Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2384
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: 47548
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:9067 original size:13 final size:13
Alignment explanation
Indices: 9049--9079 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9039 ACATTTCTTC
9049 ATGTATCGATACA
1 ATGTATCGATACA
9062 ATGTATCGATACA
1 ATGTATCGATACA
*
9075 TTGTA
1 ATGTA
9080 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9085 original size:33 final size:32
Alignment explanation
Indices: 9029--9091 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
9019 GTTACAAGCT
9029 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTC-TCATGTATCGATACA
9062 ATGTATCGATACATTGTAC-CATGTATCGAT
1 ATGTATCGATACATT-T-CTCATGTATCGAT
9092 GCAAATAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCGATACA
Found at i:9163 original size:13 final size:13
Alignment explanation
Indices: 9145--9171 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9135 ACAATTGTCC
9145 ATGTATCGATACA
1 ATGTATCGATACA
9158 ATGTATCGATACA
1 ATGTATCGATACA
9171 A
1 A
9172 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10008 original size:20 final size:21
Alignment explanation
Indices: 9983--10037 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
9973 CATTTTAAAC
9983 ATGTATCGATACATTCACTT-
1 ATGTATCGATACATTCACTTG
*
10003 ATGTATCGATACTTTCACTTG
1 ATGTATCGATACATTCACTTG
* *
10024 TTGTAGCGATACAT
1 ATGTATCGATACAT
10038 CTAGATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTG
Found at i:10711 original size:53 final size:52
Alignment explanation
Indices: 10534--10720 Score: 153
Period size: 52 Copynumber: 3.6 Consensus size: 52
10524 ATGTTAAGAA
* * * * * * * * *
10534 TGCCAATGTACTGATTCATGGCCAGCAACATTGGACATGAAGATGA-GAAGAA
1 TGCCAATGTACTGATTCAAGGCTAGCGACATCGGACTTAAAAATGACAAAG-G
* * * * *
10586 TGCCAATGTAATAATTCAAGGCCAGCGACATTGGACTTAAAAATGATAAAGG
1 TGCCAATGTACTGATTCAAGGCTAGCGACATCGGACTTAAAAATGACAAAGG
* * * * * *
10638 T-CTCAATATGCTGATTCAAGGCTAGTGATATCGGGCTTAAAGATGACAAAGGG
1 TGC-CAATGTACTGATTCAAGGCTAGCGACATCGGACTTAAAAATGACAAA-GG
10691 TGCCAATGTACTGATTCAAGGCTAGCGACA
1 TGCCAATGTACTGATTCAAGGCTAGCGACA
10721 CTAGACTTAG
Statistics
Matches: 107, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
51 1 0.01
52 76 0.71
53 29 0.27
54 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (52 bp):
TGCCAATGTACTGATTCAAGGCTAGCGACATCGGACTTAAAAATGACAAAGG
Found at i:10958 original size:33 final size:33
Alignment explanation
Indices: 10805--10965 Score: 178
Period size: 31 Copynumber: 5.1 Consensus size: 33
10795 AACCCCACCA
* *
10805 ACTTGTGTGGGCTTT-GAAAAGGGTTGCTA-TCG
1 ACTTGTGTGAGCTTTAGAAAAGGGTTGCCACT-G
10837 ACTTGTGTGAGCTTTA-AAAA-GGTTGCCACTG
1 ACTTGTGTGAGCTTTAGAAAAGGGTTGCCACTG
* * *
10868 ACTTATGTGGGCTTTAG--AAGGGTTGCCATTG
1 ACTTGTGTGAGCTTTAGAAAAGGGTTGCCACTG
*
10899 AC--GTGT-AGGCTTTAGAGAAGGGTTGCCACTG
1 ACTTGTGTGA-GCTTTAGAAAAGGGTTGCCACTG
*
10930 ACTTGTGTGAGCTTCAGAAAAGGGTTGCCACTG
1 ACTTGTGTGAGCTTTAGAAAAGGGTTGCCACTG
10963 ACT
1 ACT
10966 GCCACCGACT
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
29 10 0.09
30 2 0.02
31 49 0.45
32 19 0.17
33 28 0.26
34 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (33 bp):
ACTTGTGTGAGCTTTAGAAAAGGGTTGCCACTG
Found at i:11002 original size:41 final size:42
Alignment explanation
Indices: 10922--11006 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
