Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022476.1 Corchorus olitorius cultivar O-4 contig22509, 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: 10031
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:1114 original size:324 final size:326
Alignment explanation
Indices: 684--1277 Score: 750
Period size: 324 Copynumber: 1.8 Consensus size: 326
674 TGCATGATTT
* * * * *
684 TTGGCGCCAAAACTCCTTGAACTATCTATATTTATCTAATAAAATCTCAGTCACATTGGATTTAA
1 TTGGCGCCAAAACTACTTGAACTATCCATATTCATCTAATAAAATATCAGTCACATTGCATTTAA
* * *
749 AGATTTATTTTTACGAGCATCTAAATCTTGTATCGATTTAATTAGAAATTAATTCAG-AAAAGTA
66 AGATTTATTTTTACGAGCATCTAAATCTTATATCAATTTAATTAGAAATTAATTCAGAAAAAAT-
* * * * *
813 G-GATAAACGATATTAGAA-GCGTAAAAAAACCTTCAAT-ATTTTTGGCGTTGAATTATATATTT
130 GTGAAAAACGATATGA-AAGGCGTAAAAAAACCTCCAATCATTTTTGGCGTTAAATTATATA-TA
** * * * *
875 TTTTATGACTATTTTAGCAAAAAATTGAGGAAATATCTTTCCGGTCAATTTTTACAAAA-TTTAG
193 AATCATGACTATATTAGCAAAAAATTAAGGAAAAATCTTTCCGGTCAATTTTTACAAAATTTTAG
*
939 CCGAAATCGTGTAATATGGTTTTTTGTTAAAAATGCATTCCAGAGCCTTGGGTCAGTTTTGAATA
258 CCGAAATCATGTAATATGGTTTTTTGTTAAAAATGCATTCCAGAGCCTTGGGTCAGTTTTGAATA
1004 ATTA
323 ATTA
* * *
1008 TTGGCGCTAAGACTACTTGAGA-TATCCATATTCATCTAATCAAATATCAGTCACATTGCATTTA
1 TTGGCGCCAAAACTACTTGA-ACTATCCATATTCATCTAATAAAATATCAGTCACATTGCATTTA
* * * * * *
1072 AGGATTTGTTTTTACGAGGATCTGAATCTTATTTCAATTTAATTAGAAATTAATTTAGAAAAAAT
65 AAGATTTATTTTTACGAGCATCTAAATCTTATATCAATTTAATTAGAAATTAATTCAGAAAAAAT
* ** *
1137 GTGAAAAACGATATGAAAGGCGTGAAAAGTCCTCCAATCTTTTTTGGCGTTAAATTATATATAAA
130 GTGAAAAACGATATGAAAGGCGTAAAAAAACCTCCAATCATTTTTGGCGTTAAATTATATATAAA
* * * ** * *
1202 TCATGAGTATATTAGCCAAAAATTAAGGAAAAATTTTTCTTGTCATTTTTTGCAAAATTTTAGCC
195 TCATGACTATATTAGCAAAAAATTAAGGAAAAATCTTTCCGGTCAATTTTTACAAAATTTTAGCC
1267 GAAATCATGTA
260 GAAATCATGTA
1278 CTAATCATCA
Statistics
Matches: 224, Mismatches: 40, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
324 107 0.48
325 80 0.36
326 37 0.17
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (326 bp):
TTGGCGCCAAAACTACTTGAACTATCCATATTCATCTAATAAAATATCAGTCACATTGCATTTAA
AGATTTATTTTTACGAGCATCTAAATCTTATATCAATTTAATTAGAAATTAATTCAGAAAAAATG
TGAAAAACGATATGAAAGGCGTAAAAAAACCTCCAATCATTTTTGGCGTTAAATTATATATAAAT
CATGACTATATTAGCAAAAAATTAAGGAAAAATCTTTCCGGTCAATTTTTACAAAATTTTAGCCG
AAATCATGTAATATGGTTTTTTGTTAAAAATGCATTCCAGAGCCTTGGGTCAGTTTTGAATAATT
A
Found at i:1356 original size:2 final size:2
Alignment explanation
Indices: 1344--1374 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1334 AGACTCCTTA
1344 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1375 TAATCTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4662 original size:32 final size:32
Alignment explanation
Indices: 4616--4681 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
4606 CCATGAGGTC
4616 TTGGATTCAACTCTCACGAAATGTGAGTTTAA
1 TTGGATTCAACTCTCACGAAATGTGAGTTTAA
* **
4648 TTGGGTTCAACTCTCACGGGATGTGAGTTTAA
1 TTGGATTCAACTCTCACGAAATGTGAGTTTAA
4680 TT
1 TT
4682 TGTTTGTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (32 bp):
TTGGATTCAACTCTCACGAAATGTGAGTTTAA
Found at i:7884 original size:15 final size:15
Alignment explanation
Indices: 7864--7893 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7854 ACAGCGTTGC
7864 ATGATTTTTTGCGTT
1 ATGATTTTTTGCGTT
7879 ATGATTTTTTGCGTT
1 ATGATTTTTTGCGTT
7894 CAGACTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (15 bp):
ATGATTTTTTGCGTT
Found at i:9592 original size:658 final size:663
Alignment explanation
Indices: 8805--10022 Score: 1912
Period size: 658 Copynumber: 1.8 Consensus size: 663
8795 TTTTGCAACC
* * **
8805 ATCACGGTTTTCAGCTAAAACCGCGTTTCAGGGGCCCGGCTCAGTTTTGCACGATTTTTGGTGCC
1 ATCACGGTTTTCAGCTAAAACCGCGATTCAGGAGCCCAACTCAGTTTTGCACGATTTTTGGTGCC
* * *
8870 AAGATTCCTTGAAATATCTATATTCATCTAACCAAATCTCATCCACATTAGATTTAAGGATTTGT
