Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019762.1 Corchorus olitorius cultivar O-4 contig19795, 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: 25616
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2791 original size:29 final size:29
Alignment explanation
Indices: 2735--3020 Score: 329
Period size: 29 Copynumber: 9.0 Consensus size: 29
2725 CATTTTTTCC
2735 TTTAATTATATTTAATTATATGTCATTTTGA
1 TTTAATTATATTT--TTATATGTCATTTTGA
2766 TTTAATTATATTTTTATATGTCATTTTGA
1 TTTAATTATATTTTTATATGTCATTTTGA
*
2795 TTTACTTATATTTTTATATGTCATTTTGA
1 TTTAATTATATTTTTATATGTCATTTTGA
2824 TTTAATTATATTTTTATATGTCATTTTGA
1 TTTAATTATATTTTTATATGTCATTTTGA
2853 TTTAATTATATTTAATTATATGTCATTTTTATATGTCA
1 TTTAATTATATTT--TTATATGTCA---TT-T-TG--A
*
2891 TTTTGATTTAATTATATTTTTATATGTCATTTTGA
1 -TTT-AATT-A-TAT--TTTTATATGTCATTTTGA
2926 TTTAATTATATTTTTATATTTTTATATGTCATTTTGA
1 --T--TTA-A---TTATATTTTTATATGTCATTTTGA
2963 TTTAATTATATTTTTATATGTCATTTTGA
1 TTTAATTATATTTTTATATGTCATTTTGA
2992 TTTAATTATATTTTTATATGTCATTTTGA
1 TTTAATTATATTTTTATATGTCATTTTGA
3021 ATTGACTCTG
Statistics
Matches: 229, Mismatches: 4, Indels: 46
0.82 0.01 0.16
Matches are distributed among these distances:
29 138 0.60
31 23 0.10
32 1 0.00
33 3 0.01
34 2 0.01
35 3 0.01
36 4 0.02
37 21 0.09
38 4 0.02
39 8 0.03
40 4 0.02
41 3 0.01
42 13 0.06
44 2 0.01
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.62
Consensus pattern (29 bp):
TTTAATTATATTTTTATATGTCATTTTGA
Found at i:2886 original size:13 final size:13
Alignment explanation
Indices: 2868--2894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2858 TTATATTTAA
2868 TTATATGTCATTT
1 TTATATGTCATTT
2881 TTATATGTCATTT
1 TTATATGTCATTT
2894 T
1 T
2895 GATTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATATGTCATTT
Found at i:2934 original size:21 final size:21
Alignment explanation
Indices: 2910--2973 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2900 AATTATATTT
2910 TTATATGTCATTTTGATTTAA
1 TTATATGTCATTTTGATTTAA
2931 TTATAT-T--TTTAT-ATTT--
1 TTATATGTCATTT-TGATTTAA
2947 TTATATGTCATTTTGATTTAA
1 TTATATGTCATTTTGATTTAA
2968 TTATAT
1 TTATAT
2974 TTTTATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 8 0.22
19 8 0.22
20 1 0.03
21 12 0.33
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (21 bp):
TTATATGTCATTTTGATTTAA
Found at i:3084 original size:139 final size:138
Alignment explanation
Indices: 2800--3066 Score: 310
Period size: 139 Copynumber: 1.9 Consensus size: 138
2790 TTTGATTTAC
2800 TTATATTTTTATATGTCATTTTGATTTAATTATATTTTTATATGTCATTTTGATTTAATTATATT
1 TTATATTTTTATATGTCATTTTGATTTAATTATATTTTTATATGTCATTTTGATTTAATTATATT
* * * * * * * * *** *
2865 TAATTATATGTCATTTTTATATGTCATTTTGATTTAATTATATTTTTATATGTCATTTTGATTTA
66 T-ATTATATGTCATTTTGATATGTCACTCTGATTCAATGATATTATCATATATCATAACGAATTA
*
2930 ATTATATTT
130 ATTATATTA
2939 TTATATTTTTATATGTCATTTTGATTTAATTATATTTTTATATGTCATTTTGATTTAATTATATT
1 TTATATTTTTATATGTCATTTTGATTTAATTATATTTTTATATGTCATTTTGATTTAATTATATT
* *
3004 T-TTATATGTCATTTTGA-AT-TGACTCTG-TATCAATGGA-ATCTCATCATCTATACATAACGA
66 TATTATATGTCATTTTGATATGTCACTCTGAT-TCAAT-GATAT-T-ATCATATAT-CATAACGA
3064 ATT
126 ATT
3067 GGTGTGGTAT
Statistics
Matches: 109, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
134 1 0.01
135 11 0.10
