Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 127 of 290
Found at i:39805784 original size:17 final size:17
Alignment explanation
Indices: 39805759--39805792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39805749 ATAATTTTAA
*
39805759 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
39805776 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
39805793 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:39805809 original size:17 final size:16
Alignment explanation
Indices: 39805764--39805811 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
39805754 TTTAAATTTT
39805764 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
39805781 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
39805795 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
39805812 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:39805883 original size:18 final size:17
Alignment explanation
Indices: 39805852--39805886 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39805842 ATTATTAAGA
39805852 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
39805869 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
39805887 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:39805907 original size:128 final size:127
Alignment explanation
Indices: 39805775--39806031 Score: 394
Period size: 128 Copynumber: 2.0 Consensus size: 127
39805765 TTAAATCATA
*
39805775 TATTTA-ATTAAATCA-TAT-TAGTTATAATCATATATTATGATTTGAGTAAATTCATATAAGAA
1 TATTTATATTAAA-CAGTATATA-TT-TAATAATA-ATTATGATTTGAGTAAATTCATATAAGAA
* *
39805837 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATAATTATG
62 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG
39805902 T
127 T
** *
39805903 TATTTATATTTTACAGTATCATATTTAATAATAATTATGGTTTGAGTAAATTCATATAAGAATAT
1 TATTTATATTAAACAGTAT-ATATTTAATAATAATTATGATTTGAGTAAATTCATATAAGAATAT
39805968 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGT
65 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGT
39806031 T
1 T
39806032 TAAATATGAT
Statistics
Matches: 119, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
128 101 0.85
129 14 0.12
130 2 0.02
131 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (127 bp):
TATTTATATTAAACAGTATATATTTAATAATAATTATGATTTGAGTAAATTCATATAAGAATATT
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGT
Found at i:39806008 original size:18 final size:17
Alignment explanation
Indices: 39805980--39806014 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39805970 ATTATTAAGA
*
39805980 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39805997 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39806015 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39806134 original size:147 final size:149
Alignment explanation
Indices: 39805968--39806242 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
39805958 ATAAGAATAT
*
39805968 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
39806033 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
39806096 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
39806115 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
39806180 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
39806243 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:39806155 original size:18 final size:17
Alignment explanation
Indices: 39806127--39806161 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39806117 ATTATTAAGA
*
39806127 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39806144 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39806162 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39806372 original size:44 final size:45
Alignment explanation
Indices: 39806323--39806417 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
39806313 TTACACCTCT
* * *
39806323 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
39806367 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
39806412 ATTACA
1 ATTACA
39806418 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:39806417 original size:16 final size:16
Alignment explanation
Indices: 39806398--39806465 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
39806388 GATTTGCTAT
* * *
39806398 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
39806414 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39806430 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39806446 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39806462 TACA
1 TACA
39806466 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39809195 original size:62 final size:62
Alignment explanation
Indices: 39809125--39809275 Score: 205
Period size: 62 Copynumber: 2.4 Consensus size: 62
39809115 CACACAGTCG
* * *
39809125 GGGCACACGCCCATGTCCCTAGTCGTGTGG-CTTTGCGCCACAGATAGTGAGTTACACAGCTT
1 GGGCACACGCCCATGTCCCTAGCCGTGTGGTC-TTGCACCACAAATAGTGAGTTACACAGCTT
* * * *
39809187 GGGCACACGGCCGTGTCCCTGGCCGTGTGGTCTTGTACCACAAATAGTGAGTTACACAGCTT
1 GGGCACACGCCCATGTCCCTAGCCGTGTGGTCTTGCACCACAAATAGTGAGTTACACAGCTT
* *
39809249 GGGCACACGCCCCTGTCCCTGGCCGTG
1 GGGCACACGCCCATGTCCCTAGCCGTG
39809276 AGAACTCTGC
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
62 78 0.99
63 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (62 bp):
GGGCACACGCCCATGTCCCTAGCCGTGTGGTCTTGCACCACAAATAGTGAGTTACACAGCTT
Found at i:39812502 original size:21 final size:21
Alignment explanation
Indices: 39812476--39812615 Score: 154
Period size: 21 Copynumber: 6.7 Consensus size: 21
39812466 AGCTCGAAAC
* *
39812476 CTGAACAGAAGCTCATAAAAG
1 CTGAACAAAAGCTCATAAGAG
*
39812497 CTGAACAAAAACTCATAAGAG
1 CTGAACAAAAGCTCATAAGAG
* * *
39812518 TTGAACAGAAGCTCGTAAGAG
1 CTGAACAAAAGCTCATAAGAG
* *
39812539 CTAAACAAAAACTCATAAGAG
1 CTGAACAAAAGCTCATAAGAG
* **
39812560 TTGAACAAAAGCTTGTAAGAG
1 CTGAACAAAAGCTCATAAGAG
* **
39812581 CTAAACAAAAGCTTGTAAGAG
1 CTGAACAAAAGCTCATAAGAG
39812602 CTGAACAAAAGCTC
1 CTGAACAAAAGCTC
39812616 GAAAGTGCTA
Statistics
Matches: 98, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 98 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (21 bp):
CTGAACAAAAGCTCATAAGAG
Found at i:39812524 original size:42 final size:42
Alignment explanation
Indices: 39812477--39812629 Score: 198
Period size: 42 Copynumber: 3.6 Consensus size: 42
39812467 GCTCGAAACC
* * * *
39812477 TGAACAGAAGCTCATAAAAGCTGAACAAAAACTCATAAGAGT
1 TGAACAAAAGCTCGTAAGAGCTAAACAAAAACTCATAAGAGT
*
39812519 TGAACAGAAGCTCGTAAGAGCTAAACAAAAACTCATAAGAGT
1 TGAACAAAAGCTCGTAAGAGCTAAACAAAAACTCATAAGAGT
* * ** *
39812561 TGAACAAAAGCTTGTAAGAGCTAAACAAAAGCTTGTAAGAGC
1 TGAACAAAAGCTCGTAAGAGCTAAACAAAAACTCATAAGAGT
* *
39812603 TGAACAAAAGCTCGAAAGTGCTAAACA
1 TGAACAAAAGCTCGTAAGAGCTAAACA
39812630 GAAAGTAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 99 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (42 bp):
TGAACAAAAGCTCGTAAGAGCTAAACAAAAACTCATAAGAGT
Found at i:39812629 original size:21 final size:21
Alignment explanation
Indices: 39812479--39812634 Score: 141
Period size: 21 Copynumber: 7.4 Consensus size: 21
39812469 TCGAAACCTG
* * * *
39812479 AACAGAAGCTCATAAAAGCTG
1 AACAAAAGCTCGTAAGAGCTA
* * * *
39812500 AACAAAAACTCATAAGAGTTG
1 AACAAAAGCTCGTAAGAGCTA
*
39812521 AACAGAAGCTCGTAAGAGCTA
1 AACAAAAGCTCGTAAGAGCTA
* * * *
39812542 AACAAAAACTCATAAGAGTTG
1 AACAAAAGCTCGTAAGAGCTA
*
39812563 AACAAAAGCTTGTAAGAGCTA
1 AACAAAAGCTCGTAAGAGCTA
* *
39812584 AACAAAAGCTTGTAAGAGCTG
1 AACAAAAGCTCGTAAGAGCTA
* *
39812605 AACAAAAGCTCGAAAGTGCTA
1 AACAAAAGCTCGTAAGAGCTA
39812626 AACAGAAAG
1 AACA-AAAG
39812635 TAAAACACGA
Statistics
Matches: 110, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
21 106 0.96
22 4 0.04
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (21 bp):
AACAAAAGCTCGTAAGAGCTA
Found at i:39814180 original size:28 final size:28
Alignment explanation
Indices: 39814148--39814223 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
39814138 ATGTTTAGGG
39814148 TTAGGG-TTAGGGTTTTTGAAAAAATAAA
1 TTAGGGTTTAGGGTTTTT-AAAAAATAAA
* *
39814176 TTAGGGTTTATGGTTTTTAAAAATTAAA
1 TTAGGGTTTAGGGTTTTTAAAAAATAAA
*
39814204 TTTGGGTTTAGGGTTTTTAA
1 TTAGGGTTTAGGGTTTTTAA
39814224 TAGGTAAGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 33 0.77
29 10 0.23
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (28 bp):
TTAGGGTTTAGGGTTTTTAAAAAATAAA
Found at i:39814719 original size:126 final size:126
Alignment explanation
Indices: 39814289--39814719 Score: 539
Period size: 126 Copynumber: 3.4 Consensus size: 126
39814279 TTTTTGTATA
* * * * *
39814289 GTCAACAAAAGTACTG--AAAAGCTCTCAACTAGACACTCTTTTTGTACATTAGTTTCTT-AAAA
1 GTCAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTACTTT-TTGAAAA
* * * * *
39814351 AGTAATTTTGAGAAGATAGTTTTAAAAAAATAGGTTGAAAAACATTTCAAGCAGGATGCACT
65 AATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
* * * * * ** *
39814413 GTCAACAAAAGTACTGAAAAAAGCTTCTAGCTGGACACTCTTTTTGTATAGTAAATTATGAAAAA
1 GTCAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTACTTTTTG-AAAA
* * * * *
39814478 AATAATTTTGAGAAGATGGTTCTGAAAAAGTAGG-TCAAAAA-ATGCTTCAAGTAAGATACGCT
65 AATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACAT--TTCAAGTAGGATGCACT
* * *
39814540 GTCAGCAAAAGTATTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGAACAGTACTTTTTGAAAAA
1 GTCAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTACTTTTTGAAAAA
39814605 ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
66 ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
* *
39814666 ATCAGCAAAAGTACTGAAAAATGCTCCCAGCTAGACACTCTTTTTGTACAGTAC
1 GTCAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTAC
39814720 ATTCTGCTTG
Statistics
Matches: 260, Mismatches: 39, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
124 16 0.06
125 3 0.01
126 136 0.52
127 103 0.40
128 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (126 bp):
GTCAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTACTTTTTGAAAAA
ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
Found at i:39814815 original size:25 final size:25
Alignment explanation
Indices: 39814786--39814858 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
39814776 TTACATCAAG
39814786 AGAAATTGAAGAAGTTTAGAAGGAT
1 AGAAATTGAAGAAGTTTAGAAGGAT
* * * *
39814811 AGAAATTAAAGAAGTTCAAAAGAAT
1 AGAAATTGAAGAAGTTTAGAAGGAT
*
39814836 AAAAATTGAAGAA-TTTGAGAAGG
1 AGAAATTGAAGAAGTTT-AGAAGG
39814859 TATAAGTTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 2 0.05
25 36 0.95
ACGTcount: A:0.53, C:0.01, G:0.23, T:0.22
Consensus pattern (25 bp):
AGAAATTGAAGAAGTTTAGAAGGAT
Found at i:39817957 original size:60 final size:59
Alignment explanation
Indices: 39817891--39818018 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 59
39817881 TGTATTACCT
*
39817891 TATTCAAAAGAACTTCTATTTTATTAAATATGACAA-AATATAAAAATAATTTATACAAA-A
1 TATTCAAAACAACTTCTATTTTATT-AA-ATGA-AACAATATAAAAATAATTTATACAAATA
* * *
39817951 TATTCAAAACAACTTTTGTTTTATTAAATGAAACAATATAAAAATAATTTGTACAAATA
1 TATTCAAAACAACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTATACAAATA
*
39818010 TATTAAAAA
1 TATTCAAAA
39818019 AATAAATGCA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
57 2 0.03
58 26 0.43
59 11 0.18
60 22 0.36
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (59 bp):
TATTCAAAACAACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTATACAAATA
Found at i:39821827 original size:11 final size:11
Alignment explanation
Indices: 39821811--39821853 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
39821801 ATATTTTATA
39821811 TTTTTAATAAT
1 TTTTTAATAAT
39821822 TTTTTAAT--T
1 TTTTTAATAAT
*
39821831 TTTTT-ATAAA
1 TTTTTAATAAT
39821841 TTTTTAATAAT
1 TTTTTAATAAT
39821852 TT
1 TT
39821854 ATTTTTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
8 2 0.07
9 6 0.22
10 5 0.19
11 14 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:39821833 original size:19 final size:19
Alignment explanation
Indices: 39821811--39821848 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39821801 ATATTTTATA
*
39821811 TTTTTAATAATTTTTTAAT
1 TTTTTAATAAATTTTTAAT
*
39821830 TTTTTTATAAATTTTTAAT
1 TTTTTAATAAATTTTTAAT
39821849 AATTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAATAAATTTTTAAT
Found at i:39828460 original size:32 final size:32
Alignment explanation
Indices: 39828414--39828476 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
39828404 TCAAAACCTT
**
39828414 TCATCGTAAAATTATCATATTTGGCCATAACG
1 TCATCGTAAAATTATCATATTCAGCCATAACG
* *
39828446 TCATTGTAACATTATCATATTCAGCCATAAC
1 TCATCGTAAAATTATCATATTCAGCCATAAC
39828477 ATCTGGGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (32 bp):
TCATCGTAAAATTATCATATTCAGCCATAACG
Found at i:39828733 original size:33 final size:33
Alignment explanation
Indices: 39828695--39828762 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
39828685 GGTTTATGTT
*
39828695 TTTTCAATTTGTACAAGCTCGAGGGAGTTTTTG
1 TTTTCAATTTGTACAAACTCGAGGGAGTTTTTG
*
39828728 TTTTCAATTTGTACAAACTTGAGGGAGTTTTTG
1 TTTTCAATTTGTACAAACTCGAGGGAGTTTTTG
39828761 TT
1 TT
39828763 CCCTATGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTTCAATTTGTACAAACTCGAGGGAGTTTTTG
Found at i:39830679 original size:41 final size:40
Alignment explanation
Indices: 39830589--39830913 Score: 407
Period size: 41 Copynumber: 8.0 Consensus size: 40
39830579 TATAAAACAT
* * * *
39830589 AGAGTAATAGCGGCGTTTTTGGTAAAACGTCGCTAAAAAC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAACC
*
39830629 AGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTTAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC-TAAAACC
*
39830670 AGAGCAATAGAGGCGCTTTTGGTAAAACGCCGCTAAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCT--AAAACC
39830712 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAGAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTA-AAACC
* *
39830753 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAGAAATC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTA-AAACC
* * * * * *
39830794 GGTGTATTAGCGACGCTTTTGGTAAAACGCCGTTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCT-AAAACC
*
39830835 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCT-AAAACC
* * * * *
39830876 GGAGTATTAGCGGCACTTTTGATAAAACGCCGCTAAAA
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
39830914 GTCATATAAC
Statistics
Matches: 257, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
40 37 0.14
41 180 0.70
42 40 0.16
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (40 bp):
AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAACC
Found at i:39830956 original size:18 final size:17
Alignment explanation
Indices: 39830910--39830957 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
39830900 AAACGCCGCT
* *
39830910 AAAAGTCATATAACCCCT
1 AAAAATCATA-AACCCCA
39830928 AAAAATC-TAAACCCACA
1 AAAAATCATAAACCC-CA
39830945 AAAAATCATAAAC
1 AAAAATCATAAAC
39830958 ACTAATCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 10 0.38
18 11 0.42
ACGTcount: A:0.56, C:0.25, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAATCATAAACCCCA
Found at i:39831001 original size:23 final size:22
Alignment explanation
Indices: 39830954--39831001 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
39830944 AAAAAATCAT
* *
39830954 AAACACTAATCTATAATCCTTA
1 AAACACTAAACTATAAACCTTA
*
39830976 AAACACTAAACTCCTAAACCTTA
1 AAACACTAAACT-ATAAACCTTA
39830999 AAA
1 AAA
39831002 AATCTTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACACTAAACTATAAACCTTA
Found at i:39831346 original size:14 final size:14
Alignment explanation
Indices: 39831324--39831371 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
39831314 TTAATTATCA
*
39831324 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
39831338 TTATGGTTTAAGCT
1 TTATGGTTTAAGGT
*
39831352 ATATGGGTTTAAGGT
1 TTAT-GGTTTAAGGT
39831367 TTATG
1 TTATG
39831372 AGTTAACTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:39831371 original size:15 final size:15
Alignment explanation
Indices: 39831329--39831371 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
39831319 TATCATTATA
39831329 GTTTAAGGTTTAT-G
1 GTTTAAGGTTTATGG
* *
39831343 GTTTAAGCTATATGG
1 GTTTAAGGTTTATGG
39831358 GTTTAAGGTTTATG
1 GTTTAAGGTTTATG
39831372 AGTTAACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (15 bp):
GTTTAAGGTTTATGG
Found at i:39831429 original size:21 final size:21
Alignment explanation
Indices: 39831396--39831459 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
39831386 TAAAGGTGGT
*
39831396 TTAAGGGT-TGGGGTTTAAGG
1 TTAAGGGTGAGGGGTTTAAGG
*
39831416 TT-AGGTGTTAGGGG-TTAAGGG
1 TTAAGG-GTGAGGGGTTTAA-GG
*
39831437 TTAAGGGTGAGGGGTTTATGG
1 TTAAGGGTGAGGGGTTTAAGG
39831458 TT
1 TT
39831460 TAGGATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 19 0.53
22 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.36
Consensus pattern (21 bp):
TTAAGGGTGAGGGGTTTAAGG
Found at i:39831492 original size:14 final size:14
Alignment explanation
Indices: 39831448--39831511 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
39831438 TAAGGGTGAG
39831448 GGGTTT-ATGGTTTA
1 GGGTTTAAT-GTTTA
*
39831462 GGATTT-ATGTTTTA
1 GGGTTTAATG-TTTA
39831476 GGGTTTAATGTTTA
1 GGGTTTAATGTTTA
* *
39831490 GGGATTAAGAGTTTA
1 GGGTTTAA-TGTTTA
39831505 GGGTTTA
1 GGGTTTA
39831512 GATTAGTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
13 1 0.02
14 27 0.64
15 14 0.33
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
GGGTTTAATGTTTA
Found at i:39831512 original size:7 final size:7
Alignment explanation
Indices: 39831393--39831512 Score: 50
Period size: 7 Copynumber: 17.0 Consensus size: 7
39831383 GTTTAAAGGT
39831393 GGTTTAAG
1 GGTTT-AG
*
39831401 GG-TTGG
1 GGTTTAG
*
39831407 GGTTTAA
1 GGTTTAG
39831414 GG-TTA-
1 GGTTTAG
39831419 GGTGTTAGG
1 GGT-TTA-G
*
39831428 GGTTAAG
1 GGTTTAG
*
39831435 GGTTAAG
1 GGTTTAG
*
39831442 GG-TGAGG
1 GGTTTA-G
*
39831449 GGTTTAT
1 GGTTTAG
39831456 GGTTTAG
1 GGTTTAG
* *
39831463 GATTTAT
1 GGTTTAG
*
39831470 GTTTTAG
1 GGTTTAG
*
39831477 GGTTTAA
1 GGTTTAG
*
39831484 TGTTTAG
1 GGTTTAG
*
39831491 GGATTAAG
1 GG-TTTAG
*
39831499 AGTTTAG
1 GGTTTAG
39831506 GGTTTAG
1 GGTTTAG
39831513 ATTAGTTAGT
Statistics
Matches: 83, Mismatches: 21, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
5 2 0.02
6 8 0.10
7 59 0.71
8 11 0.13
9 3 0.04
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:39831684 original size:22 final size:22
Alignment explanation
