Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold978
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: 66592
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3616 original size:13 final size:13
Alignment explanation
Indices: 3598--3625 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3588 ATACAAAGAT
3598 CAATGTATCGATA
1 CAATGTATCGATA
3611 CAATGTATCGATA
1 CAATGTATCGATA
3624 CA
1 CA
3626 TTGAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3622 original size:33 final size:33
Alignment explanation
Indices: 3580--3645 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3570 AAATTCCCAG
3580 ATGTATCGATACAAAGA-TCAATGTATCGATACA
1 ATGTATCGATACAAAGAGT-AATGTATCGATACA
**
3613 ATGTATCGATACATTGAGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
3646 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:4473 original size:42 final size:42
Alignment explanation
Indices: 4427--4767 Score: 293
Period size: 42 Copynumber: 8.0 Consensus size: 42
4417 GATAAAGGAA
* *
4427 AAAAGGAAAACGAAATGCGTCCTGCTCTTTGAGGACAAAAGT
1 AAAAGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAAGG
4469 AAAAGGAAAAT-AAAGTGCGTCCTGCTCTTTGAGGACAAAAGAG
1 AAAAGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGACAAAAG-G
** *
4512 AAAATAAAGGAATGAAATGTGTCCTGCTCTTTGAGGAC-AAAGG
1 AAAAGGAA--AATGAAATGCGTCCTGCTCTTTGAGGACAAAAGG
* * * *
4555 AGAGAGGAAAATAAAATGCGTCATGCTCTTTGAGGACAAAAGAA
1 A-AAAGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAAG-G
* * * *
4599 AATAAGG-GAATGAAGTGTGTCCTACTCTTTGAGGAC-AAAGG
1 AA-AAGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAAGG
* ** *
4640 AGAGAGGAAAAT-AAAGTTTGTCCTGCTCTTTGAGGATAAAAGAG
1 A-AAAGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGACAAAAG-G
* * *
4684 AAAATAAGG-GAATGAAGTGTGTCCTGCTCTTTGAGGACAAAA-G
1 --AA-AAGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAAGG
* *
4727 AGAGAGGAAAAT-AAAGTGCGTTCTGCTCTTTGAGGACAAAA
1 A-AAAGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGACAAAA
4768 AAGTGCCACC
Statistics
Matches: 242, Mismatches: 36, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
41 15 0.06
42 114 0.47
43 41 0.17
44 13 0.05
45 50 0.21
46 9 0.04
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (42 bp):
AAAAGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAAGG
Found at i:4536 original size:87 final size:87
Alignment explanation
Indices: 4438--4767 Score: 504
Period size: 87 Copynumber: 3.8 Consensus size: 87
4428 AAAGGAAAAC
* * *
4438 GAAATGCGTCCTGCTCTTTGAGGACAAAAGTA-AAAGGAAAATAAAGTGCGTCCTGCTCTTTGAG
1 GAAATGTGTCCTGCTCTTTGAGGAC-AAAGGAGAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAG
*
4502 GACAAAAGAGAAAATAAAGGAAT
65 GACAAAAGAGAAAATAAGGGAAT
* *
4525 GAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAGGAAAATAAAATGCGTCATGCTCTTTGAGG
1 GAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGG
4590 AC-AAA-AGAAAATAAGGGAAT
66 ACAAAAGAGAAAATAAGGGAAT
* * **
4610 GAAGTGTGTCCTACTCTTTGAGGACAAAGGAGAGAGGAAAATAAAGTTTGTCCTGCTCTTTGAGG
1 GAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGG
*
4675 ATAAAAGAGAAAATAAGGGAAT
66 ACAAAAGAGAAAATAAGGGAAT
* * *
4697 GAAGTGTGTCCTGCTCTTTGAGGACAAAAGAGAGAGGAAAATAAAGTGCGTTCTGCTCTTTGAGG
1 GAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGG
4762 ACAAAA
66 ACAAAA
4768 AAGTGCCACC
Statistics
Matches: 221, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
85 74 0.33
86 11 0.05
87 136 0.62
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.22
Consensus pattern (87 bp):
GAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGG
ACAAAAGAGAAAATAAGGGAAT
Found at i:4654 original size:172 final size:172
Alignment explanation
Indices: 4445--4767 Score: 524
Period size: 172 Copynumber: 1.9 Consensus size: 172
4435 AACGAAATGC
* *
4445 GTCCTGCTCTTTGAGGACAAAAGTAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
1 GTCCTACTCTTTGAGGACAAAAGGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
*
4510 AGAAAATAAAGGAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAGAGGAAAATAAAATGCG
66 AGAAAATAAAGGAATGAAATGTGTCCTGCTCTTTGAGGACAAAAGAGAGAGGAAAATAAAATGCG
4575 -TCATGCTCTTTGAGGACAAAAGAAAATAAGGGAATGAAGTGT
131 TTC-TGCTCTTTGAGGACAAAAGAAAATAAGGGAATGAAGTGT
* ** *
4617 GTCCTACTCTTTGAGGAC-AAAGGAGAGAGGAAAATAAAGTTTGTCCTGCTCTTTGAGGATAAAA
1 GTCCTACTCTTTGAGGACAAAAGGA-AAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAA
* * *
4681 GAGAAAATAAGGGAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGAGAGAGGAAAATAAAGTGC
65 GAGAAAATAAAGGAATGAAATGTGTCCTGCTCTTTGAGGACAAAAGAGAGAGGAAAATAAAATGC
4746 GTTCTGCTCTTTGAGGACAAAA
130 GTTCTGCTCTTTGAGGACAAAA
4768 AAGTGCCACC
Statistics
Matches: 139, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
171 5 0.04
172 132 0.95
173 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (172 bp):
GTCCTACTCTTTGAGGACAAAAGGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
AGAAAATAAAGGAATGAAATGTGTCCTGCTCTTTGAGGACAAAAGAGAGAGGAAAATAAAATGCG
TTCTGCTCTTTGAGGACAAAAGAAAATAAGGGAATGAAGTGT
Found at i:4897 original size:122 final size:124
Alignment explanation
Indices: 4749--4978 Score: 331
Period size: 122 Copynumber: 1.9 Consensus size: 124
4739 AAAGTGCGTT
*
4749 CTGCTCTTTGAGGACAAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAG-AAAGGCGTCCTG
1 CTGCTCTTTGAGGACAAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAGAAAAGGCGTCATG
* **
4813 CTCTTTGAAGACT-GGAAGGTGCCACCAAATTGTGTGGGCTTTGCAAAGAAAAAACATC
66 CTCTTTGAAGACTAGAAAAATGCCACCAAATTGTGTGGGCTTTGCAAAGAAAAAACATC
* ** *
4871 CTGCTCTTTGAGGATAGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCGTCAT
1 CTGCTCTTTGAGGACA-AAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAGAAAAGGCGTCAT
* * *
4935 GCTTTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT
65 GCTCTTTGAAGACTAGAAAAATGCCACCAAATTGTGTGGGCTTT
4979 AAAAGGTTTC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
122 42 0.45
123 27 0.29
124 25 0.27
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (124 bp):
CTGCTCTTTGAGGACAAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAGAAAAGGCGTCATG
CTCTTTGAAGACTAGAAAAATGCCACCAAATTGTGTGGGCTTTGCAAAGAAAAAACATC
Found at i:4962 original size:63 final size:63
Alignment explanation
Indices: 4739--4984 Score: 290
Period size: 61 Copynumber: 4.0 Consensus size: 63
4729 AGAGGAAAAT
* ** *
4739 AAAGTGCGTTCTGCTCTTTGAGGAC-A-AAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAAG-
1 AAAG-GCGTCCTGCTCTTTGAGGACTAGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGA
* * ** * *
4801 AAAGGCGTCCTGCTCTTTGAAGACT-GGAAGGTGCCACCAAATTGTGTGGGCTTTGCAAA-GA
1 AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGA
** *
4862 AAAAACATCCTGCTCTTTGAGGA-TAGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGA
* *
4924 AAAGGCGTCATGCTTTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGG
4985 TTTCCTGCTC
Statistics
Matches: 155, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
60 2 0.01
61 90 0.58
62 32 0.21
63 31 0.20
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (63 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGA
Found at i:5151 original size:151 final size:151
Alignment explanation
Indices: 4869--5155 Score: 398
Period size: 151 Copynumber: 1.9 Consensus size: 151
4859 AGAAAAAACA
*
4869 TCCTGCTCTTTGAGGATAGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCGTCA
1 TCCTGCTCTTTGAGGATAGAAAAATGCCACCAACTTGTGTGGGCTTT----A--AAAAGGCATCA
* * **
4934 TGCTTTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTTTCCTGCTCCTTG
60 TGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCCTTG
4999 AGGACTAAAGGGCGAAAGGAGAGAGTG
125 AGGACTAAAGGGCGAAAGGAGAGAGTG
** *
5026 TCCTGCTCTTTGAGGACT-GGGAAATGCCACCAACTTGTGTGGGCTTT-AAAAGGCATCTTGCTC
1 TCCTGCTCTTTGAGGA-TAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGGCATCATGCTC
* *
5089 TTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA
65 TTTGAGGACT-AAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCCTTGAGGA
5154 CT
129 CT
5156 GGAAAATGCC
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
150 23 0.19
151 51 0.43
157 43 0.36
158 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (151 bp):
TCCTGCTCTTTGAGGATAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGGCATCATGCTCT
TTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCCTTGAGGACT
AAAGGGCGAAAGGAGAGAGTG
Found at i:5190 original size:55 final size:55
Alignment explanation
Indices: 5025--5388 Score: 478
Period size: 57 Copynumber: 6.4 Consensus size: 55
5015 AGGAGAGAGT
* *
5025 GTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
* * * *
5080 ATCTTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACT--AGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
5137 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
5192 GTCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACT--AGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
5249 GTCCTGCACTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGGCTTTGAAAGGAAACGGC
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT---A--AAA-GGC
* * * *
5310 ATCCTGTTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAC
1 GTCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
5366 ATCCTGCTCTTTGAGGACT-GAAA
1 GTCCTGCTCTTTGAGGACTAGAAA
5389 GGTGAGAGGA
Statistics
Matches: 273, Mismatches: 25, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
55 100 0.37
56 20 0.07
57 103 0.38
60 3 0.01
61 25 0.09
62 22 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (55 bp):
GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
Found at i:5222 original size:112 final size:112
Alignment explanation
Indices: 5025--5385 Score: 562
Period size: 112 Copynumber: 3.2 Consensus size: 112
5015 AGGAGAGAGT
* *
5025 GTCCTGCTCTTTGAGGACTGGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTGCTCT
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
5090 TTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
66 TTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
*
5137 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCT
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
5202 TTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
66 TTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
* * *
5249 GTCCTGCACTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGGCTTTGAAAGGAAACGGCATCC
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---A--AAA-GGCATCC
