Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold435
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: 249727
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 2273 characters in sequence are not A, C, G, or T
Found at i:175 original size:61 final size:62
Alignment explanation
Indices: 87--214 Score: 240
Period size: 61 Copynumber: 2.1 Consensus size: 62
77 TGTTTCAAAA
87 AAATAAATTATGAAAATATTTATATTTTTTGAATTATTTTTACAAAATTATTAATTTAATAAG
1 AAATAAATTATG-AAATATTTATATTTTTTGAATTATTTTTACAAAATTATTAATTTAATAAG
150 AAATAAATTATG-AATATTTATATTTTTTGAATTATTTTTACAAAATTATTAATTTAATAAG
1 AAATAAATTATGAAATATTTATATTTTTTGAATTATTTTTACAAAATTATTAATTTAATAAG
211 AAAT
1 AAAT
215 TTGATTAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 53 0.82
63 12 0.18
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (62 bp):
AAATAAATTATGAAATATTTATATTTTTTGAATTATTTTTACAAAATTATTAATTTAATAAG
Found at i:3363 original size:41 final size:41
Alignment explanation
Indices: 3277--3363 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
3267 TGGTTGGTCG
* * *
3277 TGTGGTAGACCATGTACATCACACAACTGTATGTTAAGCCT
1 TGTGGTAGACCATGTACATCACACAACTGTATGGTAAACCC
*** *
3318 TGTGGTAGACCATGTGGGTCACACAACTGTGTGGTAAACCC
1 TGTGGTAGACCATGTACATCACACAACTGTATGGTAAACCC
3359 TGTGG
1 TGTGG
3364 GAAGTAGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (41 bp):
TGTGGTAGACCATGTACATCACACAACTGTATGGTAAACCC
Found at i:11609 original size:19 final size:19
Alignment explanation
Indices: 11556--11609 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
11546 AAAAATTTCT
* *
11556 AAAT-TTTGGAATTTTTAT
1 AAATATTTGGAATTTTGAA
**
11574 AAATATTTTAAATTTTTGAA
1 AAATATTTGGAA-TTTTGAA
11594 AAATATTTGGAATTTT
1 AAATATTTGGAATTTT
11610 TTTCTATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (19 bp):
AAATATTTGGAATTTTGAA
Found at i:21401 original size:30 final size:30
Alignment explanation
Indices: 21360--21418 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
21350 AGCTAGACGA
* * *
21360 GCTTTCTAAAAAGTTCGTCCAGTTGGATGC
1 GCTTTCCAAAAAATTCGTCCAATTGGATGC
*
21390 GCTTTCCAAAAAATTTGTCCAATTGGATG
1 GCTTTCCAAAAAATTCGTCCAATTGGATG
21419 TGTTTTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (30 bp):
GCTTTCCAAAAAATTCGTCCAATTGGATGC
Found at i:21475 original size:20 final size:20
Alignment explanation
Indices: 21450--21489 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21440 GGGTTAGGGC
*
21450 TTATTTTAGGGTTAGAGTTT
1 TTATTTTAAGGTTAGAGTTT
*
21470 TTATTTTAAGGTTAGGGTTT
1 TTATTTTAAGGTTAGAGTTT
21490 AGGGTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (20 bp):
TTATTTTAAGGTTAGAGTTT
Found at i:23917 original size:27 final size:27
Alignment explanation
Indices: 23846--23917 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
23836 CTACCCTGTG
*
23846 TTTATTGTCCGA-TGGACTACCCCATT
1 TTTATTGTCCCAGTGGACTACCCCATT
* **
23872 TTTATTGTCCCGGCAGACTACCCCATT
1 TTTATTGTCCCAGTGGACTACCCCATT
23899 TTTATTGTCCCAGTGGACT
1 TTTATTGTCCCAGTGGACT
23918 CTATTGGTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 10 0.26
27 28 0.74
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.38
Consensus pattern (27 bp):
TTTATTGTCCCAGTGGACTACCCCATT
Found at i:24039 original size:34 final size:35
Alignment explanation
Indices: 24001--24077 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
23991 ACCGTCATTG
* *
24001 CGGTGTCGCT-TCATAGAGCCT-TAGACCGTTGTCA
1 CGGTGTCGCTCT-ATAGAACCTATAAACCGTTGTCA
* * *
24035 CGGTGTGGCTCTATGGAACCTATAAATCGTTGTCA
1 CGGTGTCGCTCTATAGAACCTATAAACCGTTGTCA
24070 CGGTGTCG
1 CGGTGTCG
24078 TCCCGAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
34 16 0.46
35 19 0.54
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (35 bp):
CGGTGTCGCTCTATAGAACCTATAAACCGTTGTCA
Found at i:24538 original size:23 final size:23
Alignment explanation
Indices: 24509--24649 Score: 129
Period size: 23 Copynumber: 6.1 Consensus size: 23
24499 ACCACATGAC
* *
24509 CCCCTTAATGAATGTTATACAAA
1 CCCCTTAATGAATGTTATGCGAA
*
24532 CCCCTTAATGAACGTTATGCGAA
1 CCCCTTAATGAATGTTATGCGAA
* ** * *
24555 CCTCTTTGTGAATGTTGTGTGAA
1 CCCCTTAATGAATGTTATGCGAA
*
24578 CCCCTTACTGAATGTTATGCGAA
1 CCCCTTAATGAATGTTATGCGAA
** * *
24601 CATCTTAGTGAATGTTATGTGAA
1 CCCCTTAATGAATGTTATGCGAA
* * * *
24624 CCCTTTAGTAAATTTTATGCGAA
1 CCCCTTAATGAATGTTATGCGAA
24647 CCC
1 CCC
24650 TGTTGGAAAA
Statistics
Matches: 94, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 94 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (23 bp):
CCCCTTAATGAATGTTATGCGAA
Found at i:24584 original size:46 final size:46
Alignment explanation
Indices: 24512--24626 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 46
24502 ACATGACCCC
* *** *
24512 CTTAATGAATGTTATACAAACCCCTTAATGAACGTTATGCGAACCT
1 CTTAGTGAATGTTATGTGAACCCCTTAATGAACGTTATGCGAACAT
* * * *
24558 CTTTGTGAATGTTGTGTGAACCCCTTACTGAATGTTATGCGAACAT
1 CTTAGTGAATGTTATGTGAACCCCTTAATGAACGTTATGCGAACAT
24604 CTTAGTGAATGTTATGTGAACCC
1 CTTAGTGAATGTTATGTGAACCC
24627 TTTAGTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (46 bp):
CTTAGTGAATGTTATGTGAACCCCTTAATGAACGTTATGCGAACAT
Found at i:24642 original size:46 final size:46
Alignment explanation
Indices: 24512--24647 Score: 146
Period size: 46 Copynumber: 3.0 Consensus size: 46
24502 ACATGACCCC
* *** * * * *
24512 CTTAATGAATGTTATACAAACCCCTTAATGAACGTTATGCGAACCT
1 CTTAGTGAATGTTATGTGAACCCCTTACTAAATGTTATGCGAACAT
* * *
24558 CTTTGTGAATGTTGTGTGAACCCCTTACTGAATGTTATGCGAACAT
1 CTTAGTGAATGTTATGTGAACCCCTTACTAAATGTTATGCGAACAT
* * *
24604 CTTAGTGAATGTTATGTGAACCCTTTAGTAAATTTTATGCGAAC
1 CTTAGTGAATGTTATGTGAACCCCTTACTAAATGTTATGCGAAC
24648 CCTGTTGGAA
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (46 bp):
CTTAGTGAATGTTATGTGAACCCCTTACTAAATGTTATGCGAACAT
Found at i:24648 original size:69 final size:69
Alignment explanation
Indices: 24509--24649 Score: 158
Period size: 69 Copynumber: 2.0 Consensus size: 69
24499 ACCACATGAC
* * *
24509 CCCCTTAATGAATGTTATACAAACCCCTTAATGAACGTTATGCGAACCTCTTTGTGAATGTTGTG
1 CCCCTTAATGAATGTTATACAAACACCTTAATGAACGTTATGCGAACCTCTTTGTAAATGTTATG
*
24574 TGAA
66 CGAA
* * * * * * * *
24578 CCCCTTACTGAATGTTATGCGAACATCTTAGTGAATGTTATGTGAACC-CTTTAGTAAATTTTAT
1 CCCCTTAATGAATGTTATACAAACACCTTAATGAACGTTATGCGAACCTCTTT-GTAAATGTTAT
24642 GCGAA
65 GCGAA
24647 CCC
1 CCC
24650 TGTTGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
68 4 0.07
69 55 0.93
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (69 bp):
CCCCTTAATGAATGTTATACAAACACCTTAATGAACGTTATGCGAACCTCTTTGTAAATGTTATG
CGAA
Found at i:26996 original size:25 final size:25
Alignment explanation
Indices: 26968--27030 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
26958 GCAAACCCTT
26968 ATGTGAACCCTTATTGCGAACAGTC
1 ATGTGAACCCTTATTGCGAACAGTC
* * *
26993 ATGTGAACCTTTAATGCGAACATTC
1 ATGTGAACCCTTATTGCGAACAGTC
*
27018 ATGCGAA-CCTTAT
1 ATGTGAACCCTTAT
27031 CCACGAGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (25 bp):
ATGTGAACCCTTATTGCGAACAGTC
