Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 180 of 279
Found at i:59057651 original size:55 final size:55
Alignment explanation
Indices: 59057546--59057651 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 55
59057536 CTGAGTAGGT
* *
59057546 AAATGTCTAATGTAGTCAAGAACCGAGATTTTGAGTTTTTCCTTTCTATGTCAGC
1 AAATGTCTAATGTAATCAAGAACCGAGATTTTGAGTTTTTCCTTACTATGTCAGC
* * * * *
59057601 AAATGTTTGATGTAATCAAGAACTGAGGTTTTTGAG-TTTTCCTTAGTATGT
1 AAATGTCTAATGTAATCAAGAACCGA-GATTTTGAGTTTTTCCTTACTATGT
59057652 ATCTGCATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 35 0.81
56 8 0.19
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (55 bp):
AAATGTCTAATGTAATCAAGAACCGAGATTTTGAGTTTTTCCTTACTATGTCAGC
Found at i:59064452 original size:23 final size:23
Alignment explanation
Indices: 59064422--59064473 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
59064412 TGCAACTTGG
59064422 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
59064445 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
59064468 TTTCAT
1 TTTCAT
59064474 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:59068904 original size:23 final size:23
Alignment explanation
Indices: 59068874--59068925 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
59068864 TGCAACTTGG
59068874 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
59068897 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
59068920 TTTCAT
1 TTTCAT
59068926 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:59070521 original size:13 final size:13
Alignment explanation
Indices: 59070503--59070528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59070493 ATTGGGGTAT
59070503 TCGAACTCTTGTA
1 TCGAACTCTTGTA
59070516 TCGAACTCTTGTA
1 TCGAACTCTTGTA
59070529 GAATTGAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TCGAACTCTTGTA
Found at i:59077449 original size:62 final size:62
Alignment explanation
Indices: 59077380--59077569 Score: 380
Period size: 62 Copynumber: 3.1 Consensus size: 62
59077370 ATTATAATTG
59077380 ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
1 ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
59077442 ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
1 ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
59077504 ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
1 ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
59077566 ATTT
1 ATTT
59077570 TGGTTCTTGA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 128 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (62 bp):
ATTTGATTACCTTGTTTTATTTTTATCTTTCCAAATATGGTGAAAAATTGATCTCAGCATTA
Found at i:59081831 original size:33 final size:33
Alignment explanation
Indices: 59081699--59081835 Score: 134
Period size: 33 Copynumber: 4.2 Consensus size: 33
59081689 TACACTCCCA
* *
59081699 TTTT-AAGTGGTACACACGAAGTGTACATACCC
1 TTTTCAAGTGGTACACACAAAGTGTACATAACC
* ** *
59081731 TTTTCAATTTATACACACAAAGTGCACATAACC
1 TTTTCAAGTGGTACACACAAAGTGTACATAACC
* * * **
59081764 TTTTCAAGT-GTACACATATAGTGTACCTTTCC
1 TTTTCAAGTGGTACACACAAAGTGTACATAACC
* * *
59081796 TTTTCAAGTGGTATACACAAAGTATACCTAACC
1 TTTTCAAGTGGTACACACAAAGTGTACATAACC
59081829 TTTTCAA
1 TTTTCAA
59081836 CTTGTACCAT
Statistics
Matches: 83, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
32 29 0.35
33 54 0.65
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (33 bp):
TTTTCAAGTGGTACACACAAAGTGTACATAACC
Found at i:59082569 original size:21 final size:19
Alignment explanation
Indices: 59082535--59082577 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
59082525 TTCTCTATTA
* *
59082535 ATAACCTTTCATTTCCTATC
1 ATAAACTTTCATTTAC-ATC
59082555 ATAAACTTTCAATTTACATC
1 ATAAACTTTC-ATTTACATC
59082575 ATA
1 ATA
59082578 TTCATCCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAACTTTCATTTACATC
Found at i:59084801 original size:17 final size:19
Alignment explanation
Indices: 59084779--59084814 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
59084769 TGTTTTCGAG
59084779 ATTTGAATT-TTT-ATTAT
1 ATTTGAATTATTTAATTAT
59084796 ATTTGAATTATTTAATTAT
1 ATTTGAATTATTTAATTAT
59084815 CCTGCATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTTGAATTATTTAATTAT
Found at i:59091217 original size:30 final size:31
Alignment explanation
Indices: 59091170--59091231 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
59091160 AGGTTAGTTT
59091170 TATAAAAAGACCCAACTACCCATCTATCTGC
1 TATAAAAAGACCCAACTACCCATCTATCTGC
*
59091201 TATAAAAA-AGCCAACTACCCATCTATCTGC
1 TATAAAAAGACCCAACTACCCATCTATCTGC
59091231 T
1 T
59091232 CTGTTCCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.39, C:0.31, G:0.06, T:0.24
Consensus pattern (31 bp):
TATAAAAAGACCCAACTACCCATCTATCTGC
Found at i:59093028 original size:57 final size:58
Alignment explanation
Indices: 59092967--59093080 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 58
59092957 TATAAATATG
*
59092967 AAAATTACTTCCATGAGGAGGGGACAAGAGAAAAAAAA-ACATATATTCCAATTAATA
1 AAAATAACTTCCATGAGGAGGGGACAAGAGAAAAAAAATACATATATTCCAATTAATA
* *
59093024 AAAATAACTTTCATGAGGAGGGGACCAGAGAAAAAAAATACATATATTCCAATTAAT
1 AAAATAACTTCCATGAGGAGGGGACAAGAGAAAAAAAATACATATATTCCAATTAAT
59093081 TGATTTACAC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 35 0.66
58 18 0.34
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (58 bp):
AAAATAACTTCCATGAGGAGGGGACAAGAGAAAAAAAATACATATATTCCAATTAATA
Found at i:59094458 original size:17 final size:17
Alignment explanation
Indices: 59094436--59094469 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59094426 ATCCACTAAT
*
59094436 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
59094453 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
59094470 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:59099097 original size:17 final size:17
Alignment explanation
Indices: 59099075--59099108 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59099065 ATCCACTAAT
*
59099075 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
59099092 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
59099109 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:59107725 original size:20 final size:20
Alignment explanation
Indices: 59107684--59107726 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
59107674 TTTGTTTAAA
*
59107684 AATATTTTTATTTAAAACAT
1 AATATTTTTATATAAAACAT
*
59107704 AATATTTGTTATATCAAA-AT
1 AATATTT-TTATATAAAACAT
59107724 AAT
1 AAT
59107727 TTTCCAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
AATATTTTTATATAAAACAT
Found at i:59109828 original size:15 final size:15
Alignment explanation
Indices: 59109808--59109836 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59109798 TTAGGTATCG
59109808 ATATTTTTGTATCTA
1 ATATTTTTGTATCTA
59109823 ATATTTTTGTATCT
1 ATATTTTTGTATCT
59109837 GTAACACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
ATATTTTTGTATCTA
Found at i:59114673 original size:22 final size:22
Alignment explanation
Indices: 59114645--59114689 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59114635 GATCCTTAAC
59114645 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
59114667 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
59114689 T
1 T
59114690 CAAGCTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTGAAAGTAATTTAATGAAAT
Found at i:59114922 original size:26 final size:28
Alignment explanation
Indices: 59114858--59114928 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
59114848 TAAGAAAATT
* * *
59114858 TATTATTA-AAAATTTTATGAAATTATA
1 TATTATTATTAAATTATATGAAATAATA