10912 AGAGAAGGGT
*
10922 TGCCACTGACTTGTGTGAGCTTCAGAAAAGGGTTGCCACTGAC
1 TGCCACCGACTTGTGTGAGCTTCAG-AAAGGGTTGCCACTGAC
* * *
10965 TGCCACCGACTTGTTTGGGCTTTAG-AAGGGTTGCCACTGAC
1 TGCCACCGACTTGTGTGAGCTTCAGAAAGGGTTGCCACTGAC
11006 T
1 T
11007 TATGTGGGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 17 0.45
43 21 0.55
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (42 bp):
TGCCACCGACTTGTGTGAGCTTCAGAAAGGGTTGCCACTGAC
Found at i:11032 original size:33 final size:33
Alignment explanation
Indices: 10965--11054 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
10955 TGCCACTGAC
* *
10965 TGCCACCGACTTGTTTGGGCTTT--AGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGAT
* *
10996 TGCCACTGACTTATGTGGGCTTTAGAGAAGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGAT
* *
11029 TGCCACCAACTTGTGTAGGCTTTAGA
1 TGCCACCGACTTGTGTGGGCTTTAGA
11055 AGAGGACTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.41
33 29 0.59
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTAGAGAAGGAT
Found at i:11132 original size:28 final size:29
Alignment explanation
Indices: 11074--11405 Score: 267
Period size: 29 Copynumber: 11.3 Consensus size: 29
11064 CCATAGAGTA
* *
11074 GTGGACTTTAAAAGCGAGTGCTACGAAGTT
1 GTGGACTTTAAAAGAG-GTGCCACGAAGTT
*
11104 GTGGA-TTTAAAA-AGGGTGCCACGCAGTT
1 GTGGACTTTAAAAGA-GGTGCCACGAAGTT
* *
11132 GTGGACTTTAAAAGCAGGTGCTATGAAGTT
1 GTGGACTTTAAAAG-AGGTGCCACGAAGTT
* * *
11162 GTGAACTTAAAAAG-GGTGCCA-TAGAGTT
1 GTGGACTTTAAAAGAGGTGCCACGA-AGTT
* * * *
11190 GTGGACTTTAAAAGAGATACAACGGAGTT
1 GTGGACTTTAAAAGAGGTGCCACGAAGTT
* *
11219 GTGGACTTTGAAGAAAAAGGTGTCACGAAGTT
1 GTGGACTTT--A-AAAGAGGTGCCACGAAGTT
* *
11251 GTGGACTTTAAAAGAGATGCCACGGAGTT
1 GTGGACTTTAAAAGAGGTGCCACGAAGTT
* * *
11280 GTGGACTTTAAAAGAGATGCCATGGAGTT
1 GTGGACTTTAAAAGAGGTGCCACGAAGTT
* * * * *
11309 ATGTACTTTGAAGAAAACGTGCCACAAAGTT
1 GTGGACTTT-AA-AAGAGGTGCCACGAAGTT
* * * *
11340 GTGAACTTTAGAAGAGATGCCACAAAGTT
1 GTGGACTTTAAAAGAGGTGCCACGAAGTT
* * * *
11369 GTGGACTTTAAAAAAGGTGCTACTAAGTC
1 GTGGACTTTAAAAGAGGTGCCACGAAGTT
11398 GTGGACTT
1 GTGGACTT
11406 CAAGAAAAGA
Statistics
Matches: 241, Mismatches: 49, Indels: 25
0.77 0.16 0.08
Matches are distributed among these distances:
27 1 0.00
28 38 0.16
29 127 0.53
30 32 0.13
31 21 0.09
32 22 0.09
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (29 bp):
GTGGACTTTAAAAGAGGTGCCACGAAGTT
Found at i:11256 original size:32 final size:29
Alignment explanation
Indices: 11074--11481 Score: 243
Period size: 29 Copynumber: 13.8 Consensus size: 29
11064 CCATAGAGTA
** *
11074 GTGGACTTTAAAAGCGAGTGCTACGAAGTT
1 GTGGACTTTAAAAAAGA-TGCCACGAAGTT
* * *
11104 GTGGA-TTTAAAAAGGGTGCCACGCAGTT
1 GTGGACTTTAAAAAAGATGCCACGAAGTT
* * * *
11132 GTGGACTTTAAAAGCAGGTGCTATGAAGTT
1 GTGGACTTTAAAA-AAGATGCCACGAAGTT
* * * *
11162 GTGAAC-TTAAAAAGGGTGCCA-TAGAGTT
1 GTGGACTTTAAAAAAGATGCCACGA-AGTT
* * * *
11190 GTGGACTTTAAAAGAGATACAACGGAGTT
1 GTGGACTTTAAAAAAGATGCCACGAAGTT
* *
11219 GTGGACTTTGAAGAAAAAGGTGTCACGAAGTT
1 GTGGACTTT--A-AAAAAGATGCCACGAAGTT
* *
11251 GTGGACTTTAAAAGAGATGCCACGGAGTT
1 GTGGACTTTAAAAAAGATGCCACGAAGTT
* * *
11280 GTGGACTTTAAAAGAGATGCCATGGAGTT
1 GTGGACTTTAAAAAAGATGCCACGAAGTT
* * *
11309 ATGTACTTTGAAGAAAACG-TGCCACAAAGTT
1 GTGGACTTT-AA-AAAA-GATGCCACGAAGTT
* * * *
11340 GTGAACTTTAGAAGAGATGCCACAAAGTT
1 GTGGACTTTAAAAAAGATGCCACGAAGTT
* * * *
11369 GTGGACTTTAAAAAAGGTGCTACTAAGTC
1 GTGGACTTTAAAAAAGATGCCACGAAGTT
* * *
