Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 53 of 352
Found at i:17113877 original size:21 final size:21
Alignment explanation
Indices: 17113853--17113892 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17113843 TAAATATGTA
*
17113853 TAAATCTAAAAAAATTAAATT
1 TAAAACTAAAAAAATTAAATT
17113874 TAAAACTAAAAAAATTAAA
1 TAAAACTAAAAAAATTAAA
17113893 CTAACATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAACTAAAAAAATTAAATT
Found at i:17120137 original size:22 final size:24
Alignment explanation
Indices: 17120097--17120162 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 24
17120087 TTTTAGTATC
*
17120097 ATTTTTATTTGTTTTAATAT-T-T-
1 ATTTTTATTT-TTTAAATATATGTG
17120119 ATTTTTATGTTTTTAAATATATGTG
1 ATTTTTAT-TTTTTAAATATATGTG
17120144 ATTTATTATATTTTTAAAT
1 ATTT-TTAT-TTTTTAAAT
17120163 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 16 0.43
23 3 0.08
24 1 0.03
25 4 0.11
26 13 0.35
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
ATTTTTATTTTTTAAATATATGTG
Found at i:17120444 original size:20 final size:20
Alignment explanation
Indices: 17120407--17120457 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
17120397 AGGACTCTTC
*
17120407 TTTTTCTC--TTTAGTTTTT
1 TTTTTCTCATTTTTGTTTTT
17120425 TTTTTCTCATTTTTGTTTTT
1 TTTTTCTCATTTTTGTTTTT
*
17120445 TCTTT-TCATTTTT
1 TTTTTCTCATTTTT
17120458 CGGGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.28
19 8 0.28
20 13 0.45
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTCTCATTTTTGTTTTT
Found at i:17126202 original size:17 final size:18
Alignment explanation
Indices: 17126180--17126228 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
17126170 GGTCCTAGAA
17126180 TATTTGGATAGATTA-TT
1 TATTTGGATAGATTAGTT
*
17126197 TATTTGAGA-AAATTAGTT
1 TATTTG-GATAGATTAGTT
*
17126215 AATTT-GATAGATTA
1 TATTTGGATAGATTA
17126229 ACTAATTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.08
17 16 0.62
18 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (18 bp):
TATTTGGATAGATTAGTT
Found at i:17129968 original size:14 final size:14
Alignment explanation
Indices: 17129949--17129978 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17129939 TTATATCGAG
17129949 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
17129963 ACCAATCCAATTCA
1 ACCAATCCAAATCA
17129977 AC
1 AC
17129979 ATATTTTCAA
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:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:17134719 original size:19 final size:20
Alignment explanation
Indices: 17134687--17134726 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
17134677 ACTATTAATT
17134687 TTAAATATTAAAATGTTTTA
1 TTAAATATTAAAATGTTTTA
*
17134707 TTAAATA-TAAAATTTTTTA
1 TTAAATATTAAAATGTTTTA
17134726 T
1 T
17134727 ATCCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAAATATTAAAATGTTTTA
Found at i:17145364 original size:14 final size:14
Alignment explanation
Indices: 17145345--17145373 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17145335 TGCAAAGGTG
17145345 TATATATATACATA
1 TATATATATACATA
17145359 TATATATATACATA
1 TATATATATACATA
17145373 T
1 T
17145374 GCACTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATATATACATA
Found at i:17146660 original size:10 final size:10
Alignment explanation
Indices: 17146636--17146669 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
17146626 TTTTTTTTCA
17146636 AAAAAAAT-T
1 AAAAAAATAT
*
17146645 ATAAAAATAT
1 AAAAAAATAT
17146655 AAAAAAATAT
1 AAAAAAATAT
17146665 AAAAA
1 AAAAA
17146670 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:17146718 original size:18 final size:19
Alignment explanation
Indices: 17146697--17146734 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17146687 AAATTTTAAA
17146697 TTAACAAA-ACATAAAAAT
1 TTAACAAATACATAAAAAT
* *
17146715 TTAAGAAATATATAAAAAT
1 TTAACAAATACATAAAAAT
17146734 T
1 T
17146735 AATTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
TTAACAAATACATAAAAAT
Found at i:17146736 original size:18 final size:17
Alignment explanation
Indices: 17146646--17146736 Score: 60
Period size: 18 Copynumber: 5.2 Consensus size: 17
17146636 AAAAAAATTA
*
17146646 TAAAAATATAAAAAAAT
1 TAAAAATATATAAAAAT
* *
17146663 ATAAAAATTATTTAAAACT
1 -TAAAAA-TATATAAAAAT
* **
17146682 TAAAAAAAT-TTTAAAT
1 TAAAAATATATAAAAAT
*
17146698 TAACAAA-ACATAAAAATT
1 TAA-AAATATATAAAAA-T
17146716 TAAGAAATATATAAAAAT
1 TAA-AAATATATAAAAAT
17146734 TAA
1 TAA
17146737 TTTTTTTGAG
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
16 8 0.14
17 9 0.16
18 23 0.41
19 16 0.29
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (17 bp):
TAAAAATATATAAAAAT
Found at i:17146972 original size:20 final size:20
Alignment explanation
Indices: 17146947--17146988 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
17146937 ATTTCATATA
17146947 TATATCACTAAAGTTATAGT
1 TATATCACTAAAGTTATAGT
17146967 TATATCACTAAAGTTATAGT
1 TATATCACTAAAGTTATAGT
17146987 TA
1 TA
17146989 AAACTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
TATATCACTAAAGTTATAGT
Found at i:17152333 original size:41 final size:41
Alignment explanation
Indices: 17152288--17152370 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
17152278 ATGGGTTGTC
17152288 TTGCAGATTACCAGGGTTTCCACTCATCATTCATCACTGGT
1 TTGCAGATTACCAGGGTTTCCACTCATCATTCATCACTGGT
17152329 TTGCAGATTACCAGGGTTTCCACTCATCATTCATCACTGGT
1 TTGCAGATTACCAGGGTTTCCACTCATCATTCATCACTGGT
17152370 T
1 T
17152371 ATGTAAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.35
Consensus pattern (41 bp):
TTGCAGATTACCAGGGTTTCCACTCATCATTCATCACTGGT
Found at i:17153479 original size:13 final size:13
Alignment explanation
Indices: 17153461--17153486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17153451 CGAATTCAAA
17153461 CCGCATTTGAGTT
1 CCGCATTTGAGTT
17153474 CCGCATTTGAGTT
1 CCGCATTTGAGTT
17153487 TGATGCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
CCGCATTTGAGTT
Found at i:17154995 original size:18 final size:17
Alignment explanation
Indices: 17154959--17154991 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17154949 AATTTAATAT
17154959 TTTTTAAATTTTTATTA
1 TTTTTAAATTTTTATTA
17154976 TTTTT-AATTATTTATT
1 TTTTTAAATT-TTTATT
17154992 TATTGTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTAAATTTTTATTA
Found at i:17156840 original size:17 final size:17
Alignment explanation
Indices: 17156808--17156846 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
17156798 ACAGCAAAGA
17156808 GAAAAAGAAAGTAAAAT
1 GAAAAAGAAAGTAAAAT
17156825 GAAAACAGAAAG-AAAAT
1 GAAAA-AGAAAGTAAAAT
17156842 GAAAA
1 GAAAA
17156847 GAAGAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (17 bp):
GAAAAAGAAAGTAAAAT
Found at i:17156852 original size:18 final size:17
Alignment explanation
Indices: 17156809--17156857 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
17156799 CAGCAAAGAG
17156809 AAAAAGAAAGTAAAATGA
1 AAAAAGAAAG-AAAATGA
*
17156827 AAACAGAAAGAAAATGA
1 AAAAAGAAAGAAAATGA
*
17156844 AAAGAAGAAGGAAA
1 AAA-AAGAAAGAAA
17156858 GAAGAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAGAAAATGA
Found at i:17170587 original size:12 final size:12
Alignment explanation
Indices: 17170570--17170602 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
17170560 ACAAAATCTG
17170570 AATTTAATTTCC
1 AATTTAATTTCC
*
17170582 AATTTAATTTCT
1 AATTTAATTTCC
17170594 AATTTAATT
1 AATTTAATT
17170603 AATTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:17176426 original size:46 final size:46
Alignment explanation
Indices: 17176359--17176450 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
17176349 AAAAAGAGAC
*
17176359 TGTTTGAACTGAGTAATCGGGATAGGATGCTTGGGTTGTCATCCTA
1 TGTTTGAACTGAGTAATCGGGATAGGATGCTTGGGTTGCCATCCTA
* *
17176405 TGTTTGAATTTAGTAATCGGGATAGGATGCTTGGGTTGCCATCCTA
1 TGTTTGAACTGAGTAATCGGGATAGGATGCTTGGGTTGCCATCCTA
17176451 GTTCGCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (46 bp):
TGTTTGAACTGAGTAATCGGGATAGGATGCTTGGGTTGCCATCCTA
Found at i:17188114 original size:52 final size:52
Alignment explanation
Indices: 17188053--17188160 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
17188043 ATAATATTTT
* *
