Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015531.1 Corchorus capsularis cultivar CVL-1 contig15552, 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: 46422
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:974 original size:27 final size:27
Alignment explanation
Indices: 943--1011 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
933 GCTCGAGGGT
943 ATTTTGGTCATTTTTGCACCCAGGGGC
1 ATTTTGGTCATTTTTGCACCCAGGGGC
* ** **
970 ATTTTGGTCATTTTCGGGCTTAGGGGC
1 ATTTTGGTCATTTTTGCACCCAGGGGC
*
997 ATTTTAGTCATTTTT
1 ATTTTGGTCATTTTT
1012 AAGTTCACCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (27 bp):
ATTTTGGTCATTTTTGCACCCAGGGGC
Found at i:1209 original size:12 final size:12
Alignment explanation
Indices: 1192--1216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1182 GATTAACTAA
1192 CTCTCAATTTAG
1 CTCTCAATTTAG
1204 CTCTCAATTTAG
1 CTCTCAATTTAG
1216 C
1 C
1217 AATAAGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CTCTCAATTTAG
Found at i:1486 original size:55 final size:55
Alignment explanation
Indices: 1402--1568 Score: 266
Period size: 55 Copynumber: 3.0 Consensus size: 55
1392 GTGGCCCAAT
1402 ATCCTTAATAAGTACACTATTGCATTTGTGTTTACAAAAAATACCAATAGTAAAA
1 ATCCTTAATAAGTACACTATTGCATTTGTGTTTACAAAAAATACCAATAGTAAAA
*
1457 ATCCTTAATAAGTACACTATTGCATTTGTGTTTACAAAAAAATACTTAATAGTAAAA
1 ATCCTTAATAAGTACACTATTGCATTTGTGTTTAC-AAAAAATAC-CAATAGTAAAA
* *
1514 ATCCTTCATAAGTACACTATTGCATTT-TGGTTTAC-AAAAATACCAATAATAAAA
1 ATCCTTAATAAGTACACTATTGCATTTGT-GTTTACAAAAAATACCAATAGTAAAA
1568 A
1 A
1569 GAGAAGAAAA
Statistics
Matches: 105, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
54 10 0.10
55 43 0.41
56 10 0.10
57 42 0.40
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (55 bp):
ATCCTTAATAAGTACACTATTGCATTTGTGTTTACAAAAAATACCAATAGTAAAA
Found at i:3464 original size:51 final size:49
Alignment explanation
Indices: 3396--3651 Score: 248
Period size: 51 Copynumber: 5.1 Consensus size: 49
3386 AATGGAACCC
* *
3396 TTGAATAAAAGACTGAATTTTTAAGTAAATTGGTAAATAAAAATATCATCT
1 TTGAATAAAAGATTGAATTTTTAAGT-AATTAGTAAATAAAAAT-TCATCT
* * * * *
3447 TTGAGTAAAAGGTTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCT
1 TTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAA-AATTCATCT
* * * * **
3498 ATGAATAAATGATTGAATGTTTAAGTAATTGGTAAGCAAAAATGTCATCT
1 TTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAAT-TCATCT
* * * * *
3548 TTGAGTAAAAGATTGAATTTTTAGGGTAATTAGTATATAAAGATTCAATCA
1 TTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATTC-ATCT
*
3599 TTGAATAAAAGATTGAATTTTTAAGT--TTAGTAAAT-AAAATGTCACCT
1 TTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAAT-TCATCT
3646 TTGAAT
1 TTGAAT
3652 TGGAAGTTTT
Statistics
Matches: 164, Mismatches: 35, Indels: 16
0.76 0.16 0.07
Matches are distributed among these distances:
47 12 0.07
48 10 0.06
49 2 0.01
50 41 0.25
51 94 0.57
52 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.37
Consensus pattern (49 bp):
TTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATTCATCT
Found at i:3577 original size:101 final size:102
Alignment explanation
Indices: 3391--3624 Score: 337
Period size: 101 Copynumber: 2.3 Consensus size: 102
3381 TAAAAAATGG
* * *
3391 AACCCTTGAATAAAAGACTGAATTTTTAAGTAAATTGGTAAATAAAAATATCATCTTTGAGTAAA
1 AACCATTGAATAAAAGATTGAATTTTTAAGTAAATTGGTAAACAAAAATATCATCTTTGAGTAAA
* *
3456 AGGTTGAATTTTTAGAGTAATTAGTAAATAAAGATTT
66 AGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTC
* * * *
3493 AACC-TATGAATAAATGATTGAATGTTTAAGT-AATTGGTAAGCAAAAATGTCATCTTTGAGTAA
1 AACCAT-TGAATAAAAGATTGAATTTTTAAGTAAATTGGTAAACAAAAATATCATCTTTGAGTAA
* *
3556 AAGATTGAATTTTTAGGGTAATTAGTATATAAAGATTC
65 AAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTC
*
