Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 15 of 198
Found at i:4773212 original size:15 final size:17
Alignment explanation
Indices: 4773187--4773220 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
4773177 TGAATATTTT
4773187 AATTATTATTTTTA-AA
1 AATTATTATTTTTACAA
4773203 AATT-TTATTTTTACAA
1 AATTATTATTTTTACAA
4773219 AA
1 AA
4773221 ATTGCATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTATTATTTTTACAA
Found at i:4776505 original size:30 final size:30
Alignment explanation
Indices: 4776471--4776535 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
4776461 TGGCAAAAAA
* * *
4776471 CTCTCAATTTTCTCCCTAGATTTTTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
*
4776501 CTCTCAAATTTCTCCTTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
4776531 CTCTC
1 CTCTC
4776536 CTTAATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.05, T:0.42
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:4778317 original size:18 final size:18
Alignment explanation
Indices: 4778294--4778330 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4778284 GCCAAGTGCA
*
4778294 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
4778312 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
4778330 T
1 T
4778331 TTCCATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:4780295 original size:127 final size:127
Alignment explanation
Indices: 4780025--4780294 Score: 382
Period size: 127 Copynumber: 2.1 Consensus size: 127
4780015 GGCCAAACAT
* * *
4780025 GAACTACTGTAGAAATAGAACGTCGACTTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * * *
4780090 CTGCTTGAAATGTTTTTGACATTATTTTTTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAACGTTTTTCACACTATTTTGTTCAGAAACGTATTATCAAAATTATTTTTTCAG
* *
4780152 GAACTACTATAGAAAAAGAACGTCCACGTGGGAGTTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * *
4780217 CTGCTTGAAGCGTTTTTCACACTA-TTTGTTCAGAATTC-TATTATCAAAATTATTTTTTCGG
66 CTGCTTGAAACGTTTTTCACACTATTTTGTTCAGAA-ACGTATTATCAAAATTATTTTTTCAG
*
4780278 GAACTACTGTAAAAAAA
1 GAACTACTGTAGAAAAA
4780295 ATAAAATCCT
Statistics
Matches: 126, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
126 45 0.36
127 81 0.64
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (127 bp):
GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAACGTTTTTCACACTATTTTGTTCAGAAACGTATTATCAAAATTATTTTTTCAG
Found at i:4780422 original size:32 final size:31
Alignment explanation
Indices: 4780353--4780419 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 31
4780343 CACAATATTA
4780353 TTTTAAACCCTAAAACCTAATTTAATTAATT
1 TTTTAAACCCTAAAACCTAATTTAATTAATT
*
4780384 TTTTAAAGCCCTTAAACCCTAATTTAATTAATT
1 TTTTAAA-CCC-TAAAACCTAATTTAATTAATT
4780417 TTT
1 TTT
4780420 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 7 0.21
32 3 0.09
33 23 0.70
ACGTcount: A:0.37, C:0.16, G:0.01, T:0.45
Consensus pattern (31 bp):
TTTTAAACCCTAAAACCTAATTTAATTAATT
Found at i:4784471 original size:30 final size:30
Alignment explanation
Indices: 4784435--4784510 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
4784425 TTTTTTTTTT
* *
4784435 GAAAAAATATAGAACTAAGTTAATTTTATA
1 GAAAAAATATAGAACTAAGCTAATTTTAAA
*
4784465 GAAAAAAT-TAAGGAACTAGGCTAATTTTAAA
1 GAAAAAATAT-A-GAACTAAGCTAATTTTAAA
*
4784496 GAAAAATTATTAGAA
1 GAAAAAATA-TAGAA
4784511 GCGTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 1 0.03
30 9 0.24
31 26 0.68
32 1 0.03
33 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.29
Consensus pattern (30 bp):
GAAAAAATATAGAACTAAGCTAATTTTAAA
Found at i:4786952 original size:25 final size:25
Alignment explanation
Indices: 4786924--4786990 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
4786914 TCTCGATCCA
* **
4786924 TATAATAGGAAGCTCATGTGAGCTG
1 TATAACAGGAAGCTCATCCGAGCTG
* *
4786949 TATAACAGGAAGCTTATCCGGGCTG
1 TATAACAGGAAGCTCATCCGAGCTG
4786974 TATAACAGGAAGCTCAT
1 TATAACAGGAAGCTCAT
4786991 AAGAGCCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (25 bp):
TATAACAGGAAGCTCATCCGAGCTG
Found at i:4787058 original size:73 final size:72
Alignment explanation
Indices: 4786979--4787144 Score: 178
Period size: 73 Copynumber: 2.3 Consensus size: 72
4786969 GGCTGTATAA
*
4786979 CAGGAAGCTCATAAGAGCCATAT-TCAGAAAACTTGT-GCGAGCCAATAACGAGTAGCTCT-GAA
1 CAGGAAGCTCATAAGAGCCATATATC-GAAAACTT-TAGCGAGCC-ATAACGAGAAGCTCTAG-A
4787041 GAGCCATTAAT
62 GAGCCATTAAT
* * * * *
4787052 CAGGAAGCTCCA-GATAGCCATATATCGAGAAGTTTAAGCGAGCCATATCGAGAAGCTCTAGAGA
1 CAGGAAGCT-CATAAGAGCCATATATCGAAAACTTT-AGCGAGCCATAACGAGAAGCTCTAGAGA
4787116 GCCATTAAT
64 GCCATTAAT
*
4787125 CAAGAAGCTCATAAAGAGCC
1 CAGGAAGCTCAT-AAGAGCC
4787145 TTTAATCGGG
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
72 3 0.04
73 57 0.74
74 17 0.22
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (72 bp):
CAGGAAGCTCATAAGAGCCATATATCGAAAACTTTAGCGAGCCATAACGAGAAGCTCTAGAGAGC
CATTAAT
Found at i:4787083 original size:25 final size:25
Alignment explanation
Indices: 4787055--4787161 Score: 69
Period size: 25 Copynumber: 4.3 Consensus size: 25
4787045 CATTAATCAG
* *
4787055 GAAGCTCCAGATAGCCATATATCGA
1 GAAGCTCAAGAGAGCCATATATCGA
* * *
4787080 GAAGTTTAAGCGAGCC--ATATCGA
1 GAAGCTCAAGAGAGCCATATATCGA
* *
4787103 GAAGCTCTAGAGAGCCAT-TAATCAA
1 GAAGCTCAAGAGAGCCATAT-ATCGA
* * *
4787128 GAAGCTCATAAAGAGCC-TTTAATCGG
1 GAAGCTCA-AGAGAGCCATAT-ATCGA
4787154 GAAGCTCA
1 GAAGCTCA
4787162 CGAAGAACCA
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
23 19 0.30
24 1 0.02
25 23 0.37
26 20 0.32
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (25 bp):
GAAGCTCAAGAGAGCCATATATCGA
Found at i:4787149 original size:26 final size:26
Alignment explanation
Indices: 4787102--4787161 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
4787092 AGCCATATCG
*
4787102 AGAAGCTC-TAGAGAGCCATTAATCA
1 AGAAGCTCATAAAGAGCCATTAATCA
* *
4787127 AGAAGCTCATAAAGAGCCTTTAATCG
1 AGAAGCTCATAAAGAGCCATTAATCA
*
4787153 GGAAGCTCA
1 AGAAGCTCA
4787162 CGAAGAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (26 bp):
AGAAGCTCATAAAGAGCCATTAATCA
Found at i:4787167 original size:26 final size:26
Alignment explanation
Indices: 4787113--4787167 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4787103 GAAGCTCTAG
*
4787113 AGAGCCATTAATCAAGAAGCTCATAA
1 AGAGCCATTAATCAAGAAGCTCACAA
* ** *
4787139 AGAGCCTTTAATCGGGAAGCTCACGA
1 AGAGCCATTAATCAAGAAGCTCACAA
4787165 AGA
1 AGA
4787168 ACCACATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAAGAAGCTCACAA
Found at i:4795821 original size:50 final size:50
Alignment explanation
Indices: 4795706--4795954 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
4795696 GATAATAACA
* * ** * *
4795706 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
4795757 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4795807 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4795857 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
4795912 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
4795955 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:4795892 original size:100 final size:104
Alignment explanation
Indices: 4795705--4795954 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
4795695 TGATAATAAC
** * *
4795705 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
4795770 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
4795807 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
4795871 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
4795912 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4795955 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:4796070 original size:13 final size:13
Alignment explanation
Indices: 4796049--4796080 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4796039 GCTTGGATCA
*
4796049 TCATCAAATAAAT
1 TCATAAAATAAAT
4796062 TCATAAAATAAAT
1 TCATAAAATAAAT
4796075 TCATAA
1 TCATAA
4796081 TTGCTAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4796327 original size:30 final size:30
Alignment explanation
Indices: 4796292--4796349 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4796282 CCTCGACTCT
*
4796292 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4796322 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4796350 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:4801869 original size:19 final size:19
Alignment explanation
Indices: 4801828--4801869 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4801818 TACTTTTTAT
*
4801828 TAATTATTAATTAATTAAT
1 TAATTATTAATTAATTAAC
*
4801847 TAATTATTTATT-ATTAGAC
1 TAATTATTAATTAATTA-AC
4801866 TAAT
1 TAAT
4801870 AATCAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTATTAATTAATTAAC
Found at i:4803106 original size:22 final size:24
Alignment explanation
Indices: 4803080--4803128 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
4803070 CTGCTCATAT
*
4803080 TTATATAAT-TAAAATATTTA-TA
1 TTATATAATATAAAACATTTATTA
*
4803102 TTATATACTATAAAACATTTATTA
1 TTATATAATATAAAACATTTATTA
4803126 TTA
1 TTA
4803129 AATATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 10 0.43
24 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATATAATATAAAACATTTATTA
Found at i:4811383 original size:20 final size:19
Alignment explanation
Indices: 4811358--4811397 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4811348 GTTTTTCTCG
* *
4811358 ATAAAATGATATATTTATCA
1 ATAAAATCATA-ATTAATCA
4811378 ATAAAATCATAATTAATCA
1 ATAAAATCATAATTAATCA
4811397 A
1 A
4811398 CTAACAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
ATAAAATCATAATTAATCA
