Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014600.1 Corchorus olitorius cultivar O-4 contig14633, 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: 20423
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1554 original size:27 final size:26
Alignment explanation
Indices: 1499--1560 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
1489 TCTAAATTTT
1499 TATTATTTTAATAATGAAATAATTAAAA
1 TATTA-TTTAATAATGAAAT-ATTAAAA
1527 TATTATTTAATAATGATAAT-TTAGAAA
1 TATTATTTAATAATGA-AATATTA-AAA
1554 TA-TATTT
1 TATTATTT
1561 GAAAAAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.25
27 16 0.50
28 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TATTATTTAATAATGAAATATTAAAA
Found at i:8643 original size:20 final size:22
Alignment explanation
Indices: 8618--8667 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
8608 GGAGAAATTG
8618 TAATAGAT-CATTTAGC-AAAT
1 TAATAGATGCATTTAGCAAAAT
8638 TAATAGATGCATTTAGCAAAAT
1 TAATAGATGCATTTAGCAAAAT
8660 TAATAGAT
1 TAATAGAT
8668 TTGCCCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 8 0.29
21 8 0.29
22 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (22 bp):
TAATAGATGCATTTAGCAAAAT
Found at i:9709 original size:19 final size:19
Alignment explanation
Indices: 9685--9722 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9675 CGGCATCAGC
9685 CAAGTAAGAAAAGGAAATG
1 CAAGTAAGAAAAGGAAATG
9704 CAAGTAAGAAAAGGAAATG
1 CAAGTAAGAAAAGGAAATG
9723 GTTCGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.26, T:0.11
Consensus pattern (19 bp):
CAAGTAAGAAAAGGAAATG
Found at i:11917 original size:14 final size:14
Alignment explanation
Indices: 11893--11932 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
11883 TTATCGGCAG
*
11893 AAAAAAGAAAAA-A
1 AAAAAATAAAAATA
11906 AATAAAATAAAAATA
1 AA-AAAATAAAAATA
11921 AAAAAATAAAAA
1 AAAAAATAAAAA
11933 GGTCAGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 2 0.08
14 19 0.79
15 3 0.12
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.10
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:16644 original size:434 final size:430
Alignment explanation
Indices: 15922--16809 Score: 1185
Period size: 434 Copynumber: 2.1 Consensus size: 430
15912 TCTTTTTAAA
* * *
15922 TTTTTTT-TATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTACA
1 TTTTTTTCTATTTGTCCAATTAAGGTGATTCAAGTGTCAATTAAAAGGTAATTTCATGATCTACA
** *
15986 ACTTTCATGAAGGACTTCAAAGCCAATTTTTAAGTTTCAATTCAAAAAAATACTTCCGAAATTTG
66 ACTTTCATGAAAAACTTCAAAGCCAATTTTTAAGTTTCAATTCAAAAAAATACTTCCCAAATTTG
* * * *
16051 CTGATTTTGATTGCCGATCTATTTAATATCATATAATTTTCGATCAACATGTCCGATTAATGTTT
131 CTGATTTTGATTACCGATCTATTTAATACCATATAATTTTAGATCAACATGTCCGATTAAAGTTT
* * * * ** *
