Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 41 of 202
Found at i:12206545 original size:13 final size:14
Alignment explanation
Indices: 12206523--12206555 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12206513 CTCATCAATA
12206523 TTTTTC-TTT-AAT
1 TTTTTCATTTAAAT
12206535 TTTTTCATTTAAAT
1 TTTTTCATTTAAAT
12206549 TTTTTCA
1 TTTTTCA
12206556 ACATCCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 3 0.16
14 10 0.53
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTCATTTAAAT
Found at i:12208039 original size:21 final size:21
Alignment explanation
Indices: 12208015--12208054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12208005 TAATGATCAG
* *
12208015 CACATTTTGGTGGTATATCCA
1 CACATTCTGGTAGTATATCCA
12208036 CACATTCTGGTAGTATATC
1 CACATTCTGGTAGTATATC
12208055 AGCGATTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (21 bp):
CACATTCTGGTAGTATATCCA
Found at i:12218142 original size:12 final size:12
Alignment explanation
Indices: 12218127--12218168 Score: 75
Period size: 12 Copynumber: 3.4 Consensus size: 12
12218117 ATATTATATA
12218127 TTTTTATATAATT
1 TTTTTATATAA-T
12218140 TTTTTATATAAT
1 TTTTTATATAAT
12218152 TTTTTATATAAT
1 TTTTTATATAAT
12218164 TTTTT
1 TTTTT
12218169 TACCAAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTATATAAT
Found at i:12218145 original size:13 final size:13
Alignment explanation
Indices: 12218127--12218170 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
12218117 ATATTATATA
12218127 TTTTTATATAATT
1 TTTTTATATAATT
12218140 TTTTTATATAA-T
1 TTTTTATATAATT
12218152 TTTTTATATAATT
1 TTTTTATATAATT
12218165 TTTTTA
1 TTTTTA
12218171 CCAAGGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATATAATT
Found at i:12218155 original size:25 final size:23
Alignment explanation
Indices: 12218120--12218170 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 23
12218110 GAATGCAATA
12218120 TTATATATTTTTATATAATTTTT
1 TTATATATTTTTATATAATTTTT
12218143 TTATATAATTTTTTATATAATTTTT
1 TTATAT-A-TTTTTATATAATTTTT
12218168 TTA
1 TTA
12218171 CCAAGGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 1 0.04
25 19 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATATATTTTTATATAATTTTT
Found at i:12218570 original size:24 final size:21
Alignment explanation
Indices: 12218535--12218577 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12218525 GATCCATTAA
12218535 AAAATAAGATGTGTGGTATTGAG
1 AAAATAAGATGT-T-GTATTGAG
*
12218558 AAAATACATATGTTGTATTG
1 AAAATA-AGATGTTGTATTG
12218578 TTCTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 7 0.39
24 5 0.28
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (21 bp):
AAAATAAGATGTTGTATTGAG
Found at i:12220102 original size:17 final size:18
Alignment explanation
Indices: 12220064--12220102 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12220054 CCCTTGTCTT
* *
12220064 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
12220082 CTAAGGGAAAGAAGAAA-
1 CTAAGGGAAAGAAGAAAG
12220099 CTAA
1 CTAA
12220103 CTAAGTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.51, C:0.10, G:0.31, T:0.08
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:12226510 original size:108 final size:109
Alignment explanation
Indices: 12226315--12226520 Score: 260
Period size: 108 Copynumber: 1.9 Consensus size: 109
12226305 GGCACCCTTG
** *
12226315 TACCAAATTTTAAAAAAAAAATTGGATGCTGAGACACTTATGGTCGACACCCTAATACCAGATTT
1 TACCAAATTTTAAAAAAAAAATTGGATGCTGAGACACTTATGACCGACACCCCAATACCAGATTT
* *
12226380 AAAAACAATTTTGGGGTACTGGAACACTGATGGCCGGCACTCCAA
66 AAAAACAA-TTCGAGGTACTGGAACACTGATGGCCGGCACTCCAA
* *
12226425 TACCAAA-TTT-AAAAAAAAATTGGGTGCTGGGACA-TTGATGACCGACACCCCAATACCAGATT
1 TACCAAATTTTAAAAAAAAAATTGGATGCTGAGACACTT-ATGACCGACACCCCAATACCAGA--
*
12226487 TTTTAAAAA-AA-TCGAGGTGCTGGAACACTGATGG
63 -TTTAAAAACAATTCGAGGTACTGGAACACTGATGG
12226521 TCGATACCCC
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
107 2 0.02
108 62 0.74
109 3 0.04
110 9 0.11
111 8 0.10
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (109 bp):
TACCAAATTTTAAAAAAAAAATTGGATGCTGAGACACTTATGACCGACACCCCAATACCAGATTT
AAAAACAATTCGAGGTACTGGAACACTGATGGCCGGCACTCCAA
Found at i:12226530 original size:55 final size:54
Alignment explanation
Indices: 12226270--12226548 Score: 206
Period size: 55 Copynumber: 5.1 Consensus size: 54
12226260 CCTTTTAAAA
* * * * *** *
12226270 TTAAAAAAAAATTGGGTGCT-GAGATACTGATGGTCGGCACCCTTGTACCAAATT
1 TTAAAAAAAAATCGGGTGCTGGA-ACACTGATGGCCGACACCCCAATACCAGATT
* * * * *
12226324 TTAAAAAAAAAATTGGATGCT-GAGACACTTATGGTCGACACCCTAATACCAGA-T
1 TT-AAAAAAAAATCGGGTGCTGGA-ACACTGATGGCCGACACCCCAATACCAGATT
** * * * * *
12226378 TTAAAAACAATTTTGGGGTACTGGAACACTGATGGCCGGCACTCCAATACCA-AAT
1 TTAAAAA-AA-AATCGGGTGCTGGAACACTGATGGCCGACACCCCAATACCAGATT
* * * *
12226433 TTAAAAAAAAATTGGGTGCTGGGACATTGATGACCGACACCCCAATACCAGATT
1 TTAAAAAAAAATCGGGTGCTGGAACACTGATGGCCGACACCCCAATACCAGATT
** * * * *
12226487 TTTTAAAAAAATCGAGGTGCTGGAACACTGATGGTCGATACCCCAGTACTAGATT
1 TTAAAAAAAAATCG-GGTGCTGGAACACTGATGGCCGACACCCCAATACCAGATT
12226542 TTAAAAA
1 TTAAAAA
12226549 CTAAATATTT
Statistics
Matches: 179, Mismatches: 39, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
53 37 0.21
54 23 0.13
55 117 0.65
56 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (54 bp):
TTAAAAAAAAATCGGGTGCTGGAACACTGATGGCCGACACCCCAATACCAGATT
Found at i:12232434 original size:22 final size:20
Alignment explanation
Indices: 12232386--12232441 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
12232376 ATATACACAT
* *
12232386 TAAAAATATAAAAATAGAAA
1 TAAATATATAAAAATACAAA
12232406 TAAATATATAAAAATTCACAAA
1 TAAATATATAAAAA-T-ACAAA
* *
12232428 TATATATAGAAAAA
1 TAAATATATAAAAA
12232442 AATAAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.43
21 1 0.03
22 16 0.53
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
TAAATATATAAAAATACAAA
Found at i:12233010 original size:22 final size:24
Alignment explanation
Indices: 12232962--12233010 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
12232952 TAAATACATT
** *
12232962 TTTTTATAATTTTATAATTATATA
1 TTTTTATAATTTTATAAAAATAAA
12232986 TTTTT-TAA-TTTATAAAAATAAA
1 TTTTTATAATTTTATAAAAATAAA
12233008 TTT
1 TTT
12233011 AAAAATTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 3 0.14
24 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTTATAATTTTATAAAAATAAA
Found at i:12233029 original size:6 final size:6
Alignment explanation
Indices: 12233020--12233055 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
12233010 TAAAAATTAC
12233020 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
12233056 TTACAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:12233146 original size:15 final size:15
Alignment explanation
Indices: 12233126--12233165 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
12233116 TATTTTATTG
12233126 TAAATTTTATTTTTA
1 TAAATTTTATTTTTA
*
12233141 TAAATTTTATTTTTT
1 TAAATTTTATTTTTA
*
12233156 TAGATTTTAT
1 TAAATTTTAT
12233166 ATATATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TAAATTTTATTTTTA
Found at i:12233155 original size:17 final size:17
Alignment explanation
Indices: 12233111--12233157 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
12233101 ATTTATTTTC
* * *
12233111 AATTATATTTTATTGTA
1 AATTTTATTTTTTTATA
12233128 AATTTTA--TTTTTATA
1 AATTTTATTTTTTTATA
12233143 AATTTTATTTTTTTA
1 AATTTTATTTTTTTA
12233158 GATTTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
AATTTTATTTTTTTATA
Found at i:12233180 original size:28 final size:28
Alignment explanation
Indices: 12233149--12233213 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
12233139 TATAAATTTT
12233149 ATTTTTTTAGATTTTATATATATTTGA-A
1 ATTTTTTTAGA-TTTATATATATTTGATA
* * * * *
12233177 ATTTTTATATATTTATTTCTATTTTATA
1 ATTTTTTTAGATTTATATATATTTGATA
12233205 ATTTTTTTA
1 ATTTTTTTA
12233214 ATGTGTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (28 bp):
ATTTTTTTAGATTTATATATATTTGATA
Found at i:12234365 original size:19 final size:19
Alignment explanation
Indices: 12234341--12234451 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
12234331 AATCTTCAGG
12234341 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12234360 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
12234379 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12234398 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
12234417 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12234436 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12234452 AGATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12234391 original size:38 final size:38
Alignment explanation
Indices: 12234348--12234451 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
12234338 AGGGATATGC
12234348 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
12234386 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
12234424 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
12234452 AGATATGATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:12234477 original size:22 final size:21