17188053 AATAAAAAAATTAACAATATTAA-TCATTTTGATTAATTAATAATATTATAAA
1 AATAAAAAAATTAACAATATTAACT-ATTTTGACTAATTAATAATACTATAAA
17188105 AATAAAAAAATTAACAATATTAACTATTTTGACTAATTAATAATACTATAAA
1 AATAAAAAAATTAACAATATTAACTATTTTGACTAATTAATAATACTATAAA
17188157 AATA
1 AATA
17188161 TAGAGATCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 52 0.98
53 1 0.02
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (52 bp):
AATAAAAAAATTAACAATATTAACTATTTTGACTAATTAATAATACTATAAA
Found at i:17189963 original size:14 final size:16
Alignment explanation
Indices: 17189934--17189967 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
17189924 TTAAATGTTT
17189934 AATATTATTGTTAAAA
1 AATATTATTGTTAAAA
17189950 AATATT-TT-TTAAAA
1 AATATTATTGTTAAAA
17189964 AATA
1 AATA
17189968 AAATATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 2 0.11
16 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATATTATTGTTAAAA
Found at i:17189972 original size:19 final size:20
Alignment explanation
Indices: 17189948--17189989 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17189938 TTATTGTTAA
17189948 AAAATATTT-TTTAAAAAAT
1 AAAATATTTATTTAAAAAAT
* *
17189967 AAAATATTTATTTTAAACAT
1 AAAATATTTATTTAAAAAAT
17189987 AAA
1 AAA
17189990 TACACGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATTTATTTAAAAAAT
Found at i:17190637 original size:18 final size:18
Alignment explanation
Indices: 17190616--17190651 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17190606 ATAGAAAATC
17190616 TATAAAAAAATATTTAAA
1 TATAAAAAAATATTTAAA
* *
17190634 TATAATAAAATTTTTAAA
1 TATAAAAAAATATTTAAA
17190652 ACTACTAAAT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAAAAAATATTTAAA
Found at i:17190780 original size:9 final size:9
Alignment explanation
Indices: 17190694--17190834 Score: 72
Period size: 10 Copynumber: 14.8 Consensus size: 9
17190684 GAAATATTAA
*
17190694 ATAAATATT
1 ATAAAAATT
17190703 AT-AAAATT
1 ATAAAAATT
17190711 ATAGAAAA-T
1 ATA-AAAATT
*
17190720 ATATAAAATA
1 ATA-AAAATT
* *
17190730 ATTAAAATG
1 ATAAAAATT
17190739 ATAAAAATCT
1 ATAAAAAT-T
**
17190749 ATAAATTTT
1 ATAAAAATT
17190758 AATAAAAAAGTT
1 -AT-AAAAA-TT
17190770 ATAAAAATT
1 ATAAAAATT
*
17190779 ATTAAAAGTAT
1 A-TAAAAAT-T
*
17190790 AAAAAAAGTT
1 ATAAAAA-TT
*
17190800 GTAAAAATT
1 ATAAAAATT
17190809 -TAAAAATAT
1 ATAAAAAT-T
17190818 ATAAGAAATT
1 ATAA-AAATT
*
17190828 ACAAAAA
1 ATAAAAA
17190835 ATAAATTTTG
Statistics
Matches: 102, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
8 14 0.14
9 32 0.31
10 42 0.41
11 12 0.12
12 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:17192873 original size:17 final size:17
Alignment explanation
Indices: 17192852--17192893 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
17192842 ACTTTACATG
17192852 TAATATATAAAATTTTAA
1 TAATATAT-AAATTTTAA
* *
17192870 -AATAAATAATTTTTAA
1 TAATATATAAATTTTAA
17192886 TAATATAT
1 TAATATAT
17192894 TATATTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATATAAATTTTAA
Found at i:17203880 original size:18 final size:18
Alignment explanation
Indices: 17203859--17203894 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17203849 TATAAATATC
17203859 ATAAACAAAAGTGTTCAA
1 ATAAACAAAAGTGTTCAA
17203877 ATAAACAAAAGTGTTCAA
1 ATAAACAAAAGTGTTCAA
17203895 CACATGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
ATAAACAAAAGTGTTCAA
Found at i:17210415 original size:36 final size:37
Alignment explanation
Indices: 17210368--17210438 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
17210358 GAGATTATTA
*
17210368 GGAGAAAGTAG-AATCTG-TGGAAATACCTGTGGATTC
1 GGAGAAAGTAGAAATCCGAT-GAAATACCTGTGGATTC
17210404 GGAGAAAGTAGAAATCCGATGAAATACCTGTGGAT
1 GGAGAAAGTAGAAATCCGATGAAATACCTGTGGAT
17210439 ATTTTCGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 11 0.34
37 20 0.62
38 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.23
Consensus pattern (37 bp):
GGAGAAAGTAGAAATCCGATGAAATACCTGTGGATTC
Found at i:17211580 original size:18 final size:20
Alignment explanation
Indices: 17211546--17211586 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
17211536 TATTATAACA
17211546 TTAAAAAAAGAACAA-TTAT
1 TTAAAAAAAGAACAATTTAT
*
17211565 TTAAAAAAAGTA-AATTTAT
1 TTAAAAAAAGAACAATTTAT
17211584 TTA
1 TTA
17211587 TTTTTTCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
TTAAAAAAAGAACAATTTAT
Found at i:17213768 original size:16 final size:16
Alignment explanation
Indices: 17213744--17213778 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17213734 ATTGATTGTC
*
17213744 AAAAATATTTTTAGAT
1 AAAAATATTTTTAAAT
*
17213760 AAAAGTATTTTTAAAT
1 AAAAATATTTTTAAAT
17213776 AAA
1 AAA
17213779 CTGAATAATT
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:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (16 bp):
AAAAATATTTTTAAAT
Found at i:17215809 original size:18 final size:18
Alignment explanation
Indices: 17215788--17215831 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17215778 ATACCAGGTG
*
17215788 TGTATCCTAGCCCTTACA
1 TGTATCCTAACCCTTACA
*
17215806 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTACA
*
17215824 TGTTTCCT
1 TGTATCCT
17215832 TTTCTCAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.41
Consensus pattern (18 bp):
TGTATCCTAACCCTTACA
Found at i:17216277 original size:24 final size:24
Alignment explanation
Indices: 17216250--17216305 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
17216240 TATTTAATAA
*
17216250 AATAAAAATTGTTTTGAATA-TTTT
1 AATAAAAATTATTTT-AATATTTTT
* *
17216274 AATAGTAAATTATTTTTATATTTTT
1 AATA-AAAATTATTTTAATATTTTT
17216299 AATAAAA
1 AATAAAA
17216306 TAGAAGTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (24 bp):
AATAAAAATTATTTTAATATTTTT
Found at i:17216289 original size:25 final size:25
Alignment explanation
Indices: 17216255--17216302 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
17216245 AATAAAATAA
*
17216255 AAATTGTTTTGAATA-TTTTAATAGT
1 AAATTATTTT-AATATTTTTAATAGT
*
17216280 AAATTATTTTTATATTTTTAATA
1 AAATTATTTTAATATTTTTAATA
17216303 AAATAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (25 bp):
AAATTATTTTAATATTTTTAATAGT
Found at i:17219533 original size:126 final size:124
Alignment explanation
Indices: 17219346--17219742 Score: 539
Period size: 126 Copynumber: 3.2 Consensus size: 124
17219336 AAGGCCAAAC
* *
17219346 AAGAACTACTGTA-AGAAAAGAGCGTCCACTGGGAGCTTTTTTTAGTCATTTTGCTGACAGTGCA
1 AAGAACTACTGTAGA-AAAAGAGCGTCCA-TGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* *
17219410 TCTTGCTTGAAGCCTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTT
64 TCTTGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTTT
*
17219471 AAGAACTACTGTAGAAAAAGAGCGTCCATGTAAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
1 AAGAACTACTGTAGAAAAAGAGCGTCCATG--GGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* *
17219536 TCTTGCTTGAAGCATTTTTGA-AGCTATTTTTTTAGAACCATCTTCTCAAAATTATTTTTTC
64 TCTTGCTTGAAGCATTTTTGACA-CTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTTT
* * * * *
17219597 AGGAACTACTATAGAAAAATAGCGTCTACATGGGAGCTTTTTTCAATAATTTTGCTGACTGTGCA
1 AAGAACTACTGTAGAAAAAGAGCGTC--CATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * * *
17219662 TCCTGCTTGAAGCATTTTTGACATTATTTTTTTAAAACCGTCTTCTCAAAATTAACTTTTCT
64 TCTTGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATT-ATTTTTTT
*
17219724 GA-AACTACTGTAGAAAAAG
1 AAGAACTACTGTAGAAAAAG
17219743 CCAAAATCCT
Statistics
Matches: 240, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
124 2 0.01
125 27 0.11
126 201 0.84
127 6 0.03
128 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (124 bp):
AAGAACTACTGTAGAAAAAGAGCGTCCATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
TTGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTTT
Found at i:17219920 original size:34 final size:32
Alignment explanation
Indices: 17219796--17219921 Score: 128
Period size: 34 Copynumber: 3.7 Consensus size: 32
17219786 CTAAACAAAA
*
17219796 AATTATTTAAAAAA-ACTAAACTCTAATTTAATT
1 AATT-TTTAAAAAACTCTAAAC-CTAATTTAATT
*
17219829 AATTTTCTTAAAAACTCTAAACCTTAATTTAATT
1 AATTTT-TAAAAAACTCTAAACC-TAATTTAATT
* * *
