Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022218.1 Corchorus olitorius cultivar O-4 contig22251, 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: 39589
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7128 original size:31 final size:31
Alignment explanation
Indices: 7092--7158 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
7082 AAACTTGGTA
7092 CCTAACGTTGCAAAATCAGCTCAAATAAGTC
1 CCTAACGTTGCAAAATCAGCTCAAATAAGTC
* *
7123 TCTAACGTTGCAAAATCAGCTCAAATCAGTC
1 CCTAACGTTGCAAAATCAGCTCAAATAAGTC
7154 CCTAA
1 CCTAA
7159 TGTCAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (31 bp):
CCTAACGTTGCAAAATCAGCTCAAATAAGTC
Found at i:9179 original size:30 final size:30
Alignment explanation
Indices: 9145--9202 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9135 TTGCACAATT
* *
9145 ACATGTTCACTCATTGGAGGTAGGAAATGC
1 ACATGTTCACTCATTGGAAGCAGGAAATGC
9175 ACATGTTCACTCATTGGAAGCAGGAAAT
1 ACATGTTCACTCATTGGAAGCAGGAAAT
9203 CTAATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (30 bp):
ACATGTTCACTCATTGGAAGCAGGAAATGC
Found at i:21990 original size:35 final size:35
Alignment explanation
Indices: 21940--22228 Score: 384
Period size: 35 Copynumber: 8.3 Consensus size: 35
21930 CAAGAAACAA
21940 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* *
21975 GATTAAGGAAGTTGGT-ATCCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAAT-CAACTTAATTCGGTGT
22010 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*
22045 AATTAAGGAAATTGGT-ATCCAACTTAATTCGATGT
1 AATTAAGGAAATTGGTAAT-CAACTTAATTCGGTGT
22080 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* *
22115 GATTAAGGAAATTGGTAATCAACTTAATCCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*** **
22150 AATTAAGGGGTTTGGTGGTCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* ** * * ** *
22185 AATTAAAGAAACCGGCAATCAACATGCTTCGGTGC
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
22220 AATTAAGGA
1 AATTAAGGA
22229 TCAAGGAAAA
Statistics
Matches: 221, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.02
35 213 0.96
36 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (35 bp):
AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
Found at i:22057 original size:19 final size:19
Alignment explanation
Indices: 22000--22057 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
21990 TATCCAACTT
22000 AATTCGGTGTAATTAAGGA
1 AATTCGGTGTAATTAAGGA
* ***
22019 AATT--G-GTAATCAACTT
1 AATTCGGTGTAATTAAGGA
22035 AATTCGGTGTAATTAAGGA
1 AATTCGGTGTAATTAAGGA
22054 AATT
1 AATT
22058 GGTATCCAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 11 0.39
17 1 0.04
18 1 0.04
19 15 0.54
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (19 bp):
AATTCGGTGTAATTAAGGA
Found at i:25547 original size:40 final size:39
Alignment explanation
Indices: 25498--25578 Score: 117
Period size: 40 Copynumber: 2.1 Consensus size: 39
25488 TCCTCCATTG
* *
25498 TTGATGGATATTTAAGAATATATATTTTAAAGGATTTATT
1 TTGAAGGATATTTAAGAATATATATTTTAAA-AATTTATT
* *
25538 TTGAAGGATATTTAAGAATGTATTTTTTAAAAATTTATT
1 TTGAAGGATATTTAAGAATATATATTTTAAAAATTTATT
25577 TT
1 TT
25579 TTAAGTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (39 bp):
TTGAAGGATATTTAAGAATATATATTTTAAAAATTTATT
Found at i:25591 original size:15 final size:15
Alignment explanation
Indices: 25548--25591 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25538 TTGAAGGATA
*
25548 TTTAAGAATGTATTT
1 TTTAAGAATATATTT
* *
25563 TTTAAAAATTTATTT
1 TTTAAGAATATATTT
*
25578 TTTAAGTATATATT
1 TTTAAGAATATATT
25592 ATGATGATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTAAGAATATATTT
Found at i:26240 original size:16 final size:16
Alignment explanation
Indices: 26207--26246 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
26197 AAACCTAGAC
26207 GACCCG-AACCCAATT
1 GACCCGAAACCCAATT
26222 GACCCGAAACCCGAA-T
1 GACCCGAAACCC-AATT
26238 GACCCGAAA
1 GACCCGAAA
26247 AAATTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.26
16 15 0.65
17 2 0.09
ACGTcount: A:0.38, C:0.38, G:0.17, T:0.07
Consensus pattern (16 bp):
