Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009419.1 Corchorus capsularis cultivar CVL-1 contig09440, 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: 35287
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1757 original size:2 final size:2
Alignment explanation
Indices: 1750--1776 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1740 TGAATACAGG
1750 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1777 CAGATACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2146 original size:19 final size:19
Alignment explanation
Indices: 2122--2159 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2112 TATCTTGATC
*
2122 TATGTTGTGTTGAATTACT
1 TATGTTATGTTGAATTACT
2141 TATGTTATGTTGAATTACT
1 TATGTTATGTTGAATTACT
2160 ATGGTACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (19 bp):
TATGTTATGTTGAATTACT
Found at i:6769 original size:28 final size:26
Alignment explanation
Indices: 6733--6801 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
6723 TTTTTAAAAA
* * *
6733 AAATCGATTTTCAATAATTATTTTTGAT
1 AAATGGATTTTCAAT-AGT-TTTTTAAT
*
6761 AAATGGATTTTCACTAGTTTTTTAAT
1 AAATGGATTTTCAATAGTTTTTTAAT
6787 AAATGGATTTTCAAT
1 AAATGGATTTTCAAT
6802 CTTTAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 21 0.58
27 2 0.06
28 13 0.36
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (26 bp):
AAATGGATTTTCAATAGTTTTTTAAT
Found at i:7054 original size:16 final size:16
Alignment explanation
Indices: 7015--7058 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
7005 TCTAAATAAG
*
7015 TAAAATAAAAAGATAT
1 TAAAATAAAAAAATAT
*
7031 TAAGATAAAAAAAT-T
1 TAAAATAAAAAAATAT
7046 TAAAAATAAAAAA
1 T-AAAATAAAAAA
7059 TGAAGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
TAAAATAAAAAAATAT
Found at i:7593 original size:11 final size:11
Alignment explanation
Indices: 7550--7587 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7540 TTCCTATGTA
*
7550 AAATAAATTAT
1 AAATTAATTAT
7561 CAAA-TAATTAT
1 -AAATTAATTAT
7572 AAATTAATTAT
1 AAATTAATTAT
7583 AAATT
1 AAATT
7588 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:12181 original size:2 final size:2
Alignment explanation
Indices: 12174--12224 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
12164 CCCTTGTCTT
12174 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
12216 TC TC CC TC T
1 TC TC TC TC T
12225 TTCTGCATGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:17502 original size:16 final size:16
Alignment explanation
Indices: 17478--17511 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17468 TTTTCTTCTG
17478 CTCTATATTCTATTGT
1 CTCTATATTCTATTGT
* *
17494 CTCTCTATTCTCTTGT
1 CTCTATATTCTATTGT
17510 CT
1 CT
17512 TTTACATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.26, G:0.06, T:0.56
Consensus pattern (16 bp):
CTCTATATTCTATTGT
Found at i:17640 original size:53 final size:53
Alignment explanation
Indices: 17556--17662 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
17546 TTGTTATCAT
* *
17556 TTCACAACAAAATTTGATTTATTAACTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTATTAACAGAATTTTCTTAAAAGAATTTATAAAA
*
17609 TTCACAACAAAATTTGATTTCTTAACAGAATTTTCTTAAAAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTATTAACAGAATTTTCTTAAAAGAATTTATAAAA
17662 T
1 T
17663 AAAACAGCCG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTATTAACAGAATTTTCTTAAAAGAATTTATAAAA
Found at i:17645 original size:14 final size:14
Alignment explanation
Indices: 17626--17655 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17616 CAAAATTTGA
*
17626 TTTCTTAACAGAAT
1 TTTCTTAAAAGAAT
17640 TTTCTTAAAAGAAT
1 TTTCTTAAAAGAAT
17654 TT
1 TT
17656 ATAAAATAAA
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:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (14 bp):
TTTCTTAAAAGAAT
Found at i:18043 original size:16 final size:16
Alignment explanation
Indices: 18022--18077 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
18012 ACCGAATCCG
18022 AATTAACCTGACCCAA
1 AATTAACCTGACCCAA
* *
18038 AATTAACCCGAACCC-G
1 AATTAACCTG-ACCCAA
* *
18054 AATTAACTTGACCTAA
