Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 137 of 221
Found at i:42190351 original size:28 final size:28
Alignment explanation
Indices: 42190320--42190385 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
42190310 TCTGGGTCGA
42190320 GCCCGACCCAATTTTTTTACTTGG-CTCG
1 GCCCGACCCAATTTTTTTACTTGGCCT-G
*
42190348 GCCCAACCCAATTTTTTTACTTGGCCTG
1 GCCCGACCCAATTTTTTTACTTGGCCTG
42190376 GCCCGACCCA
1 GCCCGACCCA
42190386 TGGACAACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.17, C:0.36, G:0.17, T:0.30
Consensus pattern (28 bp):
GCCCGACCCAATTTTTTTACTTGGCCTG
Found at i:42197976 original size:39 final size:40
Alignment explanation
Indices: 42197888--42197976 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 40
42197878 GCTTTTTAAA
* **
42197888 CGTTTTTTTTTTGTTTTCTTCTTTTTCTTCTTTCCATTTT
1 CGTTTTTTTTTTGTTTTCTTCGTTTTCCCCTTTCCATTTT
42197928 C-TTTATTTTTTCT-TTTTCTT-GTTTTCCCCTTT-CATTTT
1 CGTTT-TTTTTT-TGTTTTCTTCGTTTTCCCCTTTCCATTTT
42197966 CAGTTTTTTTT
1 C-GTTTTTTTT
42197977 ACATAGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
38 7 0.17
39 17 0.40
40 17 0.40
41 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (40 bp):
CGTTTTTTTTTTGTTTTCTTCGTTTTCCCCTTTCCATTTT
Found at i:42200106 original size:41 final size:41
Alignment explanation
Indices: 42199994--42200113 Score: 145
Period size: 41 Copynumber: 2.9 Consensus size: 41
42199984 ACCGGCTTTT
* *
42199994 AGCCTGCTAGACTTATAGT-TCGAA-ACATATCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCT-GAATA-ATTTCACCGGCATCA
* *
42200035 AGCCTGCTAGACGTATATTCTGAATAATTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCTGAATAATTTCACCGGCATCA
* * *
42200076 AGCCTGCTAGACTTAAAGTCTGAATTATTTCACTGGCA
1 AGCCTGCTAGACTTATAGTCTGAATAATTTCACCGGCA
42200114 ATAAATCCGA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 66 0.97
42 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAATAATTTCACCGGCATCA
Found at i:42205650 original size:15 final size:15
Alignment explanation
Indices: 42205566--42205657 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 15
42205556 TCTTTTTTAA
*
42205566 TTTTC-TTTTCTTCG
1 TTTTCTTTTTCTTCT
*
42205580 TTTTCTTTTTCTCACTT
1 TTTTCTTTTTCT-TC-T
* *
42205597 TTTTGATTTCTTTTTCT
1 TTTT-CTTT-TTCTTCT
* *
42205614 TTTTCTTCTTCACTTTCC
1 TTTTCTT-TT-TC-TTCT
42205632 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
42205647 TTTTCATTTTT
1 TTTTC-TTTTT
42205658 ATTACAATGT
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
14 5 0.09
15 14 0.24
16 10 0.17
17 12 0.21
18 14 0.24
19 3 0.05
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:42208250 original size:24 final size:24
Alignment explanation
Indices: 42208223--42208297 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
42208213 ATTTGATATG
*
42208223 TTCTGTATGTGAAACTGAAATTGC
1 TTCTGTATATGAAACTGAAATTGC
* * *
42208247 TTCTGCATATGTAACTG-ATTTG-
1 TTCTGTATATGAAACTGAAATTGC
*
42208269 TTCTGTATCT-AAACT-AATATTGC
1 TTCTGTATATGAAACTGAA-ATTGC
42208292 TTCTGT
1 TTCTGT
42208298 TAGCTAACCG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
21 5 0.12
22 11 0.28
23 10 0.25
24 14 0.35
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (24 bp):
TTCTGTATATGAAACTGAAATTGC
Found at i:42210471 original size:87 final size:88
Alignment explanation
Indices: 42210333--42210528 Score: 274
Period size: 87 Copynumber: 2.3 Consensus size: 88
42210323 CCCTCAAATT
* * *
42210333 AAAAAA-AAATTAAGCCCCT-CTTTTTTTTGCACTCAATTGAGTAGTTTAACTTTCAAAATGCAT
1 AAAAAAGAAATTAAGCCCCTGCTTTTTTTTGCACTCAACTGAGTACTTGAACTTTCAAAATGCAT
*
42210396 AAAAAAAACCCTCAAACTTCTTC
66 AAAAAAAACCCTCAAAATTCTTC
*
42210419 AAAAAAAGAAATTAAG-CCCTGCTTTTTTTT-CACTCAACTGGGTACTTGAACTTTCAAAATGCA
1 -AAAAAAGAAATTAAGCCCCTGCTTTTTTTTGCACTCAACTGAGTACTTGAACTTTCAAAATGCA
* *
42210482 TAAAAAAGACCCTCAAAATTTTTC
65 TAAAAAAAACCCTCAAAATTCTTC
* *
42210506 AAAACAGCAATTAAGCCCCTGCT
1 AAAAAAGAAATTAAGCCCCTGCT
42210529 CTTATTAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
86 13 0.13
87 67 0.69
88 17 0.18
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (88 bp):
AAAAAAGAAATTAAGCCCCTGCTTTTTTTTGCACTCAACTGAGTACTTGAACTTTCAAAATGCAT
AAAAAAAACCCTCAAAATTCTTC
Found at i:42210553 original size:7 final size:7
Alignment explanation
Indices: 42210531--42210584 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
42210521 CCCCTGCTCT
42210531 TATTAAA
1 TATTAAA
*
42210538 AATTTAAA
1 TA-TTAAA
42210546 TATTAAA
1 TATTAAA
42210553 TATTAAA
1 TATTAAA
42210560 TATTATAA
1 TATTA-AA
42210568 -A--AAA
1 TATTAAA
42210572 TATTAAA
1 TATTAAA
*
42210579 TTTTAA
1 TATTAA
42210585 TAGAAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 27 0.69
8 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATTAAA
Found at i:42210615 original size:27 final size:28
Alignment explanation
Indices: 42210563--42210618 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
42210553 TATTAAATAT
*
42210563 TATAAAAAATATTAAATTTTAATAGAAA
1 TATAAAAAATATTAAAATTTAATAGAAA
* *
42210591 TATAACAAAT-TTAAAATTTATTAGAAA
1 TATAAAAAATATTAAAATTTAATAGAAA
42210618 T
1 T
42210619 TAGAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (28 bp):
TATAAAAAATATTAAAATTTAATAGAAA
Found at i:42210937 original size:20 final size:19
Alignment explanation
Indices: 42210887--42210938 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
42210877 ATTTTATGAA
42210887 TTTATAAAATTTTATATAT
1 TTTATAAAATTTTATATAT
* * *
42210906 TTTTTTATATTTCTATATAT
1 TTTATAAAATTT-TATATAT
42210926 TTTATAAAATTTT
1 TTTATAAAATTTT
42210939 TACGATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATAAAATTTTATATAT
Found at i:42210938 original size:30 final size:30
Alignment explanation
Indices: 42210849--42210939 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
42210839 TTTTACGAAA
* * * * *
42210849 TTTATATTTCTTTACATTTTGTATAATTAT
1 TTTATATTTCTATAAATTTTATAAAATTTT
* *
42210879 TTTATGAATT-TATAAAATTTTAT-ATATTTT
1 TTTAT-ATTTCTAT-AAATTTTATAAAATTTT
*
42210909 TTTATATTTCTATATATTTTATAAAATTTT
1 TTTATATTTCTATAAATTTTATAAAATTTT
42210939 T
1 T
42210940 ACGATTTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
29 11 0.23
30 26 0.55
31 10 0.21
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTATATTTCTATAAATTTTATAAAATTTT
Found at i:42210947 original size:39 final size:38
Alignment explanation
Indices: 42210887--42210990 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 38
42210877 ATTTTATGAA
* * * *
42210887 TTTATAAAATTTTATA-TATTTTTTTATATTTCTATATAT
1 TTTATAAAATTTT-TACGATTTTTATAAATTTCTACA-AT
*
42210926 TTTATAAAATTTTTACGATTTTTATAAATTTGTACAAT
1 TTTATAAAATTTTTACGATTTTTATAAATTTCTACAAT
*
42210964 TTTATATATATTATTTTACGATTTTTA
1 TTTATA-A-AAT-TTTTACGATTTTTA
42210991 ATAATTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 10 0.18
39 29 0.53
40 2 0.04
41 14 0.25
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (38 bp):
TTTATAAAATTTTTACGATTTTTATAAATTTCTACAAT
Found at i:42210948 original size:20 final size:20
Alignment explanation
Indices: 42210925--42210999 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
42210915 TTTCTATATA
42210925 TTTTATAAAATTTTTACGAT
1 TTTTATAAAATTTTTACGAT
* *
42210945 TTTTAT-AAATTTGTACAAT
1 TTTTATAAAATTTTTACGAT
* *
42210964 TTTATATATATTATTTTACGAT
1 TTT-TATAAAAT-TTTTACGAT
*
42210986 TTTTA-ATAATTTTT
1 TTTTATAAAATTTTT
42211000 TAATATCTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 18 0.40
20 13 0.29
21 4 0.09
22 10 0.22
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTATAAAATTTTTACGAT
Found at i:42211166 original size:85 final size:84
Alignment explanation
Indices: 42211077--42211268 Score: 235
Period size: 86 Copynumber: 2.3 Consensus size: 84
42211067 ATAAAAGCAA
42211077 GGGCTTAATTGGTTTTTTTTTA-GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
1 GGGCTTAATTGGTTTTTTTTTAGGTTTGAGGG-CTTTTT-ATGCATTTTGAAAGTTCAAGTACCC
* **
42211141 AATTGAGTGCAAAAAAAGTAG
64 AAATGAGTGCAAAAAAAACAG
* ** * * *
42211162 GGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGCTTTTTATGCATTTTTAAAGTTTAAGTACCG
1 GGGCTTAATTGGTTTTTTT--TTAGGTTTGAGGGCTTTTTATGCATTTTGAAAGTTCAAGTACCC
*
42211227 AAATGAGTGTAAAAAAAACAG
64 AAATGAGTGCAAAAAAAACAG
*
42211248 AGGCTTAATT-GTTTTTTTTTA
1 GGGCTTAATTGGTTTTTTTTTA
42211269 AAAAGAATTT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
83 1 0.01
85 25 0.28
86 48 0.53
87 7 0.08
88 9 0.10
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (84 bp):
GGGCTTAATTGGTTTTTTTTTAGGTTTGAGGGCTTTTTATGCATTTTGAAAGTTCAAGTACCCAA
ATGAGTGCAAAAAAAACAG
Found at i:42211223 original size:86 final size:88
Alignment explanation
Indices: 42211099--42211271 Score: 242
Period size: 86 Copynumber: 2.0 Consensus size: 88
42211089 TTTTTTTTTA
* ** *
42211099 GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGTAGGG
1 GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAACAGAG
42211164 GCTTAATTGCTTTTTTTGAAAAG
66 GCTTAATTGCTTTTTTTGAAAAG
* * * *
42211187 GTTTGAGGG-CTTTTT-ATGCATTTTTAAAGTTTAAGTACCGAAATGAGTGTAAAAAAAACAGAG
1 GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAACAGAG
* *
42211250 GCTTAATTGTTTTTTTTTAAAA
66 GCTTAATTGCTTTTTTTGAAAA
42211272 AGAATTTGAG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
86 60 0.80
87 6 0.08
88 9 0.12
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (88 bp):
GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAACAGAG
GCTTAATTGCTTTTTTTGAAAAG
Found at i:42214948 original size:20 final size:21
Alignment explanation
Indices: 42214915--42214972 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
42214905 TACAAATCAA
*
42214915 TAAAAGTT-ATAAAAATTA-T
1 TAAAATTTAATAAAAATTATT
* *
42214934 TAAACTTTAATAAAAAATATT
1 TAAAATTTAATAAAAATTATT
*
42214955 TAAAATTTACTAAAAATT
1 TAAAATTTAATAAAAATT
42214973 GAAAAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 6 0.19
20 9 0.29
21 16 0.52
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTTAATAAAAATTATT
Found at i:42215351 original size:22 final size:22
Alignment explanation
Indices: 42215321--42215364 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42215311 TAATAAAAAA
**
42215321 TAAATATTTCTTATATTTTTTAT
1 TAAATATTTAATA-ATTTTTTAT
42215344 TAAA-ATTTAATAATTTTTTAT
1 TAAATATTTAATAATTTTTTAT
42215365 AACTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TAAATATTTAATAATTTTTTAT
Found at i:42215365 original size:30 final size:30
Alignment explanation
Indices: 42215290--42215376 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
42215280 AAAAATTTTT
* * *
42215290 ATAATATTTTTTTCTAATTTTTAATAAAAA
1 ATAATAATTTTTTATAATTTTTATTAAAAA
* * *
42215320 ATAA-ATATTTCTTATATTTTTTATTAAAAT