Found at i:31941 original size:22 final size:22
Alignment explanation
Indices: 31885--31943 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
31875 TGAATCATAG
*
31885 CATATCATATACATA-ACCATT
1 CATATCACATACATATACCATT
* **
31906 CATATC-CTAAACATATAGTATT
1 CATATCAC-ATACATATACCATT
31928 CATATCACATACATAT
1 CATATCACATACATAT
31944 TTAAAACTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 12 0.40
22 17 0.57
23 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (22 bp):
CATATCACATACATATACCATT
Found at i:44563 original size:17 final size:18
Alignment explanation
Indices: 44541--44582 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44531 TAAATATTGT
44541 TTAAATAATTA-AAAAAA
1 TTAAATAATTATAAAAAA
* *
44558 TTAAATTATTATACAAAA
1 TTAAATAATTATAAAAAA
44576 TTAAATA
1 TTAAATA
44583 TTTTTTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAATAATTATAAAAAA
Found at i:44584 original size:17 final size:16
Alignment explanation
Indices: 44541--44584 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
44531 TAAATATTGT
44541 TTAAATAATTAAAAAAA
1 TTAAAT-ATTAAAAAAA
*
44558 TTAAATTATTATACAAAA
1 TTAAA-TATTA-AAAAAA
44576 TTAAATATT
1 TTAAATATT
44585 TTTTCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATATTAAAAAAA
Found at i:45812 original size:19 final size:19
Alignment explanation
Indices: 45773--45812 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
45763 CAAAGTCCAT
* *
45773 AATATTGTGTAAATTTTAA
1 AATATTGTGTAAAATTCAA
45792 AATATTGTGTAAAATTCAA
1 AATATTGTGTAAAATTCAA
45811 AA
1 AA
45813 ATATATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (19 bp):
AATATTGTGTAAAATTCAA
Found at i:45813 original size:20 final size:19
Alignment explanation
Indices: 45773--45816 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
45763 CAAAGTCCAT
**
45773 AATATTGTGTAAATTTTAA
1 AATATTGTGTAAATTCAAA
45792 AATATTGTGTAAAATTCAAA
1 AATATTGTGT-AAATTCAAA
45812 AATAT
1 AATAT
45817 ATAAACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (19 bp):
AATATTGTGTAAATTCAAA
Found at i:47429 original size:15 final size:16
Alignment explanation
Indices: 47409--47438 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47399 CCCTCATTTA
47409 AAATTTT-AATAAATT
1 AAATTTTCAATAAATT
47424 AAATTTTCAATAAAT
1 AAATTTTCAATAAAT
47439 ATGCAGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTTTCAATAAATT
Found at i:54780 original size:3 final size:3
Alignment explanation
Indices: 54772--54810 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
54762 GGGTTGTACT
54772 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54811 ACTCAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:70542 original size:78 final size:78
Alignment explanation
Indices: 70413--70569 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
70403 CAAAAAAGAA
*
70413 AAACCCAGAATTTAAAACTCTCTAAAAAAGACCTAACATTTAGATTTTATTATATAGTTGAAATT
1 AAACCCAGAATTTAAAACTATCTAAAAAAGACCTAACATTTAGATTTTATTATATAGTTGAAATT
70478 TCTGAAGTTTGAG
66 TCTGAAGTTTGAG
70491 AAACCCAGAATTTAAAACTATCTAAAAAAGACCTAACATTTAGATTTTATTATATAGTTGAAATT
1 AAACCCAGAATTTAAAACTATCTAAAAAAGACCTAACATTTAGATTTTATTATATAGTTGAAATT
*
70556 TTTGAAGTTTGAG
66 TCTGAAGTTTGAG
70569 A
1 A
70570 GACTTGGCAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (78 bp):
AAACCCAGAATTTAAAACTATCTAAAAAAGACCTAACATTTAGATTTTATTATATAGTTGAAATT
TCTGAAGTTTGAG
Found at i:81882 original size:51 final size:51
Alignment explanation
Indices: 81794--81907 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 51
81784 ATATTACGGG
* * * ** *
81794 CTAAATTTGTTAAATCAGGATCAGATTGATAGCATAT-GAAAATGTTG-CGAA
1 CTAAATTTGTTAAATCAAGACCAAATTGATAAAATATGGAAAAT-TTGAAG-A
*
81845 CTAAATTTGTTAAATCAAGACCAAATTGATAAAATATGGAAACTTTGAAGA
1 CTAAATTTGTTAAATCAAGACCAAATTGATAAAATATGGAAAATTTGAAGA
81896 CTAAATTTGTTA
1 CTAAATTTGTTA
81908 TCAGGCCAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 48 0.89
52 6 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (51 bp):
CTAAATTTGTTAAATCAAGACCAAATTGATAAAATATGGAAAATTTGAAGA
Found at i:82114 original size:15 final size:16
Alignment explanation
Indices: 82094--82131 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
82084 CACGTGCATG
82094 ATATTTGG-GTATTTA
1 ATATTTGGAGTATTTA
*
82109 ATATTTGGATGTATTTG
1 ATATTTGGA-GTATTTA
82126 ATATTT
1 ATATTT
82132 TAAGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
17 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (16 bp):
ATATTTGGAGTATTTA
Found at i:92221 original size:11 final size:11
Alignment explanation
Indices: 92205--92246 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
92195 TAATTTTTAA
92205 TTTTAAAATAC
1 TTTTAAAATAC
92216 TTTTAAAATAC
1 TTTTAAAATAC
92227 TTTTAAAATAC
1 TTTTAAAATAC
92238 TTTTAAAAT
1 TTTTAAAAT
92247 TGGTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:97105 original size:33 final size:35
Alignment explanation
Indices: 97061--97135 Score: 136
Period size: 33 Copynumber: 2.2 Consensus size: 35
97051 ACGAGACAAT
97061 GATTTAAAACAAAAGAAAACATAAAAT-AAAAATA
1 GATTTAAAACAAAAGAAAACATAAAATAAAAAATA
97095 G-TTTAAAACAAAAGAAAACATAAAATAAAAAATA
1 GATTTAAAACAAAAGAAAACATAAAATAAAAAATA
97129 GATTTAA
1 GATTTAA
97136 TTAGGTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
33 25 0.64
34 9 0.23
35 5 0.13
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (35 bp):
GATTTAAAACAAAAGAAAACATAAAATAAAAAATA
Found at i:97546 original size:17 final size:18
Alignment explanation
Indices: 97524--97557 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
97514 TGAAACAAAT
97524 AAATGTC-AAATTAATAA
1 AAATGTCAAAATTAATAA
97541 AAATGTCAAAATTAATA
1 AAATGTCAAAATTAATA
97558 GCTAGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATGTCAAAATTAATAA
Found at i:100175 original size:20 final size:20
Alignment explanation
Indices: 100150--100190 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
100140 TCCTGCTGGT
100150 TGAAAGGGATGACAGGCCCC
1 TGAAAGGGATGACAGGCCCC
100170 TGAAAGGGATGACAGGCCCC
1 TGAAAGGGATGACAGGCCCC
100190 T
1 T
100191 TCTGAGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.34, T:0.12
Consensus pattern (20 bp):
TGAAAGGGATGACAGGCCCC
Found at i:106149 original size:23 final size:23
Alignment explanation
Indices: 106104--106149 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
106094 ATAAAAAATC
*
106104 TATTTAAAAAAAAGGTCAAATTT
1 TATTTAAAAAAAAGGTAAAATTT
*
106127 TATTTAAAATAAAGG-AAATATTT
1 TATTTAAAAAAAAGGTAAA-ATTT
106150 CCACTTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (23 bp):
TATTTAAAAAAAAGGTAAAATTT
Found at i:107365 original size:24 final size:24
Alignment explanation
Indices: 107335--107387 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
107325 ATATATAAAT
* *
107335 TATAAAACCTCAAAA-ATTATATA
1 TATAAAAACTCAAAATAATATATA
* *
107358 TATAAAAATTGAAAATAATATATA
1 TATAAAAACTCAAAATAATATATA
107382 TATAAA
1 TATAAA
107388 TAACAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (24 bp):
TATAAAAACTCAAAATAATATATA
Found at i:107378 original size:22 final size:22