1 AATTAACCTGACCCAA
*
18070 ATTTAACC
1 AATTAACC
18078 CGAATCCGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 3 0.10
16 23 0.77
17 4 0.13
ACGTcount: A:0.41, C:0.29, G:0.07, T:0.23
Consensus pattern (16 bp):
AATTAACCTGACCCAA
Found at i:18049 original size:32 final size:32
Alignment explanation
Indices: 18013--18109 Score: 131
Period size: 32 Copynumber: 3.0 Consensus size: 32
18003 CAATCCGAGA
*
18013 CCGAATCCGAATTAACCTGACCCAAAATTAAC
1 CCGAATCCGAATTAACCTGACCCAAATTTAAC
* * *
18045 CCGAACCCGAATTAACTTGACCTAAATTTAAC
1 CCGAATCCGAATTAACCTGACCCAAATTTAAC
* * *
18077 CCGAATCCGAATCAACCCGATCCAAATTTAAC
1 CCGAATCCGAATTAACCTGACCCAAATTTAAC
18109 C
1 C
18110 AAAACCCGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (32 bp):
CCGAATCCGAATTAACCTGACCCAAATTTAAC
Found at i:18109 original size:16 final size:17
Alignment explanation
Indices: 18068--18109 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
18058 AACTTGACCT
18068 AAATTTAACCCGAATCC
1 AAATTTAACCCGAATCC
* *
18085 GAA-TCAACCCG-ATCC
1 AAATTTAACCCGAATCC
18100 AAATTTAACC
1 AAATTTAACC
18110 AAAACCCGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.30
16 12 0.60
17 2 0.10
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.21
Consensus pattern (17 bp):
AAATTTAACCCGAATCC
Found at i:23421 original size:22 final size:22
Alignment explanation
Indices: 23379--23422 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
23369 TATTCATACG
*
23379 AAATTATAATAATCTTCCTATT
1 AAATTATAATAATCTACCTATT
*
23401 AAATTATGATAAT-TACACTATT
1 AAATTATAATAATCTAC-CTATT
23423 TTTGATGACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTATAATAATCTACCTATT
Found at i:23475 original size:62 final size:62
Alignment explanation
Indices: 23378--23529 Score: 234
Period size: 62 Copynumber: 2.5 Consensus size: 62
23368 ATATTCATAC
* * * * *
23378 GAAATTATAATAATCTTCCTATTAAATTATGATAATTACACTATTTT-TGATGACGTACTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTCTG-GGACGTACTTAT
*
23440 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTCTGGGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTCTGGGACGTACTTAT
23502 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
23530 TCAATAACGA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 81 0.98
63 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTCTGGGACGTACTTAT
Found at i:23592 original size:19 final size:19
Alignment explanation
Indices: 23564--23606 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
23554 GAGAACCTTT
*
23564 TTAT-AAATTTTTTTAACC
1 TTATGAAATTTTGTTAACC
23582 TTATGAAATTTTGTTAACC
1 TTATGAAATTTTGTTAACC
23601 TT-TGAA
1 TTATGAA
23607 GACCTTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (19 bp):
TTATGAAATTTTGTTAACC
Found at i:23785 original size:22 final size:21
Alignment explanation
Indices: 23614--24066 Score: 148
Period size: 22 Copynumber: 21.0 Consensus size: 21
23604 GAAGACCTTA
* *
23614 CTATGGAATTTTGATAACCAAC
1 CTATGAAATTTTGATAACC-TC
*
23636 ACTAT-AAGATGTTGATAACCTC
1 -CTATGAA-ATTTTGATAACCTC
* * *
23658 CATATGATATATTGATAACCAC
1 C-TATGAAATTTTGATAACCTC
* * * *
23680 GTTATGAAAATTTAAAAACCTC
1 -CTATGAAATTTTGATAACCTC
* * * *
23702 CATATG-AATTGTCAGTAATCAC
1 C-TATGAAATTTTGA-TAACCTC
*
23724 ACTCTGAAATTTTGAT-A-CTC
1 -CTATGAAATTTTGATAACCTC
*
23744 ACATTATGAAATTGTGATAACCTC
1 -C--TATGAAATTTTGATAACCTC
*
23768 GCTATGAAATTTTGATAAATCTTC
1 -CTATGAAATTTTGAT-AA-CCTC
* *
23792 CTATAAAATTTTGATAACATC
1 CTATGAAATTTTGATAACCTC
*
23813 CTTATGAAATCTTGATAA----
1 C-TATGAAATTTTGATAACCTC
*
23831 CTA-CAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCT-C
* ** *
23852 CAATGATTTTTTGATAACGTC
1 CTATGAAATTTTGATAACCTC
* *
23873 ATTATGAAATTTTG-TTACTCTCC
1 -CTATGAAATTTTGATAAC-CT-C
* * *
23896 CTATGAAATTTTGATCTACATA
1 CTATGAAATTTTGAT-AACCTC
* *
23918 TTATGAAATTTAGATAACCCTC
1 CTATGAAATTTTGATAA-CCTC
* * *
23940 TTATGAAATTTTGA-AAACTAAA
1 CTATGAAATTTTGATAACCT--C
*
23962 CTATGAAATTTTGATAACGTTC
1 CTATGAAATTTTGATAAC-CTC
* *
23984 ATATGAAATTTTGATTA-CTC
1 CTATGAAATTTTGATAACCTC
* * *
24004 CATAATAAAAGTTTAATAACCTTC
1 C-T-ATGAAATTTTGATAACC-TC
* *
