Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016342.1 Corchorus olitorius cultivar O-4 contig16375, 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: 12718
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:855 original size:10 final size:10
Alignment explanation
Indices: 830--858 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
820 CATGTAACCA
830 TCACGGTTTT
1 TCACGGTTTT
840 TC-CGGTTTT
1 TCACGGTTTT
849 TCACGGTTTT
1 TCACGGTTTT
859 GCATGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.07, C:0.21, G:0.21, T:0.52
Consensus pattern (10 bp):
TCACGGTTTT
Found at i:1655 original size:239 final size:240
Alignment explanation
Indices: 1207--1674 Score: 595
Period size: 240 Copynumber: 2.0 Consensus size: 240
1197 TAATGGCTCC
* * *
1207 TTGAAATATCTATAATCATATAACCAAATCTCAGCCACATTGGATTTAATGATTTGTTTTTACGA
1 TTGAAATATCTATAATCATATAACCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACGA
* * ** *
1272 GATTTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATAGAAAAACGATATTAGA
66 GATTCTGAATCTTGTTTCGATTGAATTAGAAATAAATTCAAAAAAAATAGAAAAAAGATATTAGA
* * * ** * * * * *
1337 AGCGTGAAAAACCCTTCAATTTTTTTGTCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
131 AGCGTGAAAAACCCTTCAATCTTTCTGGCACTCAATTATATATTTTTTATAAGAATTGTGCCAAA
*
1402 AAATTGAGG-AAAAAATTTTTAGGTCAGCTTTTACAAAATTTTAG
196 AAATTGAGGAAAAAAATTTTCAGGTCAGCTTTTACAAAATTTTAG
* * *
1446 TTGAAATATCTATATTTATCA-AAGCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACG
1 TTGAAATATCTATAATCAT-ATAACCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACG
* * *
1510 AGCA-TCTGAATCTTGTTTCGATTGAATTAGTAATTAATTCAAAAAAAAATGGAAAAAAGATATT
65 AG-ATTCTGAATCTTGTTTCGATTGAATTAGAAATAAATTC-AAAAAAAATAGAAAAAAGATATT
* * *
1574 AGAAGCTTGAAAAACCCTTTAATCTTTCTGGCACTCAATTATATATTTTTTATAAGAATTGTTTC
128 AGAAGCGTGAAAAACCCTTCAATCTTTCTGGCACTCAATTATATATTTTTTATAAGAATTG-TGC
* *
1639 CAAAAAA-TGA-GAAAAAAATTTTCGGGTCAGTTTTTA
192 CAAAAAATTGAGGAAAAAAATTTTCAGGTCAGCTTTTA
1675 GCCGAAAATC
Statistics
Matches: 194, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
239 91 0.47
240 95 0.49
241 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (240 bp):
TTGAAATATCTATAATCATATAACCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACGA
GATTCTGAATCTTGTTTCGATTGAATTAGAAATAAATTCAAAAAAAATAGAAAAAAGATATTAGA
AGCGTGAAAAACCCTTCAATCTTTCTGGCACTCAATTATATATTTTTTATAAGAATTGTGCCAAA
AAATTGAGGAAAAAAATTTTCAGGTCAGCTTTTACAAAATTTTAG
Found at i:2177 original size:331 final size:332
Alignment explanation
Indices: 1446--2932 Score: 1370
Period size: 333 Copynumber: 4.4 Consensus size: 332
1436 AAAATTTTAG
* * * * *
1446 TTGAAATATCTATATTTATCAAAGCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACGA
1 TTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGA
* * * ** *
1511 GCATCTGAATCTTGTTTCGATTGAATTAGTAATTAATTCAAAAAAAAATGGAAAAAAGATATTAG
66 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAG
* * ** * * * **
1576 AAGCTTGAAAAACCCTTTAATCTTTCTGGCACTCAATTATATA-TTTTTT-ATAAGAATTGTTTC
