Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014866.1 Kokia drynarioides strain JFW-HI SEQ_129909, whole genome shotgun sequence
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: 271135
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 294 characters in sequence are not A, C, G, or T
Found at i:16272 original size:14 final size:14
Alignment explanation
Indices: 16249--16283 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16239 TACAATATCC
*
16249 AAATAATAACAACA
1 AAATAGTAACAACA
16263 AAATAGTAACAACA
1 AAATAGTAACAACA
*
16277 TAATAGT
1 AAATAGT
16284 GAAATGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:23022 original size:5 final size:5
Alignment explanation
Indices: 23014--23057 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
23004 TAAAATAAAA
*
23014 TAATT TAATT TAATT TAATAT TAATT GTGAATT TATTT TAATT T
1 TAATT TAATT TAATT TAAT-T TAATT -T-AATT TAATT TAATT T
23058 TATGTTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 23 0.68
6 7 0.21
7 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:31315 original size:2 final size:2
Alignment explanation
Indices: 31303--31335 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31293 AGAAAGGGAG
*
31303 GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
31336 CAAGTGACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31605 original size:26 final size:26
Alignment explanation
Indices: 31576--31640 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
31566 ATAATAATTG
*
31576 CTTTTTGCCCTTTAGCCCATAATTAC
1 CTTTTTGCCCTTTAGCCCATAATCAC
31602 CTTTTTGCCCTTTAGCCCATAATCAC
1 CTTTTTGCCCTTTAGCCCATAATCAC
31628 CTTTTTGCACCTT
1 CTTTTTGC-CCTT
31641 CGACTTTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 33 0.89
27 4 0.11
ACGTcount: A:0.17, C:0.32, G:0.08, T:0.43
Consensus pattern (26 bp):
CTTTTTGCCCTTTAGCCCATAATCAC
Found at i:32463 original size:11 final size:11
Alignment explanation
Indices: 32417--32475 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
32407 CAAATATAGG
32417 ATTTTTATTTT
1 ATTTTTATTTT
* * *
32428 AATATTATATT
1 ATTTTTATTTT
* * *
32439 ATCTTTAATAT
1 ATTTTTATTTT
32450 ATTTTTATTTT
1 ATTTTTATTTT
32461 A-TTTTATTTT
1 ATTTTTATTTT
32471 ATTTT
1 ATTTT
32476 AATATTATAT
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
10 10 0.29
11 25 0.71
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:32483 original size:11 final size:11
Alignment explanation
Indices: 32434--32483 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
32424 TTTTAATATT
32434 ATATTATCTTTA
1 ATATTAT-TTTA
*
32446 ATA-TATTTTT
1 ATATTATTTTA
*
32456 ATTTTATTTT-
1 ATATTATTTTA
*
32466 ATTTTATTTTA
1 ATATTATTTTA
32477 ATATTAT
1 ATATTAT
32484 ATTACCCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 15 0.45
11 15 0.45
12 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTATTTTA
Found at i:33558 original size:20 final size:20
Alignment explanation
Indices: 33519--33578 Score: 102
Period size: 20 Copynumber: 2.9 Consensus size: 20
33509 CAAATAAACG
33519 GGAAAGAAAGAAATGAAGGAGA
1 GGAAAGAAAG-AA-GAAGGAGA
33541 GGAAAGAAAGAAGAAGGAGA
1 GGAAAGAAAGAAGAAGGAGA
33561 GGAAAGAAAGAAGAAGGA
1 GGAAAGAAAGAAGAAGGA
33579 AAGAAAGGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 26 0.68
21 2 0.05
22 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAGGAGA
Found at i:34759 original size:30 final size:30
Alignment explanation
Indices: 34700--35062 Score: 420
Period size: 30 Copynumber: 12.3 Consensus size: 30
34690 CCCTAATCTG
* **
34700 TCCAAAAATTCCA-TTTTCACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
* *
34729 TCCAAAAATTCTATTTTTAACCCTAAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
* * *
34759 TTCAAAAATTCTATTTTT-TCCCTAAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
* ***
34788 TCCAAAAATTCCA-TTTTCACCCCCGAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
*
34817 TCCAAAAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
* **
34847 TCCAAAAATTCCA--TTTCACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
**
34875 TCCAAAAA-TCCATTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
**
34904 TCCAAAAATTCCATTTTT-ACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
* *
34933 TTCAAAAA-TCTCATTTTTGACCCCAAAACT
1 TCCAAAAATTC-CATTTTTGACCCTAAAACT
*
34963 TCCAAAAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
34993 TCCAAAAATTCCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACT
* *
35023 TCCAAAAATTCCATTTTT-AGCCTTGAAACT
1 TCCAAAAATTCCATTTTTGA-CCCTAAAACT
35053 TCCAAAAATT
1 TCCAAAAATT
35063 ACTGTTTTGC
Statistics
Matches: 290, Mismatches: 34, Indels: 19
0.85 0.10 0.06
Matches are distributed among these distances:
27 4 0.01
28 25 0.09
29 95 0.33
30 164 0.57
31 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTGACCCTAAAACT
Found at i:34788 original size:59 final size:60
Alignment explanation
Indices: 34700--35062 Score: 440
Period size: 59 Copynumber: 6.2 Consensus size: 60
34690 CCCTAATCTG
* * * *
34700 TCCAAAAATTCCA-TTTTCACCCTC-GAACTTCCAAAAATTCTATTTTTAACCCTAAAACT
1 TCCAAAAATTCCATTTTTGACCC-CAAAACTTCCAAAAATTCCATTTTTAACCCTCAAACT
* * * * * * *
34759 TTCAAAAATTCTATTTTT-TCCCTAAAACTTCCAAAAATTCCA-TTTTCACCCCCGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCTCAAACT
* *
34817 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCA--TTTCACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCTCAAACT
* *
34875 TCCAAAAA-TCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTT-ACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCTCAAACT
* *
34933 TTCAAAAA-TCTCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTGACCC-CAAAACT
1 TCCAAAAATTC-CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCTC-AAACT
* * * *
34993 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTAGCCTTGAAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCTCAAACT
35053 TCCAAAAATT
1 TCCAAAAATT
35063 ACTGTTTTGC
Statistics
Matches: 269, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
57 33 0.12
58 70 0.26
59 92 0.34
60 72 0.27
61 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (60 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCTCAAACT
Found at i:37338 original size:31 final size:30
Alignment explanation
Indices: 37269--37338 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
37259 AATAAATAAA
37269 ATTTTAATATAAATAATTAATTTGTTCTTT
1 ATTTTAATATAAATAATTAATTTGTTCTTT
* * *
37299 AATATAATATATAA-AAGTTAATTTTTTCATTT
1 ATTTTAATATA-AATAA-TTAATTTGTTC-TTT
37331 -TTTTAATA
1 ATTTTAATA
37339 AAGTGAGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 11 0.34
31 18 0.56
32 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
ATTTTAATATAAATAATTAATTTGTTCTTT
Found at i:38408 original size:2 final size:2
Alignment explanation
Indices: 38401--38431 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38391 CACGGAAATG
*
38401 GA GA GA GA TA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
38432 GAAATTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
GA
Found at i:40520 original size:12 final size:12
Alignment explanation
Indices: 40498--40542 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
40488 GTTATTCATT
40498 AACATTGTTCGTG
1 AACA-TGTTCGTG
*
40511 AACATGTTCGTT
1 AACATGTTCGTG
*
40523 TA-ATGTTCGTG
1 AACATGTTCGTG
40534 AACATGTTC
1 AACATGTTC
40543 AAATAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.33
12 14 0.52
13 4 0.15
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:43108 original size:26 final size:26
Alignment explanation
