Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 37 of 344
Found at i:12403381 original size:28 final size:28
Alignment explanation
Indices: 12403345--12403442 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
12403335 ACAAAGTGCA
*
12403345 AATAACGATAAGCACCAAAGTGCAAAAT
1 AATAACGATAAGCACTAAAGTGCAAAAT
*
12403373 AATAACGATAAGCACTAAAGTGCAAATTTT
1 AATAACGATAAGCACTAAAGTGCAAA--AT
* * * *
12403403 TACAATGATAAGCACTGAAGTGCAAAAT
1 AATAACGATAAGCACTAAAGTGCAAAAT
12403431 AAT-ACGATAAGC
1 AATAACGATAAGC
12403443 GCGCTAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.14
28 27 0.47
30 23 0.40
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.20
Consensus pattern (28 bp):
AATAACGATAAGCACTAAAGTGCAAAAT
Found at i:12407515 original size:16 final size:16
Alignment explanation
Indices: 12407477--12407515 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
12407467 AAAAAAATAT
*
12407477 AAATAAAATATTCAAA
1 AAATAAAACATTCAAA
12407493 AACATAAAACATTCAAA
1 AA-ATAAAACATTCAAA
12407510 AAATAA
1 AAATAA
12407516 TCAATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAACATTCAAA
Found at i:12414494 original size:23 final size:22
Alignment explanation
Indices: 12414447--12414496 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
12414437 TTATCCATTC
*
12414447 ATAAATCTATACACTATATGCT
1 ATAAATCTATACACTATATACT
* *
12414469 ATAATATCTATACTCTATATATT
1 ATAA-ATCTATACACTATATACT
12414492 ATAAA
1 ATAAA
12414497 CAAATTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAAATCTATACACTATATACT
Found at i:12417112 original size:9 final size:9
Alignment explanation
Indices: 12417098--12417311 Score: 89
Period size: 9 Copynumber: 22.8 Consensus size: 9
12417088 TATTTTTCTC
12417098 ATAAAAATT
1 ATAAAAATT
**
12417107 ATAAAAAAA
1 ATAAAAATT
*
12417116 ACAAAAAGTT
1 ATAAAAA-TT
12417126 ATAAAAATT
1 ATAAAAATT
* *
12417135 CAGGAAACATT
1 -A-TAAAAATT
12417146 ATTAAAAA-T
1 A-TAAAAATT
*
12417155 ATTAAAATT
1 ATAAAAATT
*
12417164 GATATAAACTT
1 -ATA-AAAATT
* *
12417175 ATTAAAACT
1 ATAAAAATT
*
12417184 ATAAACA-T
1 ATAAAAATT
12417192 ATAAAAACTT
1 ATAAAAA-TT
*
12417202 ATAAATATT
1 ATAAAAATT
12417211 ATAAAAA-T
1 ATAAAAATT
12417219 AT-AAAATT
1 ATAAAAATT
*
12417227 AATAAAATTT
1 -ATAAAAATT
*
12417237 ATTTAAAA-T
1 A-TAAAAATT
12417246 A-AAAAATTT
1 ATAAAAA-TT
* *
12417255 ATTAGAATTCT
1 A-TAAAAAT-T
* *
12417266 TTAAAAATA
1 ATAAAAATT
12417275 ATAAAAATT
1 ATAAAAATT
*
12417284 GTAAAAAATT
1 AT-AAAAATT
12417294 ATAAAAATAT
1 ATAAAAAT-T
12417304 ATTAAAAA
1 A-TAAAAA
12417312 CTTGAACTAG
Statistics
Matches: 149, Mismatches: 36, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
7 8 0.05
8 16 0.11
9 56 0.38
10 48 0.32
11 21 0.14
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:12417188 original size:17 final size:17
Alignment explanation
Indices: 12417166--12417233 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
12417156 TTAAAATTGA
*
12417166 TATAAACTTATTAAAAC
1 TATAAAATTATTAAAAC
*
12417183 TATAAACA-TATAAAAAC
1 TATAAA-ATTATTAAAAC
*
12417200 TTATAAATATTA-TAAAAA
1 -TATAAA-ATTATTAAAAC
*
12417218 TATAAAATTAATAAAA
1 TATAAAATTATTAAAA
12417234 TTTATTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 4 0.10
17 25 0.60
18 11 0.26
19 2 0.05
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAATTATTAAAAC
Found at i:12417695 original size:19 final size:19
Alignment explanation
Indices: 12417663--12417710 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
12417653 TTTTGATTAC
12417663 TTTTTAT-ATATTTTAATAA
1 TTTTTATGAT-TTTTAATAA
*
12417682 TTTTTGTGATTTTTAATAA
1 TTTTTATGATTTTTAATAA
12417701 TTTTTATGAT
1 TTTTTATGAT
12417711 AAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTATGATTTTTAATAA
Found at i:12418269 original size:26 final size:26
Alignment explanation
Indices: 12418240--12418292 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12418230 TGCGGACGTA
12418240 GCAAAACTGCTGTATTTGTAAACTTC
1 GCAAAACTGCTGTATTTGTAAACTTC
12418266 GCAAAACTGCTGTATTTGTAAACTTC
1 GCAAAACTGCTGTATTTGTAAACTTC
12418292 G
1 G
12418293 TTTTGTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (26 bp):
GCAAAACTGCTGTATTTGTAAACTTC
Found at i:12422583 original size:11 final size:10
Alignment explanation
Indices: 12422567--12422622 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
12422557 AAAAAAATAT
12422567 TATTTTTATA
1 TATTTTTATA
12422577 TATTTTTA-A
1 TATTTTTATA
*
12422586 TA--TTTATT
1 TATTTTTATA
12422594 TATTTTTA-A
1 TATTTTTATA
12422603 TA-TTTTATTA
1 TATTTTTA-TA
12422613 TATTTTTATA
1 TATTTTTATA
12422623 AAACACTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 4 0.11
8 7 0.18
9 5 0.13
10 17 0.45
11 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTTATA
Found at i:12422597 original size:17 final size:18
Alignment explanation
Indices: 12422570--12422620 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
12422560 AAAATATTAT
*
12422570 TTTTATATATTTTTAATA
1 TTTTATTTATTTTTAATA
12422588 -TTTATTTATTTTTAATA
1 TTTTATTTATTTTTAATA
12422605 TTTTATTATATTTTTA
1 TTTTATT-TATTTTTA
12422621 TAAAACACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 16 0.53
18 6 0.20
19 8 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTATTTTTAATA
Found at i:12422597 original size:27 final size:27
Alignment explanation
Indices: 12422566--12422617 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12422556 AAAAAAAATA
12422566 TTATTTTTATATATTTT-TAATATTTAT
1 TTATTTTTA-ATATTTTATAATATTTAT
*
12422593 TTATTTTTAATATTTTATTATATTT
1 TTATTTTTAATATTTTATAATATTT
12422618 TTATAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TTATTTTTAATATTTTATAATATTTAT
Found at i:12425349 original size:21 final size:19
Alignment explanation
Indices: 12425315--12425376 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
12425305 TAAGCTATAT
12425315 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
12425337 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
12425359 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
12425377 GTATTTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:12425429 original size:22 final size:22
Alignment explanation
Indices: 12425401--12425443 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12425391 AAAATATGGT
*
12425401 AAAATAAATAGTATAAAAAAAC
1 AAAATAAATAATATAAAAAAAC
*
12425423 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATAAAAAAA
12425444 TATAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAATAATATAAAAAAAC
Found at i:12429776 original size:10 final size:10
Alignment explanation
Indices: 12429744--12429795 Score: 56
Period size: 11 Copynumber: 5.3 Consensus size: 10
12429734 TTATTATGAT
12429744 TTTTTAATAA
1 TTTTTAATAA
12429754 TTATTTAATAA
1 TT-TTTAATAA
*
12429765 TTTTTGATAA
1 TTTTTAATAA
12429775 -TTTT-AT-A
1 TTTTTAATAA
12429782 TTTTTAAATAA
1 TTTTT-AATAA
12429793 TTT
1 TTT
12429796 GTTGCAACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
7 1 0.03
8 6 0.17
9 4 0.11
10 11 0.31
11 14 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:12431464 original size:14 final size:14
Alignment explanation
Indices: 12431439--12431474 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
12431429 TCTTTTTATG
*
12431439 TTTTAAATTTTTTA
1 TTTTAAATATTTTA
12431453 -TTTAAATATTTTA
1 TTTTAAATATTTTA
12431466 TTTTAAATA
1 TTTTAAATA
12431475 AAATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATATTTTA
Found at i:12442066 original size:20 final size:20
Alignment explanation
Indices: 12442041--12442082 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12442031 ATTTGTAGAG
*
12442041 TATTGATGAATATTTTATAT
1 TATTGATGAATATTTCATAT
*
12442061 TATTGATGGATATTTCATAT
1 TATTGATGAATATTTCATAT
12442081 TA
1 TA
12442083 AAAATTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (20 bp):
TATTGATGAATATTTCATAT
Found at i:12442832 original size:22 final size:22
Alignment explanation
Indices: 12442807--12442850 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12442797 TAGTCTTATA
12442807 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
12442829 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
12442851 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:12442886 original size:13 final size:14
Alignment explanation
Indices: 12442870--12442911 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
12442860 TTTAAATTTT
12442870 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
12442883 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
12442898 ATTTTAAATAATAT
1 ATTTT-AATAATAT
12442912 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:12442896 original size:16 final size:16
Alignment explanation
Indices: 12442874--12442910 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12442864 AATTTTATTT
12442874 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
12442891 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
12442906 TAATA
1 TAATA
12442911 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:12442963 original size:15 final size:15
Alignment explanation
Indices: 12442943--12442999 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
12442933 ATTCAATATT
12442943 AATATTTTAATAATA
1 AATATTTTAATAATA
*
12442958 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
12442977 AATATATTAATAATA
1 AATATTTTAATAATA
*
12442992 AATGTTTT
1 AATATTTT
