Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008322.1 Corchorus capsularis cultivar CVL-1 contig08343, 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: 42839
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6729 original size:22 final size:22
Alignment explanation
Indices: 6703--6764 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
6693 TCGTGAAAAA
6703 TCGAGTCGAACTCGAGTATTCT
1 TCGAGTCGAACTCGAGTATTCT
6725 TCGAGTCGAACTCGAGTATTCT
1 TCGAGTCGAACTCGAGTATTCT
*
6747 TCGAGTCGAACACGAGTA
1 TCGAGTCGAACTCGAGTA
6765 GCTCATGAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (22 bp):
TCGAGTCGAACTCGAGTATTCT
Found at i:15232 original size:22 final size:22
Alignment explanation
Indices: 15207--15251 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
15197 AATAATTTTA
*
15207 TGGCTGTGTTTTAGGAGGGTAG
1 TGGCTGTGTTCTAGGAGGGTAG
15229 TGGCTGTGTTCTAGGAGGGTAG
1 TGGCTGTGTTCTAGGAGGGTAG
15251 T
1 T
15252 TTAGTTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.07, G:0.44, T:0.36
Consensus pattern (22 bp):
TGGCTGTGTTCTAGGAGGGTAG
Found at i:15377 original size:44 final size:45
Alignment explanation
Indices: 15294--15384 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 45
15284 GTGGTTATCT
15294 AGGAGATCGTTGGGCTCTCTCTAACGAGCCCAAAAGTTTACTTAGA
1 AGGAGATCGTTGGGCTCTCTCTAACGAGCCC-AAAGTTTACTTAGA
*
15340 AGGAGATCGTTGGGTTCTCTCTAACGAGCCC-AAGTTTACTTAGA
1 AGGAGATCGTTGGGCTCTCTCTAACGAGCCCAAAGTTTACTTAGA
15384 A
1 A
15385 CCATAGGACA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 14 0.32
46 30 0.68
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (45 bp):
AGGAGATCGTTGGGCTCTCTCTAACGAGCCCAAAGTTTACTTAGA
Found at i:22946 original size:22 final size:22
Alignment explanation
Indices: 22921--23002 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
22911 GTAGTTATTG
* *
22921 AAATTTCATACAAAGGTTACCA
1 AAATTTCATAGAAAGGTTAACA
* ** * *
22943 AAATTTCTTAGGGATGTTAATA
1 AAATTTCATAGAAAGGTTAACA
22965 AAATTTCATATGAAA-GTTAACA
1 AAATTTCATA-GAAAGGTTAACA
22987 AAATTTCATAGAAAGG
1 AAATTTCATAGAAAGG
23003 GAGGTTACCA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
21 4 0.09
22 41 0.87
23 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (22 bp):
AAATTTCATAGAAAGGTTAACA
Found at i:23066 original size:22 final size:22
Alignment explanation
Indices: 23027--23082 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
23017 TTGTGCTTAT
*
23027 CAAAATTTTCCTAGGGAGGTTAA
1 CAAAATTTT-ATAGGGAGGTTAA
*
23050 CAAAATTTTATAGGGAGGTTAT
1 CAAAATTTTATAGGGAGGTTAA
*
23072 GAAAATTTTAT
1 CAAAATTTTAT
23083 GAAGAGGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (22 bp):
CAAAATTTTATAGGGAGGTTAA
Found at i:23089 original size:22 final size:22
Alignment explanation
Indices: 23023--23100 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
23013 AAATTTGTGC
* * *
23023 TTATCAAAATTTTCCTAGGGAGG
1 TTATGAAAATTTT-ATAGAGAGG
** *
23046 TTAACAAAATTTTATAGGGAGG
1 TTATGAAAATTTTATAGAGAGG
23068 TTATGAAAATTTTAT-GAAGAGG
1 TTATGAAAATTTTATAG-AGAGG
23090 TTATCGAAAAT
1 TTAT-GAAAAT
23101 ACATAGAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 29 0.60
23 18 0.38
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (22 bp):
TTATGAAAATTTTATAGAGAGG
Found at i:23272 original size:22 final size:22
Alignment explanation
Indices: 23247--23391 Score: 137
Period size: 22 Copynumber: 6.6 Consensus size: 22
23237 TATAGGCAGA
* *
23247 TTATCAAAATTTAACAATGAGG
1 TTATCAAAATTTCATAATGAGG
* * *
23269 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGAGG
* * * *
23291 TTACCAAAATTTCACAATGTGA
1 TTATCAAAATTTCATAATGAGG
* **
23313 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAATGAGG
*
23335 TTATCGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAATGAGG
* * *
23357 TTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCATAATGAGG
*
23379 TTATCAATATTTC
1 TTATCAAAATTTC
23392 TACATTTGAG
Statistics