Alignment explanation
Indices: 12234341--12234477 Score: 114
Period size: 19 Copynumber: 6.9 Consensus size: 21
12234331 AATCTTCAGG
*
12234341 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12234360 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
12234379 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12234398 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12234417 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12234436 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
12234458 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
12234478 TTAATTTGTA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
19 79 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:12241806 original size:132 final size:132
Alignment explanation
Indices: 12241419--12241789 Score: 602
Period size: 132 Copynumber: 2.8 Consensus size: 132
12241409 CCTGTATTGA
*
12241419 TAGCGAAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
1 TAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* *
12241484 AGTAATTCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGT
66 AGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
12241549 AG
131 AG
*
12241551 TAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
1 TAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* *
12241616 AGTAATTCTACTTCCCTGGACAACAATTGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
12241681 AG
131 AG
* * *
12241683 TAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCC
1 TAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * *
12241748 AGTAA-TCATA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGA
66 AGTAATTC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGA
12241790 GTGTAAGTCC
Statistics
Matches: 222, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
131 3 0.01
132 219 0.99
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
TAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
AGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
AG
Found at i:12242177 original size:22 final size:22
Alignment explanation
Indices: 12242117--12242160 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
12242107 AATCTTCAGG
12242117 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12242136 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
12242158 GAT
1 GAT
12242161 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:12247676 original size:4 final size:4
Alignment explanation
Indices: 12247667--12247692 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12247657 TTCCTAAAAT
12247667 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
12247693 CCAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:12253406 original size:42 final size:42
Alignment explanation
Indices: 12253342--12253476 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 42
12253332 CAGGTTTATA
* * *
12253342 CTTCGGTTTAGCCAATGATGCACTTATGTGCTAGTATATTTG
1 CTTCAGTTTATCCAATGATGCACTTATGTGCCAGTATATTTG
* * *
12253384 CTTCAGTTTATCCGATGATGCACTTACGTTCCAGTATATTTG
1 CTTCAGTTTATCCAATGATGCACTTATGTGCCAGTATATTTG
** *
12253426 CTTCAGTTTATCCAATGATGTGC-TATGCTTGCCAGTATAATTG
1 CTTCAGTTTATCCAATGATGCACTTATG--TGCCAGTATATTTG
12253469 CTTCAGTT
1 CTTCAGTT
12253477 CGTTTGATGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 3 0.04
42 56 0.71
43 20 0.25
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (42 bp):
CTTCAGTTTATCCAATGATGCACTTATGTGCCAGTATATTTG
Found at i:12253577 original size:43 final size:43
Alignment explanation
Indices: 12253525--12253622 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
12253515 CGGCTTGCTC
*
12253525 GATGATGCACTATGTGTGTTAGTATCTTTTCTTTAATATATCT
1 GATGATGCACTATGTGTGTCAGTATCTTTTCTTTAATATATCT
*
12253568 GATGTTGCACTATGTGTGTCAGTATCTTTTCTTTAATATATCT
1 GATGATGCACTATGTGTGTCAGTATCTTTTCTTTAATATATCT
12253611 GATGATGCACTA
1 GATGATGCACTA
12253623 CAGTGCCAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (43 bp):
GATGATGCACTATGTGTGTCAGTATCTTTTCTTTAATATATCT
Found at i:12258505 original size:41 final size:41
Alignment explanation
Indices: 12258448--12258526 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
12258438 CCTCTAGAGA
12258448 AAGTGAAGAGTAGTCTTGGAAATGAAAATGTATTAAAACGC
1 AAGTGAAGAGTAGTCTTGGAAATGAAAATGTATTAAAACGC
12258489 AAGTGAAGAGTAGTCTTGGAAATGAAAATGTATTAAAA
1 AAGTGAAGAGTAGTCTTGGAAATGAAAATGTATTAAAA
12258527 TGCTTTGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.25
Consensus pattern (41 bp):
AAGTGAAGAGTAGTCTTGGAAATGAAAATGTATTAAAACGC
Found at i:12262094 original size:18 final size:17
Alignment explanation
Indices: 12262071--12262104 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12262061 TGAATAGAAA
12262071 ATGTGTATGATATAATGT
1 ATGTGTATGAT-TAATGT
*
12262089 ATGTGTTTGATTAATG
1 ATGTGTATGATTAATG
12262105 AATTGATGAT
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:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (17 bp):
ATGTGTATGATTAATGT
Found at i:12267607 original size:2 final size:2
Alignment explanation
Indices: 12267600--12267624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12267590 GCCCTTTCTT
12267600 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12267625 TATTAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12273841 original size:23 final size:24
Alignment explanation
Indices: 12273814--12273866 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12273804 TGTATAAAAC
*
12273814 TTATTTT-ATTGTTAATTTTGTTA
1 TTATTTTAAATGTTAATTTTGTTA
12273837 TTATTTTAAATGTTAATTTTGTTA
1 TTATTTTAAATGTTAATTTTGTTA
12273861 TTATTT
1 TTATTT
12273867 AGAGGCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (24 bp):
TTATTTTAAATGTTAATTTTGTTA
Found at i:12274525 original size:16 final size:16
Alignment explanation
Indices: 12274504--12274540 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12274494 GTTGAATTTT
*
12274504 AAAATTTTAAAATAAA
1 AAAATTATAAAATAAA
*
12274520 AAAATTATGAAATAAA
1 AAAATTATAAAATAAA
12274536 AAAAT
1 AAAAT
12274541 GAATTAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATTATAAAATAAA
Found at i:12282535 original size:21 final size:21
Alignment explanation
Indices: 12282500--12282540 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12282490 TCTTGAAAAA
12282500 CCAAAATTCTAATTTTTTTTG
1 CCAAAATTCTAATTTTTTTTG
12282521 CCAAATATTCT-ATTTTTTTT
1 CCAAA-ATTCTAATTTTTTTT
12282541 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (21 bp):
CCAAAATTCTAATTTTTTTTG
Found at i:12284158 original size:24 final size:24
Alignment explanation
Indices: 12284118--12284193 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
12284108 GACGAAGACA
12284118 AAGACGAGGGT-AGAGATGAAGATG
1 AAGACGAGGGTCA-AGATGAAGATG
*
12284142 AAGACGATGGTCAAGATGAAGATG
1 AAGACGAGGGTCAAGATGAAGATG
* * * *
12284166 AATACGGGGGTCGAGGTGAAGATG
1 AAGACGAGGGTCAAGATGAAGATG
12284190 AAGA
1 AAGA
12284194 TGATGATCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.39, T:0.14
Consensus pattern (24 bp):
AAGACGAGGGTCAAGATGAAGATG
Found at i:12289415 original size:22 final size:23
Alignment explanation
Indices: 12289349--12289415 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
12289339 TAGCGCTTAC
**
12289349 CGTTTTGCACTTCGGTGTTTA-T
1 CGTTTTGCACTTCGGTGCCTACT
** **
12289371 CGTTCCGCACTTCAATGCCTACT
1 CGTTTTGCACTTCGGTGCCTACT
12289394 -GTTTTGCACTTCGGTGCCTACT
1 CGTTTTGCACTTCGGTGCCTACT
12289416 AGGGGTGTGC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.40
Consensus pattern (23 bp):
CGTTTTGCACTTCGGTGCCTACT
Found at i:12289647 original size:13 final size:13
Alignment explanation
Indices: 12289629--12289653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12289619 ACCCAACCCA
12289629 ACCCAACCCAATT
1 ACCCAACCCAATT
12289642 ACCCAACCCAAT
1 ACCCAACCCAAT
12289654 AAAACTAAAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:12289691 original size:51 final size:53
Alignment explanation
Indices: 12289634--12289747 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 53
12289624 ACCCAACCCA
*
12289634 ACCCAATTACCCAACCCAATAAAACTAAAAATAAAGTCT-ACACTAAAG-TCT
1 ACCCAATTACCCAACCCAATAAAAATAAAAATAAAGTCTAACACTAAAGATCT
* * *
12289685 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCTAACTCTTAAGTATCT
1 ACCCAATTACCCAACCCAATAAAAATAAAAATAAAGTCTAACACTAAAG-ATCT
12289738 ACCCAATTAC
1 ACCCAATTAC
12289748 ACATGTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
50 27 0.49
51 16 0.29
53 12 0.22
ACGTcount: A:0.47, C:0.27, G:0.04, T:0.22
Consensus pattern (53 bp):
ACCCAATTACCCAACCCAATAAAAATAAAAATAAAGTCTAACACTAAAGATCT
Found at i:12289940 original size:9 final size:9
Alignment explanation
Indices: 12289922--12289997 Score: 73
Period size: 9 Copynumber: 8.4 Consensus size: 9
12289912 GTAGTGATTC
12289922 AATTCGGGT
1 AATTCGGGT
*
12289931 AATTCAGGT
1 AATTCGGGT
12289940 AATTCGGGT
1 AATTCGGGT
* *
12289949 AATTCTGTT
1 AATTCGGGT
*
12289958 AATTCGGTT
1 AATTCGGGT
*
12289967 AATTCGGTT
1 AATTCGGGT
*
12289976 AATT-TGGT
1 AATTCGGGT
*
12289984 CAATTCGGTT