1 ATAATA-ATTTTTTATAATTTTTATTAAAAA
*
42215350 TTAATAATTTTTTATAACTTTTTATTA
1 ATAATAATTTTTTATAA-TTTTTATTA
42215377 TTTTTTGCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
29 1 0.02
30 34 0.76
31 10 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
ATAATAATTTTTTATAATTTTTATTAAAAA
Found at i:42219463 original size:25 final size:26
Alignment explanation
Indices: 42219403--42219487 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
42219393 AATTTTCTCG
* *
42219403 AAATTTTA-CAGGAGGCAAAATCGCCA
1 AAATTTTACCAGGA-GTAAAATAGCCA
42219429 AAATTTTACCAGGAGTAAAATAGCC-
1 AAATTTTACCAGGAGTAAAATAGCCA
* *
42219454 AAATTTTACCAAGG-GTAAAATTGTCA
1 AAATTTTACC-AGGAGTAAAATAGCCA
42219480 AAATTTTA
1 AAATTTTA
42219488 TTGGGGTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
25 19 0.37
26 28 0.54
27 5 0.10
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (26 bp):
AAATTTTACCAGGAGTAAAATAGCCA
Found at i:42222426 original size:16 final size:15
Alignment explanation
Indices: 42222384--42222426 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
42222374 GGACGAATAC
*
42222384 ATTTCTCG-ATGTCG
1 ATTTCTCGAATGTTG
42222398 ATTTCTC-AATGTTG
1 ATTTCTCGAATGTTG
42222412 ATTTTCTCGAATGTT
1 A-TTTCTCGAATGTT
42222427 TACAGGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 6 0.24
16 6 0.24
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (15 bp):
ATTTCTCGAATGTTG
Found at i:42226262 original size:18 final size:18
Alignment explanation
Indices: 42226221--42226262 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42226211 TTCATGATTC
42226221 ATAA-TTTTTAATTTTTA
1 ATAATTTTTTAATTTTTA
*
42226238 ATTATTTTTTCAATTTTT-
1 ATAATTTTTT-AATTTTTA
42226256 ATAATTT
1 ATAATTT
42226263 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.52
19 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATAATTTTTTAATTTTTA
Found at i:42226330 original size:29 final size:30
Alignment explanation
Indices: 42226262--42226330 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
42226252 TTTTATAATT
*
42226262 TATA-TTTTTTTCATTTTGTAATAATTTTA
1 TATATTTTTTTTCATCTTGTAATAATTTTA
42226291 -ATAATTCTTTTTTCA-CTT-TAATAAGTTTTA
1 TAT-ATT-TTTTTTCATCTTGTAATAA-TTTTA
42226321 TATATTTTTT
1 TATATTTTTT
42226331 ATGATTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
28 2 0.06
29 11 0.32
30 11 0.32
31 10 0.29
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (30 bp):
TATATTTTTTTTCATCTTGTAATAATTTTA
Found at i:42228003 original size:101 final size:102
Alignment explanation
Indices: 42227877--42228061 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
42227867 AAAGTGATGG
* * *
42227877 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGAATGATAATGGTCACATGTGTAGT
42227940 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
*
42227978 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
42228043 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
42228062 TGAACCGAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 7 0.09
101 37 0.47
102 34 0.44
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:42228008 original size:51 final size:51
Alignment explanation
Indices: 42227873--42228068 Score: 236
Period size: 51 Copynumber: 3.9 Consensus size: 51
42227863 AGTGAAAGTG
* * *
42227873 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* *
42227922 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * * * * * *
42227973 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
*
42228025 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
42228069 AACATCATTG
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.33
51 79 0.64
52 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
Found at i:42228063 original size:26 final size:26
Alignment explanation
Indices: 42227983--42228063 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
42227973 TTCGATCACG
42227983 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
42228009 CGTGTA-T-CGAATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
42228034 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
42228060 TGTG
1 TGTG
42228064 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:42228101 original size:102 final size:101
Alignment explanation
Indices: 42227885--42228072 Score: 261
Period size: 102 Copynumber: 1.9 Consensus size: 101
42227875 GGTCACGTGT
* * *
42227885 GTAGTACTATGTGCAGGCTACTATGTGTACTGGAATGATAGGTCGCATGTGTAGTACTATGTGCA
1 GTAGTACTATGTGCAGGCTACTACGTGTACTCGAATGATAGGTCACATGTGTAGTACTATGTGCA
* * * **
42227950 GGCTACTATGCGTACCGGATAGTTTCGATCACGTGT
66 GGCTACTATGCGAACCGAACAGTTTCGATCACGTAA
*
42227986 GTAGTACTATGTGCAGGCTACTACGTGTA-TCGAATGGTAATGGTCACATGTGTAGTACTATGTG
1 GTAGTACTATGTGCAGGCTACTACGTGTACTCGAATGAT-A-GGTCACATGTGTAGTACTATGTG
*
42228050 CAGGCTACTATGTGAACCGAACA
64 CAGGCTACTATGCGAACCGAACA
42228073 TCATTGATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 7 0.09
101 29 0.38
102 41 0.53
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (101 bp):
GTAGTACTATGTGCAGGCTACTACGTGTACTCGAATGATAGGTCACATGTGTAGTACTATGTGCA
GGCTACTATGCGAACCGAACAGTTTCGATCACGTAA
Found at i:42228120 original size:44 final size:45
Alignment explanation
Indices: 42228065--42228158 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
42228055 TACTATGTGA
* *
42228065 ACCGAACATCATTGATTAGTAA-GTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
42228109 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
42228154 ACCGA
1 ACCGA
42228159 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 20 0.44
45 25 0.56
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:42230381 original size:30 final size:28
Alignment explanation
Indices: 42230322--42230396 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 28
42230312 TTTTAAAATT
42230322 TTATAAAA-ATTCAAAAATAAATAAAAA
1 TTATAAAATATTCAAAAATAAATAAAAA
42230349 TTATAAAATATTCCAAATATATAAAT-AAAA
1 TTATAAAATATT-CAAA-A-ATAAATAAAAA
*
42230379 TTATAAAATATTAAAAAA
1 TTATAAAATATTCAAAAA
42230397 ATATTACTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 9 0.21
28 4 0.09
29 7 0.16
30 17 0.40
31 6 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
TTATAAAATATTCAAAAATAAATAAAAA
Found at i:42230402 original size:21 final size:21
Alignment explanation
Indices: 42230363--42230402 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42230353 AAAATATTCC
*
42230363 AAATATATAAATAAAATTATA
1 AAATATATAAAAAAAATTATA
42230384 AAATAT-TAAAAAAATATTA
1 AAATATATAAAAAAA-ATTA
42230403 CTAATCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATATAAAAAAAATTATA
Found at i:42240868 original size:12 final size:12
Alignment explanation
Indices: 42240834--42240888 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
42240824 TATCTAGAAA
*
42240834 TAATA-TTATTT
1 TAATATTTAATT
42240845 TAATAGTTTAATAT
1 TAATA-TTTAAT-T
42240859 TAA-ATTTAATT
1 TAATATTTAATT
42240870 TAATATTT-ATCT
1 TAATATTTAAT-T
42240882 TAATATT
1 TAATATT
42240889 ATTTTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 11 0.29
12 18 0.47
13 5 0.13
14 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:42240873 original size:17 final size:17
Alignment explanation
Indices: 42240851--42240944 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 17
42240841 ATTTTAATAG
42240851 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
*
42240868 TTTAATATT-TATCTTAA
1 TTTAATATTAAAT-TTAA
*
42240885 TATT-ATTTTATTAATTTAA
1 T-TTAATATTA--AATTTAA
42240904 --TAATATTAAAGTGATT-A
1 TTTAATATTAAA-T--TTAA
*
42240921 TCTTAATATTTAATTTAA
1 T-TTAATATTAAATTTAA
42240939 TTTAAT
1 TTTAAT
42240945 GATAAGGTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 26
0.66 0.06 0.29
Matches are distributed among these distances:
15 2 0.03
16 4 0.07
17 31 0.53
18 6 0.10
19 5 0.08
20 11 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:42250161 original size:17 final size:17
Alignment explanation
Indices: 42250139--42250176 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42250129 TATTATTTAT
42250139 TTAATTAATTGAATTAA
1 TTAATTAATTGAATTAA
* *
42250156 TTAATTAATTTACTTAA
1 TTAATTAATTGAATTAA
42250173 TTAA
1 TTAA
42250177 ATTATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATTAATTGAATTAA
Found at i:42259427 original size:43 final size:43
Alignment explanation
Indices: 42259313--42259432 Score: 154
Period size: 42 Copynumber: 2.8 Consensus size: 43
42259303 CATAGGATTC
* *
42259313 CGATATGTGATTACGTGTAAGACCATGCCTGGGACATCGGCGT
1 CGATATATGATTACGTGTAAGACCATGTCTGGGACATCGGCGT
* *
42259356 CG-TATATGATTTCGTGTAAGACCCTGTCTGGGACAGT-GGCGT
1 CGATATATGATTACGTGTAAGACCATGTCTGGGACA-TCGGCGT
* * *
42259398 CGATATTTGATTACATGTAAGATCATGTCTGGGAC
1 CGATATATGATTACGTGTAAGACCATGTCTGGGAC
42259433 GTTGGCATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 36 0.55
43 30 0.45
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
CGATATATGATTACGTGTAAGACCATGTCTGGGACATCGGCGT
Found at i:42262984 original size:33 final size:33
Alignment explanation
Indices: 42262942--42263074 Score: 130
Period size: 31 Copynumber: 4.1 Consensus size: 33
42262932 AAAAATTAGA
*
42262942 TTATATATCATTAAATTAAATTATTTAAATATT
1 TTATTTATCATTAAATTAAATTATTTAAATATT
* * *
42262975 TTATGTATCATTATATTGAATTATTTAAATA--
1 TTATTTATCATTAAATTAAATTATTTAAATATT
* *
42263006 TAATTTATCATTATATTAAATTATTT-AA-ATT
1 TTATTTATCATTAAATTAAATTATTTAAATATT
* * ** *
42263037 TTATTTATTATTATATTTACTTTTTTTAAATATT
1 TTATTTATCATTA-AATTAAATTATTTAAATATT
42263071 TTAT
1 TTAT
42263075 ATGTCATAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.01
30 2 0.02
31 34 0.41
32 8 0.10
33 30 0.37
34 7 0.09
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (33 bp):
TTATTTATCATTAAATTAAATTATTTAAATATT
Found at i:42263018 original size:31 final size:31
Alignment explanation
Indices: 42262941--42263053 Score: 145
Period size: 31 Copynumber: 3.6 Consensus size: 31
42262931 AAAAAATTAG
* *
42262941 ATTATATATCATTAAATTAAATTATTTAAAT
1 ATTATTTATCATTATATTAAATTATTTAAAT
* *
42262972 ATTTTATGTATCATTATATTGAATTATTTAAAT
1 A--TTATTTATCATTATATTAAATTATTTAAAT
*
42263005 ATAATTTATCATTATATTAAATTATTTAAAT
1 ATTATTTATCATTATATTAAATTATTTAAAT
* *
42263036 TTTATTTATTATTATATT
1 ATTATTTATCATTATATT
42263054 TACTTTTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
31 43 0.61
33 28 0.39
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTATTTATCATTATATTAAATTATTTAAAT
Found at i:42264446 original size:39 final size:38
Alignment explanation
Indices: 42264360--42264446 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 38
42264350 TATTTAATAC
*