* * * *
5314 TGTTCTTTGAGGACT-AGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAC
60 TGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
*
5366 ATCCTGCTCTTTGAGGACTG
1 GTCCTGCTCTTTGAGGACTG
5386 AAAGGTGAGA
Statistics
Matches: 229, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
112 154 0.67
115 1 0.00
117 54 0.24
118 20 0.09
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (112 bp):
GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
TTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
Found at i:6393 original size:10 final size:10
Alignment explanation
Indices: 6380--6409 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6370 CTCTTTTTTC
6380 TTTTTTGTTT
1 TTTTTTGTTT
6390 TTTTTTGTTT
1 TTTTTTGTTT
6400 TTTTTT-TTT
1 TTTTTTGTTT
6409 T
1 T
6410 GCCTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:6393 original size:17 final size:16
Alignment explanation
Indices: 6359--6424 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
6349 AAGCAAGTTC
* * *
6359 TTTTCTTTTCTCTCTT
1 TTTTCTTTTTTTTTTT
6375 TTTTCTTTTTTGTTTTT
1 TTTTCTTTTTT-TTTTT
*
6392 TTTTGTTTTTTTTTTT
1 TTTTCTTTTTTTTTTT
**
6408 TTGCCTTTTCTTTTTTT
1 TTTTCTTTT-TTTTTTT
6425 AAAAAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
16 21 0.51
17 20 0.49
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTT
Found at i:18827 original size:76 final size:76
Alignment explanation
Indices: 18590--18913 Score: 348
Period size: 79 Copynumber: 4.2 Consensus size: 76
18580 ATAACGGGGC
* * * *
18590 TGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGATTTAGA
1 TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA---TGAAAAATTGATGTTTTAGA
*
18655 AATAAAATCAGGAT
63 AATAAAACCAGGAT
* * * *
18669 TAGAGAATCCCCTCGGAAATAAGGGGGTTGGAGTATCCCCGACTATGAAAAATTGATGTTTTAGA
1 TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTTTTAGA
* *
18734 AATAAAACCGGGGT
63 AATAAAACCAGGAT
* *
18748 TGGAGTACCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAT
1 TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAT
18813 AAAACCAGGAT
66 AAAACCAGGAT
* * * * * *
18824 TGGAATGTCCCCT-AAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTT-GA
1 TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA-TG-AAAAATTGA-TGTTTTAG-
*
18887 AAATAAAATC-GGAGT
62 AAATAAAACCAGGA-T
18902 TGGAGTATCCCC
1 TGGAGTATCCCC
18914 GATTATGGAA
Statistics
Matches: 208, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
75 26 0.12
76 45 0.22
77 10 0.05
78 26 0.12
79 100 0.48
82 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (76 bp):
TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAAT
AAAACCAGGAT
Found at i:18891 original size:154 final size:156
Alignment explanation
Indices: 18584--18913 Score: 411
Period size: 154 Copynumber: 2.1 Consensus size: 156
18574 GAGATAATAA
* * *
18584 CGGGGCTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA-T-TGAAAAATCGATGA
* ** *
18649 TTTAGAAATAAAATCAGGATTAGAGAATCCCCTCGGAAATAAGGGGGTTGGAGTATCCCCGACTA
64 TTTAGAAATAAAACCAGGATTAGAGAATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGACTA
*
18714 TGAAAAATTGATGTTTTAGAAATAAAAC
129 TGAAAAATAGATGTTTTAGAAATAAAAC
* * * *
18742 CGGGGTTGGAGTACCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGA-TGAAAAATTGATGTTT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGAAAAATCGATGATT
* *
18806 TAGAAATAAAACCAGGATT-G-GAATGTCCCCT-AAAAATAACGGGGTTGGAGTATCCCCGATTG
66 TAGAAATAAAACCAGGATTAGAGAA--TCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGACTA
* *
18868 TGAAAAGTCAG-TGTTTT-GAAAATAAAAT
129 TGAAAAAT-AGATGTTTTAG-AAATAAAAC
*
18896 CGGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
18914 GATTATGGAA
Statistics
Matches: 150, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
153 4 0.03
154 64 0.43
155 39 0.26
158 43 0.29
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (156 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGAAAAATCGATGATT
TAGAAATAAAACCAGGATTAGAGAATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGACTATG
AAAAATAGATGTTTTAGAAATAAAAC
Found at i:18911 original size:51 final size:50
Alignment explanation
Indices: 18849--19015 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 50
18839 AAATAACGGG
*
18849 GTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-TCAGTGTTTTGAAAATAAAATCGGA
**
18900 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTT-AGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATCAGTGTTTTGA-AAATAAAATCGGA
* * * * * *
18951 GTTGGAGTATCCCCGATTAAGAAAAATTAATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATCAGTGTTTTGAAAATAAAATCGGA
19001 GATTGGAGTATCCCC
1 G-TTGGAGTATCCCC
19016 AAGATGAAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
50 3 0.03
51 93 0.92
52 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATCAGTGTTTTGAAAATAAAATCGGA
Found at i:21369 original size:13 final size:13
Alignment explanation
Indices: 21351--21375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21341 TACAATGAGC
21351 AATGTATCGATAT
1 AATGTATCGATAT
21364 AATGTATCGATA
1 AATGTATCGATA
21376 CAAATTGTGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:26381 original size:191 final size:189
Alignment explanation