Indices: 43072--43126 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
43062 AAAGATTGGT
43072 TGTTAGTAATGTTGCGTTGCTGTCTG
1 TGTTAGTAATGTTGCGTTGCTGTCTG
43098 TGTTAGTAATGTTGCGTTGCTGTCTG
1 TGTTAGTAATGTTGCGTTGCTGTCTG
43124 TGT
1 TGT
43127 CATTCACTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.11, C:0.11, G:0.31, T:0.47
Consensus pattern (26 bp):
TGTTAGTAATGTTGCGTTGCTGTCTG
Found at i:43233 original size:23 final size:22
Alignment explanation
Indices: 43206--43252 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
43196 ATTCACCCTC
43206 TAATTTTATAAAATTTAT-TTTTT
1 TAATTTT-T-AAATTTATGTTTTT
43229 TAATTTTTAAATTTATGTTTTT
1 TAATTTTTAAATTTATGTTTTT
43251 TA
1 TA
43253 TCGAATCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.35
22 8 0.35
23 7 0.30
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TAATTTTTAAATTTATGTTTTT
Found at i:45022 original size:18 final size:18
Alignment explanation
Indices: 44999--45041 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
44989 TAATAGGTTT
44999 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
45017 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
45035 TTAATTA
1 TTAATTA
45042 CACCTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:47766 original size:10 final size:12
Alignment explanation
Indices: 47743--47785 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
47733 TAAGGGTTTG
47743 TTTAATATTGTT
1 TTTAATATTGTT
47755 TTTAATATT-TT
1 TTTAATATTGTT
* *
47766 TTTAGTATTGCT
1 TTTAATATTGTT
47778 TTTAATAT
1 TTTAATAT
47786 GCAGTTTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (12 bp):
TTTAATATTGTT
Found at i:48905 original size:23 final size:22
Alignment explanation
Indices: 48871--48926 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
48861 ATAGTATACA
*
48871 ATGTTTTTCTCTGCTTCTTAGC
1 ATGTTTTTCTCTGCTTCTTAAC
*
48893 ATGTTTTTCCTCTGTTTCTTAAC
1 ATGTTTTT-CTCTGCTTCTTAAC
48916 ATG-TTTTCTCT
1 ATGTTTTTCTCT
48927 TTTTTTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 4 0.13
22 12 0.39
23 15 0.48
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.57
Consensus pattern (22 bp):
ATGTTTTTCTCTGCTTCTTAAC
Found at i:56020 original size:59 final size:59
Alignment explanation
Indices: 55952--56150 Score: 246
Period size: 59 Copynumber: 3.4 Consensus size: 59
55942 TTCGAGGTTT
* * * *
55952 AAAATGGAA-TTTTCGAA-TTTTCGAGGGTAAAAATAGATTTTTTGGAAATTTTGGATTCA
1 AAAATGGAATTTTTGGAAGTTTT-GAGGGTAAAAATGGAATTTTTGGAAGTTTTGG-TTCA
*
56011 AAAATGGAATTTTTGGAAGTTTTGA-GGTTAAAATGGAATTTTTGGAAGTTTTGAGGTT-A
1 AAAATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTT--GGTTCA
* *
56070 AAAATGGAATTTTTGGAAGTTTTG-GGGTTAAAAATGGAATTTTTGGAAGTTTTAGGGTCG
1 AAAATGGAATTTTTGGAAGTTTTGAGGG-TAAAAATGGAATTTTTGGAAGTTTT-GGTTCA
56130 AAAATGGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
56151 CAAGGACCTC
Statistics
Matches: 125, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
59 63 0.50
60 56 0.45
61 6 0.05
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGTTCA
Found at i:56024 original size:30 final size:29
Alignment explanation
Indices: 55947--56150 Score: 243
Period size: 30 Copynumber: 6.9 Consensus size: 29
55937 AGAGTTTCGA
* *
55947 GGTTTAAAATGGAA-TTTTCGAA-TTTTCG
1 GGTTAAAAATGGAATTTTTGGAAGTTTT-G
* * * *
55975 AGGGTAAAAATAGATTTTTTGGAAATTTTG
1 -GGTTAAAAATGGAATTTTTGGAAGTTTTG
*
56005 GATTCAAAAATGGAATTTTTGGAAGTTTTG
1 GGTT-AAAAATGGAATTTTTGGAAGTTTTG
56035 AGGTT-AAAATGGAATTTTTGGAAGTTTTG
1 -GGTTAAAAATGGAATTTTTGGAAGTTTTG
56064 AGGTTAAAAATGGAATTTTTGGAAGTTTTGG
1 -GGTTAAAAATGGAATTTTTGGAAGTTTT-G
56095 GGTTAAAAATGGAATTTTTGGAAGTTTTAG
1 GGTTAAAAATGGAATTTTTGGAAGTTTT-G
**
56125 GGTCGAAAATGGAATTTTTGGAAGTT
1 GGTTAAAAATGGAATTTTTGGAAGTT
56151 CAAGGACCTC
Statistics
Matches: 155, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
29 41 0.26
30 106 0.68
31 8 0.05
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (29 bp):
GGTTAAAAATGGAATTTTTGGAAGTTTTG
Found at i:56835 original size:28 final size:28
Alignment explanation
Indices: 56804--56858 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
56794 CGCTTTTTTC
56804 CCTTTGGGCCTACTGCAGGATTTTTCCT
1 CCTTTGGGCCTACTGCAGGATTTTTCCT
56832 CCTTTGGGCCTACTGCAGGATTTTTCC
1 CCTTTGGGCCTACTGCAGGATTTTTCC
56859 CTTTTTTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.29, G:0.22, T:0.38
Consensus pattern (28 bp):
CCTTTGGGCCTACTGCAGGATTTTTCCT
Found at i:60600 original size:97 final size:98
Alignment explanation
Indices: 60415--60601 Score: 236
Period size: 97 Copynumber: 1.9 Consensus size: 98
60405 GAAAAGGATG
* * *
60415 TTCGATTATCTCGATTTGATGAAAAAGTCGCACAGAGTAAGTTAAGGCACGAATTTTCAGAATCA
1 TTCGATTATCTCGATTTGATGAAAAAATCGCACAGAGTAAGTTAAGGCACAAATTTTCAAAATCA
* *
60480 GAGATAAAAAAACATTACCTTGATTAAAGGGTA
66 GAAATAAAAAAACATTACATTGATTAAAGGGTA
* **
60513 TTCGATTAT-TCCGATTTGA-GAAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAACT
1 TTCGATTATCT-CGATTTGATGAAAAAATCGCACAGAGTAAGTTAAGGCACAAATTTTCAAAA-T
* * *
60576 C-GAAATAAAAGAATATTGCATTGATT
64 CAGAAATAAAAAAACATTACATTGATT
60602 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
97 57 0.75
98 19 0.25
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (98 bp):
TTCGATTATCTCGATTTGATGAAAAAATCGCACAGAGTAAGTTAAGGCACAAATTTTCAAAATCA
GAAATAAAAAAACATTACATTGATTAAAGGGTA
Found at i:61030 original size:30 final size:30
Alignment explanation
Indices: 60936--61033 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
60926 ACATGGTAAT
* * *
60936 TTTTTGGAAAAAATCGGGGCCAAAAATGAAA
1 TTTTTGG-AGAAATTGGGGTCAAAAATGAAA
*
60967 -TTTTGG-GAAGTTCGGGGGT--AAAATGATAA
1 TTTTTGGAGAAATT--GGGGTCAAAAATGA-AA
60996 TTTTTGGAGAAATTGGGGTCAAAAATGAAA
1 TTTTTGGAGAAATTGGGGTCAAAAATGAAA
61026 TTTTTGGA
1 TTTTTGGA
61034 TGTTTGGGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
28 10 0.18
29 7 0.13
30 26 0.47
31 12 0.22
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.31
Consensus pattern (30 bp):
TTTTTGGAGAAATTGGGGTCAAAAATGAAA
Found at i:61043 original size:59 final size:59
Alignment explanation
Indices: 60859--61298 Score: 394
Period size: 58 Copynumber: 7.5 Consensus size: 59
60849 TTTTGGACAC
* *** * *
60859 TCGGAGGTAAAATGGTAA-TTTTGAGAACGTTTGGGGTCAAAAATG-GATTTTTAGACA-T
1 TCGGGGGTAAAATGGTAATTTTTG-GAAAAATTGGGGTCAAAAATGAAATTTTTGGA-AGT
** * * * *
60917 TCAAGGGTAACATGGTAATTTTTTGGAAAAAATCGGGGCCAAAAATGAAATTTTGGGAAGT
1 TCGGGGGTAAAATGGTAA-TTTTTGG-AAAAATTGGGGTCAAAAATGAAATTTTTGGAAGT
* * *
60978 TCGGGGGTAAAATGATAATTTTTGGAGAAATTGGGGTCAAAAATGAAATTTTTGGATGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGAAATTTTTGGAAGT
* * * *
61037 TTGGGGGTAAAATGATAATTTTT-AAAAAATTAGGGTCAAAATTATG--ATTTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAA--ATGAAATTTTTGGAAGT
* * * * * * * * *
61095 TAGGGGGTAAAATGAT-TTTTTTCGAAAAATTGAGGTTAAAATTG-AGTTTTTGGAAAT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGAAATTTTTGGAAGT
* * *
61152 TCGGGGGTAAAATGGTAATTTTTGGAAAAATCT-AGGTTAAAAATGAAATTTTTTGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAAAT-TGGGGTCAAAAATGAAATTTTTGGAAGT
* * * * * *
61211 TCGGGGGTAAAATGGTAATCTTTGGAAAAAATCGGGGTTAAAAATGGATTTTTTGGAAAT
1 TCGGGGGTAAAATGGTAATTTTTGG-AAAAATTGGGGTCAAAAATGAAATTTTTGGAAGT
* *
61271 TTGAGGGTAAAATGGTAATTTTTGGAAA
1 TCGGGGGTAAAATGGTAATTTTTGGAAA
61299 TCGAGGTAAA
Statistics
Matches: 315, Mismatches: 53, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
56 2 0.01
57 29 0.09
58 92 0.29
59 90 0.29
60 80 0.25
61 22 0.07
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGAAATTTTTGGAAGT
Found at i:61089 original size:58 final size:57
