Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005408.1 Corchorus capsularis cultivar CVL-1 contig05426, 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: 2969
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Found at i:86 original size:31 final size:31
Alignment explanation
Indices: 13--238 Score: 209
Period size: 31 Copynumber: 7.0 Consensus size: 31
3 GTGCCTTGTC
*
13 CCCTTGGCTTTGGCGTCGGCATTTGCCGATGG
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGAT-G
* * *
45 CCTTTGGCCTTGGCGTCCGCATTTGCCGATT
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGATG
*
76 CCCTTGGCCTTGGCGTCGGAATTTGCCGATGG
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGAT-G
* * * *
108 CCCTTGGTCTTGGAGTCAGCATTTGACGATG
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGATG
* *
139 CCCATGGCCTTGGCGTCGGCATTTGCAGATTCG
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGA-T-G
* * * *
172 CTTTGCCTTGGCGTATGGCCTAGGCATTTCCCGATG
1 C----CCTTGGCCT-TGGCGTCGGCATTTGCCGATG
* * *
208 CCCATGTCCTAGGCGTCGGCATTTGCCGATG
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGATG
239 GGGCCCGGTA
Statistics
Matches: 154, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
31 68 0.44
32 59 0.38
33 2 0.01
36 2 0.01
37 8 0.05
38 15 0.10
ACGTcount: A:0.11, C:0.29, G:0.30, T:0.31
Consensus pattern (31 bp):
CCCTTGGCCTTGGCGTCGGCATTTGCCGATG
Found at i:120 original size:63 final size:63
Alignment explanation
Indices: 13--164 Score: 223
Period size: 63 Copynumber: 2.4 Consensus size: 63
3 GTGCCTTGTC
* * * * * *
13 CCCTTGGCTTTGGCGTCGGCATTTGCCGATGGCCTTTGGCCTTGGCGTCCGCATTTGCCGATT
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGAGTCAGCATTTGACGATG
* *
76 CCCTTGGCCTTGGCGTCGGAATTTGCCGATGGCCCTTGGTCTTGGAGTCAGCATTTGACGATG
1 CCCTTGGCCTTGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGAGTCAGCATTTGACGATG
*
139 CCCATGGCCTTGGCGTCGGCATTTGC
1 CCCTTGGCCTTGGCGTCGGCATTTGC
165 AGATTCGCTT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 79 1.00
ACGTcount: A:0.09, C:0.29, G:0.31, T:0.31
Consensus pattern (63 bp):
CCCTTGGCCTTGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGAGTCAGCATTTGACGATG
Found at i:820 original size:10 final size:10
Alignment explanation
Indices: 805--845 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
795 GCTAAGTCGG
*
805 TGTAGGACCT
1 TGTAGAACCT
*
815 TGTAGGACCT
1 TGTAGAACCT
*
825 TGTAGAACGT
1 TGTAGAACCT
835 TGTAGAACCT
1 TGTAGAACCT
845 T
1 T
846 CTAGCACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (10 bp):
TGTAGAACCT
Found at i:1566 original size:25 final size:25
Alignment explanation
Indices: 1538--1591 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1528 AGCTTTTCGA
* * *
1538 TGCCAATGGCCTTGGCGTCGGCATT
1 TGCCAATGCCCCTGGCATCGGCATT
*
1563 TGCCGATGCCCCTGGCATCGGCATT
1 TGCCAATGCCCCTGGCATCGGCATT
1588 TGCC
1 TGCC