Indices: 26084--26430 Score: 523
Period size: 191 Copynumber: 1.8 Consensus size: 189
26074 CGAGATTCCG
* * * * *
26084 TTGTAGCAGATTGTGATCGTGATTATGATCAGAGACAAAAAAAGATATTTGCTGCAAGTAGAGCT
1 TTGTAGCAGATTGTGATCATAATCATGATCAGAGACAAAAAAAGATATTTGCTACAAGTAGAGCC
* * *
26149 ATATGATGATTTTTAAATTGATCCAATGGTGTAGATCTTGGGTTAATATTACGAGCTAATGATCT
66 ATATGATGATTCTCAAATTGATCCAATAGTGTAGATCTTGGGTTAATATTACGAGCTAATGATCT
* *
26214 TTTGAGGTGGAGATTGTTAGGTATCTGAAGCGGCTTATTTAGTTTCGACAGTAATTTTA
131 CTAGAGGTGGAGATTGTTAGGTATCTGAAGCGGCTTATTTAGTTTCGACAGTAATTTTA
* * * *
26273 TTGTTGCAGATTGTGATCATAATCATGATCGGAGACATACAAGAAGATATTTGCTACAAGTGGAG
1 TTGTAGCAGATTGTGATCATAATCATGATCAGAGACA-A-AAAAAGATATTTGCTACAAGTAGAG
* * *
26338 CCATATGATGATTCTCAAATTGATCTAGTAGTGTAGATCTTGGGTTAATGTTACGAGCTAATGAT
64 CCATATGATGATTCTCAAATTGATCCAATAGTGTAGATCTTGGGTTAATATTACGAGCTAATGAT
26403 CTCTAGAGGTGGAGATTGTTAGGTATCT
129 CTCTAGAGGTGGAGATTGTTAGGTATCT
26431 AAAGTGACAT
Statistics
Matches: 139, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
189 32 0.23
190 1 0.01
191 106 0.76
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (189 bp):
TTGTAGCAGATTGTGATCATAATCATGATCAGAGACAAAAAAAGATATTTGCTACAAGTAGAGCC
ATATGATGATTCTCAAATTGATCCAATAGTGTAGATCTTGGGTTAATATTACGAGCTAATGATCT
CTAGAGGTGGAGATTGTTAGGTATCTGAAGCGGCTTATTTAGTTTCGACAGTAATTTTA
Found at i:27844 original size:92 final size:90
Alignment explanation
Indices: 27722--27903 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 90
27712 TCCCCTGTAA
27722 CCTGGCAAGAACAACTCTGTGACGCTTTTGACTATTTTGTTGTCCATAGTTATTATCAAAAGGCA
1 CCTGGCAAGAACAACTCTGTGACGCTTTTGACTATTTTGTTGTCCATAGTTATTATCAAAAGGCA
* *
27787 TAATAATGCTCTGATTCCTTGAAGT
66 CAAAAATGCTCTGATTCCTTGAAGT
* * *
27812 CCTGGCACTAGAACAACTCTTTGACTCTTTTGACTATTTTGTTGTCCATATTTATTATCAAAAGG
1 CCTGGCA--AGAACAACTCTGTGACGCTTTTGACTATTTTGTTGTCCATAGTTATTATCAAAAGG
*
27877 CACAAAAATGTTCTGATTCCTTGAAGT
64 CACAAAAATGCTCTGATTCCTTGAAGT
27904 ATCAAAAAGG
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
90 7 0.08
92 77 0.92
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (90 bp):
CCTGGCAAGAACAACTCTGTGACGCTTTTGACTATTTTGTTGTCCATAGTTATTATCAAAAGGCA
CAAAAATGCTCTGATTCCTTGAAGT
Found at i:30420 original size:139 final size:139
Alignment explanation
Indices: 30183--30461 Score: 558
Period size: 139 Copynumber: 2.0 Consensus size: 139
30173 AACATTCTTA
30183 TCATCTTCCTGTTATTTTAAGTTAATATACTAATTACCTTAAATTATACTACTTTTCACAATTTG
1 TCATCTTCCTGTTATTTTAAGTTAATATACTAATTACCTTAAATTATACTACTTTTCACAATTTG
30248 ATACCTAAAGAAAAAATTTTTCAATTAAATACTTAAATTTTACTTCCTTCACACATATTAATTTA
66 ATACCTAAAGAAAAAATTTTTCAATTAAATACTTAAATTTTACTTCCTTCACACATATTAATTTA
30313 AAACTTAAC
131 AAACTTAAC
30322 TCATCTTCCTGTTATTTTAAGTTAATATACTAATTACCTTAAATTATACTACTTTTCACAATTTG
1 TCATCTTCCTGTTATTTTAAGTTAATATACTAATTACCTTAAATTATACTACTTTTCACAATTTG
30387 ATACCTAAAGAAAAAATTTTTCAATTAAATACTTAAATTTTACTTCCTTCACACATATTAATTTA
66 ATACCTAAAGAAAAAATTTTTCAATTAAATACTTAAATTTTACTTCCTTCACACATATTAATTTA
30452 AAACTTAAC
131 AAACTTAAC
30461 T
1 T
30462 GTACTGATAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (139 bp):
TCATCTTCCTGTTATTTTAAGTTAATATACTAATTACCTTAAATTATACTACTTTTCACAATTTG
ATACCTAAAGAAAAAATTTTTCAATTAAATACTTAAATTTTACTTCCTTCACACATATTAATTTA
AAACTTAAC
Found at i:33881 original size:2 final size:2
Alignment explanation
Indices: 33870--33905 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
33860 TTTTTACCTC
*
33870 AT AT AC AT AT 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 AT AT AT AT AT
33906 TTTCTATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34134 original size:16 final size:17
Alignment explanation
Indices: 34113--34145 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
34103 TTTTTTATAT
34113 TTTTATTA-AAATTAAA
1 TTTTATTATAAATTAAA
34129 TTTTATTATAAATTAAA
1 TTTTATTATAAATTAAA
34146 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTATTATAAATTAAA
Found at i:34359 original size:53 final size:53
Alignment explanation
Indices: 34302--34681 Score: 203
Period size: 53 Copynumber: 7.1 Consensus size: 53
34292 ATTGATAGAA
* * *
34302 AAAAAAATTATTTTATTCTTTTTATTTTTTTCTTTCCAAACAATCGTACCAAT
1 AAAAAAATTATTTTATTCTCTTCATTTTTTTCTTTCCAAACAATCATACCAAT
* * * * * *
34355 AAAAAATATTTTTTTA-TCTCTTTATTTTTTTCTTTTCGATCAATCATATCAAT
1 AAAAAA-ATTATTTTATTCTCTTCATTTTTTTCTTTCCAAACAATCATACCAAT
* * * * *
34408 ---AAATTTATTTTTATT-TTTTCACTTTTTCTTTTTTCCAACCAATTATACCAAT
1 AAAAAAATTA-TTTTATTCTCTTCA-TTTTT-TTCTTTCCAAACAATCATACCAAT
* * * * *
34460 AAAAAAA-TATTTTTTTCTCTTCATTTTTTTCTTTTCGACCAATCATATCAAT
1 AAAAAAATTATTTTATTCTCTTCATTTTTTTCTTTCCAAACAATCATACCAAT
* * * * **
34512 ---AAATTTTTTTTATT-TTTTCACTTTTTTTTCTTTTCAATTAATCATACCAAT
1 AAAAAAATTATTTTATTCTCTTCA--TTTTTTTCTTTCCAAACAATCATACCAAT
* * * * * **
34563 AAAAAATATT-TTTTTTATCTTTTCAATTTTTTTTTCTTAT-CGACCAATTATATTAAT
1 AAAAAA-ATTATTTTAT-TCTCTTC-A--TTTTTTTCTT-TCCAAACAATCATACCAAT
* * *
34620 -AAAAAATTATTTT-TATCTTTTCACTTTTTCTTCTTTTCAACCAATCATACCAAT
1 AAAAAAATTATTTTAT-TCTCTTCA-TTTTT-TTCTTTCCAAACAATCATACCAAT
34674 AATAAAAA
1 AA-AAAAA
34682 AAAAAATTAT
Statistics
Matches: 255, Mismatches: 47, Indels: 47
0.73 0.13 0.13
Matches are distributed among these distances:
49 10 0.04
50 19 0.07
