Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2739_ERROPOS718940
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: 90639
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 499 characters in sequence are not A, C, G, or T
Found at i:1643 original size:2 final size:2
Alignment explanation
Indices: 1616--1665 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
1606 TTAAATAATA
* * *
1616 AT AT AG AT AT AT A- AT AT -T TT AA AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
1657 AT AT AT AT A
1 AT AT AT AT A
1666 AAACACTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1647 original size:28 final size:28
Alignment explanation
Indices: 1605--1660 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1595 TAGTCAGGAG
1605 TTTAAATAATAATATAGATATATA-ATAT
1 TTTAAATAATAATAT-GATATATATATAT
1633 TTTAAAT-ATATATATGATATATATATAT
1 TTTAAATAATA-ATATGATATATATATAT
1661 ATATAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTAAATAATAATATGATATATATATAT
Found at i:6793 original size:13 final size:14
Alignment explanation
Indices: 6777--6809 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6767 TTCAAAGCTT
6777 AATTT-CTTTTAAA
1 AATTTACTTTTAAA
*
6790 AATTTATTTTTAAA
1 AATTTACTTTTAAA
6804 AATTTA
1 AATTTA
6810 TAAAACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTACTTTTAAA
Found at i:6802 original size:14 final size:14
Alignment explanation
Indices: 6783--6810 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6773 GCTTAATTTC
6783 TTTTAAAAATTTAT
1 TTTTAAAAATTTAT
6797 TTTTAAAAATTTAT
1 TTTTAAAAATTTAT
6811 AAAACATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAAATTTAT
Found at i:7567 original size:17 final size:19
Alignment explanation
Indices: 7533--7570 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7523 TTTAATGACG
*
7533 TTTTACAAATATATAATTT
1 TTTTAAAAATATATAATTT
7552 TTTTAAAAAT-TA-AATTT
1 TTTTAAAAATATATAATTT
7569 TT
1 TT
7571 AAAAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 2 0.11
19 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAAAAATATATAATTT
Found at i:9919 original size:20 final size:18
Alignment explanation
Indices: 9886--9926 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
9876 GAAATGGAAT
*
9886 TAAATTGTAATTTTAGTA
1 TAAATTGTAATTTTAGAA
9904 TAAATTTGTGAATTTTAGAA
1 TAAA-TTGT-AATTTTAGAA
9924 TAA
1 TAA
9927 TAAAGGGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TAAATTGTAATTTTAGAA
Found at i:16944 original size:16 final size:16
Alignment explanation
Indices: 16923--16992 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
16913 TTTGGTTCGC
* * *
16923 TGTATTGGATTAGAGA
1 TGTAATGGAATAGAGG
* *
16939 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
16955 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
16971 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
16987 TGTAAT
1 TGTAAT
16993 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:17248 original size:18 final size:17
Alignment explanation
Indices: 17226--17260 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17216 TTATTATTAA
*
17226 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17244 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17261 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17374 original size:14 final size:15
Alignment explanation
Indices: 17325--17376 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17315 ATAAAATATA
17325 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
17340 TATTAAATATATTAT
1 AATTAAATATATTAT
17355 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
17368 AATTTAATA
1 AATTAAATA
17377 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:17519 original size:128 final size:125
Alignment explanation
Indices: 17212--17629 Score: 667
Period size: 120 Copynumber: 3.4 Consensus size: 125
17202 ATATTTAAAT
17212 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
* *
17277 TCTGATATGAATTTACTCAAATAATAATATATGATACTAT-AAA-ATAT-A-AA-TTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATATAATAATTTAAC
*
17332 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
17397 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAATAATTTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAT-A--TAATAATTTAAC
*
17460 ATAATTATTATTAAATATATCTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
* *
17525 TCTTATATGAATTTACTCAAATCATAATATATTATACTATAAAAG--ATAAT--TTGAA-
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATATAATAATTTAAC
* *
17580 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
17630 TAAAATAATT
Statistics
Matches: 280, Mismatches: 10, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
