Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013336.1 Corchorus olitorius cultivar O-4 contig13369, 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: 31434
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:2281 original size:26 final size:26
Alignment explanation
Indices: 2199--2281 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 26
2189 AAAGTGCTAA
2199 AATAAGTCACAGATCAAGTACACATT
1 AATAAGTCACAGATCAAGTACACATT
** *
2225 AATTTG-CATCATAAGTC-A-TAACCACATT
1 AATAAGTCA-CA-GA-TCAAGT-A-CACATT
2253 AATAAGTCACAGATCAAGTACACATT
1 AATAAGTCACAGATCAAGTACACATT
2279 AAT
1 AAT
2282 TTGCATCATA
Statistics
Matches: 43, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
25 2 0.05
26 18 0.42
27 6 0.14
28 15 0.35
29 2 0.05
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.27
Consensus pattern (26 bp):
AATAAGTCACAGATCAAGTACACATT
Found at i:2281 original size:54 final size:54
Alignment explanation
Indices: 2199--2305 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
2189 AAAGTGCTAA
2199 AATAAGTCACAGATCAAGTACACATTAATTTGCATCATAAGTCATAACCACATT
1 AATAAGTCACAGATCAAGTACACATTAATTTGCATCATAAGTCATAACCACATT
2253 AATAAGTCACAGATCAAGTACACATTAATTTGCATCATAAGTCATAACCACAT
1 AATAAGTCACAGATCAAGTACACATTAATTTGCATCATAAGTCATAACCACAT
2306 AAGTACAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (54 bp):
AATAAGTCACAGATCAAGTACACATTAATTTGCATCATAAGTCATAACCACATT
Found at i:14539 original size:20 final size:20
Alignment explanation
Indices: 14514--14553 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14504 TAATCCTTTC
14514 CTTTGAGTAATTGATTAGGT
1 CTTTGAGTAATTGATTAGGT
14534 CTTTGAGTAATTGATTAGGT
1 CTTTGAGTAATTGATTAGGT
14554 GATATGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (20 bp):
CTTTGAGTAATTGATTAGGT
Found at i:14931 original size:880 final size:864
Alignment explanation
Indices: 13410--14996 Score: 2831
Period size: 880 Copynumber: 1.8 Consensus size: 864
13400 TACCCGTTTC
13410 TCTCCCTCTCCATCTCTCTCGCCTCTTTGATCTCCACTGTATCATCATTGCTTTTCTCTCCAAAA
1 TCTCCCTCTCCATCTCTCTCGCCTCTTTGATCTCCACTGTATCATCATTGCTTTTCTCTCCAAAA
13475 CAAAAACAAGGCAAAGAGTTCAAGGATTTGACTTTCTTTTATCTTCTCACATGTTATTTGTGGCT
66 CAAAAACAAGGCAAAGAGTTCAAGGATTTGACTTTCTTTTATCTTCTCACATGTTATTTGTGGCT
*
13540 TCCTTGCCATAAATTAAACTCTTTGTTTTTTTTTTTTCGATCAATGCAGCCTTTTCTTTCCTATC
131 TCCTTGCCATAAATTAAACTCTTTGTTTTTTTTTTTTCGA-CAATGCAGCCTTTTCTTCCCTATC
13605 TAATTTGTTGTATCCTTTGTTAAGCCATTATAATAAAAGTAATCCTTTCCTTTGAGTAATTGATT
195 TAATTTGTTGTATCCTTTGTTAAGCCATTATAATAAAAGTAATCCTTTCCTTTGAGTAATTGATT
13670 AGGTGATATGAATTTCAACATTTAATTGCTTGATTTGTTAATTTTCATCGTCATTGTTTGTGATA
