Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019801.1 Corchorus olitorius cultivar O-4 contig19834, 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: 36443
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:1456 original size:23 final size:23
Alignment explanation
Indices: 1430--1477 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1420 TTGAACAAAC
*
1430 CTCTCAAATAAACCAAATGGTTT
1 CTCTCAAATAAACCAAACGGTTT
*
1453 CTCTCAAATAAACCAAGCGGTTT
1 CTCTCAAATAAACCAAACGGTTT
1476 CT
1 CT
1478 ATTAGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (23 bp):
CTCTCAAATAAACCAAACGGTTT
Found at i:2221 original size:16 final size:16
Alignment explanation
Indices: 2208--2251 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
2198 GTAAAAAAAC
2208 GAAACCCCAAAAAATT
1 GAAACCCCAAAAAATT
*
2224 GAAACCCTAAAAAATT
1 GAAACCCCAAAAAATT
2240 GAAACCCCAAAA
1 GAAACCCCAAAA
2252 GGTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.25, G:0.07, T:0.11
Consensus pattern (16 bp):
GAAACCCCAAAAAATT
Found at i:7610 original size:36 final size:36
Alignment explanation
Indices: 7570--7642 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
7560 ATATAATTAT
*
7570 AATTATCATTATCATAAAATAAAAAA-ATAATTTTAA
1 AATTATAATTATCAT-AAATAAAAAACATAATTTTAA
7606 AATTATAATTATCATAAATAAAAAATCATAATTTTAA
1 AATTATAATTATCATAAATAAAAAA-CATAATTTTAA
7643 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 10 0.29
36 14 0.41
37 10 0.29
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (36 bp):
AATTATAATTATCATAAATAAAAAACATAATTTTAA
Found at i:15595 original size:2 final size:2
Alignment explanation
Indices: 15588--15620 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15578 AGAAAATCCT
15588 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
15621 TTGTTTACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20127 original size:26 final size:26
Alignment explanation
Indices: 20097--20149 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
20087 AGATGAAAAC
**
20097 AGAGAAATCGAGAAAATGATTGGAAA
1 AGAGAAATCGAGAAAACAATTGGAAA
20123 AGAGAAATCGAGAAAACAATTGGAAA
1 AGAGAAATCGAGAAAACAATTGGAAA
20149 A
1 A
20150 AACTTAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.25, T:0.13
Consensus pattern (26 bp):
AGAGAAATCGAGAAAACAATTGGAAA
Found at i:21153 original size:107 final size:108
Alignment explanation
Indices: 20994--21205 Score: 304
Period size: 107 Copynumber: 2.0 Consensus size: 108
20984 TTTGTATTCT
* ***
20994 TTTTAGAAATTAAATATAAATTAATGTCACTGAAAGTTTAGTTCCAAATTAAAATTTTAATTTAA
1 TTTTAGAAATTAAATATAAACTAATGTCACTGAAAGTTTAACACCAAATTAAAATTTTAATTTAA
* * * *
21059 TTTTAATGGTAAATTCTAAAATTAATAATTTATTGTTATAGGG
66 TTTTAAAGGTAAATTCCAAAATAAATAATTTATTATTATAGGG
21102 TTTTAG-AATTAAAATATAAAACTAATGTCACT-AAA-TTTAACACCAAATTAAAATTTTAATTT
1 TTTTAGAAATT-AAATAT-AAACTAATGTCACTGAAAGTTTAACACCAAATTAAAATTTTAATTT
*
21164 TATTTTAAAGGTAAATTCCAAAATAAATAATTTATTATTATA
64 AATTTTAAAGGTAAATTCCAAAATAAATAATTTATTATTATA
21206 AAGTTTTACA
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 65 0.70
108 15 0.16
109 13 0.14
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (108 bp):
TTTTAGAAATTAAATATAAACTAATGTCACTGAAAGTTTAACACCAAATTAAAATTTTAATTTAA
TTTTAAAGGTAAATTCCAAAATAAATAATTTATTATTATAGGG
Found at i:27419 original size:36 final size:37
Alignment explanation
Indices: 27347--27423 Score: 93
Period size: 41 Copynumber: 2.0 Consensus size: 37
27337 ATTTGTCCGT
27347 CCTAATAATTAAGATAATAAAGTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGATAATAAAGTAAAT-C---TTTAGCCCC
* *
27388 CCTAATAATTAAGGTAATAAATTAAAT-TTTAGCCCC