1592 GATGTCCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.11, C:0.33, G:0.30, T:0.26
Consensus pattern (25 bp):
TGCCAATGCCCCTGGCATCGGCATT
Found at i:1603 original size:25 final size:25
Alignment explanation
Indices: 1550--1603 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
1540 CCAATGGCCT
* *
1550 TGGCGTCGGCATTTGCCGATGCCCC
1 TGGCATCGGCATTTGCCGATGCCCA
*
1575 TGGCATCGGCATTTGCCGATGTCCA
1 TGGCATCGGCATTTGCCGATGCCCA
1600 TGGC
1 TGGC
1604 CTTGTCGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.11, C:0.31, G:0.31, T:0.26
Consensus pattern (25 bp):
TGGCATCGGCATTTGCCGATGCCCA
Found at i:1678 original size:63 final size:62
Alignment explanation
Indices: 1538--1735 Score: 221
Period size: 63 Copynumber: 3.3 Consensus size: 62
1528 AGCTTTTCGA
*
1538 TGCCAATGGCCTTGGCGTCGGCATTTGCCGATG-CC----CCTGGCATCGGCATTTGCCGA-
1 TGCCCATGGCCTTGGCGTCGGCATTTGCCGATGCCCATGGCCTGGCATCGGCATTTGCCGAT
* * * * *
1594 TGTCCATGGCCTTGTCGTCGGCATTTGCTGATGCCCATGGCCTAGGCGTCGGCATTTGCTGAT
1 TGCCCATGGCCTTGGCGTCGGCATTTGCCGATGCCCATGGCCT-GGCATCGGCATTTGCCGAT
* *
1657 TGCCCATGGTCTTGGCGTCGGCA-TTACCGATGGCCCATGGCCTTGGCATCGGCATTTGCCGAT
1 TGCCCATGGCCTTGGCGTCGGCATTTGCCGAT-GCCCATGGCC-TGGCATCGGCATTTGCCGAT
* * *
1720 GGCCCTTGCCCTTGGC
1 TGCCCATGGCCTTGGC
1736 CGTGATGGTT
Statistics
Matches: 116, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
56 29 0.25
57 2 0.02
61 3 0.03
62 22 0.19
63 59 0.51
64 1 0.01
ACGTcount: A:0.11, C:0.31, G:0.30, T:0.28
Consensus pattern (62 bp):
TGCCCATGGCCTTGGCGTCGGCATTTGCCGATGCCCATGGCCTGGCATCGGCATTTGCCGAT
Found at i:1733 original size:32 final size:31
Alignment explanation
Indices: 1535--1735 Score: 218
Period size: 31 Copynumber: 6.6 Consensus size: 31
1525 ATAAGCTTTT
*
1535 CGATGCCAATGGCCTTGGCGTCGGCATTTGC
1 CGATGCCCATGGCCTTGGCGTCGGCATTTGC
*
1566 CGATG-CC----CC-TGGCATCGGCATTTGC
1 CGATGCCCATGGCCTTGGCGTCGGCATTTGC
* *
1591 CGATGTCCATGGCCTTGTCGTCGGCATTTGC
1 CGATGCCCATGGCCTTGGCGTCGGCATTTGC
* *
1622 TGATGCCCATGGCCTAGGCGTCGGCATTTGC
1 CGATGCCCATGGCCTTGGCGTCGGCATTTGC
* * *
1653 TGATTGCCCATGGTCTTGGCGTCGGCA-TTAC
1 CGA-TGCCCATGGCCTTGGCGTCGGCATTTGC
*
1684 CGATGGCCCATGGCCTTGGCATCGGCATTTGC
1 CGAT-GCCCATGGCCTTGGCGTCGGCATTTGC
* *
1716 CGATGGCCCTTGCCCTTGGC
1 CGAT-GCCCATGGCCTTGGC
1736 CGTGATGGTT
Statistics
Matches: 144, Mismatches: 17, Indels: 17
0.81 0.10 0.10
Matches are distributed among these distances:
25 20 0.14
26 4 0.03
30 4 0.03
31 74 0.51
32 42 0.29
ACGTcount: A:0.11, C:0.31, G:0.30, T:0.27
Consensus pattern (31 bp):
CGATGCCCATGGCCTTGGCGTCGGCATTTGC
Found at i:2650 original size:329 final size:328
Alignment explanation
Indices: 1735--2688 Score: 1318
Period size: 329 Copynumber: 2.9 Consensus size: 328
1725 TTGCCCTTGG
* * * *
1735 CCGTGATGGTTAGTACACGATTTTGACTACATATTTGCTGAAAATGACCTAAAAAATTATTTCCT
1 CCGTGATGG-T-GTACACGATTTTGGCTAAAAATTTGCTGAAAATGACCCAAAAAATT-TTTCCT
* * *
