Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 23 of 27
Found at i:3702761 original size:33 final size:31
Alignment explanation
Indices: 3702694--3702782 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 31
3702684 TTACGACAAC
*
3702694 TATC-TTTCAGGGCTAAGATAAAAACCTCCT
1 TATCTTTTCAGGGCTAAGATAGAAACCTCCT
*
3702724 TATCTTTTCACGGGCTAAGATAGAACCTCTCCT
1 TATCTTTTCA-GGGCTAAGATAGAAAC-CTCCT
*
3702757 TATCTTTTTCAAAGGCTAAGATAGAA
1 TATC-TTTTC-AGGGCTAAGATAGAA
3702783 TCTTTCAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 4 0.08
31 5 0.10
32 14 0.27
33 9 0.18
34 18 0.35
35 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (31 bp):
TATCTTTTCAGGGCTAAGATAGAAACCTCCT
Found at i:3703277 original size:32 final size:32
Alignment explanation
Indices: 3703236--3703306 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
3703226 TACTATTCAC
* *
3703236 ATGTATCGATACATGAACAATGATGAACAGTG
1 ATGTATCGATACATGAACAATGATCAACAGTA
* *
3703268 ATGTATCGATACATGAATAATGATCAATAGTA
1 ATGTATCGATACATGAACAATGATCAACAGTA
3703300 ATGTATC
1 ATGTATC
3703307 AATTAAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACATGAACAATGATCAACAGTA
Found at i:3703384 original size:20 final size:19
Alignment explanation
Indices: 3703340--3703391 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
3703330 TGCGAGTTTT
*
3703340 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAA
3703359 ATGTATCGATACTAA-GCAAA
1 ATGTATCGATAC-AATG-AAA
3703379 ATGTATCGATACA
1 ATGTATCGATACA
3703392 TTTGGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (19 bp):
ATGTATCGATACAATGAAA
Found at i:3704746 original size:13 final size:13
Alignment explanation
Indices: 3704728--3704754 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3704718 TACACCAAGT
3704728 ATGTATCGATACA
1 ATGTATCGATACA
3704741 ATGTATCGATACA
1 ATGTATCGATACA
3704754 A
1 A
3704755 AAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3709932 original size:32 final size:32
Alignment explanation
Indices: 3709891--3709951 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3709881 TACTATTCAC
* *
3709891 ATGTATCGATACATGAACAGCGATGAACAATG
1 ATGTATCGATACATAAACAGCGATCAACAATG
*
3709923 ATGTATCGATACATAAACAGTGATCAACA
1 ATGTATCGATACATAAACAGCGATCAACA
3709952 GTAAGTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (32 bp):
ATGTATCGATACATAAACAGCGATCAACAATG
Found at i:3720778 original size:29 final size:29
Alignment explanation
Indices: 3720741--3720944 Score: 237
Period size: 29 Copynumber: 7.0 Consensus size: 29
3720731 CTTTTTTCCA
* *
3720741 AAAGTCCACGACTCAGTGGCACCCTTTTT
1 AAAGTCCACAACTCTGTGGCACCCTTTTT
* * * * * *
3720770 AAAGTCCACGACTCAGTGGTATCTCTTCTC
1 AAAGTCCACAACTCTGTGGCA-CCCTTTTT
* *
3720800 AAAGTCCAAAACTTTGTGGCACCCTTTTT
1 AAAGTCCACAACTCTGTGGCACCCTTTTT
*
3720829 AAAGTCCTCAACTCTGTGGCACCCTTTTT
1 AAAGTCCACAACTCTGTGGCACCCTTTTT
* *
3720858 AAAGTCCATAACTCTGTGGCCCCCTTTTT
1 AAAGTCCACAACTCTGTGGCACCCTTTTT
* *
3720887 AAAGTCCACAACTCTGTGACACCTTTTTT
1 AAAGTCCACAACTCTGTGGCACCCTTTTT
* * *
3720916 AAAGTCCATAACTCTATGGCCCCCTTTTT
1 AAAGTCCACAACTCTGTGGCACCCTTTTT
3720945 CTTTTTAAGT
Statistics
Matches: 147, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
29 126 0.86
30 21 0.14
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (29 bp):
AAAGTCCACAACTCTGTGGCACCCTTTTT
Found at i:3720999 original size:34 final size:34
Alignment explanation
Indices: 3720917--3721002 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
3720907 ACCTTTTTTA
* * * *
3720917 AAGTCCATAACTCTATGGCCCCCTTTTTCTTTTT
1 AAGTCCACAACTCTGTGGCCCCATTTTTCTTGTT
*
3720951 AAGTCCACAACTCTGTGGCTCCATTTTTCTTGTT
1 AAGTCCACAACTCTGTGGCCCCATTTTTCTTGTT
*
3720985 AATTCCACAACTCTGTGG
1 AAGTCCACAACTCTGTGG
3721003 TACCTTTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (34 bp):
AAGTCCACAACTCTGTGGCCCCATTTTTCTTGTT
Found at i:3721049 original size:31 final size:31
Alignment explanation
Indices: 3721011--3721257 Score: 300
Period size: 31 Copynumber: 7.9 Consensus size: 31
3721001 GGTACCTTTT
*
3721011 CTTCTAAAGCCCACACAAGTAGGTGGTAACC
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACC
*
3721042 CTTCTAAAGCCCACACAAGTTGGTGGCAACC
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACC
* * ** *
3721073 CTTCTAAAGCTCGCACAAGTCTGTGGCAATC
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACC
*
3721104 CTTCTAAAGCTCACACAAGTTA-GTGGCAACC
1 CTTCTAAAGCCCACACAAG-TAGGTGGCAACC
*
3721135 CTTCTAAAGCCCACACAAGTCA-ATGGCAACC
1 CTTCTAAAGCCCACACAAGT-AGGTGGCAACC
* *
3721166 CTTCTTTAAAGCCCACACAAGTTGATGGCAACC
1 CTTC--TAAAGCCCACACAAGTAGGTGGCAACC
* * *
3721199 CTTCTAAAGCCAAAACAAGTCGGTGGCAACC
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACC
* *
3721230 CTTCTAAAGTCCACACAAGTTGGTGGCA
1 CTTCTAAAGCCCACACAAGTAGGTGGCA
3721258 CTTTTCAGTC
Statistics
Matches: 190, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 159 0.84
32 1 0.01
33 29 0.15
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (31 bp):
CTTCTAAAGCCCACACAAGTAGGTGGCAACC
Found at i:3721079 original size:62 final size:62
Alignment explanation
Indices: 3721011--3721257 Score: 334
Period size: 62 Copynumber: 4.0 Consensus size: 62
3721001 GGTACCTTTT
*
3721011 CTTCTAAAGCCCACACAAGTAGGTGGTAACCCTTCTAAAGCCCACACAAGTTGGTGGCAACC
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACCCTTCTAAAGCCCACACAAGTTGGTGGCAACC
* * ** * * *
3721073 CTTCTAAAGCTCGCACAAGTCTGTGGCAATCCTTCTAAAGCTCACACAAGTTAGTGGCAACC
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACCCTTCTAAAGCCCACACAAGTTGGTGGCAACC
* *
3721135 CTTCTAAAGCCCACACAAGTCA-ATGGCAACCCTTCTTTAAAGCCCACACAAGTTGATGGCAACC
1 CTTCTAAAGCCCACACAAGT-AGGTGGCAACCCTTC--TAAAGCCCACACAAGTTGGTGGCAACC
* * * *
3721199 CTTCTAAAGCCAAAACAAGTCGGTGGCAACCCTTCTAAAGTCCACACAAGTTGGTGGCA
1 CTTCTAAAGCCCACACAAGTAGGTGGCAACCCTTCTAAAGCCCACACAAGTTGGTGGCA
3721258 CTTTTCAGTC
Statistics
Matches: 159, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
62 105 0.66
64 54 0.34
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (62 bp):
CTTCTAAAGCCCACACAAGTAGGTGGCAACCCTTCTAAAGCCCACACAAGTTGGTGGCAACC
Found at i:3721201 original size:126 final size:124
Alignment explanation
Indices: 3721011--3721257 Score: 356
Period size: 126 Copynumber: 2.0 Consensus size: 124
3721001 GGTACCTTTT
* * *
3721011 CTTCTAAAGCCCACACAAGTAGGTGGTAACCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCTT
1 CTTCTAAAGCCCACACAAGTAGATGGCAACCCTTCTAAAGCCCACACAAGTTGATGGCAACCCTT
** * *
3721076 CTAAAGCTC-GCACAAGTCTGTGGCAATCCTTCTAAAG-CTCACACAAGTTAGTGGCAACC
66 CTAAAGC-CAAAACAAGTCGGTGGCAACCCTTCTAAAGTC-CACACAAGTTAGTGGCAACC
3721135 CTTCTAAAGCCCACACAAGTCA-ATGGCAACCCTTCTTTAAAGCCCACACAAGTTGATGGCAACC
1 CTTCTAAAGCCCACACAAGT-AGATGGCAACCCTTC--TAAAGCCCACACAAGTTGATGGCAACC
*
3721199 CTTCTAAAGCCAAAACAAGTCGGTGGCAACCCTTCTAAAGTCCACACAAGTTGGTGGCA
63 CTTCTAAAGCCAAAACAAGTCGGTGGCAACCCTTCTAAAGTCCACACAAGTTAGTGGCA
3721258 CTTTTCAGTC
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
124 31 0.28
125 2 0.02
126 76 0.69
127 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (124 bp):
CTTCTAAAGCCCACACAAGTAGATGGCAACCCTTCTAAAGCCCACACAAGTTGATGGCAACCCTT
CTAAAGCCAAAACAAGTCGGTGGCAACCCTTCTAAAGTCCACACAAGTTAGTGGCAACC
Found at i:3721523 original size:52 final size:53
Alignment explanation
Indices: 3721430--3721529 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 53
3721420 TAGTTGGTGG
*
3721430 CATCATCTTTAAAGTCCAACGTCGCGAGCCTTGAATCAGCACTTTGGCACCCT
1 CATCATCTTTAAAGTCCAACGTCGCGAGCCTTGAATCAGCACATTGGCACCCT
* * *
3721483 CATCATCTTTAAA-TCTAATGTTGCTG-GCCTTGAAGT-AGCACATTGGC
1 CATCATCTTTAAAGTCCAACGTCGC-GAGCCTTGAA-TCAGCACATTGGC
3721530 GTGATACCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 26 0.63
53 15 0.37
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (53 bp):
CATCATCTTTAAAGTCCAACGTCGCGAGCCTTGAATCAGCACATTGGCACCCT
Found at i:3722295 original size:13 final size:13
Alignment explanation
Indices: 3722277--3722302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3722267 TACAGCAAGT
3722277 ATGTATCGATACA
1 ATGTATCGATACA
3722290 ATGTATCGATACA
1 ATGTATCGATACA
3722303 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3724553 original size:21 final size:21
Alignment explanation
Indices: 3724520--3724564 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3724510 TTGCAAGTTG
*
3724520 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3724542 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3724562 AAA
1 AAA
3724565 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3728494 original size:13 final size:13
Alignment explanation
Indices: 3728476--3728501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3728466 ACATTTTTCT
3728476 TTGTATCGATACA
1 TTGTATCGATACA
3728489 TTGTATCGATACA
1 TTGTATCGATACA
3728502 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3731064 original size:13 final size:13
Alignment explanation
Indices: 3731046--3731071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3731036 TACAGCAAGT
3731046 ATGTATCGATACA
1 ATGTATCGATACA
3731059 ATGTATCGATACA
1 ATGTATCGATACA
3731072 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3733364 original size:19 final size:19
Alignment explanation
Indices: 3733329--3733365 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3733319 CAAGTGATCG
* *
3733329 ATGAAAAAAGAAGTGAAAA
1 ATGAAAAAAAAAATGAAAA
3733348 ATGAAAAAAAAAATGAAA
1 ATGAAAAAAAAAATGAAA
3733366 CTTTAAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
ATGAAAAAAAAAATGAAAA
Found at i:3733557 original size:16 final size:16
Alignment explanation
Indices: 3733538--3733590 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
3733528 TTTAAATTCG