3594 AATCATTGAATAAAAGATTGAATTTTTAAGT
1 AACCATTGAATAAAAGATTGAATTTTTAAGT
3625 TTAGTAAATA
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
101 90 0.77
102 27 0.23
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.36
Consensus pattern (102 bp):
AACCATTGAATAAAAGATTGAATTTTTAAGTAAATTGGTAAACAAAAATATCATCTTTGAGTAAA
AGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTC
Found at i:4414 original size:47 final size:48
Alignment explanation
Indices: 4360--4471 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 48
4350 GTAAAAAGAA
** * *
4360 AATCAGTAAATCAGTAAAAAAAGATTAATC-GGAGTCAAAGTGATGGT
1 AATCAGTAAATCAGTAAAAAAAGATTAATCAAAAGTCAAAGTAATAGT
* * *
4407 AATCAGTAAATCAGTGAAAAGAGATTAATCAAAAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAAAAAAAGATTAATCAAAAGTCAAAGTAATAGT
*
4455 AATCGGTAAATCAGTAA
1 AATCAGTAAATCAGTAA
4472 TCAAGTAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
47 28 0.51
48 27 0.49
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (48 bp):
AATCAGTAAATCAGTAAAAAAAGATTAATCAAAAGTCAAAGTAATAGT
Found at i:4569 original size:33 final size:31
Alignment explanation
Indices: 4503--4569 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
4493 AGTAAATTGA
* * *
4503 TAATTACGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAAAAATTAATCAG
4534 TAATTAAGAGTCAAGGTAAAAAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAAAAAT--TAATCAG
4567 TAA
1 TAA
4570 ATCAGTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 21 0.68
33 10 0.32
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.25
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAAAAATTAATCAG
Found at i:4587 original size:72 final size:71
Alignment explanation
Indices: 4432--4588 Score: 167
Period size: 72 Copynumber: 2.2 Consensus size: 71
4422 GAAAAGAGAT
* * * *
4432 TAATCAAAAGTCAAGGTAATAGTAATCGGTAAATCAGTAATCAAGTAAAAACATAGTAATCAGTA
1 TAATTAAAAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAACATAGTAATCAGTA
*
4497 AATTGA
66 AATAGA
** * *
4503 TAATTACGAGTCAAGGTAAGAGATTAATCAGTAATTAAG-AGTCAAGGTAAAAA-ATAGTAATCA
1 TAATTAAAAGTCAAGGTAAGAG--TAATCAGTAAATAAGTAATCAA-GTAAAAACATAGTAATCA
4566 GTAAATCAG-
63 GTAAAT-AGA
*
4575 TGATTAAAAGTCAA
1 TAATTAAAAGTCAA
4589 TAGATTGATC
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
71 18 0.26
72 32 0.46
73 20 0.29
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.25
Consensus pattern (71 bp):
TAATTAAAAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAACATAGTAATCAGTA
AATAGA
Found at i:4756 original size:6 final size:7
Alignment explanation
Indices: 4736--4769 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4726 AGGAGTAATT
4736 AGTAAAA
1 AGTAAAA
4743 AGTAAAA
1 AGTAAAA
4750 AGTAAAAA
1 AGT-AAAA
*
4758 AGTAAAG
1 AGTAAAA
4765 AGTAA
1 AGTAA
4770 TCAGCAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (7 bp):
AGTAAAA
Found at i:4759 original size:15 final size:15
Alignment explanation
Indices: 4739--4769 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4729 AGTAATTAGT
4739 AAAAAGTAAAAAGTA
1 AAAAAGTAAAAAGTA
*
4754 AAAAAGTAAAGAGTA
1 AAAAAGTAAAAAGTA
4769 A
1 A
4770 TCAGCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (15 bp):
AAAAAGTAAAAAGTA
Found at i:4779 original size:35 final size:36
Alignment explanation
Indices: 4740--4853 Score: 112
Period size: 35 Copynumber: 3.2 Consensus size: 36
4730 GTAATTAGTA
4740 AAAAGTAA-AA-AGTAAAAAAGTAAAGAGTAATCAGC
1 AAAAGTAAGAATAGT-AAAAAGTAAAGAGTAATCAGC
* *
4775 AAAAG-AAGAATGGTAAAAAGTAAAGAATAATCAG-
1 AAAAGTAAGAATAGTAAAAAGTAAAGAGTAATCAGC
* * * *
4809 TAAAGGAAGAATGGTAAAGAGTAAAG-GATAATCAGC
1 AAAAGTAAGAATAGTAAAAAGTAAAGAG-TAATCAGC
4845 AAAAAGTAA
1 -AAAAGTAA
4854 AAAGATCATC
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
34 6 0.09
