Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002080.1 Corchorus olitorius cultivar O-4 contig02080, 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, 750
Length: 1251
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Found at i:89 original size:2 final size:2
Alignment explanation
Indices: 82--144 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
72 CTTATTATCC
* * * *
82 AT AT AT AT AT AT AT AT AT AT AT AC AT AC AC AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
145 CTAGTTTTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:351 original size:21 final size:22
Alignment explanation
Indices: 327--379 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
317 GAATTTCGAG
* *
327 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATAAAATTTTGTT
348 AACCTTCTTATAAAATTTTGTT
1 AACCTTCTTATAAAATTTTGTT
*
370 AACCTCCTTA
1 AACCTTCTTA
380 AGGAATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.51
Consensus pattern (22 bp):
AACCTTCTTATAAAATTTTGTT
Found at i:458 original size:45 final size:44
Alignment explanation
Indices: 400--495 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 44
390 AAGACCTCAC
* * *
400 TATGAAATTTTGATAACTTCCGA-ATGAAATTTTGATAACCAACAT
1 TATGAAATGTTGATAACCTCC-ATATGAAATATTGATAACC-ACAT
* * *
445 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGT
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCACAT
489 TATGAAA
1 TATGAAA
496 ATTTAAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 10 0.23
45 33 0.77
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (44 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCACAT
Found at i:479 original size:22 final size:22
Alignment explanation
Indices: 360--803 Score: 210
Period size: 22 Copynumber: 20.4 Consensus size: 22
350 CCTTCTTATA
* * *
360 AAATTTTGTTAACCTCCTTAAG
1 AAATTTTGATAACCTCCATATG
*
382 GAATTTTGA-AGACCT-CACTATG
1 AAATTTTGATA-ACCTCCA-TATG
*
404 AAATTTTGATAACTTCCGA-ATG
1 AAATTTTGATAACCTCC-ATATG
**
426 AAATTTTGATAACCAACATTATG
1 AAATTTTGATAACCTCCA-TATG
* *
449 AGATGTTGATAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
* * * **
471 ATATATTGATAACCACGTTATG
1 AAATTTTGATAACCTCCATATG
* * * *
493 AAAATTTAAAAACCTACATATG
1 AAATTTTGATAACCTCCATATG
*
515 -AATTGTT-AGTAA--TCACACTCTG
1 AAATT-TTGA-TAACCTC-CA-TATG
537 AAATTTTGATAA--TCACACTATG
1 AAATTTTGATAACCTC-CA-TATG
* *
559 AAATTGTGATAACCTCGC-TATA
1 AAATTTTGATAACCTC-CATATG
* * *
581 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCCATATG
* *
604 AAATTTTAATAACCTCCTTATG
1 AAATTTTGATAACCTCCATATG
* * *
626 AAATCTTAATAA----C-TA-C
1 AAATTTTGATAACCTCCATATG
*
642 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCATATG
** *
664 ATTTTTTGATAACCT-TATTATG
1 AAATTTTGATAACCTCCA-TATG
* * *
686 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCATATG
*
708 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CATATG
* **
730 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCTCCA-TATG
*
752 AAAATTTTGATAACCTTCATATG
1 -AAATTTTGATAACCTCCATATG
* *
775 AAATTTTGATATCCTCC--CTG
1 AAATTTTGATAACCTCCATATG
795 AAATTTTGA
1 AAATTTTGA
804 CTACTCCATA
Statistics
Matches: 325, Mismatches: 67, Indels: 62
0.72 0.15 0.14
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 13 0.04
21 15 0.05
22 218 0.67
23 57 0.18
24 9 0.03
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCCATATG
Found at i:602 original size:23 final size:23
Alignment explanation
Indices: 569--637 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
559 AAATTGTGAT
*
569 AACCTCGCTATAAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
592 AACCTCCCTATAAAATTTTAAT-
1 AACCTCCCTATAAAATTTTAATA
* * *
614 AACCTCCTTATGAAATCTTAATA
1 AACCTCCCTATAAAATTTTAATA