Indices: 39831659--39831703 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39831649 ATTATTTTAA
*
39831659 GGTTTATGGATTATGGA-TTATG
1 GGTTTAGGGATTAT-GATTTATG
*
39831681 GGTTTAGGGTTTATGATTTATG
1 GGTTTAGGGATTATGATTTATG
39831703 G
1 G
39831704 TTATGTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (22 bp):
GGTTTAGGGATTATGATTTATG
Found at i:39832110 original size:6 final size:7
Alignment explanation
Indices: 39832077--39832141 Score: 85
Period size: 8 Copynumber: 8.6 Consensus size: 7
39832067 AATTCTTCAA
39832077 AAAAATT
1 AAAAATT
39832084 GAAAAATT
1 -AAAAATT
39832092 GAAAAATT
1 -AAAAATT
39832100 AAAAATT
1 AAAAATT
39832107 AAAAATT
1 AAAAATT
39832114 AAAAACTT
1 AAAAA-TT
39832122 AAAAATTT
1 AAAAA-TT
39832130 AAAAACTT
1 AAAAA-TT
39832138 AAAA
1 AAAA
39832142 TTTTAATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
7 19 0.35
8 35 0.65
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:39832215 original size:23 final size:24
Alignment explanation
Indices: 39832175--39832220 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
39832165 CATATTTCAG
* *
39832175 TTAAAAAAATCAATATT-CAAAAT
1 TTAAAAAAATAAAAATTCCAAAAT
39832198 TTAAAAAAATAAAAATTCCAAAA
1 TTAAAAAAATAAAAATTCCAAAA
39832221 AATAATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (24 bp):
TTAAAAAAATAAAAATTCCAAAAT
Found at i:39834840 original size:17 final size:17
Alignment explanation
Indices: 39834818--39834854 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
39834808 CTTGATCCTC
39834818 TGTTAAATGTAATTAAA
1 TGTTAAATGTAATTAAA
39834835 TGTTAAATGTAATTAAA
1 TGTTAAATGTAATTAAA
39834852 TGT
1 TGT
39834855 AATTAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TGTTAAATGTAATTAAA
Found at i:39834869 original size:10 final size:10
Alignment explanation
Indices: 39834820--39834866 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
39834810 TGATCCTCTG
39834820 TTAAATGTAA
1 TTAAATGTAA
39834830 TTAAATG---
1 TTAAATGTAA
39834837 TTAAATGTAA
1 TTAAATGTAA
39834847 TTAAATGTAA
1 TTAAATGTAA
39834857 TTAATATGTA
1 TTAA-ATGTA
39834867 TTACAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 7 0.21
10 21 0.64
11 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (10 bp):
TTAAATGTAA
Found at i:39834876 original size:16 final size:15
Alignment explanation
Indices: 39834855--39834884 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39834845 AATTAAATGT
39834855 AATTAATATGTATTAC
1 AATTAATATG-ATTAC
39834871 AATTAATATGATTA
1 AATTAATATGATTA
39834885 ACTTAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
AATTAATATGATTAC
Found at i:39834877 original size:20 final size:20
Alignment explanation
Indices: 39834820--39834866 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
39834810 TGATCCTCTG
39834820 TTAAATGTAATTAAATG---
1 TTAAATGTAATTAAATGTAA
39834837 TTAAATGTAATTAAATGTAA
1 TTAAATGTAATTAAATGTAA
39834857 TTAATATGTA
1 TTAA-ATGTA
39834867 TTACAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 17 0.65
20 4 0.15
21 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (20 bp):
TTAAATGTAATTAAATGTAA
Found at i:39837776 original size:43 final size:43
Alignment explanation
Indices: 39837705--39837801 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
39837695 TTTTTATGAC
* *
39837705 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGAA-
1 CTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCCT-AAT
39837748 CTTTAGCGGCGTTTATGGGATAAA-CGCCGCTAAAGGTCCTAAT
1 CTTTAGCGGCGTTTATGGGA-AAAGCGCCGCTAAAGGTCCTAAT
*
39837791 CTTTAGTGGCG
1 CTTTAGCGGCG
39837802 CCATCTATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
42 2 0.04
43 44 0.90
44 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCCTAAT
Found at i:39850074 original size:12 final size:12
Alignment explanation
Indices: 39850057--39850083 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39850047 TTGTAAAAAT
39850057 AATATTAGATTA
1 AATATTAGATTA
39850069 AATATTAGATTA
1 AATATTAGATTA
39850081 AAT
1 AAT
39850084 TTAATACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (12 bp):
AATATTAGATTA
Found at i:39856407 original size:30 final size:30
Alignment explanation
Indices: 39856372--39856429 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39856362 AACAGGGGAC
* *
39856372 ACACGCCCATGTGGCTAGGCCGTGTGTCAG
1 ACACGCCCATATGGCCAGGCCGTGTGTCAG
*
39856402 ACACGCCCGTATGGCCAGGCCGTGTGTC
1 ACACGCCCATATGGCCAGGCCGTGTGTC
39856430 TCACATAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.19
Consensus pattern (30 bp):
ACACGCCCATATGGCCAGGCCGTGTGTCAG
Found at i:39859524 original size:20 final size:18
Alignment explanation
Indices: 39859474--39859525 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
39859464 CTTGTGGATA
39859474 AATATTAAATTAA-ACTT
1 AATATTAAATTAATACTT
39859491 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-AC-TT
39859511 AATATTAAATTAATA
1 AATATTAAATTAATA
39859526 AAATACTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 4 0.13
20 14 0.47
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATACTT
Found at i:39874657 original size:45 final size:45
Alignment explanation
Indices: 39874608--39874729 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
39874598 GATGCCGATG
* * *
39874608 TCCCAGATATGGTCTTACATGTAACCACATATATTGATGCCAACA
1 TCCCAGACATGGTCTTACACGTAAACACATATATTGATGCCAACA
* *
39874653 TCCCAGACATGGTCTTACACGTAAACACATTTATTGATGCCAACG
1 TCCCAGACATGGTCTTACACGTAAACACATATATTGATGCCAACA
*
39874698 TCCCAGACGTGGTCTTACACG-AGAACACATAT
1 TCCCAGACATGGTCTTACACGTA-AACACATAT
39874730 TAGATCCTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 68 0.99
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (45 bp):
TCCCAGACATGGTCTTACACGTAAACACATATATTGATGCCAACA
Found at i:39884597 original size:148 final size:148
Alignment explanation
Indices: 39884329--39884623 Score: 536
Period size: 148 Copynumber: 2.0 Consensus size: 148
39884319 GTACTCAGCT
* *
39884329 GATTTCTTCTATAGTTGAAAAACATGGCTGGAAAATATTTTGCCTTCATCCCGGCGATGTTCTCA
1 GATTTCTTCTATAGTTGAAAAACATGACTGGAAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
*
39884394 CAAAGGTTGTAATGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
66 CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
39884459 GTATGGTTTACCTGAGGC
131 GTATGGTTTACCTGAGGC
*
39884477 GATTTCTTCTATAGTTGAAAAACATGACTGGCAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
1 GATTTCTTCTATAGTTGAAAAACATGACTGGAAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
*
39884542 CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTTTCCAGATGATGTACTCCATCAACGCACA
66 CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
*
39884607 GTATGGTTTACTTGAGG
131 GTATGGTTTACCTGAGG
39884624 TCTAGATGAA
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 141 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (148 bp):
GATTTCTTCTATAGTTGAAAAACATGACTGGAAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
GTATGGTTTACCTGAGGC
Found at i:39885937 original size:18 final size:18
Alignment explanation
Indices: 39885914--39885949 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39885904 TTGGGGGTGT
39885914 GTTGTACTTATTGTATGC
1 GTTGTACTTATTGTATGC
39885932 GTTGTACTTATTGTATGC
1 GTTGTACTTATTGTATGC
39885950 ATTAGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (18 bp):
GTTGTACTTATTGTATGC
Found at i:39889687 original size:12 final size:12
Alignment explanation
Indices: 39889670--39889694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39889660 TTTTAATAAT
39889670 ATTTAATATTAA
1 ATTTAATATTAA
39889682 ATTTAATATTAA
1 ATTTAATATTAA
39889694 A
1 A
39889695 GTGATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:39892326 original size:17 final size:18
Alignment explanation
Indices: 39892299--39892337 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
39892289 TTCTCCTCCT
39892299 CTAAGGGGAAAC-AGAAA
1 CTAAGGGGAAACAAGAAA
39892316 GCTAA-GGGAAACAAGAAA
1 -CTAAGGGGAAACAAGAAA
39892334 CTAA
1 CTAA
39892338 CTAAGACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.54, C:0.13, G:0.26, T:0.08
Consensus pattern (18 bp):
CTAAGGGGAAACAAGAAA
Found at i:39893385 original size:5 final size:5
Alignment explanation
Indices: 39893375--39893402 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39893365 TTTTGACTAG
39893375 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
39893403 GGTATCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:39893766 original size:20 final size:21
Alignment explanation
Indices: 39893727--39893766 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39893717 AAGGGCTATT
*
39893727 TTGTAAAGTTTGTAAAATAAG
1 TTGTAAAGTGTGTAAAATAAG
*
39893748 TTGTAAA-TGTGTGAAATAA
1 TTGTAAAGTGTGTAAAATAA
39893767 TTAAAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGTAAAGTGTGTAAAATAAG
Found at i:39896746 original size:18 final size:18
Alignment explanation
Indices: 39896661--39896748 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
39896651 TTCTTTTGTT
** *
39896661 TCTTTTTCTAATTCATTT
1 TCTTTTTCTTTTTCATTC
*
39896679 TC-TCTTCTTTTTCAATT-
1 TCTTTTTCTTTTTC-ATTC
** * *
39896696 TCTTTTTCACTCTCAATC
1 TCTTTTTCTTTTTCATTC
39896714 TCTTTTTGCTCTTTTTCATTC
1 TC-TTTT--TCTTTTTCATTC
