Alignment explanation
Indices: 40855162--40855224 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
40855152 CTAAGATTAC
40855162 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
40855183 ATATCAAATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
40855202 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
40855223 AT
1 AT
40855225 CCTTGAAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.47
21 20 0.53
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:40874467 original size:19 final size:20
Alignment explanation
Indices: 40874411--40874468 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 20
40874401 TGTTATAATT
40874411 TTTTTAAAATATAAATTTTAGAA
1 TTTTTAAAA-AT--ATTTTAGAA
*
40874434 TTTTTATAAATATTTTA-AA
1 TTTTTAAAAATATTTTAGAA
40874453 -TTTTAAAAATCATTTT
1 TTTTTAAAAAT-ATTTT
40874469 GAAAATTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 6 0.19
22 2 0.06
23 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTTAAAAATATTTTAGAA
Found at i:40890159 original size:25 final size:25
Alignment explanation
Indices: 40890120--40890170 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
40890110 ATGATATAAT
*
40890120 ACTTATTATAATCTTTTAAATTATA
1 ACTTATCATAATCTTTTAAATTATA
*
40890145 ACTTATCATATTCTTTTAAATTATA
1 ACTTATCATAATCTTTTAAATTATA
40890170 A
1 A
40890171 TTTTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (25 bp):
ACTTATCATAATCTTTTAAATTATA
Found at i:40892635 original size:18 final size:17
Alignment explanation
Indices: 40892574--40892637 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
40892564 TGTCACCTCA
*
40892574 ATAAATAATTT-AAAATT
1 ATAAA-AATTTAAAAAAT
*
40892591 ATAAAAATATTCAAAAAT
1 ATAAAAAT-TTAAAAAAT
*
40892609 AAAAGAAATTTAAAAAAT
1 ATAA-AAATTTAAAAAAT
40892627 GATAAAAATTT
1 -ATAAAAATTT
40892638 TATTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 22 0.56
19 7 0.18
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAAATTTAAAAAAT
Found at i:40899319 original size:30 final size:29
Alignment explanation
Indices: 40899283--40899349 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40899273 TTTAATTAAT
* *
40899283 TTTTTAAAATTTA-AAAAATATTTTTATAAG
1 TTTTTAAAACTTATAAAAATA-TTTTA-AAA
40899313 TTTTT-AAACTTATAAAAATATTTTAAAA
1 TTTTTAAAACTTATAAAAATATTTTAAAA
40899341 TTTTTAAAA
1 TTTTTAAAA
40899350 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 14 0.42
30 12 0.36
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTTTAAAACTTATAAAAATATTTTAAAA
Found at i:40900407 original size:20 final size:19
Alignment explanation
Indices: 40900371--40900409 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
40900361 ATTAAAGGAG
* *
40900371 AAATTAAATTAATTTGATT
1 AAATTAAATCAAATTGATT
40900390 AAATTCAAATCAAATTGATT
1 AAATT-AAATCAAATTGATT
40900410 TGAATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
AAATTAAATCAAATTGATT
Found at i:40901678 original size:21 final size:21
Alignment explanation
Indices: 40901654--40901696 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
40901644 ACCTAAACCC
40901654 TAAACTTATAAAAATA-TTTTT
1 TAAA-TTATAAAAATAGTTTTT
*
40901675 TAAATTTTAAAAATAGTTTTT
1 TAAATTATAAAAATAGTTTTT
40901696 T
1 T
40901697 TTATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TAAATTATAAAAATAGTTTTT
Found at i:40903321 original size:60 final size:60
Alignment explanation
Indices: 40903228--40903349 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
40903218 TGATAAAGGG
40903228 AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
1 AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
*
40903288 AAAGAAATAACTATCCAAACAGAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
1 AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
40903348 AA
1 AA
40903350 TGCTTAGCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (60 bp):
AAAGAAATAACTATCCAAACAAAGAAGAGAAAAGAGAATAATATTCTTTTGTTATTCAAA
Found at i:40907300 original size:21 final size:21
Alignment explanation
Indices: 40907276--40907315 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40907266 TTTTTTAAGC
40907276 CAACACACCAATTTTGACTAT
1 CAACACACCAATTTTGACTAT
** *
40907297 CAACATGCCTATTTTGACT
1 CAACACACCAATTTTGACT
40907316 GGCATAATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (21 bp):
CAACACACCAATTTTGACTAT
Found at i:40908631 original size:20 final size:19
Alignment explanation
Indices: 40908606--40908655 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
40908596 TAATATATTT
40908606 TATTATTAAAATATTAAAAA
1 TATTATTAAAAT-TTAAAAA
* *
40908626 TATTATTTAAACTTTAAAAT
1 TATTA-TTAAAATTTAAAAA
40908646 TATTAATTAA
1 TATT-ATTAA
40908656 CGTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTATTAAAATTTAAAAA
Found at i:40908661 original size:19 final size:20
Alignment explanation
Indices: 40908619--40908662 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40908609 TATTAAAATA
* *
40908619 TTAAAAATATTATTTAAACT
1 TTAAAAATATTAATTAAACG
*
40908639 TTAAAATTATTAATT-AACG
1 TTAAAAATATTAATTAAACG
40908658 TTAAA
1 TTAAA
40908663 TTTTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAAAATATTAATTAAACG
Found at i:40912125 original size:43 final size:43
Alignment explanation
Indices: 40912061--40912243 Score: 294
Period size: 43 Copynumber: 4.3 Consensus size: 43
40912051 TTCTAAAAAT
* *
40912061 GCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAATC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* * *
40912104 GCCACTAAAGATCAAAACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
*
40912147 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTCTTCCCACAAAC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
40912190 GCCGCTAAAGAACAAGACTTTTAGCGGCGCTTTTCCCATAAAC
1 GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
40912233 GCCGCTAAAGA
1 GCCGCTAAAGA
40912244 TTATGACCTT
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:40915675 original size:21 final size:22
Alignment explanation
Indices: 40915628--40915698 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 22
40915618 GAAATATCAA
*
40915628 AATAAAAATCAACTG-AAAT-CC
1 AATAAAAA-CAACTGAAAATAAC
*
40915649 AAATAAAAAGAAC-GAAAATTAAC
1 -AATAAAAACAACTGAAAA-TAAC
40915672 -AT-AAAACAACTGAAAATAAC
1 AATAAAAACAACTGAAAATAAC
40915692 AATAAAA
1 AATAAAA
40915699 CGGGGGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
20 12 0.30
21 15 0.38
22 12 0.30
23 1 0.03
ACGTcount: A:0.66, C:0.13, G:0.06, T:0.15
Consensus pattern (22 bp):
AATAAAAACAACTGAAAATAAC
Found at i:40916323 original size:9 final size:9
Alignment explanation
Indices: 40916309--40916361 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
40916299 GTTTAAATTT
40916309 TTTTTAAAA
1 TTTTTAAAA
40916318 TTTTTAAAA
1 TTTTTAAAA
**
40916327 AATTTAAAA
1 TTTTTAAAA
40916336 TCTTTTAAAA
1 T-TTTTAAAA
40916346 TTCATTTTAAAA
1 -T--TTTTAAAA
40916358 TTTT
1 TTTT
40916362 AAATCACGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 19 0.53
10 7 0.19
11 2 0.06
12 8 0.22
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:40916733 original size:21 final size:18
Alignment explanation
Indices: 40916691--40916746 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
40916681 CAAAACACGC
*
40916691 AAAAAACTGAACTGGATA
1 AAAAAACTGAACCGGATA
40916709 AAAAAACTGAACCGAGCACTA
1 AAAAAACTGAACCG-G-A-TA
* *
40916730 AAAATACTGAACGGGAT
1 AAAAAACTGAACCGGAT
40916747 GGGAGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
20 2 0.06
21 14 0.44
ACGTcount: A:0.52, C:0.16, G:0.18, T:0.14
Consensus pattern (18 bp):
AAAAAACTGAACCGGATA
Found at i:40916972 original size:21 final size:21
Alignment explanation
Indices: 40916948--40916987 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40916938 TTTAACACAT
*
40916948 AACCTCTAAACCTTAAACCCC
1 AACCTCTAAACCATAAACCCC
*
40916969 AACCTTTAAACCATAAACC
1 AACCTCTAAACCATAAACC
40916988 ATAAACCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCTCTAAACCATAAACCCC
Found at i:40916992 original size:14 final size:14
Alignment explanation
Indices: 40916975--40917028 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
40916965 CCCCAACCTT
40916975 TAAACCATAAACCA
1 TAAACCATAAACCA
* *
40916989 TAAACCATAACCCC
1 TAAACCATAAACCA
* *
40917003 TAAACCCATAATCTA
1 TAAA-CCATAAACCA
*
40917018 TAAACCTTAAA
1 TAAACCATAAA
40917029 ATGGTAACAC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:40917058 original size:14 final size:14
Alignment explanation
Indices: 40917038--40917086 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
40917028 AATGGTAACA
*
40917038 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
* *
40917052 TCTAAACCATATAC
1 CCTAAACCATAAAC
* *
40917066 CCTAAACCAAAAAA
1 CCTAAACCATAAAC
40917080 CCTAAAC
1 CCTAAAC
40917087 TATAGTGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:40917333 original size:41 final size:41
Alignment explanation
Indices: 40917266--40917633 Score: 477
Period size: 41 Copynumber: 9.0 Consensus size: 41
40917256 TTTAAATCCT
40917266 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * *
40917307 TGAGCATTAGTGGCGTTTTTTAAAAAACGCCGCTAAAG-CC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * * * *
40917347 TAAGCATTAGCGGCGCTTCCCCAAAAACGCCACTAAGGCTC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * *
40917388 TGAGCATTAGCGGCGCTTCCCCAAAAACGCCACTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * * *
40917429 TGACCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAACCT
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * *
40917470 TGAGCATTAGCGACGCTTCCTCAAAAACGCCGCTAAAGCCT
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* * *
40917511 TAAGCATTAGCGGTGCTTTCTCAAAAACGCCGCTAAATCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
* ** * *
40917552 TGATCATTAGCGATGCTTTCTCAAAAACGCCTCTAAATCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
40917593 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
40917634 CGGAAGCTCA
Statistics
Matches: 284, Mismatches: 42, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
40 31 0.11
41 253 0.89
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
Found at i:40929854 original size:18 final size:19
Alignment explanation
