Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023030.1 Corchorus olitorius cultivar O-4 contig23063, 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: 12382
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5238 original size:56 final size:56
Alignment explanation
Indices: 5148--5261 Score: 194
Period size: 56 Copynumber: 2.0 Consensus size: 56
5138 TATCCATTTC
* *
5148 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTTTATTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
5204 CTTTCACACAATAAATGTTATAATAAATTC-TATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAA-TCATATCCCCCTATCTCTACTTAATTATT
5260 CT
1 CT
5262 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 53 0.96
57 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:9581 original size:22 final size:22
Alignment explanation
Indices: 9269--9769 Score: 223
Period size: 22 Copynumber: 23.0 Consensus size: 22
9259 TACAAGAACT
*
9269 TCCCTATGAAATTTTGTTAACC
1 TCCCTATGAAATTTTGATAACC
* **
9291 TCCCTAT-ACAATTTTGAAAATA
1 TCCCTATGA-AATTTTGATAACC
** * *
9313 TTACTAT-AAAATTTGATGACC
1 TCCCTATGAAATTTTGATAACC
*
9334 T-CCTAGTGAAATTTTGATAGCC
1 TCCCTA-TGAAATTTTGATAACC
9356 ATCCACT-T-AAATTTTGATAACC
1 -TCC-CTATGAAATTTTGATAACC
* * * * *
9378 ACACTATAAAATTTTGGTAATC
1 TCCCTATGAAATTTTGATAACC
* * * * *
9400 TCCATGTGAAATGTTGGTAAGC
1 TCCCTATGAAATTTTGATAACC
* * * *
9422 ACACTATGATATTTTTTATAACC
1 TCCCTATGA-AATTTTGATAACC
* *
9445 TCCTTATGAAATCTTAGTGATTA--
1 TCCCTATGAAAT-TT--TGATAACC
* * *
9468 -CACTGTGAAATTTTGATAA-T
1 TCCCTATGAAATTTTGATAACC
* * * *
9488 TACACC-ATGAAATTGTAATGATC
1 T-C-CCTATGAAATTTTGATAACC
** *
9511 TCGGTATGAAATTTTGATAAACA
1 TCCCTATGAAATTTTGAT-AACC
* * *
9534 TTCATATAAAATTTTGATAAACC
1 TCCCTATGAAATTTTGAT-AACC
* *
9557 TCCCTATAAAATTTTAATAACC
1 TCCCTATGAAATTTTGATAACC
*
9579 TCCTTATGAAATTTTGATAA--
1 TCCCTATGAAATTTTGATAACC
*
9599 TCAC-A--AAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
** *
9618 TCCCTATGATTTTTTGATAACT
1 TCCCTATGAAATTTTGATAACC
** *
9640 TCATTATGAAA-TTTGTTAACC
1 TCCCTATGAAATTTTGATAACC
9661 TCCCTATGAAATTTTGATAA--
1 TCCCTATGAAATTTTGATAACC
* * *
9681 ACCCTATAAAATTTTGA-AAAC
1 TCCCTATGAAATTTTGATAACC
** *
9702 TAAACTATGAAATTTTGATATCC
1 T-CCCTATGAAATTTTGATAACC
*
9725 TCCCTATGAAATTTTGATAA-T
1 TCCCTATGAAATTTTGATAACC
* *
9746 TCCCCTTTGAAATTTTAATAACC
1 T-CCCTATGAAATTTTGATAACC
9769 T
1 T
9770 TCGAAATTTT
Statistics
Matches: 348, Mismatches: 100, Indels: 61
0.68 0.20 0.12
Matches are distributed among these distances:
17 12 0.03
19 11 0.03
20 23 0.07
21 33 0.09
22 204 0.59
23 58 0.17
24 1 0.00
25 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TCCCTATGAAATTTTGATAACC
Found at i:9618 original size:39 final size:41
Alignment explanation
Indices: 9564--9721 Score: 137
Period size: 39 Copynumber: 3.8 Consensus size: 41
9554 ACCTCCCTAT
* *
9564 AAAATTTTAATAACCTCCTTATGAAATTTTGATAA-TCA-C
1 AAAATTTTGATAACCTCCCTATGAAATTTTGATAACTCATC
** *
9603 AAAATTTTGATAACCTCCCTATGATTTTTTGATAACTTCATT
1 AAAATTTTGATAACCTCCCTATGAAATTTTGATAAC-TCATC
* *
9645 ATGAAA-TTTGTTAACCTCCCTATGAAATTTTGATAAACCCTAT-
1 A--AAATTTTGATAACCTCCCTATGAAATTTTGAT-AACTC-ATC
* **
9688 AAAATTTTGA-AAACTAAACTATGAAATTTTGATA
1 AAAATTTTGATAACCT-CCCTATGAAATTTTGATA
9722 TCCTCCCTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
39 31 0.32
41 11 0.11
42 20 0.21
43 27 0.28
44 8 0.08
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (41 bp):
AAAATTTTGATAACCTCCCTATGAAATTTTGATAACTCATC
Found at i:9733 original size:85 final size:82
Alignment explanation
Indices: 9519--9821 Score: 211
Period size: 85 Copynumber: 3.6 Consensus size: 82
9509 TCTCGGTATG
* * * *
9519 AAATTTTGATAAAC-ATTCATATAAAATTTTGATAAACCTCCCTATAAAATTTTAATAACCTCCT
1 AAATTTTGATAAACTA-AC-TATGAAATTTTGAT-AACCTCCCTATGAAATTTT-ATAACCTCCC
*
9583 TATGAAATTTTGATAATCACA
62 TATGAAATTTTGATAACCACA
* ** ** * **
9604 AAATTTTGATAACCTCCCTATGATTTTTTGATAACTTCATTATGAAATTTGT-TAACCTCCCTAT
1 AAATTTTGATAAACTAACTATGAAATTTTGATAACCTCCCTATGAAATTT-TATAACCTCCCTAT
*
9668 GAAATTTTGATAAACCCTATA
65 GAAATTTTGAT-AA-CC-ACA
* *
9689 AAATTTTGA-AAACTAAACTATGAAATTTTGATATCCTCCCTATGAAATTTTGATAA-TTCCCCT
1 AAATTTTGATAAACT-AACTATGAAATTTTGATAACCTCCCTATGAAATTTT-ATAACCT-CCCT
* * * *
9752 TTGAAATTTTAATAACCTTCG
63 ATGAAATTTTGATAACC-ACA
* ** * * *
9773 AAATTTTGGTAACCAC-AAAAATGCAATTTCGATAACCTCCCTTTGAAAT
1 AAATTTTGATAA--ACTAACTATGAAATTTTGATAACCTCCCTATGAAAT
9822 ACCACACTCT
Statistics
Matches: 171, Mismatches: 35, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
82 22 0.13
83 16 0.09
84 29 0.17
85 84 0.49
86 18 0.11
87 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (82 bp):
AAATTTTGATAAACTAACTATGAAATTTTGATAACCTCCCTATGAAATTTTATAACCTCCCTATG
AAATTTTGATAACCACA
Done.