39896735 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
39896749 CTCACTTGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 12 0.23
18 22 0.42
19 4 0.08
20 4 0.08
21 10 0.19
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.65
Consensus pattern (18 bp):
TCTTTTTCTTTTTCATTC
Found at i:39899328 original size:48 final size:46
Alignment explanation
Indices: 39899223--39899531 Score: 151
Period size: 48 Copynumber: 6.5 Consensus size: 46
39899213 ACTCGTATCA
* *
39899223 ACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCACAATATGAAAGCCAGTGTAAG
*
39899269 ACATGTCTGGGACATGCATCGGCCTCGAGATAT-ACAAGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCAC-A-ATATGA-AAGCCAGTGTAAG
* * * * * * *** *
39899317 ACATGCCTGGGACATG--GCGTCAAC-TTGTTGTGTGTCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCACAAT-ATGAAAGCCAGTGTAAG
* * * * * *
39899361 ACCTATCTGGGACACGGCATC-GACACCGATAGATGAGAGCCAGTGTAAG
1 ACATGTCTGGGACA-TGCATCGGCCA-C-A-ATATGAAAGCCAGTGTAAG
* **
39899410 ACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGTTAGTGTAAG
1 A-CATGTCTGGGACAT-GCATCGGCCAC-A-ATATGAAAGCCAGTGTAAG
* * * **** * **
39899460 ACCTATCTGGGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAG
1 ACATGTCTGGGACAT-GCATCGGCCACAATATGAAAGCCAGTGTAAG
*
39899507 ACCATGTCTGGGACTTGGCATCGGC
1 A-CATGTCTGGGACAT-GCATCGGC
39899532 ATCGTATCCC
Statistics
Matches: 194, Mismatches: 53, Indels: 30
0.70 0.19 0.11
Matches are distributed among these distances:
43 1 0.01
44 22 0.11
45 1 0.01
46 30 0.15
47 19 0.10
48 49 0.25
49 35 0.18
50 35 0.18
51 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (46 bp):
ACATGTCTGGGACATGCATCGGCCACAATATGAAAGCCAGTGTAAG
Found at i:39899408 original size:49 final size:49
Alignment explanation
Indices: 39899252--39899529 Score: 180
Period size: 48 Copynumber: 5.8 Consensus size: 49
39899242 CGGCCACATT
* * * * *
39899252 ATGAGAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGAT
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGAGAG
* ** * * * **
39899300 AT-ACAAGCCAGTGTAAGACATGCCTGGGACATGGCGTC-AACTTG-TTG
1 ATGA-AAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGAGAG
* * * *
39899347 -TG--TGTCAGTGTAAGACCTATCTGGGACACGGCATCGACAC-CGATAG
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGAC-CTCGAGAG
* * * *
39899393 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT
1 ATGAAAGCCAGTGTAAGACC-TATCTGGGACATGGCATCGACCTCGAGAG
** * * *
39899443 ATGAAAGTTAGTGTAAGACCTATCTGGGACATGGCATCGACTTTGA-TG
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGAGAG
** * *
39899491 -TGCTAGCCAGTGTAAGACCATGTCTGGGACTTGGCATCG
1 ATGAAAGCCAGTGTAAGACC-TATCTGGGACATGGCATCG
39899530 GCATCGTATC
Statistics
Matches: 177, Mismatches: 41, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
44 26 0.15
45 2 0.01
46 4 0.02
47 18 0.10
48 48 0.27
49 40 0.23
50 39 0.22
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (49 bp):
ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGAGAG
Found at i:39899526 original size:97 final size:99
Alignment explanation
Indices: 39899353--39899531 Score: 281
Period size: 97 Copynumber: 1.8 Consensus size: 99
39899343 GTTGTGTGTC
39899353 AGTGTAAGACCTATCTGGGACACGGCATCGACACCGATAGATGAGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACCTATCTGGGACACGGCATCGACACCGATAGATGAGAGCCAGTGTAAGACCATGTC
39899418 TGGGACATGGCATCGGCCTCGAGATATGAAAGTT
66 TGGGACATGGCATCGGCCTCGAGATATGAAAGTT
* *** **
39899452 AGTGTAAGACCTATCTGGGACATGGCATCGACTTTGAT-G-TGCTAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACCTATCTGGGACACGGCATCGACACCGATAGATGAGAGCCAGTGTAAGACCATGTC
*
39899515 TGGGACTTGGCATCGGC
66 TGGGACATGGCATCGGC
39899532 ATCGTATCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 38 0.52
98 1 0.01
99 34 0.47
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (99 bp):
AGTGTAAGACCTATCTGGGACACGGCATCGACACCGATAGATGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCGGCCTCGAGATATGAAAGTT
Found at i:39902651 original size:56 final size:50
Alignment explanation
Indices: 39902537--39902657 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 50
39902527 AGGATTAGAA
39902537 TTAATCATATTAATATTAAATTAATAAAATATTATCAAGATAAAAAATAAAT
1 TTAAT-AT-TTAATATTAAATTAATAAAATATTATCAAGATAAAAAATAAAT
* * * *
39902589 TAAATATTTAATATTAATATTAATAAAATATTATCTAA-ATAAATATTTAAT
1 TTAATATTTAATATTAA-ATTAATAAAATATTATC-AAGATAAAAAATAAAT
39902640 TT-A-ATTTAATATTAAATT
1 TTAATATTTAATATTAAATT
39902658 TGTTAAAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
48 3 0.05
49 12 0.19
50 11 0.18
51 30 0.48
52 6 0.10
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (50 bp):
TTAATATTTAATATTAAATTAATAAAATATTATCAAGATAAAAAATAAAT
Found at i:39930215 original size:17 final size:17
Alignment explanation
Indices: 39930195--39930229 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39930185 CAAATGAAGC
39930195 CTCACTAACACCTCTAT
1 CTCACTAACACCTCTAT
39930212 CTCACTAACACCTCTAT
1 CTCACTAACACCTCTAT
39930229 C
1 C
39930230 AAGGCCACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (17 bp):
CTCACTAACACCTCTAT
Found at i:39930859 original size:16 final size:15
Alignment explanation
Indices: 39930833--39930869 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
39930823 GTACGTAATA
*
39930833 TTTTGTTTTTCTTTT
1 TTTTTTTTTTCTTTT
39930848 TTCTTTTTTTTCTTTT
1 TT-TTTTTTTTCTTTT
39930864 TTTTTT
1 TTTTTT
39930870 GAGGGGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTCTTTT
Found at i:39931690 original size:17 final size:18
Alignment explanation
Indices: 39931657--39931690 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39931647 ATTGTAATCA
*
39931657 AAAATAAAAATTTCCCAC
1 AAAATAAAAATTACCCAC
39931675 AAAATAAAAA-TACCCA
1 AAAATAAAAATTACCCA
39931691 TTACCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAATAAAAATTACCCAC
Found at i:39932071 original size:15 final size:16
Alignment explanation
Indices: 39932050--39932082 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39932040 AGAATTTATT
*
39932050 TTAAAAAATTTTTAAA
1 TTAAAATATTTTTAAA
39932066 TTAAAATATTTTTAAA
1 TTAAAATATTTTTAAA
39932082 T
1 T
39932083 GTATTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATATTTTTAAA
Found at i:39932993 original size:15 final size:15
Alignment explanation
Indices: 39932973--39933002 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39932963 ATTGAATTAA
39932973 TTTTATTTTTAAAAT
1 TTTTATTTTTAAAAT
39932988 TTTTATTTTTAAAAT
1 TTTTATTTTTAAAAT
39933003 AAATAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATTTTTAAAAT
Found at i:39934159 original size:23 final size:21
Alignment explanation
Indices: 39934129--39934177 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
39934119 ATTTATTACA
*
39934129 GTTTTTAAATTAAGGTTTTAGT
1 GTTTTT-AATTAAGGGTTTAGT
*
39934151 GTTTATTAATTAGGGGTTTAGT
1 GTTT-TTAATTAAGGGTTTAGT
39934173 GTTTT
1 GTTTT
39934178 AGGGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.88
23 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.55
Consensus pattern (21 bp):
GTTTTTAATTAAGGGTTTAGT
Found at i:39934171 original size:8 final size:8
Alignment explanation
Indices: 39934160--39934217 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
39934150 TGTTTATTAA
*
39934160 TTAGGGGT
1 TTAGGGTT
*
39934168 TTAGTGTT
1 TTAGGGTT
39934176 TTAGGGTT
1 TTAGGGTT
39934184 TTA---TT
1 TTAGGGTT
*
39934189 ATTAGGCTT
1 -TTAGGGTT
39934198 TTAGGGTTT
1 TTAGGG-TT
39934207 TTAGGGTT
1 TTAGGGTT
39934215 TTA
1 TTA
39934218 AAGTTAGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 2 0.05
6 3 0.07
8 26 0.63
9 10 0.24
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (8 bp):
TTAGGGTT
Found at i:39934201 original size:30 final size:31
Alignment explanation
Indices: 39934142--39934238 Score: 96
Period size: 30 Copynumber: 3.2 Consensus size: 31
39934132 TTTAAATTAA
* *
39934142 GGTTTTAGTG-TTTATTAATTAGGGGTTTAG
1 GGTTTTAGGGTTTTATTAATTAGGCGTTTAG
* *
39934172 TGTTTTAGGGTTTTATT-ATTAGGCTTTTAG
1 GGTTTTAGGGTTTTATTAATTAGGCGTTTAG
*
39934202 GGTTTTTAGGGTTTTA--AAGTTAGG-GTTTAT
1 GG-TTTTAGGGTTTTATTAA-TTAGGCGTTTAG
39934232 GGTTTTA
1 GGTTTTA
39934239 ATTGATTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.09
30 27 0.48
31 24 0.43
ACGTcount: A:0.19, C:0.01, G:0.28, T:0.53
Consensus pattern (31 bp):
GGTTTTAGGGTTTTATTAATTAGGCGTTTAG
Found at i:39937872 original size:7 final size:7
Alignment explanation
Indices: 39937862--39937890 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
39937852 CAAAATTAAA
39937862 AATGTCC
1 AATGTCC
39937869 AATGTCC
1 AATGTCC
39937876 AATGTCC
1 AATGTCC
39937883 AA-GTCC
1 AATGTCC
39937889 AA
1 AA
39937891 CCAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (7 bp):
AATGTCC
Found at i:39947997 original size:14 final size:17
Alignment explanation
Indices: 39947965--39948002 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
39947955 GATTATAAAG
39947965 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
39947982 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
39947996 TATATTA
1 TATATTA
39948003 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:39951112 original size:12 final size:12
Alignment explanation