11398 GTGGACTTCAAGAAAAGATGCTACTG-AGTC
1 GTGGACTTTAA-AAAAGATGCCAC-GAAGTT
* ** *
11428 GTGGACTTTGAGAGTAGATGCCACTG-AGTC
1 GTGGACTTT-AAAAAAGATGCCAC-GAAGTT
* *
11458 ATGGACTTTGAGAAAAGATGCCAC
1 GTGGACTTT-AAAAAAGATGCCAC
11482 TTAGTCGTGT
Statistics
Matches: 301, Mismatches: 62, Indels: 30
0.77 0.16 0.08
Matches are distributed among these distances:
27 1 0.00
28 31 0.10
29 141 0.47
30 84 0.28
31 21 0.07
32 23 0.08
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (29 bp):
GTGGACTTTAAAAAAGATGCCACGAAGTT
Found at i:11380 original size:89 final size:90
Alignment explanation
Indices: 11157--11381 Score: 301
Period size: 89 Copynumber: 2.5 Consensus size: 90
11147 AGGTGCTATG
* * * *
11157 AAGTTGTGAACTTAAAAAG-GGTGCCATAGAGTTGTGGACTTTAAAAGAGATACAACGGAGTTGT
1 AAGTTGTGAACTTTAAAAGAGATGCCACAGAGTTGTGGACTTTAAAAGAGATACAACGGAGTTAT
* * *
11221 GGACTTTGAAGAAAAAGGTGTCACG
66 GGACTTTGAAGAAAAACGTGCCACA
* * * * *
11246 AAGTTGTGGACTTTAAAAGAGATGCCACGGAGTTGTGGACTTTAAAAGAGATGCCATGGAGTTAT
1 AAGTTGTGAACTTTAAAAGAGATGCCACAGAGTTGTGGACTTTAAAAGAGATACAACGGAGTTAT
*
11311 GTACTTTGAAG-AAAACGTGCCACA
66 GGACTTTGAAGAAAAACGTGCCACA
* *
11335 AAGTTGTGAACTTTAGAAGAGATGCCACAAAGTTGTGGACTTTAAAA
1 AAGTTGTGAACTTTAAAAGAGATGCCACAGAGTTGTGGACTTTAAAA
11382 AAGGTGCTAC
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
89 70 0.59
90 48 0.41
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.26
Consensus pattern (90 bp):
AAGTTGTGAACTTTAAAAGAGATGCCACAGAGTTGTGGACTTTAAAAGAGATACAACGGAGTTAT
GGACTTTGAAGAAAAACGTGCCACA
Found at i:11420 original size:30 final size:30
Alignment explanation
Indices: 11219--11563 Score: 191
Period size: 29 Copynumber: 11.3 Consensus size: 30
11209 CAACGGAGTT
* * * *
11219 GTGGACTTTGAAGAAAAAGGTGTCACGAAGTT
1 GTGGACTTT-AAG-AAAAGATGCCACTAAGTC
* ** *
11251 GTGGACTTTAA-AAGAGATGCCACGGAGTT
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
* * *
11280 GTGGACTTTAA-AAGAGATGCCA-TGGAGTT
1 GTGGACTTTAAGAAAAGATGCCACT-AAGTC
* * * *
11309 ATGTACTTTGAAGAAAACG-TGCCACAAAGTT
1 GTGGACTTT-AAGAAAA-GATGCCACTAAGTC
* * * *
11340 GTGAACTTT-AGAAGAGATGCCACAAAGTT
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
* *
11369 GTGGACTTTAA-AAAAGGTGCTACTAAGTC
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
* * *
11398 GTGGACTTCAAGAAAAGATGCTACTGAGTC
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
* ** *
11428 GTGGACTTTGAGAGTAGATGCCACTGAGTC
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
* * *
11458 ATGGACTTTGAGAAAAGATGCCACTTAGTC
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
* * *
11488 GTGTACTTTAAGAAGATAAAAAAAGTGCCACTGAGTC
1 GTGGACTTT---AAG---AAAAGA-TGCCACTAAGTC
* * *
11525 GTGGACTTTGAGAAAAGAAGCCACTGAGTC
1 GTGGACTTTAAGAAAAGATGCCACTAAGTC
11555 AG-GGACTTT
1 -GTGGACTTT
11564 GAAAAGGAAC
Statistics
Matches: 257, Mismatches: 40, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.00
29 96 0.37
30 95 0.37
31 27 0.11
32 10 0.04
33 2 0.01
34 2 0.01
36 5 0.02
37 19 0.07
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (30 bp):
GTGGACTTTAAGAAAAGATGCCACTAAGTC
Found at i:11563 original size:67 final size:72
Alignment explanation
Indices: 11446--11640 Score: 206
Period size: 72 Copynumber: 2.8 Consensus size: 72
11436 TGAGAGTAGA
* * * *
11446 TGCCACTGAGTCATGGACTTTGAGAAAAGATGCCACTTAGTCGTGTACTTT-AAGAA-G-A-TA-
1 TGCCACTGAGTCGTGGACTTTGAGAAAAGAAGCCACTGAGTCGTGGACTTTGAA-AAGGAACTAT
11506 AAA-AAAG
65 AAATAAAG
