Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 180 of 228
Found at i:53866655 original size:26 final size:28
Alignment explanation
Indices: 53866626--53866687 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
53866616 GAACTTATTT
53866626 AATT-ATT-TTTAATAATATATG-GACTA
1 AATTGATTATTTAATAATATA-GAGACTA
53866652 AATTGATTCATTTAATAATATAGAGACTA
1 AATTGATT-ATTTAATAATATAGAGACTA
*
53866681 ATTTGAT
1 AATTGAT
53866688 CCAGTCTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
28 1 0.03
29 23 0.74
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.44
Consensus pattern (28 bp):
AATTGATTATTTAATAATATAGAGACTA
Found at i:53868313 original size:18 final size:18
Alignment explanation
Indices: 53868290--53868327 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
53868280 TCCAAGACCG
53868290 GCGGTTTGCGAGACTTAA
1 GCGGTTTGCGAGACTTAA
*
53868308 GCGGTTTGTGAGACTTAA
1 GCGGTTTGCGAGACTTAA
53868326 GC
1 GC
53868328 TCTAGCCCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (18 bp):
GCGGTTTGCGAGACTTAA
Found at i:53879171 original size:64 final size:64
Alignment explanation
Indices: 53879056--53879185 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 64
53879046 CGAGCATCCC
* * * * *
53879056 GATCGGTAGTAATCCTGCATGTGTTGCGTACATACCGCAACTATTTGTGAGCGTCCTGTTATAT
1 GATCGATAGTAATCCTACATGTGTTGCGGACATACCACAACTATTTATGAGCGTCCTGTTATAT
* ** * *
53879120 GATCGATAGTGATCCTACATGTGTTGCGGACATACCACAGTTCTTTATGAGCTTCCTGTTATAT
1 GATCGATAGTAATCCTACATGTGTTGCGGACATACCACAACTATTTATGAGCGTCCTGTTATAT
53879184 GA
1 GA
53879186 CTCTCTAGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (64 bp):
GATCGATAGTAATCCTACATGTGTTGCGGACATACCACAACTATTTATGAGCGTCCTGTTATAT
Found at i:53879402 original size:23 final size:24
Alignment explanation
Indices: 53879368--53879441 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 24
53879358 AGCTCAAATA
53879368 AGCTTC-CTGATA-GACTCTTTGTG
1 AGCTTCTCTGATATG-CTCTTTGTG
*
53879391 AGCTTCTC-GATATGCTTTTTGTG
1 AGCTTCTCTGATATGCTCTTTGTG
53879414 AGCTTCT-TGATTAATGGCTCTTTGTG
1 AGCTTCTCTGA-T-AT-GCTCTTTGTG
53879440 AG
1 AG
53879442 TTTCCTGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
23 27 0.63
24 3 0.07
25 2 0.05
26 11 0.26
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (24 bp):
AGCTTCTCTGATATGCTCTTTGTG
Found at i:53879456 original size:26 final size:27
Alignment explanation
Indices: 53879400--53879459 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
53879390 GAGCTTCTCG
* *
53879400 ATAT-GCTTTTTGTGAGCTTCTTGATT
1 ATATGGCTCTTTGTGAGCTTCCTGATT
*
53879426 A-ATGGCTCTTTGTGAGTTTCCTG-TT
1 ATATGGCTCTTTGTGAGCTTCCTGATT
53879451 ATATGGCTC
1 ATATGGCTC
53879460 GAGAGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (27 bp):
ATATGGCTCTTTGTGAGCTTCCTGATT
Found at i:53883539 original size:13 final size:13
Alignment explanation
Indices: 53883521--53883545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53883511 TAAAAGTTTG
53883521 AGGGAGAGTAAAT
1 AGGGAGAGTAAAT
53883534 AGGGAGAGTAAA
1 AGGGAGAGTAAA
53883546 ATTTTGGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (13 bp):
AGGGAGAGTAAAT
Found at i:53883897 original size:9 final size:9
Alignment explanation
Indices: 53883883--53883919 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53883873 TATAGTTTGA
53883883 TATTCGAAT
1 TATTCGAAT
53883892 TATTCGAAT
1 TATTCGAAT
*
53883901 TATTCGAGT
1 TATTCGAAT
53883910 TATTCGAAT
1 TATTCGAAT
53883919 T
1 T
53883920 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53884055 original size:16 final size:16
Alignment explanation
Indices: 53884034--53884065 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53884024 CCCCTACGCT
53884034 AAACAGCTGTCGTGCC
1 AAACAGCTGTCGTGCC
*
53884050 AAACAGTTGTCGTGCC
1 AAACAGCTGTCGTGCC
53884066 CACAATGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (16 bp):
AAACAGCTGTCGTGCC
Found at i:53889611 original size:24 final size:23
Alignment explanation
Indices: 53889578--53889625 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
53889568 AGATTGAAAG
* *
53889578 CCAAAACGTGTTAGGTTAGCAGA
1 CCAAAACGTGCTAGGGTAGCAGA
*
53889601 CCAAAGACGTGCTAGGGTAGTAGA
1 CCAAA-ACGTGCTAGGGTAGCAGA
53889625 C
1 C
53889626 TTTTAGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (23 bp):
CCAAAACGTGCTAGGGTAGCAGA
Found at i:53891845 original size:22 final size:21
Alignment explanation
Indices: 53891807--53891866 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
53891797 TAATATTATA
*
53891807 TTTATATTTTAAGTTTATTTC
1 TTTATATTTTAAATTTATTTC
53891828 TTTATATTTTAAAATTTATTTC
1 TTTATATTTT-AAATTTATTTC
53891850 TTT-TAGTATTTAAATTT
1 TTTATA-T-TTTAAATTT
53891867 CATGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 12 0.34
22 20 0.57
23 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATATTTTAAATTTATTTC
Found at i:53895400 original size:29 final size:29
Alignment explanation
Indices: 53895367--53895425 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
53895357 TTCGATCTCT
*
53895367 ATATTTTTAAAATATTTTTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
*
53895396 ATATTTTTATAATATTATTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
53895425 A
1 A
53895426 ATGGTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATTTTTAAAATATTATTAATTAGTTCA
Found at i:53897666 original size:31 final size:28
Alignment explanation
Indices: 53897611--53897710 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
53897601 GGTTTAGGGA
* *
53897611 TTTTAAA-AATTAAATCAAGATTTAGCATTT
1 TTTTAAATAATTAAAT-TAGTTTTAG--TTT
***
53897641 TTTTAAATAATTAAATTAGGTTTTAGGGGG
1 TTTTAAATAATTAAATTA-GTTTTA-GTTT
53897671 TTTTAAATAAATTAAATTAGTGTTTAGTTT
1 TTTTAAAT-AATTAAATTAGT-TTTAGTTT
53897701 TTTTAAATAA
1 TTTTAAATAA
53897711 CTTTGTGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.04
30 27 0.47
31 27 0.47
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (28 bp):
TTTTAAATAATTAAATTAGTTTTAGTTT
Found at i:53897705 original size:30 final size:31
Alignment explanation
Indices: 53897638--53897710 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
53897628 AGATTTAGCA
53897638 TTTTTTTAAAT-AATTAAATTAGGTTTTAGG
1 TTTTTTTAAATAAATTAAATTAGGTTTTAGG
***
53897668 GGGTTTTAAATAAATTAAATTA-GTGTTTA-G
1 TTTTTTTAAATAAATTAAATTAGGT-TTTAGG
53897698 TTTTTTTAAATAA
1 TTTTTTTAAATAA
53897711 CTTTGTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTTTTTAAATAAATTAAATTAGGTTTTAGG
Found at i:53897923 original size:126 final size:126
Alignment explanation
Indices: 53897762--53898032 Score: 470
Period size: 126 Copynumber: 2.2 Consensus size: 126
53897752 AATAAGGATT
* *
53897762 TTTTTCTACAGTAATTCTTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
* * *
53897827 ACGCTTCAAGCACGATGCACTGTCAGCAAAATTGATGAAAAAGGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
*
53897888 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
* *
53897953 ACGCTTTAAGCAGGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
53898014 TTTTTCTACAGTAGTTCCT
1 TTTTTCTACAGTAGTTCCT
53898033 ATTTGGCCTT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 136 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCACGACGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACACTC
Found at i:53901484 original size:18 final size:18
Alignment explanation
Indices: 53901458--53901500 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53901448 GACTGGGAAA
* *
53901458 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
53901476 AGGATACATATCAGGGCT
1 AGGATACATATAAGGGCT
53901494 AGGATAC
1 AGGATAC
53901501 GCATTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:53902229 original size:7 final size:7
Alignment explanation
Indices: 53902219--53902243 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53902209 AGATATACAT
53902219 AATACTA
1 AATACTA
53902226 AATACTA
1 AATACTA
53902233 AATACTA
1 AATACTA
53902240 AATA
1 AATA
53902244 TGAAACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53903121 original size:10 final size:10
Alignment explanation
Indices: 53903108--53903135 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
53903098 AAAATTATAA
53903108 AATTAAAATT
1 AATTAAAATT
53903118 AATTAAAATT
1 AATTAAAATT
53903128 AATTAAAA
1 AATTAAAA
53903136 GAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTAAAATT
Found at i:53903354 original size:30 final size:30
Alignment explanation
Indices: 53903320--53903384 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
53903310 ATTAATTAAA
53903320 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
* *
53903350 GAGAGCTTTGATAAATTTAGGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
53903380 GAGAG
1 GAGAG
53903385 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (30 bp):
GAGAGCTTTGAAAAATTTAAGGAGAAATTT
Found at i:53905942 original size:22 final size:23
Alignment explanation
Indices: 53905899--53905943 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53905889 TTTCAATAAA
*
53905899 TAAAAAAATAAAATTATTAATAT
1 TAAAAAAATAAAATTATAAATAT
* *
53905922 TAAAACAATATAA-TATAAATAT
1 TAAAAAAATAAAATTATAAATAT
53905944 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAAAATAAAATTATAAATAT
Found at i:53906903 original size:8 final size:8
Alignment explanation
Indices: 53906886--53906916 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
53906876 CCTTTTACTA
*
53906886 TATATTTG
1 TATATATG
53906894 TATATATG
1 TATATATG
53906902 TATATATG
1 TATATATG
53906910 TATATAT
1 TATATAT