*
59114885 TATTATTATTAAATTATATGTAATAATA
1 TATTATTATTAAATTATATGAAATAATA
59114913 -ATTATT-TTAAATTATA
1 TATTATTATTAAATTATA
59114929 CAAATTCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 10 0.26
27 14 0.36
28 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
TATTATTATTAAATTATATGAAATAATA
Found at i:59115125 original size:16 final size:17
Alignment explanation
Indices: 59115090--59115124 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
59115080 ATTATTAAGA
59115090 ATTTTATTAAAATATAT
1 ATTTTATTAAAATATAT
59115107 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59115125 TAAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59115335 original size:44 final size:45
Alignment explanation
Indices: 59115286--59115380 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
59115276 TTACACCTCT
* * *
59115286 ATTACATTCAACCAAACAG-AGTTTTACTATTACGCCTGTATTCC
1 ATTACATTCAACCAAACAGTAGATTTACTATTACACCTCTATTCC
* *
59115330 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGTAGATTTACTATTACACCTCTATTCC
59115375 ATTACA
1 ATTACA
59115381 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 19 0.42
45 26 0.58
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGTAGATTTACTATTACACCTCTATTCC
Found at i:59115380 original size:16 final size:16
Alignment explanation
Indices: 59115361--59115412 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
59115351 GATTTGCTAT
* *
59115361 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
59115377 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
59115393 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
59115409 TACA
1 TACA
59115413 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:59121643 original size:29 final size:30
Alignment explanation
Indices: 59121611--59121669 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
59121601 TTTGGTTTAA
*
59121611 TATGTAATTATATATAT-AAACTTTGATTT
1 TATGTAATTATATACATAAAACTTTGATTT
* *
59121640 TATGTAATTTTATACATAAAATTTTGATTT
1 TATGTAATTATATACATAAAACTTTGATTT
59121670 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (30 bp):
TATGTAATTATATACATAAAACTTTGATTT
Found at i:59125354 original size:21 final size:23
Alignment explanation
Indices: 59125310--59125354 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
59125300 AAGTTATAGC
*
59125310 ATGACTCGATTTAACTTGTTTAA
1 ATGACTCGATTTAACTTATTTAA
*
59125333 ATGACTC-ATTTTA-TTATTTAA
1 ATGACTCGATTTAACTTATTTAA
59125354 A
1 A
59125355 GAATAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (23 bp):
ATGACTCGATTTAACTTATTTAA
Found at i:59125779 original size:14 final size:14
Alignment explanation
Indices: 59125756--59125792 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
59125746 ATTTTTAAGA
59125756 TTTTTG-TTTAGGG
1 TTTTTGTTTTAGGG
59125769 TTTTTGTTTTA-GG
1 TTTTTGTTTTAGGG
59125782 TTTTT-TTTTAG
1 TTTTTGTTTTAG
59125793 ATTTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.08, C:0.00, G:0.22, T:0.70
Consensus pattern (14 bp):
TTTTTGTTTTAGGG
Found at i:59125798 original size:12 final size:12
Alignment explanation
Indices: 59125747--59125799 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
59125737 CGATTTAGGA
*
59125747 TTTTTAAGATTT
1 TTTTTTAGATTT
* *
59125759 TTGTTTAGGGTTT
1 TTTTTTA-GATTT
*
59125772 TTGTTTTAGGTTT
1 TT-TTTTAGATTT
59125785 TTTTTTAGATTT
1 TTTTTTAGATTT
59125797 TTT
1 TTT
59125800 AATTTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
12 17 0.50
13 13 0.38
14 4 0.12
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.70
Consensus pattern (12 bp):
TTTTTTAGATTT
Found at i:59126951 original size:4 final size:4
Alignment explanation
Indices: 59126942--59126967 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
59126932 CCTACAAGTT
59126942 ATGC ATGC ATGC ATGC ATGC ATGC AT
1 ATGC ATGC ATGC ATGC ATGC ATGC AT
59126968 CTCATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (4 bp):
ATGC
Found at i:59128383 original size:63 final size:63
Alignment explanation
Indices: 59128284--59128411 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
59128274 AAATCACACG
59128284 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
1 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
59128347 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
1 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
59128410 TA
1 TA
59128412 CGTTAGAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (63 bp):
TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
Found at i:59128993 original size:4 final size:4
Alignment explanation
Indices: 59128984--59129009 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
59128974 CCTACAAGTT
59128984 ATGC ATGC ATGC ATGC ATGC ATGC AT
1 ATGC ATGC ATGC ATGC ATGC ATGC AT
59129010 CTCATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (4 bp):
ATGC
Found at i:59130425 original size:63 final size:63
Alignment explanation
Indices: 59130326--59130453 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
59130316 AAATCACACG
59130326 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
1 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
59130389 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
1 TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
59130452 TA
1 TA
59130454 CGTTAGAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (63 bp):
TAAAATTCATATTCATATGCATAAAACCTACCTGAAACCTCACCAACCTGTTTTAAATTAGTA
Found at i:59130792 original size:23 final size:23
Alignment explanation
Indices: 59130750--59130795 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
59130740 ATTTGCAACT
*
59130750 TTTATCATAAAGCAAAGCTCAAA
1 TTTATCATAAAACAAAGCTCAAA
* *
59130773 TTTATCATAAAACGATGCTCAAA
1 TTTATCATAAAACAAAGCTCAAA
59130796 ACCAGCAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (23 bp):
TTTATCATAAAACAAAGCTCAAA
Found at i:59132122 original size:94 final size:94
Alignment explanation
Indices: 59131950--59132126 Score: 232
Period size: 94 Copynumber: 1.9 Consensus size: 94
59131940 ATGCTCAGTC
* *
59131950 TTACCTCATAAATAAATGATAATTTCTTCACTATTTTCTTTAAAAAATTCATTTTAATCCGATAT
1 TTACCTCATAAATAAATGATAATTTCTTCACTATTTTCTTTAAAAAATTAATTTTAATCCGACAT
*** * *
59132015 TAGTTAGAGAATACTCTTATATATCACAT
66 TAACCAAAAAATACTCTTATATATCACAT
* * *
59132044 TTACCTTATAAATAAGTGATAATTTCTTCACTATTTT-TGTTAAAAAGTTAATTTTAATCTC-AC
1 TTACCTCATAAATAAATGATAATTTCTTCACTATTTTCT-TTAAAAAATTAATTTTAATC-CGAC
59132107 ATTAACCAAAAAATACTCTT
64 ATTAACCAAAAAATACTCTT
59132127 GTAGCTCACC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
93 1 0.01
94 69 0.97
95 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (94 bp):
TTACCTCATAAATAAATGATAATTTCTTCACTATTTTCTTTAAAAAATTAATTTTAATCCGACAT
TAACCAAAAAATACTCTTATATATCACAT
Found at i:59132777 original size:141 final size:144
Alignment explanation
Indices: 59132494--59132766 Score: 381
Period size: 141 Copynumber: 1.9 Consensus size: 144
59132484 AAAAATAATA
* ** *
59132494 TTAATCCCATATTAGCTGGAGAACACTTGCATACCCACTATTTTCATAAGCTCTTTAGAGTTTCT
1 TTAATCCCATATTAGCTAGAGAACACTCCCATACCCAATATTTTCATAAGCTCTTTAGAGTTTCT
* * * * * *
59132559 TTCCTTTTAAGGAAATTTATGAGAGATAACTTATAGTTTAAAGTTATTTATATATTATTGATATG
66 TTCCTTTTAAAGAAATTCACGAGAGAGAACTTATAGCTTAAAGTTATTTATATATTATCGATATG
59132624 AACGATGATGATTT
131 AACGATGATGATTT
* * * *
59132638 TTAATCCCATTTTATCTAGAGAACACTCCCATACTCAATATTTTCATAAGCT-TTTCGAGTTTC-
1 TTAATCCCATATTAGCTAGAGAACACTCCCATACCCAATATTTTCATAAGCTCTTTAGAGTTTCT
* *
59132701 TTCC-TTTAAAGAAATTCACGAGAGAGAGCTTATAGCTTGAAGTTATTTATATATTATCGATATG