12443000 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:12448050 original size:37 final size:37
Alignment explanation
Indices: 12447996--12448073 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
12447986 TATTTCAAGA
12447996 CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
1 CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
*
12448033 CAAGATTAATTATTAAAATAGTTATTTTTGTTTGTCT
1 CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
12448070 CAAG
1 CAAG
12448074 TTATATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (37 bp):
CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
Found at i:12450462 original size:2 final size:2
Alignment explanation
Indices: 12450457--12450494 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
12450447 CAAGTTTTAC
* *
12450457 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12450495 TACTTAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12451112 original size:25 final size:23
Alignment explanation
Indices: 12451056--12451120 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
12451046 TCTTATTTTT
*
12451056 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
12451075 TATTTGTTTTTATATTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
12451098 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
12451121 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 5 0.13
21 2 0.05
23 6 0.15
24 3 0.08
25 12 0.31
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:12454790 original size:40 final size:39
Alignment explanation
Indices: 12454669--12454802 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 39
12454659 GACTTCAAGT
* * *
12454669 CGATGAGACATTGGATGTCAAATTATTACTTC-AGATTAATT
1 CGATGAGACACTGGGTGTC-AATTATTACTTCGA-ATT-ATC
* * * ** *
12454710 TGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGAATTATC
*
12454747 CGATGAGACACTGGGTGTCAACTTATTGCTTCGAATTATC
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGAATTATC
**
12454787 CGATGAGGTACTGGGT
1 CGATGAGACACTGGGT
12454803 ACCAAGCTGG
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
37 19 0.27
38 9 0.13
39 2 0.03
40 27 0.38
41 14 0.20
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGAATTATC
Found at i:12457661 original size:15 final size:16
Alignment explanation
Indices: 12457641--12457677 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
12457631 CCATGTAAAC
*
12457641 ACAAAACAAACAAAA-
1 ACAAAACAAAAAAAAT
12457656 ACAAAACAAAAAAAAT
1 ACAAAACAAAAAAAAT
12457672 ACAAAA
1 ACAAAA
12457678 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (16 bp):
ACAAAACAAAAAAAAT
Found at i:12457662 original size:11 final size:11
Alignment explanation
Indices: 12457637--12457678 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
12457627 GGGCCCATGT
12457637 AAACACAAAAC-
1 AAACA-AAAACA
12457648 AAACAAAAACA
1 AAACAAAAACA
12457659 AAACAAAAA-A
1 AAACAAAAACA
12457669 AATACAAAAA
1 AA-ACAAAAA
12457679 ATATATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:12459901 original size:131 final size:131
Alignment explanation
Indices: 12459716--12460075 Score: 431
Period size: 131 Copynumber: 2.7 Consensus size: 131
12459706 ATAAGCATTC
* * * * *
12459716 ATTC-AAAAATTCTTCAAAAACGAAGACGAGATTCGTTGTTTGGCAATTCGCGGAATCGTGCCCT
1 ATTCTAAAAATTCTTC-AAAACGAAGGCGAGATTCGATATTT-GAAATTCGCGGAATCATGCCCT
12459780 AACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCA
64 AACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCA
**
12459845 TGT
129 CAT
* * *
12459848 CTT-TTAAAATTCTTCAAAACGAAGGCGAGATTCGATATTTAGTAATTCGCGGAATCATGCCCTA
1 ATTCTAAAAATTCTTCAAAACGAAGGCGAGATTCGATATTT-GAAATTCGCGGAATCATGCCCTA
* * * *
12459912 ACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAGATTTCATTCAC
65 ACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCAC
12459977 AT
130 AT
* * * * * *
12459979 ATTCTAAAAATTATTTAAAACGAAGGCAATATTC-ACATTTGAAAATTCG-AGAATCATGCCCTA
1 ATTCTAAAAATTCTTCAAAACGAAGGCGAGATTCGATATTTG-AAATTCGCGGAATCATGCCCTA
* * ** *
12460042 TCGTGCTGGGTTGTGATTTCTCGTTTGCTCAAAA
65 ACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAA
12460076 CGATCGAACA
Statistics
Matches: 197, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
130 43 0.22
131 117 0.59
132 37 0.19
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (131 bp):
ATTCTAAAAATTCTTCAAAACGAAGGCGAGATTCGATATTTGAAATTCGCGGAATCATGCCCTAA
CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACA
T
Found at i:12464497 original size:13 final size:14
Alignment explanation
Indices: 12464475--12464506 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
12464465 GAGATCTTCA
12464475 AAAAATAATAAAAT
1 AAAAATAATAAAAT
12464489 AAAAA-AATAAAAT
1 AAAAATAATAAAAT
12464502 AAAAA
1 AAAAA
12464507 GAAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:12465824 original size:45 final size:44
Alignment explanation
Indices: 12465773--12466223 Score: 139
Period size: 45 Copynumber: 10.2 Consensus size: 44
12465763 GAAATTGAAA
**
12465773 TGAAGCAGATCGAAGACGGTGAATCTGAGCTTCCTGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCAATCT-AGCTTCCTGAAGTTGCAG
** ** * * * *
12465818 TGAAGCAGATTTAAG-CCACCAACCTAGCTCCCTAAAGTTGTAG
1 TGAAGCAGATCGAAGACGGCCAATCTAGCTTCCTGAAGTTGCAG
* * * * **** * *
12465861 TGGAGTAG-GCTAA-AATTTCAGATCTCGTTTCCTTGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCA-ATCTAGCTTCC-TGAAGTTGCAG
* *
12465905 TAAAGCAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCAATCT-AGCTTCCTGAAGTTGCAG
** ** * * * *
12465950 TGAAGCAGATTTAAG-CCACCAACCTAGCTCCCTAAAGTTGTAG
1 TGAAGCAGATCGAAGACGGCCAATCTAGCTTCCTGAAGTTGCAG
* * * * **** * * *
12465993 TGGAGTAG-GCTAA-AATTTCAGGTCTTGTTTTCCTGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCA-ATCTAG-CTTCCTGAAGTTGCAG
* * *
12466037 TGAAACAGATCGAAGACGGCGAATCTGAGCTTCATGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCAATCT-AGCTTCCTGAAGTTGCAG
* ** ** * * *
12466082 TGAAGGAGATTTAAG-CCACCATTCTAGTTTCCT-AAGGTTGTAG
1 TGAAGCAGATCGAAGACGGCCAATCTAGCTTCCTGAA-GTTGCAG
* * * * **** * * *
12466125 TGGAGTAG-GCTAA-AATTTCAGATATTGTTTTCCTGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCA-ATCTAG-CTTCCTGAAGTTGCAG
** *
12466169 TGAAATAGATCGAAGACGGCGAATCTGAGCTTCCTGAAGTTGCAG
1 TGAAGCAGATCGAAGACGGCCAATCT-AGCTTCCTGAAGTTGCAG
12466214 TGAAGCAGAT
1 TGAAGCAGAT
12466224 TTAAGCCACC
Statistics
Matches: 274, Mismatches: 112, Indels: 40
0.64 0.26 0.09
Matches are distributed among these distances:
42 17 0.06
43 73 0.27
44 66 0.24
45 105 0.38
46 13 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
TGAAGCAGATCGAAGACGGCCAATCTAGCTTCCTGAAGTTGCAG
Found at i:12465972 original size:132 final size:132
Alignment explanation
Indices: 12465747--12466935 Score: 1372
Period size: 132 Copynumber: 9.1 Consensus size: 132
12465737 GCTAAAATTT
* * * *
12465747 TAGATCTTGTTTCCTTGAAATTGAAATGAAGCAGATCGAAGACGGTGAATCTGAGCTTCCTGAAG
1 TAGATCTTGTTTCC-TGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTTCCTGAAG
* * *
12465812 TTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT-AAAA
65 TTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGA
12465876 TT-
130 TTA
* * *
12465878 TCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTGAGCTTCCTGAA
1 T-AGATCTTGTTTCC-TGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTTCCTGAA
* * *
12465943 GTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT-AAA
64 GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAG
12466007 ATT-
129 ATTA
* * *
12466010 TCAGGTCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCATGAA
1 T-AGATCTTG-TTTCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTTCCTGAA
* * * * *
12466075 GTTGCAGTGAAGGAGATTTAAGCCACCATTCTAGTTTCCTAAGGTTGTAGTGGAGTAGGCT-AAA
64 GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAG
12466139 ATT-
129 ATTA
* **
12466142 TCAGATATTGTTTTCCTGAAGTTGCAGTGAAATAGATCGAAGACGGCGAATCTGAGCTTCCTGAA
1 T-AGATCTTG-TTTCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTTCCTGAA
*
12466207 GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTTCCTAAGGTTGTAGTGGAGTAGGCTGAAG
64 GTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAG
12466272 ATTA
129 ATTA
* ** *
12466276 TAGATCTTGTTTCCCTG-AGATTGTAGTGGGGCAGATCGAAGACGGTGAATCT-AGGCTTCCTGA
1 TAGATCTTGTTT-CCTGAAG-TTGCAGTGAAGCAGATCGAAGACGGCGAATCTGA-GCTTCCTGA
* * * * *
12466339 TGATGCAGCGAAGCAAATTTAAG----CATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAA
63 AGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAA
12466400 GATTA
128 GATTA
*
12466405 TAGATCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCCTGAAG
1 TAGATCTTG-TTTCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTTCCTGAAG
*
12466470 TTGCAGTGAA-CAGATTTAAGCCACCATCCTAGCTTCCTAAGGTTGTAGTGGAGTAGGCTGAAGA
65 TTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGA
12466534 TTA
130 TTA
**
12466537 TAGATCTTGTTTTCCTG-AGATTGCAGTGGGGCAGATCGAAGACGGCGAATCT-AGGCTTCCTGA
1 TAGATCTTG-TTTCCTGAAG-TTGCAGTGAAGCAGATCGAAGACGGCGAATCTGA-GCTTCCTGA
* * * *
12466600 TGATGCAGCGAAGCAGATTTAAG----CATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAA
63 AGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAA
12466661 GATTA
128 GATTA
** *
12466666 TAGATCTTGTTTCCCTG-AGATTGCAGTGGGGCAGATCGAAGACGGTGAATCT-AGGCTTCCTGA
1 TAGATCTTGTTT-CCTGAAG-TTGCAGTGAAGCAGATCGAAGACGGCGAATCTGA-GCTTCCTGA
* * * ** *
12466729 TGTTGCAGTAAAGCAAATTTAAG-CA--AGTCCTAGCTTTCTAAAGTTGTAGTGGAGTAGGCTGA