17219863 AATTTATTTAAAACCCCTAAAACCTAATTTAATT
1 AATTT-TTAAAAAACTCT-AAACCTAATTTAATT
17219897 AATTTTTAAAAAAACCTCTAAACCT
1 AATTTTT-AAAAAA-CTCTAAACCT
17219922 TGGTTTATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.03
33 13 0.16
34 55 0.70
35 9 0.11
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (32 bp):
AATTTTTAAAAAACTCTAAACCTAATTTAATT
Found at i:17223198 original size:16 final size:17
Alignment explanation
Indices: 17223177--17223209 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17223167 CATAATTTTT
17223177 AAAATAT-TAATTTAAA
1 AAAATATATAATTTAAA
*
17223193 AAAATATATATTTTAAA
1 AAAATATATAATTTAAA
17223210 TACTGTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATATAATTTAAA
Found at i:17224753 original size:23 final size:23
Alignment explanation
Indices: 17224716--17224760 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17224706 CATCGTTTCA
*
17224716 TATATTATTATCAATTCACAATTT
1 TATATCATTATCAATTCA-AATTT
17224740 TATATCATT-TCAATTCAAATT
1 TATATCATTATCAATTCAAATT
17224761 ATACATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATCATTATCAATTCAAATTT
Found at i:17230000 original size:5 final size:5
Alignment explanation
Indices: 17229992--17230051 Score: 104
Period size: 5 Copynumber: 12.2 Consensus size: 5
17229982 ATTATTAAAC
*
17229992 TAATA TAATA TAATA TAATA TAGTA TAATA T-ATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
17230041 TAATA TAATA T
1 TAATA TAATA T
17230052 TTAAACTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
4 4 0.08
5 48 0.92
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:17230064 original size:29 final size:29
Alignment explanation
Indices: 17229994--17230051 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
17229984 TATTAAACTA
*
17229994 ATATAATATAATATAATATAGTATAATAT
1 ATATAATATAATATAATATAATATAATAT
17230023 ATATAATATAATATAATATAATATAATAT
1 ATATAATATAATATAATATAATATAATAT
17230052 TTAAACTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATAATATAATATAATATAATATAATAT
Found at i:17231160 original size:10 final size:10
Alignment explanation
Indices: 17231145--17231173 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
17231135 ATTATATACC
17231145 ATATAATATG
1 ATATAATATG
17231155 ATATAATATG
1 ATATAATATG
17231165 ATATAATAT
1 ATATAATAT
17231174 ATTATGAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
ATATAATATG
Found at i:17233877 original size:1 final size:1
Alignment explanation
Indices: 17233871--17233898 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17233861 TATAATTCCC
17233871 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
17233899 CTCAATTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17236721 original size:192 final size:192
Alignment explanation
Indices: 17236393--17236782 Score: 753
Period size: 192 Copynumber: 2.0 Consensus size: 192
17236383 CTATAATTTG
17236393 AATATGGCATGGCTTATGGATTACAGAGAGTAGAGGAGATAACATAGGTGAAGGTTGTATATATC
1 AATATGGCATGGCTTATGGATTACAGAGAGTAGAGGAGATAACATAGGTGAAGGTTGTATATATC
* *
17236458 TGAACCATTCGCCATGCTTTGATTTAGACTATGGAAAGATGTGAGTGATAGAGATAACACAGTAG
66 TGAACCATTCGCCATGCTTTGATTTAGACTATGGAAAGATGTGAGTGATAGAGATAAAACAATAG
17236523 TTCCAAACAAACAGGCAACCACCACTGGGCTTTCTCATTCCCTTTTTTTATGCCAATGCCTA
131 TTCCAAACAAACAGGCAACCACCACTGGGCTTTCTCATTCCCTTTTTTTATGCCAATGCCTA
*
17236585 TATATGGCATGGCTTATGGATTACAGAGAGTAGAGGAGATAACATAGGTGAAGGTTGTATATATC
1 AATATGGCATGGCTTATGGATTACAGAGAGTAGAGGAGATAACATAGGTGAAGGTTGTATATATC
17236650 TGAACCATTCGCCATGCTTTGATTTAGACTATGGAAAGATGTGAGTGATAGAGATAAAACAATAG
66 TGAACCATTCGCCATGCTTTGATTTAGACTATGGAAAGATGTGAGTGATAGAGATAAAACAATAG
17236715 TTCCAAACAAACAGGCAACCACCACTGGGCTTTCTCATTCCCTTTTTTTATGCCAATGCCTA
131 TTCCAAACAAACAGGCAACCACCACTGGGCTTTCTCATTCCCTTTTTTTATGCCAATGCCTA
17236777 AATATG
1 AATATG
17236783 CAGGGGACAC
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 194 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (192 bp):
AATATGGCATGGCTTATGGATTACAGAGAGTAGAGGAGATAACATAGGTGAAGGTTGTATATATC
TGAACCATTCGCCATGCTTTGATTTAGACTATGGAAAGATGTGAGTGATAGAGATAAAACAATAG
TTCCAAACAAACAGGCAACCACCACTGGGCTTTCTCATTCCCTTTTTTTATGCCAATGCCTA
Found at i:17236898 original size:6 final size:6
Alignment explanation
Indices: 17236889--17236948 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
17236879 TTTTTCTAAC
17236889 ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA
1 ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA
17236937 ATAGGA ATAGGA
1 ATAGGA ATAGGA
17236949 TGGTTTAAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
ATAGGA
Found at i:17239113 original size:21 final size:21
Alignment explanation
Indices: 17239088--17239128 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17239078 TGGGTGGATT
17239088 AGCTCTCATGAGCTTCTGTTC
1 AGCTCTCATGAGCTTCTGTTC
*
17239109 AGCTCTTATGAGCTTCTGTT
1 AGCTCTCATGAGCTTCTGTT
17239129 AGCGATGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (21 bp):
AGCTCTCATGAGCTTCTGTTC
Found at i:17240227 original size:21 final size:21
Alignment explanation
Indices: 17240189--17240228 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17240179 CCTGCAGTCC
* * *
17240189 AAAATTTTCAACTTTTTTCCT
1 AAAATTTGCAAATATTTTCCT
17240210 AAAATTTGCAAATATTTTC
1 AAAATTTGCAAATATTTTC
17240229 GATTTAGTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (21 bp):
AAAATTTGCAAATATTTTCCT
Found at i:17240766 original size:24 final size:24
Alignment explanation
Indices: 17240739--17240784 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17240729 TAATGGTTTG
* *
17240739 TTTTATTTTAATCATTTTAATTTT
1 TTTTAATTTAATCAATTTAATTTT
17240763 TTTTAATTTAATCAATTTAATT
1 TTTTAATTTAATCAATTTAATT
17240785 AAAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTAATTTAATCAATTTAATTTT
Found at i:17243475 original size:19 final size:19
Alignment explanation
Indices: 17243453--17243490 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17243443 AAAAAACAAT
*
17243453 AAAATTTAATAAAATTAAC
1 AAAATGTAATAAAATTAAC
*
17243472 AAAATGTATTAAAATTAAC
1 AAAATGTAATAAAATTAAC
17243491 CTAAATGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATGTAATAAAATTAAC
Found at i:17244028 original size:32 final size:32
Alignment explanation
Indices: 17243989--17244055 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
17243979 AACATTAAAG
17243989 AATGATCAAATAATTTCGTTGATTAAATGGTT
1 AATGATCAAATAATTTCGTTGATTAAATGGTT
17244021 AATGATCAAATAATTTCGTTGATTAAATGGTT
1 AATGATCAAATAATTTCGTTGATTAAATGGTT
17244053 AAT
1 AAT
17244056 TAAAGCTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (32 bp):
AATGATCAAATAATTTCGTTGATTAAATGGTT
Found at i:17246214 original size:3 final size:3
Alignment explanation
Indices: 17246206--17246236 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17246196 TCAATACCAA
17246206 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17246237 CTTACCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17246870 original size:17 final size:19
Alignment explanation
Indices: 17246836--17246873 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
17246826 AAACTTTTAA
17246836 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
17246855 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
17246872 TT
1 TT
17246874 CCTTCCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:17250574 original size:46 final size:46
Alignment explanation
Indices: 17250522--17250650 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
17250512 TATTTTGGCA
17250522 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
17250568 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
17250614 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17250651 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:17252828 original size:40 final size:39
Alignment explanation
Indices: 17252773--17252906 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 39
17252763 ACCAGTTTGG
*
17252773 CACCCAGTGCCTCATCGGAAAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGAAAATCCGAAGT-ATAAATTGA
* * *
17252813 CACCCAGTGTCTCATCGGCTAAA-CCGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGG-AAAATCCGAAGTATAAATTGA
* *