131 AAGCGTGAAAAACCCTTCAATCTTTCTGGCGTTGAATTATATATTTTTTTCA-AAGTATT-ATGG
* *
1639 CAAAAAA-TGAGAAAAAAATTTTCGGGTCAG----T------TTTTAGCCGAAAATCGTGTACAA
194 CAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCG-AAATCGTATACAA
* * * * * * *
1693 AACATCACTGTTTTTGGGCTAAAAACGCGTTTCGGGGTCTCGACTCAGTTTTCCATGGTTTTTGG
258 ACCATCACGGTTTTT-GGCTAAAAACGCGTTT-GGAGTCTCGGCTCAGATTTGCATGATTTTTGG
1758 CATAAAGA-TGCC
321 CATAAAGACT-CC
* ** * * * *
1770 TTGAAATATCTATATGCATTTAACCAAATCTCGGGCACATTGCATTTAAGGATTTGTTTTTACGA
1 TTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGA
* * *
1835 GCATCTGAATCTTGTTTAGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAAGGAAATTAG
66 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAG
* * *
1900 AAGCGTGAAAAACCCTTCAAT-TTCTCCGGTGTTGAAATATATATTTTTTTCAAAGTATCT-T-G
131 AAGCGTGAAAAACCCTTCAATCTT-TCTGGCGTTGAATTATATATTTTTTTCAAAGTAT-TATGG
* *
1962 CAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTATACAAA
194 CAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTATACAAA
* * * * * *
2027 GCATCACGGTTTTTGGCTAAAAATGCGTTCTGGAGCCCCGGCTCA-ATTTGCTTAATTTTTGGCA
259 CCATCACGGTTTTTGGCTAAAAACGCGTT-TGGAGTCTCGGCTCAGATTTGCATGATTTTTGGCA
2091 TAAAGACTCC
323 TAAAGACTCC
*
2101 TTGAAATATCTATATTCATCAAACCAAATCTCAGGCACATTGGATTTAAAGATTTGTTTTTACGA
1 TTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGA
* * * * *
2166 GCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGGAAAAAATGG-AAAACAATATTAG
66 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAG
* * * * * * *
2230 AAGCGTG-AAAATCCTGTTAGTCTTTTTGGCGTTGAGTTATATATTTTTTTCTAAGTATTGTGGC
131 AAGCGTGAAAAACCCT-TCAATCTTTCTGGCGTTGAATTATATATTTTTTTCAAAGTATTATGGC
* * * *
2294 AAAAAATTCA-GATAAAAATTTTCGGGTTAGTTTTTAGCCGAAATCGTGTGTA-CGCGAAGCCCT
195 AAAAAATTGAGGA-AAAAATTTTCGGGTCAGTTTTT-G-CAAAAT--T-T-TAGC-CGAA---AT
* ** ** * *
2357 CTGATGCTGAGTTGCTTTTTACCATCACAATTTTTGAGCTAAAAACGCGTTTCGAGGTCGCGGCT
249 C----G-T-A--TAC---AAACCATCACGGTTTTTG-GCTAAAAACGCGTTTGGA-GTCTCGGCT
* * *
2422 CAGTTTTGCATTATTTTTGGCAAAAAGACTCC
301 CAGATTTGCATGATTTTTGGCATAAAGACTCC
* * * * * *
2454 TTGAAATAACTATATTCTTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTATTTTTACGA
1 TTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGA
* * *
2519 GCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCTGAAAAAAATGGAAAAACGATATTGG
66 GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAG
* ** * * * * * * ** *
2584 AATCGTG-AAAATTCTTCAATTTTTTTGGTGTAGTATTATATA-TATTTTCTGACTATTATGGCA
131 AAGCGTGAAAAACCCTTCAATCTTTCTGGCGTTGAATTATATATTTTTTTCAAAGTATTATGGCA
* * * * *
2647 AAAAATTGAGGAAAAACTTTTCGGTTCAGTTTTTGCAAAATTTTAACCGAAATCGTGTACTAACC
196 AAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTATACAAACC
* * * * *
2712 ATCACGATTTTTTTGGCTAAAAACGCATTCCGAAGACTCGGCTCA-ATTTTGCATGATTTTTGGC
261 ATCACG--GTTTTTGGCTAAAAACGCGTT-TGGAGTCTCGGCTCAGA-TTTGCATGATTTTTGGC
*
2776 ACAAAGACT-C
322 ATAAAGACTCC
* *** * * * *
2786 TTAGAATTATCTATATTCATTGGACCAAATCTCAGACACATTGGATATAAAGATTTTTTTTTACA