Alignment explanation
Indices: 107347--107388 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
107337 TAAAACCTCA
*
107347 AAAATTATATATATAAAAATTG
1 AAAATAATATATATAAAAATTG
*
107369 AAAATAATATATATATAAAT
1 AAAATAATATATATAAAAAT
107389 AACAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATAATATATATAAAAATTG
Found at i:109333 original size:38 final size:38
Alignment explanation
Indices: 109194--109326 Score: 194
Period size: 38 Copynumber: 3.5 Consensus size: 38
109184 ACCGCCCTAC
* * *
109194 TGAGAACATGATAAGCATGTCTACTGTTAATAATGAAT
1 TGAGTACATGTTAAACATGTCTACTGTTAATAATGAAT
* * *
109232 TGAGTACGTATTAAACATGTCTACTGTTATTAATGAAT
1 TGAGTACATGTTAAACATGTCTACTGTTAATAATGAAT
* *
109270 TGAGTACAAGTTAAACATGTCTATTGTTAATAATGAAT
1 TGAGTACATGTTAAACATGTCTACTGTTAATAATGAAT
109308 TGAGTACATGTTAAACATG
1 TGAGTACATGTTAAACATG
109327 CCTATTGCTA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 83 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (38 bp):
TGAGTACATGTTAAACATGTCTACTGTTAATAATGAAT
Found at i:110480 original size:20 final size:20
Alignment explanation
Indices: 110438--110495 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
110428 TTTTAATAAA
*
110438 TTAAAAATATAAAAAAATGT
1 TTAAAAATATAAAAAAATAT
* **
110458 TTAAAAATATAAATATTTAT
1 TTAAAAATATAAAAAAATAT
*
110478 TTAAAAAT-TAAGAAAATA
1 TTAAAAATATAAAAAAATA
110496 ATATGGATGA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
TTAAAAATATAAAAAAATAT
Found at i:113332 original size:2 final size:2
Alignment explanation
Indices: 113325--113350 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
113315 CAACTTTTAC
113325 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
113351 GAAAATTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115492 original size:2 final size:2
Alignment explanation
Indices: 115485--115513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
115475 GTAAATACTA
115485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115514 AAACTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116275 original size:19 final size:19
Alignment explanation
Indices: 116239--116280 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
116229 TGGAAAATTA
*
116239 AAAAAATTATAAAGTTATTT
1 AAAAAATTATAAAATTA-TT
116259 AAAAAATTA-AAAATTATT
1 AAAAAATTATAAAATTATT
116277 AAAA
1 AAAA
116281 GTATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAATTATAAAATTATT
Found at i:116281 original size:29 final size:28
Alignment explanation
Indices: 116232--116290 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
116222 TTTAATTTGG
*
116232 AAAATTAAAAAAATTATAAAGTTATTTAA
1 AAAATTAAAAAAATTATAAAG-TATATAA
*
116261 AAAATTAAAAATTATTA-AAAGTATATAA
1 AAAATTAAAAA-AATTATAAAGTATATAA
116289 AA
1 AA
116291 TATATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 8 0.30
29 15 0.56
30 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAATTAAAAAAATTATAAAGTATATAA
Found at i:118491 original size:31 final size:31
Alignment explanation
Indices: 118440--118518 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
118430 TTCTAAGGAA
* * *
118440 TAAATTATCTCTATTGATTTTTGATACTACC
1 TAAAATATCCCTATTAATTTTTGATACTACC
* **
118471 TAAAATATCCCTATTAATTTTTTATGTTACC
1 TAAAATATCCCTATTAATTTTTGATACTACC
*
118502 TAAAATATCCTTATTAA
1 TAAAATATCCCTATTAA
118519 CTACTAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (31 bp):
TAAAATATCCCTATTAATTTTTGATACTACC
Found at i:118611 original size:31 final size:30
Alignment explanation
Indices: 118575--118647 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
118565 CACTATTACC
* *
118575 TTAATTTAATTACAATATATAACATTTTAAT
1 TTAATTTAATTACAATAAATAACA-ATTAAT
* * *
118606 TTAATTTAATCACATTAAATAATAATTAAT
1 TTAATTTAATTACAATAAATAACAATTAAT
118636 TTAATTTAATTA
1 TTAATTTAATTA
118648 TCATATCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAATTTAATTACAATAAATAACAATTAAT
Found at i:127531 original size:15 final size:15
Alignment explanation
Indices: 127513--127542 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
127503 ATGAGTTAAC
127513 TAAGTTTAATTAATT
1 TAAGTTTAATTAATT
127528 TAAGTTTAATTAATT
1 TAAGTTTAATTAATT
127543 AACTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TAAGTTTAATTAATT
Found at i:128581 original size:29 final size:30
Alignment explanation
Indices: 128523--128584 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
128513 TACACCCTAT
128523 TCTTTGTAGTTTTCGTACATTTGAAATTTAA
1 TCTTTGTAGTTTTC-TACATTTGAAATTTAA
*
128554 TCTTTGTA-TTTT-TACTTTTAGAAATTTAA
1 TCTTTGTAGTTTTCTACATTT-GAAATTTAA
128583 TC
1 TC
128585 CTTTAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
29 11 0.38
30 4 0.14
31 8 0.28
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (30 bp):
TCTTTGTAGTTTTCTACATTTGAAATTTAA
Found at i:133846 original size:15 final size:14
Alignment explanation
Indices: 133802--133838 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
133792 TAAAGATGAG
133802 TTAATTAAGTTTAA
1 TTAATTAAGTTTAA
133816 TTAATTTAAGTTTAA
1 TTAA-TTAAGTTTAA
133831 TTAATTAA
1 TTAATTAA
133839 CTATTAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TTAATTAAGTTTAA
Found at i:143896 original size:110 final size:109
Alignment explanation
Indices: 143605--143926 Score: 472
Period size: 110 Copynumber: 3.0 Consensus size: 109
143595 GAAATTCAAG
*
143605 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACTCAGCACATTAGGGCACG-TTCCTC
1 AGGATATTTGGCTATTTGGTTAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* **
143667 AAATTTCCAAACGCAAAACATTGCCTTA-TTTGAAATTTTTGGA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* *
143710 AGGATATTTGGCTATTTGGTTAAACGAGAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTTAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
*
143775 GAATTTTCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* * *
143819 AGGATATTTAGCTATTTGGTTGAACGAGAAAAAATCGAAACCCAGCACATTAAGGCACGTTTCCT
1 AGGATATTTGGCTATTTGGTTAAACGAG-AAAAATCGAAACCCAGCACATTAGGGCACGTTTCCT
* * * *
143884 CGAATTTCCAAACGCTAAATATTGCCTCATTTAGAAAATTTTT
65 CGAATTTCCAAACGCAAAACATTGCCTTATTTTG-AAATTTTT
143927 CCTTTTTGAA
Statistics
Matches: 194, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
105 28 0.14
107 26 0.13
108 31 0.16
109 39 0.20
110 62 0.32
111 8 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTTAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:143998 original size:20 final size:20
Alignment explanation
Indices: 143962--143999 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
143952 GCATAATGGA
*
143962 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
143982 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
144000 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:144225 original size:12 final size:12
Alignment explanation
Indices: 144210--144234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
144200 TATGAAAAAA
144210 TATATATATATG
1 TATATATATATG
144222 TATATATATATG
1 TATATATATATG
144234 T
1 T