Alignment explanation
Indices: 60892--61298 Score: 329
Period size: 59 Copynumber: 6.9 Consensus size: 57
60882 AGAACGTTTG
* ** * * **
60892 GGGTCAAAAATGGATTTTTAGACA-TTCAAGGGTAACATGGTAATTTTTTGGAAAAAATCG
1 GGGTCAAAAAT-GATTTTTGGA-AGTTCGGGGGTAAAATGATAA-TTTTTGG-AAAAATTA
* * * *
60952 GGGCCAAAAATGAAATTTTGGGAAGTTCGGGGGTAAAATGATAATTTTTGGAGAAATTG
1 GGGTCAAAAATG--ATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAAAATTA
* * *
61011 GGGTCAAAAATGAAATTTTTGGATGTTTGGGGGTAAAATGATAATTTTT-AAAAAATTA
1 GGGTCAAAAATG--ATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAAAATTA
* * *
61069 GGGTCAAAATTATGATTTTTGGAAGTTAGGGGGTAAAATGAT-TTTTTTCGAAAAATT-
1 GGGTCAAAA--ATGATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAAAATTA
* * * *
61126 GAGGTTAAAATTGAGTTTTTGGAAATTCGGGGGTAAAATGGTAATTTTTGGAAAAATCTA
1 G-GGTCAAAAATGA-TTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAAAAT-TA
* * * * **
61186 -GGTTAAAAATGAAATTTTTTGAAGTTCGGGGGTAAAATGGTAATCTTTGGAAAAAATCG
1 GGGTCAAAAATG--ATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGG-AAAAATTA
* * * * *
61245 GGGTTAAAAATGGATTTTTTGGAAATTTGAGGGTAAAATGGTAATTTTTGGAAA
1 GGGTCAAAAAT-GA-TTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAA
61299 TCGAGGTAAA
Statistics
Matches: 292, Mismatches: 38, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
56 3 0.01
57 30 0.10
58 77 0.26
59 90 0.31
60 69 0.24
61 23 0.08
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (57 bp):
GGGTCAAAAATGATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAAAATTA
Found at i:61292 original size:29 final size:29
Alignment explanation
Indices: 60982--61444 Score: 183
Period size: 29 Copynumber: 16.0 Consensus size: 29
60972 GGAAGTTCGG
* *
60982 GGGTAAAATGATAATTTTTGGAGAAATTG-
1 GGGTAAAATGGTAATTTTTGGA-AATTTGA
* ** *
61011 GGGTCAAAAAT-GAAATTTTTGGATGTTTGG
1 GGGT--AAAATGGTAATTTTTGGAAATTTGA
* ** *
61041 GGGTAAAATGATAATTTTTAAAAAATT-A
1 GGGTAAAATGGTAATTTTTGGAAATTTGA
** * * * *
61069 GGGTCAAAATTATGATTTTTGGAAGTTAGG
1 GGGT-AAAATGGTAATTTTTGGAAATTTGA
* * * *
61099 GGGTAAAATGAT-TTTTTTCGAAAAATTGA
1 GGGTAAAATGGTAATTTTT-GGAAATTTGA
* * * * *
61128 GGTTAAAATTG-AGTTTTTGGAAATTCGG
1 GGGTAAAATGGTAATTTTTGGAAATTTGA
*
61156 GGGTAAAATGGTAATTTTTGGAAAAATCT-A
1 GGGTAAAATGGTAATTTTTGG--AAATTTGA
* * * * * *
61186 GGTTAAAAAT-GAAATTTTTTGAAGTTCGG
1 GGGT-AAAATGGTAATTTTTGGAAATTTGA
* * *
61215 GGGTAAAATGGTAATCTTTGGAAAAAATCG-
1 GGGTAAAATGGTAATTTTTGG--AAATTTGA
*
61245 GGGTTAAAAATGG-ATTTTTTGGAAATTTGA
1 GGG-T-AAAATGGTAATTTTTGGAAATTTGA
*
61275 GGGTAAAATGGTAATTTTTGGAAA-TCGA
1 GGGTAAAATGGTAATTTTTGGAAATTTGA
*
61303 -GGTAAAAATGG-AATCTTT-GAAAGTTT-A
1 GGGT-AAAATGGTAATTTTTGGAAA-TTTGA
* * * ** *
61330 GGGTTAAAGGGTATTTTTTTAAAATTTTA
1 GGGTAAAATGGTAATTTTTGGAAATTTGA
*
61359 GGGCTAAAAT-GTAATTTTTGAAAAGTTT-A
1 GGG-TAAAATGGTAATTTTTGGAAA-TTTGA
* *
61388 GGGTCAAAAT-GTAATTTTTGAAAAAATT-A
1 GGGT-AAAATGGTAATTTTTG-GAAATTTGA
61417 GGGTTAAAAT-GTAATTTTT-GAAAGTTTG
1 GGG-TAAAATGGTAATTTTTGGAAA-TTTG
61445 GGGACCTCCA
Statistics
Matches: 325, Mismatches: 75, Indels: 68
0.69 0.16 0.15
Matches are distributed among these distances:
26 4 0.01
27 18 0.06
28 69 0.21
29 152 0.47
30 48 0.15
31 27 0.08
32 7 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAATTTGA
Found at i:61349 original size:56 final size:57
Alignment explanation
Indices: 61121--61348 Score: 176
Period size: 60 Copynumber: 4.0 Consensus size: 57
61111 TTTTTTCGAA
* * * * * * *
61121 AAATTGAGGTT-AAAATTGAGTTTTTGGAAATTCGGGGGTAAAATGGTAATTTTTGG
1 AAATCGAGGTTAAAAATGGAATCTTTGGAAATTTGAGGGTAAAAGGGTAATTTTTGG
* * * * * * * * *
61177 AAAAATCTAGGTTAAAAATGAAATTTTTTGAAGTTCGGGGGTAAAATGGTAATCTTTGG
1 --AAATCGAGGTTAAAAATGGAATCTTTGGAAATTTGAGGGTAAAAGGGTAATTTTTGG
* * * *
61236 AAAAAATCGGGGTTAAAAATGGATTTTTTGGAAATTTGAGGGTAAAATGGTAATTTTTGG
1 ---AAATCGAGGTTAAAAATGGAATCTTTGGAAATTTGAGGGTAAAAGGGTAATTTTTGG
* *
61296 AAATCGAGG-TAAAAATGGAATCTTT-GAAAGTTT-AGGGTTAAAGGGTATTTTTT
1 AAATCGAGGTTAAAAATGGAATCTTTGGAAA-TTTGAGGGTAAAAGGGTAATTTTT
61349 TAAAATTTTA
Statistics
Matches: 144, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
55 21 0.15
56 17 0.12
57 8 0.06
58 9 0.06
59 39 0.27
60 50 0.35
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
AAATCGAGGTTAAAAATGGAATCTTTGGAAATTTGAGGGTAAAAGGGTAATTTTTGG
Found at i:63051 original size:13 final size:13
Alignment explanation
Indices: 63010--63051 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
63000 AAAACTTGGG
63010 TTGTATTTGGACT
1 TTGTATTTGGACT
*
63023 TT-TATATTCGGGCT
1 TTGTAT-TT-GGACT
63037 TTGTATTTGGACT
1 TTGTATTTGGACT
63050 TT
1 TT
63052 TTGTAATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 8 0.33
15 3 0.12
ACGTcount: A:0.14, C:0.10, G:0.21, T:0.55
Consensus pattern (13 bp):
TTGTATTTGGACT
Found at i:63056 original size:15 final size:14
Alignment explanation
Indices: 63010--63063 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 14
63000 AAAACTTGGG
63010 TTGTATTTGGACTT
1 TTGTATTTGGACTT
* * *
63024 TTATATTCGGGC-T
1 TTGTATTTGGACTT
63037 TTGTATTTGGACTTT
1 TTGTATTTGGAC-TT
*
63052 TTGTAATTGGAC
1 TTGTATTTGGAC
63064 ATTATTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.32
14 9 0.29
15 12 0.39
ACGTcount: A:0.17, C:0.09, G:0.22, T:0.52
Consensus pattern (14 bp):
TTGTATTTGGACTT
Found at i:63094 original size:23 final size:23
Alignment explanation
Indices: 63067--63113 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
63057 ATTGGACATT
63067 ATTTA-AATAAACTTTAAATTTAA
1 ATTTATAATAAA-TTTAAATTTAA
63090 ATTTATAATAAATTTAAATTTAA
1 ATTTATAATAAATTTAAATTTAA
63113 A
1 A
63114 ATAAATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTATAATAAATTTAAATTTAA
Found at i:63101 original size:17 final size:17
Alignment explanation
Indices: 63081--63125 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
63071 AAATAAACTT
*
63081 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
63098 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
63115 TAAATCTAAAT
1 TAAATTTAAAT
63126 CCTGTTGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:63863 original size:21 final size:23
Alignment explanation
Indices: 63839--63880 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
63829 TTTTTCTGCA
*
63839 TTTGTCTTTTG-CTCT-TGTTGC
1 TTTGCCTTTTGTCTCTGTGTTGC
63860 TTTGCCTTTTGTCTCTGTGTT
1 TTTGCCTTTTGTCTCTGTGTT
63881 TTCTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.62
Consensus pattern (23 bp):
TTTGCCTTTTGTCTCTGTGTTGC
Found at i:64173 original size:17 final size:18
Alignment explanation
Indices: 64133--64180 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
64123 GGTTTGTTAT
*
64133 ATTTT-AATGTAAATCGAC
1 ATTTTAAAT-TAAATAGAC
64151 ATTTTAAATTAAATAGA-
1 ATTTTAAATTAAATAGAC
*
64168 ATTTTAATTTAAA
1 ATTTTAAATTAAA
64181 ATTTTATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 12 0.44
18 12 0.44
19 3 0.11
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTTAAATTAAATAGAC
Found at i:64182 original size:18 final size:18
Alignment explanation
Indices: 64133--64180 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
64123 GGTTTGTTAT
* *
64133 ATTTTAATGTAAATCGAC
1 ATTTTAATTTAAATAGAC
*
64151 ATTTTAAATTAAATAGA-
1 ATTTTAATTTAAATAGAC
64168 ATTTTAATTTAAA
1 ATTTTAATTTAAA
64181 ATTTTATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTTAATTTAAATAGAC
Found at i:69300 original size:25 final size:25
Alignment explanation
Indices: 69249--69301 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
69239 TGTTTACTTC
* *
69249 TATACATTGGGTTGAATGCTAGTTG
1 TATACATTCGGTTAAATGCTAGTTG
*