24028 C--T--AA-TTTGGTAACCATA
1 CTATGAAATTTTGATAACC-TC
24045 CTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCTC
24066 C
1 C
24067 CCAGAAATAC
Statistics
Matches: 315, Mismatches: 75, Indels: 82
0.67 0.16 0.17
Matches are distributed among these distances:
16 11 0.03
17 12 0.04
18 3 0.01
19 1 0.00
20 9 0.03
21 25 0.08
22 194 0.62
23 46 0.15
24 14 0.04
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:24129 original size:22 final size:22
Alignment explanation
Indices: 24080--24224 Score: 132
Period size: 22 Copynumber: 6.6 Consensus size: 22
24070 GAAATACCAC
* * *
24080 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
24103 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
*
24124 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCTCTT
* * * * *
24146 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
* * *
24168 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCTT
*
24190 TATGTAATTTTGATAACCTCGTT
1 TATGAAATTTTGATAACCTC-TT
24213 T-TGAAATTTTGA
1 TATGAAATTTTGA
24225 AATTGGACCA
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
21 3 0.03
22 92 0.94
23 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:24130 original size:44 final size:44
Alignment explanation
Indices: 24080--24224 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 44
24070 GAAATACCAC
* *
24080 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
* * * * * *
24124 TATGAAATTTTGATAACCTC-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCTT
* *
24168 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TT
24213 T-TGAAATTTTGA
1 TATGAAATTTTGA
24225 AATTGGACCA
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
43 5 0.06
44 70 0.88
45 5 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
Found at i:24533 original size:30 final size:31
Alignment explanation
Indices: 24496--24563 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
24486 TAATGGCAAT
*
24496 TTAGAAATATGATTTT-AAAA-AATGGTACAA
1 TTAGAAATATG-TTTTAAAAATAAGGGTACAA
*
24526 TTGGAAATATGTTTTAAAAATAAGGGTACAA
1 TTAGAAATATGTTTTAAAAATAAGGGTACAA
24557 TTAGAAA
1 TTAGAAA
24564 ACATAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 4 0.12
30 14 0.42
31 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (31 bp):
TTAGAAATATGTTTTAAAAATAAGGGTACAA
Found at i:33502 original size:1 final size:1
Alignment explanation
Indices: 33496--33527 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
33486 GAAGTCTGTC
33496 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33528 AGATATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33802 original size:10 final size:10
Alignment explanation
Indices: 33787--33822 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
33777 ATACCTCGAT
*
33787 ATATCCGTTA
1 ATATCCGTAA
33797 ATATCCGTAA
1 ATATCCGTAA
*
33807 ATATCCATAA
1 ATATCCGTAA
33817 ATATCC
1 ATATCC
33823 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:34332 original size:34 final size:32
Alignment explanation
Indices: 34308--34377 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
34298 CACATTGTTG
*
34308 TCAA-AATATCTGTTTCAATTAAGTCTAGGTT
1 TCAATAATATCTGTTTCAATTAAGTCCAGGTT
**
34339 TCAACTTAATATCTGTTTCAATTAAGTCTGGGTT
1 TCAA--TAATATCTGTTTCAATTAAGTCCAGGTT
34373 TCAAT
1 TCAAT
34378 TAAGTCTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 1 0.03
34 30 0.86
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (32 bp):
TCAATAATATCTGTTTCAATTAAGTCCAGGTT
Found at i:34341 original size:17 final size:17
Alignment explanation
Indices: 34319--34390 Score: 94
Period size: 17 Copynumber: 4.2 Consensus size: 17
34309 CAAAATATCT
*
34319 GTTTCAATTAAGTCTAG
1 GTTTCAATTAAGTCTGG
*
34336 GTTTCAACTTAATATCT--
1 GTTTCAA-TTAA-GTCTGG
34353 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
34370 GTTTCAATTAAGTCTGG
1 GTTTCAATTAAGTCTGG
34387 GTTT
1 GTTT
34391 TGGTCATCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.06
16 4 0.08
17 35 0.71
18 4 0.08
19 3 0.06
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.44
Consensus pattern (17 bp):
GTTTCAATTAAGTCTGG
Done.