Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 5 of 214
Found at i:1454171 original size:17 final size:16
Alignment explanation
Indices: 1454131--1454172 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1454121 AAGTATTTTA
* *
1454131 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
1454147 AAAA-ATTTAAAAAAT
1 AAAATATTTAAAAAAT
1454162 AAATATATTTA
1 AAA-ATATTTA
1454173 TTATATCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:1459747 original size:27 final size:27
Alignment explanation
Indices: 1459695--1459749 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1459685 AATTTTAAAA
** *
1459695 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTGATTTTT
*
1459722 TATTTTTAAAATAAATTTTTGGTTTTT
1 TATTTTTAAAATAAATTTTTGATTTTT
1459749 T
1 T
1459750 TAAAAAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATAAATTTTTGATTTTT
Found at i:1459748 original size:28 final size:27
Alignment explanation
Indices: 1459695--1459751 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1459685 AATTTTAAAA
* *
1459695 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATAATTTTTGTATTTTT
1459722 TATTTTTAAAATAAATTTTTGGT-TTTTT
1 TATTTTTAAAAT-AATTTTT-GTATTTTT
1459750 TA
1 TA
1459752 AAAAATGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
28 13 0.50
29 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATAATTTTTGTATTTTT
Found at i:1460057 original size:30 final size:30
Alignment explanation
Indices: 1460008--1460067 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1459998 GCACTCAGAT
* * *
1460008 TATTGTGATAAACTAAAACAC-AATAAAAA
1 TATTGTGAAAAAATAAAACACGAAAAAAAA
1460037 TATTGTGAAAAAAATAAAACACGAAAAAAAA
1 TATTGTG-AAAAAATAAAACACGAAAAAAAA
1460068 AATGAAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 12 0.46
31 7 0.27
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (30 bp):
TATTGTGAAAAAATAAAACACGAAAAAAAA
Found at i:1460078 original size:18 final size:19
Alignment explanation
Indices: 1460044--1460080 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1460034 AAATATTGTG
1460044 AAAAAAATAAAACACGAAA
1 AAAAAAATAAAACACGAAA
*
1460063 AAAAAAATGAAA-ACGAAA
1 AAAAAAATAAAACACGAAA
1460081 TTATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.05
Consensus pattern (19 bp):
AAAAAAATAAAACACGAAA
Found at i:1460395 original size:17 final size:17
Alignment explanation
Indices: 1460363--1460396 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1460353 CGAAAATACT
1460363 AACTACAATAATAACAA
1 AACTACAATAATAACAA
1460380 AACTAACAATAA-AACAA
1 AACT-ACAATAATAACAA
1460397 GTGTTATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.15
Consensus pattern (17 bp):
AACTACAATAATAACAA
Found at i:1460705 original size:12 final size:12
Alignment explanation
Indices: 1460688--1460712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1460678 GGTATACTTG
1460688 AATACTCTTTCA
1 AATACTCTTTCA
1460700 AATACTCTTTCA
1 AATACTCTTTCA
1460712 A
1 A
1460713 GTATGTAAGT
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:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
AATACTCTTTCA
Found at i:1461462 original size:15 final size:15
Alignment explanation
Indices: 1461444--1461482 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1461434 TATTTCATTT
*
1461444 TTAAATATTGTATTA
1 TTAAATATTATATTA
*
1461459 TTAAACATTATATTA
1 TTAAATATTATATTA
*
1461474 TTAACTATT
1 TTAAATATT
1461483 TTATCATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAAATATTATATTA
Found at i:1472549 original size:39 final size:41
Alignment explanation
Indices: 1472492--1472575 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 41
1472482 TTTAAAATTC
*
1472492 AAAA-ATATAAAAACTATTTTTA-AAAATT-AAAATTTTAA
1 AAAATATATAAAAAATATTTTTATAAAATTAAAAATTTTAA
** *
1472530 AAAATATATAAAAAATATTTTTATAATTTTAAAAATTTTTA
1 AAAATATATAAAAAATATTTTTATAAAATTAAAAATTTTAA
1472571 AAAAT
1 AAAAT
1472576 TAATTAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
38 4 0.10
39 17 0.44
40 4 0.10
41 14 0.36
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (41 bp):
AAAATATATAAAAAATATTTTTATAAAATTAAAAATTTTAA
Found at i:1472940 original size:16 final size:15
Alignment explanation
Indices: 1472896--1472945 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1472886 TCATAATACA
*
1472896 TATTTTTTATACTACT
1 TATTTTTTATATTA-T
*
1472912 TA-TTTTAATATTAT
1 TATTTTTTATATTAT
1472926 TATTTTTTATA--AT
1 TATTTTTTATATTAT
1472939 TATTTTT
1 TATTTTT
1472946 GGGTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 16 0.53
16 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTATATTAT
Found at i:1479297 original size:15 final size:15
Alignment explanation
Indices: 1479277--1479307 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1479267 TTTGAAATTT
1479277 AAAATTAAAAATAAA
1 AAAATTAAAAATAAA
*
1479292 AAAATTAAAATTAAA
1 AAAATTAAAAATAAA
1479307 A
1 A
1479308 TTACCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATTAAAAATAAA
Found at i:1479299 original size:21 final size:21
Alignment explanation
Indices: 1479275--1479333 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1479265 CTTTTGAAAT
1479275 TTAAAATTAAAAATAAAAAAA
1 TTAAAATTAAAAATAAAAAAA
* **
1479296 TTAAAATTAAAATTACCAAAA
1 TTAAAATTAAAAATAAAAAAA
*
1479317 -GAGAAATTAAAAATAAA
1 TTA-AAATTAAAAATAAA
1479334 GTTTGAGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (21 bp):
TTAAAATTAAAAATAAAAAAA
Found at i:1480714 original size:21 final size:22
Alignment explanation
Indices: 1480690--1480786 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 22
1480680 TTAGCCATTC
1480690 TATTGTTT-TTACTATTT-TTAT
1 TATT-TTTATTACTATTTATTAT
1480711 TATTTTTATTACTATTTATTAT
1 TATTTTTATTACTATTTATTAT
**
1480733 TATACTGCTATGTACCTATTTATATAT
1 TAT--TTTTAT-TA-CTATTTAT-TAT
*
1480760 TA-TTTTATTA-TA-CTATTAT
1 TATTTTTATTACTATTTATTAT
*
1480779 TTTTTTTA
1 TATTTTTA
1480787 ACTGTTTCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
19 4 0.06
20 11 0.18
21 15 0.24
22 7 0.11
23 2 0.03
24 8 0.13
25 2 0.03
26 8 0.13
27 5 0.08
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (22 bp):
TATTTTTATTACTATTTATTAT
Found at i:1480719 original size:9 final size:9
Alignment explanation
Indices: 1480690--1480733 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1480680 TTAGCCATTC
*
1480690 TATTGTTTT
1 TATTATTTT
*
1480699 TACTATTTT
1 TATTATTTT
1480708 TATTATTTT
1 TATTATTTT
*
1480717 TATTACTATT
1 TATTA-TTTT
1480727 TATTATT
1 TATTATT
1480734 ATACTGCTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (9 bp):
TATTATTTT
Found at i:1480776 original size:16 final size:15
Alignment explanation
Indices: 1480752--1480781 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1480742 ATGTACCTAT
1480752 TTATATATTATTTTA
1 TTATATATTATTTTA
1480767 TTATACTATTATTTT
1 TTATA-TATTATTTT
1480782 TTTTAACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATTATTTTA
Found at i:1488508 original size:46 final size:45
Alignment explanation
Indices: 1488409--1488615 Score: 355
Period size: 46 Copynumber: 4.6 Consensus size: 45
1488399 TTTGAGTACT
*
1488409 TCTGATCAAGTGACAAAGTGATAAGTGGTAACTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1488454 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1488500 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
1488546 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
1488591 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1488616 ATCATACGTA
Statistics
Matches: 158, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
43 12 0.08
44 5 0.03
45 50 0.32
46 91 0.58
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:1488583 original size:91 final size:91
Alignment explanation
Indices: 1488409--1488615 Score: 357
Period size: 91 Copynumber: 2.3 Consensus size: 91
1488399 TTTGAGTACT
1488409 TCTGATCAAGTGACAAAGTGATAAGTGGTAACTTAGCTACACTTATCTGATCAAGTGACAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAACTTAGCTACACTTATCTGATCAAGTGACAAAGTG
*
1488474 ATAAGTGGTAGCTTTAGCTACACTTA
66 ATAAGTGGTAGCTCTAGCTACACTTA
*
1488500 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAAC-TTAGCTACACTTATCTGATCAAGTGACAAAGT
1488565 GATAAGTGGTAGC-CTAGCTACACTTA
65 GATAAGTGGTAGCTCTAGCTACACTTA
*
1488591 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1488616 ATCATACGTA
Statistics
Matches: 112, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
89 12 0.11
90 5 0.04
91 50 0.45
92 45 0.40
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (91 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAACTTAGCTACACTTATCTGATCAAGTGACAAAGTG
ATAAGTGGTAGCTCTAGCTACACTTA
Found at i:1492341 original size:32 final size:32
Alignment explanation
Indices: 1492300--1492364 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1492290 ATAGGTGTTG
1492300 TATCTATGTTGACAATTTTAACTTGGTACTTA
1 TATCTATGTTGACAATTTTAACTTGGTACTTA
1492332 TATCTATGTTGACAATTTTAACTTGGTACTTA
1 TATCTATGTTGACAATTTTAACTTGGTACTTA
1492364 T
1 T
1492365 CTTGATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (32 bp):
TATCTATGTTGACAATTTTAACTTGGTACTTA
Found at i:1495387 original size:31 final size:31
