Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009726.1 Corchorus capsularis cultivar CVL-1 contig09747, 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: 55882
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:204 original size:16 final size:16
Alignment explanation
Indices: 179--209 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
169 TCTGGTTAGT
*
179 TTATTGTTATTACTAC
1 TTATTATTATTACTAC
195 TTATTATTATTACTA
1 TTATTATTATTACTA
210 GTAGCTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATTATTATTACTAC
Found at i:3158 original size:30 final size:30
Alignment explanation
Indices: 3122--3178 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3112 TTGATGAAAT
*
3122 AAGTCAACTGTGTATTTACAGCAGGATTCA
1 AAGTCAACAGTGTATTTACAGCAGGATTCA
* *
3152 AAGTCAACAGTTTGTTTACAGCAGGAT
1 AAGTCAACAGTGTATTTACAGCAGGAT
3179 CCAAGATTGA
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:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (30 bp):
AAGTCAACAGTGTATTTACAGCAGGATTCA
Found at i:3221 original size:21 final size:21
Alignment explanation
Indices: 3195--3245 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3185 TTGAAGTCGA
* *
3195 AAATCATGTTGCCATGTTCGC
1 AAATCATGTTACCATGTCCGC
*
3216 AAATCATGTTACCGTGTCCGC
1 AAATCATGTTACCATGTCCGC
3237 AAATCATGT
1 AAATCATGT
3246 AGATTGATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (21 bp):
AAATCATGTTACCATGTCCGC
Found at i:3329 original size:2 final size:2
Alignment explanation
Indices: 3322--3346 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3312 TTACTGCAGG
3322 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3347 ATCTATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9880 original size:30 final size:30
Alignment explanation
Indices: 9846--9902 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
9836 ATGATGAAAT
*
9846 AAGTCAACTGTGTATTTACAGCAGGATTCA
1 AAGTCAACAGTGTATTTACAGCAGGATTCA
* * *
9876 AAGTCAACAGTTTGTTTACAGTAGGAT
1 AAGTCAACAGTGTATTTACAGCAGGAT
9903 CCAAGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (30 bp):
AAGTCAACAGTGTATTTACAGCAGGATTCA
Found at i:9945 original size:21 final size:21
Alignment explanation
Indices: 9919--9969 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
9909 TTGAAGCCGG
*
9919 AAATCATGTTGCCGTGTCCGC
1 AAATCATGTTACCGTGTCCGC
*
9940 AAATCATGTTACCGTGTCTGC
1 AAATCATGTTACCGTGTCCGC
9961 AAATCATGT
1 AAATCATGT
9970 AGATTGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (21 bp):
AAATCATGTTACCGTGTCCGC
Found at i:13256 original size:2 final size:2
Alignment explanation
Indices: 13249--13285 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
13239 ATTGATTAGT
*
13249 TA TA TA TA AA TA TA -A T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13286 TAAGGGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19253 original size:2 final size:2
Alignment explanation
Indices: 19246--19282 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19236 CTTGGACCTA
19246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19283 ACAACTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22102 original size:33 final size:32
Alignment explanation
Indices: 22031--22103 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 32
22021 ATTTGATGAG
* * *
22031 TGAAGAAGAGGCTAAAAGTGATGTTGTGGATG
1 TGAAGAAGAGCCTAAAAGGGATGTTGTGGATC
* *
22063 TG--GAAGAGCCTAAGAGGGATGTTGTTGGTTC
1 TGAAGAAGAGCCTAAAAGGGATGTTG-TGGATC
22094 TGAAGAAGAG
1 TGAAGAAGAG
22104 GAGTCGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
30 19 0.58
31 6 0.18
32 2 0.06
33 6 0.18
ACGTcount: A:0.32, C:0.05, G:0.38, T:0.25
Consensus pattern (32 bp):
TGAAGAAGAGCCTAAAAGGGATGTTGTGGATC
Found at i:22375 original size:27 final size:27
Alignment explanation
Indices: 22335--22553 Score: 294
Period size: 27 Copynumber: 8.1 Consensus size: 27
22325 TGTTGGAGAG
*
22335 AAGGAAGGTGAATTGGAAAATATATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
* *
22362 AAGGAAGGTCAATTGCAAAATGTATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
** *
22389 AAGGAAGGTGAATTGGTTAATGTGTCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
*
22416 AAGGAAGGTGAATTGGAAAATGCATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
* *
22443 CAGGAAGGTGAATTGGAAAATGCATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
*
22470 AAGGAAGGTGAATTGGAAAATGCATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
*
22497 AAGGAAGGTGAATTGGTAAATGTATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
* ** * *
22524 AAGGAAAGTGAACAGGAACATGCATCA
1 AAGGAAGGTGAATTGGAAAATGTATCA
22551 AAG
1 AAG
22554 AATCTAGAAG
Statistics
Matches: 170, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 170 1.00
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.21
Consensus pattern (27 bp):
AAGGAAGGTGAATTGGAAAATGTATCA
Found at i:36676 original size:3 final size:3
Alignment explanation
Indices: 36668--36725 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
36658 GAATCTCCAA
36668 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36716 AAT AAT AAT A
1 AAT AAT AAT A
36726 GGGGTAGGGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43420 original size:1 final size:1
Alignment explanation
Indices: 43414--43450 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
43404 CACATTTCGG
43414 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43451 GTCTTTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:49943 original size:12 final size:12
Alignment explanation
Indices: 49926--49951 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49916 ACGATCACTC
49926 CGTCAGAAGGTA
1 CGTCAGAAGGTA
49938 CGTCAGAAGGTA
1 CGTCAGAAGGTA
49950 CG
1 CG
49952 ACACATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.19, G:0.35, T:0.15
Consensus pattern (12 bp):
CGTCAGAAGGTA
Found at i:51887 original size:17 final size:18
Alignment explanation
Indices: 51865--51900 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
51855 GTTATTAGAA
51865 GTATGCTCTG-TTTTAGG
1 GTATGCTCTGTTTTTAGG
51882 GTATGCTCTGTTTTTAGG
1 GTATGCTCTGTTTTTAGG
51900 G
1 G
51901 GGCAGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.11, C:0.11, G:0.31, T:0.47
Consensus pattern (18 bp):
GTATGCTCTGTTTTTAGG
Done.