42264360 AATAAAATATTTATTATATTTATCAGTGTTTTTTAATAT
1 AATAAAATATTCATTATATTTATCAGTGTTTTTT-ATAT
*
42264399 AATAAAATATTCATTATATTTATGGTAGTGTTTTTT-T-T
1 AATAAAATATTCATTATATTTAT--CAGTGTTTTTTATAT
42264437 AATATAAATA
1 AATA-AAATA
42264447 CTTTTTAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
38 5 0.12
39 28 0.65
41 10 0.23
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (38 bp):
AATAAAATATTCATTATATTTATCAGTGTTTTTTATAT
Found at i:42273942 original size:20 final size:20
Alignment explanation
Indices: 42273899--42273940 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
42273889 TAAAGAAAGT
42273899 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAGTAATG
42273919 AAATGCAAAT-GAAAGTAA-G
1 AAATGC-AATGGAAAGTAATG
42273938 AAA
1 AAA
42273941 ATTTGGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGCAATGGAAAGTAATG
Found at i:42274419 original size:15 final size:16
Alignment explanation
Indices: 42274399--42274428 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42274389 TGGTGCCTTA
42274399 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
42274414 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
42274429 AGCATGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:42280600 original size:49 final size:49
Alignment explanation
Indices: 42280547--42280706 Score: 146
Period size: 49 Copynumber: 3.3 Consensus size: 49
42280537 ATGCATGGTT
* * *
42280547 TAATTAAAATGCAAACTAAATAAACAAATGAGCTACATAATGCATGACA
1 TAATTAAAATGCAAACTTAATAAACATATGAGATACATAATGCATGACA
* * * * * *
42280596 TAATTTAATATGC-AACTTAATTAACATAGGAGTTACTTAATACATGACA
1 TAA-TTAAAATGCAAACTTAATAAACATATGAGATACATAATGCATGACA
** * * *
42280645 TAATTAAAACACAAACTTTATGAACATATGAGATGCATTAATGCATGA-A
1 TAATTAAAATGCAAACTTAATAAACATATGAGATACA-TAATGCATGACA
42280694 TTAATT-AAATGCA
1 -TAATTAAAATGCA
42280707 GAAAACATAA
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
48 6 0.07
49 59 0.68
50 22 0.25
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (49 bp):
TAATTAAAATGCAAACTTAATAAACATATGAGATACATAATGCATGACA
Found at i:42280750 original size:32 final size:31
Alignment explanation
Indices: 42280695--42280774 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 31
42280685 ATGCATGAAT
* *
42280695 TAATT-AAATGCAGAAAACATAATGTAAATCA
1 TAATTAAAATGCA-AACACATAATGCAAATCA
*
42280726 TAATTAAAGATGCAAACACATAATGCAAGTCA
1 TAATTAAA-ATGCAAACACATAATGCAAATCA
42280758 TAATTAAATATGCAAAC
1 TAATTAAA-ATGCAAAC
42280775 TTATTAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.12
32 33 0.77
33 5 0.12
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (31 bp):
TAATTAAAATGCAAACACATAATGCAAATCA
Found at i:42284925 original size:44 final size:44
Alignment explanation
Indices: 42284876--42285203 Score: 140
Period size: 44 Copynumber: 7.5 Consensus size: 44
42284866 GATCTACTCT
* *
42284876 CTGCAACTTTAGAGAGATAAGATCCA-AGGTTTTAATCTGCTCCA
1 CTGCAACTTTAGGGAGATAAGAT-CATAGGTTTTAATCTGCCCCA
* * * * *
42284920 CTGCAACCTCAGGGAGATAGGATTATCGGTTTTAATCTGCCCCA
1 CTGCAACTTTAGGGAGATAAGATCATAGGTTTTAATCTGCCCCA
* * * * *
42284964 CTGCAACTTCT-GGGAGATAAGAT--TTGCCATCTTCAGTCTGCCTCA
1 CTGCAACTT-TAGGGAGATAAGATCATAG--GT-TTTAATCTGCCCCA
* * * *
42285009 CTGCAACTTTA-GGAGGATAAGA-C-TTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTTAGGGA-GATAAGATCATAGGTT--TTAATCTGCCCCA
* * * *** * *
42285053 CTGTAACTTCAGGGAGATAAGA-C-TA-GATGCGATCTG-CTCT
1 CTGCAACTTTAGGGAGATAAGATCATAGGTTTTAATCTGCCCCA
* * * * *
42285093 CTGCAACTTCAGGGACATAAGATC-TAAGGTTTTAATCCGCTCTA
1 CTGCAACTTTAGGGAGATAAGATCAT-AGGTTTTAATCTGCCCCA
* * * * * * * *
42285137 TTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCG
1 CTGCAACTTTAGGGAGATAAGATCATAGGTTTTAATCTGCCCCA
* *
42285181 CTACAACTTCAGGGAGATAAGAT
1 CTGCAACTTTAGGGAGATAAGAT
42285204 TTGCCATCTT
Statistics
Matches: 214, Mismatches: 54, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
40 21 0.10
41 6 0.03
42 4 0.02
43 9 0.04
44 140 0.65
45 34 0.16
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
CTGCAACTTTAGGGAGATAAGATCATAGGTTTTAATCTGCCCCA
Found at i:42285173 original size:217 final size:217
Alignment explanation
Indices: 42284823--42285385 Score: 892
Period size: 217 Copynumber: 2.6 Consensus size: 217
42284813 ACTGGTATGT
* * * * * *
42284823 TTAGTCTGCCCCACTGCAATTTCAGGGGGATAAGGCTAGATGCGATCTACTCTCTGCAACTTTAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * * *
42284888 AGAGATAAGATCCAAGGTTTTAATCTGCTCCACTGCAACCTCAGGGAGATAGGATTATCGGTTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
* *
42284953 AATCTGCCCCACTGCAACTTCTGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
131 AATCTGCCCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
42285018 TAGGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
*
42285040 TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * * *
42285105 GGACATAAGATCTAAGGTTTTAATCCGCTCTATTGCAACTTCAGGGAGATAGGATTATCGGCTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
* * *
42285170 AATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGCAACTT
131 AATCTGCCCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
42285235 CAGGAGGATAAGACTTGCTTAC
196 CAGGAGGATAAGACTTGCTTAC
*
42285257 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
** *
42285322 AGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCCAGGGAGATAGGATTATCGGCT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTT-CAGGGAGATAGGATTATCGGCT
42285386 ACGAATTTGT
Statistics
Matches: 315, Mismatches: 30, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
217 293 0.93
218 22 0.07
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (217 bp):
TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
AGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTT
AATCTGCCCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
CAGGAGGATAAGACTTGCTTAC
Found at i:42285276 original size:44 final size:43
Alignment explanation
Indices: 42284911--42285373 Score: 256
Period size: 44 Copynumber: 10.7 Consensus size: 43
42284901 AAGGTTTTAA
* * * * * *
42284911 TCTGCTCCACTGCAACCTCAGGGAGATAGGATTATCGGT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T-GCTACTTAG
* * * *
42284955 TCTGCCCCACTGCAACTTCTGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA-CTT-AG
*
42285000 TCTGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAG
* * * * *
42285044 TCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAG
* * * * * *
42285085 TCTGCT-CTCTGCAACTTCAGGGACATAAGATCTAAGGT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTACTTAG
* * * * * *
42285128 TCCGCTCTATTGCAACTTCAGGGAGATAGGATTATCGGCT--TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTACTTAG
* * * *
42285172 TCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGCCATCTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA-C-TTAG
42285217 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TACTTAG
* * *
42285261 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTACTTAG
* * * * *
42285302 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGAT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTACTTAG
*
42285345 TCCGCTCCACTGCAACTTCCAGGGAGATA
1 TCTGCTCCACTGCAACTT-CAGGGAGATA
42285374 GGATTATCGG
Statistics
Matches: 332, Mismatches: 55, Indels: 63
0.74 0.12 0.14
Matches are distributed among these distances:
40 43 0.13
41 16 0.05
42 12 0.04
43 21 0.06
44 157 0.47
45 81 0.24
46 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTAG
Found at i:42298716 original size:31 final size:31
Alignment explanation
Indices: 42298680--42298753 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 31
42298670 GTTATATACC
*
42298680 TATATACATACATGCGTTTTTATA-A-TGTATA
1 TATATACATACA--CATTTTTATACACTGTATA
*
42298711 TATATACACGTACACATTTTTATACACTGTCTA
1 TATATACA--TACACATTTTTATACACTGTATA
42298744 TATATACATA
1 TATATACATA
42298754 TATATACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
31 19 0.51
32 1 0.03
33 17 0.46
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (31 bp):
TATATACATACACATTTTTATACACTGTATA
Found at i:42298804 original size:21 final size:21
Alignment explanation
Indices: 42298780--42298822 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42298770 CTTTATATTT
42298780 TATAACTTATATGCATA-TCTA
1 TATAAC-TATATGCATATTCTA
* *
42298801 TATATCTATGTGCATATTCTA
1 TATAACTATATGCATATTCTA
42298822 T
1 T
42298823 TTTCATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (21 bp):
TATAACTATATGCATATTCTA
Found at i:42300800 original size:55 final size:55
Alignment explanation
Indices: 42300703--42300810 Score: 139
Period size: 55 Copynumber: 2.0 Consensus size: 55
42300693 AGCTATAACT
* * * *
42300703 AAGTTTTCGTATTTCTACATAAAGCTAATATTTCTCACTATCATATAATTAAACA
1 AAGTTGTCGTATTTCTACATAAAGCTAATATCTCTAACTATCAAATAATTAAACA
*
42300758 AAGTTGTCGTATTTCTACAATAAAG-T-ATGATCTCTAATTATCAAATAATTAAA
1 AAGTTGTCGTATTTCTAC-ATAAAGCTAAT-ATCTCTAACTATCAAATAATTAAA
42300811 ATAAGAGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
54 2 0.04
55 38 0.83
56 6 0.13
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (55 bp):
AAGTTGTCGTATTTCTACATAAAGCTAATATCTCTAACTATCAAATAATTAAACA
Found at i:42307394 original size:21 final size:21
Alignment explanation
Indices: 42307355--42307403 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
42307345 AACAATTTTC
*
42307355 TTTT-TCCTTTTTTTCCCTCCT
1 TTTTCTCCTTTCTTTCCCT-CT
42307376 TTTTCTCCTTTCTTT-CCTCT
1 TTTTCTCCTTTCTTTCCCTCT
42307396 TTCTTCTC
1 TT-TTCTC
42307404 TAACCCCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 9 0.36
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTCTCCTTTCTTTCCCTCT
Found at i:42314640 original size:31 final size:30
Alignment explanation
Indices: 42314595--42314682 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 30
42314585 TTAATGATGC
*
42314595 ATAAAATATTTTAAA-AACTTAAATATAATA
1 ATAAATTATTTTAAACAA-TTAAATATAATA
* *
42314625 ATAAATTATATTTAAACAATTTAATATAATG
1 ATAAATTAT-TTTAAACAATTAAATATAATA
* * *
42314656 ATAAA-T-GTTTAAATAATTTAATATAAT
1 ATAAATTATTTTAAACAATTAAATATAAT
42314683 GTTACATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 19 0.37
30 9 0.18
31 21 0.41
32 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAATTATTTTAAACAATTAAATATAATA
Found at i:42315451 original size:33 final size:33
Alignment explanation
Indices: 42315394--42315487 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
42315384 ACTCAAACTT
* * * *
42315394 TTACCTAGACCTTATGCATACAACAATCAATTC
1 TTACCTAGGCCATATACATGCAACAATCAATTC
*
42315427 TTACCTTA-GCCATATACATGCAACAATCGATTC
1 TTACC-TAGGCCATATACATGCAACAATCAATTC
*
42315460 TTACCTAGGTCATATACATGCAACAATC