69274 TATACATTTCGGTTAAATGTTAG-TG
1 TATACA-TTCGGTTAAATGCTAGTTG
69299 TAT
1 TAT
69302 TTTGATTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (25 bp):
TATACATTCGGTTAAATGCTAGTTG
Found at i:69460 original size:19 final size:20
Alignment explanation
Indices: 69433--69478 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
69423 TGATAGTATT
69433 ATTTAGATTTGAAGTT-ATTGG
1 ATTT-GATTTGAA-TTGATTGG
69454 -TTTGATTTGAATTGATTGG
1 ATTTGATTTGAATTGATTGG
69473 ATTTGA
1 ATTTGA
69479 ATTTATAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 13 0.57
20 8 0.35
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (20 bp):
ATTTGATTTGAATTGATTGG
Found at i:69712 original size:43 final size:43
Alignment explanation
Indices: 69548--69715 Score: 153
Period size: 43 Copynumber: 3.9 Consensus size: 43
69538 AAATTTGTAT
* * * *
69548 GAAAAACGTCGCTAAATAACATGTTCTATAGCTG-GGTTTGTGG
1 GAAAAGCGCCGCTAAAGAACATGTTCTATAGC-GATGTTTGTGG
* * * * ***
69591 GAAAAGCGCCGCTAAAGAATATGGTCTTTATCGGCATTTGT-G
1 GAAAAGCGCCGCTAAAGAACATGTTCTATAGCGATGTTTGTGG
* * *
69633 AAAATAGCGCCGCTAAAG-ACAATGTTCTTTAACGATGTTTGTGG
1 GAAA-AGCGCCGCTAAAGAAC-ATGTTCTATAGCGATGTTTGTGG
*
69677 GAAAAGCGCCGCTAAAGACCATGTTCTATAGCGATGTTT
1 GAAAAGCGCCGCTAAAGAACATGTTCTATAGCGATGTTT
69716 TTCCACATAA
Statistics
Matches: 100, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 6 0.06
43 89 0.89
44 5 0.05
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAGAACATGTTCTATAGCGATGTTTGTGG
Found at i:70294 original size:16 final size:17
Alignment explanation
Indices: 70273--70307 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
70263 TTGAATCAAT
*
70273 TTTTATATTTTTAA-AA
1 TTTTATAATTTTAATAA
70289 TTTTATAATTTTAATAA
1 TTTTATAATTTTAATAA
70306 TT
1 TT
70308 ACTTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATAATTTTAATAA
Found at i:72736 original size:18 final size:17
Alignment explanation
Indices: 72709--72743 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
72699 ACCCTAAACT
*
72709 CTAACTTAATCTTAACC
1 CTAACTTAATATTAACC
72726 CTAACCTTAATATTAACC
1 CTAA-CTTAATATTAACC
72744 AAACCCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (17 bp):
CTAACTTAATATTAACC
Found at i:80378 original size:31 final size:31
Alignment explanation
Indices: 80325--80383 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
80315 TATTTAAGTT
*
80325 AATTGAGTTATTCGGATCAACTCAAATAAAA
1 AATTAAGTTATTCGGATCAACTCAAATAAAA
* * *
80356 AATTAAGTTTTTCGGTTTAACTCAAATA
1 AATTAAGTTATTCGGATCAACTCAAATA
80384 TAAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
AATTAAGTTATTCGGATCAACTCAAATAAAA
Found at i:81808 original size:6 final size:7
Alignment explanation
Indices: 81787--81811 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
81777 GTCACATGTA
81787 TTAATTT
1 TTAATTT
81794 TTAATTT
1 TTAATTT
81801 TTAATTT
1 TTAATTT
81808 TTAA
1 TTAA
81812 AATACAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTAATTT
Found at i:82959 original size:20 final size:20
Alignment explanation
Indices: 82934--82979 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
82924 AATTTGTTCA
82934 ACTTTACTTTTATTAAAAAC
1 ACTTTACTTTTATTAAAAAC
82954 ACTTTACTTTTATTAAAAAC
1 ACTTTACTTTTATTAAAAAC
82974 ACTTTA
1 ACTTTA
82980 ATTTGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
ACTTTACTTTTATTAAAAAC
Found at i:83876 original size:31 final size:31
Alignment explanation
Indices: 83839--83976 Score: 115
Period size: 31 Copynumber: 4.5 Consensus size: 31
83829 GGATCCCAAA
*
83839 AAGTTTAGGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAAAAAAAAGTGTC
* * **
83870 AAGTTTAGTTACTAAATTAGGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAAAAAAAAGTGTC
* * * *
83901 AAGTTTAAGTACCGACTTGGACAAAAAA-----
1 AAGTTTAGGTACCAAATT--AAAAAAAAGTGTC
*
83929 AACTTTAGGTACCAAATTAAAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAAAAAAAAGTGTC
* *
83960 AAGTTCAAGTACCAAAT
1 AAGTTTAGGTACCAAAT
83977 ATTATATTAA
Statistics
Matches: 80, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
26 7 0.09
28 14 0.17
31 53 0.66
33 6 0.08
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAAAAAAAAGTGTC
Found at i:83930 original size:90 final size:90
Alignment explanation
Indices: 83784--83976 Score: 253
Period size: 90 Copynumber: 2.1 Consensus size: 90
83774 TTAAAAAAGG
* ** *
83784 TTAGGTACCAAATTAGGAAAAAGAGTTAAGTTCAAGTACCAAATTGGATCCCAAAAAGTTTAGGT
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGGATCAAAAAAACTTTAGGT
*
83849 ACCAACTTAAAAAAAAGTGTCAAGT
66 ACCAAATTAAAAAAAAGTGTCAAGT
* * * * * *
83874 TTAGTTACTAAATTAGGAAAAAGTGTCAAGTTTAAGTACCGACTTGGA-CAAAAAAAACTTTAGG
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGGATC-AAAAAAACTTTAGG
83938 TACCAAATTAAAAAAAAGTGTCAAGT
65 TACCAAATTAAAAAAAAGTGTCAAGT
* *
83964 TCAAGTACCAAAT
1 TTAGGTACCAAAT
83977 ATTATATTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 1 0.01
90 86 0.99
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGGATCAAAAAAACTTTAGGT
ACCAAATTAAAAAAAAGTGTCAAGT
Found at i:84273 original size:56 final size:55
Alignment explanation
Indices: 84187--84428 Score: 241
Period size: 56 Copynumber: 4.3 Consensus size: 55
84177 CTCAAGTGAC
* * **
84187 CCAAACGACGCTATAAATTAATGCAACTTATACAACAATCTCAAGTGACAAAGCGT
1 CCAAACGACGCTACAAACT-ATGCAACTTATATGACAATCTCAAGTGACAAAGCGT
* * * *
84243 CCAAACAACGCTACAAACTATCGCAACTTATATGGCAATCTCAAGTGACAAAACAT
1 CCAAACGACGCTACAAACTAT-GCAACTTATATGACAATCTCAAGTGACAAAGCGT
* * * * * * *
84299 CCAAACAATGCTACAAACTATTACAACTTATATGGCAATATTAAGTGACAAAGTGT
1 CCAAACGACGCTACAAACTA-TGCAACTTATATGACAATCTCAAGTGACAAAGCGT
** * * * *
84355 CCAAACGACATTATAAACTATGGCAATTTATATGATAATCTCCAGTGACAAAGCGT
1 CCAAACGACGCTACAAACTAT-GCAACTTATATGACAATCTCAAGTGACAAAGCGT
* *
84411 TCAAACGAGGCTACAAAC
1 CCAAACGACGCTACAAAC
84429 CATTGTGGTC
Statistics
Matches: 150, Mismatches: 33, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
55 3 0.02
56 146 0.97
57 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (55 bp):
CCAAACGACGCTACAAACTATGCAACTTATATGACAATCTCAAGTGACAAAGCGT
Found at i:101844 original size:6 final size:7
Alignment explanation
Indices: 101812--101852 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
101802 TTTTATTCAT
101812 AAAAAGA
1 AAAAAGA
101819 CAAAAAGA
1 -AAAAAGA
101827 CAAAAAGA
1 -AAAAAGA
101835 AAAAAGA
1 AAAAAGA
101842 AAAAAGA
1 AAAAAGA
101849 AAAA
1 AAAA
101853 TATATTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 18 0.55
8 15 0.45
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:102008 original size:26 final size:27
Alignment explanation
Indices: 101956--102013 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
101946 ATTGATATAA
101956 ATAAATATATTTAATTATTATAAATTT
1 ATAAATATATTTAATTATTATAAATTT
**
101983 -TAAAT-TACTTTAATTATTATTCATTT
1 ATAAATATA-TTTAATTATTATAAATTT
102009 ATAAA
1 ATAAA
102014 AAGGTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 21 0.78
27 4 0.15
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAAATATATTTAATTATTATAAATTT
Found at i:103283 original size:21 final size:21
Alignment explanation
Indices: 103258--103301 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
103248 AACAACGATG
*
103258 ACGGTAAAATTAATTATTGTA
1 ACGGTAAAATTAAATATTGTA
* *
103279 ACGGTGAGATTAAATATTGTA
1 ACGGTAAAATTAAATATTGTA
103300 AC
1 AC
103302 AATGAGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (21 bp):
ACGGTAAAATTAAATATTGTA
Found at i:103307 original size:21 final size:21
Alignment explanation
Indices: 103266--103312 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
103256 TGACGGTAAA
* **
