Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022238.1 Corchorus olitorius cultivar O-4 contig22271, 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: 26394
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:6592 original size:3 final size:3
Alignment explanation
Indices: 6586--6615 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6576 ATTCAATTGT
6586 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6616 TATATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13369 original size:2 final size:2
Alignment explanation
Indices: 13362--13396 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
13352 ATATAAATTC
13362 AT AT AT AT GA- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
13397 ATTAGATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15333 original size:47 final size:47
Alignment explanation
Indices: 15280--15451 Score: 265
Period size: 47 Copynumber: 3.7 Consensus size: 47
15270 AAACACACTG
*
15280 CTAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTATATT
1 CTAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTTTATT
15327 CTAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTTTATT
1 CTAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTTTATT
* * * * * *
15374 TTAGTAAATTTAATTGACACCAGAGGTTGTCAAATCAGAATTTTCTT
1 CTAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTTTATT
*
15421 -TAGTAAATTTAATTGACACCAGAAGTTGTCA
1 CTAGTAAATTTAATTGACACCAAAAGTTGTCA
15452 CACAAGAAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 30 0.26
47 87 0.74
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (47 bp):
CTAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTTTATT
Found at i:15477 original size:93 final size:93
Alignment explanation
Indices: 15281--15495 Score: 260
Period size: 94 Copynumber: 2.3 Consensus size: 93
15271 AACACACTGC
* *
15281 TAGTAAATTTAATTGACACCAAAAGTTGTCAAATTAAAATTATATTCTAGTAAATTTAATTGACA
1 TAGTAAATTTAATTGACACCAGAAGTTGTCAAATCAAAATTATATTCTAGTAAATTTAATTGACA
** *
15346 CCAAAAGTTGTCAAATTAAAATTTTATTT
66 CCAAAAGTTGTCAAAAGAAAATATTA-TT
* * * *
15375 TAGTAAATTTAATTGACACCAGAGGTTGTCAAATCAGAATTTTCTT-TAGTAAATTTAATTGACA
1 TAGTAAATTTAATTGACACCAGAAGTTGTCAAATCAAAATTATATTCTAGTAAATTTAATTGACA
*
15439 CCAGAAGTTGTCACACAAGAAAATATTA-T
66 CCAAAAGTTGTCA-A-AAGAAAATATTATT
* *
15468 TATTCAA-TT--TTGACACCAGAAGTTGTCA
1 TAGTAAATTTAATTGACACCAGAAGTTGTCA
15496 TACTTAAGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
90 18 0.17
92 2 0.02
93 36 0.34
94 41 0.39
95 9 0.08
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (93 bp):
TAGTAAATTTAATTGACACCAGAAGTTGTCAAATCAAAATTATATTCTAGTAAATTTAATTGACA
CCAAAAGTTGTCAAAAGAAAATATTATT
Found at i:18728 original size:25 final size:25
Alignment explanation
Indices: 18700--18761 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
18690 GTAATTTTTG
*
18700 TGGGCTATTATAGAAGCCA-TCATTA
1 TGGGCTATTATAGAAGCCAGT-ATCA
* * *
18725 TGGGCAATTATAGAGGCTAGTATCA
1 TGGGCTATTATAGAAGCCAGTATCA
18750 TGGGCTATTATA
1 TGGGCTATTATA
18762 ATGGCCATGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (25 bp):
TGGGCTATTATAGAAGCCAGTATCA
Found at i:22966 original size:8 final size:8
Alignment explanation
Indices: 22955--22979 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