17252850 CACCCAGTGCCTTATC-AAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGAA--AATCCGAAGTA-TAAATTGA
*
17252891 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
17252907 AACTCAAGGT
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
35 1 0.01
37 23 0.30
38 6 0.08
40 22 0.29
41 24 0.32
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGAAAATCCGAAGTATAAATTGA
Found at i:17252855 original size:37 final size:38
Alignment explanation
Indices: 17252769--17252906 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 38
17252759 ACACACCAGT
*
17252769 TTGGCACCCAGTGCCTCATCGGAAAATTCGAAGTAATAAA
1 TTGGCACCCAGTGCCTCATCGGAAAATCCGAAG--ATAAA
* * *
17252809 TTGACACCCAGTGTCTCATCGGCTAAA-CCGAAG-TAAA
1 TTGGCACCCAGTGCCTCATCGG-AAAATCCGAAGATAAA
* *
17252846 TTGGCACCCAGTGCCTTATC-AAATTAATCCGAAGTAGTAAA
1 TTGGCACCCAGTGCCTCATCGGAA--AATCCGAAG-A-TAAA
* *
17252887 TTGACACCCAGTGTCTCATC
1 TTGGCACCCAGTGCCTCATC
17252907 AACTCAAGGT
Statistics
Matches: 79, Mismatches: 12, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
35 1 0.01
37 23 0.29
38 6 0.08
40 25 0.32
41 24 0.30
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (38 bp):
TTGGCACCCAGTGCCTCATCGGAAAATCCGAAGATAAA
Found at i:17253738 original size:17 final size:18
Alignment explanation
Indices: 17253706--17253740 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
17253696 TGAACCCTAA
17253706 CTTTTTCTCCTTTCTTTCC
1 CTTTTTCT-CTTTCTTTCC
17253725 CTTTTTCT-TTTCTTTC
1 CTTTTTCTCTTTCTTTC
17253741 GTTTTGCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCC
Found at i:17253793 original size:5 final size:5
Alignment explanation
Indices: 17253783--17253829 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
17253773 TTTTACTTAT
17253783 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
17253830 CTTAAACATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:17254708 original size:11 final size:11
Alignment explanation
Indices: 17254694--17254735 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
17254684 TTGTTTTTTT
17254694 TACTATTTTAC
1 TACTATTTTAC
*
17254705 TACTATTTCAC
1 TACTATTTTAC
* *
17254716 TACTATGTTGC
1 TACTATTTTAC
17254727 TACTATTTT
1 TACTATTTT
17254736 GTTGTTATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (11 bp):
TACTATTTTAC
Found at i:17254921 original size:16 final size:16
Alignment explanation
Indices: 17254893--17254926 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
17254883 TTTATTTTAA
17254893 TATTTTTATTATTTTT
1 TATTTTTATTATTTTT
17254909 TATTTATTA-TATTTTT
1 TATTT-TTATTATTTTT
17254925 TA
1 TA
17254927 AAAAAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTTTATTATTTTT
Found at i:17259098 original size:21 final size:20
Alignment explanation
Indices: 17259074--17259112 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17259064 CCTTTATAAG
*
17259074 GTAATCTTTCTCTTTCTATTT
1 GTAATCTTTCAC-TTCTATTT
*
17259095 GTAATTTTTCACTTCTAT
1 GTAATCTTTCACTTCTAT
17259113 GTTTTGCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (20 bp):
GTAATCTTTCACTTCTATTT
Found at i:17261271 original size:34 final size:34
Alignment explanation
Indices: 17261228--17261330 Score: 181
Period size: 34 Copynumber: 3.0 Consensus size: 34
17261218 TTTCGCCTTT
17261228 TTGTTCAAAGTGGAAAGGAGATTGATTTGGTGTG
1 TTGTTCAAAGTGGAAAGGAGATTGATTTGGTGTG
17261262 TTGTTCAAAGTGGAAAGGAGATTGATTTGGTGTG
1 TTGTTCAAAGTGGAAAGGAGATTGATTTGGTGTG
*
17261296 TTGTTCAAAATGGAAAGGAGATTGATTCT-GTGTG
1 TTGTTCAAAGTGGAAAGGAGATTGATT-TGGTGTG
17261330 T
1 T
17261331 AACCTGGATT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
34 66 0.99
35 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.36
Consensus pattern (34 bp):
TTGTTCAAAGTGGAAAGGAGATTGATTTGGTGTG
Found at i:17263896 original size:15 final size:15
Alignment explanation
Indices: 17263876--17263904 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17263866 TGGAAGAGAG
17263876 GAGGAGGAGGAAGAA
1 GAGGAGGAGGAAGAA
17263891 GAGGAGGAGGAAGA
1 GAGGAGGAGGAAGA
17263905 GGGTGGCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (15 bp):
GAGGAGGAGGAAGAA
Found at i:17267092 original size:12 final size:13
Alignment explanation
Indices: 17267075--17267113 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
17267065 TGCAAAAAAT
17267075 AAAAAT-ATTTTA
1 AAAAATAATTTTA
* *
17267087 AAAAATAAATATA
1 AAAAATAATTTTA
17267100 AAAAATAATTTTA
1 AAAAATAATTTTA
17267113 A
1 A
17267114 TTTTTTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:17267295 original size:19 final size:18
Alignment explanation
Indices: 17267273--17267321 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
17267263 AATTAAAATA
**
17267273 TATTTTTATTTTATTTATT
1 TATTTTTATAATATTT-TT
*
17267292 TATTTTCTAAAATATTTTT
1 TATTTT-TATAATATTTTT
17267311 TATTTTTATAA
1 TATTTTTATAA
17267322 GACTAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTTATAATATTTTT
Found at i:17267516 original size:28 final size:27
Alignment explanation
Indices: 17267476--17267547 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 27
17267466 TGGAGTTAAC
*
17267476 TTTTAAATGATTTTTATTATTTTTTAAT-T
1 TTTTAAA--ATTTTTATT-TTATTTAATAT
*
17267505 TTTTGAAAATTTTGAATTTTATTTAATAT
1 TTTT-AAAATTTT-TATTTTATTTAATAT
*
17267534 TTTTATAATTTTTA
1 TTTTAAAATTTTTA
17267548 ATAATGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.03
28 20 0.56
29 12 0.33
30 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTAAAATTTTTATTTTATTTAATAT
Found at i:17267594 original size:15 final size:14
Alignment explanation
Indices: 17267567--17267601 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
17267557 TACAAATTAA
17267567 TAAAA-TATTTTTT
1 TAAAATTATTTTTT
17267580 TAAAATTATTTTTT
1 TAAAATTATTTTTT
17267594 TAAAATTA
1 TAAAATTA
17267602 AGCTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAAAATTATTTTTT
Found at i:17267846 original size:48 final size:48
Alignment explanation
Indices: 17267775--17267869 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
17267765 ATTATACCTT
17267775 GATATATACTTAATGTTCTTTTTAAAGAAAAAATTTACAACATTCCTA
1 GATATATACTTAATGTTCTTTTTAAAGAAAAAATTTACAACATTCCTA
17267823 GATATATACTTAATGTTCTTTTTAAAGAAAAAATTTACAACATTCCT
1 GATATATACTTAATGTTCTTTTTAAAGAAAAAATTTACAACATTCCT
17267870 TCTTTTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (48 bp):
GATATATACTTAATGTTCTTTTTAAAGAAAAAATTTACAACATTCCTA
Found at i:17270334 original size:27 final size:28
Alignment explanation
Indices: 17270297--17270436 Score: 175
Period size: 27 Copynumber: 5.2 Consensus size: 28
17270287 AGCATGGCTG
* *
17270297 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
17270323 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
*
17270351 CCAGA-ACAGATATATGTGGCAAAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
17270378 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
17270405 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
17270432 CCAGA
1 CCAGA
17270437 ACGCTTCCTC
Statistics
Matches: 104, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
26 5 0.05
27 82 0.79
28 17 0.16
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:17270568 original size:26 final size:27
Alignment explanation
Indices: 17270539--17270614 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 27
17270529 CAAAATTAAC
* *
17270539 CCTAGGGGTATAACGGTAATTTT-GTA
1 CCTAGGGGTATAACAGTAATTTTCATA
17270565 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATAACAGTAATTTT-CATA
* *
17270593 CATAGGGGTATTACAGTAATTT
1 CCTAGGGGTATAACAGTAATTT
17270615 AGCTACTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 22 0.50
28 22 0.50
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (27 bp):
CCTAGGGGTATAACAGTAATTTTCATA
Found at i:17270608 original size:28 final size:26
Alignment explanation
Indices: 17270541--17270614 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 26
17270531 AAATTAACCC
* * *
17270541 TAGGGGTATAACGGTAATTTTGTACC
1 TAGGGGTATAACAGTAATTTTATACA
17270567 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTT--ATACA
*
17270595 TAGGGGTATTACAGTAATTT
1 TAGGGGTATAACAGTAATTT
17270615 AGCTACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 20 0.48
28 22 0.52