3733538 AGTCATTTTTAGTTCA
1 AGTCATTTTTAGTTCA
* * *
3733554 AGTCACTTTAAGCTCA
1 AGTCATTTTTAGTTCA
*
3733570 AGTC-TTTCTTAGTTTA
1 AGTCATTT-TTAGTTCA
3733586 AGTCA
1 AGTCA
3733591 ATCGAATTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 2 0.07
16 26 0.93
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (16 bp):
AGTCATTTTTAGTTCA
Found at i:3739298 original size:21 final size:21
Alignment explanation
Indices: 3739269--3739309 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3739259 GTATTTGTAT
3739269 ACCCTAGAAAGTATCGATACAG
1 ACCCTAG-AAGTATCGATACAG
3739291 ACCC-AGAAGTATCGATACA
1 ACCCTAGAAGTATCGATACA
3739310 AATTACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 2 0.11
22 4 0.21
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (21 bp):
ACCCTAGAAGTATCGATACAG
Found at i:3741734 original size:23 final size:22
Alignment explanation
Indices: 3741708--3741750 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3741698 CAAATAGGCT
* *
3741708 AAAATTTTTTAATAAAATTAATA
1 AAAAATTTTAAAT-AAATTAATA
3741731 AAAAATTTTAAATAAATTAA
1 AAAAATTTTAAATAAATTAA
3741751 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTTTAAATAAATTAATA
Found at i:3741754 original size:16 final size:15
Alignment explanation
Indices: 3741733--3741762 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3741723 AATTAATAAA
3741733 AAATTTTAAATAAATT
1 AAATTTTAAA-AAATT
3741749 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
3741763 AAAGTCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTTTAAAAAATT
Found at i:3749060 original size:20 final size:20
Alignment explanation
Indices: 3749016--3749085 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
3749006 CTATAATTTG
* * *
3749016 TATCGATACAACAAGTTAATA
1 TATCGATAC-ATAAGTAAATC
* *
3749037 TATCAATACCTAAGTAAATC
1 TATCGATACATAAGTAAATC
* *
3749057 TATCGATACATAAGTGAATG
1 TATCGATACATAAGTAAATC
3749077 TATCGATAC
1 TATCGATAC
3749086 TAAACCTTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 32 0.80
21 8 0.20
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (20 bp):
TATCGATACATAAGTAAATC
Found at i:3753579 original size:141 final size:142
Alignment explanation
Indices: 3753239--3753581 Score: 430
Period size: 141 Copynumber: 2.4 Consensus size: 142
3753229 AACCAAGGGC
* * ** * ** *
3753239 ATACGAAAAGTTTGTG-A-ATTTTTATACCCCTACGGACGACTATAGGAATGA-TAGAAGGCTTG
1 ATACGAAAAGTTT-TGAAGATTTCTATATCCCTACGGATAACCATAGGAAT-ATTAGAAATCTTC
* **
3753301 AAAAATTTAAGATAATAATTTTTATTTAATTTTCAATTTTCAAAAAAATCATTTTGTACCTTAAT
64 AAAAATTTAAGATAATAATTTCTATTTAATTTTCAATTTTCAAAAAAATCATTTCATACCTTAAT
3753366 AGAGAAACAAAAAG
129 AGAGAAACAAAAAG
3753380 ATACGAAAAGTTTTGAAGATTTCTATATCCCTACGGATAACCATAGGAATATTAGAAATCTTCAA
1 ATACGAAAAGTTTTGAAGATTTCTATATCCCTACGGATAACCATAGGAATATTAGAAATCTTCAA
** * *
3753445 AAA-TTAAGATAATAATTTCTATTTAATTTTTTATTTT-AAAAAAATTCATTTCATACTTTAATG
66 AAATTTAAGATAATAATTTCTATTTAATTTTCAATTTTCAAAAAAA-TCATTTCATACCTTAATA
* *
3753508 GAGAACCGAAAAG
130 GAGAAACAAAAAG
*
3753521 ATAC-AAAAGGTTTTGAAGATTTCTATA-CCTTTACGGATAACCATAGGAATATTAGAAATCT
1 ATACGAAAA-GTTTTGAAGATTTCTATATCC-CTACGGATAACCATAGGAATATTAGAAATCT
3753582 ACCAAAATGA
Statistics
Matches: 178, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
140 15 0.08
141 123 0.69
142 40 0.22
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (142 bp):
ATACGAAAAGTTTTGAAGATTTCTATATCCCTACGGATAACCATAGGAATATTAGAAATCTTCAA
AAATTTAAGATAATAATTTCTATTTAATTTTCAATTTTCAAAAAAATCATTTCATACCTTAATAG
AGAAACAAAAAG
Found at i:3754353 original size:10 final size:10
Alignment explanation
Indices: 3754330--3754379 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
3754320 ATTTTTTGTA
3754330 TTTTCTCTCTT
1 TTTTCTCTC-T
*
3754341 TTTTCTTTCT
1 TTTTCTCTCT
3754351 TTTTCTCTCT
1 TTTTCTCTCT
* *
3754361 TTTTTTGTCT
1 TTTTCTCTCT
3754371 TTTT-TCTCT
1 TTTTCTCTCT
3754380 CCACTTGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 4 0.12
10 22 0.65
11 8 0.24
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTCTCTCT
Found at i:3754356 original size:21 final size:21
Alignment explanation
Indices: 3754330--3754380 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
3754320 ATTTTTTGTA
*
3754330 TTTTCTCTCTTTTTTCTTTC-T
1 TTTTCTCTCTTTTTT-TGTCTT
3754351 TTTTCTCTCTTTTTTTGTCTT
1 TTTTCTCTCTTTTTTTGTCTT
3754372 TTTTCTCTC
1 TTTTCTCTC
3754381 CACTTGCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTCTCTTTTTTTGTCTT
Found at i:3755254 original size:166 final size:167
Alignment explanation
Indices: 3754973--3755286 Score: 481
Period size: 166 Copynumber: 1.9 Consensus size: 167
3754963 AACAATCTAT
* * * * *
3754973 CCGAGAACCTTTATGGAATAGAAAATTCGATTTTTTTAGAAATAGGGGCACTTTAAGGAAAAAGA
1 CCGAAAACCTTTATGGAATAGAAAATTCGAGTTTTTCAGAAATAGGGGAAATTTAAGGAAAAAGA
* * *
3755038 TGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTGATTCATTATGAATTAAATGATGATATT
66 TGAAAAACTCATAAAAATAAAGGAATTTTTCAAAACTGATTCAATATGAATTAAATGATGATATT
3755103 TGATGAATGTTAAAAATTTCAAACTGAGAAAAACCCC
131 TGATGAATGTTAAAAATTTCAAACTGAGAAAAACCCC
*
3755140 CCGAAAACCTTTATGGAATAGAAAATTC-AGTTTTTCATAAATA-GGGAAATTTGAAGGAAAAA-
1 CCGAAAACCTTTATGGAATAGAAAATTCGAGTTTTTCAGAAATAGGGGAAATTT-AAGGAAAAAG
* *
3755202 ATGAAAAACTCATAAAAATAAAAGGAATTTTTCAAATCTGATTTAATATGAATTAAATGATGATA
65 ATGAAAAACTCATAAAAAT-AAAGGAATTTTTCAAAACTGATTCAATATGAATTAAATGATGATA
*
3755267 TTTGATGAATTTTAAAAATT
129 TTTGATGAATGTTAAAAATT
3755287 ATAAACCACA
Statistics
Matches: 133, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
165 25 0.19
166 81 0.61
167 27 0.20
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (167 bp):
CCGAAAACCTTTATGGAATAGAAAATTCGAGTTTTTCAGAAATAGGGGAAATTTAAGGAAAAAGA
TGAAAAACTCATAAAAATAAAGGAATTTTTCAAAACTGATTCAATATGAATTAAATGATGATATT
TGATGAATGTTAAAAATTTCAAACTGAGAAAAACCCC
Found at i:3755389 original size:166 final size:164
Alignment explanation
Indices: 3755027--3755459 Score: 415
Period size: 166 Copynumber: 2.6 Consensus size: 164
3755017 GGGGCACTTT
* * * * *
3755027 AAGGAAAAAGATGAAAAACTCATGAAAAT-AAATGAATTTTTCAAAACTGATTCATTATGAATTA
1 AAGGAAAAA-AAGAAAAACTAATAAAAATAAAAGGAATTTTTC-AAACTGATTTATTATGAATTA
* * * ** **
3755091 AATGATGATATTTGATGAATGTTAAAAATT-TCAAACTGAGAAAAACCCCCCGAAAACCTTTATG
64 AATGATGATATTTGATGAATTTTAAAAATTAT-AAAC-CACAAAAACCCCCCGAAAACAATTACA
* * * * * *
3755155 GAATAGAAAATTCAGTTTTTCATAAATAGGGAAATTTG
127 GAATAGAAAACTCAGTATTTCAAAAAAAGGAAAATTTC
* * *
3755193 AAGGAAAAAATGAAAAACTCATAAAAATAAAAGGAATTTTTCAAATCTGATTTAATATGAATTAA
1 AAGGAAAAAAAGAAAAACTAATAAAAATAAAAGGAATTTTTCAAA-CTGATTTATTATGAATTAA
* * * *
3755258 ATGATGATATTTGATGAATTTTAAAAATTATAAACCACAAAAGAGCTCCCTGAAAATAATTACAT
65 ATGATGATATTTGATGAATTTTAAAAATTATAAACCACAAAA-A-CCCCCCGAAAACAATTACAG
* *
3755323 AGTAGAAAACTCAGTATTT-AAAAAAATGAAGAATTTC
128 AATAGAAAACTCAGTATTTCAAAAAAAGGAA-AATTTC
* * * * * * *
3755360 AAGGAAAAAAAGGAAAATTAAT-GAAATAAAAGGAATTTTTTGAAACTAATTTATTTTGAGTTAA
1 AAGGAAAAAAAGAAAAACTAATAAAAATAAAAGGAA-TTTTTCAAACTGATTTATTATGAATTAA
* * * *
3755424 ATAATAATCTTTGATGAATTTTAAAATTTATAAACC
65 ATGATGATATTTGATGAATTTTAAAAATTATAAACC
3755460 TGAGAAAATA
Statistics
Matches: 223, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
165 26 0.12
166 137 0.61
167 60 0.27
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.30
Consensus pattern (164 bp):
AAGGAAAAAAAGAAAAACTAATAAAAATAAAAGGAATTTTTCAAACTGATTTATTATGAATTAAA
TGATGATATTTGATGAATTTTAAAAATTATAAACCACAAAAACCCCCCGAAAACAATTACAGAAT
AGAAAACTCAGTATTTCAAAAAAAGGAAAATTTC
Found at i:3760120 original size:20 final size:19
Alignment explanation
Indices: 3760095--3760168 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
3760085 AACCCTAATT
3760095 TGTATTGATACATACCAAAA
1 TGTATTGATACATA-CAAAA
*
3760115 TGTATTGATACAATACACAA
1 TGTATTGATAC-ATACAAAA
*
3760135 TGTATTGATACATTACATGAA
1 TGTATTGATACA-TACA-AAA
*
3760156 TATATTGATACAT
1 TGTATTGATACAT
3760169 CTATTGGTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.02
20 31 0.65
21 16 0.33
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (19 bp):
TGTATTGATACATACAAAA
Found at i:3760218 original size:112 final size:112
Alignment explanation
Indices: 3760021--3760259 Score: 316
Period size: 112 Copynumber: 2.1 Consensus size: 112
3760011 CTCAGGTTTG
* * * * * *
3760021 AATGTATCGATACATTACATGAATGTATCGATATATTTGTTGGTAGTAGCTAAGGAAATCCTGAA
1 AATGTATCGATACATTACATGAATATATCGATACATCTATTGGTAGTAGCTAAAGAAATCCAGAA
*
3760086 ACCCTAATTTGTATTGATACATACCAAAATGTATTGATACAATACAC
66 ACCCTAATTTGTATTGATACATACCAAAATGTATTAATACAATACAC
* *
3760133 AATGTATTGATACATTACATGAATATATTGATACATCTATTGGTAGTAGCTAAAGAAATCCAGAA
1 AATGTATCGATACATTACATGAATATATCGATACATCTATTGGTAGTAGCTAAAGAAATCCAGAA
* * * ** * *
3760198 ATCCTTATTTGTATTGATACATATCAGGATGTATTAATACAATATAT
66 ACCCTAATTTGTATTGATACATACCAAAATGTATTAATACAATACAC
* *
3760245 TATTTATCGATACAT
1 AATGTATCGATACAT
3760260 AAAAAATGTA
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
112 108 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (112 bp):
AATGTATCGATACATTACATGAATATATCGATACATCTATTGGTAGTAGCTAAAGAAATCCAGAA
ACCCTAATTTGTATTGATACATACCAAAATGTATTAATACAATACAC
Found at i:3762173 original size:20 final size:20
Alignment explanation
Indices: 3762150--3762201 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3762140 ATATTGCTTA
3762150 GTATCGATACATGGTAAATT
1 GTATCGATACATGGTAAATT
3762170 GTATCGATACATGGTAAATT
1 GTATCGATACATGGTAAATT
*
3762190 ATATCGATACAT
1 GTATCGATACAT
3762202 TAAGCCCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGGTAAATT
Found at i:3762244 original size:52 final size:52
Alignment explanation
Indices: 3762166--3762325 Score: 248
Period size: 52 Copynumber: 3.1 Consensus size: 52
3762156 ATACATGGTA