1 -AATTCGGGT
12289994 AATT
1 AATT
12289998 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 2 0.04
9 52 0.93
10 2 0.04
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:12289953 original size:27 final size:27
Alignment explanation
Indices: 12289922--12289997 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
12289912 GTAGTGATTC
12289922 AATTCGGGTAATTCAGG-TAATTCGGGT
1 AATTCGGGTAATTC-GGTTAATTCGGGT
* * *
12289949 AATTCTGTTAATTCGGTTAATTCGGTT
1 AATTCGGGTAATTCGGTTAATTCGGGT
*
12289976 AATT-TGGTCAATTCGGTTAATT
1 AATTCGGGT-AATTCGGTTAATT
12289998 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.12
27 38 0.88
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (27 bp):
AATTCGGGTAATTCGGTTAATTCGGGT
Found at i:12289976 original size:18 final size:18
Alignment explanation
Indices: 12289922--12289997 Score: 93
Period size: 18 Copynumber: 4.2 Consensus size: 18
12289912 GTAGTGATTC
12289922 AATTCGGGTAATTCAGG-T
1 AATTCGGGTAATTC-GGTT
*
12289940 AATTCGGGTAATTCTGTT
1 AATTCGGGTAATTCGGTT
*
12289958 AATTCGGTTAATTCGGTT
1 AATTCGGGTAATTCGGTT
*
12289976 AATT-TGGTCAATTCGGTT
1 AATTCGGGT-AATTCGGTT
12289994 AATT
1 AATT
12289998 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 3 0.06
18 48 0.94
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:12292466 original size:33 final size:33
Alignment explanation
Indices: 12292404--12292498 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 33
12292394 GGACTTTATC
*
12292404 TGTTCTGTGTTTATTGTCCCAGCGAACTATCTA
1 TGTTCTGTGTTTATTGTCCCAACGAACTATCTA
* * *
12292437 TGTTCTGTGTTTATTGTCCTAAC-AGACTATTTC
1 TGTTCTGTGTTTATTGTCCCAACGA-ACTATCTA
* * *
12292470 TGTTATGTGTTTACTAT-CCAACGAACTAT
1 TGTTCTGTGTTTATTGTCCCAACGAACTAT
12292499 ATTTGTCATG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 10 0.19
33 42 0.81
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTTCTGTGTTTATTGTCCCAACGAACTATCTA
Found at i:12293810 original size:25 final size:25
Alignment explanation
Indices: 12293757--12293810 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12293747 AAAGATAAAC
* *
12293757 ATTAAATTAAATTTATATAACTACT
1 ATTAAATTAAATTAATATAAATACT
12293782 -TTAATATTAAATTAATA-AAATACT
1 ATTAA-ATTAAATTAATATAAATACT
12293806 ATTAA
1 ATTAA
12293811 GATAAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTAAATTAAATTAATATAAATACT
Found at i:12298823 original size:42 final size:43
Alignment explanation
Indices: 12298731--12298824 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
12298721 ACATAGTTAG
** * *
12298731 CCCATTGATGAATACTATACACAAGTAAACTTTATACAATTCG
1 CCCATTGGCGAATACTATACACAAGCAAACTTTATACAATTCA
**
12298774 CCCATTGGCGAATACTATACACAAGCAGTCTTT-TACAATTCA
1 CCCATTGGCGAATACTATACACAAGCAAACTTTATACAATTCA
12298816 CCCATTGGC
1 CCCATTGGC
12298825 AAAATACCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
42 17 0.38
43 28 0.62
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (43 bp):
CCCATTGGCGAATACTATACACAAGCAAACTTTATACAATTCA
Found at i:12300044 original size:20 final size:20
Alignment explanation
Indices: 12300020--12300119 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
12300010 AAGTACTTGT
*
12300020 AGTTTATCTGCAATACTGGT
1 AGTTTATCTGCAATACTGGC
* * *** *
12300040 GGTTTGTCCATAATACTAGC
1 AGTTTATCTGCAATACTGGC
* *
12300060 ATTTTATCTGCAATACTGGT
1 AGTTTATCTGCAATACTGGC
* * * **
12300080 GGCTTGTCCACAATACTGGC
1 AGTTTATCTGCAATACTGGC
*
12300100 AGTTTATCTGTAATACTGGC
1 AGTTTATCTGCAATACTGGC
12300120 GACTTGTCCA
Statistics
Matches: 52, Mismatches: 28, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
AGTTTATCTGCAATACTGGC
Found at i:12300077 original size:40 final size:40
Alignment explanation
Indices: 12300020--12300170 Score: 178
Period size: 40 Copynumber: 3.8 Consensus size: 40
12300010 AAGTACTTGT
*
12300020 AGTTTATCTGCAATACTGGTGGTTTGTCCATAATACTAGC
1 AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAGC
* * *
12300060 ATTTTATCTGCAATACTGGTGGCTTGTCCACAATACTGGC
1 AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAGC
* * * *
12300100 AGTTTATCTGTAATACTGGCGACTTGTCCATAATACT-GAT
1 AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAG-C
* **
12300140 AGTTTATCTGCGATTACCAGTGGCTTGTCCA
1 AGTTTATCTGC-AATACTGGTGGCTTGTCCA
12300171 CAAACGACTG
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 78 0.84
41 14 0.15
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (40 bp):
AGTTTATCTGCAATACTGGTGGCTTGTCCATAATACTAGC
Found at i:12305966 original size:6 final size:7
Alignment explanation
Indices: 12305937--12305965 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
12305927 CCTAAATACT
12305937 AAACTC-
1 AAACTCA
12305943 AAACTCA
1 AAACTCA
12305950 AAACTCA
1 AAACTCA
12305957 AAACTCA
1 AAACTCA
12305964 AA
1 AA
12305966 CCCTAAATTA
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:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACTCA
Found at i:12306045 original size:14 final size:14
Alignment explanation
Indices: 12306026--12306052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12306016 CAAACCCGAA
12306026 CCTGAACCTTGAAT
1 CCTGAACCTTGAAT
12306040 CCTGAACCTTGAA
1 CCTGAACCTTGAA
12306053 CCTAGGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (14 bp):
CCTGAACCTTGAAT
Found at i:12316649 original size:24 final size:24
Alignment explanation
Indices: 12316615--12316666 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12316605 TTTCTAGAAG
* * *
12316615 ATTTAGTATTTATGAGTATAATGT
1 ATTTAGCATTTATGAGCATAATAT
*
12316639 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
12316663 ATTT
1 ATTT
12316667 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:12319753 original size:24 final size:24
Alignment explanation
Indices: 12319688--12319741 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12319678 TCTTTCTAGA
** * *
12319688 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAACATTTATTAGCATAAT
12319712 ATATTTAACATTTATTAGCATAAT
1 ATATTTAACATTTATTAGCATAAT
12319736 ATATTT
1 ATATTT
12319742 GACTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
ATATTTAACATTTATTAGCATAAT
Found at i:12321355 original size:23 final size:24
Alignment explanation
Indices: 12321327--12321372 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
12321317 TTGTTATATG
12321327 TATATACATACATACAT-TTTTTA
1 TATATACATACATACATATTTTTA
*
12321350 TATATATATACATACATATTTTT
1 TATATACATACATACATATTTTT
12321373 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATACATACATACATATTTTTA
Found at i:12321384 original size:27 final size:27
Alignment explanation
Indices: 12321314--12321375 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
12321304 TTTACTTCAA
*
12321314 ATTTTGTTATATGTATATACATACATAC
1 ATTTT-TTATATATATATACATACATAC
12321342 ATTTTTTATATATATATACATACATA-
1 ATTTTTTATATATATATACATACATAC
*
12321368 TTTTTTTA
1 ATTTTTTA
12321376 ATTTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.22
27 20 0.62
28 5 0.16
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTTTTATATATATATACATACATAC
Found at i:12321447 original size:20 final size:19
Alignment explanation
Indices: 12321424--12321470 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
12321414 ATTTATTTTT
12321424 ATATTTTATAACTTATATAC
1 ATATTTTATAAC-TATATAC
* *
12321444 ATATCTATATATCTATATAC
1 ATAT-TTTATAACTATATAC
12321464 AT-TTTTA
1 ATATTTTA
12321471 ATTTTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 1 0.04
20 13 0.57
21 6 0.26
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTTATAACTATATAC
Found at i:12322479 original size:173 final size:173
Alignment explanation
Indices: 12322221--12322573 Score: 636
Period size: 173 Copynumber: 2.0 Consensus size: 173
12322211 ATTCTTCTAA
12322221 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
1 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
* * * *
12322286 GGTGTTAATCCTTTCTCGTACGTAACCGACTCTCGAACTCGTTTTCTGAATTTTGTGGACCAAAA
66 GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCATTTTCTGAATTTTGTGGACCAAAA
* *
12322351 TCGTTGTTTTAATAAAATCGAATCGTTTATTAAAAATAACCAC
131 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
*
12322394 GTTTTCAATTTTCGACATCAAGACATTAGCTAATTAACTAGGTACCAATTTTTGGGCGTTACGAG
1 GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
12322459 GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCATTTTCTGAATTTTGTGGACCAAAA
66 GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCATTTTCTGAATTTTGTGGACCAAAA
12322524 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
131 TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
12322567 -TTTTCAA
1 GTTTTCAA
12322574 GGTGATCTGA
Statistics
Matches: 173, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
172 7 0.04
173 166 0.96
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (173 bp):
GTTTTCAATTTTCGACATCAAGACATTAGCTAATCAACTAGGTACCAATTTTTGGGCGTTACGAG
GGTGCTAATCCTTCCTCGTACGTAACCGACTCCCGAACTCATTTTCTGAATTTTGTGGACCAAAA
TCGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCAC
Found at i:12332501 original size:45 final size:45
Alignment explanation