144235 TTTAAGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:146290 original size:50 final size:49
Alignment explanation
Indices: 146236--146409 Score: 150
Period size: 50 Copynumber: 3.4 Consensus size: 49
146226 CGGAGAAATT
* * *
146236 AGATTCGTCGTCGTAGATTCAATCTATTTCATTTCACCGCCAGGGAAGTA
1 AGATTCG-CGTCGTAGCTTCAATCTATTTCACTACACCGCCAGGGAAGTA
* * * ** * *
146286 AGATTCGCTGTTGTAGCTTCAATCTATTTAACCACAATGTCGGGGAAGTA
1 AGATTCGC-GTCGTAGCTTCAATCTATTTCACTACACCGCCAGGGAAGTA
* * * **
146336 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTTGGGAAAGTA
1 AGATTCG-CGTCGTAGCTTCAATCTATTTCACTACACCGCCAGGG-AAGTA
* *
146387 AGATTCGCCGTTGTGGCTTCAAT
1 AGATTCG-CGTCGTAGCTTCAAT
146410 TTTTTAAATT
Statistics
Matches: 98, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
49 1 0.01
50 70 0.71
51 27 0.28
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (49 bp):
AGATTCGCGTCGTAGCTTCAATCTATTTCACTACACCGCCAGGGAAGTA
Found at i:146448 original size:50 final size:50
Alignment explanation
Indices: 146278--147419 Score: 720
Period size: 50 Copynumber: 22.9 Consensus size: 50
146268 TTCACCGCCA
* ***
146278 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTT-AACCACAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGCAATGTCG
* * ** * ** *
146328 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTTG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATG-TCG
* * *
146379 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATTTTTTAAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * **** *
146429 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGC-ATCG-CC
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTCG
* * *
146478 GGGAAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * **** * *
146528 GGGAAGCAAGATTCGCCGTCGTAGCTTCAAT-TTGTTCCGCTGC-ATCGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTT-TTAAATTGCAAT-GTCG
* * * *
146578 GGAAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * * ** * ** * ** *
146628 AGGAAGGAAGATTTGCCGTCATAGCTTCAATCTGTTCCACTGCACCGCTTG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATG-TCG
* * * *
146679 GGAAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGTAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * * * * * ** *
146729 GGGAAGCAAAATTCGTCATTGTAGCTTCAATCTGTT---CTGCTACATCACC
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGC-A-ATGTCG
* *
146778 TGGAAGTAAGATTCGCTGTTGT-GACTTCAATCTTTTAAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTTTTAAATTGCAATGTCG
* * * * * ** * * *
146828 AGGAAGGAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTG-TATCG-CC
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTCG
* * *
146877 TGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * **** *
146927 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCG-CC
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTCG
* * * *
146976 TGGAAGTAAGATTCACCGTTATAGCTTCAATCTTTTAAATTACAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * ***** *
147026 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCAGC-ATCG-CC
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTCG
* * *
147075 TGGAAGTAAGATTCGCCATTGT-GACTTCAATCTTTTAAATTACAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTTTTAAATTGCAATGTCG
* * * ****
147125 GGGAAGCAAGATTCGTCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGTC-
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTCG
* * * * *
147174 TGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGTAATGTTG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
*** * * * **** * *
147224 GGGAAACGAGATTCGCCGTCGTAGTTTCAATCTGTTCCGCTGC-ATCGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTCG
* * * *
147274 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
** * * * * * *** * * *
147324 GGGAAGCGATATTCACCGTCGTTGCTTCAATCTATTCCGTTGCATTGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
* * * *
147374 GAGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTAAATTGCAAT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAAT
147420 CTATGGTTTC
Statistics
Matches: 794, Mismatches: 265, Indels: 66
0.71 0.24 0.06
Matches are distributed among these distances:
47 2 0.00
48 3 0.00
49 220 0.28
50 484 0.61
51 82 0.10
52 3 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG
Found at i:146531 original size:99 final size:99
Alignment explanation
Indices: 146236--147419 Score: 1497
Period size: 99 Copynumber: 11.9 Consensus size: 99
146226 CGGAGAAATT
* * * * ** * * * *
146236 AGATTCGTCGTCGTAGATTCAATCTATTTCATTTCACCGCCAGGGAAGTAAGATTCGCTGTTGTA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCC-GGGAAGTAAGATTCGCCGTTGTG
*** *
146301 GCTTCAATCTATTT-AACCACAATGTCGGGGAAGTA
65 GCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCA
* * *
146336 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTTGGGAAAGTAAGATTCGCCGTTGT
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC-CGGG-AAGTAAGATTCGCCGTTGT
*
146401 GGCTTCAATTTTTTAAATTGCAATGTCGGGGAAGCA
64 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * *
146437 AGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCGCCGGGAAGTAAGATTCGTCGTTGTGG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
*
146502 CCTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
66 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * *
146536 AGATTCGCCGTCGTAGCTTCAATTTGTTCCGCTGCATCGCCTGGAAAGTAAGATTCACCGTTGTG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCC-GGGAAGTAAGATTCGCCGTTGTG
* * *
146601 GCTTCAATCTTTTTAATTGCAATGTCGAGGAAGGA
65 GCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * * *
146636 AGATTTGCCGTCATAGCTTCAATCTGTTCCACTGCACCGCTTGGGAAAGTAAGATTCACCGTTGT
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGC-CGGG-AAGTAAGATTCGCCGTTGT
*
146701 GGCTTCAATCTTTTAAATTGTAATGTCGGGGAAGCA
64 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * * * * * * *
146737 AAATTCGTCATTGTAGCTTCAATCTGTTCTGCTACATCACCTGGAAGTAAGATTCGCTGTTGTGA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
* *
146802 CTTCAATCTTTTAAATTGCAATGTCGAGGAAGGA
66 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * *
146836 AGATTCGCCATCGTAGCTTCAATCTGTTCCACTGTATCGCCTGGAAGTAAGATTCGTCGTTGTGG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
146901 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
66 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * *
146935 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCACCGTTATAG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
*
147000 CTTCAATCTTTTAAATTACAATGTCGGGGAAGCA
66 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * *
147034 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCAGCATCGCCTGGAAGTAAGATTCGCCATTGTGA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
*
147099 CTTCAATCTTTTAAATTACAATGTCGGGGAAGCA
66 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * *
147133 AGATTCGTCGTTGTAGCTTCAATCTGTTCCGCTGCATCGTCTGGAAGTAAGATTCACCGTTGTGG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