1 TT-GAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACG
* *
2851 AGCATCTAAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTA
65 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTA
2916 GAAGCGTGAAAAACCCT
130 GAAGCGTGAAAAACCCT
2933 AAAACTGTTT
Statistics
Matches: 952, Mismatches: 156, Indels: 100
0.79 0.13 0.08
Matches are distributed among these distances:
323 9 0.01
324 165 0.17
325 11 0.01
326 2 0.00
328 1 0.00
329 8 0.01
330 51 0.05
331 160 0.17
332 38 0.04
333 194 0.20
334 21 0.02
335 3 0.00
336 1 0.00
337 6 0.01
338 1 0.00
339 1 0.00
340 2 0.00
343 2 0.00
344 1 0.00
345 1 0.00
346 7 0.01
347 2 0.00
348 3 0.00
350 5 0.01
351 17 0.02
352 66 0.07
353 150 0.16
354 24 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (332 bp):
TTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGA
GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAG
AAGCGTGAAAAACCCTTCAATCTTTCTGGCGTTGAATTATATATTTTTTTCAAAGTATTATGGCA
AAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTATACAAACC
ATCACGGTTTTTGGCTAAAAACGCGTTTGGAGTCTCGGCTCAGATTTGCATGATTTTTGGCATAA
AGACTCC
Found at i:3794 original size:321 final size:320
Alignment explanation
Indices: 3035--4164 Score: 861
Period size: 311 Copynumber: 3.5 Consensus size: 320
3025 CTCAATTCGC
* ** * * *
3035 ATGATTTTTGACGTAAAGACTGCTTGAAATATCTATATTCAT-TGAACCAAATCTCAGCTACATT
1 ATGATTTTTGGCAAAAAGACTCCTTGAAATAACTATATTCATCT-AACCAAATCTCAGCCACATT
* * * * * * * *
3099 GGATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG
65 GGATTTAAGGATTTGTTTTTACAAACATCTAAATCTGGTTTCGATTTAATTAAAAATAAATTC--
* * * ** * * ** *
3164 AAA-AAAATGGTAAAACGATATTAGAAGCACGAAAAACTCTTCAATCTTTTT-GGCGTTGAATTA
128 AAACAAAATGGAAAAACAATATTAGAAACGTGAAAAACCCGTCAAT-TTTTTCGGAATTAAATTA
* * * * * * *
3227 TATATTTTTTTGTGAGTATTGT-GG-CAAAAATTGAGAAAAAACA-TTTCGGGTAAGTTTTTGCA
192 TATA-TATTTTATGAGTATTATGGGAAAAAAATTCAGAAAAAA-ATTTTCAGGTCA------GC-
* * * * *
3289 AAATTTTAGCCAAAATCGTATACTAACTTTCACGGTTTTTGGCTAAAAACGCG-TTCTAGAGCCC
248 ---TTTTAGCCGAAATCGTGTACTAAC-ATCACAGTTTTTGGCTAAAAACGCGTTTC-AG-GGCC
* *
3353 CGGCTCA-ATTTGC
307 CGGCTCAGTTTTGA
* * * *
3366 TTGATTTTTGGCGTAAAA-ACTCCTTGAAA-AATCTATATTCATCAAACCAAATCTCAACCACAT
1 ATGATTTTTGGC-AAAAAGACTCCTTGAAATAA-CTATATTCATCTAACCAAATCTCAGCCACAT
* * * * * ** ** *
3429 TGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTCAAATTGATTCG
64 TGGATTTAAGGATTTGTTTTTACAAACATCTAAATCTGGTTTCGATTTAATTAAAAATAAATTCA
* * ** * *
3494 GA-AAAATGGAAAATCAATATTAGAAACGTGAAAGGCCCGTCAGTCTTTTT-GGAATTGAATTAT
129 AACAAAATGGAAAAACAATATTAGAAACGTGAAAAACCCGTCAAT-TTTTTCGGAATTAAATTAT
* * * * * *
3557 TTATTTTTTAT-AGGTATTATGGTAAAAAAGTTCATAAAAAAATTTTC-GAGTTAGC-TTTAGCC
193 ATATATTTTATGA-GTATTATGGGAAAAAAATTCAGAAAAAAATTTTCAG-GTCAGCTTTTAGCC
*
3619 GAAATCGTGTACTAACCATCACAGTTTTTGGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTT
256 GAAATCGTGTACTAA-CATCACAGTTTTT-GGCTAAAAACGCGTTTCAGGGCC-CGGCTCAGTTT
3684 TGA
318 TGA
* * *
3687 ATGATTTTTGGCAAAAAGACTTCTTGAAATAACTATATCCATCTAACCAAATTTCAGCCACATTG