53906917 AGCAAACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TATATATG
Found at i:53911757 original size:41 final size:41
Alignment explanation
Indices: 53911705--53911786 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
53911695 ATATTTTATT
* * *
53911705 TTATGTTTTAGTAGTTTATTAGAATAAGTGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
53911746 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
53911787 CAATTAGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
Found at i:53920243 original size:3 final size:3
Alignment explanation
Indices: 53920235--53920291 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
53920225 GGACTCGTAT
* *
53920235 TCA TCA TCA TCA TCA TCA T-A ACAA TAA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA TCA TCA
53920280 TCA TCA TCA TCA
1 TCA TCA TCA TCA
53920292 AAAGAAGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:53921480 original size:10 final size:10
Alignment explanation
Indices: 53921465--53921501 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
53921455 TTTTTTAAAA
*
53921465 ATTAAAAATC
1 ATTAAAAATT
53921475 ATT-AAAATT
1 ATTAAAAATT
53921484 ATTAAAAATT
1 ATTAAAAATT
53921494 A-TAAAAAT
1 ATTAAAAAT
53921502 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 15 0.60
10 10 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:53921500 original size:19 final size:19
Alignment explanation
Indices: 53921465--53921501 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53921455 TTTTTTAAAA
*
53921465 ATTAAAAATCATTAAAATT
1 ATTAAAAATCATAAAAATT
*
53921484 ATTAAAAATTATAAAAAT
1 ATTAAAAATCATAAAAAT
53921502 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAATCATAAAAATT
Found at i:53921521 original size:48 final size:48
Alignment explanation
Indices: 53921428--53921519 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
53921418 TTTTAAAATT
* *
53921428 TTAAAATTTTTAAAAATATAAGAACTATTTTTTAAAAATTAAAAATCA
1 TTAAAATTATTAAAAATATAAGAAATATTTTTTAAAAATTAAAAATCA
*
53921476 TTAAAATTATTAAAAATTATAA-AAATATTTTTT-AAATTTAAAAA
1 TTAAAATTATTAAAAA-TATAAGAAATATTTTTTAAAAATTAAAAA
53921520 ATTAAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 10 0.25
48 25 0.62
49 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (48 bp):
TTAAAATTATTAAAAATATAAGAAATATTTTTTAAAAATTAAAAATCA
Found at i:53925313 original size:30 final size:32
Alignment explanation
Indices: 53925279--53925337 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
53925269 TAAATTAATG
*
53925279 AAATATGTTG-ATTTTTTTTA-ATATTTAAGT
1 AAATAGGTTGTATTTTTTTTATATATTTAAGT
*
53925309 AAATAGGTTGTCTTTTTTTTATATATTTA
1 AAATAGGTTGTATTTTTTTTATATATTTA
53925338 TCGGTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 9 0.36
32 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (32 bp):
AAATAGGTTGTATTTTTTTTATATATTTAAGT
Found at i:53928872 original size:50 final size:50
Alignment explanation
Indices: 53928748--53928996 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
53928738 GATAATAACA
* * ** * *
53928748 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
53928799 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
53928849 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
53928899 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
53928954 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
53928997 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:53928926 original size:100 final size:104
Alignment explanation
Indices: 53928747--53928996 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
53928737 TGATAATAAC
**
53928747 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
53928812 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
53928849 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
53928912 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
53928954 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53928997 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:53929112 original size:13 final size:13
Alignment explanation
Indices: 53929091--53929122 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53929081 GCTTGGATCA
*
53929091 TCATCAAATAAAT
1 TCATAAAATAAAT
53929104 TCATAAAATAAAT
1 TCATAAAATAAAT
53929117 TCATAA
1 TCATAA
53929123 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:53929369 original size:30 final size:30
Alignment explanation
Indices: 53929334--53929391 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53929324 CCTCGACTCT
*
53929334 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
53929364 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53929392 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53938518 original size:16 final size:16
Alignment explanation
Indices: 53938497--53938527 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53938487 CAAAATTCTT
53938497 GGACAATCTTCTCATG
1 GGACAATCTTCTCATG
*
53938513 GGACAATCTTTTCAT
1 GGACAATCTTCTCAT
53938528 TCCATATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (16 bp):
GGACAATCTTCTCATG
Found at i:53939161 original size:31 final size:31
Alignment explanation
Indices: 53939123--53939186 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53939113 GCCAAACAAT
53939123 TTAGTGTAATTACTACTACCATACGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
* *
53939154 TTAGTGTAATTACTACTAGCATATGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
53939185 TT
1 TT
53939187 GCTCTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (31 bp):
TTAGTGTAATTACTACTACCATACGCAAATA
Found at i:53945755 original size:11 final size:11
Alignment explanation
Indices: 53945739--53945779 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
53945729 ATTTTCTCAT
53945739 AAAAAATTATA
1 AAAAAATTATA
53945750 AAAAAA-TA-A
1 AAAAAATTATA
53945759 AATAAAATTATA
1 AA-AAAATTATA
*
53945771 AAAATATTA
1 AAAAAATTA
53945780 AAATTGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.12
10 6 0.23
11 14 0.54
12 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:53945767 original size:21 final size:22
Alignment explanation
Indices: 53945741--53945783 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
53945731 TTTCTCATAA
53945741 AAAATTATAAAAA-AATAAAAT
1 AAAATTATAAAAATAATAAAAT
*
53945762 AAAATTATAAAAATATTAAAAT
1 AAAATTATAAAAATAATAAAAT
53945784 TGATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATTATAAAAATAATAAAAT
Found at i:53945782 original size:28 final size:28
Alignment explanation
Indices: 53945751--53945875 Score: 81
Period size: 27 Copynumber: 4.2 Consensus size: 28
53945741 AAAATTATAA
53945751 AAAAATAAAATAAAATTATAAAAATATT
1 AAAAATAAAATAAAATTATAAAAATATT
* * * *
53945779 AAAATTGATATAAAATTATTAAAATTATT
1 AAAAATAAAATAAAATTA-TAAAAATATT
*
53945808 AAAATTATAAATTATTATAATTATTATAAAAATATA
1 AAAA--ATAAA--A-TA-AA--ATTATAAAAATATT
** * *
53945844 AAAAATCTAAT-AAATTATAAAATTAAT
1 AAAAATAAAATAAAATTATAAAAATATT
53945871 AAAAA
1 AAAAA
53945876 ATTATTTAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
27 16 0.22
28 15 0.20
29 15 0.20
31 3 0.04
32 1 0.01
33 1 0.01
34 5 0.07
35 2 0.03
36 12 0.16
37 4 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
AAAAATAAAATAAAATTATAAAAATATT
Found at i:53945790 original size:20 final size:20
Alignment explanation
Indices: 53945767--53945804 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53945757 AAAATAAAAT
53945767 TATAAAAATATTAAAATTGA
1 TATAAAAATATTAAAATTGA
*
53945787 TATAAAATTATTAAAATT
1 TATAAAAATATTAAAATT
53945805 ATTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TATAAAAATATTAAAATTGA
Found at i:53945877 original size:19 final size:19
Alignment explanation
Indices: 53945737--53945880 Score: 56
Period size: 19 Copynumber: 7.6 Consensus size: 19
53945727 ATATTTTCTC
*
53945737 ATAAAAAATTATAAAA-AA
1 ATAAAAAATTATAAAATTA
*
53945755 ATAAAATAAAATTATAAAAAT-
1 AT--AA-AAAATTATAAAATTA
* *
53945776 ATTAAAATTGATATAAAATT-
1 ATAAAAAAT--TATAAAATTA
*
53945796 AT-TAAAATTATTAAAATT-
1 ATAAAAAATTA-TAAAATTA
**
53945814 ATAAATTATTAT--AATTA
1 ATAAAAAATTATAAAATTA
*
53945831 TTATAAAAA-TATAAAA--A
1 ATA-AAAAATTATAAAATTA
*
53945848 ATCTAATAAATTATAAAATTA
1 A--TAAAAAATTATAAAATTA
53945869 ATAAAAAATTAT
1 ATAAAAAATTAT
53945881 TTAAAATATT
Statistics
Matches: 94, Mismatches: 15, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
16 4 0.04
17 8 0.09
18 23 0.24
19 31 0.33
20 12 0.13
21 16 0.17
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (19 bp):
ATAAAAAATTATAAAATTA
Found at i:53946408 original size:9 final size:9
Alignment explanation
Indices: 53946396--53946586 Score: 64
Period size: 9 Copynumber: 20.0 Consensus size: 9
53946386 TTTTATGATT
53946396 TTTTTATAA
1 TTTTTATAA
53946405 TTTTTATAA
1 TTTTTATAA
**
53946414 GTTCATATCAA
1 -TTTTTAT-AA
* *
53946425 TTTTAATAC
1 TTTTTATAA
* *
53946434 TATTTATGA
1 TTTTTATAA
*
53946443 TTTTAATAGAA
1 TTTT--TATAA
* *
53946454 TTTTAATATG
1 TTTTTATA-A
53946464 TTTTTATAAA
1 TTTTTAT-AA
*
53946474 TTTTTAAATA
1 TTTTTATA-A
*
53946484 TGTTTTATTA
1 T-TTTTATAA
*
53946494 CTTTTATAAA
1 TTTTTAT-AA
*
53946504 TTTTATAGAA
1 TTTT-TATAA
*
53946514 TTTTTAT-G
1 TTTTTATAA
53946522 TTTTTGATAA
1 TTTTT-ATAA
*
53946532 TATTTATAA
1 TTTTTATAA
*
53946541 GTTTATATCAA
1 -TTTTTAT-AA
*
53946552 TTTTCAT-A
1 TTTTTATAA
53946560 TATTTT-TAA
1 T-TTTTATAA
* *
53946569 TATTTATAT
1 TTTTTATAA
53946578 TTTTTATAA
1 TTTTTATAA
53946587 ATATTTTCTG
Statistics
Matches: 127, Mismatches: 38, Indels: 34
0.64 0.19 0.17
Matches are distributed among these distances:
8 11 0.09
9 49 0.39
10 48 0.38
11 19 0.15
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:53946463 original size:22 final size:22
Alignment explanation
Indices: 53946438--53946490 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
53946428 TAATACTATT
53946438 TATGATTTTAATAGAA-TTTT-AA
1 TATG-TTTTAATA-AATTTTTAAA
*
53946460 TATGTTTTTATAAATTTTTAAA
1 TATGTTTTAATAAATTTTTAAA
53946482 TATGTTTTA
1 TATGTTTTA
53946491 TTACTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 11 0.41
22 14 0.52
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
TATGTTTTAATAAATTTTTAAA
Found at i:53946477 original size:20 final size:19
Alignment explanation
Indices: 53946438--53946588 Score: 73
Period size: 20 Copynumber: 7.8 Consensus size: 19
53946428 TAATACTATT
*
53946438 TATGATTTTAATAGAATTTTAA
1 TATG-TTTTTATA-AATTTT-A
53946460 TATGTTTTTATAAATTTTTAAA
1 TATGTTTTTATAAA-TTTT--A
* *
53946482 TATG-TTTTATTACTTTTA
1 TATGTTTTTATAAATTTTA
**
53946500 TA-AATTTTATAGAATTTT-
1 TATGTTTTTATA-AATTTTA
53946518 TATGTTTTTGAT-AATATTTA
1 TATGTTTTT-ATAAAT-TTTA
* * *
53946538 TAAGTTTATATCAATTTTCA
1 TATGTTTTTATAAATTTT-A
* *
53946558 TATATTTTTA-ATA-TTTA
1 TATGTTTTTATAAATTTTA
53946575 TAT-TTTTTATAAAT
1 TATGTTTTTATAAAT
53946589 ATTTTCTGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
16 6 0.06
17 6 0.06
18 17 0.17
19 18 0.18
20 26 0.26
21 18 0.18
22 10 0.10
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TATGTTTTTATAAATTTTA
Found at i:53946554 original size:38 final size:37
Alignment explanation
Indices: 53946507--53946611 Score: 88
Period size: 38 Copynumber: 2.8 Consensus size: 37
53946497 TTATAAATTT
53946507 TATAGAATTTTTATGTTTTTGATAATATTTATAAGTTTA
1 TATA-AATTTTTATGTTTTTGATAATATTTAT-AGTTTA
* * * * *
53946546 TATCAATTTTCATATATTTT--TAATATTTATATTTTT
1 TATAAATTTTTATGT-TTTTGATAATATTTATAGTTTA
* * *
53946582 TATAAATATTTTCTGTTATTGATATTATTT
1 TATAAAT-TTTTATGTTTTTGATAATATTT
53946612 TTATGGGAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
36 13 0.25
37 15 0.29
38 16 0.31
39 7 0.14
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (37 bp):
TATAAATTTTTATGTTTTTGATAATATTTATAGTTTA
Found at i:53949975 original size:93 final size:94
Alignment explanation
Indices: 53949816--53950128 Score: 517
Period size: 93 Copynumber: 3.3 Consensus size: 94
53949806 ATCAGGTATA
53949816 TTGATCT-ATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
53949880 ACACTATCGGGTATGTAATATTATCTTAT
66 ACACTATCGGGTATGTAATATTATCTTAT
53949909 TTGATCT-ATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
*
53949973 ACACTATTGGGTATGTAATATTATCTTAT
66 ACACTATCGGGTATGTAATATTATCTTAT
*
53950002 TTGAT-TCATTTAGTTGGAGGGTAAAATTTTACTATTTGATTGATGGAATGTAAGATTATTTATT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAA-A--A-TTATT
*
53950066 TAGTACACCATCGGGTATGTAATATTATCTTAT
62 TAGTACACTATCGGGTATGTAATATTATCTTAT
* *
53950099 TTG-TTTCATTTAGCTGGAGGGTAAAATTTT
1 TTGATCTCATTTAGTTGGAGGGTAAAATTTT
53950129 TGATAAAATG
Statistics
Matches: 209, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
92 1 0.00
93 142 0.68
94 1 0.00
96 2 0.01
97 63 0.30
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (94 bp):
TTGATCTCATTTAGTTGGAGGGTAAAATTTTACTGTTTGATTGATGGAATGTAAAATTATTTAGT
ACACTATCGGGTATGTAATATTATCTTAT
Found at i:53964968 original size:113 final size:112
Alignment explanation
Indices: 53964807--53965351 Score: 442
Period size: 114 Copynumber: 4.8 Consensus size: 112
53964797 AAATCTCAAG
* * *
53964807 ACCAACACGCAGCGTTCTGGTGTTGATGTATATTGGC-ATTAGTGGCGCTTACGAACAAACGCCG
1 ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-GCAATTAGTGGCGCTTATGAA-AAACGCC-
* * * *
53964871 GC-AATGTATAGTATTAGCGGCGCTTAGTGGAAGTGCTGCAAAAGATGTTA
62 GCTAAAGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATCTTA
* * * *
53964921 GCCAAAACGCAGAGTTTGGTCTTGATGTATATTTCAATTAGTGGCGCTTATAAATAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GA-AAAACGCCGC
* ** * * * *
53964986 TAATGTATAGTATTAGCGGCGCAGAGCCT-TAAACGCCGCAAGACATCTTA
64 TAAAGTATAGTATTAGCGGCGCTTAG--TGGAAGCGCCGCAAAAGATCTTA
* * ** * * * *
53965036 ATCAAAACGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGCGTTTAAGGAAAACACCAGC
1 ACCAAAACGCAGCGT-TTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCC-GC
* * * * * *
53965101 -AAAGGATAGT-TATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTA
64 TAAAGTATAGTAT-TAGCGGCGCTTAGTGG-AAGCGCCGCAAAAGATCTTA
* * *
53965150 ACCAAAACGCAGAGTTTGGTCTTGAGGTGTATTAG-AATTAGTGGCGCTTGATGAAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATT-GCAATTAGTGGCGCTT-ATGAAAAACGCCGC
*
53965214 TAAAGTATA-TCATTAGCGGCG-TTTGTGGAACGCGCCGC-AAAGTATCTTA
64 TAAAGTATAGT-ATTAGCGGCGCTTAGTGGAA-GCGCCGCAAAAG-ATCTTA
* * * * ** * *
53965263 ACCAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGGCGCAAATGGGAAAACGCCAC
1 ACCAAAACGCAGCGTTT-GGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GAAAAACGCCGC
* *
53965328 TGAAGCATAGTATTAGCGGCGCTT
64 TAAAGTATAGTATTAGCGGCGCTT
53965352 TTACCGAAAC
Statistics
Matches: 342, Mismatches: 66, Indels: 45
0.75 0.15 0.10
Matches are distributed among these distances:
112 7 0.02
113 100 0.29
114 170 0.50
115 33 0.10
116 32 0.09
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (112 bp):
ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCCGCTA
AAGTATAGTATTAGCGGCGCTTAGTGGAAGCGCCGCAAAAGATCTTA
Found at i:53965475 original size:18 final size:18
Alignment explanation
Indices: 53965454--53965489 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
53965444 TCATTTTATA
53965454 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
53965472 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
53965490 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:53965844 original size:29 final size:29
Alignment explanation
Indices: 53965811--53965867 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
53965801 AAGGGTTGTA
*
53965811 ATTTAGGGGTTATAGATTAAGAGTCAGGG
1 ATTTAAGGGTTATAGATTAAGAGTCAGGG
* * * *
53965840 ATTTAAGGTTTATGGATTCAGTGTCAGG
1 ATTTAAGGGTTATAGATTAAGAGTCAGG
53965868 TTAGGCTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.32, T:0.35
Consensus pattern (29 bp):
ATTTAAGGGTTATAGATTAAGAGTCAGGG
Found at i:53966445 original size:7 final size:7
Alignment explanation
Indices: 53966435--53966495 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
53966425 GACTTTTACT
53966435 GTTTGGG
1 GTTTGGG
**
53966442 GTTTTAAG
1 G-TTTGGG
*
53966450 GTTTAGG
1 GTTTGGG
*
53966457 GTTTAGG
1 GTTTGGG
53966464 GTTTGGG
1 GTTTGGG
53966471 GTTTGGG
1 GTTTGGG
53966478 GTTTGGG
1 GTTTGGG
*
53966485 GTTTGAG
1 GTTTGGG
53966492 GTTT
1 GTTT
53966496 AAGGTTTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 43 0.90
8 5 0.10
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:53966500 original size:7 final size:7
Alignment explanation
Indices: 53966444--53966503 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
53966434 TGTTTGGGGT
*
53966444 TTTAAGG
1 TTTAGGG
53966451 TTTAGGG
1 TTTAGGG
53966458 TTTAGGG
1 TTTAGGG
*
53966465 TTTGGGG
1 TTTAGGG
*
53966472 TTTGGGG
1 TTTAGGG
*
53966479 TTTGGGG
1 TTTAGGG
53966486 TTT-GAGG
1 TTTAG-GG
*
53966493 TTTAAGG
1 TTTAGGG
53966500 TTTA
1 TTTA
53966504 CAAATTATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
6 1 0.02
7 47 0.98
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:53967081 original size:74 final size:74
Alignment explanation
Indices: 53967003--53967230 Score: 211
Period size: 74 Copynumber: 3.1 Consensus size: 74
53966993 TGAAATGTTG
53967003 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
1 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
53967068 GAAACGGCT
66 GAAACGGCT
* * * * ** * * *
53967077 TCGTTTTGAGT-TATAG--TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGT
1 TCGTTTT-TGTCTATTGTATTAGTGGCGTTTTTC-GGAAACGCCACAACATTGGGTAA--ACTG-
*** *
53967136 TTATTGAAATGTTG-T
61 TTGGGGAAACG--GCT
53967151 T-GTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
1 TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
*
53967215 GAAACGACT
66 GAAACGGCT
53967224 TCGTTTT
1 TCGTTTT
53967231 GAGTAATAGT
Statistics
Matches: 112, Mismatches: 27, Indels: 30
0.66 0.16 0.18
Matches are distributed among these distances:
71 3 0.03
72 17 0.15
73 32 0.29
74 39 0.35
75 18 0.16
76 3 0.03
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (74 bp):
TCGTTTTTGTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGG
GAAACGGCT
Found at i:53967106 original size:147 final size:147
Alignment explanation
Indices: 53966946--53967272 Score: 591
Period size: 147 Copynumber: 2.2 Consensus size: 147
53966936 TACGTTGCTA
*
53966946 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
*
53967011 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
66 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
*
53967076 TTCGTTTTGAGTTATAG
131 TTCGTTTTGAGTAATAG
*
53967093 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
53967158 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
66 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
53967223 TTCGTTTTGAGTAATAG
131 TTCGTTTTGAGTAATAG
* * *
53967240 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATT
1 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT
53967273 GTTCAAACAT
Statistics
Matches: 173, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 173 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (147 bp):
TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