Found at i:4815432 original size:28 final size:28
Alignment explanation
Indices: 4815399--4815460 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
4815389 CTCTCCCCAA
4815399 CAAAAATTACAAAATAATTAAAAAAATTT
1 CAAAAATT-CAAAATAATTAAAAAAATTT
* * *
4815428 TAAAAATTCAAAATATTTATAAAAATTT
1 CAAAAATTCAAAATAATTAAAAAAATTT
4815456 CAAAA
1 CAAAA
4815461 TTTATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (28 bp):
CAAAAATTCAAAATAATTAAAAAAATTT
Found at i:4815463 original size:18 final size:18
Alignment explanation
Indices: 4815420--4815466 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
4815410 AAATAATTAA
4815420 AAAAATTT-TAAAAATTC
1 AAAAATTTATAAAAATTC
4815437 AAAATATTTATAAAAATTTC
1 AAAA-ATTTATAAAAA-TTC
4815457 -AAAATTTATA
1 AAAAATTTATA
4815467 TATTTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 11 0.41
19 9 0.33
20 3 0.11
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTTATAAAAATTC
Found at i:4815468 original size:20 final size:19
Alignment explanation
Indices: 4815414--4815461 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
4815404 ATTACAAAAT
* *
4815414 AATTAAAAAAATTT-TAAA
1 AATTCAAAATATTTATAAA
4815432 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
4815451 AATTTCAAAAT
1 AA-TTCAAAAT
4815462 TTATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 6 0.23
20 8 0.31
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:4815908 original size:17 final size:15
Alignment explanation
Indices: 4815863--4815900 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4815853 ACTGGTATAG
*
4815863 AAAATATAGTTAAAC
1 AAAATATATTTAAAC
*
4815878 ATAATATATTTAAAC
1 AAAATATATTTAAAC
4815893 AAAATATA
1 AAAATATA
4815901 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAATATATTTAAAC
Found at i:4816089 original size:26 final size:23
Alignment explanation
Indices: 4816060--4816114 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
4816050 GTGGATAATT
4816060 TTTAATGAAAAATTAATTTACTTTTA
1 TTTAAT-AAAAA-TAATTTA-TTTTA
* *
4816086 TTTAAATAATAATAATTTATTTTT
1 TTT-AATAAAAATAATTTATTTTA
4816110 TTTAA
1 TTTAA
4816115 AAACAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.08
24 7 0.27
25 7 0.27
26 7 0.27
27 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAATAAAAATAATTTATTTTA
Found at i:4816124 original size:25 final size:25
Alignment explanation
Indices: 4816067--4816124 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
4816057 ATTTTTAATG
*
4816067 AAAAATTAATTTACTTTTATTTAAA
1 AAAAAATAATTTACTTTTATTTAAA
* * *
4816092 TAATAATAATTTA-TTTTTTTTAAA
1 AAAAAATAATTTACTTTTATTTAAA
4816116 AACAAAATA
1 AA-AAAATA
4816125 TAATATTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAAAATAATTTACTTTTATTTAAA
Found at i:4818313 original size:22 final size:20
Alignment explanation
Indices: 4818271--4818311 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4818261 TAAGTGACAT
4818271 TTAATATCTCAAAATATATA
1 TTAATATCTCAAAATATATA
4818291 TTAATATCTCAAAATATATA
1 TTAATATCTCAAAATATATA
4818311 T
1 T
4818312 ATCTCCTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATATCTCAAAATATATA
Found at i:4823049 original size:11 final size:11
Alignment explanation
Indices: 4823033--4823063 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
4823023 AAATTAATCA
4823033 TTCTCTTCGCT
1 TTCTCTTCGCT
4823044 TTCTCTTCGCT
1 TTCTCTTCGCT
4823055 TTCATCTTC
1 TTC-TCTTC
4823064 ATCTAAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.03, C:0.35, G:0.06, T:0.55
Consensus pattern (11 bp):
TTCTCTTCGCT
Found at i:4823189 original size:17 final size:17
Alignment explanation
Indices: 4823167--4823200 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4823157 GGGAGGTTTT
4823167 CCTTTTCTGTCTTTCCC
1 CCTTTTCTGTCTTTCCC
* *
4823184 CCTTTTGTTTCTTTCCC
1 CCTTTTCTGTCTTTCCC
4823201 TTCTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.38, G:0.06, T:0.56
Consensus pattern (17 bp):
CCTTTTCTGTCTTTCCC
Found at i:4828355 original size:3 final size:3
Alignment explanation
Indices: 4828347--4828375 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4828337 CAAATTTTAT
4828347 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4828376 GAAACTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4829964 original size:18 final size:16
Alignment explanation
Indices: 4829910--4829969 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 16
4829900 CGATGCAATC
4829910 AAAATATAAAATATAAA
1 AAAAT-TAAAATATAAA
*
4829927 TATAAATTAAAATCTAAA
1 -A-AAATTAAAATATAAA
4829945 AAAACTTAAAAATATAAA
1 AAAA-TT-AAAATATAAA
4829963 AATAATT
1 AA-AATT
4829970 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 24 0.67
19 6 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAAAATATAAA
Found at i:4831270 original size:20 final size:21
Alignment explanation
Indices: 4831241--4831279 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4831231 ATTTTAACAT
4831241 TAATAATTTTAA-ATTTTAAG
1 TAATAATTTTAATATTTTAAG
*
4831261 TAATATTTTTAATATTTTA
1 TAATAATTTTAATATTTTA
4831280 TTGACAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TAATAATTTTAATATTTTAAG
Found at i:4832260 original size:2 final size:2
Alignment explanation
Indices: 4832253--4832280 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4832243 AGTTTTTATG
4832253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4832281 GAAATCCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4834920 original size:37 final size:37
Alignment explanation
Indices: 4834878--4834983 Score: 144
Period size: 37 Copynumber: 2.8 Consensus size: 37
4834868 TATATTTATT
*
4834878 TTTTAAAAT-TTTAATATTACTTTTTAATTTTTTTAAA
1 TTTTAAAATATTTAACA-TACTTTTTAATTTTTTTAAA
*
4834915 TTTTAAAATATTTTACATACTTTTTAATTTTTTTAAA
1 TTTTAAAATATTTAACATACTTTTTAATTTTTTTAAA
*
4834952 TTTTAAAATATTTTTAAAATA-TTTTTAATTTT
1 TTTTAAAATA--TTTAACATACTTTTTAATTTT
4834984 AAAATATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
37 39 0.63
38 16 0.26
39 7 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTTAAAATATTTAACATACTTTTTAATTTTTTTAAA
Found at i:4834966 original size:28 final size:29
Alignment explanation
Indices: 4834935--4835026 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 29
4834925 TTTTACATAC
4834935 TTTT-TAATTTTTTTAAATTTTAAAATAT
1 TTTTATAATTTTTTTAAATTTTAAAATAT
* *
4834963 TTTTAAAATATTTTT-AATTTTAAAATAT
1 TTTTATAATTTTTTTAAATTTTAAAATAT
* *
4834991 TTTTAAAATACTTTTTTTAATTTTTAAAA-AT
1 TTTT---ATAATTTTTTTAAATTTTAAAATAT
4835022 TTTTA
1 TTTTA
4835027 AAATAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 22 0.42
29 8 0.15
31 14 0.26
32 9 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTATAATTTTTTTAAATTTTAAAATAT
Found at i:4834968 original size:11 final size:11
Alignment explanation
Indices: 4834952--4835031 Score: 77
Period size: 11 Copynumber: 7.9 Consensus size: 11
4834942 TTTTTTTAAA
4834952 TTTTAAAATAT
1 TTTTAAAATAT
4834963 TTTTAAAATAT
1 TTTTAAAATAT
4834974 TTTT---A-A-
1 TTTTAAAATAT
4834980 TTTTAAAATAT
1 TTTTAAAATAT
4834991 TTTTAAAATACT
1 TTTTAAAATA-T
**
4835003 TTTT-TTA-AT
1 TTTTAAAATAT
4835012 TTTTAAAA-AT
1 TTTTAAAATAT
4835022 TTTTAAAATA
1 TTTTAAAATA
4835032 AAAATGGGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
6 4 0.07
7 1 0.02
8 1 0.02
9 6 0.11
10 13 0.23
11 27 0.47
12 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:4834994 original size:17 final size:17
Alignment explanation
Indices: 4834963--4834996 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4834953 TTTAAAATAT
4834963 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
4834980 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
4834997 AATACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:4838904 original size:7 final size:8
Alignment explanation
Indices: 4838886--4838925 Score: 53
Period size: 8 Copynumber: 4.6 Consensus size: 8
4838876 TTTACATTAC
4838886 TTTTTAAT
1 TTTTTAAT
4838894 TTTTTAAT
1 TTTTTAAT
4838902 TTTTTACAT
1 TTTTTA-AT
4838911 ACTTTTTAAT
1 --TTTTTAAT
4838921 TTTTT
1 TTTTT
4838926 TTAAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 19 0.66
9 2 0.07
10 2 0.07
11 6 0.21
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTAAT
Found at i:4838906 original size:28 final size:28
Alignment explanation
Indices: 4838870--4838925 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
4838860 TTTAAATTTA
4838870 AATTATTTTACATTACTTTTTAATTTTTT
1 AATTATTTTACA-TACTTTTTAATTTTTT
4838899 AATT-TTTTACATACTTTTTAATTTTTT
1 AATTATTTTACATACTTTTTAATTTTTT
4838926 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.59
28 7 0.26
29 4 0.15
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (28 bp):
AATTATTTTACATACTTTTTAATTTTTT
Found at i:4838926 original size:29 final size:28
Alignment explanation
Indices: 4838870--4838962 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
4838860 TTTAAATTTA
4838870 AATTATTTTACATTACTTTTTAA-TTTTTT
1 AATT-TTTTACA-TACTTTTTAATTTTTTT
4838899 AATTTTTTACATACTTTTTAATTTTTTTT
1 AATTTTTTACATACTTTTTAA-TTTTTTT
* * * *
4838928 AAATTTTAAAATA-TTTTTAAAATATTTTT
1 AATTTTTTACATACTTTTT--AATTTTTTT
4838957 AATTTT
1 AATTTT
4838963 AAAATATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 10 0.18
28 12 0.22
29 31 0.56
30 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (28 bp):
AATTTTTTACATACTTTTTAATTTTTTT
Found at i:4838944 original size:17 final size:17
Alignment explanation
Indices: 4838942--4838975 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4838932 TTTAAAATAT
*
4838942 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTAAA
4838959 TTTTAAAATATTTTAAA
1 TTTTAAAATATTTTAAA
4838976 ATACTTTTTT
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:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAATATTTTAAA
Found at i:4838963 original size:28 final size:28
Alignment explanation
Indices: 4838923--4838989 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 28
4838913 TTTTTAATTT
4838923 TTTTTAAATTTTAAAATATTTTTAAAATA-
1 TTTTT-AATTTTAAAATA-TTTTAAAATAC
4838952 TTTTTAATTTTAAAATATTTTAAAATAC
1 TTTTTAATTTTAAAATATTTTAAAATAC
4838980 TTTTTTAATT
1 -TTTTTAATT
4838990 ATTTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 10 0.28
28 12 0.33
29 14 0.39
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTTAATTTTAAAATATTTTAAAATAC
Found at i:4839000 original size:11 final size:10
Alignment explanation
Indices: 4838930--4838999 Score: 65
Period size: 10 Copynumber: 7.0 Consensus size: 10
4838920 TTTTTTTTAA
4838930 ATTTTAAAAT
1 ATTTTAAAAT
4838940 ATTTTTAAAAT
1 A-TTTTAAAAT
*
4838951 ATTTT--TA-
1 ATTTTAAAAT
4838958 ATTTTAAAAT
1 ATTTTAAAAT
4838968 ATTTTAAAAT
1 ATTTTAAAAT
* *
4838978 ACTTTTTTAATT
1 A--TTTTAAAAT
4838990 ATTTTAAAAT
1 ATTTTAAAAT
4839000 TTTAAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 1 0.02
10 23 0.48
11 10 0.21
12 8 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:4840147 original size:30 final size:31
Alignment explanation
Indices: 4840095--4840152 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
4840085 AAAAATAAAA
4840095 AAAATTGAATTTTAACCCCTAAA-TTTTCCT
1 AAAATTGAATTTTAACCCCTAAACTTTTCCT
* *
4840125 AAAATT-ATATTTTAAGCGCTAAACTTTT
1 AAAATTGA-ATTTTAACCCCTAAACTTTT
4840153 TTAAATTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 19 0.79
31 4 0.17
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (31 bp):
AAAATTGAATTTTAACCCCTAAACTTTTCCT
Found at i:4840189 original size:30 final size:29
Alignment explanation
Indices: 4840149--4840259 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
4840139 AGCGCTAAAC
* *
4840149 TTTTTTAAATTACATTTTGACCCATCAAAT
1 TTTTTGAAATTACATTTTGACCCATC-AAG
4840179 TTTTTGAAATTACATTTTGACCCATCAAG
1 TTTTTGAAATTACATTTTGACCCATCAAG
4840208 TTTTTGAAATTACATTTTGACCCATCAAG
1 TTTTTGAAATTACATTTTGACCCATCAAG
4840237 TTTTTGAAATTACATTTTGACCC
1 TTTTTGAAATTACATTTTGACCC
4840260 CTATATTTTC
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
29 54 0.68
30 25 0.32
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (29 bp):
TTTTTGAAATTACATTTTGACCCATCAAG
Found at i:4840189 original size:59 final size:58
Alignment explanation
Indices: 4840126--4840259 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 58
4840116 AATTTTCCTA
* * * *
4840126 AAATTATATTTTAAGCGC-TAAACTTTTTTAAATTACATTTTGACCCATCAAATTTTTTG
1 AAATTACATTTTAA-CCCATAAACTTTTTGAAATTACATTTTGACCCATC-AAGTTTTTG
* * *
4840185 AAATTACATTTTGACCCATCAAGTTTTTGAAATTACATTTTGACCCATCAAGTTTTTG
1 AAATTACATTTTAACCCATAAACTTTTTGAAATTACATTTTGACCCATCAAGTTTTTG
*
4840243 AAATTACATTTTGACCC
1 AAATTACATTTTAACCC
4840260 CTATATTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 27 0.40
59 40 0.60
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (58 bp):
AAATTACATTTTAACCCATAAACTTTTTGAAATTACATTTTGACCCATCAAGTTTTTG
Found at i:4840651 original size:15 final size:14
Alignment explanation
Indices: 4840632--4840697 Score: 68
Period size: 13 Copynumber: 4.8 Consensus size: 14
4840622 GTGAAGAGGG
4840632 AAGAAGAAAAAGAA
1 AAGAAGAAAAAGAA
4840646 GAAGAAAGAAATAA-AA
1 -AAG-AAGAAA-AAGAA
*
4840662 AAGAA-AAAAGGAA
1 AAGAAGAAAAAGAA
4840675 AA-AAGAAAAAGAA
1 AAGAAGAAAAAGAA
4840688 AA-AAGAAAAA
1 AAGAAGAAAAA
4840698 ATTAATAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 3 0.07
13 24 0.53
14 2 0.04
15 6 0.13
16 8 0.18
17 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAGAAGAAAAAGAA
Found at i:4840654 original size:7 final size:7
Alignment explanation
Indices: 4840638--4840698 Score: 72
Period size: 7 Copynumber: 8.7 Consensus size: 7
4840628 AGGGAAGAAG
4840638 AAAAAG-
1 AAAAAGA
*
4840644 AAGAAGA
1 AAAAAGA
*
4840651 AAGAAATA
1 AA-AAAGA
4840659 AAAAAGA
1 AAAAAGA
4840666 AAAAAGGA
1 AAAAA-GA
4840674 AAAAAG-
1 AAAAAGA
4840680 AAAAAGA
1 AAAAAGA
4840687 AAAAAGA
1 AAAAAGA
4840694 AAAAA
1 AAAAA
4840699 TTAATAGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
6 11 0.23
7 24 0.51
8 12 0.26
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:4840664 original size:21 final size:19
Alignment explanation
Indices: 4840638--4840698 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
4840628 AGGGAAGAAG
4840638 AAAAAGAAGAAGAAAGAAATA
1 AAAAAGAAGAA-AAAGAAA-A
*
4840659 AAAAAGAA-AAAAGGAAAA
1 AAAAAGAAGAAAAAGAAAA
4840677 AAGAAA-AAGAAAAAAGAAAA
1 AA-AAAGAAG-AAAAAGAAAA
4840697 AA
1 AA
4840699 TTAATAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 5 0.14
19 9 0.26
20 13 0.37
21 8 0.23
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAAAAAGAAAA
Found at i:4840668 original size:6 final size:6
Alignment explanation
Indices: 4840635--4840697 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
4840625 AAGAGGGAAG
* *
4840635 AAGAAA AAGAAG AAG--A AAGAAA TA-AAA AAGAAAA AAGGAAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA AA-G-AAA AAGAAA
4840683 AAGAAAA AAGAAA AA
1 AAG-AAA AAGAAA AA
4840698 ATTAATAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 3 0.06
5 4 0.09
6 21 0.45
7 12 0.26
8 7 0.15
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:4840698 original size:15 final size:15
Alignment explanation
Indices: 4840632--4840698 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
4840622 GTGAAGAGGG
*
4840632 AAGAAGAAAAAG-AAG
1 AAGAA-AAAAAGAAAA
* *
4840647 AAGAAAGAAATAAAA
1 AAGAAAAAAAGAAAA
*
4840662 AAGAAAAAAGGAAAA
1 AAGAAAAAAAGAAAA
4840677 AAG--AAAAAGAAAA
1 AAGAAAAAAAGAAAA
4840690 AAGAAAAAA
1 AAGAAAAAA
4840699 TTAATAGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 12 0.29
14 4 0.10
15 26 0.62
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (15 bp):
AAGAAAAAAAGAAAA
Found at i:4840854 original size:25 final size:25
Alignment explanation
Indices: 4840826--4840902 Score: 88
Period size: 24 Copynumber: 3.1 Consensus size: 25
4840816 AAGTAGCTGC
4840826 CCAACAGGCCCAACAGCCTAGCAGG
1 CCAACAGGCCCAACAGCCTAGCAGG
* *
4840851 CCAACA-GCCCAACAGCTTGGCAGG
1 CCAACAGGCCCAACAGCCTAGCAGG
*
4840875 CCAGCAGGCCCATCACAG-C-AGCAGG
1 CCAACAGGCCCA--ACAGCCTAGCAGG
4840900 CCA
1 CCA
4840903 GCAGATTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 21 0.48
25 19 0.43
27 4 0.09
ACGTcount: A:0.30, C:0.40, G:0.25, T:0.05
Consensus pattern (25 bp):
CCAACAGGCCCAACAGCCTAGCAGG
Found at i:4840864 original size:8 final size:8
Alignment explanation
Indices: 4840824--4840866 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
4840814 CAAAGTAGCT
4840824 GCCCAACA
1 GCCCAACA
4840832 GGCCCAACA
1 -GCCCAACA
* *
4840841 GCCTAGCA
1 GCCCAACA
*
4840849 GGCCAACA
1 GCCCAACA
4840857 GCCCAACA
1 GCCCAACA
4840865 GC
1 GC
4840867 TTGGCAGGCC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.33, C:0.44, G:0.21, T:0.02
Consensus pattern (8 bp):
GCCCAACA
Found at i:4841309 original size:17 final size:17
Alignment explanation
Indices: 4841287--4841346 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
4841277 CTTTTAAAAA
4841287 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
* *
4841304 AAAAATTTTCGGGCTTTC
1 AAAAA-TTTCGTGTTTTC
*
4841322 AAAAATTT-TTGTGTTTC
1 AAAAATTTCGTGT-TTTC
4841339 AAAAATTT
1 AAAAATTT
4841347 TCGTATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.03
17 20 0.56
18 15 0.42
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:4841347 original size:17 final size:18
Alignment explanation
Indices: 4841286--4841350 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
4841276 CCTTTTAAAA
* *
4841286 AAAAAATTTCGTGTTTTC
1 AAAAATTTTCGTGCTTTC
*
4841304 AAAAATTTTCGGGCTTTC
1 AAAAATTTTCGTGCTTTC
*
4841322 AAAAATTTTTGTG-TTTC
1 AAAAATTTTCGTGCTTTC
4841339 AAAAATTTTCGT
1 AAAAATTTTCGT
4841351 ATTAAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 15 0.37
18 26 0.63
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGCTTTC
Found at i:4841445 original size:18 final size:18
Alignment explanation
Indices: 4841399--4841485 Score: 77
Period size: 18 Copynumber: 4.7 Consensus size: 18
4841389 TGTTTTTGTA
* *
4841399 TTTTCAACAAATTCTCGTG
1 TTTTCAAAAAAAT-TCGTG
*
4841418 TTTTTAAAAAAAATTCGTG
1 -TTTTCAAAAAAATTCGTG
* *
4841437 TTTTGAAAAAATTTCCGTG
1 TTTTCAAAAAAATT-CGTG
* *
4841456 -TTTCAAAAATATTCTTG
1 TTTTCAAAAAAATTCGTG
4841473 TTTTCAAAAAAAT
1 TTTTCAAAAAAAT
4841486 ATTCTCGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
17 3 0.05
18 33 0.60
19 9 0.16
20 10 0.18
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTTCAAAAAAATTCGTG
Found at i:4841513 original size:38 final size:37
Alignment explanation
Indices: 4841424--4841514 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 37
4841414 CGTGTTTTTA
* * *
4841424 AAAAAAATTCGTGTTTT-GAAAAAATTTCCGTGTTTC
1 AAAAATATTCATGTTTTCAAAAAAATTTCCGTGTTTC
*
4841460 AAAAATATTCTTGTTTTCAAAAAAATATTCTCGTGTTTC
1 AAAAATATTCATGTTTTCAAAAAAAT-TTC-CGTGTTTC
* *
4841499 -AACATTTTCATGTTTT
1 AAAAATATTCATGTTTT
4841515 AAAGATTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 15 0.33
37 7 0.15
38 16 0.35
39 8 0.17
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (37 bp):
AAAAATATTCATGTTTTCAAAAAAATTTCCGTGTTTC
Found at i:4841569 original size:33 final size:34
Alignment explanation
Indices: 4841490--4841575 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
