Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011122.1 Corchorus olitorius cultivar O-4 contig11155, 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: 58392
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5260 original size:31 final size:31
Alignment explanation
Indices: 5225--5283 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
5215 ACAATAGAAT
5225 CTAGTGATTGATAGTAGTAACAAAATGATTG
1 CTAGTGATTGATAGTAGTAACAAAATGATTG
5256 CTAGTGATTGATAGTAGTAACAAAATGA
1 CTAGTGATTGATAGTAGTAACAAAATGA
5284 AGCTTAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31
Consensus pattern (31 bp):
CTAGTGATTGATAGTAGTAACAAAATGATTG
Found at i:9842 original size:22 final size:22
Alignment explanation
Indices: 9814--9857 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9804 GAATAAAAGA
9814 GAAACTTAAACTAAAATCTTTC
1 GAAACTTAAACTAAAATCTTTC
9836 GAAACTTAAACTAAAATCTTTC
1 GAAACTTAAACTAAAATCTTTC
9858 AATTAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
GAAACTTAAACTAAAATCTTTC
Found at i:15167 original size:14 final size:14
Alignment explanation
Indices: 15148--15184 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
15138 AACCTGGGTA
15148 AGAATTTCAATTGC
1 AGAATTTCAATTGC
15162 AGAATTTCAATTGC
1 AGAATTTCAATTGC
15176 AGAATTTCA
1 AGAATTTCA
15185 TTATACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (14 bp):
AGAATTTCAATTGC
Found at i:23210 original size:13 final size:13
Alignment explanation
Indices: 23169--23216 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
23159 TTATTAACAT
23169 TAAAT-ATACAAA
1 TAAATAATACAAA
* **
23181 TATAATTATTTAAA
1 TA-AATAATACAAA
23195 TAAATAATACAAA
1 TAAATAATACAAA
23208 TAAATAATA
1 TAAATAATA
23217 TATAATAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 2 0.07
13 20 0.69
14 7 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAATACAAA
Found at i:23223 original size:27 final size:26
Alignment explanation
Indices: 23169--23223 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
23159 TTATTAACAT
* *
23169 TAAATATACAAATATAATTATTTAAA
1 TAAATATACAAATATAATAATATAAA
23195 TAAATAATACAAATA-AATAATATATAA
1 TAAAT-ATACAAATATAATAATATA-AA
23222 TA
1 TA
23224 GTGATTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAATATACAAATATAATAATATAAA
Found at i:36890 original size:29 final size:30
Alignment explanation
Indices: 36827--36891 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
36817 AGAATGGGGG
* *
36827 CAAAACGTCCCAAAATTGAAGTTCATGAGA
1 CAAAACGTCCCAAAATTGAAATTCAAGAGA
* * *
36857 TAAAATGT-CCAAAATTGAAATTCAAGGGA
1 CAAAACGTCCCAAAATTGAAATTCAAGAGA
36886 CAAAAC
1 CAAAAC
36892 TTCAAACGCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (30 bp):
CAAAACGTCCCAAAATTGAAATTCAAGAGA
Found at i:39561 original size:30 final size:31
Alignment explanation
Indices: 39487--39561 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
39477 GACTGAGGGC
* *
39487 GTAAAACGTCCTAGAATTGAAACTCAGAGAA
1 GTAAAACGTCCAAAAATTGAAACTCAGAGAA
* * * *
39518 GCAAAATGTCCAAAAATTGAAATTCAG-GAG
1 GTAAAACGTCCAAAAATTGAAACTCAGAGAA
39548 GTAAAACGTCCAAA
1 GTAAAACGTCCAAA
39562 TGCTATAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 14 0.39
31 22 0.61
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (31 bp):
GTAAAACGTCCAAAAATTGAAACTCAGAGAA
Found at i:44606 original size:24 final size:23
Alignment explanation
Indices: 44574--44620 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44564 TGAATATTCT
*
44574 CAATATTGACATGGACAAAAAAGC
1 CAATATTGAC-TCGACAAAAAAGC
* *
44598 CAATCTTGACTCTACAAAAAAGC
1 CAATATTGACTCGACAAAAAAGC