136 4 0.04
137 20 0.18
138 7 0.06
139 66 0.61
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.57
Consensus pattern (138 bp):
TTATATTTTTATATGTCATTTTGATTTAATTATATTTTTATATGTCATTTTGATTTAATTATATT
TATTATATGTCATTTTGATATGTCACTCTGATTCAATGATATTATCATATATCATAACGAATTAA
TTATATTA
Found at i:8650 original size:22 final size:22
Alignment explanation
Indices: 8625--8930 Score: 141
Period size: 22 Copynumber: 14.1 Consensus size: 22
8615 GAATTGTTAG
*
8625 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
8647 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
8669 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
8691 TAAAC-CTTCCTATAAAATTTTGA
1 TAATCAC--ACTATGAAATTTTGA
* * * *
8714 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
* * *
8737 TAATCTC-CTTGTGAAATCTTG-
1 TAATCACAC-TATGAAATTTTGA
*
8758 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
8775 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
8797 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
8819 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
8841 T-GTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* *
8863 TAA-CCCTCCTATGAAATTTTGA
1 TAATCAC-ACTATGAAATTTTGA
* *
8885 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
8907 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
8929 TA
1 TA
8931 TCCTGCCTGA
Statistics
Matches: 219, Mismatches: 47, Indels: 36
0.73 0.16 0.12
Matches are distributed among these distances:
16 7 0.03
17 1 0.00
18 1 0.00
19 3 0.01
21 9 0.04
22 159 0.73
23 35 0.16
24 3 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:8854 original size:44 final size:43
Alignment explanation
Indices: 8454--8930 Score: 272
Period size: 44 Copynumber: 10.9 Consensus size: 43
8444 TTAACCTTCT
* * * * * *
8454 TATGAAATTCTGTTAACCTCCCTAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA-ACAT-AC
* * * * *
8498 TATCAAATTTTGATAACTTCCCAATGAAATTTTGGTAACCAACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-C-ATAC
* * * * *
8543 TATGAGATGTTGATAACCTCCATATGATATTATATTGATAAC-CAC
1 TATGAAATTTTGATAACCTCCCTATGA-A--ATTTTGATAACATAC
* * * * *
8588 GTTATGAAAATTTGAAAACCTTCATATG-AATTGTT-AGTAATCACAC
1 --TATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CATAC
* * * * * * *
8634 TCTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACAT-AC
* * * *
8678 TATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACAT-AC
* * * * *
8724 TATAAAATTTTGATAATCTCCTTGTGAAATCTTGATAAC-TAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAC
** * *
8766 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACAT-AC
* * *
8806 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATGTACATAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATAC
* *
8850 TATGAAATTTTGATAACC-CTCCTATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAAC-ATAC
* *
8894 TATGAAATTTTGATAACCTTCATATGAAATTTTGATA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA
8931 TCCTGCCTGA
Statistics
Matches: 331, Mismatches: 75, Indels: 54
0.72 0.16 0.12
Matches are distributed among these distances:
38 29 0.09
39 1 0.00
40 1 0.00
42 1 0.00
43 8 0.02
44 168 0.51
45 69 0.21
46 24 0.07
47 22 0.07
48 8 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAC
Found at i:9144 original size:22 final size:22