Alignment explanation
Indices: 1495317--1495393 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
1495307 TTCTTTAATT
* *
1495317 TGATTAATTTTGGTCTTAGTATTTTTTGAAA
1 TGATAAATTTTAGTCTTAGTATTTTTTGAAA
*
1495348 TGATAAATTTTAGTCTTTGTACTTTTTT-AAA
1 TGATAAATTTTAGTCTTAGTA-TTTTTTGAAA
*
1495379 -GTTGAAATTTTAGTC
1 TGAT-AAATTTTAGTC
1495394 CCGATCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 2 0.05
31 32 0.80
32 6 0.15
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.53
Consensus pattern (31 bp):
TGATAAATTTTAGTCTTAGTATTTTTTGAAA
Found at i:1496426 original size:10 final size:10
Alignment explanation
Indices: 1496406--1496437 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1496396 CAGAATAAGC
1496406 TATTT-TATA
1 TATTTATATA
1496415 TATTTATATA
1 TATTTATATA
1496425 TATTTATATA
1 TATTTATATA
1496435 TAT
1 TAT
1496438 ATCTTGGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTATATA
Found at i:1507073 original size:54 final size:54
Alignment explanation
Indices: 1507014--1507151 Score: 159
Period size: 54 Copynumber: 2.5 Consensus size: 54
1507004 GGCAAACCGA
* ** *
1507014 AAGATTTTGAAAATCTTATAAGTATATGGTTGCGATCTTAAATTGGCGAACTGT
1 AAGATTTTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAAATGT
* * * * * *
1507068 AAGATTCTGAAAATCTTATAAATAAAAGGTCGTGATCTTAAATCAGTGAAATGT
1 AAGATTTTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAAATGT
* *
1507122 AAGATTTCTAAAAATCGTATAAGTATATGG
1 AAGATTT-TGAAAATCTTATAAGTATATGG
1507152 CGGCTGTGAC
Statistics
Matches: 67, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
54 50 0.75
55 17 0.25
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (54 bp):
AAGATTTTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAAATGT
Found at i:1512086 original size:25 final size:25
Alignment explanation
Indices: 1512064--1512171 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
1512054 GAGTGCTCAT
1512064 TCGAGCACATA-AACGAGAAGCTCTG
1 TCGAGC-CATATAACGAGAAGCTCTG
*
1512089 TTGAGCCATATAACGAGAAGCTCCTG
1 TCGAGCCATATAACGAGAAGCT-CTG
* * *
1512115 T-GAGCTATGTAACGGGAAGCTCAT-
1 TCGAGCCATATAACGAGAAGCTC-TG
*
1512139 ACGAGCCA-ATATA-GAGAAGCTCTG
1 TCGAGCCATATA-ACGAGAAGCTCTG
**
1512163 GAGAGCCAT
1 TCGAGCCAT
1512172 TAATTGGGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 21 0.32
25 40 0.61
26 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
TCGAGCCATATAACGAGAAGCTCTG
Found at i:1512115 original size:26 final size:25
Alignment explanation
Indices: 1512066--1512136 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
1512056 GTGCTCATTC
1512066 GAGCACATA-AACGAGAAGCT-CTGTT
1 GAGC-CATATAACGAGAAGCTCCTG-T
1512091 GAGCCATATAACGAGAAGCTCCTGT
1 GAGCCATATAACGAGAAGCTCCTGT
* * *
1512116 GAGCTATGTAACGGGAAGCTC
1 GAGCCATATAACGAGAAGCTC
1512137 ATACGAGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
24 4 0.10
25 34 0.83
26 3 0.07
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGAGAAGCTCCTGT
Found at i:1519057 original size:14 final size:14
Alignment explanation
Indices: 1519040--1519073 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1519030 TGGGTTGAGA
1519040 AAATAATT-TAATTT
1 AAATAATTGTAA-TT
1519054 AAATAATTGTAATT
1 AAATAATTGTAATT
1519068 AAATAA
1 AAATAA
1519074 ATAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AAATAATTGTAATT
Found at i:1519744 original size:26 final size:26
Alignment explanation
Indices: 1519715--1519768 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1519705 AATCCGAAAG
1519715 TTTGCAACAAGTTAACAACTACAATC
1 TTTGCAACAAGTTAACAACTACAATC
*
1519741 TTTGCAGCAAGTTAACAACTACAATC
1 TTTGCAACAAGTTAACAACTACAATC
1519767 TT
1 TT
1519769 AAACTTGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (26 bp):
TTTGCAACAAGTTAACAACTACAATC
Found at i:1520446 original size:17 final size:17
Alignment explanation
Indices: 1520398--1520448 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1520388 TTAACAAAGT
*
1520398 TAGCACATTTGGTGA-C
1 TAGCACATTTGATGAGC
* *
1520414 TCGCAC-TTTTAGTGAGC
1 TAGCACATTTGA-TGAGC
1520431 TAGCACATTTGATGAGC
1 TAGCACATTTGATGAGC
1520448 T
1 T
1520449 CATAATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 3 0.11
16 8 0.30
17 12 0.44
18 4 0.15
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (17 bp):
TAGCACATTTGATGAGC
Found at i:1531086 original size:46 final size:46
Alignment explanation
Indices: 1531019--1531221 Score: 365
Period size: 46 Copynumber: 4.5 Consensus size: 46
1531009 TGATCAGTGA
1531019 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1531065 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1531111 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1531157 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1531203 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
1531222 ATCACATATA
Statistics
Matches: 153, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
44 12 0.08
45 5 0.03
46 136 0.89
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:1532555 original size:49 final size:49
Alignment explanation
Indices: 1532478--1532619 Score: 178
Period size: 49 Copynumber: 2.9 Consensus size: 49
1532468 ATGTGAAAAT
1532478 GTGATTATGTGATCTTCGTGTAAGACCATAGCTGGGCTATGGCATC-GATAA
1 GTGA-TATGTGAT-TTCGTGTAAGACCATAGCTGGGCTATGGCATCTG-TAA
* * * *
1532529 GTGATATGTGATTTTGTGTAAAACCATAGCTGGGTTATGGCATCTGTAT
1 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCTGTAA
* * * *
1532578 GTGATATGTGATTACATGTAAGACCATAGTTGGACTATGGCA
1 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCA
1532620 ATGTGAAAAC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 66 0.84
50 9 0.11
51 4 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (49 bp):
GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCTGTAA
Found at i:1537397 original size:45 final size:46
Alignment explanation
Indices: 1537326--1537526 Score: 329
Period size: 45 Copynumber: 4.5 Consensus size: 46
1537316 TGATCAGTGA
1537326 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
*
1537372 CGAGTGACAAAGTG-TAAGTGGTAGCTTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
*
1537417 CAATTGACAAAGTG-TAAGTGGTAGCTTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
* *
1537462 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
*
1537508 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
1537527 ATCACATATA
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
44 12 0.08
45 92 0.63
46 43 0.29
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
Found at i:1541058 original size:18 final size:18
Alignment explanation
Indices: 1541035--1541070 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1541025 GTTTTATTCA
1541035 AAGATTTCTAGGTTTTCT
1 AAGATTTCTAGGTTTTCT
* *
1541053 AAGATTTTTGGGTTTTCT
1 AAGATTTCTAGGTTTTCT
1541071 CATTCAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (18 bp):
AAGATTTCTAGGTTTTCT
Found at i:1541409 original size:20 final size:19
Alignment explanation
Indices: 1541353--1541410 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1541343 TAATTATTTC
* *
1541353 TTATATATATATTTTAGAGT
1 TTATATATA-ATTTTATAAT
1541373 TTATATATAATTTTTATAAT
1 TTATATATAA-TTTTATAAT
*
1541393 TTATATTTAGATTTTATA
1 TTATATATA-ATTTTATA
1541411 TAGTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATATATAATTTTATAAT
Found at i:1541537 original size:20 final size:19
Alignment explanation
Indices: 1541512--1541572 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
1541502 ATTTATATAC
1541512 ATATTTTTTCGAAATTTTAT
1 ATATTTTTTC-AAATTTTAT
* *
1541532 ATATTTATTTCTATTTTTAT
1 ATATTT-TTTCAAATTTTAT
**
1541552 A-ATTTTTT-AAGGTTTAT
1 ATATTTTTTCAAATTTTAT
1541569 ATAT
1 ATAT
1541573 GTTTGGCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 4 0.12
20 14 0.41
21 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
ATATTTTTTCAAATTTTAT
Found at i:1542184 original size:21 final size:22
Alignment explanation
Indices: 1542134--1542188 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1542124 TAGTGAGATG
*
1542134 ACAACAAAACAATGGAAAAATA
1 ACAACAAAACAATGGAAAAACA
* * *
1542156 GCAGCAAAATAAT-GAAAAACA
1 ACAACAAAACAATGGAAAAACA
1542177 ACAACAAAACAA
1 ACAACAAAACAA
1542189 CAAGTTTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.67, C:0.16, G:0.09, T:0.07
Consensus pattern (22 bp):
ACAACAAAACAATGGAAAAACA
Found at i:1542967 original size:29 final size:30
Alignment explanation
Indices: 1542935--1542991 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1542925 TTTGATATAA
1542935 TTTTTTTATA-ACTTTCCTATTTTCTAACT
1 TTTTTTTATATACTTTCCTATTTTCTAACT
** *
1542964 TTTTTTTATATTTTTTGCTATTTTCTAA
1 TTTTTTTATATACTTTCCTATTTTCTAA
1542992 TTAATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTTTTATATACTTTCCTATTTTCTAACT
Found at i:1556751 original size:16 final size:16
Alignment explanation
Indices: 1556714--1556752 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1556704 TTTGGTTCAG
*
1556714 TGTAATGGAATAGAGC
1 TGTAATTGAATAGAGC
* *
1556730 TATAATTGAATAGAGT
1 TGTAATTGAATAGAGC
1556746 TGTAATT
1 TGTAATT