66 TTCCTTTTAAAGAAATTCACGAGAGAGAACTTATAGCTTAAAGTTATTTATATATTATCGATATG
59132765 AA
131 AA
59132767 TGGTGGTGAT
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
141 54 0.48
142 4 0.04
143 10 0.09
144 45 0.40
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (144 bp):
TTAATCCCATATTAGCTAGAGAACACTCCCATACCCAATATTTTCATAAGCTCTTTAGAGTTTCT
TTCCTTTTAAAGAAATTCACGAGAGAGAACTTATAGCTTAAAGTTATTTATATATTATCGATATG
AACGATGATGATTT
Found at i:59133070 original size:15 final size:16
Alignment explanation
Indices: 59133043--59133073 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
59133033 TACAATTTTA
59133043 AATTTACTTATTAAAT
1 AATTTACTTATTAAAT
59133059 AATTTA-TTATTAAAT
1 AATTTACTTATTAAAT
59133074 TCAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTACTTATTAAAT
Found at i:59133570 original size:19 final size:19
Alignment explanation
Indices: 59133517--59133572 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
59133507 TCTTTCTCCA
* *
59133517 CAAAA-ATTTAAAAAAAAT
1 CAAAATATTTATAAAAATT
* *
59133535 CAAAATAACTT-TCAAAATT
1 CAAAAT-ATTTATAAAAATT
59133554 CAAAATATTTATAAAAATT
1 CAAAATATTTATAAAAATT
59133573 TCAAGATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.28
19 18 0.62
20 3 0.10
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (19 bp):
CAAAATATTTATAAAAATT
Found at i:59144820 original size:14 final size:14
Alignment explanation
Indices: 59144803--59144833 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59144793 TTTATATCTG
59144803 TTTTATGATTTATA
1 TTTTATGATTTATA
*
59144817 TTTTATGGTTTATA
1 TTTTATGATTTATA
59144831 TTT
1 TTT
59144834 AAAATTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (14 bp):
TTTTATGATTTATA
Found at i:59147510 original size:24 final size:25
Alignment explanation
Indices: 59147482--59147528 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
59147472 GGAAATAAAA
*
59147482 TTATAATTTTATTA-TTTTAATAGT
1 TTATAATTTTATAATTTTTAATAGT
*
59147506 TTATATTTTTATAATTTTTAATA
1 TTATAATTTTATAATTTTTAATA
59147529 AATTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTATAATTTTATAATTTTTAATAGT
Found at i:59149412 original size:7 final size:7
Alignment explanation
Indices: 59149388--59149449 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
59149378 AACATTTTTC
59149388 TTTTAAA
1 TTTTAAA
* *
59149395 ATTTCAA
1 TTTTAAA
59149402 TTTTAAA
1 TTTTAAA
59149409 TTTTAAA
1 TTTTAAA
** *
59149416 ACTTAAC
1 TTTTAAA
*
59149423 TCTTAAA
1 TTTTAAA
*
59149430 CTTTAAA
1 TTTTAAA
59149437 TTTTAAA
1 TTTTAAA
*
59149444 TGTTAA
1 TTTTAA
59149450 TTACTTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (7 bp):
TTTTAAA
Found at i:59149449 original size:28 final size:29
Alignment explanation
Indices: 59149403--59149458 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
59149393 AAATTTCAAT
59149403 TTTAAATTTTAAAACTTAACT-CTTAAAC
1 TTTAAATTTTAAAACTTAACTACTTAAAC
** *
59149431 TTTAAATTTTAAATGTTAATTACTTAAA
1 TTTAAATTTTAAAACTTAACTACTTAAA
59149459 AATTTAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (29 bp):
TTTAAATTTTAAAACTTAACTACTTAAAC
Found at i:59151806 original size:27 final size:28
Alignment explanation
Indices: 59151775--59151827 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
59151765 AATTTTTAAA
*
59151775 ATTTTAAATTAAT-AAAAGTAAAATTAT
1 ATTTTAAATTAATAAAAAATAAAATTAT
*
59151802 ATTTTAAATTACTAAAAAATAAAATT
1 ATTTTAAATTAATAAAAAATAAAATT
59151828 TTGATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
ATTTTAAATTAATAAAAAATAAAATTAT
Found at i:59152819 original size:30 final size:30
Alignment explanation
Indices: 59152785--59152845 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
59152775 ATGAAATAAT
* * * * *
59152785 AACAAAATAGTGAGAAAACAAGAAAATAGC
1 AACAAAACAGTAAAAAAACAAAAAAAAAGC
59152815 AACAAAACAGTAAAAAAACAAAAAAAAAGC
1 AACAAAACAGTAAAAAAACAAAAAAAAAGC
59152845 A
1 A
59152846 GCAATTCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.07
Consensus pattern (30 bp):
AACAAAACAGTAAAAAAACAAAAAAAAAGC
Found at i:59154985 original size:6 final size:6
Alignment explanation
Indices: 59154971--59155045 Score: 105
Period size: 6 Copynumber: 12.5 Consensus size: 6
59154961 CTTTTTGTTA
*
59154971 TCTCTC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
* * * *
59155019 TCTCTC TCTCTC TCTCTC TCTCTC TCT
1 TCTCCC TCTCCC TCTCCC TCTCCC TCT
59155046 ACCTTTTGGA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TCTCCC
Found at i:59156127 original size:21 final size:19
Alignment explanation
Indices: 59156103--59156153 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
59156093 ATTATTTTAG
59156103 TTTTTTATTTAATTTTGCATA
1 TTTTTTATTTAATTTT--ATA
59156124 TTTTTTATAATTAATTTTATA
1 TTTTTTAT--TTAATTTTATA
*
59156145 TTATTTATT
1 TTTTTTATT
59156154 AAATCACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
21 18 0.67
23 8 0.30
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTTATTTAATTTTATA
Found at i:59164799 original size:23 final size:22
Alignment explanation
Indices: 59164740--59164800 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
59164730 TTCAAATAAA
*
59164740 AATTTAAAAAATTAATTACAAT
1 AATTAAAAAAATTAATTACAAT
*
59164762 AATTAAAAAATATTATTTACAA-
1 AATTAAAAAA-ATTAATTACAAT
59164784 AATTAATTAAAAATTAA
1 AATTAA--AAAAATTAA
59164801 ACGTGTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 15 0.45
23 14 0.42
24 4 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAAAAAAATTAATTACAAT
Found at i:59165347 original size:27 final size:27
Alignment explanation
Indices: 59165317--59165371 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
59165307 ATAGTATGAT
*
59165317 ATAATTTAAA-CCCTAAAAACCCAACCC
1 ATAACTTAAATCCC-AAAAACCCAACCC
*
59165344 ATAACTTAAATTCCAAAAACCCAACCC
1 ATAACTTAAATCCCAAAAACCCAACCC
59165371 A
1 A
59165372 AAAATACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (27 bp):
ATAACTTAAATCCCAAAAACCCAACCC
Found at i:59165706 original size:30 final size:30
Alignment explanation
Indices: 59165672--59165731 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
59165662 TTTAATTCGA
59165672 GTTAAATGATTTTGAACAAGTTAATAGTTC
1 GTTAAATGATTTTGAACAAGTTAATAGTTC
59165702 GTTAAATGATTTTGAACAAGTTAATAGTTC
1 GTTAAATGATTTTGAACAAGTTAATAGTTC
59165732 AGTTTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (30 bp):
GTTAAATGATTTTGAACAAGTTAATAGTTC
Found at i:59173865 original size:18 final size:19
Alignment explanation
Indices: 59173844--59173883 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
59173834 TATTTAAAGA
59173844 TTATAAAT-GTTGGAATTT
1 TTATAAATAGTTGGAATTT
* *
59173862 TTATAAATATTTTGAATTT
1 TTATAAATAGTTGGAATTT
59173881 TTA
1 TTA
59173884 AAAAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (19 bp):
TTATAAATAGTTGGAATTT
Found at i:59173880 original size:19 final size:20
Alignment explanation
Indices: 59173856--59173899 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
59173846 ATAAATGTTG
*
59173856 GAATTTTT-ATAAATATTTT
1 GAATTTTTAAAAAATATTTT
*
59173875 GAATTTTTAAAAAATGTTTT
1 GAATTTTTAAAAAATATTTT
59173895 GAATT
1 GAATT
59173900 CTTTTTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (20 bp):
GAATTTTTAAAAAATATTTT
Found at i:59178625 original size:11 final size:10
Alignment explanation
Indices: 59178603--59178634 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
59178593 TGCTTTTATT
59178603 AAAAATTAAA
1 AAAAATTAAA
59178613 AAAAATTATAA
1 AAAAATTA-AA
59178624 AAAAATTAAA
1 AAAAATTAAA
59178634 A
1 A
59178635 TCAATAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:59178759 original size:10 final size:10