11513 TGCCACTGAGTCGTGGACTTTGAGAAAAGAAGCCACTGAGTCAG-GGACTTTGAAAAGGAACTAT
1 TGCCACTGAGTCGTGGACTTTGAGAAAAGAAGCCACTGAGTC-GTGGACTTTGAAAAGGAACTAT
**
11577 AAATAGGG
65 AAATAAAG
* * * * * * *
11585 TGCCACTAAGTCGTGGACTTCGAGAAAAGATGTCACTTAGTCATGGTCTTTGAAAA
1 TGCCACTGAGTCGTGGACTTTGAGAAAAGAAGCCACTGAGTCGTGGACTTTGAAAA
11641 AGGATGCCAC
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
67 47 0.44
68 4 0.04
69 1 0.01
70 2 0.02
71 3 0.03
72 50 0.47
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (72 bp):
TGCCACTGAGTCGTGGACTTTGAGAAAAGAAGCCACTGAGTCGTGGACTTTGAAAAGGAACTATA
AATAAAG
Found at i:11685 original size:29 final size:28
Alignment explanation
Indices: 11583--11702 Score: 89
Period size: 30 Copynumber: 4.1 Consensus size: 28
11573 CTATAAATAG
* * *
11583 GGTGCCACTAAGTCGTGGACTTCGAGAAAA
1 GGTGCCACTAAGTCATGAACTT-TA-AAAA
* * * **
11613 GATGTCACTTAGTCATGGTCTTTGAAAAA
1 GGTGCCACTAAGTCATGAACTTT-AAAAA
*
11642 GGATGCCACTAAGTCGTGAACTTTAAAGAA
1 GG-TGCCACTAAGTCATGAACTTTAAA-AA
*
11672 GGTGCCA-TAGAGTCATGAACTTCAAAAA
1 GGTGCCACTA-AGTCATGAACTTTAAAAA
11700 GGT
1 GGT
11703 TACTTTATTA
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
28 7 0.10
29 27 0.38
30 38 0.53
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (28 bp):
GGTGCCACTAAGTCATGAACTTTAAAAA
Found at i:12556 original size:33 final size:33
Alignment explanation
Indices: 12514--12597 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
12504 AAACGTTGAC
* *
12514 TTAACAAGAAGGGTGATACGGTTTGATTTATTT
1 TTAACAAGAAAGGTGATACGATTTGATTTATTT
*
12547 TTAACAAGAAAGGTGATACGATTTGGTTTATTT
1 TTAACAAGAAAGGTGATACGATTTGATTTATTT
* **
12580 CTGGCAAGAAAGGTGATA
1 TTAACAAGAAAGGTGATA
12598 TGATGGTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (33 bp):
TTAACAAGAAAGGTGATACGATTTGATTTATTT
Found at i:12842 original size:10 final size:10
Alignment explanation
Indices: 12827--12869 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
12817 GTAAGGGGAA
12827 TTTAGTTTTT
1 TTTAGTTTTT
12837 TTTAGTTGTTT
1 TTTAGTT-TTT
*
12848 TTT-GTTGTT
1 TTTAGTTTTT
12857 TTT-GTTTTT
1 TTTAGTTTTT
12866 TTTA
1 TTTA
12870 TGAAGACGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 13 0.45
10 10 0.34
11 6 0.21
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79
Consensus pattern (10 bp):
TTTAGTTTTT
Found at i:12892 original size:18 final size:18
Alignment explanation
Indices: 12869--12910 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12859 TGTTTTTTTT
* *
12869 ATGAAGACGATTGATTGA
1 ATGAAGACAACTGATTGA
*
12887 ATGAAGATAACTGATTGA
1 ATGAAGACAACTGATTGA
12905 ATGAAG
1 ATGAAG
12911 TTGACAATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.26, T:0.26
Consensus pattern (18 bp):
ATGAAGACAACTGATTGA
Found at i:14789 original size:13 final size:13
Alignment explanation
Indices: 14771--14795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14761 TAATTCATCA
14771 TGTATCGATACAT
1 TGTATCGATACAT
14784 TGTATCGATACA
1 TGTATCGATACA
14796 ATGTGCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14793 original size:33 final size:33
Alignment explanation
Indices: 14769--14848 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
14759 TATAATTCAT
14769 CATGTATCGATACATTGTATCGATACAATGTGC
1 CATGTATCGATACATTGTATCGATACAATGTGC
*
14802 CATGTATCGATACATTGTATCGGTACAATGTGC
1 CATGTATCGATACATTGTATCGATACAATGTGC
14835 CATGTATCGATACA
1 CATGTATCGATACA
14849 AATAGTGGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (33 bp):