4841480 AAAAATATTC
* * *
4841490 TCGTG-TTTC-AACATTTTCATGTTTTAAAGATT
1 TCGTGTTTTCAAAAATTCTCATGTTCTAAAGATT
* *
4841522 TGGTGTTTTCAAAAATTCTCATGTTCTAAA-TTT
1 TCGTGTTTTCAAAAATTCTCATGTTCTAAAGATT
4841555 TCGTGTTTTCAAAAAATTCTC
1 TCGTGTTTTC-AAAAATTCTC
4841576 GTATTTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 4 0.09
33 15 0.33
34 26 0.58
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.48
Consensus pattern (34 bp):
TCGTGTTTTCAAAAATTCTCATGTTCTAAAGATT
Found at i:4842794 original size:40 final size:40
Alignment explanation
Indices: 4842737--4842829 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 40
4842727 TAAACAAAAA
*
4842737 AAAAATTAGAAAA-TTTAAAAAAGTATTTTAAAAGTA-TCTT
1 AAAAA-TAAAAAATTTTAAAAAAGTATTTTAAAA-TATTCTT
*
4842777 AAAAATAAAAAATTTTAAAAAAGTATTTTAAAATATTTTT
1 AAAAATAAAAAATTTTAAAAAAGTATTTTAAAATATTCTT
4842817 AAAAATAAAAAAT
1 AAAAATAAAAAAT
4842830 ATATATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 8 0.16
40 41 0.84
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (40 bp):
AAAAATAAAAAATTTTAAAAAAGTATTTTAAAATATTCTT
Found at i:4852417 original size:288 final size:288
Alignment explanation
Indices: 4851898--4852517 Score: 1051
Period size: 288 Copynumber: 2.2 Consensus size: 288
4851888 GGATCCAAAA
* * *
4851898 ATAAAGAAGTATGTCATTTTCATAGATGTTTTCGATAAATTATCATCCTATTATCAAAAGTTGTT
1 ATAAAGAAGTATGTCATTTTCATAGATGTTTTCGATAAAGTATCATCATATTATCAAAAGTTATT
* *
4851963 CATGATGATAAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATGGAAGCTCTAAATGATGA
66 CATAATGATAAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATAGAAGCTCTAAATGATGA
4852028 AGACCCTTTAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCA
131 AGACCCTTTAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCA
*
4852093 CAAGGGAGAAGAGGCAACCACAATACTTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATT
196 CAAGGGAGAAGAGGCAACCACAATACCTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATT
* * *
4852158 ACTTTATACTTCTTTATTGGAGAAATGG
261 ACTTCATACTTCTTTATTAGAGAAATAG
* *
4852186 ATGAAGAAGTATGTCATTTTTATAGATGTTTTCGATAAAGTATCATCATATTATCAAAAGTTATT
1 ATAAAGAAGTATGTCATTTTCATAGATGTTTTCGATAAAGTATCATCATATTATCAAAAGTTATT
* *
4852251 CATAATGATGAGAAAAGTAGCTTACAACTACTTCCTGAAAGCAACATAGAAGCTCTAAATGATGA
66 CATAATGATAAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATAGAAGCTCTAAATGATGA
* * * * *
4852316 AGATCCTTTAACATCTGATACCTTAGATGTGGAAGGTGGTGAGCAAGAACTCCAAAGGAAATCCA
131 AGACCCTTTAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCA
* *
4852381 CAAGGGAGAAGAGGCAACCACAATACCTGAAAGATTATGTGGTGCAAACCAACAATTGTTCAATT
196 CAAGGGAGAAGAGGCAACCACAATACCTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATT
4852446 ACTTCATACTTCTTTATTAGAGAAATAG
261 ACTTCATACTTCTTTATTAGAGAAATAG
*
4852474 ATAAAGAAGTATGTCATTTTCATAGATGTTTTCAATAAAGTATC
1 ATAAAGAAGTATGTCATTTTCATAGATGTTTTCGATAAAGTATC
4852518 TGTTGAGATT
Statistics
Matches: 309, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
288 309 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (288 bp):
ATAAAGAAGTATGTCATTTTCATAGATGTTTTCGATAAAGTATCATCATATTATCAAAAGTTATT
CATAATGATAAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATAGAAGCTCTAAATGATGA
AGACCCTTTAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCA
CAAGGGAGAAGAGGCAACCACAATACCTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATT
ACTTCATACTTCTTTATTAGAGAAATAG
Found at i:4859402 original size:2 final size:2
Alignment explanation
Indices: 4859395--4859420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4859385 CGCAAAAGTA
4859395 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4859421 GAAATATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4862093 original size:17 final size:18
Alignment explanation
Indices: 4862071--4862105 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4862061 TTATATCTTC
*
4862071 TTATAATTAAAT-TTTTG
1 TTATAAATAAATATTTTG
4862088 TTATAAATAAATATTTTG
1 TTATAAATAAATATTTTG
4862106 GGTACAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTATAAATAAATATTTTG
Found at i:4864148 original size:21 final size:22
Alignment explanation
Indices: 4864122--4864165 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
4864112 GGTTTTAACG
4864122 TTCAAGTTCATCCAT-AAAGGT
1 TTCAAGTTCATCCATAAAAGGT
4864143 TTCAAGTTCATCCATAAAAGGT
1 TTCAAGTTCATCCATAAAAGGT
4864165 T
1 T
4864166 AGCCATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (22 bp):
TTCAAGTTCATCCATAAAAGGT
Found at i:4881648 original size:30 final size:29
Alignment explanation
Indices: 4881614--4881706 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
4881604 GCCAGGGGGG
4881614 CCAAAATTTTTTGAAAATTTTAATTAGGCC
1 CCAAAATTTTTT-AAAATTTTAATTAGGCC
* * *
4881644 CCAAAATTATTTAAAAGTTCTAATTAAGCC
1 CCAAAATTTTTTAAAA-TTTTAATTAGGCC
* * * *
4881674 TTCCAAAAGTTCTAAAAATTTTAATTAGACC
1 --CCAAAATTTTTTAAAATTTTAATTAGGCC
4881705 CC
1 CC
4881707 TTCAGTTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
29 6 0.12
30 22 0.44
31 10 0.20
32 12 0.24
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (29 bp):
CCAAAATTTTTTAAAATTTTAATTAGGCC
Found at i:4883134 original size:36 final size:36
Alignment explanation
Indices: 4883087--4883158 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
4883077 AAGGAGAGTA
4883087 AATCTGACCTGAATTATCAAATTCTCAAACGTAGTT
1 AATCTGACCTGAATTATCAAATTCTCAAACGTAGTT
4883123 AATCTGACCTGAATTATCAAATTCTCAAACGTAGTT
1 AATCTGACCTGAATTATCAAATTCTCAAACGTAGTT
4883159 TTCTATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
AATCTGACCTGAATTATCAAATTCTCAAACGTAGTT
Found at i:4884193 original size:18 final size:18
Alignment explanation
Indices: 4884161--4884211 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
4884151 TAAAAAAAGT
4884161 ATTTTAAAAATATTTTAAA
1 ATTTTAAAAA-ATTTTAAA
4884180 ATTTTAAAAAA-TTTAAA
1 ATTTTAAAAAATTTTAAA
*
4884197 ATATTTAAAATATTT
1 AT-TTTAAAAAATTT
4884212 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.28
18 9 0.31
19 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTAAAAAATTTTAAA
Found at i:4884212 original size:18 final size:17
Alignment explanation
Indices: 4884161--4884214 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
4884151 TAAAAAAAGT
4884161 ATTTTAAAAATATTTTAAA
1 ATTTT-AAAATA-TTTAAA
*
4884180 ATTTTAAAAAATTTAAA
1 ATTTTAAAATATTTAAA
4884197 ATATTTAAAATATTTAAA
1 AT-TTTAAAATATTTAAA
4884215 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 8 0.25
18 19 0.59
19 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTAAAATATTTAAA
Found at i:4884215 original size:8 final size:9
Alignment explanation
Indices: 4884167--4884214 Score: 71
Period size: 9 Copynumber: 5.3 Consensus size: 9
4884157 AAGTATTTTA
4884167 AAAATATTTT
1 AAAATA-TTT
4884177 AAAAT-TTT
1 AAAATATTT
*
4884185 AAAAAATTT
1 AAAATATTT
4884194 AAAATATTT
1 AAAATATTT
4884203 AAAATATTT
1 AAAATATTT
4884212 AAA
1 AAA
4884215 TTAAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
8 7 0.20
9 23 0.66
10 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:4887863 original size:11 final size:11
Alignment explanation
Indices: 4887847--4887877 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4887837 TATATATATT
4887847 TAAAAATTATA
1 TAAAAATTATA
*
4887858 TAAAAATAATA
1 TAAAAATTATA
4887869 TAAAAATTA
1 TAAAAATTA
4887878 ATACAGGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:4894350 original size:20 final size:19
Alignment explanation
Indices: 4894325--4894369 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
4894315 AAATATGTAA
4894325 ATTTAA-CCTTAAATCTTAT
1 ATTTAATCCTTAAAT-TTAT
*
4894344 ATATTAATGCTTAAATTTAT
1 AT-TTAATCCTTAAATTTAT
4894364 ATTTAA
1 ATTTAA
4894370 GGATTAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTAATCCTTAAATTTAT
Found at i:4897448 original size:23 final size:23
Alignment explanation
Indices: 4897406--4897449 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4897396 TAATTAATTT
* *
4897406 TGAAGATAAAAAAGATAAAAAGG
1 TGAAGATAAAAAAAAAAAAAAGG
4897429 TGAAGATAAAAAAAAAAAAAA
1 TGAAGATAAAAAAAAAAAAAA
4897450 TCCTTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (23 bp):
TGAAGATAAAAAAAAAAAAAAGG
Found at i:4908926 original size:12 final size:13
Alignment explanation
Indices: 4908895--4908920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4908885 TGATTATTTG
4908895 AATATAAATTTTT
1 AATATAAATTTTT
4908908 AATATAAATTTTT
1 AATATAAATTTTT
4908921 TTATAACATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATAAATTTTT
Found at i:4910893 original size:13 final size:13
Alignment explanation
Indices: 4910875--4910899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4910865 CTAAATCATA
4910875 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
4910888 ATTTTAGTAAAA
1 ATTTTAGTAAAA
4910900 CCTTTTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:4915827 original size:16 final size:16
Alignment explanation
Indices: 4915806--4915854 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
4915796 CGCTGTATTG
*
4915806 GAATAGAGGCGTAATA
1 GAATAGAGGTGTAATA
*
4915822 GAATAGAGGTGTAATG
1 GAATAGAGGTGTAATA
*
4915838 GATTAGAGGTGTAATA
1 GAATAGAGGTGTAATA
4915854 G
1 G
4915855 CAAATCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.39, C:0.02, G:0.35, T:0.24
Consensus pattern (16 bp):
GAATAGAGGTGTAATA
Found at i:4916108 original size:18 final size:17
Alignment explanation
Indices: 4916066--4916120 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
4916056 TTAATCATAT
4916066 TTAAACATA-ATAA-TTA
1 TTAAA-ATATATAATTTA
* *
4916082 TT-AAATATATTA-TAA