* * * *
147198 CTTCAATCTTTTAAATTGTAATGTTGGGGAAACG
66 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* *
147232 AGATTCGCCGTCGTAGTTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCC-GGGAAGTAAGATTCGCCGTTGTG
* * *
147297 GCTTCAATCTTTTAAATTACAATGTCAGGGAAGCG
65 GCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
* * * * * * * *
147332 ATATTCACCGTCGTTGCTTCAATCTATTCCGTTGCATTGCCTGAGAAGTAAGATTCGCCATTGTG
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCC-GGGAAGTAAGATTCGCCGTTGTG
*
147397 GCTTTAATCTTTTAAATTGCAAT
65 GCTTCAATCTTTTAAATTGCAAT
147420 CTATGGTTTC
Statistics
Matches: 954, Mismatches: 123, Indels: 14
0.87 0.11 0.01
Matches are distributed among these distances:
99 533 0.56
100 261 0.27
101 160 0.17
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (99 bp):
AGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCGGGAAGTAAGATTCGCCGTTGTGG
CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCA
Found at i:148719 original size:7 final size:7
Alignment explanation
Indices: 148707--148754 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
148697 TTGGCCTCTC
148707 CTTTTTT
1 CTTTTTT
148714 C-TTTTT
1 CTTTTTT
*
148720 CTTTTCT
1 CTTTTTT
148727 CTTCTTTT
1 CTT-TTTT
*
148735 -TTTCTT
1 CTTTTTT
148741 CTTTTTT
1 CTTTTTT
148748 CTTTTTT
1 CTTTTTT
148755 TTTGAATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 9 0.26
7 22 0.65
8 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:148724 original size:11 final size:10
Alignment explanation
Indices: 148708--148757 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
148698 TGGCCTCTCC
148708 TTTTTTCTTTT
1 TTTTTTC-TTT
148719 TCTTTTCTCTTCT
1 T-TTTT-TCTT-T
*
148732 TTTTTTCTTC
1 TTTTTTCTTT
148742 TTTTTTCTTT
1 TTTTTTCTTT
148752 TTTTTT
1 TTTTTT
148758 GAATCTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 15 0.44
11 5 0.15
12 10 0.29
13 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:148727 original size:21 final size:21
Alignment explanation
Indices: 148703--148757 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
148693 TACCTTGGCC
148703 TCTCCTTTTTTCTTT-TTCTTT
1 TCTCCTTTTTT-TTTCTTCTTT
148724 TCT-CTTCTTTTTTTCTTCTTT
1 TCTCCTT-TTTTTTTCTTCTTT
*
148745 T-TTCTTTTTTTTT
1 TCTCCTTTTTTTTT
148758 GAATCTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TCTCCTTTTTTTTTCTTCTTT
Found at i:148733 original size:23 final size:22
Alignment explanation
Indices: 148702--148757 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
148692 TTACCTTGGC
* *
148702 CTCTCCTTTTTTCTTTTTCTTTT
1 CTCTTCTTTTTTCTTCTT-TTTT
148725 CTCTTCTTTTTTTCTTCTTTTTT
1 CTCTTC-TTTTTTCTTCTTTTTT
148748 CT-TT-TTTTTT
1 CTCTTCTTTTTT
148758 GAATCTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.20
22 2 0.07
23 11 0.37
24 11 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
CTCTTCTTTTTTCTTCTTTTTT
Found at i:148738 original size:18 final size:18
Alignment explanation
Indices: 148715--148755 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
148705 TCCTTTTTTC
148715 TTTTTCTT-TTCTCTTCTT
1 TTTTTCTTCTT-TCTTCTT
*
148733 TTTTTCTTCTTTTTTCTT
1 TTTTTCTTCTTTCTTCTT
148751 TTTTT
1 TTTTT
148756 TTGAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTCTTCTTTCTTCTT
Found at i:153360 original size:110 final size:109
Alignment explanation
Indices: 153069--153390 Score: 427
Period size: 110 Copynumber: 3.0 Consensus size: 109
153059 GAAATTCAAG
*
153069 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * * **
153131 AAATTTCCAAAAGCAAAACATTGCCTTA-TTTGAAATTTTTGGA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
* * * * * *
153174 AGGATATTTGGCCATTTAGTTGAACGAGAAAAATCGAAACCTAGCATATTAGGGCACATTTTCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
153239 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
* *
153283 AGGATATTTAGCTATTTGGTTGAACGAGAAAAAATCGAAACCCAGCACATTAGTGCACGTTTCCT
1 AGGATATTTGGCTATTTGGTTGAACGAG-AAAAATCGAAACCCAGCACATTAGGGCACGTTTCCT
* * * * *
153348 CGAATTTCCAAACGCTAAATATTGCATCATTTAGAAAATTTTT
65 CGAATTTCCAAACGCAAAACATTGCCTTATTT-TAAAATTTTT
153391 CCTTTTTGAA
Statistics
Matches: 186, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
105 25 0.13
107 25 0.13
108 31 0.17
109 37 0.20
110 59 0.32
111 9 0.05
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
Found at i:153456 original size:20 final size:21
Alignment explanation
Indices: 153413--153457 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
153403 ATGGTGTTAT
*
153413 AATATGCATAATGGAATAATA
1 AATATGCATAATGGAACAATA
153434 AATATG-ATAATGTGAACAA-A
1 AATATGCATAATG-GAACAATA
153454 AATA
1 AATA
153458 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (21 bp):
AATATGCATAATGGAACAATA
Found at i:153687 original size:12 final size:12
Alignment explanation
Indices: 153670--153694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
153660 AAATATGAAA
153670 TATATATATATG
1 TATATATATATG
153682 TATATATATATG
1 TATATATATATG
153694 T
1 T
153695 TTTAAGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:153821 original size:18 final size:17
Alignment explanation
Indices: 153794--153827 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
153784 TATTTTAAAA
153794 TTATTAAATATAAAAGT
1 TTATTAAATATAAAAGT
153811 TTATGTAAATATAAAAG
1 TTAT-TAAATATAAAAG
153828 GATTAGCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
TTATTAAATATAAAAGT
Found at i:154129 original size:12 final size:12
Alignment explanation
Indices: 154112--154136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
154102 AAGAATTGCA
154112 ACCCAATACGTT
1 ACCCAATACGTT
154124 ACCCAATACGTT
1 ACCCAATACGTT
154136 A
1 A
154137 GTGTATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
ACCCAATACGTT
Found at i:155099 original size:3 final size:3
Alignment explanation
Indices: 155085--155130 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
155075 CAAATGAGCA
* * *
155085 AAT AAT AGT AAT AAT AAT AAT TAT GAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
155131 CGAAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:155598 original size:12 final size:12
Alignment explanation
Indices: 155581--155605 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
155571 AAGAATTGCA
155581 ACCCAATACGTT
1 ACCCAATACGTT
155593 ACCCAATACGTT
1 ACCCAATACGTT
155605 A
1 A
155606 GTGTATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
ACCCAATACGTT
Found at i:156568 original size:3 final size:3
Alignment explanation
Indices: 156554--156599 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
156544 CAAATGAGCA
* * *
156554 AAT AAT AGT AAT AAT AAT AAT TAT GAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
156600 CGAAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:162076 original size:14 final size:14
Alignment explanation
Indices: 162057--162083 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
162047 TATAATTATT
162057 TTATTTAATATTTA
1 TTATTTAATATTTA
162071 TTATTTAATATTT