1 TTACCTAGGCCATATACATGCAACAATC
42315488 TATTTCATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.04
33 49 0.92
34 2 0.04
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.30
Consensus pattern (33 bp):
TTACCTAGGCCATATACATGCAACAATCAATTC
Found at i:42315796 original size:2 final size:2
Alignment explanation
Indices: 42315789--42315814 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42315779 TTACGAAGCG
42315789 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
42315815 TATATATACA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42316605 original size:74 final size:71
Alignment explanation
Indices: 42316427--42316605 Score: 198
Period size: 71 Copynumber: 2.5 Consensus size: 71
42316417 AACTTTATTT
* * ** * * * * **
42316427 GATGTTGCTCACTCAAGCTGTCAAGAATCTGCAACACGTGCTAGATCTTAGTCATTGACAAAGTA
1 GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAACACATACTAGATCTCAACCATTGACAAAGTA
42316492 TAATGC
66 TAATGC
* *
42316498 GATGCTACTCACTCAAGTTGCTGAGAATCCGCAACACATACTAGATCTCAACCATTG-CTAAAGT
1 GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAACACATACTAGATCTCAACCATTGAC-AAAGT
42316562 ATAATGATC
65 ATAATG--C
*
42316571 TTATGCTGCTCACTCAAGTTGTTGAGAATCCGCAA
1 -GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAA
42316606 TTTATGTTGG
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
70 1 0.01
71 56 0.63
73 1 0.01
74 31 0.35
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (71 bp):
GATGCTGCTCACTCAAGTTGTTGAGAATCCGCAACACATACTAGATCTCAACCATTGACAAAGTA
TAATGC
Found at i:42319046 original size:21 final size:22
Alignment explanation
Indices: 42319014--42319054 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
42319004 AGAATTTTGA
42319014 AAAATAAATAAATAAA-AATTAT
1 AAAATAAATAAA-AAATAATTAT
42319036 AAAAT-AATAAAAAATAATT
1 AAAATAAATAAAAAATAATT
42319055 TTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 10 0.56
22 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATAAATAAAAAATAATTAT
Found at i:42328192 original size:84 final size:84
Alignment explanation
Indices: 42328083--42328378 Score: 520
Period size: 84 Copynumber: 3.5 Consensus size: 84
42328073 CAAAGGATCC
* * *
42328083 CGGTGAAATTAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCATCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
42328148 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* *
42328167 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATATCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
42328232 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
*
42328251 CGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
*
42328316 CCTTTCACAATCAAGGATG
66 CCTTTCACAATCAAGGATA
*
42328335 CGGTGGAATCAGCACTTGGCAACCACCTTATAATCAATGATACG
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACG
42328379 AGTTCACATA
Statistics
Matches: 202, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 202 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:42328370 original size:42 final size:42
Alignment explanation
Indices: 42328038--42328378 Score: 370
Period size: 42 Copynumber: 8.1 Consensus size: 42
42328028 TAACTGATAC
* **
42328038 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATC-AAGGAT
* * * *
42328081 CCCGGTGAAATTAGCACTTAGCAACCACCTTATAATCAATGAT
1 -ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* * *
42328124 ACGG-GGAATCATCACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGAT
*
42328166 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* * *
42328208 ACGG-GGAATCAGCACATATCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGAT
* *
42328250 ACGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
* * *
42328292 ACGG-GGAATCAACACATAGCAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGAT
* * *
42328334 GCGGTGGAATCAGCACTTGGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
42328376 ACG
1 ACG
42328379 AGTTCACATA
Statistics
Matches: 248, Mismatches: 37, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
40 6 0.02
41 59 0.24
42 84 0.34
43 63 0.25
44 36 0.15
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
Found at i:42328413 original size:26 final size:26
Alignment explanation
Indices: 42328383--42328463 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
42328373 GATACGAGTT
42328383 CACATAGTAGCCTGCACATAATACTA
1 CACATAGTAGCCTGCACATAATACTA
*
42328409 CACAT-GT-GACCAT-CAC-T-ATCCGATA
1 CACATAGTAG-CC-TGCACATAATAC--TA
* *
42328434 CACGTAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCTGCACATAATACTA
42328460 CACA
1 CACA
42328464 CGTGATCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 18
0.64 0.08 0.28
Matches are distributed among these distances:
23 3 0.07
24 2 0.05
25 14 0.34
26 18 0.44
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (26 bp):
CACATAGTAGCCTGCACATAATACTA
Found at i:42332275 original size:10 final size:10
Alignment explanation
Indices: 42332260--42332345 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
42332250 TTTGAAATAT
42332260 TTTAATATAA
1 TTTAATATAA
42332270 TTTAATATAA
1 TTTAATATAA
** *
42332280 AAT-ATTTAA
1 TTTAATATAA
42332289 TTTCAAAATATAA
1 TTT---AATATAA
*
42332302 TTTAAAATAA
1 TTTAATATAA
42332312 ---AATAT--
1 TTTAATATAA
*
42332317 TTTAA-ATAT
1 TTTAATATAA
42332326 TTTAATATAA
1 TTTAATATAA
42332336 TTTAATATAA
1 TTTAATATAA
42332346 AAATAATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 20
0.66 0.10 0.23
Matches are distributed among these distances:
7 6 0.11
8 2 0.04
9 11 0.19
10 30 0.53
13 8 0.14
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAATATAA
Found at i:42332285 original size:34 final size:33
Alignment explanation
Indices: 42332242--42332347 Score: 144
Period size: 34 Copynumber: 3.2 Consensus size: 33
42332232 AAATATAAAA
42332242 ATAAAATATTTGAAATATTTTAATATAATTTAAT
1 ATAAAATATTT-AAATATTTTAATATAATTTAAT
** *
42332276 ATAAAATATTT-AAT-TTCAAAATATAATTTAAA
1 ATAAAATATTTAAATATT-TTAATATAATTTAAT
42332308 ATAAAATATTTTAAATATTTTAATATAATTTAAT
1 ATAAAATA-TTTAAATATTTTAATATAATTTAAT
42332342 ATAAAA
1 ATAAAA
42332348 ATAATTATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
31 2 0.03
32 23 0.37
33 3 0.05
34 32 0.52
35 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
ATAAAATATTTAAATATTTTAATATAATTTAAT
Found at i:42332365 original size:32 final size:31
Alignment explanation
Indices: 42332263--42332365 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 31
42332253 GAAATATTTT
42332263 AATATAATTTAATATAAAATATTTA-ATTTCAA
1 AATATAATTTAATATAAAATATTTATA-TT-AA
* **
42332295 AATATAATTTAAAATAAAATATTTTAAATATTTT
1 AATATAATTTAATATAAAATA-TTT--ATATTAA
*
42332329 AATATAATTTAATATAAAAATAATTATATTAA
1 AATATAATTTAATAT-AAAATATTTATATTAA
42332361 AATAT
1 AATAT
42332366 TAATAAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 30 0.51
33 3 0.05
34 16 0.27
35 9 0.15
36 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
AATATAATTTAATATAAAATATTTATATTAA
Found at i:42332421 original size:59 final size:57
Alignment explanation
Indices: 42332347--42332460 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 57
42332337 TTAATATAAA
* *
42332347 AATAATTATATTAAAATATTAATAAATTATATATTTTATTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAATATGAATAAATTATATA-TTT-TTTCATTAAATTATATTTAAT
* * * *
42332406 AATAATTATATTAAAATATGATTAGATTATTTATTTTTTCATTAAATTATTTTTA
1 AATAATTATATTAAAATATGAATAAATTATATATTTTTTCATTAAATTATATTTA
42332461 TATATTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 17 0.35
58 3 0.06
59 29 0.59
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (57 bp):
AATAATTATATTAAAATATGAATAAATTATATATTTTTTCATTAAATTATATTTAAT
Found at i:42332465 original size:87 final size:86
Alignment explanation
Indices: 42332373--42332546 Score: 316
Period size: 87 Copynumber: 2.0 Consensus size: 86
42332363 TATTAATAAA
*
42332373 TTATATA-TTTTA-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAGATTAT
1 TTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
42332436 TTATTTTTTCATTAAATTATTT
66 TTATTTTTT-ATTAAATTATTT
42332458 TTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
1 TTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
42332523 TTATTTTTTATTAAATTATTT
66 TTATTTTTTATTAAATTATTT
42332544 TTA
1 TTA
42332547 ATAATAATCG
Statistics
Matches: 86, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
85 7 0.08
86 20 0.23
87 59 0.69
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (86 bp):
TTATATATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
TTATTTTTTATTAAATTATTT
Found at i:42332535 original size:30 final size:29
Alignment explanation
Indices: 42332414--42332537 Score: 94
Period size: 30 Copynumber: 4.2 Consensus size: 29
42332404 ATAATAATTA
*
42332414 TATTAAAATATGATTAGATTATTTATTTTT
1 TATTAAAATATGATTAAATTATTTA-TTTT
* **
42332444 TCATTAAATTATTTTTATATATT-TTTATTTT
1 T-ATTAAAATATGATTA-A-ATTATTTATTTT
* * * * *
42332475 TATTAAATTAT-ATTTAA-TA-ATAATTA
1 TATTAAAATATGATTAAATTATTTATTTT
42332501 TATTAAAATATGATTAAATTATTTATTTTT
1 TATTAAAATATGATTAAATTATTTA-TTTT
42332531 TATTAAA
1 TATTAAA
42332538 TTATTTTTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
26 15 0.21
27 6 0.08
28 3 0.04
29 4 0.06
30 20 0.28
31 17 0.24
32 4 0.06
33 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (29 bp):
TATTAAAATATGATTAAATTATTTATTTT
Found at i:42332747 original size:16 final size:15
Alignment explanation
Indices: 42332726--42332793 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
42332716 TAAATTATTG
*
42332726 ATTACATCTTTATTCC
1 ATTACAT-TCTATTCC
42332742 ATTACAGTTCTATTCC
1 ATTACA-TTCTATTCC
*
42332758 ATTACAACTCTATTCC
1 ATTAC-ATTCTATTCC
*
42332774 ATAATA-ATTTTATTCC
1 AT--TACATTCTATTCC
42332790 ATTA
1 ATTA
42332794 TAGCGAACCA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.05
16 38 0.86
17 2 0.05
18 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.01, T:0.46
Consensus pattern (15 bp):
ATTACATTCTATTCC
Found at i:42332763 original size:32 final size:32
Alignment explanation
Indices: 42332726--42332793 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
42332716 TAAATTATTG
* * * *
42332726 ATTACATCTTTATTCCATTACAGTTCTATTCC
1 ATTACAACTCTATTCCATAACAATTCTATTCC
* *
42332758 ATTACAACTCTATTCCATAATAATTTTATTCC
1 ATTACAACTCTATTCCATAACAATTCTATTCC
42332790 ATTA
1 ATTA
42332794 TAGCGAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTACAACTCTATTCCATAACAATTCTATTCC
Found at i:42333276 original size:15 final size:15
Alignment explanation
Indices: 42333256--42333307 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