Alignment explanation
Indices: 59178730--59178796 Score: 64
Period size: 10 Copynumber: 6.7 Consensus size: 10
59178720 ATTGTAATTT
59178730 TTTATAAAAA
1 TTTATAAAAA
*
59178740 TTGTAAAAAAA
1 TT-TATAAAAA
59178751 TTTAT-AAAA
1 TTTATAAAAA
* *
59178760 TATATAGAAA
1 TTTATAAAAA
* *
59178770 TATAAAAAAA
1 TTTATAAAAA
*
59178780 TTTATAAAAT
1 TTTATAAAAA
59178790 TTTATAA
1 TTTATAA
59178797 CGTCGTAAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 8 0.17
10 29 0.63
11 9 0.20
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:59178795 original size:60 final size:59
Alignment explanation
Indices: 59178690--59178835 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 59
59178680 TAAAAATTAT
* * ** *
59178690 AATATATATAAATAGT-AA-AAACATAAAAAAATTGTAATTTTTTATAAAAATTGTAA-AAA
1 AATATATA-AAATA-TAAAGAAATATAAAAAAATTATAAAATTTTAT-AAAATCGTAAGAAA
* * **
59178749 AATTTATAAAATATATAGAAATATAAAAAAATTTATAAAATTTTATAACGTCGTAAGAAA
1 AATATATAAAATATAAAGAAATATAAAAAAA-TTATAAAATTTTATAAAATCGTAAGAAA
*
59178809 AATATATAAAATGTAAAGAAATATAAA
1 AATATATAAAATATAAAGAAATATAAA
59178836 TTTCGTAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
57 1 0.01
58 6 0.08
59 26 0.37
60 38 0.54
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (59 bp):
AATATATAAAATATAAAGAAATATAAAAAAATTATAAAATTTTATAAAATCGTAAGAAA
Found at i:59179068 original size:19 final size:18
Alignment explanation
Indices: 59179048--59179112 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
59179038 ATTTTTAATA
59179048 AATTTTAATATTTTTTCT
1 AATTTTAATATTTTTTCT
* * *
59179066 AAAATTTATTA-TTTAT-T
1 -AATTTTAATATTTTTTCT
*
59179083 ATTTTTAATATTTTTTTCT
1 AATTTTAATA-TTTTTTCT
59179102 AATTTCTAATA
1 AATTT-TAATA
59179113 AGAGCATGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 8 0.24
19 13 0.38
20 5 0.15
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTTAATATTTTTTCT
Found at i:59186223 original size:21 final size:22
Alignment explanation
Indices: 59186197--59186239 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
59186187 ATTCAACCCC
59186197 AAGGTTTAAGGTTT-GGGTTTT
1 AAGGTTTAAGGTTTAGGGTTTT
*
59186218 AAGGTTTAGGGTTTAGGGTTTT
1 AAGGTTTAAGGTTTAGGGTTTT
59186240 TGGTTATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (22 bp):
AAGGTTTAAGGTTTAGGGTTTT
Found at i:59186244 original size:21 final size:21
Alignment explanation
Indices: 59186197--59186255 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
59186187 ATTCAACCCC
*
59186197 AAGGTTTAAGGTTTGGGTTTT
1 AAGGTTTAGGGTTTGGGTTTT
59186218 AAGGTTTAGGGTTTAGGGTTTT
1 AAGGTTTAGGGTTT-GGGTTTT
*
59186240 -TGG-TTATGGGTTTGGG
1 AAGGTTTA-GGGTTTGGG
59186256 GTTCAGGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 6 0.18
21 21 0.62
22 7 0.21
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.46
Consensus pattern (21 bp):
AAGGTTTAGGGTTTGGGTTTT
Found at i:59186257 original size:7 final size:7
Alignment explanation
Indices: 59186199--59186267 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
59186189 TCAACCCCAA
*
59186199 GGTTTAA
1 GGTTTAG
59186206 GGTTT-G
1 GGTTTAG
*
59186212 GGTTTTAA
1 GG-TTTAG
59186220 GGTTTAG
1 GGTTTAG
59186227 GGTTTAG
1 GGTTTAG
**
59186234 GGTTTTT
1 GGTTTAG
59186241 GG-TTATG
1 GGTTTA-G
*
59186248 GGTTTGG
1 GGTTTAG
*
59186255 GGTTCAG
1 GGTTTAG
59186262 GGTTTA
1 GGTTTA
59186268 AAGATTTGTG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
6 4 0.09
7 39 0.83
8 4 0.09
ACGTcount: A:0.13, C:0.01, G:0.39, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:59190693 original size:3 final size:3
Alignment explanation
Indices: 59190685--59190717 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
59190675 TCTCTCCATT
59190685 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
59190718 AAACAGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:59196205 original size:21 final size:21
Alignment explanation
Indices: 59196154--59196206 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
59196144 TTAGATTATA
59196154 TTTTAATTATTTTTTTAAAAAT
1 TTTTAA-TATTTTTTTAAAAAT
*
59196176 TTATATAATA-TTTTTTAAACTAT
1 TT-T-TAATATTTTTTTAAA-AAT
59196199 TTTTAATA
1 TTTTAATA
59196207 CAAATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 5 0.19
22 12 0.44
23 7 0.26
24 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAATATTTTTTTAAAAAT
Found at i:59198665 original size:21 final size:22
Alignment explanation
Indices: 59198639--59198697 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
59198629 GTTTTAAGAA
*
59198639 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
59198660 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
59198682 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
59198698 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:59198712 original size:26 final size:24
Alignment explanation
Indices: 59198668--59198715 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
59198658 ATTTGTTTTA
*
59198668 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
59198692 ATATTTGATTTATTATATTTTTAA
1 ATATTTG-TTT-TTATATTTTTAA
59198716 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:59210171 original size:23 final size:23
Alignment explanation
Indices: 59210145--59210197 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
59210135 ATGTATTCTT
*
59210145 AGAAGCTCACTATGATTATTC-GG
1 AGAAGCTCACCATGATTA-TCGGG
59210168 AGAAGCTCACCATGATTATCGGG
1 AGAAGCTCACCATGATTATCGGG
59210191 AGAAGCT
1 AGAAGCT
59210198 ATCTGGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (23 bp):
AGAAGCTCACCATGATTATCGGG
Found at i:59212013 original size:15 final size:15
Alignment explanation
Indices: 59211993--59212023 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59211983 GTGCAGGCCA
*
59211993 TAATTTTGGAAATGG
1 TAATTTTGAAAATGG
59212008 TAATTTTGAAAATGG
1 TAATTTTGAAAATGG
59212023 T
1 T
59212024 TCTTCCCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (15 bp):
TAATTTTGAAAATGG
Found at i:59215833 original size:19 final size:20
Alignment explanation
Indices: 59215796--59215834 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
59215786 ATAAAATAAT
*
59215796 AAATAATTCATTAAGTTAAA
1 AAATAACTCATTAAGTTAAA
*
59215816 AAATAACTC-TTAATTTAAA
1 AAATAACTCATTAAGTTAAA
59215835 GAAAATAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATAACTCATTAAGTTAAA
Found at i:59215898 original size:20 final size:21
Alignment explanation
Indices: 59215852--59215892 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59215842 GATGTAATAA
*
59215852 TCTAAAATTTTTATTTCAAGC
1 TCTAAAATTTTTATTACAAGC
*
59215873 TCTAAACTTTTTATTACAAG
1 TCTAAAATTTTTATTACAAG
59215893 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (21 bp):
TCTAAAATTTTTATTACAAGC
Found at i:59217337 original size:18 final size:18
Alignment explanation
Indices: 59217314--59217350 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59217304 ATTTCTCCTC
* *
59217314 TGTTTTTTTATTTTTCTT
1 TGTTTTGTTATCTTTCTT
59217332 TGTTTTGTTATCTTTCTT
1 TGTTTTGTTATCTTTCTT
59217350 T
1 T
59217351 TTGCTAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.78
Consensus pattern (18 bp):
TGTTTTGTTATCTTTCTT
Found at i:59218147 original size:79 final size:79
Alignment explanation
Indices: 59218055--59218200 Score: 186
Period size: 79 Copynumber: 1.8 Consensus size: 79
59218045 ACGCCTCTGG
*** * * *
59218055 GTTACTCTGTTGATAAAGAATATGTGACATTTGAT-TATGTTAGATTGATTGTTACTGATTCTGA
1 GTTACTCTGTTGATAAAGAATATACAACATCT-ATAAATGTTAGACTGATTGTTACTGATTCTGA
59218119 TTTATAACCCTTTAT
65 TTTATAACCCTTTAT
* * * *