63 AGTTGCAGTGAAGCAGATTTAAGCCACCA-TCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGA
* *
12466791 GGATTG
127 AGATTA
* * * * * ***
12466797 TAGATCTCGTCTCCCTGAAGTTGCAGTGAGGCAAATCAAAGACGATAAATCTTG-GCTTCCTGAA
1 TAGATCTTGT-TTCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATC-TGAGCTTCCTGAA
* * * * * *
12466861 GATGCAGCGAAGCAGATTTAAG-CA--AGTCCTAGCTCCTTAAAGTTGTAGTGAAGTGGGCTGAA
64 GTTGCAGTGAAGCAGATTTAAGCCACCA-TCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAA
*
12466923 GATTG
128 GATTA
*
12466928 TAGGTCTT
1 TAGATCTT
12466936 ATCTTCTCGA
Statistics
Matches: 943, Mismatches: 90, Indels: 50
0.87 0.08 0.05
Matches are distributed among these distances:
128 12 0.01
129 217 0.23
130 7 0.01
131 150 0.16
132 471 0.50
133 85 0.09
134 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (132 bp):
TAGATCTTGTTTCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTGAGCTTCCTGAAGT
TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGAT
TA
Found at i:12466527 original size:261 final size:259
Alignment explanation
Indices: 12465747--12466935 Score: 1448
Period size: 261 Copynumber: 4.5 Consensus size: 259
12465737 GCTAAAATTT
* * * *
12465747 TAGATCTTGTTTCCTTGAAATTGAAATGAAGCAGATCGAAGACGGTGAATCTGAGCTTCCTGAAG
1 TAGATCTTGTTTCCCTG-AATTGCAGTGAGGCAGATCGAAGACGGTGAATCTG-GCTTCCTGAAG
* * * * *
12465812 TTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT-AAAA
64 ATGCAGCGAAGCAGATTTAAG----CATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGA
* *
12465876 TTTCAGATCTCG-TTTCCTTGAAGTTGCAGT-AAAGCAGATCGAAGACGGCAAATCTGAGCTTCC
125 TTT-AGATCTTGTTTTCC-TGAAGTTGCAGTGAAA-CAGATCGAAGACGGCGAATCTGAGCTTCC
* *
12465939 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT
187 TGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTTCCTAAAGTTGTAGTGGAGTAGGCT
*
12466004 -AAAATT-
252 GAAGATTA
* * ** * *
12466010 TCAGGTCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCATGAA
1 T-AGATCTTGTTTCCCTGAA-TTGCAGTGAGGCAGATCGAAGACGGTGAATCTG-GCTTCCTGAA
* * * * * * *
12466075 GTTGCAGTGAAGGAGATTTAAGCCACCATTCTAGTTTCCTAAGGTTGTAGTGGAGTAGGCT-AAA
63 GATGCAGCGAAGCAGATTTAAG----CATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAG
* *
12466139 ATTTCAGATATTGTTTTCCTGAAGTTGCAGTGAAATAGATCGAAGACGGCGAATCTGAGCTTCCT
124 ATTT-AGATCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCCT
*
12466204 GAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTTCCTAAGGTTGTAGTGGAGTAGGCTG
188 GAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTTCCTAAAGTTGTAGTGGAGTAGGCTG
12466269 AAGATTA
253 AAGATTA
* * *
12466276 TAGATCTTGTTTCCCTGAGATTGTAGTGGGGCAGATCGAAGACGGTGAATCTAGGCTTCCTGATG
1 TAGATCTTGTTTCCCTGA-ATTGCAGTGAGGCAGATCGAAGACGGTGAATCT-GGCTTCCTGAAG
* *
12466341 ATGCAGCGAAGCAAATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAAGATTAT
64 ATGCAGCGAAGCAGATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATT-T
12466406 AGATCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCCTGAAGT
128 AGATCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCCTGAAGT
*
12466471 TGCAGTGAA-CAGATTTAAGCCACCATCCTAGCTTCCTAAGGTTGTAGTGGAGTAGGCTGAAGAT
193 TGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTTCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
12466535 TA
258 TA
* * * *
12466537 TAGATCTTGTTTTCCTGAGATTGCAGTGGGGCAGATCGAAGACGGCGAATCTAGGCTTCCTGATG
1 TAGATCTTGTTTCCCTGA-ATTGCAGTGAGGCAGATCGAAGACGGTGAATCT-GGCTTCCTGAAG
*
12466602 ATGCAGCGAAGCAGATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAAGATTAT
64 ATGCAGCGAAGCAGATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATT-T
* *** * *
12466667 AGATCTTGTTTCCCTG-AGATTGCAGTGGGGCAGATCGAAGACGGTGAATCT-AGGCTTCCTGAT
128 AGATCTTGTTTTCCTGAAG-TTGCAGTGAAACAGATCGAAGACGGCGAATCTGA-GCTTCCTGAA
* * * *
12466730 GTTGCAGTAAAGCAAATTTAAG-CA--AGTCCTAGCTTTCTAAAGTTGTAGTGGAGTAGGCTGAG
191 GTTGCAGTGAAGCAGATTTAAGCCACCA-TCCTAGCTTCCTAAAGTTGTAGTGGAGTAGGCTGAA
*
12466792 GATTG
255 GATTA
* * * * * *
12466797 TAGATCTCGTCTCCCTGAAGTTGCAGTGAGGCAAATCAAAGACGATAAATCTTGGCTTCCTGAAG
1 TAGATCTTGTTTCCCTGAA-TTGCAGTGAGGCAGATCGAAGACGGTGAATC-TGGCTTCCTGAAG
* * * *
12466862 ATGCAGCGAAGCAGATTTAAGCAAGTCCTAGCTCCTTAAAGTTGTAGTGAAGTGGGCTGAAGATT
64 ATGCAGCGAAGCAGATTTAAGC-A-TCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATT
*
12466927 GTAGGTCTT
127 -TAGATCTT
12466936 ATCTTCTCGA
Statistics
Matches: 833, Mismatches: 75, Indels: 37
0.88 0.08 0.04
Matches are distributed among these distances:
259 2 0.00
260 113 0.14
261 280 0.34
262 128 0.15
263 4 0.00
264 222 0.27
265 81 0.10
266 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (259 bp):
TAGATCTTGTTTCCCTGAATTGCAGTGAGGCAGATCGAAGACGGTGAATCTGGCTTCCTGAAGAT
GCAGCGAAGCAGATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTTAGA
TCTTGTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCCTGAAGTTGC
AGTGAAGCAGATTTAAGCCACCATCCTAGCTTCCTAAAGTTGTAGTGGAGTAGGCTGAAGATTA
Found at i:12467233 original size:44 final size:44
Alignment explanation
Indices: 12467115--12468090 Score: 1310
Period size: 44 Copynumber: 22.1 Consensus size: 44
12467105 CAAGACCAGA
* *
12467115 CAGATTTGGCGTCTTTGTATTGGCAGAGAGCAGATCGAAGCTAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
12467159 CAGATTTGGGCGTCTCTGTATTGCCAGAGAGCAGATCAAAGATAG
1 CAGATTT-GGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
12467204 CAGATTTGGCGTCTCTGTATTGGCGGAGAGTCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAG-CAGATCGAAGATAG
* * *
12467249 CAGATTTGACTTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
12467293 CAGATTTGGCGTCTCTGTATTGGCAAAAAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
12467337 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCATATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
12467381 CAGATTTGGCGTCTCTGTATTGGCGGAAAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
12467425 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
12467469 TAGATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
12467513 TAGATTTGGCGTCTCTGTATTAGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
**
12467557 CAGATTTGGCGTCTCTGTATTGGTGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
12467601 TAGATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* ** * *
12467645 TAGATTTGGTATCTCTGTATTGACAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
12467689 CAGATTTGGCGTCTCTGTATCGTCGGAGGGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
12467733 CAGATTTGGTGTCTCTGTATTGTCAGAGGGCAGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
12467776 TTAAATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 -CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *** *
12467821 CAGATTTGGCGTCTCTGTATCGTTGGAGGGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
12467865 TAAATTTGGCGTCTTTGTATTGGCGGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
12467909 TAGATTTGGCGTCTCTGTATTGTCAGAGAGCGGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
12467952 ACAGATTTGGCGTCTCTGTATTGGCAGAGGGCAGATCGAAGATGG
1 -CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * **
12467997 CAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATTAAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
12468040 ACAGATTTGGCATCTCTGTATTGGCAGAGAACAGCTCGAAAATAA
1 -CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
12468085 CAGATT
1 CAGATT
12468091 GGTGTTCCTG
Statistics
Matches: 830, Mismatches: 94, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
43 2 0.00
44 745 0.90
45 83 0.10
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
Found at i:12468329 original size:15 final size:16
Alignment explanation
Indices: 12468309--12468345 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
12468299 CCGTGTAAAC
*
12468309 ACAAAACAAACAAAA-
1 ACAAAACAAAAAAAAT
12468324 ACAAAACAAAAAAAAT
1 ACAAAACAAAAAAAAT
12468340 ACAAAA
1 ACAAAA
12468346 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (16 bp):
ACAAAACAAAAAAAAT
Found at i:12468330 original size:11 final size:11
Alignment explanation
Indices: 12468305--12468346 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
12468295 GGGCCCGTGT
12468305 AAACACAAAAC-
1 AAACA-AAAACA
12468316 AAACAAAAACA
1 AAACAAAAACA
12468327 AAACAAAAA-A
1 AAACAAAAACA
12468337 AATACAAAAA
1 AA-ACAAAAA
12468347 ATATATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:12470636 original size:131 final size:132
Alignment explanation
Indices: 12470386--12470669 Score: 419
Period size: 131 Copynumber: 2.2 Consensus size: 132
12470376 GCATTCATTC
* *
12470386 AAAAATTCTTCAAAAACGAAGACGAGATTCATTGTTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATTCTTC-AAAACGAAGACGAGATTCATTATTTAGCAATTCGCGGAATCGTGCCCTAACGT
* **
12470451 GTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCATGTCT
65 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCT
12470516 T-T
130 TCT
* *
12470518 TAAAATTCTTCAAAACGAAGACGAGATTCGA-TATTTAGTAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATTCTTCAAAACGAAGACGAGATTC-ATTATTTAGCAATTCGCGGAATCGTGCCCTAACGT
* * * *
12470582 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAGATTTCATTCACATCT
65 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCT
12470647 TCT
130 TCT
* *
12470650 AAAAATTATTTAAAACGAAG
1 AAAAATTCTTCAAAACGAAG
12470670 GAAATATTCG
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
131 107 0.79