42333246 GCTACAAAAC
42333256 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
42333271 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
42333290 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
42333305 ATT
1 ATT
42333308 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:42333293 original size:19 final size:19
Alignment explanation
Indices: 42333269--42333305 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42333259 TATTATTAAT
*
42333269 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
42333288 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
42333306 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:42333358 original size:13 final size:13
Alignment explanation
Indices: 42333340--42333364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42333330 TTGTGAAGAA
42333340 TATTATTAAAATT
1 TATTATTAAAATT
42333353 TATTATTAAAAT
1 TATTATTAAAAT
42333365 AAAATTAAAA
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:0.00, T:0.52
Consensus pattern (13 bp):
TATTATTAAAATT
Found at i:42352821 original size:18 final size:18
Alignment explanation
Indices: 42352781--42352823 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
42352771 AATTTAAAAG
* * *
42352781 ATTAAAAAATTATATATT
1 ATTAAAAAATTAAAAATC
*
42352799 TTTAAAAAATTAAAAATC
1 ATTAAAAAATTAAAAATC
42352817 ATTAAAA
1 ATTAAAA
42352824 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAAAAAATTAAAAATC
Found at i:42358737 original size:8 final size:8
Alignment explanation
Indices: 42358724--42358752 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
42358714 GGTCTATGCG
42358724 TGTAGAAA
1 TGTAGAAA
42358732 TGTAGAAA
1 TGTAGAAA
42358740 TGTAGAAA
1 TGTAGAAA
42358748 TGTAG
1 TGTAG
42358753 TAAAACTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (8 bp):
TGTAGAAA
Found at i:42359394 original size:33 final size:33
Alignment explanation
Indices: 42359352--42359500 Score: 230
Period size: 33 Copynumber: 4.5 Consensus size: 33
42359342 TCAACATAAG
42359352 TGATTGGAACATCTATCAGGGCAGCTTCATCGA-
1 TGATTGGAACATCTATCAGGGCAGCTTCATC-AT
42359385 TGATTGGAACATCTATCAGGGCAGCTTCATCGA-
1 TGATTGGAACATCTATCAGGGCAGCTTCATC-AT
* *
42359418 TGATTGGAACATCTATCGGGGCAGCTTCGTCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
**
42359451 TGATTGGAACATCTATTGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
42359484 TGATTGGAACATCTATC
1 TGATTGGAACATCTATC
42359501 GGGGGAGATT
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 1 0.01
33 109 0.99
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAT
Found at i:42371047 original size:29 final size:29
Alignment explanation
Indices: 42371013--42371072 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
42371003 TTGGCTATTA
* *
42371013 AAAATTTTCAAATAAGGAAGTTTTCTTTC
1 AAAATTTTCAAATAAGGAAATTTTCATTC
42371042 AAAATTTTCAAATAAGGAAATTTTCATTC
1 AAAATTTTCAAATAAGGAAATTTTCATTC
42371071 AA
1 AA
42371073 TTATGGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAATTTTCAAATAAGGAAATTTTCATTC
Found at i:42371064 original size:16 final size:16
Alignment explanation
Indices: 42371014--42371067 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
42371004 TGGCTATTAA
42371014 AAATTTTCAAATAAGG
1 AAATTTTCAAATAAGG
* ** *
42371030 AAGTTTTC-TTTCA--
1 AAATTTTCAAATAAGG
42371043 AAATTTTCAAATAAGG
1 AAATTTTCAAATAAGG
42371059 AAATTTTCA
1 AAATTTTCA
42371068 TTCAATTATG
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
13 7 0.26
14 2 0.07
15 2 0.07
16 16 0.59
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (16 bp):
AAATTTTCAAATAAGG
Found at i:42371133 original size:21 final size:21
Alignment explanation
Indices: 42371108--42371153 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
42371098 AGCCTTTTTT
42371108 TTAATAGGTATGTTTTTATCA
1 TTAATAGGTATGTTTTTATCA
*
42371129 TTAATAGGTATGTTTTTGTCA
1 TTAATAGGTATGTTTTTATCA
42371150 TTAA
1 TTAA
42371154 CCTGTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (21 bp):
TTAATAGGTATGTTTTTATCA
Found at i:42381287 original size:50 final size:50
Alignment explanation
Indices: 42381211--42381441 Score: 259
Period size: 50 Copynumber: 4.6 Consensus size: 50
42381201 TTGGGTAAAT
* *
42381211 AGGTCCCGTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
* * * *
42381261 AGGTCCCATATAAGACCACGTTTGGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
** * *
42381311 AGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
** * * * * *
42381361 AACTCCCATGGAAGACCATATTTGGGACATGGCATTGGCA--GTACATGAA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAG
** *
42381410 ACATCCCATGTAAAACCATGTCTGGGACATGG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGG
42381442 TTTTGGCATG
Statistics
Matches: 152, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 31 0.20
50 120 0.79
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
Found at i:42389755 original size:24 final size:24
Alignment explanation
Indices: 42389728--42389906 Score: 151
Period size: 24 Copynumber: 7.3 Consensus size: 24
42389718 CAGCTCATAT
**
42389728 GAGCATACCAATTACAGCTTTTGA
1 GAGCATACCAATTACAGCTCGTGA
* * * *
42389752 GAGCATACTGATTTATAGCTCGTGT
1 GAGCATAC-CAATTACAGCTCGTGA
* * *
42389777 GTGCATATCAATTACAGCTTGTGA
1 GAGCATACCAATTACAGCTCGTGA
* *
42389801 GAGCATACCGATTTACAGCTCGTGT
1 GAGCATACC-AATTACAGCTCGTGA
* *
42389826 GTGCATATCAATTACAGCTCGTGA
1 GAGCATACCAATTACAGCTCGTGA
* * *
42389850 GAGCATATCGATTTACAGCTCGTGT
1 GAGCATA-CCAATTACAGCTCGTGA
* * * *
42389875 GAGCATATCGATTACAACTCGTGT
1 GAGCATACCAATTACAGCTCGTGA
42389899 GAGCATAC
1 GAGCATAC
42389907 ATGTATAGGA
Statistics
Matches: 119, Mismatches: 33, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
24 64 0.54
25 55 0.46
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
GAGCATACCAATTACAGCTCGTGA
Found at i:42389782 original size:25 final size:24
Alignment explanation
Indices: 42389752--42389905 Score: 157
Period size: 24 Copynumber: 6.3 Consensus size: 24
42389742 CAGCTTTTGA
*
42389752 GAGCATACTGATTTATAGCTCGTGT
1 GAGCATA-TGATTTACAGCTCGTGT
* * * * *
42389777 GTGCATATCAATTACAGCTTGTGA
1 GAGCATATGATTTACAGCTCGTGT
*
42389801 GAGCATACCGATTTACAGCTCGTGT
1 GAGCATA-TGATTTACAGCTCGTGT
* * * *
42389826 GTGCATATCAATTACAGCTCGTGA
1 GAGCATATGATTTACAGCTCGTGT
42389850 GAGCATATCGATTTACAGCTCGTGT
1 GAGCATAT-GATTTACAGCTCGTGT
*
42389875 GAGCATATCGA-TTACAACTCGTGT
1 GAGCATAT-GATTTACAGCTCGTGT
42389899 GAGCATA
1 GAGCATA
42389906 CATGTATAGG
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
24 57 0.54
25 48 0.46
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (24 bp):
GAGCATATGATTTACAGCTCGTGT
Found at i:42389791 original size:49 final size:49
Alignment explanation
Indices: 42389730--42389906 Score: 248
Period size: 49 Copynumber: 3.6 Consensus size: 49
42389720 GCTCATATGA
* * *
42389730 GCATACCAATTACAGCTTTTGAGAGCATACTGATTTATAGCTCGTGTGT
1 GCATATCAATTACAGCTTGTGAGAGCATACTGATTTACAGCTCGTGTGT
*
42389779 GCATATCAATTACAGCTTGTGAGAGCATACCGATTTACAGCTCGTGTGT
1 GCATATCAATTACAGCTTGTGAGAGCATACTGATTTACAGCTCGTGTGT
* *
42389828 GCATATCAATTACAGCTCGTGAGAGCATA-TCGATTTACAGCTCGTGTGA
1 GCATATCAATTACAGCTTGTGAGAGCATACT-GATTTACAGCTCGTGTGT
* * * *
42389877 GCATATCGATTACAACTCGTGTGAGCATAC
1 GCATATCAATTACAGCTTGTGAGAGCATAC
42389907 ATGTATAGGA
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 116 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (49 bp):
GCATATCAATTACAGCTTGTGAGAGCATACTGATTTACAGCTCGTGTGT
Found at i:42392526 original size:5 final size:5
Alignment explanation
Indices: 42392518--42392561 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
42392508 TACTGTACTT
* *
42392518 ACCTC ACCTC ACCTC ACCTT ACCTT ACCTC ACCTC ACCTC ACCT
1 ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCT
42392562 TGTGGCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.20, C:0.55, G:0.00, T:0.25
Consensus pattern (5 bp):
ACCTC
Found at i:42395800 original size:30 final size:29
Alignment explanation
Indices: 42395764--42395826 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
42395754 AGAAAAAGCC
42395764 TTTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
42395794 TTTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTTCAAAATTTACCGAAATGGGCCA
42395823 TTTT
1 TTTT
42395827 CCAGGAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (29 bp):
TTTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:42399386 original size:10 final size:10
Alignment explanation
Indices: 42399371--42399395 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42399361 CAGATCTAAC
42399371 ATTATGTAAA
1 ATTATGTAAA
42399381 ATTATGTAAA
1 ATTATGTAAA
42399391 ATTAT
1 ATTAT
42399396 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:42399520 original size:56 final size:57
Alignment explanation
Indices: 42399378--42399521 Score: 152
Period size: 56 Copynumber: 2.5 Consensus size: 57
42399368 AACATTATGT
* * *
42399378 AAAATTATGTAAAATTATTAAGCCAAAAAAATTTTCTTAATGGTTAGAAAAATTTATC
1 AAAA-TATGTAAAATTATTAAGCCAAAAAAATTGTCTTAATAGTTAGAAAAATGTATC
* * * ** *
42399436 -AAATAATCTCAAATTATTAAGTCC--AAAAATTGTGTTAATAGTTATTAAAGTGT-TC
1 AAAAT-ATGTAAAATTATTAAG-CCAAAAAAATTGTCTTAATAGTTAGAAAAATGTATC
42399491 AAAATATGTAAAATTATTAAGCCAAAAAAAT
1 AAAATATGTAAAATTATTAAGCCAAAAAAAT
42399522 ATGTAAAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
54 2 0.03
55 16 0.23
56 33 0.47
57 17 0.24
58 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.35
Consensus pattern (57 bp):
AAAATATGTAAAATTATTAAGCCAAAAAAATTGTCTTAATAGTTAGAAAAATGTATC
Found at i:42399524 original size:26 final size:26
Alignment explanation
Indices: 42399491--42399545 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
42399481 TAAAGTGTTC
42399491 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
42399517 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
42399543 AAA
1 AAA
42399546 CTTTAGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAATATGTAAAATTATTAAGCCAAA
Found at i:42399596 original size:28 final size:28
Alignment explanation
Indices: 42399547--42400114 Score: 631
Period size: 28 Copynumber: 19.4 Consensus size: 28
42399537 GCCAAAAAAC
* * *
42399547 TTTAGGTTAGTTTTGGGTTTTTAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
* *
42399575 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
1 TTTAGGTTA-GATTAGGGTTTTTAGTTAA
*
42399604 TTTAGGTTATATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42399632 TTTAGGTTAGATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
42399660 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAATTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
