Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011236.1 Corchorus olitorius cultivar O-4 contig11269, 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: 30752
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1909 original size:36 final size:36
Alignment explanation
Indices: 1862--1931 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1852 TTCAATAACC
* *
1862 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1898 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1932 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3471 original size:31 final size:31
Alignment explanation
Indices: 3415--3479 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3405 ACAGTTTTGT
**
3415 AACGTTTGATCCTGAATTGCTCATTTGAG-CA
1 AACGTTTGATCCTGAATTGAACATTT-AGCCA
3446 AACGTTAT-ATCCTGAATTGAACATTTAGCCA
1 AACGTT-TGATCCTGAATTGAACATTTAGCCA
3477 AAC
1 AAC
3480 TTAATGCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 27 0.90
32 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (31 bp):
AACGTTTGATCCTGAATTGAACATTTAGCCA
Found at i:4275 original size:210 final size:203
Alignment explanation
Indices: 3912--4329 Score: 671
Period size: 210 Copynumber: 2.0 Consensus size: 203
3902 GCTTAATAAC
* *
3912 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATCAGTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTAAATGTTATTAATTTTTTTAAGTCTAAGATCACTAACAAAGTTGTAGTGAATA
3977 AGATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTT
66 AGATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTT
*
4042 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTT-CAAAATTATAAAAGATATTAAGGA
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTACAAAATTATAAAAGATAATAA-GA
4106 TCCGATTTA
195 TCCGATTTA
*
4115 TTTATCAATGGTAAATGTTATTAA-TTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTAAATGTTATTAATTTTTTTAAGTCTAAGATCACTAACAAAGTTGTAGTGAATA
* *
4179 AGATACAACACATTACTATTATATATATATATATAGAACTATA-ACCAAAAAAATTAGTTGAACA
66 AGATACAACACA-T--TA-T-TAT-TATATATAT--AACTATACA-AAAAAAAAGTAGTTGAACA
4243 TTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTACAAAATTATAAAAGA
122 TTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTACAAAATTATAAAAGA
4308 TAATAAGATCCGATTTA
187 TAATAAGATCCGATTTA
4325 TTTAT
1 TTTAT
4330 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
202 50 0.25
203 24 0.12
205 2 0.01
206 1 0.01
207 3 0.02
208 9 0.05
209 1 0.01
210 89 0.45
211 20 0.10
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTAAATGTTATTAATTTTTTTAAGTCTAAGATCACTAACAAAGTTGTAGTGAATA
AGATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTACAAAATTATAAAAGATAATAAGAT
CCGATTTA
Found at i:4504 original size:39 final size:40
Alignment explanation
Indices: 4439--4519 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
4429 ATACCTAAGA
*
4439 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
* * *
4478 ATTTGATTATTGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
4518 AT
1 AT
4520 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:13586 original size:25 final size:25
Alignment explanation
Indices: 13558--13609 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
13548 AAGTTTTTTT
13558 AATTGAAAAAAAAATACAAAAAGTA
1 AATTGAAAAAAAAATACAAAAAGTA
13583 AATTGAAAAAAAAATACAAAAAGTA
1 AATTGAAAAAAAAATACAAAAAGTA
13608 AA
1 AA
13610 AGGAACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (25 bp):
AATTGAAAAAAAAATACAAAAAGTA
Found at i:17489 original size:17 final size:17
Alignment explanation
Indices: 17459--17519 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
17449 ATTCCGACAG
* *
17459 CAGGAGTCAGGCTGCAA
1 CAGGAATCACGCTGCAA
17476 CAGGAATCACGCTGCAA
1 CAGGAATCACGCTGCAA
* * *
17493 CAAGAGTCACACTGCAA
1 CAGGAATCACGCTGCAA
*
17510 CAGCAATCAC
1 CAGGAATCAC
17520 ATGGCAGTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.36, C:0.30, G:0.23, T:0.11
Consensus pattern (17 bp):
CAGGAATCACGCTGCAA
Found at i:28472 original size:45 final size:45
Alignment explanation
Indices: 28407--28501 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
28397 CAACAATTAT
* * *
28407 TATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAGAA
1 TATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGGACTAGAA
* *
28452 TATTAGTTTTATTTTAATGAATTACCTAGAGATGGAGTACTAGAA
1 TATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGGACTAGAA
28497 T-TTAG
1 TATTAG
28502 GTAATGCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (45 bp):
TATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGGACTAGAA
Found at i:28859 original size:51 final size:51
Alignment explanation
Indices: 28793--28897 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
28783 TTAAAACTAC
28793 AATATATACTATATATTAATTTTAGTGGCTATGGAAATTACTTAAAGGCCA
1 AATATATACTATATATTAATTTTAGTGGCTATGGAAATTACTTAAAGGCCA
28844 AATATATACTATATATTAATTTTAGTGGCTATGGAAATTACTTAAAGGCCA
1 AATATATACTATATATTAATTTTAGTGGCTATGGAAATTACTTAAAGGCCA
28895 AAT
1 AAT
28898 TGAGGATTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (51 bp):
AATATATACTATATATTAATTTTAGTGGCTATGGAAATTACTTAAAGGCCA
Done.