Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017813.1 Corchorus olitorius cultivar O-4 contig17846, 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: 43786
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3460 original size:35 final size:36
Alignment explanation
Indices: 3413--3481 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
3403 TTCAATAACC
* *
3413 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
3449 TTACAT-TTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
3482 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.22, C:0.10, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:4380 original size:203 final size:203
Alignment explanation
Indices: 3981--4391 Score: 736
Period size: 203 Copynumber: 2.0 Consensus size: 203
3971 GCTTAATAAC
3981 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
4046 GATACAACACATTATTATTATATATAAAACTATACCCAAAAAAAGGTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTATATATAAAACTATACCCAAAAAAAGGTAGTTGAACATTAGTGGTT
*
4111 GATTTATTAAATTAAATTAGATCAATGTCAAACAAATTTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
4176 CCGATTTA
196 CCGATTTA
*
4184 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
4249 GATACAACATATTACTATTATATATATAGAACTATACCGAAAAAAA-TTAGTTGAACATTAGTGG
66 GATACAACACATTACTATTATATATA-A-AACTATACCCAAAAAAAGGTAGTTGAACATTAGTGG
4313 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAG
129 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
4377 ATCCGATTTA
194 ATCCGATTTA
4387 TTTAT
1 TTTAT
4392 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
203 106 0.53
204 78 0.39
205 16 0.08
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCCAAAAAAAGGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
CCGATTTA
Found at i:4555 original size:39 final size:40
Alignment explanation
Indices: 4501--4581 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
4491 ATACCTAAGA
*
4501 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
4540 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
4580 AT
1 AT
4582 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:4915 original size:35 final size:36
Alignment explanation
Indices: 4868--4936 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
4858 TTCAATAACC
* **
4868 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTAATTATCATATTTCTTA
4904 TTACAT-TTTTGTAATTTTAATTATCATATTTCT
1 TTACATCTTTTGTAATTTTAATTATCATATTTCT
4937 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 24 0.80
36 6 0.20
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTAATTATCATATTTCTTA
Found at i:6589 original size:39 final size:40
Alignment explanation
Indices: 6535--6615 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
6525 ATACCTAAGA
*
6535 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
6574 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
6614 AT
1 AT
6616 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:23462 original size:25 final size:25
Alignment explanation
Indices: 23420--23482 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
23410 CAAGCTCCTT
** *
23420 AAGAGGGACCGCCTCAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
*
23445 AAGAGGGAATGCCACAAGCTCTCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
23470 AAGAGGGAATGCC
1 AAGAGGGAATGCC
23483 CCAAAGAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.33, C:0.30, G:0.27, T:0.10
Consensus pattern (25 bp):
AAGAGGGAATGCCACAAGCTCCCCA
Found at i:23488 original size:16 final size:16
Alignment explanation
Indices: 23467--23498 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23457 CACAAGCTCT