132 29 0.21
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (132 bp):
AAAAATTCTTCAAAACGAAGACGAGATTCATTATTTAGCAATTCGCGGAATCGTGCCCTAACGTG
TTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCTT
CT
Found at i:12470728 original size:131 final size:131
Alignment explanation
Indices: 12470386--12470742 Score: 389
Period size: 131 Copynumber: 2.7 Consensus size: 131
12470376 GCATTCATTC
* * ** *
12470386 AAAAATTCTTCAAAAACGAAGACGAGATTC-ATTGTTTGGCAATTCGCGGAATCGTGCCCTAACG
1 AAAAATTATTC-AAAACGAAGACAAGATTCGA-CATTTGACAATTCGCGGAATCGTGCCCTAACG
**
12470450 TGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCATGTC
64 TGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATC
12470515 TTT
129 TTT
* * * * *
12470518 TAAAATTCTTCAAAACGAAGACGAGATTCGATATTT-AGTAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATTATTCAAAACGAAGACAAGATTCGACATTTGA-CAATTCGCGGAATCGTGCCCTAACGT
* * * * *
12470582 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAGATTTCATTCACATCT
65 GTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCT
12470647 TCT
130 T-T
* * * * *
12470650 AAAAATTATTTAAAACGAAGGA-AATATTCGACATTTGACAATTCG-AGAATCATGCCCTATCGT
1 AAAAATTATTCAAAACGAA-GACAAGATTCGACATTTGACAATTCGCGGAATCGTGCCCTAACGT
* * ** **
12470713 GCTGTGTTGTGATTTCTTGTTTGCTCAAAA
65 GTTGGGTTGCAATTTCGCGTTTGCTCAAAA
12470743 CGATCGAACA
Statistics
Matches: 192, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
131 144 0.75
132 45 0.23
133 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (131 bp):
AAAAATTATTCAAAACGAAGACAAGATTCGACATTTGACAATTCGCGGAATCGTGCCCTAACGTG
TTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCTT
T
Found at i:12471637 original size:20 final size:20
Alignment explanation
Indices: 12471614--12471655 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12471604 TTCTTTCTTG
*
12471614 TTTT-GTATTTTTATCATTTA
1 TTTTAGTATATTTAT-ATTTA
*
12471634 TTTTATTATATTTATATTTA
1 TTTTAGTATATTTATATTTA
12471654 TT
1 TT
12471656 CTTTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTAGTATATTTATATTTA
Found at i:12471653 original size:15 final size:16
Alignment explanation
Indices: 12471619--12471655 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
12471609 TCTTGTTTTG
12471619 TATTT-TTATCATTTA
1 TATTTATTATCATTTA
12471634 T-TTTATTAT-ATTTA
1 TATTTATTATCATTTA
12471648 TATTTATT
1 TATTTATT
12471656 CTTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATTATCATTTA
Found at i:12472097 original size:3 final size:3
Alignment explanation
Indices: 12472089--12472113 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12472079 GCATATGTGA
12472089 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
12472114 TTGATAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12474950 original size:19 final size:19
Alignment explanation
Indices: 12474914--12474964 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
12474904 TGGCACACAT
*
12474914 AGCGCATACTAGCA-CACGA
1 AGCGCATACT-GGAGCACGA
*
12474933 AGTGCATACTGGAGCACGA
1 AGCGCATACTGGAGCACGA
*
12474952 AGCGCATCCTGGA
1 AGCGCATACTGGA
12474965 ACCTGAGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.14
Consensus pattern (19 bp):
AGCGCATACTGGAGCACGA
Found at i:12477721 original size:9 final size:9
Alignment explanation
Indices: 12477707--12477795 Score: 54
Period size: 10 Copynumber: 9.2 Consensus size: 9
12477697 CGTTTGTATA
12477707 TATAATTTT
1 TATAATTTT
12477716 TATAATTTT
1 TATAATTTT
* *
12477725 TAAAAATTT
1 TATAATTTT
*
12477734 TAAAAGTTATT
1 TATAA-TT-TT
12477745 TA-AATTTTCT
1 TATAA-TTT-T
*
12477755 TATAATTCAT
1 TATAATT-TT
*
12477765 AATAATTTT
1 TATAATTTT
*
12477774 TAAATATTTT
1 TATA-ATTTT
12477784 TATAATTATT
1 TATAATT-TT
12477794 TA
1 TA
12477796 AGAATCCACT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
9 28 0.44
10 29 0.46
11 6 0.10
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (9 bp):
TATAATTTT
Found at i:12478759 original size:31 final size:30
Alignment explanation
Indices: 12478701--12478775 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
12478691 AAGTATAAAC
12478701 TCATAATATAAA-ATAAATCATCACCAAAAG
1 TCATAATATAAATATAAA-CATCACCAAAAG
12478731 TCATAATATAAATATTAAA-AGTCACCAAAAG
1 TCATAATATAAATA-TAAACA-TCACCAAAAG
*
12478762 TCATAATGTAAATA
1 TCATAATATAAATA
12478776 AAGTAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 13 0.32
31 24 0.59
32 4 0.10
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
TCATAATATAAATATAAACATCACCAAAAG
Found at i:12486913 original size:17 final size:18
Alignment explanation
Indices: 12486891--12486925 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12486881 ACAATCACAC
12486891 TCATAT-ATATATATAAG
1 TCATATCATATATATAAG
12486908 TCATATCCATATATATAA
1 TCATAT-CATATATATAA
12486926 ATTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (18 bp):
TCATATCATATATATAAG
Found at i:12498385 original size:12 final size:12
Alignment explanation
Indices: 12498368--12498397 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
12498358 TTTGATTAGA
12498368 TTATTTCATGAG
1 TTATTTCATGAG
12498380 TTATTTCATGAG
1 TTATTTCATGAG
12498392 TTATTT
1 TTATTT
12498398 TTTTGATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTATTTCATGAG
Found at i:12498514 original size:45 final size:46
Alignment explanation
Indices: 12498462--12498554 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
12498452 TAACTTATAT
12498462 ATCAAAATTGTTAAGTGA-TTGTTTTTGTGCTCTATTAATGAATAA
1 ATCAAAATTGTTAAGTGATTTGTTTTTGTGCTCTATTAATGAATAA
*
12498507 ATCAAAATTGTTAAGTGATTTTTTTTTTGTGCTCTATTAATGAATAA
1 ATCAAAATTGTTAAGTGA-TTTGTTTTTGTGCTCTATTAATGAATAA
12498554 A
1 A
12498555 ACAATTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 18 0.40
47 27 0.60
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (46 bp):
ATCAAAATTGTTAAGTGATTTGTTTTTGTGCTCTATTAATGAATAA
Found at i:12499643 original size:30 final size:30
Alignment explanation
Indices: 12499609--12499669 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
12499599 TATTAGTATG
*
12499609 TCAATTTTAGGATTTTTTTATAATCCATAT
1 TCAATTTTAGGATTTTTATATAATCCATAT
12499639 TCAATTTTAGGATTTTTATATAATCCATAT
1 TCAATTTTAGGATTTTTATATAATCCATAT
12499669 T
1 T
12499670 AAGGAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (30 bp):
TCAATTTTAGGATTTTTATATAATCCATAT
Found at i:12502901 original size:161 final size:161
Alignment explanation
Indices: 12502629--12502937 Score: 476
Period size: 161 Copynumber: 1.9 Consensus size: 161
12502619 CCCAAGACGG
* * *
12502629 ATTGAAAAAAATTGCCACTTACAAAGCTGTTGAGTTCGTTGAGATGAGTTCGGGCACAGGTCCAA
1 ATTGAAAAAAATTGCCACTTACAAAGCTATTGAGTTAGTTGAGATGAGTCCGGGCACAGGTCCAA
*
12502694 TAGCCAAACATGTCATAGGTCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACAC
66 TAGCCAAACATATCATAGGTCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACAC
12502759 CAAAACCCTTTTGATAATGCTCCGACAAGGA
131 CAAAACCCTTTTGATAATGCTCCGACAAGGA
* * ** **
12502790 ATTGAAAAAAATTTCCACTTACAAAGCTATTGAGTTAGTTGAGTTGAGTCCGGGCAGGGGTTTAA
1 ATTGAAAAAAATTGCCACTTACAAAGCTATTGAGTTAGTTGAGATGAGTCCGGGCACAGGTCCAA
* * * *
12502855 TCGCCAAACATATCGT-GGATCGAATCGGGGAGTTGCTCCGACAAGGCATTGTTCATCTACCACA
66 TAGCCAAACATATCATAGG-TCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACA
12502919 CCAAAACCCTTTTGATAAT
130 CCAAAACCCTTTTGATAAT
12502938 ACTCTAAAAT
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
160 2 0.02
161 131 0.98
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (161 bp):
ATTGAAAAAAATTGCCACTTACAAAGCTATTGAGTTAGTTGAGATGAGTCCGGGCACAGGTCCAA
TAGCCAAACATATCATAGGTCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACAC
CAAAACCCTTTTGATAATGCTCCGACAAGGA
Found at i:12506097 original size:13 final size:15
Alignment explanation
Indices: 12506063--12506097 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
12506053 CATAAATGTA
12506063 TTTTTTTCACTTATT
1 TTTTTTTCACTTATT
12506078 TTTTTTTCACTT-TT
1 TTTTTTTCACTTATT
12506092 TTTTTT
1 TTTTTT
12506098 GAGAACAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTCACTTATT
Found at i:12507239 original size:22 final size:22
Alignment explanation
Indices: 12507214--12507318 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 22
12507204 AGAAATAGCA
12507214 AAATAAAAATAATAATTATAAT
1 AAATAAAAATAATAATTATAAT
* *
12507236 AAATTAAAAAT-ATAAGTATAAG
1 AAA-TAAAAATAATAATTATAAT
*
12507258 AAA-AATAAATTAATTAATTAATTATT
1 AAATAA-AAA-TAA-TAATT-A-TAAT
*
12507284 AAAATAAAAATAAATAA-TATAAC
1 -AAATAAAAAT-AATAATTATAAT
*
12507307 AATTAAAAATAA
1 AAATAAAAATAA
12507319 AACAAAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 25 0.38
23 10 0.15
24 5 0.08
25 2 0.03
26 6 0.09
27 8 0.12
28 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATAAAAATAATAATTATAAT
Found at i:12510515 original size:17 final size:18
Alignment explanation
Indices: 12510482--12510518 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
12510472 GTTAGTAAAT
12510482 TAAAAGTAAAACAAAAAA
1 TAAAAGTAAAACAAAAAA
12510500 TAAAA-TAAAA-ATAAAAA
1 TAAAAGTAAAACA-AAAAA
12510517 TA
1 TA
12510519 GCTAAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 12 0.67
18 5 0.28
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (18 bp):
TAAAAGTAAAACAAAAAA
Found at i:12510601 original size:115 final size:114
Alignment explanation
Indices: 12510428--12510657 Score: 390
Period size: 115 Copynumber: 2.0 Consensus size: 114
12510418 GGGTTTCTTC