1556753 AGTAATTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (16 bp):
TGTAATTGAATAGAGC
Found at i:1556982 original size:58 final size:58
Alignment explanation
Indices: 1556919--1557044 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 58
1556909 TTTTAAAAAG
* * *
1556919 ATTATTATTAAAGATAATTTAATAAAAATAATAAATAGTTTAACCATATT-TTAACATA
1 ATTATTATTAAAGATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
1556977 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAGATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
1557035 ATTATTATTA
1 ATTATTATTA
1557045 TATGAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 21 0.35
58 39 0.65
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAGATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:1557080 original size:58 final size:57
Alignment explanation
Indices: 1556919--1557081 Score: 145
Period size: 58 Copynumber: 2.8 Consensus size: 57
1556909 TTTTAAAAAG
* * * * ** *
1556919 ATTATTATTAAAGATAATTTAATAAAAATAATAAATAGTTTAACCATATT-TTAACATA
1 ATTATTATT-AATATAATTTAA-AAAAATAATATATAATCTAATAAAATTCTTAACATA
* * *
1556977 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATT-AATATAATTTAAAAAAATAATATATAATCTAATAAAATTCTTAACATA
1557035 ATTATTATT-ATATGAA-TTAAAAAATCATAATATATAATACT-ATAAAA
1 ATTATTATTAATAT-AATTTAAAAAA--ATAATATATAAT-CTAATAAAA
1557082 ATAATATATA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
56 11 0.12
57 23 0.26
58 55 0.61
59 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (57 bp):
ATTATTATTAATATAATTTAAAAAAATAATATATAATCTAATAAAATTCTTAACATA
Found at i:1557910 original size:98 final size:98
Alignment explanation
Indices: 1557795--1557987 Score: 296
Period size: 98 Copynumber: 2.0 Consensus size: 98
1557785 ATATAAAAAT
* * * * *
1557795 TTTAAAAGAACATCCACTCGTCCAAGATTTAAGAAACCACACCTAATACGTTAGGGCACGATCCC
1 TTTAAAAAAACATCCACTCATCCAAGATTTAAAAAACCACACCCAATACGTTAGGGCACAATCCC
1557860 TTTAGAATCCCAAACTCAGAATATTTCCTTTAA
66 TTTAGAATCCCAAACTCAGAATATTTCCTTTAA
* * *
1557893 TTTAAAAAAACATCCACTTATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAAAACATCCACTCATCCAAGATTTAAAAAACCACACCCAATACGTTAGGGCACAATCCC
* *
1557958 TTTAGAATCTCAAACTCGGAATATTTCCTT
66 TTTAGAATCCCAAACTCAGAATATTTCCTT
1557988 CATGATTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 85 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
TTTAAAAAAACATCCACTCATCCAAGATTTAAAAAACCACACCCAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCAGAATATTTCCTTTAA
Found at i:1558267 original size:12 final size:12
Alignment explanation
Indices: 1558250--1558274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1558240 AACGAGCAAC
1558250 ATAATATAAATG
1 ATAATATAAATG
1558262 ATAATATAAATG
1 ATAATATAAATG
1558274 A
1 A
1558275 AAGCACAAAT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:1558791 original size:8 final size:8
Alignment explanation
Indices: 1558778--1558802 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1558768 AGAAAGGAAA
1558778 ATTTCCCT
1 ATTTCCCT
1558786 ATTTCCCT
1 ATTTCCCT
1558794 ATTTCCCT
1 ATTTCCCT
1558802 A
1 A
1558803 AACGGCGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTCCCT
Found at i:1559790 original size:14 final size:14
Alignment explanation
Indices: 1559771--1559803 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1559761 CACTATTTGG
*
1559771 TTTGGGCCTCTGAA
1 TTTGGGCCACTGAA
1559785 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
1559799 TTTGG
1 TTTGG
1559804 TTTTGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.36
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:1562643 original size:41 final size:41
Alignment explanation
Indices: 1562598--1562866 Score: 403
Period size: 41 Copynumber: 6.6 Consensus size: 41
1562588 GGTTTTAAAA
*
1562598 CCTAGCAGGCTAAGTGTCGGTGATCTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
*
1562639 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* *
1562680 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* * *
1562721 TCTAGCAGACTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* ** *
1562762 CCTAGCAGGCTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
*
1562803 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* * *
1562844 CCTAACAAGCTAAGTGCCAGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
1562867 ATCTGTTTAA
Statistics
Matches: 207, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 207 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
Found at i:1566463 original size:14 final size:14
Alignment explanation
Indices: 1566444--1566473 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1566434 ACCATTAGTA
1566444 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
*
1566458 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
1566472 AA
1 AA
1566474 TGTGTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:1566535 original size:16 final size:16
Alignment explanation
Indices: 1566516--1566549 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1566506 GACGTTTAAT
*
1566516 ATGATTTTTTTGTAGC
1 ATGATTTGTTTGTAGC
1566532 ATGATTTGTTTGTAGC
1 ATGATTTGTTTGTAGC
1566548 AT
1 AT
1566550 TTTACTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.53
Consensus pattern (16 bp):
ATGATTTGTTTGTAGC
Found at i:1566737 original size:28 final size:27
Alignment explanation
Indices: 1566676--1566737 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
1566666 ATAACATAAA
*
1566676 TTAAAGATATCAAAAATAAAAATAGTT
1 TTAAATATATCAAAAATAAAAATAGTT
* *
1566703 TTAAAATATATTAAAAGATTAAAATAGTT
1 TT-AAATATATCAAAA-ATAAAAATAGTT
1566732 TTAAAT
1 TTAAAT
1566738 GAAACATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.07
28 15 0.50
29 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (27 bp):
TTAAATATATCAAAAATAAAAATAGTT
Found at i:1567255 original size:42 final size:42
Alignment explanation
Indices: 1567197--1567447 Score: 283
Period size: 42 Copynumber: 6.0 Consensus size: 42
1567187 ACGTTTACAG
*
1567197 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * *
1567239 AAAAAAATGTCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * * *
1567280 AAAAAAGACACCGCTAAAGGTCATGTTCTTTCGCAGCGC-TTA
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * *
1567322 AAGAAAAAGGCCGCTAAAGATCATGTTCTTTAGAGGCTC-TTA
1 AA-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * * *
1567364 ACGAAAAATGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTTG
1 A-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * * *
1567407 CATAAAACGCCGCGAAAGATCATGTTTTTTAGCGGCGCTTT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTT
1567448 TATCACAAAC
Statistics
Matches: 176, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
41 9 0.05
42 161 0.91
43 6 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
Found at i:1567430 original size:126 final size:126
Alignment explanation
Indices: 1567199--1567446 Score: 313
Period size: 126 Copynumber: 2.0 Consensus size: 126
1567189 GTTTACAGAA
* * * *
1567199 AAAAACGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTTAAAAAAAATGTCGCTAAAGGTCATGT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTTAAAAAAAATGCCGCTAAAGATCATGC
* * *
1567264 TCTTTAGCGGCGCTTAAAAAAAGACACCGCTAAAGGTCATGTTCTTTCGCAGCGCTTAAAG
66 TCTTTAGCGGCGCTTAAAAAAAGACACCGCGAAAGATCATGTTCTTTAGCAGCGCTTAAAG
* *
1567325 AAAAAGGCCGCTAAAGATCATGTTCTTTAG-AG-GCTCTTAACGAAAAATGCCGCTAAAGATCAT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCT-TTAA-AAAAAATGCCGCTAAAGATCAT
** * * * *
1567388 GCTCTTTAGCGGCGCTTTGCATAAA-ACGCCGCGAAAGATCATGTTTTTTAGCGGCGCTT
64 GCTCTTTAGCGGCGC-TTAAAAAAAGACACCGCGAAAGATCATGTTCTTTAGCAGCGCTT
1567447 TTATCACAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
124 3 0.03
125 5 0.05
126 90 0.87
127 6 0.06
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (126 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTTAAAAAAAATGCCGCTAAAGATCATGC
TCTTTAGCGGCGCTTAAAAAAAGACACCGCGAAAGATCATGTTCTTTAGCAGCGCTTAAAG
Found at i:1567535 original size:87 final size:86
Alignment explanation
Indices: 1567390--1567549 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 86
1567380 AAGATCATGC
* ** *
1567390 TCTTTAGCGGCGCTTTGCATAAAACGCCGCGAAAGATCATGTTTTTTAGCGGCGCTTTTATCACA
1 TCTTTAGCGGCGCTTTGCATAAAACGCCGCGAAAGAGCATGACTTTTAGCGGCGCTTTTATCAAA
1567455 AACGCCACAAAAAAGTAAAGT
66 AACGCCACAAAAAAGTAAAGT
* * * * *
1567476 TCTTTAGCGGCGCTTT-CTTCACAAACGCCGCTAGAGAGCATGACTTTTATCGGCGCTTTTATGA
1 TCTTTAGCGGCGCTTTGCAT-A-AAACGCCGCGAAAGAGCATGACTTTTAGCGGCGCTTTTATCA
1567540 AAAACGCCAC
64 AAAACGCCAC
1567550 TAATTTTGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 2 0.03
86 17 0.27
87 44 0.70
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTGCATAAAACGCCGCGAAAGAGCATGACTTTTAGCGGCGCTTTTATCAAA
AACGCCACAAAAAAGTAAAGT
Found at i:1567945 original size:21 final size:21
Alignment explanation
Indices: 1567921--1567971 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1567911 TTCTTTTGAA
*
1567921 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
1567942 CCTCTGCTTCCCTTGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
1567963 CCTCTGCTT