Indices: 12332452--12332551 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
12332442 ATAGATCAAT
* * *
12332452 GAAGATAGCAGATTTTGCTTTCCTGTACTGACAGCAAAGCAGATC
1 GAAGATACCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGATC
* * *
12332497 GAAGACACCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATC
1 GAAGATACCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGATC
12332542 GAAGATACCA
1 GAAGATACCA
12332552 TAGTTTGCAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (45 bp):
GAAGATACCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGATC
Found at i:12332623 original size:50 final size:50
Alignment explanation
Indices: 12332579--12332891 Score: 172
Period size: 50 Copynumber: 6.3 Consensus size: 50
12332569 GATTGAGGTC
* *
12332579 ACAATGGCGAATCTTACTT-CCTTAGCGGTGCAGTGGAACAGATTGAAGCT
1 ACAACGGCGAATCTTACTTCCCTT-GCGGTACAGTGGAACAGATTGAAGCT
* *
12332629 ACAACGGCGAATCTTATTTCCCTTGTGGTACAGTGGAACAGATTGAAGCT
1 ACAACGGCGAATCTTACTTCCCTTGCGGTACAGTGGAACAGATTGAAGCT
** * ** * * * * * *
12332679 ACAACGATGAATCTTGCTTTCCC--GACATTGCAAT-TAAAAGATTGAGGCC
1 ACAACGGCGAATCTTAC-TTCCCTTG-CGGTACAGTGGAACAGATTGAAGCT
* * * ** * *
12332728 ACAACGACGAATCTTACTTTCCTGGCGGTGTAGTGGAATAAATTGAAGCT
1 ACAACGGCGAATCTTACTTCCCTTGCGGTACAGTGGAACAGATTGAAGCT
* * * * ** * * * * *
12332778 ACAATGGTGAATCTTGCTTCCC-CGACATTACAAT-TAAAAGA-TCAAGGCC
1 ACAACGGCGAATCTTACTTCCCTTG-CGGTACAGTGGAACAGATTGAA-GCT
** * * *
12332827 ACAACGGCGAATCTTACTTTTCTGGCGGTGCAGCGGAACAGATTGAAGCT
1 ACAACGGCGAATCTTACTTCCCTTGCGGTACAGTGGAACAGATTGAAGCT
* *
12332877 ACAACGACAAATCTT
1 ACAACGGCGAATCTT
12332892 GCTTAACATT
Statistics
Matches: 190, Mismatches: 62, Indels: 22
0.69 0.23 0.08
Matches are distributed among these distances:
48 7 0.04
49 60 0.32
50 111 0.58
51 12 0.06
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
ACAACGGCGAATCTTACTTCCCTTGCGGTACAGTGGAACAGATTGAAGCT
Found at i:12332734 original size:49 final size:49
Alignment explanation
Indices: 12332668--12332941 Score: 148
Period size: 49 Copynumber: 5.6 Consensus size: 49
12332658 ACAGTGGAAC
* * *
12332668 AGATTGAAGCTACAACGATGAATCTTGCTTTCCCGACATTGCAATTAAA
1 AGATTGAAGCCACAACGACGAATCTTACTTTCCCGACATTGCAATTAAA
* * * ** * * *
12332717 AGATTGAGGCCACAACGACGAATCTTACTTTCCTGGCGGTGTAGTGGAATA
1 AGATTGAAGCCACAACGACGAATCTTACTTTCCCGACATTGCAAT-TAA-A
* * ** * * *
12332768 A-ATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTACAATTAAA
1 AGATTGAAGCCACAACGACGAATCTTACTTTCCCGACATTGCAATTAAA
* * * * * ** *** *
12332816 AGA-TCAAGGCCACAACGGCGAATCTTACTTTTCTGGCGGTGCAGCGGAAC
1 AGATTGAA-GCCACAACGACGAATCTTACTTTCCCGACATTGCA-ATTAAA
* * * *
12332866 AGATTGAAGCTACAACGACAAATCTTGC-TT---AACATTGCAATTAAA
1 AGATTGAAGCCACAACGACGAATCTTACTTTCCCGACATTGCAATTAAA
*
12332911 AGATTGAGGCCACAAC-AGCGAATCTTACTTT
1 AGATTGAAGCCACAACGA-CGAATCTTACTTT
12332942 TCTGGTGAAT
Statistics
Matches: 158, Mismatches: 59, Indels: 19
0.67 0.25 0.08
Matches are distributed among these distances:
44 1 0.01
45 24 0.15
46 7 0.04
48 5 0.03
49 64 0.41
50 52 0.33
51 5 0.03
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (49 bp):
AGATTGAAGCCACAACGACGAATCTTACTTTCCCGACATTGCAATTAAA
Found at i:12332740 original size:99 final size:99
Alignment explanation
Indices: 12332618--12332946 Score: 400
Period size: 99 Copynumber: 3.4 Consensus size: 99
12332608 GCAGTGGAAC
* * * * * *
12332618 AGATTGAAGCTACAACGGCGAATCTTA-TTTCCCTTGTGGTACAGTGGAACAGATTGAAGCTACA
1 AGATTGAGGCCACAACGACGAATCTTACTTT-CCTGGCGGTGCAGTGGAACAGATTGAAGCTACA
12332682 ACGATGAATCTTGCTTTCCCGACATTGCAATTAAA
65 ACGATGAATCTTGCTTTCCCGACATTGCAATTAAA
* * *
12332717 AGATTGAGGCCACAACGACGAATCTTACTTTCCTGGCGGTGTAGTGGAATAAATTGAAGCTACAA
1 AGATTGAGGCCACAACGACGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAA
* * * *
12332782 TGGTGAATCTTGCTTCCCCGACATTACAATTAAA
66 CGATGAATCTTGCTTTCCCGACATTGCAATTAAA
** * * *
12332816 AGATCAAGGCCACAACGGCGAATCTTACTTTTCTGGCGGTGCAGCGGAACAGATTGAAGCTACAA
1 AGATTGAGGCCACAACGACGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAA
** *
12332881 CGACAAATCTTGC-TT---AACATTGCAATTAAA
66 CGATGAATCTTGCTTTCCCGACATTGCAATTAAA
*
12332911 AGATTGAGGCCACAAC-AGCGAATCTTACTTTTCTGG
1 AGATTGAGGCCACAACGA-CGAATCTTACTTTCCTGG
12332947 TGAATAGATT
Statistics
Matches: 197, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
95 45 0.23
98 1 0.01
99 148 0.75
100 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (99 bp):
AGATTGAGGCCACAACGACGAATCTTACTTTCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAA
CGATGAATCTTGCTTTCCCGACATTGCAATTAAA
Found at i:12334794 original size:22 final size:23
Alignment explanation
Indices: 12334762--12334808 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
12334752 TTGTTATATG
*
12334762 TATATACATACATACAT-TTTTT
1 TATATACATACATAAATATTTTT
*
12334784 TATATATATACATAAATATTTTT
1 TATATACATACATAAATATTTTT
12334807 TA
1 TA
12334809 ATTTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATACATACATAAATATTTTT
Found at i:12334880 original size:20 final size:19
Alignment explanation
Indices: 12334857--12334903 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
12334847 ATTTATTTTT
12334857 ATATTTTATAACTTATATAC
1 ATATTTTATAAC-TATATAC
* *
12334877 ATATCTATATATCTATATAC
1 ATAT-TTTATAACTATATAC
12334897 AT-TTTTA
1 ATATTTTA
12334904 ATTTTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 1 0.04
20 13 0.57
21 6 0.26
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTTATAACTATATAC
Found at i:12336106 original size:14 final size:14
Alignment explanation
Indices: 12336087--12336115 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12336077 GACAAAGCCT
12336087 ATACTTTAATTGTG
1 ATACTTTAATTGTG
12336101 ATACTTTAATTGTG
1 ATACTTTAATTGTG
12336115 A
1 A
12336116 AACTGAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (14 bp):
ATACTTTAATTGTG
Found at i:12338125 original size:24 final size:24
Alignment explanation
Indices: 12338074--12338125 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12338064 AATTGAGTTT
* * *
12338074 CTTTTCCTAGTTAAACCCTACTAT
1 CTTTTCCTAGTCAAACCCTAATAA
* *
12338098 CTTTTCCTAGTCGAACTCTAATAA
1 CTTTTCCTAGTCAAACCCTAATAA
12338122 CTTT
1 CTTT
12338126 AGGGATATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (24 bp):
CTTTTCCTAGTCAAACCCTAATAA
Found at i:12345617 original size:25 final size:25
Alignment explanation
Indices: 12345582--12345629 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12345572 AAGAATCCCA
12345582 GTTTTCCTTTGACTGGGTCTAGCCG
1 GTTTTCCTTTGACTGGGTCTAGCCG
*
12345607 GTTTTCTTTTGACTGGGTCTAGC
1 GTTTTCCTTTGACTGGGTCTAGC
12345630 AGCCGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.21, G:0.27, T:0.44
Consensus pattern (25 bp):
GTTTTCCTTTGACTGGGTCTAGCCG
Found at i:12348076 original size:13 final size:13
Alignment explanation
Indices: 12348058--12348082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12348048 TTTAGTATTG
12348058 CTTTTAAAAAGTA
1 CTTTTAAAAAGTA
12348071 CTTTTAAAAAGT
1 CTTTTAAAAAGT
12348083 GTTAGTGGAA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
CTTTTAAAAAGTA
Found at i:12355520 original size:17 final size:17
Alignment explanation
Indices: 12355498--12355530 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12355488 ACCCGAAAAA
*
12355498 ATTATTATTTTATCGAG
1 ATTATTAATTTATCGAG
12355515 ATTATTAATTTATCGA
1 ATTATTAATTTATCGA
12355531 TAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (17 bp):
ATTATTAATTTATCGAG
Found at i:12355546 original size:27 final size:26
Alignment explanation
Indices: 12355516--12355579 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
12355506 TTTATCGAGA
12355516 TTATTAATTTATCGATAAATAAATATT
1 TTATTAATTTATCGATAAATAAATA-T
* *
12355543 TTATTACTTTATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATAAATAT
12355569 TTATTAATTTA
1 TTATTAATTTA
12355580 GAGAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATAAATAT
Found at i:12355700 original size:36 final size:39
Alignment explanation
Indices: 12355653--12355730 Score: 117
Period size: 36 Copynumber: 2.1 Consensus size: 39
12355643 AATGAATCAA
*
12355653 AATTAATTGGTTCATGTAA-C-AAAA-AAAAAAAGAGTT
1 AATTAATTGGTTCATGTAACCAAAAAGAAAAAAAAAGTT
*
12355689 AATTGATTGGTTCATGTAACCAAAAAGAAAAAAAAAGTT
1 AATTAATTGGTTCATGTAACCAAAAAGAAAAAAAAAGTT
12355728 AAT
1 AAT
12355731 AGTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 18 0.49
37 1 0.03
38 4 0.11
39 14 0.38
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (39 bp):
AATTAATTGGTTCATGTAACCAAAAAGAAAAAAAAAGTT
Found at i:12371122 original size:12 final size:12
Alignment explanation
Indices: 12371092--12371124 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12371082 TATATATTTT
12371092 AAAATT-ATATA
1 AAAATTAATATA
12371103 AAAA-TAATATA
1 AAAATTAATATA
12371114 AAAATTAATAT
1 AAAATTAATAT
12371125 GGGTGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:12373725 original size:13 final size:13
Alignment explanation
Indices: 12373707--12373734 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12373697 TTCTGCCACC
12373707 AAAAATTTGCAAT