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTATACA
Found at i:17272092 original size:26 final size:26
Alignment explanation
Indices: 17272056--17272139 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
17272046 CATGAAATTC
17272056 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
17272082 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
17272108 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
17272134 TTATCA
1 TTATCA
17272140 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:17272555 original size:21 final size:22
Alignment explanation
Indices: 17272530--17272570 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17272520 AAAGTATTAA
17272530 TGAG-AATTATCTTTAAAAAAT
1 TGAGAAATTATCTTTAAAAAAT
* *
17272551 TGAGAAATTATTTTTCAAAA
1 TGAGAAATTATCTTTAAAAA
17272571 TCTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAGAAATTATCTTTAAAAAAT
Found at i:17273028 original size:31 final size:32
Alignment explanation
Indices: 17272993--17273054 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
17272983 TTAAAAATAT
* * *
17272993 ATTTTATATTTTTCAATAATT-TTAATTTTAA
1 ATTTTAAATTTTTAAAAAATTATTAATTTTAA
17273024 ATTTTAAATTTTTAAAAAATTAATTAATTTT
1 ATTTTAAATTTTTAAAAAATT-ATTAATTTT
17273055 TGATGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
33 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTTAAATTTTTAAAAAATTATTAATTTTAA
Found at i:17273880 original size:20 final size:21
Alignment explanation
Indices: 17273846--17273899 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
17273836 TGATGATATT
*
17273846 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
17273867 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
17273887 TTTTATTATTTTA
1 TTATATTATTTTA
17273900 TTATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:17276100 original size:46 final size:46
Alignment explanation
Indices: 17276048--17276366 Score: 496
Period size: 46 Copynumber: 6.9 Consensus size: 46
17276038 GTGTGCTCTT
* *
17276048 TGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGACAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
17276094 TGATATGAAATGTGTCAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
17276140 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
17276186 TGTTATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
17276232 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*** *
17276278 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * * * *
17276324 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
17276367 TCATGTCAAA
Statistics
Matches: 255, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 254 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:17277692 original size:16 final size:14
Alignment explanation
Indices: 17277654--17277693 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
17277644 ATCGGATTCG
17277654 TAAATATTTA-TTA
1 TAAATATTTATTTA
17277667 TAAATA-TTATTTA
1 TAAATATTTATTTA
17277680 T-AATA-TTATTTA
1 TAAATATTTATTTA
17277692 TA
1 TA
17277694 GTGATGCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATATTTATTTA
Found at i:17280118 original size:39 final size:39
Alignment explanation
Indices: 17280029--17280123 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 39
17280019 GATATTTTTG
* *
17280029 ATATAAAAT-ATATATTATATATTATATTAACTTAATAT
1 ATATAATATAATATATAATATATTATATTAACTTAATAT
17280067 -T-TAAGTATTAATATATAATATATTATATT-A-TTATATTAT
1 ATATAA-TA-TAATATATAATATATTATATTAACTTA-A-TAT
17280106 ATATAATATAATATATAA
1 ATATAATATAATATATAA
17280124 AACATAAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
36 3 0.06
37 5 0.10
38 3 0.06
39 31 0.65
40 3 0.06
41 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
ATATAATATAATATATAATATATTATATTAACTTAATAT
Found at i:17280123 original size:7 final size:7
Alignment explanation
Indices: 17280029--17280123 Score: 58
Period size: 7 Copynumber: 14.1 Consensus size: 7
17280019 GATATTTTTG
*
17280029 ATATAAA
1 ATATATA
17280036 ATATATA
1 ATATATA
*
17280043 TTATATA
1 ATATATA
*
17280050 TTATATTA
1 ATATA-TA
*
17280058 A-CT-TA
1 ATATATA
*
17280063 ATATTTA
1 ATATATA
17280070 AGTAT-TA
1 A-TATATA
17280077 ATATATA
1 ATATATA
*
17280084 ATATATT
1 ATATATA
17280091 ATAT-TA
1 ATATATA
* *
17280097 TTATATT
1 ATATATA
17280104 ATATAT-
1 ATATATA
17280110 A-ATATA
1 ATATATA
17280116 ATATATA
1 ATATATA
17280123 A
1 A
17280124 AACATAAAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 7 0.10
6 10 0.14
7 48 0.69
8 5 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (7 bp):
ATATATA
Found at i:17281321 original size:22 final size:22
Alignment explanation
Indices: 17281292--17281348 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
17281282 TAGCACGTTA
17281292 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* * *
17281315 -GTGCTCTCTATATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
17281336 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
17281349 CGTTTGTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:17285717 original size:26 final size:25
Alignment explanation
Indices: 17285691--17285742 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
17285681 AAAGATAAAA
*
17285691 TAAATAAAAATTATAAAGTTATTAAATT
1 TAAATAAAAAATATAAA--TATTAAA-T
*
17285719 TTAATAAAAAATATAAATATTAAA
1 TAAATAAAAAATATAAATATTAAA
17285743 AATTAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
28 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
TAAATAAAAAATATAAATATTAAAT
Found at i:17285843 original size:21 final size:21
Alignment explanation
Indices: 17285792--17285845 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
17285782 AAGTCGTAAG
17285792 AAAATTATAAAAAAATATAAA
1 AAAATTATAAAAAAATATAAA
* **
17285813 GAAA-TATAAAATTCATA-AAA
1 AAAATTATAAAA-AAATATAAA
17285833 AAAATTATAAAAA
1 AAAATTATAAAAA
17285846 TATTATACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATTATAAAAAAATATAAA
Found at i:17285844 original size:11 final size:11
Alignment explanation
Indices: 17285792--17285852 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
17285782 AAGTCGTAAG
17285792 AAAATTATAAA
1 AAAATTATAAA
17285803 AAAA-TATAAA
1 AAAATTATAAA
*
17285813 GAAA-TAT---
1 AAAATTATAAA
17285820 AAAATTCATAAAA
1 AAAATT-AT-AAA
17285833 AAAATTATAAA
1 AAAATTATAAA
*
17285844 AATATTATA
1 AAAATTATA
17285853 CCAAAAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 2 0.05
10 12 0.29
11 15 0.37
12 2 0.05
13 6 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:17286062 original size:19 final size:19
Alignment explanation
Indices: 17286025--17286147 Score: 67
Period size: 19 Copynumber: 6.3 Consensus size: 19
17286015 AATGAATTTC
*
17286025 ATAAAATTTGTTATGATTTTT
1 ATAAAA-TT-TTATAATTTTT
17286046 ATAAAATTTTATAATTTTT
1 ATAAAATTTTATAATTTTT
17286065 -TAAAGATTTT-TATATATTTT
1 ATAAA-ATTTTATA-AT-TTTT
* * * **
17286085 CT-GACTTTTAATAAAATTT
1 ATAAAATTTT-ATAATTTTT
*
17286104 A-AATATTTT-TATATTTTT
1 ATAAAATTTTATA-ATTTTT
*
17286122 ATTAAAATTTAATAATTTTT
1 A-TAAAATTTTATAATTTTT
17286142 ATAAAA
1 ATAAAA
17286148 AAATTATTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
17 2 0.03
18 11 0.14
19 33 0.42
20 21 0.27
21 11 0.14
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (19 bp):
ATAAAATTTTATAATTTTT
Found at i:17286066 original size:20 final size:21
Alignment explanation
Indices: 17286041--17286084 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
17286031 TTTGTTATGA
17286041 TTTTTATAA-AATTTTATA-AT
1 TTTTTA-AAGAATTTTATATAT
*
17286061 TTTTTAAAGATTTTTATATAT
1 TTTTTAAAGAATTTTATATAT
17286082 TTT
1 TTT
17286085 CTGACTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTAAAGAATTTTATATAT
Found at i:17286121 original size:28 final size:28
Alignment explanation
Indices: 17286090--17286144 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
17286080 ATTTTCTGAC
17286090 TTTTAATAAAATTTAA-ATATTTTTATAT
1 TTTTAATAAAATTTAATA-ATTTTTATAT
*
17286118 TTTTATTAAAATTTAATAATTTTTATA
1 TTTTAATAAAATTTAATAATTTTTATA
17286145 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTAATAAAATTTAATAATTTTTATAT
Found at i:17286133 original size:38 final size:37
Alignment explanation