CATGTATCGATACATTGTATCGATACAATGTGC
Found at i:14809 original size:20 final size:20
Alignment explanation
Indices: 14784--14849 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
14774 ATCGATACAT
14784 TGTATCGATACAATGTGCCA
1 TGTATCGATACAATGTGCCA
14804 TGTATCGATAC-A--T----
1 TGTATCGATACAATGTGCCA
*
14817 TGTATCGGTACAATGTGCCA
1 TGTATCGATACAATGTGCCA
14837 TGTATCGATACAA
1 TGTATCGATACAA
14850 ATAGTGGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 23 0.62
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
TGTATCGATACAATGTGCCA
Found at i:14903 original size:20 final size:19
Alignment explanation
Indices: 14878--14931 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
14868 CTGCCAGTTT
**
14878 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
* *
14898 CATGTATTGATACGATGAA
1 CATGTATCGATACAATGAA
14917 CATGTATCGATACAA
1 CATGTATCGATACAA
14932 AGCATAATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:17452 original size:13 final size:13
Alignment explanation
Indices: 17434--17471 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
17424 ATAGTAACCC
17434 ATGTATCGATACA
1 ATGTATCGATACA
17447 ATGTATCGAT--A
1 ATGTATCGATACA
*
17458 TTGTATCGATACA
1 ATGTATCGATACA
17471 A
1 A
17472 AGAATATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:18524 original size:13 final size:13
Alignment explanation
Indices: 18506--18530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18496 CATTTTATGG
18506 TGTATCGATACAA
1 TGTATCGATACAA
18519 TGTATCGATACA
1 TGTATCGATACA
18531 TACTTTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:23323 original size:13 final size:13
Alignment explanation
Indices: 23305--23335 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23295 ACAATTCATC
23305 ATGTATCGATACA
1 ATGTATCGATACA
23318 ATGTATCGATACA
1 ATGTATCGATACA
*
23331 TTGTA
1 ATGTA
23336 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23329 original size:33 final size:33
Alignment explanation
Indices: 23283--23351 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
23273 CCATTAAAAG
* *
23283 CAATGTATTGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGCACCATGTATCGATA
*
23316 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGCACCATGTATCGATA
23349 CAA
1 CAA
23352 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTGCACCATGTATCGATA
Found at i:23445 original size:32 final size:33
Alignment explanation
Indices: 23401--23465 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
23391 ACAATTGTCC
* *
23401 ATGTATCTATACAATGAACAA-GTATCGATACA
1 ATGTATCGATACAAAGAACAATGTATCGATACA
* *
23433 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAGAACAATGTATCGATACA
23466 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGAACAATGTATCGATACA
Found at i:24119 original size:46 final size:46
Alignment explanation
Indices: 24052--24155 Score: 181
Period size: 46 Copynumber: 2.3 Consensus size: 46
24042 GCATTTCTAA
*
24052 TTCTCCCCCTTTGTCAAATATTAAAAAATTTATTTATTTTCAATAT
1 TTCTCCCCCTTTGTCAAATATTAAAAAAATTATTTATTTTCAATAT
**
24098 TTCTCCCTGTTTGTCAAATATTAAAAAAATTATTTATTTTCAATAT
1 TTCTCCCCCTTTGTCAAATATTAAAAAAATTATTTATTTTCAATAT
24144 TTCTCCCCCTTT
1 TTCTCCCCCTTT
24156 TTGTTATAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (46 bp):
TTCTCCCCCTTTGTCAAATATTAAAAAAATTATTTATTTTCAATAT
Found at i:26590 original size:21 final size:21
Alignment explanation
Indices: 26566--26663 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
