Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008600.1 Corchorus capsularis cultivar CVL-1 contig08621, whole genome shotgun sequence
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: 63384
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9103 original size:13 final size:14
Alignment explanation
Indices: 9084--9122 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
9074 AGTTTCTTTT
9084 TTGAGTTAGTTTCG
1 TTGAGTTAGTTTCG
*
9098 TT-AGTTTGTTTCG
1 TTGAGTTAGTTTCG
*
9111 TTGAGTCAGTTT
1 TTGAGTTAGTTT
9123 GTGTTGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.13, C:0.08, G:0.26, T:0.54
Consensus pattern (14 bp):
TTGAGTTAGTTTCG
Found at i:9123 original size:18 final size:18
Alignment explanation
Indices: 9100--9144 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
9090 TAGTTTCGTT
9100 AGTTTGTTTCGTTGAGTC
1 AGTTTGTTTCGTTGAGTC
*
9118 AGTTTGTGTT-GTTGAGTT
1 AGTTTGT-TTCGTTGAGTC
9136 AGTTT-TTTC
1 AGTTTGTTTC
9145 AATAGTCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 19 0.79
19 2 0.08
ACGTcount: A:0.11, C:0.07, G:0.27, T:0.56
Consensus pattern (18 bp):
AGTTTGTTTCGTTGAGTC
Found at i:12614 original size:29 final size:28
Alignment explanation
Indices: 12543--12620 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
12533 TAAAAGTACA
* *
12543 AAATTGGTCCCTCAAGTGGAGCGAAAATAGC
1 AAATTAGTCCCTCAAGT-GA--AAAAATAGC
*
12574 AAATTGGTCCCTCAAGTGAAAAAATATGC
1 AAATTAGTCCCTCAAGTGAAAAAATA-GC
* *
12603 AATTTAGTCCCTGAAGTG
1 AAATTAGTCCCTCAAGTG
12621 GAGTTAACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 6 0.14
29 17 0.40
30 2 0.05
31 17 0.40
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (28 bp):
AAATTAGTCCCTCAAGTGAAAAAATAGC
Found at i:12844 original size:30 final size:31
Alignment explanation
Indices: 12784--12853 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
12774 AAAATTGGTG
*
12784 AGGGACCCAATTGCTCAATTAACTCAACTTC
1 AGGGACCCAATTACTCAATTAACTCAACTTC
* *
12815 AGGGACTCAATTACTC-ATTAAGTTC-ACTTC
1 AGGGACCCAATTACTCAATTAA-CTCAACTTC
*
12845 AAGGACCCA
1 AGGGACCCA
12854 TTTGCACATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (31 bp):
AGGGACCCAATTACTCAATTAACTCAACTTC
Found at i:14891 original size:17 final size:19
Alignment explanation
Indices: 14869--14907 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
14859 AAGAGACAAT
*
14869 AAAATATGGAG-A-GGAAG
1 AAAATATGAAGAAGGGAAG
14886 AAAATATGAAGAAGGGAAG
1 AAAATATGAAGAAGGGAAG
14905 AAA
1 AAA
14908 TTGTTCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (19 bp):
AAAATATGAAGAAGGGAAG
Found at i:15101 original size:11 final size:11
Alignment explanation
Indices: 15087--15124 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15077 ATTCATAACA
15087 AATTTATAATT
1 AATTTATAATT
15098 AATTTATAATT
1 AATTTATAATT
15109 -ATTTGATAATT
1 AATTT-ATAATT
*
15120 TATTT
1 AATTT
15125 TATATTGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:16527 original size:30 final size:31
Alignment explanation
Indices: 16493--16575 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
16483 TCATATATTG
* *
16493 CACAAAAAT-GTTTAATTTAATCCATGTACT
1 CACAAAAATGGGTCAATTTAATCCATGTACT
* *
16523 CACAAAATTGGGTCAATTTATTCCATGTACT
1 CACAAAAATGGGTCAATTTAATCCATGTACT
* * * *
16554 CATAAGATTGAGTCAATTTAAT
1 CACAAAAATGGGTCAATTTAAT
16576 TAAAGCACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 8 0.18
31 36 0.82
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (31 bp):
CACAAAAATGGGTCAATTTAATCCATGTACT
Found at i:16548 original size:31 final size:31
Alignment explanation
Indices: 16506--16575 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
16496 AAAAATGTTT
*
16506 AATTTAATCCATGTACTCACAAAATTGGGTC
1 AATTTAATCCATGTACTCACAAAATTGAGTC
* * *
16537 AATTTATTCCATGTACTCATAAGATTGAGTC
1 AATTTAATCCATGTACTCACAAAATTGAGTC