66 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCATCCACATTAAATTTAAGGATTTGT
** * *
8935 TTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTG-AAAAATTGGAAAAATA
131 TTTTACAAGCATCAAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACA
*
8999 ATATTGGAAACGTTAAAAGCCCTTCAATCTTTTTGACGTCGAATTATATATTTTTTTATGAGTAT
196 ATATTAGAAACGTTAAAAGCCCTTCAATCTTTTTGACGTCGAATTATATA-TTTTTTATGAGTAT
*
9064 TTTAGCCAAAAATTGAGGAAATATCTTTCCGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
260 TTTACCCAAAAATTGAGGAAATATCTTTCCGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * *
9129 ACTAAGCATCAC-G-GTTTTTGGCTAAATACGCGTTCCAGGGCCACGGTTCTGTTTTGCATGATT
325 ACTAAGCATCACAGTGTTTTTGGCTAAAAACGCGTTCCAGCGCCACGGCTCTGTTTTGCATGATT
*
9192 TTTGGCGCCGAGACTCCTTAAAATATCTTTATTCATCTAATCAAATCTCAGGCACATT-AGATTT
390 TTTGGCACCGAGACTCCTTAAAATATCTTTATTCATCTAATCAAATCTCAGGCACATTGA-ATTT
*
9256 AAGGATTTGTTTTTATGTGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AAA-ATA
454 AAGGATTTGTTTTTATGTGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAAAATATA
9319 TGAAAAACGATATT-AAATGCGTGAAAAGTCCTCAAATTCTTTTAACGTTGAATTATATATTTTT
519 TGAAAAACGATATTGAAA-GCGTGAAAAGTCCTCAAATTCTTTTAACGTTGAATTATATATTTTT
9383 TATGAGTATTTTCGCTAGATATCGAGCAAAGATCTTTCGGATCAATTTTTGCAAAGTTTTAGCCG
583 TATGAGTATTTTCGCTAGATATCGAGCAAAGATCTTTCGGATCAATTTTTGCAAAGTTTTAGCCG
9448 AAATCATGTACTAACT
648 AAATCATGTACTAACT
** * *
9464 ATCACGGTTTTCAGCTAAAAGTGC-ATTCCGGAGCCCAACTCAGTTTTGCATGATTTTTGGTGCC
1 ATCACGGTTTTCAGCTAAAACCGCGATTCAGGAGCCCAACTCAGTTTTGCACGATTTTTGGTGCC
**
9528 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCATTGACATTAAATTTAAGGATTTGT
66 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCATCCACATTAAATTTAAGGATTTGT
*
9593 TTTTACGAGCATCAAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACA
131 TTTTACAAGCATCAAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACA
** * *
9658 ATATTAGAAGTGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGATTATT
196 ATATTAGAAACGTTAAAAGCCCTTCAATCTTTTTGACGTCGAATTATATATTTTTTATGAGTATT
* ** * *
9723 TTACCCAATAATTGAGGAAATATCTTTTGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTA
261 TTACCCAAAAATTGAGGAAATATCTTTCCGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
* ** * * *
9788 TTAATTATCACAGTTTTTTTTTGGCTAAAAACGCTTTCCAGCGCCACGGCTCTGTTTTGTATGAT
326 CTAAGCATCACAG--TGTTTTTGGCTAAAAACGCGTTCCAGCGCCACGGCTCTGTTTTGCATGAT
* *
9853 TTTTGGCACCTAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGGCACATTGAATTT
389 TTTTGGCACCGAGACTCCTTAAAATATCTTTATTCATCTAATCAAATCTCAGGCACATTGAATTT
*
9918 AAGGATTTGTTTTTATGTGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAAAAAATA
454 AAGGATTTGTTTTTATGTGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC--AAAATA
* *
9983 TATGAAAAACGATATTGAAAGCGTGAAAAGTTCTCCAATT
517 TATGAAAAACGATATTGAAAGCGTGAAAAGTCCTCAAATT
10023 TGGCGTTGA
Statistics
Matches: 503, Mismatches: 45, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
658 220 0.44
659 83 0.17
662 158 0.31
663 1 0.00
665 3 0.01
666 35 0.07
667 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (663 bp):
ATCACGGTTTTCAGCTAAAACCGCGATTCAGGAGCCCAACTCAGTTTTGCACGATTTTTGGTGCC
AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCATCCACATTAAATTTAAGGATTTGT
TTTTACAAGCATCAAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACA
ATATTAGAAACGTTAAAAGCCCTTCAATCTTTTTGACGTCGAATTATATATTTTTTATGAGTATT
TTACCCAAAAATTGAGGAAATATCTTTCCGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
CTAAGCATCACAGTGTTTTTGGCTAAAAACGCGTTCCAGCGCCACGGCTCTGTTTTGCATGATTT
TTGGCACCGAGACTCCTTAAAATATCTTTATTCATCTAATCAAATCTCAGGCACATTGAATTTAA
GGATTTGTTTTTATGTGAATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAAAATATATG
AAAAACGATATTGAAAGCGTGAAAAGTCCTCAAATTCTTTTAACGTTGAATTATATATTTTTTAT
GAGTATTTTCGCTAGATATCGAGCAAAGATCTTTCGGATCAATTTTTGCAAAGTTTTAGCCGAAA
TCATGTACTAACT
Done.