103266 ATTAATTATTGTAACGGTGAG
1 ATTAAATATTGTAACAATGAG
103287 ATTAAATATTGTAACAATGAG
1 ATTAAATATTGTAACAATGAG
103308 ATTAA
1 ATTAA
103313 TAACAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (21 bp):
ATTAAATATTGTAACAATGAG
Found at i:113769 original size:78 final size:78
Alignment explanation
Indices: 113679--113837 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 78
113669 TCTAATCTCT
*
113679 AATGAGTGTATTTTTTAAAGTTGTAAATTCATAAGCGAAATAAATTATAAAATAAATGCAAAATA
1 AATGAGTGTATTTTTTAAAGTTGTAAATTCATAAGCCAAATAAATTATAAAATAAATGCAAAATA
*
113744 TATTATACTTATA
66 TATTATACTAATA
* * *
113757 AATGAGTGTATTTTTTAAAGTTGTAAATTCGTATGCCAAATAAATTATATAATAAATGCAAAATA
1 AATGAGTGTATTTTTTAAAGTTGTAAATTCATAAGCCAAATAAATTATAAAATAAATGCAAAATA
113822 TATTATACTAATA
66 TATTATACTAATA
113835 AAT
1 AAT
113838 ATTAAATTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.38
Consensus pattern (78 bp):
AATGAGTGTATTTTTTAAAGTTGTAAATTCATAAGCCAAATAAATTATAAAATAAATGCAAAATA
TATTATACTAATA
Found at i:113815 original size:23 final size:24
Alignment explanation
Indices: 113789--113837 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
113779 GTAAATTCGT
*
113789 ATGCCAAATAAATTATA-TAATAA
1 ATGCAAAATAAATTATACTAATAA
*
113812 ATGCAAAATATATTATACTAATAA
1 ATGCAAAATAAATTATACTAATAA
113836 AT
1 AT
113838 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
ATGCAAAATAAATTATACTAATAA
Found at i:115040 original size:2 final size:2
Alignment explanation
Indices: 115033--115060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
115023 TCACTCAAAA
115033 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115061 TTTGTGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:122416 original size:40 final size:40
Alignment explanation
Indices: 122341--122426 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
122331 TCACTACCGG
* * * *
122341 TTCAGTGGTATTCTTGCAGTGTTTACAGTGCCATTG-TCAA
1 TTCAGTGGTAATCTTGAAGTGTTTACAATACCATTGCT-AA
* *
122381 TTCAGTTGTAATCTTGAAGTGTTTACAATATCATTGCTAA
1 TTCAGTGGTAATCTTGAAGTGTTTACAATACCATTGCTAA
122421 TTCAGT
1 TTCAGT
122427 AAATATTCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (40 bp):
TTCAGTGGTAATCTTGAAGTGTTTACAATACCATTGCTAA
Found at i:131217 original size:28 final size:28
Alignment explanation
Indices: 131148--131240 Score: 109
Period size: 27 Copynumber: 3.4 Consensus size: 28
131138 TAACAAACAA
* *
131148 CAAAATTTAAAACAAAGGATAACAACAG
1 CAAAATTTAAAATAAAGGATAACACCAG
* *
131176 C-AAATTCAAAATAAATGATAACACCAG
1 CAAAATTTAAAATAAAGGATAACACCAG
* **
131203 CAAAATTTAAAATAAAGGACAACACTTG
1 CAAAATTTAAAATAAAGGATAACACCAG
131231 -AAAATTTAAA
1 CAAAATTTAAA
131241 CACATGCTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
27 33 0.60
28 22 0.40
ACGTcount: A:0.58, C:0.14, G:0.09, T:0.19
Consensus pattern (28 bp):
CAAAATTTAAAATAAAGGATAACACCAG
Found at i:143078 original size:25 final size:25
Alignment explanation
Indices: 143050--143101 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
143040 AGGAAGAATC
*
143050 CTACTTTTCTTCATCACAACCATCT
1 CTACTTTTCTTCACCACAACCATCT
143075 CTACTTTTCTTCACCACAACCATCT
1 CTACTTTTCTTCACCACAACCATCT
143100 CT
1 CT
143102 TCAAGGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (25 bp):
CTACTTTTCTTCACCACAACCATCT
Found at i:145300 original size:19 final size:19
Alignment explanation
Indices: 145276--145316 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
145266 ATTTTTAGAA
145276 ATTCTAATT-AGAAGATATT
1 ATTCTAATTAAG-AGATATT
145295 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGATATT
145314 ATT
1 ATT
145317 TTCTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
ATTCTAATTAAGAGATATT
Found at i:149415 original size:19 final size:19
Alignment explanation
Indices: 149391--149431 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
149381 GTTTTTTGAG
*
149391 ATTCTAACTAGGAGATATT
1 ATTCTAACTAAGAGATATT
*
149410 ATTCTAATTAAGAGATATT
1 ATTCTAACTAAGAGATATT
149429 ATT
1 ATT
149432 TCCTTAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (19 bp):
ATTCTAACTAAGAGATATT
Found at i:153289 original size:27 final size:27
Alignment explanation
Indices: 153255--153306 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
153245 AATGTTGATG
*
153255 AAATTATTGCTGAAATGAGAATCAATT
1 AAATTATTGCTGAAATGAAAATCAATT
153282 AAATTATTGCTGAAATGAAAATCAA
1 AAATTATTGCTGAAATGAAAATCAA
153307 GTGTTCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (27 bp):
AAATTATTGCTGAAATGAAAATCAATT
Found at i:155910 original size:29 final size:30
Alignment explanation
Indices: 155878--155936 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
155868 TATGGTTTAA
155878 TGTGTAATTATATACAT-AAACTTTGATTT
1 TGTGTAATTATATACATGAAACTTTGATTT
* *
155907 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTATATACATGAAACTTTGATTT
155937 GATCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (30 bp):
TGTGTAATTATATACATGAAACTTTGATTT
Found at i:156115 original size:31 final size:30
Alignment explanation
Indices: 156079--156147 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
156069 GATTAAATTA
*
156079 AAATTAAAGTTTCAAGTATATATTTGAATC
1 AAATTAAAGTTTCAAGTATATAATTGAATC
* * *
156109 ATAATTAGAGTTTCACGTGTATAATTGAATC
1 A-AATTAAAGTTTCAAGTATATAATTGAATC
156140 AAATTAAA
1 AAATTAAA
156148 ATTTATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATAATTGAATC
Found at i:156321 original size:17 final size:18
Alignment explanation
Indices: 156299--156344 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
156289 GTATATTTTT
*
156299 ATTTAAATATTTGTT-AC
1 ATTTAAATATTTGTTCAA
*
156316 ATTT-AATATTTATTCAA
1 ATTTAAATATTTGTTCAA
156333 ATTTAAAT-TTTG
1 ATTTAAATATTTG
156345 ATTATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.38
17 12 0.50
18 3 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (18 bp):
ATTTAAATATTTGTTCAA
Found at i:162094 original size:27 final size:27
Alignment explanation
Indices: 162033--162110 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
162023 TGTTTAGTGT
* * * *
162033 CCCAACGAACCATCTCGTGTTTAACGC
1 CCCATCGAACTATCCCGTGTTTAACAC
* *
162060 CACGTCGAACTATCCCGTGTTTAACAC
1 CCCATCGAACTATCCCGTGTTTAACAC
*
162087 CCCATCGAACTATCCCATGTTTAA
1 CCCATCGAACTATCCCGTGTTTAA
162111 TGTCATCGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.26
Consensus pattern (27 bp):
CCCATCGAACTATCCCGTGTTTAACAC
Found at i:162428 original size:45 final size:45
Alignment explanation
Indices: 162364--162464 Score: 184
Period size: 45 Copynumber: 2.2 Consensus size: 45
162354 ATGCAATAGC
162364 GTCTTACTCATTGTTATCATGATGCCATAACATTTTTCAGCTATG
1 GTCTTACTCATTGTTATCATGATGCCATAACATTTTTCAGCTATG
*
162409 GTCTTACTCATTGTTATCATGATGCCATAGCATTTTTCAGCTATG
1 GTCTTACTCATTGTTATCATGATGCCATAACATTTTTCAGCTATG
*
162454 GTCCTACTCAT
1 GTCTTACTCAT
162465 CTTTGTGTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (45 bp):
GTCTTACTCATTGTTATCATGATGCCATAACATTTTTCAGCTATG
Found at i:168479 original size:27 final size:28
Alignment explanation
Indices: 168449--168533 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 28
168439 CTAGCGGACC
*
168449 ATCCCGTGTTTAATGTCCT-GTCGAATT
1 ATCCCGTGTTTAATGTCCTCGTCGAACT
* * *
168476 ATCCCATGTTTAACGT-CTCGTCGGACT
1 ATCCCGTGTTTAATGTCCTCGTCGAACT
* * **
168503 ATACTGTGTTTAATGTCC-CGTTAAACT
1 ATCCCGTGTTTAATGTCCTCGTCGAACT
168530 ATCC
1 ATCC
168534 ATGATATTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 2 0.05
27 41 0.93
28 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (28 bp):
ATCCCGTGTTTAATGTCCTCGTCGAACT
Found at i:168737 original size:45 final size:45
Alignment explanation