51 31 0.12
52 37 0.15
53 54 0.21
54 42 0.16
55 19 0.07
56 19 0.07
57 23 0.09
58 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.01, T:0.53
Consensus pattern (53 bp):
AAAAAAATTATTTTATTCTCTTCATTTTTTTCTTTCCAAACAATCATACCAAT
Found at i:34473 original size:104 final size:104
Alignment explanation
Indices: 34304--34815 Score: 527
Period size: 104 Copynumber: 4.8 Consensus size: 104
34294 TGATAGAAAA
* * * * * *
34304 AAAAATTATTTTATTCTTTTTA-TTTTT-TTCTTTCCAAACAATCGTACCAATAAAAAATATTTT
1 AAAAATTTTTTTATT-TTTTCACTTTTTCTT-TTTTCAACCAATCATACCAATAAAAAA-ATATT
*
34367 TTTATCTCTTT-A-TTTTTTTCTTTTCGATCAATCATATCAAT
63 TTTATCT-TTTCACTTTTTTTCTTTTCGACCAATCATATCAAT
* *
34408 -AAATTTATTTTTATTTTTTCACTTTTTCTTTTTTCCAACCAATTATACCAATAAAAAAATATTT
1 AAAAATT-TTTTTATTTTTTCACTTTTTCTTTTTT-CAACCAATCATACCAATAAAAAAATATTT
* *
34472 TTTTCTCTTCA-TTTTTTTCTTTTCGACCAATCATATCAAT
64 TTATCTTTTCACTTTTTTTCTTTTCGACCAATCATATCAAT
* * ** *
34512 -AAATTTTTTTTATTTTTTCACTTTTTTTTCTTTTCAATTAATCATACCAATAAAAAATATTTTT
1 AAAAATTTTTTTATTTTTTCACTTTTTCTT-TTTTCAACCAATCATACCAATAAAAAA-A-TATT
* * * *
34576 TTTATCTTTTCAATTTTTTTTTCTTATCGACCAATTATATTAAT
63 TTTATCTTTTC-A-CTTTTTTTCTTTTCGACCAATCATATCAAT
* *
34620 AAAAAATTATTTTTATCTTTTCACTTTTTCTTCTTTTCAACCAATCATACCAATAATAAAAAAAA
1 -AAAAATT-TTTTTATTTTTTCACTTTTTCTT-TTTTCAACCAATCATACCAAT-A-AAAAAATA
*** * *
34685 AAATTATCTTTTCACTTTTTTTCTTTTTGACCGATCATATCAAT
61 TTTTTATCTTTTCACTTTTTTTCTTTTCGACCAATCATATCAAT
* * * *
34729 GAAAATTTTTTTATCTTTT-ACTTTTTCTTATTTTCAGCTAATCATACCAATAAAAAAATATTTT
1 AAAAATTTTTTTATTTTTTCACTTTTTCTT-TTTTCAACCAATCATACCAATAAAAAAATA-TTT
34793 TTATCTTTTCACTTTTTTTCTTT
64 TTATCTTTTCACTTTTTTTCTTT
34816 AATTTTCTTT
Statistics
Matches: 346, Mismatches: 45, Indels: 33
0.82 0.11 0.08
Matches are distributed among these distances:
103 54 0.16
104 72 0.21
105 58 0.17
106 30 0.09
107 12 0.03
108 32 0.09
109 24 0.07
110 6 0.02
111 51 0.15
112 2 0.01
113 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.53
Consensus pattern (104 bp):
AAAAATTTTTTTATTTTTTCACTTTTTCTTTTTTCAACCAATCATACCAATAAAAAAATATTTTT
ATCTTTTCACTTTTTTTCTTTTCGACCAATCATATCAAT
Found at i:34489 original size:55 final size:55
Alignment explanation
Indices: 34300--34815 Score: 341
Period size: 54 Copynumber: 9.6 Consensus size: 55
34290 AAATTGATAG
* * * * *
34300 AAAAAAAAATTATTTTATTCTTTTTATTTTTTTC--TTTCCAAACAATCGTACCAAT
1 AAAAAAATATT-TTTTA-TCTTTTCATTTTTTTCTTTTTTCAACCAATCATACCAAT
* * *
34355 -AAAAAATATTTTTTTATCTCTTT-ATTTTTTTC--TTTTCGATCAATCATATCAAT
1 AAAAAAATA-TTTTTTATCT-TTTCATTTTTTTCTTTTTTCAACCAATCATACCAAT
** * * *
34408 --AAATTTA-TTTTTATTTTTTCA-CTTTTTCTTTTTTCCAACCAATTATACCAAT
1 AAAAAAATATTTTTTATCTTTTCATTTTTTTCTTTTTT-CAACCAATCATACCAAT
* * *
34460 AAAAAAATATTTTTT-TCTCTTCATTTTTTTC--TTTTCGACCAATCATATCAAT
1 AAAAAAATATTTTTTATCTTTTCATTTTTTTCTTTTTTCAACCAATCATACCAAT
* * * **
34512 ----AAATTTTTTTTATTTTTTCACTTTTTTT-TCTTTTCAATTAATCATACCAAT
1 AAAAAAATATTTTTTATCTTTTCA-TTTTTTTCTTTTTTCAACCAATCATACCAAT
* * * * **
34563 AAAAAATATTTTTTTTATCTTTTCAATTTTTTT-TTCTTATCGACCAATTATATTAAT
1 AAAAAA-ATATTTTTTATCTTTTC-ATTTTTTTCTT-TTTTCAACCAATCATACCAAT
* *
34620 AAAAAATTA-TTTTTATCTTTTCA-CTTTTTCTTCTTTTCAACCAATCATACCAAT
1 AAAAAAATATTTTTTATCTTTTCATTTTTTTCTT-TTTTCAACCAATCATACCAAT
* **** * * *
34674 AATAAAAAAAAAAATTATCTTTTCACTTTTTTTC-TTTTT-GACCGATCATATCAAT
1 AA-AAAAATATTTTTTATCTTTTCA-TTTTTTTCTTTTTTCAACCAATCATACCAAT
* * * *
34729 --GAAAAT-TTTTTTATCTTTT-A-CTTTTTCTTATTTTCAGCTAATCATACCAAT
1 AAAAAAATATTTTTTATCTTTTCATTTTTTTCTT-TTTTCAACCAATCATACCAAT
34780 AAAAAAATATTTTTTATCTTTTCACTTTTTTTCTTT
1 AAAAAAATATTTTTTATCTTTTCA-TTTTTTTCTTT
34816 AATTTTCTTT
Statistics
Matches: 357, Mismatches: 69, Indels: 69
0.72 0.14 0.14
Matches are distributed among these distances:
48 16 0.04
49 16 0.04
50 21 0.06
51 41 0.11
52 36 0.10
53 42 0.12
54 61 0.17
55 47 0.13
56 41 0.11
57 30 0.08
58 6 0.02
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.53
Consensus pattern (55 bp):
AAAAAAATATTTTTTATCTTTTCATTTTTTTCTTTTTTCAACCAATCATACCAAT
Found at i:34754 original size:217 final size:211
Alignment explanation
Indices: 34305--34811 Score: 600
Period size: 217 Copynumber: 2.4 Consensus size: 211
34295 GATAGAAAAA
* * * *
34305 AAAATTATTTTATTCTTTT--TATTTTTTTCTTTCCAAACAATCGTACCAATAAAAAATA-TTTT
1 AAAATTTTTTTA-TCTTTTACT-TTTTTTTCTTTTCAAATAATCATACCAATAAAAAATATTTTT
* * * *
34367 TTTATCTCTTT--A--TTTTTTTCTTTTCGATCAATCATATCAATAAATTTATTTTTATTTTTTC
64 TTTATCT-TTTCAATTTTTTTTTCTTATCGACCAATCATATCAATAAAATTATTTTTATCTTTTC
* * *** *
34428 ACTTTTTCTTTTTTCCAACCAATTATACCAATAAAAAAATATTTTTTTCTCTTCATTTTTTTCTT
128 ACTTTTTCTTTTTTCCAACCAATCATACCAATAAAAAAAAAAAATTATCTCTTCATTTTTTTCTT
34493 TTCGACCAATCATATCAAT
193 TTCGACCAATCATATCAAT
* * *
34512 AAATTTTTTTTATTTTTTCACTTTTTTTTCTTTTCAATTAATCATACCAATAAAAAATATTTTTT
1 AAAATTTTTTTATCTTTT-ACTTTTTTTTCTTTTCAAATAATCATACCAATAAAAAATATTTTTT
* *
34577 TTATCTTTTCAATTTTTTTTTCTTATCGACCAATTATATTAATAAAAAATTATTTTTATCTTTTC
65 TTATCTTTTCAATTTTTTTTTCTTATCGACCAATCATATCAAT--AAAATTATTTTTATCTTTTC
*
34642 ACTTTTTCTTCTTTT-CAACCAATCATACCAATAATAAAAAAAAAAATTATCTTTTCACTTTTTT
128 ACTTTTTCTT-TTTTCCAACCAATCATACCAAT-A-AAAAAAAAAAATTATCTCTTCA-TTTTTT
* *
34706 TCTTTTTGACCGATCATATCAAT
189 TCTTTTCGACCAATCATATCAAT