*
23467 CCAAAGAGGGAATGCC
1 CCAAAGAGGAAATGCC
23483 CCAAAGAGGAAATGCC
1 CCAAAGAGGAAATGCC
23499 ACAAGCTCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.28, T:0.06
Consensus pattern (16 bp):
CCAAAGAGGAAATGCC
Found at i:23497 original size:41 final size:41
Alignment explanation
Indices: 23440--23523 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
23430 GCCTCAAGCT
* *
23440 CCCCAAAGAGGGAATGCCACAAGCTCTCCAAAGAGGGAATG
1 CCCCAAAGAGGAAATGCCACAAGCTCCCCAAAGAGGGAATG
23481 CCCCAAAGAGGAAATGCCACAAGCTCCCCAAAGAGGGAATG
1 CCCCAAAGAGGAAATGCCACAAGCTCCCCAAAGAGGGAATG
23522 CC
1 CC
23524 TCAAGCTCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.30, G:0.25, T:0.08
Consensus pattern (41 bp):
CCCCAAAGAGGAAATGCCACAAGCTCCCCAAAGAGGGAATG
Found at i:23515 original size:25 final size:25
Alignment explanation
Indices: 23481--23596 Score: 155
Period size: 25 Copynumber: 4.7 Consensus size: 25
23471 AGAGGGAATG
*
23481 CCCCAAAGAGGAAATGCCACAAGCT
1 CCCCAAAGAGGGAATGCCACAAGCT
*
23506 CCCCAAAGAGGGAATGCCTCAAGCT
1 CCCCAAAGAGGGAATGCCACAAGCT
*
23531 CCCCAAAGAGGGAATGCCA-TA-CT
1 CCCCAAAGAGGGAATGCCACAAGCT
* *
23554 CCCCAAAGATGGAATACCACAAGCT
1 CCCCAAAGAGGGAATGCCACAAGCT
* *
23579 CCCCTAAGAGGGACTGCC
1 CCCCAAAGAGGGAATGCC
23597 TTGCTCCCCA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 19 0.24
24 2 0.03
25 57 0.73
ACGTcount: A:0.34, C:0.33, G:0.22, T:0.11
Consensus pattern (25 bp):
CCCCAAAGAGGGAATGCCACAAGCT
Found at i:23577 original size:48 final size:48
Alignment explanation
Indices: 23481--23612 Score: 156
Period size: 48 Copynumber: 2.7 Consensus size: 48
23471 AGAGGGAATG
* * * *
23481 CCCCAAAGAGGAAATGCCACAAGCTCCCCAAAGAGGGAATGCCTCAAGCT
1 CCCCAAAGAGGGAATGCCA-TA-CTCCCCAAAGAGGGAATACCACAAGCT
*
23531 CCCCAAAGAGGGAATGCCATACTCCCCAAAGATGGAATACCACAAGCT
1 CCCCAAAGAGGGAATGCCATACTCCCCAAAGAGGGAATACCACAAGCT
* * * *
23579 CCCCTAAGAGGGACTGCCTTGCTCCCCAAGAGAG
1 CCCCAAAGAGGGAATGCCATACTCCCCAA-AGAG
23613 ACATTAAATC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
48 49 0.69
49 4 0.06
50 18 0.25
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.12
Consensus pattern (48 bp):
CCCCAAAGAGGGAATGCCATACTCCCCAAAGAGGGAATACCACAAGCT
Found at i:23727 original size:65 final size:65
Alignment explanation
Indices: 23600--24061 Score: 635
Period size: 65 Copynumber: 7.1 Consensus size: 65
23590 GACTGCCTTG
* * *
23600 CTCCCCAAGAGAGACATTAAATCAGGTCGTGCGACGTAAGACCCCAGTGGTTGGCCCACCTGCAG
1 CTCCCC-AGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAG
23665 T
65 T
** * * *
23666 CTCCTTAGAGGGACGTTGAATAAGGTCGTGTGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
1 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
*
23731 CTCCCCAGAGGGACGTTAAATCAGGTCGTGTGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
1 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
* * *
23796 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTATGACCTCAGTGGTTGGCCCCCCTGCAGT
1 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
* * *
23861 CT-CCTAGAGGGACGTTAAATCAGGTCGTGCGCCATAAGA-CCCAGT-GTGGGGCCCACCTGCAG
1 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGT-TGGCCCACCTGCAG
23923 T
65 T
* * * *
23924 CTCCCCAAAGGGACGTTAAATCAGGTGGTGCGTCGTAAGACCCCAGTGGTTGGCCCCCCTTGCAG
1 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACC-TGCAG
23989 T
65 T
* * ** * *
23990 CTCCCCAGTGGAACGTTAAATCAGGTCGTGTACCGTAAAACCCCAATGGTTGGCCC-CCTGCAGT
1 CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
*
24054 TTCCCCAG
1 CTCCCCAG
24062 TAGAACAAAC
Statistics
Matches: 352, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