TTCGTTTTGAGTAATAG
Found at i:53967156 original size:73 final size:74
Alignment explanation
Indices: 53966945--53967176 Score: 183
Period size: 73 Copynumber: 3.1 Consensus size: 74
53966935 TTACGTTGCT
* *
53966945 ATTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTT
1 ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
* *
53967010 TGTCTATTG
66 AGTCTATAG
* * ** * * * *** *
53967019 TATTAGTGGCGTTTTTC-GGAAACGCCACAACATTGGGTAA--ACTG-TTGGGGAAACG--GCTT
1 -ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGTTTATTGAAATGTTG-TT
53967078 CGTTTTGAGT-TATAG
61 -GTTTT-AGTCTATAG
53967093 -TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
1 ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
* *
53967157 TGTCTATTG
66 AGTCTATAG
53967166 TATTAGTGGCG
1 -ATTAGTGGCG
53967177 TTTTTCGGAA
Statistics
Matches: 114, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
71 3 0.03
72 18 0.16
73 31 0.27
74 31 0.27
75 28 0.25
76 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (74 bp):
ATTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTT
AGTCTATAG
Found at i:53967263 original size:73 final size:71
Alignment explanation
Indices: 53967021--53967273 Score: 181
Period size: 73 Copynumber: 3.5 Consensus size: 71
53967011 GTCTATTGTA
* * * *
53967021 TTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGCTTCGTTTTGA
1 TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAAC-GCTTCGTTTTGA
53967086 GTTATAG
65 GTTATAG
* * * * *** * * *
53967093 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATT--TTAATTA-TGTTTATTGAAATGTTGTTGTT
1 TTAGTGGCGCTTTAC-TGAAACGCCACAAAATTGGGTAA--ACTG-TTGGGGAAACGCT-TCGTT
* *
53967155 TT-TGTCTATTG
61 TTGAGT-TATAG
* * * *
53967166 TATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGACTTCGTTTT
1 --TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACG-CTTCGTTTT
*
53967231 GAGTAATAG
63 GAGTTATAG
*
53967240 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATTG
1 TTAGTGGCGCTTTAC-TGAAACGCCACAAAATTG
53967274 TTCAAACATT
Statistics
Matches: 131, Mismatches: 36, Indels: 27
0.68 0.19 0.14
Matches are distributed among these distances:
71 3 0.02
72 32 0.24
73 45 0.34
74 30 0.23
75 18 0.14
76 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (71 bp):
TTAGTGGCGCTTTACTGAAACGCCACAAAATTGGGTAAACTGTTGGGGAAACGCTTCGTTTTGAG
TTATAG
Found at i:53967290 original size:147 final size:146
Alignment explanation
Indices: 53966946--53967326 Score: 543
Period size: 147 Copynumber: 2.6 Consensus size: 146
53966936 TACGTTGCTA
* * **
53966946 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAATGTTGTCGTTTTT
*
53967011 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
*
53967076 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTAATAG
* ** *
53967093 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAATGTTGTCGTTTTT
53967158 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
65 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
53967223 TTCGTTTTGAGTAATAG
130 TTCGTTTTGAGTAATAG
* * * * *
53967240 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATTGTTCAA-ACATTTGTTGAAACGTTGCCG-TTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATT-TT-AATACATTTATTGAAATGTTGTCGTTTT
* *
53967303 TGT-AAATGTTATTAGTGGCGTTTT
64 TGTCTATTG-TATTAGTGGCGTTTT
53967327 ACCGAAAATG
Statistics
Matches: 216, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
145 3 0.01
146 21 0.10
147 188 0.87
148 2 0.01
149 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (146 bp):
TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAATACATTTATTGAAATGTTGTCGTTTTTG
TCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGACT
TCGTTTTGAGTAATAG
Found at i:53967359 original size:147 final size:146
Alignment explanation
Indices: 53966946--53967398 Score: 482
Period size: 147 Copynumber: 3.1 Consensus size: 146
53966936 TACGTTGCTA
* * ** * *
53966946 TTAGTGGCGCTTTCCATAAAACGCCGTAAAATTTTAATTATGTTTATTGAAATGTTGTCGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAACGTTGCCGTTTTT
** * * *
53967011 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGGC
65 GTAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
53967076 TTCGTTTTGAGTTATAG
130 TTCGTTTTGAGTTATAG
* ** * **
53967093 TTAGTGGCGCTTTCCATAAAACGCCGCAAAATTTTAATTATGTTTATTGAAATGTTGTTGTTTTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAA-TACATTTATTGAAACGTTGCCGTTTTT
** * *
53967158 GTCTATTGTATTAGTGGCGTTTTTCGGAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
65 GTAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGAC
*
53967223 TTCGTTTTGAGTAATAG
130 TTCGTTTTGAGTTATAG
* * *
53967240 TTAGTGGCGCTTTACTTGAAACGCCGCAAAATTGTTCAA-ACATTTGTTGAAACGTTGCCG-TTT
1 TTAGTGGCGCTTTACATAAAACGCCGCAAAATT-TT-AATACATTTATTGAAACGTTGCCGTTTT
* ***** * ** *
53967303 TGTAAA-TGTTATTAGTGGCGTTTTACCGAAAATGCCATGGGTTTGAGGT-AAGTGTTGATGAAG
64 TGTAAATTG-TATTAGTGGCGTTTT-CCGAAAACGCCACAACATTG-GGTAAACTGTTGGGGAAA
**
53967366 CGACCGCGTTTTGAGTTATAG
126 CGACTTCGTTTTGAGTTATAG
53967387 TTAGTGGCGCTT
1 TTAGTGGCGCTT
53967399 AGTTTAAAAC
Statistics
Matches: 271, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
145 2 0.01
146 22 0.08
147 240 0.89
148 5 0.02
149 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (146 bp):
TTAGTGGCGCTTTACATAAAACGCCGCAAAATTTTAATACATTTATTGAAACGTTGCCGTTTTTG
TAAATTGTATTAGTGGCGTTTTCCGAAAACGCCACAACATTGGGTAAACTGTTGGGGAAACGACT
TCGTTTTGAGTTATAG
Found at i:53968835 original size:10 final size:10
Alignment explanation
Indices: 53968820--53968856 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
53968810 GTTATGGGTA
53968820 AATTTTAAAT
1 AATTTTAAAT
53968830 AATTTTAAAT
1 AATTTTAAAT
**
53968840 AATTTTATTT
1 AATTTTAAAT
53968850 AATTTTA
1 AATTTTA
53968857 TAATTATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AATTTTAAAT
Found at i:53968893 original size:17 final size:17
Alignment explanation
Indices: 53968871--53968903 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53968861 TATTCGAATA
53968871 TATATTCATAATTATAC
1 TATATTCATAATTATAC
*
53968888 TATATTTATAATTATA
1 TATATTCATAATTATA
53968904 GATTTGCAAT
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:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATTCATAATTATAC
Found at i:53968923 original size:16 final size:16
Alignment explanation
Indices: 53968899--53968934 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53968889 ATATTTATAA
*
53968899 TTATAGATTTGCAATT
1 TTATAGATTTACAATT
*
53968915 TTATCGATTTACAATT
1 TTATAGATTTACAATT
53968931 TTAT
1 TTAT
53968935 TTCAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATAGATTTACAATT
Found at i:53969339 original size:13 final size:13
Alignment explanation
Indices: 53969323--53969381 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
53969313 TTACTAAAAT
*
53969323 TTACTTTAATATA
1 TTACTTAAATATA
*
53969336 TTACTTGAATATA
1 TTACTTAAATATA
53969349 TTACTTAAATA-A
1 TTACTTAAATATA
*
53969361 TTTACTTAAATACA
1 -TTACTTAAATATA
53969375 TTACTTA
1 TTACTTA
53969382 CTAAAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.95
14 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:53969650 original size:16 final size:16
Alignment explanation
Indices: 53969629--53969953 Score: 90
Period size: 16 Copynumber: 19.8 Consensus size: 16
53969619 ACACTTATTA
53969629 AACTTACATAATACAT
1 AACTTACATAATACAT
*
53969645 AACTTACAT-GT---T
1 AACTTACATAATACAT
53969657 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
53969673 GACTTATATAAAATTCTCAAAT
1 AACTTACAT--AA---T-ACAT
53969695 AAACTTACATAATACAT
1 -AACTTACATAATACAT
* *
53969712 TAGTTACATAATAACTTATAT
1 AACTTACATAAT-AC----AT
53969733 AAACTTACATAATACA-
1 -AACTTACATAATACAT
*
53969749 CA-TTAC-T--TACAT
1 AACTTACATAATACAT
* * *
53969761 AGCATACATAACTTACAC
1 AACTTACATAA--TACAT
* *
53969779 AACTTAAATAATACAA
1 AACTTACATAATACAT
53969795 AACTTACATAACCTACAT
1 AACTTACATAA--TACAT
*
53969813 AACCTACATAATACAT
1 AACTTACATAATACAT
*
53969829 AA-TAAC-T--TAC--
1 AACTTACATAATACAT
53969839 AACTTACATAACATACAT
1 AACTTACAT-A-ATACAT
* **
53969857 TACTTTGATAACTCACAT
1 AACTTACATAA-T-ACAT
53969875 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
53969891 AACTTAAATAGCTTACTT
1 AACTTACATA--ATACAT
53969909 AA--TACATAACTTACAT
1 AACTTACATAA--TACAT
* * *
53969925 AACTTATACACGTACAT
1 AACTTACATA-ATACAT
53969942 AACTTACATAAT
1 AACTTACATAAT
53969954 TGACTTAATA
Statistics
Matches: 221, Mismatches: 45, Indels: 86
0.63 0.13 0.24
Matches are distributed among these distances:
10 2 0.01
11 7 0.03
12 14 0.06
13 5 0.02
14 6 0.03
15 4 0.02
16 77 0.35
17 22 0.10
18 57 0.26
21 7 0.03
22 13 0.06
23 7 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:53969734 original size:9 final size:9
Alignment explanation
Indices: 53969722--53969952 Score: 153
Period size: 9 Copynumber: 26.4 Consensus size: 9
53969712 TAGTTACATA
*
53969722 ATAACTTAT
1 ATAACTTAC
53969731 ATAAACTTAC
1 AT-AACTTAC
*
53969741 ATAA-TACAC
1 ATAACT-TAC
*
53969750 ATTACTTAC
1 ATAACTTAC
* *
53969759 ATAGCATAC
1 ATAACTTAC
53969768 ATAACTTAC
1 ATAACTTAC
* *
53969777 ACAACTTAA
1 ATAACTTAC
53969786 ATAA--TAC
1 ATAACTTAC
*
53969793 AAAACTTAC
1 ATAACTTAC
*
53969802 ATAACCTAC
1 ATAACTTAC
*
53969811 ATAACCTAC
1 ATAACTTAC
*
53969820 ATAATACATA-
1 AT-A-ACTTAC
53969830 ATAACTTAC
1 ATAACTTAC
53969839 --AACTTAC
1 ATAACTTAC
*
53969846 ATAACATAC
1 ATAACTTAC
* **
53969855 ATTACTTTG
1 ATAACTTAC
*
53969864 ATAACTCAC
1 ATAACTTAC
53969873 ATAACTTAC