* * ** *
34729 GAAAATTTTTTTATCTTTTACTTTTTCTTATTTTCAGCTAATCATACCAATAAAAAA-ATATTTT
1 -AAAATTTTTTTATCTTTTACTTTTTTTTCTTTTCAAATAATCATACCAATAAAAAATATTTTTT
*
34793 TTATCTTTTCACTTTTTTT
65 TTATCTTTTCAATTTTTTT
34812 CTTTAATTTT
Statistics
Matches: 255, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
206 5 0.02
207 10 0.04
208 36 0.14
209 12 0.05
210 1 0.00
212 25 0.10
214 44 0.17
215 5 0.02
216 40 0.16
217 61 0.24
218 16 0.06
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.53
Consensus pattern (211 bp):
AAAATTTTTTTATCTTTTACTTTTTTTTCTTTTCAAATAATCATACCAATAAAAAATATTTTTTT
TATCTTTTCAATTTTTTTTTCTTATCGACCAATCATATCAATAAAATTATTTTTATCTTTTCACT
TTTTCTTTTTTCCAACCAATCATACCAATAAAAAAAAAAAATTATCTCTTCATTTTTTTCTTTTC
GACCAATCATATCAAT
Found at i:34832 original size:11 final size:11
Alignment explanation
Indices: 34805--34842 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
34795 ATCTTTTCAC
34805 TTTTTTTC-TT
1 TTTTTTTCTTT
**
34815 TAATTTTCTTT
1 TTTTTTTCTTT
34826 TTTTTTTCTTT
1 TTTTTTTCTTT
34837 TTTTTT
1 TTTTTT
34843 CATTTTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:34842 original size:21 final size:21
Alignment explanation
Indices: 34805--34848 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
34795 ATCTTTTCAC
*
34805 TTTTTTTCTTTAATTTTCTTT
1 TTTTTTTCTTTAATTTTCATT
**
34826 TTTTTTTCTTTTTTTTTCATT
1 TTTTTTTCTTTAATTTTCATT
34847 TT
1 TT
34849 ATCAAGTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTCTTTAATTTTCATT
Found at i:34848 original size:11 final size:10
Alignment explanation
Indices: 34805--34848 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
34795 ATCTTTTCAC
34805 TTTTTTTCTT
1 TTTTTTTCTT
**
34815 TAATTTTCTTT
1 TTTTTTTC-TT
34826 TTTTTTTCTT
1 TTTTTTTCTT
*
34836 TTTTTTTCAT
1 TTTTTTTCTT
34846 TTT
1 TTT
34849 ATCAAGTAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:36018 original size:15 final size:15
Alignment explanation
Indices: 35979--36019 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
35969 AATGTTATTG
*
35979 TTGAAAGAAATTTGCA
1 TTGAAA-AAATTTGAA
35995 TTAGAAAAAATTTGAA
1 TT-GAAAAAATTTGAA
36011 TTGAAAAAA
1 TTGAAAAAA
36020 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (15 bp):
TTGAAAAAATTTGAA
Found at i:37133 original size:2 final size:2
Alignment explanation
Indices: 37126--37157 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37116 TAAAACTAAC
37126 AT AT AT 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 AT AT AT
37158 TTAATACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37320 original size:2 final size:2
Alignment explanation
Indices: 37313--37348 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
37303 ATATAAACTC
37313 AT AT AT AT AT 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 AT AT AT AT AT
37349 TCATGTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37645 original size:2 final size:2
Alignment explanation
Indices: 37640--37674 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37630 CGTGTGTGTG
37640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37675 TCATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38436 original size:2 final size:2
Alignment explanation
Indices: 38431--38481 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
38421 GTTTTTAGAT
38431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38473 TA TA TA TA T
1 TA TA TA TA T
38482 GATCATGTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38790 original size:25 final size:24
Alignment explanation
Indices: 38760--38809 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
38750 AGTATTATTT
38760 AATATAAATTTAAATATAATATAAA
1 AATATAAATTTAAATAT-ATATAAA
**
38785 AATATAAATTTTTATATATATAAA
1 AATATAAATTTAAATATATATAAA
38809 A
1 A
38810 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATAAATTTAAATATATATAAA
Found at i:42408 original size:2 final size:2
Alignment explanation
Indices: 42401--42435 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42391 AAAGTTTCTC
42401 AT AT AT 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 AT AT AT A
42436 ACAAAACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43139 original size:13 final size:13
Alignment explanation
Indices: 43121--43145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43111 GAGAAATGTA
43121 AGCCAAATATTAT
1 AGCCAAATATTAT
43134 AGCCAAATATTA
1 AGCCAAATATTA
43146 CAATTTACAA
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
AGCCAAATATTAT
Found at i:47634 original size:16 final size:17
Alignment explanation
Indices: 47615--47656 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
47605 TAACTTTAAT
47615 TAAAAATAAATAA-AGA
1 TAAAAATAAATAAGAGA
*
47631 TAAAAATTAATTAAGAGA
1 TAAAAA-TAAATAAGAGA
47649 TAGAAAAT
1 TA-AAAAT
47657 CAAACAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 6 0.27
18 6 0.27
19 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (17 bp):
TAAAAATAAATAAGAGA
Found at i:49062 original size:2 final size:2
Alignment explanation
Indices: 49057--49081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49047 AAAATTTAGG
49057 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49082 GAATAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49593 original size:25 final size:25