35 52 0.79
36 2 0.03
37 6 0.09
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.15
Consensus pattern (36 bp):
AAAAGTAAGAATAGTAAAAAGTAAAGAGTAATCAGC
Found at i:4967 original size:21 final size:21
Alignment explanation
Indices: 4943--5153 Score: 122
Period size: 21 Copynumber: 9.5 Consensus size: 21
4933 TCAGTAGAAG
* *
4943 GTAATCATTAAGAGTAAAACA
1 GTAATCAGTAAGAGTAAAATA
* * * * *
4964 GTAACCAGTGAGAGCAAAGTG
1 GTAATCAGTAAGAGTAAAATA
* *
4985 GTAATTAGTAAGAGTCAAATA
1 GTAATCAGTAAGAGTAAAATA
*
5006 GTAATCAGTAAGAAGTAAAAGA
1 GTAATCAGTAAG-AGTAAAATA
*
5028 GTAATCAGTAAAAAAGGAGCAGAAAATA
1 GTAATCAGT----AA-GAG--TAAAATA
*
5056 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAGT--AAGAGTAAAATA
* *
5079 GTAATCAGTAAAAAGTAAGAA-G
1 GTAATCAGT-AAGAGTAA-AATA
**
5101 GTAATCAACAAGAGTAAAATA
1 GTAATCAGTAAGAGTAAAATA
*
5122 GTAATCAGTACAAAGTAAAGA-A
1 GTAATCAGTA-AGAGTAAA-ATA
5144 -TAATCAGTAA
1 GTAATCAGTAA
5154 AATAATGATG
Statistics
Matches: 149, Mismatches: 29, Indels: 25
0.73 0.14 0.12
Matches are distributed among these distances:
20 3 0.02
21 63 0.42
22 40 0.27
23 17 0.11
25 3 0.02
26 8 0.05
27 1 0.01
28 14 0.09
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (21 bp):
GTAATCAGTAAGAGTAAAATA
Found at i:5037 original size:15 final size:15
Alignment explanation
Indices: 5019--5074 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
5009 ATCAGTAAGA
5019 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
5034 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
5048 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
5062 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
5075 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:9135 original size:5 final size:5
Alignment explanation
Indices: 9118--9157 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
9108 TATATTGTAG
*
9118 TAAGA TAAAA TAAGA TAAGA TAAGA T-A-A TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
9158 TTCATTCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 27 0.87
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:12711 original size:89 final size:89
Alignment explanation
Indices: 12560--12738 Score: 331
Period size: 89 Copynumber: 2.0 Consensus size: 89
12550 TTTTAGGTGC
12560 AATTTTGTATGGTGCCCACCCCAACTTGGTCATTAGTGCACACCTTATCGATTAATTGAATATTG
1 AATTTTGTATGGTGCCCACCCCAACTTGGTCATTAGTGCACACCTTATCGATTAATTGAATATTG
12625 TACCCTTAAACCAGTCTATGAGCT
66 TACCCTTAAACCAGTCTATGAGCT
* *
12649 AATTTTGTATGGTGCCCACCCTAACTTGGTTATTAGTGCACACCTTATCGATTAATTGAATATTG
1 AATTTTGTATGGTGCCCACCCCAACTTGGTCATTAGTGCACACCTTATCGATTAATTGAATATTG
*
12714 TGCCCTTAAACCAGTCTATGAGCT
66 TACCCTTAAACCAGTCTATGAGCT
12738 A
1 A
12739 TTAAGAAAAC
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (89 bp):
AATTTTGTATGGTGCCCACCCCAACTTGGTCATTAGTGCACACCTTATCGATTAATTGAATATTG
TACCCTTAAACCAGTCTATGAGCT
Found at i:16800 original size:31 final size:28
Alignment explanation
Indices: 16742--16805 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 28
16732 TGACACGTGG
*
16742 CACGTGTCCTTTTGTGCACATGGCATGC
1 CACGTGTCCTTTTGTACACATGGCATGC
*
16770 CACGTGTCACTTTTTGGTACACGTGGCATGC
1 CACGTGTC-C-TTTT-GTACACATGGCATGC
16801 CACGT
1 CACGT
16806 CGGACATCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 8 0.26
29 1 0.03
30 4 0.13
31 18 0.58
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.31
Consensus pattern (28 bp):
CACGTGTCCTTTTGTACACATGGCATGC
Found at i:23460 original size:15 final size:15
Alignment explanation
Indices: 23440--23471 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23430 CATATTTATT
23440 CAAAGATGAGTTTGG
1 CAAAGATGAGTTTGG
23455 CAAAGATGAGTTTGG
1 CAAAGATGAGTTTGG
23470 CA
1 CA
23472 CTTGATAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.25
Consensus pattern (15 bp):