16568 AATTTAAT
1 AATTTAAT
16576 TAAAGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
AATTTAATCCATGTACTCACAAAATTGAGTC
Found at i:18815 original size:25 final size:24
Alignment explanation
Indices: 18780--18838 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
18770 TTCAAACCCT
* *
18780 AAACTTAATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
18805 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
18829 AAA-TTCATTT
1 AAACTTCATTT
18839 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 8 0.26
25 16 0.52
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:18877 original size:26 final size:26
Alignment explanation
Indices: 18848--18915 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
18838 TTCCTTCATT
18848 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
18874 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
18900 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
18916 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:18939 original size:52 final size:51
Alignment explanation
Indices: 18848--18951 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
18838 TTCCTTCATT
* *
18848 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
18900 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
18951 T
1 T
18952 CATAAATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 11 0.24
52 28 0.62
53 6 0.13
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:19179 original size:21 final size:22
Alignment explanation
Indices: 19144--19189 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
19134 AAAAATTATA
**
19144 AAAAGGGGGGACGGTATTTAGC
1 AAAAGGGGGGACGGTAAATAGC
19166 AAAAGGGGGG-CGGTAAATAGC
1 AAAAGGGGGGACGGTAAATAGC
19187 AAA
1 AAA
19190 CCCTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.13
Consensus pattern (22 bp):
AAAAGGGGGGACGGTAAATAGC
Found at i:21982 original size:11 final size:11
Alignment explanation
Indices: 21968--22005 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
21958 ATTCATAACA
21968 AATTTATAATT
1 AATTTATAATT
21979 AATTTATAATT
1 AATTTATAATT
21990 -ATTTGATAATT
1 AATTT-ATAATT
*
22001 TATTT
1 AATTT
22006 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:22779 original size:17 final size:17
Alignment explanation
Indices: 22759--22791 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22749 CCCAGATTAT
22759 CAGTGAT-CTAAGATCAG
1 CAGTGATGC-AAGATCAG
22776 CAGTGATGCAAGATCA
1 CAGTGATGCAAGATCA
22792 TTGTTGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (17 bp):
CAGTGATGCAAGATCAG
Found at i:23790 original size:30 final size:30
Alignment explanation
Indices: 23708--23792 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
23698 TAAATTTAAT
* * *
23708 TGACACCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAAAAGTTGTCATGATTTTGCAAC
* *
23738 TGACACCAGATGTTGTCATGATTTTGCAAC
1 TGACACCAAAAGTTGTCATGATTTTGCAAC
23768 TGACACCAAAAGTTGTCATGATTTT
1 TGACACCAAAAGTTGTCATGATTTT
23793 ACGTTTGGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (30 bp):
TGACACCAAAAGTTGTCATGATTTTGCAAC
Found at i:26225 original size:12 final size:12
Alignment explanation
Indices: 26208--26235 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
26198 GAGCACCTAT
26208 ATATTTTTAATA
1 ATATTTTTAATA
26220 ATATTTTTAATA
1 ATATTTTTAATA
26232 ATAT
1 ATAT
26236 ATATATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTTTAATA
Found at i:26237 original size:14 final size:13
Alignment explanation
Indices: 26205--26237 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
26195 AATGAGCACC
26205 TATATATTTTTAA
1 TATATATTTTTAA
26218 TA-ATATTTTTAA
1 TATATATTTTTAA
26230 TAATATAT
1 T-ATATAT
26238 ATATGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.61
13 3 0.17
14 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATATTTTTAA
Found at i:26304 original size:11 final size:12
Alignment explanation
Indices: 26290--26318 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
26280 TGATATTTTA
26290 TTATTAAAATG-
1 TTATTAAAATGT
26301 TTATTAAAATGT
1 TTATTAAAATGT
26313 TTATTA
1 TTATTA
26319 TATTATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TTATTAAAATGT
Found at i:37598 original size:89 final size:90
Alignment explanation
Indices: 37498--37671 Score: 287
Period size: 91 Copynumber: 1.9 Consensus size: 90
37488 TTATACAATA
* *
37498 TCATTTAAGAAATATATTT-AAAAAATTCTAATAGATCTAAGTTTTTTAATTAAAATGGTAAAAT
1 TCATTTAAGAAATATATTTAAAAAAATTCTAATAGATATAAGTTTTTTAATTAAAATAGTAAAAT
37562 AATAAAAATAAAATAGTTACTGTAG
66 AATAAAAATAAAATAGTTACTGTAG
*
37587 TCATTTAAGAAATATATTTAAAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAA
1 TCATTTAAGAAATATATTT-AAAAAAATTCTAATAGATATAAGTTTTTTAATTAAAATAGTAAAA
**
37652 TGGTAAAAATAAAATAGTTA
65 TAATAAAAATAAAATAGTTA
37672 TAAATATATT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 19 0.24
91 59 0.76
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.37
Consensus pattern (90 bp):
TCATTTAAGAAATATATTTAAAAAAATTCTAATAGATATAAGTTTTTTAATTAAAATAGTAAAAT
AATAAAAATAAAATAGTTACTGTAG
Found at i:41066 original size:33 final size:34
Alignment explanation
Indices: 41023--41091 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
41013 CTAAACAAAT
*
41023 AAAGATTTTAC-AAAAAGATTTACTAATAAAAAC
1 AAAGAGTTTACAAAAAAGATTTACTAATAAAAAC
*
41056 AAAGAGTTTACAAAAAATATTTACTAATAAAAAC
1 AAAGAGTTTACAAAAAAGATTTACTAATAAAAAC
41090 AA
1 AA
41092 TTATATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 10 0.30
34 23 0.70
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (34 bp):
AAAGAGTTTACAAAAAAGATTTACTAATAAAAAC
Found at i:41401 original size:31 final size:31
Alignment explanation
Indices: 41330--41401 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
41320 GTCTATCAGC
*
41330 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* * *
41361 TAATT-ATTTGTTTAATTTTATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTAATTT
41391 GTTTTAATTTG
1 -TTTTAATTTG
41402 CAATAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.24, C:0.04, G:0.10, T:0.62
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:41650 original size:31 final size:31
Alignment explanation
Indices: 41615--41687 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
41605 AACCTAAGAT
* * *
41615 CGAACCCGAAATACTTGAACCTGACATAGCC
1 CGAACCCGAAATACCTAAACCTGACAGAGCC
* **
41646 CGAACCCAAAAATACCTAAATTTGACAGAGCC
1 CGAACCC-GAAATACCTAAACCTGACAGAGCC
41678 CGAACCCGAA
1 CGAACCCGAA
41688 TGAACCCGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.40, C:0.32, G:0.15, T:0.14
Consensus pattern (31 bp):
CGAACCCGAAATACCTAAACCTGACAGAGCC
Found at i:42706 original size:20 final size:20
Alignment explanation
Indices: 42681--42720 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42671 TATGTTCTTA
42681 GTTGTTTTTAA-AGATTAGAG
1 GTTGTTTTTAACA-ATTAGAG
42701 GTTGTTTTTAACAATTAGAG
1 GTTGTTTTTAACAATTAGAG
42721 ATGTTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTGTTTTTAACAATTAGAG
Found at i:42725 original size:19 final size:20
Alignment explanation
Indices: 42683--42726 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42673 TGTTCTTAGT
*
42683 TGTTTTTAAAGATTAGAGGT
1 TGTTTTTAAAGATTAGAGGA
42703 TGTTTTTAACA-ATTAGA-GA
1 TGTTTTTAA-AGATTAGAGGA
42722 TGTTT
1 TGTTT
42727 GATCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (20 bp):
TGTTTTTAAAGATTAGAGGA
Found at i:44027 original size:23 final size:23
Alignment explanation
Indices: 43994--44065 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
43984 TCTTTGTTTA
*
43994 TTTTGGAACTCCTATGTGAGAGC
1 TTTTGGAACTCCTTTGTGAGAGC
*
44017 TTTTGGTACTCCTTTGTGAGAGC