* *
42399694 TTTAGGTTAGATTA-GGTTTTAAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
42399721 TTTAGGTTAGATTAGGGTTTTTAGGTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42399749 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
* * *
42399783 TTTAGGTTATATTA-GGTTTTAAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
42399810 TTTAGGTTAGATTAGGGTTTTTAGGTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
42399838 TTTAAGTTAGGGTTAGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A-TTAGGGTTTTTAGTTAA
* * *
42399871 TTTAGGTTAGATTA-GGTTTTAAATTAC
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42399898 TTTAGGTTAGATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42399926 TTTAGGTTAGGCTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA-G---A--TTAGGGTTTTTAGTTAA
* *
42399960 TTTAGGTTAGATTA-GGTTTTAAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42399987 TTTAGGTTAGATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
*
42400015 TTTAGGTTAGATTATGGTTTTTAGTTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42400043 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
* *
42400077 TTTAGGTTAGATTAGGTTTTTTAATTAA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAA
42400105 TTTAGGTTAG
1 TTTAGGTTAG
42400115 TGTTAGGTTA
Statistics
Matches: 471, Mismatches: 35, Indels: 68
0.82 0.06 0.12
Matches are distributed among these distances:
27 99 0.21
28 201 0.43
29 29 0.06
30 8 0.02
31 1 0.00
32 7 0.01
33 25 0.05
34 101 0.21
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (28 bp):
TTTAGGTTAGATTAGGGTTTTTAGTTAA
Found at i:42399737 original size:89 final size:89
Alignment explanation
Indices: 42399547--42400131 Score: 834
Period size: 89 Copynumber: 6.6 Consensus size: 89
42399537 GCCAAAAAAC
* * * *
42399547 TTTAGGTTAGTTTTGGGTTTTTAATTAATTTAGGTTA-GG-T---TTAGGGTTTTTAATTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
* * *
42399607 AGGTTATATTAGGGTTTTTAGTTAA
66 AGGTTAGATTA-GGTTTTAAATTAA
*
42399632 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAATTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
42399697 AGGTTAGATTAGGTTTTAAATTAA
66 AGGTTAGATTAGGTTTTAAATTAA
*
42399721 TTTAGGTTAGATTAGGGTTTTTAGGTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
*
42399786 AGGTTATATTAGGTTTTAAATTAA
66 AGGTTAGATTAGGTTTTAAATTAA
* *
42399810 TTTAGGTTAGATTAGGGTTTTTAGGTAATTTAAGTTAGGGTTA-GTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
*
42399874 AGGTTAGATTAGGTTTTAAATTAC
66 AGGTTAGATTAGGTTTTAAATTAA
*
42399898 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGCTTAGGTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
42399963 AGGTTAGATTAGGTTTTAAATTAA
66 AGGTTAGATTAGGTTTTAAATTAA
*
42399987 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTA--G--A--TTATGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
* *
42400046 AGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
66 AGGTTA--G--A--TTA-GGTTTTAAATTAA
* * *
42400077 TTTAGGTTAGATTAGGTTTTTTAATTAATTTAGGTTAGTGTTAGGTTAGGGTTTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTT
42400132 CAATTAAATT
Statistics
Matches: 458, Mismatches: 23, Indels: 27
0.90 0.05 0.05
Matches are distributed among these distances:
83 25 0.05
85 36 0.08
86 2 0.00
87 2 0.00
88 83 0.18
89 223 0.49
90 76 0.17
92 1 0.00
94 1 0.00
96 9 0.02
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (89 bp):
TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
AGGTTAGATTAGGTTTTAAATTAA
Found at i:42399904 original size:177 final size:177
Alignment explanation
Indices: 42399547--42400131 Score: 848
Period size: 177 Copynumber: 3.3 Consensus size: 177
42399537 GCCAAAAAAC
* * *
42399547 TTTAGGTTAGTTTTGGGTTTTTAATTAATTTAGGTTA-GG-T---TTAGGGTTTTTAATTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
* *
42399607 AGGTTATATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGG
66 AGGTTATATTA-GGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGG
*
42399672 TTAGGTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGTTTTAAATTAA
130 TTA-GTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGTTTTAAATTAA
**
42399721 TTTAGGTTAGATTAGGGTTTTTAGGTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
* *
42399786 AGGTTATATTAGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGGTAATTTAAGTTAGGGT
66 AGGTTATATTAGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGT
*
42399851 TAGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGTTTTAAATTAC
131 TAGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGTTTTAAATTAA
* *
42399898 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGCTTAGGTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
*
42399963 AGGTTAGATTAGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTA--G-
66 AGGTTATATTAGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGT
* * *
42400025 -A-TTATGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
131 TAGTTAGGGTTTTTAGTTAATTTAGGTTA--G--A--TTA-GGTTTTAAATTAA
* *
42400077 TTTAGGTTAGATTAGGTTTTTTAATTAATTTAGGTTAGTGTTAGGTTAGGGTTTT
1 TTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTT
42400132 CAATTAAATT
Statistics
Matches: 375, Mismatches: 24, Indels: 19
0.90 0.06 0.05
Matches are distributed among these distances:
172 25 0.07
173 1 0.00
174 34 0.09
175 3 0.01
176 2 0.01
177 164 0.44
178 55 0.15
179 91 0.24
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (177 bp):
TTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
AGGTTATATTAGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGT
TAGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGTTTTAAATTAA
Found at i:42400098 original size:62 final size:62
Alignment explanation
Indices: 42399547--42400131 Score: 532
Period size: 62 Copynumber: 9.9 Consensus size: 62
42399537 GCCAAAAAAC
* *
42399547 TTTAGGTTAG-TTTTGGGTTTTTAATTAATTTAGGTTA-GG-T---TTAGGGTTTTTAATTAA
1 TTTAGGTTAGATTAT-GGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
* * *
42399604 TTTAGGTTATATTAGGGTTTTTAGTTAATTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
* * *
42399660 TTTAGGTTAGGGTTAGGTTAGGGTTTTTAATTAATTTAGGTTA--G--A--TTA-GGTTTTAAAT
1 TTTAGGTTA--G--A--TTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGT
42399718 TAA
60 TAA
* **
42399721 TTTAGGTTAGATTAGGGTTTTTAGGTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
* * *
42399783 TTTAGGTTATATTA-GGTTTTAAATTAATTTAGGTTA--G--A--TTAGGGTTTTTAGGTAA
1 TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
* * * * *
42399838 TTTAAGTTAGGGTTAGTTAGGGTTTTTAGTTAATTTAGGTTA--G--A--TTA-GGTTTTAAATT
1 TTTAGGTTA--G--A-TTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTT
*
42399896 AC
61 AA
* * *
42399898 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGCTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
*
42399960 TTTAGGTTAGATTA-GGTTTTAAATTAATTTAGGTTA--G--A--TTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
*
42400015 TTTAGGTTAGATTATGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
1 TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
*
42400077 TTTAGGTTAGATTA-GGTTTTTTAATTAATTTAGGTTAGTGTTAGGTTAGGGTTTT
1 TTTAGGTTAGATTATGG-TTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTT
42400132 CAATTAAATT
Statistics
Matches: 454, Mismatches: 38, Indels: 67
0.81 0.07 0.12
Matches are distributed among these distances:
55 105 0.23
56 47 0.10
57 34 0.07
58 4 0.01
59 5 0.01
60 22 0.05
61 92 0.20
62 145 0.32
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (62 bp):
TTTAGGTTAGATTATGGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
Found at i:42400223 original size:26 final size:25
Alignment explanation
Indices: 42400192--42400240 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
42400182 CTTAAAAAAT
42400192 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
42400218 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
42400241 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:42400389 original size:24 final size:24
Alignment explanation
Indices: 42400355--42400406 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42400345 GCGGCTGTTA
*
42400355 TTCCTCTGGTGGTGATTGTGGTCC
1 TTCCTCCGGTGGTGATTGTGGTCC
* *
42400379 TTCCTCCGGTGGTGGTTGTGGTTC
1 TTCCTCCGGTGGTGATTGTGGTCC
42400403 TTCC
1 TTCC
42400407 GGTTCCGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.02, C:0.23, G:0.33, T:0.42
Consensus pattern (24 bp):
TTCCTCCGGTGGTGATTGTGGTCC
Found at i:42400705 original size:18 final size:18
Alignment explanation
Indices: 42400661--42400706 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
42400651 TATTCGGAAA
* *
42400661 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
42400679 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
42400697 AGGAAACATA
1 AGGATACATA
42400707 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:42401361 original size:7 final size:7
Alignment explanation
Indices: 42401351--42401380 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
42401341 TTATATACAT
42401351 AATACTA
1 AATACTA
42401358 AATACTA
1 AATACTA
42401365 AATACTA
1 AATACTA
42401372 AATA-TA
1 AATACTA
42401378 AAT
1 AAT
42401381 TGACTAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:42402447 original size:30 final size:31
Alignment explanation
Indices: 42402394--42402457 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
42402384 GCCATTGATG
42402394 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
* *
42402425 AAAATATAAAAAAA-TTATAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
42402455 AAA
1 AAA
42402458 TGGATTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:42402495 original size:40 final size:40
Alignment explanation
Indices: 42402451--42402526 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
42402441 ATAATTATTT
42402451 TTAAAAATG-GATTTGAGAGAATATTGGAAGGAAATTAAAA
1 TTAAAAATGAG-TTTGAGAGAATATTGGAAGGAAATTAAAA
* *
42402491 TTAAATATGAGTTTGAGAGAATTTTGGAAGGAAATT
1 TTAAAAATGAGTTTGAGAGAATATTGGAAGGAAATT
42402527 GAGAGGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (40 bp):
TTAAAAATGAGTTTGAGAGAATATTGGAAGGAAATTAAAA
Found at i:42404113 original size:11 final size:11
Alignment explanation
Indices: 42404097--42404123 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42404087 AACTTGAACA
42404097 AAAATAAAAAT
1 AAAATAAAAAT
42404108 AAAATAAAAAT
1 AAAATAAAAAT
42404119 AAAAT
1 AAAAT
42404124 TACATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:42420612 original size:15 final size:16
Alignment explanation