GACCCGAAACCCAATT
Found at i:27931 original size:49 final size:48
Alignment explanation
Indices: 27812--27941 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 48
27802 CATTTTTACT
* *
27812 GCACTCTTTTTCTCAATTTTTACAACAAAATTGAACTTTTAATTTTCCTC
1 GCAC-CTTTTTCTCAATTTTTGC-ACAAAATTGAACTTTTAATTTTCCCC
*
27862 GCACCTTTTTCTCAATTTTTGCATCAAAATTGAA-TATTTACTTTTCCCC
1 GCACCTTTTTCTCAATTTTTGCA-CAAAATTGAACT-TTTAATTTTCCCC
* *
27911 GCATCC-TTTTATCAATTTTTGGACAAAATTG
1 GCA-CCTTTTTCTCAATTTTTGCACAAAATTG
27942 GTTGGCACGC
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
48 10 0.14
49 56 0.78
50 6 0.08
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.45
Consensus pattern (48 bp):
GCACCTTTTTCTCAATTTTTGCACAAAATTGAACTTTTAATTTTCCCC
Found at i:28366 original size:21 final size:21
Alignment explanation
Indices: 28326--28366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28316 TTCTTTTTAG
*
28326 TAAGTTTAGCCCTAATTTCAC
1 TAAGTTTAGCCCTAAATTCAC
28347 TAAGTTTAGTCCC-AAATTCA
1 TAAGTTTAG-CCCTAAATTCA
28367 AATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAGTTTAGCCCTAAATTCAC
Found at i:32181 original size:2 final size:2
Alignment explanation
Indices: 32165--32210 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
32155 AACGACAAAC
*
32165 AT AT AT ACT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32208 AT A
1 AT A
32211 AATAGTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:34130 original size:10 final size:10
Alignment explanation
Indices: 34115--34145 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
34105 AAACCTCTGT
34115 CTTTGTAAAA
1 CTTTGTAAAA
34125 CTTTGTAAAAA
1 CTTTGT-AAAA
34136 CTTTGTAAAA
1 CTTTGTAAAA
34146 TTATGACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (10 bp):
CTTTGTAAAA
Found at i:34137 original size:11 final size:11
Alignment explanation
Indices: 34115--34145 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
34105 AAACCTCTGT
34115 CTTTGT-AAAA
1 CTTTGTAAAAA
34125 CTTTGTAAAAA
1 CTTTGTAAAAA
34136 CTTTGTAAAA
1 CTTTGTAAAA
34146 TTATGACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (11 bp):
CTTTGTAAAAA
Found at i:36214 original size:8 final size:7
Alignment explanation
Indices: 36186--36212 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
36176 TGAAAATAGA
36186 AAAAAAG
1 AAAAAAG
36193 AAAAAAG
1 AAAAAAG
36200 AAAAAAG
1 AAAAAAG
36207 AAAAAA
1 AAAAAA
36213 AGGCAGGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:37425 original size:63 final size:63
Alignment explanation
Indices: 37353--37493 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
37343 AATGATTAGT
**
37353 TTGTAAATTTGTCTTCATATAC-TTAAATAAATTGCAAATTTGTCCCCATTTACAATTAATGCA
1 TTGTAAATTTGTCCCCATATACATT-AATAAATTGCAAATTTGTCCCCATTTACAATTAATGCA
* ** * **
37416 TTGTAAATTTGTCCCCATTTACAATTAATGCATTGTAAATTTGTCCCCATTTGTAATTAATGCA
1 TTGTAAATTTGTCCCCATATAC-ATTAATAAATTGCAAATTTGTCCCCATTTACAATTAATGCA
* *
37480 TTGGAAAATTGTCC
1 TTGTAAATTTGTCC
37494 TTATTCAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
63 19 0.29
64 45 0.68
65 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (63 bp):
TTGTAAATTTGTCCCCATATACATTAATAAATTGCAAATTTGTCCCCATTTACAATTAATGCA
Found at i:37429 original size:32 final size:32
Alignment explanation
Indices: 37383--37493 Score: 177
Period size: 32 Copynumber: 3.5 Consensus size: 32
37373 ACTTAAATAA
*
37383 ATTGCAAATTTGTCCCCATTTACAATTAATGC
1 ATTGTAAATTTGTCCCCATTTACAATTAATGC
37415 ATTGTAAATTTGTCCCCATTTACAATTAATGC
1 ATTGTAAATTTGTCCCCATTTACAATTAATGC
**
37447 ATTGTAAATTTGTCCCCATTTGTAATTAATGC
1 ATTGTAAATTTGTCCCCATTTACAATTAATGC
* *
37479 ATTGGAAAATTGTCC
1 ATTGTAAATTTGTCC
37494 TTATTCAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (32 bp):
ATTGTAAATTTGTCCCCATTTACAATTAATGC
Found at i:39553 original size:2 final size:2
Alignment explanation
Indices: 39546--39587 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
39536 TTTATAATAG
39546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39588 AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.