Indices: 39951097--39951123 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39951087 TAAAAATATT
39951097 AATAAAAAATAG
1 AATAAAAAATAG
39951109 AATAAAAAATAG
1 AATAAAAAATAG
39951121 AAT
1 AAT
39951124 TTGAATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
AATAAAAAATAG
Found at i:39951472 original size:29 final size:28
Alignment explanation
Indices: 39951422--39951481 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
39951412 TTTCCACCAC
*
39951422 TTTTTAAAAAAACTGACCTATTTCCTTAA
1 TTTTTAAAAAAACTGACCTA-TTCCATAA
* *
39951451 TTTTTAAAAAAA-TGGCTTTATTCCATAA
1 TTTTTAAAAAAACTGAC-CTATTCCATAA
39951479 TTT
1 TTT
39951482 ATCTCATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (28 bp):
TTTTTAAAAAAACTGACCTATTCCATAA
Found at i:39970542 original size:18 final size:18
Alignment explanation
Indices: 39970506--39970542 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39970496 TTGGTTTTCG
* *
39970506 AATTCGAATAACTCTAAT
1 AATTCGAATAAATCAAAT
39970524 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
39970542 A
1 A
39970543 CCAAATTATA
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:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:39970661 original size:31 final size:31
Alignment explanation
Indices: 39970595--39970661 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
39970585 CTCTTTACTT
****
39970595 CCCCCAAAACTTTTACTCCCTCCCACTTTTT
1 CCCCCAAAACTTTTACTCCCTCCCACTCCCA
39970626 CCCCCAAAACTTTTACTCCCCTCCCA-TCCCA
1 CCCCCAAAACTTTTACT-CCCTCCCACTCCCA
39970657 CCCCC
1 CCCCC
39970662 TTCTACCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.19, C:0.54, G:0.00, T:0.27
Consensus pattern (31 bp):
CCCCCAAAACTTTTACTCCCTCCCACTCCCA
Found at i:39973844 original size:50 final size:50
Alignment explanation
Indices: 39973779--39974122 Score: 307
Period size: 50 Copynumber: 6.9 Consensus size: 50
39973769 ACCGAAGCTC
* * * *
39973779 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGGCCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * * *
39973829 TCTGGTACACGTAGTAGCCTACA-TTAGTACTACGCACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * ** *
39973878 TTTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAA
* * * * * * * * *
39973930 -CGGGTACGCATAGTAGTCTGCACTTAGTACTACACACATGGCTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * ** *
39973979 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAA
* ** * * *
39974031 T-GGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
*
39974080 TCTAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
39974123 TCACAATGGA
Statistics
Matches: 227, Mismatches: 60, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
49 46 0.20
50 110 0.48
51 68 0.30
52 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
Found at i:39973960 original size:51 final size:51
Alignment explanation
Indices: 39973889--39974066 Score: 207
Period size: 51 Copynumber: 3.5 Consensus size: 51
39973879 TTGATACACG
* *
39973889 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
* * * ** * * * * *
39973940 TAGTAGTCTGCACTTAGTACTACACACATG-GCTTAA-CCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACATGATC-GAAGTTAACGGGTACGCA
* *
39973990 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAATGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
39974041 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
39974067 TGCGACCTAT
Statistics
Matches: 100, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
50 39 0.39
51 61 0.61
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
Found at i:39973986 original size:101 final size:101
Alignment explanation
Indices: 39973790--39974121 Score: 397
Period size: 101 Copynumber: 3.3 Consensus size: 101
39973780 CTGGTACGCA
* * ** * * * * *
39973790 TAGTAGCCTGCACTTAGTACTACACATGTG-GCCTA-TCAATCTGGTACACGTAGTAGCCTACA-
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACGCATAGTAGCCTGCAC
* * * *
39973852 TTAGTACTACGCACGTGACTTAACCATTTGATACACG
65 TTAGTACTACACACATGGCTTAACCATCTGATACACG
* *
39973889 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGTCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACT
39973954 TAGTACTACACACATGGCTTAACCATCTGATACACG
66 TAGTACTACACACATGGCTTAACCATCTGATACACG
* * *
39973990 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAATGGGTATGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACT
* * *
39974055 TAGTACT--ACACATGCGACCTATCAATCT-AGTACACG
66 TAGTACTACACACATG-G-CTTAACCATCTGA-TACACG
39974091 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
39974122 CTCACAATGG
Statistics
Matches: 203, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
99 35 0.17
100 21 0.10
101 147 0.72
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACT
TAGTACTACACACATGGCTTAACCATCTGATACACG
Found at i:39976707 original size:41 final size:42
Alignment explanation
Indices: 39976649--39976733 Score: 163
Period size: 41 Copynumber: 2.0 Consensus size: 42
39976639 ATACTCAATA
39976649 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
1 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
39976691 TATA-CCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
1 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
39976732 TA
1 TA
39976734 ATGCTTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
Found at i:39990125 original size:38 final size:38
Alignment explanation
Indices: 39990034--39990186 Score: 198
Period size: 38 Copynumber: 4.0 Consensus size: 38
39990024 GAATCCAATC
* * * * *
39990034 ACCACCACAAAGCCTGCGGGACTTTAAGCTCGGATATAAT
1 ACCAGCACGAAGCCTACGGGA-TTTAA-CCCGGATATATT
* *
39990074 ACTAGCACTAAGCCTACGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTACGGGATTTAACCCGGATATATT
* *
39990112 ACCAGTACGAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTACGGGATTTAACCCGGATATATT
*
39990150 ACCAGCACGAAGCCTACGGGACTTAACCCGGATATAT
1 ACCAGCACGAAGCCTACGGGATTTAACCCGGATATAT
39990187 ATCGAGTGCT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 78 0.78
39 5 0.05
40 17 0.17
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (38 bp):
ACCAGCACGAAGCCTACGGGATTTAACCCGGATATATT
Found at i:39990157 original size:76 final size:78
Alignment explanation
Indices: 39990043--39990186 Score: 229
Period size: 76 Copynumber: 1.9 Consensus size: 78
39990033 CACCACCACA
* * * *
39990043 AAGCCTGCGGGACTTTAAGCTCGGATATAATACTAGCACTAAGCCTACGGGATTTAACCCGGATA
1 AAGCCTGCGGGACTTTAAGCCCGGATATAATACCAGCACGAAGCCTACGGGACTTAACCCGGATA
39990108 TATTACCAGTACG
66 TATTACCAGTACG
*
39990121 AAGCCTGCGGGA-TTTAA-CCCGGATATATTACCAGCACGAAGCCTACGGGACTTAACCCGGATA
1 AAGCCTGCGGGACTTTAAGCCCGGATATAATACCAGCACGAAGCCTACGGGACTTAACCCGGATA
39990184 TAT
66 TAT
39990187 ATCGAGTGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 44 0.72
77 5 0.08
78 12 0.20
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (78 bp):
AAGCCTGCGGGACTTTAAGCCCGGATATAATACCAGCACGAAGCCTACGGGACTTAACCCGGATA
TATTACCAGTACG
Found at i:39999466 original size:93 final size:93
Alignment explanation
Indices: 39999312--39999490 Score: 238
Period size: 93 Copynumber: 1.9 Consensus size: 93
39999302 CTTACATACG
* **
39999312 TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTTATCTGTGTTGATGCCAT
1 TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCAC-TATCTGGGCCGATGCCAT
*
39999377 GTCCTAAACAGGTTTTACACTAACAAACC
65 GTCCTAAACAGGTCTTACACTAACAAACC
*
39999406 TCAA-GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAGGCCGATGCC
1 TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCT-CACTATC-TG-GGCCGATGCC
* *
39999468 ATGTCCTAGATAGGTCTTACACT
63 ATGTCCTAAACAGGTCTTACACT
39999491 GGCTCTCACT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
91 4 0.05
92 3 0.04
93 64 0.85
94 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (93 bp):
TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTATCTGGGCCGATGCCATG
TCCTAAACAGGTCTTACACTAACAAACC
Found at i:39999540 original size:49 final size:48
Alignment explanation
Indices: 39999317--39999539 Score: 206
Period size: 49 Copynumber: 4.7 Consensus size: 48
39999307 ATACGTCAAG
*
39999317 GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTTATCTGT
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCAC-TATCTGT
** * * * ** * **
39999366 GTTGATGCCATGTCCTAAACAGGTTTTACACTA--ACAAAC-CTC-AA
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCACTATCTGT
*
39999410 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAG
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCT-CACTATC-TG-T
* *
39999459 GCCGATGCCATGTCCTAGATAGGTCTTACACTGGCTCTCACTTATCTGT
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCAC-TATCTGT
* * *
39999508 GTCGATGTCATGTCCTAGACAGGTTTTACACT
1 GCCGATGCCATGTCCTAGACAGGTCTTACACT
39999540 GACACACACA
Statistics
Matches: 136, Mismatches: 28, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
44 29 0.21
45 2 0.01
46 3 0.02
47 3 0.02
49 92 0.68
50 3 0.02
51 4 0.03
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (48 bp):
GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCACTATCTGT
Found at i:40006339 original size:54 final size:54
Alignment explanation
Indices: 40006249--40006356 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
40006239 AAAAAGGAAA
* *
40006249 AGGAAGGAACGGACGCACGCTAGTCAAACTTTGAAGAAACACCAGATTTGTCTT
