Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007704.1 Corchorus capsularis cultivar CVL-1 contig07725, 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: 8805
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:317 original size:30 final size:30
Alignment explanation
Indices: 271--373 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 30
261 TCACCTAAAT
*
271 CAGATTTATTTCCAATGCTATCAACCAAAA
1 CAGAATTATTTCCAATGCTATCAACCAAAA
* *
301 CAGGATTATTTGCAATGCTATAATCAACCAAAA
1 CAGAATTATTTCCAATGC--T-ATCAACCAAAA
* **
334 CAGAATTGTTTTTAATGCTATGTTCAACCAAAA
1 CAGAATTATTTCCAATGCTA---TCAACCAAAA
367 CAGAATT
1 CAGAATT
374 GTTTTCATCA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
30 16 0.27
31 1 0.02
32 1 0.02
33 42 0.70
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (30 bp):
CAGAATTATTTCCAATGCTATCAACCAAAA
Found at i:374 original size:33 final size:33
Alignment explanation
Indices: 290--380 Score: 128
Period size: 33 Copynumber: 2.8 Consensus size: 33
280 TTCCAATGCT
* * *
290 ATCAACCAAAACAGGATTATTTGCAATGCTATA
1 ATCAACCAAAACAGAATTGTTTTCAATGCTATA
* *
323 ATCAACCAAAACAGAATTGTTTTTAATGCTATG
1 ATCAACCAAAACAGAATTGTTTTCAATGCTATA
*
356 TTCAACCAAAACAGAATTGTTTTCA
1 ATCAACCAAAACAGAATTGTTTTCA
381 TCACAATTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (33 bp):
ATCAACCAAAACAGAATTGTTTTCAATGCTATA
Found at i:442 original size:34 final size:33
Alignment explanation
Indices: 404--525 Score: 147
Period size: 33 Copynumber: 3.7 Consensus size: 33
394 CCAAAACAGA
* *
404 TTTAGTTTTATTGCTAAACAACACTCAAATTAGG
1 TTTAGTATCATTGC-AAACAACACTCAAATTAGG
* ** *
438 TTTAGTATCATCGCAAACAACA-TCTAAAACAGA
1 TTTAGTATCATTGCAAACAACACTC-AAATTAGG
*
471 TTTAGTGTCATTGCAAACAACACTCAAATTAGG
1 TTTAGTATCATTGCAAACAACACTCAAATTAGG
*
504 TTTAGTATCATCGCAAACAACA
1 TTTAGTATCATTGCAAACAACA
526 TCTAAAACAC
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.79
34 13 0.18
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (33 bp):
TTTAGTATCATTGCAAACAACACTCAAATTAGG
Found at i:457 original size:33 final size:33
Alignment explanation
Indices: 419--525 Score: 153
Period size: 33 Copynumber: 3.2 Consensus size: 33
409 TTTTATTGCT
419 AAACAACACTCAAATTAGGTTTAGTATCATCGC
1 AAACAACACTCAAATTAGGTTTAGTATCATCGC
** * * *
452 AAACAACA-TCTAAAACAGATTTAGTGTCATTGC
1 AAACAACACTC-AAATTAGGTTTAGTATCATCGC
485 AAACAACACTCAAATTAGGTTTAGTATCATCGC
1 AAACAACACTCAAATTAGGTTTAGTATCATCGC
518 AAACAACA
1 AAACAACA
526 TCTAAAACAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.94
34 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (33 bp):
AAACAACACTCAAATTAGGTTTAGTATCATCGC
Found at i:508 original size:66 final size:67
Alignment explanation
Indices: 391--534 Score: 254
Period size: 66 Copynumber: 2.2 Consensus size: 67
381 TCACAATTAG
* * *
391 CATCCAAAACAGATTTAGTTTTATTGCTAAACAACACTCAAATTAGGTTTAGTATCATCGCAAAC
1 CATCTAAAACAGATTTAGTGTCATTGCTAAACAACACTCAAATTAGGTTTAGTATCATCGCAAAC
456 AA
66 AA
458 CATCTAAAACAGATTTAGTGTCATTGC-AAACAACACTCAAATTAGGTTTAGTATCATCGCAAAC
1 CATCTAAAACAGATTTAGTGTCATTGCTAAACAACACTCAAATTAGGTTTAGTATCATCGCAAAC
522 AA
66 AA
524 CATCTAAAACA
1 CATCTAAAACA
535 CTCTTTTCAA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
66 50 0.68
67 24 0.32
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (67 bp):
CATCTAAAACAGATTTAGTGTCATTGCTAAACAACACTCAAATTAGGTTTAGTATCATCGCAAAC
AA
Found at i:3077 original size:33 final size:33
Alignment explanation
Indices: 2979--3078 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 33
2969 CAAGTGTCCG
* **
2979 GGTGTAGC-CGGGCATGGCCATGTCGCGTGGCC
1 GGTGTTGCGCGGGCATCTCCATGTCGCGTGGCC
* * * *
3011 AGTGATG-GCCGGGCATCTCCATGTTGCATGGCC
1 GGTGTTGCG-CGGGCATCTCCATGTCGCGTGGCC
3044 GGTGTTGCGCGGGCATCTCCATGTCGCGTGGCC
1 GGTGTTGCGCGGGCATCTCCATGTCGCGTGGCC
3077 GG
1 GG
3079 ATCTCCAAGT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
32 4 0.07
33 49 0.91
34 1 0.02
ACGTcount: A:0.10, C:0.28, G:0.40, T:0.22
Consensus pattern (33 bp):
GGTGTTGCGCGGGCATCTCCATGTCGCGTGGCC
Found at i:3084 original size:21 final size:21
Alignment explanation
Indices: 3058--3099 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3048 TTGCGCGGGC
* *
3058 ATCTCCATGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
3079 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
3100 TCACTTGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.33, G:0.31, T:0.21
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:7089 original size:30 final size:30
Alignment explanation
Indices: 7053--7115 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
7043 CATCTTCAAG
*
7053 TCCATGATAAGTCCTTGG-TGCATCATTCCC
1 TCCATGATAAG-CCTTGGACGCATCATTCCC
7083 TCCATGATAAGCCTTGGACGCATCATTCCC
1 TCCATGATAAGCCTTGGACGCATCATTCCC
7113 TCC
1 TCC
7116 CCCTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGACGCATCATTCCC
Done.