Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010993.1 Corchorus capsularis cultivar CVL-1 contig11014, 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: 322808
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:273559 original size:34 final size:30
Alignment explanation
Indices: 273497--273556 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
273487 TTGGATAAAA
273497 GGAAATAAATTAATTACTTTAGATTGATTG
1 GGAAATAAATTAATTACTTTAGATTGATTG
*
273527 GGAAATATATTAATTACTTTAGATTGATTG
1 GGAAATAAATTAATTACTTTAGATTGATTG
273557 ATTAATTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (30 bp):
GGAAATAAATTAATTACTTTAGATTGATTG
Found at i:275699 original size:40 final size:40
Alignment explanation
Indices: 275644--275723 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
275634 AACAATAGGT
275644 TAACTTGCAGTCATATACTTACAGACTAGAGAGAGAGGAA
1 TAACTTGCAGTCATATACTTACAGACTAGAGAGAGAGGAA
275684 TAACTTGCAGTCATATACTTACAGACTAGAGAGAGAGGAA
1 TAACTTGCAGTCATATACTTACAGACTAGAGAGAGAGGAA
275724 GATCTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (40 bp):
TAACTTGCAGTCATATACTTACAGACTAGAGAGAGAGGAA
Found at i:292223 original size:15 final size:15
Alignment explanation
Indices: 292200--292247 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
292190 TTCTGCACAA
292200 CATGATTGTTTGCAC
1 CATGATTGTTTGCAC
* *
292215 CATGGTTGTTCGCAC
1 CATGATTGTTTGCAC
* *
292230 CATTATGGTTTGCAC
1 CATGATTGTTTGCAC
292245 CAT
1 CAT
292248 TGTTGTTGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (15 bp):
CATGATTGTTTGCAC
Found at i:292243 original size:30 final size:30
Alignment explanation
Indices: 292207--292263 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
292197 CAACATGATT
292207 GTTTGCACCATGGTTGTTCGCACCATTATG
1 GTTTGCACCATGGTTGTTCGCACCATTATG
* * *
292237 GTTTGCACCATTGTTGTTGGCGCCATT
1 GTTTGCACCATGGTTGTTCGCACCATT
292264 CACCCTAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.39
Consensus pattern (30 bp):
GTTTGCACCATGGTTGTTCGCACCATTATG
Found at i:296752 original size:18 final size:19
Alignment explanation
Indices: 296714--296752 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
296704 CCAAACATAT
*
296714 TTTCCATATAATTACTTAA
1 TTTCCATATAATTAATTAA
*
296733 TTTCCATA-ATTTAATTAA
1 TTTCCATATAATTAATTAA
296751 TT
1 TT
296753 AAATTAGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTCCATATAATTAATTAA
Found at i:298194 original size:15 final size:15
Alignment explanation
Indices: 298171--298263 Score: 98
Period size: 15 Copynumber: 6.2 Consensus size: 15
298161 AGCGAACACT
*
298171 TTCGGTGCCATCA-A
1 TTCGGTGCCATCACC
298185 TTCTGGTGCCATCACC
1 TTC-GGTGCCATCACC
* *
298201 TTGGGTGCCATCATC
1 TTCGGTGCCATCACC
*
298216 TTCGGTGCCATCATC
1 TTCGGTGCCATCACC
* *
298231 TTAGGTGCCATCATC
1 TTCGGTGCCATCACC
* *
298246 TTCGATGCCATGACC
1 TTCGGTGCCATCACC
298261 TTC
1 TTC
298264 CTCTATGGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
14 3 0.04
15 63 0.93
16 2 0.03
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.32
Consensus pattern (15 bp):
TTCGGTGCCATCACC
Found at i:298210 original size:30 final size:30
Alignment explanation
Indices: 298174--298262 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
298164 GAACACTTTC
*
298174 GGTGCCATCA-ATTCTGGTGCCATCACCTTG