1800 CAATTTTCAGATAAAATACTCATAAAATATATAATGATTTAACTCCAAAAATATTATTAGAGGAC
63 CAATTTTCGGATAAAATACTCATAAAAT-TAT-ATGATTTAACACC-AAAA-A-TATTGGAGGAC
* * *
1865 TTTTTACATTTTTAATA-TAATTTT-TTATATTTTTCTGAATTAATTTCTAATTAAATCGCACCA
123 TTTTCACGTTTTTAATATTAATTTTCATAT-TTTTTCTGAATTAATTTCTAATTAAATCGCACCA
* *
1928 AAATTCATATGCTCGAAAAAACAAATTCTTAAAATTCAAAGTAGCTGAGATTTGG--TGATGAAT
187 AAATTCATAT-CTAGAAAAAACAAATTCTT-AAATTCAATGTAGCTGAGATTTGGTTTGATGAAT
* * **
1991 ATAGATATTT-TAGGAGTCTTGGCACAAAAAATCACTCAAAACTGAGCCGGAGCTCTGGAACGCA
250 ATAGATATTTCAAGGAGTCTTGGCACAAAAAATCACTCAAAACCGAGCCGGAGCTCCAGAACGCA
**
2055 TTTTTAGCCAAATT
315 TTTTTAGCCAAAAA
**
2069 CCGTGATGGGTTAGTACACGATTTTGGCTAAAAATTTGCTGAAAATGACCCAAAATTTTTTTTCC
1 CCGTGAT-GG-T-GTACACGATTTTGGCTAAAAATTTGCTGAAAATGACCCAAAA-AATTTTTCC
* *
2134 TCAATTTTAGGATAAAATACTCATAAAAAATATATGATTTAACACCAAAAATATTGGAGGACTTT
62 TCAATTTTCGGATAAAATACTCAT-AAAATTATATGATTTAACACCAAAAATATTGGAGGACTTT
*
2199 TCACGTTTTTAATATCAATTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGCACCAAAAT
126 TCACGTTTTTAATATTAATTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGCACCAAAAT
*
2263 TCATA---AGAAAAAACAAATTCTTAAATTCAATGTAGCTGAAATTTGGTTTGATGAATATAGAT
191 TCATATCTAGAAAAAACAAATTCTTAAATTCAATGTAGCTGAGATTTGGTTTGATGAATATAGAT
* * *
2325 ATTTCAAGGAGTATTGGCACAAAAAATCACTCAAAACCGAGCCGGGGCTCCATAACGCATTTTTA
256 ATTTCAAGGAGTCTTGGCACAAAAAATCACTCAAAACCGAGCCGGAGCTCCAGAACGCATTTTTA
2390 GCCAAAAA
321 GCCAAAAA
* * *
2398 CCGTGAT-G-GTACATGATTTTGGCTAAAAATTTGCTGAAAATGACCCAAAAAATTTTTGGCACA
1 CCGTGATGGTGTACACGATTTTGGCTAAAAATTTGCTGAAAATGACCCAAAAAATTTTT-CCTCA
* *
2461 ATTTTTCGGATAAAATACTCATAAAATTATATGATTTAAAACCAAAAATATTGGAGGAGTTTTCA
65 A-TTTTCGGATAAAATACTCATAAAATTATATGATTTAACACCAAAAATATTGGAGGACTTTTCA
* *
2526 CGTTTTTAATATTAATTTTCATATTTTTTTTGAATTCATTTCTAATTAAATCGCACCAAAATTCA
129 CGTTTTTAATATTAATTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGCACCAAAATTCA
*
2591 TATTCTAGAAAAAACAAATTCTTAAATTCAATGTACCTGAGATTTGGTTTGATGAATATAGATAT
194 TA-TCTAGAAAAAACAAATTCTTAAATTCAATGTAGCTGAGATTTGGTTTGATGAATATAGATAT
* * *
2656 TTCAAGGAATCTTGGCACAAAATATCCCTCAAA
258 TTCAAGGAGTCTTGGCACAAAAAATCACTCAAA
2689 CCCTAAACCC
Statistics
Matches: 560, Mismatches: 45, Indels: 35
0.88 0.07 0.05
Matches are distributed among these distances:
323 5 0.01
324 107 0.19
325 60 0.11
326 22 0.04
327 17 0.03
328 18 0.03
329 152 0.27
331 68 0.12
332 7 0.01
333 6 0.01
334 19 0.03
335 73 0.13
336 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (328 bp):
CCGTGATGGTGTACACGATTTTGGCTAAAAATTTGCTGAAAATGACCCAAAAAATTTTTCCTCAA
TTTTCGGATAAAATACTCATAAAATTATATGATTTAACACCAAAAATATTGGAGGACTTTTCACG
TTTTTAATATTAATTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGCACCAAAATTCATA
TCTAGAAAAAACAAATTCTTAAATTCAATGTAGCTGAGATTTGGTTTGATGAATATAGATATTTC
AAGGAGTCTTGGCACAAAAAATCACTCAAAACCGAGCCGGAGCTCCAGAACGCATTTTTAGCCAA
AAA
Done.