1 TTTTGGAACTCCTTTGTGAGAGC
*
44040 TTTTGGGACTCCTTTGTGAGAGC
1 TTTTGGAACTCCTTTGTGAGAGC
44063 TTT
1 TTT
44066 GTCTATTGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.42
Consensus pattern (23 bp):
TTTTGGAACTCCTTTGTGAGAGC
Found at i:47363 original size:31 final size:31
Alignment explanation
Indices: 47292--47363 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
47282 ATCCATCAAC
47292 TTTTAATTTGTTTAATTTAAGGCTTACATTT
1 TTTTAATTTGTTTAATTTAAGGCTTACATTT
** * *
47323 TAATGATTTGTTTAATTTAATGCTTA-ATTT
1 TTTTAATTTGTTTAATTTAAGGCTTACATTT
47353 GTTTTAATTTG
1 -TTTTAATTTG
47364 CAATCATTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.58
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTACATTT
Found at i:52210 original size:64 final size:64
Alignment explanation
Indices: 52131--52324 Score: 352
Period size: 64 Copynumber: 3.0 Consensus size: 64
52121 AATCATTGGA
*
52131 ATTCAAATAAAAGATCTGAAGTCACAGGTGTGATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
1 ATTCAAATAAAAGATCTGAAGTCACAGGTGAGATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
*
52195 ATTCAAATAAAAGATCTGAAGTCACAGGTGAAATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
1 ATTCAAATAAAAGATCTGAAGTCACAGGTGAGATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
* *
52259 ATTCAAATAAAAAATCTGAAGTCACATGTGAGATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
1 ATTCAAATAAAAGATCTGAAGTCACAGGTGAGATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
52323 AT
1 AT
52325 GACAACTTGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 125 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (64 bp):
ATTCAAATAAAAGATCTGAAGTCACAGGTGAGATTTACTCTGTAAAGACTGCCCGTTAAAGTAT
Found at i:57578 original size:6 final size:6
Alignment explanation
Indices: 57567--57609 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
57557 TTCTTTTAAT
57567 ATATAC ATATAC ATATAC ATATAC ATATAC ATGCATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC AT--ATAC ATATA
57610 TATGTATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 29 0.83
8 6 0.17
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:60505 original size:82 final size:82
Alignment explanation
Indices: 60368--60531 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
60358 ATGCTTCTTA
*
60368 AAACAAATGATGAGCTCAAAATTCATGGGTAAAATTTAAACTGTGCAAGTCTATGACAAATGAAA
1 AAACAAATGATGAGCTCAAAACTCATGGGTAAAATTTAAACTGTGCAAGTCTATGACAAATGAAA
60433 GACAGAAGCATAGAAAG
66 GACAGAAGCATAGAAAG
*
60450 AAACAAATGATGAGCTCAAAACTCATGGGTAAAATTTGAACTGTGCAAGTCTATGACAAATGAAA
1 AAACAAATGATGAGCTCAAAACTCATGGGTAAAATTTAAACTGTGCAAGTCTATGACAAATGAAA
*
60515 GCCAGAAGCATAGAAAG
66 GACAGAAGCATAGAAAG
60532 CAACTCGCTA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.20
Consensus pattern (82 bp):
AAACAAATGATGAGCTCAAAACTCATGGGTAAAATTTAAACTGTGCAAGTCTATGACAAATGAAA
GACAGAAGCATAGAAAG
Found at i:63358 original size:21 final size:19
Alignment explanation
Indices: 63322--63384 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 19
63312 ATAAAAGTAA
*
63322 ATATATATT-TATTATAAT
1 ATATATATTAAATTATAAT
63340 ATATATATATACAATTATAAT
1 ATATATAT-TA-AATTATAAT
*
63361 ATATAAATTAAA-TAT-AT
1 ATATATATTAAATTATAAT
63378 ATATATA
1 ATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 8 0.21
18 11 0.28
19 3 0.08
20 2 0.05
21 15 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATTAAATTATAAT
Found at i:63362 original size:13 final size:14
Alignment explanation
Indices: 63339--63378 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
63329 TTTATTATAA
63339 TATATATATATACAAT
1 TATA-ATATATA-AAT
63355 TATAATATATAAAT
1 TATAATATATAAAT
63369 TA-AATATATA
1 TATAATATATA
63379 TATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 7 0.29
16 4 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
TATAATATATAAAT
Done.