Alignment explanation
Indices: 9119--9222 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 22
9109 TTGGCCCCTC
*
9119 TATGAAATTTTTATAATCACAT
1 TATGAAATTTTGATAATCACAT
* *
9141 TATGTAATTTTGATAAGCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
* *
9164 T-TGAAATTTTGATAATAACAC
1 TATGAAATTTTGATAATCACAT
*
9185 TAT-AAATTTTGATAATCTTC-T
1 TATGAAATTTTGATAATC-ACAT
*
9206 TAT-AAGTTTTGATAATC
1 TATGAAATTTTGATAATC
9223 TGATCTCTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.03
21 30 0.45
22 29 0.44
23 2 0.03
24 3 0.05
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:9244 original size:25 final size:22
Alignment explanation
Indices: 9167--9245 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 22
9157 GCTCGCTTTG
** *
9167 AAATTTTGATAAT-AACACTAT
1 AAATTTTGATAATCTTCTCTAT
9188 AAATTTTGATAATCTTCT-TAT
1 AAATTTTGATAATCTTCTCTAT
*
9209 AAGTTTTGATAATCTGATCTCTAT
1 AAATTTTGATAATCT--TCTCTAT
*
9233 GAAATTTCGATAA
1 -AAATTTTGATAA
9246 CCACTCTCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 30 0.64
22 1 0.02
23 3 0.06
24 3 0.06
25 10 0.21
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCTTCTCTAT
Found at i:9267 original size:21 final size:22
Alignment explanation
Indices: 9227--9268 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9217 ATAATCTGAT
9227 CTCTATGAAATTTCGATAACCA
1 CTCTATGAAATTTCGATAACCA
* *
9249 CTCTCTGAGATTT-GATAACC
1 CTCTATGAAATTTCGATAACC
9269 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (22 bp):
CTCTATGAAATTTCGATAACCA
Found at i:10635 original size:539 final size:526
Alignment explanation
Indices: 9630--10694 Score: 1578
Period size: 539 Copynumber: 2.0 Consensus size: 526
9620 TAGACTCGTT
* *
9630 TGAGTCCATGAAGTCCAAATAGTCAAGTCAGATGTTTTGAAGTCTAAATCTGATATTCTTAGACC
1 TGAGTCCATGAAGTCCAAATAGTCAAGCCAGATGTTTTGAAATCTAAATCTGATATTCTTAGACC
* *
9695 CAATTCGTTAATATGGAAGCCCAAAGAATGAATCCAAGTCCAATCAGTAATTATGATTCAGCCCT
66 CAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATGATTCAGCCCT
* * * *
9760 GATGCAGCATTGTTAAATCTTATTTAAAGGAGGACTTCACAAGAGAAGTTTGGAAGAAATTTCAT
131 AATGCAGCATTGTTAAATCCTATTTAAAGGAGGACTTCACAAAAGAAGTTTGGAAGAAAATTCAT
* * *
9825 AACTTTTGATTCAGAGCTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCT
196 AACTTTTGATCCAGAACTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGACGATTCCAAGATCT
* * * * * * * *
9890 ACAGCTTTTATGCTTATCTTGAGACCTAATTCTGTCGTTTTGGTGGACTATTTTACCTTTGAAAT
261 ACAACTTTTATGCTTATCTCGAGACCTAATTCTGCCGTATCGATGGACGATTTTACCCTTGAAAT
* * * *
9955 TTCTGGACATAATTGATCTTCTCCTAAACGGACTTTGAGAATGTTTTAGACGAAAATTCAGATGC
326 TTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATCTTTTAGACGAAAATTCAGATGC
10020 TAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGGATAATCTAAATT
391 TAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGGATAATCTAAATT
*
10085 GTCATTATTTTAATAGTGGAATAATTAAAATATTATGTAATAATGGCAATTTAGAAATATATTTG
456 GTCATTATTTTAATAGTGGAATAATTAAAATATTATGTAATAATGGCAATTTAGAAATATA-TTA
10150 AAAAAAA
520 AAAAAAA
*
10157 TGAGTCCATGAAGTCCAAATTGTCAAGCCAGAT-TTATTGAAATCTAAATCTGATATTCTTAGAC
1 TGAGTCCATGAAGTCCAAATAGTCAAGCCAGATGTT-TTGAAATCTAAATCTGATATTCTTAGAC
* * *
10221 CCAATTCGTTAATATGGAAGCCCAAAGTAGGAGTGCAAATCCAATCAGTAATTATGATGCAGTAA
