Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019345.1 Corchorus olitorius cultivar O-4 contig19378, 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: 87101
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:127 original size:27 final size:26
Alignment explanation
Indices: 96--147 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
86 TTTTTCAGAT
96 ATATTTCTAA-ATTGCCATTATTAAAGA
1 ATATTT-TAATATT-CCATTATTAAAGA
123 ATATTTTAATTATTCCATTATTAAA
1 ATATTTTAA-TATTCCATTATTAAA
148 ATAATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATTTTAATATTCCATTATTAAAGA
Found at i:1515 original size:26 final size:26
Alignment explanation
Indices: 1486--1536 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1476 ATTATTAAAA
1486 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
1512 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
1537 CTACAGTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Found at i:7791 original size:15 final size:15
Alignment explanation
Indices: 7755--7795 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
7745 TCCAAAATTT
* *
7755 AAATAAAAGAAAGGG
1 AAATAAAGGAAAAGG
7770 AAA-AAAGGAAAAGG
1 AAATAAAGGAAAAGG
7784 AAATAAAGGAAA
1 AAATAAAGGAAA
7796 TTAATAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (15 bp):
AAATAAAGGAAAAGG
Found at i:11106 original size:31 final size:31
Alignment explanation
Indices: 11068--11129 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11058 CAAACTTAAA
11068 TTTGAACCTATTATATTAAATCCCATGACTT
1 TTTGAACCTATTATATTAAATCCCATGACTT
11099 TTTGAACCTATTATATTAAATCCCATGACTT
1 TTTGAACCTATTATATTAAATCCCATGACTT
11130 GCAAATTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (31 bp):
TTTGAACCTATTATATTAAATCCCATGACTT
Found at i:12676 original size:56 final size:57
Alignment explanation
Indices: 12605--12720 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 57
12595 TTATTTTGTA
12605 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTG-AAG
1 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
*
12661 GAATAATTAAGTAGAGATAGGGGGATGGGATTTATTATAACATTTATTGTGTGAAAG
1 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
12718 GAA
1 GAA
12721 ACAGATAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 52 0.90
57 6 0.10
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.33
Consensus pattern (57 bp):
GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
Found at i:13090 original size:107 final size:107
Alignment explanation
Indices: 12904--13119 Score: 387
Period size: 107 Copynumber: 2.0 Consensus size: 107
12894 AATATGTAAC
*
12904 AAGCAGGGCGGCCGGCGCTTGCGCTGCAGTCATCTTCTTATTAAGGCTATATTTTTTTGTAATTG
1 AAGCAGGGCGGCCGGCGCTTGCGCTGCAGTCATCTTCTTATTAAGGCTATATTTTTCTGTAATTG
12969 TTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTGTAAATT
66 TTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTGTAAATT
* * *
13011 AAGCAGGGTGGCCTGCGCTTGCGCTGCAGTCATCTTCTTATTAAGGCTATATTTTTCTGTAGTTG
1 AAGCAGGGCGGCCGGCGCTTGCGCTGCAGTCATCTTCTTATTAAGGCTATATTTTTCTGTAATTG
*
13076 TTTAAGTCGGTTAGTAAGAAGATATTGCATTGGCTGTAAATT
66 TTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTGTAAATT
13118 AA
1 AA
13120 TTCTCATACA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (107 bp):
AAGCAGGGCGGCCGGCGCTTGCGCTGCAGTCATCTTCTTATTAAGGCTATATTTTTCTGTAATTG
TTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTGTAAATT
Found at i:13249 original size:42 final size:43
Alignment explanation
Indices: 13198--13291 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
13188 AGTGTATTAC
*
13198 CTAA-ATTCTACTCCT-TCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCTCTCTAGATAATTCATCAAAATAAAG
* *
13239 TTAATATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAG
1 CTAATATTCTACTCCT-C-TCTCTAGATAATTCATCAAAATAAAG
13284 CTAATATT
1 CTAATATT
13292 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 11 0.24
45 31 0.69
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (43 bp):
CTAATATTCTACTCCTCTCTCTAGATAATTCATCAAAATAAAG
Found at i:26558 original size:24 final size:24
Alignment explanation
Indices: 26526--26574 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
26516 ACTACTGAAT
26526 AGACTAGTTTACAATTGACGGAAC
1 AGACTAGTTTACAATTGACGGAAC
26550 AGACTAGTTTACAATTGACGGAAC
1 AGACTAGTTTACAATTGACGGAAC
26574 A
1 A
26575 CTGCACATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (24 bp):
AGACTAGTTTACAATTGACGGAAC
Found at i:32452 original size:15 final size:14
Alignment explanation
Indices: 32417--32455 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
32407 GTGCAAAAGG
32417 AAATAACTAAAACA
1 AAATAACTAAAACA
* *
32431 AAATAACTTAAAGA
1 AAATAACTAAAACA
32445 AAATTAACTAA
1 AAA-TAACTAA
32456 TTATTATAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAACTAAAACA
Found at i:33785 original size:15 final size:14
Alignment explanation
Indices: 33750--33788 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
33740 GTGCAATAGG
33750 AAATAACTAAAACA
1 AAATAACTAAAACA
* *
33764 AAATAACTTAAAGA
1 AAATAACTAAAACA
33778 AAATTAACTAA
1 AAA-TAACTAA
33789 TTATTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAACTAAAACA
Found at i:33867 original size:5 final size:5
Alignment explanation
Indices: 33853--33882 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
33843 TCAAGTAATT
*
33853 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
33883 GGAGGGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:34141 original size:20 final size:21
Alignment explanation
Indices: 34108--34154 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
34098 AAAACAAAAG
* *
34108 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
34129 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
34148 AAGAAAA
1 AAAAAAA
34155 GAGATGACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:37170 original size:42 final size:43
Alignment explanation
Indices: 37120--37213 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
37110 AGTGCATTAC
* * *
37120 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTATTAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
37161 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
37206 CTAATATT
1 CTAATATT
37214 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:38161 original size:42 final size:44
Alignment explanation
Indices: 38114--38201 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
38104 TTACCTAAAC
* * *
38114 TCTACT-C-CATCTCTAGGTAATTTATCAAAATAAAGCTAATAT
1 TCTACTCCGCATCTCTAGATAATTCATCAAAATAAAACTAATAT
38156 TCTACTCCTGCATCTCTAGATAATTCATCAAAATAAAACTAATAT
1 TCTACTCC-GCATCTCTAGATAATTCATCAAAATAAAACTAATAT
38201 T
1 T
38202 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 6 0.15
43 1 0.03
45 33 0.82
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (44 bp):
TCTACTCCGCATCTCTAGATAATTCATCAAAATAAAACTAATAT
Found at i:41244 original size:2 final size:2
Alignment explanation
Indices: 41237--41273 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
41227 CATTTCATTC
* *
41237 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41274 CACACAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:43634 original size:49 final size:49
Alignment explanation
Indices: 43545--43639 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
43535 ATATATGATA
* * * *
43545 ATATTTACAATATAATAAAAGCATACTTGAAACATAACTTAGACTTCTG
1 ATATTTACAACAAAATAAAAGCATACTTCAAACATAACTTACACTTCTG
* * * *
43594 ATATTTACAACAAAATGAAAGCATAGTTCAGACATGACTTACACTT
1 ATATTTACAACAAAATAAAAGCATACTTCAAACATAACTTACACTT
43640 AGTTTAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (49 bp):
ATATTTACAACAAAATAAAAGCATACTTCAAACATAACTTACACTTCTG
Found at i:59762 original size:113 final size:108
Alignment explanation
Indices: 59561--59763 Score: 262
Period size: 113 Copynumber: 1.8 Consensus size: 108
59551 AATCAATGTT
* * * * *
59561 AAATTTGAGATTTATCCTTTAAAAATAAAACATTTTTATAATTGTGGTTAAACCTTATCAATAGG
1 AAATTTGAGATTTACCCTTTAAAAATAAAACATTTTTATAATTGTGGCTAAAACTTATCAACAAG
59626 TATTTAAACTTATTTTTCCAAAACCCTATGATAATAGGTTTCA
66 TATTTAAACTTATTTTTCCAAAACCCTATGATAATAGGTTTCA
* * **
59669 AAATTTGAGATTTACCCTTTAAAAAATAAAATATATATTTATAATTATTGGACTAAAACTTATTG
1 AAATTTGAGATTTACCCTTT-AAAAATAAAACAT-T-TTTATAATT-GTGG-CTAAAACTTATCA
* *
59734 ACAAGTATTTAAATTTATTTTTCTAAAACC
61 ACAAGTATTTAAACTTATTTTTCCAAAACC
59764 TTTTTTATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
108 19 0.24
109 12 0.15
110 1 0.01
111 9 0.11
112 3 0.04
113 35 0.44
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (108 bp):
AAATTTGAGATTTACCCTTTAAAAATAAAACATTTTTATAATTGTGGCTAAAACTTATCAACAAG
TATTTAAACTTATTTTTCCAAAACCCTATGATAATAGGTTTCA
Found at i:60676 original size:54 final size:54
Alignment explanation
Indices: 60594--60702 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
60584 ATTGCTTCCG
60594 TTAGCCAAATCCATAAAAATAATCACTTCTACCAAAAGTGGTCACATGTTTGTA
1 TTAGCCAAATCCATAAAAATAATCACTTCTACCAAAAGTGGTCACATGTTTGTA
*
60648 TTAGCCAAATCCATAAAAATAATCACTTCTACCAAGAGTGGTCACATGTTTGTA
1 TTAGCCAAATCCATAAAAATAATCACTTCTACCAAAAGTGGTCACATGTTTGTA
60702 T
1 T
60703 AGTTGACTTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (54 bp):
TTAGCCAAATCCATAAAAATAATCACTTCTACCAAAAGTGGTCACATGTTTGTA
Found at i:60914 original size:19 final size:19
Alignment explanation
Indices: 60878--60916 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
60868 TTACATTCCG
* **
60878 TGAGAGTAGAACTTAAGAC
1 TGAGAATAGAACCCAAGAC
60897 TGAGAATAGAACCCAAGAC
1 TGAGAATAGAACCCAAGAC
60916 T
1 T
60917 TTATGGTCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (19 bp):
TGAGAATAGAACCCAAGAC
Done.