1 ATGATTTTTGGCAAAAAGACTCCTTGAAATAACTATATTCATCTAACCAAATCTCAGCCACATTG
* **
3752 GGTTTAAGGATTTGTTTTTTTAAACATCTAAATCTGGTTTCGATTTAATTAAAAATAAATTCAAA
66 GATTTAAGGATTTGTTTTTACAAACATCTAAATCTGGTTTCGATTTAATTAAAAATAAATTCAAA
* * ** **
3817 CAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTTCAATTTTTTCGGTGTTAAATTATATA
131 CAAAATGGAAAAACAATATTAGAAACGTGAAAAACCCGTCAATTTTTTCGGAATTAAATTATATA
* * * * *
3882 TATTTTCTGAGTATTGTGGGAAAAAAATTGAGAAAAAAGTTTTCAGGTCAGCTTTTAGACGAAAT
196 TATTTTATGAGTATTATGGGAAAAAAATTCAGAAAAAAATTTTCAGGTCAGCTTTTAGCCGAAAT
* * * *
3947 CGTG---T---A-C-GA-TTTTTGGCTAAAAATGCGTTTCAGGGCCCGACTCAGTTTTGT
261 CGTGTACTAACATCACAGTTTTTGGCTAAAAACGCGTTTCAGGGCCCGGCTCAGTTTTGA
* * * * *
3998 ATGGTTTTAGGCATAAAGACACCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG
1 ATGATTTTTGGCAAAAAGACTCCTTGAAATAACTATATTCATCTAACCAAATCTCAGCCACATTG
* * ** * * ** *
4063 TATTTAAGGATTAT-TTTTTACGAGTATCTGAATTTTTTTTCGATTTAATTAGAAATAAATTCGT
66 GATTTAAGGATT-TGTTTTTACAAACATCTAAATCTGGTTTCGATTTAATTAAAAATAAATTC--
* * * **
4127 AAAAAAAATTGAAAAAAATATATTAGAATTGTGAAAAA
128 AAACAAAATGGAAAAACA-ATATTAGAAACGTGAAAAA
4165 TCCTCCAAAT
Statistics
Matches: 654, Mismatches: 121, Indels: 65
0.78 0.14 0.08
Matches are distributed among these distances:
311 117 0.18
312 22 0.03
313 19 0.03
314 18 0.03
315 1 0.00
316 1 0.00
319 33 0.05
320 27 0.04
321 113 0.17
322 87 0.13
323 17 0.03
324 2 0.00
327 1 0.00
328 13 0.02
329 54 0.08
330 21 0.03
331 105 0.16
332 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (320 bp):
ATGATTTTTGGCAAAAAGACTCCTTGAAATAACTATATTCATCTAACCAAATCTCAGCCACATTG
GATTTAAGGATTTGTTTTTACAAACATCTAAATCTGGTTTCGATTTAATTAAAAATAAATTCAAA
CAAAATGGAAAAACAATATTAGAAACGTGAAAAACCCGTCAATTTTTTCGGAATTAAATTATATA
TATTTTATGAGTATTATGGGAAAAAAATTCAGAAAAAAATTTTCAGGTCAGCTTTTAGCCGAAAT
CGTGTACTAACATCACAGTTTTTGGCTAAAAACGCGTTTCAGGGCCCGGCTCAGTTTTGA
Found at i:10556 original size:16 final size:18
Alignment explanation
Indices: 10537--10577 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
10527 TATACTTTCA
10537 TTTTTTATAAT-TA-ATG
1 TTTTTTATAATATATATG
*
10553 TTTTTTATAATATATATT
1 TTTTTTATAATATATATG
10571 TTTTTTA
1 TTTTTTA
10578 AACTATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
18 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTTATAATATATATG
Found at i:11492 original size:13 final size:14
Alignment explanation
Indices: 11475--11507 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
11465 TCATATACAG
11475 AATCTTCAATTATT
1 AATCTTCAATTATT
11489 -ATCTTCAATTATT
1 AATCTTCAATTATT
11502 AATCTT
1 AATCTT
11508 TTCATAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (14 bp):
AATCTTCAATTATT
Found at i:11995 original size:15 final size:15
Alignment explanation
Indices: 11975--12006 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11965 GTCACCCTTC
*
11975 AGGACCCGGATGTAT
1 AGGACCCGCATGTAT
11990 AGGACCCGCATGTAT
1 AGGACCCGCATGTAT
12005 AG
1 AG
12007 TCTGCTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (15 bp):
AGGACCCGCATGTAT
Done.