Matches: 96, Mismatches: 27, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 96 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAGG
Found at i:23299 original size:44 final size:44
Alignment explanation
Indices: 23136--23390 Score: 148
Period size: 44 Copynumber: 5.8 Consensus size: 44
23126 TCTCATAGGT
* * *
23136 AGGTTATCGAAA-TTTCATGGTCTGGTTACCAAAATTT---TATG
1 AGGTTATC-AAATTTTCATAGTGTGGTTACCAAAATTTAACAATG
* * * ** *
23177 ATGTTATCAAAATTTTCATAGTGCGGTTACC-AATTTTATTTAGTG
1 AGGTTATC-AAATTTTCATAGTGTGGTTACCAAAATTTA-ACAATG
* * * * * *
23222 TGATTATTAAAATTTT-ATAG-GCAGATTATCAAAATTTAACAATG
1 AGGTTA-TCAAATTTTCATAGTG-TGGTTACCAAAATTTAACAATG
*
23266 AGGTTATCGAAA-TTTCATAGTGTGGTTACCAAAATTTCACAATG
1 AGGTTATC-AAATTTTCATAGTGTGGTTACCAAAATTTAACAATG
* * * * * * * *
23310 TGATTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATG
1 AGGTTATCAAATTTTCATAGTGTGGTTACCAAAATTTAACAATG
* * * *
23354 AGGTTATCAAATTTTCAAAATGTGGTTATCAATATTT
1 AGGTTATCAAATTTTCATAGTGTGGTTACCAAAATTT
23391 CTACATTTGA
Statistics
Matches: 161, Mismatches: 41, Indels: 21
0.72 0.18 0.09
Matches are distributed among these distances:
41 15 0.09
42 15 0.09
43 8 0.05
44 103 0.64
45 19 0.12
46 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (44 bp):
AGGTTATCAAATTTTCATAGTGTGGTTACCAAAATTTAACAATG
Found at i:23300 original size:66 final size:63
Alignment explanation
Indices: 23136--23368 Score: 163
Period size: 66 Copynumber: 3.6 Consensus size: 63
23126 TCTCATAGGT
* * *
23136 AGGTTATCGAAATTTCATGGTCTGGTTACCAAAATTTTAT-GATG-TTATCAAAATTTTCATAGT
1 AGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTTATAGA-GATTATCAAAATTTACA-A-T
23199 G
63 G
* * * * **
23200 CGGTTA-C-CAATTTTATTTAGTGTGATTATTAAAATTTTATAGGCAGATTATCAAAATTTAACA
1 AGGTTATCGAAATTTCA--TAGTGTGGTTACCAAAATTTTATA-G-AGATTATCAAAATTT-ACA
23263 ATG
61 ATG
* * * *
23266 AGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTCACAATGTGATTATC-AAATTTTCATAG
1 AGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTTA-TA-GAGATTATCAAAATTTACA-A-
*
23330 GG
62 TG
* * *
23332 AGGTTATCGAAATTTCATAATGAGGTTATC-AAATTTT
1 AGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTT
23369 CAAAATGTGG
Statistics
Matches: 132, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
62 6 0.05
63 1 0.01
64 25 0.19
65 13 0.10
66 62 0.47
67 17 0.13
68 8 0.06
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (63 bp):
AGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTTATAGAGATTATCAAAATTTACAATG
Found at i:23370 original size:66 final size:67
Alignment explanation
Indices: 23265--23390 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 67
23255 ATTTAACAAT
* * *
23265 GAGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTCACAATGTGATTATCAA-ATTTTCATA
1 GAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGTGATTATCAATATTTTCATA
23329 GG
66 GG
* * *
23331 GAGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTGGTTATCAATATTT
1 GAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGTGATTATCAATATTT
23391 CTACATTTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
66 49 0.92
67 4 0.08
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (67 bp):
GAGGTTATCGAAATTTCATAATGAGGTTACCAAAATTTCAAAATGTGATTATCAATATTTTCATA
GG
Found at i:23391 original size:44 final size:44
Alignment explanation
Indices: 23247--23391 Score: 175
Period size: 44 Copynumber: 3.3 Consensus size: 44
23237 TATAGGCAGA
*
23247 TTATCAAAATTTAACAATGAGGTTATCGAAA-TTTCATAGTGTGG
1 TTATCAAAATTTCACAATGAGGTTATC-AAATTTTCATAGTGTGG
* * * * *
23291 TTACCAAAATTTCACAATGTGATTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
* * * *
23335 TTATCGAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
*
23379 TTATCAATATTTC
1 TTATCAAAATTTC
23392 TACATTTGAG
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 3 0.04
44 80 0.96
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGTGTGG
Found at i:23801 original size:154 final size:154
Alignment explanation
Indices: 23521--23828 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 154
23511 TAAAGCTTTC
23521 TAAGAAGTCTAAAACCTCAACTTCCCGATTTAACACGTGTGAGCACCAAACGTTGTTCTCAAGAA
1 TAAGAAGTCTAAAACCTCAACTTCCCGATTTAACACGTGTGAGCACCAAACGTTGTTCTCAAGAA
23586 AACGTTCAATACAAATACATTATTTGTGAAGCCAACGCTCAAATGTTGTGTTTCAGAGTGAGTAA
66 AACGTTCAATACAAATACATTATTTGTGAAGCCAACGCTCAAATGTTGTGTTTCAGAGTGAGTAA
23651 GCTAATTGTAAAGTGGGTTTTCCA
131 GCTAATTGTAAAGTGGGTTTTCCA
23675 TAAGAAGTCTAAAACCTCAACTTCCCGATTTAACACGTGTGAGCACCAAACGTTGTTCTCAAGAA
1 TAAGAAGTCTAAAACCTCAACTTCCCGATTTAACACGTGTGAGCACCAAACGTTGTTCTCAAGAA
*
23740 AAGGTTCAATACAAATACATTATTTGTGAAGCCAACGCTCAAATGTTGTGTTTCAGAGTGAGTAA
66 AACGTTCAATACAAATACATTATTTGTGAAGCCAACGCTCAAATGTTGTGTTTCAGAGTGAGTAA
23805 GCTAATTGTAAAGTGGGTTTTCCA
131 GCTAATTGTAAAGTGGGTTTTCCA
23829 GAAAAACAAA
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (154 bp):
TAAGAAGTCTAAAACCTCAACTTCCCGATTTAACACGTGTGAGCACCAAACGTTGTTCTCAAGAA
AACGTTCAATACAAATACATTATTTGTGAAGCCAACGCTCAAATGTTGTGTTTCAGAGTGAGTAA
GCTAATTGTAAAGTGGGTTTTCCA
Found at i:28341 original size:20 final size:22
Alignment explanation
Indices: 28297--28341 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28287 CCCCTGTACA
**
28297 TGCCATGTCACCAGGGCTCTCC
1 TGCCATGTCACCAAAGCTCTCC
28319 TGCCATGTCACCAAAG-T-TCC
1 TGCCATGTCACCAAAGCTCTCC
28339 TGC
1 TGC
28342 AAGAGGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.18, C:0.38, G:0.20, T:0.24
Consensus pattern (22 bp):
TGCCATGTCACCAAAGCTCTCC
Found at i:35652 original size:31 final size:31
Alignment explanation
Indices: 35605--35711 Score: 160
Period size: 31 Copynumber: 3.5 Consensus size: 31
35595 GTTTTCCGAC
* *
35605 GTGGCATGCCATGTGTACTAAAAAGTGACAT
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
* *
35636 GTGGCATACCACGTGTACCAAAAAGTGACAC
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
* *
35667 GTGTCATGTCACGTGTACCAAAAAGTGACAT
1 GTGGCATGCCACGTGTACCAAAAAGTGACAT
35698 GTGGCATGCCACGT
1 GTGGCATGCCACGT
35712 CGGACACCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.22
Consensus pattern (31 bp):
GTGGCATGCCACGTGTACCAAAAAGTGACAT
Found at i:36318 original size:13 final size:13
Alignment explanation
Indices: 36300--36329 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36290 TGTCAGCATT
36300 TTATTGGTCAAGA
1 TTATTGGTCAAGA
36313 TTATTGGTCAAGA
1 TTATTGGTCAAGA
36326 TTAT
1 TTAT
36330 GGATGAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (13 bp):
TTATTGGTCAAGA
Found at i:38665 original size:2 final size:2
Alignment explanation
Indices: 38654--38693 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
38644 ATTTCCTCAG
*
38654 TA TA TA -A TA TA TA AA 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 TA TA TA TA TA TA TA T
38694 CTTATATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39749 original size:12 final size:12
Alignment explanation
Indices: 39728--39758 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39718 AGTCGGTTTG
39728 TTTTTT-CTTTT
1 TTTTTTCCTTTT
39739 TTTTTTCCTTTT
1 TTTTTTCCTTTT
39751 TTTTTTCC
1 TTTTTTCC
39759 AATGAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCCTTTT
Found at i:42566 original size:26 final size:26
Alignment explanation
Indices: 42535--42586 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42525 AAAATTATGT
42535 TTTTTCCAGCAATTTAATTATATAAG
1 TTTTTCCAGCAATTTAATTATATAAG
42561 TTTTTCCAGCAATTTAATTATATAAG
1 TTTTTCCAGCAATTTAATTATATAAG
42587 ATTACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTTCCAGCAATTTAATTATATAAG
Found at i:42814 original size:2 final size:2
Alignment explanation
Indices: 42807--42839 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42797 GTAAAACTAG
42807 TA TA TA 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 TA TA TA T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.