3762166 AATTGTATCGATACATGGTAAATTATATCGATACATTAAGCCCAATGACTAT
1 AATTGTATCGATACATGGTAAATTATATCGATACATTAAGCCCAATGACTAT
3762218 AATTGTATCGATACATGGTAAATTATATCGATACATTAAGCCCAATGACTAT
1 AATTGTATCGATACATGGTAAATTATATCGATACATTAAGCCCAATGACTAT
** * * * * * *
3762270 AATTGTATCGATACATTATGAATTGTATCGATACATTGAGTCCAATGGCTAG
1 AATTGTATCGATACATGGTAAATTATATCGATACATTAAGCCCAATGACTAT
3762322 AATT
1 AATT
3762326 TCAAATCCAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 100 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (52 bp):
AATTGTATCGATACATGGTAAATTATATCGATACATTAAGCCCAATGACTAT
Found at i:3763117 original size:19 final size:20
Alignment explanation
Indices: 3763093--3763144 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3763083 GCTTTATGTT
* *
3763093 TTGTATCGATACATGCTC-A
1 TTGTATCGATACATACGCAA
3763112 TTGTATCGATACATACGCAA
1 TTGTATCGATACATACGCAA
*
3763132 TTGTATAGATACA
1 TTGTATCGATACA
3763145 AGAAACTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATACGCAA
Found at i:3764833 original size:9 final size:9
Alignment explanation
Indices: 3764806--3764843 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3764796 GTCAACCATC
3764806 GAAGATGAT
1 GAAGATGAT
*
3764815 AAAGATGAT
1 GAAGATGAT
3764824 GAAGATGAT
1 GAAGATGAT
*
3764833 GATGATGAT
1 GAAGATGAT
3764842 GA
1 GA
3764844 CGAAGTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.24
Consensus pattern (9 bp):
GAAGATGAT
Found at i:3765294 original size:16 final size:16
Alignment explanation
Indices: 3765268--3765309 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3765258 GAAAGAAAAT
*
3765268 AAATCAAAATTTGTTGA
1 AAAT-AAAATTTCTTGA
3765285 AAATAAAA-TTCTTGA
1 AAATAAAATTTCTTGA
*
3765300 AAAGAAAATT
1 AAATAAAATT
3765310 ATTGAACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
16 5 0.23
17 4 0.18
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (16 bp):
AAATAAAATTTCTTGA
Found at i:3765323 original size:16 final size:15
Alignment explanation
Indices: 3765281--3765315 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3765271 TCAAAATTTG
* *
3765281 TTGAAAATAAAATTC
1 TTGAAAAGAAAATTA
3765296 TTGAAAAGAAAATTA
1 TTGAAAAGAAAATTA
3765311 TTGAA
1 TTGAA
3765316 CTAGAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.31
Consensus pattern (15 bp):
TTGAAAAGAAAATTA
Found at i:3769585 original size:21 final size:21
Alignment explanation
Indices: 3769561--3769608 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3769551 CAATTCCTTT
3769561 TCAAAATTCATCT-TTTTCATA
1 TCAAAA-TCATCTGTTTTCATA
3769582 TCAAAATCATCTGTTTTC--A
1 TCAAAATCATCTGTTTTCATA
3769601 TCAAAATC
1 TCAAAATC
3769609 TCCATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.35
20 6 0.23
21 11 0.42
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (21 bp):
TCAAAATCATCTGTTTTCATA
Found at i:3769593 original size:20 final size:22
Alignment explanation
Indices: 3769561--3769601 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3769551 CAATTCCTTT
3769561 TCAAAATTCATCT-TTTTCATA
1 TCAAAATTCATCTGTTTTCATA
3769582 TCAAAA-TCATCTGTTTTCAT
1 TCAAAATTCATCTGTTTTCAT
3769602 CAAAATCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.32, C:0.20, G:0.02, T:0.46
Consensus pattern (22 bp):
TCAAAATTCATCTGTTTTCATA
Found at i:3771958 original size:20 final size:20
Alignment explanation
Indices: 3771933--3771982 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3771923 CCCTAGAAAA
3771933 TATCGATACA-TATCCTGATG
1 TATCGATACATTATCCT-ATG
* *
3771953 TATCGATACATTATTCTTTG
1 TATCGATACATTATCCTATG
3771973 TATCGATACA
1 TATCGATACA
3771983 ATGTATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTATCCTATG
Found at i:3771994 original size:33 final size:32
Alignment explanation
Indices: 3771950--3772014 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3771940 ACATATCCTG
* *
3771950 ATGTATCGATACATTATTCTTTGTATCGATACA
1 ATGTATCGATACA-TACTCATTGTATCGATACA
* *
3771983 ATGTATTGATACATGCTCATTGTATCGATACA
1 ATGTATCGATACATACTCATTGTATCGATACA
3772015 TACTCAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (32 bp):
ATGTATCGATACATACTCATTGTATCGATACA
Found at i:3772029 original size:20 final size:19
Alignment explanation
Indices: 3771981--3772035 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3771971 TGTATCGATA
* *
3771981 CAATGTATTGATACATGCT
1 CAATGTATCGATACATACT
*
3772000 CATTGTATCGATACATACT
1 CAATGTATCGATACATACT
3772019 CAATCGTATCGATACAT
1 CAAT-GTATCGATACAT
3772036 GAAACTGGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (19 bp):
CAATGTATCGATACATACT
Found at i:3772087 original size:20 final size:20
Alignment explanation
Indices: 3772062--3772099 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3772052 ACCCTAAGTG
*
3772062 AAATGTATTGATACATTGGA
1 AAATGTATCGATACATTGGA
3772082 AAATGTATCGATACATTG
1 AAATGTATCGATACATTG
3772100 TATCGATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTGGA
Found at i:3774166 original size:35 final size:35
Alignment explanation
Indices: 3774097--3774166 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
3774087 TAAGTGATTG
*
3774097 AGAGGTTTTATCTTAGCCTTTGAAAAAGATAGGGAA
1 AGAGGTTTTATCTTAGCCGTT-AAAAAGATAGGGAA
3774133 AGAGGTTTTATCTTAGCCCGTT-AAAAGATAGGGA
1 AGAGGTTTTATCTTAG-CCGTTAAAAAGATAGGGA
3774167 GGCTTCTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 12 0.38
36 16 0.50
37 4 0.12
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (35 bp):
AGAGGTTTTATCTTAGCCGTTAAAAAGATAGGGAA
Found at i:3775698 original size:28 final size:28
Alignment explanation
Indices: 3775659--3775713 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3775649 TTTTTTCATA
*
3775659 ATCGGGGGTACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
3775687 ATCGGGGATACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
3775714 TCGAGGGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:3775721 original size:28 final size:27
Alignment explanation
Indices: 3775661--3775733 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
3775651 TTTTCATAAT
*
3775661 CGGGGGTACTCCAACCCCGTTATTTCA
1 CGGGGATACTCCAACCCCGTTATTTCA
3775688 TCGGGGATACTCCAACCCCGTTATTTTCGA
1 -CGGGGATACTCCAACCCCGTTA-TTTC-A
*
3775718 -GGGGATACCCCAACCC
1 CGGGGATACTCCAACCC
3775734 TGGCTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.23
Consensus pattern (27 bp):
CGGGGATACTCCAACCCCGTTATTTCA
Found at i:3775783 original size:79 final size:78
Alignment explanation
Indices: 3775687--3776000 Score: 398
Period size: 79 Copynumber: 4.0 Consensus size: 78
3775677 CCGTTATTTC
* *
3775687 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACCCCAACCCTGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC-GGTTTTATTTCTAAAAT
* *
3775752 ATTAATTTCTCATA
65 ATCAATTTTTCATA
* * * *
3775766 ATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCGGTTTTATTTCTAAAAT
3775831 ATCAATTTTTCATA
65 ATCAATTTTTCATA
* * *
3775845 GTCGGGGATACTCCAACCCCCTTA-TTTCTGAGGGGATACTCCAATCCCGATTTTATTTCT-AAA
1 ATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAA-CCCGGTTTTATTTCTAAAA
*
3775908 TCATCAATTTTTCACA
64 T-ATCAATTTTTCATA
* * * *
3775924 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATAGTCCAACCCCGTTATTATCTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCGGTT-TTATTTCTAAAAT
*
3775989 ATTAAATTTTTC
65 A-TCAATTTTTC
3776001 GTTGGGAGAT
Statistics
Matches: 203, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
78 11 0.05
79 172 0.85
80 20 0.10
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCGGTTTTATTTCTAAAATA
TCAATTTTTCATA
Found at i:3778050 original size:4 final size:4
Alignment explanation
Indices: 3778041--3778065 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3778031 TATTTTGAGG
3778041 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
3778066 GTTTTATCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:3780944 original size:1 final size:1
Alignment explanation
Indices: 3780938--3780975 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
3780928 AGAGTGTTTG
* *
3780938 AAAAAAAAAAAAAAAAACAAAACAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3780976 TTCCAAATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3781027 original size:20 final size:20
Alignment explanation
Indices: 3780975--3781056 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 20
3780965 AAAAAAAAAA
3780975 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
3780994 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
3781015 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
*
3781035 ATTCTACAATTGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
3781056 A
1 A
3781057 GGGTCCCAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.06
20 18 0.33
21 33 0.61
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:3781036 original size:41 final size:40
Alignment explanation
Indices: 3780975--3781056 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
3780965 AAAAAAAAAA
* *
3780975 ATTCCAAATGTATCGATACATTTGTAGAA-TGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAATTGTATCGATAC
3781015 ATTCACAAATGTATCGATACATTCTACAATTGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAATTGTATCGATAC
3781056 A
1 A
3781057 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 10 0.26
41 28 0.74
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAATTGTATCGATAC
Found at i:3781116 original size:19 final size:19
Alignment explanation
Indices: 3781092--3781159 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3781082 AATTCAACGA
