Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012681.1 Corchorus olitorius cultivar O-4 contig12714, 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: 31609
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Found at i:9474 original size:49 final size:46
Alignment explanation
Indices: 9374--9514 Score: 174
Period size: 49 Copynumber: 2.9 Consensus size: 46
9364 AGCGTGCCAG
* * * *
9374 TCAATTTTGTCAAAAAATTGATAAAAAGTGTAGTGAAAATTAAAAGA
1 TCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGT-AAAAATAAAAGA
*
9421 TCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAGT
1 TCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTAAAAATAAAAGA
*
9470 TCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTAAAAAGTAAA
1 TCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTAAAAA-TAAA
9515 GGATTGCTTG
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
47 19 0.23
48 22 0.27
49 39 0.47
50 3 0.04
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (46 bp):
TCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTAAAAATAAAAGA
Found at i:23422 original size:15 final size:15
Alignment explanation
Indices: 23402--23438 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
23392 TTATTGTTCA
23402 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
23417 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
23432 CACCATT
1 CACCATT
23439 CACCCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (15 bp):
CACCATTGTTATTCG
Found at i:24361 original size:49 final size:46
Alignment explanation
Indices: 24256--24397 Score: 176
Period size: 49 Copynumber: 3.0 Consensus size: 46
24246 GAGCGTGCCA
* * *
24256 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAGTGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGT-AAAAATAAAAG
*
24303 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATGAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTAAAAATAAAAG
* *
24352 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTAAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTAAAAA-TAAA
24398 GGATTGCTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
47 20 0.24
48 21 0.25
49 39 0.47
50 3 0.04
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (46 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTAAAAATAAAAG
Found at i:26576 original size:17 final size:17
Alignment explanation
Indices: 26539--26577 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
26529 AACTGCAATG
* *
26539 AATTTTTGAATTTTCAG
1 AATTTTTGAATCTTCAA
*
26556 AATTTTTGAATCTTGAA
1 AATTTTTGAATCTTCAA
26573 AATTT
1 AATTT
26578 GAAAGTTGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (17 bp):
AATTTTTGAATCTTCAA
Found at i:28301 original size:29 final size:29
Alignment explanation
Indices: 28168--28358 Score: 140
Period size: 29 Copynumber: 6.5 Consensus size: 29
28158 AGGATCACCT
* *
28168 AGGGGCATTTTGGTCATTT-T-CAAAAATCC
1 AGGGGCATTTTGGTCATTTCTGC--ACATTC
* *
28197 AGGGGCACTTTGGTCATTT-TTCACATTC
1 AGGGGCATTTTGGTCATTTCTGCACATTC
** * * * *
28225 AATGGCATTATGGTTATTTTTTGCACATTT
1 AGGGGCATTTTGGTCA-TTTCTGCACATTC
* **
28255 AGGGGGTATTTTTATCATTTCTGCACATTC
1 A-GGGGCATTTTGGTCATTTCTGCACATTC
28285 AGGGGCATTTTGGTCATTTC--CACATATC
1 AGGGGCATTTTGGTCATTTCTGCACAT-TC
**
28313 TAGGGGCATTTTGGTCATTTCTGCATGTTC
1 -AGGGGCATTTTGGTCATTTCTGCACATTC
*
28343 AGGGGGTATTTTGGTC
1 A-GGGGCATTTTGGTC
28359 TTTTTTGCGC
Statistics
Matches: 128, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
27 5 0.04
28 17 0.13
29 59 0.46
30 36 0.28
31 11 0.09
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTCTGCACATTC
Found at i:30497 original size:11 final size:11
Alignment explanation
Indices: 30481--30505 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30471 AGATAATTTC
30481 TTTCTTCTAGT
1 TTTCTTCTAGT
30492 TTTCTTCTAGT
1 TTTCTTCTAGT
30503 TTT
1 TTT
30506 TAGGCAAAGG
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:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTCTTCTAGT
Found at i:31295 original size:15 final size:15
Alignment explanation
Indices: 31265--31321 Score: 105
Period size: 15 Copynumber: 3.7 Consensus size: 15
31255 TTACTTTGCT
31265 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
31281 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
31296 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
31311 TTGTTTTCTGT
1 TTGTTTTCTGT
31322 CAATCTCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 32 0.78
16 9 0.22
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.