1 CCTCTGCTT
1567972 TAATTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:1573473 original size:7 final size:7
Alignment explanation
Indices: 1573463--1573508 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
1573453 TGATATATTT
1573463 TTATGTA
1 TTATGTA
1573470 TTATGTAA
1 TTATGT-A
1573478 GTTATGTAA
1 -TTATGT-A
1573487 GTTATGTA
1 -TTATGTA
1573495 TTATGTA
1 TTATGTA
1573502 TTATGTA
1 TTATGTA
1573509 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:1573484 original size:9 final size:9
Alignment explanation
Indices: 1573470--1573808 Score: 311
Period size: 9 Copynumber: 39.4 Consensus size: 9
1573460 TTTTTATGTA
1573470 TTATGTAAG
1 TTATGTAAG
1573479 TTATGTAAG
1 TTATGTAAG
1573488 TTATGT-A-
1 TTATGTAAG
1573495 TTATGT-A-
1 TTATGTAAG
1573502 TTATGTAAG
1 TTATGTAAG
1573511 -TACTGTAAG
1 TTA-TGTAAG
*
1573520 TAATGTAAG
1 TTATGTAAG
1573529 TTATGTAAG
1 TTATGTAAG
*
1573538 TAATGT-A-
1 TTATGTAAG
1573545 TTATGTAAG
1 TTATGTAAG
*
1573554 TTGTGTATA-
1 TTATGTA-AG
*
1573563 ATAT-TAA-
1 TTATGTAAG
*
1573570 TTATGTGAG
1 TTATGTAAG
*
1573579 TTGTGT-A-
1 TTATGTAAG
*
1573586 TAATGTAAG
1 TTATGTAAG
*
1573595 TTAAG-AAGG
1 TTATGTAA-G
1573604 TTATGT-A-
1 TTATGTAAG
* *
1573611 TAATATAAG
1 TTATGTAAG
*
1573620 TTATTTAAG
1 TTATGTAAG
1573629 TTATGTAAG
1 TTATGTAAG
1573638 TTATGTAAG
1 TTATGTAAG
*
1573647 TTGTGT-A-
1 TTATGTAAG
*
1573654 TAATGTAAG
1 TTATGTAAG
1573663 TTATGTAAG
1 TTATGTAAG
* *
1573672 TTATTTAAT
1 TTATGTAAG
1573681 TTATGTAAG
1 TTATGTAAG
1573690 TTATGTAAG
1 TTATGTAAG
* *
1573699 TTATTTAAT
1 TTATGTAAG
1573708 TTATGTAAG
1 TTATGTAAG
* *
1573717 TTATTTAAT
1 TTATGTAAG
1573726 TTATGTAAG
1 TTATGTAAG
1573735 TTATGTAAG
1 TTATGTAAG
1573744 TTATGTAAG
1 TTATGTAAG
* *
1573753 TTATTTAAT
1 TTATGTAAG
1573762 TTATGTAAG
1 TTATGTAAG
1573771 TTATGTAAG
1 TTATGTAAG
*
1573780 TTATGTATG
1 TTATGTAAG
1573789 TTATGT-A-
1 TTATGTAAG
*
1573796 TTATGTTAG
1 TTATGTAAG
1573805 TTAT
1 TTAT
1573809 TATGTTATTA
Statistics
Matches: 269, Mismatches: 42, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
7 40 0.15
8 18 0.07
9 209 0.78
10 2 0.01
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1573835 original size:29 final size:30
Alignment explanation
Indices: 1573803--1573907 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 30
1573793 GTATTATGTT
1573803 AGTTAT-TATGTTATTATATAAGTTATGCA
1 AGTTATATATGTTATTATATAAGTTATGCA
* **
1573832 AGTTTCTATATATG-T-TTATAT-ATTGTATGTT
1 AG--T-TATATATGTTATTATATAAGT-TATGCA
1573863 AGTTAT-TATGTTATTATATAAGTTATGCA
1 AGTTATATATGTTATTATATAAGTTATGCA
* *
1573892 AGATATATAAGTTATT
1 AGTTATATATGTTATT
1573908 TAAGTTATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
27 4 0.07
28 4 0.07
29 18 0.31
30 12 0.20
31 13 0.22
32 4 0.07
33 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (30 bp):
AGTTATATATGTTATTATATAAGTTATGCA
Found at i:1573964 original size:22 final size:23
Alignment explanation
Indices: 1573936--1573978 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1573926 TATAAAGTAT
* *
1573936 TATGTAATTTAT-TATGTTATTA
1 TATGTAAGTTATGTAAGTTATTA
1573958 TATGTAAGTTATGTAAGTTAT
1 TATGTAAGTTATGTAAGTTAT
1573979 GCAAGCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (23 bp):
TATGTAAGTTATGTAAGTTATTA
Found at i:1574027 original size:83 final size:79
Alignment explanation
Indices: 1573865--1574061 Score: 254
Period size: 83 Copynumber: 2.4 Consensus size: 79
1573855 TGTATGTTAG
* * * * *
1573865 TTATTATGTTATTATA-TAAGTTATGCAAGATATATAAGTTATTTAAGTTATTATGTTATTATAT
1 TTATTATGTTATTATATTAAGTTATGTAAGTTATACAAGTTATTTAAGTTATTA-GTTATAACAT
*
1573929 AAAGTATTATGTAAT
65 AAAGTACTATGTAAT
*
1573944 TTATTATGTTATTATATGTAAGTTATGTAAGTTATGCAAGCTTATATTTAAGTTATGTA-TTATA
1 TTATTATGTTATTATAT-TAAGTTATGTAAGTTATACAAG--T-TATTTAAGTTAT-TAGTTATA
1574008 ACATAAAGTACTATGTAAT
61 ACATAAAGTACTATGTAAT
1574027 TTATTATGTTATTATATATAAGTTATGTAAGTTAT
1 TTATTATGTTATTATAT-TAAGTTATGTAAGTTAT
1574062 TATGTAAGTT
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
79 16 0.15
81 18 0.17
83 56 0.54
84 12 0.12
85 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.49
Consensus pattern (79 bp):
TTATTATGTTATTATATTAAGTTATGTAAGTTATACAAGTTATTTAAGTTATTAGTTATAACATA
AAGTACTATGTAAT
Found at i:1574059 original size:9 final size:9
Alignment explanation
Indices: 1574045--1574122 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
1574035 TTATTATATA
1574045 TAAGTTATG
1 TAAGTTATG
1574054 TAAGTTATTATG
1 TAAG---TTATG
1574066 TAAGTTATG
1 TAAGTTATG
* *
1574075 CAAGCTTAAATA
1 TAAG-TT--ATG
1574087 TAAGTTATG
1 TAAGTTATG
*
1574096 T-A-TTATA
1 TAAGTTATG
*
1574103 TAAGTTTTG
1 TAAGTTATG
1574112 TAAGTTATG
1 TAAGTTATG
1574121 TA
1 TA
1574123 CGTGGTGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 28 0.53
10 2 0.04
11 2 0.04
12 14 0.26
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1574066 original size:12 final size:12
Alignment explanation
Indices: 1574049--1574073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1574039 TATATATAAG
1574049 TTATGTAAGTTA
1 TTATGTAAGTTA
1574061 TTATGTAAGTTA
1 TTATGTAAGTTA
1574073 T
1 T
1574074 GCAAGCTTAA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:1574071 original size:21 final size:21
Alignment explanation
Indices: 1574041--1574119 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
1574031 TATGTTATTA
1574041 TATATAAGTTATGTAAGTTAT
1 TATATAAGTTATGTAAGTTAT
* *
1574062 TATGTAAGTTATGCAAGCTTA-
1 TATATAAGTTATGTAAG-TTAT
*
1574083 AATATAAGTTA--T--G-TAT
1 TATATAAGTTATGTAAGTTAT
*
1574099 TATATAAGTTTTGTAAGTTAT
1 TATATAAGTTATGTAAGTTAT
1574120 GTACGTGGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
15 2 0.05
16 9 0.20
17 1 0.02
18 1 0.02
20 1 0.02
21 27 0.61
22 3 0.07
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (21 bp):
TATATAAGTTATGTAAGTTAT
Found at i:1574244 original size:16 final size:16
Alignment explanation
Indices: 1574219--1574256 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1574209 GAAAACGAAG
*
1574219 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
1574234 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
1574250 TAAATTT
1 TAAATTT
1574257 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:1574271 original size:13 final size:13
Alignment explanation
Indices: 1574253--1574280 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1574243 ATACAAATAA
1574253 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1574266 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1574279 AT
1 AT
1574281 AAAATTAATA
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:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1574319 original size:61 final size:61
Alignment explanation
Indices: 1574138--1574406 Score: 367
Period size: 62 Copynumber: 4.4 Consensus size: 61
1574128 TGTATTATGT
* * *
1574138 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAA
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
* ** * *
1574199 CACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
** *
1574261 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTGTTACTAACAAATTTAGAA
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
* ** * * *
1574322 CACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
1574384 AACTTATTTAGAAAACTTATAAA
1 AACTTATTTAGAAAACTTATAAA
1574407 TTTAGAAAAC
Statistics
Matches: 178, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
61 72 0.40
62 106 0.60
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (61 bp):
AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
Found at i:1574357 original size:123 final size:123
Alignment explanation
Indices: 1574138--1574406 Score: 511
Period size: 123 Copynumber: 2.2 Consensus size: 123
1574128 TGTATTATGT
*
1574138 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
1574203 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
*
1574261 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTGTTACTAACAAATTTAGAACACT
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
*
1574326 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
1574384 AACTTATTTAGAAAACTTATAAA
1 AACTTATTTAGAAAACTTATAAA
1574407 TTTAGAAAAC
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 143 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (123 bp):
AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAA
Found at i:1574367 original size:16 final size:16
Alignment explanation
Indices: 1574342--1574379 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1574332 GAAAACGAAG
*
1574342 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
*
1574357 TAAATTTTAATGCAAA
1 TAAATTTTAATACAAA
1574373 TAAATTT
1 TAAATTT
1574380 AGAAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:1574394 original size:13 final size:13
Alignment explanation
Indices: 1574376--1574403 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1574366 ATGCAAATAA
1574376 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1574389 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1574402 AT
1 AT
1574404 AAATTTAGAA