1 AAAAATTTGCAAT
12373720 AAAAATTTGCAAT
1 AAAAATTTGCAAT
12373733 AA
1 AA
12373735 TACCCTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAAATTTGCAAT
Found at i:12376505 original size:18 final size:20
Alignment explanation
Indices: 12376468--12376507 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12376458 AATATTGGAT
*
12376468 CTATATTTTCACTATTATCC
1 CTATATTTTCACTATAATCC
12376488 CTAT-TTTTCACTA-AATCC
1 CTATATTTTCACTATAATCC
12376506 CT
1 CT
12376508 TGAATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (20 bp):
CTATATTTTCACTATAATCC
Found at i:12381204 original size:43 final size:42
Alignment explanation
Indices: 12381141--12381294 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 42
12381131 AGCTCGTACA
* *
12381141 ATGCC-ATATCCCGGATATGGTCTTACATGTTAATGCATATCG
1 ATGCCAATATCCCAGACATGGTCTTACATGTTAAT-CATATCG
* *
12381183 ATGCCACTATCCCAGACATGGTCTTATATG--AATCATATACG
1 ATGCCAATATCCCAGACATGGTCTTACATGTTAATCATAT-CG
* * **
12381224 ATGCCAATGTCCCAGACATGGTCTTACACGTTTTCTCACT-TCG
1 ATGCCAATATCCCAGACATGGTCTTACATG-TTAATCA-TATCG
* *
12381267 ATGCCAATTTCCTAGACATGGTCTTACA
1 ATGCCAATATCCCAGACATGGTCTTACA
12381295 CGAAATCACA
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
40 5 0.05
41 31 0.33
42 5 0.05
43 48 0.51
44 4 0.04
45 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (42 bp):
ATGCCAATATCCCAGACATGGTCTTACATGTTAATCATATCG
Found at i:12381488 original size:30 final size:30
Alignment explanation
Indices: 12381440--12381823 Score: 605
Period size: 30 Copynumber: 12.9 Consensus size: 30
12381430 GACAATATAT
*
12381440 ATGTATA--CATAAACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
* *
12381468 ATGTATATCTATATACAAATCAATTCGGTA
1 ATGTATATCCATATACAAATCAATTCGGCA
12381498 ATGTATATCCATATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
*
12381528 ATGTATATCCTTATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
* *
12381558 ACGTATATCTATATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
* *
12381588 ACGTATATCTATATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
* *
12381618 ATGTATATCCATATACAAAACAATTCAGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
12381648 ATGTATATCCATATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
*
12381678 ATGTATATCCATATACAAATCAATTTGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
* *
12381708 ATGTATATCTATATA-AAAACTAATTCGGCA
1 ATGTATATCCATATACAAATC-AATTCGGCA
12381738 ATGTATATCCATATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
12381768 ATGTATATCCATATACAAATCAATTCGGCA
1 ATGTATATCCATATACAAATCAATTCGGCA
*
12381798 ATGTATACCCATATAC-AATCAATTCG
1 ATGTATATCCATATACAAATCAATTCG
12381824 AAAATATATA
Statistics
Matches: 330, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
28 7 0.02
29 14 0.04
30 305 0.92
31 4 0.01
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (30 bp):
ATGTATATCCATATACAAATCAATTCGGCA
Found at i:12391685 original size:19 final size:19
Alignment explanation
Indices: 12391661--12391753 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
12391651 AATAAATTAC
*
12391661 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
*
12391680 TCATCTTAGCTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * * *
12391699 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
12391715 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
12391734 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
12391753 T
1 T
12391754 GCTGGAATAA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 7 0.13
18 6 0.11
19 38 0.69
20 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:12391705 original size:54 final size:54
Alignment explanation
Indices: 12391642--12391763 Score: 217
Period size: 54 Copynumber: 2.3 Consensus size: 54
12391632 ATAAGTATTT
*
12391642 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGCTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGCTAATTA
* *
12391696 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGCTAATTA
12391750 AGTTGCTGGAATAA
1 AGTTGCTGGAATAA
12391764 TTTATTGTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGCTAATTA
Found at i:12391725 original size:26 final size:26
Alignment explanation
Indices: 12391640--12391725 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
12391630 GAATAAGTAT
12391640 TTAGTTGCTGGAATAAATTACTCATC
1 TTAGTTGCTGGAATAAATTACTCATC
** * * ** *
12391666 TTAGTTAATTGAGTTCATCTTAGCTAAT-
1 TTAGTTGCTGGA-AT-AAATTA-CTCATC
*
12391694 TAAGTTGCTGGAATAAATTACTCATC
1 TTAGTTGCTGGAATAAATTACTCATC
12391720 TTAGTT
1 TTAGTT
12391726 AATTAAGTTC
Statistics
Matches: 40, Mismatches: 16, Indels: 8
0.62 0.25 0.12
Matches are distributed among these distances:
25 4 0.10
26 18 0.45
27 2 0.05
28 12 0.30
29 4 0.10
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (26 bp):
TTAGTTGCTGGAATAAATTACTCATC
Found at i:12397105 original size:9 final size:9
Alignment explanation
Indices: 12397091--12397118 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12397081 TTTTGTTACA
12397091 ACAATTAAT
1 ACAATTAAT
12397100 ACAATTAAT
1 ACAATTAAT
12397109 ACAATTAAT
1 ACAATTAAT
12397118 A
1 A
12397119 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:12397140 original size:68 final size:68
Alignment explanation
Indices: 12397061--12397224 Score: 319
Period size: 68 Copynumber: 2.4 Consensus size: 68
12397051 TCAAGTTTGT
*
12397061 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
12397126 AAA
66 AAA
12397129 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
12397194 AAA
66 AAA
12397197 TTTACTAATCAAATGTTAGATTTTATTA
1 TTTACTAATCAAATGTTAGATTTTATTA
12397225 ATAATTTGAT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 95 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:12397171 original size:9 final size:9
Alignment explanation
Indices: 12397159--12397186 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12397149 TTTTATTACA
12397159 ACAATTAAT
1 ACAATTAAT
12397168 ACAATTAAT
1 ACAATTAAT
12397177 ACAATTAAT
1 ACAATTAAT
12397186 A
1 A
12397187 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:12397261 original size:16 final size:16
Alignment explanation
Indices: 12397242--12397283 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12397232 GATAATTTGA
*
12397242 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
*
12397258 TAATTTTAATCACAAT
1 TAATTTTAATAACAAT
*
12397274 TAGTTTTAAT
1 TAATTTTAAT
12397284 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:12399292 original size:18 final size:19
Alignment explanation
Indices: 12399258--12399296 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
12399248 ATTCTATTCC
12399258 ATTAAATAAATTATTAAAA
1 ATTAAATAAATTATTAAAA
*
12399277 ATTAAA-AAA-TATTTAAA
1 ATTAAATAAATTATTAAAA
12399294 ATT
1 ATT
12399297 GATTTCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTAAATAAATTATTAAAA
Found at i:12402915 original size:14 final size:14
Alignment explanation
Indices: 12402889--12402918 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
12402879 GTATTCAGCG
12402889 AAGGGAAGAAAAAT
1 AAGGGAAGAAAAAT
12402903 AAGGAGAAGAAAAAT
1 AAGG-GAAGAAAAAT
12402918 A
1 A
12402919 TTTCTTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
AAGGGAAGAAAAAT
Found at i:12411069 original size:13 final size:14
Alignment explanation
Indices: 12411038--12411070 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12411028 ATTAAAAGCA
12411038 AAAAAATAAGGTAT
1 AAAAAATAAGGTAT
12411052 AAAAAATAAGTGT-T
1 AAAAAATAAG-GTAT
12411066 AAAAA
1 AAAAA
12411071 GAATTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (14 bp):
AAAAAATAAGGTAT
Found at i:12412737 original size:23 final size:23
Alignment explanation
Indices: 12412711--12412757 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12412701 TAAAGTACGC
* *
12412711 TTACAACTGAAAAGAAACCTAAA
1 TTACAACTAAAAAGAAAACTAAA
* *
12412734 TTACAAGTAAAAATAAAACTAAA
1 TTACAACTAAAAAGAAAACTAAA
12412757 T
1 T
12412758 AGAAAATGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (23 bp):
TTACAACTAAAAAGAAAACTAAA
Found at i:12417084 original size:47 final size:47
Alignment explanation
Indices: 12417025--12417154 Score: 145
Period size: 47 Copynumber: 2.8 Consensus size: 47
12417015 AAAAGCTGCT
* * * *
12417025 AATACGTTGTGGATGAACCACTACTCGAGTAGAT-AGTTGCCGACTAA
1 AATACGTTGTGGATAAACCACTAATCGAGCAGATGA-TTGCAGACTAA
* * * *
12417072 AATATGTTGTGGATAAATCACTAATTGAGCAGATGATTGGAGACTAA
1 AATACGTTGTGGATAAACCACTAATCGAGCAGATGATTGCAGACTAA
* **
12417119 AATACGTTGTGGATAAACCATTGGTCGAGCAGATGA
1 AATACGTTGTGGATAAACCACTAATCGAGCAGATGA
12417155 ATACCGACTA
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
47 67 0.99
48 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (47 bp):
AATACGTTGTGGATAAACCACTAATCGAGCAGATGATTGCAGACTAA
Found at i:12418345 original size:17 final size:16
Alignment explanation
Indices: 12418302--12418346 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
12418292 TTTGATGTAA
12418302 GAGAGGAAAGAAAAGG
1 GAGAGGAAAGAAAAGG
*
12418318 AAGA-GAGAAGAAATAGG
1 GAGAGGA-AAGAAA-AGG
