Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011766.1 Corchorus capsularis cultivar CVL-1 contig11787, 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: 45186
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:444 original size:2 final size:2
Alignment explanation
Indices: 437--474 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
427 ATTGCAGAGA
437 AT AT AT AT AT AT AT AT AT 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
475 GGTCATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23487 original size:29 final size:29
Alignment explanation
Indices: 23435--23532 Score: 144
Period size: 29 Copynumber: 3.4 Consensus size: 29
23425 CGTTAGGTTG
* *
23435 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAATGT-CCAAGATTGAAGTTC
*
23465 AGGGGGCAAAATGTCCAAGATTGAAGTTT
1 AGGGGGCAAAATGTCCAAGATTGAAGTTC
*
23494 AGGGGGCAAAATGTCCAAGATTGAATTTC
1 AGGGGGCAAAATGTCCAAGATTGAAGTTC
23523 A-GGGGCAAAA
1 AGGGGGCAAAA
23533 CGTACGCTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 9 0.14
29 41 0.65
30 13 0.21
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (29 bp):
AGGGGGCAAAATGTCCAAGATTGAAGTTC
Found at i:24015 original size:43 final size:43
Alignment explanation
Indices: 23967--24049 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
23957 TCACATGCAA
*
23967 GCACATGACTGAATTCTGTTACGGCAGGGGCAAAGTGTCCCAC
1 GCACATGACTGAATTCTGTTACGGCAGGGACAAAGTGTCCCAC
*
24010 GCACATGACTGAATTCTGTTACGGTAGGGACAAAGTGTCC
1 GCACATGACTGAATTCTGTTACGGCAGGGACAAAGTGTCC
24050 TTATTTCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23
Consensus pattern (43 bp):
GCACATGACTGAATTCTGTTACGGCAGGGACAAAGTGTCCCAC
Found at i:31156 original size:3 final size:3
Alignment explanation
Indices: 31150--31175 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31140 AAAAAAAAAA
31150 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
31176 ACAGCTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34364 original size:27 final size:27
Alignment explanation
Indices: 34312--34368 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 27
34302 TACTAAGATT
34312 AAAATATTGTAAGTCCTTTCACCAAAAAA
1 AAAATATTGTAAGTCC--TCACCAAAAAA
34341 AAAATATTGTAAGTCC-CACTCAAAAAA
1 AAAATATTGTAAGTCCTCAC-CAAAAAA
34368 A
1 A
34369 TATTGAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 3 0.11
27 8 0.30
29 16 0.59
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATATTGTAAGTCCTCACCAAAAAA
Found at i:38647 original size:5 final size:6
Alignment explanation
Indices: 38635--38665 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
38625 AGATGATCGC
*
38635 TTGTTT TTGTTT TTGTTT TTGTTT TTCTTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT T
38666 CGTAGCGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (6 bp):
TTGTTT
Found at i:39994 original size:35 final size:36
Alignment explanation
Indices: 39955--40025 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
39945 ATCTTTTACT
*
39955 TTTCA-TCACCATTGTTTTTACAAGGTGTAATCTTG
1 TTTCATTCACCATTATTTTTACAAGGTGTAATCTTG
* *
39990 TTTCATTCACCCTTATTTTTATAAGGTGTAATCTTG
1 TTTCATTCACCATTATTTTTACAAGGTGTAATCTTG
40026 CTTCGGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.48
Consensus pattern (36 bp):
TTTCATTCACCATTATTTTTACAAGGTGTAATCTTG
Found at i:42442 original size:97 final size:97
Alignment explanation
Indices: 42328--42522 Score: 300
Period size: 97 Copynumber: 2.0 Consensus size: 97
42318 TTTAGGGTTT
* *
42328 AGGGAAGGGTAAATACTTTAGAAACTCACAATATATGCTACCACATTTTTTAATAACAATACCAA
1 AGGGAACGGTAAATACTTTAGAAACTCACAATATATGCTACCACAATTTTTAATAACAATACCAA
*
42393 ACATTATTTACATTTTTCTACTCCAATTAAAA
66 ACATTATTTACATTTTTCTACCCCAATTAAAA
* * * ***
42425 AGGGAACGGTAAGTACTTTAGAAACTCATAATATATTCTACCACAATTTTTAATAGTGATACCAA
1 AGGGAACGGTAAATACTTTAGAAACTCACAATATATGCTACCACAATTTTTAATAACAATACCAA
*
42490 ACATTATTTACATTTTTTTACCCCAATTAAAA
66 ACATTATTTACATTTTTCTACCCCAATTAAAA
42522 A
1 A
42523 AAAGTAAATC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 88 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.34
Consensus pattern (97 bp):
AGGGAACGGTAAATACTTTAGAAACTCACAATATATGCTACCACAATTTTTAATAACAATACCAA
ACATTATTTACATTTTTCTACCCCAATTAAAA
Found at i:44801 original size:21 final size:21
Alignment explanation
Indices: 44790--44830 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44780 TGTATATGTT
*
44790 AGATTTGTTACTATACAGATA
1 AGATTTGTTACTGTACAGATA
44811 AGATTTGTTACTGTACAGAT
1 AGATTTGTTACTGTACAGAT
44831 GAAAATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
AGATTTGTTACTGTACAGATA
Done.