Indices: 17286026--17286137 Score: 100
Period size: 38 Copynumber: 2.9 Consensus size: 37
17286016 ATGAATTTCA
* **
17286026 TAAAATTTGTTATGATTTTTATAAAATTTTATAATTTTT
1 TAAAATTT-TTAT-ATTTTTATAAAATTTAATAATAATT
* * **
17286065 TAAAGATTTTTATATATTTTCTGACTTTTAATAA-AATT
1 TAAA-ATTTTTATAT-TTTTATAAAATTTAATAATAATT
17286103 TAAATATTTTTATATTTTTATTAAAATTTAATAAT
1 TAAA-ATTTTTATATTTTTA-TAAAATTTAATAAT
17286138 TTTTATAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
37 4 0.07
38 28 0.49
39 21 0.37
40 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (37 bp):
TAAAATTTTTATATTTTTATAAAATTTAATAATAATT
Found at i:17295049 original size:14 final size:12
Alignment explanation
Indices: 17295000--17295063 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
17294990 CAAAATATTT
*
17295000 AAATTTATT-TA
1 AAATTAATTATA
* *
17295011 AATTTACTTATA
1 AAATTAATTATA
* *
17295023 ATATCAATTATA
1 AAATTAATTATA
17295035 AAATTAAATTTATA
1 AAATT-AA-TTATA
17295049 AAA-TAATTATA
1 AAATTAATTATA
17295060 AAAT
1 AAAT
17295064 ATTTTAATTG
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
11 14 0.35
12 15 0.38
13 3 0.08
14 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATTAATTATA
Found at i:17301003 original size:48 final size:49
Alignment explanation
Indices: 17300932--17301156 Score: 219
Period size: 48 Copynumber: 4.7 Consensus size: 49
17300922 GGGTAAATTA
* * * *
17300932 CCGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCACATGTCGAGG
1 CCGATGTCATGTTCCAGACATGGTCTTACACTGAGCTCTCATATCGAGG
* * * * *
17300980 CCGATG-CTATGTTCCAGACATGGTCTTACAGT-AGCTCTCGTCTCAATG
1 CCGATGTC-ATGTTCCAGACATGGTCTTACACTGAGCTCTCATATCGAGG
* * * * **
17301028 CCGATGTCATGTTCCAAATATGGTCTTACACT-AGCTGTCATAACGTTG
1 CCGATGTCATGTTCCAGACATGGTCTTACACTGAGCTCTCATATCGAGG
* *
17301076 CCGATGTCATGTTCCAAACATGGTCTTACACTG-GCTCTCATAAT-GTGG
1 CCGATGTCATGTTCCAGACATGGTCTTACACTGAGCTCTCAT-ATCGAGG
* *
17301124 CCGATGTCATGTCCCAGACATGATCTTACACTG
1 CCGATGTCATGTTCCAGACATGGTCTTACACTG
17301157 GCACACATAT
Statistics
Matches: 149, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
47 2 0.01
48 145 0.97
49 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
CCGATGTCATGTTCCAGACATGGTCTTACACTGAGCTCTCATATCGAGG
Found at i:17308629 original size:43 final size:41
Alignment explanation
Indices: 17308582--17308749 Score: 142
Period size: 43 Copynumber: 4.0 Consensus size: 41
17308572 TCTACGACGT
* *
17308582 TGGCATCGATTTGAGATATCGTGTAAGACCGTGTCTGGGACA
1 TGGCATCGATTTGAGAT-TCATGTAAGACCATGTCTGGGACA
* ** *
17308624 CTGGCATCGATTAGAGATTTTGTGTAAGACCATGTTTGGGACA
1 -TGGCATCGATTTGAGA-TTCATGTAAGACCATGTCTGGGACA
* * * *
17308667 TCGGCATCGTATTT--TATTCATGTAAGACCCTATCTGGGATA
1 T-GGCATCG-ATTTGAGATTCATGTAAGACCATGTCTGGGACA
* * *
17308708 GTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGAC
1 -TGGCATCGATTTGAGATT-CATGTAAGACCATGTCTGGGAC
17308750 GTTGGCATTG
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
40 3 0.03
41 26 0.26
42 6 0.06
43 61 0.61
44 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (41 bp):
TGGCATCGATTTGAGATTCATGTAAGACCATGTCTGGGACA
Found at i:17308756 original size:43 final size:43
Alignment explanation
Indices: 17308560--17308757 Score: 129
Period size: 43 Copynumber: 4.7 Consensus size: 43
17308550 TATGATTTCG
** * *
17308560 TGTAAGACCACGTCTACGACGTTGGCATCGATTTGAGA-TATCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGAGATTA-CA
** ** ***
17308603 TGTAAGACCGTGTCTGGGACACTGGCATCGAT-TAGAGATTTTG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATAT-GAGATTACA
* * * * ***
17308646 TGTAAGACCATGTTTGGGACATCGGCATCG-TATTTTATT-CA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGAGATTACA
* * *
17308687 TGTAAGACC-CTATCTGGGATAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATATGAGATTACA
17308730 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
17308758 TGTACGATAT
Statistics
Matches: 119, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
41 22 0.18
42 13 0.11
43 82 0.69
44 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGAGATTACA
Found at i:17308757 original size:84 final size:85
Alignment explanation
Indices: 17308560--17308757 Score: 204
Period size: 84 Copynumber: 2.3 Consensus size: 85
17308550 TATGATTTCG
** * * *
17308560 TGTAAGACCACGTCTACGACGTTGGCATCGATTTGAGATATCGTGTAAGACCGTGTCTGGGACAC
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATTT-AGATATCATGTAAGACCCTATCTGGGACAC
***
17308625 TGGCATCGATTAGAGATTTTG
65 TGGCATCGATTAGAGATTACA
* * * * * * *
17308646 TGTAAGACCATGTTTGGGACATCGGCATCGTATTT-TAT-TCATGTAAGACCCTATCTGGGATAG
1 TGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTAGATATCATGTAAGACCCTATCTGGGACAC
*
17308709 TGGCATCGA-TATGTGATTACA
65 TGGCATCGATTA-GAGATTACA
17308730 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
17308758 TGTACGATAT
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
83 2 0.02
84 58 0.64
85 2 0.02
86 24 0.27
87 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (85 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTTAGATATCATGTAAGACCCTATCTGGGACACT
GGCATCGATTAGAGATTACA
Found at i:17310868 original size:59 final size:59
Alignment explanation
Indices: 17310776--17310894 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
17310766 GGATATGTAC
*
17310776 AAAGGGATGATGTGATATATGTACTTGTATATGTAATGAAATATGCTTAACCATAATTT
1 AAAGGGATGATGTGATATATGCACTTGTATATGTAATGAAATATGCTTAACCATAATTT
17310835 AAAGGGATGATGTGATATATGCACTTGTATATGTAATGAAATATGCTTAACCATAATTT
1 AAAGGGATGATGTGATATATGCACTTGTATATGTAATGAAATATGCTTAACCATAATTT
17310894 A
1 A
17310895 TGTATTCGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (59 bp):
AAAGGGATGATGTGATATATGCACTTGTATATGTAATGAAATATGCTTAACCATAATTT
Found at i:17311394 original size:24 final size:25
Alignment explanation
Indices: 17311331--17311396 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
17311321 CTTACAGATT
* *
17311331 TTTCAACTCGTAAAAGCTTATCGTA
1 TTTCAGCTCGTAAGAGCTTATCGTA
* *
17311356 TTTCAGCTTGGAAGAGCTTATCG-A
1 TTTCAGCTCGTAAGAGCTTATCGTA
**
17311380 TTTTGGCTCGTAAGAGC
1 TTTCAGCTCGTAAGAGC
17311397 ATACATGTAC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTCAGCTCGTAAGAGCTTATCGTA
Found at i:17312588 original size:21 final size:21
Alignment explanation
Indices: 17312564--17312617 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
17312554 ACAGCCTGAA
17312564 ACACGGGCGTGTCCCATAGCC
1 ACACGGGCGTGTCCCATAGCC
* * *
17312585 ACACGGGCATGTCCCCTGGCC
1 ACACGGGCGTGTCCCATAGCC
17312606 ACACGGGCGTGT
1 ACACGGGCGTGT
17312618 AACCCCTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.37, G:0.31, T:0.15
Consensus pattern (21 bp):
ACACGGGCGTGTCCCATAGCC
Found at i:17314341 original size:26 final size:26
Alignment explanation
Indices: 17314293--17314361 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 26
17314283 ATAGTAAAAT
* * *
17314293 AAAATGTTTAGATGAAACAATTATAC
1 AAAATGGTTATATGAAACAATTACAC
* * *
17314319 AAAATGGTTATATGGAACGATTACAT
1 AAAATGGTTATATGAAACAATTACAC
* *
17314345 GAAATGGTTATGTGAAA
1 AAAATGGTTATATGAAA
17314362 ATATATGTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (26 bp):
AAAATGGTTATATGAAACAATTACAC
Found at i:17317657 original size:30 final size:30
Alignment explanation
Indices: 17317621--17317681 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
17317611 TTCCCGAGCC
17317621 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
17317651 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
17317681 T
1 T
17317682 GTATTAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:17318152 original size:46 final size:46
Alignment explanation
Indices: 17318102--17318274 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
17318092 TGGTTGAGCA
17318102 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
17318148 TCCGAACTCGTTGAGTTGAGTCCGAGCTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
17318193 CATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
17318241 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
17318275 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.57
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:17324587 original size:22 final size:21