* *
12510428 TAGTCATAAACTAAAGACACCTGCCAGAAGCAAATAAAAGAAATGTTAGTAAATTAAAAGTAAAA
1 TAGTCATAAACTAAAGACACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAAA
*
12510493 CAAAAAATAAAATAAAAATAAAAATAGCTAAAGTAATAAAAATCTAGTGT
66 -AAAAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
12510543 TAGTCATAAACTAAAGGA-ACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAA
1 TAGTCATAAACTAAA-GACACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAA
**
12510607 AATGAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
65 AAAAAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
12510657 T
1 T
12510658 CCTAATATTT
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
114 47 0.43
115 60 0.55
116 2 0.02
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (114 bp):
TAGTCATAAACTAAAGACACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAAA
AAAAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
Found at i:12510632 original size:17 final size:17
Alignment explanation
Indices: 12510592--12510629 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12510582 GAAACGTAAG
*
12510592 TAAATTAAAAGTAAAAA
1 TAAAATAAAAGTAAAAA
*
12510609 TGAAATAAAA-TAAAAA
1 TAAAATAAAAGTAAAAA
12510625 TAAAA
1 TAAAA
12510630 ATAGATAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAGTAAAAA
Found at i:12511744 original size:30 final size:30
Alignment explanation
Indices: 12511710--12511767 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
12511700 CACAGACTGG
*
12511710 CACATGGGCGTGTGGCCAGCCAGTGTGGCT
1 CACATGGGCGTATGGCCAGCCAGTGTGGCT
*
12511740 CACATGGGCGTATGGCCAGCCCGTGTGG
1 CACATGGGCGTATGGCCAGCCAGTGTGG
12511768 AAATGTCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.19
Consensus pattern (30 bp):
CACATGGGCGTATGGCCAGCCAGTGTGGCT
Found at i:12522547 original size:20 final size:20
Alignment explanation
Indices: 12522522--12522571 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
12522512 TGGCTTAAAA
12522522 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
12522542 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
12522559 GTGGTAGTGGATT
1 TTGGTAGTGGATT
12522572 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:12527189 original size:20 final size:20
Alignment explanation
Indices: 12527164--12527213 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
12527154 TGGCTTAAAA
12527164 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
12527184 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
12527201 GTGGTAGTGGATT
1 TTGGTAGTGGATT
12527214 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:12530168 original size:28 final size:28
Alignment explanation
Indices: 12530136--12530205 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 28
12530126 TAAAATTTCA
12530136 AAAAATTATAAAAATTATTTTTAAAAAT-T
1 AAAAATTATAAAAATTA--TTTAAAAATAT
* *
12530165 AAAAATCAT-TAAATTATTTAAAAATAT
1 AAAAATTATAAAAATTATTTAAAAATAT
*
12530192 GAAAATTATAAAAA
1 AAAAATTATAAAAA
12530206 AAATATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 9 0.26
27 8 0.24
28 9 0.26
29 8 0.24
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATTATAAAAATTATTTAAAAATAT
Found at i:12533098 original size:17 final size:17
Alignment explanation
Indices: 12533076--12533110 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12533066 AAATTATTTG
12533076 TTTTGTTTACTATTCAC
1 TTTTGTTTACTATTCAC
12533093 TTTTGTTTACTATTCAC
1 TTTTGTTTACTATTCAC
12533110 T
1 T
12533111 CCCTTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTGTTTACTATTCAC
Found at i:12533700 original size:16 final size:17
Alignment explanation
Indices: 12533674--12533706 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12533664 TATACAATAT
*
12533674 AAAATTATAAATTTATG
1 AAAATTATAAAATTATG
12533691 AAAA-TATAAAATTATG
1 AAAATTATAAAATTATG
12533707 TACCATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAAATTATAAAATTATG
Found at i:12533777 original size:22 final size:21
Alignment explanation
Indices: 12533745--12533786 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
12533735 ATATTTTGAA
*
12533745 ATATATATAAAAATTTATAAT
1 ATATATATAAAAATTAATAAT
12533766 ATATAATATAAAAATTAATAA
1 ATAT-ATATAAAAATTAATAA
12533787 AAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATATAAAAATTAATAAT
Found at i:12533795 original size:32 final size:33
Alignment explanation
Indices: 12533751--12533812 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
12533741 TGAAATATAT
*
12533751 ATAAAAATTTAT-AATATATAATA-TAAAAATTA
1 ATAAAAAATTATAAATATAT-ATACTAAAAATTA
12533783 ATAAAAAATTATAAATATATATACTAAAAA
1 ATAAAAAATTATAAATATATATACTAAAAA
12533813 GCATGTCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (33 bp):
ATAAAAAATTATAAATATATATACTAAAAATTA
Found at i:12533952 original size:16 final size:16
Alignment explanation
Indices: 12533901--12533954 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
12533891 TAATGTAAAT
12533901 TTTTTATAT-TTTTAA
1 TTTTTATATATTTTAA
* *
12533916 TAATTTATATAATTTAAAA
1 T-TTTTATAT-ATTT-TAA
12533935 TTTTTATATATTTTAA
1 TTTTTATATATTTTAA
12533951 TTTT
1 TTTT
12533955 CAATTGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 13 0.42
17 4 0.13
18 10 0.32
19 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTATATATTTTAA
Found at i:12541512 original size:26 final size:26
Alignment explanation
Indices: 12541476--12541527 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12541466 GGGGTTATTT
12541476 TAAATTGCCTGTAAAATTGTATCAGA
1 TAAATTGCCTGTAAAATTGTATCAGA
12541502 TAAATTGCCTGTAAAATTGTATCAGA
1 TAAATTGCCTGTAAAATTGTATCAGA
12541528 ATAAGCCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (26 bp):
TAAATTGCCTGTAAAATTGTATCAGA
Found at i:12542350 original size:21 final size:21
Alignment explanation
Indices: 12542325--12542375 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
12542315 TAGCCAACAC
12542325 GGCCGTGTGAATTTTGGGCCA
1 GGCCGTGTGAATTTTGGGCCA
*
12542346 GGCCGTGTGAATTTTGGGCTA
1 GGCCGTGTGAATTTTGGGCCA
12542367 GGCCGTGTG
1 GGCCGTGTG
12542376 GGCCACACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.18, G:0.41, T:0.29
Consensus pattern (21 bp):
GGCCGTGTGAATTTTGGGCCA
Found at i:12545796 original size:30 final size:30
Alignment explanation
Indices: 12545734--12545796 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
12545724 AACTTATTTA
*
12545734 TTGTTAATTTTGTTATTATTTTAAAAGTAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
12545764 TTGTTAATTTTGTTATTATTTTAGAAA-CAT
1 TTGTTAATTTTGTTATTATTTTA-AAAGCAT
12545794 TTG
1 TTG
12545797 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAAGCAT
Found at i:12548898 original size:14 final size:14
Alignment explanation
Indices: 12548879--12548908 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12548869 TCTCTTAATT
12548879 TTTAAAATAATTAA
1 TTTAAAATAATTAA
12548893 TTTAAAATAATTAA
1 TTTAAAATAATTAA
12548907 TT
1 TT
12548909 ACATTATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAAAATAATTAA
Found at i:12551780 original size:21 final size:20
Alignment explanation
Indices: 12551754--12551798 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
12551744 CTACGTGGCA
*
12551754 AGTTAACTGGCCACATTAGC
1 AGTTAACTGGCCACATCAGC
*
12551774 TAGTTAACTTGCCACATCAGC
1 -AGTTAACTGGCCACATCAGC
12551795 AGTT
1 AGTT
12551799 CTGTTAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:12552363 original size:21 final size:21
Alignment explanation
Indices: 12552314--12552368 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
12552304 ATTGTAAATG
12552314 TAATATTAA-TTATGATTTTT
1 TAATATTAATTTATGATTTTT
*
12552334 TAA-ATTTAATTTAT-TTTTATT
1 TAATA-TTAATTTATGATTT-TT
12552355 TAATATTAAGTTTA
1 TAATATTAA-TTTA
12552369 AAATAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.03
20 10 0.34
21 13 0.45
22 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TAATATTAATTTATGATTTTT
Found at i:12553907 original size:21 final size:21
Alignment explanation
Indices: 12553881--12553920 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12553871 CGCACAGTAG
**
12553881 CCTGTGTTGTGACATAGGGGC
1 CCTGTGTTGCAACATAGGGGC
12553902 CCTGTGTTGCAACATAGGG
1 CCTGTGTTGCAACATAGGG
12553921 TCTGTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (21 bp):
CCTGTGTTGCAACATAGGGGC
Found at i:12557206 original size:28 final size:29
Alignment explanation
Indices: 12557152--12557215 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
12557142 ATTAAACCAA
* * *
12557152 AATTTTATTATTTTTAGGGGGCAAAATGT
1 AATTTTATTATTTTTAGGAGGAAAAATAT
*
12557181 AATTTTATTATTTTTA-GATGAAAAATAT
1 AATTTTATTATTTTTAGGAGGAAAAATAT
12557209 AATTTTA
1 AATTTTA
12557216 CCATTACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (29 bp):
AATTTTATTATTTTTAGGAGGAAAAATAT
Found at i:12560100 original size:15 final size:17
Alignment explanation
Indices: 12560065--12560097 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12560055 AATGCAGTAA
*
12560065 TAAAATATATTATATTT
1 TAAAAAATATTATATTT
12560082 TAAAAAATATTA-ATTT
1 TAAAAAATATTATATTT
12560098 AAACTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAAATATTATATTT
Found at i:12560120 original size:21 final size:20
Alignment explanation
Indices: 12560066--12560121 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 20
12560056 ATGCAGTAAT
* *
12560066 AAAATA-TATTATATTTTAA
1 AAAATATTATTAAATTTAAA