22945 CATTATTAAA
22955 TAATTATT
1 TAATTATT
22963 TAATTATT
1 TAATTATT
22971 TAATTATT
1 TAATTATT
22979 T
1 T
22980 TAATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTATT
Found at i:24270 original size:22 final size:22
Alignment explanation
Indices: 24130--24318 Score: 148
Period size: 22 Copynumber: 8.5 Consensus size: 22
24120 TAATTTCATG
* **
24130 AGGTTATCAAAATTCCATAGTG
1 AGGTTATCAAAATTTCATAGAA
* * *
24152 TGGTTACCAAAATTTCATATGGA
1 AGGTTATCAAAATTTCATA-GAA
* *
24175 A-GTTATCAAAATTTCATGGGA
1 AGGTTATCAAAATTTCATAGAA
* *
24196 AGGTTACCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGAA
* *
24218 TGGTTACCAAAATTTCATAGAA
1 AGGTTATCAAAATTTCATAGAA
* *
24240 TCAGGTTATTAAAATTTCTTAGAA
1 --AGGTTATCAAAATTTCATAGAA
** *
24264 AGGTTATTGAAATTTCATA-ATG
1 AGGTTATCAAAATTTCATAGA-A
* * *
24286 TGGTTATCACAATTTTATAGAA
1 AGGTTATCAAAATTTCATAGAA
24308 AGGTTATCAAA
1 AGGTTATCAAA
24319 GAGTTTATCA
Statistics
Matches: 133, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
21 5 0.04
22 108 0.81
23 2 0.02
24 18 0.14
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGAA
Found at i:24521 original size:22 final size:22
Alignment explanation
Indices: 24323--24886 Score: 157
Period size: 22 Copynumber: 26.1 Consensus size: 22
24313 ATCAAAGAGT
* *
24323 TTATCAAAATGTCATA-GTAAGG
1 TTATCAAAATTTCATATG-GAGG
*
24345 TTAT-AAGAATTTCATA-GTGTGG
1 TTATCAA-AATTTCATATG-GAGG
* *
24367 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATATGGAGG
* * **
24389 TTA-CTGATATTTCATGGGGAGG
1 TTATC-AAAATTTCATATGGAGG
*
24411 TTATCAAAATTTCATA-GTATGG
1 TTATCAAAATTTCATATGGA-GG
* *
24433 TTA-CTAAA--T--TA-GGAAGC
1 TTATCAAAATTTCATATGG-AGG
* * *
24450 TTATTAAACTTTTACTATGGA-G
1 TTATCAAAATTTCA-TATGGAGG
* *
24472 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATATGGAGG
* *
24492 ATATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATGGAGG
* **
24514 TTATCAAATTTTCATAGTTTA-G
1 TTATCAAAATTTCATA-TGGAGG
* * * *
24536 TTTTCAAATTTTCATA-GTATG
1 TTATCAAAATTTCATATGGAGG
* * *
24557 TAGATCAAAATTGCATAGGGAGG
1 T-TATCAAAATTTCATATGGAGG
*
24580 TTATCAAAA--T--T-TGTA-G
1 TTATCAAAATTTCATATGGAGG
* *
24596 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCATATGGAGG
* *
24618 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATATGGAGG
* **
24640 TTTATCAAAATTTTATAACGAGG
1 -TTATCAAAATTTCATATGGAGG
*
24663 TTATCACAATTTCATAGTGTGA--
1 TTATCAAAATTTCATA-TG-GAGG
* *
24685 TCATCAAAATTTCAGAGTGTGA--
1 TTATCAAAATTTCATA-TG-GAGG
24707 TTA-CTAACAA-TTCATATGGAGG
1 TTATC-AA-AATTTCATATGGAGG
* * * ** * *
24729 TTTTTAAATTTTCATAACGTGA
1 TTATCAAAATTTCATATGGAGG
* * *
24751 TTATCAATATATCATATAGAGG
1 TTATCAAAATTTCATATGGAGG
* * * **
24773 TTATTAATATCTCATAGTGTTGG
1 TTATCAAAATTTCATA-TGGAGG
*
24796 TTATCAAAATTTCAT-TCGGAAG
1 TTATCAAAATTTCATAT-GGAGG
24818 TTATCAAAATTTCATA-GTGAGG
1 TTATCAAAATTTCATATG-GAGG
* * * *
24840 TCT-TCAAAATTCCTTAGGGATG
1 T-TATCAAAATTTCATATGGAGG
* *
24862 TTAAT-AAAATTTCATAAGAAGG
1 TT-ATCAAAATTTCATATGGAGG
24884 TTA
1 TTA
24887 AAAAAAATTT
Statistics
Matches: 400, Mismatches: 98, Indels: 89
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.02
17 9 0.02
18 5 0.01
19 5 0.01
20 18 0.05
21 21 0.05
22 276 0.69
23 53 0.13
24 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGG
Done.