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:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1574411 original size:17 final size:17
Alignment explanation
Indices: 1574372--1574421 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1574362 TTTAATGCAA
1574372 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
1574388 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
1574402 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
1574419 ATA
1 ATA
1574422 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:1577711 original size:7 final size:7
Alignment explanation
Indices: 1577665--1577696 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1577655 TTAAACACTG
1577665 AAACCCT
1 AAACCCT
1577672 AAACCCT
1 AAACCCT
1577679 AAACCCT
1 AAACCCT
1577686 AAACCCT
1 AAACCCT
1577693 AAAC
1 AAAC
1577697 ATTATAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:1578700 original size:20 final size:20
Alignment explanation
Indices: 1578648--1578702 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
1578638 CGCTGAAATG
* *
1578648 TAAACTCTAAACCTTAAAAC
1 TAAACTCTAAGCCCTAAAAC
* * *
1578668 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCTAAGCCCTAAAAC
1578689 TAAACTCTAAGCCC
1 TAAACTCTAAGCCC
1578703 AGAACACAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.40, C:0.35, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAACTCTAAGCCCTAAAAC
Found at i:1579384 original size:114 final size:114
Alignment explanation
Indices: 1579184--1579398 Score: 319
Period size: 114 Copynumber: 1.9 Consensus size: 114
1579174 TATCCCAATA
*
1579184 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAGCAATAAAACAGTAGCGTTTT
1 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTAGCGTTTT
* *
1579249 GTCCAAATTTTTTCCTTAAATTAGATATCTTTACCGCCCAATTCAATCT
66 GTCCAAATTCTTTCCTCAAATTAGATATCTTTACCGCCCAATTCAATCT
*
1579298 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGCAATAAAATGAAACAATAAAAC-GATA-CTGTT
1 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAG-TAGC-GTT
* * *
1579361 TTG-CTCACATTCTTTCCTCAAATTTGTTATCTTTACCG
64 TTGTC-CAAATTCTTTCCTCAAATTAGATATCTTTACCG
1579399 GCGTTTCTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
113 3 0.03
114 88 0.97
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (114 bp):
TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTAGCGTTTT
GTCCAAATTCTTTCCTCAAATTAGATATCTTTACCGCCCAATTCAATCT
Found at i:1579980 original size:17 final size:18
Alignment explanation
Indices: 1579960--1580012 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1579950 TTTGGTGACT
*
1579960 TCGCATTTTTAG-TGAGC
1 TCGCACTTTTAGATGAGC
* *
1579977 TCGCACATTT-GATAAGC
1 TCGCACTTTTAGATGAGC
*
1579994 TCGCAGTTTTAGATGAGC
1 TCGCACTTTTAGATGAGC
1580012 T
1 T
1580013 TGCAAGTGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 1 0.04
17 20 0.71
18 7 0.25
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (18 bp):
TCGCACTTTTAGATGAGC
Found at i:1582829 original size:32 final size:32
Alignment explanation
Indices: 1582793--1582896 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 32
1582783 TTATGATTAA
1582793 ACTTAATCACTTTAATATTAAATTAATATAAT
1 ACTTAATCACTTTAATATTAAATTAATATAAT
* *
1582825 ACTT-ATCAAGATAAATATTATATTAAATTTAATATTAA-
1 ACTTAATC-A-CT---T-TAATATTAAA-TTAATA-TAAT
*
1582863 A-TTAATCACTTTAATATTAAATTAATAAAAT
1 ACTTAATCACTTTAATATTAAATTAATATAAT
1582894 ACT
1 ACT
1582897 ATTTAGATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
30 2 0.04
31 10 0.18
32 15 0.27
33 2 0.04
36 2 0.04
37 12 0.21
38 10 0.18
39 3 0.05
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (32 bp):
ACTTAATCACTTTAATATTAAATTAATATAAT
Found at i:1582871 original size:69 final size:68
Alignment explanation
Indices: 1582788--1582932 Score: 227
Period size: 68 Copynumber: 2.1 Consensus size: 68
1582778 TTCAATTATG
* *
1582788 ATTAAACTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTATATTAAAT
1 ATTAAA-TTAATCACTTTAATATTAAATTAATAAAATAC-TATCAAGATAAATATTAAATTAAAT
1582853 TTAAT
64 TTAAT
** *
1582858 ATTAAATTAATCACTTTAATATTAAATTAATAAAATACTATTTAGATAAGTATTAAATTAAATTT
1 ATTAAATTAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAATTT
1582923 AAT
66 AAT
1582926 ATTAAAT
1 ATTAAAT
1582933 CTATTAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 33 0.47
69 31 0.44
70 6 0.09
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (68 bp):
ATTAAATTAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAATTT
AAT
Found at i:1582946 original size:68 final size:69
Alignment explanation
Indices: 1582805--1582949 Score: 186
Period size: 68 Copynumber: 2.1 Consensus size: 69
1582795 TTAATCACTT
* *
1582805 TAATATTAAATTAATATAATACTTATCAAGATAAATATTATATTAAATTTAATATTAAATTAATC
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATTAATC
***
1582870 ACTT
66 AAAA
** *
1582874 TAATATTAAATTAATAAAATAC-TATTTAGATAAGTATTAAATTAAATTTAATATTAAATCT-AT
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAT-TAAT
*
1582937 TAAAA
65 CAAAA
1582942 TAATATTA
1 TAATATTA
1582950 TTTTTAGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
68 44 0.67
69 22 0.33
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (69 bp):
TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATTAATC
AAAA
Found at i:1583212 original size:11 final size:11
Alignment explanation
Indices: 1583196--1583255 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
1583186 ATATATTTTT
1583196 TATTTTTAAAA
1 TATTTTTAAAA
1583207 TA-TTTTAAAA
1 TATTTTTAAAA
*
1583217 TACTTTTT---T
1 TA-TTTTTAAAA
*
1583226 TATTTTTTAAA
1 TATTTTTAAAA
1583237 TATTTTTAAAA
1 TATTTTTAAAA
1583248 TACTTTTT
1 TA-TTTTT
1583256 TAATTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 10 0.25
11 14 0.35
12 9 0.22
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:1583226 original size:31 final size:31
Alignment explanation
Indices: 1583191--1583267 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1583181 TAAATATATA
1583191 TTTTTTATTTTTAAAATA-TTTTAAAATACT
1 TTTTTTATTTTTAAAATATTTTTAAAATACT
*
1583221 TTTTTTATTTTTTAAATATTTTTAAAATACT
1 TTTTTTATTTTTAAAATATTTTTAAAATACT
*
1583252 TTTTTAATTTTCTAAA
1 TTTTTTATTTT-TAAA
1583268 TTTTTTTGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 17 0.40
31 22 0.52
32 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTATTTTTAAAATATTTTTAAAATACT
Found at i:1583273 original size:30 final size:28
Alignment explanation
Indices: 1583191--1583273 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 28
1583181 TAAATATATA
*
1583191 TTTTTTATTTTTAAAATATTTTAAAATAC
1 TTTTTTATTTTT-AAATTTTTTAAAATAC
1583220 TTTTTTTATTTTTTAAATATTTTTAAAATAC
1 -TTTTTTA-TTTTTAAAT-TTTTTAAAATAC
1583251 TTTTTTAATTTTCTAAATTTTTT
1 TTTTTT-ATTTT-TAAATTTTTT
1583274 TGGTGTTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
30 26 0.54
31 22 0.46
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTTATTTTTAAATTTTTTAAAATAC
Found at i:1598192 original size:23 final size:23
Alignment explanation
Indices: 1598166--1598219 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1598156 CCCGCCCATT
*
1598166 TTTTAATAAA-TACAAAAAATTTA
1 TTTTAA-AAATTACAAAAAATGTA
**
1598189 TTTTAAAAATTTTAAAAAATGTA
1 TTTTAAAAATTACAAAAAATGTA
1598212 TTTTAAAA
1 TTTTAAAA
1598220 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTAAAAATTACAAAAAATGTA
Found at i:1598206 original size:24 final size:24
Alignment explanation
Indices: 1598179--1598229 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
1598169 TAATAAATAC
*
1598179 AAAAAATTTATTTTAAAA-ATTTT
1 AAAAAATGTATTTTAAAATATTTT
1598202 AAAAAATGTATTTTAAAATATTTT
1 AAAAAATGTATTTTAAAATATTTT
1598226 AAAA
1 AAAA
1598230 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAAAATGTATTTTAAAATATTTT
Found at i:1598234 original size:39 final size:40
Alignment explanation
Indices: 1598193--1598286 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
1598183 AATTTATTTT
1598193 AAAAATTTTAAAAAATGTATTTT-AAAATATTTTAAAATTA
1 AAAAATTTTAAAAAA-GTATTTTAAAAATATTTTAAAATTA
** *
1598233 AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAATTTA
1 AAAAATTTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
*
1598273 AAAAAATTTAAAAA
1 AAAAATTTTAAAAA
1598287 TAAATATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 7 0.15
40 40 0.85
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAAATTTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:1599009 original size:16 final size:17
Alignment explanation
Indices: 1598983--1599020 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1598973 TTCAACATAT
1598983 TTTTATAA-TTTTAATAA
1 TTTTATAATTTTTAA-AA
1599000 TTTT-TAATTTTTAAAA
1 TTTTATAATTTTTAAAA
1599016 TTTTA
1 TTTTA
1599021 ATAACTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATAATTTTTAAAA
Found at i:1600451 original size:12 final size:12
Alignment explanation
Indices: 1600418--1600451 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1600408 TTATTAAAAA
*
1600418 ATAATAAAATTT
1 ATAAAAAAATTT
1600430 ATAAACAAAATTT
1 ATAAA-AAAATTT
1600443 ATAAAAAAA
1 ATAAAAAAA
1600452 AAAAGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAAAAAAATTT
Found at i:1600452 original size:13 final size:13
Alignment explanation
Indices: 1600423--1600452 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1600413 AAAAAATAAT
*
1600423 AAAATTTATAAAC
1 AAAATTTATAAAA
1600436 AAAATTTATAAAA
1 AAAATTTATAAAA
1600449 AAAA
1 AAAA
1600453 AAAGTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATTTATAAAA
Found at i:1601041 original size:22 final size:23
Alignment explanation
Indices: 1601005--1601048 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1600995 AATTTTGTTT
*
1601005 ATAATTTTTATAATTTTAAAAAA
1 ATAATTTTTAAAATTTTAAAAAA
1601028 ATAA-TTTTAAAATTTTAAAAA
1 ATAATTTTTAAAATTTTAAAAA
1601049 GGATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAATTTTTAAAATTTTAAAAAA
Found at i:1602452 original size:12 final size:13
Alignment explanation
Indices: 1602432--1602461 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1602422 AGCCAACAAA
1602432 TATTATTTATTTT
1 TATTATTTATTTT
1602445 TATT-TTTATTTT
1 TATTATTTATTTT
1602457 TATTA
1 TATTA
1602462 GTAGTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:1606891 original size:43 final size:42
Alignment explanation
Indices: 1606822--1606940 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
1606812 TTTCAGAAAT
* * ** **
1606822 AAACGCCGCTAAAGATCATGGCCTTTAGCGGCGTTTGTGGGA-
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCAT-TCCGAC
* *
1606864 AAAGCGCCGCTAAAGACCATGATCTTTAGCGGCGCATTCCTAC
1 AAA-CGCCGCTAAAGACCATGACCTTTAGCGGCGCATTCCGAC
1606907 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC
1606941 TGTTACCACA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 35 0.53
43 31 0.47
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCATTCCGAC
Found at i:1608910 original size:5 final size:5
Alignment explanation
Indices: 1608866--1608892 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1608856 GATTCTTGTT
1608866 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1608893 GGTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1611336 original size:107 final size:105
Alignment explanation
Indices: 1611097--1611406 Score: 415
Period size: 107 Copynumber: 2.9 Consensus size: 105
1611087 TTTTATTTTG
* * * * * **
1611097 AACAAAATGACCCCATTTTGCTATTCTAAAAAAATTTTATTTTGTTTTTTATAAATTGATTTAAA
1 AACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTATAAATTGATTTATT
*
1611162 TTTTGCGGCG-TTTTTAAAAAACGCCGCTATTTCATCTTG
66 TTTTGCGGCGTTTTTTAAAAAACGCCGCTATTTCATCTTC
** * * *
1611201 AACAAAATGACGTCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATATATTGATTTGTT
1 AACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTATAAATTGATTTATT
* *
1611266 TTTTGTGGCGTTTTTATAAAAAAACGCCGCTATTTCATTTTC
66 TTTTGCGGCGTTTTT-T-AAAAAACGCCGCTATTTCATCTTC
*
1611308 AGCAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTATAAATTGATTTATT
1 AACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTATAAATTGATTTATT
* *
1611373 TTTTGCGGCATTTTTTTTTAAAAACGCCGCTATT
66 TTTTGCGGC--GTTTTTTAAAAAACGCCGCTATT
1611407 GCTTACCTTT
Statistics
Matches: 178, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
104 63 0.35
105 4 0.02
106 1 0.01
107 104 0.58
108 1 0.01
109 5 0.03
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (105 bp):
AACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTATAAATTGATTTATT
TTTTGCGGCGTTTTTTAAAAAACGCCGCTATTTCATCTTC
Found at i:1612377 original size:36 final size:36
Alignment explanation
Indices: 1612336--1612406 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1612326 ACTTTAAATC
* *
1612336 CCTAACTCTTAACCCCTAACATCT-AACCCCTAAACT
1 CCTAACCCTTAAACCCTAA-ATCTCAACCCCTAAACT
* *
1612372 CCTAACCCTTAAACCTTAAATCTCAACCCTTAAAC
1 CCTAACCCTTAAACCCTAAATCTCAACCCCTAAAC
1612407 CATAATCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.25
Consensus pattern (36 bp):
CCTAACCCTTAAACCCTAAATCTCAACCCCTAAACT
Found at i:1612378 original size:15 final size:14
Alignment explanation
Indices: 1612335--1612379 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1612325 AACTTTAAAT
*
1612335 CCCTAACTCTTAAC
1 CCCTAACTCCTAAC
1612349 CCCTAACAT-CTAAC
1 CCCTAAC-TCCTAAC
1612363 CCCTAAACTCCTAAC
1 CCCT-AACTCCTAAC
1612378 CC
1 CC
1612380 TTAAACCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAACTCCTAAC
Found at i:1612424 original size:14 final size:14
Alignment explanation
Indices: 1612406--1612447 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1612396 AACCCTTAAA
1612406 CCATAATCCCTAAT
1 CCATAATCCCTAAT
*
1612420 TCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
1612435 CCATACTCCCTAA
1 CCATAATCCCTAA
1612448 ACCTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:1612444 original size:15 final size:15
Alignment explanation
Indices: 1612402--1612448 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1612392 TCTCAACCCT
1612402 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
1612416 T-AATTCATAATCCC
1 TAAATCCATAATCCC
*
1612430 TAAATCCATACTCCC
1 TAAATCCATAATCCC
1612445 TAAA
1 TAAA
1612449 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:1612652 original size:15 final size:15
Alignment explanation
Indices: 1612634--1612684 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1612624 CCTAGCATGT
1612634 CTAACCCTTAAATCC
1 CTAACCCTTAAATCC
*
1612649 CTAACCCTCT-AACCC
1 CTAACCCT-TAAATCC
*
1612664 CTAAACCTTAAATCC
1 CTAACCCTTAAATCC
1612679 C-AACCC
1 CTAACCC
1612685 CTAATCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 5 0.17
15 24 0.80
16 1 0.03
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (15 bp):
CTAACCCTTAAATCC
Found at i:1613240 original size:114 final size:113
Alignment explanation
Indices: 1613014--1613550 Score: 679
Period size: 114 Copynumber: 4.7 Consensus size: 113
1613004 AGCATTTTTG
** *
1613014 GCCGCTAAATCCCTAAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGAATTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAG-GTTTTTTGCGGCGCTTTC
* *
1613079 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAT
65 TTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * *
1613128 GCCGCTAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTCAGGTTTTTTGCGGCGCTTTCT
1 GCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCT
*
1613193 TAAAAACGCCGCAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAC
66 TAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAAC
* * * *
1613242 GCCACTAAATCCCCGAAAGCT-AACAAAACGGTGTCGTTGGGTTTAGGATTTCTTGCGGCG-TTT
1 GCCGCTAAATCCCCGAAAGCTCAA-AAAACGGCGTCGTTGGGCTTAGG-TTTTTTGCGGCGCTTT
* * * *
1613305 -TTGAGGAAGCGCCGCTAAATCCTTGAGCATTAGCGGCGCTTTAC-TAAAAAC
64 CTT-A-AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTT-CTTAAAAAC
* * *
1613356 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAGTTTTTTTGCGGCACTTT-
1 GCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTT-AGGTTTTTTGCGGCGCTTTC
* *
1613420 TATCAAAAACACCGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTTAAAAAC
65 T-T-AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * **** *
1613471 GCCACTAAACCCCCGAAAGCTTGGGAAACGGTGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCT
1 GCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCT
*
1613536 CAAAAACGCCGCTAA
66 TAAAAACGCCGCTAA
1613551 TGCTTATTTT
Statistics
Matches: 367, Mismatches: 44, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
113 75 0.20
114 162 0.44
115 127 0.35
116 3 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (113 bp):
GCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCT
TAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
Found at i:1614890 original size:22 final size:21
Alignment explanation
Indices: 1614848--1614900 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1614838 AATATTAAAA
**
1614848 ATATATT-TTATAATATTTTT
1 ATATATTATTATAATAAATTT
1614868 ATATATTATTATAATTAAATTT
1 ATATATTATTATAA-TAAATTT
* *
1614890 AAATACTATTA
1 ATATATTATTA
1614901 GTAAACATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 14 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATATTATTATAATAAATTT
Found at i:1631274 original size:18 final size:17
Alignment explanation
Indices: 1631251--1631288 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
1631241 AAAAAAATGT
1631251 AATAATGTAATCTCATGC
1 AATAATGTAATCTCAT-C
1631269 AATAATGTAATCTCATC
1 AATAATGTAATCTCATC
1631286 AAT
1 AAT
1631289 TACATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
AATAATGTAATCTCATC
Found at i:1640703 original size:18 final size:17
Alignment explanation
Indices: 1640670--1640708 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1640660 TTTTATAAAT
1640670 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1640688 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1640705 TGTG
1 TGTG
1640709 GAAGGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1640953 original size:23 final size:23
Alignment explanation
Indices: 1640926--1641047 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
1640916 AGTGTTATTG
*
1640926 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