Alignment explanation
Indices: 49558--49608 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
49548 AAATAAATAA
* *
49558 TAAATTAAAAAAGATATGTATTTTTT
1 TAAATTAAAAAAG-TAAGAATTTTTT
49584 TAAA-TAAAAAAGTAAGAATTTTTT
1 TAAATTAAAAAAGTAAGAATTTTTT
49608 T
1 T
49609 TTCTTATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.48
25 8 0.35
26 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (25 bp):
TAAATTAAAAAAGTAAGAATTTTTT
Found at i:49761 original size:11 final size:11
Alignment explanation
Indices: 49728--49766 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
49718 GTTATTATTT
49728 ATTTTAAAAAA
1 ATTTTAAAAAA
*
49739 ATTATAATAAAAA
1 ATT-TTA-AAAAA
49752 ATTTTAAAAAA
1 ATTTTAAAAAA
49763 ATTT
1 ATTT
49767 GTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 12 0.50
12 4 0.17
13 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:49840 original size:18 final size:17
Alignment explanation
Indices: 49817--49850 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
49807 CTTTTATGTA
49817 AATTAATTAAAATTAATT
1 AATTAATT-AAATTAATT
49835 AATTAATTAAATTAAT
1 AATTAATTAAATTAAT
49851 ATTATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAATTAAATTAATT
Found at i:50123 original size:4 final size:4
Alignment explanation
Indices: 50114--50143 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
50104 TATACCATTT
50114 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
50144 TTAATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:50745 original size:13 final size:13
Alignment explanation
Indices: 50727--50751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50717 TATATATTTT
50727 ATTTTTAAAATAC
1 ATTTTTAAAATAC
50740 ATTTTTAAAATA
1 ATTTTTAAAATA
50752 TATGTTATCT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTTAAAATAC
Found at i:51220 original size:2 final size:2
Alignment explanation
Indices: 51203--51239 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
51193 CATTCCTATG
51203 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51240 GTGGTACAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:53729 original size:24 final size:25
Alignment explanation
Indices: 53702--53753 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
53692 AATAAAACTC
* *
53702 AAAAAAATTA-CAATCTAAAAATTT
1 AAAAAAATTATAAATATAAAAATTT
*
53726 AAAAAAATTATAAATATTAAAATTT
1 AAAAAAATTATAAATATAAAAATTT
53751 AAA
1 AAA
53754 TTTATCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAAATTATAAATATAAAAATTT
Found at i:54198 original size:18 final size:18
Alignment explanation
Indices: 54164--54197 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54154 TATATCCAAG
*
54164 TTAAAGTATATTTTTTTA
1 TTAAAGCATATTTTTTTA
54182 TTAAAGCAT-TTTTTTT
1 TTAAAGCATATTTTTTT
54198 TCAAATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (18 bp):
TTAAAGCATATTTTTTTA
Found at i:54349 original size:27 final size:25
Alignment explanation
Indices: 54319--54372 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
54309 TTTGCATGTA
54319 AAAAACAAAATTTAATTTTTAAAAATT
1 AAAAACAAAATTTAA--TTTAAAAATT
***
54346 AAAAATTTAATTTAATTTAAAAATT
1 AAAAACAAAATTTAATTTAAAAATT
54371 AA
1 AA
54373 TCTTTCGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
27 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAACAAAATTTAATTTAAAAATT
Found at i:54350 original size:22 final size:24
Alignment explanation
Indices: 54325--54372 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
54315 TGTAAAAAAC
54325 AAAATTTAA-TT-TTTAAAAATTA
1 AAAATTTAATTTATTTAAAAATTA
54347 AAAATTTAATTTAATTTAAAAATTA
1 AAAATTTAATTT-ATTTAAAAATTA
54372 A
1 A
54373 TCTTTCGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 2 0.09
25 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATTTAATTTATTTAAAAATTA
Found at i:54753 original size:6 final size:6
Alignment explanation
Indices: 54744--54803 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
54734 ATCGAAATAA
* * *
54744 TTAAAT TTAATAT TTAATAT TT-AA- TAAAAT ATAAAT TTAAAC TTAAATT
1 TTAAAT TTAA-AT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T
54793 TTAAAT TTAAA
1 TTAAAT TTAAA
54804 CTAAAAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 24 0.55
7 16 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:54790 original size:19 final size:18
Alignment explanation
Indices: 54768--54809 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
54758 TAATATTTAA
54768 TAAAATATAAATTTAAAC
1 TAAAATATAAATTTAAAC
* *
54786 TTAAATTTTAAATTTAAAC
1 -TAAAATATAAATTTAAAC
54805 TAAAA
1 TAAAA
54810 AACTATCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATATAAATTTAAAC
Found at i:54803 original size:13 final size:12
Alignment explanation
Indices: 54744--54803 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
54734 ATCGAAATAA
54744 TTAAATTTAATAT
1 TTAAATTTAA-AT
54757 TTAATATTT-AA-
1 TTAA-ATTTAAAT
* *
54768 TAAAATATAAAT
1 TTAAATTTAAAT
*
54780 TTAAACTTAAATT
1 TTAAATTTAAA-T
54793 TTAAATTTAAA
1 TTAAATTTAAA
54804 CTAAAAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
10 3 0.08
11 5 0.14
12 9 0.24
13 16 0.43
14 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:56154 original size:14 final size:13
