Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019962.1 Corchorus olitorius cultivar O-4 contig19995, 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: 19057
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:376 original size:24 final size:24
Alignment explanation
Indices: 331--409 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 24
321 TAATATCAAA
*
331 TAATAAC-AGAAAT-AATTT-ATT
1 TAATAACTAAAAATCAATTTAATT
352 TAATAACTAAAAATCAATTTAATTTATT
1 TAATAACTAAAAATCAATTT-A---ATT
*
380 TAATAACTAAAAATCAATTTAATC
1 TAATAACTAAAAATCAATTTAATT
404 TAATAA
1 TAATAA
410 AATCAATTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
21 7 0.14
22 5 0.10
23 5 0.10
24 8 0.16
27 1 0.02
28 23 0.47
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (24 bp):
TAATAACTAAAAATCAATTTAATT
Found at i:377 original size:28 final size:28
Alignment explanation
Indices: 343--402 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
333 ATAACAGAAA
343 TAATTTATTTAATAACTAAAAATCAATT
1 TAATTTATTTAATAACTAAAAATCAATT
371 TAATTTATTTAATAACTAAAAATCAATT
1 TAATTTATTTAATAACTAAAAATCAATT
399 TAAT
1 TAAT
403 CTAATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATTTATTTAATAACTAAAAATCAATT
Found at i:401 original size:19 final size:21
Alignment explanation
Indices: 377--425 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
367 AATTTAATTT
377 ATTTAATAACT-A-AAAATCA
1 ATTTAATAACTAATAAAATCA
396 ATTTAAT--CTAATAAAATCA
1 ATTTAATAACTAATAAAATCA
415 ATTTAATAACT
1 ATTTAATAACT
426 GAAATTGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 1 0.04
19 21 0.81
21 2 0.08
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTAATAACTAATAAAATCA
Found at i:863 original size:17 final size:18
Alignment explanation
Indices: 837--877 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
827 TAATTACAAT
*
837 AATAAATAATTATAGT-A
1 AATAATTAATTATAGTCA
854 AATAATTAATTATAGTCA
1 AATAATTAATTATAGTCA
872 AATAAT
1 AATAAT
878 AAAATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (18 bp):
AATAATTAATTATAGTCA
Found at i:1229 original size:19 final size:19
Alignment explanation
Indices: 1205--1243 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1195 CATGATGTTC
1205 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
1224 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
1243 T
1 T
1244 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Found at i:3194 original size:20 final size:21
Alignment explanation
Indices: 3169--3208 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3159 TAAAAACTAC
3169 AAGAACTCCG-AATGGAGTAT
1 AAGAACTCCGCAATGGAGTAT
*
3189 AAGAACTCCGCGATGGAGTA
1 AAGAACTCCGCAATGGAGTA
3209 AAAACCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGAACTCCGCAATGGAGTAT
Found at i:3219 original size:28 final size:28
Alignment explanation
Indices: 3187--3241 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3177 CGAATGGAGT
3187 ATAAGAACTCCGCGATGGAGTAAAAACC
1 ATAAGAACTCCGCGATGGAGTAAAAACC
* * * *
3215 ATAAGACCTCTGCGATTGAGTATAAAC
1 ATAAGAACTCCGCGATGGAGTAAAAAC
3242 TAACACGACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (28 bp):
ATAAGAACTCCGCGATGGAGTAAAAACC
Found at i:18448 original size:27 final size:28
Alignment explanation
Indices: 18418--18472 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
18408 TTTTAATAAG
* *
18418 TATTCTTTTTAG-TTATTTAATTTTTTT
1 TATTCTTTTTAGATGATTTAACTTTTTT
*
18445 TATTTTTTTTAGATGATTTAACTTTTTT
1 TATTCTTTTTAGATGATTTAACTTTTTT
18473 ATTAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (28 bp):
TATTCTTTTTAGATGATTTAACTTTTTT
Found at i:18473 original size:27 final size:27
Alignment explanation
Indices: 18418--18475 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
18408 TTTTAATAAG
* *
18418 TATTCTTTTTAGTTATTTAATTTTTTT
1 TATTCTTTTTAGTGATTTAATCTTTTT
*
18445 TATTTTTTTTAGATGATTTAA-CTTTTT
1 TATTCTTTTTAG-TGATTTAATCTTTTT
18472 TATT
1 TATT
18476 AATAATTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (27 bp):
TATTCTTTTTAGTGATTTAATCTTTTT
Found at i:18483 original size:20 final size:20
Alignment explanation
Indices: 18447--18484 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18437 ATTTTTTTTA
*
18447 TTTTTTTTAGATGATTTAAC
1 TTTTTTTTAGATAATTTAAC
18467 TTTTTTATTA-ATAATTTA
1 TTTTTT-TTAGATAATTTA
18485 CTCTCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTTTTAGATAATTTAAC
Done.