59218134 GTTACTTTGTTGATTAGGAATATACAATATCTATAAATGTTAGACTGATTGTTACTGATTCTGAT
1 GTTACTCTGTTGATAAAGAATATACAACATCTATAAATGTTAGACTGATTGTTACTGATTCTGAT
59218199 TT
66 TT
59218201 GCAACCGTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
78 2 0.04
79 54 0.96
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (79 bp):
GTTACTCTGTTGATAAAGAATATACAACATCTATAAATGTTAGACTGATTGTTACTGATTCTGAT
TTATAACCCTTTAT
Found at i:59225020 original size:21 final size:20
Alignment explanation
Indices: 59224977--59225026 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
59224967 GGTCACTTCG
* *
59224977 TTCTT-TTTTTCCAAGTTAT
1 TTCTTCTTTTTCCAAATTAC
*
59224996 TTCTCTCTTTTTCCAAATTGC
1 TTCT-TCTTTTTCCAAATTAC
59225017 TTCTTCTTTT
1 TTCTTCTTTT
59225027 CTTTTGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 15 0.58
ACGTcount: A:0.12, C:0.22, G:0.04, T:0.62
Consensus pattern (20 bp):
TTCTTCTTTTTCCAAATTAC
Found at i:59226191 original size:39 final size:39
Alignment explanation
Indices: 59226143--59226218 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
59226133 TCGGCCACCA
* * *
59226143 CAGGTATAGTATCAAGATGATTTGGAGCGACAGTGGCCG
1 CAGGGATAGTAGCAAGATGATTTGGAGCCACAGTGGCCG
59226182 CAGGGATAGTAGCAAGATGATTTGGAGCCACAGTGGC
1 CAGGGATAGTAGCAAGATGATTTGGAGCCACAGTGGC
59226219 ACGGTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.21
Consensus pattern (39 bp):
CAGGGATAGTAGCAAGATGATTTGGAGCCACAGTGGCCG
Found at i:59226635 original size:41 final size:41
Alignment explanation
Indices: 59226586--59226667 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
59226576 TTATGCTTTT
*
59226586 AGGTTTACGAGTACTCCATTTGCTTTTTTGCTTTTCTCATC
1 AGGTTTACGAGTACTCCATTTCCTTTTTTGCTTTTCTCATC
59226627 AGGTTTACGAGTACTCCATTTCCTTTTTTGCTTTTCTCATC
1 AGGTTTACGAGTACTCCATTTCCTTTTTTGCTTTTCTCATC
59226668 TCGTTTTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (41 bp):
AGGTTTACGAGTACTCCATTTCCTTTTTTGCTTTTCTCATC
Found at i:59229409 original size:21 final size:20
Alignment explanation
Indices: 59229371--59229409 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
59229361 GCGGATATTG
*
59229371 AAAAATAATAAATTTTATAA
1 AAAAATAATAAATATTATAA
*
59229391 AAAAATGAATTAATATTAT
1 AAAAAT-AATAAATATTAT
59229410 TAAACAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAAATAATAAATATTATAA
Found at i:59230116 original size:16 final size:16
Alignment explanation
Indices: 59230083--59230116 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59230073 ACGTGGTGTT
* *
59230083 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
59230099 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
59230115 AA
1 AA
59230117 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:59232943 original size:21 final size:21
Alignment explanation
Indices: 59232917--59232960 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
59232907 AGACGAGCAA
* *
59232917 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
59232938 TACTCCAAAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
59232959 TA
1 TA
59232961 ACAGCCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:59233591 original size:16 final size:16
Alignment explanation
Indices: 59233558--59233591 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59233548 GGAGATTGTT
* *
59233558 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
59233574 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
59233590 AA
1 AA
59233592 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:59241683 original size:22 final size:22
Alignment explanation
Indices: 59241658--59241705 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
59241648 TAACAAGTTC
*
59241658 AATT-AATTAATATAAATTATTA
1 AATTAAATTAAT-TAAATTAATA
*
59241680 AATTAAATTAATTAATTTAATA
1 AATTAAATTAATTAAATTAATA
59241702 AATT
1 AATT
59241706 TATGATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTAAATTAATTAAATTAATA
Found at i:59241693 original size:14 final size:14
Alignment explanation
Indices: 59241658--59241699 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
59241648 TAACAAGTTC
59241658 AATTAATT-AATATA
1 AATTAATTAAAT-TA
59241672 AATT-ATTAAATTA
1 AATTAATTAAATTA
*
59241685 AATTAATTAATTTA
1 AATTAATTAAATTA
59241699 A
1 A
59241700 TAAATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTAATTAAATTA
Found at i:59248149 original size:31 final size:31
Alignment explanation
Indices: 59248114--59248177 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
59248104 TAATTATACA
*
59248114 ATAATTGCTTGTGTGGGTAACCATTGTAATT
1 ATAATTGCTTGTGTGGATAACCATTGTAATT
59248145 ATAATTGCTTGTGTGGATAACCATTGTAATT
1 ATAATTGCTTGTGTGGATAACCATTGTAATT
59248176 AT
1 AT
59248178 TGAGTCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (31 bp):
ATAATTGCTTGTGTGGATAACCATTGTAATT
Found at i:59249191 original size:17 final size:18
Alignment explanation
Indices: 59249169--59249209 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
59249159 TTTAGAATTT
* *
59249169 TTTTTATCGT-ATTGATA
1 TTTTTATAGTAATTAATA
59249186 TTTTTATAGTAATTAATA
1 TTTTTATAGTAATTAATA
59249204 TTTTTA
1 TTTTTA
59249210 AAACATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (18 bp):
TTTTTATAGTAATTAATA
Found at i:59255263 original size:9 final size:9
Alignment explanation
Indices: 59255249--59255280 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
59255239 TTATATTTAC
59255249 TATTATATT
1 TATTATATT
59255258 TATTATATT
1 TATTATATT
59255267 TATTATATT
1 TATTATATT
59255276 ATATT
1 -TATT
59255281 TTACTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTATATT
Found at i:59255334 original size:3 final size:3
Alignment explanation
Indices: 59255326--59255375 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
59255316 TCTTGTATCT
* * *
59255326 TTA TTA TTA TTG CTA TTA TTG TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
59255372 TTA T
1 TTA T
59255376 ATTTGTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:59255505 original size:25 final size:25
Alignment explanation
Indices: 59255444--59255506 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
59255434 TATGCAAATA
* * *
59255444 TTTTAATACTATATTACGTATGTAT
1 TTTTAATGCCATATTACGTATATAT
* *
59255469 TTTTCATCGCCATATTATGTATATAT
1 TTTTAAT-GCCATATTACGTATATAT
59255495 TTTTAATGCCAT
1 TTTTAATGCCAT
59255507 GTGTACACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.51
Consensus pattern (25 bp):
TTTTAATGCCATATTACGTATATAT
Found at i:59255662 original size:24 final size:22
Alignment explanation
Indices: 59255633--59255680 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
59255623 TAGTGTGTAT
59255633 TATTATATGTACATATACTCTCAA
1 TATTATAT-T-CATATACTCTCAA
* *
59255657 TATTATATTCTTATACTCTTAA
1 TATTATATTCATATACTCTCAA
59255679 TA
1 TA
59255681 CCATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATATTCATATACTCTCAA
Found at i:59255686 original size:22 final size:22
Alignment explanation
Indices: 59255646--59255687 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
59255636 TATATGTACA
**
59255646 TATACTCTCAATATTATATTCT
1 TATACTCTCAATACCATATTCT
*
59255668 TATACTCTTAATACCATATT
1 TATACTCTCAATACCATATT
59255688 ATTCTTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (22 bp):
TATACTCTCAATACCATATTCT
Found at i:59256105 original size:21 final size:24
Alignment explanation
Indices: 59256074--59256132 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 24
59256064 TTTCAATATT
*
59256074 TATTTTATATATATGTAAATA-T-
1 TATTGTATATATATGTAAATACTA
* *
59256096 TA-TGTATATATTTTTAAATACTA
1 TATTGTATATATATGTAAATACTA
59256119 TATTGTATATATAT
1 TATTGTATATATAT
