Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006773.1 Corchorus capsularis cultivar CVL-1 contig06794, 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: 23128
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1271 original size:73 final size:73
Alignment explanation
Indices: 1152--1328 Score: 300
Period size: 73 Copynumber: 2.4 Consensus size: 73
1142 ACCCGGGTCA
* * *
1152 TTTCAACTTCAGTTTCAGTCGACTGAAATGGCATTTTACTGTTTATACAGAAAGAACATAACAGA
1 TTTCAACTTCTGTTTTAGTCGACTGAAATGGCATTTTACTGTTTATACAGAAAGAACACAACAGA
1217 CTGGGCGC
66 CTGGGCGC
* *
1225 TTTCAATTTCTGTTTTAGTCGACTGAAATGGCATTTTACTGTTTATACAGAAAGGACACAACAGA
1 TTTCAACTTCTGTTTTAGTCGACTGAAATGGCATTTTACTGTTTATACAGAAAGAACACAACAGA
1290 CTGGGCGC
66 CTGGGCGC
*
1298 TTTCAACTTCTGTTTTAGTCTACTGAAATGG
1 TTTCAACTTCTGTTTTAGTCGACTGAAATGG
1329 TTCATTTTCC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 97 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (73 bp):
TTTCAACTTCTGTTTTAGTCGACTGAAATGGCATTTTACTGTTTATACAGAAAGAACACAACAGA
CTGGGCGC
Found at i:14893 original size:18 final size:18
Alignment explanation
Indices: 14870--14904 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14860 CAATTGCTGG
14870 TTTAATATTTAATATATT
1 TTTAATATTTAATATATT
* *
14888 TTTAATTTTTTATATAT
1 TTTAATATTTAATATAT
14905 ATTATACATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAATATTTAATATATT
Found at i:17541 original size:29 final size:30
Alignment explanation
Indices: 17485--17546 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
17475 ATATTTATCT
* *
17485 TATAATGAGTAGTTTTTTTTTCTAAAATTGG
1 TATAATGAGTAG-TTTTTTATCTAAAATGGG
*
17516 TATAATGGGTAG-TTTTTATCTAAAATGGG
1 TATAATGAGTAGTTTTTTATCTAAAATGGG
17545 TA
1 TA
17547 GTTTTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (30 bp):
TATAATGAGTAGTTTTTTATCTAAAATGGG
Found at i:18261 original size:21 final size:21
Alignment explanation
Indices: 18223--18449 Score: 255
Period size: 21 Copynumber: 10.9 Consensus size: 21
18213 TATATGAAAC
* * *
18223 TTTGGGGTTAGACTATCAATA
1 TTTGGGGTTTGACCATCAAGA
*
18244 TTTAGGGTTTGACCATCAAGA
1 TTTGGGGTTTGACCATCAAGA
* * * *
18265 TTTAGGGCTTGACTAT-AAAA
1 TTTGGGGTTTGACCATCAAGA
* *
18285 TTTGGGGTTAGACTATCAAGA
1 TTTGGGGTTTGACCATCAAGA
18306 TTTGGGGTTTGACCATCAAGA
1 TTTGGGGTTTGACCATCAAGA
*
18327 TTTGGGGTTTGACTATCAA-A
1 TTTGGGGTTTGACCATCAAGA
*
18347 TTTGGGGTTTGACTATCAAGA
1 TTTGGGGTTTGACCATCAAGA
* ***
18368 TTTGGGGTGTGACCATTTTGA
1 TTTGGGGTTTGACCATCAAGA
*
18389 TATT-GGGTTTGACAATCAA-A
1 T-TTGGGGTTTGACCATCAAGA
18409 CTTTGGGGTTTGACCATCAAGA
1 -TTTGGGGTTTGACCATCAAGA
18431 TTTGGGGTTTGACCATCAA
1 TTTGGGGTTTGACCATCAA
18450 AAGTTTTGTG
Statistics
Matches: 175, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