1 TTATTTAATATTT
162084 GATAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTAATATTTA
Found at i:162362 original size:18 final size:18
Alignment explanation
Indices: 162325--162362 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
162315 AATATAAAAA
*
162325 AATTACAAATACAATTAT
1 AATTACAAATACAATCAT
*
162343 AATTACAAATATAATCAT
1 AATTACAAATACAATCAT
162361 AA
1 AA
162363 ATAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTACAAATACAATCAT
Found at i:162812 original size:35 final size:35
Alignment explanation
Indices: 162766--162835 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
162756 GACTAAATTC
162766 ACAATTAATAATAAATTTGCATGCCATTTGAGTAT
1 ACAATTAATAATAAATTTGCATGCCATTTGAGTAT
162801 ACAATTAATAATAAATTTGCATGCCATTTGAGTAT
1 ACAATTAATAATAAATTTGCATGCCATTTGAGTAT
162836 TTAAGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (35 bp):
ACAATTAATAATAAATTTGCATGCCATTTGAGTAT
Found at i:165365 original size:131 final size:131
Alignment explanation
Indices: 165182--165448 Score: 437
Period size: 131 Copynumber: 2.0 Consensus size: 131
165172 CTCGCATTTG
165182 TTTTTATTTAAAACACATTTATTTTAGTTTTAAAAGGATATTCAGTTATTTAGGTTCAACGCCAG
1 TTTTTATTTAAAACACATTTATTTTAGTTTTAAAAGGATATTCAGTTATTTAGGTTCAACGCCAG
* * *
165247 AAAAATC-AAAACCCAGTAAGTTAAGGCACAACTTCTCAAATTTTTAAATATGGAATATTGCCTT
66 AAAAATCGAAAA-CCAGTAAGTTAAGGCACAACTTCTCAAATTTCTAAATATGAAATATTACCTT
165311 TA
130 TA
* * *
165313 TTTTTATTTAAAACACATTTATTTTAGTTTTAAAAGGATATTCGGTTATTTAGGTTTAACGCGAG
1 TTTTTATTTAAAACACATTTATTTTAGTTTTAAAAGGATATTCAGTTATTTAGGTTCAACGCCAG
* * *
165378 AAAAATCGAAAACCAGTAAGTTAGGGCACAACTTTTCGAATTTCTAAATATGAAATATTACCTTT
66 AAAAATCGAAAACCAGTAAGTTAAGGCACAACTTCTCAAATTTCTAAATATGAAATATTACCTTT
165443 A
131 A
165444 TTTTT
1 TTTTT
165449 CGAAATTTTC
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 122 0.97
132 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (131 bp):
TTTTTATTTAAAACACATTTATTTTAGTTTTAAAAGGATATTCAGTTATTTAGGTTCAACGCCAG
AAAAATCGAAAACCAGTAAGTTAAGGCACAACTTCTCAAATTTCTAAATATGAAATATTACCTTT
A
Found at i:165845 original size:12 final size:12
Alignment explanation
Indices: 165828--165857 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
165818 AAATAGATCG
*
165828 TAATAATAGATA
1 TAATAATAAATA
165840 TAATAATAAATA
1 TAATAATAAATA
165852 TAATAA
1 TAATAA
165858 AAGAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:169625 original size:57 final size:60
Alignment explanation
Indices: 169493--169630 Score: 178
Period size: 57 Copynumber: 2.3 Consensus size: 60
169483 ATTGACGGTA
169493 AAAAGGATCTAGCCCGGACAGGTGATCCTATCCTGATATAGCCCTTCCGAAGAATATGTGTG
1 AAAAGGATCTAGCCCGGACAGGTGATCC-AT-CTGATATAGCCCTTCCGAAGAATATGTGTG
* *
169555 AAAAAGATCTAGCCCGGACAGGTGAT-C-T-TGATATAGGCC-TCCTGAAGAATATGTG-G
1 AAAAGGATCTAGCCCGGACAGGTGATCCATCTGATATAGCCCTTCC-GAAGAATATGTGTG
*
169611 AAAATGGATTTAGCCCGGAC
1 AAAA-GGATCTAGCCCGGAC
169631 GAGTAATCCA
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
56 8 0.11
57 35 0.50
59 1 0.01
61 1 0.01
62 25 0.36
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (60 bp):
AAAAGGATCTAGCCCGGACAGGTGATCCATCTGATATAGCCCTTCCGAAGAATATGTGTG
Found at i:169812 original size:67 final size:67
Alignment explanation
Indices: 169704--169838 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
169694 GTAATTGTCG
*
169704 TTGCAAGGGATTTAGCCTGGACTGGTAATCCCGCAGTAAGAAATGAGGTTTGCGGGAGTGTGCTC
1 TTGCAAGGGATTTAGCCTGGACTGGTAATCCCGCAGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
169769 TC
66 TC
* *
169771 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAAGGGATTTAGCCTGGACTGGTAATCCCGCAGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
169836 TC
66 TC
169838 T
1 T
169839 GAATTGGAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (67 bp):
TTGCAAGGGATTTAGCCTGGACTGGTAATCCCGCAGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
TC
Found at i:170894 original size:17 final size:17
Alignment explanation
Indices: 170872--170908 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
170862 TCTCTGTCCC
170872 TAGTACTGACATTCTCT
1 TAGTACTGACATTCTCT
170889 TAGTACTGACATTCTCT
1 TAGTACTGACATTCTCT
170906 TAG
1 TAG
170909 AACTCTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (17 bp):
TAGTACTGACATTCTCT
Found at i:172812 original size:11 final size:11
Alignment explanation
Indices: 172796--172820 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
172786 AATCTTCTTA
172796 TTCTTTTTTTT
1 TTCTTTTTTTT
172807 TTCTTTTTTTT
1 TTCTTTTTTTT
172818 TTC
1 TTC
172821 ACCTAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:192125 original size:28 final size:29
Alignment explanation
Indices: 192085--192146 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
192075 ATTTCCCTCA
*
192085 TTTTCTCTCACTTT-ATTTATATTTGAAAT
1 TTTTATCTCACTTTCATTTA-ATTTGAAAT
**
192114 TTTTATCT-ACTTTCATTTAATTTTTAAT
1 TTTTATCTCACTTTCATTTAATTTGAAAT
192142 TTTTA
1 TTTTA
192147 GAATTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATCTCACTTTCATTTAATTTGAAAT
Found at i:195396 original size:29 final size:32
Alignment explanation
Indices: 195330--195401 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
195320 AAAAAAATGT
195330 ACGTATATATATATATATATATATGATAGCAA
1 ACGTATATATATATATATATATATGATAGCAA
* * *
195362 A-ATATATGTGTATATATATAT-TG-TAG-AA
1 ACGTATATATATATATATATATATGATAGCAA
195390 ACGTATATATAT
1 ACGTATATATAT
195402 TTAATGTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.09
29 10 0.30
30 2 0.06
31 17 0.52
32 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (32 bp):
ACGTATATATATATATATATATATGATAGCAA
Found at i:195428 original size:12 final size:12
Alignment explanation
Indices: 195411--195435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
195401 TTTAATGTAT
195411 ATAACAAAATTA
1 ATAACAAAATTA
195423 ATAACAAAATTA
1 ATAACAAAATTA
195435 A
1 A
195436 AAAGGTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACAAAATTA
Found at i:198699 original size:29 final size:29
Alignment explanation
Indices: 198667--198725 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
198657 TAATATGAGG
*
198667 TAAATAAAAGTGATTGTTTTTATAGTTTA
1 TAAATAAAAGTGATTATTTTTATAGTTTA
198696 TAAATAAAAGTGATTATTTTTATAGTTTA
1 TAAATAAAAGTGATTATTTTTATAGTTTA
198725 T
1 T
198726 CCTATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (29 bp):
TAAATAAAAGTGATTATTTTTATAGTTTA
Found at i:203343 original size:29 final size:30
Alignment explanation
Indices: 203271--203349 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
203261 ACAAATAAAA
*
203271 GTAAATAAATAATTAATTAATTAAAGCACT
1 GTAAATAAATAAATAATTAATTAAAGCACT
203301 -TAAATAAA-ATAATAATGATAA-T-AAGCA-T
1 GTAAATAAATA-AATAAT--TAATTAAAGCACT
203329 GTAAATAAATAAATAAATTAA
1 GTAAATAAATAAAT-AATTAA
203350 CACCAAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
28 5 0.12
29 29 0.69
30 5 0.12
31 3 0.07
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.30
Consensus pattern (30 bp):
GTAAATAAATAAATAATTAATTAAAGCACT
