Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019950.1 Corchorus olitorius cultivar O-4 contig19983, 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: 64819
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:883 original size:333 final size:334
Alignment explanation
Indices: 1--1194 Score: 1770
Period size: 333 Copynumber: 3.6 Consensus size: 334
* * * * *
1 GGCATTTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGTAAAAAACTTTCGGGTC
1 GGCA-TTGAATTATATATTTTTTGTGAGTATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTC
*
66 AGTTTTTTCAAAAATTTTAGCCAAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCGC
65 AGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCGC
* *
131 TATGGGACCCCGGCTCAG-TTTGCATGATTTTTAGTGCCAAGACTCCTTGAAATATCTTTATTCA
130 TATGGGACCCCGGCTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTTTATTCA
* * * * *
195 TTTAACCAAATCTCAGTCGCAATGGGTTTAAGGATTTATTTTTGCGAGCATCTGAATCATGTTCC
195 TCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTGTTTTTGCGAGCATCTGAATCATGTTTC
** *
260 GATTTGCTTAAAAATTAATTTGGAAAAAATTTTGAAAAACGATATTAGAAGCGTGAAAGGCCCTT
260 GATTTAATTAAAAATTAATTTGGAAAAAATTTTGAAAAACGATATTAGAAGCGTGAAAAGCCCTT
325 CAATCTTTTT
325 CAATCTTTTT
335 GGCATTGAATTATATATTTTTTTGTGAGTATTGTGGCAAAAAAATGGAGGAAAAAATTTTCGGGT
1 GGCATTGAATTATATA-TTTTTTGTGAGTATTGTGGC-AAAAAATGGAGGAAAAAATTTTCGGGT
* * *
400 CAATTTTTTCAAAAATTTTAGTCG-AATCGTGTACTAACCATAATGATTTTTGGCTAAAAATGCG
64 CAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCG
464 CTATGGGACCCCGGCTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTTTATTC
129 CTATGGGACCCCGGCTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTTTATTC
**
529 ATCTAACCAAATCTCAGCCGCAAAT-GATTTAAGGATTTGTTTTTATGAGCATCTGAATCATGTT
194 ATCTAACCAAATCTCAGCCGC-AATGGATTTAAGGATTTGTTTTTGCGAGCATCTGAATCATGTT
* * * *
593 TCGATTTAATTAGAAATTAATTTGGACAAAATTTTGAAAAACGATATTAGAAACGTGAAAAACCC
258 TCGATTTAATTAAAAATTAATTTGGAAAAAATTTTGAAAAACGATATTAGAAGCGTGAAAAGCCC
658 TTCAATCTTTTT
323 TTCAATCTTTTT
* * * * *
670 GGCGTTGAATTATATA-TTTTTGTGAGTATTGTGGCCAAAAGTTGAGG-AAAAATGTTTTGGGTC
1 GGCATTGAATTATATATTTTTTGTGAGTATTGTGGCAAAAAATGGAGGAAAAAAT-TTTCGGGTC
* * ** * * * *
733 AGTTTCTTCAAAAATCTTAGTTGAAATCCTCTACTAACCATCATGATTTTTGCCTAAAAATGCAC
65 AGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCGC
* **
798 TATAGGG-CCCCGGCTCAGTTTTGAATGATTTTTGGTGTCAAGACTCCTTGAAATATCTTTATTC
130 TAT-GGGACCCCGGCTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTTTATTC
* * **
862 ATCTAACCAAATCTTAGCCGCAATGGTTTTAAGGATTTGCCTTTGCGAGCATCTGAATCATGTTT
194 ATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTGTTTTTGCGAGCATCTGAATCATGTTT
*
927 CGATTTAGTTAAAAATTAATTTGGAAAAAATTTTGAAAAACGATATTAGAAGCGTGAAAAGCCCT
259 CGATTTAATTAAAAATTAATTTGGAAAAAATTTTGAAAAACGATATTAGAAGCGTGAAAAGCCCT
*
992 TCAATATTTTT
324 TCAATCTTTTT
*
1003 GGCATTGAATTATATATTTTTTGTGAGTATTTTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCA
1 GGCATTGAATTATATATTTTTTGTGAGTATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTC-
*
1068 ATTTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCG
65 A-GTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCG
* * * * * * *
1133 TTCTTGGATCCCGGCTTAGTTTTGCTTGATTTTTGGTACCAAGACTCCTTGAGATATCTTTA
129 CTATGGGACCCCGGCTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTTTA
1195 ACGTTACAAA
Statistics
Matches: 768, Mismatches: 79, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
331 6 0.01
332 39 0.05
333 264 0.34
334 118 0.15
335 235 0.31
336 106 0.14
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (334 bp):
GGCATTGAATTATATATTTTTTGTGAGTATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCA
GTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCGCT
ATGGGACCCCGGCTCAGTTTTGCATGATTTTTGGTACCAAGACTCCTTGAAATATCTTTATTCAT
CTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTGTTTTTGCGAGCATCTGAATCATGTTTCG
ATTTAATTAAAAATTAATTTGGAAAAAATTTTGAAAAACGATATTAGAAGCGTGAAAAGCCCTTC
AATCTTTTT
Found at i:3079 original size:32 final size:31
Alignment explanation
Indices: 3009--3081 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
2999 TCAAATTGAT
* * *
3009 AGACAAAATAGCCCTCGAATTTTGACATAGA
1 AGACAAAATAACCCTCAAATTTTGACAAAGA
3040 AGAACAAAATAACCCTCAAATTTTGACAAAGTA
1 AG-ACAAAATAACCCTCAAATTTTGACAAAG-A
*
3073 CGACAAAAT
1 AGACAAAAT
3082 GTTCTTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 2 0.06
32 32 0.89
33 2 0.06
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (31 bp):
AGACAAAATAACCCTCAAATTTTGACAAAGA
Found at i:13246 original size:19 final size:20
Alignment explanation
Indices: 13224--13261 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13214 AATTATTTTA
*
13224 ATATTATATTTTTA-TTAAT
1 ATATTACATTTTTACTTAAT
13243 ATATTACATTTTTACTTAA
1 ATATTACATTTTTACTTAA
13262 AAACTACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTACATTTTTACTTAAT
Found at i:15560 original size:2 final size:2
Alignment explanation
Indices: 15553--15587 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15543 CCCTATTGTA
15553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15588 CAAATAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20401 original size:148 final size:148
Alignment explanation
Indices: 20133--20432 Score: 548
Period size: 148 Copynumber: 2.0 Consensus size: 148
20123 TCTTGTTGTC
20133 TTTTCATAGCAACTGAATATTAGTTGAATTTAGTTTTCATTTTATCCTCATAGTGATTACATAGA
1 TTTTCATAGCAACTGAATATTAGTTGAATTTAGTTTTCATTTTATCCTCATAGTGATTACATAGA
*
20198 AAAATTGCATTTACTACTCTCCAGCAGTCCAGCTCGTTAGAATCTCATTCATTTGGTTGAGTGGT
66 AAAATTGCATTTACTACTCTCCAGCAGTCCAGCTCGTTAGAAACTCATTCATTTGGTTGAGTGGT
20263 CAGTACCTATGACTAAAG
131 CAGTACCTATGACTAAAG
20281 TTTTCATAGCAACTGAATATTAGTTGAATTTAGTTTTCATTTTATCCTCATAGTGATTACATAGA
1 TTTTCATAGCAACTGAATATTAGTTGAATTTAGTTTTCATTTTATCCTCATAGTGATTACATAGA
*
20346 AAAATTGCATTTACTAC-CTTCCAGCAGTCCAGCTGGTTAGAAACTCATTCATTTGGTTGAGTGG
66 AAAATTGCATTTACTACTC-TCCAGCAGTCCAGCTCGTTAGAAACTCATTCATTTGGTTGAGTGG
**
20410 TCAGTACCTATGTTTAAAG
130 TCAGTACCTATGACTAAAG
20429 TTTT
1 TTTT
20433 GATAAAACCC
Statistics
Matches: 147, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 1 0.01
148 146 0.99
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (148 bp):
TTTTCATAGCAACTGAATATTAGTTGAATTTAGTTTTCATTTTATCCTCATAGTGATTACATAGA
AAAATTGCATTTACTACTCTCCAGCAGTCCAGCTCGTTAGAAACTCATTCATTTGGTTGAGTGGT
CAGTACCTATGACTAAAG
Found at i:26681 original size:6 final size:6
Alignment explanation
Indices: 26670--26696 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26660 TTTTTTACAA
26670 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
26697 TTGGTTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:26753 original size:3 final size:3
Alignment explanation
Indices: 26745--26773 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
26735 TTTTAATTGA
26745 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
26774 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:54554 original size:30 final size:30
Alignment explanation
Indices: 54520--54578 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
54510 ATGAAAGATA
* *
54520 AATTAATTTGAGAAGTTAAAAAGAAAAAAG
1 AATTAATTTAAGAAGTCAAAAAGAAAAAAG
* *
54550 AATTATTTTAAGGAGTCAAAAAGAAAAAA
1 AATTAATTTAAGAAGTCAAAAAGAAAAAA
54579 AAAATTTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (30 bp):
AATTAATTTAAGAAGTCAAAAAGAAAAAAG
Found at i:57441 original size:2 final size:2
Alignment explanation
Indices: 57434--57462 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57424 TGAGAAAAGA
57434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57463 CGTCCATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.