3781092 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3781111 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3781126 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3781143 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3781160 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3781130 original size:32 final size:32
Alignment explanation
Indices: 3781094--3781156 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3781084 TTCAACGATT
*
3781094 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3781126 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3781157 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3781131 original size:13 final size:13
Alignment explanation
Indices: 3781113--3781137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3781103 ACATAAGTTT
3781113 TGTATCGATACAA
1 TGTATCGATACAA
3781126 TGTATCGATACA
1 TGTATCGATACA
3781138 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3781217 original size:13 final size:13
Alignment explanation
Indices: 3781199--3781224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3781189 CATTTTTCTG
3781199 TGTATCGATACAT
1 TGTATCGATACAT
3781212 TGTATCGATACAT
1 TGTATCGATACAT
3781225 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3781221 original size:33 final size:33
Alignment explanation
Indices: 3781179--3781245 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3781169 GCCAAGGAAA
***
3781179 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3781212 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3781245 T
1 T
3781246 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3783657 original size:51 final size:53
Alignment explanation
Indices: 3783588--3783930 Score: 214
Period size: 51 Copynumber: 6.5 Consensus size: 53
3783578 AGTTTATCAA
* * * * *
3783588 TTCTCCACAATCGTGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
3783639 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
3783693 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
3783751 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * * *
3783800 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAGACACTAA-
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAAT
* *
3783851 TT-TTCTATAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
3783905 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
3783931 CTCGTTATTT
Statistics
Matches: 228, Mismatches: 36, Indels: 53
0.72 0.11 0.17
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 5 0.02
51 67 0.29
52 35 0.15
53 27 0.12
54 54 0.24
55 23 0.10
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:3783772 original size:28 final size:27
Alignment explanation
Indices: 3783705--3783773 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
3783695 CTTCACAATC
**
3783705 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
3783732 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
3783760 GGGGATACTCCAAC
1 GGGGATACTCCAAC
3783774 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:3783919 original size:105 final size:104
Alignment explanation
Indices: 3783588--3783929 Score: 329
Period size: 105 Copynumber: 3.2 Consensus size: 104
3783578 AGTTTATCAA
* * * * *
3783588 TTCTCCACAATCGTGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTTCACAATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAGACACTAATTTTCTATAATCGG
*
3783653 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
65 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
* * * ** ** * *** *
3783693 TTCTTCACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA-CCCCGT-TATT
1 TTCTTCACAATCGGGGATACTCCAATCCGGTTTTATTTTC-AAGACACT--AATTTTC-TATA-A
* * *
3783755 TCCGAGGGGATACTCCAACTCCGGTTTTA--TCGC-TAAAACACTAAT
61 T-C--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAAACACCAAT
3783800 TT-TTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAGACACTAATTTTCTATAATCG
1 TTCTT-CACAATCGGGGATACTCCAATCC-GGTTTTATTTTCAAGACACTAATTTTCTATAATCG
*
3783864 GGGATACTCCAACTCTGATTTTATTTCCAAAAAACACCAAT
64 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
3783905 TTCTTCACAATCGGGGATACTCCAA
1 TTCTTCACAATCGGGGATACTCCAA
3783930 CCTCGTTATT
Statistics
Matches: 182, Mismatches: 37, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
103 28 0.15
104 7 0.04
105 60 0.33
106 12 0.07
107 40 0.22
108 7 0.04
109 28 0.15
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (104 bp):
TTCTTCACAATCGGGGATACTCCAATCCGGTTTTATTTTCAAGACACTAATTTTCTATAATCGGG
GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
Found at i:3783946 original size:28 final size:29
Alignment explanation
Indices: 3783914--3783991 Score: 113
Period size: 28 Copynumber: 2.7 Consensus size: 29
3783904 TTTCTTCACA
* *
3783914 ATCGGGGATACTCCAACCTCGTTATTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTCT
3783942 ATCGGGGATACTCCAACCCCGTTACTTCT
1 ATCGGGGATACTCCAACCCCGTTACTTCT
**
3783971 AGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3783992 GCTTTATTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 26 0.58
29 19 0.42
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTACTTCT
Found at i:3793360 original size:54 final size:55
Alignment explanation
Indices: 3793214--3793398 Score: 239
Period size: 55 Copynumber: 3.4 Consensus size: 55
3793204 TTCACCCTTT
* * * * *
3793214 AGTCCTCAAAGAGCAAGACACCTTTCAAAGCTCGCACAAGTTGGTGGCACCTT-TC
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCC
* * * *
3793269 AGTCCTCAAAGAGCAAGATGTCTTTTAAAGCCTACACAACTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
* *
3793324 AGTCCTC-AAGAGCAGGACGCCTTTTAAAGCCCACACAAGTAGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
*
3793378 AGTCCTCAAAGAGCATGACGC
1 AGTCCTCAAAGAGCAAGACGC
3793399 TCTCTCCTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
54 51 0.46
55 61 0.54
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
Found at i:3793480 original size:56 final size:56
Alignment explanation
Indices: 3793414--3793546 Score: 171
Period size: 56 Copynumber: 2.4 Consensus size: 56
3793404 CCTTTCACCC
*
3793414 TTTAGTCCTCAAAGAGCAGGACAG-CTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 TTTAGTCCTCAAAGAGCAGGACAGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTT
*** *
3793470 TTTAGTCCTCAAAGAATGGGA-AGCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGACAGCCTTTCAAAGCCCACACAAGTTGGTGGCACTT
***
3793525 CCCAGTCCTCAAAGAGCAGGAC
1 TTTAGTCCTCAAAGAGCAGGAC
3793547 GCTCTCTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
55 19 0.30
56 45 0.70
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (56 bp):
TTTAGTCCTCAAAGAGCAGGACAGCCTTTCAAAGCCCACACAAGTTGGTGGCACTT
Found at i:3793533 original size:150 final size:147
Alignment explanation
Indices: 3793263--3793712 Score: 555
Period size: 150 Copynumber: 3.0 Consensus size: 147
3793253 GTTGGTGGCA
* * * * *
3793263 CCTTTCAGTCCTCAAAGAGCAAGA-TGTCTTTTAAAGCCTACACAACTTGGTGGCACTTCCCAGT
1 CCTTT-AGTCCTCAAAGAGCAAGACTG-CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGT
* *
3793327 CCTCAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTAGGTGGCACTTCCCAGTCCTCAAAGAGC
64 CCTCAA-AGAAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
*
3793392 ATGACGCTCTCTCCTTTCAC
128 AGGACGCTCTCTCCTTTCAC
* * * *
3793412 CCTTTAGTCCTCAAAGAGCAGGACAGCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTC
1 CCTTTAGTCCTCAAAGAGCAAGACTGCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTC
*
3793477 CTCAAAGAATGGGAAGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
65 CTCAAAGAA--GGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
* *
3793542 AGGACGCTCTCTCATTTCGC
128 AGGACGCTCTCTCCTTTCAC
* *
3793562 CCTTTAGTCCTCAAAGAGTAAGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTC
1 CCTTTAGTCCTCAAAGAGCAAGACTGCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTC
* *
3793627 CTCAAAGACAGGACGCTTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTTA
65 CTCAAAGA-AGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCA
* *
3793691 AAGAGAAGGACGC-CTTTCCTTT
122 AAGAGCAGGACGCTCTCTCCTTT
3793713 TCAAAGCCCA
Statistics
Matches: 261, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
148 45 0.17
149 21 0.08
150 135 0.52
151 1 0.00
154 7 0.03
155 49 0.19
156 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (147 bp):
CCTTTAGTCCTCAAAGAGCAAGACTGCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
TCAAAGAAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGG
ACGCTCTCTCCTTTCAC
Found at i:3793575 original size:94 final size:94
Alignment explanation
Indices: 3793470--3793643 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 94
3793460 GTGGCATTTT
**
3793470 TTTAGTCCTCAAAGAATGGGAAGCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCCAGTCCT
1 TTTAGTCCTCAAAGAATAAGAAGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCCAGTCCT
3793534 CAAAGAGCAGGACGCTCTCTCATTTCGCCC
66 CAAAGA-CAGGACGCTCTCTCATTTCGCCC
* ** * *
3793564 TTTAGTCCTCAAAGAGTAAGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCT
1 TTTAGTCCTCAAAGAATAAGAAGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCCAGTCCT
3793629 CAAAGACAGGACGCT
66 CAAAGACAGGACGCT
3793644 TTTTCCTTTC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 57 0.79
95 15 0.21
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (94 bp):
TTTAGTCCTCAAAGAATAAGAAGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCCAGTCCT
CAAAGACAGGACGCTCTCTCATTTCGCCC
Found at i:3793660 original size:61 final size:61
Alignment explanation
Indices: 3793586--3793761 Score: 232
Period size: 61 Copynumber: 2.9 Consensus size: 61
3793576 AGAGTAAGAC
* * *
3793586 TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGA-CAGGACGCTTTT
1 TCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGACGC-CTT