1 GGTGCCATCATATTC-GGTGCCATCACCTTA
* *
298204 GGTGCCATCATCTTCGGTGCCATCATCTTA
1 GGTGCCATCATATTCGGTGCCATCACCTTA
* * *
298234 GGTGCCATCATCTTCGATGCCATGACCTT
1 GGTGCCATCATATTCGGTGCCATCACCTT
298263 CCTCTATGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 49 0.94
31 3 0.06
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.31
Consensus pattern (30 bp):
GGTGCCATCATATTCGGTGCCATCACCTTA
Found at i:298255 original size:45 final size:45
Alignment explanation
Indices: 298171--298256 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
298161 AGCGAACACT
* *
298171 TTCGGTGCCATCAATTCTGGTGCCATCACCTTGGGTGCCATCATC
1 TTCGGTGCCATCAATTCTGGTGCCATCACCTTCGATGCCATCATC
*
298216 TTCGGTGCCATC-A-TCTTAGGTGCCATCATCTTCGATGCCAT
1 TTCGGTGCCATCAATTC-T-GGTGCCATCACCTTCGATGCCAT
298257 GACCTTCCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 2 0.06
44 2 0.06
45 32 0.89
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.33
Consensus pattern (45 bp):
TTCGGTGCCATCAATTCTGGTGCCATCACCTTCGATGCCATCATC
Found at i:302101 original size:22 final size:22
Alignment explanation
Indices: 302073--302114 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
302063 GCTTGAGAGT
*
302073 TTGAAAGCACAGAGCTTGATTG
1 TTGAAAGCACAAAGCTTGATTG
302095 TTGAAAGCACAAAGCTTGAT
1 TTGAAAGCACAAAGCTTGAT
302115 CTGATTTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (22 bp):
TTGAAAGCACAAAGCTTGATTG
Found at i:309166 original size:20 final size:21
Alignment explanation
Indices: 309129--309167 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
309119 TCCTTTGGGT
* *
309129 GCTTTTTTTTTTGTCAAGACA
1 GCTTATTTTGTTGTCAAGACA
309150 GCTTATTTTGTTG-CAAGA
1 GCTTATTTTGTTGTCAAGA
309168 GCAACTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (21 bp):
GCTTATTTTGTTGTCAAGACA
Found at i:311447 original size:31 final size:29
Alignment explanation
Indices: 311375--311448 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
311365 TGCCGTCACA
**
311375 ATCAATTTGGGATATAACGTTTCAAAACG
1 ATCAATTAAGGATATAACGTTTCAAAACG
* * **
311404 ATCATTTCAGGATATAACGTTATCCAATCCG
1 ATCAATTAAGGATATAACGTT-T-CAAAACG
311435 ATCAATTAAGGATA
1 ATCAATTAAGGATA
311449 AAATTGGACG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 18 0.50
30 1 0.03
31 17 0.47
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (29 bp):
ATCAATTAAGGATATAACGTTTCAAAACG
Found at i:311899 original size:15 final size:12
Alignment explanation
Indices: 311870--311894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
311860 GTCTCCAAAA
311870 GCTTCTTCAATG
1 GCTTCTTCAATG
311882 GCTTCTTCAATG
1 GCTTCTTCAATG
311894 G
1 G
311895 AGGCTATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GCTTCTTCAATG
Found at i:313727 original size:2 final size:2
Alignment explanation
Indices: 313720--313745 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
313710 ATTTTTATCT
313720 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
313746 GTTTCCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:314312 original size:31 final size:32
Alignment explanation
Indices: 314261--314322 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
314251 AAGATTGAAA
314261 TATGAAAAATGACAAGAACAA-GTAAGAACTTG
1 TATGAAAAATGACAAGAACAATG-AAGAACTTG
314293 TATGAAAAA-GTA-AAGAACAATGAAGAACTT