Indices: 168686--168885 Score: 143
Period size: 45 Copynumber: 4.4 Consensus size: 45
168676 TGGCACAGTG
* * * *
168686 TCTTTCAACCATGGTCTTACACATTTGTAACATGGTTCCAAAACA
1 TCTTTCAGCTATGGTCTTACACATTTGTAACATGATGCCAAAACA
* * * * * *
168731 TCTTTCAGTTATGGTCTTACTCATTTTTATCATGATGCCATAGCA
1 TCTTTCAGCTATGGTCTTACACATTTGTAACATGATGCCAAAACA
* * * * * *
168776 TCTTTCAGCTATTGTCTTACGCATTTTTATCATGATGTCATATA-A
1 TCTTTCAGCTATGGTCTTACACATTTGTAACATGATGCCA-AAACA
* * * * * * * *
168821 TCTTTCAACTATTGTCTTACTCATTTTTATCATGATGTCATAGCA
1 TCTTTCAGCTATGGTCTTACACATTTGTAACATGATGCCAAAACA
*
168866 TCTTTCA-ATAATGGTCTTAC
1 TCTTTCAGCT-ATGGTCTTAC
168886 TTATATTGGC
Statistics
Matches: 128, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.01
45 127 0.99
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (45 bp):
TCTTTCAGCTATGGTCTTACACATTTGTAACATGATGCCAAAACA
Found at i:168814 original size:23 final size:23
Alignment explanation
Indices: 168744--168814 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
168734 TTCAGTTATG
*
168744 GTCTTACTCATTTTTATCATGAT
1 GTCTTACGCATTTTTATCATGAT
* * * *
168767 GCCATA-GCATCTTTCAGC-T-ATT
1 GTCTTACGCAT-TTTTATCATGA-T
168789 GTCTTACGCATTTTTATCATGAT
1 GTCTTACGCATTTTTATCATGAT
168812 GTC
1 GTC
168815 ATATAATCTT
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 18 0.53
24 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (23 bp):
GTCTTACGCATTTTTATCATGAT
Found at i:168886 original size:45 final size:44
Alignment explanation
Indices: 168729--168886 Score: 208
Period size: 45 Copynumber: 3.5 Consensus size: 44
168719 GGTTCCAAAA
* *
168729 CATCTTTCAGTTATGGTCTTACTCATTTTTATCATGATGCCATAG
1 CATCTTTCA-ATATGGTCTTACTCATTTTTATCATGATGTCATAG
* * * *
168774 CATCTTTCAGCTATTGTCTTACGCATTTTTATCATGATGTCATAT
1 CATCTTTCA-ATATGGTCTTACTCATTTTTATCATGATGTCATAG
* *
168819 AATCTTTCAACTATTGTCTTACTCATTTTTATCATGATGTCATAG
1 CATCTTTCAA-TATGGTCTTACTCATTTTTATCATGATGTCATAG
168864 CATCTTTCAATAATGGTCTTACT
1 CATCTTTCAAT-ATGGTCTTACT
168887 TATATTGGCG
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 1 0.01
45 99 0.99
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (44 bp):
CATCTTTCAATATGGTCTTACTCATTTTTATCATGATGTCATAG
Found at i:175259 original size:14 final size:14
Alignment explanation
Indices: 175240--175267 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
175230 GAATTTAATT
175240 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
175254 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
175268 AACATGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:176128 original size:22 final size:22
Alignment explanation
Indices: 176103--176145 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
176093 TTTATGTTCA
*
176103 TTAAATGAATATAATTT-CATGC
1 TTAAATAAAT-TAATTTGCATGC
*
176125 TTAATTAAATTAATTTGCATG
1 TTAAATAAATTAATTTGCATG
176146 ACCCACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
TTAAATAAATTAATTTGCATGC
Found at i:177919 original size:42 final size:43
Alignment explanation
Indices: 177864--178091 Score: 143
Period size: 42 Copynumber: 5.4 Consensus size: 43
177854 TATGCTCCAA
* * *
177864 CCGAGTCATAAGTCATCCTTTTTAAACA-AATATTATGCTCTA-
1 CCGAGACATAAGTCTTCCTTTTTAAACATAATATCATGCT-TAC
* *
177906 CTGAGACATAAGTCTTCC--TTTAAACATAATCTCATGCTTATC
1 CCGAGACATAAGTCTTCCTTTTTAAACATAATATCATGCTTA-C
* * *
177948 CCGAGACATAAGTCTTCC--TTTAAACATAATCTCGTGCTCATC
1 CCGAGACATAAGTCTTCCTTTTTAAACATAATATCATGCTTA-C
** * ** * *
177990 CTAAGTCACGAGTCTTCC--TTTAAACATAATCTCATGCTCATC
1 CCGAGACATAAGTCTTCCTTTTTAAACATAATATCATGCTTA-C
* * * * *
178032 CCGAGACTTGAGTCTTCC--TTTAAACATAATCTCATGGTCATC
1 CCGAGACATAAGTCTTCCTTTTTAAACATAATATCATGCTTA-C
* *
178074 CCGATACATGAGTCTTCC
1 CCGAGACATAAGTCTTCC
178092 ATTTATACAT
Statistics
Matches: 161, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
40 10 0.06
41 9 0.06
42 142 0.88
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (43 bp):
CCGAGACATAAGTCTTCCTTTTTAAACATAATATCATGCTTAC
Found at i:178004 original size:84 final size:84
Alignment explanation
Indices: 177916--178074 Score: 273
Period size: 84 Copynumber: 1.9 Consensus size: 84
177906 CTGAGACATA
*
177916 AGTCTTCCTTTAAACATAATCTCATGCTTATCCCGAGACATAAGTCTTCCTTTAAACATAATCTC
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATAAGTCTTCCTTTAAACATAATCTC
*
177981 GTGCTCATCCTAAGTCACG
66 ATGCTCATCCTAAGTCACG
* *
178000 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACTTGAGTCTTCCTTTAAACATAATCTC
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATAAGTCTTCCTTTAAACATAATCTC
*
178065 ATGGTCATCC
66 ATGCTCATCC
178075 CGATACATGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.34
Consensus pattern (84 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATAAGTCTTCCTTTAAACATAATCTC
ATGCTCATCCTAAGTCACG
Found at i:178087 original size:84 final size:85
Alignment explanation
Indices: 177911--178101 Score: 269
Period size: 84 Copynumber: 2.3 Consensus size: 85
177901 CTCTACTGAG
* *
177911 ACATAAGTCTTCCTTTAAACATAATCTCATGCTTATCCCGAGACATAAGTCTTCCTTTAAACATA
1 ACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATAAGTCTTCCTTTAAACATA
* *
177976 ATCTCGTGCTCATCCTAAGT
66 ATCTCATGCTCATCCCAAGT
* * *
177996 -CACGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACTTGAGTCTTCCTTTAAACATA
1 ACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATAAGTCTTCCTTTAAACATA
* *
178060 ATCTCATGGTCATCCCGA-T
66 ATCTCATGCTCATCCCAAGT
*
178079 ACATGAGTCTTCCATTTATACAT
1 ACATGAGTCTTCC-TTTAAACAT
178102 CAATTGATTC
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 1 0.01
84 84 0.90
85 8 0.09
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (85 bp):
ACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATAAGTCTTCCTTTAAACATA
ATCTCATGCTCATCCCAAGT
Found at i:178806 original size:17 final size:18
Alignment explanation
Indices: 178781--178814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
178771 ATTCTTGATC
178781 TAAAATAA-TAATTTCAT
1 TAAAATAATTAATTTCAT
*
178798 TAAATTAATTAATTTCA
1 TAAAATAATTAATTTCA
178815 ACAGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATAATTAATTTCAT
Found at i:187114 original size:25 final size:25
Alignment explanation
Indices: 187080--187210 Score: 118
Period size: 26 Copynumber: 5.1 Consensus size: 25
187070 AAATGTTCGA
* *
187080 TGATTATTAGCAGGCTTTGAGTCGG
1 TGATTATTAGCAGGCTTCGAGCCGG
*
187105 TGATTTTTAGCAGGCTTCGAGCCGG
1 TGATTATTAGCAGGCTTCGAGCCGG
* * * * *
187130 TGATTAATTAGCAAGATTCAAGCTGA
1 TGATT-ATTAGCAGGCTTCGAGCCGG
* *
187156 TGATTAATTAGCAGGCTTTGAGCTGG
1 TGATT-ATTAGCAGGCTTCGAGCCGG
* * *
187182 TGATTAATTAGTAGGTTTCAAGCCGG
1 TGATT-ATTAGCAGGCTTCGAGCCGG
187208 TGA
1 TGA
187211 ATGTCTAGTA
Statistics
Matches: 86, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
25 27 0.31
26 59 0.69
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (25 bp):
TGATTATTAGCAGGCTTCGAGCCGG
Found at i:192728 original size:17 final size:17
Alignment explanation
Indices: 192695--192737 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
192685 ATTTCGTTTG
*
192695 TTTATTGTTCTTTATTTA
1 TTTATT-TTCATTATTTA
192713 TTTATTTTCATTATTTA
1 TTTATTTTCATTATTTA
192730 TTTATTTT
1 TTTATTTT
192738 TATCTCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTATTTTCATTATTTA
Found at i:193312 original size:2 final size:2
Alignment explanation
Indices: 193305--193351 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
193295 NNNNNNNNNN
193305 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193347 TA TA T
1 TA TA T
193352 TGCATTTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:199557 original size:384 final size:384