1640949 TTCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1640972 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1640995 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1641018 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1641041 ATCAGTG
1 ATCAGTG
1641048 TGGCACTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1640979 original size:46 final size:46
Alignment explanation
Indices: 1640926--1641047 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
1640916 AGTGTTATTG
*
1640926 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGACTACAT
*
1640972 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGACTACAT
* *
1641018 ATCAGTGGTAGCTTCAGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
1641048 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGACTACAT
Found at i:1643146 original size:16 final size:16
Alignment explanation
Indices: 1643113--1643166 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1643103 AAAAGATCCA
**
1643113 AGCCCGAGAAAATTTG
1 AGCCCGAGAAAACCTG
*
1643129 AGCCCGACAAAACCTG
1 AGCCCGAGAAAACCTG
**
1643145 AGCTTGAGAAAACCTG
1 AGCCCGAGAAAACCTG
1643161 AGCCCG
1 AGCCCG
1643167 TAACAAACTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.35, C:0.28, G:0.24, T:0.13
Consensus pattern (16 bp):
AGCCCGAGAAAACCTG
Found at i:1643913 original size:15 final size:15
Alignment explanation
Indices: 1643884--1643927 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 15
1643874 AGAATGTATT
1643884 ATTATTATATATAATA
1 ATTATTAT-TATAATA
1643900 ATTATTATTATAAT-
1 ATTATTATTATAATA
1643914 A-TA-TATTATAATA
1 ATTATTATTATAATA
1643927 A
1 A
1643928 AAGATATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.33
13 3 0.11
14 1 0.04
15 6 0.22
16 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:1644221 original size:235 final size:242
Alignment explanation
Indices: 1643665--1644246 Score: 647
Period size: 241 Copynumber: 2.4 Consensus size: 242
1643655 ATATAATTAT
* ** *
1643665 TATAATATAGATTATAATAAAAAAGATATAGTATTACATGATATTATAATGTTTAATTGTCGATG
1 TATAATATAGATTATAATAAAAGA-ATATAGTATTACATGATATTATAATGTTTAATCATTGATG
* *
1643730 CATATATATAAAAATTATTAATATA-T-TATA-TGATATGATATAACATTATGTAATATAGTAAG
65 CATATATAT--AAACTATAAATATAGTATATACT-ATATGATATAACATTATGTAATATAGTAAG
* * * * *
1643792 AGGGCTAACTTTCAAATATACGAAATGTATAGAGACTTAAAGCATGTTTCAACAAAAAATAATAA
127 AGGGCTAACTTTCAAATATACAAAAAGTATAAAAACTTAAAGCATATTTCAACAAAAAATAATAA
* * * * *
1643857 TATATAATAAGTAACATAGAATGTATTATTATTATATATAATAATTATTAT
192 TATATAACAAGTAACATAGAATGTATAATAATTATATATAATAATTACTAC
* ** *
1643908 TATAATATATATTATAATAAAAG-ATATAGTATTACATGATAACATAATGTTTAACCATTGATGC
1 TATAATATAGATTATAATAAAAGAATATAGTATTACATGATATTATAATGTTTAATCATTGATGC
* *
1643972 ATATATAAAAACTATAAATATAGTATATACTATATGATATAACATTATGTAATATAGTAGGAGGG
66 ATATATATAAACTATAAATATAGTATATACTATATGATATAACATTATGTAATATAGTAAGAGGG
* * * * **
1644037 CT-ACTTTTAAATGTACAAAAAGTATAAAAACTTAAAGCGTATTTCAAC-CAGTATAAT-A-ATA
131 CTAACTTTCAAATATACAAAAAGTATAAAAACTTAAAGCATATTTCAACAAAAAATAATAATATA
*
1644098 -AACAA-T-A-ATA-TAT-TATAATAATTA-ATAT-ATAATGTACTAC
196 TAACAAGTAACATAGAATGTATAATAATTATATATAATAAT-TACTAC
* * * *
1644138 TATCAGATTATAGAATATAATAAAAGATATATAGTATTACGTTATATTACAATGTTTAATCATTG
1 TAT-A-A-TATAGATTATAATAAAAGA-ATATAGTATTACATGATATTATAATGTTTAATCATTG
* * *
1644203 ATGCATATACATAAACTATGAATATAGTATATACTACATGATAT
62 ATGCATATATATAAACTATAAATATAGTATATACTATATGATAT
1644247 GATATAACAT
Statistics
Matches: 289, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
229 5 0.02
230 11 0.04
231 10 0.03
232 3 0.01
233 19 0.07
234 1 0.00
235 72 0.25
236 4 0.01
237 3 0.01
238 1 0.00
239 18 0.06
240 39 0.13
241 81 0.28
242 1 0.00
243 21 0.07
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (242 bp):
TATAATATAGATTATAATAAAAGAATATAGTATTACATGATATTATAATGTTTAATCATTGATGC
ATATATATAAACTATAAATATAGTATATACTATATGATATAACATTATGTAATATAGTAAGAGGG
CTAACTTTCAAATATACAAAAAGTATAAAAACTTAAAGCATATTTCAACAAAAAATAATAATATA
TAACAAGTAACATAGAATGTATAATAATTATATATAATAATTACTAC
Found at i:1652468 original size:187 final size:186
Alignment explanation
Indices: 1652145--1652526 Score: 656
Period size: 187 Copynumber: 2.0 Consensus size: 186
1652135 TCAACAACCG
* *
1652145 AGTGATTTTGGCCCCATTTTTAATAATTTTTATGTTTTGGAGATCGTTACAACTATGTCCAGCTA
1 AGTGATTTTGGCCCCATTTTTAATAATTTTTATGTTTTAGAGATCGTTACAACTAGGTCCAGCTA
*
1652210 ACTCATACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAATGAACCTTGTGATG
66 ACTCATACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAACGAACCTTGTGATG
1652275 TTAGATGTTAAATGATGAATTTAAAATATTATTTTTTTATTTAAAAGTATTTTATTA
131 TTAGATGTTAAATGATGAATTTAAAATATTA-TTTTTTATTTAAAAGTATTTTATTA
* * *
1652332 TGTGATTTTGGCCCCGTTTTTAATAATTTTTATGTTTTAGAGATCGTTACAACTAGGTCCAGCTT
1 AGTGATTTTGGCCCCATTTTTAATAATTTTTATGTTTTAGAGATCGTTACAACTAGGTCCAGCTA
* * * * *
1652397 GCTCGTACCTTCGATTTTGAAACTGTTAAAGAATTTGAATGTTGCCATCAGCGAACCTTGTGATT
66 ACTCATACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAACGAACCTTGTGATG
1652462 TTAGATGTTAAATGATGAATTTAAAATATTATTTTTTATTTAAAAGTATTTTATTA
131 TTAGATGTTAAATGATGAATTTAAAATATTATTTTTTATTTAAAAGTATTTTATTA
1652518 AGTGATTTT
1 AGTGATTTT
1652527 TGATAAATTT
Statistics
Matches: 183, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
186 33 0.18
187 150 0.82
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (186 bp):
AGTGATTTTGGCCCCATTTTTAATAATTTTTATGTTTTAGAGATCGTTACAACTAGGTCCAGCTA
ACTCATACCTTCGATTTTGAAACTGTCAAAGAATTTGAATGTTGCCATCAACGAACCTTGTGATG
TTAGATGTTAAATGATGAATTTAAAATATTATTTTTTATTTAAAAGTATTTTATTA
Found at i:1653209 original size:21 final size:21
Alignment explanation
Indices: 1653183--1653225 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1653173 TTCAAGTGGA
1653183 TCAGCTCTTATGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
1653204 TCAGCTCTTATGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
1653225 T
1 T
1653226 TGGCGTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTAT
Found at i:1667978 original size:13 final size:13
Alignment explanation
Indices: 1667960--1668010 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
1667950 TAAAAATGAA
1667960 AATAAAATAAAAT
1 AATAAAATAAAAT
* *
1667973 AGTAAAATTAAAT
1 AATAAAATAAAAT
1667986 AATAATAATAATAAT
1 AATAA-AATAA-AAT
1668001 AATAATAATA
1 AATAA-AATA
1668011 GGAAAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 15 0.47
14 4 0.12
15 13 0.41
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:1667991 original size:3 final size:3
Alignment explanation
Indices: 1667983--1668010 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1667973 AGTAAAATTA
1667983 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1668011 GGAAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1672040 original size:28 final size:27
Alignment explanation
Indices: 1672012--1672075 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
1672002 GTTAATGAAA
1672012 TATATATTAACATATTTAAATAAAAAAAT
1 TATA-ATTAACA-ATTTAAATAAAAAAAT
* *
1672041 TATCAATTATCAATTTAAATAAATAAAT
1 TAT-AATTAACAATTTAAATAAAAAAAT
*
1672069 TAAAATT
1 TATAATT
1672076 TAGTATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 17 0.55
29 9 0.29
30 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
TATAATTAACAATTTAAATAAAAAAAT
Found at i:1672168 original size:23 final size:24
Alignment explanation
Indices: 1672142--1672203 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
1672132 TAAATATTAA
*
1672142 TAAATTTAAATAAAATAAT-AATT
1 TAAATTTAAATAAAATAATAAAAT
**
1672165 TAAAAATAAATAAAATAATAAAAT
1 TAAATTTAAATAAAATAATAAAAT
1672189 TACATATTTAAATAA
1 TA-A-ATTTAAATAA
1672204 TACAATTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 17 0.55
24 5 0.16
25 1 0.03
26 8 0.26
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAATTTAAATAAAATAATAAAAT
Found at i:1672175 original size:18 final size:18
Alignment explanation
Indices: 1672139--1672177 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1672129 TTTTAAATAT
*
1672139 TAATAAATTTAAATAAAA
1 TAATAAATTTAAAAAAAA
1672157 TAAT-AATTTAAAAATAAA
1 TAATAAATTTAAAAA-AAA
1672175 TAA
1 TAA
1672178 AATAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAAATTTAAAAAAAA
Found at i:1672186 original size:12 final size:12
Alignment explanation
Indices: 1672148--1672186 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1672138 TTAATAAATT
1672148 TAAATAAAATAA
1 TAAATAAAATAA
* *
1672160 TAATTTAAA-AA
1 TAAATAAAATAA
1672171 TAAATAAAATAA
1 TAAATAAAATAA
1672183 TAAA
1 TAAA
1672187 ATTACATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:1681281 original size:130 final size:130
Alignment explanation
Indices: 1681048--1681311 Score: 528
Period size: 130 Copynumber: 2.0 Consensus size: 130
1681038 TATATTCTAC
1681048 ATGCTTGTAGGGCACGAGAAATGAGAGTGAGCAGAGAGGTCATTTTGACAGTATGAACAACCATA
1 ATGCTTGTAGGGCACGAGAAATGAGAGTGAGCAGAGAGGTCATTTTGACAGTATGAACAACCATA
1681113 GATATCTCTTGTTACTTTGAAATGATCAGGTAAAACTAACAATACAACTTCATGGCAAAGACTAT
66 GATATCTCTTGTTACTTTGAAATGATCAGGTAAAACTAACAATACAACTTCATGGCAAAGACTAT
1681178 ATGCTTGTAGGGCACGAGAAATGAGAGTGAGCAGAGAGGTCATTTTGACAGTATGAACAACCATA