1 TATGAAAAATG-ACAAGAACAATGAAGAACTT
314323 TTAGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.19
Consensus pattern (32 bp):
TATGAAAAATGACAAGAACAATGAAGAACTTG
Found at i:315624 original size:158 final size:159
Alignment explanation
Indices: 315328--315634 Score: 445
Period size: 158 Copynumber: 1.9 Consensus size: 159
315318 GGCCGCACAA
* *
315328 CACAGGGTATGGGCGGCTTAACCATGATATTAGAGTGTCAATAATGTAGACATGCCACATATACT
1 CACAGGGTATGGACGGCCTAACCATGATATTAGAGTGTCAATAATGTAGACATGCCACATATACT
** * * * * *
315393 AAGTTCATATTGCATCTCATGTGTCTGCACGCAGTATGATATAATCGTTTCACTTGAAGAATTAA
66 AAGACCATATTGCATCCCATGTCTCTACACGCAGTATGATATAATCGTTGCACTTGAAGAACTAA
315458 TTCACTTACTACGCCTGAACACCACGCAG
131 TTCACTTACTACGCCTGAACACCACGCAG
* ** * * *
315487 CACA-GGTATGGACGGCCTAATCATGATATTAGAGTGTGTATAATGTAGGCATGTCGCATATACT
1 CACAGGGTATGGACGGCCTAACCATGATATTAGAGTGTCAATAATGTAGACATGCCACATATACT
*
315551 AAGACCATATTGCATCCCATGTCTCTACGCGCAGTATGATATAATCGTTGCACTTGAAGAACTAA
66 AAGACCATATTGCATCCCATGTCTCTACACGCAGTATGATATAATCGTTGCACTTGAAGAACTAA
* *
315616 TTCCCTTACTGCGCCTGAA
131 TTCACTTACTACGCCTGAA
315635 GGCCGTGCAA
Statistics
Matches: 130, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
158 126 0.97
159 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (159 bp):
CACAGGGTATGGACGGCCTAACCATGATATTAGAGTGTCAATAATGTAGACATGCCACATATACT
AAGACCATATTGCATCCCATGTCTCTACACGCAGTATGATATAATCGTTGCACTTGAAGAACTAA
TTCACTTACTACGCCTGAACACCACGCAG
Found at i:319394 original size:14 final size:14
Alignment explanation
Indices: 319375--319402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
319365 TTCTGTCCTG
319375 ATAGCGCTAAGTAT
1 ATAGCGCTAAGTAT
319389 ATAGCGCTAAGTAT
1 ATAGCGCTAAGTAT
319403 TTTTTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
ATAGCGCTAAGTAT
Found at i:322600 original size:21 final size:21
Alignment explanation
Indices: 322557--322600 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
322547 TATAAGGGGG
* *
322557 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCCACTT
322578 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCACTT
322599 TT
1 TT
322601 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCACTT
Found at i:322628 original size:14 final size:15
Alignment explanation
Indices: 322599--322642 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
322589 CGCCCCACTT
*
322599 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
322614 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
322628 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
322643 ACTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:322723 original size:33 final size:31
Alignment explanation
Indices: 322686--322797 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 31
322676 GCGAAGCCTC
* *
322686 CCCACTGGGGCGGCTTCACCATGGGCAGGCCG
1 CCCACTGGGGCGGCTTCGCCA-AGGCAGGCCG
322718 TCCCACTGGGGCGGCTTCGCCAAGGCAGGCCG
1 -CCCACTGGGGCGGCTTCGCCAAGGCAGGCCG
* *
322750 CCCTCATGGGGCGGCTTCGCCACGGCAGGCCG
1 CCCAC-TGGGGCGGCTTCGCCAAGGCAGGCCG
322782 CCC-CGGTGGGGCGGCT
1 CCCAC--TGGGGCGGCT
322798 AGACCAAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.07
32 47 0.65
33 20 0.28
ACGTcount: A:0.10, C:0.38, G:0.39, T:0.12
Consensus pattern (31 bp):
CCCACTGGGGCGGCTTCGCCAAGGCAGGCCG
Done.