12560085 AAAATATTAATTTAAACTTTAAA
1 AAAATATT-A-TTAAA-TTTAAA
12560108 AAAATATTATTAAA
1 AAAATATTATTAAA
12560122 AAATAACTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 6 0.19
22 5 0.16
23 13 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTATTAAATTTAAA
Found at i:12565575 original size:23 final size:23
Alignment explanation
Indices: 12565549--12565596 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
12565539 ATTGACTTTA
*
12565549 TCATTATGTAATGTTGTTCATTC
1 TCATTATATAATGTTGTTCATTC
12565572 TCATTATATAATGTTGTTCATTC
1 TCATTATATAATGTTGTTCATTC
12565595 TC
1 TC
12565597 TTTTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (23 bp):
TCATTATATAATGTTGTTCATTC
Found at i:12570421 original size:15 final size:16
Alignment explanation
Indices: 12570401--12570431 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12570391 TTATAGTTGT
12570401 TAAAAT-AAATAAAAA
1 TAAAATAAAATAAAAA
12570416 TAAAATAAAATAAAAA
1 TAAAATAAAATAAAAA
12570432 AACACACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:12579738 original size:51 final size:51
Alignment explanation
Indices: 12579662--12579778 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
12579652 CGGATCACAT
* *
12579662 TTATCACTTGTCACTTGTCAGTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
12579713 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
12579764 TTATCCCTTGTCACT
1 TTATCACTTGTCACT
12579779 GATCAAAAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:12586007 original size:12 final size:12
Alignment explanation
Indices: 12585990--12586023 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
12585980 CCGTCCGGCC
12585990 TATATTAATTTT
1 TATATTAATTTT
12586002 TATATT-ATTTT
1 TATATTAATTTT
12586013 TATA-TAATTTT
1 TATATTAATTTT
12586024 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:12589299 original size:15 final size:14
Alignment explanation
Indices: 12589266--12589299 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12589256 TTTAGAACTT
*
12589266 TAATTATTTAATTA
1 TAATTATTTAATAA
12589280 TAATTATTTAAATAA
1 TAATTATTT-AATAA
12589295 TAATT
1 TAATT
12589300 TAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTATTTAATAA
Found at i:12613065 original size:310 final size:310
Alignment explanation
Indices: 12612503--12613125 Score: 1167
Period size: 310 Copynumber: 2.0 Consensus size: 310
12612493 AATACACGCC
*
12612503 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGGAAACTTGTTTTCTCTCTTTTCAAT
1 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
12612568 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
66 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
* *
12612633 GTTCTTCACACTCCGATTTGCCAATAAACCTTTTCTGGAGGGTCGGTTAAAGCCTTTGGTGGAGT
131 GTTATTCACACTCCGATTTGCCAAGAAACCTTTTCTGGAGGGTCGGTTAAAGCCTTTGGTGGAGT
*
12612698 TTGTTGAAGTCTTTCTTCAAAGGGTTCCATCGAACATCGCCTTTCATTCATCTTTATGCCTATCT
196 TTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATCT
*
12612763 TTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTCTCTTTTATGAA
261 TTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
12612813 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
1 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
*
12612878 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTGGTT
66 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
*
12612943 GTTATTCACACTCCGATTTGCCAAGAAACCTTTAT-TGGAGGGTCGGTTAGAGCCTTTGGTGGAG
131 GTTATTCACACTCCGATTTGCCAAGAAACCTTT-TCTGGAGGGTCGGTTAAAGCCTTTGGTGGAG
12613007 TTTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATC
195 TTTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATC
12613072 TTTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
260 TTTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
12613123 CCT
1 CCT
12613126 TCTTCTAACA
Statistics
Matches: 305, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
310 304 1.00
311 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (310 bp):
CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
GTTATTCACACTCCGATTTGCCAAGAAACCTTTTCTGGAGGGTCGGTTAAAGCCTTTGGTGGAGT
TTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATCT
TTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
Found at i:12619500 original size:6 final size:6
Alignment explanation
Indices: 12619489--12619515 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12619479 ACAACATAAT
12619489 TATACA TATACA TATACA TATACA TAT
1 TATACA TATACA TATACA TATACA TAT
12619516 TAATTCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
TATACA
Found at i:12621284 original size:20 final size:20
Alignment explanation
Indices: 12621258--12621305 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
12621248 GTACTTACCT
*
12621258 TAATATTAT-TAAATTAAAT
1 TAATATTATATAAATTAAAA
*
12621277 TAAATATTATATATATTAAAA
1 T-AATATTATATAAATTAAAA
12621298 TAATATTA
1 TAATATTA
12621306 CTTTTGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.60
21 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATTATATAAATTAAAA
Found at i:12625775 original size:15 final size:15
Alignment explanation
Indices: 12625755--12625786 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12625745 ATGCATGCAA
*
12625755 AAATATGAAAGACAT
1 AAATATAAAAGACAT
12625770 AAATATAAAAGACAT
1 AAATATAAAAGACAT
12625785 AA
1 AA
12625787 CAGTGGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:12625882 original size:26 final size:26
Alignment explanation
Indices: 12625853--12625909 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
12625843 GTTGACTACA
*
12625853 ATAGTGACTATTCCGAAATGTC-TTCT
1 ATAGTGACTATTACGAAATGTCATT-T
*
12625879 ATAGTGACTATTACGAGATGTCATTT
1 ATAGTGACTATTACGAAATGTCATTT
12625905 ATAGT
1 ATAGT
12625910 TCCAACTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (26 bp):
ATAGTGACTATTACGAAATGTCATTT
Found at i:12626740 original size:155 final size:155
Alignment explanation
Indices: 12626458--12626775 Score: 539
Period size: 155 Copynumber: 2.1 Consensus size: 155
12626448 TATAAGGGTC
* *
12626458 ATACACATGACAAGGTCAATGGATAAAGTAGTTGGATGAATTACTTACATAAAGAGTATATAATA
1 ATACACATGACAAGGTCAATGGATAAAGCAGTTGGATGAATTACTTACATAAAGAGTAAATAATA
*
12626523 AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTTGCCAGAA
66 AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTCGCCAGAA
12626588 TAGGGTTA-CGAGGTATTACCGGATA
131 TAGGGTTATC-AGGTATTACCGGATA
* *
12626613 ATACACATGACAAGGTCAATTGATAAAGCAGTTGGATGAATTATTTACATAAAGAGTAAATAATA
1 ATACACATGACAAGGTCAATGGATAAAGCAGTTGGATGAATTACTTACATAAAGAGTAAATAATA
* *
12626678 AGGAGTTTTCAATCATGGTACTTATTGTAGACTGTAACACCCCTAACTCGTATTCGTCGCCAGAA
66 AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTCGCCAGAA
* *
12626743 TAGGGTTATCATGTATTATCGGATA
131 TAGGGTTATCAGGTATTACCGGATA
12626768 ATACACAT
1 ATACACAT
12626776 CATTCACATA
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
155 152 0.99
156 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (155 bp):
ATACACATGACAAGGTCAATGGATAAAGCAGTTGGATGAATTACTTACATAAAGAGTAAATAATA
AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTCGCCAGAA
TAGGGTTATCAGGTATTACCGGATA
Found at i:12627843 original size:21 final size:21
Alignment explanation
Indices: 12627819--12627874 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
12627809 TACCAAAATG
12627819 ACACTAGTCTATACATGCCAT
1 ACACTAGTCTATACATGCCAT
12627840 ACACTAGTCTATACATGCCAT
1 ACACTAGTCTATACATGCCAT
*
12627861 ACACTA-TATATACA
1 ACACTAGTCTATACA
12627875 AAGCTTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.29
Consensus pattern (21 bp):
ACACTAGTCTATACATGCCAT
Found at i:12630412 original size:48 final size:52
Alignment explanation
Indices: 12630353--12630479 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 52
12630343 ATTTAATAGT
* *
12630353 TTTAATATTAAATTAAATTTAATAGTTATC-T-TA-AT-AGTATTTTATTAA
1 TTTAATATTAAATTAAATTTAATACTTATCATGTAGATAAATATTTTATTAA
* *
12630401 TTTAATGTTAAATTAAATTTAATACTTATCATGTAGATAAATGTTTTATTAA
1 TTTAATATTAAATTAAATTTAATACTTATCATGTAGATAAATATTTTATTAA
12630453 TTTAATAAATTTAATATTAAATTTAAT
1 TTTAAT--A-TTAA-ATTAAATTTAAT
12630480 GTAATATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
48 28 0.42
49 1 0.02
50 2 0.03
51 2 0.03
52 17 0.26
55 4 0.06
56 12 0.18
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (52 bp):
TTTAATATTAAATTAAATTTAATACTTATCATGTAGATAAATATTTTATTAA
Found at i:12630467 original size:61 final size:58
Alignment explanation
Indices: 12630399--12630517 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 58
12630389 GTATTTTATT
* * * *
12630399 AATTTAATGTTAAATTAAATTTAATACTTATCATGTAGATAAATGTTTTATTAATTTAATA
1 AATTTAATATTAAATTAAATGTAATACTTATC-T-T-GATAAATATTATATTAATTTAATA
* * *
12630460 AATTTAATATTAAATTTAATGTAATATTTATCTTGATAATTATTATATTAATTTAATA
1 AATTTAATATTAAATTAAATGTAATACTTATCTTGATAAATATTATATTAATTTAATA
12630518 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 21 0.41
59 1 0.02
60 1 0.02
61 28 0.55
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (58 bp):
AATTTAATATTAAATTAAATGTAATACTTATCTTGATAAATATTATATTAATTTAATA
Found at i:12631253 original size:43 final size:43
Alignment explanation
Indices: 12631205--12631290 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
12631195 TGGAAGGTAA
12631205 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
1 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