CAAAGATGAGTTTGG
Found at i:25072 original size:14 final size:14
Alignment explanation
Indices: 25051--25099 Score: 73
Period size: 14 Copynumber: 3.4 Consensus size: 14
25041 ATTTCAAGGA
25051 TTTTTTTTTG-TTT
1 TTTTTTTTTGCTTT
25064 TTGTTTTTTTGCTTTT
1 TT-TTTTTTTGC-TTT
25080 TTTTTTTTTGCTTT
1 TTTTTTTTTGCTTT
25094 TTTTTT
1 TTTTTT
25100 ACCCCCTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.06
14 17 0.52
15 9 0.27
16 5 0.15
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTGCTTT
Found at i:25072 original size:15 final size:15
Alignment explanation
Indices: 25051--25099 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
25041 ATTTCAAGGA
25051 TTTTTTTTTG-TTTT
1 TTTTTTTTTGCTTTT
*
25065 TGTTTTTTTGCTTTT
1 TTTTTTTTTGCTTTT
25080 TTTTTTTTTGCTTTT
1 TTTTTTTTTGCTTTT
25095 TTTTT
1 TTTTT
25100 ACCCCCTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 9 0.28
15 23 0.72
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTGCTTTT
Found at i:25460 original size:23 final size:24
Alignment explanation
Indices: 25428--25473 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
25418 AGACAATAGA
*
25428 AAAAAGCTCTCACAAAGGAGTCCC
1 AAAAAGCTCTCACAAAGAAGTCCC
*
25452 AAAAA-CTCTCACTAAGAAGTCC
1 AAAAAGCTCTCACAAAGAAGTCC
25474 AAATAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.15
Consensus pattern (24 bp):
AAAAAGCTCTCACAAAGAAGTCCC
Found at i:25839 original size:6 final size:6
Alignment explanation
Indices: 25799--25838 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
25789 GGAAATGGTC
* *
25799 AATACT AATACT AATACT AATGCT AATACT AATAAT AATA
1 AATACT AATACT AATACT AATACT AATACT AATACT AATA
25839 AGAGTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (6 bp):
AATACT
Found at i:26688 original size:6 final size:6
Alignment explanation
Indices: 26677--26717 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
26667 TGGTCAAAAA
*
26677 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC CTTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
26718 GCTTTGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTC
Found at i:26999 original size:22 final size:21
Alignment explanation
Indices: 26967--27007 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
26957 GTGGATTTCC
*
26967 TCTATTTGGTACCCACTCCCCT
1 TCTATTCGGTACCCA-TCCCCT
26989 TCTATTCGGTACCCATCCC
1 TCTATTCGGTACCCATCCC
27008 TCATTTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.15, C:0.41, G:0.10, T:0.34
Consensus pattern (21 bp):
TCTATTCGGTACCCATCCCCT
Found at i:32133 original size:23 final size:23
Alignment explanation
Indices: 32106--32155 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
32096 GAATCTTAGA
32106 GCCTTCAATGTGTTTGTTATCTT
1 GCCTTCAATGTGTTTGTTATCTT
32129 GCCTTCAATGTGTTTGTTATCTT
1 GCCTTCAATGTGTTTGTTATCTT
32152 GCCT
1 GCCT
32156 AAGTGAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.50
Consensus pattern (23 bp):
GCCTTCAATGTGTTTGTTATCTT
Found at i:33076 original size:18 final size:18
Alignment explanation
Indices: 33050--33084 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33040 AATAGTAAAA
*
33050 AAAATGCAATTAGGAAAC
1 AAAAGGCAATTAGGAAAC
33068 AAAAGGCAATTAGGAAA
1 AAAAGGCAATTAGGAAA
33085 AGGCAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.09, G:0.20, T:0.14
Consensus pattern (18 bp):
AAAAGGCAATTAGGAAAC
Found at i:36511 original size:20 final size:20
Alignment explanation
Indices: 36486--36531 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
36476 TGTTTTGCTC
36486 TGCTTCCTTTAATTAGAATA
1 TGCTTCCTTTAATTAGAATA
*
36506 TGCTTCCTTTAATTAGAATC
1 TGCTTCCTTTAATTAGAATA
36526 TGCTTC
1 TGCTTC
36532 AAGCATGTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (20 bp):
TGCTTCCTTTAATTAGAATA
Done.