Alignment explanation
Indices: 198827--199985 Score: 2052
Period size: 384 Copynumber: 3.0 Consensus size: 384
198817 ATTGTAATTT
* * *
198827 TGAACAGGCTCAAGCTAAGAGGAGGGCACCTGACAAGTCCATTAGAGAAGACCAGGACAAGATAG
1 TGAACAGGCTCAAGCT-A-A-GAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
* *
198892 ACAGGAGTGTTCCTGCTTCGTCCGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGAAT
63 ACAGGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
* *
198957 GAAGCTTTCATTAGATCCAAGAAAGTGCACAAGCCCATCTCAATTGAGAGGAATGACACTGCTCG
128 GAAGCTTTCATTAGACCCAAGAAAGTGCACAAGCCCAACTCAATTGAGAGGAATGACACTGCTCG
* *
199022 CACTCATGAGGTGTGTTTTTGGATGTTGTTTTGTGAAATCTTAGAATTTTCTTTTACCATGAAGT
193 CACTCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
199087 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
258 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
*
199152 CTCCTTCGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
323 CTCCTTTGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
199214 TGAACAGGCTCAAGCTAAGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGGACA
1 TGAACAGGCTCAAGCTAAGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGGACA
*
199279 GGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGTTAAGGAGGGGGATGAA
66 GGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGATGAA
** *
199344 GCTTTCATTAGACCCAAGAAAGTGTGCAAGCCCAACTCAATTGAGAGGAATGACACTGCTCGGAC
131 GCTTTCATTAGACCCAAGAAAGTGCACAAGCCCAACTCAATTGAGAGGAATGACACTGCTCGCAC
199409 TCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGTTTA
196 TCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGTTTA
*
199474 AGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCACCTGCTAAATTTTCTC
261 AGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTTCTC
199539 CTTTGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
326 CTTTGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
*
199598 TGAATAGGCTCAAGCTAAGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGGACA
1 TGAACAGGCTCAAGCTAAGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGGACA
199663 GGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGATGAA
66 GGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGATGAA
*
199728 GCTTTCATTAGACCCAAGAAAGTGCACAAGCCCAACTCAATTGAGAGGAATGACACTGTTCGCAC
131 GCTTTCATTAGACCCAAGAAAGTGCACAAGCCCAACTCAATTGAGAGGAATGACACTGCTCGCAC
* * * *
199793 TCATGAGGTGTGTACTTGGATGTTGTTTTGTAAAATATTGGAATTTTCTTTTACCATGAAATTTA
196 TCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGTTTA
*
199858 AGGCTTATCCTTTCATTACACTGCATGCTGTAACTTGTAATTGTAATCTCCTGCTAAATTTTCTC
261 AGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTTCTC
*
199923 CTTCT-TACG-TGTCATTGTTATAACCAATTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
326 CTT-TGTACGCT-TCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
199982 TGAA
1 TGAA
199986 ATCTTGGGAG
Statistics
Matches: 742, Mismatches: 28, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
383 1 0.00
384 722 0.97
385 2 0.00
386 1 0.00
387 16 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (384 bp):
TGAACAGGCTCAAGCTAAGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGGACA
GGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGATGAA
GCTTTCATTAGACCCAAGAAAGTGCACAAGCCCAACTCAATTGAGAGGAATGACACTGCTCGCAC
TCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGTTTA
AGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTTCTC
CTTTGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
Found at i:205862 original size:30 final size:30
Alignment explanation
Indices: 205828--205979 Score: 182
Period size: 30 Copynumber: 5.1 Consensus size: 30
205818 CCTCTTTAGG
205828 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
* * *
205858 CTTCTCACCGTCTTTGGGCTTT-TCGGGTTT
1 CTTCTCAGCTTCTTTGGG-TTTCTCCGGTTT
* * *
205888 CTTCTCCGCTTCCTTGGGTTTTTCCGGTTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
* *
205918 CTTCTCGGCTTCTTTGGGTTTTTCCGGTTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
* * *
205948 CTTCTCAGCTTCTTTCGGCTTCT-CGGCTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
205977 CTT
1 CTT
205980 TAGGTTTGAC
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
29 11 0.10
30 91 0.87
31 3 0.03
ACGTcount: A:0.02, C:0.28, G:0.20, T:0.49
Consensus pattern (30 bp):
CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
Found at i:206987 original size:60 final size:60
Alignment explanation
Indices: 206876--207045 Score: 211
Period size: 61 Copynumber: 2.8 Consensus size: 60
206866 ACTTAACACA
* *
206876 TTTTCTTAATTTAGCACTTAAA-TTTTTTT-TATTCAATTTGGTACTTAAACTTGACA-TT
1 TTTTCTTAATTTAGTAC-TAAACTTTTTTTATATTCAATTTGATACTTAAACTTGACATTT
* * * *
206934 TTTTCTTAATTTTGTATCTAAACTTTTTTTAGATCCAATTTGATACTTGAACTTGACATTT
1 TTTTCTTAATTTAGTA-CTAAACTTTTTTTATATTCAATTTGATACTTAAACTTGACATTT
* * *
206995 TTTTCCTAATTTAGTACCTAAGCTTTTTTTATATTCAATTTGATACCTAAA
1 TTTTCTTAATTTAGTA-CTAAACTTTTTTTATATTCAATTTGATACTTAAA
207046 TTTATTAAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
58 18 0.19
59 8 0.09
60 23 0.24
61 45 0.48
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (60 bp):
TTTTCTTAATTTAGTACTAAACTTTTTTTATATTCAATTTGATACTTAAACTTGACATTT
Found at i:207335 original size:33 final size:30
Alignment explanation
Indices: 207285--207386 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 30
207275 CCAAGCTTAG
*
207285 GTACCAAATTAGAAAAAAAGTGTCAAGTTTGA
1 GTACCAAATTAGAAAAAAAG-GT-AAGTTTAA
*
207317 GTACCAAATTGGACAAAAAA---AAGTTTAA
1 GTACCAAATTAGA-AAAAAAGGTAAGTTTAA
*
207345 GTACCAAATTAAAAAAAAAAGAGTGAAGTTTAA
1 GTACCAAATT-AGAAAAAAAG-GT-AAGTTTAA
207378 GTACCAAAT
1 GTACCAAAT
207387 ATTATATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
28 23 0.39
29 1 0.02
32 12 0.20
33 23 0.39
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.23
Consensus pattern (30 bp):
GTACCAAATTAGAAAAAAAGGTAAGTTTAA
Found at i:207345 original size:91 final size:90
Alignment explanation
Indices: 207191--207362 Score: 229
Period size: 91 Copynumber: 1.9 Consensus size: 90
207181 TAAAAAAAAA
* * * * **
207191 TTAGGTATCAAATTAAGAAAAAGAGTCAAGTTTGGGTGCCAAATTGGATCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAAAAAAAAGAGTCAAGTTTGAGTACCAAATTGGATCAAAAAAAGTTTAAGT
** *
207256 GTCAACTTAAAAAAAAGTACCAAGC
66 ACCAAATTAAAAAAAAGTACCAAGC
*
207281 TTAGGTACCAAATTAGAAAAAAAGTGTCAAGTTTGAGTACCAAATTGGA-CAAAAAAAAGTTTAA
1 TTAGGTACCAAATTA-AAAAAAAGAGTCAAGTTTGAGTACCAAATTGGATC-AAAAAAAGTTTAA
207345 GTACCAAATTAAAAAAAA
64 GTACCAAATTAAAAAAAA
207363 AAGAGTGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
90 15 0.21
91 55 0.79
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (90 bp):
TTAGGTACCAAATTAAAAAAAAGAGTCAAGTTTGAGTACCAAATTGGATCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAGTACCAAGC
Found at i:209819 original size:21 final size:22
Alignment explanation
Indices: 209780--209821 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
209770 TTTGATCCAT
*
209780 TTTAATTCTTATCATTTTTTAA
1 TTTAATCCTTATCATTTTTTAA
209802 TTTAATCCTTAT-ATTTTTTA
1 TTTAATCCTTATCATTTTTTA
209822 TGTTCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAATCCTTATCATTTTTTAA
Found at i:224096 original size:18 final size:17
Alignment explanation
Indices: 224066--224112 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
224056 TTTTGAGTAG
*
224066 TTATA-TTTTTTTAGAT
1 TTATATTTTTTTTAAAT
224082 TTATATTTTTATTTAAAT
1 TTATATTTTT-TTTAAAT
224100 TCTATCATTTTTT
1 T-TAT-ATTTTTT
224113 AATGGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
