Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016328.1 Corchorus olitorius cultivar O-4 contig16361, 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: 98833
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1897 original size:21 final size:21
Alignment explanation
Indices: 1871--1937 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
1861 TATAACATGT
*
1871 TTATGGGCTTTGCTTGGCAGG
1 TTATGGGCTTTGCCTGGCAGG
*
1892 TTATGGGCATTGCCTGGCAGG
1 TTATGGGCTTTGCCTGGCAGG
1913 TTATGGGCTTTGCCTGGCAGG
1 TTATGGGCTTTGCCTGGCAGG
1934 TTAT
1 TTAT
1938 AACATGTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.12, C:0.16, G:0.36, T:0.36
Consensus pattern (21 bp):
TTATGGGCTTTGCCTGGCAGG
Found at i:3581 original size:19 final size:19
Alignment explanation
Indices: 3531--3571 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3521 ATAGGAAAAT
* * *
3531 ATGATCAATGTTTGGTGTA
1 ATGATCATTATTTGATGTA
3550 ATGATCATTATTTGATGTA
1 ATGATCATTATTTGATGTA
3569 ATG
1 ATG
3572 GTATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (19 bp):
ATGATCATTATTTGATGTA
Found at i:15630 original size:13 final size:13
Alignment explanation
Indices: 15612--15639 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15602 TTTTATTTTG
15612 TTTTTATTAGTAA
1 TTTTTATTAGTAA
15625 TTTTTATTAGTAA
1 TTTTTATTAGTAA
15638 TT
1 TT
15640 AATTAGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTTATTAGTAA
Found at i:16288 original size:4 final size:4
Alignment explanation
Indices: 16279--16305 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16269 TGGAAATAGT
16279 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
16306 TACCATGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:21508 original size:20 final size:22
Alignment explanation
Indices: 21469--21512 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
21459 TTGGGTTTTC
*
21469 AGGGCAAAGATGATGAAAGAAA
1 AGGGCAAAGAGGATGAAAGAAA
21491 AGGGCAAA-AGGA-GAAAGAAA
1 AGGGCAAAGAGGATGAAAGAAA
21511 AG
1 AG
21513 AGAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.57, C:0.05, G:0.34, T:0.05
Consensus pattern (22 bp):
AGGGCAAAGAGGATGAAAGAAA
Found at i:31915 original size:2 final size:2
Alignment explanation
Indices: 31908--31941 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31898 CCCAAAGTGT
31908 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31942 AGTGATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32140 original size:110 final size:109
Alignment explanation
Indices: 32026--32240 Score: 358
Period size: 110 Copynumber: 2.0 Consensus size: 109
32016 GCATTTGATC
* * *
32026 ACTTAAATCATTCATTAAGAGAGATCTAATGCTTTTGCAGCAGTACCTGACTACCTGAACATATG
1 ACTTAAATCATTCATCAAGAAAGATCTAATGCTCTTGCAGCAGTACCTGACTACCTGAACATATG
*
32091 AACATTGCCTCAATATCACTATGAAAAAAAAATTATTTGATCAAT