59256133 ATTCTTAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 15 0.50
22 3 0.10
23 2 0.07
24 10 0.33
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (24 bp):
TATTGTATATATATGTAAATACTA
Found at i:59256149 original size:27 final size:29
Alignment explanation
Indices: 59256100--59256159 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
59256090 AAATATTATG
*
59256100 TATATATTTTTAAATACTATATT-GTATA
1 TATATATTCTTAAATACTATATTAGTATA
*
59256128 TATATATTCTT-AGTACTATATTACGTATA
1 TATATATTCTTAAATACTATATTA-GTATA
59256157 TAT
1 TAT
59256160 TATGTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 10 0.36
29 8 0.29
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.52
Consensus pattern (29 bp):
TATATATTCTTAAATACTATATTAGTATA
Found at i:59258522 original size:50 final size:50
Alignment explanation
Indices: 59258447--59258541 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
59258437 TAATCATAAT
*
59258447 GAACTTAACCGAATAGATTTTTTGTCTCTTAGATGGGGTCCACAGTCAAA
1 GAACTTAACCGAATAGATTCTTTGTCTCTTAGATGGGGTCCACAGTCAAA
*
59258497 GAACTTATCCGAATAGATTCTTTGTCTCTTAGATGGGGTCCACAG
1 GAACTTAACCGAATAGATTCTTTGTCTCTTAGATGGGGTCCACAG
59258542 ACTTTAACCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (50 bp):
GAACTTAACCGAATAGATTCTTTGTCTCTTAGATGGGGTCCACAGTCAAA
Found at i:59259161 original size:19 final size:21
Alignment explanation
Indices: 59259137--59259176 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
59259127 ATTTGACATT
*
59259137 AATATTTCAA-TCA-TAATAA
1 AATATTTAAACTCACTAATAA
59259156 AATATTTAAACTCACTAATAA
1 AATATTTAAACTCACTAATAA
59259177 TATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATTTAAACTCACTAATAA
Found at i:59259176 original size:21 final size:19
Alignment explanation
Indices: 59259137--59259197 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
59259127 ATTTGACATT
*
59259137 AATATTTCAATCATAATAA
1 AATATTTAAATCATAATAA
59259156 AATATTTAAACTCACTAAT--
1 AATATTTAAA-TCA-TAATAA
**
59259175 AATATTATAAAAAATAATAA
1 AATATT-TAAATCATAATAA
59259195 AAT
1 AAT
59259198 TTCATATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATTTAAATCATAATAA
Found at i:59259462 original size:16 final size:16
Alignment explanation
Indices: 59259441--59259474 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
59259431 TTCACATATT
59259441 ATTTCTTCTTAACCTA
1 ATTTCTTCTTAACCTA
59259457 ATTTCTTCTTAACCTA
1 ATTTCTTCTTAACCTA
59259473 AT
1 AT
59259475 AAGGTCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTCTTCTTAACCTA
Found at i:59260683 original size:6 final size:6
Alignment explanation
Indices: 59260655--59260696 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
59260645 ATCACTAAAT
*
59260655 AATTTAA AATTTA AGAATTA AATTTA AATTTA AATTTA AATT
1 AATTT-A AATTTA A-ATTTA AATTTA AATTTA AATTTA AATT
59260697 AATTATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:59263547 original size:19 final size:21
Alignment explanation
Indices: 59263511--59263550 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
59263501 TTTTATAGTA
*
59263511 TTATTAGTGAGTTTAAATATT
1 TTATTAGTGAGTTAAAATATT
59263532 TTATTA-TGA-TTAAAATATT
1 TTATTAGTGAGTTAAAATATT
59263551 AATGTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TTATTAGTGAGTTAAAATATT
Found at i:59265371 original size:14 final size:14
Alignment explanation
Indices: 59265348--59265377 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59265338 ACACAAAAAA
*
59265348 CAAAACAAAAAGAG
1 CAAAAAAAAAAGAG
59265362 CAAAAAAAAAAGAG
1 CAAAAAAAAAAGAG
59265376 CA
1 CA
59265378 GTAGAACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.13, G:0.13, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAGAG
Found at i:59268874 original size:12 final size:12
Alignment explanation
Indices: 59268852--59268880 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59268842 TAAATGTCTC
59268852 TAAAA-TAATAA
1 TAAAATTAATAA
59268863 TAAAATTAATAA
1 TAAAATTAATAA
59268875 TAAAAT
1 TAAAAT
59268881 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:59268885 original size:18 final size:19
Alignment explanation
Indices: 59268855--59268895 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
59268845 ATGTCTCTAA
59268855 AATAATAATAAAATTA-AT
1 AATAATAATAAAATTATAT
59268873 AATAA-AATAAAAATTATAT
1 AATAATAAT-AAAATTATAT
59268892 AATA
1 AATA
59268896 TGAAAGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAATAAAATTATAT
Found at i:59273165 original size:9 final size:9
Alignment explanation
Indices: 59273138--59273172 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
59273128 TTCAGTTAGC
59273138 TATTTACAA
1 TATTTACAA
59273147 TATTTTACAA
1 TA-TTTACAA
*
59273157 TATTGACAA
1 TATTTACAA
59273166 TATTTAC
1 TATTTAC
59273173 TAAATATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (9 bp):
TATTTACAA
Found at i:59273233 original size:22 final size:21
Alignment explanation
Indices: 59273191--59273230 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
59273181 ACTTAAAAAG
59273191 TAAATCACATACTTTTTTTAT
1 TAAATCACATACTTTTTTTAT
59273212 TAAATCACATACTTTTTTT
1 TAAATCACATACTTTTTTT
59273231 TATGTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATCACATACTTTTTTTAT
Found at i:59276803 original size:34 final size:34
Alignment explanation
Indices: 59276735--59276840 Score: 149
Period size: 34 Copynumber: 3.1 Consensus size: 34
59276725 TGTAATGAAA
*
59276735 TTGAGAGTTTTGCCACTCCAAGTCATCCCATAAAT
1 TTGAGAGTGTTGCCACTCCAAGTC-TCCCATAAAT
* * *
59276770 TTGAGAGTGTTCCCACTCCAAGTCTTCCGTAAAT
1 TTGAGAGTGTTGCCACTCCAAGTCTCCCATAAAT
* *
59276804 TTGAGAGTGTTGTCACTCCAAGTCTCCCATAGAT
1 TTGAGAGTGTTGCCACTCCAAGTCTCCCATAAAT
59276838 TTG
1 TTG
59276841 TGAATAATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
34 40 0.65
35 22 0.35
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (34 bp):
TTGAGAGTGTTGCCACTCCAAGTCTCCCATAAAT
Found at i:59279897 original size:63 final size:63
Alignment explanation
Indices: 59279813--59279931 Score: 193
Period size: 63 Copynumber: 1.9 Consensus size: 63
59279803 CATGCTCGTG
* * *
59279813 TCCCTGGCCGTATGGTTTTTGTACCACAAACAGTGAGTTACATGGTCTAGACACACGCCCGTA
1 TCCCTGGCCGTATGGTCTTTGTACCACAAACAGTGAGTTACACGGCCTAGACACACGCCCGTA
* *
59279876 TCCCTGGCCGTGTGGTCTTTGTACCACAAACAGTGAGTTATACGGCCTAGACACAC
1 TCCCTGGCCGTATGGTCTTTGTACCACAAACAGTGAGTTACACGGCCTAGACACAC
59279932 ACCCATGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (63 bp):
TCCCTGGCCGTATGGTCTTTGTACCACAAACAGTGAGTTACACGGCCTAGACACACGCCCGTA
Found at i:59281506 original size:16 final size:17
Alignment explanation
Indices: 59281466--59281506 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
59281456 AAAACACATG
59281466 TATAAAAATCATTTTAT
1 TATAAAAATCATTTTAT
* *
59281483 TAT-TAAATGATTTT-T
1 TATAAAAATCATTTTAT
59281498 TATAAAAAT
1 TATAAAAAT
59281507 TTATCATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.20
16 13 0.65
17 3 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TATAAAAATCATTTTAT
Found at i:59289130 original size:79 final size:78
Alignment explanation
Indices: 59288990--59289207 Score: 321
Period size: 79 Copynumber: 2.8 Consensus size: 78
59288980 GAGTCACATC
* *
59288990 TCATGTAA-ATGTAGTGAATCAGGATTACCTTTTCAGGTCAAATCCTACCCACCTTAAGTTATCA
1 TCATGTAACA-GTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTATCA
59289054 TAAAGAATCATATA
65 TAAAGAATCATATA
** * * *
59289068 TTGTGTAACAGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATTCATCTTAGGTTATCA
1 TCATGTAACAGTAGCGAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTATCA
*
59289133 TAATGAATCATATA
