Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017887.1 Corchorus olitorius cultivar O-4 contig17920, 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: 14843
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:68 original size:2 final size:2
Alignment explanation
Indices: 61--98 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
51 ATCAATATCA
61 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
99 ATACAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86 original size:17 final size:17
Alignment explanation
Indices: 64--97 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54 AATATCAATA
64 TATATATATATATATAT
1 TATATATATATATATAT
81 TATATATATATATATAT
1 TATATATATATATATAT
98 AATACAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:1394 original size:27 final size:27
Alignment explanation
Indices: 1340--1396 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1330 CAGCAGCCAA
* * * *
1340 AATCCGTTGGTATAAAACGGTTGCACC
1 AATCCATTGGTATAAAACCGCTACACC
*
1367 AATCCATTGGTATAAAACCGCTATACC
1 AATCCATTGGTATAAAACCGCTACACC
1394 AAT
1 AAT
1397 GAAATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (27 bp):
AATCCATTGGTATAAAACCGCTACACC
Found at i:8774 original size:332 final size:328
Alignment explanation
Indices: 7657--9204 Score: 1385
Period size: 331 Copynumber: 4.7 Consensus size: 328
7647 TTTTACGAGC
* * * * * *
7657 AAATAAGAAATACGATATTAAAAGCGTGGAAAGCCCTCCAATGTTTTTGGCGTTCAA-T-TATAT
1 AAATAGGAAAAACGATATTAAAA-CGTGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT
* *** *
7720 ATTTTATGAGTATTTTAGCCAAAAATTGAGGAGAA-ATCTTTCAATTCAATTTTTACAAAATTTT
65 ATTTTATGAGTATTTTAGCCAAAAATTGAGGA-AATATATTTCGGGTCAATTTTTGCAAAATTTT
* * *
7784 TGCCGAAATCGTGTACTAACTAATCATCACGG-TTTTTGACTAAAAACGCATTCCGGAGACCCAC
129 AGCCGAAATCGTG---TAA-TAATCATCACGGTTTTTTG-CTAAAAA-GCGTTTCGG-GACCC-C
* ** * * * *
7848 -CTCAATTTTGCATGATTTTTGGCTTCTAGACTACTTGAAATATCTATATTAATCTAATAAAATC
186 GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATA
* ** * ***
7912 TCAGCCACATTGGATTTAAGGGTTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTTCT
251 TCAGCCACATTGCATTTAAGGAATTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGA
* *
7977 AATTAAATCGGAAA
316 AATTAATTC-AAAA
* ** * *
7991 AAATAGGAAAAACAATATTAAAAACGACAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATAT
1 AAATAGGAAAAACGATATT-AAAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT
* * * * * **
8056 TTTTTATGATTATTTTAGCCAAAATTTGAGGAAATATCTTTCGGCTCAATTTTTATAAAATTTTA
65 ATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTA
* * * * * *
8121 GCCGAAATCGTGT--TAACCATCACAGTTTTTGGCTAAAAAAGC-ATTCCGAAGCCCCGACTCAG
130 GCCGAAATCGTGTAATAATCATCACGGTTTTTTGCT-AAAAAGCGTTTCGGGA-CCCCG-CTCAG
* * * * * *
8183 TTTCGCATGATTTTTGGCGCCAAGACTCCTTGAGATATCCATATACATCTAATCAAATCTCAGCC
192 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATATCAGCC
* * * * *
8248 ACATTGGATTTAA-AAATTTGTTTTTATGAGCATCTAATATTCTTGTTTCGATTTAATTAGAATT
257 ACATTGCATTTAAGGAA-TTGTTTTTACGAGCATCTAA-A-TCTTATTTCGATTTAATTAGAAAT
* *
8312 TAATTTAGAA
319 TAATTCAAAA
* * * * * **
8322 AAATATGAAAAACGATATTAAAAACATGAAAAGTCCTCCAATCTGTTTGGCCATAAATTATATAT
1 AAATAGGAAAAACGATATT-AAAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT
* * * * * * *
8387 ATATTATGAGTATTTTATCCAAAAATTGATGAAACATTTTTCGGGTCATTTTTTGCAAAAGTTTA
65 ATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTA
* * *
8452 ACCAAAATCGTGTACTAATCATCACGGTTTTTTGCTAAAAATGCGTTTCGGGACCCCAGCTCAGT
130 GCCGAAATCGTGTAATAATCATCACGGTTTTTTGCTAAAAA-GCGTTTCGGGACCCC-GCTCAGT
* * * *
8517 TTTGCATGATTTTTGGCGCCGAGACTGCTTGAAATATCTATATTCATCTAAAAAAATATTAGCCA
193 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATATCAGCCA
* *
8582 CATTGCATTTAAGGAATTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTATT
258 CATTGCATTTAAGGAATTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAAT
8647 TCATAAA
323 TCA-AAA
* * * * * *
8654 AAATATGAAAAACGATATTAAAAGGTTGAAAAGGCCTTCAATCTTTTTAGCGTTGAATTATATTT
1 AAATAGGAAAAACGATATTAAAACG-TGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT
* * * * *
8719 TTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATATTTCGGGACAATTTTTGCAAAATTTTA
65 ATTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTA
* * * *** *
8784 GCCGAAATCGTGTAATAATCATCACGATTTTTGGCTAAAAA-CGTGTTCCGGTGTCCGGTACAGT
130 GCCGAAATCGTGTAATAATCATCACGGTTTTTTGCTAAAAAGCGT-TTCGGGACCCCGCT-CAGT
* * * *
8848 TTTGCATGATTTTTTGCGCCGATACTCCTTGAAATATCTATATTCATC---T---A-A-C--CTA
193 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATATCAGCCA
* ** *
8903 -A-T-C---TGAGCCATTGTTTTTA-GAAGCATCTGAAT-TATATTTCGATTTAATTA-AAATTA
258 CATTGCATTTAAGGAATTGTTTTTACG-AGCATCTAAATCT-TATTTCGATTTAATTAGAAATTA
8959 ATTC-AAA
321 ATTCAAAA
**
8966 AAATAGGAAAAATAATATTAGAAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT
1 AAATAGGAAAAACGATATTA-AAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATAT
** * * * * *** * *
9031 AGATTATGAGTATTGTGGTTC-AAAATTGAGGAAAAATATTTCAAATCCATTTTTGCAAAATATT
65 ATTTTATGAGTATTTTAG-CCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTT
* ** * ** * *
9095 AGCCAAAATCGTGTAATAATCATCACTCTTTTTTTTTGCTAAAAAGACGTTCCGAGTTCCCGGGT
129 AGCCGAAATCGTGTAATAATCATCA--C-GGTTTTTTGCTAAAAAG-CGTTTCG-GGACCCCGCT
*
9160 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGGAATATCTAT
189 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTAT
9205 TGTTTCGATT
Statistics
Matches: 1004, Mismatches: 178, Indels: 82
0.79 0.14 0.06
Matches are distributed among these distances:
312 130 0.13
313 4 0.00
314 12 0.01
315 51 0.05
316 43 0.04
317 9 0.01
318 1 0.00
319 1 0.00
320 1 0.00
321 2 0.00
324 1 0.00
325 1 0.00
328 2 0.00
329 6 0.01
330 109 0.11
331 217 0.22
332 170 0.17
333 116 0.12
334 50 0.05
335 7 0.01
336 71 0.07
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (328 bp):
AAATAGGAAAAACGATATTAAAACGTGAAAAGCCCTTCAATCTTTTTGGCGTTAAATTATATATA
TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAG
CCGAAATCGTGTAATAATCATCACGGTTTTTTGCTAAAAAGCGTTTCGGGACCCCGCTCAGTTTT
GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAAATATCAGCCACAT
TGCATTTAAGGAATTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCA
AAA
Found at i:9811 original size:338 final size:335
Alignment explanation
Indices: 9318--10508 Score: 1207
Period size: 337 Copynumber: 3.5 Consensus size: 335
9308 GAGTATCCAG
* * *
9318 AAATTGA-G-AAAATATCTTCTGGGTCAATTTTTGCAAAATTTTAGCAGAAATCGTGTAATAATC
1 AAATTGAGGAAAAATAT-TTC-GGGT-AATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAACC
* * * * *
9381 ACCATGGTTTTTGGCTAAAAACGCGTTTCAAGGCCCCAGGTCGGTTTTGCATGATTCTTTGCG--
63 ATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATT-TTTG-GTA
* * **
9444 CCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTTAGCTGCATTGCATTTAAGGATTT
126 CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGGATTT
* * * *
9509 AATTTTACGAGTCTCTGAATTTTGTTTCAATTTAATTAGACATTAATTCAGAAAAAATATGAAAA
191 ATTTTTACGAGTCTCTAAATCTTGTTTCGATTTAATTAGACATTAATT-AGAAAAAATATGAAAA
* *
9574 A-TATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATATATATTTC
255 ACTATATTAAAAGCGTGAAAAGTCTTCCAATATTTTTGGCGTT-AATTATATATATATATATTTA
*
9638 ATGAGTGTTTTAGCCAA
319 ATGAGTATTTTAGCCAA
*
9655 AAATTGAGGAAAAATTTTTCGGGTAATTTTTTGCAAAATTTTAGCC-AGAATCGTGTAGTAACCA
1 AAATTGAGGAAAAATATTTCGGGTAA-TTTTTGCAAAATTTTAGCCGA-AATCGTGTAGTAACCA
* * * * *
9719 TCACGGTTTTTTTGCTAAAAATGCGTTTCGCGGCCCCAGCTCTGTTTTGCATGATTTTTGGTATC
64 TCACGG-TTTTTGGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGGTACC
* * * * * * *
9784 GAGACTCCTTGAAATTTCTATATTCATCTAATCAAATCTCAACCACAATACATTTAAGAATTTAT
128 AAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGGATTTAT
* * * *