120 149 0.53
121 7 0.03
122 2 0.01
123 5 0.02
125 2 0.01
126 1 0.00
127 2 0.01
128 112 0.40
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (125 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATATAATAATTTAAC
Found at i:17756 original size:40 final size:40
Alignment explanation
Indices: 17670--17745 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
17660 AGTGAGTAAG
* *
17670 AATTGAACTCTAAAAATAAAAAAAAAACATAACCATATAG
1 AATTGAACTCTAAAAATAAAAAAAAAACATAAACATATAC
17710 AATTGAACTCTAAAAATAAAAAAATAAA-A-AAACATA
1 AATTGAACTCTAAAAATAAAAAAA-AAACATAAACATA
17746 ACCATATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
39 6 0.18
40 25 0.74
41 3 0.09
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.20
Consensus pattern (40 bp):
AATTGAACTCTAAAAATAAAAAAAAAACATAAACATATAC
Found at i:18275 original size:145 final size:145
Alignment explanation
Indices: 18012--18301 Score: 571
Period size: 145 Copynumber: 2.0 Consensus size: 145
18002 TAACCTCCAA
18012 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
1 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
18077 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
66 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
18142 TAGCTACTTGAAATG
131 TAGCTACTTGAAATG
18157 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
1 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
*
18222 GCATTGATAAATCAGGAAAAATAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
66 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
18287 TAGCTACTTGAAATG
131 TAGCTACTTGAAATG
18302 GTACATTTTA
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 144 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (145 bp):
CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
TAGCTACTTGAAATG
Found at i:21793 original size:16 final size:16
Alignment explanation
Indices: 21753--21794 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
21743 GTTTCTTTTT
*
21753 TAATTATAAATAAATA
1 TAATTAAAAATAAATA
21769 TAATTAAAAATAAAT-
1 TAATTAAAAATAAATA
*
21784 TAATTTAAAAT
1 TAATTAAAAAT
21795 TTGACTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATTAAAAATAAATA
Found at i:24490 original size:15 final size:17
Alignment explanation
Indices: 24470--24504 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
24460 GTTGAACTAG
24470 ATTTTAAT-ATTT-TTA
1 ATTTTAATGATTTCTTA
24485 ATTTTAATGATTTCTTA
1 ATTTTAATGATTTCTTA
24502 ATT
1 ATT
24505 GAGTCGGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 4 0.22
17 6 0.33
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAATGATTTCTTA
Found at i:31302 original size:12 final size:13
Alignment explanation
Indices: 31285--31321 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
31275 GAACCGGACA
31285 CGAACCGAA-CTC
1 CGAACCGAAGCTC
31297 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
31309 CGAACCGTAGCTC
1 CGAACCGAAGCTC
31322 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:32061 original size:14 final size:14
Alignment explanation
Indices: 32042--32071 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
32032 ACACTTGGAT
32042 AACTCCATTACTGG
1 AACTCCATTACTGG
*
32056 AACTCCTTTACTGG
1 AACTCCATTACTGG
32070 AA
1 AA
32072 TCAGTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (14 bp):
AACTCCATTACTGG
Found at i:32237 original size:21 final size:21
Alignment explanation
Indices: 32211--32251 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
32201 CCTTGTTGAT
32211 TTGTCGTGTCTGGATCAGGAC
1 TTGTCGTGTCTGGATCAGGAC
32232 TTGTCGTGTCTGGATCAGGA
1 TTGTCGTGTCTGGATCAGGA
32252 TTTGGTCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (21 bp):
TTGTCGTGTCTGGATCAGGAC
Found at i:37391 original size:4 final size:4
Alignment explanation
Indices: 37382--37418 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
37372 GTAAGCTTCA
**
37382 TATG TATG TATG TGCG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
37419 GGATTATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:42853 original size:21 final size:21
Alignment explanation
Indices: 42821--42861 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42811 AGGCTCGAGG
42821 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
42842 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
42862 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:46407 original size:145 final size:145
Alignment explanation
Indices: 46144--46433 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
46134 TAACCTCCAA
46144 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
1 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