637 A
1 A
638 CTACAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTAATA
Found at i:674 original size:105 final size:104
Alignment explanation
Indices: 537--733 Score: 234
Period size: 105 Copynumber: 1.9 Consensus size: 104
527 TCACACTCTG
* *
537 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATAAAATTTTAATAAACCTCCCTA
1 AAATTTTGATAACCACACTATGAAATTGTGATAACCTCACTATAAAATTTT-ATAAACCTCCCTA
602 TAAAATTTTAATAA-CCTCCTTATGAAATCTTAATAACTAC
65 TAAAATTTTAATAACCCT-CTTATGAAATCTTAATAACTAC
* * ** * * * * * * *
642 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTTATTATGAAATTTTGTTAATCTCCCTAT
1 AAATTTTGATAACCACACTATGAAATTGTGATAACCTCACTATAAAATTTTATAAACCTCCCTAT
* *
707 GAAATTTTGATAACCCTCTTATGAAAT
66 AAAATTTTAATAACCCTCTTATGAAAT
734 TTTGAAAACT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
104 32 0.42
105 44 0.58
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (104 bp):
AAATTTTGATAACCACACTATGAAATTGTGATAACCTCACTATAAAATTTTATAAACCTCCCTAT
AAAATTTTAATAACCCTCTTATGAAATCTTAATAACTAC
Found at i:935 original size:22 final size:22
Alignment explanation
Indices: 886--1156 Score: 146
Period size: 22 Copynumber: 12.4 Consensus size: 22
876 GAAATACCAC
* * *
886 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
909 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
* *
930 TATGAAATTTTGATAACTTCTC
1 TATGAAATTTTGATAACCTCTT
* * * * *
952 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
*** *
974 TATGAAATTTTGATATTTTCAT
1 TATGAAATTTTGATAACCTCTT
* *
996 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-TT
** **
1019 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCTT
1040 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCTCTT
1060 CCTAT-AAATTTTGATAACCTGATCTT
1 --TATGAAATTTTGATAACC---TCTT
* * * *
1086 TATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAACCTCTT
* *
1108 TATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCTT
* * *
1128 TATCAAATTTTGGT-A-CTCCT
1 TATGAAATTTTGATAACCTCTT
1148 TATGAAATT
1 TATGAAATT
1157 AAGACTTTTA
Statistics
Matches: 187, Mismatches: 48, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.01
20 17 0.09
21 29 0.16
22 117 0.63
23 3 0.02
24 3 0.02
25 12 0.06
26 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:999 original size:66 final size:66
Alignment explanation
Indices: 910--1079 Score: 175
Period size: 66 Copynumber: 2.6 Consensus size: 66
900 AATCACATTT
* * * * * * ** *
910 TGAAAATTTGATAA-CCTCTTTATGAAATTTTGATAACTTCTCTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCTTC-TTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACAACAC
974 TA
65 TA
* * * *
976 TGAAATTTTGAT-ATTTTCATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACAC
1 TGAAATTTTGATAATCTTC-TTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACAACAC
1040 TA
65 TA
*
1042 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAACCT
1 TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCT
1080 GATCTTTATG
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
65 15 0.18
66 65 0.76
67 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (66 bp):
TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACAACACT
A
Found at i:1235 original size:22 final size:22
Alignment explanation
Indices: 1175--1249 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
1165 TATTTCTTCA
*
1175 TATGAAATTTTGATAAGCACAC
1 TATGAAATTTTGATAACCACAC
** *
1197 TAAAAAACTTTTAATAACCACAC
1 TATGAAA-TTTTGATAACCACAC
* *
1220 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
1242 TATGAAAT
1 TATGAAAT
1250 AT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 25 0.58
23 18 0.42
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Done.