260 AGGTGATATGAATTTCAACATTTAATTGCTTGATTTGTTAATTTTCATCGTCATTGTTTGTGATA
* *
13735 TACGTATGAACAATAAATACAAAGAGGGGATGAAAATGAAATCAATTAAAGCTTCATATTTGGAA
325 TACGTATGAACAATAAATACAAAGAGGGGATGAAAACGAAATCAATTAAAACTTCATATTTGGAA
13800 ATTGATATAATCAAAAACAAAATCAAAGAAAGAGCTTAATCAACGATGGCATAAGAAATAACAAC
390 ATTGATATAATCAAAAACAAAATCAAAGAAAGAGCTTAATCAACGATGGCATAAGAAATAACAAC
*
13865 GAGAGGGTGAGGACTGAGGAAGACGACGATTTATAGAAAATAAGTTAAGCAATTTTTTCCCAAGA
455 GAGAGGGTGAGGACTGAGGAAGACGACGATTTATAGAAAATAAGTTAAGCAATTTTTCCCCAAGA
13930 CACGGTAATTCTAATTACATTATTATTATTAATAAGTAATAACTGAAATCATAATTTATATTCAA
520 CACGGTAATTCTAATTACATTATTATTATTAATAAGTAATAACTGAAATCATAATTTATATTCAA
13995 TAATTATTATTAAGGGCCTTGACAATTTTAATTTTTTATTTTAGTAAGGCGGCAGCTTGTGGATG
585 TAATTATTATTAAGGGCCTTGACAATTTTAATTTTTTATTTTAGTAAGGCGGCAGCTTGTGGATG
*
14060 ACTGATAGTGTATGGAAGTTATACACTGTCAGTGCATCAAATATAAACTC-TATATTTGATGCAC
650 ACTGACAGTGTATGGAAGTTATACACTGTCAGTGCATCAAATATAAACTCATATATTTGATGCAC
14124 TGACAGTATATAGCTTCCATACACTGTCAGTCATCCACAAGCTGCCACCTCATAAAAAATAAAAT
715 TGACAGTATATAGCTTCCATACACTGTCAGTCATCCACAAGCTGCCACCTCATAAAAAATAAAAT
14189 GAAAATTATTAAGGTCCCTATTGATAAATATTAACAAATGATAATTTTAATTAATTAGAAATGAT
780 GAAAATTATTAAGGTCCCTATTGATAAATATTAACAAATGATAATTTTAATTAATTAGAAATGAT
14254 AGGTAATTAAACTGAAACCT
845 AGGTAATTAAACTGAAACCT
14274 TCTCCCTCTCCATCTCTCTCGCCTCTTTGATCTCCACTGTATCATCATTGCTTTTCTCTCCAAAA
1 TCTCCCTCTCCATCTCTCTCGCCTCTTTGATCTCCACTGTATCATCATTGCTTTTCTCTCCAAAA
14339 CAAAAACAAGGCAAAGAGTTCAAGGATTTGACTTTCTTTTATCTTCTCACATGTTATTTGTGGCT
66 CAAAAACAAGGCAAAGAGTTCAAGGATTTGACTTTCTTTTATCTTCTCACATGTTATTTGTGGCT
*
14404 TCCTTGCCATAAATTAAACTCTTTG-TTTTTTTTTTTC-A-GATGCAGCCTTTTCTTCCCTATCT
131 TCCTTGCCATAAATTAAACTCTTTGTTTTTTTTTTTTCGACAATGCAGCCTTTTCTTCCCTATCT
14466 AATTTGTTGTATCCTTTGTTAAGCCATTATAATAAAAGTAATCCTTTCCTTTGAGTAATTGATTA
196 AATTTGTTGTATCCTTTGTTAAGCCATTATAATAAAAGTAATCCTTT-C----------------
14531 GGTCTTTGAGTAATTGATTAGGTGATATGAATTTCAACATTTAATTGCTTGATTTGTTAATTTTC
244 ---CTTTGAGTAATTGATTAGGTGATATGAATTTCAACATTTAATTGCTTGATTTGTTAATTTTC
*
14596 ATCTTCATTGTTTGTGATATACGTATGAACAATAAATACAAAGAGGGGATGAAAACGAAATCAAT
306 ATCGTCATTGTTTGTGATATACGTATGAACAATAAATACAAAGAGGGGATGAAAACGAAATCAAT
14661 TAAAACTTCATATTTGGAAATTGATATAATCAAAAACAAAATCAAAGAAAGAGCTTAATCAACGA
371 TAAAACTTCATATTTGGAAATTGATATAATCAAAAACAAAATCAAAGAAAGAGCTTAATCAACGA
**
14726 TGGTGTAAGAAATAACAACGAGAGGGTGAGGACTGAGGAAGACGACGATTTATAGAAAATAAGTT
436 TGGCATAAGAAATAACAACGAGAGGGTGAGGACTGAGGAAGACGACGATTTATAGAAAATAAGTT
*
14791 AAGCGATTTTTCCCCAAGACACGGTAATTCTAATTACATTATTATTATTAATAAGTAATAACTGA