1 ATAACTTAC
53969882 ATAA--TAC
1 ATAACTTAC
*
53969889 ATAACTTAA
1 ATAACTTAC
*
53969898 ATAGCTTAC
1 ATAACTTAC
*
53969907 TTAA--TAC
1 ATAACTTAC
53969914 ATAACTTAC
1 ATAACTTAC
53969923 ATAACTT--
1 ATAACTTAC
*
53969930 ATACACGTAC
1 ATA-ACTTAC
53969940 ATAACTTAC
1 ATAACTTAC
53969949 ATAA
1 ATAA
53969953 TTGACTTAAT
Statistics
Matches: 169, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
7 28 0.17
8 8 0.05
9 114 0.67
10 15 0.09
11 4 0.02
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:53969744 original size:38 final size:38
Alignment explanation
Indices: 53969657--53969748 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 38
53969647 CTTACATGTT
*
53969657 AACTTACATAATACATGACTTATATAAAATTCTCAAATA
1 AACTTACATAATACATGACTTACATAAAA-TCTCAAATA
* * * *
53969696 AACTTACATAATACATTAGTTACATAATAA-CTTATATA
1 AACTTACATAATACATGACTTACATAA-AATCTCAAATA
53969734 AACTTACATAATACA
1 AACTTACATAATACA
53969749 CATTACTTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 21 0.45
39 24 0.51
40 2 0.04
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (38 bp):
AACTTACATAATACATGACTTACATAAAATCTCAAATA
Found at i:53969812 original size:43 final size:45
Alignment explanation
Indices: 53969734--53969856 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 45
53969724 AACTTATATA
* * * *
53969734 AACTTACATAATACACATTACTTACATAGCATACATAACTTACAC
1 AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
* *
53969779 AACTTAAATAATACA-A-AACTTACATAACCTACATAACCTACAT
1 AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
* *
53969822 AA--TACATAATA-ACTTACAACTTACATAACATACAT
1 AACTTAAATAATACAC--ATAACTTACATAACATACAT
53969857 TACTTTGATA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
40 1 0.02
41 8 0.12
43 25 0.38
44 18 0.27
45 14 0.21
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.28
Consensus pattern (45 bp):
AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
Found at i:53969814 original size:25 final size:25
Alignment explanation
Indices: 53969764--53969814 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53969754 CTTACATAGC
* *
53969764 ATACATAACTTACACAACTTAAATA
1 ATACAAAACTTACACAACCTAAATA
* *
53969789 ATACAAAACTTACATAACCTACATA
1 ATACAAAACTTACACAACCTAAATA
53969814 A
1 A
53969815 CCTACATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (25 bp):
ATACAAAACTTACACAACCTAAATA
Found at i:53969905 original size:25 final size:25
Alignment explanation
Indices: 53969864--53969968 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
53969854 CATTACTTTG
* *
53969864 ATAACTCACATAACTTACATAATAC
1 ATAACTTAAATAACTTACATAATAC
* *
53969889 ATAACTTAAATAGCTTACTTAATAC
1 ATAACTTAAATAACTTACATAATAC
* * * *
53969914 ATAACTTACATAACTTATACACGTAC
1 ATAACTTAAATAACTTACATA-ATAC
* *
53969940 ATAACTTACATAA-TTGACTTAATAC
1 ATAACTTAAATAACTT-ACATAATAC
53969965 ATAA
1 ATAA
53969969 ATATATATCA
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
25 46 0.72
26 18 0.28
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAACTTAAATAACTTACATAATAC
Found at i:53969960 original size:51 final size:50
Alignment explanation
Indices: 53969864--53969968 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 50
53969854 CATTACTTTG
* *
53969864 ATAACTCACATAACTTACATAATACATAACTTAAATAGCTTACTTAATAC
1 ATAACTCACATAACTTACACAATACATAACTTAAATAGATTACTTAATAC
* * * *
53969914 ATAACTTACATAACTTATACACGTACATAACTTACATA-ATTGACTTAATAC
1 ATAACTCACATAACTTACACA-ATACATAACTTAAATAGATT-ACTTAATAC
53969965 ATAA
1 ATAA
53969969 ATATATATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 20 0.43
51 27 0.57
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (50 bp):
ATAACTCACATAACTTACACAATACATAACTTAAATAGATTACTTAATAC
Found at i:53974229 original size:7 final size:7
Alignment explanation
Indices: 53974212--53974244 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
53974202 AGAGAAAGAA
53974212 AAAAAAT
1 AAAAAAT
53974219 -AAAAAT
1 AAAAAAT
53974225 AAAAAAT
1 AAAAAAT
53974232 AAAAAAT
1 AAAAAAT
53974239 AAAAAA
1 AAAAAA
53974245 ACGAATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:53974230 original size:14 final size:15
Alignment explanation
Indices: 53974211--53974245 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
53974201 CAGAGAAAGA
53974211 AAAAAAAT-AAAAAT
1 AAAAAAATAAAAAAT
53974225 -AAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
53974239 AAAAAAA
1 AAAAAAA
53974246 CGAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:53978421 original size:21 final size:21
Alignment explanation
Indices: 53978395--53978444 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
53978385 CTACAACTTA
*
53978395 AAGCAGAGGCGGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* * *
53978416 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
53978437 AAGCAGAG
1 AAGCAGAG
53978445 CAGGCCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:53978836 original size:42 final size:41
Alignment explanation
Indices: 53978726--53978841 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 41
53978716 GTTTTTGTAT
* * * *
53978726 AAAAGCGCCGCTAAAGAACATGTTCTTTAGTGGGGTTTAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAA
* *****
53978767 AAAAACGCCACTATTTTTCATGTTCTTTAGCGGCGCTTAAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAA-A
* *
53978809 ATAAACGCCGCTAAAGAACATGATCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGG
53978842 TGTTTTTTTC
Statistics
Matches: 56, Mismatches: 18, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
41 30 0.54
42 26 0.46
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAA
Found at i:53978861 original size:42 final size:42
Alignment explanation
Indices: 53978814--53978911 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
53978804 TAAGAATAAA
*
53978814 CGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * *
53978856 TGCCGCTAAAGTACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
53978898 CGCCGCTAAAGAAC
1 CGCCGCTAAAGAAC
53978912 TCAAAGCGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:53979871 original size:14 final size:15
Alignment explanation
Indices: 53979832--53979873 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53979822 TTTTAACATA
*
53979832 ATTATTATTAAATAT
1 ATTATAATTAAATAT
53979847 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53979861 A-TATAATTTAATA
1 ATTATAATTAAATA
53979874 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53979984 original size:18 final size:17
Alignment explanation
Indices: 53979963--53979997 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53979953 TTATTATTAA
*
53979963 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53979981 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53979998 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53980036 original size:120 final size:120
Alignment explanation
Indices: 53979829--53980236 Score: 723
Period size: 120 Copynumber: 3.4 Consensus size: 120
53979819 ATATTTTAAC
*
53979829 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
53979894 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT-AA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
53979948 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
53980013 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
53980069 ATAATTATTATTAAATAAAATTTAATTAAAATATATGATTTAATAAAATTTTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
53980134 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
53980189 ATAATTATTATTAAATATATTTTAATT-AAA-ATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
53980237 TAAAATAATT
Statistics
Matches: 279, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
118 18 0.06
119 3 0.01
120 256 0.92
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:53980204 original size:26 final size:26
Alignment explanation
Indices: 53980175--53980317 Score: 86
Period size: 26 Copynumber: 5.7 Consensus size: 26
53980165 TGATACTATA
*
53980175 AAATATAATTTGAAATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
* *
53980201 AAATATATTTTAATTAA-AA-TATGATT
1 AAATATAATTTAA--AATAATTATTATT
* * *
53980227 TAATAAAATTTAAAATAATTATTACT
1 AAATATAATTTAAAATAATTATTATT
** * *
53980253 -AATA-AATTT--TCTTA-TATGAATT
1 AAATATAATTTAAAATAATTAT-TATT
**
53980275 -TGTATAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
53980300 AAATATAATTTAATAATA
1 AAATATAATTTAA-AATA
53980318 TATAATTTCA
Statistics
Matches: 85, Mismatches: 21, Indels: 21
0.67 0.17 0.17
Matches are distributed among these distances:
21 3 0.04
22 6 0.07
23 5 0.06
24 7 0.08
25 11 0.13
26 45 0.53
27 6 0.07
28 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (26 bp):
AAATATAATTTAAAATAATTATTATT
Found at i:53980320 original size:15 final size:15
Alignment explanation
Indices: 53980277--53980330 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
53980267 TATGAATTTG
53980277 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
53980291 -ATTA-TTATTAA-A
1 TATAATTTAATAATA
53980303 TATAATTTAATAATA
1 TATAATTTAATAATA
*
53980318 TATAATTTCATAA
1 TATAATTTAATAA
53980331 AATTCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 6 0.19
15 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:53980363 original size:71 final size:73
Alignment explanation
Indices: 53980282--53980417 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 73
53980272 ATTTGTATAA
*
53980282 TTTAAAATAATTATTATTAAATATAATTTAAT-A-ATATATAATTTCATAAAATTCTTGATAATA
