Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019968.1 Corchorus olitorius cultivar O-4 contig20001, 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: 5520
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Found at i:84 original size:20 final size:20
Alignment explanation
Indices: 59--99 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
49 ATGAAAGTCT
*
59 AAGGCCCAAGGATGCAAATA
1 AAGGCCCAAGCATGCAAATA
79 AAGGCCCAAGCATGCAAATA
1 AAGGCCCAAGCATGCAAATA
99 A
1 A
100 TTAAACAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (20 bp):
AAGGCCCAAGCATGCAAATA
Found at i:524 original size:27 final size:28
Alignment explanation
Indices: 493--570 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
483 AAGTGAACCT
493 AAAATGACCAAAATGCCCTTAGA-CGTG
1 AAAATGACCAAAATGCCCTTAGATCGTG
* * * * *
520 CAAATGACTAAAATGCCCCTGGATCTTG
1 AAAATGACCAAAATGCCCTTAGATCGTG
548 AAAATGACCAAAATGCCCCTTAG
1 AAAATGACCAAAATG-CCCTTAG
571 TTGATCCTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 19 0.47
28 16 0.40
29 5 0.12
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCTTAGATCGTG
Found at i:553 original size:28 final size:27
Alignment explanation
Indices: 493--567 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
483 AAGTGAACCT
*
493 AAAATGACCAAAATGCCCTTAGACGTG
1 AAAATGACCAAAATGCCCCTAGACGTG
* * * *
520 CAAATGACTAAAATGCCCCTGGATCTTG
1 AAAATGACCAAAATGCCCCTAGA-CGTG
548 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
568 TAGTTGATCC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 19 0.47
28 21 0.52
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAGACGTG
Found at i:1072 original size:51 final size:50
Alignment explanation
Indices: 872--1656 Score: 1210
Period size: 51 Copynumber: 15.5 Consensus size: 50
862 AATCAACTTA
* * * * *
872 TTTGAATTGTCTTCTAATCCAATATTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCC
* * *
922 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCC
* * *
972 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTCCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCC
* *
1022 TTTGAACTATCTGCCAATTCAATCTTTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAAT-TTTAAAAGGACCGTCTTCCGCTTATCC
* *
1073 TTTGAACTGTCTAGCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
*
1124 TTTGAACTGTCTACCAATTCAATCTTTAAAAGGACCATCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAAT-TTTAAAAGGACCGTCTTCCGCTTATCC
* *
1175 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCGGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
* *
1226 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCGGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
*
1277 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
* *
1328 TTTGAACTGTCTACCAATTCAATTCTAAAAGGACTGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCC
* *
1378 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCGGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
1429 TTTGAACTGTCTACCAATTCAATCTTTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAAT-TTTAAAAGGACCGTCTTCCGCTTATCC
* *
1480 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCATCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
1531 TTTGAACTGTCTACCAATTCAATTCTTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-TTAAAAGGACCGTCTTCCGCTTATCC
*
1582 TTTGAATTGTCTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTCAATT-T-TAAAAGGACCGTCTTCCGCTTATCC
1634 TTTGAACTGTCTACCAATTCAAT
1 TTTGAACTGTCTACCAATTCAAT
1657 CTTGAAAAAA
Statistics
Matches: 690, Mismatches: 37, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
50 164 0.24
51 477 0.69
52 49 0.07
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (50 bp):
TTTGAACTGTCTACCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCC
Found at i:1369 original size:305 final size:306
Alignment explanation
Indices: 898--1658 Score: 1339
Period size: 305 Copynumber: 2.5 Consensus size: 306
888 ATCCAATATT
* *
898 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAA-TCTTAAAAGGATCGTCTT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTTAAAAGGACCGTCTT
* * *
962 CCGCTTATCCTTTGAACTGTCTTCCAATTCAA-TCTTAAAAGGACCGTCTCCCGCTTATCCTTTG
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTG
* * * *
1026 AACTATCTGCCAATTCAATCTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTAGCAAT
131 AACTGTCTACCAATTCAATCTCTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAAT
1091 TCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAAAAG
196 TCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAAAAG
1156 GACCATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
261 GACCATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
* *
1202 AAAAGGACCGTCTTCGGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTTAAAAGGACCGTCTT
*
1267 CGGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTG
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTG
*
1332 AACTGTCTACCAATTCAAT-TCTAAAAGGACTGTCTTCCGCTTATCCTTTGAACTGTCTACCAAT
131 AACTGTCTACCAATTCAATCTCTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAAT
*
1396 TCAATTCTAAAAAGGACCGTCTTCGGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAAAAG
196 TCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAAAAG
*
1461 GACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
261 GACCATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
*
1507 AAAAGGACCATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTTAAAAGGACCGTCTT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTTAAAAGGACCGTCTT
*
1572 CCGCTTATCCTTTGAATTGTCTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATCCTTT
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA-AAAAGGACCGTCTTCCGCTTATCCTTT
1637 GAACTGTCTACCAATTCAATCT
130 GAACTGTCTACCAATTCAATCT
1659 TGAAAAAAAA
Statistics
Matches: 433, Mismatches: 20, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
304 44 0.10
305 294 0.68
306 94 0.22
307 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (306 bp):
AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTTAAAAGGACCGTCTT
CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTG
AACTGTCTACCAATTCAATCTCTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAAT
TCAATTCTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAAAAG
GACCATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
Found at i:1786 original size:50 final size:50
Alignment explanation
Indices: 1716--1909 Score: 275
Period size: 50 Copynumber: 3.9 Consensus size: 50
1706 AAACCAAGGT
* * *
1716 TTGA-AAT-GACTCGTACGGAAACGAGCTCGGCTTGTGGAAAAGCCTATG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* * *
1764 TTGATAATGGACTCATATGGAAACGAGTTTGGCTTGTGGAAAATCCTATG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* *
1814 TTGATAATCGACTCGTATAGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
* * *
1864 TTGATAATCGACTCGTATGGAAACGAGTTTGACTTATGAAAAAGCC
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1910 AAAACATTCG
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
48 4 0.03
49 3 0.02
50 123 0.95
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (50 bp):
TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
Found at i:3148 original size:19 final size:19
Alignment explanation
Indices: 3097--3149 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
3087 CTTTCGTCGG
3097 CCTTATGTCTTCAATTAGA
1 CCTTATGTCTTCAATTAGA
*
3116 CCTGCAATTGTCTTCAATTAGA
1 CCT--TA-TGTCTTCAATTAGA
3138 CCTTATGTCTTC
1 CCTTATGTCTTC
3150 TTTCGCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 10 0.34
20 1 0.03
21 1 0.03
22 17 0.59
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.42
Consensus pattern (19 bp):
CCTTATGTCTTCAATTAGA
Found at i:5040 original size:11 final size:11
Alignment explanation
Indices: 5012--5047 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5002 TTAATTCACT
*
5012 TTTGTTTTGAA
1 TTTGATTTGAA
5023 CTTTGATTTGAA
1 -TTTGATTTGAA
5035 TTTGATTTGAA
1 TTTGATTTGAA
5046 TT
1 TT
5048 ACTTAACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (11 bp):
TTTGATTTGAA
Done.