20 39 0.22
21 133 0.76
22 3 0.02
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (21 bp):
TTTGGGGTTTGACCATCAAGA
Found at i:18299 original size:62 final size:61
Alignment explanation
Indices: 18223--18449 Score: 301
Period size: 62 Copynumber: 3.7 Consensus size: 61
18213 TATATGAAAC
* * *
18223 TTTGGGGTTAGACTATCAATATTTAGGGTTTGACCATCAAGATTTAGGGCTTGACTATAAAA
1 TTTGGGGTTAGACTATCAAGATTTGGGGTTTGACCATCAAGATTT-GGGTTTGACTATAAAA
*
18285 TTTGGGGTTAGACTATCAAGATTTGGGGTTTGACCATCAAGATTTGGGGTTTGACTATCAAA
1 TTTGGGGTTAGACTATCAAGATTTGGGGTTTGACCATCAAGATTT-GGGTTTGACTATAAAA
* * *** * *
18347 TTTGGGGTTTGACTATCAAGATTTGGGGTGTGACCATTTTGATATTGGGTTTGACAATCAAAC
1 TTTGGGGTTAGACTATCAAGATTTGGGGTTTGACCATCAAGAT-TTGGGTTTGACTAT-AAAA
* *
18410 TTTGGGGTTTGACCATCAAGATTTGGGGTTTGACCATCAA
1 TTTGGGGTTAGACTATCAAGATTTGGGGTTTGACCATCAA
18450 AAGTTTTGTG
Statistics
Matches: 145, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
62 106 0.73
63 39 0.27
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (61 bp):
TTTGGGGTTAGACTATCAAGATTTGGGGTTTGACCATCAAGATTTGGGTTTGACTATAAAA
Found at i:18371 original size:83 final size:83
Alignment explanation
Indices: 18223--18451 Score: 268
Period size: 83 Copynumber: 2.7 Consensus size: 83
18213 TATATGAAAC
* * * * *
18223 TTTGGGGTTAGACTATCAATATTTAGGGTTTGACCATCAAGATTTAGGGCTTGACTAT-AAAATT
1 TTTGGGGTTTGACAATCAA-ATTTGGGGTTTGACCATCAAGATTTGGGGTTTGACTATCAAAATT
*
18287 TGGGGT-TAGACTATCAAGA
65 TGGGGTGT-GACCATCAAGA
* * *
18306 TTTGGGGTTTGACCATCAAGATTTGGGGTTTGACTATCAA-ATTTGGGGTTTGACTATCAAGATT
1 TTTGGGGTTTGACAATCAA-ATTTGGGGTTTGACCATCAAGATTTGGGGTTTGACTATCAAAATT
***
18370 TGGGGTGTGACCATTTTGA
65 TGGGGTGTGACCATCAAGA
*
18389 TATT-GGGTTTGACAATCAAACTTTGGGGTTTGACCATCAAGATTTGGGGTTTGACCATCAAAA
1 T-TTGGGGTTTGACAATCAAA-TTTGGGGTTTGACCATCAAGATTTGGGGTTTGACTATCAAAA
18452 GTTTTGTGGT
Statistics
Matches: 125, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
82 16 0.13
83 86 0.69
84 23 0.18
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.36
Consensus pattern (83 bp):
TTTGGGGTTTGACAATCAAATTTGGGGTTTGACCATCAAGATTTGGGGTTTGACTATCAAAATTT
GGGGTGTGACCATCAAGA
Found at i:18625 original size:18 final size:18
Alignment explanation
Indices: 18560--18625 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 18
18550 AAACTCCAAG
18560 ATGCTAAATTCAAATGCT
1 ATGCTAAATTCAAATGCT
*
18578 ATGCTTCCACCATTCAACTAT-CT
1 ATGC-T--A-AATTCAA--ATGCT
18601 AATGCTAAATTCAAATGCT
1 -ATGCTAAATTCAAATGCT
18620 ATGCTA
1 ATGCTA
18626 TGCTATGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 6 0.16
21 2 0.05
22 6 0.16
23 3 0.08
24 6 0.16
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (18 bp):
ATGCTAAATTCAAATGCT
Done.