1 TTAAAATATATAATTTA
4916097 TTAAAATATATAATTTA
1 TTAAAATATATAATTTA
4916114 TTAAAAT
1 TTAAAAT
4916121 TCTTAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 3 0.09
15 9 0.28
16 11 0.34
17 9 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATATATAATTTA
Found at i:4916234 original size:14 final size:15
Alignment explanation
Indices: 4916185--4916236 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
4916175 ATAAAATATA
4916185 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
4916200 TATTAAATATATTAT
1 AATTAAATATATTAT
4916215 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
4916228 AATTTAATA
1 AATTAAATA
4916237 AAATTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:4916238 original size:59 final size:58
Alignment explanation
Indices: 4916069--4916240 Score: 152
Period size: 59 Copynumber: 2.9 Consensus size: 58
4916059 ATCATATTTA
* * * *
4916069 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTATTAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAA-TATAAAT
* * * * * * * *
4916128 AA-ATTATATTCTTATATGAATTTACTGA-AATCATAATATATGATACT-ATAAAATATAAATT
1 AACA-TA-ATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATATAAA-T
4916189 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAAT
4916241 TTTAATAATT
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
58 4 0.05
59 30 0.36
60 17 0.20
61 29 0.35
62 4 0.05
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (58 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATATAAAT
Found at i:4916600 original size:20 final size:20
Alignment explanation
Indices: 4916553--4916591 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4916543 AATTTAAAAT
*
4916553 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
4916573 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
4916592 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:4916894 original size:11 final size:12
Alignment explanation
Indices: 4916864--4916899 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
4916854 ATGTATTAAT
4916864 TTATTTTTCATA
1 TTATTTTTCATA
*
4916876 TTATTTTTGATA
1 TTATTTTTCATA
4916888 TTATTTTT-ATA
1 TTATTTTTCATA
4916899 T
1 T
4916900 CATGTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (12 bp):
TTATTTTTCATA
Found at i:4916914 original size:23 final size:24
Alignment explanation
Indices: 4916853--4916915 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
4916843 TAATTTATTG
4916853 CATGTATTAATTTATTTTTCATAT
1 CATGTATTAATTTATTTTTCATAT
* * *
4916877 TAT-TTTTGATATTATTTTT-ATAT
1 CATGTATTAAT-TTATTTTTCATAT
4916900 CATGTATTAATTTATT
1 CATGTATTAATTTATT
4916916 GCATGTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (24 bp):
CATGTATTAATTTATTTTTCATAT
Found at i:4926332 original size:6 final size:6
Alignment explanation
Indices: 4926321--4926351 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4926311 CCTTTCCTTT
4926321 CGATGC CGATGC CGATGC CGATGC CGATGC C
1 CGATGC CGATGC CGATGC CGATGC CGATGC C
4926352 TCTGATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CGATGC
Found at i:4926845 original size:3 final size:3
Alignment explanation
Indices: 4926837--4926878 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4926827 TCCTTAAACC
4926837 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
4926879 TCATTGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:4936568 original size:16 final size:16
Alignment explanation
Indices: 4936549--4936581 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4936539 GAATGGACTC
*
4936549 TGTTTCTTTTCTTCTT
1 TGTTTCTTTTATTCTT
4936565 TGTTTCTTTTATTCTT
1 TGTTTCTTTTATTCTT
4936581 T
1 T
4936582 TACTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTTATTCTT
Found at i:4936615 original size:3 final size:3
Alignment explanation
Indices: 4936607--4936637 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4936597 TTGTATTAAT
4936607 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4936638 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4938732 original size:30 final size:31
Alignment explanation
Indices: 4938698--4938779 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
4938688 AAGAAAAAAG
*
4938698 TTTTTACCAACTTTTAAGGGCCCCAAATTTT
1 TTTTTACCAACTTTTAAGGGCCCAAAATTTT
** * ***
4938729 TTTTT-TTAGCTTTTAAGGATTCAAAATTTT
1 TTTTTACCAACTTTTAAGGGCCCAAAATTTT
4938759 TCTTTTACCAACTTTTAAGGG
1 T-TTTTACCAACTTTTAAGGG
4938780 ACTTAAAAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
30 19 0.50
31 9 0.24
32 10 0.26
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTTTACCAACTTTTAAGGGCCCAAAATTTT
Found at i:4939448 original size:17 final size:17
Alignment explanation
Indices: 4939417--4939722 Score: 158
Period size: 17 Copynumber: 17.5 Consensus size: 17
4939407 AAAAAAAACG
*
4939417 AAATTTTCG-AACACGA
1 AAATTTTTGAAACACGA
*
4939433 AAATTTTAGAAACACGA
1 AAATTTTTGAAACACGA
** *
4939450 ATTTTTTTTAAAACACGA
1 A-AATTTTTGAAACACGA
*
4939468 CAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
* *
4939485 GAATTTTTCAAAACAC-A
1 AAATTTTT-GAAACACGA
* * *
4939502 AATTTTATTAAAAAAACATGA
1 AAATTT-TT---GAAACACGA
* * *
4939523 CAATTTGTGAAACACTA
1 AAATTTTTGAAACACGA
* * ** *
4939540 GAGTCATTGAAAACACGG
1 AAATTTTTG-AAACACGA
* *
4939558 AAATTTGTGAAAAACGA
1 AAATTTTTGAAACACGA
* *
4939575 AATTTTTTGAAGCAC-A
1 AAATTTTTGAAACACGA
4939591 GAAATTTTTAGAAAACACGA
1 -AAATTTTT-G-AAACACGA
*
4939611 AAA-TTTTGAATCACCG-
1 AAATTTTTGAAACA-CGA
4939627 AAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
*
4939645 AGATTTTTGAAACACCG-
1 AAATTTTTGAAACA-CGA
* *
4939662 AAATTTTTGAAAATACGT
1 AAATTTTTG-AAACACGA
*
4939680 AGATTTTTGAAACACTG-
1 AAATTTTTGAAACAC-GA
4939697 AAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
*
4939715 GAATTTTT
1 AAATTTTT
4939723 TTTACATAAA
Statistics
Matches: 218, Mismatches: 50, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
16 16 0.07
17 106 0.49
18 75 0.34
19 8 0.04
20 8 0.04
21 5 0.02
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (17 bp):
AAATTTTTGAAACACGA
Found at i:4939474 original size:18 final size:17
Alignment explanation
Indices: 4939426--4939723 Score: 126
Period size: 18 Copynumber: 16.9 Consensus size: 17
4939416 GAAATTTTCG
*
4939426 AACACGAAA-ATTTTAGA
1 AACACGAAATTTTTTA-A
*
4939443 AACACGAATTTTTTTTAA
1 AACACGAA-ATTTTTTAA
*
4939461 AACACGACAA-TTTTTGA
1 AACACGA-AATTTTTTAA
*
4939478 AACACGAGAATTTTTCAA
1 AACACGA-AATTTTTTAA
4939496 AACAC-AAATTTTATTAAAAA
1 AACACGAAATTTT-TT---AA
* * *
4939516 AACATGACAA-TTTGTGA
1 AACACGA-AATTTTTTAA
* * ** *
4939533 AACACTAGAGTCATTGAA
1 AACACGA-AATTTTTTAA
* *
4939551 AACACGGAAATTTGTGAA
1 AACAC-GAAATTTTTTAA
*
4939569 AA-ACGAAATTTTTTGA
1 AACACGAAATTTTTTAA
* *
4939585 AGCACAGAAATTTTTAGAA
1 AACAC-GAAATTTTT-TAA
* *
4939604 AACACGAAA-ATTTTGA
1 AACACGAAATTTTTTAA
* *
4939620 ATCACCGAAATTTTTGAA
1 AACA-CGAAATTTTTTAA
*
4939638 AACACGAAGA-TTTTTGA
1 AACACGAA-ATTTTTTAA
*
4939655 AACACCGAAATTTTTGAA
1 AACA-CGAAATTTTTTAA
* * *
4939673 AATACGTAGA-TTTTTGA
1 AACACG-AAATTTTTTAA
*
4939690 AACACTGAAATTTTTGAA
1 AACAC-GAAATTTTTTAA
4939708 AACACGAGAATTTTTT
1 AACACGA-AATTTTTT
4939724 TTACATAAAC
Statistics
Matches: 204, Mismatches: 53, Indels: 47
0.67 0.17 0.15
Matches are distributed among these distances:
16 20 0.10
17 73 0.36
18 86 0.42
19 12 0.06
20 7 0.03
21 4 0.02
22 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (17 bp):
AACACGAAATTTTTTAA
Found at i:4939722 original size:35 final size:33
Alignment explanation
Indices: 4939414--4939722 Score: 223
Period size: 35 Copynumber: 8.8 Consensus size: 33
4939404 TTTAAAAAAA
* *
4939414 ACGAAATTTTCG--AACACGAAAATTTTAGAAAC
1 ACGAAATTTTTGAAAACACG-AAATTTTTGAAAC
* *
4939446 ACGAATTTTTTTTAAAACACGACAATTTTTGAAAC
1 ACGAA-ATTTTTGAAAACACGA-AATTTTTGAAAC
* *
4939481 ACGAGAATTTTTCAAAACAC-AAATTTTATTAAAAAAAC
1 ACGA-AATTTTTGAAAACACGAAA-TTT-TT---GAAAC
* * * * **
4939519 ATGACAATTTGTG-AAACACTAGAGTCATTGAAAAC
1 ACGA-AATTTTTGAAAACACGA-AATTTTTG-AAAC
* *
4939554 ACGGAAATTTGTGAAAA-ACGAAATTTTTTGAAGC
1 AC-GAAATTTTTGAAAACACGAAA-TTTTTGAAAC
* *
4939588 ACAGAAATTTTTAGAAAACACGAAAATTTTGAATC
1 AC-GAAATTTTT-GAAAACACGAAATTTTTGAAAC
4939623 ACCGAAATTTTTGAAAACACGAAGATTTTTGAAAC
1 A-CGAAATTTTTGAAAACACGAA-ATTTTTGAAAC
* *
4939658 ACCGAAATTTTTGAAAATACGTAGATTTTTGAAAC
1 A-CGAAATTTTTGAAAACACG-AAATTTTTGAAAC
4939693 ACTGAAATTTTTGAAAACACGAGAATTTTT
1 AC-GAAATTTTTGAAAACACGA-AATTTTT
4939723 TTTACATAAA
Statistics
Matches: 223, Mismatches: 31, Indels: 43
0.75 0.10 0.14
Matches are distributed among these distances:
32 5 0.02
33 6 0.03
34 32 0.14
35 142 0.64
36 14 0.06
37 8 0.04
38 15 0.07
39 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (33 bp):
ACGAAATTTTTGAAAACACGAAATTTTTGAAAC
Found at i:4939883 original size:19 final size:18
Alignment explanation
Indices: 4939839--4939904 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 18
4939829 TCGCTGCCTT
*
4939839 ATTTTTGAAAACACGAATAT
1 ATTTTTG-AAACACGAA-AA
*
4939859 TTTTTTGAAACACGAGAAAA
1 ATTTTTGAAACAC--GAAAA
*
4939879 ATTTTTG-AAGACGAAAA
1 ATTTTTGAAACACGAAAA
4939896 A-TTTTGAAA
1 ATTTTTGAAA
4939905 GATAGAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.13
17 8 0.21
19 10 0.26
20 13 0.33
21 3 0.08
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (18 bp):
ATTTTTGAAACACGAAAA
Found at i:4940163 original size:26 final size:25
Alignment explanation
Indices: 4940119--4940175 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
4940109 TTAAAAATAT
* *
4940119 AAATACAAAAATATAAAAATGCACA
1 AAATACAAAAATATAAAAATGAAAA