501 AAGCAATTTTTCCCCAAGACACGGTAATTCTAATTACATTATTATTATTAATAAGTAATAACTGA
*
14856 AATCATAATTTATATTCAATAATTATTATTAAGGGCCTTGACAATTTTAATTTTTTATTTTAGTG
566 AATCATAATTTATATTCAATAATTATTATTAAGGGCCTTGACAATTTTAATTTTTTATTTTAGTA
* * *
14921 AGGTGGCAGCTTGTGGATGATTGACAGTGTGTGGAAGTTATACACTGTCAGTGCATCAAATATAA
631 AGGCGGCAGCTTGTGGATGACTGACAGTGTATGGAAGTTATACACTGTCAGTGCATCAAATATAA
14986 ACTCATATATT
696 ACTCATATATT
14997 ATTTATGGTT
Statistics
Matches: 688, Mismatches: 14, Indels: 25
0.95 0.02 0.03
Matches are distributed among these distances:
860 69 0.10
861 1 0.00
862 1 0.00
863 12 0.02
864 155 0.23
880 444 0.65
881 6 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (864 bp):
TCTCCCTCTCCATCTCTCTCGCCTCTTTGATCTCCACTGTATCATCATTGCTTTTCTCTCCAAAA
CAAAAACAAGGCAAAGAGTTCAAGGATTTGACTTTCTTTTATCTTCTCACATGTTATTTGTGGCT
TCCTTGCCATAAATTAAACTCTTTGTTTTTTTTTTTTCGACAATGCAGCCTTTTCTTCCCTATCT
AATTTGTTGTATCCTTTGTTAAGCCATTATAATAAAAGTAATCCTTTCCTTTGAGTAATTGATTA
GGTGATATGAATTTCAACATTTAATTGCTTGATTTGTTAATTTTCATCGTCATTGTTTGTGATAT
ACGTATGAACAATAAATACAAAGAGGGGATGAAAACGAAATCAATTAAAACTTCATATTTGGAAA
TTGATATAATCAAAAACAAAATCAAAGAAAGAGCTTAATCAACGATGGCATAAGAAATAACAACG
AGAGGGTGAGGACTGAGGAAGACGACGATTTATAGAAAATAAGTTAAGCAATTTTTCCCCAAGAC
ACGGTAATTCTAATTACATTATTATTATTAATAAGTAATAACTGAAATCATAATTTATATTCAAT
AATTATTATTAAGGGCCTTGACAATTTTAATTTTTTATTTTAGTAAGGCGGCAGCTTGTGGATGA
CTGACAGTGTATGGAAGTTATACACTGTCAGTGCATCAAATATAAACTCATATATTTGATGCACT
GACAGTATATAGCTTCCATACACTGTCAGTCATCCACAAGCTGCCACCTCATAAAAAATAAAATG
AAAATTATTAAGGTCCCTATTGATAAATATTAACAAATGATAATTTTAATTAATTAGAAATGATA
GGTAATTAAACTGAAACCT
Found at i:15351 original size:21 final size:21
Alignment explanation
Indices: 15312--15352 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15302 TGGCAGAAGA
**
15312 AAAAAAAGTTAGCCCTTAGGG
1 AAAAAAAGTTAGAACTTAGGG
*
15333 AAAAAAAGTTAGAATTTAGG
1 AAAAAAAGTTAGAACTTAGG
15353 CCAGACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (21 bp):
AAAAAAAGTTAGAACTTAGGG
Found at i:19811 original size:43 final size:43
Alignment explanation
Indices: 19753--19884 Score: 255
Period size: 43 Copynumber: 3.1 Consensus size: 43
19743 AAAGGGTACT
*
19753 TTGCAAATTCAAGAGAGTAGGTTTTTCCTCACTTTGGAAATAC
1 TTGCAAATTCAAGAGAGTAGTTTTTTCCTCACTTTGGAAATAC
19796 TTGCAAATTCAAGAGAGTAGTTTTTTCCTCACTTTGGAAATAC
1 TTGCAAATTCAAGAGAGTAGTTTTTTCCTCACTTTGGAAATAC
19839 TTGCAAATTCAAGAGAGTAGTTTTTTCCTCACTTTGGAAATAC
1 TTGCAAATTCAAGAGAGTAGTTTTTTCCTCACTTTGGAAATAC
19882 TTG
1 TTG
19885 TGAGTTATTA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (43 bp):
TTGCAAATTCAAGAGAGTAGTTTTTTCCTCACTTTGGAAATAC
Done.