1 ATGCTTGTAGGGCACGAGAAATGAGAGTGAGCAGAGAGGTCATTTTGACAGTATGAACAACCATA
1681243 GATATCTCTTGTTACTTTGAAATGATCAGGTAAAACTAACAATACAACTTCATGGCAAAGACTAT
66 GATATCTCTTGTTACTTTGAAATGATCAGGTAAAACTAACAATACAACTTCATGGCAAAGACTAT
1681308 ATGC
1 ATGC
1681312 AATTGCCAGA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 134 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (130 bp):
ATGCTTGTAGGGCACGAGAAATGAGAGTGAGCAGAGAGGTCATTTTGACAGTATGAACAACCATA
GATATCTCTTGTTACTTTGAAATGATCAGGTAAAACTAACAATACAACTTCATGGCAAAGACTAT
Found at i:1686724 original size:15 final size:14
Alignment explanation
Indices: 1686699--1686738 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1686689 TTTCAATTTT
1686699 ATTTT-AATAATAA
1 ATTTTAAATAATAA
1686712 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
1686726 ATTTTAAATAATA
1 ATTTTAAATAATA
1686739 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:1690283 original size:21 final size:20
Alignment explanation
Indices: 1690243--1690285 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1690233 TTTGAAAATC
*
1690243 AAAATAATAAAAATATATTA
1 AAAATAATAAAAATAAATTA
1690263 AAAATTAA-AAAAAGTAAATTA
1 AAAA-TAATAAAAA-TAAATTA
1690284 AA
1 AA
1690286 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATAATAAAAATAAATTA
Found at i:1692730 original size:11 final size:11
Alignment explanation
Indices: 1692705--1692768 Score: 76
Period size: 11 Copynumber: 5.9 Consensus size: 11
1692695 TATAATTTCA
*
1692705 AAAAAATATAT
1 AAAAAATTTAT
*
1692716 -AAAAATTTCT
1 AAAAAATTTAT
*
1692726 AAAAAATATAT
1 AAAAAATTTAT
*
1692737 AAAAAATTTCT
1 AAAAAATTTAT
*
1692748 AAAAAATATAT
1 AAAAAATTTAT
1692759 AAAAAATTTA
1 AAAAAATTTA
1692769 AAATTTTCTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
10 8 0.19
11 35 0.81
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAATTTAT
Found at i:1692741 original size:22 final size:22
Alignment explanation
Indices: 1692698--1692767 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
1692688 CAAAATTTAT
*
1692698 AATTTCAAAAAAATATAT-AAA
1 AATTTCTAAAAAATATATAAAA
1692719 AATTTCTAAAAAATATATAAAA
1 AATTTCTAAAAAATATATAAAA
1692741 AATTTCTAAAAAATATATAAAA
1 AATTTCTAAAAAATATATAAAA
1692763 AATTT
1 AATTT
1692768 AAAATTTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 17 0.36
22 30 0.64
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTTCTAAAAAATATATAAAA
Found at i:1693791 original size:15 final size:17
Alignment explanation
Indices: 1693766--1693803 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1693756 ATGTAATTTT
*
1693766 CTATTTGAACA-TACAA
1 CTATTTCAACATTACAA
1693782 -TATTTCAACATTACAA
1 CTATTTCAACATTACAA
1693798 CTATTT
1 CTATTT
1693804 TTAATCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (17 bp):
CTATTTCAACATTACAA
Found at i:1702114 original size:14 final size:14
Alignment explanation
Indices: 1702095--1702128 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1702085 ATCATTTTGC
1702095 TATTATATTATTAT
1 TATTATATTATTAT
* *
1702109 TATTATATTGTTGT
1 TATTATATTATTAT
1702123 TATTAT
1 TATTAT
1702129 TTGAATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:1706175 original size:26 final size:26
Alignment explanation
Indices: 1706146--1706211 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
1706136 GCAACATACG
*
1706146 TATAAAGGTTACACCTTGAACATAAA
1 TATAAAGGTCACACCTTGAACATAAA
* *
1706172 TATACAGGTCACACCTTGAACATAAG
1 TATAAAGGTCACACCTTGAACATAAA
1706198 TATAAAGGTCACAC
1 TATAAAGGTCACAC
1706212 ACAAGGTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (26 bp):
TATAAAGGTCACACCTTGAACATAAA
Found at i:1706522 original size:99 final size:99
Alignment explanation
Indices: 1706411--1706610 Score: 364
Period size: 99 Copynumber: 2.0 Consensus size: 99
1706401 AAAAAATCTT
* * *
1706411 ATTTTTGAGTGATAATAGTGTAACTTACCTTAATTATTATTTAAATCGATAAATTAATACTTTTT
1 ATTTTAGAGTGATAATAGTGTAACTTACCCTAACTATTATTTAAATCGATAAATTAATACTTTTT
1706476 AATTATATTTAATAATTCAATTAATTTTACATTA
66 AATTATATTTAATAATTCAATTAATTTTACATTA
*
1706510 ATTTTAGAGTGATAATAGTGTAACTTACCCTAACTATTATTTAAATTGATAAATTAATACTTTTT
1 ATTTTAGAGTGATAATAGTGTAACTTACCCTAACTATTATTTAAATCGATAAATTAATACTTTTT
1706575 AATTATATTTAATAATTCAATTAATTTTACATTA
66 AATTATATTTAATAATTCAATTAATTTTACATTA
1706609 AT
1 AT
1706611 AATTAAAAAT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.47
Consensus pattern (99 bp):
ATTTTAGAGTGATAATAGTGTAACTTACCCTAACTATTATTTAAATCGATAAATTAATACTTTTT
AATTATATTTAATAATTCAATTAATTTTACATTA
Found at i:1716235 original size:23 final size:23
Alignment explanation
Indices: 1716208--1716254 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1716198 CTTCAACCTC
*
1716208 TTTCTCCTTATGCTTCTTTTCTT
1 TTTCTCCTTATGCTTCTTCTCTT
* * *
1716231 TTTCTTCTTCTTCTTCTTCTCTT
1 TTTCTCCTTATGCTTCTTCTCTT
1716254 T
1 T
1716255 ATCTTCTTTT
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:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTCTCCTTATGCTTCTTCTCTT
Found at i:1717930 original size:41 final size:38
Alignment explanation
Indices: 1717873--1717963 Score: 148
Period size: 41 Copynumber: 2.3 Consensus size: 38
1717863 AATATATTTA
1717873 TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTAATTTTAAAATA-TTTTAAAATACT
1717912 TTTTTTATTATTTTTTAATTTTAAAATATTTTAAAATAC-
1 TTTTTTA--ATTTTTTAATTTTAAAATATTTTAAAATACT
1717951 TTTTTTAATTTTT
1 TTTTTTAATTTTT
1717964 AAAATAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
37 6 0.12
39 14 0.28
40 11 0.22
41 19 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTTTTAATTTTTTAATTTTAAAATATTTTAAAATACT
Found at i:1728995 original size:216 final size:216
Alignment explanation
Indices: 1728621--1729272 Score: 1205
Period size: 216 Copynumber: 3.0 Consensus size: 216
1728611 ACCAATAGAT
*
1728621 TAGAGACATCAGTTTAGGTTTCAAACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
1 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
* *
1728686 ATCTAATTAAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTACATG
66 ATCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
**
1728751 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGTT
131 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
1728816 AAACAGATGACTCCTCTAAAC
196 AAACAGATGACTCCTCTAAAC
* *
1728837 TAGAGACATCAGTTTTGGTTTCAGACATTTGATCTAAGCCGTTTCATAAAATTATTTAAATTTAA
1 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
1728902 ATCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
66 ATCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
1728967 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
131 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
1729032 AAACAGATGACTCCTCTAAAC
196 AAACAGATGACTCCTCTAAAC
*
1729053 TAGAGACATCAGTTTAGGTTTCAGACATTTGACCTAAGCCATTTCATAAAATTATTTAAATTTAA
1 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
*
1729118 ACCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
66 ATCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
* *
1729183 GCACAAAGTTAAAATATCAAGTCTTTTGGAGAACAGATGATAAATTAATTGTTTTATGACATGGA
131 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
1729248 AAACAGATGACTCCTCTAAAC
196 AAACAGATGACTCCTCTAAAC
1729269 TAGA
1 TAGA
1729273 TCAGGTTCAA
Statistics
Matches: 423, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
216 423 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (216 bp):
TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
ATCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
AAACAGATGACTCCTCTAAAC
Found at i:1731020 original size:206 final size:205
Alignment explanation
Indices: 1730612--1731021 Score: 631
Period size: 206 Copynumber: 2.0 Consensus size: 205
1730602 AAAGTGGGAG
* *
1730612 CTTGAATTAACAATGTTTCATAAATCCAACAACCCTGACTACAAATCCACTCACAATGAAAGGAT
1 CTTGAATTAACAATGTTTCATAAATCCAACAACCCTGACTACAAATCCACCCACAATGAAAAGAT
** * *
1730677 ATCATAATCAAAGTAAAACCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGA
66 ATCATAATCAAAGTAAAACCATAACATGCAAGTTTGTGAGAATCTTGATAACCAAGCAGCAATGA
* * * * *
1730742 AAAGCCATGTTCAGATAGATGAGTAAAGCTTTGGAATGGTAACTAACTCTTACACCCAGACCTCG
131 AAAGCCAAGTTCAGATAGAAGAGTAAAGCTTTAGAATGGTAACCAACTCTGACACCCAGACCTCG
1730807 AACTAAGAAA
196 AACTAAGAAA
*
1730817 CTTGAATTAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACCCACAATGAAAAGAT
1 CTTGAATTAACAATGTTTCATAAATCCAACAACCCTGACTACAAATCCACCCACAATGAAAAGAT
* * *
1730882 ATCATAATCGAAGTAAAAATCATAACATGCAAGTTTGTGAGAATCTTGATAACCAAGCAGCTATG
66 ATCATAATCAAAGT-AAAACCATAACATGCAAGTTTGTGAGAATCTTGATAACCAAGCAGCAATG
* * ** *
1730947 AAAAGTCAAGTTCAGATAGAAGAGTAATGCTTTAGAATGGTAACCAACTCTGACACCTGGGCCTC
130 AAAAGCCAAGTTCAGATAGAAGAGTAAAGCTTTAGAATGGTAACCAACTCTGACACCCAGACCTC
1731012 GAACTAAGAA
195 GAACTAAGAA
1731022 GAAACTTATT
Statistics
Matches: 184, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
205 75 0.41
206 109 0.59
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (205 bp):
CTTGAATTAACAATGTTTCATAAATCCAACAACCCTGACTACAAATCCACCCACAATGAAAAGAT
ATCATAATCAAAGTAAAACCATAACATGCAAGTTTGTGAGAATCTTGATAACCAAGCAGCAATGA
AAAGCCAAGTTCAGATAGAAGAGTAAAGCTTTAGAATGGTAACCAACTCTGACACCCAGACCTCG
AACTAAGAAA
Done.