1 CCTAATAATTAAGATAATAAAGTAAATCTTTAGCCCC
27424 TAGTTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 9 0.26
41 25 0.74
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (37 bp):
CCTAATAATTAAGATAATAAAGTAAATCTTTAGCCCC
Found at i:27554 original size:25 final size:25
Alignment explanation
Indices: 27526--27585 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
27516 ACACGTCAGG
*
27526 AGGGTCAAGTGGAGGGACAAATTGA
1 AGGGTCAAGTGGAAGGACAAATTGA
* *
27551 AGGGTTAAGTGGAAGGACAAATTGG
1 AGGGTCAAGTGGAAGGACAAATTGA
27576 AGGGTCAAGT
1 AGGGTCAAGT
27586 AGCAATACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.40, T:0.18
Consensus pattern (25 bp):
AGGGTCAAGTGGAAGGACAAATTGA
Found at i:28691 original size:15 final size:15
Alignment explanation
Indices: 28667--28739 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
28657 TTCCTATAGA
28667 AGGC-GAGGTTGGGG
1 AGGCGGAGGTTGGGG
*
28681 AGGCGGAGGTTGGGT
1 AGGCGGAGGTTGGGG
** *
28696 AGATTGG-GG-TGCTGG
1 AG-GCGGAGGTTG-GGG
28711 AGGCGGAGGTTGGGG
1 AGGCGGAGGTTGGGG
* *
28726 TGGCGAAGGTTGGG
1 AGGCGGAGGTTGGG
28740 TAGGTTGGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
14 8 0.18
15 32 0.73
16 4 0.09
ACGTcount: A:0.14, C:0.07, G:0.60, T:0.19
Consensus pattern (15 bp):
AGGCGGAGGTTGGGG
Found at i:28721 original size:45 final size:44
Alignment explanation
Indices: 28667--28757 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
28657 TTCCTATAGA
* *
28667 AGGCGAGGTTGGGGAGGCGGAGGTTGGGTAGATTGGGGTGCTGG
1 AGGCGAGGTTGGGGAGGCGAAGGTTGGGTAGATTGGGATGCTGG
* * *
28711 AGGCGGAGGTTGGGGTGGCGAAGGTTGGGTAGGTTGGGATGGTGG
1 AGGC-GAGGTTGGGGAGGCGAAGGTTGGGTAGATTGGGATGCTGG
28756 AG
1 AG
28758 ATTGGGGTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.14, C:0.05, G:0.59, T:0.21
Consensus pattern (44 bp):
AGGCGAGGTTGGGGAGGCGAAGGTTGGGTAGATTGGGATGCTGG
Found at i:31495 original size:23 final size:24
Alignment explanation
Indices: 31462--31548 Score: 108
Period size: 23 Copynumber: 3.7 Consensus size: 24
31452 AATATTAGAA
31462 TATTAAATTGTT-TTATCATCATC
1 TATTAAATTGTTATTATCATCATC
* *
31485 TATTAATTTGTTATTAT--TCTATA
1 TATTAAATTGTTATTATCATC-ATC
*
31508 TATTAAATTGTTTTTATCATCATC
1 TATTAAATTGTTATTATCATCATC
*
31532 TATTAATTTGTTATTAT
1 TATTAAATTGTTATTAT
31549 TCTATATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.04
23 28 0.53
24 21 0.40
25 2 0.04
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (24 bp):
TATTAAATTGTTATTATCATCATC
Found at i:31533 original size:47 final size:46
Alignment explanation
Indices: 31461--31558 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 46
31451 GAATATTAGA
31461 ATATTAAATTGTTTTATCATCATCTATTAATTTGTTATTATTCTAT
1 ATATTAAATTGTTTTATCATCATCTATTAATTTGTTATTATTCTAT
31507 ATATTAAATTGTTTTTATCATCATCTATTAATTTGTTATTATTCTAT
1 ATATTAAATTG-TTTTATCATCATCTATTAATTTGTTATTATTCTAT
31554 ATATT
1 ATATT
31559 TGTGTGTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 11 0.22
47 40 0.78
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (46 bp):
ATATTAAATTGTTTTATCATCATCTATTAATTTGTTATTATTCTAT
Found at i:31558 original size:23 final size:23
Alignment explanation
Indices: 31485--31558 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
31475 TATCATCATC
31485 TATTAATTTGTTATTATTCTATA
1 TATTAATTTGTTATTATTCTATA
* * *
31508 TATTAAATTGTTTTTA-TCATCATC
1 TATTAATTTGTTATTATTC-T-ATA
31532 TATTAATTTGTTATTATTCTATA
1 TATTAATTTGTTATTATTCTATA
31555 TATT
1 TATT
31559 TGTGTGTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.05
23 21 0.50
24 17 0.40
25 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (23 bp):
TATTAATTTGTTATTATTCTATA
Done.