Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009122.1 Corchorus capsularis cultivar CVL-1 contig09143, 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: 74704
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:782 original size:30 final size:30
Alignment explanation
Indices: 746--810 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
736 AAATGGAAAT
746 AACTTATCATTCTTTAATTCGTCCAAAAAG
1 AACTTATCATTCTTTAATTCGTCCAAAAAG
776 AACTTATCATTCTTTAATTCGTCCAAAAAG
1 AACTTATCATTCTTTAATTCGTCCAAAAAG
806 AACTT
1 AACTT
811 TTTGAGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (30 bp):
AACTTATCATTCTTTAATTCGTCCAAAAAG
Found at i:4567 original size:1 final size:1
Alignment explanation
Indices: 4520--4548 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
4510 AATAAAAAGC
4520 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4549 CAGATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9114 original size:162 final size:163
Alignment explanation
Indices: 8777--9343 Score: 395
Period size: 168 Copynumber: 3.4 Consensus size: 163
8767 TTGCACGAGC
* * * * * ** * *
8777 TTTTCAGCAACCGACTGTGGGAAGAGAGATTTCAAGCTACTGCATCTTCTTATCTCCAAAGATTC
1 TTTT-AGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCATC-T-TCTCCAAAGTTTC
* * * * * **
8842 CAACTTTTGTAGCA-CT---TCATCAGCACCTTCCAATATCTCCTCAAAAATTTGCTCCAACTTA
63 CAACTTTGGTAGCACCTCGATCATTACCACCTTCC---ATCCCCTCAAAAATTTGCTTCAACACA
* * * * ** * * * *
8903 TGGCAGCCATCTATATTGAGGCTTTTTAACTGCACGAGCA
125 TCGCAGTCAACTATTTTGACACTTTTCAATTGAACAAG-A
** * *
8943 TTTTAGCAACCCCCAGTGGAAACACTGATTTCAGGCTACCACAT-ATC-T-T-CAAAGTTTCCAA
1 TTTTAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCATCTTCTCCAAAGTTTCCAA
* *
9004 C-TTGGATAGCGCC-CGATCATTATCACCTTCCATCCCCTCATCAAAAATTTG-TTCCAACACAT
66 CTTTGG-TAGCACCTCGATCATTACCACCTTCCAT-CCC-C-TCAAAAATTTGCTT-CAACACAT
**
9066 CGCATGT-AGTTATTTTGACACTTTTCAATTGAACAAGA
126 CGCA-GTCAACTATTTTGACACTTTTCAATTGAACAAGA
* * * * * * *
9104 TTTCTAGCAACTGGCGGTGGAAAGAGAGATTTCAGGTTACCACATCCTCTTACCTCCAATGTTTC
1 TTT-TAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCATCTT--CTCCAAAGTTTC
* * * * * *
9169 CAACTTTTGTAGCACCTTATGATCATTACCACCTTCGATCCCCTCGAAAATTTGCTTCAGCATAT
63 CAACTTTGGTAGCACC-T-CGATCATTACCACCTTCCATCCCCTCAAAAATTTGCTTCAACACAT
9234 CGCAGTCAACTATTTTGACACTTTTCAATTGAACAAGA
126 CGCAGTCAACTATTTTGACACTTTTCAATTGAACAAGA
* * *
9272 TTTTTAGTAACCGATGGTGGAAACACAGATTTCACGCTACCACATC-TCGTTATCTCCAAAGTTT
1 -TTTTAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCATC--T-TCTCCAAAGTTT
9336 CCAACTTT
62 CCAACTTT
9344 TTCAAGAACC
Statistics
Matches: 314, Mismatches: 60, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
158 3 0.01
159 18 0.06
160 4 0.01
161 7 0.02
162 87 0.28
163 3 0.01
164 3 0.01
165 30 0.10
166 4 0.01
167 5 0.02
168 119 0.38
169 10 0.03
170 4 0.01
171 17 0.05
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (163 bp):
TTTTAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCATCTTCTCCAAAGTTTCCAA
CTTTGGTAGCACCTCGATCATTACCACCTTCCATCCCCTCAAAAATTTGCTTCAACACATCGCAG
TCAACTATTTTGACACTTTTCAATTGAACAAGA
Found at i:13864 original size:16 final size:14
Alignment explanation
Indices: 13843--13928 Score: 73
Period size: 16 Copynumber: 5.4 Consensus size: 14