1 AGGAAGGAACGGACGCACGCTAGTCAAACTTCGAAGAAACACCAGATTTATCTT
*
40006303 AGGAAGGAACGGACGCACGCTAGTCAGACTTCGAAGAAACACCAGATTTATCTT
1 AGGAAGGAACGGACGCACGCTAGTCAAACTTCGAAGAAACACCAGATTTATCTT
40006357 CTAACTCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (54 bp):
AGGAAGGAACGGACGCACGCTAGTCAAACTTCGAAGAAACACCAGATTTATCTT
Found at i:40020910 original size:40 final size:40
Alignment explanation
Indices: 40020805--40021021 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
40020795 CGGATGATAA
* * *
40020805 CCGGGGTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
40020845 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40020884 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40020924 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
40020964 CCGAGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
40021004 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40021022 TACTTGGTTT
Statistics
Matches: 161, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 50 0.31
40 111 0.69
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40028494 original size:12 final size:12
Alignment explanation
Indices: 40028477--40028505 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40028467 TTATAATTTA
40028477 TTCTTAACAACT
1 TTCTTAACAACT
40028489 TTCTTAACAACT
1 TTCTTAACAACT
40028501 TTCTT
1 TTCTT
40028506 CATCTTCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
TTCTTAACAACT
Found at i:40031741 original size:21 final size:20
Alignment explanation
Indices: 40031717--40031755 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40031707 GAGTATTTTG
40031717 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
40031738 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
40031756 ATTAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:40032396 original size:48 final size:48
Alignment explanation
Indices: 40032319--40032545 Score: 312
Period size: 48 Copynumber: 4.7 Consensus size: 48
40032309 TTAGGGGATA
* *
40032319 CATTGTTTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCAAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
* * * *
40032367 CATTCATTTGGATTTGGGCCATGATATTGGCACTTCAAGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
* * *
40032415 CATTAATTTGGCTTTGGGCCATGATATTGGCACTTCGGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
* * * *
40032463 AATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGAGTGCGAGATAT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCT-T
*
40032512 -ATTGAATTGGCTTCGGGCCATGATATTGGCACTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTT
40032546 AGTGTGCGGG
Statistics
Matches: 158, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
48 157 0.99
49 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (48 bp):
CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
Found at i:40038153 original size:16 final size:17
Alignment explanation
Indices: 40038132--40038164 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40038122 TTCGTTTTTG
40038132 TTCTAT-TTTTTATGAT
1 TTCTATGTTTTTATGAT
*
40038148 TTCTATGTTTTTGTGAT
1 TTCTATGTTTTTATGAT
40038165 CGTTGCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (17 bp):
TTCTATGTTTTTATGAT
Found at i:40041433 original size:42 final size:41
Alignment explanation
Indices: 40041386--40041539 Score: 141
Period size: 42 Copynumber: 3.6 Consensus size: 41
40041376 TGTGATTTTT
* *
40041386 TGTAAGACCATATCTGGGATATGGCATCGATATGTGATTTCA
1 TGTAAGACCATAT-TGGGATATGGCATCGATATATGATTCCA
* * * ** *
40041428 TGTAAGACCATGTTTGGGACATGGCATCGATATAAGACACCG
1 TGTAAGACCAT-ATTGGGATATGGCATCGATATATGATTCCA
*
40041470 TGTAAGA-CATAGTTGGGCTATTGGCATCGATATATGA-TCCTA
1 TGTAAGACCATA-TTGGGATA-TGGCATCGATATATGATTCC-A
*
40041512 TGTAAGTACCATATATCGGATATGGCAT
1 TGTAAG-ACCATAT-TGGGATATGGCAT
40041540 TGGCATCTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
41 11 0.12
42 60 0.67
43 9 0.10
44 9 0.10
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (41 bp):
TGTAAGACCATATTGGGATATGGCATCGATATATGATTCCA
Found at i:40049282 original size:44 final size:42
Alignment explanation
Indices: 40049214--40049361 Score: 162
Period size: 44 Copynumber: 3.5 Consensus size: 42
40049204 TATGTGCTTT
40049214 CGTGTAAGACCACGTCT-GAGACGTTGGCATCGACTTATGATTTA
1 CGTGTAAGACCACGTCTAGA-ACGTTGGCATCGA-TT-TGATTTA
40049258 CGTGTAAGACCACGTCTAGAACGTTGGCATCGTATTTGATTT-
1 CGTGTAAGACCACGTCTAGAACGTTGGCATCG-ATTTGATTTA
* *
40049300 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGA-TTA
1 CGTGTAAGACCAC-GTCTAGAAC-GTTGGCATCG--ATTTGATTTA
*
40049343 CATGTAAGACCACGTCTAG
1 CGTGTAAGACCACGTCTAG
40049362 GACATCGGTA
Statistics
Matches: 93, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
41 1 0.01
42 28 0.30
43 29 0.31
44 32 0.34
45 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTAGAACGTTGGCATCGATTTGATTTA
Found at i:40049337 original size:43 final size:43
Alignment explanation
Indices: 40049201--40049364 Score: 183
Period size: 43 Copynumber: 3.8 Consensus size: 43
40049191 ACATAGGATC
* * *
40049201 CGATATGTGCTTTCGTGTAAGACCACGTCTGAGACGTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
40049244 CGACT-TATGATTTACGTGTAAGACCACGTCTAGAACGTTGGCAT
1 CGA-TATTTGATTT-CGTGTAAGACCACGTCTGGGACGTTGGCAT
40049288 CG-TATTTGATTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATTTGATTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* * *
40049330 CGATATTTGATTACATGTAAGACCACGTCTAGGAC
1 CGATATTTGATTTCGTGTAAGACCACGTCTGGGAC
40049365 ATCGGTATTG
Statistics
Matches: 103, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.26
43 44 0.43
44 31 0.30
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:40052916 original size:24 final size:24
Alignment explanation
Indices: 40052884--40052954 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
40052874 CTGTCAGGAG
40052884 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
40052908 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
40052932 AGGATTTAGGAGAAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
40052955 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.37, C:0.00, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:40052966 original size:48 final size:48
Alignment explanation
Indices: 40052884--40052977 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
40052874 CTGTCAGGAG
** * *
40052884 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGGAT
1 AGGATTTAGGAGAAGATAAGGGA-AGGATCTAGGAGCTGATCAAGGGAT
40052932 AGGATTTAGGAGAAGATAAGGG-AGGAAATCTAGGAGCTGATCAAGG
1 AGGATTTAGGAGAAGATAAGGGAAGG--ATCTAGGAGCTGATCAAGG
40052978 AACAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
46 3 0.08
48 32 0.82
49 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.37, T:0.23
Consensus pattern (48 bp):
AGGATTTAGGAGAAGATAAGGGAAGGATCTAGGAGCTGATCAAGGGAT
Found at i:40054410 original size:27 final size:26
Alignment explanation
Indices: 40054371--40054481 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 26
40054361 GGAAACGTCT
*
40054371 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
40054398 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
*
40054425 TGGTGGTTCTGCCACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTG-ATC
* * *
40054453 TGGTGACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
40054479 TGG
1 TGG
40054482 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.68
28 16 0.22
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:40054474 original size:54 final size:54
Alignment explanation
Indices: 40054371--40054481 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
40054361 GGAAACGTCT
*
40054371 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTC
* * * *
40054425 TGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTC
40054479 TGG
1 TGG
40054482 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTC
Found at i:40055546 original size:28 final size:29
Alignment explanation
Indices: 40055473--40055560 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
40055463 AGCATGGCTG
* * * *
40055473 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
40055500 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
40055529 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
40055557 CCAG
1 CCAG
40055561 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:40055713 original size:28 final size:28
Alignment explanation
Indices: 40055666--40055758 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
40055656 AAATTAACCC
* * *
40055666 TAGGGGTACAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
40055694 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
40055722 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
40055750 TAGGGGTAT
1 TAGGGGTAT
40055759 TCTAGTACAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:40064514 original size:28 final size:28
Alignment explanation
Indices: 40064474--40064538 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
40064464 ATGTACTAGA
*
40064474 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
40064502 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
40064530 ATACCCCTA
1 ATACCCCTA