Alignment explanation
Indices: 17324551--17324609 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
17324541 TAAAAGGTTT
* *
17324551 TTACAAATCAAATCTCTATGA
1 TTACAAATCATATCTCTAAGA
17324572 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATC-TCTAAGA
*
17324595 TTACATATCATATCT
1 TTACAAATCATATCT
17324610 ACGATTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.15
22 18 0.55
23 10 0.30
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.37
Consensus pattern (21 bp):
TTACAAATCATATCTCTAAGA
Found at i:17326429 original size:5 final size:5
Alignment explanation
Indices: 17326419--17326447 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
17326409 CTATTTTTAT
17326419 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
17326448 AAGAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:17329231 original size:22 final size:21
Alignment explanation
Indices: 17329193--17329237 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
17329183 CATCTATCCA
17329193 TTTAATTATTTTAACTTCATAC
1 TTTAATTATTTTAACTTCA-AC
*
17329215 TTTAATCTA-TTTGACTTCAAC
1 TTTAAT-TATTTTAACTTCAAC
17329236 TT
1 TT
17329238 ACTTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 15 0.71
23 2 0.10
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAATTATTTTAACTTCAAC
Found at i:17329764 original size:21 final size:21
Alignment explanation
Indices: 17329725--17329763 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17329715 ATATTCGAGC
17329725 AATCATTTAACATATAAAAGT
1 AATCATTTAACATATAAAAGT
*
17329746 AATCATTTTACAT-TAAAA
1 AATCATTTAACATATAAAA
17329764 AAAAATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (21 bp):
AATCATTTAACATATAAAAGT
Found at i:17330666 original size:14 final size:15
Alignment explanation
Indices: 17330647--17330686 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
17330637 ATTTCACTTA
17330647 AAAATTTAAATTT-T
1 AAAATTTAAATTTAT
17330661 AAAATTTAAAATTTAT
1 AAAATTT-AAATTTAT
*
17330677 AAAAATTAAA
1 AAAATTTAAA
17330687 AATGATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 9 0.39
16 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTAAATTTAT
Found at i:17349414 original size:18 final size:19
Alignment explanation
Indices: 17349385--17349422 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
17349375 TGTTTTAAAT
*
17349385 TATTTATGAAAATTTTATA
1 TATTTATGAAAAATTTATA
17349404 TATTT-TGAAAAATTTATA
1 TATTTATGAAAAATTTATA
17349422 T
1 T
17349423 GACATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TATTTATGAAAAATTTATA
Found at i:17350973 original size:44 final size:42
Alignment explanation
Indices: 17350896--17350986 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 42
17350886 CATTTACTAA
* *
17350896 TCCAAAAAGAGTGACAAAATCACATATACCAGTTGTAAATGC
1 TCCAAAAAGAGTGAAAAAATCACACATACCAGTTGTAAATGC
*
17350938 TCCAAAAAGAGTGAAAAAAAATTACACATACCAGTTGTAAATGC
1 TCCAAAAAGAGTG--AAAAAATCACACATACCAGTTGTAAATGC
17350982 TCCAA
1 TCCAA
17350987 TCAAAATTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 13 0.30
44 31 0.70
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (42 bp):
TCCAAAAAGAGTGAAAAAATCACACATACCAGTTGTAAATGC
Found at i:17353110 original size:17 final size:17
Alignment explanation
Indices: 17353088--17353122 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17353078 AGGAAATGGG
*
17353088 TGAAAAAATGGCAAAAT
1 TGAAAAAATGCCAAAAT
*
17353105 TGAAAAATTGCCAAAAT
1 TGAAAAAATGCCAAAAT
17353122 T
1 T
17353123 AGCTAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (17 bp):
TGAAAAAATGCCAAAAT
Found at i:17353177 original size:11 final size:11
Alignment explanation
Indices: 17353161--17353185 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17353151 ATATCTAGAA
17353161 TTCTCTTCATT
1 TTCTCTTCATT
17353172 TTCTCTTCATT
1 TTCTCTTCATT
17353183 TTC
1 TTC
17353186 ATCAGCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:17354471 original size:25 final size:25
Alignment explanation
Indices: 17354442--17354493 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
17354432 AAGAATAATT
**
17354442 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
17354467 TGAATATCCGATATTGCTTACTAAA
1 TGAATATCCGATATTGCCTAATAAA
17354492 TG
1 TG
17354494 TCAAACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:17361754 original size:59 final size:58
Alignment explanation
Indices: 17361621--17361765 Score: 166
Period size: 59 Copynumber: 2.5 Consensus size: 58
17361611 CTATAAAGCT
* * * * *
17361621 TTCAAAGA-CTAACTTGAACAAAAAAAATTCAAGTCCCAATATAGGAACATTTGTCAAG
1 TTCAAA-ATCTAACTTGAAAAAAAAAAATTCAAGTCCCAATATAGAAACAATTATCAAA
* * * *
17361679 TTCAAAGTCTACCTTGAATAAAAAAAAATTCATGTCCTAATATAGAAACAATTATCAAA
1 TTCAAAATCTAACTTGAA-AAAAAAAAATTCAAGTCCCAATATAGAAACAATTATCAAA
* *
17361738 TTTAAAATCTAACTTGAAAAAAGAAAAT
1 TTCAAAATCTAACTTGAAAAAAAAAAAT
17361766 CCAGACCTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 24 0.33
59 48 0.67
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (58 bp):
TTCAAAATCTAACTTGAAAAAAAAAAATTCAAGTCCCAATATAGAAACAATTATCAAA
Found at i:17368041 original size:19 final size:19
Alignment explanation
Indices: 17368017--17368062 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
17368007 ATAATTTTCA
17368017 CATTTTACAAATAAATCCC
1 CATTTTACAAATAAATCCC
17368036 CATTTTACAAATAAATCCC
1 CATTTTACAAATAAATCCC
*
17368055 TATTTTAC
1 CATTTTAC
17368063 GTTTTCAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (19 bp):
CATTTTACAAATAAATCCC
Found at i:17374137 original size:10 final size:10
Alignment explanation
Indices: 17374122--17374194 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
17374112 CTTTTCTTGC
17374122 TCTTTTTCTT
1 TCTTTTTCTT
17374132 TCTTTTTCTT
1 TCTTTTTCTT
* *
17374142 TCGCTTTACTT
1 TC-TTTTTCTT
*
17374153 CTCTGTTTCTAT
1 -TCTTTTTCT-T
*
17374165 TC-TTTTGTT
1 TCTTTTTCTT
17374174 TC-TTTTCTAT
1 TCTTTTTCT-T
17374184 TCTTTTTCTT
1 TCTTTTTCTT
17374194 T
1 T
17374195 TATTTAAACA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
9 8 0.16
10 21 0.42
11 18 0.36
12 3 0.06
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.71
Consensus pattern (10 bp):
TCTTTTTCTT
Found at i:17383411 original size:18 final size:18
Alignment explanation
Indices: 17383388--17383422 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17383378 ACAAAGAAGA
17383388 AAAG-AAGGAAAGAAAGGG
1 AAAGAAAGGAAA-AAAGGG
17383406 AAAGAAAGGAAAAAAGG
1 AAAGAAAGGAAAAAAGG
17383423 AAATTAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
AAAGAAAGGAAAAAAGGG
Found at i:17384098 original size:18 final size:19
Alignment explanation
Indices: 17384063--17384101 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
17384053 TAAGTATTGA
17384063 TATTGAATTGAATGAAAATG
1 TATTGAATTG-ATGAAAATG
17384083 TATTGAATTG-TGAAAATG
1 TATTGAATTGATGAAAATG
17384101 T
1 T
17384102 GTGAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
TATTGAATTGATGAAAATG
Found at i:17388011 original size:38 final size:39
Alignment explanation
Indices: 17387919--17388011 Score: 95
Period size: 38 Copynumber: 2.4 Consensus size: 39
17387909 TTTTTTCTAT
*
17387919 AAAATAAGAATATATTATTTTAACATATAGTTTTGTTTAAC
1 AAAATAAGAATATATTATTTT-A-ATATAGTTATGTTTAAC
*
17387960 AAAAT-TGATATATATATATTTGT-ATATA-TTAT-TTTAAC
1 AAAATAAGA-ATATAT-TATTT-TAATATAGTTATGTTTAAC
17387998 AAAATAAGAATATA
1 AAAATAAGAATATA
17388012 CTGTTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
38 16 0.36
39 5 0.11
40 7 0.16
41 11 0.24
42 5 0.11
43 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (39 bp):
AAAATAAGAATATATTATTTTAATATAGTTATGTTTAAC
Found at i:17400361 original size:177 final size:177
Alignment explanation
Indices: 17400049--17400619 Score: 910
Period size: 177 Copynumber: 3.2 Consensus size: 177
17400039 GAAATTGCAG
* *
17400049 ATCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCACCAGCCTTATTTCTCTGAGGTAGC
1 ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
* * *
17400114 AAGAGAGCAGGTTGAAGGTACAAGTCTTATCTTCCTGAGGTAGCAAGAAAGTAGACTAAAATTGC
66 AAGAGAGCAGGTTGAAGGTACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAATTAC
* *
17400179 AGATCTTATCTCCATGTATCGGCTATGGAGCATATCGAAGATGGCGA