13833 GAACTCGCCC
13843 GACCCGAGACCCGAAT
1 GACCCGA-ACCC-AAT
13859 GACCCGTAACCCAGAT
1 GACCCG-AACCCA-AT
13875 GACCCGAGACCCAAAT
1 GACCCGA-ACCC-AAT
13891 GACCCGTAACCCAGAT
1 GACCCG-AACCCA-AT
*
13907 AACCCGAAACCCGAAT
1 GACCCG-AACCC-AAT
13923 GACCCG
1 GACCCG
13929 TAACTCGAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
15 3 0.05
16 53 0.88
17 4 0.07
ACGTcount: A:0.34, C:0.38, G:0.20, T:0.08
Consensus pattern (14 bp):
GACCCGAACCCAAT
Found at i:13884 original size:32 final size:32
Alignment explanation
Indices: 13843--13932 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
13833 GAACTCGCCC
13843 GACCCGAGACCCGAATGACCCGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
*
13875 GACCCGAGACCCAAATGACCCGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
* *
13907 AACCCGAAACCCGAATGACCCGTAAC
1 GACCCGAGACCCGAATGACCCGTAAC
13933 TCGAGTGATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.34, C:0.38, G:0.19, T:0.09
Consensus pattern (32 bp):
GACCCGAGACCCGAATGACCCGTAACCCAGAT
Found at i:14783 original size:16 final size:15
Alignment explanation
Indices: 14764--14820 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 15
14754 AGACCTGGTA
*
14764 GACCCGAAATCCGTAT
1 GACCCGAAACCCG-AT
14780 GACCCGAAACCCAGAT
1 GACCCGAAACCC-GAT
*
14796 GACCTGAAACCCGAAT
1 GACCCGAAACCCG-AT
14812 GACCCGAAA
1 GACCCGAAA
14821 AAACTGTCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.11
Consensus pattern (15 bp):
GACCCGAAACCCGAT
Found at i:14840 original size:17 final size:18
Alignment explanation
Indices: 14811--14853 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
14801 GAAACCCGAA
*
14811 TGACCCGAAAAAACTGTC
1 TGACCCAAAAAAACTGTC
14829 TGACCCAAAAAAACTGTC
1 TGACCCAAAAAAACTGTC
*
14847 TAACCCA
1 TGACCCA
14854 TTTGACCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.16
Consensus pattern (18 bp):
TGACCCAAAAAAACTGTC
Found at i:17410 original size:55 final size:55
Alignment explanation
Indices: 17351--17476 Score: 234
Period size: 55 Copynumber: 2.3 Consensus size: 55
17341 ATTGAAGGCC
17351 ACACCATCAGGATCAATTTATTAGTCCCGATGGTGTGAGCAATTTTTATTTGACA
1 ACACCATCAGGATCAATTTATTAGTCCCGATGGTGTGAGCAATTTTTATTTGACA
*
17406 ACACCATCAGGATCAATTTTTTAGTCCCGATGGTGTGAGCAATTTTTATTTGACA
1 ACACCATCAGGATCAATTTATTAGTCCCGATGGTGTGAGCAATTTTTATTTGACA
*
17461 ACACCATCAGGTTCAA
1 ACACCATCAGGATCAA
17477 GCTATTTGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (55 bp):
ACACCATCAGGATCAATTTATTAGTCCCGATGGTGTGAGCAATTTTTATTTGACA
Found at i:22037 original size:18 final size:18
Alignment explanation
Indices: 21993--22038 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
21983 AAGGAAAAAC
21993 AGTAGAAACACCATTACA
1 AGTAGAAACACCATTACA
*
22011 A-TCAAAAACACCATTACA
1 AGT-AGAAACACCATTACA
22029 AGTAGAAACA
1 AGTAGAAACA
22039 GTTTTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.54, C:0.22, G:0.09, T:0.15
Consensus pattern (18 bp):
AGTAGAAACACCATTACA
Found at i:27242 original size:165 final size:165
Alignment explanation
Indices: 27015--27330 Score: 415
Period size: 165 Copynumber: 1.9 Consensus size: 165
27005 CATCCGATCT
* *
27015 TTAGCACCTTCCATCTCCTCAAAAATTTGCTCCAACACATCGCATGTACTTATTGTGACACTTCT