Alignment explanation
Indices: 56128--56152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56118 AAGTATATTT
56128 AAGGTTTTTTTTA
1 AAGGTTTTTTTTA
56141 AAGGTTTTTTTT
1 AAGGTTTTTTTT
56153 TATATATTCA
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
AAGGTTTTTTTTA
Found at i:58829 original size:21 final size:20
Alignment explanation
Indices: 58780--58853 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 20
58770 TAAAAATTTT
58780 AAAAAT-TATTTTTATATTA
1 AAAAATATATTTTTATATTA
**
58799 ATATTTATATATTTTTATAATTA
1 A-A-AAATATATTTTTAT-ATTA
58822 AAAAATAT-TTTTTAATTATTA
1 AAAAATATATTTTT-A-TATTA
*
58843 AATAATA-ATTT
1 AAAAATATATTT
58854 AGATAGAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 6 0.14
21 20 0.47
22 11 0.26
23 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAAATATATTTTTATATTA
Found at i:59957 original size:50 final size:50
Alignment explanation
Indices: 59903--60108 Score: 324
Period size: 50 Copynumber: 4.1 Consensus size: 50
59893 CTTAGAGTCA
59903 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
*
59953 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTAAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* * * *
60003 AACAATTATGGTCACCTCCCTCTATTGTCAAAGTTTGGTGAAGGATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* * *
60053 AACAATTATGGCCACCT-CTCTCTATTATCAAAGGTTGGTGAAGGATAGTC
1 AACAATTATGGCCACCTCCT-TCTATTGTCAAAGGTTGGTGAAGAATCGTC
60103 AACAAT
1 AACAAT
60109 GGCAACAACT
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 1 0.01
50 143 0.99
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (50 bp):
AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
Found at i:64561 original size:50 final size:50
Alignment explanation
Indices: 64507--64699 Score: 300
Period size: 50 Copynumber: 3.9 Consensus size: 50
64497 CTTAGAGTCA
*
64507 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGATGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
64557 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* *
64607 AACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
** *
64657 AACAATTATGATCACCTCTCTT-TATTG-CTAAAGGTCGGTGAAG
1 AACAATTATGGCCACCTC-CTTCTATTGTC-AAAGGTTGGTGAAG
64700 GATAGTCACC
Statistics
Matches: 135, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
49 1 0.01
50 132 0.98
51 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (50 bp):
AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
Found at i:65353 original size:11 final size:11
Alignment explanation
Indices: 65339--65396 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
65329 TATATATTTT
65339 ATTATATTATA
1 ATTATATTATA
*
65350 ATTATATTTAAA
1 ATTATA-TTATA
*
65362 ATTATATATTTA
1 ATTATAT-TATA
65374 A-TATATTAATA
1 ATTATATT-ATA
65385 ATTTATATTATA
1 A-TTATATTATA
65397 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 1 0.03
11 15 0.39
12 16 0.42
13 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATATTATA
Found at i:65356 original size:29 final size:26
Alignment explanation
Indices: 65315--65397 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 26
65305 TAATTGGTTC
65315 ATTTATATAATATTTATATATTTTATTAT
1 ATTTA-AT-ATATTTATA-ATTTTATTAT
*
65344 ATTATAATTATATTTA-AA-ATTA-TAT
1 ATT-TAA-TATATTTATAATTTTATTAT
*
65369 ATTTAATATATTAATAATTTATATTAT
1 ATTTAATATATTTATAATTT-TATTAT
65396 AT
1 AT
65398 AAATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
23 7 0.16
24 5 0.11
25 7 0.16
26 5 0.11
27 6 0.13
28 1 0.02
29 11 0.24
30 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTAATATATTTATAATTTTATTAT
Found at i:65365 original size:23 final size:22
Alignment explanation
Indices: 65339--65396 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
65329 TATATATTTT
65339 ATTATATTATAATTATATTTAA-A
1 ATTATATTATAA-TATA-TTAATA
*
65362 ATTATATATTTAATATATTAATA
1 ATTATAT-TATAATATATTAATA
65385 ATTTATATTATA
1 A-TTATATTATA
65397 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.13
23 16 0.53
24 10 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTATATTATAATATATTAATA
Found at i:65368 original size:35 final size:38
Alignment explanation
Indices: 65317--65402 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 38
65307 ATTGGTTCAT
*
65317 TTATATAATATTTATATATTTTATTATATT-ATAA-TTATA
1 TTATATAA-A-TTATATA-TTTAATATATTAATAATTTATA
65356 TT-TA-AAATTATATATTTAATATATTAATAATTTATA
1 TTATATAAATTATATATTTAATATATTAATAATTTATA
65392 TTATATAAATT
1 TTATATAAATT
65403 TTAAAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
34 10 0.24
35 11 0.26
36 8 0.19
37 4 0.10
38 7 0.17
39 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
TTATATAAATTATATATTTAATATATTAATAATTTATA
Found at i:66019 original size:19 final size:20
Alignment explanation
Indices: 65975--66026 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
65965 ATAAATACTT
*
65975 CACAAATAAAACATGGAAAAA
1 CACAAATAAAA-ATCGAAAAA
65996 -A-AAATAAAAA-CGAAAAA
1 CACAAATAAAAATCGAAAAA
66013 CACAAATACAAAAT
1 CACAAATA-AAAAT
66027 ACAATTCCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 6 0.23
18 2 0.08
19 13 0.50
20 5 0.19
ACGTcount: A:0.71, C:0.13, G:0.06, T:0.10
Consensus pattern (20 bp):
CACAAATAAAAATCGAAAAA
Done.