* * *
3793647 TCCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTTAAAGAGAAGGACGCCTT
1 TCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGACGCCTT
* * *
3793707 TCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TTGTCCTCAAAGAGTAGGA
1 TCC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGA
3793762 TGCACTTTAT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
60 19 0.19
61 79 0.79
62 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (61 bp):
TCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGACGCCTT
Found at i:3793801 original size:42 final size:42
Alignment explanation
Indices: 3793742--3793935 Score: 194
Period size: 42 Copynumber: 4.5 Consensus size: 42
3793732 GTGGCACTTT
* *
3793742 TTTGTCCTCAAAGAGTAGGATGCACTTTATTTTCTTCTTTCC
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTCTTTCC
* * * **
3793784 TTTGTCCTCAAAGAGTAGGACACACTTCATTCCCTTCTTTTCTC
1 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTC-TTTC-C
* ** * *
3793828 TTTTATCCTCAAAGAGCATTACGCACTTTATTTTCTTTTTTCT
1 -TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTCTTTCC
*
3793871 TTTGTCCTCAAAGAGCAGGACGCA-TTTCATTTTCCTTTTTTCC
1 TTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTT-CTTCTTTCC
*
3793914 TTTATCCTCGAAA-AGCAGGACG
1 TTTGTCCTC-AAAGAGCAGGACG
3793936 TACTCCTTTT
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
41 3 0.02
42 58 0.46
43 29 0.23
44 8 0.06
45 28 0.22
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTCTTTCC
Found at i:3793900 original size:87 final size:85
Alignment explanation
Indices: 3793763--3793930 Score: 232
Period size: 87 Copynumber: 2.0 Consensus size: 85
3793753 AGAGTAGGAT
*
3793763 GCACTTTATTTTCTTCTTTCCTTTGTCCTCAAAGAGTAGGACACACTTCA-TTCCCTTCTTTTCT
1 GCACTTTATTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCCTT-TTTTC-
3793827 CTTTTATCCTC-AAAGAGCATTAC
64 C-TTTATCCTCGAAA-AGCATTAC
* * * * *
3793850 GCACTTTATTTTCTTTTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTTTTCCT
1 GCACTTTATTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCCTTTTTTCCT
3793915 TTATCCTCGAAAAGCA
66 TTATCCTCGAAAAGCA
3793931 GGACGTACTC
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
85 13 0.18
86 4 0.05
87 50 0.68
88 6 0.08
ACGTcount: A:0.20, C:0.26, G:0.10, T:0.44
Consensus pattern (85 bp):
GCACTTTATTTTCTTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTTCATTTCCCTTTTTTCCT
TTATCCTCGAAAAGCATTAC
Found at i:3793997 original size:41 final size:40
Alignment explanation
Indices: 3793941--3794040 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
3793931 GGACGTACTC
* *
3793941 CTTTTCACTTTGTCCTCAAGAAGCAGGACACT-TTCCTTTTCT
1 CTTTTC-CTTTGTCCTCAAGAAGCAAGAC-CTATTCC-ATTCT
* * *
3793983 TTTTTCCTTTGTCCTCAAGGAGCAAGACCTATTTCATTCT
1 CTTTTCCTTTGTCCTCAAGAAGCAAGACCTATTCCATTCT
3794023 CTTTTCCTTTGTCCTCAA
1 CTTTTCCTTTGTCCTCAA
3794041 AAAGTGGCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
40 23 0.45
41 23 0.45
42 5 0.10
ACGTcount: A:0.18, C:0.28, G:0.11, T:0.43
Consensus pattern (40 bp):
CTTTTCCTTTGTCCTCAAGAAGCAAGACCTATTCCATTCT
Found at i:3794590 original size:20 final size:20
Alignment explanation
Indices: 3794565--3794673 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 20
3794555 TTTTCACAAT
3794565 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
* ***
3794585 TTGTATCGATACATTCTGGG
1 TTGTATCGATACATTGTTCA
* *
3794605 TT-TACCCA-A-A-TG-T-A
1 TTGTATCGATACATTGTTCA
* *
3794619 ATGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
3794639 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
3794659 ATGTATCGATACATT
1 TTGTATCGATACATT
3794674 CAGGCATTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
14 1 0.01
15 4 0.06
16 2 0.03
17 2 0.03
18 3 0.04
19 6 0.09
20 49 0.73
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:3797248 original size:28 final size:27
Alignment explanation
Indices: 3797207--3797260 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
3797197 TTTTTTCATA
3797207 ATCGGGGTACTCCAACCCCATTATTTC
1 ATCGGGGTACTCCAACCCCATTATTTC
*
3797234 ATCGGGGATACTCCAACCCCGTTATTT
1 ATCGGGG-TACTCCAACCCCATTATTT
3797261 TCGAGGGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (27 bp):
ATCGGGGTACTCCAACCCCATTATTTC
Found at i:3797268 original size:28 final size:27
Alignment explanation
Indices: 3797209--3797279 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
3797199 TTTTCATAAT
3797209 CGGGG-TACTCCAACCCCATTATTTCA
1 CGGGGATACTCCAACCCCATTATTTCA
*
3797235 TCGGGGATACTCCAACCCCGTTATTTTCGA
1 -CGGGGATACTCCAACCCCATTA-TTTC-A
*
3797265 -GGGGATACCCCAACC
1 CGGGGATACTCCAACC
3797280 ATGGCTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.13
28 29 0.74
29 4 0.10
30 1 0.03
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.24
Consensus pattern (27 bp):
CGGGGATACTCCAACCCCATTATTTCA
Found at i:3797360 original size:107 final size:107
Alignment explanation
Indices: 3797122--3797361 Score: 317
Period size: 108 Copynumber: 2.2 Consensus size: 107
3797112 AATACCAATT
* * *
3797122 TTTCATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCAAACCCTGGCTTTATATCTA
1 TTTCA-CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACCCAAACCATGGCTTTATATCTA
** *
3797187 AAAATATTGTTTTTTTCATAATCGGGGTACTCCAACCCCATTA
65 AAAATATTGAATTTCTCATAATCGGGGTACTCCAACCCCATTA
* *
3797230 TTTCATCGGGGATACTCCAACCCCGTTATTT-TCGAGGGGATACCCCAACCATGGCTTTATTTCT
1 TTTCA-CGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACCCAAACCATGGCTTTATATCT
*
3797294 -AAAATATT-AATTTCTCATAATCGGGGATACTCCAACCCCGTTA
64 AAAAATATTGAATTTCTCATAATCGGGG-TACTCCAACCCCATTA
3797337 TTTTCGA-GGGGATACTCCAACCCCG
1 -TTTC-ACGGGGATACTCCAACCCCG
3797362 GTTTTATTTC
Statistics
Matches: 119, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
106 15 0.13
107 42 0.35
108 61 0.51
109 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (107 bp):
TTTCACGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACCCAAACCATGGCTTTATATCTAA
AAATATTGAATTTCTCATAATCGGGGTACTCCAACCCCATTA
Found at i:3797368 original size:79 final size:79
Alignment explanation
Indices: 3797234--3797547 Score: 373
Period size: 79 Copynumber: 4.0 Consensus size: 79
3797224 CCATTATTTC
* ** *
3797234 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACCCCAACCATGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
*
3797299 ATTAATTTCTCATA
66 ATCAATTTCTCATA
*
3797313 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
*
3797378 ATCAATTTTTCATA
66 ATCAATTTCTCATA
* * ** * * * *
3797392 GTTGGGGATACTCCAACCCCCATATTTTCGAGAGGATACTCTAATCCCGATTTTATTTCT-AAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
*
3797456 CATCAATTTTTC-TCA
66 -ATCAATTTCTCAT-A
** * * *
3797471 ATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGATACTTCAACCCC-GTTATTATCTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT-TTATTTCTAAAA
*
3797535 TATTAAATTTCTC
65 TA-TCAATTTCTC
3797548 GTCAGGAGAT
Statistics
Matches: 199, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
78 6 0.03
79 181 0.91
80 12 0.06
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAT
ATCAATTTCTCATA
Found at i:3798989 original size:21 final size:22
Alignment explanation
Indices: 3798965--3799033 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
3798955 ACTAGAGAAG
3798965 AAAATGAATGAGTTGGAAAA-A
1 AAAATGAATGAGTTGGAAAATA
* * *
3798986 AAAA-GAAATGTGTTGCAAAATG
1 AAAATG-AATGAGTTGGAAAATA
**
3799008 AAAATG-ATGAGTTGGCTAATA
1 AAAATGAATGAGTTGGAAAATA
3799029 AAAAT
1 AAAAT
3799034 AAAAAATTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 1 0.03
21 31 0.84
22 4 0.11
23 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.22, T:0.23
Consensus pattern (22 bp):
AAAATGAATGAGTTGGAAAATA
Found at i:3802051 original size:20 final size:19
Alignment explanation
Indices: 3802028--3802078 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3802018 ACACCCAAAT
* *
3802028 GTATCAATACATATTGCTTA
1 GTATCGATACATATT-CCTA
*
3802048 GTATCGATACATGTTCCTA
1 GTATCGATACATATTCCTA
3802067 GTATCGATACAT
1 GTATCGATACAT
3802079 CATGAATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATTCCTA
Found at i:3804256 original size:21 final size:22
Alignment explanation
Indices: 3804232--3804300 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
3804222 GAACTAGAGG
**
3804232 AGAAAATGAATGAGTTGGAA-A
1 AGAAAATGAATGAGTTACAAGA
*
3804253 AGAAAATAAATGAGTTACAAGA
1 AGAAAATGAATGAGTTACAAGA
* *
3804275 AGAAAATG-ATGAATTA-AATA
1 AGAAAATGAATGAGTTACAAGA
3804295 AGAAAA
1 AGAAAA
3804301 ATAAAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.22
21 24 0.59
22 8 0.20
ACGTcount: A:0.59, C:0.01, G:0.20, T:0.19
Consensus pattern (22 bp):
AGAAAATGAATGAGTTACAAGA
Found at i:3805203 original size:31 final size:32
Alignment explanation
Indices: 3805141--3805235 Score: 86
Period size: 36 Copynumber: 2.9 Consensus size: 32
3805131 CCTTACAACA
* * * * *
3805141 CTATCTTTTGAAGGCTAGGGTGGAA-CTT-TT
1 CTATCTTTTCAAGGCTAAGATAGAACCTTCTC
3805171 CTATCTTTTCACAGGCTAAGATAGAACCTTTCTCC
1 CTATCTTTTCA-AGGCTAAGATAGAACC-TTCT-C
3805206 CTATCTTTTTCAAAGGCTAAGATAGAACCT
1 CTATC-TTTTC-AAGGCTAAGATAGAACCT
3805236 CTCAACCACT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
30 10 0.19
31 11 0.21
32 1 0.02
33 2 0.04
34 1 0.02
35 6 0.11
36 21 0.40
37 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (32 bp):
CTATCTTTTCAAGGCTAAGATAGAACCTTCTC
Found at i:3811129 original size:36 final size:33
Alignment explanation
Indices: 3811048--3811143 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 33
3811038 CTTCTAACAT
3811048 TATCTTTT-AAAGGCTAAGATAGAA-C-CTACC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTACC
* *