9849 TTTTAAGAG-CATCTAAATCTTATTTCGATTTAATTAGAAATTAATTA-AGAAAATATGAAAAAC
193 TTTTACGAGTC-TCTAAATCTTGTTTCGATTTAATTAGACATTAATTAGAAAAAATATGAAAAAC
* * * * * *
9912 TATATTAAAAGTGTGAATAGTCTTCCAATCTTTTTAGAGTTGAATTATATATATATATATTTTAT
257 TATATTAAAAGCGTGAAAAGTCTTCCAATATTTTTGGCGTT-AATTATATATATATATATTTAAT
*
9977 GAGTATTTTAGAC-A
321 GAGTATTTTAGCCAA
* * * * * * * *
9991 AAAGTGAGGAAAAATATTTCTGGTTAGTTATTGCAATATATTAGTCGAAATCGTGTACGTTAGTC
1 AAATTGAGGAAAAATATTTC-GGGTAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-G-TA-AC
* * *
10056 GAAATCACGATTTTTGGCTAAAAACGCGTTTCGAGGCCCCAGGTCAGTTTTGCATGATTTTT--T
62 --CATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGGT
** * * * * *
10119 ACGCTAAGACTATTTAAAATATATCTATATTTATCTAACCAAATCTTAGCCAAATTGTATTTAAG
125 AC-C-AAGACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAG
* * * * *
10184 GATTTATTTTTACGAGTATCTAAATCTTGTTTTGATTTAATCA-TCAATTAATTTGGAAATAAAA
186 GATTTATTTTTACGAGTCTCTAAATCTTGTTTCGATTTAATTAGAC-ATTAA-TTAG-AA-AAAA
* * * * * *
10248 TAGGAAAAACGATATTATAAGCGTGAAAAAGGT-TTTCAATTTTTTTGGCGTTGA--AT-TATAT
247 TATGAAAAACTATATTAAAAGCGTG-AAAA-GTCTTCCAATATTTTTGGCGTTAATTATATATAT
* * * *
10309 AT-T-TTTAATGATTATTTTCGCTAG
310 ATATATTTAATGAGTATTTTAGCCAA
* *
10333 AAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGCAGTAACCAT
1 AAATTGAGGAAAAATATTTCGGGT-AATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAACCAT
* * * *
10398 CACGGTTTTCGGCTAAAAACGCGTTCCGAGGCCCGA-CTCAGTTTTGCATGATTTTCGGTACCAA
65 CACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGGTACCAA
* * *
10462 GACTCCTTGAAATATCTATTTTCATCTTA-CAAAATCTCAGCCACATT
130 GACTCCTTGAAATATCTATATTCATCTAATC-AAATCTTAGCCACATT
10509 ATTTGAATCT
Statistics
Matches: 698, Mismatches: 123, Indels: 69
0.78 0.14 0.08
Matches are distributed among these distances:
333 1 0.00
334 29 0.04
335 2 0.00
336 87 0.12
337 162 0.23
338 146 0.21
339 9 0.01
340 56 0.08
341 26 0.04
342 122 0.17
343 9 0.01
344 2 0.00
345 1 0.00
346 26 0.04
347 18 0.03
348 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (335 bp):
AAATTGAGGAAAAATATTTCGGGTAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAACCATC
ACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTTTTGGTACCAAG
ACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGGATTTATTTT
TACGAGTCTCTAAATCTTGTTTCGATTTAATTAGACATTAATTAGAAAAAATATGAAAAACTATA
TTAAAAGCGTGAAAAGTCTTCCAATATTTTTGGCGTTAATTATATATATATATATTTAATGAGTA
TTTTAGCCAA
Found at i:12581 original size:49 final size:48
Alignment explanation
Indices: 12480--12621 Score: 173
Period size: 49 Copynumber: 3.0 Consensus size: 48
12470 GAGCGTGCTA
* * * *
12480 ATCAATTTTGTCAAAAAATTGATAGAAAGTGC-AGTGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAAAG
12527 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTGAAAAATAAAAG
* * *
12576 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAA
12622 GGATTGCTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
47 15 0.18
48 25 0.30
49 40 0.48
50 3 0.04
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (48 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAAAG
Found at i:13917 original size:9 final size:9
Alignment explanation
Indices: 13901--13934 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
13891 TTCATTTAAA
13901 TTCC-TAAT
1 TTCCATAAT
13909 TTCCATAAT
1 TTCCATAAT
*
13918 TTCCCTAAT
1 TTCCATAAT
13927 TTCCATAA
1 TTCCATAA
13935 GTAATTTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
TTCCATAAT
Found at i:14663 original size:23 final size:22
Alignment explanation
Indices: 14637--14682 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
14627 ACCCAATGAA
14637 ATTTTTGT-TAACCACCCTTATGT
1 ATTTTT-TATAACCACCCTT-TGT
*
14660 ATTTTTTATAACCATCCTTTGT
1 ATTTTTTATAACCACCCTTTGT
14682 A
1 A
14683 ATCTTGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTTTTTATAACCACCCTTTGT
Done.