62 2 0.01
63 20 0.06
64 79 0.22
65 192 0.55
66 59 0.17
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (65 bp):
CTCCCCAGAGGGACGTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGT
Found at i:24014 original size:194 final size:195
Alignment explanation
Indices: 23616--24053 Score: 650
Period size: 193 Copynumber: 2.3 Consensus size: 195
23606 AAGAGAGACA
* *
23616 TTAAATCAGGTCGTGCGACGTAAGACCCCAGTGGTTGGCCCACCTGCAGTCTCCTTAGAGGGACG
1 TTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCCCCTGCAGTCTCCTTAGAGGGACG
* * * * *
23681 TTGAATAAGGTCGTGTGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGTCTCCCCAGAGGGACG
66 TTAAATAAGGTCGTGCGCCATAAGACCCCAGTGGTGGGCCCACCTGCAGTCTCCCCAAAGGGACG
* *
23746 TTAAATCAGGTCGTGTGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGTCTCCCCAGAGGGACG
131 TTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGTCTCCCCAGAGGAACG
* *
23811 TTAAATCAGGTCGTGCGCCGTATGACCTCAGTGGTTGGCCCCCCTGCAGTCTCC-TAGAGGGACG
1 TTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCCCCTGCAGTCTCCTTAGAGGGACG
*
23875 TTAAATCAGGTCGTGCGCCATAAGA-CCCAGT-GTGGGGCCCACCTGCAGTCTCCCCAAAGGGAC
66 TTAAATAAGGTCGTGCGCCATAAGACCCCAGTGGT-GGGCCCACCTGCAGTCTCCCCAAAGGGAC
* * * *
23938 GTTAAATCAGGTGGTGCGTCGTAAGACCCCAGTGGTTGGCCCCCCTTGCAGTCTCCCCAGTGGAA
130 GTTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACC-TGCAGTCTCCCCAGAGGAA
24003 CG
194 CG
** * *
24005 TTAAATCAGGTCGTGTACCGTAAAACCCCAATGGTTGG-CCCCCTGCAGT
1 TTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCCCCTGCAGT
24054 TTCCCCAGTA
Statistics
Matches: 219, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
192 2 0.01
193 85 0.39
194 82 0.37
195 50 0.23
ACGTcount: A:0.21, C:0.30, G:0.29, T:0.21
Consensus pattern (195 bp):
TTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCCCCTGCAGTCTCCTTAGAGGGACG
TTAAATAAGGTCGTGCGCCATAAGACCCCAGTGGTGGGCCCACCTGCAGTCTCCCCAAAGGGACG
TTAAATCAGGTCGTGCGCCGTAAGACCCCAGTGGTTGGCCCACCTGCAGTCTCCCCAGAGGAACG
Found at i:25779 original size:77 final size:77
Alignment explanation
Indices: 25652--25805 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
25642 GTTAAATTTG
*
25652 TGTCTAAATTTTAGAAATAATTTTGAGTTATCACAATTTTAAATGGCTAAATATACAATACACCC
1 TGTCTAAATTTTAGAAATAATTTTGAGGTATCACAATTTTAAATGGCTAAATATACAATACACCC
*
25717 TCAGTGGAGTTT
66 TCAGTAGAGTTT
* *
25729 TGTCTAAATTTTAGAAATAATTTTGAGGTATCACAATTTTAAATGGCTAAATATACAGTACACCG
1 TGTCTAAATTTTAGAAATAATTTTGAGGTATCACAATTTTAAATGGCTAAATATACAATACACCC
25794 TCAGTAGAGTTT
66 TCAGTAGAGTTT
25806 AGTAGACTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (77 bp):
TGTCTAAATTTTAGAAATAATTTTGAGGTATCACAATTTTAAATGGCTAAATATACAATACACCC
TCAGTAGAGTTT
Found at i:41660 original size:15 final size:15
Alignment explanation
Indices: 41637--41669 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
41627 AATGAAGAAA
*
41637 CTATTTTAAATAAAT
1 CTATCTTAAATAAAT
41652 CTATCTTAAATAAAT
1 CTATCTTAAATAAAT
41667 CTA
1 CTA
41670 AGTCTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (15 bp):
CTATCTTAAATAAAT
Found at i:42025 original size:28 final size:30
Alignment explanation
Indices: 41984--42058 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
41974 TGGCGCTGAG
* *
41984 AGTTTAGGAGGCAAAACGTCCAAA-ATA-A
1 AGTTCAGGGGGCAAAACGTCCAAACATACA
* *
42012 AGTTCAGTGGGCAAAACGTCCAAATCGTACA
1 AGTTCAGGGGGCAAAACGTCCAAA-CATACA
42043 AGTTCAGGGGGCAAAA
1 AGTTCAGGGGGCAAAA
42059 GGGTATTAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 21 0.54
30 2 0.05
31 16 0.41
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (30 bp):
AGTTCAGGGGGCAAAACGTCCAAACATACA
Done.