Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011140.1 Corchorus capsularis cultivar CVL-1 contig11161, 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: 16636
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:669 original size:27 final size:27
Alignment explanation
Indices: 631--685 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
621 TGAGCCTTCC
631 TGACGTATTTATCTAGTCTAAGTTGTA
1 TGACGTATTTATCTAGTCTAAGTTGTA
658 TGACGTATTTATCTAGTCTAAGTTGTA
1 TGACGTATTTATCTAGTCTAAGTTGTA
685 T
1 T
686 AAATAGGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (27 bp):
TGACGTATTTATCTAGTCTAAGTTGTA
Found at i:7468 original size:21 final size:22
Alignment explanation
Indices: 7444--7493 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
7434 ATTCATTTAC
*
7444 TATTA-TCTGTAAATCTCGTTT
1 TATTACTCTGTAAATCTCCTTT
* *
7465 TATTACTTTGTAAATGTCCTTT
1 TATTACTCTGTAAATCTCCTTT
7487 TATTACT
1 TATTACT
7494 TCTCTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (22 bp):
TATTACTCTGTAAATCTCCTTT
Found at i:7477 original size:22 final size:22
Alignment explanation
Indices: 7451--7494 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7441 TACTATTATC
*
7451 TGTAAATCTCGTTTTATTACTT
1 TGTAAATCTCCTTTTATTACTT
*
7473 TGTAAATGTCCTTTTATTACTT
1 TGTAAATCTCCTTTTATTACTT
7495 CTCTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (22 bp):
TGTAAATCTCCTTTTATTACTT
Found at i:7961 original size:26 final size:27
Alignment explanation
Indices: 7927--7979 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
7917 TTGTATGTCA
*
7927 CTCATATTCTGATA-TCTTATCTTTGT
1 CTCACATTCTGATATTCTTATCTTTGT
*
7953 CTCACATTCTGATATTTTTATCTTTGT
1 CTCACATTCTGATATTCTTATCTTTGT
7980 ATTGTCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.55
Consensus pattern (27 bp):
CTCACATTCTGATATTCTTATCTTTGT
Found at i:14941 original size:57 final size:57
Alignment explanation
Indices: 14860--14969 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
14850 ATTAAAAATC
14860 ATTTCACTGTACATGCATGGTCAAACCCCAAAGAATGATAATCAAACCACAAAAAAG
1 ATTTCACTGTACATGCATGGTCAAACCCCAAAGAATGATAATCAAACCACAAAAAAG
* * * * * *
14917 ATTTCATTGTACATGTATGGTCAAACCCCAAAGATTGGTAGTCAAACCCCAAA
1 ATTTCACTGTACATGCATGGTCAAACCCCAAAGAATGATAATCAAACCACAAA
14970 GTTTGATTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (57 bp):
ATTTCACTGTACATGCATGGTCAAACCCCAAAGAATGATAATCAAACCACAAAAAAG
Found at i:14960 original size:21 final size:20
Alignment explanation
Indices: 14936--15234 Score: 339
Period size: 21 Copynumber: 14.4 Consensus size: 20
14926 TACATGTATG
* *
14936 GTCAAACCCCAAAGATTGGTA
1 GTCAAACCCCAAA-TTTGATA
*
14957 GTCAAACCCCAAAGTTTGATT
1 GTCAAACCCCAAA-TTTGATA
14978 GTCAAACCCCAAAATTTGATA
1 GTCAAACCCC-AAATTTGATA
* *
14999 ATCAAACCCGAAAGTTTGATA
1 GTCAAACCCCAAA-TTTGATA
* *
15020 GTCAAACACCGAATTTGATA
1 GTCAAACCCCAAATTTGATA
15040 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAA-TTTGATA
15061 GTCAAACCCCAAAATTTGATA
1 GTCAAACCCC-AAATTTGATA
*
15082 GTCAAACCCTAAATTTTGATA
1 GTCAAACCCCAAA-TTTGATA
* **
15103 GTCAAACTCTGAATTTGATA
1 GTCAAACCCCAAATTTGATA
*
15123 ATCAAACCCCAAAATTTGATA
1 GTCAAACCCC-AAATTTGATA
15144 GTCAAACCCCAAATTTTGATA
1 GTCAAACCCCAAA-TTTGATA
* * *
15165 GTTAAACCTCGAATTTGATA
1 GTCAAACCCCAAATTTGATA
15185 GTCAAACCCCAAAATTTGAT-
1 GTCAAACCCC-AAATTTGATA
15205 GATCAAACCCCAAAGTTTGATA
1 G-TCAAACCCCAAA-TTTGATA
*
15227 ATCAAACC
1 GTCAAACC
15235 ATGTTAAACC
Statistics
Matches: 240, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
20 60 0.25
21 174 0.73
22 6 0.03
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (20 bp):
GTCAAACCCCAAATTTGATA