1 TTAGCACCCTCCATCTCCTCAAAAACTTGCTCCAACACATCGCATGTACTTATTGTGACACTTCT
* * * * * *
27080 CAATTGAACAAGATTTTTAGCAACTGGCGGTGGAAAGAGAGATTTCAGGTTACCACATCCTC-TT
66 CAACTGAACAAGATTTTTAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACAT-CTCGTT
** *
27144 ATCTCCAATGTTTCCAACTTTTGTAGCACCTCATCA
130 ATCTCCAAAATTACCAACTTTTGTAGCACCTCATCA
* * *
27180 TTAGCACCCTCCATCTCCTCAAAAACTTGCTCTAAGATATCGCA-GTCAGC-TATT-TCGACACT
1 TTAGCACCCTCCATCTCCTCAAAAACTTGCTCCAACACATCGCATGT-A-CTTATTGT-GACACT
* * *
27242 TTTCAACTGAACAAGATTTTTAGCAACCGATGGTGGAAACACAGATTTCAGGCTACCACATTTCG
63 TCTCAACTGAACAAGATTTTTAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCTCG
27307 TTATCTCCAAAATTACCAACTTTT
128 TTATCTCCAAAATTACCAACTTTT
27331 TCAGGAACCC
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
164 5 0.04
165 124 0.95
166 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (165 bp):
TTAGCACCCTCCATCTCCTCAAAAACTTGCTCCAACACATCGCATGTACTTATTGTGACACTTCT
CAACTGAACAAGATTTTTAGCAACCGACGGTGGAAACACAGATTTCAGGCTACCACATCTCGTTA
TCTCCAAAATTACCAACTTTTGTAGCACCTCATCA
Found at i:46699 original size:22 final size:22
Alignment explanation
Indices: 46671--46715 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
46661 GATGGGTGAG
46671 TCTCCCAACAGGAACTGCTGCT
1 TCTCCCAACAGGAACTGCTGCT
*
46693 TCTCCCAACAGGAATTGCTGCT
1 TCTCCCAACAGGAACTGCTGCT
46715 T
1 T
46716 ACTTAAGGTC
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:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (22 bp):
TCTCCCAACAGGAACTGCTGCT
Found at i:60855 original size:18 final size:18
Alignment explanation
Indices: 60828--60862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60818 GAGATGGTAT
*
60828 AAGTGTTCAAATTTACAA
1 AAGTGATCAAATTTACAA
*
60846 AAGTGATCAATTTTACA
1 AAGTGATCAAATTTACA
60863 TAAATCCACG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGTGATCAAATTTACAA
Found at i:62389 original size:6 final size:6
Alignment explanation
Indices: 62375--62426 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
62365 TGCCCCTTTC
* *
62375 TTTCCT TTTCTT TTTCTT TTTTTT TTTGCTTTT TTGTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT-C--TT TT-TCTT TTTCTT TTTCTT
62427 GTCTTCTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 29 0.74
7 4 0.10
9 5 0.13
10 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:74358 original size:21 final size:21
Alignment explanation
Indices: 74334--74377 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
74324 GTTAACTGGA
74334 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
74355 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
74376 TT
1 TT
74378 TACGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:74681 original size:33 final size:34
Alignment explanation
Indices: 74621--74704 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
74611 GCTCAACCAC
**
74621 GGCAGAGCCGCCCCACTGGGGGCGGCTTCACCATG
1 GGCAG-GCCGCCCCGGTGGGGGCGGCTTCACCATG
74656 GGCAGGCCGCCCCGGT-GGGGCGGCTTCACCATG
1 GGCAGGCCGCCCCGGTGGGGGCGGCTTCACCATG
74689 GGCAGGCCGCCCCGGT
1 GGCAGGCCGCCCCGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 33 0.70
34 9 0.19
35 5 0.11
ACGTcount: A:0.11, C:0.38, G:0.40, T:0.11
Consensus pattern (34 bp):
GGCAGGCCGCCCCGGTGGGGGCGGCTTCACCATG
Done.