Found at i:203394 original size:4 final size:4
Alignment explanation
Indices: 203385--203416 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
203375 TAACATAATA
203385 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
203417 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:203658 original size:3 final size:3
Alignment explanation
Indices: 203650--203678 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
203640 AATAAGTAGG
203650 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
203679 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:209572 original size:90 final size:91
Alignment explanation
Indices: 209415--209611 Score: 274
Period size: 90 Copynumber: 2.2 Consensus size: 91
209405 TTTAAGGGTG
* * * *
209415 CAAAAA-GCCCTCAAACTTTTTCAAAAATAGCAACTAAACCCCCTTTTTTTTTTTTGCACTCATT
1 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAACTAAACCCCCTCTTTTTTTTTTGCACTCAAT
209479 TGGGTACTTAAACTTTCAAAATACAT
66 TGGGTACTTAAACTTTCAAAATACAT
* * *
209505 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGC-AGTTAAGCCCCTACTTTTTTTTTT-CACTCAA
1 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAACTAAACCCCCT-CTTTTTTTTTTGCACTCAA
* *
209568 TTGGGTACTTGAACTTTCAAAATGCAT
65 TTGGGTACTTAAACTTTCAAAATACAT
*
209595 CAAAAAGACCCTCAAAC
1 CAAAAAGGCCCTCAAAC
209612 TTAAAAAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
90 62 0.65
91 33 0.35
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (91 bp):
CAAAAAGGCCCTCAAACCTTTTCAAAAAAAGCAACTAAACCCCCTCTTTTTTTTTTGCACTCAAT
TGGGTACTTAAACTTTCAAAATACAT
Found at i:209837 original size:20 final size:19
Alignment explanation
Indices: 209792--209845 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
209782 ATAAAATCAA
209792 TAAAATTT-ATAAAAA-AT
1 TAAAATTTAATAAAAATAT
*
209809 TAAAGTTTAATAAAAATATT
1 TAAAATTTAATAAAAATA-T
*
209829 TAAAATTTATTAAAAAT
1 TAAAATTTAATAAAAAT
209846 TAGAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 1 0.03
20 16 0.52
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAAATTTAATAAAAATAT
Found at i:213667 original size:61 final size:61
Alignment explanation
Indices: 213574--213700 Score: 139
Period size: 61 Copynumber: 2.1 Consensus size: 61
213564 TATATTAAAA
* * * *
213574 TTTTTAGAATTAGAACTAAATTGCTAATTTTTGAAAATATTAAGGGTTAAATTTATTAATT
1 TTTTTAGAATTAGAACTAAAATGCTAAGTTTTGAAAACATTAAGGGCTAAATTTATTAATT
* * ** * * *
213635 TTTTTAGAATTTGAACTAAAATGAC-AGGTTTTGTTAACATTCAGGGCTAAATTTGTTGATT
1 TTTTTAGAATTAGAACTAAAATG-CTAAGTTTTGAAAACATTAAGGGCTAAATTTATTAATT
213696 TTTTT
1 TTTTT
213701 TATATCTAGG
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 53 0.98
62 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGCTAAGTTTTGAAAACATTAAGGGCTAAATTTATTAATT
Found at i:215966 original size:92 final size:88
Alignment explanation
Indices: 215778--216008 Score: 264
Period size: 90 Copynumber: 2.5 Consensus size: 88
215768 TTTAAGGGTG
** * * * *
215778 CAAAAAGCCCTCAAACTTTTTCAAAACTAGCAACTAAACCCCTGCTCTTTTTTTTTACACTCATT
1 CAAAAAGCCCTCAAAC-TTTTCAAAAAAAGCAATTAAGCCCCT--ACTTTTTTTTTACACTCAAT
215843 TGGGAACTTGAACTTTCAAAATACAT
63 TGGGAACTTGAACTTTCAAAATACAT
*
215869 CAAAAAGGCCCTCAAACATTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACTCAATT
1 CAAAAA-GCCCTCAAAC-TTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTACACTCAATT
* **
215934 GGGTACTTGAACTTTCAAAATGTAT
64 GGGAACTTGAACTTTCAAAATACAT
* * ***
215959 CAAAAAAACTCTCAAACTTAAAAAAAAAAAGCAATTAAGCCCCTACTTTT
1 C-AAAAAGCCCTCAAACTT-TTCAAAAAAAGCAATTAAGCCCCTACTTTT
216009 ATTAAAAATT
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
89 2 0.02
90 76 0.63
91 11 0.09
92 32 0.26
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (88 bp):
CAAAAAGCCCTCAAACTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTACACTCAATTGG
GAACTTGAACTTTCAAAATACAT
Found at i:216090 original size:46 final size:45
Alignment explanation
Indices: 216023--216119 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
216013 AAAATTAGAG
* * * *
216023 AAAAAATTAAAATCAATAAAATCTAT-AATATTATTAAATTTTAAT
1 AAAAAATTAAAATCAAAAAAATATATAAAAATTATAAAATTTT-AT
*
216068 AAAAAATTAAAAT-ATTAAAAAATATATAAAAATTGTAAAATTTTAT
1 AAAAAATTAAAATCA--AAAAAATATATAAAAATTATAAAATTTTAT
216114 AAAAAA
1 AAAAAA
216120 GTTTAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 13 0.30
46 17 0.39
47 13 0.30
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (45 bp):
AAAAAATTAAAATCAAAAAAATATATAAAAATTATAAAATTTTAT
Found at i:218435 original size:18 final size:19
Alignment explanation
Indices: 218403--218438 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
218393 GAAAAAGTGC
218403 AAAAATAAAATAAAATATA
1 AAAAATAAAATAAAATATA
218422 AAAAATAAAA-AAAATAT
1 AAAAATAAAATAAAATAT
218439 TCTATGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAATAAAATAAAATATA
Found at i:224370 original size:19 final size:22
Alignment explanation
Indices: 224346--224385 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
224336 AGGCCCACTC
224346 AACCC-AATTA-AT-AGCCCAA
1 AACCCAAATTACATCAGCCCAA
224365 AACCCAAATTACATCAGCCCA
1 AACCCAAATTACATCAGCCCA
224386 TATACTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 2 0.11
22 6 0.33
ACGTcount: A:0.45, C:0.35, G:0.05, T:0.15
Consensus pattern (22 bp):
AACCCAAATTACATCAGCCCAA
Found at i:225335 original size:3 final size:3
Alignment explanation
Indices: 225316--225374 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
225306 TGCAATTCAT
*
225316 TTA TTA TTTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
225362 TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TT
225375 CACATGCATC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:231901 original size:17 final size:16
Alignment explanation
Indices: 231879--231918 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
231869 CTAATTCTAA
231879 ATTTTTAATAAAAAATC
1 ATTTTTAA-AAAAAATC
231896 ATTTTT-AAAAAAATC
1 ATTTTTAAAAAAAATC
231911 ATTTTTAA
1 ATTTTTAA
231919 CCTTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.64
16 2 0.09
17 6 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTTAAAAAAAATC
Found at i:232479 original size:50 final size:52
Alignment explanation
Indices: 232393--232514 Score: 142
Period size: 56 Copynumber: 2.3 Consensus size: 52
232383 AGTTTGGTCC
*
232393 CAATTGTCTATTGACTATAAATTTAACTCCAC-AAAAAG-GGCTAAGACTAT
1 CAATTGTCTATTGACTATAAATTTAACTCCACAAAAAAGAGACTAAGACTAT
* * *
232443 CAATTGTCTATTGACTA-CACTTTAACTCGACAAAAAAAGACAAAGACTAAGACTAT
1 CAATTGTCTATTGACTATAAATTTAACTCCAC-AAAAAAG----AGACTAAGACTAT
232499 CAATTGTCTATTGACT
1 CAATTGTCTATTGACT
232515 TCACACTTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
49 11 0.18
50 17 0.28
51 6 0.10
56 27 0.44
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (52 bp):
CAATTGTCTATTGACTATAAATTTAACTCCACAAAAAAGAGACTAAGACTAT
Found at i:234580 original size:20 final size:20
Alignment explanation
Indices: 234506--234580 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 20
234496 TATTATTTAA