66 AACATTGCCTCAATATCACTATG-AAAAAAAATGATTTGATCAAT
32136 ACTTAAATCATTCATCAAGAAAGATCTAATGCTCTTGCAGCAGTACCTGACTACCTGAACATATG
1 ACTTAAATCATTCATCAAGAAAGATCTAATGCTCTTGCAGCAGTACCTGACTACCTGAACATATG
* * *
32201 AACATTGCCTCGATATCGCTATGGAAAAAAATGATTTGAT
66 AACATTGCCTCAATATCACTATGAAAAAAAATGATTTGAT
32241 AAATTTCGGA
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
109 15 0.15
110 83 0.85
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (109 bp):
ACTTAAATCATTCATCAAGAAAGATCTAATGCTCTTGCAGCAGTACCTGACTACCTGAACATATG
AACATTGCCTCAATATCACTATGAAAAAAAATGATTTGATCAAT
Found at i:32596 original size:110 final size:110
Alignment explanation
Indices: 32403--32624 Score: 444
Period size: 110 Copynumber: 2.0 Consensus size: 110
32393 ACGGTAAACA
32403 ATTCCATTTTCCATTAATTTATAATCCTACTAAATACATGTCTACCAAAGGGCACATATGGTATA
1 ATTCCATTTTCCATTAATTTATAATCCTACTAAATACATGTCTACCAAAGGGCACATATGGTATA
32468 TACTTTCAGTTGGTAAAAATACTTCATCACACAGAAATGTCAATG
66 TACTTTCAGTTGGTAAAAATACTTCATCACACAGAAATGTCAATG
32513 ATTCCATTTTCCATTAATTTATAATCCTACTAAATACATGTCTACCAAAGGGCACATATGGTATA
1 ATTCCATTTTCCATTAATTTATAATCCTACTAAATACATGTCTACCAAAGGGCACATATGGTATA
32578 TACTTTCAGTTGGTAAAAATACTTCATCACACAGAAATGTCAATG
66 TACTTTCAGTTGGTAAAAATACTTCATCACACAGAAATGTCAATG
32623 AT
1 AT
32625 CAAAGATCTA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (110 bp):
ATTCCATTTTCCATTAATTTATAATCCTACTAAATACATGTCTACCAAAGGGCACATATGGTATA
TACTTTCAGTTGGTAAAAATACTTCATCACACAGAAATGTCAATG
Found at i:36328 original size:29 final size:29
Alignment explanation
Indices: 36296--36371 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
36286 CCATCACATT
36296 GAAAAGTATTGCATATTCAAAACCAAAAA
1 GAAAAGTATTGCATATTCAAAACCAAAAA
36325 GAAAAGTATTGCATATTCAAAACCAAAAA
1 GAAAAGTATTGCATATTCAAAACCAAAAA
36354 GAAAAGTATTGCATATTC
1 GAAAAGTATTGCATATTC
36372 GTTTTTGAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (29 bp):
GAAAAGTATTGCATATTCAAAACCAAAAA
Found at i:44329 original size:24 final size:24
Alignment explanation
Indices: 44299--44353 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
44289 CTGTGGAGAT
* *
44299 TGATGATGCTT-TGGTGATTGAAGA
1 TGATGATACTTCTGATGA-TGAAGA
*
44323 TGATGATATTTCTGATGATGAAGA
1 TGATGATACTTCTGATGATGAAGA
44347 TGATGAT
1 TGATGAT
44354 CATGAAGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (24 bp):
TGATGATACTTCTGATGATGAAGA
Found at i:52598 original size:1 final size:1
Alignment explanation
Indices: 52592--52619 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
52582 AGCAAAAGTT
52592 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
52620 GAAAGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:79638 original size:15 final size:16
Alignment explanation
Indices: 79612--79649 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