* *
4940144 AAATACTAATAATATTAAAATGAAAA
1 AAATAC-AAAAATATAAAAATGAAAA
4940170 AAATAC
1 AAATAC
4940176 GAGCATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATACAAAAATATAAAAATGAAAA
Found at i:4940280 original size:17 final size:17
Alignment explanation
Indices: 4940258--4940307 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
4940248 ACAAATTGAA
4940258 CCTTTTTTTTTCTTTTC
1 CCTTTTTTTTTCTTTTC
*
4940275 CCTTTTTTCTT-TTTTC
1 CCTTTTTTTTTCTTTTC
*
4940291 TCTTTTTTTCTTCTTTT
1 CCTTTTTTT-TTCTTTT
4940308 TTTTTTTCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 12 0.43
17 12 0.43
18 4 0.14
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
CCTTTTTTTTTCTTTTC
Found at i:4940286 original size:7 final size:7
Alignment explanation
Indices: 4940263--4940314 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
4940253 TTGAACCTTT
4940263 TTTTTTC
1 TTTTTTC
**
4940270 TTTTCCC
1 TTTTTTC
4940277 TTTTTTC
1 TTTTTTC
4940284 TTTTTTC
1 TTTTTTC
*
4940291 TCTTTT-
1 TTTTTTC
*
4940297 TTTCTTC
1 TTTTTTC
4940304 TTTTTT-
1 TTTTTTC
4940310 TTTTT
1 TTTTT
4940315 CTGGCCTGCT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
6 9 0.25
7 27 0.75
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:4940296 original size:14 final size:12
Alignment explanation
Indices: 4940278--4940316 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
4940268 TCTTTTCCCT
4940278 TTTTTCTTTTTTC
1 TTTTT-TTTTTTC
*
4940291 TCTTTTTTTCTTC
1 T-TTTTTTTTTTC
4940304 TTTTTTTTTTTC
1 TTTTTTTTTTTC
4940316 T
1 T
4940317 GGCCTGCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 11 0.48
13 8 0.35
14 4 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:4940307 original size:9 final size:8
Alignment explanation
Indices: 4940259--4940316 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
4940249 CAAATTGAAC
4940259 CTTTTTTT
1 CTTTTTTT
*
4940267 -TTCTTTTC
1 CTT-TTTTT
*
4940275 CCTTTTTT
1 CTTTTTTT
4940283 CTTTTTTCT
1 CTTTTTT-T
4940292 CTTTTTTT
1 CTTTTTTT
*
4940300 CTTCTTTT
1 CTTTTTTT
4940308 -TTTTTTT
1 CTTTTTTT
4940315 CT
1 CT
4940317 GGCCTGCTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 8 0.20
8 23 0.57
9 9 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTTT
Found at i:4940313 original size:17 final size:17
Alignment explanation
Indices: 4940259--4940316 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
4940249 CAAATTGAAC
4940259 CTTTTTTT-TTCTTTTC-
1 CTTTTTTTCTT-TTTTCT
*
4940275 CCTTTTTTCTTTTTTCT
1 CTTTTTTTCTTTTTTCT
*
4940292 CTTTTTTTCTTCTTT-T
1 CTTTTTTTCTTTTTTCT
4940308 -TTTTTTTCT
1 CTTTTTTTCT
4940317 GGCCTGCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.24
16 13 0.35
17 15 0.41
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTTTTTCTTTTTTCT
Found at i:4940643 original size:10 final size:10
Alignment explanation
Indices: 4940624--4940694 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
4940614 ACTGAATTAA
4940624 TTTT-TTTCT
1 TTTTCTTTCT
4940633 TTTTCTTTCT
1 TTTTCTTTCT
4940643 TTTTC-TTCT
1 TTTTCTTTCT
* *
4940652 TCCTTCTTCCT
1 T-TTTCTTTCT
4940663 TTCTTCTTT-T
1 TT-TTCTTTCT
4940673 TCTTTC-TTCTT
1 T-TTTCTTTC-T
4940684 TTTTCTTTCT
1 TTTTCTTTCT
4940694 T
1 T
4940695 CCCCGTTCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
9 11 0.22
10 24 0.48
11 15 0.30
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:4940808 original size:17 final size:17
Alignment explanation
Indices: 4940776--4940852 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 17
4940766 ACGCTCCTCC
4940776 CTTTTCTTTCTCTTCTTTT
1 CTTTT-TTT-TCTTCTTTT
4940795 CTTTTTTTTCTTC--TT
1 CTTTTTTTTCTTCTTTT
*
4940810 -TGTTTTTTCTTGCTTGTT
1 CTTTTTTTTCTT-CTT-TT
*
4940828 GTTGTTTTTTCTT-TCTTT
1 CTT-TTTTTTCTTCT-TTT
4940846 CTTTTTT
1 CTTTTTT
4940853 ATTTTTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
17 9 0.19
18 10 0.21
19 7 0.15
20 9 0.19
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (17 bp):
CTTTTTTTTCTTCTTTT
Found at i:4940857 original size:20 final size:19
Alignment explanation
Indices: 4940777--4940849 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
4940767 CGCTCCTCCC
4940777 TTTTCTTTCTCTTCTTT-TCT
1 TTTTCTTTCT-TTCTTTGT-T
4940797 TTTT-TTTC-TTCTTTGTT
1 TTTTCTTTCTTTCTTTGTT
*
4940814 TTTTCTTGCTTGT-TGTTGTT
1 TTTTCTTTCTT-TCT-TTGTT
4940834 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
4940850 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 9 0.20
20 21 0.47
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTCTTTGTT
Found at i:4941281 original size:59 final size:58
Alignment explanation
Indices: 4941189--4941335 Score: 179
Period size: 59 Copynumber: 2.5 Consensus size: 58
4941179 GGGCCGAATC
*
4941189 GTAATTTTGAGAAAGTTTAAGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
1 GTAATTTAGA-AAAGTTT-AGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
* * ** *
4941249 GTAATTTAGAAAAGTTTAGGTGTTGAATTGTAATTTTGAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTAGAAAAGTTTAGG-GTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
*
4941308 GCAATTTTAGAAAAGTTTAGAGG-TCAAA
1 GTAA-TTTAGAAAAGTTTAG-GGTTCAAA
4941336 AAGCAAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
58 3 0.04
59 46 0.61
60 25 0.33
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GTAATTTAGAAAAGTTTAGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
Found at i:4941327 original size:30 final size:31
Alignment explanation
Indices: 4941189--4941336 Score: 164
Period size: 30 Copynumber: 5.0 Consensus size: 31
4941179 GGGCCGAATC
* *
4941189 GTAATTTT-GAGAAAGTTTAAGGGTTCAAAT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
* *
4941219 GTAATTTCA-AGAAAGTTTAGGGGTCAAAAT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
* * *
4941249 GTAA-TTTAGA-AAAGTTTAGGTGTTGAATT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
4941278 GTAATTTT-GAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
* * *
4941308 GCAATTTTAGA-AAAGTTTAGAGGTCAAAA
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAA
4941337 AGCAAAAAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
29 24 0.24
30 72 0.73
31 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (31 bp):
GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
Found at i:4941703 original size:74 final size:72
Alignment explanation
Indices: 4941528--4942713 Score: 1159
Period size: 75 Copynumber: 15.7 Consensus size: 72
4941518 CTCGGCGTGC
* * * ** * **
4941528 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCTTCGAAAAACAAAAATCGAAAATAC
1 GACCCGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTTAAAAAACATAAATTAAAAATAC
4941593 CTC-GACATGT
65 CTCAG-C--GT
* * * * * *
4941603 GCCCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAACATGAATTGAAAAATA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAACATAAATT-AAAAATA
*
4941668 CCTCGGCGT
64 CCTCAGCGT
* * * * *
4941677 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAACATAAA-TT--AA-AA
* *
4941742 ATACCTCGGCAT
61 ATACCTCAGCGT
** * * *
4941754 GGTCCAAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAACATAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTAAAAAACATAAA-TT--AA-A
* * *
4941819 AATACATCGGCAT
60 AATACCTCAGCGT
** * * *
4941832 GGTCCTAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAACATAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTAAAAAACATAAA-TT--AA-A
* *
4941897 AATACATCAGCAT
60 AATACCTCAGCGT
** * * * * *
4941910 GGTCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTGAAAAACATAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTAAAAAACATAAA-TT--AA-A
* *
4941975 AATACCTCGGCAT
60 AATACCTCAGCGT
** * * *
4941988 GGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAGACATAAATTAAAAATA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAA-ACATAAATTAAAAATA
*
4942053 CCTCAGTGT
64 CCTCAGCGT
4942062 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGACATAAATTAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTT--AAAAA-ACATAAATTAAAAA
4942127 TACCTCAGCGT
62 TACCTCAGCGT
* *
4942138 GACCCGAGGCTCAATTCACCTCTTTATTATGAGTTGATTTTTTTTAAAAAAGACATAAATTAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA---TTTTT-AAAAA-ACATAAATTAAAA
*
4942203 ATACCTAAGCGT
61 ATACCTCAGCGT
4942215 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT--AAAAA-ACATAAATTAAAAAT
*
4942280 ACCTCAGTGT
63 ACCTCAGCGT
* * **
4942290 GACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAAAAAAACCGAAATTAAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT---TAAAAAACATAAATTAAAAAT
4942355 ACCTCAGCGT
63 ACCTCAGCGT
* **
4942365 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAGACCGAAATTAAAAAT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT--TAAAAA-ACATAAATTAAAAAT
4942430 ACCTCAGCGT
63 ACCTCAGCGT
* * * *
4942440 GACCCGAGGCTTAACTCACCTCTATGTTATGAGTTGATTTTAAAAAAAAAAGACATAAATTAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT----TAAAAA-ACATAAATTAAAA
*
4942505 ACACCTCAGCGT
61 ATACCTCAGCGT
* **
4942517 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAGACCGAAATTAAAAATA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT-TAAAAA-ACATAAATTAAAAATA
4942582 CCTCAGCGT
64 CCTCAGCGT
* **
4942591 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAGACCGAAATTAAAAATA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT-TAAAAA-ACATAAATTAAAAATA
4942656 CCTCAGCGT
64 CCTCAGCGT
*
4942665 GACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATATTTAAAAAA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAA
4942714 AACAGAAAGT
Statistics