234506 TTAAAATTGTTTTA-TTA-T
1 TTAAAATTGTTTTATTTATT
*
234524 TTAAAATTGTTTTATATATCT
1 TTAAAATTGTTTTATTTAT-T
* **
234545 TTTAAA-TGCAACTTATTTATT
1 TTAAAATTG--TTTTATTTATT
234566 TTAAAATTGTTTTAT
1 TTAAAATTGTTTTAT
234581 ATACCTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
18 14 0.33
19 2 0.05
20 6 0.14
21 12 0.28
22 9 0.21
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.57
Consensus pattern (20 bp):
TTAAAATTGTTTTATTTATT
Found at i:236187 original size:89 final size:92
Alignment explanation
Indices: 236045--236256 Score: 265
Period size: 89 Copynumber: 2.3 Consensus size: 92
236035 CCTCAAACTT
* * * *
236045 TTTCAAAAATAGCAACTAAACCCCT-GTTCTTTTTATGCACTCATTTGGGTACTTGAACTTTCAA
1 TTTCAAAAAAAGCAATTAAACCCCTACTT-TTTTTATGCACTCAATTGGGTACTTGAACTTTCAA
236109 AATACATCAAAAAGGAC-CTC-AA-AAAA
65 AATACATCAAAAA-GACTCTCAAATAAAA
*
236135 TTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTT-TGCACTCAATTGGGTACTTGAACTTTCAAA
1 TTTCAAAAAAAGCAATTAAACCCCTACTTTTTTTATGCACTCAATTGGGTACTTGAACTTTCAAA
* *
236199 ATGCATCAAAAAGTCTCTCAAAATAAAA
66 ATACATCAAAAAGACTCTC-AAATAAAA
** *
236227 AAT-AAAAAAAGCAATTAATCCCCTACTTTT
1 TTTCAAAAAAAGCAATTAAACCCCTACTTTT
236257 ATTAAAAATT
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
88 2 0.02
89 43 0.40
90 27 0.25
91 30 0.28
92 5 0.05
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (92 bp):
TTTCAAAAAAAGCAATTAAACCCCTACTTTTTTTATGCACTCAATTGGGTACTTGAACTTTCAAA
ATACATCAAAAAGACTCTCAAATAAAA
Found at i:236663 original size:20 final size:20
Alignment explanation
Indices: 236630--236696 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
236620 AAAGAATTCT
*
236630 AATTTTTAAT-AAATTTTTA
1 AATTTTTATTAAAATTTTTA
*
236649 AATTTTTATTAAAATTTAATA
1 AATTTTTATTAAAATTT-TTA
*
236670 AATTTTT-CTAAAATTTTT-
1 AATTTTTATTAAAATTTTTA
*
236688 TATTTTTAT
1 AATTTTTAT
236697 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.15
19 10 0.26
20 14 0.36
21 9 0.23
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTATTAAAATTTTTA
Found at i:236666 original size:18 final size:19
Alignment explanation
Indices: 236630--236667 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
236620 AAAGAATTCT
*
236630 AATTTTTAATAAATTTTTA
1 AATTTTTAATAAATATTTA
*
236649 AATTTTTATTAAA-ATTTA
1 AATTTTTAATAAATATTTA
236667 A
1 A
236668 TAAATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTTAATAAATATTTA
Found at i:240123 original size:70 final size:71
Alignment explanation
Indices: 239889--240197 Score: 476
Period size: 72 Copynumber: 4.3 Consensus size: 71
239879 GAATTGACAA
* * * * *
239889 TGGAATTTGTCCACTCAATTGGTTACACAACAAGTTTAAACGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTT-CCCA
239954 ATGATCT
65 ATGATCT
* ** * *
239961 TGGAATTTGTCCACTCAACTGGTTCTGCGAGAAGTCTAAATCAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTT-CCCA
240026 ATGATCT
65 ATGATCT
* *
240033 TGGAATTTGTCCACTCAATTGGTTCCCCCACAAGTTTAAATGAGTGAGTTGCAAGAGGTT-CCAA
1 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCAA
240097 TGATCT
66 TGATCT
*
240103 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTTCCAA
1 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCAA
240168 TGATCT
66 TGATCT
240174 TGGAATTTGTCCACTCAATTGGTT
1 TGGAATTTGTCCACTCAATTGGTT
240198 GTCTCCCAAG
Statistics
Matches: 218, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
70 68 0.31
71 34 0.16
72 116 0.53
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (71 bp):
TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCAA
TGATCT
Found at i:240161 original size:142 final size:142
Alignment explanation
Indices: 239889--240197 Score: 503
Period size: 142 Copynumber: 2.2 Consensus size: 142
239879 GAATTGACAA
239889 TGGAATTTGTCCACTCAATTGGTTACACAACAAGTTTAAACGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTACACAACAAGTTTAAACGAGTGAGTTGCAAGAGGTT-CCCA
** *
239954 ATGATCTTGGAATTTGTCCACTCAACTGGTTCTGCGAGAAGTCTAAATCAGTGAGTTGCAAGAGG
65 ATGATCTTGGAATTTGTCCACTCAACTGGTTCCCCGACAAGTCTAAATCAGTGAGTTGCAAGAGG
240019 TTCCCCAATGATCT
130 TT-CCCAATGATCT
* * * *
240033 TGGAATTTGTCCACTCAATTGGTTCCCCCACAAGTTTAAATGAGTGAGTTGCAAGAGGTT-CCAA
1 TGGAATTTGTCCACTCAATTGGTTACACAACAAGTTTAAACGAGTGAGTTGCAAGAGGTTCCCAA
* *
240097 TGATCTTGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGT
66 TGATCTTGGAATTTGTCCACTCAACTGGTTCCCCGACAAGTCTAAATCAGTGAGTTGCAAGAGGT
*
240162 TTCCAATGATCT
131 TCCCAATGATCT
240174 TGGAATTTGTCCACTCAATTGGTT
1 TGGAATTTGTCCACTCAATTGGTT
240198 GTCTCCCAAG
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
141 34 0.22
142 65 0.42
144 56 0.36
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (142 bp):
TGGAATTTGTCCACTCAATTGGTTACACAACAAGTTTAAACGAGTGAGTTGCAAGAGGTTCCCAA
TGATCTTGGAATTTGTCCACTCAACTGGTTCCCCGACAAGTCTAAATCAGTGAGTTGCAAGAGGT
TCCCAATGATCT
Found at i:244634 original size:62 final size:61
Alignment explanation
Indices: 244538--244662 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 61
244528 TACCAAGTAT
* *
244538 CATAATAAAACATATATTGATAATTTAGGTACCACATTAAACATTTTCAAAGCACATGTAC
1 CATAATAAAACACATATTGATAATTCAGGTACCACATTAAACATTTTCAAAGCACATGTAC
* * * * *
244599 CATAATAATAACACATATTGATAGTTCAGGTACCACATTATATATTTTCAAAGTACTTGTAC
1 CATAATAA-AACACATATTGATAATTCAGGTACCACATTAAACATTTTCAAAGCACATGTAC
244661 CA
1 CA
244663 CTAAACATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 8 0.14
62 48 0.86
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.33
Consensus pattern (61 bp):
CATAATAAAACACATATTGATAATTCAGGTACCACATTAAACATTTTCAAAGCACATGTAC
Found at i:246548 original size:16 final size:16
Alignment explanation
Indices: 246527--246561 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
246517 TTAAACATAT
246527 ATTTTTCATTCATAGA
1 ATTTTTCATTCATAGA
246543 ATTTTTCATTCATAGA
1 ATTTTTCATTCATAGA
246559 ATT
1 ATT
246562 GATTACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (16 bp):
ATTTTTCATTCATAGA
Found at i:247661 original size:91 final size:90
Alignment explanation
Indices: 247496--247725 Score: 275
Period size: 91 Copynumber: 2.5 Consensus size: 90
247486 TTTAAGGGTG
* * * * * * * *
247496 CAAAAA-GCCCACAAACGTTTTCAAAAATAGCAACTAAACCCCT-GTTCTTTTTATGCACTCATT
1 CAAAAAGGCCCTCAAAC-TTTTAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTATGCACTCAAT
*
247559 TGAGAACTTGAACTTTCAAAATACAT
65 TGAGAACTTGAACTTTCAAAATACAA
*
247585 CAAAAAGGCCCTCAAACATTTTAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTTGCACTCAAT
1 CAAAAAGGCCCTCAAAC-TTTTAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTATGCACTCAAT
* * *
247650 TGGGTACTTGAACTTTCAAAATGCAA
65 TGAGAACTTGAACTTTCAAAATACAA
* * *
247676 CAAAAAGACCCTCAAACTTTAAAAAAAAAAGAAATTAAGCCCCTACTTTT
1 CAAAAAGGCCCTCAAACTTT-TAAAAAAAAGCAATTAAGCCCCTACTTTT
247726 ATTAAAAATT
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
89 6 0.05
90 34 0.28
91 81 0.67
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (90 bp):
CAAAAAGGCCCTCAAACTTTTAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTATGCACTCAATT
GAGAACTTGAACTTTCAAAATACAA
Done.