12418335 GAGAGGAAAGAA
1 GAGAGGAAAGAA
12418347 TATTCTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 2 0.08
16 9 0.38
17 11 0.46
18 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (16 bp):
GAGAGGAAAGAAAAGG
Found at i:12425391 original size:41 final size:41
Alignment explanation
Indices: 12425334--12425442 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 41
12425324 TGATCGAATG
* * * *
12425334 TAATTCAGACTTATTGTCTAGTAGGCTTGATGCCGGTGATA
1 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGATA
*
12425375 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGATA
* * *
12425416 TTATTCGGACT-ATAAGTCTAGCAGGCT
1 TAATTCAGACTCAT-TGTCTAGCAGGCT
12425443 AAAAGCCGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
40 2 0.03
41 57 0.97
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGATA
Found at i:12425589 original size:21 final size:21
Alignment explanation
Indices: 12425540--12425589 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
12425530 ACGTGATATG
12425540 TAAATAA-TATATATATTTGA
1 TAAATAAGTATATATATTTGA
*
12425560 -AGATCAAGTATATATATTTGA
1 TAAAT-AAGTATATATATTTGA
12425581 TAAATAAGT
1 TAAATAAGT
12425590 TTGATGGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 17 0.68
22 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (21 bp):
TAAATAAGTATATATATTTGA
Found at i:12426680 original size:22 final size:22
Alignment explanation
Indices: 12426647--12426688 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
12426637 TTGGCAAGCC
12426647 TATAAGTCTAAGCTTCACCATG
1 TATAAGTCTAAGCTTCACCATG
12426669 TATAAGGT-TAAGCTTCACCA
1 TATAA-GTCTAAGCTTCACCA
12426689 AGTTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
TATAAGTCTAAGCTTCACCATG
Found at i:12434499 original size:15 final size:15
Alignment explanation
Indices: 12434479--12434510 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12434469 CATTTCACTA
*
12434479 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
12434494 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
12434509 TT
1 TT
12434511 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:12437669 original size:45 final size:45
Alignment explanation
Indices: 12437601--12437693 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
12437591 TCAGATACTT
* *
12437601 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
* *
12437646 GGTGGAATCAGCACATAGTAACCACCTTACTAATCAATGATGTTC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
12437691 GGT
1 GGT
12437694 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:12437755 original size:51 final size:50
Alignment explanation
Indices: 12437695--12437882 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
12437685 ATGTTCGGTT
*
12437695 CACATAGTAGCCTGCACATAGTACTACACATGTGACTATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACTA-TACCATCCGATA
* * * *
12437746 CACATAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CTATACCATCCGATA
* * * * *
12437797 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTAT--CATTCTAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CTATACCATCCGA-TA
* *
12437847 CACGTAGTAGCCTGCATATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGAC
12437883 CATCACTTTC
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 4 0.03
50 32 0.28
51 77 0.67
52 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACTATACCATCCGATA
Found at i:12437881 original size:101 final size:101
Alignment explanation
Indices: 12437697--12437881 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
12437687 GTTCGGTTCA
*
12437697 CATAGTAGCCTGCACATAGTACTACACATGTGACTATTACCATCCGATACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACTATTA-CATCCGATACACATAGTAGCCTGCA
12437762 CATAGTACTACACACGTGATCAAAACTATCTGATACG
65 CATAGTACTACACACGTGATCAAAACTATCTGATACG
* * *
12437799 CATAGTAGCCTGCACATAGTACTACACATGCGACCTA-T-CATTCTAGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGA-CTATTACATCCGA-TACACATAGTAGCCTGC
*
12437862 ATATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
12437882 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 5 0.07
101 35 0.46
102 33 0.43
103 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACTATTACATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCAAAACTATCTGATACG
Found at i:12445091 original size:19 final size:20
Alignment explanation
Indices: 12445056--12445097 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
12445046 AATTGAGAAA
12445056 AAAAACCAACTTAAAT-ATT
1 AAAAACCAACTTAAATAATT
*
12445075 AAAAACCAAAC-TCAATAATT
1 AAAAACC-AACTTAAATAATT
12445095 AAA
1 AAA
12445098 TAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAACCAACTTAAATAATT
Found at i:12447432 original size:2 final size:2
Alignment explanation
Indices: 12447425--12447463 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12447415 TGTCCCATCT
12447425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12447464 TTACATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12447938 original size:9 final size:9
Alignment explanation
Indices: 12447924--12447954 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12447914 GTTAAACGAA
12447924 TCGAGTTAT
1 TCGAGTTAT
*
12447933 TCGAGTTAA
1 TCGAGTTAT
12447942 TCGAGTTAT
1 TCGAGTTAT
12447951 TCGA
1 TCGA
12447955 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12451856 original size:21 final size:23
Alignment explanation
Indices: 12451809--12451858 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12451799 AGAAAAGAGG
**
12451809 GAAAAAGAAGGAACGATAGAATG
1 GAAAAAGAAGGAACGATAGAAAA
12451832 GAAAAAGAAGGAA-GA-AGAAAA
1 GAAAAAGAAGGAACGATAGAAAA
12451853 GAAAAA
1 GAAAAA
12451859 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.04
Consensus pattern (23 bp):
GAAAAAGAAGGAACGATAGAAAA
Found at i:12455587 original size:18 final size:19
Alignment explanation
Indices: 12455549--12455606 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
12455539 ACTCCCCCTA
*
12455549 TTTACTTTCCCTC-AAAC-T
1 TTTA-TTTCCCCCAAAACTT
12455567 TTTA-TTCCCCCAAAACTT
1 TTTATTTCCCCCAAAACTT
*
12455585 TTTATTTTCCCCCTAAACTT
1 TTTA-TTTCCCCCAAAACTT
12455605 TT
1 TT
12455607 ACTTCTCACC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 9 0.26
20 15 0.44
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTATTTCCCCCAAAACTT
Found at i:12455618 original size:20 final size:18
Alignment explanation
Indices: 12455557--12455618 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 18
12455547 TATTTACTTT
12455557 CCCTCAAACTTTTATTC-C
1 CCCT-AAACTTTTATTCTC
* *
12455575 CCCAAAACTTTTTATTTTCC
1 CCCTAAAC-TTTTATTCT-C
12455595 CCCTAAACTTTTACTTCTC
1 CCCTAAACTTTTA-TTCTC
12455614 ACCCT
1 -CCCT
12455619 TTACTCTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 4 0.11
18 10 0.29
19 6 0.17
20 15 0.43
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (18 bp):
CCCTAAACTTTTATTCTC
Found at i:12457498 original size:24 final size:22
Alignment explanation
Indices: 12457471--12457517 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
12457461 TTAATATTTT
*
12457471 TATTTTTTAATTTATTTATATATA
1 TATTCTTTAATTT-TTTA-ATATA
*
12457495 TATTCTTTCATTTTTTAATATA
1 TATTCTTTAATTTTTTAATATA
12457517 T
1 T
12457518 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 4 0.19
24 11 0.52
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTCTTTAATTTTTTAATATA
Found at i:12457788 original size:21 final size:19
Alignment explanation
Indices: 12457751--12457789 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
12457741 ATAATATTCT
*
12457751 TATATAATACTATTTTATA
1 TATATAATACTAATTTATA
12457770 TATATATATACATAATTTAT
1 TATATA-ATAC-TAATTTAT
12457790 GTTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATAATACTAATTTATA
Found at i:12458372 original size:17 final size:18
Alignment explanation
Indices: 12458340--12458373 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12458330 GCTCTTGTGT
12458340 GTATTGTATTGCTTATTG
1 GTATTGTATTGCTTATTG
*
12458358 GTATT-TATTGGTTATT
1 GTATTGTATTGCTTATT
12458374 TGTAGTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (18 bp):
GTATTGTATTGCTTATTG
Found at i:12459307 original size:30 final size:29
Alignment explanation
Indices: 12459249--12459309 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
12459239 TTCAAATTTG
* *
12459249 AATATAAATAAAATTATTTAATACAATTA
1 AATATAAATAAAAGTAATTAATACAATTA
* *
12459278 AATATAATATCAAAGTAATTAATATAATTA
1 AATATAA-ATAAAAGTAATTAATACAATTA
12459308 AA
1 AA
12459310 AAAGCAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (29 bp):
AATATAAATAAAAGTAATTAATACAATTA
Found at i:12461739 original size:16 final size:15
Alignment explanation
Indices: 12461720--12461773 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
12461710 AAATTATTAT
*
12461720 GAAATAAAAGAATAGA
1 GAAATAAAAGAACA-A
12461736 GAAAGTAAAAGAACAA
1 GAAA-TAAAAGAACAA
**
12461752 GAAATAGGAGAACAA
1 GAAATAAAAGAACAA
12461767 -AAATAAA
1 GAAATAAA
12461774 CGTATGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 9 0.28
17 9 0.28
