Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015914.1 Corchorus capsularis cultivar CVL-1 contig15935, 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: 32366
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:1438 original size:12 final size:13
Alignment explanation
Indices: 1421--1449 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1411 AAAAAAGGGG
1421 GGCAGCATT-CAT
1 GGCAGCATTACAT
1433 GGCAGCATTACAT
1 GGCAGCATTACAT
1446 GGCA
1 GGCA
1450 TCTCACCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (13 bp):
GGCAGCATTACAT
Found at i:4462 original size:55 final size:57
Alignment explanation
Indices: 4396--4550 Score: 226
Period size: 55 Copynumber: 2.7 Consensus size: 57
4386 ATTGATGATT
*
4396 AAGAGTCAAGGTAATAGTAATCAGTAAATTAGTAATTAAGTAAAAAGAGATTAA-T-
1 AAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTA
*
4451 CAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTA
1 AAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTA
*
4508 AAGAGACAAGGTAAAAATAGTAATCAGTAAATC-GATAATTAAG
1 AAGAGTCAAGGT---AATAGTAATCAGTAAATCAG-TAATTAAG
4551 AGTAAAAGTG
Statistics
Matches: 90, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
55 52 0.58
56 1 0.01
57 10 0.11
59 1 0.01
60 26 0.29
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (57 bp):
AAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTA
Found at i:4713 original size:24 final size:25
Alignment explanation
Indices: 4676--4731 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
4666 AATTAAGAAG
*
4676 AGATTGATAATTAAAGTGGTAATTA
1 AGATTCATAATTAAAGTGGTAATTA
*
4701 AGATTCAT-ATTAAAGTGGTAATTG
1 AGATTCATAATTAAAGTGGTAATTA
4725 AGATTCA
1 AGATTCA
4732 AAGTAAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (25 bp):
AGATTCATAATTAAAGTGGTAATTA
Found at i:4915 original size:16 final size:16
Alignment explanation
Indices: 4890--4945 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
4880 GTAAGATAGA
4890 AAGT-AAAATGGTATT
1 AAGTAAAAATGGTATT
*
4905 AAGTAAAAATGGCATT
1 AAGTAAAAATGGTATT
* * *
4921 AGGTCAAAATGATATT
1 AAGTAAAAATGGTATT
4937 AAGTAAAAA
1 AAGTAAAAA
4946 GGGTCAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.27
Consensus pattern (16 bp):
AAGTAAAAATGGTATT
Found at i:4956 original size:25 final size:25
Alignment explanation
Indices: 4922--4969 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4912 AATGGCATTA
4922 GGTCAAAATGATATTAAGTAAAAAG
1 GGTCAAAATGATATTAAGTAAAAAG
*
4947 GGTCAAAATGGTATTAAGTAAAA
1 GGTCAAAATGATATTAAGTAAAA
4970 GAGTAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (25 bp):
GGTCAAAATGATATTAAGTAAAAAG
Found at i:9496 original size:22 final size:21
Alignment explanation
Indices: 9406--9504 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 21
9396 CATGGTGTAA
*
9406 TTATCAAATTTTCATAAGGAGG
1 TTATCAAATTTT-ATAAGAAGG
* *
9428 TTA-CAAAATTTTATAGGAAAG
1 TTATC-AAATTTTATAAGAAGG
* * * *
9449 TTATCAAAATTTCATAATACGA
1 TTATC-AAATTTTATAAGAAGG
9471 TTATCGAAATTTTATAAGAAGG
1 TTATC-AAATTTTATAAGAAGG
9493 TTATTCAAATTT
1 TTA-TCAAATTT
9505 CATAGTAAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
21 10 0.17
22 48 0.80
23 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (21 bp):
TTATCAAATTTTATAAGAAGG
Found at i:9524 original size:36 final size:36
Alignment explanation
Indices: 9477--9548 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
9467 ACGATTATCG
9477 AAATTTTATAAGAAGGTTATTCAAATTTCATAGTAA
1 AAATTTTATAAGAAGGTTATTCAAATTTCATAGTAA
9513 AAATTTTATAAGAAGGTTATTCAAATTTCATAGTAA
1 AAATTTTATAAGAAGGTTATTCAAATTTCATAGTAA
9549 GATTGTCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (36 bp):
AAATTTTATAAGAAGGTTATTCAAATTTCATAGTAA
Found at i:9685 original size:22 final size:21
Alignment explanation
Indices: 9609--9693 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 21
9599 ATTTTATGAT
9609 GTGATTATA-AAAATTTCATAG
1 GTGATTA-ACAAAATTTCATAG
*
9630 ATG-TTAACAAAATTTCATAAG
1 GTGATTAACAAAATTTCAT-AG
* **
9651 GAT-ATCAGTAAAATTTCATAG
1 G-TGATTAACAAAATTTCATAG
*
9672 TGTGATTAACAAAAATTCATAG
1 -GTGATTAACAAAATTTCATAG
9694 ATATCTTATC
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.27
21 7 0.14
22 28 0.57
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (21 bp):
GTGATTAACAAAATTTCATAG