Indices: 40929833--40929870 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
40929823 ATCAATATTT
40929833 TTAT-AAAAATATCGATAC
1 TTATAAAAAATATCGATAC
40929851 TTATGAAAAAATATCGATAC
1 TTAT-AAAAAATATCGATAC
40929871 CACGGGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TTATAAAAAATATCGATAC
Found at i:40932258 original size:29 final size:30
Alignment explanation
Indices: 40932226--40932415 Score: 116
Period size: 29 Copynumber: 6.6 Consensus size: 30
40932216 TTTTTTCGAG
* *
40932226 TTTTATAGTTCTGCCATTA-TTTTCTAGAA
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
* *
40932255 TTTTATAGTTTTGCCCCTAGTTTTCT-GGA
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
* * * * *
40932284 TTTTTTAATTATGCCACTATTTTTCTAG-T
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
* *
40932313 TTTTATAGTTTTGCCACTGGTTTTCCA-AA
1 TTTTATAGTTTTGCCACTAGTTTTCTAGAA
** *
40932342 GTTTTCA-A-TTCAGCCACT--TTTTTTAG-A
1 -TTTT-ATAGTTTTGCCACTAGTTTTCTAGAA
* **
40932369 TTTTACAAATTTGCCACTA-TTTT-TAAGAA
1 TTTTATAGTTTTGCCACTAGTTTTCT-AGAA
40932398 -TTTATAGTTTTGCCACTA
1 TTTTATAGTTTTGCCACTA
40932416 TTCTTCAAAA
Statistics
Matches: 123, Mismatches: 27, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
25 1 0.01
26 5 0.04
27 14 0.11
28 21 0.17
29 69 0.56
30 12 0.10
31 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.51
Consensus pattern (30 bp):
TTTTATAGTTTTGCCACTAGTTTTCTAGAA
Found at i:40932358 original size:58 final size:57
Alignment explanation
Indices: 40932237--40932392 Score: 147
Period size: 58 Copynumber: 2.7 Consensus size: 57
40932227 TTTATAGTTC
* *** * *
40932237 TGCCA-TTATTTTCTAGAATTTTATAGTTTTGCCCCTAGTTTTCTGGATTTTTTAATTA
1 TGCCACTT-TTTTCTAG-ATTTTATAGTTTTGCCACTAGTTTTCCAAAGTTTTCAATTA
* *
40932295 TGCCACTATTTTTCTAGTTTTTATAGTTTTGCCACTGGTTTTCCAAAGTTTTCAATTCA
1 TGCCACT-TTTTTCTAGATTTTATAGTTTTGCCACTAGTTTTCCAAAGTTTTCAATT-A
* ** *
40932354 -GCCACTTTTTT-TAGATTTTACAAATTTGCCACTATTTTT
1 TGCCACTTTTTTCTAGATTTTATAGTTTTGCCACTAGTTTT
40932393 AAGAATTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
56 22 0.27
57 5 0.06
58 43 0.53
59 10 0.12
60 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (57 bp):
TGCCACTTTTTTCTAGATTTTATAGTTTTGCCACTAGTTTTCCAAAGTTTTCAATTA
Found at i:40932391 original size:28 final size:28
Alignment explanation
Indices: 40932354--40932417 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
40932344 TTTCAATTCA
* *
40932354 GCCACT-TTTTTTAGATTTTACAAATTT
1 GCCACTATTTTTAAGAATTTACAAATTT
* **
40932381 GCCACTATTTTTAAGAATTTATAGTTTT
1 GCCACTATTTTTAAGAATTTACAAATTT
40932409 GCCACTATT
1 GCCACTATT
40932418 CTTCAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (28 bp):
GCCACTATTTTTAAGAATTTACAAATTT
Found at i:40933448 original size:37 final size:36
Alignment explanation
Indices: 40933367--40933456 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 36
40933357 TTGAACCGTA
* *
40933367 TTGAATTGATTGATATACGAGACTGTTTGTTATCATG
1 TTGAATTGATTGATATACGAAACTGTTTGTCAT-ATG
* **
40933404 TTAAATTGATTGATATGTGAAACTGTTTGTCAT-TG
1 TTGAATTGATTGATATACGAAACTGTTTGTCATATG
40933439 TACTGAATTGATTGATAT
1 T--TGAATTGATTGATAT
40933457 TACTGTACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 3 0.07
37 42 0.93
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (36 bp):
TTGAATTGATTGATATACGAAACTGTTTGTCATATG
Found at i:40934470 original size:20 final size:20
Alignment explanation
Indices: 40934445--40934506 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
40934435 ACAATTTTAA
* *
40934445 AATCAAGTGAAAATGATTTT
1 AATCAAGTCAAAATAATTTT
*
40934465 AATCAAGTCAAAATAATTTC
1 AATCAAGTCAAAATAATTTT
* *
40934485 AATCAAGTTAAAATTATTTT
1 AATCAAGTCAAAATAATTTT
40934505 AA
1 AA
40934507 GACATCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
AATCAAGTCAAAATAATTTT
Found at i:40934525 original size:40 final size:40
Alignment explanation
Indices: 40934445--40934532 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
40934435 ACAATTTTAA
*
40934445 AATCAAGTGAAAATGATTTTAATCAAGTCAAAATAATTTC
1 AATCAAGTGAAAATGATTTTAAACAAGTCAAAATAATTTC
* * *
40934485 AATCAAGTTAAAATTATTTTAAGAC-A-TCAAAATGATTTTC
1 AATCAAGTGAAAATGATTTTAA-ACAAGTCAAAAT-AATTTC
*
40934525 AAACAAGT
1 AATCAAGT
40934533 CAGGATTGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 7 0.17
40 33 0.80
41 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (40 bp):
AATCAAGTGAAAATGATTTTAAACAAGTCAAAATAATTTC
Found at i:40935782 original size:25 final size:25
Alignment explanation
Indices: 40935736--40935783 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
40935726 CACACGGCCG
* *
40935736 TGTGAAATAATGTAGGCCGTGTGCT
1 TGTGAAATAATGTAGACAGTGTGCT
40935761 TGTGAAATCAA-GTAGACAGTGTG
1 TGTGAAAT-AATGTAGACAGTGTG
40935784 GACCACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.29
Consensus pattern (25 bp):
TGTGAAATAATGTAGACAGTGTGCT
Found at i:40941519 original size:18 final size:21
Alignment explanation
Indices: 40941491--40941530 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
40941481 ATATATATGT
40941491 ATTATTTTAAAA-AT-AAAAA
1 ATTATTTTAAAATATGAAAAA