1 TTTAAAATAATTAATATTAAATATAATTTAATAAGATATATAATTTCATAAAATTCTTGATAATA
53980345 AATTTTCT
66 AATTTTCT
*
53980353 TTTAGAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAAT
1 TTTAAAATAATTAATATTAAATATAATTTAATAA-GATATATAATTTCATAAAATTCTTGATAAT
53980418 TTAATCATGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
71 30 0.50
72 1 0.02
74 29 0.48
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (73 bp):
TTTAAAATAATTAATATTAAATATAATTTAATAAGATATATAATTTCATAAAATTCTTGATAATA
AATTTTCT
Found at i:53987563 original size:6 final size:6
Alignment explanation
Indices: 53987540--53987575 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
53987530 ATATACATAG
* *
53987540 TCAGAT TTAGAA TCAGAT TCAGAT TCAGAT TCAGAT
1 TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT
53987576 AACAGAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (6 bp):
TCAGAT
Found at i:53988109 original size:32 final size:32
Alignment explanation
Indices: 53988034--53988115 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
53988024 GGGCCCAGAT
* * *
53988034 ACCCGTGTGGCCCATACACCCAGATTGGCCTT
1 ACCCGTGTGGCCCACACGCCCAGATTGGCCTA
* * *
53988066 ACCCATATGGCCCACACGCCCAGTTTGGCC-A
1 ACCCGTGTGGCCCACACGCCCAGATTGGCCTA
53988097 AGCCCGTGTGGCCCACACG
1 A-CCCGTGTGGCCCACACG
53988116 TCCACACCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 1 0.02
32 40 0.98
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.17
Consensus pattern (32 bp):
ACCCGTGTGGCCCACACGCCCAGATTGGCCTA
Found at i:53989164 original size:29 final size:32
Alignment explanation
Indices: 53989131--53989189 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
53989121 TGCATCTTGT
53989131 AAAAA-TTGAAAAA-ATA-AAATAAAAAAAGA
1 AAAAATTTGAAAAATATATAAATAAAAAAAGA
* *
53989160 AAAAATTTTAAAAATATATAACTAAAAAAA
1 AAAAATTTGAAAAATATATAAATAAAAAAA
53989190 TTAATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 7 0.28
31 3 0.12
32 10 0.40
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (32 bp):
AAAAATTTGAAAAATATATAAATAAAAAAAGA
Found at i:53995314 original size:46 final size:46
Alignment explanation
Indices: 53995242--53995352 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 46
53995232 GTAAAAGTAT
* *
53995242 ATTT-ATAATATTTT-ATAAATATCGTAAATAACAGATA-TCAACTTG
1 ATTTAATAAT-TTTTAATGAATATCGTAAAAAACAGATACT-AACTTG
* *
53995287 ATTTAATACTTTTTAATGAATATCGTAAAAAACAGATACTAGCTTG
1 ATTTAATAATTTTTAATGAATATCGTAAAAAACAGATACTAACTTG
53995333 ATTTAATAATTTTTAATGAA
1 ATTTAATAATTTTTAATGAA
53995353 AATATTAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
45 8 0.14
46 49 0.84
47 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (46 bp):
ATTTAATAATTTTTAATGAATATCGTAAAAAACAGATACTAACTTG
Found at i:53999183 original size:115 final size:115
Alignment explanation
Indices: 53998979--53999311 Score: 377
Period size: 115 Copynumber: 2.9 Consensus size: 115
53998969 ACGGATAGTG
* *
53998979 AAAGCGCCGCAAAATAT-TTGAACCAAAACGCATCGTTTTGGTATTGATGTATACTAGAATTAGT
1 AAAGCGCCGCAAAATATCTT-AACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
* * *
53999043 GGCGTTTACGGTAAAACGCCGCTAAACCATAGTATTAGCAGCGATT-CTTTG-
65 GGCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGCAGCCATTAC--TGA
** * * *
53999094 CTAGCGCCGCAAAATATCCTAACTAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTAGTG
1 AAAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTG
* ** * *
53999159 GCGCTTACGGGAAACCGCCGCTAAAGAATAGTATTAGCGGCCCTTACTGA
66 GCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGCAGCCATTACTGA
* * ***
53999209 AAAGCGCCACAAAATATCTTAACCT-AAACGCATAGTTTTAACCTTGATGTATACTAGAATTAGT
1 AAAGCGCCGCAAAATATCTTAA-CTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
** ** *
53999273 GGCGCTTACTAGAAAACGCCATTAAATCATAGTATTAGC
65 GGCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGC
53999312 GGCGCTTTTT
Statistics
Matches: 182, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
114 2 0.01
115 176 0.97
116 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (115 bp):
AAAGCGCCGCAAAATATCTTAACTAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTG
GCGCTTACGGGAAAACGCCGCTAAACCATAGTATTAGCAGCCATTACTGA
Found at i:53999575 original size:84 final size:84
Alignment explanation
Indices: 53999414--53999576 Score: 231
Period size: 84 Copynumber: 1.9 Consensus size: 84
53999404 GGTGAAGCGC
* * **
53999414 CGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTTA
1 CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTA
*
53999479 CGTTGAAACGCCGCCAAAA
66 CGGTGAAACGCCGCCAAAA
*
53999498 CGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCGT-GATGTATACTAAAATTAGTGGCGCTT
1 CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTC-TCGATGTATACTAAAATTAGTGGCGCTT
*
53999562 AGGGT-AAACCGCCGC
65 ACGGTGAAA-CGCCGC
53999577 GAAAGCATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 3 0.04
84 66 0.94
85 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (84 bp):
CGCAAAATACCTGAACCAAAACGCAGCGTTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTA
CGGTGAAACGCCGCCAAAA
Found at i:54000657 original size:114 final size:115
Alignment explanation
Indices: 54000397--54000717 Score: 314
Period size: 114 Copynumber: 2.8 Consensus size: 115
54000387 AGCAAAACAG
* * * *
54000397 TGTCG-TTTTGTCTGAT-TTTTTAGTGGCGTTT-TGACTAAAACGCCGCAAAAGGAGT-TATATT
1 TGTCGTTTTTATCT-ATGTTTTTAGTGGCGTTTGT-ACCAAAACACCGCAAAAGGA-TATGTATT
** * * * * ** *
54000458 AGTGGCGTTTTACAAAAAAACGCCACAATT-TTGTTTTTAGTC-ACTGTTAAGCGT
63 AGTGGCGTTTTA-TTATAAACGCCGCAATTATT-TTATTAGGCTTTTG-TAAACGT
* * * * * *
54000512 TGTCGTTTTTATGTATGTTTTTAGTGGCGTTTTTACTAAACCACCGCAAAATGATTTGTATTAGT
1 TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGT
* *
54000577 GGCGTTTTTTTGT-AACGCCGCAATTATTTTATTAGGCTTTTGTAAACGT
66 GGCGTTTTATTATAAACGCCGCAATTATTTTATTAGGCTTTTGTAAACGT
* ** *
54000626 TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACGCCGGTAAAGGATATGTTTTAGT
1 TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGT
54000691 GGCGTTTTATTATAAACGCCGCAATTA
66 GGCGTTTTATTATAAACGCCGCAATTA
54000718 AGTTTTAAGT
Statistics
Matches: 170, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
114 90 0.53
115 25 0.15
116 54 0.32
117 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (115 bp):
TGTCGTTTTTATCTATGTTTTTAGTGGCGTTTGTACCAAAACACCGCAAAAGGATATGTATTAGT
GGCGTTTTATTATAAACGCCGCAATTATTTTATTAGGCTTTTGTAAACGT
Found at i:54000952 original size:40 final size:40
Alignment explanation
Indices: 54000897--54000973 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
54000887 TCCCTAATTT
* *
54000897 CCCATTTCCTATTCCCCCAACTTCCCCGATTTCATTTTCC
1 CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTTCC
* *
54000937 CCCAATTCCTTTTCCCCCAATTTCCCCGATTTAATTT
1 CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTT
54000974 CCCTAAATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.17, C:0.42, G:0.03, T:0.39
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAACTTCCCCGATTTAATTTTCC
Found at i:54000961 original size:16 final size:16
Alignment explanation
Indices: 54000920--54000961 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
54000910 CCCCCAACTT
* *
54000920 CCCCGATTTCATTTTC
1 CCCCAATTTCCTTTTC
54000936 CCCCAA-TTCCTTTTC
1 CCCCAATTTCCTTTTC
54000951 CCCCAATTTCC
1 CCCCAATTTCC
54000962 CCGATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.14, C:0.45, G:0.02, T:0.38
Consensus pattern (16 bp):
CCCCAATTTCCTTTTC
Found at i:54002473 original size:15 final size:15
Alignment explanation
Indices: 54002453--54002485 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
54002443 AAGTTTTCTA
54002453 TATTAGTATTAAATT
1 TATTAGTATTAAATT
54002468 TATTAGTATTAAATT
1 TATTAGTATTAAATT
54002483 TAT
1 TAT
54002486 AAGTTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTAGTATTAAATT
Found at i:54002482 original size:43 final size:45
Alignment explanation
Indices: 54002434--54002545 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
54002424 ATAAGTTTTC
* *
54002434 TAAATTTATAAGTTTTCTATATTAGT-AT-TAAATTTATTAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGATCTAAATTTATTAGTAT
*
54002477 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTATTAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGATCTAAATTTATTAGTAT
* *
54002522 TAATTTTTTAAGTTTTCTAAATAA
1 TAAATTTATAAGTTTTCTAAATAA
54002546 TTATATCACC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 24 0.39
44 1 0.02
45 37 0.60
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (45 bp):
TAAATTTATAAGTTTTCTAAATAAGTGATCTAAATTTATTAGTAT
Found at i:54002673 original size:17 final size:17
Alignment explanation
Indices: 54002653--54002736 Score: 122
Period size: 17 Copynumber: 5.2 Consensus size: 17
54002643 TTAATATCTA
54002653 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
*
54002670 TATAAGTGTTCTAAATT
1 TATAAGTTTTCTAAATT
54002687 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
54002704 TATAAGTTTTCT--A--
1 TATAAGTTTTCTAAATT
*
54002717 TATAAGTGTTCTAAATT
1 TATAAGTTTTCTAAATT
54002734 TAT
1 TAT
54002737 TAGTAATAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
13 11 0.18
15 2 0.03
17 47 0.78
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:54002832 original size:24 final size:26
Alignment explanation
Indices: 54002805--54002860 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
54002795 TTATATATCT
* *
54002805 TACATAATACATAAC-TACATAA-CA
1 TACATAATACAGAACTTACATAATAA
54002829 TACATAATACAGAACTTACATAATAA
1 TACATAATACAGAACTTACATAATAA