Found at i:9781 original size:2 final size:2
Alignment explanation
Indices: 9774--9810 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9764 CCAACTGTAC
9774 AT 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 AT A
9811 CTAGGTTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13951 original size:15 final size:15
Alignment explanation
Indices: 13931--13962 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13921 ATTTTCAAGG
13931 AAGACCGAATTTTCA
1 AAGACCGAATTTTCA
*
13946 AAGACCTAATTTTCA
1 AAGACCGAATTTTCA
13961 AA
1 AA
13963 TTTCACAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (15 bp):
AAGACCGAATTTTCA
Found at i:16112 original size:10 final size:10
Alignment explanation
Indices: 16097--16148 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
16087 TCAACACCAA
16097 GCCATGCCCG
1 GCCATGCCCG
16107 GCCATGCCCG
1 GCCATGCCCG
16117 GCCATGTCCGCG
1 GCCATG-CC-CG
*
16129 CACCATGCCCG
1 -GCCATGCCCG
16140 GCCAATGCC
1 GCC-ATGCC
16149 ATGCCATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 18 0.50
11 9 0.25
12 4 0.11
13 5 0.14
ACGTcount: A:0.13, C:0.48, G:0.27, T:0.12
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:16140 original size:33 final size:32
Alignment explanation
Indices: 16098--16164 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
16088 CAACACCAAG
*
16098 CCATGCCCGGCC-ATGCCCGGCCATGTCCGCGCA
1 CCATGCCCGGCCAATGCCAGGCCA--TCCGCGCA
*
16131 CCATGCCCGGCCAATGCCATGCCATCCGCGCA
1 CCATGCCCGGCCAATGCCAGGCCATCCGCGCA
16163 CC
1 CC
16165 TCACCGAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 10 0.32
33 12 0.39
34 9 0.29
ACGTcount: A:0.15, C:0.49, G:0.24, T:0.12
Consensus pattern (32 bp):
CCATGCCCGGCCAATGCCAGGCCATCCGCGCA
Found at i:18565 original size:25 final size:25
Alignment explanation
Indices: 18537--18616 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 25
18527 ACTAATTATC
18537 CTCTTCTTAATTATTACCACTTTTA
1 CTCTTCTTAATTATTACCACTTTTA
* *
18562 CTCTTCTT-TTTCTCTACCA-TTTTA
1 CTCTTCTTAATTAT-TACCACTTTTA
* * *
18586 CTCTT-TGAATTACTGATCACCTTTTA
1 CTCTTCTTAATTA-TTACCA-CTTTTA
18612 CTCTT
1 CTCTT
18617 TACTGATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.02
24 18 0.42
25 14 0.33
26 10 0.23
ACGTcount: A:0.19, C:0.26, G:0.03, T:0.53
Consensus pattern (25 bp):
CTCTTCTTAATTATTACCACTTTTA
Found at i:18652 original size:21 final size:21
Alignment explanation
Indices: 18623--18692 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
18613 TCTTTACTGA
*
18623 TTACTTCTTGCTAATTACCATT
1 TTAC-TCTTACTAATTACCATT
* * *
18645 TTGCTCTTACTGATTACTATT
1 TTACTCTTACTAATTACCATT
* * *
18666 TTACTCTTTACCATTTACCTTT
1 TTACTC-TTACTAATTACCATT
18688 TTACT
1 TTACT
18693 GATTAATATT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.53
Consensus pattern (21 bp):
TTACTCTTACTAATTACCATT
Found at i:18821 original size:26 final size:27
Alignment explanation
Indices: 18775--18842 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
18765 CTCTTTACTG
**
18775 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
18801 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
18827 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
18843 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:18994 original size:16 final size:16
Alignment explanation
Indices: 18975--19029 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
18965 CGATTGCTTC
18975 TTTTACTTTCACTCTA
1 TTTTACTTTCACTCTA
*
18991 TTTTACTGATT-ACT-TC
1 TTTTACT--TTCACTCTA
*
19007 TTTTACTTTCACTCCA
1 TTTTACTTTCACTCTA
19023 TTTTACT
1 TTTTACT
19030 GATTACTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 22 0.69
17 3 0.09
18 2 0.06
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTTACTTTCACTCTA
Found at i:18994 original size:32 final size:32
Alignment explanation
Indices: 18956--19039 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
18946 CTCTTGATTA
* *
18956 CCATTTTACCGATTGCTTCTTTTACTTTCACT
1 CCATTTTACTGATTACTTCTTTTACTTTCACT
*
18988 CTATTTTACTGATTACTTCTTTTACTTTCACT
1 CCATTTTACTGATTACTTCTTTTACTTTCACT
19020 CCATTTTACTGATTACTTCT
1 CCATTTTACTGATTACTTCT
19040 CTTGGTTACC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.52
Consensus pattern (32 bp):
CCATTTTACTGATTACTTCTTTTACTTTCACT
Done.