26556 AAAAATTTCA
*
26566 AATGTATCGATAGATTTGTAG
1 AATGTATCGATACATTTGTAG
*
26587 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
26608 AATGTGTCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
* *
26629 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
26650 AATGTATCGATACA
1 AATGTATCGATACA
26664 GGGTCCCAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 3 0.04
21 66 0.96
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:26779 original size:20 final size:20
Alignment explanation
Indices: 26754--26808 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
26744 GCCAAGGAAA
*
26754 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
26774 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
26794 TGTATCGATACATTT
1 TGTATCGATACATTT
26809 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:29211 original size:51 final size:51
Alignment explanation
Indices: 29155--29275 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
29145 CAACTCTCCG
*
29155 CAATCGGGGATATTCCAACTCCGATTTTATTTCTAAAACACCCA-TTTTCCA
1 CAATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCCACTTTT-CA
* * *
29206 TAATCGGGGATACTT-CAACTCCGATTTTATTTCCAAAGCACCGACTTTTCA
1 CAATCGGGGATA-TTCCAACTCCGATTTTATTTCCAAAACACCCACTTTTCA
*
29257 CAATCGAGGATATTCCAAC
1 CAATCGGGGATATTCCAAC
29276 GCTGTTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
50 2 0.03
51 53 0.87
52 6 0.10
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
CAATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCCACTTTTCA
Found at i:29371 original size:27 final size:27
Alignment explanation
Indices: 29333--29385 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29323 CATCAATTTC
*
29333 TCATTGGGGATACTCCAACCTCGTTAA
1 TCATCGGGGATACTCCAACCTCGTTAA
29360 TCATCGGGGATACTCCAACCTCGTTA
1 TCATCGGGGATACTCCAACCTCGTTA
29386 CCTCCGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCTCGTTAA
Found at i:29405 original size:28 final size:27
Alignment explanation
Indices: 29338--29407 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
29328 ATTTCTCATT
**
29338 GGGGATACTCCAACCTCGTTAATCATC
1 GGGGATACTCCAACCTCGTTAATCAGA
* *
29365 GGGGATACTCCAACCTCGTTACCTCCGA
1 GGGGATACTCCAACCTCGTTA-ATCAGA
*
29393 GGGGATATTCCAACC
1 GGGGATACTCCAACC
29408 CCGACTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCTCGTTAATCAGA
Found at i:29511 original size:52 final size:51
Alignment explanation
Indices: 29394--29614 Score: 160
Period size: 52 Copynumber: 4.3 Consensus size: 51
29384 TACCTCCGAG
* ** * * *** * *
29394 GGGATATTCCAACCCCGACTTTATTCCCAAAATATTGATTTTTCATAATCG
1 GGGATACTCCAACCCCGGTTTTATTCTCAAAACACCAATTTTTCACAATCC
* * *
29445 GGGATACTCTAACCCTGGTTTTATTGCT-AAAACACTAATTTTTCCACAATCC
1 GGGATACTCCAACCCCGGTTTTATT-CTCAAAACACCAATTTTT-CACAATCC
* * ** *
29497 GGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCG
1 GGGATACTCCAACCCCGGTTTTATTCTCAAAACACCAATTTTTC-ACAATCC
* * * *
29549 GGGATACTCAAACTCCGATTTTATT-TCCAAAA-ATGCCAATTTTTCACAATCA
1 GGGATACTCCAACCCCGGTTTTATTCT-CAAAACA--CCAATTTTTCACAATCC
*
29601 AGGATACTCCAACC
1 GGGATACTCCAACC
29615 TCGTTATTTC
Statistics
Matches: 134, Mismatches: 29, Indels: 13
0.76 0.16 0.07
Matches are distributed among these distances:
51 36 0.27
52 89 0.66
53 9 0.07
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGTTTTATTCTCAAAACACCAATTTTTCACAATCC
Found at i:29663 original size:28 final size:28
Alignment explanation