Found at i:15049 original size:83 final size:82
Alignment explanation
Indices: 14955--15234 Score: 393
Period size: 83 Copynumber: 3.4 Consensus size: 82
14945 CAAAGATTGG
* *
14955 TAGTCAAACCCCAAAGTTTGATTGTCAAACCCCAAAATTTGATAATCAAACCCGAAAGTTTGATA
1 TAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCCGAAA-TTTGATA
15020 GTCAAACACCGAATTTGA
65 GTCAAACACCGAATTTGA
*
15038 TAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCCTAAATTTTGATA
1 TAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCCGAAA-TTTGATA
* *
15103 GTCAAACTCTGAATTTGA
65 GTCAAACACCGAATTTGA
* * * *
15121 TAATCAAACCCCAAAATTTGATAGTCAAACCCCAAATTTTGATAGTTAAACCTCG-AATTTGATA
1 TAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACC-CGAAATTTGATA
* *
15185 GTCAAACCCCAAAATTTGA
65 GTCAAACACC-GAATTTGA
*
15204 T-GATCAAACCCCAAAGTTTGATAATCAAACC
1 TAG-TCAAACCCCAAAGTTTGATAGTCAAACC
15235 ATGTTAAACC
Statistics
Matches: 177, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
82 15 0.08
83 161 0.91
84 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (82 bp):
TAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAGTCAAACCCGAAATTTGATAG
TCAAACACCGAATTTGA
Found at i:15050 original size:62 final size:63
Alignment explanation
Indices: 14937--15234 Score: 372
Period size: 62 Copynumber: 4.8 Consensus size: 63
14927 ACATGTATGG
* *
14937 TCAAACCCCAAAGA-TTGGTAGTCAAACCCCAAAGTTTGATTGTCAAACCCCAAAATTTGATAA
1 TCAAACCCCAAA-ATTTGATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAA
* * * * * *
15000 TCAAACCCGAAAGTTTGATAGTCAAACACCGAA-TTTGATAGTCAAACCCCAAAGTTTGATAG
1 TCAAACCCCAAAATTTGATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAA
* * * **
15062 TCAAACCCCAAAATTTGATAGTCAAACCCTAAATTTTGATAGTCAAA-CTCTGAATTTGATAA
1 TCAAACCCCAAAATTTGATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAA
* * * * *
15124 TCAAACCCCAAAATTTGATAGTCAAACCCCAAATTTTGATAGTTAAACCTC-GAATTTGATAG
1 TCAAACCCCAAAATTTGATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAA
*
15186 TCAAACCCCAAAATTTGAT-GATCAAACCCCAAAGTTTGATAATCAAACC
1 TCAAACCCCAAAATTTGATAG-TCAAACCCCAAAGTTTGATAGTCAAACC
15235 ATGTTAAACC
Statistics
Matches: 207, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
61 1 0.00
62 163 0.79
63 43 0.21
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (63 bp):
TCAAACCCCAAAATTTGATAGTCAAACCCCAAAGTTTGATAGTCAAACCCCAAAATTTGATAA
Found at i:15375 original size:16 final size:16
Alignment explanation
Indices: 15354--15385 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15344 ATGTATGTAC
15354 ATGTATTAATTTAATT
1 ATGTATTAATTTAATT
15370 ATGTATTAATTTAATT
1 ATGTATTAATTTAATT
15386 TTAATAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATGTATTAATTTAATT
Found at i:16358 original size:26 final size:25
Alignment explanation
Indices: 16317--16399 Score: 98
Period size: 26 Copynumber: 3.2 Consensus size: 25
16307 TTAATTGTTA
16317 ATATCATATATATATATATATCAATAT
1 ATAT-ATATATATATATATATCAA-AT
16344 ATATATATATATATATATATCAAAT
1 ATATATATATATATATATATCAAAT
* *
16369 CGT-TACAATATATATATATATCAAAT
1 -ATATA-TATATATATATATATCAAAT
16395 A-ATAT
1 ATATAT
16400 TTAGTAGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
25 6 0.12
26 39 0.80
27 4 0.08
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (25 bp):
ATATATATATATATATATATCAAAT
Found at i:16383 original size:2 final size:2
Alignment explanation
Indices: 16317--16363 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
16307 TTAATTGTTA
16317 AT AT CAT AT AT AT AT AT AT AT CA- AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
16360 AT AT
1 AT AT
16364 CAAATCGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.