65 TAAAGAATCATATA
* *
59289147 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTA
1 TCATGTAACAGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTA
59289208 CCAAAGTGAA
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
78 52 0.42
79 71 0.58
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (78 bp):
TCATGTAACAGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTATCAT
AAAGAATCATATA
Found at i:59289256 original size:40 final size:40
Alignment explanation
Indices: 59289185--59289322 Score: 143
Period size: 40 Copynumber: 3.5 Consensus size: 40
59289175 CTTTTCAGGT
* * * *
59289185 CAAATCCTATCCGCCTT-AAGTTACCAAAGTGAATCATGAA
1 CAAATCCTATCCACTTTAAAG-TACTATAGTGAATCATGAA
* * * * *
59289225 TAAATCCTATTCATTTTAAATTACTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAAGTACTATAGTGAATCATGAA
* * *
59289265 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCATGAA
1 CAAATCCTATCCACTTTAAAGTACTATAGTGAATCATGAA
*
59289305 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
59289323 TATTCTCGAA
Statistics
Matches: 78, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 76 0.97
41 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAAGTACTATAGTGAATCATGAA
Found at i:59292494 original size:3 final size:3
Alignment explanation
Indices: 59292486--59292562 Score: 54
Period size: 3 Copynumber: 26.0 Consensus size: 3
59292476 AGGATGAAAC
* * * *
59292486 AAT AAT AAT -AT AA- AAT AAA AAT AAC AAT ACATT AAT AAG AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
*
59292531 AAT -AT ATT AAT -AT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
59292563 GATGATGATG
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
2 8 0.14
3 43 0.75
4 4 0.07
5 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59292550 original size:20 final size:19
Alignment explanation
Indices: 59292486--59292554 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
59292476 AGGATGAAAC
*
59292486 AATAATAATATA-AAATAAA
1 AATAATAATATATTAAT-AA
* *
59292505 AATAACAATACATTAATAA
1 AATAATAATATATTAATAA
*
59292524 GAGTAATAATATATTAATATA
1 -AATAATAATATATTAATA-A
59292545 AATAATAATA
1 AATAATAATA
59292555 ATAATAATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
19 12 0.30
20 27 0.68
21 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAATAATATATTAATAA
Found at i:59292739 original size:3 final size:3
Alignment explanation
Indices: 59292724--59292902 Score: 82
Period size: 3 Copynumber: 58.3 Consensus size: 3
59292714 AGTAATGTAT
* * * * *
59292724 TAA TAA GAA TAA TAA T-A TAT TAC TAA TAA TAA TCA TGAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* ** * *
59292769 TAA TAA TAC TAA T-A TTT TAAA TAA -GA TAA TAA TAA TTGA TAGA -AA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TA-A TAA
* * * * * *
59292814 GTAG TAG TAA TAA TACA TTAA TAA GAG TAA TAG TAA TAA TAA TAA AAA
1 -TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59292862 TAA TAA TAGA T-A TAA TAA TAA TAA -ATA TAA TAA TAAA TAA T
1 TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA T
59292903 TAATTTGAAA
Statistics
Matches: 132, Mismatches: 28, Indels: 32
0.69 0.15 0.17
Matches are distributed among these distances:
2 9 0.07
3 107 0.81
4 14 0.11
5 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:59292824 original size:26 final size:25
Alignment explanation
Indices: 59292795--59292906 Score: 85
Period size: 26 Copynumber: 4.6 Consensus size: 25
59292785 TTAAATAAGA
* *
59292795 TAATAATAATTGATAGAAAGTAGTAG
1 TAATAATAATTAATA-AAAGTAATAG
*
59292821 TAATAATACATTAATAAGAGTAATAG
1 TAATAATA-ATTAATAAAAGTAATAG
*
59292847 TAATAATAA-TAA-AAATAATAATAG
1 TAATAATAATTAATAAA-AGTAATAG
*
59292871 -ATATAATAA-TAAT-AAA-T-ATAA
1 TA-ATAATAATTAATAAAAGTAATAG
59292892 TAATAAATAATTAAT
1 TAAT-AATAATTAAT
59292907 TTGAAAATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
21 5 0.07
22 7 0.10
23 8 0.11
24 22 0.30
25 1 0.01
26 24 0.33
27 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (25 bp):
TAATAATAATTAATAAAAGTAATAG
Found at i:59293600 original size:45 final size:45
Alignment explanation
Indices: 59293539--59293626 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
59293529 ATATAATTTT
59293539 TATATATATAAACAGATTTGTAAAGGAAAAAAAGAAGAAAGGATA
1 TATATATATAAACAGATTTGTAAAGGAAAAAAAGAAGAAAGGATA
59293584 TATATATATAAACAGATTTGTAAAGGAAAAAAAGAAGAAAGGA
1 TATATATATAAACAGATTTGTAAAGGAAAAAAAGAAGAAAGGA
59293627 AACTAACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.58, C:0.02, G:0.18, T:0.22
Consensus pattern (45 bp):
TATATATATAAACAGATTTGTAAAGGAAAAAAAGAAGAAAGGATA
Found at i:59300579 original size:15 final size:17
Alignment explanation
Indices: 59300559--59300598 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
59300549 AATTTTTAAA
59300559 AATATTTTAAT-A-TTT
1 AATATTTTAATAATTTT
59300574 AATA-TTTAATAATTTT
1 AATATTTTAATAATTTT
59300590 ATATATTTT
1 A-ATATTTT
59300599 TTATTTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 4 0.19
17 3 0.14
18 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATATTTTAATAATTTT
Found at i:59300603 original size:24 final size:24
Alignment explanation
Indices: 59300562--59300614 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
59300552 TTTTAAAAAT
59300562 ATTTTAATATTTAATATTTAAT-A
1 ATTTTAATATTTAATATTTAATGA
** *
59300585 ATTTTATATATTTTTTATTTATTGA
1 ATTTTA-ATATTTAATATTTAATGA
59300610 ATTTT
1 ATTTT
59300615 TTTATATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 13 0.52
25 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTTTAATATTTAATATTTAATGA
Found at i:59306999 original size:27 final size:27
Alignment explanation
Indices: 59306969--59307131 Score: 200
Period size: 27 Copynumber: 6.0 Consensus size: 27
59306959 AAATAAATAA
* *
59306969 AAAGTTCCCACATTAACCTTTGCAATC
1 AAAGTTCACATATTAACCTTTGCAATC
*
59306996 AAAGTTGCAATATATTAACCTTTGCAATC
1 AAAGTT-C-ACATATTAACCTTTGCAATC
* * *
59307025 AAAGTTGAGATATTAAACTTTGCAATC
1 AAAGTTCACATATTAACCTTTGCAATC
* *
59307052 AAAGTTCCCATATTAACCTTTCCAATC
1 AAAGTTCACATATTAACCTTTGCAATC
* * *
59307079 CAAGTTGACATATTAAACTTTGCAATC
1 AAAGTTCACATATTAACCTTTGCAATC
*
59307106 AAAGTTCCCATATTAACCTTTGCAAT
1 AAAGTTCACATATTAACCTTTGCAAT
59307132 TAGTTTGCCG
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
27 90 0.79
28 1 0.01
29 23 0.20
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
AAAGTTCACATATTAACCTTTGCAATC
Found at i:59307086 original size:54 final size:54
Alignment explanation
Indices: 59306980--59307131 Score: 232
Period size: 54 Copynumber: 2.8 Consensus size: 54
59306970 AAGTTCCCAC
* ** *
59306980 ATTAACCTTTGCAATCAAAGTTGCAATATATTAACCTTTGCAATCAAAGTTGAGAT
1 ATTAAACTTTGCAATCAAAGTT-C-CCATATTAACCTTTGCAATCAAAGTTGACAT
* *
59307036 ATTAAACTTTGCAATCAAAGTTCCCATATTAACCTTTCCAATCCAAGTTGACAT
1 ATTAAACTTTGCAATCAAAGTTCCCATATTAACCTTTGCAATCAAAGTTGACAT
59307090 ATTAAACTTTGCAATCAAAGTTCCCATATTAACCTTTGCAAT
1 ATTAAACTTTGCAATCAAAGTTCCCATATTAACCTTTGCAAT
59307132 TAGTTTGCCG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 67 0.75
55 1 0.01
56 21 0.24
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (54 bp):
ATTAAACTTTGCAATCAAAGTTCCCATATTAACCTTTGCAATCAAAGTTGACAT
Found at i:59307127 original size:81 final size:82
Alignment explanation
Indices: 59306969--59307131 Score: 229
Period size: 81 Copynumber: 2.0 Consensus size: 82
59306959 AAATAAATAA
* * * * *
59306969 AAAGTTCCCACATTAACCTTTGCAATCAAAGTTGCAATATATTAACCTTTGCAATCAAAGTTGAG
1 AAAGTTCCCACATTAACCTTTCCAATCAAAGTTG-AACATATTAAACTTTGCAATCAAAGTTCAC
59307034 ATATTAAACTTTGCAATC
65 ATATTAAACTTTGCAATC