Indices: 42420592--42420626 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
42420582 AAATTGTTAT
42420592 TTATTATCATTATC-A
1 TTATTATCATTATCTA
*
42420607 TTATTATTATTATCTA
1 TTATTATCATTATCTA
42420623 TTAT
1 TTAT
42420627 CTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATCATTATCTA
Found at i:42426707 original size:32 final size:32
Alignment explanation
Indices: 42426671--42426734 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42426661 GTCTAAACGT
42426671 CATTATTCTAATAAAATACATCTTTGCATTCA
1 CATTATTCTAATAAAATACATCTTTGCATTCA
42426703 CATTATTCTAATAAAATACATCTTTGCATTCA
1 CATTATTCTAATAAAATACATCTTTGCATTCA
42426735 TTTTTGAGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (32 bp):
CATTATTCTAATAAAATACATCTTTGCATTCA
Found at i:42429014 original size:50 final size:50
Alignment explanation
Indices: 42428882--42429014 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 50
42428872 AGGTTACAGT
* * * * * *
42428882 GGAGCAGATTGAAACCACGACGGTGAATCTTACTCCCCTGGTGGTGTAGT
1 GGAGCAGATTGAAGCCACGACGGCGAATCTTATTCCCCTGATGGTATAGC
** * * *
42428932 GGAATAGATTGAAGCCGCGACGGCGAATCTTATTTCCCTGATGTTATAGC
1 GGAGCAGATTGAAGCCACGACGGCGAATCTTATTCCCCTGATGGTATAGC
*
42428982 GGAGCAGATTGAAGCCATGACGGCGAATCTTAT
1 GGAGCAGATTGAAGCCACGACGGCGAATCTTAT
42429015 CTCTTTTGTG
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (50 bp):
GGAGCAGATTGAAGCCACGACGGCGAATCTTATTCCCCTGATGGTATAGC
Found at i:42429424 original size:265 final size:267
Alignment explanation
Indices: 42428937--42429463 Score: 752
Period size: 265 Copynumber: 2.0 Consensus size: 267
42428927 GTAGTGGAAT
* * * *
42428937 AGATTGAAGCCGCGACGGCGAATCTTATTTCCCTGATGTTATAGCGGAGCAGATTGAAGCCATGA
1 AGATTGAAGCCGCAACGACGAATCTTATTTCCCTGACGTTATAGCGGAGCAGATTGAAGCCACGA
* * *
42429002 CGGCGAATCTTATCTCTTTTGTGTTAAGGTCTAGATTAGCTAAAGTACAGCAGATTGAAGCTATG
66 CAGCGAATCTTATCTCTTTGGTGTTAAGGTCTAGATTAGCTAAAGTACAGCAGATTGAAGCCATG
* * *
42429067 GGCAGCGAATCCTATTTCTTTAGCGTTATAGTGGAGCAGATTGAAACCACGATGGTGAATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCGTTACAGTGGAGCAGATTGAAACCACGACGGTGAATCTTAC
* * * * *
42429132 TCCCCTAGCGGTGTAGTGGAACAGATTGAAGCTGCGACGGCGAATCTAG-TTCCCCAACATTACA
196 TCCCCTAGCAGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTAGTTTCCCCAACATTACA
42429196 ATTTAAA
261 ATTTAAA
* ** *
42429203 AGATTGAAGTCGCAACGACGAATCTTATTTCGTTGGCGTTATAGCGGAGCAGATTGAAGCC-CGA
1 AGATTGAAGCCGCAACGACGAATCTTATTTCCCTGACGTTATAGCGGAGCAGATTGAAGCCACGA
* * * * * *
42429267 CAGCGAATCTTATCTCTTTGGTGTTAAGGTTTGGATTAGCTGAAGTAGAGCGGATTGAAGCCGTG
66 CAGCGAATCTTATCTCTTTGGTGTTAAGGTCTAGATTAGCTAAAGTACAGCAGATTGAAGCCATG
*
42429332 GGCAGCGAATCCTATCTCTTTGGCGTTACAGTGGAGCAGATTGAAACCACGACGGTGAATCTTAC
131 GGCAGCGAATCCTATCTCTTTAGCGTTACAGTGGAGCAGATTGAAACCACGACGGTGAATCTTAC
* * * * * *
42429397 TCCTCTGGCAGTGCAGTGGATCAGATTGAAGCTACAACGGCAAATCTTGTTTCCTCAACATTGCA
196 TCCCCTAGCAGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTAGTTTCCCCAACATTACA
42429462 AT
261 AT
42429464 GGTGAATCTT
Statistics
Matches: 228, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
265 159 0.70
266 69 0.30
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (267 bp):
AGATTGAAGCCGCAACGACGAATCTTATTTCCCTGACGTTATAGCGGAGCAGATTGAAGCCACGA
CAGCGAATCTTATCTCTTTGGTGTTAAGGTCTAGATTAGCTAAAGTACAGCAGATTGAAGCCATG
GGCAGCGAATCCTATCTCTTTAGCGTTACAGTGGAGCAGATTGAAACCACGACGGTGAATCTTAC
TCCCCTAGCAGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTAGTTTCCCCAACATTACA
ATTTAAA
Found at i:42429538 original size:44 final size:44
Alignment explanation
Indices: 42429468--42429845 Score: 216
Period size: 44 Copynumber: 8.8 Consensus size: 44
42429458 TGCAATGGTG
*
42429468 AATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * **
42429512 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAA-ACTTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * * * *
42429555 GGATCTTATCTCTCTGAAGTTGTAG-AGAGTAGA-T--CG-CATCT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
** * * *
42429596 TGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-T
* *
42429639 AAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGAC-A-
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAT
* *
42429685 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * *
42429729 AAT-TCTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAACCACA-
1 AATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * ** * * *
42429773 AATTTTATCTCTCTGAAGTTGCAG-AAAGCAGATCACATCC---
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
42429813 AGTCTTATCTCCCTGAAGTTGCAATGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
42429846 CATAAGACAC
Statistics
Matches: 259, Mismatches: 52, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
40 41 0.16
41 13 0.05
42 4 0.02
43 25 0.10
44 139 0.54
45 28 0.11
46 6 0.02
47 1 0.00
48 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:42429706 original size:45 final size:44
Alignment explanation
Indices: 42429598--42429885 Score: 176
Period size: 44 Copynumber: 6.6 Consensus size: 44
42429588 TCGCATCTTG
*
42429598 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
*
42429642 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGACAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTAAG-CAAA
*
42429687 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCA--AAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-AA
* * * *
42429731 T-TCTATCTCCCAGAAGTTGCAGTGGAGCGGATTAA--AACCACAAA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA--GCAAA
* * ** * * * * *
42429775 TTTTATCTCTCTGAAGTTGCAG-AAAGCAGA-TCA--CATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
*
42429815 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACATAAG-ACA-CAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-TAAGTA-AGCAAA
* *
42429859 TCTTATTTCCC-CAAGGTTGCAGTGGAG
1 TCTTATCTCCCTGAA-GTTGCAGTGGAG
42429886 TGGATTGAAA
Statistics
Matches: 194, Mismatches: 31, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
40 21 0.11
41 6 0.03
42 6 0.03
43 15 0.08
44 103 0.53
45 39 0.20
46 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
Found at i:42429781 original size:133 final size:128
Alignment explanation
Indices: 42429598--42429943 Score: 328
Period size: 128 Copynumber: 2.7 Consensus size: 128
42429588 TCGCATCTTG
* * * *
42429598 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA--GCAAGTCTTATC-CTCCTGAAGTT
1 TCTTATCTCCCAGAAGTTGCAGTGGAGCGGATTAA--AACCGCAAATCTTATCTCT-CTGAAGTT
* * * *
42429660 GCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCA-AAG
63 GCAG-AAAGCAGA-T-AACAT--CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGA-CATAAG
* * *
42429724 CCGATAAT
122 AC-ACAAA
* *
42429732 TC-TATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAACCACAAATTTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAACCGCAAATCTTATCTCTCTGAAGTTGCA
* * *
42429796 GAAAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACATAAGACACAAA
66 GAAAGCAGATAACATCAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACATAAGACACAAA
* * * * *
42429859 TCTTATTTCCCCA-AGGTTGCAGTGGAGTGGATTGAAACCGCAGATCTTATCTCTCTGAAGTTGC
1 TCTTATCT-CCCAGAAGTTGCAGTGGAGCGGATTAAAACCGCAAATCTTATCTCTCTGAAGTTGC
**
42429923 AGAGAA-CAGATCGCATCAAAT
65 AGA-AAGCAGATAACATCAAAT
42429944 TCATCTTTAA
Statistics
Matches: 179, Mismatches: 26, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
127 7 0.04
128 100 0.56
129 6 0.03
130 3 0.02
131 3 0.02
132 6 0.03
133 50 0.28
134 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (128 bp):
TCTTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAACCGCAAATCTTATCTCTCTGAAGTTGCA
GAAAGCAGATAACATCAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACATAAGACACAAA
Found at i:42429878 original size:128 final size:128
Alignment explanation
Indices: 42429687--42429939 Score: 334
Period size: 128 Copynumber: 2.0 Consensus size: 128
42429677 AGATGACAAA
* * * *
42429687 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGCCGATAATTCTATCTCCCAGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGATCAAAGACGACAAATCTATCTCCCAGAAGTTGCA
*
42429752 GTGGAGCGGATTAAAACCACAAATTTTATCTCTCTGAAGTTGCAGA-AAGCAGATCACATCCAG
66 GTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGAGAA-CAGATCACATCCAG
* *
42429815 TCTTATCTCCCTGAAGTTGCAATGGAGCAGA-CATAAGAC-ACAAATCTTATTTCCCCA-AGGTT
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGATCA-AAGACGACAAATC-TATCT-CCCAGAAGTT
* * * * *
42429877 GCAGTGGAGTGGATTGAAACCGCAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATC
63 GCAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGAGAACAGATCACATC
42429940 AAATTCATCT
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
127 7 0.06
128 96 0.88
129 6 0.06
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAATGGAGCAGATCAAAGACGACAAATCTATCTCCCAGAAGTTGCA
GTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGAGAACAGATCACATCCAG
Found at i:42429880 original size:217 final size:217
Alignment explanation
Indices: 42429468--42429882 Score: 575
Period size: 217 Copynumber: 1.9 Consensus size: 217
42429458 TGCAATGGTG
* *
42429468 AATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATCAAAGCCAATAATCCTATCTCCCAGAAGTTG
* ***** * * * * **
42429533 TAGTGGAGCGGATTAAAACTTTGGATCTTATCTCTCTGAAGTTGTAGAGAGTAGATCGCATCTTG
66 CAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCACATCCAG
* * **
42429598 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
131 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAATCTTATCCTCCCCAAGTTGCA
42429663 GTGAGGCAGACTGAAGATGACA
196 GTGAGGCAGACTGAAGATGACA
* * *
42429685 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGCCGATAATTCTATCTCCCAGAAGTTG
1 AATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATCAAAGCCAATAATCCTATCTCCCAGAAGTTG
*
42429750 CAGTGGAGCGGATTAAAACCACAAATTTTATCTCTCTGAAGTTGCAGAAAGCAGATCACATCCAG
66 CAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCACATCCAG
*
42429815 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACATAAG-ACA-CAAATCTTAT-TTCCCCAAGGTT
131 TCTTATCTCCCTGAAGTTGCAATGGAGCAGAC-TAAGTA-AGCAAATCTTATCCTCCCCAA-GTT
42429877 GCAGTG
193 GCAGTG
42429883 GAGTGGATTG
Statistics
Matches: 172, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
216 5 0.03
217 162 0.94
218 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
AATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATCAAAGCCAATAATCCTATCTCCCAGAAGTTG
CAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCACATCCAG
TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAATCTTATCCTCCCCAAGTTGCA
GTGAGGCAGACTGAAGATGACA
