Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019533.1 Corchorus olitorius cultivar O-4 contig19566, 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: 26141
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:330 original size:41 final size:41
Alignment explanation
Indices: 284--544 Score: 432
Period size: 41 Copynumber: 6.4 Consensus size: 41
274 TTTTTATCTC
284 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
*
325 TGCAATTTAGTCCCTGATTTAAGATTCTAATTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
*
366 TGCAATTTAGTCCCTGATTTAAGATTCTAATTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
*
407 TGCAATTTAGTCCCTGATTCAAGATTCTATTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
*
448 TGCAATTTAGTCCCTGATTTAAGATTCTCTTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
* * * *
489 TGCAATTTAGTCACTGATTTAGGATTTTAGTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
* *
530 TTCAATTTGGTCCCT
1 TGCAATTTAGTCCCT
545 AGTTTTAGAA
Statistics
Matches: 207, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 207 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (41 bp):
TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
Found at i:575 original size:123 final size:123
Alignment explanation
Indices: 284--577 Score: 369
Period size: 123 Copynumber: 2.4 Consensus size: 123
274 TTTTTATCTC
* * * * *
284 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGATGCAATTTAGTCCCTGATTTAAGA
1 TGCAATTTAGTCCCTGATTCAAAATTCGATTTACAAATTGATGCAATTTAGTCCCTGATTTAAGA
*
349 TTCTAATTACTATTTGATGCAATTTAGTCCCTGATTTAAGATTCTAATTACTATTTGA
66 TTCTAATTACTATTTGATGCAATTTAGTCACTGATTTAAGATTCTAATTACTATTTGA
* * * *
407 TGCAATTTAGTCCCTGATTCAAGATTCTATTTACTATTTGATGCAATTTAGTCCCTGATTTAAGA
1 TGCAATTTAGTCCCTGATTCAAAATTCGATTTACAAATTGATGCAATTTAGTCCCTGATTTAAGA
** * * *
472 TTCTCTTTACTATTTGATGCAATTTAGTCACTGATTTAGGATTTTAGTTACTATTTGA
66 TTCTAATTACTATTTGATGCAATTTAGTCACTGATTTAAGATTCTAATTACTATTTGA
* * * *
530 TTCAATTTGGTCCCTAGTTTTAGAAATT-GATGTTA-AAATTG-TGCAATT
1 TGCAATTTAGTCCCT-GATTCA-AAATTCGAT-TTACAAATTGATGCAATT
578 GGATACTTGA
Statistics
Matches: 153, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
123 136 0.89
124 10 0.07
125 7 0.05
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (123 bp):
TGCAATTTAGTCCCTGATTCAAAATTCGATTTACAAATTGATGCAATTTAGTCCCTGATTTAAGA
TTCTAATTACTATTTGATGCAATTTAGTCACTGATTTAAGATTCTAATTACTATTTGA
Found at i:5620 original size:22 final size:22
Alignment explanation
Indices: 5592--5634 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5582 TTTCCCGCAA
* *
5592 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCAGGGCAGGACTTGTC
5614 CAAGTCCAGGGCAGGACTTGT
1 CAAGTCCAGGGCAGGACTTGT
5635 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (22 bp):
CAAGTCCAGGGCAGGACTTGTC
Found at i:14577 original size:10 final size:11
Alignment explanation
Indices: 14557--14581 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14547 AAACCAAAGG
14557 AAAGAAAAAAA
1 AAAGAAAAAAA
14568 AAAGAAAAAAA
1 AAAGAAAAAAA
14579 AAA
1 AAA
14582 AAGGAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:16476 original size:15 final size:15
Alignment explanation
Indices: 16456--16486 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16446 TTACCCATGT
16456 TATAATATATATATA
1 TATAATATATATATA
16471 TATAATATATATATA
1 TATAATATATATATA
16486 T
1 T
16487 TTAGTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATATATATATA
Found at i:16478 original size:13 final size:13
Alignment explanation
Indices: 16462--16486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16452 ATGTTATAAT
16462 ATATATATATATA
1 ATATATATATATA
16475 ATATATATATAT
1 ATATATATATAT
16487 TTAGTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:19333 original size:18 final size:16
Alignment explanation
Indices: 19294--19351 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 16
19284 CAGATCTGTC
19294 CAGTTTTTATTTGAGT
1 CAGTTTTTATTTGAGT
**
19310 TTGTTTTTGAGTTTGAGT
1 CAGTTTTT-A-TTTGAGT
*
19328 CAGTTTGTTTTTTCGAGT
1 CAGTTT-TTATTT-GAGT
19346 CAGTTT
1 CAGTTT
19352 CGAGTCTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 21 0.64
19 2 0.06
ACGTcount: A:0.14, C:0.07, G:0.22, T:0.57
Consensus pattern (16 bp):
CAGTTTTTATTTGAGT
Found at i:22348 original size:2 final size:2
Alignment explanation
Indices: 22341--22366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22331 GGAAATGTGA
22341 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
22367 TAATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23552 original size:18 final size:18
Alignment explanation
Indices: 23529--23567 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
23519 AAATAATTAA
23529 ATAAAAATAATAAATCGC
1 ATAAAAATAATAAATCGC
23547 ATAAAAATAATAAATCGC
1 ATAAAAATAATAAATCGC
23565 ATA
1 ATA
23568 TTAATCTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAAAAATAATAAATCGC
Found at i:24320 original size:273 final size:274
Alignment explanation
Indices: 23810--24356 Score: 974
Period size: 273 Copynumber: 2.0 Consensus size: 274
23800 CTAACTTGGC
* *
23810 TTTTCTTGCAACTCTTTTTGTCTTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
1 TTTTCTTGCAACTCCTTTTGTCTGTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
*
23875 GCATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGC
66 GCATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGC
23940 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
131 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
*
24005 GCAATTTCTTTGATTAACTCGGCATTTTAACCAAAATTATTAACTTTAAGAGAACAAAA-TTTTG
196 GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTTG
*
24069 TTGCAGATATCAGT
261 TTACAGATATCAGT
24083 TTTTCCTTGCAACTCCTTTT-TC-GTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATACCATC
1 TTTT-CTTGCAACTCCTTTTGTCTGTTTGGTTTTTCATATGCTTGTCTTGGCAAATCAT-CCATC
*
24146 GAGCATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGGCTCTTCTTGA
64 GAGCATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGA
* *
24211 GTTTTCTCTTTTCTACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATT
129 GCTTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATT
24276 TTGCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTT
194 TTGCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTT
*
24341 TGTTATAGATATCAGT
259 TGTTACAGATATCAGT
24357 GCTAGTTCCA
Statistics
Matches: 262, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
272 34 0.13
273 197 0.75
274 31 0.12
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (274 bp):
TTTTCTTGCAACTCCTTTTGTCTGTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGA
GCATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGC
TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTTG
TTACAGATATCAGT
Done.