79602 TGCTCCCTTG
79612 CTTCCTTCTTCTCTTT
1 CTTCCTTCTTCTCTTT
*
79628 CTTCC-TCTTCTTTTT
1 CTTCCTTCTTCTCTTT
79643 C-TCCTTC
1 CTTCCTTC
79650 CTTTCCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 12 0.60
16 5 0.25
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTTCCTTCTTCTCTTT
Found at i:85483 original size:46 final size:46
Alignment explanation
Indices: 85416--85508 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
85406 ATACAAGTGG
*
85416 TTCGGCTCGTGCTGGCGCGTCGAGTGTTAAAATTTTTTTTAAGAAT
1 TTCGGCTCGCGCTGGCGCGTCGAGTGTTAAAATTTTTTTTAAGAAT
*
85462 TTCGGCTCGCGTTGGCGCGTCGAGTGTTAAAATTTTTTTTAAGAAT
1 TTCGGCTCGCGCTGGCGCGTCGAGTGTTAAAATTTTTTTTAAGAAT
85508 T
1 T
85509 ACTTCTATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (46 bp):
TTCGGCTCGCGCTGGCGCGTCGAGTGTTAAAATTTTTTTTAAGAAT
Found at i:98127 original size:614 final size:612
Alignment explanation
Indices: 97374--98826 Score: 1773
Period size: 616 Copynumber: 2.4 Consensus size: 612
97364 GTATTGTTGC
* * *
97374 AAAAAATTGAGAAAAAAATTTTCGGTTCAGTTTTTAACCGAAATCGTGTACGTTACATCATA-GT
1 AAAAAATTGAGTAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACG-TACATCA-AGGT
*
97438 TTTTGGCTAACAACGCGTTCCGAAGCCCGACTCAATTTTACATGATTTTGGGTGCAAAGACTCCT
64 TTTTGGCTAAAAACGCGTTCCG-AGCCCGACTCAATTTTACATGATTTTGGGTGCAAAGACTCCT
* * *
97503 TGATATATCTATATTCATCTAACGAAATCTCAGCCAAATTGGATTTAAGGATTGTTTTTACGTGT
128 TGAAATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTGTTTTTACGTGA
* *
97568 ATGTGAATCTTGTTTCGATTTAATTAGAAAATAATTCCGAAAAAAGTTGGAAAAATAATATTAGA
193 ATCTGAATCTTGTTTCGATTTAATTAGAAAATAATTACGAAAAAAGTTGGAAAAATAATATTAGA
* * * * * **
97633 AGCGTGAAAAAACCTTTAATCTTTTTGGCGTTGAATTATTTTTTTTTTTGAGTAGTGT-G-GGAA
258 AGCGTGAAAAAACCTCTAATCTTTTTGGCATTGAATTATATATTTTTCTGAGTAGTGTAGAAAAA
* *
97696 AAAA-TTGAGGAAAATTTTTCGAGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCA
323 AAAAGTTGAGGAAAATTTTTCGAGTCAATTTTAGAAAAATTTTAGCCGAAATCGTGT-CTAACCA
* * ** *
97760 TAACGTTTTTTTTTGCTGAAAACGCGTGATGCGGATGAGG-TAAATATATCATATATGGATCGTA
387 TAACG--TTTTTTGGCTAAAAACGCGACATGCGGAT-AGGATAAATATATCATAAATGGATCGTA
* * *
97824 TGGACCATCAGAAGTCCATTCGAAAAGGCGTGTAA-AGTTTTGGATTTTGGGCTTGAAATTCTTG
449 TGGACCATCAGAAGTCCATTCGAAAAGGCGTGTAACA-TTTTGGATTTTGGGCCTGAAATTCCTA
** * * * **
97888 GGGGTGGGTCAACTTAAAGAGGCCATAACTTTCAAACCGTAAATCGGTTTAACTGTTATAATACC
513 CAGGTGGGTCAACTAAAAAAGGCCATAACTTTCAAACCATAAATCGGTTTAACAATTATAATACC
* * * *
97953 TTTCCGTAGACTTATTTGAACCGAATATGCTATGG
578 TTTCCGGAGACTGATTTGAACCGAACACGCTATGG
* * * *
97988 AAAAATTTGAGTCAAAATTTTTCGGGGCAGTTTTTAGCCGAAATCGTGTAC-TAACCATCAAGGT
1 AAAAAATTGAGTAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACGT-A-CATCAAGGT
* ** * * ** *
98052 TTTTGAG-TAATAACATGTTCCAGAGCCC-AGCTCCATTTTGCATGAATTTT-GGCACAAAGATT