Matches: 1017, Mismatches: 73, Indels: 44
0.90 0.06 0.04
Matches are distributed among these distances:
73 13 0.01
74 234 0.23
75 261 0.26
76 83 0.08
77 193 0.19
78 233 0.23
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (72 bp):
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAACATAAATTAAAAATACC
TCAGCGT
Found at i:4941832 original size:78 final size:78
Alignment explanation
Indices: 4941587--4942330 Score: 703
Period size: 78 Copynumber: 9.7 Consensus size: 78
4941577 CAAAAATCGA
* * *
4941587 AAATACCTCGACATGTGCCCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
1 AAATACCTCGGCATG-G-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
* *
4941651 ACATGAA-TT-GAA-
64 ACATAAATTTAAAAG
* ** *
4941663 AAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAT
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
*
4941727 AGAAATTTAAAAG
66 ATAAATTTAAAAG
* *
4941740 AAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAAC
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
4941805 ATAAATTTAAAAG
66 ATAAATTTAAAAG
* * *
4941818 AAATACATCGGCATGGTCCTAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAAC
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
4941883 ATAAATTTAAAAG
66 ATAAATTTAAAAG
* * * *
4941896 AAATACATCAGCATGGTCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTGAAAAAC
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
4941961 ATAAATTTAAAAG
66 ATAAATTTAAAAG
**
4941974 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTAAAAAAGA
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA-A
4942038 CATAAA-TT--AA-
65 CATAAATTTAAAAG
* ** ** * * *
4942048 AAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTAAAAAAA
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT--GAAAA
4942112 GACATAAA-TT--AA-
64 -ACATAAATTTAAAAG
* * ** * ** * *
4942124 AAATACCTCAGCGTGACCCGAGGCTCAATTCACCTCT-TTATTATGAGTTGATTTTTTTTAAAAA
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTT-GAAA
4942188 AGACATAAA-TT--AA-
63 A-ACATAAATTTAAAAG
** * ** * * **
4942201 AAATACCTAAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAG
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-TGAAAA-
4942265 ACATAAA-TT--AA-
64 ACATAAATTTAAAAG
* ** ** ** *
4942276 AAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTT
1 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
4942331 AAAAAAAAAA
Statistics
Matches: 611, Mismatches: 46, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
73 12 0.02
74 85 0.14
75 78 0.13
76 80 0.13
77 123 0.20
78 233 0.38
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (78 bp):
AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
ATAAATTTAAAAG
Found at i:4941986 original size:234 final size:226
Alignment explanation
Indices: 4941605--4942731 Score: 873
Period size: 227 Copynumber: 5.0 Consensus size: 226
4941595 CGACATGTGC
* * * *
4941605 CCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATGAATTGAAAAATAC
1 CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAACATAAATTAAAAAATAC
* * * * * *
4941669 CTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATT
66 ATCAGCATGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTGAAAAACAGAAATT
* **
4941734 TAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTG
131 TAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTAA
* *
4941799 AAAA-ACATAAATTTAAAAGAAATACATCGGCATGG
195 AAAAGACATAAA-TT--AA-AAATACATCAGCATGA
* *
4941834 TCCTAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAACATAAATTTAAAAGAAA
1 CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAACATAAA-TT-AAA-AAA
** *
4941899 TACATCAGCATGGTCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTTGAAAAACATA
63 TACATCAGCATGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAA-TTTTTGAAAAACAGA
*
4941964 AATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
127 AATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* **
4942029 TAAAAAAGACATAAATTAAAAATACCTCAGTGTGA
192 TAAAAAAGACATAAATTAAAAATACATCAGCATGA
* *
4942064 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTAAAAAAAGACATAAATT-AAAAA
1 CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTT--GAAAA-ACATAAATTAAAAAA
* * * * ** * * *
4942127 TACCTCAGCGTGACCCGAGGCTCAATTCACCTCT-TTATTATGAGTTGATTTTTTTTAAAAA-AG
63 TACATCAGCATGACCCGAGGCTCAACTCACCTATCGCAATATGAGTT-A-ATTTTTGAAAAACAG
* * ** * ** * * *
4942190 ACA--TAAATTAAAAATACCTAAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA
126 AAATTTAAA--AGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* **
4942252 TTTTTAAAAAAAGACATAAATTAAAAATACCTCAGTGTGA
189 -TTTT-AAAAAAGACATAAATTAAAAATACATCAGCATGA
* * *** **
4942292 CCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTAAAAAAAAAACCGAAATT-AAAAAT
1 CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT--TTGAAAAACATAAATTAAAAAAT
* * * * * * * *
4942355 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTAAAAAAAAGACC
64 ACATCAGCATGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTGAAAAACAGA--
* * * ** * * * *
4942418 GAAATT--AA-AAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCTATG--TTATGAGTTGAT
127 -AATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCT-CGCAATATGAGTTGAT
* * *
4942478 TTTAAAAAAAAAAGACATAAATTAAAAACACCTCAGCGTGA
190 TTT----AAAAAAGACATAAATTAAAAATACATCAGCATGA
* *** **
4942519 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAAGACCGAAATT-AAAAATA
1 CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAA-ACATAAATTAAAAAATA
* * * * * * ** *
4942582 CCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAAGACCGAA
65 CATCAGCATGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTT-TGAAAA-ACAGAA
* * ** * * * *
4942646 A-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATATT
128 ATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TT
* * *
4942707 TAAAAAAAACAGAAAGTGAAAAATA
192 TAAAAAAGACATAAA-TTAAAAATA
4942732 TTTCTTGAAA
Statistics
Matches: 788, Mismatches: 74, Indels: 77
0.84 0.08 0.08
Matches are distributed among these distances:
223 12 0.02
224 21 0.03
225 100 0.13
226 89 0.11
227 183 0.23
228 126 0.16
229 56 0.07
230 47 0.06
231 10 0.01
232 9 0.01
233 55 0.07
234 80 0.10
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (226 bp):
CCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAACATAAATTAAAAAATAC
ATCAGCATGACCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTGAAAAACAGAAATT
TAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAA
AAAGACATAAATTAAAAATACATCAGCATGA
Found at i:4943612 original size:15 final size:14
Alignment explanation
Indices: 4943588--4943626 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
4943578 TTGATTTTTC
4943588 TTTTTCTTTTCTTTG
1 TTTTT-TTTTCTTTG
*
4943603 TTTTGTTTTTGTTTG
1 TTTT-TTTTTCTTTG
4943618 TTTTTTTTT
1 TTTTTTTTT
4943627 GTCCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 16 0.73
16 1 0.05
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:4949919 original size:16 final size:16
Alignment explanation
Indices: 4949887--4949938 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4949877 TTTTTTTGTT
* *
4949887 TTTTAAAAAAACGAAA
1 TTTTAGAAACACGAAA
*
4949903 TTTTCG-AACACGAAAA
1 TTTTAGAAACACG-AAA
4949919 TTTTAGAAACACGAAA
1 TTTTAGAAACACGAAA
4949935 TTTT
1 TTTT
4949939 TTTTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (16 bp):
TTTTAGAAACACGAAA
Found at i:4949931 original size:17 final size:17
Alignment explanation
Indices: 4949887--4949975 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
4949877 TTTTTTTGTT
* *
4949887 TTTTAAAAAAACG-AAA
1 TTTTAGAAACACGAAAA
*
4949903 TTTTCG-AACACGAAAA
1 TTTTAGAAACACGAAAA
*
4949919 TTTTAGAAACACGAAATTTT
1 TTTTAGAAACACGAAA---A
*
4949939 TTTTA-AAACACGACAA
1 TTTTAGAAACACGAAAA
* * *
4949955 TTTTTGACACACGAGAA
1 TTTTAGAAACACGAAAA
4949972 TTTT
1 TTTT
4949976 TCAAAACACA
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
15 5 0.09
16 16 0.28
17 22 0.39
19 9 0.16
20 5 0.09
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (17 bp):
TTTTAGAAACACGAAAA
Found at i:4949947 original size:19 final size:21
Alignment explanation
Indices: 4949919--4949959 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
4949909 AACACGAAAA
4949919 TTTTAGAAACACGA-AATTTT
1 TTTTAGAAACACGACAATTTT
4949939 TTTTA-AAACACGACAATTTT
1 TTTTAGAAACACGACAATTTT
4949959 T
1 T
4949960 GACACACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTAGAAACACGACAATTTT
Found at i:4949992 original size:53 final size:51
Alignment explanation
Indices: 4949885--4950000 Score: 130
Period size: 52 Copynumber: 2.3 Consensus size: 51
4949875 TTTTTTTTTG
4949885 TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
1 TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
* * * *
4949936 TTTTTTTAAAACACGACAATTTTTGACACACGAGAATTTTTCA-AAACAC--AAT
1 TTTTTTAAAAAAACGA-AATTTTCGA-ACACGA-AAATTTT-AGAAACACGAAAT
*
4949988 TTTTTAAAAAAAA
1 TTTTTTAAAAAAA
4950001 AACATGACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
51 14 0.26
52 21 0.39
53 6 0.11
54 12 0.22
55 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.33
Consensus pattern (51 bp):
TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
Found at i:4950053 original size:18 final size:18
Alignment explanation
Indices: 4950031--4950314 Score: 202
Period size: 18 Copynumber: 16.1 Consensus size: 18
4950021 ACTAGAGTCA
4950031 TTGAAAACACGGAAATTT
1 TTGAAAACACGGAAATTT
*
4950049 GTGAAAA-AC-GAAATTTT
1 TTGAAAACACGGAAA-TTT
* *
4950066 TTG-AAGCACAGAAATTT
1 TTGAAAACACGGAAATTT
*