12631248 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
1 GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
12631291 CGACATTAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.26
Consensus pattern (43 bp):
GAGTATCTGGTCTCTGTATCCCTAGGGATGCAAGAAGCAGTGG
Found at i:12634084 original size:24 final size:24
Alignment explanation
Indices: 12634057--12634107 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12634047 TAAAAATAAT
*
12634057 TATATTAAAAATATTATTAAATTA
1 TATATTAAAAATATTACTAAATTA
* * *
12634081 TATATTAATATTTTTACTAAATTA
1 TATATTAAAAATATTACTAAATTA
12634105 TAT
1 TAT
12634108 TCAATAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTAAAAATATTACTAAATTA
Found at i:12647408 original size:32 final size:32
Alignment explanation
Indices: 12647362--12647441 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
12647352 TGTCAATCAT
* *
12647362 TTCAATAACCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
* * *
12647394 TTCAATATCTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
12647426 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
12647442 CTAAAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 2 0.05
32 38 0.95
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.25
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:12651303 original size:50 final size:50
Alignment explanation
Indices: 12651228--12651367 Score: 181
Period size: 50 Copynumber: 2.8 Consensus size: 50
12651218 ACCATGGCAA
** *
12651228 CAAGGATAAGCGAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGAT
1 CAAGGATAAGTAAAAGTGATAAGTAATAGCTTCGGCTACAATTATCTGAT
*
12651278 CAAGGATAAGTAAAAGTGATAAGTAATAGCTCCGGCTACAATTATCTGAT
1 CAAGGATAAGTAAAAGTGATAAGTAATAGCTTCGGCTACAATTATCTGAT
* * * * **
12651328 CAAGGACAAATGACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 CAAGGATAAGT-AAAAGTGATAAGTAATAGCTTCGGCTAC
12651368 CTGATCAGTG
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 55 0.71
51 23 0.29
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (50 bp):
CAAGGATAAGTAAAAGTGATAAGTAATAGCTTCGGCTACAATTATCTGAT
Found at i:12651381 original size:31 final size:31
Alignment explanation
Indices: 12651343--12651491 Score: 226
Period size: 31 Copynumber: 4.8 Consensus size: 31
12651333 ACAAATGACA
12651343 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
12651374 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
12651405 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
12651436 AATGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
12651467 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
12651492 AAGTGACAAG
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:12652862 original size:16 final size:18
Alignment explanation
Indices: 12652841--12652877 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12652831 AATCATAAAG
12652841 AAATAA-AAATAAAA-AT
1 AAATAATAAATAAAATAT
*
12652857 AAATAATACATAAAATAT
1 AAATAATAAATAAAATAT
12652875 AAA
1 AAA
12652878 GTTTAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAATAAATAAAATAT
Found at i:12669387 original size:18 final size:18
Alignment explanation
Indices: 12669360--12669416 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
12669350 CCCAACTACT
*
12669360 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
12669378 GTATATGTGAATAGTATC
1 GTATACGTGAATAGTACC
12669396 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
12669414 GTA
1 GTA
12669417 AACGGTCGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:12673881 original size:23 final size:23
Alignment explanation
Indices: 12673855--12673911 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
12673845 TTAGTATCAC
12673855 AACTTAATTGAACCGTAAACCGT
1 AACTTAATTGAACCGTAAACCGT
12673878 AACTTAATTGAACCGTAAACCGT
1 AACTTAATTGAACCGTAAACCGT
12673901 AACTTAATTGA
1 AACTTAATTGA
12673912 TGAAATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (23 bp):
AACTTAATTGAACCGTAAACCGT
Found at i:12674629 original size:44 final size:44
Alignment explanation
Indices: 12674579--12674667 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
12674569 AGTTTCTAGA
* *
12674579 AGATGTTTTATTTTAACTCTTTATAACAACTTTTCACTTATAAT
1 AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
12674623 AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
1 AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
12674667 A
1 A
12674668 ATATCCATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.47
Consensus pattern (44 bp):
AGATGTTTGATTTTAACCCTTTATAACAACTTTTCACTTATAAT
Found at i:12674789 original size:24 final size:20
Alignment explanation
Indices: 12674747--12674787 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12674737 ACGTAAAATT
12674747 ATAGTTATTTCATATAAGCA
1 ATAGTTATTTCATATAAGCA
12674767 ATAGTTATTTCATATAAGCA
1 ATAGTTATTTCATATAAGCA
12674787 A
1 A
12674788 GCCTATCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (20 bp):
ATAGTTATTTCATATAAGCA
Found at i:12676630 original size:10 final size:10
Alignment explanation
Indices: 12676615--12676639 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12676605 ATAGAAGATA
12676615 TTATTTTGTT
1 TTATTTTGTT
12676625 TTATTTTGTT
1 TTATTTTGTT
12676635 TTATT
1 TTATT
12676640 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (10 bp):
TTATTTTGTT
Found at i:12676654 original size:18 final size:17
Alignment explanation
Indices: 12676624--12676661 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
12676614 ATTATTTTGT
*
12676624 TTTATTTTGTTTTATTA
1 TTTATTTTATTTTATTA
12676641 TTTATTTTTATTTTATTA
1 TTTA-TTTTATTTTATTA
12676659 TTT
1 TTT
12676662 TAGAATAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTATTTTATTTTATTA
Found at i:12677848 original size:18 final size:18
Alignment explanation
Indices: 12677827--12677861 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12677817 TATTTATTTA
* *
12677827 GTAACAGTCAGTTATTCG
1 GTAACAATCAATTATTCG
12677845 GTAACAATCAATTATTC
1 GTAACAATCAATTATTC
12677862 AATAATAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (18 bp):
GTAACAATCAATTATTCG
Found at i:12677927 original size:18 final size:18
Alignment explanation
Indices: 12677900--12678084 Score: 151
Period size: 18 Copynumber: 10.3 Consensus size: 18
12677890 AATTGATCAG
*
12677900 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* * *
12677918 TTATTTAGTAA-AATCAG
1 TTATTCAGTAACAGTCAA
* * *
12677935 GTATTCAGTAACAATTAA
1 TTATTCAGTAACAGTCAA
*
12677953 GTTATTCAGTAGCAGTC-A
1 -TTATTCAGTAACAGTCAA
* *
12677971 TTCATTCAGTGACAATCAA
1 TT-ATTCAGTAACAGTCAA
* * *
12677990 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
12678008 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
*
12678027 -TATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* * *
12678044 TTATCCGGTAACAGTTAA
1 TTATTCAGTAACAGTCAA
* *
12678062 TTATTCAGTAATAATCAA
1 TTATTCAGTAACAGTCAA
12678080 TTATT
1 TTATT
12678085 TTATACCTTT
Statistics
Matches: 131, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
17 17 0.13
18 98 0.75
19 16 0.12
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:12677962 original size:62 final size:62
Alignment explanation
Indices: 12677834--12677949 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 62
12677824 TTAGTAACAG
* * * * *
12677834 TCAGTTATTCGGTAACAATCAATTATTCAATAATAACCAGTTATTCAGTATCGATCAATTGA
1 TCAGTTATCCAGTAACAATCAATTATTCAATAATAACCAGGTATTCAGTAACAATCAATTGA
* * * *
12677896 TCAGTTATCCAGTAACAGTCAATTATTTAGTAA-AATCAGGTATTCAGTAACAAT
1 TCAGTTATCCAGTAACAATCAATTATTCAATAATAACCAGGTATTCAGTAACAAT
12677950 TAAGTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
61 17 0.38
62 28 0.62
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (62 bp):
TCAGTTATCCAGTAACAATCAATTATTCAATAATAACCAGGTATTCAGTAACAATCAATTGA
Found at i:12678044 original size:54 final size:54
Alignment explanation
Indices: 12677807--12678072 Score: 173
Period size: 54 Copynumber: 4.8 Consensus size: 54
12677797 TCATTAACAA
* * * * * *
12677807 TCAG-AACAATTATTTATTTAGTAAC-AGTCAGTTATTCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTATTCAGTAACAATTCAGTTATTCAGTAACAGTCAA-TAT
* * * * *
12677860 TCAATAATAACCAGTTATTCAGTATCGATCAATTGATCAGTTATCCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTATTCAGTA---A-CAA-T--TCAGTTATTCAGTAACAGTCAA-TAT
* ** * * *
12677922 TTAGTAA-AATCAGGTATTCAGTAACAATTAAGTTATTCAGTAGCAGTCATTCAT
1 TCAGTAACAATCAATTATTCAGTAACAATTCAGTTATTCAGTAACAGTCAAT-AT
* *
12677976 TCAGTGACAATCAATTATTCAGTAA-TATTCAGTTATTCAGTAACAGTCTAATAT
1 TCAGTAACAATCAATTATTCAGTAACAATTCAGTTATTCAGTAACAGTC-AATAT
* * * * * *
12678030 CCAGTAACAGTCAATTATCCGGTAACAGTT-AATTATTCAGTAA
1 TCAGTAACAATCAATTATTCAGTAACAATTCAGTTATTCAGTAA
12678073 TAATCAATTA
Statistics
Matches: 166, Mismatches: 34, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
53 4 0.02
54 93 0.56
55 19 0.11
56 1 0.01
57 4 0.02
58 2 0.01
59 1 0.01
61 14 0.08
62 28 0.17
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (54 bp):
TCAGTAACAATCAATTATTCAGTAACAATTCAGTTATTCAGTAACAGTCAATAT
Found at i:12678317 original size:45 final size:45
Alignment explanation
Indices: 12678260--12678369 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 45
12678250 ACAGAAACAG
* * * *
12678260 TAACAGTAACAGTAATAGTATTCAACACACAAAGTGCTGAATTGA
1 TAACTGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
* *