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.09
Consensus pattern (15 bp):
GAAATAAAAGAACAA
Found at i:12465598 original size:19 final size:19
Alignment explanation
Indices: 12465576--12465613 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12465566 TCAATCATCC
12465576 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
12465595 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
12465614 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:12475927 original size:15 final size:15
Alignment explanation
Indices: 12475907--12475938 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12475897 CTTACTTCCT
12475907 TCGTCAGCATCCTCA
1 TCGTCAGCATCCTCA
12475922 TCGTCAGCATCCTCA
1 TCGTCAGCATCCTCA
12475937 TC
1 TC
12475939 CTCATCCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.12, T:0.28
Consensus pattern (15 bp):
TCGTCAGCATCCTCA
Found at i:12475938 original size:6 final size:6
Alignment explanation
Indices: 12475929--12475983 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
12475919 TCATCGTCAG
* * *
12475929 CATCCT CATCCT CATCCT CTTCCT CA---T CATCCT CTTCCT CCTCCT
1 CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT
*
12475974 CATCAT CATC
1 CATCCT CATC
12475984 ATCGTCATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
3 3 0.08
6 37 0.93
ACGTcount: A:0.15, C:0.49, G:0.00, T:0.36
Consensus pattern (6 bp):
CATCCT
Found at i:12475958 original size:21 final size:21
Alignment explanation
Indices: 12475934--12475986 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12475924 GTCAGCATCC
*
12475934 TCATCCTCATCCTCTTCCTCA
1 TCATCCTCATCCTCCTCCTCA
*
12475955 TCATCCTCTTCCTCCTCCTCA
1 TCATCCTCATCCTCCTCCTCA
*
12475976 TCATCATCATC
1 TCATCCTCATC
12475987 GTCATCTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.47, G:0.00, T:0.38
Consensus pattern (21 bp):
TCATCCTCATCCTCCTCCTCA
Found at i:12475960 original size:15 final size:15
Alignment explanation
Indices: 12475940--12475968 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12475930 ATCCTCATCC
12475940 TCATCCTCTTCCTCA
1 TCATCCTCTTCCTCA
12475955 TCATCCTCTTCCTC
1 TCATCCTCTTCCTC
12475969 CTCCTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.41
Consensus pattern (15 bp):
TCATCCTCTTCCTCA
Found at i:12477843 original size:28 final size:28
Alignment explanation
Indices: 12477803--12477858 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
12477793 TAACAAAAAG
12477803 AAAACCAAAAACAATTATGGGTGTCACC
1 AAAACCAAAAACAATTATGGGTGTCACC
12477831 AAAACCAAAAACAATTATGGGTGTCACC
1 AAAACCAAAAACAATTATGGGTGTCACC
12477859 CACCTTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.18
Consensus pattern (28 bp):
AAAACCAAAAACAATTATGGGTGTCACC
Found at i:12479743 original size:283 final size:281
Alignment explanation
Indices: 12478697--12480252 Score: 1762
Period size: 283 Copynumber: 5.5 Consensus size: 281
12478687 CTATTTTTAA
* * * * *
12478697 AATTTAGTTGACGGTTATTCATG-TCGTTAAGATTAATGATAGATTTAGTAA--GTAAATAAAAA
1 AATTGAGTTGAC-GTCATTCATGAT-GTTAAGCTTAAAGAAAGATTTAGTAAGTGTAAATAAAAA
* * * * * ** * *
12478759 TAATAATTAGGTTTAAGTTATAGCGTTGTAATTTAGGATAAATCTAAATTATGGTGCCAATATTT
64 TAATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAATATTC
* * *
12478824 ATTGTTTTATAATAATTACTATATCTCTATAATTTAGTTGACGTCATTCGTCATGTCAAGCTCAA
129 ATTATTTTATAATAATTACTATATCTTTATAATTTAGTTGACGTCATTCGTCATGTTAAGCTCAA
* * * * *
12478889 TAATAGAATTAGTAAGT-AAAATGGAGTTAATGTTTAGATTTAAACAATAATACTATTTTTTTTT
194 TGATAGATTTAGTAAGTAAAAATGGAATTAATGTTTAGATTTAAACAATAATA-T-TATTTTTAT
* *
12478953 TAAATTTATGTTTAATAATTTCTTC
257 AAAATTTATGTTTAATAATTTCTAC
* * * * * *
12478978 AATTGAATTGACG-CTATTTATTATGTTAAGCATAAAGAAAGATCTAGTAAGTGTAAATAAAAGT
1 AATTGAGTTGACGTC-ATTCATGATGTTAAGCTTAAAGAAAGATTTAGTAAGTGTAAATAAAAAT
* * * * *
12479042 GATGTTTAGATTCAAGTCATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCTAATATTCA
65 AATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAATATTCA
* * * * * *
12479107 TTATTTTATAATAATTACTATATCTCTATAATCTAGTTAACGTCATTGGTCATGTTAAGCCCGAT
130 TTATTTTATAATAATTACTATATCTTTATAATTTAGTTGACGTCATTCGTCATGTTAAGCTCAAT
* * *
12479172 GATAGATTTAGTAAATAAAAATGGAATTAATGTTTAGATTTAAACAAT-A-A-TA-TTTAAAAAA
195 GATAGATTTAGTAAGTAAAAATGGAATTAATGTTTAGATTTAAACAATAATATTATTTTTATAAA
* *
12479233 AATTATGTTTAATAATTTCTGC
260 ATTTATGTTTAATAATTTCTAC
* * * ***
12479255 AATTGAGTTGATGTCATTCATAATGTTAAGCTTAAAAAAAGATTTAGTAAGTGTAAATAAACGGA
1 AATTGAGTTGACGTCATTCATGATGTTAAGCTTAAAGAAAGATTTAGTAAGTGTAAATAAAAATA
* * * * *
12479320 ATATGTAGATTCAAGTTAGAACGCTATAATTTAGGATAAGTCTAAATTATGGTGCCAATATTCAT
66 ATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAATATTCAT
* * * *
12479385 TATTTTATCATAATTATTATTTCTTTATAATTTAGTTGACGTCATTGGTCATGTTAAGCTCAATG
131 TATTTTATAATAATTACTATATCTTTATAATTTAGTTGACGTCATTCGTCATGTTAAGCTCAATG
* *
12479450 ATAGATTTAGTAAGTAAAAATGGAACTACTGTTTAGATTTAAACAATAATATTATTTTTATAAAA
196 ATAGATTTAGTAAGTAAAAATGGAATTAATGTTTAGATTTAAACAATAATATTATTTTTATAAAA
* *
12479515 TTTATGTTTAATCATCTCTAC
261 TTTATGTTTAATAATTTCTAC
** * *
12479536 AATTGAGTAAACGTCATTCATGATATTAAACTTAAA-AAAGATTTAGTAAGTGTAAATAAACGTA
1 AATTGAGTTGACGTCATTCATGATGTTAAGCTTAAAGAAAGATTTAGTAAGTGTAAATAAA---A
* * *
12479600 ATATATATTTAGATTTAAGTTATAACACTATAATTTAGGTTAGGTCTAAATTATGGCACCAATAT
63 ATA-ATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAATAT
* ** * * * *
12479665 TCATTA-TTTATGATAATTACTATATCTTTATAATAAACTTGACGTCATTTGTCGTATTAAGCTC
127 TCATTATTTTATAATAATTACTATATCTTTATAATTTAGTTGACGTCATTCGTCATGTTAAGCTC
* * *
12479729 AATGATATATTTAGTAAGTAAAAATGAAATTAATGTTCAGATTTAAACAATAATA-TATTTTT-T
192 AATGATAGATTTAGTAAGTAAAAATGGAATTAATGTTTAGATTTAAACAATAATATTATTTTTAT
12479792 AAAAATTTATGTTTAATAATTTCTAC
257 -AAAATTTATGTTTAATAATTTCTAC
* * * * * * * *
12479818 AATTGAGTTGACGTGATTCATGATGTAAAGCTTAAAGAAAGAATCAATAAGTATAAATGAAAGTA
1 AATTGAGTTGACGTCATTCATGATGTTAAGCTTAAAGAAAGATTTAGTAAGTGTAAATAAAAATA
* ** * * * ** * *
12479883 ATGTTTAGATTTAAGCAATAACGCAATAATTTAGGATATGTCTAATTTATGATG-TAATTATTTA
66 ATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAA-TATTCA
* * * * * * * *
12479947 TTATTTTATAA-ATTTACTATATTTTTAAAATTTAGTTGACGGTTATTCGTGACGTTAAGATTAA
130 TTATTTTATAATAATTACTATATCTTTATAATTTAGTTGAC-GTCATTCGTCATGTTAAGCTCAA
* *
12480011 TGATAGATTTAGTAAGTAAAAAATGAAATTAATGTTTAGATTTAAACAATAATATTATTCTTTTT
194 TGATAGATTTAGTAAGT-AAAAATGGAATTAATGTTTAGATTTAAACAATAATATTATT-TTTAT
*
12480076 AAAATTTATGCTTAATAATTTCTAC
257 AAAATTTATGTTTAATAATTTCTAC
* * *
12480101 AATTGAGTT-ACG-CAATTCTTGATGTTAAGCTTAAAGAAAGATTTTAATAAGGGTAAATAAACA
1 AATTGAGTTGACGTC-ATTCATGATGTTAAGCTTAAAGAAAGA-TTTAGTAAGTGTAAATAAA-A
* * *
12480164 A-AATATTTAGATTTAAGTTATAACACTATAATTTAGGATAGGTCTACATTATGGCGTCAATATT
63 ATAATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAATATT
* *
12480228 CACTATTTTATAATAATTACAATAT
128 CATTATTTTATAATAATTACTATAT
12480253 TTCTAAAATT
Statistics
Matches: 1070, Mismatches: 177, Indels: 53
0.82 0.14 0.04
Matches are distributed among these distances:
277 237 0.22
278 5 0.00
279 75 0.07
280 93 0.09
281 103 0.10
282 226 0.21
283 259 0.24
284 72 0.07
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (281 bp):
AATTGAGTTGACGTCATTCATGATGTTAAGCTTAAAGAAAGATTTAGTAAGTGTAAATAAAAATA
ATATTTAGATTTAAGTTATAACGCTATAATTTAGGATAGGTCTAAATTATGGCGCCAATATTCAT
TATTTTATAATAATTACTATATCTTTATAATTTAGTTGACGTCATTCGTCATGTTAAGCTCAATG
ATAGATTTAGTAAGTAAAAATGGAATTAATGTTTAGATTTAAACAATAATATTATTTTTATAAAA
TTTATGTTTAATAATTTCTAC
Found at i:12483882 original size:32 final size:30
Alignment explanation
Indices: 12483811--12483888 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
12483801 GTAAGGGTTA
* *
12483811 ATTTCATTTTTT-TAATATTATTAATTTTT
1 ATTTAATTTTTTATAATATAATTAATTTTT
12483840 ATTTAA-TTTTTATAATATAATTAATATTTT
1 ATTTAATTTTTTATAATATAATTAAT-TTTT
12483870 -TTATAATTTTTTTATAATA
1 ATT-TAA-TTTTTTATAATA
12483889 GCAGTAGATC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 5 0.12
29 19 0.45
30 7 0.17
32 11 0.26
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTAATTTTTTATAATATAATTAATTTTT
Found at i:12485009 original size:43 final size:43
Alignment explanation
Indices: 12484944--12485145 Score: 244
Period size: 43 Copynumber: 4.7 Consensus size: 43
12484934 GAACAAGGCC
* * * * *
12484944 TTTAGCGGCACTTTTTCAACAAACGTCGCTAAAGATCATGACT
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGACT
*
12484987 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGTTCATGACT
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGACT
* * * * *
12485030 TTTAGCGGCGCTATTCCCACAAACACCACGATAGATCATCACT
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGACT
* * * * *
12485073 TTTAGCGACGCTTTTCCCACAAATGCCACTATAGAACA-GACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGACT
*
12485115 TTTAGCGACGCTTTTCCCACAAACGCCGCTA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTA
12485146 AAAACATATC
Statistics
Matches: 137, Mismatches: 22, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
42 31 0.23
43 106 0.77
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATGACT
Found at i:12485479 original size:43 final size:43