64 TTTTG-GCTAAAAACGCGTTCC-GAGCCCGA-CTCAATTTTACATG-ATTTTGGGTGCAAAGACT
* * * * * *
98114 CCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGACTTAAGAATTCATTTTTAC
125 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATT-GTTTTTAC
* * ** * * *
98179 GAGCATCTGTTTCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAAGTTGGAAAAATGATAT
189 GTGAATCTGAATCTTGTTTCGATTTAATTAGAAAATAATTACGAAAAAAGTTGGAAAAATAATAT
98244 TAGAAGCGTGAAAAAACCTCTAATCTTTTTGGCATTGAATTATATATTTTTCTGAGTAGTGTAGC
254 TAGAAGCGTGAAAAAACCTCTAATCTTTTTGGCATTGAATTATATATTTTTCTGAGTAGTGTAG-
* *
98309 AAAAAAAAAGTTGAGGAAATTTTTTCGGGTCAATTTTAGAAAAATTTTAGCCGAAATCGTGTCTA
318 AAAAAAAAAGTTGAGGAAAATTTTTCGAGTCAATTTTAGAAAAATTTTAGCCGAAATCGTGTCTA
* * ** *
98374 ACCTTCACGTTTTTTGGCTAAAAATTCGACATGCGGATAGGATAGATATATCATAAATGGATCGT
383 ACCATAACGTTTTTTGGCTAAAAACGCGACATGCGGATAGGATAAATATATCATAAATGGATCGT
** * * *
98439 ATGGACTGTCAGAAGTCCGTTCGAAATGGTGTGTAACATTTTGGATTTTGGGCCTGAAATTCCTA
448 ATGGACCATCAGAAGTCCATTCGAAAAGGCGTGTAACATTTTGGATTTTGGGCCTGAAATTCCTA
* * * *
98504 CAGGTGGGTGAACTAAAAAATGCCATAGCTTTCAAACCATAAATCGGTTTTACAATTATAATACC
513 CAGGTGGGTCAACTAAAAAAGGCCATAACTTTCAAACCATAAATCGGTTTAACAATTATAATACC
* * *
98569 TTTCCGGAGACTGATTTGAACCTACCACGCTGTGG
578 TTTCCGGAGACTGATTTGAACCGAACACGCTATGG
* * * * *
98604 AAAAAATTGAGTAAAAACTTTTCGGGTTAGTTTTTAGCCAAAATCGTGTACGT--TTCACGGTTT
1 AAAAAATTGAGTAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACGTACATCAAGGTTT
* *
98667 TTGGCTAAAAACGCGTTCCGGAGCCCGACTCAATTTTCCATGATTTTGGGTGCAAAGACACCTTG
66 TTGGCTAAAAACGCGTTCC-GAGCCCGACTCAATTTTACATGATTTTGGGTGCAAAGACTCCTTG
* * * * *
98732 AAAAATCTATATTCATTTTTACCAAATCTCAG-AAACATTGGATTTAAAGATTTGTTTTTAC-TA
130 AAATATCTATATTCA-TCTAACCAAATCTCAGCCAA-ATTGGATTTAAGGA-TTGTTTTTACGT-
*
98795 GAATCTGAATCTTGTTTCAATTTAATTAGAAA
191 GAATCTGAATCTTGTTTCGATTTAATTAGAAA
98827 TTTATTC
Statistics
Matches: 704, Mismatches: 113, Indels: 44
0.82 0.13 0.05
Matches are distributed among these distances:
612 7 0.01
613 70 0.10
614 202 0.29
615 132 0.19
616 227 0.32
617 2 0.00
618 16 0.02
619 48 0.07
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (612 bp):
AAAAAATTGAGTAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACGTACATCAAGGTTT
TTGGCTAAAAACGCGTTCCGAGCCCGACTCAATTTTACATGATTTTGGGTGCAAAGACTCCTTGA
AATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTGTTTTTACGTGAATC
TGAATCTTGTTTCGATTTAATTAGAAAATAATTACGAAAAAAGTTGGAAAAATAATATTAGAAGC
GTGAAAAAACCTCTAATCTTTTTGGCATTGAATTATATATTTTTCTGAGTAGTGTAGAAAAAAAA
AGTTGAGGAAAATTTTTCGAGTCAATTTTAGAAAAATTTTAGCCGAAATCGTGTCTAACCATAAC
GTTTTTTGGCTAAAAACGCGACATGCGGATAGGATAAATATATCATAAATGGATCGTATGGACCA
TCAGAAGTCCATTCGAAAAGGCGTGTAACATTTTGGATTTTGGGCCTGAAATTCCTACAGGTGGG
TCAACTAAAAAAGGCCATAACTTTCAAACCATAAATCGGTTTAACAATTATAATACCTTTCCGGA
GACTGATTTGAACCGAACACGCTATGG
Done.