40941510 ATTA-TTTAAAATATGAAAAA
1 ATTATTTTAAAATATGAAAAA
40941530 A
1 A
40941531 ATAAGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATTATTTTAAAATATGAAAAA
Found at i:40941983 original size:15 final size:16
Alignment explanation
Indices: 40941950--40941985 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40941940 TGAATGGGTC
*
40941950 TCAACCTCTTTTATTA
1 TCAACCCCTTTTATTA
40941966 TCAACCCCTTTT-TTA
1 TCAACCCCTTTTATTA
40941981 TCAAC
1 TCAAC
40941986 AACTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (16 bp):
TCAACCCCTTTTATTA
Found at i:40944811 original size:101 final size:102
Alignment explanation
Indices: 40944691--40944875 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 102
40944681 AAAGGGATGG
* *
40944691 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG-ATGATAATGGTCACATGTGTAGT
40944754 ACTACT-TGCAGGCTACTATGCGTACTGGATAGTTTCAA
65 ACTA-TGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
* *
40944792 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGATAATGGTCACATGTGTAGTA
40944857 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
40944876 TGAACCGAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 32 0.42
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACTGGATAGTTTCAA
Found at i:40944852 original size:51 final size:49
Alignment explanation
Indices: 40944687--40944873 Score: 198
Period size: 51 Copynumber: 3.7 Consensus size: 49
40944677 AGTGAAAGGG
* *
40944687 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGG-ATGGT
* * * *
40944738 A-GGTCGCATGTGTAGTACTACT-TGCAGGCTACTATGCGTACTGGATAGT
1 ATGGTCACATGTGTAGTACTA-TGTGCAGGCTACTACGTGTAC-GGATGGT
* ** * *
40944787 TTCAATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATGGT
40944838 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
40944874 TGTGAACCGA
Statistics
Matches: 110, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
49 4 0.04
50 36 0.33
51 68 0.62
52 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (49 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATGGT
Found at i:40944877 original size:26 final size:26
Alignment explanation
Indices: 40944797--40944877 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
40944787 TTCAATCACG
40944797 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
40944823 CGTGTA-T-CAGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
40944848 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
40944874 TGTG
1 TGTG
40944878 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:40947662 original size:50 final size:50
Alignment explanation
Indices: 40947603--40947714 Score: 208
Period size: 50 Copynumber: 2.3 Consensus size: 50
40947593 CATTCAAAAT
40947603 TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
1 TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
*
40947653 TAACCATTCAAGAGCTTCAAACACTTAACAAGACACATATACATATCATA
1 TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
40947703 TAACCA-TCAAGA
1 TAACCATTCAAGA
40947715 ACAAGTATTA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 6 0.10
50 55 0.90
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (50 bp):
TAACCATTCAAGAGCGTCAAACACTTAACAAGACACATATACATATCATA
Found at i:40948310 original size:22 final size:20
Alignment explanation
Indices: 40948289--40948365 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
40948279 CTGAGTAGTA
*
40948289 GGCACCGAAGTGCGAATCAGT
1 GGCACCGAAGTGC-AAACAGT
** *
40948310 AAACACCGAAATGCAAACAGT
1 -GGCACCGAAGTGCAAACAGT
*
40948331 GGCACCAAAGTGCAAACAGT
1 GGCACCGAAGTGCAAACAGT
**
40948351 GGCATTGAAGTGCAA
1 GGCACCGAAGTGCAA
40948366 TCTCATACAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 28 0.64
21 6 0.14
22 10 0.23
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (20 bp):
GGCACCGAAGTGCAAACAGT
Found at i:40949344 original size:22 final size:20
Alignment explanation
Indices: 40949308--40949366 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
40949298 GACCCGATCC
40949308 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
40949330 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
40949351 AAATATTTTAAAAATA
1 ATTTATTTTAAAAATA
40949367 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:40949363 original size:11 final size:11
Alignment explanation
Indices: 40949349--40949488 Score: 83
Period size: 11 Copynumber: 12.4 Consensus size: 11
40949339 AAAAATTAAA
40949349 AAAAATATTTT
1 AAAAATATTTT
40949360 AAAAATATTTT
1 AAAAATATTTT
* **
40949371 AAAATTAAAAAATT
1 -AAA--AATATTTT
40949385 AAAAAGTATTTT
1 AAAAA-TATTTT
40949397 AAAAATATTTT
1 AAAAATATTTT
* **
40949408 AAAATTAAAAAATT
1 -AAA--AATATTTT
40949422 AAAAAGTATTTT
1 AAAAA-TATTTT
40949434 AAAAATATTTT
1 AAAAATATTTT
*
40949445 --AAA-A-TTA
1 AAAAATATTTT
* *
40949452 AAAAATA-ATA
1 AAAAATATTTT
40949462 AAAAAGTATTTT
1 AAAAA-TATTTT
40949474 AAAAATATTTT
1 AAAAATATTTT
40949485 AAAA
1 AAAA
40949489 TTAAAAAATT
Statistics
Matches: 100, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
7 2 0.02
8 1 0.01
9 6 0.06
10 8 0.08
11 39 0.39
12 28 0.28
13 6 0.06