4950083 TTAGAAAACAC-GAAAATT
1 TT-GAAAACACGGAAATTT
*
4950101 TTG-AATCACCGG-AATTT
1 TTGAAAACA-CGGAAATTT
*
4950118 TTAAAAACAC-GAAGATTT
1 TTGAAAACACGGAA-ATTT
* * *
4950136 TTG-AAGCACCGAAAATT
1 TTGAAAACACGGAAATTT
4950153 TTGAAAACAC-GAAGATTT
1 TTGAAAACACGGAA-ATTT
*
4950171 TTG-AAACACCGAAATTT
1 TTGAAAACACGGAAATTT
*
4950188 TTGAAAACACGTG-GATTT
1 TTGAAAACACG-GAAATTT
*
4950206 TTG-AAACAC-GAATTTTTT
1 TTGAAAACACGGAA--ATTT
* *
4950224 TTGAAAATACGAAAATTT
1 TTGAAAACACGGAAATTT
* * *
4950242 TTTAAAACACAGATATTT
1 TTGAAAACACGGAAATTT
*
4950260 TT-AAAACACGGGAATTT
1 TTGAAAACACGGAAATTT
**
4950277 TTG-AAACACTAAAATTT
1 TTGAAAACACGGAAATTT
4950294 TTGAAAACACGAGAAATTT
1 TTGAAAACACG-GAAATTT
4950313 TT
1 TT
4950315 TTTACATAAA
Statistics
Matches: 208, Mismatches: 34, Indels: 47
0.72 0.12 0.16
Matches are distributed among these distances:
15 1 0.00
16 11 0.05
17 85 0.41
18 90 0.43
19 19 0.09
20 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (18 bp):
TTGAAAACACGGAAATTT
Found at i:4950070 original size:35 final size:35
Alignment explanation
Indices: 4950035--4950314 Score: 241
Period size: 35 Copynumber: 8.0 Consensus size: 35
4950025 GAGTCATTGA
*
4950035 AAACACGGAAATTTGTGAAAA-ACGAA-ATTTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAGA-TTTTTG
* * *
4950069 AAGCACAGAAATTTTTAGAAAACACGAA-AATTTTG
1 AAACACGGAAATTTTT-GAAAACACGAAGATTTTTG
* *
4950104 AATCACCGG-AATTTTTAAAAACACGAAGATTTTTG
1 AAACA-CGGAAATTTTTGAAAACACGAAGATTTTTG
* * *
4950139 AAGCACCGAAAATTTTGAAAACACGAAGATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAGATTTTTG
* **
4950174 AAACACCGAAATTTTTGAAAACACGTGGATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAGATTTTTG
* * * *
4950209 AAACAC-GAATTTTTTTTGAAAATACGAAAATTTTTTA
1 AAACACGGAA--ATTTTTGAAAACACGAAGA-TTTTTG
* * *
4950246 AAACACAGATATTTTT-AAAACACG-GGAATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAG-ATTTTTG
** *
4950280 AAACACTAAAATTTTTGAAAACACGAGAAATTTTT
1 AAACACGGAAATTTTTGAAAACACGA-AGATTTTT
4950315 TTTACATAAA
Statistics
Matches: 200, Mismatches: 33, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
34 46 0.23
35 108 0.54
36 33 0.17
37 11 0.05
38 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (35 bp):
AAACACGGAAATTTTTGAAAACACGAAGATTTTTG
Found at i:4950193 original size:17 final size:17
Alignment explanation
Indices: 4950035--4950314 Score: 151
Period size: 17 Copynumber: 15.9 Consensus size: 17
4950025 GAGTCATTGA
* *
4950035 AAACACGGAAATTTGTG
1 AAACACCGAAATTTTTG
*
4950052 AAA-AACGAAATTTTTTG
1 AAACACCGAAA-TTTTTG
* *
4950069 AAGCACAGAAATTTTTAG
1 AAACACCGAAATTTTT-G
*
4950087 AAA-ACACGAAAATTTTG
1 AAACAC-CGAAATTTTTG
* *
4950104 AATCACCGGAATTTTT-
1 AAACACCGAAATTTTTG
*
4950120 AAAAACACGAAGATTTTTG
1 AAACAC-CGAA-ATTTTTG
* *
4950139 AAGCACCGAAAATTTTG
1 AAACACCGAAATTTTTG
4950156 AAA-ACACGAAGATTTTTG
1 AAACAC-CGAA-ATTTTTG
4950174 AAACACCGAAATTTTTG
1 AAACACCGAAATTTTTG
**
4950191 AAA-ACACGTGGATTTTTG
1 AAACAC-CG-AAATTTTTG
*
4950209 AAACA-CGAATTTTTTTTG
1 AAACACCGAA--ATTTTTG
* *
4950227 AAA-ATACGAAAATTTTTTA
1 AAACA-CCG-AAA-TTTTTG
* * *
4950246 AAACACAGATATTTTTA
1 AAACACCGAAATTTTTG
* *
4950263 AAACACGGGAATTTTTG
1 AAACACCGAAATTTTTG
**
4950280 AAACACTAAAATTTTTG
1 AAACACCGAAATTTTTG
*
4950297 AAAACACGAGAAATTTTT
1 -AAACAC-CGAAATTTTT
4950315 TTTACATAAA
Statistics
Matches: 201, Mismatches: 39, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
16 13 0.06
17 91 0.45
18 68 0.34
19 26 0.13
20 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
AAACACCGAAATTTTTG
Found at i:4950473 original size:21 final size:20
Alignment explanation
Indices: 4950432--4950475 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4950422 CGCTGCCTTA
* *
4950432 TTTTTGAAAACACGAATATT
1 TTTTTGAAAACAAGAAAATT
4950452 TTTTTGAAACACAAGAAAATT
1 TTTTTGAAA-ACAAGAAAATT
4950473 TTT
1 TTT
4950476 AAAGACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTTGAAAACAAGAAAATT
Found at i:4950498 original size:19 final size:20
Alignment explanation
Indices: 4950460--4950499 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4950450 TTTTTTTGAA
* *
4950460 ACACAAGAAAATTTTTAAAG
1 ACACAAGAAAAATTTGAAAG
4950480 ACACAA-AAAAATTTGAAAG
1 ACACAAGAAAAATTTGAAAG
4950499 A
1 A
4950500 TAGAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (20 bp):
ACACAAGAAAAATTTGAAAG
Found at i:4950679 original size:6 final size:6
Alignment explanation
Indices: 4950659--4950708 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
4950649 AAAAGTATTC
* *
4950659 AAAA-T AAAA-T AAAATT AAAATT -GAATT AAATTT AAAATTT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT
4950705 AAAA
1 AAAA
4950709 ATATAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
5 13 0.34
6 19 0.50
7 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:4950757 original size:26 final size:25
Alignment explanation
Indices: 4950713--4950769 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
4950703 TTAAAAATAT
* *
4950713 AAATACAAAAATATAAAAATGCACA
1 AAATACAAAAATATAAAAATGAAAA
* *
4950738 AAATACTAATAATATTAAAATGAAAA
1 AAATAC-AAAAATATAAAAATGAAAA
4950764 AAATAC
1 AAATAC
4950770 GAGCATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATACAAAAATATAAAAATGAAAA
Found at i:4953703 original size:30 final size:28
Alignment explanation
Indices: 4953669--4953809 Score: 149
Period size: 30 Copynumber: 4.8 Consensus size: 28
4953659 CATAATTTTG
*
4953669 AGAAAGTTTAAGGGTTCAAATGTAATTT
1 AGAAAGTTTAAGGGTTAAAATGTAATTT
* *
4953697 CAAGAAAGTTTAGGGGTCAAAATGTAATTT
1 --AGAAAGTTTAAGGGTTAAAATGTAATTT
* *
4953727 AGAAAAGTTT-AGGTGTTGAATTGTAATTTT
1 AG-AAAGTTTAAGG-GTTAAAATGTAA-TTT
*
4953757 GAGAAAGTTTAAGGGTTAAAATGAAATTTT
1 -AGAAAGTTTAAGGGTTAAAATGTAA-TTT
4953787 AGAAAAGTTTAAGGGTTAAAATG
1 AG-AAAGTTTAAGGGTTAAAATG
4953810 CAAAAAAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
28 4 0.04
29 18 0.19
30 68 0.72
31 5 0.05
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.34
Consensus pattern (28 bp):
AGAAAGTTTAAGGGTTAAAATGTAATTT
Found at i:4953752 original size:59 final size:58
Alignment explanation
Indices: 4953661--4953809 Score: 172
Period size: 59 Copynumber: 2.5 Consensus size: 58
4953651 GGCCGAATCA
* *
4953661 TAATTTTGAGAAAGTTTAAGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAATG
1 TAATTTAGA-AAAGTTT-AGGGTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAATG
* * ** *
4953721 TAATTTAGAAAAGTTTAGGTGTTGAATTGTAATTTTGAGAAAGTTTAAGGGTTAAAATG
1 TAATTTAGAAAAGTTTAGG-GTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAATG
* *
4953780 AAATTTTAGAAAAGTTTAAGGGTTAAAATG
1 TAA-TTTAGAAAAGTTT-AGGGTTCAAATG
4953810 CAAAAAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
58 3 0.04
59 42 0.55
60 28 0.37
61 3 0.04
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (58 bp):
TAATTTAGAAAAGTTTAGGGTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAATG
Found at i:4954648 original size:23 final size:25
Alignment explanation
Indices: 4954603--4954654 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
4954593 TTAATAAATT
*
4954603 AAAACATTATATTGAAAATAATGAA
1 AAAACATTAGATTGAAAATAATGAA
*
4954628 AAAATATTAGATT-AAAA-AATGAA
1 AAAACATTAGATTGAAAATAATGAA
4954651 AAAA
1 AAAA
4954655 AATATTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 11 0.44
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (25 bp):
AAAACATTAGATTGAAAATAATGAA
Found at i:4958252 original size:31 final size:33
Alignment explanation
Indices: 4958181--4958259 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 33
4958171 ATATATGAAT
*
4958181 TATAAATAAGTTATAAAATATGTATGGGTATAGGTA
1 TATATATAA-TTATAAAATATGTAT-GGTATA-GTA
4958217 TATATATATATTATAAAA-ATGTAT-GTAT-GTA
1 TATATATA-ATTATAAAATATGTATGGTATAGTA
4958248 TATATATAATTA
1 TATATATAATTA
4958260 AATCCAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 4 0.10
31 11 0.27
33 4 0.10
35 6 0.15
36 15 0.37
37 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.42
Consensus pattern (33 bp):
TATATATAATTATAAAATATGTATGGTATAGTA
Found at i:4960328 original size:24 final size:26
Alignment explanation
Indices: 4960268--4960339 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 26
4960258 ATGACTCTTT
* *
4960268 GGAGCTTCTCGATTAAAGGCTCTTCCA
1 GGAGCTTCCCG-TTAATGGCTCTTCCA
*
4960295 TGAGCTTCCCGTTAATGGCTC-TCC-
1 GGAGCTTCCCGTTAATGGCTCTTCCA
* *
4960319 GGAGCTTCCCGATATTGGCTC
1 GGAGCTTCCCGTTAATGGCTC
4960340 GCTTGAACCT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 18 0.46
25 3 0.08
26 9 0.23
27 9 0.23
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.31
Consensus pattern (26 bp):
GGAGCTTCCCGTTAATGGCTCTTCCA
Found at i:4960387 original size:25 final size:24
Alignment explanation
Indices: 4960359--4960422 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
4960349 TTCTCAATAT
**
4960359 TGGCTCGTATGAGCTTCCGGTTATA
1 TGGCTCGTATGAGCTTCCCATT-TA
* * *
4960384 TGGCTCGAAAGAGTTTCCCATTTA
1 TGGCTCGTATGAGCTTCCCATTTA
4960408 TGTGCTCGTATGAGC
1 TG-GCTCGTATGAGC
4960423 ATTTCCGAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (24 bp):
TGGCTCGTATGAGCTTCCCATTTA
Found at i:4963416 original size:20 final size:21
Alignment explanation
Indices: 4963388--4963440 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
4963378 CCCGAACCCT
*
4963388 AAACCCTAAACCATGAAT-CA
1 AAACACTAAACCATGAATACA
** *
4963408 AAACACTAAACTTTGAATACT
1 AAACACTAAACCATGAATACA
4963429 AAACACTAAACC
1 AAACACTAAACC
4963441 TTAAATCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.51, C:0.26, G:0.04, T:0.19
Consensus pattern (21 bp):
AAACACTAAACCATGAATACA
Done.