46209 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
66 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
46274 TAGCTACTTGAAATG
131 TAGCTACTTGAAATG
46289 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
1 CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
46354 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
66 GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
46419 TAGCTACTTGAAATG
131 TAGCTACTTGAAATG
46434 GTACATTTTA
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (145 bp):
CTTCATGTGTCCATTCCACAAGTTAAGGGAAAAAGCAATCTCTGCCAATTCTGGATTTATATGAT
GCATTGATAAATCAGGAAAAACAATCTTTCTGACTCCTAATCACACCAAAAGGAGAAGGGGAGAG
TAGCTACTTGAAATG
Found at i:49924 original size:16 final size:16
Alignment explanation
Indices: 49884--49925 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
49874 GTTTCTTTTT
*
49884 TAATTATAAATAAATA
1 TAATTAAAAATAAATA
49900 TAATTAAAAATAAAT-
1 TAATTAAAAATAAATA
*
49915 TAATTTAAAAT
1 TAATTAAAAAT
49926 TTGACTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATTAAAAATAAATA
Found at i:52621 original size:15 final size:17
Alignment explanation
Indices: 52601--52635 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
52591 GTTGAACTAG
52601 ATTTTAAT-ATTT-TTA
1 ATTTTAATGATTTCTTA
52616 ATTTTAATGATTTCTTA
1 ATTTTAATGATTTCTTA
52633 ATT
1 ATT
52636 GAGTCGGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 4 0.22
17 6 0.33
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAATGATTTCTTA
Found at i:55182 original size:14 final size:14
Alignment explanation
Indices: 55163--55192 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55153 ACACTTGGAT
55163 AACTCCATTACTGG
1 AACTCCATTACTGG
*
55177 AACTCCTTTACTGG
1 AACTCCATTACTGG
55191 AA
1 AA
55193 TCAGTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (14 bp):
AACTCCATTACTGG
Found at i:55358 original size:21 final size:21
Alignment explanation
Indices: 55332--55372 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
55322 CCTTGTTGAT
55332 TTGTCGTGTCTGGATCAGGAC
1 TTGTCGTGTCTGGATCAGGAC
55353 TTGTCGTGTCTGGATCAGGA
1 TTGTCGTGTCTGGATCAGGA
55373 TTTGGTCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (21 bp):
TTGTCGTGTCTGGATCAGGAC
Found at i:60510 original size:4 final size:4
Alignment explanation
Indices: 60501--60537 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
60491 GTAAGCTTCA
**
60501 TATG TATG TATG TGCG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
60538 GGATTATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:65972 original size:21 final size:21
Alignment explanation
Indices: 65940--65980 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
65930 AGGCTCGAGG
65940 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
65961 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
65981 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:71689 original size:15 final size:17
Alignment explanation
Indices: 71669--71703 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
71659 GTTGAACTAG
71669 ATTTTAAT-ATTT-TTA
1 ATTTTAATGATTTCTTA
71684 ATTTTAATGATTTCTTA
1 ATTTTAATGATTTCTTA
71701 ATT
1 ATT
71704 GAGTCGGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 4 0.22
17 6 0.33
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAATGATTTCTTA
Found at i:74238 original size:14 final size:14
Alignment explanation
Indices: 74219--74248 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
74209 ACACTTGGAT
74219 AACTCCATTACTGG
1 AACTCCATTACTGG
*
74233 AACTCCTTTACTGG
1 AACTCCATTACTGG
74247 AA
1 AA
74249 TCAGTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (14 bp):
AACTCCATTACTGG
Found at i:74413 original size:21 final size:21
Alignment explanation
Indices: 74387--74427 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
74377 TCCTTGTTGA
74387 TTGTCGTGTCTGGATCAGGAC
1 TTGTCGTGTCTGGATCAGGAC
74408 TTGTCGTGTCTGGATCAGGA
1 TTGTCGTGTCTGGATCAGGA
74428 TTTGGTCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (21 bp):
TTGTCGTGTCTGGATCAGGAC
Found at i:79562 original size:4 final size:4
Alignment explanation
Indices: 79553--79589 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
79543 GTAAGCTTCA
**
79553 TATG TATG TATG TGCG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
79590 GGATTATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:85020 original size:21 final size:21
Alignment explanation
Indices: 84988--85028 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
84978 AGGCTCGAGG
84988 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
85009 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
85029 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Done.