12678305 TAAC-GATAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGG
1 TAACTG-TAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
12678350 TAACTGTAACAGTAACAGTA
1 TAACTGTAACAGTAACAGTA
12678370 ACAGTAACAG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 1 0.02
45 56 0.97
46 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (45 bp):
TAACTGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
Found at i:12678364 original size:6 final size:6
Alignment explanation
Indices: 12678349--12678381 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12678339 TGCCGAATCG
*
12678349 GTAACT GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
12678382 GTCGGCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (6 bp):
GTAACA
Found at i:12680045 original size:137 final size:137
Alignment explanation
Indices: 12679812--12680085 Score: 494
Period size: 137 Copynumber: 2.0 Consensus size: 137
12679802 CCCATTCAGT
12679812 TAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
1 TAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
12679877 GATAACAGTATGGCCCATAAGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCC
66 GATAACAGTATGGCCCATAAGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCC
12679942 ATTTGGG
131 ATTTGGG
* *
12679949 TAACAGTGGTACTGGGCCAGAGCCCTTTTCATATTACAATAAACTGGGCCTTAGCCCCTTATTTA
1 TAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
* * * *
12680014 GATAATAGTATGGCCCATAGGCCTATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
66 GATAACAGTATGGCCCATAAGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCC
12680079 ATTTGGG
131 ATTTGGG
12680086 GAGACTACTC
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 131 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (137 bp):
TAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
GATAACAGTATGGCCCATAAGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCC
ATTTGGG
Found at i:12681907 original size:26 final size:26
Alignment explanation
Indices: 12681871--12681954 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
12681861 CATGAAATTC
12681871 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12681897 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
12681923 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
12681949 TTATCA
1 TTATCA
12681955 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:12683208 original size:16 final size:16
Alignment explanation
Indices: 12683189--12683227 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12683179 AATTTTTCCC
*
12683189 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
12683205 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
12683221 TCTTTCC
1 TTTTTCC
12683228 CCTGCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:12693642 original size:13 final size:13
Alignment explanation
Indices: 12693624--12693658 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
12693614 AAATAGAAGA
*
12693624 TATTATTTTGTTT
1 TATTATTTTATTT
12693637 TATTA-TTTATTT
1 TATTATTTTATTT
12693649 TATTATTTTA
1 TATTATTTTA
12693659 GAATAGGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TATTATTTTATTT
Found at i:12697464 original size:25 final size:23
Alignment explanation
Indices: 12697407--12697464 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
12697397 AGAACAATAG
12697407 TAAA-ATAAT-GATATTAATACC
1 TAAATATAATAGATATTAATACC
*
12697428 TAAATACAAATAGATATATAATACC
1 TAAATA-TAATAGATAT-TAATACC
12697453 TAAAATATAATA
1 T-AAATATAATA
12697465 ATAACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.13
22 1 0.03
23 3 0.10
24 5 0.17
25 12 0.40
26 5 0.17
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (23 bp):
TAAATATAATAGATATTAATACC
Found at i:12697465 original size:17 final size:17
Alignment explanation
Indices: 12697441--12697479 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
12697431 ATACAAATAG
* *
12697441 ATAT-ATAATACCTAAA
1 ATATAATAATAACAAAA
12697457 ATATAATAATAACAAAA
1 ATATAATAATAACAAAA
12697474 ATATAA
1 ATATAA
12697480 ATAGATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
ATATAATAATAACAAAA
Found at i:12697492 original size:17 final size:17
Alignment explanation
Indices: 12697472--12697510 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12697462 ATAATAACAA
12697472 AAATATAAATAGATAAG
1 AAATATAAATAGATAAG
12697489 AAATATAAATAGATAAG
1 AAATATAAATAGATAAG
*
12697506 TAATA
1 AAATA
12697511 AGAAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (17 bp):
AAATATAAATAGATAAG
Found at i:12697671 original size:3 final size:3
Alignment explanation
Indices: 12697663--12697726 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
12697653 TAAGATGGCG
12697663 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12697711 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
12697727 CGACATAACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12698026 original size:18 final size:18
Alignment explanation
Indices: 12697946--12698026 Score: 60
Period size: 18 Copynumber: 4.5 Consensus size: 18
12697936 AAGACTAAGA
* *
12697946 TAATAATAATAGTAAT-G
1 TAATAATAACAGAAATAG
*
12697963 ATAATAAT-ACAAAAAATAG
1 -TAATAATAAC-AGAAATAG
**
12697982 TAATAACT-ACATTAATAG
1 TAATAA-TAACAGAAATAG
*
12698000 AAATAATAACAGAAATAG
1 TAATAATAACAGAAATAG
12698018 TAATAATAA
1 TAATAATAA
12698027 TAGTGCTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
17 2 0.04
18 44 0.88
19 4 0.08
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (18 bp):
TAATAATAACAGAAATAG
Found at i:12699606 original size:13 final size:14
Alignment explanation
Indices: 12699588--12699616 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12699578 TTAAAATTGT
12699588 ATAAAAA-TTAAAA
1 ATAAAAACTTAAAA
12699601 ATAAAAACTTAAAA
1 ATAAAAACTTAAAA
12699615 AT
1 AT
12699617 GGAAAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAAAACTTAAAA
Found at i:12700126 original size:24 final size:24
Alignment explanation
Indices: 12700063--12700114 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12700053 TTTCTAGAAG
* * **
12700063 ATTTAGTATTTATGAGAATAATAT
1 ATTTAGCATTTATTAGCGTAATAT
12700087 ATTTAGCATTTATTAGCGTAATAT
1 ATTTAGCATTTATTAGCGTAATAT
12700111 ATTT
1 ATTT
12700115 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCGTAATAT
Found at i:12709804 original size:22 final size:22
Alignment explanation
Indices: 12709769--12709813 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12709759 AAATAAGTTG
* *
12709769 TTTTGTTGTTATTTCACTATTA
1 TTTTGTTATCATTTCACTATTA
**
12709791 TTTTGTTATCATTTTGCTATTA
1 TTTTGTTATCATTTCACTATTA
12709813 T
1 T
12709814 ATTAATACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTGTTATCATTTCACTATTA
Found at i:12712088 original size:22 final size:23
Alignment explanation
Indices: 12712063--12712133 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
12712053 TGGGTTTTTG
12712063 ATTTTTTTATTGCA-TTATATTA
1 ATTTTTTTATTGCAGTTATATTA
* * *
12712085 A-TTTGTTATTGTAGTTATATTG
1 ATTTTTTTATTGCAGTTATATTA
* * *
12712107 ATTTTTTTAGTGTAGTTAT-TAA
1 ATTTTTTTATTGCAGTTATATTA
12712129 ATTTT
1 ATTTT
12712134 GTATAGTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 10 0.25
22 15 0.38
23 15 0.38
ACGTcount: A:0.25, C:0.01, G:0.11, T:0.62
Consensus pattern (23 bp):
ATTTTTTTATTGCAGTTATATTA
Found at i:12712124 original size:23 final size:23
Alignment explanation
Indices: 12712060--12712125 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
12712050 GATTGGGTTT
*
12712060 TTGATTTTTTTATTGCA-TTATA
1 TTGATTTTTTTATTGTAGTTATA
* *
12712082 TT-AATTTGTTATTGTAGTTATA
1 TTGATTTTTTTATTGTAGTTATA
*
12712104 TTGATTTTTTTAGTGTAGTTAT
1 TTGATTTTTTTATTGTAGTTAT
12712126 TAAATTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.31
22 9 0.25
23 16 0.44
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.62
Consensus pattern (23 bp):
TTGATTTTTTTATTGTAGTTATA
Found at i:12715776 original size:2 final size:2
Alignment explanation
Indices: 12715769--12715795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12715759 ACAAATACAA
12715769 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
12715796 CCTTAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:12718661 original size:25 final size:26
Alignment explanation
Indices: 12718631--12718682 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12718621 TTTAAATTAA
*
12718631 TAAATGA-AAAATTAC-AGTTTACCCT
1 TAAATGATAAAATT-CTAGTTTAACCT
12718656 TAAATGATAAAATTCTAGTTTAACCT
1 TAAATGATAAAATTCTAGTTTAACCT
12718682 T
1 T
12718683 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (26 bp):
TAAATGATAAAATTCTAGTTTAACCT
Found at i:12718900 original size:20 final size:21
Alignment explanation
Indices: 12718862--12718901 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12718852 CTAAAGTCTA
*
12718862 ATTAAGTAACAAAACTATTAC
1 ATTAAGTAACAAAAATATTAC
*
12718883 ATTAA-TAATAAAAATATTA
1 ATTAAGTAACAAAAATATTA
12718902 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
ATTAAGTAACAAAAATATTAC
Found at i:12719071 original size:22 final size:22
Alignment explanation
Indices: 12719043--12719084 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12719033 TTTATATATA
*
12719043 AAAATTATA-TTTATTTAATTAC
1 AAAATTAGATTTTA-TTAATTAC
12719065 AAAATTAGATTTTATTAATT
1 AAAATTAGATTTTATTAATT
12719085 TTAATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATTAGATTTTATTAATTAC
Done.