* * *
59307052 AAAGTTCCCATATTAACCTTTCCAATCCAAGTTG-ACATATTAAACTTTGCAATCAAAGTTCCCA
1 AAAGTTCCCACATTAACCTTTCCAATCAAAGTTGAACATATTAAACTTTGCAATCAAAGTTCACA
*
59307116 TATTAACCTTTGCAAT
66 TATTAAACTTTGCAAT
59307132 TAGTTTGCCG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 40 0.56
83 31 0.44
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (82 bp):
AAAGTTCCCACATTAACCTTTCCAATCAAAGTTGAACATATTAAACTTTGCAATCAAAGTTCACA
TATTAAACTTTGCAATC
Found at i:59307374 original size:36 final size:36
Alignment explanation
Indices: 59307334--59307417 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
59307324 AAAATACTAA
* *
59307334 TTTAAATTTATTTTAGATCTAT-ATAATTTTTTATTT
1 TTTAAATTTATTTTA-ATATATAATAATTTTATATTT
** *
59307370 TTTAAAAATATTTTAATATTTAATAATTTTATATTT
1 TTTAAATTTATTTTAATATATAATAATTTTATATTT
**
59307406 TTTTTATTTATT
1 TTTAAATTTATT
59307418 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (36 bp):
TTTAAATTTATTTTAATATATAATAATTTTATATTT
Found at i:59307383 original size:18 final size:17
Alignment explanation
Indices: 59307361--59307408 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
59307351 TCTATATAAT
59307361 TTTTTATTTTTTAAAAA
1 TTTTTATTTTTTAAAAA
* * *
59307378 TATTTTAATATTTAATAA
1 T-TTTTATTTTTTAAAAA
59307396 TTTTATATTTTTT
1 TTTT-TATTTTTT
59307409 TTATTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTATTTTTTAAAAA
Found at i:59307871 original size:59 final size:60
Alignment explanation
Indices: 59307779--59307938 Score: 261
Period size: 59 Copynumber: 2.7 Consensus size: 60
59307769 CAAGTGGGCC
*
59307779 GTTGTGGTCTATTCTGGGCGGACCCATATTGACAATTTAATTATTTTTGTAATTGTT-AT
1 GTTGTGGTCTATTCTGGGCGGACCCATATTGACAATTTAATTATTTTTGTAATTCTTAAT
*
59307838 GTTGTGGTCTATTCTGGGCGGAACCATATTGACAATTTAATTATTTTTGTAATTCTTAAT
1 GTTGTGGTCTATTCTGGGCGGACCCATATTGACAATTTAATTATTTTTGTAATTCTTAAT
** *
59307898 -TTACGGTCTATTCTGGGTGGACCCATATTGACAATTTAATT
1 GTTGTGGTCTATTCTGGGCGGACCCATATTGACAATTTAATT
59307939 GGACACTAAG
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 92 0.98
60 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (60 bp):
GTTGTGGTCTATTCTGGGCGGACCCATATTGACAATTTAATTATTTTTGTAATTCTTAAT
Found at i:59308367 original size:25 final size:25
Alignment explanation
Indices: 59308339--59308387 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
59308329 GTTTGAAGAG
*
59308339 TAATA-TATTTTAATATATTATATTT
1 TAATATTATTTT-ATATAATATATTT
59308364 TAATATTATTTTATATAATATATT
1 TAATATTATTTTATATAATATATT
59308388 AAAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TAATATTATTTTATATAATATATTT
Found at i:59308371 original size:13 final size:15
Alignment explanation
Indices: 59308342--59308388 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
59308332 TGAAGAGTAA
59308342 TATATTTTAATATAT
1 TATATTTTAATATAT
59308357 TATATTTTAATATTAT
1 TATATTTTAATA-TAT
* *
59308373 TTTA-TATAATATAT
1 TATATTTTAATATAT
59308387 TA
1 TA
59308389 AAATTTGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 18 0.64
16 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTTTAATATAT
Found at i:59308411 original size:30 final size:30
Alignment explanation
Indices: 59308349--59308412 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
59308339 TAATATATTT
* * * *
59308349 TAATATATTATATTTTAATATTATTTTATA
1 TAATATATTAAAATTTAATATGATTTGATA
* *
59308379 TAATATATTAAAATTTGATATGATTTGCTA
1 TAATATATTAAAATTTAATATGATTTGATA
59308409 TAAT
1 TAAT
59308413 TAAAATATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
TAATATATTAAAATTTAATATGATTTGATA
Found at i:59310543 original size:50 final size:50
Alignment explanation
Indices: 59310465--59310641 Score: 275
Period size: 50 Copynumber: 3.5 Consensus size: 50
59310455 CCATGGCAAC
59310465 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
59310515 AAATGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TGA
*
59310565 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
59310615 CAAGTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
59310642 CTGATCAGTG
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
49 3 0.03
50 87 0.75
51 26 0.22
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:59310655 original size:31 final size:31
Alignment explanation
Indices: 59310617--59310765 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
59310607 ACAAATGACA
*
59310617 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
59310648 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
59310679 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
59310710 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
59310741 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
59310766 AAGTGACAAG
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:59310853 original size:47 final size:46
Alignment explanation
Indices: 59310783--59310947 Score: 169
Period size: 47 Copynumber: 3.7 Consensus size: 46
59310773 AAGTGATTTC
* *
59310783 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
59310829 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
59310876 CGTGTAAGACCATAGCTGGGCTATGGCATC-----GATATATGAATA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATG-ATA
* * * *
59310918 TGTGTAAGACCATAGCTGGGCTATGGCATC
1 CGTATAAGACCATATCTGGGATATGGCATC
59310948 ATTATGTGAA
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 7 0.07
42 31 0.29
46 27 0.25
47 41 0.39
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:59310935 original size:42 final size:43
Alignment explanation
Indices: 59310877--59310991 Score: 171
Period size: 42 Copynumber: 2.7 Consensus size: 43
59310867 TATGTGATTC
*
59310877 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
59310919 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
59310961 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
59310992 GAAAACGAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:59311972 original size:19 final size:19
Alignment explanation
Indices: 59311950--59311988 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
59311940 GCAATTTATA
59311950 TAATTATATCATAT-TTAAT
1 TAATTATAT-ATATGTTAAT
*
59311969 TAATTTTATATATGTTAAT
1 TAATTATATATATGTTAAT
59311988 T
1 T
59311989 TAAAATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TAATTATATATATGTTAAT
Found at i:59312709 original size:30 final size:30
Alignment explanation
Indices: 59312675--59312737 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
59312665 AATATATTAC
59312675 TTATATCAAATCA-TA-TCAAATTATAATATA
1 TTATATCAAAT-AGTAGT-AAATTATAATATA
*
59312705 TTATATCAAATAGTAGTAAATTTTAATATA
1 TTATATCAAATAGTAGTAAATTATAATATA
59312735 TTA
1 TTA
59312738 AACTATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.93
31 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (30 bp):
TTATATCAAATAGTAGTAAATTATAATATA
Found at i:59315483 original size:22 final size:23
Alignment explanation
Indices: 59315458--59315503 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
59315448 CAACCAAATC
59315458 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
59315480 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
59315503 A
1 A
59315504 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:59315509 original size:23 final size:23
Alignment explanation
Indices: 59315465--59315509 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
59315455 ATCAATTCAA
*
59315465 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
59315488 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
59315510 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Done.