Indices: 29602--29671 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
29592 TCACAATCAA
* * **
29602 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
* *
29630 GAATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
29658 GGATACTCCAACCC
1 GGATACTCCAACCC
29672 TGGCTTTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:31822 original size:4 final size:4
Alignment explanation
Indices: 31813--31847 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
31803 TCTTGAGGTG
* *
31813 TTTA TTTA TTTA TTTA TTTA TTTA TATA TCTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
31848 TTTTTGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:42177 original size:10 final size:10
Alignment explanation
Indices: 42162--42227 Score: 51
Period size: 11 Copynumber: 6.1 Consensus size: 10
42152 CATTCTCTTC
42162 AAAAAAAAGA
1 AAAAAAAAGA
*
42172 AAAAAAAACAA
1 AAAAAAAA-GA
*
42183 AACAAAAAAAA
1 AA-AAAAAAGA
42194 ACAAAACAAAGA
1 A-AAAA-AAAGA
* *
42206 AAAAGAGAGA
1 AAAAAAAAGA
42216 AAAGAAAAAGA
1 AAA-AAAAAGA
42227 A
1 A
42228 CCTGCTTAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
10 15 0.33
11 18 0.40
12 12 0.27
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:42189 original size:15 final size:15
Alignment explanation
Indices: 42162--42209 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
42152 CATTCTCTTC
*
42162 AAAA-AAAAGAAAAA
1 AAAACAAAACAAAAA
42176 AAAACAAAACAAAAA
1 AAAACAAAACAAAAA
42191 AAAACAAAACAAAGAA
1 AAAACAAAACAAA-AA
42207 AAA
1 AAA
42210 GAGAGAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 4 0.13
15 22 0.71
16 5 0.16
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (15 bp):
AAAACAAAACAAAAA
Found at i:43280 original size:59 final size:59
Alignment explanation
Indices: 43188--44021 Score: 1400
Period size: 59 Copynumber: 14.3 Consensus size: 59
43178 CCTTCCGCTT
43188 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43247 TTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43306 TTCAATCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43365 TTCAGTCCTAAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43424 TACAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43483 TTCAGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
43542 TTCAGTCCTCAAAGAGTGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTAGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
43601 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
43660 TTCAGTCCTCAAAGAGCAGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43719 TTCAGTCCTCAAAGAGAGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
43778 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTAGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
43837 TTCAGTCCTCAAAGAGCGGGACACCTTTTTTTTTAAAGCCCACACAAGTTGGTGGTACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
** *
43896 TTCAGTCCTCAAAGAGCAAGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGCACT
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
43950 TTCAGTCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTT
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-C
*
44005 TTTAGTCCTCAAAGAGC
1 TTCAGTCCTCAAAGAGC
44022 AGGATACACT
Statistics
Matches: 740, Mismatches: 34, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
54 74 0.10
55 17 0.02
58 3 0.00
59 646 0.87
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (59 bp):
TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:44907 original size:13 final size:13
Alignment explanation
Indices: 44889--44914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44879 CATTTTTCTG
44889 TGTATCGATACAT
1 TGTATCGATACAT
44902 TGTATCGATACAT
1 TGTATCGATACAT
44915 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:44911 original size:33 final size:33
Alignment explanation
Indices: 44869--44932 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
44859 GCCAAGGAAA
***
44869 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
44902 TGTATCGATACATGGATCTTTGTATCGATAC
1 TGTATCGATACATGGATCTGTGTATCGATAC
44933 GTTTGGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:47275 original size:51 final size:50
Alignment explanation
Indices: 47220--47337 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 50
47210 ATTTTTGTTG
* * * * *
47220 ATCGGGGATATTCCAACTCTGATTTTATTTCTAAAACACCTATTTTCCATA
1 ATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCGACTTT-CACA
*
47271 ATCGGGGATACTT-CAACTCCGATTTTATTTCCAAAGCACCGACTTTCACA
1 ATCGGGGATA-TTCCAACTCCGATTTTATTTCCAAAACACCGACTTTCACA
47321 ATCGGGGATATTCCAAC
1 ATCGGGGATATTCCAAC
47338 CCCGTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
49 2 0.03
50 17 0.29
51 38 0.64
52 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (50 bp):
ATCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACCGACTTTCACA
Found at i:47431 original size:26 final size:27
Alignment explanation
Indices: 47395--47469 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
47385 CATTAATTTT
*
47395 TCATTGGGGATACTCCAACCCGTTA-A
1 TCATAGGGGATACTCCAACCCGTTACA
* *
47421 TCATCGGGGATACTCCAACCTCGTTACC
1 TCATAGGGGATACTCCAACC-CGTTACA
**
47449 TCCGAGGGGATACTCCAACCC
1 TCATAGGGGATACTCCAACCC
47470 CGACTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 19 0.45
27 6 0.14
28 17 0.40
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (27 bp):
TCATAGGGGATACTCCAACCCGTTACA
Found at i:47466 original size:28 final size:26
Alignment explanation
Indices: 47400--47469 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 26
47390 ATTTTTCATT
**
47400 GGGGATACTCCAACCCGTTAATCATC
1 GGGGATACTCCAACCCGTTAATCAGA
* *
47426 GGGGATACTCCAACCTCGTTACCTCCGA
1 GGGGATACTCCAACC-CGTTA-ATCAGA
47454 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
47470 CGACTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 15 0.39
27 6 0.16
28 17 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.20
Consensus pattern (26 bp):
GGGGATACTCCAACCCGTTAATCAGA
Found at i:47497 original size:102 final size:104
Alignment explanation
Indices: 47321--47520 Score: 260
Period size: 102 Copynumber: 1.9 Consensus size: 104
47311 GACTTTCACA
* ** * ** * *
47321 ATCGGGGATATTCCAACCCCGTTATTTCTGAAGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGACACTCCAACCCCGACTTTATTCCCAAAAC
47386 ATTAATTTTTCAT-T-GGGGATACTCCAACCCGTTAATC
66 ATTAATTTTTCATATCGGGGATACTCCAACCCGTTAATC
* * * *
47423 ATCGGGGATACTCCAACCTCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGACACTCCAACCCCGACTTTATTCCCAAAAC
*
47488 ATTGATTTTTCATAATCGGGGATACTCCAACCC
66 ATTAATTTTTCAT-ATCGGGGATACTCCAACCC
47521 CGTTTTTATT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
102 65 0.79
104 1 0.01
105 16 0.20
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (104 bp):
ATCGGGGATACTCCAACCCCGTTACCTCCGAAGGGACACTCCAACCCCGACTTTATTCCCAAAAC
ATTAATTTTTCATATCGGGGATACTCCAACCCGTTAATC
Done.