18 7 0.27
19 4 0.15
20 6 0.23
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (17 bp):
TTATATTTTTTTTAAAT
Found at i:225098 original size:6 final size:6
Alignment explanation
Indices: 225089--225113 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
225079 CGCCACCTTT
225089 GAAACC GAAACC GAAACC GAAACC G
1 GAAACC GAAACC GAAACC GAAACC G
225114 CGTTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAACC
Found at i:235464 original size:16 final size:15
Alignment explanation
Indices: 235443--235473 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
235433 AAGAAAGCCA
235443 AATAATAATTCTTCAT
1 AATAATAATT-TTCAT
235459 AATAATAATTTTCAT
1 AATAATAATTTTCAT
235474 TATTAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAATTTTCAT
Found at i:235741 original size:48 final size:48
Alignment explanation
Indices: 235680--235778 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
235670 ATATATATTT
235680 TATTAGGATACCTTTACTTTCATAAAATGTCCAATGTGATATTTGAAC
1 TATTAGGATACCTTTACTTTCATAAAATGTCCAATGTGATATTTGAAC
* * *
235728 TATTAGGATACCTTTACTTTCATAAAATGTCCAATTTGGTATTTGGAC
1 TATTAGGATACCTTTACTTTCATAAAATGTCCAATGTGATATTTGAAC
235776 TAT
1 TAT
235779 CAATATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (48 bp):
TATTAGGATACCTTTACTTTCATAAAATGTCCAATGTGATATTTGAAC
Found at i:240425 original size:15 final size:15
Alignment explanation
Indices: 240394--240440 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
240384 GTTAAAAATT
240394 ATAAAAACATTCA-AAA
1 ATAAAAA-ATT-ATAAA
240410 ATAAAAAATTATAAA
1 ATAAAAAATTATAAA
* *
240425 AAAAAAAATCATAAA
1 ATAAAAAATTATAAA
240440 A
1 A
240441 ATTCAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 20 0.71
16 7 0.25
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAAAATTATAAA
Found at i:240441 original size:15 final size:16
Alignment explanation
Indices: 240406--240442 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
240396 AAAAACATTC
*
240406 AAAAATAAAAAATTAT
1 AAAAATAAAAAATCAT
240422 AAAAA-AAAAAATCAT
1 AAAAATAAAAAATCAT
240437 AAAAAT
1 AAAAAT
240443 TCAAAGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAAATCAT
Found at i:243948 original size:84 final size:81
Alignment explanation
Indices: 243857--244195 Score: 362
Period size: 84 Copynumber: 4.0 Consensus size: 81
243847 AGAAGAGAAA
* ***
243857 AAGAAGGCAGTTGAAGAAAGAAAACTTG-TCGATTTGGAGATGGCTAAAGCAAGCGAGTTGAGGA
1 AAGAAGGCTGTTGAAGAAAGAAAAC-TGCT-GATTTGGAGATGGCTAAAGC-AG-GAGCAAAGGA
243921 AGATTGCAGAAGAAACTAAG
62 AGATTGCAGAAGAAACTAAG
* * * *
243941 AAAAAGGCTGTTGATGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCGGAGAAGCAAAGGAA
1 AAGAAGGCTGTTGAAGAAAGAAAA-CTGCTGATTTGGAGATGGCTAAAGC--AGGAGCAAAGGAA
*
244006 GATTTCTA-AAGAAACTAAG
63 GATTGC-AGAAGAAACTAAG
* * *
244025 AAGAAGGCTGTTGAAGAAAGAAAACGTGCTGATTTAGAGATGGCTGAAGCAGTGAAGCAGAGGAA
1 AAGAAGGCTGTTGAAGAAAGAAAAC-TGCTGATTTGGAGATGGCTAAAGCAG-G-AGCAAAGGAA
*
244090 GATTGCAGAAGAAAAC-ATG
63 GATTGCAGAAG-AAACTAAG
* * *
244109 AAGAAGGCTGTTGAAGTAAGAAAACAAGCTGATATT-GAGTTGGCTAAAGCAGAAGAGCAAAGGA
1 AAGAAGGCTGTTGAAGAAAGAAAAC-TGCTGAT-TTGGAGATGGCTAAAGCAG--GAGCAAAGGA
244173 AGATTGCAGAAGAAACTAAG
62 AGATTGCAGAAGAAACTAAG
244193 AAG
1 AAG
244196 GCTGTTGAAG
Statistics
Matches: 216, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
82 2 0.01
83 5 0.02
84 198 0.92
85 11 0.05
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (81 bp):
AAGAAGGCTGTTGAAGAAAGAAAACTGCTGATTTGGAGATGGCTAAAGCAGGAGCAAAGGAAGAT
TGCAGAAGAAACTAAG
Found at i:244155 original size:168 final size:168
Alignment explanation
Indices: 243857--244195 Score: 429
Period size: 168 Copynumber: 2.0 Consensus size: 168
243847 AGAAGAGAAA
* * **
243857 AAGAAGGCAGTTGAAGAAAGAAAACTTGTCGATTTGGAGATGGCTAAAGCAAGCGAGTTGAGGAA
1 AAGAAGGCAGTTGAAGAAAGAAAACGTGTCGATTTAGAGATGGCTAAAGCAAGCGAGCAGAGGAA
* ***
243922 GATTGCAGAAGAAACTAAGAAAAAGGCTGTTGATGAAAGAAAATGTGCTGATTTGGAGATGGCTA
66 GATTGCAGAAGAAACTAAGAAAAAGGCTGTTGAAGAAAGAAAACAAGCTGATTTGGAGATGGCTA
* *
243987 AAGC-GGAGAAGCAAAGGAAGATTTCTA-AAGAAACTAAG
131 AAGCAGAAG-AGCAAAGGAAGATTGC-AGAAGAAACTAAG
* * *
244025 AAGAAGGCTGTTGAAGAAAGAAAACGTG-CTGATTTAGAGATGGCTGAAGC-AGTGAAGCAGAGG
1 AAGAAGGCAGTTGAAGAAAGAAAACGTGTC-GATTTAGAGATGGCTAAAGCAAGCG-AGCAGAGG
* * * *
244088 AAGATTGCAGAAGAAAAC-ATGAAGAAGGCTGTTGAAGTAAGAAAACAAGCTGATATT-GAGTTG
64 AAGATTGCAGAAG-AAACTAAGAAAAAGGCTGTTGAAGAAAGAAAACAAGCTGAT-TTGGAGATG
244151 GCTAAAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAACTAAG
127 GCTAAAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAACTAAG
244193 AAG
1 AAG
244196 GCTGTTGAAG
Statistics
Matches: 148, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
167 5 0.03
168 134 0.91
169 9 0.06
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (168 bp):
AAGAAGGCAGTTGAAGAAAGAAAACGTGTCGATTTAGAGATGGCTAAAGCAAGCGAGCAGAGGAA
GATTGCAGAAGAAACTAAGAAAAAGGCTGTTGAAGAAAGAAAACAAGCTGATTTGGAGATGGCTA
AAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAACTAAG
Found at i:256623 original size:5 final size:5
Alignment explanation
Indices: 256613--256638 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
256603 ATCCACTTAT
256613 ACGCC ACGCC ACGCC ACGCC ACGCC A
1 ACGCC ACGCC ACGCC ACGCC ACGCC A
256639 AGCAAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACGCC
Found at i:266313 original size:29 final size:30
Alignment explanation
Indices: 266279--266352 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
266269 TTGTACCTAC
266279 ATATTATTTTAATAAA-TAA-TTTATAACCT
1 ATATTATTTTAATAAATTAATTTTAT-ACCT
***
266308 ATATTATTTTAA-AAATTAATTTTATTTTT
1 ATATTATTTTAATAAATTAATTTTATACCT
266337 ATATTATTTTAATAAA
1 ATATTATTTTAATAAA
266353 ATCCCAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.08
29 28 0.72
30 8 0.21
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATTATTTTAATAAATTAATTTTATACCT
Found at i:267555 original size:2 final size:2
Alignment explanation
Indices: 267550--267587 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
267540 AAAAAAAGAA
*
267550 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
267588 TTCAAAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:268055 original size:6 final size:6
Alignment explanation
Indices: 268008--268080 Score: 74
Period size: 6 Copynumber: 12.2 Consensus size: 6
267998 GAGATAGGAA
* * *
268008 GGATAA GGATAA GGATAG GGATAG GAATAG GGATAG GGATAG GGATAG
1 GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG
* * * * *
268056 AGATAG AGATGG GGACAG AGATAG G
1 GGATAG GGATAG GGATAG GGATAG G
268081 AGTAGGCATA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.40, C:0.01, G:0.44, T:0.15
Consensus pattern (6 bp):
GGATAG
Found at i:268070 original size:18 final size:18
Alignment explanation
Indices: 268021--268098 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
268011 TAAGGATAAG
* * *
268021 GATAGGGATAGGAATAGG
1 GATAGAGATAGGGATAGA
*
268039 GATAGGGATAGGGATAGA
1 GATAGAGATAGGGATAGA
* *
268057 GATAGAGATGGGGACAGA
1 GATAGAGATAGGGATAGA
*
268075 GATAG-GAGTAGGCATAGA
1 GATAGAGA-TAGGGATAGA
268093 GATAGA
1 GATAGA
268099 TATAAGGAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
17 2 0.04
18 48 0.96
ACGTcount: A:0.40, C:0.03, G:0.42, T:0.15
Consensus pattern (18 bp):
GATAGAGATAGGGATAGA
Found at i:269962 original size:3 final size:3
Alignment explanation
Indices: 269954--269995 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
269944 TTTGACCAGC
269954 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
269996 ACAACAACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.