54002855 TACATA
1 TACATA
54002861 CCGTACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.50
25 7 0.25
26 7 0.25
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.27
Consensus pattern (26 bp):
TACATAATACAGAACTTACATAATAA
Found at i:54002834 original size:9 final size:9
Alignment explanation
Indices: 54002789--54003083 Score: 205
Period size: 9 Copynumber: 34.4 Consensus size: 9
54002779 ATAATTATAT
*
54002789 ATAAGCTTAT
1 ATAA-CTTAC
*
54002799 ATATCTTAC
1 ATAACTTAC
54002808 ATAA--TAC
1 ATAACTTAC
54002815 ATAAC-TAC
1 ATAACTTAC
*
54002823 ATAACATAC
1 ATAACTTAC
54002832 ATAA--TAC
1 ATAACTTAC
*
54002839 AGAACTTAC
1 ATAACTTAC
54002848 ATAA-TAATAC
1 ATAACT--TAC
* *
54002858 ATACCGTAC
1 ATAACTTAC
* *
54002867 ATAAATTAA
1 ATAACTTAC
*
54002876 ATAAGTTAC
1 ATAACTTAC
54002885 ATAA--TAC
1 ATAACTTAC
* **
54002892 ACAA-AAAC
1 ATAACTTAC
*
54002900 AAAAACTTAC
1 -ATAACTTAC
54002910 ATAACTTAC
1 ATAACTTAC
54002919 ATAA--TAC
1 ATAACTTAC
* *
54002926 ACAACTGAC
1 ATAACTTAC
54002935 ATAACTTAC
1 ATAACTTAC
54002944 ATAA--TAC
1 ATAACTTAC
*
54002951 ACAACTTAC
1 ATAACTTAC
54002960 ATAACTTAC
1 ATAACTTAC
54002969 ATAA--TAC
1 ATAACTTAC
*
54002976 ATAATTTAC
1 ATAACTTAC
54002985 ATAACTTAC
1 ATAACTTAC
*
54002994 ATAA--GAC
1 ATAACTTAC
54003001 ATAACTTAC
1 ATAACTTAC
* *
54003010 ATAAGTTTC
1 ATAACTTAC
54003019 ATAA--TAC
1 ATAACTTAC
*
54003026 ACAACTTAC
1 ATAACTTAC
*
54003035 ACAACTTAC
1 ATAACTTAC
54003044 ATAACTTAC
1 ATAACTTAC
* *
54003053 ACAACTTAT
1 ATAACTTAC
54003062 ATAACTTAC
1 ATAACTTAC
54003071 ATAACTTAC
1 ATAACTTAC
54003080 ATAA
1 ATAA
54003084 TAAATAACTT
Statistics
Matches: 228, Mismatches: 37, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
7 49 0.21
8 11 0.05
9 157 0.69
10 11 0.05
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (9 bp):
ATAACTTAC
Found at i:54002848 original size:16 final size:16
Alignment explanation
Indices: 54002811--54002853 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
54002801 ATCTTACATA
*
54002811 ATACATAACTACATAAC
1 ATACATAA-TACAGAAC
54002828 ATACATAATACAGAAC
1 ATACATAATACAGAAC
*
54002844 TTACATAATA
1 ATACATAATA
54002854 ATACATACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.26
Consensus pattern (16 bp):
ATACATAATACAGAAC
Found at i:54002867 original size:19 final size:19
Alignment explanation
Indices: 54002826--54002870 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
54002816 TAACTACATA
*
54002826 ACATACATAATACAGAACTT
1 ACATA-ATAATACAGAACGT
* *
54002846 ACATAATAATACATACCGT
1 ACATAATAATACAGAACGT
54002865 ACATAA
1 ACATAA
54002871 ATTAAATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.24
Consensus pattern (19 bp):
ACATAATAATACAGAACGT
Found at i:54002931 original size:16 final size:17
Alignment explanation
Indices: 54002903--54003094 Score: 150
Period size: 16 Copynumber: 11.4 Consensus size: 17
54002893 CAAAAACAAA
54002903 AACTTACATAACTTACAT
1 AACTTACATAAC-TACAT
*
54002921 AA--TACACAACTGACAT
1 AACTTACATAACT-ACAT
*
54002937 AACTTACATAA-TACAC
1 AACTTACATAACTACAT
54002953 AACTTACATAACTTACAT
1 AACTTACATAAC-TACAT
*
54002971 AA--TACATAATTTACAT
1 AACTTACATAA-CTACAT
*
54002987 AACTTACATAA-GACAT
1 AACTTACATAACTACAT
* *
54003003 AACTTACATAAGTTTCAT
1 AACTTACATAA-CTACAT
* *
54003021 AA--TACACAACTTACAC
1 AACTTACATAAC-TACAT
*
54003037 AACTTACATAACTTACAC
1 AACTTACATAAC-TACAT
*
54003055 AACTTATATAACTTACAT
1 AACTTACATAAC-TACAT
*
54003073 AACTTACATAA-TAAAT
1 AACTTACATAACTACAT
54003089 AACTTA
1 AACTTA
54003095 TTCCTAAATC
Statistics
Matches: 144, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.01
16 77 0.53
17 1 0.01
18 65 0.45
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (17 bp):
AACTTACATAACTACAT
Found at i:54002931 original size:25 final size:25
Alignment explanation
Indices: 54002903--54003074 Score: 245
Period size: 25 Copynumber: 6.8 Consensus size: 25
54002893 CAAAAACAAA
54002903 AACTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
54002928 AACTGACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
54002953 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAC
* * *
54002978 AATTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAC
* *
54003003 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAC
*
54003028 AACTTACACAACTTACATAACTTACAC
1 AACTTACATAACTTACATAA--TACAC
*
54003055 AACTTATATAACTTACATAA
1 AACTTACATAACTTACATAA
54003075 CTTACATAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
25 107 0.82
27 23 0.18
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:54004981 original size:21 final size:21
Alignment explanation
Indices: 54004914--54004982 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
54004904 CAACTTAAAA
* * *
54004914 CAGAGGCAGCAACGAGGGAAG
1 CAGAGGCTGCAGCGAGAGAAG
*
54004935 CAGAAGCTGCAGCGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
54004956 CAGAGGCCT-CAGCGAGAGAAG
1 CAGAGG-CTGCAGCGAGAGAAG
54004977 CAGAGG
1 CAGAGG
54004983 TTCAAAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 40 0.95
22 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.41, T:0.03
Consensus pattern (21 bp):
CAGAGGCTGCAGCGAGAGAAG
Found at i:54005403 original size:43 final size:43
Alignment explanation
Indices: 54005355--54005455 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
54005345 ATCCCAAAAT
*
54005355 TAGTGGCGTTTTTTAAAAAAGCGCCGCTAAA-AGTCA-TATCATA
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCGAAAGAG-CACTA-CATA
* * * * *
54005398 TAGTGGCGTTTGTGAAATAAGCGCCGCGAAAGAGCACTACTTT
1 TAGTGGCGTTTTTTAAAAAAGCGCCGCGAAAGAGCACTACATA
54005441 TAGTGGCGTTTTTTA
1 TAGTGGCGTTTTTTA
54005456 CCAAGTGCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 44 0.92
44 4 0.08
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
TAGTGGCGTTTTTTAAAAAAGCGCCGCGAAAGAGCACTACATA
Found at i:54005508 original size:42 final size:42
Alignment explanation
Indices: 54005415--54005643 Score: 183
Period size: 43 Copynumber: 5.4 Consensus size: 42
54005405 GTTTGTGAAA
* * * * *
54005415 TAAGCGCCGCGAAAGAGCACTACTTTTAGTGGCGTTTTTTAC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
* * *
54005457 CAAGTGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
* * * * * * * *
54005499 TAAACGCCGCTAAAGATCATGT-TTCTTTAACTGTGTTTTCTCC
1 TAAGCGCCGCTAAAGAACAT-TACT-TTTAGCGGCGTTTTTTTC
* * * *
54005542 CAAGCGCCGCTAAAGAACATGA-TCATTAGCAGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTTC
* *
54005584 TTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTC
1 -TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
*
54005627 TGTAAGCGCCGCAAAAG
1 --TAAGCGCCGCTAAAG
54005644 TTAGCGACAT
Statistics
Matches: 146, Mismatches: 35, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
42 64 0.44
43 68 0.47
44 14 0.10
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTTC
Found at i:54005537 original size:85 final size:86
Alignment explanation
Indices: 54005448--54005605 Score: 212
Period size: 85 Copynumber: 1.8 Consensus size: 86
54005438 TTTTAGTGGC
* * * * * *
54005448 GTTTTTTACCAAGTGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTTTTC-TAAACGCCGCTA
1 GTTTTCTACCAAGCGCCGCTAAAGAACATGATC-ATTAGCAGCGTTTTTTTCTTAAACGCCGCTA
*
54005511 AAGATCATGTTTCTTTAACTGT
65 AAGAACATGTTTCTTTAACTGT
* *
54005533 GTTTTCTCCCAAGCGCCGCTAAAGAACATGATCATTAGCAGCGTTTTTTTCTTAAGCGCCGCTAA
1 GTTTTCTACCAAGCGCCGCTAAAGAACATGATCATTAGCAGCGTTTTTTTCTTAAACGCCGCTAA
54005598 AGAACATG
66 AGAACATG
54005606 ACCTTTAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 42 0.68
86 20 0.32
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (86 bp):
GTTTTCTACCAAGCGCCGCTAAAGAACATGATCATTAGCAGCGTTTTTTTCTTAAACGCCGCTAA
AGAACATGTTTCTTTAACTGT
Found at i:54005622 original size:85 final size:84
Alignment explanation
Indices: 54005415--54005622 Score: 204
Period size: 85 Copynumber: 2.5 Consensus size: 84
54005405 GTTTGTGAAA
* * * * * * * *
54005415 TAAGCGCCGCGAAAGAGCACT-ACTTTTAGTGGCGTTTTTTACCAAGTGCCGCTATAGAACATTA
1 TAAGCGCCGCTAAAGAACA-TGACCTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGA
* *
54005479 CTTTTAGCGGCGTTTTTTTC
65 CTATTAGCAGCGTTTTTTTC
* * ** * * * *
54005499 TAAACGCCGCTAAAGATCATGTTTCTTTAACTGTGTTTTCTCCCAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATG-ACCTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGA
54005564 -TCATTAGCAGCGTTTTTTTC
65 CT-ATTAGCAGCGTTTTTTTC
54005584 TTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT
1 -TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT
54005623 TTTCTGTAAG
Statistics
Matches: 96, Mismatches: 24, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
83 1 0.01
84 17 0.18
85 59 0.61
86 19 0.20
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (84 bp):
TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTCTACCAAGCGCCGCTAAAGAACATGAC
TATTAGCAGCGTTTTTTTC
Found at i:54006161 original size:24 final size:25
Alignment explanation
Indices: 54006123--54006174 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
54006113 ACACGTTAGC
54006123 AAACAAAAATATATAAATAT-AAAT
1 AAACAAAAATATATAAATATAAAAT
* * *
54006147 AAACAAATATTTATATATATAAAAT
1 AAACAAAAATATATAAATATAAAAT
54006172 AAA
1 AAA
54006175 TTGAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAACAAAAATATATAAATATAAAAT
Found at i:54009789 original size:42 final size:42
Alignment explanation
Indices: 54009743--54009826 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
54009733 CAAATTGACG
54009743 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