44621 ACAGCTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (23 bp):
CAATATTGACTCGACAAAAAAGC
Found at i:48023 original size:9 final size:9
Alignment explanation
Indices: 48009--48044 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
47999 TGCTAAGTTC
48009 TTCTTTCTT
1 TTCTTTCTT
48018 TTCTTT-TT
1 TTCTTTCTT
48026 TT-TTTCTT
1 TTCTTTCTT
48034 TTCTTTCTT
1 TTCTTTCTT
48043 TT
1 TT
48045 TCACAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.12
8 8 0.32
9 14 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:48032 original size:11 final size:11
Alignment explanation
Indices: 48006--48046 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
47996 CTTTGCTAAG
48006 TTCTTCTTTCTT
1 TTCTT-TTTCTT
*
48018 TTCTTTTTTTT
1 TTCTTTTTCTT
48029 TTC-TTTTC-T
1 TTCTTTTTCTT
48038 TTCTTTTTC
1 TTCTTTTTC
48047 ACAATTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 4 0.15
10 9 0.35
11 8 0.31
12 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:48033 original size:16 final size:17
Alignment explanation
Indices: 48012--48045 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
48002 TAAGTTCTTC
48012 TTTCTTTTCTTT-TTTT
1 TTTCTTTTCTTTCTTTT
48028 TTTCTTTTCTTTCTTTT
1 TTTCTTTTCTTTCTTTT
48045 T
1 T
48046 CACAATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTCTTTTCTTTCTTTT
Found at i:49937 original size:30 final size:30
Alignment explanation
Indices: 49902--49961 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
49892 AATTTTGTCC
*
49902 TCCATGATAGTTATCCCATGTTTTGTAGCA
1 TCCATGATAGTCATCCCATGTTTTGTAGCA
49932 TCCATGATAGTCATCCCATGTTTTGTAGCA
1 TCCATGATAGTCATCCCATGTTTTGTAGCA
49962 AAACTCTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (30 bp):
TCCATGATAGTCATCCCATGTTTTGTAGCA
Found at i:55781 original size:9 final size:10
Alignment explanation
Indices: 55750--55781 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
55740 TTGTTTAATT
55750 AAATTGACAA
1 AAATTGACAA
55760 AAATTGACAA
1 AAATTGACAA
55770 AAATTGACAA
1 AAATTGACAA
55780 AA
1 AA
55782 CCCTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (10 bp):
AAATTGACAA
Found at i:57551 original size:30 final size:31
Alignment explanation
Indices: 57512--57642 Score: 151
Period size: 30 Copynumber: 4.3 Consensus size: 31
57502 CGATGCCAGA
57512 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGG
* *
57543 CCC-TATTTGAGCATTTTCGATAACGCTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGG
* ** ** * *
57573 CCCTTATTTGACCAAATT-AA-AATATCAGA
1 CCCTTATTTGAGCATTTTCAATAACGTTAGG
*
57602 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGG
57633 CCCTTATTTG
1 CCCTTATTTG
57643 GTCAAATTAA
Statistics
Matches: 78, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 19 0.24
30 30 0.38
31 29 0.37
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGG
Found at i:57616 original size:60 final size:60
Alignment explanation
Indices: 57546--57701 Score: 233
Period size: 60 Copynumber: 2.6 Consensus size: 60
57536 CGTTAGGCCC
* *
57546 TATTTGAGCATTTTCGATAACGCTAGGCCCTTATTTGACCAAATTAAAATATCAGACCCT
1 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGACCCT
** * *
57606 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGATCCT
1 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGACCCT
*
57666 TATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTT
1 TATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTT
57702 AAACAATTAG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 87 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (60 bp):
TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGACCCT
Done.