Alignment explanation
Indices: 12485413--12485499 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
12485403 ACATATGCAA
* * * *
12485413 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATAAAGGAAATCTT
* *
12485456 GGTAATAAAATATATAATACATTTACTTAATAAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATAAAGGAAATCTT
12485499 G
1 G
12485500 TACATCATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATAAAGGAAATCTT
Found at i:12488475 original size:9 final size:9
Alignment explanation
Indices: 12488458--12488494 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12488448 TATAGTTTGA
12488458 TATTCGAAT
1 TATTCGAAT
*
12488467 TATTTGAAT
1 TATTCGAAT
*
12488476 TATTCGAGT
1 TATTCGAAT
12488485 TATTCGAAT
1 TATTCGAAT
12488494 T
1 T
12488495 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12490453 original size:23 final size:24
Alignment explanation
Indices: 12490427--12490475 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
12490417 TTTAAATATA
12490427 TATATATGT-ATATTTATTTCTTT
1 TATATATGTAATATTTATTTCTTT
*
12490450 TATATATGTACATATTTATTTTTTT
1 TATATATGTA-ATATTTATTTCTTT
12490475 T
1 T
12490476 CAACTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
25 14 0.61
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TATATATGTAATATTTATTTCTTT
Found at i:12490465 original size:21 final size:22
Alignment explanation
Indices: 12490427--12490471 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
12490417 TTTAAATATA
* *
12490427 TATATATGTATATTTATTTCTTT
1 TATATATGTACA-TTATTTATTT
12490450 TATATATGTACA-TATTTATTT
1 TATATATGTACATTATTTATTT
12490471 T
1 T
12490472 TTTTCAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TATATATGTACATTATTTATTT
Found at i:12490941 original size:4 final size:4
Alignment explanation
Indices: 12490934--12490968 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
12490924 TTGATTTATT
12490934 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
12490969 CTATACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:12493263 original size:29 final size:29
Alignment explanation
Indices: 12493213--12493273 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
12493203 CTAATTAATC
* * *
12493213 TAAACCCTAAACCCTTAGCCCCT-ATCTCT
1 TAAACCCTAAACCATAAACCCCTAATC-CT
*
12493242 TAAACCCTAAATCATAAACCCCTAATCCT
1 TAAACCCTAAACCATAAACCCCTAATCCT
12493271 TAA
1 TAA
12493274 GTACTCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (29 bp):
TAAACCCTAAACCATAAACCCCTAATCCT
Found at i:12493827 original size:41 final size:40
Alignment explanation
Indices: 12493759--12494072 Score: 351
Period size: 41 Copynumber: 7.7 Consensus size: 40
12493749 TACTTTTTGT
* *
12493759 GGCGTTTTTCCAAAAACGCCGTTAAAGACCGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGACCGAGCATTAGC
*
12493799 GGCGCTTTTTCAAAAACGCCGCTAAAAGACCAGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCT-AAAGACC-GAGCATTAGC
* *
12493841 GGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGAC-CGAGCATTAGC
* * *
12493882 GGTGCTTTTCCAAAAACGCCGCTAAAGGCTAGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGAC-CGAGCATTAGC
*
12493923 GGCGCTTTTCCAAAAAACGCCGCTAAAGACCAGAGCATTACC
1 GGCGCTTTTCC-AAAAACGCCGCTAAAGACC-GAGCATTAGC
* *** *
12493965 GACGAACTTCCAAAAACGCCGCTAAAGACCAGAACATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGACC-GAGCATTAGC
* * * * *
12494006 GACGCATTTCCAAAAACGCCGCTAAAGCCCCAAGCACTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAG-ACCGAGCATTAGC
* *
12494047 GGCGCTTCTT-GAGAAACGCCGCTAAA
1 GGCGCTT-TTCCAAAAACGCCGCTAAA
12494073 TCCCTGAAAA
Statistics
Matches: 240, Mismatches: 27, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
40 20 0.08
41 150 0.62
42 70 0.29
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (40 bp):
GGCGCTTTTCCAAAAACGCCGCTAAAGACCGAGCATTAGC
Found at i:12493902 original size:83 final size:81
Alignment explanation
Indices: 12493759--12494072 Score: 371
Period size: 83 Copynumber: 3.8 Consensus size: 81
12493749 TACTTTTTGT
* * * *
12493759 GGCGTTTTTCCAAAAACGCCGTTAAAGACCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAA
1 GGCGCTTTTCCAAAAACGCCGCTAAAGACAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCT-A
12493824 AAGACCAGAGCATTAGC
65 AAGACCAGAGCATTAGC
* *
12493841 GGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTAGCGGTGCTTTTCCAAAAACGCCGCTA
1 GGCGCTTTTCCAAAAACGCCGCTAAAGAC-AGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTA
* *
12493906 AAGGCTAGAGCATTAGC
65 AAGACCAGAGCATTAGC
* * ***
12493923 GGCGCTTTTCCAAAAAACGCCGCTAAAGACCAGAGCATTACCGACGAACTTCCAAAAACGCCGCT
1 GGCGCTTTTCC-AAAAACGCCGCTAAAGA-CAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCT
*
12493988 AAAGACCAGAACATTAGC
64 AAAGACCAGAGCATTAGC
* * * * * *
12494006 GACGCATTTCCAAAAACGCCGCTAAAGCCCCA-AGCACTAGCGGCGCTTCTT-GAGAAACGCCGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAG--ACAGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGC
12494069 TAAA
63 TAAA
12494073 TCCCTGAAAA
Statistics
Matches: 197, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
82 92 0.47
83 104 0.53
84 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (81 bp):
GGCGCTTTTCCAAAAACGCCGCTAAAGACAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAA
AGACCAGAGCATTAGC
Found at i:12493983 original size:124 final size:123
Alignment explanation
Indices: 12493764--12494072 Score: 381
Period size: 124 Copynumber: 2.5 Consensus size: 123
12493754 TTTGTGGCGT
* * *
12493764 TTTTCCAAAAACGCCGTTAAAGACCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGAC
1 TTTTCCAAAAACGCCGCTAAAGACAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAGAC
* * *** * * * **
12493829 CAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACTAGAGCATTAGCGGTGC
66 CAGAGCATTACCGACGAACTTCCAAAAACGCCGCTAAAGACCAGAACATTAGCGACGC
*
12493887 TTTTCCAAAAACGCCGCTAAAGGCTAGAGCATTAGCGGCGCTTTTCCAAAAAACGCCGCT-AAAG
1 TTTTCCAAAAACGCCGCTAAAGAC-AGAGCATTAGCGGCGCTTTTCC-AAAAACGCCGCTAAAAG
12493951 ACCAGAGCATTACCGACGAACTTCCAAAAACGCCGCTAAAGACCAGAACATTAGCGACGC
64 ACCAGAGCATTACCGACGAACTTCCAAAAACGCCGCTAAAGACCAGAACATTAGCGACGC
* * * * *
12494011 ATTTCCAAAAACGCCGCTAAAGCCCCA-AGCACTAGCGGCGCTTCTT-GAGAAACGCCGCTAAA
1 TTTTCCAAAAACGCCGCTAAAG--ACAGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGCTAAA
12494073 TCCCTGAAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
123 33 0.20
124 112 0.70
125 15 0.09
126 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.18
Consensus pattern (123 bp):
TTTTCCAAAAACGCCGCTAAAGACAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAGAC
CAGAGCATTACCGACGAACTTCCAAAAACGCCGCTAAAGACCAGAACATTAGCGACGC
Found at i:12495421 original size:30 final size:29
Alignment explanation
Indices: 12495335--12495410 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
12495325 AAAACAAAAT
*
12495335 CCATCTCGTTAAAA-TATTTTTTTCAGAAC
1 CCATCTCGTCAAAATTA-TTTTTTCAGAAC
* * * *
12495364 ACATCACGACAAATTTATTTTTTCAGAAC
1 CCATCTCGTCAAAATTATTTTTTCAGAAC
12495393 CCATCTCGTCAAAATTAT
1 CCATCTCGTCAAAATTAT
12495411 ATTTCCCAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
CCATCTCGTCAAAATTATTTTTTCAGAAC
Found at i:12495574 original size:59 final size:63
Alignment explanation
Indices: 12495500--12495635 Score: 181
Period size: 65 Copynumber: 2.2 Consensus size: 63
12495490 TATTTTTCCT
* *
12495500 AAACACTAAACAATTAAAAATATAATAC-TTAA-T-TTT-TCCTAAACCTTAATAAAACCCTA
1 AAACACTAAACAATTAAAAACATAATACTTTAATTATTTATCCTAAACCCTAATAAAACCCTA
* *
12495559 AAACTCTAAACAATTAAAAACATAATACTTTAATTTAATTTATCCTAAACCCTAATCAAACCCTA
1 AAACACTAAACAATTAAAAACATAATACTTTAA-TT-ATTTATCCTAAACCCTAATAAAACCCTA
*
12495624 AAACCCTAAACA
1 AAACACTAAACA
12495636 TAGGCCTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 26 0.39
60 4 0.06
62 1 0.02
64 3 0.05
65 32 0.48
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (63 bp):
AAACACTAAACAATTAAAAACATAATACTTTAATTATTTATCCTAAACCCTAATAAAACCCTA
Found at i:12501420 original size:19 final size:18
Alignment explanation
Indices: 12501398--12501456 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
12501388 TTACAAAAAG
12501398 AAATTAAAATAATTTTCAA
1 AAATTAAAATAATTTT-AA
12501417 AAATTCAAAAT-ATTTATAA
1 AAATT-AAAATAATTT-TAA
*
12501436 AAATTTTAAA-AATTTTAA
1 AAA-TTAAAATAATTTTAA
12501454 AAA
1 AAA
12501457 ATTTCAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 6 0.17
19 21 0.60
20 8 0.23
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTAAAATAATTTTAA
Found at i:12501455 original size:8 final size:9
Alignment explanation
Indices: 12501408--12501466 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
12501398 AAATTAAAAT
12501408 AATTTTCAAA
1 AATTTT-AAA
*
12501418 AA-TTCAAA
1 AATTTTAAA
12501426 ATATTTATAAA
1 A-ATTT-TAAA
12501437 AATTTTAAA
1 AATTTTAAA
12501446 AATTTTAAAA
1 AATTTT-AAA
*
12501456 AATTTCAAA
1 AATTTTAAA
12501465 AA
1 AA
12501467 AATATGTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
8 4 0.10
9 18 0.43
10 16 0.38
11 4 0.10
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (9 bp):
AATTTTAAA
Done.