16116 CTCAAGTGTTGGTTAAAAGGTTATTGCATGATCTACGACTTTTGTGAAGGACCCGAAAGCTAAAT
196 CTCAAATATCGGTTAAAAGGTTATTGCATGATCTACCACTTTCATAAAGGACCCGAAAGCTAAAT
* * * * * *
16181 TTTATCTACGAGTTCCATTAAGTGTTCAAAAGTGAATTTTTATATTTCAAGATCTCCATCAATAA
261 TTGATCTACAAGTTCCATGAAGGGTTCAAAAGGGAATTTTTATATTTCAAGATCTCCATCAACAA
** * * * *
16246 ACATTTTTTTATTTGGATTATTTATGAAATGACCCTCATATTTTTCTACTTTATACTACTTAGTC
326 ACAGATTCTTATTTGGATTATTAATCAAATGACCCTCATAATTTTCTACTTTATACTACTTAGTC
* *
16311 CTTTACTAATTCTATCTTAATCGATTTAACGC-TTAAGCTTCT
391 CTTTACAAATTCTATCTTAATCGATTTAACACTTTAA--TT-T
* *
16353 TTTTTTTCTATTTGTCCAATTAAGGTGATTCAGGTGTCAATTAAAAGGTAATTTCATGATCTCCA
1 TTTTTTTCTATTTGTCCAATTAAGGTGATTCAAGTGTCAATTAAAAGGTAATTTCATGATCTACA
*
16418 ACTTTCATGAAAAAC-TCAAAAGCCAATTTTTACA-TTTCAATTCAAATAAAAATGCTTCCCAAA
66 ACTTTCATGAAAAACTTC-AAAGCCAATTTTTA-AGTTTCAATTC-AA-AAAAATACTTCCCAAA
* * * * * *
16481 TTTGGTGGTTTTGATTATCGTTCTATTTAATACCATATAATTTTAGATCCACATGTGCGATTAAA
127 TTTGCTGATTTTGATTACCGATCTATTTAATACCATATAATTTTAGATCAACATGTCCGATTAAA
* *
16546 GTAATT-T-AAATATCGGTTAAAAGGTTATTGCGTGATCTACCACTTTCATAAAGTACCCGAAAG
192 GT--TTCTCAAATATCGGTTAAAAGGTTATTGCATGATCTACCACTTTCATAAAGGACCCGAAAG
* * * * *
16609 CTAAATTTGATTTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTGAAGATCTCTAT
255 CTAAATTTGATCTACAAGTTCCATGAAGGGTTCAAAAGGGAATTTTTATATTTCAAGATCTCCAT
*
16674 CAACAAACAGATTCTTATTTGGATTATTAATCAAATGACCCTTATAATTTTCTACTTTATACTAC
320 CAACAAACAGATTCTTATTTGGATTATTAATCAAATGACCCTCATAATTTTCTACTTTATACTAC
* *
16739 TTAGTCCTTTACAAATTCTATTTTACTCGATTTAACACTTTAATTT
385 TTAGTCCTTTACAAATTCTATCTTAATCGATTTAACACTTTAATTT
*
16785 TTTTTATTCTATTTGTCTAATTAAG
1 TTTTT-TTCTATTTGTCCAATTAAG
16810 ATAATTCATG
Statistics
Matches: 397, Mismatches: 51, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
431 9 0.02
432 94 0.24
433 23 0.06
434 264 0.66
435 5 0.01
436 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (430 bp):
TTTTTTTCTATTTGTCCAATTAAGGTGATTCAAGTGTCAATTAAAAGGTAATTTCATGATCTACA
ACTTTCATGAAAAACTTCAAAGCCAATTTTTAAGTTTCAATTCAAAAAAATACTTCCCAAATTTG
CTGATTTTGATTACCGATCTATTTAATACCATATAATTTTAGATCAACATGTCCGATTAAAGTTT
CTCAAATATCGGTTAAAAGGTTATTGCATGATCTACCACTTTCATAAAGGACCCGAAAGCTAAAT
TTGATCTACAAGTTCCATGAAGGGTTCAAAAGGGAATTTTTATATTTCAAGATCTCCATCAACAA
ACAGATTCTTATTTGGATTATTAATCAAATGACCCTCATAATTTTCTACTTTATACTACTTAGTC
CTTTACAAATTCTATCTTAATCGATTTAACACTTTAATTT
Found at i:18116 original size:12 final size:12
Alignment explanation
Indices: 18099--18127 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18089 ATAGCACTAA
18099 AATTATTATACT
1 AATTATTATACT
18111 AATTATTATACT
1 AATTATTATACT
18123 AATTA
1 AATTA
18128 ATTTTAGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTATACT
Done.