40064539 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:40064706 original size:27 final size:27
Alignment explanation
Indices: 40064645--40064734 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
40064635 AGGAAGCGTC
40064645 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
40064673 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
40064700 CTTGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
40064729 CTGGTG
1 CTGGTG
40064735 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 25 0.47
29 6 0.11
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:40065734 original size:10 final size:10
Alignment explanation
Indices: 40065717--40065750 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
40065707 AGCCTGTAAG
40065717 TATTCTGAAT
1 TATTCTGAAT
*
40065727 TTTTCTGAAT
1 TATTCTGAAT
40065737 GTATTCTGAAT
1 -TATTCTGAAT
40065748 TAT
1 TAT
40065751 CTATCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:40072290 original size:28 final size:28
Alignment explanation
Indices: 40072250--40072311 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
40072240 ATGTACTACA
*
40072250 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
40072278 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
40072306 ATACCC
1 ATACCC
40072312 TTAGGGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:40072479 original size:27 final size:27
Alignment explanation
Indices: 40072431--40072510 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
40072421 CTAGTGGCTA
40072431 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAA-TATCTGTTCTGGTGGCCC
* *
40072459 TGCCACATATATCTGTTCTGGTGGCTC
1 TGCCACAAATATCTGTTCTGGTGGCCC
40072486 TGCCACAAAATATCTGTATCTGGTG
1 TGCCAC-AAATATCTGT-TCTGGTG
40072511 ACTCTGTCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
27 23 0.49
28 17 0.36
29 7 0.15
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
TGCCACAAATATCTGTTCTGGTGGCCC
Found at i:40072529 original size:55 final size:56
Alignment explanation
Indices: 40072424--40072535 Score: 147
Period size: 55 Copynumber: 2.0 Consensus size: 56
40072414 AAGCGTCCTA
* *
40072424 GTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-TCTG
1 GTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTG
* * * *
40072479 GTGGCTCTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTATCTG
1 GTGGCTATGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTATCTG
40072535 G
1 G
40072536 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
55 28 0.57
56 21 0.43
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (56 bp):
GTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTG
Found at i:40078453 original size:3 final size:3
Alignment explanation
Indices: 40078445--40078489 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
40078435 ATTTCCGGCA
*
40078445 AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
40078490 GAGAGGAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40078575 original size:14 final size:14
Alignment explanation
Indices: 40078526--40078588 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
40078516 TGAGAGAAGA
40078526 AAAAAGAA--AAAG
1 AAAAAGAAGGAAAG
40078538 AAAAAGAGAAGGAGAAG
1 -AAAA-AGAAGGA-AAG
* * *
40078555 AAGAAGAGGGAAGG
1 AAAAAGAAGGAAAG
40078569 AAAAAGAAGGAAAG
1 AAAAAGAAGGAAAG
40078583 AAAAAG
1 AAAAAG
40078589 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 4 0.10
14 23 0.57
15 6 0.15
16 4 0.10
17 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGGAAAG
Found at i:40078575 original size:17 final size:17
Alignment explanation
Indices: 40078531--40078588 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
40078521 GAAGAAAAAA
*
40078531 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
40078549 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
40078568 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
40078582 GAAAAAG
1 GAAAAAG
40078589 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:40079405 original size:146 final size:146
Alignment explanation
Indices: 40079164--40079775 Score: 652
Period size: 147 Copynumber: 4.1 Consensus size: 146
40079154 ATTTTATGCT
* * * * *
40079164 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAACAATATGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAAAAAAGTGCT
* *
40079229 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAAATA-TTGAAATAATACATTTGAAACATTAT
66 AAAATCAGGGTTATTTATTAAATAAATATAAAAAAATACTT-AAATAATACATTTAAAACATTAT
40079293 GTACTAAAATAATATGAA
130 GTACTAAAATAATAT-AA
*
40079311 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-T
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAAAAAAGTGCT
* * * *
40079374 CAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACCTAATACATTTG
66 -AAAATCAGGGTTATTTATTAAATAAATAT-AAAAAA-A--TAC-T--TA-A-ATAATACATTTA
* * *
40079439 AAACATTTTTTGCTAAAATAATATAAAA
121 AAACATTATGTACTAAAATAATAT--AA
* * * *
40079467 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAAAAAAGTGCT
** * *
40079531 AAAATCAGGGTTATTTATTAAA-AAATAT-TTAAAACACTTAAATAATATATTTAAAACATTATG
66 AAAATCAGGGTTATTTATTAAATAAATATAAAAAAATACTTAAATAATACATTTAAAACATTATG
* *
40079594 TACTAAAATAAGGGTTTTA
131 TACTAAAATAA---TATAA
* *
40079613 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAAATACG-AAAAAGTG
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAAAAAAGTG
* * * *
40079675 -TCAAAATCAGTGTTATTTATTAAATTAATAT-AAAAAATACTTACATAATACATTTAAAACCTT
64 CT-AAAATCAGGGTTATTTATTAAATAAATATAAAAAAATACTTAAATAATACATTTAAAACATT
* * *
40079738 TTTTTCTAAAATAATATAA
128 ATGTACTAAAATAATATAA
*
40079757 AAAATAATATACGAAAATA
1 AAAATAAAATACGAAAATA
40079776 TTTTACTTAT
Statistics
Matches: 389, Mismatches: 54, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
142 10 0.03
143 2 0.01
144 7 0.02
145 29 0.07
146 84 0.22
147 109 0.28
148 18 0.05
149 1 0.00
150 4 0.01
152 2 0.01
153 4 0.01
154 2 0.01
155 36 0.09
156 80 0.21
157 1 0.00
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (146 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAAAAAAGTGCT
AAAATCAGGGTTATTTATTAAATAAATATAAAAAAATACTTAAATAATACATTTAAAACATTATG
TACTAAAATAATATAA
Found at i:40079513 original size:15 final size:14
Alignment explanation
Indices: 40079453--40079517 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 14
40079443 ATTTTTTGCT
*
40079453 AAAATAATATAAAA
1 AAAATAATATAGAA
*
40079467 AAAATAAAATAGGAA
1 AAAATAATATA-GAA
**
40079482 AATAAT-ATATTTTAA
1 AA-AATAATA-TAGAA
40079497 AAAATAATATACGAA
1 AAAATAATATA-GAA
40079512 AAAATA
1 AAAATA
40079518 TGAATAAAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
14 14 0.36
15 21 0.54
16 4 0.10
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (14 bp):
AAAATAATATAGAA
Found at i:40079551 original size:302 final size:300
Alignment explanation
Indices: 40079164--40079724 Score: 864
Period size: 302 Copynumber: 1.9 Consensus size: 300
40079154 ATTTTATGCT
40079164 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAACAATATGAATAAAGTGCT
1 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAACAATATGAATAAAGTGCT
*
40079229 AAAATCAGGGTTATTTATTAAAAAA-ATATAAAAAAATATTGAAATAATACATTTGAAACATTAT
66 AAAATCAGGGTTATTTATTAAAAAATAT-TAAAAAAA-ATT-AAATAATACATTTAAAACATTAT
40079293 GTACTAAAATAA-TATGAAGAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATAC-A
128 GTACTAAAATAAGTATGAA-AAATAAATAATACGAAAATAATATA-TTTAAAAAA-AAGATACGA
*
40079354 AAAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACA
190 AAAAAATACG-AAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAACACTTACA
40079419 TAATATACCTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
253 TAATATACCTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
**
40079467 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACGAAAA-AATATGAATAAAGTGCT
1 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAACAATATGAATAAAGTGCT
* * * *
40079531 AAAATCAGGGTTATTTATTAAAAAATATTTAAAACACTTAAATAATATATTTAAAACATTATGTA
66 AAAATCAGGGTTATTTATTAAAAAATATTAAAAAAAATTAAATAATACATTTAAAACATTATGTA
* * * *
40079596 CTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATATTTAAAAAAAAGATACGAAAAA
131 CTAAAATAA--GTATGAAAAATAAATAATACGAAAATAATATATTTAAAAAAAAGATACGAAAAA
* *
40079661 AATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATATAAAAAATACTTACATAATA
194 AATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTACATAATA
40079725 CATTTAAAAC
Statistics
Matches: 237, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
300 33 0.14
301 20 0.08
302 95 0.40
303 73 0.31
304 16 0.07
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (300 bp):
AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAACAATATGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAATATTAAAAAAAATTAAATAATACATTTAAAACATTATGTA
CTAAAATAAGTATGAAAAATAAATAATACGAAAATAATATATTTAAAAAAAAGATACGAAAAAAA
TACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTACATAATATAC
CTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
Found at i:40079571 original size:20 final size:22
Alignment explanation
Indices: 40079548--40079588 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40079538 GGGTTATTTA
40079548 TTAAA-AA-ATATTTAAAACAC
1 TTAAATAATATATTTAAAACAC
40079568 TTAAATAATATATTTAAAACA