14 10 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40949397 original size:37 final size:37
Alignment explanation
Indices: 40949339--40949504 Score: 269
Period size: 37 Copynumber: 4.3 Consensus size: 37
40949329 AATTTATTTT
*
40949339 AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTA
1 AAAAATT--AAAAAGTATTTTAAAAATATTTTAAAATTA
40949378 AAAAATTAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAGTATTTTAAAAATATTTTAAAATTA
40949415 AAAAATTAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAGTATTTTAAAAATATTTTAAAATTA
40949452 AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAT--T-AAAAAGTATTTTAAAAATATTTTAAAATTA
40949492 AAAAATTTAAAAA
1 AAAAA-TTAAAAA
40949505 ATAAATATAT
Statistics
Matches: 122, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
37 72 0.59
38 5 0.04
39 9 0.07
40 35 0.29
41 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (37 bp):
AAAAATTAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:40949454 original size:29 final size:29
Alignment explanation
Indices: 40949416--40949477 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
40949406 TTAAAATTAA
* * *
40949416 AAAATTAAAAAGTATTTTAAAAA-TATTTT
1 AAAATTAAAAAATA-ATAAAAAAGTATTTT
40949445 AAAATTAAAAAATAATAAAAAAGTATTTT
1 AAAATTAAAAAATAATAAAAAAGTATTTT
40949474 AAAA
1 AAAA
40949478 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTAAAAAATAATAAAAAAGTATTTT
Found at i:40949499 original size:16 final size:17
Alignment explanation
Indices: 40949358--40949517 Score: 83
Period size: 17 Copynumber: 8.8 Consensus size: 17
40949348 AAAAAATATT
*
40949358 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
40949375 TTAAAAA-ATTAAAAAGTA
1 TTAAAAATATTTAAAA--A
*
40949393 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTAAAAA
*
40949412 TTAAAAA-ATTAAAAAGTA
1 TTAAAAATATTTAAAA--A
*
40949430 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTAAAAA
**
40949449 TTAAAAAATAATAAAAAAGTA
1 TT-AAAAAT-ATTTAAAA--A
*
40949470 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTAAAAA
40949489 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
40949505 ATAAATATATTTA
1 TTAAAAATATTTA
40949518 TTATATCGGG
Statistics
Matches: 109, Mismatches: 17, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
16 25 0.23
17 28 0.26
18 8 0.07
19 8 0.07
20 14 0.13
21 18 0.17
22 6 0.06
23 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:40949517 original size:17 final size:16
Alignment explanation
Indices: 40949475--40949517 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
40949465 AAGTATTTTA
* *
40949475 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
40949491 AAAAAATTTAAAAAAT
1 AAAATATTTAAAAAAT
40949507 AAATATATTTA
1 AAA-ATATTTA
40949518 TTATATCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:40950721 original size:12 final size:12
Alignment explanation
Indices: 40950700--40950735 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
40950690 AAGATCTCTC
40950700 CATA-TCTTTTG
1 CATATTCTTTTG
40950711 CATATTCTTTTG
1 CATATTCTTTTG
40950723 CATATTCTTTTG
1 CATATTCTTTTG
40950735 C
1 C
40950736 TTACAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (12 bp):
CATATTCTTTTG
Found at i:40951456 original size:12 final size:13
Alignment explanation
Indices: 40951439--40951471 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
40951429 TTCCCTTTTA
40951439 TTTAACATAA-TT
1 TTTAACATAAGTT
40951451 TTTAAC-TAAGTT
1 TTTAACATAAGTT
40951463 TTTAACATA
1 TTTAACATA
40951472 TAAACAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 14 0.74
13 2 0.11
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (13 bp):
TTTAACATAAGTT
Found at i:40951734 original size:29 final size:30
Alignment explanation
Indices: 40951699--40951758 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
40951689 ACAAATGTTT
*
40951699 ACTAAAAATATTTACAAGCTCAGTTT-ATA
1 ACTAAAAATAATTACAAGCTCAGTTTCATA
*
40951728 ACTAAAAATAATTACAAGCTTAGTTTCATA
1 ACTAAAAATAATTACAAGCTCAGTTTCATA
40951758 A
1 A
40951759 ATAAGGTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (30 bp):
ACTAAAAATAATTACAAGCTCAGTTTCATA
Found at i:40953159 original size:5 final size:5
Alignment explanation
Indices: 40953149--40953173 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40953139 TAGTCTCTAC
40953149 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
40953174 GCTAATGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:40954333 original size:24 final size:24
Alignment explanation
Indices: 40954306--40954361 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
40954296 TATCATGTAC
* *
40954306 TATTATTTTA-AGTTTTTCATATAT
1 TATTATTTTAGA-TTTATCACATAT
*
40954330 TATTATTTTGGATTTATCACATAT
1 TATTATTTTAGATTTATCACATAT
40954354 TATTATTT
1 TATTATTT
40954362 AATTTCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (24 bp):
TATTATTTTAGATTTATCACATAT
Found at i:40966067 original size:27 final size:27
Alignment explanation
Indices: 40966031--40966440 Score: 455
Period size: 27 Copynumber: 15.2 Consensus size: 27
40966021 AGAGGTCTAT
*
40966031 AAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