131 AGATCTTATCTCCATGTATCGGCTATGGAGTAGATCGAAGATGGCGA
*
17400226 ATCTTATCTCCATGTATCGG-TAATAGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAG
1 ATCTTATCTCCATGTATCGGCT-ATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAG
* * * * *
17400290 CAAGAGAGCAGGTTGAAGGTACAAGTCTTATCTTCCTAAGGTAGTAAGGAAGCAAACTGAAATTC
65 CAAGAGAGCAGGTTGAAGGTACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAATTA
17400355 CAGATCTTATCTCCATGTATCGGCTATGGAGTAGATCGAAGATGGCGA
130 CAGATCTTATCTCCATGTATCGGCTATGGAGTAGATCGAAGATGGCGA
* * * *
17400403 ATCTTATCTCTATGTATCGGTTATGGAGCAGATTTTAGCCACCGGTCTTATCTCTCTGAGGTAGC
1 ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
*
17400468 AAGAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAAATTA
66 AAGAGAGCAGGTTGAAGGTACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACT-AAAATTA
* * * *
17400533 CAAATCTTATCTCCATGTATTGGCTATAGAATAGATCGAAGATGGCGA
130 CAGATCTTATCTCCATGTATCGGCTATGGAGTAGATCGAAGATGGCGA
*
17400581 ATCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGC
1 ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
17400620 TATTGGCTTT
Statistics
Matches: 364, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
176 1 0.00
177 275 0.76
178 88 0.24
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (177 bp):
ATCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGC
AAGAGAGCAGGTTGAAGGTACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAAATTAC
AGATCTTATCTCCATGTATCGGCTATGGAGTAGATCGAAGATGGCGA
Found at i:17412072 original size:21 final size:21
Alignment explanation
Indices: 17412048--17412087 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17412038 TTTAAATTAT
17412048 ATATTT-ATTCTTAATTTTTAA
1 ATATTTCATT-TTAATTTTTAA
*
17412069 ATATTTCATTTTATTTTTT
1 ATATTTCATTTTAATTTTT
17412088 TTTAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
ATATTTCATTTTAATTTTTAA
Found at i:17412664 original size:23 final size:23
Alignment explanation
Indices: 17412632--17412682 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
17412622 ATAAAATTAA
*
17412632 AAAATTAAAT-TA-ATTATGAGTAG
1 AAAATCAAATATATATT-TGAG-AG
17412655 AAAATCAAATATATATTTGAGAG
1 AAAATCAAATATATATTTGAGAG
17412678 AAAAT
1 AAAAT
17412683 ATTTTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 16 0.64
24 6 0.24
25 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (23 bp):
AAAATCAAATATATATTTGAGAG
Found at i:17415695 original size:42 final size:42
Alignment explanation
Indices: 17415632--17415758 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
17415622 CTTCGTTTTC
** * *
17415632 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
17415675 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
17415716 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
17415757 TC
1 TC
17415759 TCACTGATGT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:17415900 original size:31 final size:31
Alignment explanation
Indices: 17415865--17416075 Score: 286
Period size: 31 Copynumber: 6.8 Consensus size: 31
17415855 CTTGTCACTT
*
17415865 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
17415896 GTAGCCGGAGCTACCA-TTATTCATTGATCAG
1 GTAGCCGAAGCTACCACTT-TTCACTGATCAG
* *
17415927 GTAGCCGGAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
17415958 GTAGCCGGAA-CTACCACTTTTCACTGATTAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
17415989 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
17416020 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
17416051 GTAGCTGGAA-CTACCACTTTTCACT
1 GTAGC-CGAAGCTACCACTTTTCACT
17416076 TGTCATTTGT
Statistics
Matches: 166, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
30 4 0.02
31 155 0.93
32 7 0.04
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:17416024 original size:93 final size:93
Alignment explanation
Indices: 17415865--17416075 Score: 318
Period size: 93 Copynumber: 2.3 Consensus size: 93
17415855 CTTGTCACTT
* * *
17415865 GTAGCC-GAAGCTACCACTATTCACTGATCAGGTAGCCGGAGCTACCATTATTCATTGATCAGGT
1 GTAGCCGGAA-CTACCACTTTTCACTGATCAGGTAGCCGGAACTACCATTATTCACTGATCAGGT
* * *
17415929 AGCCGGAGCTACCACTTTTCACTGATTAG
65 AGCAGAAGCTACCACTTTTCACTGATCAG
*
17415958 GTAGCCGGAACTACCACTTTTCACTGATTAGGTAGCCGGAACTACCACTT-TTCACTGATCAGGT
1 GTAGCCGGAACTACCACTTTTCACTGATCAGGTAGCCGGAACTACCA-TTATTCACTGATCAGGT
17416022 AGCAGAAGCTACCACTTTTCACTGATCAG
65 AGCAGAAGCTACCACTTTTCACTGATCAG
*
17416051 GTAGCTGGAACTACCACTTTTCACT
1 GTAGCCGGAACTACCACTTTTCACT
17416076 TGTCATTTGT
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
93 103 0.95
94 5 0.05
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (93 bp):
GTAGCCGGAACTACCACTTTTCACTGATCAGGTAGCCGGAACTACCATTATTCACTGATCAGGTA
GCAGAAGCTACCACTTTTCACTGATCAG
Found at i:17418884 original size:39 final size:39
Alignment explanation
Indices: 17418836--17418982 Score: 186
Period size: 39 Copynumber: 3.8 Consensus size: 39
17418826 TTAATAGGGG
*
17418836 TAAACTACTGTATTGAATAATTGATAGTTACTGAATAAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * * *
17418875 TAAATTACTGTATTGAATAATTAATAGTTATTGAATAAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * *
17418914 TAAACTACTGCACTGAATATTTGATAGTTACTGAATGAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * * *
17418953 TAAATTACTATACTGAATAACTGATTGTTA
1 TAAACTACTGTACTGAATAATTGATAGTTA
17418983 TTGATTGTTT
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 92 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (39 bp):
TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
Found at i:17418893 original size:21 final size:20
Alignment explanation
Indices: 17418836--17418923 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 20
17418826 TTAATAGGGG
17418836 TAAACTACTGTATTGAATAA-
1 TAAA-TACTGTATTGAATAAC
** * *
17418856 TTGATAGT-TACTGAATAAC
1 TAAATACTGTATTGAATAAC
17418875 TAAATTACTGTATTGAATAA-
1 TAAA-TACTGTATTGAATAAC
* *
17418895 TTAATAGT-TATTGAATAAC
1 TAAATACTGTATTGAATAAC
17418914 TAAACTACTG
1 TAAA-TACTG
17418924 CACTGAATAT
Statistics
Matches: 50, Mismatches: 12, Indels: 11
0.68 0.16 0.15
Matches are distributed among these distances:
18 19 0.38
19 11 0.22
20 11 0.22
21 9 0.18
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (20 bp):
TAAATACTGTATTGAATAAC
Found at i:17418908 original size:18 final size:18
Alignment explanation
Indices: 17418846--17418912 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
17418836 TAAACTACTG
*
17418846 TATTGAATAATTGATAGT
1 TATTGAATAATTAATAGT
* * *
17418864 TACTGAATAACTAAATTACT
1 TATTGAATAA-TTAA-TAGT
17418884 GTATTGAATAATTAATAGT
1 -TATTGAATAATTAATAGT
17418903 TATTGAATAA
1 TATTGAATAA
17418913 CTAAACTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 19 0.49
19 5 0.13
20 6 0.15
21 9 0.23
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.40
Consensus pattern (18 bp):
TATTGAATAATTAATAGT
Found at i:17418970 original size:78 final size:78
Alignment explanation
Indices: 17418836--17418986 Score: 221
Period size: 78 Copynumber: 1.9 Consensus size: 78
17418826 TTAATAGGGG
* * * * *
17418836 TAAACTACTGTATTGAATAATTGATAGTTACTGAATAACTAAATTACTGTATTGAATAATTAATA
1 TAAACTACTGCACTGAATAATTGATAGTTACTGAATAACTAAATTACTATACTGAATAACTAATA
17418901 GTTATTGAATAAC
66 GTTATTGAATAAC
* * * *
17418914 TAAACTACTGCACTGAATATTTGATAGTTACTGAATGACTAAATTACTATACTGAATAACTGATT
1 TAAACTACTGCACTGAATAATTGATAGTTACTGAATAACTAAATTACTATACTGAATAACTAATA
17418979 GTTATTGA
66 GTTATTGA
17418987 TTGTTTGATA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (78 bp):
TAAACTACTGCACTGAATAATTGATAGTTACTGAATAACTAAATTACTATACTGAATAACTAATA
GTTATTGAATAAC
Found at i:17421409 original size:19 final size:19
Alignment explanation
Indices: 17421385--17421446 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
17421375 TTTATACATT
17421385 TTTATTTTAATATGCACAA
1 TTTATTTTAATATGCACAA
** **
17421404 TTTA--TTACCAT-CA-TT
1 TTTATTTTAATATGCACAA
17421419 TTTATTTTAATATGCACAA
1 TTTATTTTAATATGCACAA
17421438 TTTATTTTA
1 TTTATTTTA
17421447 TTGTTTTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
15 4 0.13
16 2 0.06
17 10 0.32
18 2 0.06
19 13 0.42
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTATTTTAATATGCACAA
Done.