65 CCAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAG----TA--AT----T-A
* *
10286 TGATTCAGCCCTAATGCAGCATTGTTAAATCCTATTTAAAGGAGGGCTTCACAAAAGCAGTTTTG
119 TGATTCAGCCCTAATGCAGCATTGTTAAATCCTATTTAAAGGAGGACTTCACAAAAGAAG-TTTG
* *
10351 GAAGAAAATTCATAACTTTTGATCCAGAACTCAGAAAAAT-CAAAATGAGGTACCGTTTGAAGGA
183 GAAGAAAATTCATAACTTTTGATCCAGAACTCAGAAAAATGC-AAATGAGGTACCGTTGGAAAGA
* *
10415 CGATTCCAAGATCTACAACTTTTATGTTTATCTCGAGACTTAATTCTGCCGTATCGATGGACGAT
247 CGATTCCAAGATCTACAACTTTTATGCTTATCTCGAGACCTAATTCTGCCGTATCGATGGACGAT
* *
10480 TTTGCCCTT-AAATTTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATCTTTTGGA
312 TTTACCCTTGAAA-TTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATCTTTTAGA
* * *
10544 CGAAAATTCAGATGTTAAAGATGATGTGGGGCATCCCTATTGGCCATGTTGGATTCTAATTAATG
376 CGAAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATG
* * * *
10609 AGGATAATCTAAATTTTCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGGGAAT
441 AGGATAATCTAAATTGTCATTATTTTAATAGTGGAATAATTAAAATATTATGTAATAATGGCAAT
10674 TTAGAAATATATTAAAAAAAA
506 TTAGAAATATATTAAAAAAAA
10695 GGTATAATCG
Statistics
Matches: 480, Mismatches: 43, Indels: 19
0.89 0.08 0.04
Matches are distributed among these distances:
526 2 0.00
527 101 0.21
531 2 0.00
533 2 0.00
537 1 0.00
538 69 0.14
539 303 0.63
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (526 bp):
TGAGTCCATGAAGTCCAAATAGTCAAGCCAGATGTTTTGAAATCTAAATCTGATATTCTTAGACC
CAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATGATTCAGCCCT
AATGCAGCATTGTTAAATCCTATTTAAAGGAGGACTTCACAAAAGAAGTTTGGAAGAAAATTCAT
AACTTTTGATCCAGAACTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGACGATTCCAAGATCT
ACAACTTTTATGCTTATCTCGAGACCTAATTCTGCCGTATCGATGGACGATTTTACCCTTGAAAT
TTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATCTTTTAGACGAAAATTCAGATGC
TAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGGATAATCTAAATT
GTCATTATTTTAATAGTGGAATAATTAAAATATTATGTAATAATGGCAATTTAGAAATATATTAA
AAAAAA
Found at i:20316 original size:24 final size:24
Alignment explanation
Indices: 20289--20374 Score: 163
Period size: 24 Copynumber: 3.6 Consensus size: 24
20279 TTTTAACCCC
20289 TTTTATGTTGATTGTTTGTGGATT
1 TTTTATGTTGATTGTTTGTGGATT
*
20313 TTTTATGTTGATTGTTTGTGGATC
1 TTTTATGTTGATTGTTTGTGGATT
20337 TTTTATGTTGATTGTTTGTGGATT
1 TTTTATGTTGATTGTTTGTGGATT
20361 TTTTATGTTGATTG
1 TTTTATGTTGATTG
20375 CTTGGGTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.13, C:0.01, G:0.24, T:0.62
Consensus pattern (24 bp):
TTTTATGTTGATTGTTTGTGGATT
Found at i:20491 original size:13 final size:13
Alignment explanation
Indices: 20473--20512 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
20463 CATTGTGTAG
20473 ATTTGTGTGGGTA
1 ATTTGTGTGGGTA
20486 ATTTGTGT-GG--
1 ATTTGTGTGGGTA
20496 ATTTGTGTGGGTA
1 ATTTGTGTGGGTA
20509 ATTT
1 ATTT
20513 CAGCTATGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (13 bp):
ATTTGTGTGGGTA
Found at i:20498 original size:23 final size:23
Alignment explanation
Indices: 20465--20512 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
20455 TTATTGTGCA
20465 TTGTGTAGATTTGTGTGGGTAAT
1 TTGTGTAGATTTGTGTGGGTAAT
*
20488 TTGTGTGGATTTGTGTGGGTAAT
1 TTGTGTAGATTTGTGTGGGTAAT
20511 TT
1 TT
20513 CAGCTATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (23 bp):
TTGTGTAGATTTGTGTGGGTAAT
Done.