3811078 TATCTTTTCACAGGCTAAGATAGAACCTTTCTCCC
1 TATCTTTTCAAAGGCTAAGATAGAACC--TCTACC
*
3811113 TATCTTTTTCAAAGGCTAAGATAAAACCTCT
1 TATC-TTTTCAAAGGCTAAGATAGAACCTCT
3811144 CAATCACTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.14
31 15 0.27
32 1 0.02
34 3 0.05
35 8 0.14
36 21 0.38
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.33
Consensus pattern (33 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTACC
Found at i:3811544 original size:20 final size:20
Alignment explanation
Indices: 3811519--3811558 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3811509 TACACGCTCC
*
3811519 AATGTATCGATATAATTCAT
1 AATGTATCGATACAATTCAT
3811539 AATGTATCGATACAATTCAT
1 AATGTATCGATACAATTCAT
3811559 TTGAAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACAATTCAT
Found at i:3811743 original size:33 final size:34
Alignment explanation
Indices: 3811701--3811767 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3811691 TTTCATGGTA
*
3811701 TATCGATACAATG-AACATGTATCGATACATTTG
1 TATCGATACAAAGCAACATGTATCGATACATTTG
* * *
3811734 TATCGATACAAAGCAATATGTATTGATATATTTG
1 TATCGATACAAAGCAACATGTATCGATACATTTG
3811768 GGTGTGTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (34 bp):
TATCGATACAAAGCAACATGTATCGATACATTTG
Found at i:3817494 original size:61 final size:58
Alignment explanation
Indices: 3817399--3818057 Score: 752
Period size: 61 Copynumber: 11.4 Consensus size: 58
3817389 TCCATTTACT
* * * *
3817399 TTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAGCTCACATAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGATGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGCACC
3817460 TTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGATGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
3817521 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAATTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGATGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
3817582 TTTCAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGATGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
3817643 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACATAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGATGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* *
3817704 TTTCAGTCCTCAAAGAGCAGGA---CACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTTCAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * *
3817758 TTTCCAGTCCTCAAAGAGCA-G--GCCGCCTTTTAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
*
3817813 TTTCCAGTCCTCAAAGAGCAGGATG--T-CTTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * *
3817868 TTTCCAGTCCTCAAAGAGTA-G--GCCGCCTTTTAAAGCCCACACAAGTTGGTGGCA-T
1 TTT-CAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
*
3817923 TTTCCAGTCCTCAAAGAGCAGGATG--T-CTTTCAAA-CCCACACGAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
* * * *
3817978 TTTCAGTCCTCAAAGAGAAGGA---CGCCTTTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTCAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
*
3818033 TTTTAGTCCTCAAAGAGCAGGATGC
1 TTTCAGTCCTCAAAGAGCAGGATGC
3818058 ACTTTATTTT
Statistics
Matches: 546, Mismatches: 33, Indels: 41
0.88 0.05 0.07
Matches are distributed among these distances:
52 1 0.00
54 49 0.09
55 238 0.44
56 2 0.00
58 3 0.01
61 253 0.46
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (58 bp):
TTTCAGTCCTCAAAGAGCAGGATGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
Found at i:3817706 original size:29 final size:28
Alignment explanation
Indices: 3817673--3817756 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 28
3817663 GATGCCTTTT
3817673 CCTTTCAAAGCCCACATAAGTTGGTGGCA
1 CCTTTCAAAGCCCACA-AAGTTGGTGGCA
* * * **
3817702 CCTTTC--AGTCCTCAAAG-AGCAGGACA
1 CCTTTCAAAGCCCACAAAGTTGGTGG-CA
3817728 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAAAGCCCACA-AAGTTGGTGGCA
3817757 TTTTCCAGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
25 3 0.08
26 11 0.28
27 6 0.15
28 6 0.15
29 11 0.28
30 3 0.08
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAAGTTGGTGGCA
Found at i:3817766 original size:55 final size:55
Alignment explanation
Indices: 3817396--3818054 Score: 718
Period size: 55 Copynumber: 11.5 Consensus size: 55
3817386 TTGTCCATTT
* * *
3817396 ACTTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAGCTCACATAAGTTGGTGGC
1 ACTTTTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817457 ACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGC
1 ACTTTTCAGTCCTCAAAGAGCAGGA---C---GCCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817518 ACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAATTTGGTGGC
1 ACTTTTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817579 ACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGC
1 ACTTTTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817640 ACCTTTT-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACATAAGTTGGTGGC
1 A-CTTTTCAGTCCTCAAAGAGCAGGA---C---GCCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817701 ACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGC
1 ACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817756 A-TTTTCCAGTCCTCAAAGAGCAGGCCGCCTTTTAAAGCCCACACAAGTTGGTGGC
1 ACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
* *
3817811 A-TTTTCCAGTCCTCAAAGAGCAGGATGTCTTTCAAAGCCCACACAAGTTGGTGGC
1 ACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
* * *
3817866 A-TTTTCCAGTCCTCAAAGAGTAGGCCGCCTTTTAAAGCCCACACAAGTTGGTGGC
1 ACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
* * *
3817921 A-TTTTCCAGTCCTCAAAGAGCAGGATGTCTTTCAAA-CCCACACGAGTTGGTGGC
1 ACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
* * *
3817975 ACCTTTCAGTCCTCAAAGAGAAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGC
1 ACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
*
3818030 ACTTTTTAGTCCTCAAAGAGCAGGA
1 ACTTTTCAGTCCTCAAAGAGCAGGA
3818055 TGCACTTTAT
Statistics
Matches: 533, Mismatches: 42, Indels: 52
0.85 0.07 0.08
Matches are distributed among these distances:
54 48 0.09
55 249 0.47
58 2 0.00
60 4 0.01
61 224 0.42
62 4 0.01
64 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
ACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGC
Found at i:3818212 original size:119 final size:117
Alignment explanation
Indices: 3818034--3818256 Score: 276
Period size: 119 Copynumber: 1.9 Consensus size: 117
3818024 GGTGGCACTT
* * *
3818034 TTTAGTCCTCAAAGAGCAGGATGCACTTTATTTTCTTCTTTCTTTCGTCCTCAAAGAGCAGGACG
1 TTTAGTCCTCAAAGAGCAGGA-GCACTTTATTTTCTTCTTCCTTTCGTCCTCAAAGAGCAAGACA
*
3818099 TATTTCGTTTCCCTTTTTCCTTTGTCCTCGAAAAA-TGGGACGTACCCTTTTTCAC
65 TATTTC-ATTCCC-TTTTCCTTTGTCCTC-AAAAAGTGGGACGTACCCTTTTTCAC
* *
3818154 TTTA-TCCTC-AAGAAGCAGGA-CACTTTCTTTTTCTTCTCTCCCTTT-GTCCTCAAGGAGCAAG
1 TTTAGTCCTCAAAG-AGCAGGAGCACTTT-ATTTTCTTCT-T-CCTTTCGTCCTCAAAGAGCAAG
*
3818215 ACATATTTCATTCTCTTTTCCTTTGTCCTCAAAAAGTGGGAC
62 ACATATTTCATTCCCTTTTCCTTTGTCCTCAAAAAGTGGGAC
3818257 ACCCCTTCCA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
116 5 0.05
117 27 0.30
118 16 0.18
119 35 0.38
120 8 0.09
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.39
Consensus pattern (117 bp):
TTTAGTCCTCAAAGAGCAGGAGCACTTTATTTTCTTCTTCCTTTCGTCCTCAAAGAGCAAGACAT
ATTTCATTCCCTTTTCCTTTGTCCTCAAAAAGTGGGACGTACCCTTTTTCAC
Found at i:3818942 original size:19 final size:19
Alignment explanation
Indices: 3818918--3818967 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
3818908 AAACAGTAAA
3818918 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
3818937 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
3818956 TGTATCGATACA
1 TGTATCGATACA
3818968 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:3819018 original size:21 final size:21
Alignment explanation
Indices: 3818992--3819033 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3818982 AGCTACTGCC
3818992 AAGGAAACATATCGATACATT
1 AAGGAAACATATCGATACATT
**
3819013 AAGGAAATGTATCGATACATT
1 AAGGAAACATATCGATACATT
3819034 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (21 bp):
AAGGAAACATATCGATACATT
Found at i:3819038 original size:13 final size:13
Alignment explanation
Indices: 3819020--3819045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3819010 ATTAAGGAAA
3819020 TGTATCGATACAT
1 TGTATCGATACAT
3819033 TGTATCGATACAT
1 TGTATCGATACAT
3819046 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3821567 original size:28 final size:28
Alignment explanation
Indices: 3821535--3821605 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
3821525 ATTTTTCATC
* *
3821535 GGGGATACTCCAATCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
3821563 GGGGATACTCAAACCCCATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
3821591 GGGGATACCCCAACC
1 GGGGATACTCCAACC
3821606 TCGACTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:3821683 original size:107 final size:104
Alignment explanation
Indices: 3821459--3821686 Score: 312
Period size: 104 Copynumber: 2.2 Consensus size: 104
3821449 TTTCACAATC
* * * **
3821459 GGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCAAACCCCATTATTTCCGAGGGGACACCCCAACCCCGACTTTATTTCTAAAACATC
* * *
3821524 AATTTTTCATCGGGGATACTCCAATCCCGTTATTTTCGA
66 AATTTTTAATCGGGGATACTCCAACCCCGTTATTTTCAA
* * * * *
3821563 GGGGATACTCAAACCCCATTATTTTCGAGGGGATACCCCAACCTCGACTTTATTTCTAAAATATT
1 GGGGATACTCAAACCCCATTATTTCCGAGGGGACACCCCAACCCCGACTTTATTTCTAAAACATC
3821628 AATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCAA
66 AATTT-T--TAATCGGGGATACTCCAACCCCGTTATTTTCAA
3821670 GGGGATACTCAAACCCC
1 GGGGATACTCAAACCCC
3821687 GGTTTTATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