Found at i:42432507 original size:120 final size:119
Alignment explanation
Indices: 42432285--42432547 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
42432275 TCCTCGTTCA
* * **
42432285 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * *
42432350 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
42432403 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
42432468 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
42432524 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42432548 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 36 0.30
120 80 0.66
121 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:42432508 original size:40 final size:40
Alignment explanation
Indices: 42432285--42432494 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
42432275 TCCTCGTTCA
* * * ** *
42432285 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42432324 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42432364 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42432404 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
42432444 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
42432484 AAGGCCTTCGG
1 AATGCCTTCGG
42432495 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:42432531 original size:80 final size:80
Alignment explanation
Indices: 42432288--42432547 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 80
42432278 TCGTTCAAAT
* * * ** * * *
42432288 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
42432352 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
* * *
42432367 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
42432432 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
** * **
42432447 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
*
42432511 ATTC-ACTTAGCAC-AAA
65 A-ACAAC-TAGCACGAAA
*
42432527 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
42432548 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 33 0.21
80 120 0.75
81 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ACAACTAGCACGAAA
Found at i:42432556 original size:41 final size:41
Alignment explanation
Indices: 42432479--42432556 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42432469 TTAGTATCTC
* * *
42432479 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42432520 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42432557 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42440243 original size:40 final size:40
Alignment explanation
Indices: 42440182--42440420 Score: 295
Period size: 40 Copynumber: 6.0 Consensus size: 40
42440172 CATAGCCCGT
* * *
42440182 TTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGA
1 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
*
42440221 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
42440261 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
42440301 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
* * * * **
42440341 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGA
1 TTTAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA
* * * * * *
42440381 TATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 TTTAATAAC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
42440421 CAGCATTCAA
Statistics
Matches: 178, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.08
40 155 0.87
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
Found at i:42440429 original size:41 final size:41
Alignment explanation
Indices: 42440352--42440429 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42440342 TTAGTATCTC
* * *
42440352 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42440393 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42440430 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42451731 original size:15 final size:15
Alignment explanation
Indices: 42451711--42451741 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42451701 GACGGTTCCG
42451711 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
42451726 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
42451741 T
1 T
42451742 ACTGATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:42455189 original size:20 final size:19
Alignment explanation
Indices: 42455159--42455242 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
42455149 GATGTTAGAA
42455159 TATTAATTCTATTATATATT
1 TATT-ATTCTATTATATATT
42455179 TATCTATTCTATTATATA--
1 TAT-TATTCTATTATATATT
*
42455197 TA-TATTCTAATATATATT
1 TATTATTCTATTATATATT
42455215 AGTATTATT-T-TTATATTATT
1 --TATTATTCTATTATA-TATT
42455235 TATCTATT
1 TAT-TATT
42455243 TCTTATCTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 8 0.15
20 23 0.43
21 5 0.09
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTATTCTATTATATATT
Found at i:42455204 original size:16 final size:17
Alignment explanation
Indices: 42455164--42455213 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
42455154 TAGAATATTA
42455164 ATTCTATTATATATTTATCT
1 ATTCTATTATATA--TA-CT
42455184 ATTCTATTATATATA-T
1 ATTCTATTATATATACT
*
42455200 ATTCTAATATATAT
1 ATTCTATTATATAT
42455214 TAGTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCTATTATATATACT
Found at i:42456968 original size:18 final size:18
Alignment explanation
Indices: 42456947--42456983 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42456937 AATTCGACGC
* *
42456947 AGTGGATAAATTAGATAA
1 AGTGGAAAAATGAGATAA
42456965 AGTGGAAAAATGAGATAA
1 AGTGGAAAAATGAGATAA
42456983 A
1 A
42456984 CCAGCTTCAT
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:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (18 bp):
AGTGGAAAAATGAGATAA
Found at i:42459852 original size:17 final size:17
Alignment explanation
Indices: 42459830--42459863 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42459820 ATAGATTCGC
*
42459830 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
42459847 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
42459864 AATATACGAA
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:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:42472266 original size:6 final size:6
Alignment explanation
Indices: 42472257--42472298 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
42472247 ATCGTTATTT
*
42472257 ATTATC ATTATC ATTATC ATTATC ATTATC TATTATC TTTAT
1 ATTATC ATTATC ATTATC ATTATC ATTATC -ATTATC ATTAT
42472299 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTATC
Found at i:42472280 original size:18 final size:19
Alignment explanation
Indices: 42472244--42472298 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
42472234 ATTGTTATTT
* *
42472244 ATTATCGTTATTTATTATC
1 ATTATCATTATCTATTATC
42472263 ATTATCATTATC-ATTATC
1 ATTATCATTATCTATTATC
42472281 ATTATCTATTATCT-TTAT
1 ATTATC-ATTATCTATTAT
42472299 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTATCATTATCTATTATC
Found at i:42472293 original size:13 final size:13
Alignment explanation
Indices: 42472238--42472298 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
42472228 AAGAAAATTG
* *
42472238 TTATTTATTATCG
1 TTATCTATTATCA
*
42472251 TTATTTATTATCA
1 TTATCTATTATCA
42472264 TTATC-ATTATCA
1 TTATCTATTATCA
42472276 TTATC-ATTATCTA
1 TTATCTATTATC-A
42472289 TTATCT-TTAT
1 TTATCTATTAT
42472299 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 18 0.41
13 26 0.59
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.59
Consensus pattern (13 bp):
TTATCTATTATCA
Found at i:42472994 original size:13 final size:14
Alignment explanation
Indices: 42472960--42472997 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
42472950 TGCTTTTATA
42472960 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
42472975 TAT-TTATTT-GTT
1 TATATTATTTCGTT
42472987 TATATTATTTC
1 TATATTATTTC
42472998 TATGCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:42475062 original size:20 final size:20
Alignment explanation
Indices: 42475039--42475089 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
42475029 CACAAACTTT
42475039 TCTTTGTTCATGTATAGCAG
1 TCTTTGTTCATGTATAGCAG
*
42475059 TCTTTGTTCATGTATAGTAG
1 TCTTTGTTCATGTATAGCAG
* *
42475079 CCTTTTTTCAT
1 TCTTTGTTCAT
42475090 TTAAAATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.51
Consensus pattern (20 bp):
TCTTTGTTCATGTATAGCAG
Found at i:42476869 original size:62 final size:62
Alignment explanation
Indices: 42476759--42476881 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 62
42476749 TGTAAGTGTG
*
42476759 ATTTTGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCCA
1 ATTTCGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCCA
* * *
42476821 ATTTCGTCCTGTTTTTAATGATTTTTATGTTTTTGAAGTCGCAGCTTAATCTACCTAGCCC
1 ATTTCGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCC
42476882 GAGGACTAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (62 bp):
ATTTCGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCCA
Found at i:42491412 original size:21 final size:21
Alignment explanation
Indices: 42491386--42491435 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
42491376 AAGGTGGAAG
* *
42491386 TTATGTGGCAGCTATCTACGA
1 TTATGTGGCAGCTATCGACAA
* *
42491407 TTATGTGGCTGTTATCGACAA
1 TTATGTGGCAGCTATCGACAA
42491428 TTATGTGG
1 TTATGTGG
42491436 TGGCTTGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
TTATGTGGCAGCTATCGACAA
Found at i:42493638 original size:21 final size:21
Alignment explanation
Indices: 42493596--42493638 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42493586 TACAAATAGG
**
42493596 ACATTAAAACATACATTTCAT
1 ACATTAAAACATACATAACAT
* *
42493617 ACATTAATATATACATAACAT
1 ACATTAAAACATACATAACAT
42493638 A
1 A
42493639 AATCATTCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (21 bp):
ACATTAAAACATACATAACAT
Found at i:42500875 original size:43 final size:43
Alignment explanation
Indices: 42500822--42500964 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
42500812 TTTGGGATTG
* * * *
42500822 CGCCACTAAAGACCATGACCTTTAGCTGCACTTTT-TTGACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCACTTTTCCT-ACAAA
** *
42500865 CGCCGCTAAAGACCCTGATATTTAGCGGCACTTTTCCTACAAT
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCACTTTTCCTACAAA
* * *
42500908 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTCTTTCC-ACGAG
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCACT-TTTCCTACAAA
*
42500951 TGCCGCTAAAGACC
1 CGCCGCTAAAGACC
42500965 ACGACAAAGC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 79 0.93
44 6 0.07
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGACCCTGACCTTTAGCGGCACTTTTCCTACAAA
Done.