1 TTAAATAATATATTTAAAACA
40079589 TTATGTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
TTAAATAATATATTTAAAACAC
Found at i:40086180 original size:21 final size:20
Alignment explanation
Indices: 40086155--40086194 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40086145 CTTCTTTTTT
*
40086155 TCTTCTCCTTTTTCTTCCTTC
1 TCTTCTCCTTTCT-TTCCTTC
40086176 TCTTCTCCTTTCTTTCCTT
1 TCTTCTCCTTTCTTTCCTT
40086195 TTATTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TCTTCTCCTTTCTTTCCTTC
Found at i:40086193 original size:9 final size:10
Alignment explanation
Indices: 40086153--40086195 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
40086143 ACCTTCTTTT
40086153 TTTCTTCTCC
1 TTTCTTCTCC
40086163 TTT-TTCTTCC
1 TTTCTTC-TCC
40086173 TTCTCTTCTCC
1 TT-TCTTCTCC
40086184 TTTCTT-TCC
1 TTTCTTCTCC
40086193 TTT
1 TTT
40086196 TATTTTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 6 0.20
12 3 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTCTTCTCC
Found at i:40086319 original size:27 final size:27
Alignment explanation
Indices: 40086289--40086358 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40086279 GACCCACACA
*
40086289 ACTGGTGCCGCCTCTGTCAGAGACAAC
1 ACTGGTGCCGCCTCTGCCAGAGACAAC
*
40086316 ACTGGTGCCGCCTCTGCCAGAGGCAAC
1 ACTGGTGCCGCCTCTGCCAGAGACAAC
*
40086343 ACTGGTACCGCCTCTG
1 ACTGGTGCCGCCTCTG
40086359 GCACCCACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.19, C:0.36, G:0.27, T:0.19
Consensus pattern (27 bp):
ACTGGTGCCGCCTCTGCCAGAGACAAC
Found at i:40086438 original size:15 final size:15
Alignment explanation
Indices: 40086396--40086429 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40086386 CTTTTTTTCG
*
40086396 TTTTTC-AACTTTTT
1 TTTTTCAAAGTTTTT
40086410 TTTTTCAAAGTTTTT
1 TTTTTCAAAGTTTTT
40086425 TTTTT
1 TTTTT
40086430 TACTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTCAAAGTTTTT
Found at i:40091934 original size:20 final size:19
Alignment explanation
Indices: 40091905--40091948 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
40091895 TCGTAAACGC
*
40091905 ATTTTTTATTTTCATTTTA
1 ATTTTTTATTTTAATTTTA
40091924 ATTTTTATATTTTAATTTTA
1 ATTTTT-TATTTTAATTTTA
40091944 ATTTT
1 ATTTT
40091949 GAGACATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTTATTTTAATTTTA
Found at i:40092170 original size:21 final size:20
Alignment explanation
Indices: 40092146--40092205 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 20
40092136 AATAAAATCA
40092146 TAAAAATAAAATGTATATTTT
1 TAAAAATAAAAT-TATATTTT
*
40092167 TAAAAAAATTAAAAATCAT-TTTT
1 T--AAAAA-T-AAAATTATATTTT
40092190 TAAAAATAAAATTATA
1 TAAAAATAAAATTATA
40092206 ATTTATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
19 7 0.22
20 1 0.03
21 6 0.19
23 10 0.31
24 3 0.09
25 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAAATAAAATTATATTTT
Found at i:40092209 original size:22 final size:22
Alignment explanation
Indices: 40092145--40092214 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
40092135 AAATAAAATC
40092145 ATAAAAATAAAATGTATATTTTT
1 ATAAAAATAAAAT-TATATTTTT
*
40092168 AAAAAAATTAAAA--ATCATTTTT
1 ATAAAAA-TAAAATTAT-ATTTTT
*
40092190 -TAAAAATAAAATTATA-ATTT
1 ATAAAAATAAAATTATATTTTT
40092210 ATAAA
1 ATAAA
40092215 TTATGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
20 8 0.21
21 12 0.31
22 8 0.21
23 6 0.15
24 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
ATAAAAATAAAATTATATTTTT
Found at i:40097404 original size:2 final size:2
Alignment explanation
Indices: 40097397--40097432 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40097387 CTAATAAAGC
40097397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40097433 TAAATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40097586 original size:31 final size:29
Alignment explanation
Indices: 40097550--40097628 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 29
40097540 TATTAAAATT
*
40097550 ATACATAAATTTTAATTTAATGTGTAATATC
1 ATACATAAATTTTAATTT--TATGTAATATC
* * *
40097581 ATACATAAATTTTGATTTTATGTAATTTT
1 ATACATAAATTTTAATTTTATGTAATATC
*
40097610 ATATATGAAATTTTAATTT
1 ATACAT-AAATTTTAATTT
40097629 GATTTAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.32
30 11 0.27
31 17 0.41
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (29 bp):
ATACATAAATTTTAATTTTATGTAATATC
Found at i:40099455 original size:27 final size:27
Alignment explanation
Indices: 40099402--40099455 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
40099392 ATGACATCAA
** *
40099402 AGATAGTCTGACGGGACGTTAAGCACG
1 AGATAGTCTGACGAAACGTTAAACACG
40099429 AGATAGTCTGACGAAAC-TCTAAACACG
1 AGATAGTCTGACGAAACGT-TAAACACG
40099456 TAAATTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (27 bp):
AGATAGTCTGACGAAACGTTAAACACG
Found at i:40100799 original size:19 final size:18
Alignment explanation
Indices: 40100777--40100822 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
40100767 AATAATAACG
*
40100777 ATAATATTAAAAATAAGTA
1 ATAATAATAAAAAT-AGTA
*
40100796 ATAATAATGAAAATAGTA
1 ATAATAATAAAAATAGTA
*
40100814 AGAATAATA
1 ATAATAATA
40100823 TGGTATTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (18 bp):
ATAATAATAAAAATAGTA
Found at i:40100810 original size:28 final size:28
Alignment explanation
Indices: 40100767--40100820 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40100757 CATATATGTA
* *
40100767 AATAATAACGATAATATTAAAAATAAGT
1 AATAATAACGAAAATAGTAAAAATAAGT
* *
40100795 AATAATAATGAAAATAGTAAGAATAA
1 AATAATAACGAAAATAGTAAAAATAA
40100821 TATGGTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (28 bp):
AATAATAACGAAAATAGTAAAAATAAGT
Found at i:40100819 original size:18 final size:19
Alignment explanation
Indices: 40100786--40100821 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40100776 GATAATATTA
*
40100786 AAAATAAGTAATAATAATG
1 AAAATAAGTAAGAATAATG
40100805 AAAAT-AGTAAGAATAAT
1 AAAATAAGTAAGAATAAT
40100822 ATGGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (19 bp):
AAAATAAGTAAGAATAATG
Found at i:40103529 original size:90 final size:87
Alignment explanation
Indices: 40103370--40103662 Score: 351
Period size: 90 Copynumber: 3.3 Consensus size: 87
40103360 TCACTTCATT
* * ** * *
40103370 TCTCGCAATATGAATTGACTCTTT-AAAAATAGACGTT--AAAACAGAAATTAAAAATAGCTCAG
1 TCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCAG
*
40103432 CACGTGAGCTAAGGCTCAACTCACC
65 --CGTGAGCTGAGGCTCAACTCACC
*
40103457 TCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAATACCTCAG
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTG-AAAAACAGAAATTGAAAATACCTCAG
*
40103522 CTTGTGAGCCGAGGCTCAACTCACC
65 C--GTGAGCTGAGGCTCAACTCACC
* *
40103547 TCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAACAGAAATTGAAAATTCCTCA
1 TCTCGCAATATGAGTTGA--TTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCA
** *
40103612 GCGTGCCCTGAGGCTCAACTCACT
64 GCGTGAGCTGAGGCTCAACTCACC
*
40103636 TATCGCAATATGAGTTGA-TTTTGAAAA
1 TCTCGCAATATGAGTTGATTTTTGAAAA
40103663 CAGAAATAAA
Statistics
Matches: 181, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
86 13 0.07
87 27 0.15
88 1 0.01
89 35 0.19
90 61 0.34
91 26 0.14
92 18 0.10
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (87 bp):
TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCAGC
GTGAGCTGAGGCTCAACTCACC
Found at i:40120711 original size:49 final size:49
Alignment explanation
Indices: 40120630--40120751 Score: 210
Period size: 49 Copynumber: 2.5 Consensus size: 49
40120620 AATAACACGC
40120630 CAAATAAATTTCAT-AAAAATAAATCTAATCAACCTAAAACACACATAA
1 CAAATAAATTTCATAAAAAATAAATCTAATCAACCTAAAACACACATAA
*
40120678 CAAATAAATTTCATAAAAAATAAATCTAATCAACTTAAAACACACATAA
1 CAAATAAATTTCATAAAAAATAAATCTAATCAACCTAAAACACACATAA
*
40120727 CAAATAAATTACATAAAAAAATAAA
1 CAAATAAATTTCAT-AAAAAATAAA
40120752 ACATTCTTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
48 14 0.20
49 46 0.66
50 10 0.14
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (49 bp):
CAAATAAATTTCATAAAAAATAAATCTAATCAACCTAAAACACACATAA
Found at i:40121151 original size:9 final size:9
Alignment explanation
Indices: 40121137--40121161 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40121127 CGTCCTCTCA
40121137 TTCTCCTTC
1 TTCTCCTTC
40121146 TTCTCCTTC
1 TTCTCCTTC
40121155 TTCTCCT
1 TTCTCCT
40121162 AAAAATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
TTCTCCTTC
Found at i:40123712 original size:20 final size:20
Alignment explanation
Indices: 40123689--40123727 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40123679 TTATTTAAAT
40123689 AATAATTTTATAAATAAAAA
1 AATAATTTTATAAATAAAAA
*
40123709 AATATTTTTATAAATAAAA
1 AATAATTTTATAAATAAAA
40123728 TAATTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATTTTATAAATAAAAA
Found at i:40124344 original size:19 final size:20
Alignment explanation
Indices: 40124304--40124352 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
40124294 ATAATTTTGC
40124304 ATGTATTTTT-TTAAATATT
1 ATGTATTTTTATTAAATATT
40124323 ATGTATTTTTATTGAAA-A-T
1 ATGTATTTTTATT-AAATATT
*
40124342 ATGAATTTTTA
1 ATGTATTTTTA
40124353 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 21 0.78
20 3 0.11
21 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
ATGTATTTTTATTAAATATT
Done.