104 60 0.56
105 1 0.01
107 47 0.44
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (104 bp):
GGGGATACTCAAACCCCATTATTTCCGAGGGGACACCCCAACCCCGACTTTATTTCTAAAACATC
AATTTTTAATCGGGGATACTCCAACCCCGTTATTTTCAA
Found at i:3821751 original size:78 final size:78
Alignment explanation
Indices: 3821563--3821842 Score: 328
Period size: 79 Copynumber: 3.6 Consensus size: 78
3821553 TTATTTTCGA
* * * * * * * *
3821563 GGGGATACTCAAACCCCATTATTTTCGAGGGGATACCCCAACCTCGACTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC
*
3821628 AATTTCTCATAATC
66 AATTT-TTATAATC
* *
3821642 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCAAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC
*
3821707 AATTTTTATAGTC
66 AATTTTTATAATC
* * * * * * *
3821720 GGGGATACTTCAACCCCGTTA-TTTCTGAGGGGATGCTCCAATCCCAATTTTATTTCCAAATCAT
1 GGGGATACTCCAACCCCGTTATTTTC-AAGGGGATACTCCAACCCCGATTTTATTTCTAAAACAT
* * *
3821784 CGATTTTTCACAACC
65 CAATTTTT-ATAATC
3821799 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCC
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCC
3821843 TGTTATTATC
Statistics
Matches: 169, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
77 4 0.02
78 63 0.37
79 98 0.58
80 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC
AATTTTTATAATC
Found at i:3821871 original size:79 final size:78
Alignment explanation
Indices: 3821563--3821879 Score: 302
Period size: 79 Copynumber: 4.0 Consensus size: 78
3821553 TTATTTTCGA
* * * * * * *
3821563 GGGGATACTCAAACCCCATTATTTTCGAGGGGATACCCCAACCTC-GACTTTATTTCTAAAATAT
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCTG-TTTTATTTCCAAAATAT
3821627 TAATTTCTCATAATC
65 TAATTT-TCATAATC
* * * * *
3821642 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCAAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCTGTTTTATTTCCAAAATATT
* *
3821707 AATTTTTATAGTC
66 AATTTTCATAATC
* * * * **
3821720 GGGGATACTTCAACCCCGTTA-TTTCTGAGGGGATGCTCCAATCCCAATTTTATTTCC-AAATCA
1 GGGGATACTCCAACCCCGTTATTTTC-AAGGGGATACTCCAACCCCTGTTTTATTTCCAAAAT-A
* * * *
3821783 TCGATTTTTCACAACC
64 T-TAATTTTCATAATC
*
3821799 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAA-CCCTGTTATTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCTGTT-TTATTTCCAAAATAT
*
3821863 TAAATTTTC-TCATC
65 T-AATTTTCATAATC
3821877 GGG
1 GGG
3821880 AAATGTATTC
Statistics
Matches: 193, Mismatches: 37, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
77 7 0.04
78 62 0.32
79 115 0.60
80 9 0.05
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCTGTTTTATTTCCAAAATATT
AATTTTCATAATC
Found at i:3823700 original size:52 final size:52
Alignment explanation
Indices: 3823622--3823761 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 52
3823612 TCTGGAATGA
* * * *
3823622 AAATGTATAGATACATT-TTCCATTGTATTGATACATTATGGGTTTTTAACCC
1 AAATGTATCGATACATTCTT-CATTGTATAGATACATTATAGGTTTTCAACCC
* * *
3823674 AAATGTATCGATACATTCTTCATTGTATAAATACATTCTAGGTTTTCGACCC
1 AAATGTATCGATACATTCTTCATTGTATAGATACATTATAGGTTTTCAACCC
* * *
3823726 AAATCTATCGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTCTTCATTGTATAGATACAT
3823762 GCATGCAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
52 74 0.97
53 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATAGATACATTATAGGTTTTCAACCC
Found at i:3830684 original size:1 final size:1
Alignment explanation
Indices: 3830678--3830727 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
3830668 AAAGTGTTTG
***
3830678 AAAAAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3830728 TTTAAATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.94, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:3830715 original size:25 final size:25
Alignment explanation
Indices: 3830681--3830729 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3830671 GTGTTTGAAA
3830681 AAAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAAATTG
3830706 AAAAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAAAATT
3830730 TAAATGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.90, C:0.00, G:0.02, T:0.08
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAAAAAATTG
Found at i:3830756 original size:21 final size:21
Alignment explanation
Indices: 3830732--3830788 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3830722 AAAAAATTTA
3830732 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3830753 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3830774 AATGTATCGATACAT
1 AATGTATCGATACAT
3830789 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3830868 original size:19 final size:19
Alignment explanation
Indices: 3830844--3830911 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3830834 AATTCAACAA
3830844 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3830863 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3830878 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3830895 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3830912 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3830883 original size:13 final size:13
Alignment explanation
Indices: 3830865--3830889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3830855 ACATAAGTTT
3830865 TGTATCGATACAA
1 TGTATCGATACAA
3830878 TGTATCGATACA
1 TGTATCGATACA
3830890 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3830887 original size:32 final size:32
Alignment explanation
Indices: 3830846--3830908 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3830836 TTCAACAATT
*
3830846 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3830878 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3830909 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3830969 original size:13 final size:13
Alignment explanation
Indices: 3830951--3830976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3830941 CATTTTTCTG
3830951 TGTATCGATACAT
1 TGTATCGATACAT
3830964 TGTATCGATACAT
1 TGTATCGATACAT
3830977 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3830973 original size:33 final size:33
Alignment explanation
Indices: 3830931--3830997 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3830921 GCCAAGGAAA
***
3830931 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3830964 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3830997 T
1 T
3830998 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3833518 original size:28 final size:29
Alignment explanation
Indices: 3833449--3833521 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 29
3833439 CTTCACAATC
*
3833449 GGGGACACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCGTTAATCATCGA
*
3833478 --GGATACTCCAACCCCGTT-AT-TTCTGA
1 GGGGATACTCCAACCCCGTTAATCATC-GA
3833504 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3833522 ACTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
27 17 0.44
28 16 0.41
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.21
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTAATCATCGA
Found at i:3833566 original size:51 final size:51
Alignment explanation
Indices: 3833504--3833674 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
3833494 TTATTTCTGA
* * *
3833504 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
3833555 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
3833608 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3833660 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3833675 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3833693 original size:28 final size:28
Alignment explanation
Indices: 3833657--3833738 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3833647 ATTTTTCACA
*
3833657 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3833685 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3833713 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3833739 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3882380 original size:9 final size:9
Alignment explanation
Indices: 3882366--3882425 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
3882356 TTCTCTTCAA
3882366 AAAAAAAAG
1 AAAAAAAAG
3882375 AAAAAAAA-
1 AAAAAAAAG
*
3882383 AACAAAAA-
1 AAAAAAAAG
* *
3882391 AAACAAAAC
1 AAAAAAAAG
3882400 AAAGAAAAAG
1 AAA-AAAAAG
* *
3882410 AGAGAAAAG
1 AAAAAAAAG
3882419 AAAAAAA
1 AAAAAAA
3882426 CCTACTTAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
8 13 0.32
9 21 0.52
10 6 0.15
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3882380 original size:11 final size:11
Alignment explanation
Indices: 3882363--3882393 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3882353 ACCTTCTCTT
3882363 CAAAAAAAAAA
1 CAAAAAAAAAA
*
3882374 GAAAAAAAAAA
1 CAAAAAAAAAA
3882385 CAAAAAAAA
1 CAAAAAAAA
3882394 CAAAACAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.06, G:0.03, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:3883476 original size:55 final size:55
Alignment explanation
Indices: 3883391--3884068 Score: 1016
Period size: 55 Copynumber: 12.3 Consensus size: 55
3883381 TCCGCTTTTT
*
3883391 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3883446 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
3883501 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
3883556 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
3883611 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3883666 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
3883721 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3883776 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
3883831 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
3883886 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