*
54009785 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAGAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
54009827 AATTCCGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (42 bp):
GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
Found at i:54011955 original size:4 final size:4
Alignment explanation
Indices: 54011946--54011979 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
54011936 AAGTTTTATT
54011946 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
54011980 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:54011987 original size:22 final size:22
Alignment explanation
Indices: 54011929--54011988 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
54011919 AAGTGGCCCA
*
54011929 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
54011953 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
54011974 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
54011989 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:54015780 original size:4 final size:4
Alignment explanation
Indices: 54015771--54015804 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
54015761 AAGTTTTATT
54015771 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
54015805 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:54015812 original size:22 final size:22
Alignment explanation
Indices: 54015754--54015813 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
54015744 AAGTGGCCCA
*
54015754 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
54015778 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
54015799 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
54015814 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:54019477 original size:6 final size:6
Alignment explanation
Indices: 54019466--54019500 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
54019456 GTAATTAGTG
54019466 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
54019501 CACACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:54019507 original size:18 final size:18
Alignment explanation
Indices: 54019468--54019508 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
54019458 AATTAGTGAT
* *
54019468 ACATATACATATACATAT
1 ACATATACATATACACAC
54019486 ACATATACATATACACAC
1 ACATATACATATACACAC
54019504 ACATA
1 ACATA
54019509 CAAATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (18 bp):
ACATATACATATACACAC
Found at i:54019595 original size:16 final size:16
Alignment explanation
Indices: 54019576--54019610 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54019566 TAGATAAATA
*
54019576 CATACATACAGACATG
1 CATACATAAAGACATG
*
54019592 CATACATAAATACATG
1 CATACATAAAGACATG
54019608 CAT
1 CAT
54019611 GCATGCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (16 bp):
CATACATAAAGACATG
Found at i:54032210 original size:18 final size:18
Alignment explanation
Indices: 54032189--54032275 Score: 120
Period size: 18 Copynumber: 4.8 Consensus size: 18
54032179 CGTTTACGAT
54032189 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
* *
54032207 ACTATTCACGTATGCGGT
1 ACTATTCACGTATACGGC
* *
54032225 ACTATTTACATATACGGC
1 ACTATTCACGTATACGGC
*
54032243 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
54032261 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
54032276 AGTAGTTGGG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:54042605 original size:22 final size:21
Alignment explanation
Indices: 54042574--54042615 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54042564 TTATTTAATT
*
54042574 TAAATTTTTTATGATGTAAAAA
1 TAAATATTTTAT-ATGTAAAAA
*
54042596 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATGTAAAA
54042616 TACTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAATATTTTATATGTAAAAA
Found at i:54048529 original size:48 final size:48
Alignment explanation
Indices: 54048461--54048620 Score: 250
Period size: 48 Copynumber: 3.3 Consensus size: 48
54048451 AAGGTATATT
* * *
54048461 TGTCTTTCACTATTTGCACTCTTAGAGTTGGTAC-TTTATTGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTA-TGTATGGCA
*
54048509 TGTCATTCATTATTTTCACTCTTAGAGTTGGTGCTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
* *
54048557 TGTCATTCATTATTTTCACTCTTAGATTTTGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
54048605 TGTCATTCATTATTTT
1 TGTCATTCATTATTTT
54048621 TATTGATAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 100 0.96
49 4 0.04
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (48 bp):
TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
Found at i:54053602 original size:3 final size:3
Alignment explanation
Indices: 54053594--54053646 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
54053584 AATACACCAA
54053594 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54053641 AAT AAT
1 AAT AAT
54053647 GGTAAGAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:54066091 original size:13 final size:13
Alignment explanation
Indices: 54066075--54066120 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
54066065 CTTTGCTTTT
54066075 GAAAAGTGCTGTG
1 GAAAAGTGCTGTG
* *
54066088 GAAAAGTGCTTTT
1 GAAAAGTGCTGTG
* *
54066101 GAGAAGTGTTGTG
1 GAAAAGTGCTGTG
54066114 GAAAAGT
1 GAAAAGT
54066121 TTGGTTTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (13 bp):
GAAAAGTGCTGTG
Found at i:54066097 original size:26 final size:26
Alignment explanation
Indices: 54066068--54066120 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
54066058 AGTTCTTCTT
54066068 TGCTTTTGAAAAGTGCTGTGGAAAAG
1 TGCTTTTGAAAAGTGCTGTGGAAAAG
* *
54066094 TGCTTTTGAGAAGTGTTGTGGAAAAG
1 TGCTTTTGAAAAGTGCTGTGGAAAAG
54066120 T
1 T
54066121 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.34
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTGTGGAAAAG
Found at i:54069166 original size:16 final size:18
Alignment explanation
Indices: 54069128--54069165 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
54069118 TTGATTCATA
*
54069128 TTTTATCCGAGTCTAATT
1 TTTTATCCAAGTCTAATT
54069146 TTTTATCCAAGTCT-ATT
1 TTTTATCCAAGTCTAATT
54069163 TTT
1 TTT
54069166 AGTACCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (18 bp):
TTTTATCCAAGTCTAATT
Found at i:54071804 original size:1 final size:1
Alignment explanation
Indices: 54071798--54071823 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
54071788 ACACACACAC
54071798 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
54071824 CAGGAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:54074350 original size:3 final size:3
Alignment explanation
Indices: 54074342--54074379 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54074332 ACCGTGCATG
54074342 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54074380 ATTGTAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54074551 original size:34 final size:35
Alignment explanation
Indices: 54074513--54074597 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 35
54074503 TTATAAACAT
54074513 TAAAAAATTATTTTAAAA-ATAATAAAAAT-AAAAA
1 TAAAAAA-TATTTTAAAAGATAATAAAAATAAAAAA
**
54074547 T-AAAAATATTTTAAAAGTATTTTAAAAATAAAAAA
1 TAAAAAATATTTTAAAAG-ATAATAAAAATAAAAAA
54074582 TAAAAAAATATATTTA
1 T-AAAAAATAT-TTTA
54074598 TTATATTCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.23
33 5 0.12
34 10 0.23
35 6 0.14
37 8 0.19
38 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (35 bp):
TAAAAAATATTTTAAAAGATAATAAAAATAAAAAA
Found at i:54074561 original size:11 final size:11
Alignment explanation
Indices: 54074547--54074576 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54074537 AAAATAAAAA
54074547 TAAAAATATTT
1 TAAAAATATTT
*
54074558 TAAAAGTATTT
1 TAAAAATATTT
54074569 TAAAAATA
1 TAAAAATA
54074577 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:54076916 original size:3 final size:3
Alignment explanation
Indices: 54076908--54076934 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54076898 AACCCTTGAC
54076908 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
54076935 ATCCATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54077933 original size:126 final size:126
Alignment explanation
Indices: 54077689--54077991 Score: 318
Period size: 126 Copynumber: 2.4 Consensus size: 126
54077679 GTTAGAAGCT
* *
54077689 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTAATGGTGAAATGCTTGATGAAAA
1 CGCTATGAGAAGGATCAAAATACATCCAGAGATA--G-T-G--ATGGTGATATGCTCGATGAAAA
* * ** * * * * * *
54077754 TAGATCTACTGGCTCTCATAGTGAGGAGCAAGATCAGCACTTATTGGTAGAAGGGCGACGTAATG
60 TAGATCAACTGACTCTCATAGCAAGAAGCAAGATCAGAACTTATCGATAGAAGGCCAACGTAATG
*
54077819 GT
125 GA
* * *
54077821 TGCTATGAGAAGGAACAAAATGCATCCAGAGATAGTGATGGTGATATGCTCGATGAAAATAGATC
1 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGATATGCTCGATGAAAATAGATC
* * * * *
54077886 AACTGATTCTCGTAGCAAGAAGCACGGTGAGAACTTATCGATAGAAGGCCAACGTAATGGA
66 AACTGACTCTCATAGCAAGAAGCAAGATCAGAACTTATCGATAGAAGGCCAACGTAATGGA
* * * * *
54077947 CGCTACGAGAAAGATCAAGATACTTCCAGAGATGGTGATGGTGAT
1 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGAT
54077992 GGTGATGGTG
Statistics
Matches: 142, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
126 108 0.76
128 1 0.01
129 1 0.01
130 1 0.01
132 31 0.22
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (126 bp):
CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGATATGCTCGATGAAAATAGATC
AACTGACTCTCATAGCAAGAAGCAAGATCAGAACTTATCGATAGAAGGCCAACGTAATGGA
Done.