40966058 AAATGACCGAAATACCCCCATAGGGT-
1 AAATGACCGAAATACCCCCATAGGGTA
* ** ** *
40966084 AAATAACTAAAATACCCTTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** *
40966111 AAATGATTGAAATACTCTCCATAGGGTA
1 AAATGACCGAAATAC-CCCCATAGGGTA
* ** *
40966139 GAATGATAGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
40966166 GAATGACCGAAATACACCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40966193 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
40966220 GAATGATCGAAATA-CCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
40966246 AATTGACCGAAATACCCCGATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
40966273 AAATGACTGAAATACCCCTATAGGGTT
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40966300 AAATAATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40966327 GAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
40966354 AAATGACCAAAATGCCCTCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40966381 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40966408 AAATAACCGAAATACCCCCATAGAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
40966435 AAATGA
1 AAATGA
40966441 TTGTTATACC
Statistics
Matches: 322, Mismatches: 58, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
26 42 0.13
27 259 0.80
28 21 0.07
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:40966877 original size:29 final size:31
Alignment explanation
Indices: 40966835--40966901 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
40966825 AACTACATAT
* *
40966835 CTGCACTGATTAATGATATT-GTACTG-TTA
1 CTGCATTGATTAATGATATTAATACTGTTTA
40966864 CTGCATTGATTAATGATATTACATACTGTTTA
1 CTGCATTGATTAATGATATTA-ATACTGTTTA
40966896 CTGCAT
1 CTGCAT
40966902 GACTGATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 5 0.15
32 9 0.27
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (31 bp):
CTGCATTGATTAATGATATTAATACTGTTTA
Found at i:40978579 original size:22 final size:20
Alignment explanation
Indices: 40978543--40978601 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
40978533 GACCCAGCCC
40978543 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
40978565 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
40978586 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
40978602 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:40978603 original size:11 final size:11
Alignment explanation
Indices: 40978583--40978687 Score: 81
Period size: 11 Copynumber: 10.4 Consensus size: 11
40978573 TAAAAATTAA
40978583 AAAAAGTATTTT
1 AAAAA-TATTTT
40978595 AAAAATATTTT
1 AAAAATATTTT
40978606 --AAA-A--TT
1 AAAAATATTTT
40978612 AAAAA-ATTTT
1 AAAAATATTTT
*
40978622 GAAAAGTATTTT
1 -AAAAATATTTT
40978634 AAAAATATTTT
1 AAAAATATTTT
40978645 --AAA-A--TT
1 AAAAATATTTT
40978651 AAAAA-ATTTT
1 AAAAATATTTT
*
40978661 GAAAAGTATTTT
1 -AAAAATATTTT
40978673 AAAAATATTTT
1 AAAAATATTTT
40978684 AAAA
1 AAAA
40978688 TTAAAAAATA
Statistics
Matches: 77, Mismatches: 4, Indels: 25
0.73 0.04 0.24
Matches are distributed among these distances:
6 4 0.05
8 10 0.13
9 6 0.08
10 4 0.05
11 38 0.49
12 15 0.19
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40978619 original size:39 final size:39
Alignment explanation
Indices: 40978574--40978716 Score: 214
Period size: 39 Copynumber: 3.6 Consensus size: 39
40978564 AATTTATTTT
40978574 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
***
40978613 AAAAATTTTGAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
***
40978652 AAAAATTTTGAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
*
40978691 AAAAATAATAAAAAAGTATTTTAAAA
1 AAAAATTA-AAAAAAGTATTTTAAAA
40978717 TTAAAAAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 81 0.84
40 15 0.16
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (39 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:40978694 original size:29 final size:29
Alignment explanation
Indices: 40978673--40978733 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
40978663 AAAGTATTTT
40978673 AAAAA-TATTTTAAAATTAAAAAATAATA
1 AAAAAGTATTTTAAAATTAAAAAATAATA
*
40978701 AAAAAGTATTTTAAAATTAAAAAA-AATT
1 AAAAAGTATTTTAAAATTAAAAAATAATA
40978729 AAAAA
1 AAAAA
40978734 CTAAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAATAATA
Found at i:40978727 original size:78 final size:78
Alignment explanation
Indices: 40978584--40978733 Score: 221
Period size: 78 Copynumber: 1.9 Consensus size: 78
40978574 AAAAATTAAA
* ** ***
40978584 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTTGAAAAGTATTTTAAAAATATTTTAAAA
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATATAAAAAAGTATTTTAAAAATATAAAAAAA
40978649 TTAAAAAATTTTG
66 TTAAAAAATTTTG
*
40978662 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAAAAAAGTATTTTAAAATTA-AAAAAA
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAT-ATAAAAAAGTATTTTAAAAATATAAAAAA
40978726 ATTAAAAA
65 ATTAAAAA
40978734 CTAAATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
78 46 0.72
79 18 0.28
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (78 bp):
AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATATAAAAAAGTATTTTAAAAATATAAAAAAA
TTAAAAAATTTTG
Found at i:40979228 original size:17 final size:17
Alignment explanation
Indices: 40979206--40979240 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40979196 ATTTTTATAG
40979206 TTTAATAATAATTTTAA
1 TTTAATAATAATTTTAA
* *
40979223 TTTAATACTTATTTTAA
1 TTTAATAATAATTTTAA
40979240 T
1 T
40979241 AGTATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATAATAATTTTAA
Found at i:40981934 original size:17 final size:18
Alignment explanation
Indices: 40981898--40981936 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40981888 CCATCGTCCT
* *
40981898 CTAAGGGGAAATAGATAA
1 CTAAGGGAAAAAAGATAA
40981916 CTAAGGGAAAAAAGA-AA
1 CTAAGGGAAAAAAGATAA
40981933 CTAA
1 CTAA
40981937 CTAAGTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.56, C:0.08, G:0.23, T:0.13
Consensus pattern (18 bp):
CTAAGGGAAAAAAGATAA
Found at i:40984822 original size:16 final size:15
Alignment explanation
Indices: 40984787--40984822 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40984777 CATTCATTCA
*
40984787 TGCATTTAGATTATT
1 TGCATTTAGATTAAT
40984802 TGCATTTAGATTTAAT
1 TGCATTTAGA-TTAAT
40984818 TGCAT
1 TGCAT
40984823 AGGGATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (15 bp):
TGCATTTAGATTAAT
Found at i:40987847 original size:45 final size:47
Alignment explanation
Indices: 40987794--40987885 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
40987784 ATTTATACCT
*
40987794 GAATACATAGCTAATACCTACATTCG-A-ATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
40987839 GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
40987886 ATCATATACA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 25 0.57
46 1 0.02
47 18 0.41
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (47 bp):
GAATACATAGCTAATACATACATTCGAATATATATATATACATATTC
Found at i:40987866 original size:25 final size:25
Alignment explanation
Indices: 40987794--40987868 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
40987784 ATTTATACCT
*
40987794 GAATACATAGCTAATACCTACATTC
1 GAATACATAGCTAATACATACATTC
*
40987819 GAATATATA--T-ATACAT--ATTC
1 GAATACATAGCTAATACATACATTC
40987839 GAATACATAGCTAATACATACATTC
1 GAATACATAGCTAATACATACATTC
40987864 GAATA
1 GAATA
40987869 TATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 12 0.29
22 6 0.14
23 7 0.17
25 17 0.40
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (25 bp):
GAATACATAGCTAATACATACATTC
Found at i:40987881 original size:20 final size:20
Alignment explanation
Indices: 40987812--40987881 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
40987802 AGCTAATACC
40987812 TACATTCGAATATATATATA
1 TACATTCGAATATATATATA
* * *
40987832 CATATTCGAATACATAGCTAATACA
1 TACATTCGAAT--ATA--T-ATATA
40987857 TACATTCGAATATATATATA
1 TACATTCGAATATATATATA
40987877 TACAT
1 TACAT
40987882 ATTCATCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 18 0.46
21 1 0.03
22 3 0.08
23 3 0.08
24 1 0.03
25 13 0.33
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (20 bp):
TACATTCGAATATATATATA
Found at i:40988256 original size:16 final size:16
Alignment explanation
Indices: 40988235--40988269 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40988225 CACCGGCTTT
40988235 TAGCCTGCTAGACCTA
1 TAGCCTGCTAGACCTA
40988251 TAGCCTGCTAGACCTA
1 TAGCCTGCTAGACCTA
40988267 TAG
1 TAG
40988270 TCCGAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (16 bp):
TAGCCTGCTAGACCTA
Found at i:40988326 original size:41 final size:41
Alignment explanation
Indices: 40988252--40988360 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
40988242 CTAGACCTAT
* * * * * * *
40988252 AGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
*
40988293 AGCCTGTTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
* *
40988334 AGTCTGCTAGACGTAAAGTCTGTATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTA
40988361 CATTCGATCA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
Found at i:40991334 original size:27 final size:27
Alignment explanation
Indices: 40991295--40991447 Score: 173
Period size: 27 Copynumber: 5.7 Consensus size: 27
40991285 AGAGGCCAGT
40991295 AAATGA-CATAAATACCCCCATAGGGTA
1 AAATGACCA-AAATACCCCCATAGGGTA
* *
40991322 AAATGACCAAAATACCCTCATAGGGAA
1 AAATGACCAAAATACCCCCATAGGGTA
* * * *
40991349 AAATAACCGAAATACCTCCATAGGATA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
40991376 AAATGACCAAAATACCCCCATAAGATA
1 AAATGACCAAAATACCCCCATAGGGTA
** *
40991403 AAATGACTGAAATACCCTCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
40991430 AAATAACTAAAATACCCC
1 AAATGACCAAAATACCCC
40991448 TTATAGGAGA
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
27 103 0.98
28 2 0.02
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:40991433 original size:81 final size:81
Alignment explanation
Indices: 40991295--40991445 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 81
40991285 AGAGGCCAGT
* * *
40991295 AAATGACATAAATACCCCCATAGGGTAAAATGACCAAAATACCCTCATAGGGAAAAATAACCGAA
1 AAATGACATAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGAAAAATAACCAAA
40991360 ATACCTCCATAGGATA
66 ATACCTCCATAGGATA
** * *
40991376 AAATGACCA-AAATACCCCCATAAGATAAAATGACTGAAATACCCTCATAGGGTAAAATAACTAA
1 AAATGA-CATAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGAAAAATAACCAA
40991440 AATACC
65 AATACC
40991446 CCTTATAGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 60 0.97
82 2 0.03
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (81 bp):
AAATGACATAAATACCCCCATAAGATAAAATGACCAAAATACCCTCATAGGGAAAAATAACCAAA
ATACCTCCATAGGATA
Found at i:40991659 original size:26 final size:26
Alignment explanation
Indices: 40991630--40991683 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
40991620 TTGCCACATT
*
40991630 TACTGTTACTGGCAGCTTCGCTGCGA
1 TACTATTACTGGCAGCTTCGCTGCGA
*
40991656 TACTATTACTGGCAGCTTTGCTGCGA
1 TACTATTACTGGCAGCTTCGCTGCGA
40991682 TA
1 TA
40991684 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTCGCTGCGA
Found at i:40991849 original size:28 final size:28
Alignment explanation
Indices: 40991791--40991854 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
40991781 ACTGTACTGA
* *
40991791 TACTGTATTGGGCTAAAGCCCACATTGT
1 TACTGTATTGGGCTAAAGCCCACACTAT
* * * *
40991819 TACTGTATTGGGCTCAGGCTCAGACTAT
1 TACTGTATTGGGCTAAAGCCCACACTAT
40991847 TACTGTAT
1 TACTGTAT
40991855 GTCGTATACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (28 bp):
TACTGTATTGGGCTAAAGCCCACACTAT
Found at i:40995936 original size:17 final size:18
Alignment explanation
Indices: 40995906--40995948 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40995896 TCCCTCACCT
**
40995906 TTTCTTTTTTGTTCT-TC
1 TTTCTTTTCGGTTCTCTC
40995923 TTTCTTTTCGGTTCTCTC
1 TTTCTTTTCGGTTCTCTC
40995941 TTCTCTTT
1 TT-TCTTT
40995949 GATTGTCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 4 0.18
19 5 0.23
ACGTcount: A:0.00, C:0.23, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTCTTTTCGGTTCTCTC
Found at i:40997780 original size:9 final size:9
Alignment explanation
Indices: 40997766--40997844 Score: 104
Period size: 9 Copynumber: 8.6 Consensus size: 9
40997756 TTTGGTTAAA
*
40997766 AATTACTCG
1 AATTACCCG
*
40997775 AATTACCTG
1 AATTACCCG
40997784 AATTACCCG
1 AATTACCCG
40997793 AATTACCCG
1 AATTACCCG
40997802 AATTACCCG
1 AATTACCCG
*
40997811 AAAATTACCCA
1 --AATTACCCG
*
40997822 AATTACCAG
1 AATTACCCG
40997831 AATTACCCG
1 AATTACCCG
40997840 AATTA
1 AATTA
40997845 AATCACTACA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
9 53 0.87
11 8 0.13
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:41000940 original size:62 final size:57
Alignment explanation
Indices: 41000856--41000988 Score: 178
Period size: 62 Copynumber: 2.3 Consensus size: 57
41000846 TCCAAAAATA
* * *
41000856 ATATTATTTTAAT-TGTTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATT
1 ATATTATTTTAATATATTTAATATTAAATTTAATCTAAT-ATTATC-T-T-GATAAATATT
41000916 ATATTATTTTAATAATATTTAATATTAAATTTAATCTAATATTATCTTGATAAATATT
1 ATATTATTTTAAT-ATATTTAATATTAAATTTAATCTAATATTATCTTGATAAATATT
*
41000974 ATATTAATTTAATAT
1 ATATTATTTTAATAT
41000989 TAAAGTGATT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
57 2 0.03
58 22 0.33
59 1 0.01
60 14 0.21
61 5 0.07
62 23 0.34
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (57 bp):
ATATTATTTTAATATATTTAATATTAAATTTAATCTAATATTATCTTGATAAATATT
Found at i:41000985 original size:58 final size:62
Alignment explanation
Indices: 41000871--41000987 Score: 179
Period size: 58 Copynumber: 2.0 Consensus size: 62
41000861 ATTTTAATTG
* * *
41000871 TTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTATATTATTTTAATAATA
1 TTTAATATTAAATTTAATCTAATGATTATCTTGTAGATAAATATTATATTAATTTAATAATA
41000933 TTTAATATTAAATTTAATCTAAT-ATTATC-T-T-GATAAATATTATATTAATTTAATA
1 TTTAATATTAAATTTAATCTAATGATTATCTTGTAGATAAATATTATATTAATTTAATA
41000988 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 23 0.44
59 1 0.02
60 1 0.02
61 5 0.10
62 22 0.42
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (62 bp):
TTTAATATTAAATTTAATCTAATGATTATCTTGTAGATAAATATTATATTAATTTAATAATA
Found at i:41002114 original size:9 final size:9
Alignment explanation
Indices: 41002100--41002151 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
41002090 TTTGGTTAAA
41002100 AATTACCCG
1 AATTACCCG
41002109 AATTACCCG
1 AATTACCCG
*
41002118 AAAATTACCCA
1 --AATTACCCG
*
41002129 AAATACCCG
1 AATTACCCG
*
41002138 AATTACCCA
1 AATTACCCG
41002147 AATTA
1 AATTA
41002152 AATCACTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 28 0.78
11 8 0.22
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:41002123 original size:20 final size:20
Alignment explanation
Indices: 41002098--41002151 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
41002088 TTTTTGGTTA
*
41002098 AAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCG
*
41002118 AAAATTACCCAAAATACCCG
1 AAAATTACCCAAATTACCCG
41002138 --AATTACCCAAATTA
1 AAAATTACCCAAATTA
41002152 AATCACTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.42
20 18 0.58
ACGTcount: A:0.46, C:0.28, G:0.06, T:0.20
Consensus pattern (20 bp):
AAAATTACCCAAATTACCCG
Done.