3883941 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
3883996 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
3884051 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
3884069 TACAATTTAT
Statistics
Matches: 589, Mismatches: 25, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
54 12 0.02
55 567 0.96
56 10 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:3883662 original size:29 final size:29
Alignment explanation
Indices: 3883629--3883772 Score: 108
Period size: 29 Copynumber: 5.2 Consensus size: 29
3883619 AAGAGCAGGA
3883629 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
3883658 CACCT-TT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
3883683 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
* * * * **
3883713 CACCT-TT-CAGTCCTCA-AAG-AGCAGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
3883738 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
3883768 CACCT
1 CACCT
3883773 TTCAGTCCTC
Statistics
Matches: 83, Mismatches: 20, Indels: 24
0.65 0.16 0.19
Matches are distributed among these distances:
25 6 0.07
26 16 0.19
27 17 0.20
28 17 0.20
29 21 0.25
30 6 0.07
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:3883743 original size:26 final size:26
Alignment explanation
Indices: 3883658--3883802 Score: 87
Period size: 26 Copynumber: 5.3 Consensus size: 26
3883648 AAGTTGGTGG
*
3883658 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3883684 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3883713 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3883739 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3883768 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
3883794 CACCTTTCA
1 CACCTTTCA
3883803 AAGCCCACAC
Statistics
Matches: 85, Mismatches: 24, Indels: 20
0.66 0.19 0.16
Matches are distributed among these distances:
25 6 0.07
26 25 0.29
27 16 0.19
28 16 0.19
29 16 0.19
30 6 0.07
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:3884669 original size:1 final size:1
Alignment explanation
Indices: 3884663--3884708 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
3884653 AAAGTGTTTG
***
3884663 AAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3884709 TTTAAATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:3884694 original size:25 final size:25
Alignment explanation
Indices: 3884660--3884708 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3884650 GATAAAGTGT
3884660 TTGAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAA
3884685 TTGAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAA
3884709 TTTAAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (25 bp):
TTGAAAAAAAAAAAAAAAAAAAAAA
Found at i:3884696 original size:24 final size:24
Alignment explanation
Indices: 3884664--3884710 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3884654 AAGTGTTTGA
3884664 AAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAATTG
3884688 AAAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAAATT
3884711 TAAATGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.89, C:0.00, G:0.02, T:0.09
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAAAAATTG
Found at i:3884737 original size:21 final size:21
Alignment explanation
Indices: 3884713--3884769 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3884703 AAAAAATTTA
3884713 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3884734 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3884755 AATGTATCGATACAT
1 AATGTATCGATACAT
3884770 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3884849 original size:19 final size:19
Alignment explanation
Indices: 3884825--3884892 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3884815 AATTCAACAA
3884825 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3884844 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3884859 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3884876 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3884893 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3884864 original size:13 final size:13
Alignment explanation
Indices: 3884846--3884870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3884836 ACATAAGTTT
3884846 TGTATCGATACAA
1 TGTATCGATACAA
3884859 TGTATCGATACA
1 TGTATCGATACA
3884871 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3884868 original size:32 final size:32
Alignment explanation
Indices: 3884827--3884889 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3884817 TTCAACAATT
*
3884827 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3884859 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3884890 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3884950 original size:13 final size:13
Alignment explanation
Indices: 3884932--3884957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3884922 CATTTTTCTG
3884932 TGTATCGATACAT
1 TGTATCGATACAT
3884945 TGTATCGATACAT
1 TGTATCGATACAT
3884958 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3884954 original size:33 final size:33
Alignment explanation
Indices: 3884912--3884978 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3884902 GCCAAGGAAA
***
3884912 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3884945 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3884978 T
1 T
3884979 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3887498 original size:28 final size:29
Alignment explanation
Indices: 3887429--3887501 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 29
3887419 CTTCACAATC
*
3887429 GGGGACACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCGTTAATCATCGA
*
3887458 --GGATACTCCAACCCCGTT-AT-TTCTGA
1 GGGGATACTCCAACCCCGTTAATCATC-GA
3887484 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3887502 ACTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
27 17 0.44
28 16 0.41
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.21
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTAATCATCGA
Found at i:3887546 original size:51 final size:51
Alignment explanation
Indices: 3887484--3887654 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
3887474 TTATTTCTGA
* * *
3887484 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
3887535 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
3887588 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3887640 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3887655 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3887673 original size:28 final size:28
Alignment explanation
Indices: 3887637--3887718 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3887627 ATTTTTCACA
*
3887637 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3887665 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3887693 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3887719 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3890344 original size:149 final size:149
Alignment explanation
Indices: 3890046--3890553 Score: 655
Period size: 149 Copynumber: 3.4 Consensus size: 149
3890036 GTGCCTAAAT
* * * * * * *
3890046 ATCCT-AGAGGACTTGGATAAGATCAAAATAAACCCATTCCTAATTCATACCTTCGGCGTAGAAG
1 ATCCTAAG-GGACTTGAAAAAGATAAAAACAAACCCACTCCTAATTCATACCTTCAGCGTAGAAA
* * * * * *
3890110 TGGACTCAGTAGTTTTATAAAACTAAGCTTC-AGGGAAAATGCTAAAATATCCCTAAGGTTTACG
65 AGGAC-CGGTAGTTTTATAAGACTAGGTTTCGA-GGAAAATGCTAAAATATCCCTAAGGTTTACC
*
3890174 ATCAACTTAGAAGTGCCCGGTG
128 ATCGACTTAGAAGTGCCCGGTG
* * *
3890196 ATCCTAAGGGACTTGAAAAAGATAAAAATAGACCCACTCCTAATTCATACCTTTAGCGTAGAAAA
1 ATCCTAAGGGACTTGAAAAAGATAAAAACAAACCCACTCCTAATTCATACCTTCAGCGTAGAAAA
* *
3890261 GGACCGGTAGTTTTATAAGACTAGGTTTCGAGGAAAATGCTAAAATATCCCTAAGATTGACCATC
66 GGACCGGTAGTTTTATAAGACTAGGTTTCGAGGAAAATGCTAAAATATCCCTAAGGTTTACCATC
*
3890326 GACTTAAAAGTGCCCGGTG
131 GACTTAGAAGTGCCCGGTG
** *
3890345 ATCCTAAGGTCCTTGAAAAAGATAAAAACAAACCCACTCCTAATTCATAACTTCAGCGTA-AAAG
1 ATCCTAAGGGACTTGAAAAAGATAAAAACAAACCCACTCCTAATTCATACCTTCAGCGTAGAAA-
* * * * *
3890409 CGGACCCGATAGTTTTATAAGACTAGGTTTTGAGAAAAATGCTAAAATATCCTTAAGGTTTACCA
65 AGGA-CCGGTAGTTTTATAAGACTAGGTTTCGAGGAAAATGCTAAAATATCCCTAAGGTTTACCA
*
3890474 -CGACTTAGAAGTGTCCGGTG
129 TCGACTTAGAAGTGCCCGGTG
* * *
3890494 ATCCTAAGGGACTGGAAAAAGATAAAAACAAATCCACTCCTAATTCATACCTTCAACGTA
1 ATCCTAAGGGACTTGAAAAAGATAAAAACAAACCCACTCCTAATTCATACCTTCAGCGTA
3890554 AGAGTGACAA
Statistics
Matches: 315, Mismatches: 39, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
148 3 0.01
149 198 0.63
150 112 0.36
151 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (149 bp):
ATCCTAAGGGACTTGAAAAAGATAAAAACAAACCCACTCCTAATTCATACCTTCAGCGTAGAAAA
GGACCGGTAGTTTTATAAGACTAGGTTTCGAGGAAAATGCTAAAATATCCCTAAGGTTTACCATC
GACTTAGAAGTGCCCGGTG
Found at i:3892336 original size:10 final size:9
Alignment explanation
Indices: 3892321--3892356 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
3892311 GATTTTCCTA
3892321 TTTTTCTCTT
1 TTTTTCT-TT
3892331 TTTTTCTTGT
1 TTTTTCTT-T
3892341 TTTTTCTTT
1 TTTTTCTTT
3892350 TTTTTCT
1 TTTTTCT
3892357 CTTGGAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3892673 original size:5 final size:5
Alignment explanation
Indices: 3892657--3892716 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
3892647 ACTAGTTTTG
* *
3892657 AAATA AAGTA AAATA AAATA AAATA ATCAA-A AAATA AAAGA AAATTA
1 AAATA AAATA AAATA AAATA AAATA A--AATA AAATA AAATA AAA-TA
*
3892704 AAATT AAA-A AAAT
1 AAATA AAATA AAAT
3892717 TATAAACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 5 0.11
5 31 0.70
6 6 0.14
7 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (5 bp):
AAATA
Done.