Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021108.1 Corchorus olitorius cultivar O-4 contig21141, 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: 22137
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:1500 original size:29 final size:29
Alignment explanation
Indices: 1467--1533 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1457 TTTCATGAAT
*
1467 ATAAATAATAATAGTATATATTATAATCG
1 ATAAATAATAATAGTATATATTATAATCA
* * *
1496 ATAAATCATAATATTATATATTATCATCA
1 ATAAATAATAATAGTATATATTATAATCA
*
1525 AAAAATAAT
1 ATAAATAAT
1534 TATTAGAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (29 bp):
ATAAATAATAATAGTATATATTATAATCA
Found at i:2180 original size:22 final size:23
Alignment explanation
Indices: 2147--2191 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2137 AGTTAGCTGG
2147 ATTACAATTATAATGGATTATTA
1 ATTACAATTATAATGGATTATTA
*
2170 ATTAC-ATTATAGTGGATTATTA
1 ATTACAATTATAATGGATTATTA
2192 CTATATATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.44
Consensus pattern (23 bp):
ATTACAATTATAATGGATTATTA
Found at i:2286 original size:27 final size:26
Alignment explanation
Indices: 2251--2301 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2241 TCCATAATTA
*
2251 ATAAAAAAGTTGAATCATCTAAAAAAT
1 ATAAAAAAGTTAAATCA-CTAAAAAAT
*
2278 ATAAAAAAGTTAAATGACTAAAAA
1 ATAAAAAAGTTAAATCACTAAAAA
2302 GAATACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.24
Consensus pattern (26 bp):
ATAAAAAAGTTAAATCACTAAAAAAT
Found at i:2418 original size:13 final size:13
Alignment explanation
Indices: 2400--2427 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2390 TATAGTAGTA
2400 ATAGTAAGATAAG
1 ATAGTAAGATAAG
2413 ATAGTAAGATAAG
1 ATAGTAAGATAAG
2426 AT
1 AT
2428 GATTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (13 bp):
ATAGTAAGATAAG
Found at i:5936 original size:5 final size:5
Alignment explanation
Indices: 5926--5950 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5916 TATGATTTCT
5926 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
5951 AAGGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:11779 original size:330 final size:330
Alignment explanation
Indices: 10031--13835 Score: 3325
Period size: 331 Copynumber: 11.6 Consensus size: 330
10021 CCATGATGGT
* * *
10031 AAAAA-TGACCCAAAAGATTTTTCCTCAATTTTTGTCAAAAATACCCATAAAAAAATATATAATT
1 AAAAATTGACCGAAAA-ATTTTTCCTCAATTTTTGGCAAAAATACTCAT-AAAAAATATATAATT
* * * * *
10095 CAGTGCCAAAAAGATTGGAGGACTTGTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATT
64 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATT
* * * *
10160 AATTTCTAATTAAATCGAAATAAGATTCAGATGCAT-GTAAAAATAAATCTTTAATTCCAATGTG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCAATGTG
** * * * * *
10224 TTTGACATTTGATTAGATGAATAAAGATATTTTAAGGAGTCTCGGCACCAAAAATCATGCAAAAC
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * ** * * * ** *
10289 AAAGTCATGACCCTGGAACACGTTTTTAGCCAAAAACTATGATGGTTAGTACACGATTTCGGTTA
258 TAAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG-TAGTACACGATTTCGGCTA
10354 AAATTTTGC
322 AAATTTTGC
** * * * *
10363 AAAAATTGACACGAAGGATATTTCCTCAATTTTTTGCTAAAATACTCAT-AAAAATATATGATTT
1 AAAAATTGAC-CGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATAT-AATT
* * * * * * **
10427 GACAT--AAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAAT
64 CA-ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAAT
* * * *
10490 TAATTTCTAATTAAATCAAAATAAGATTTAGATGCTTGTAAAAACAAATCCTTAAAATCCAATGT
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGT
* * * * *
10555 GCCT-AGATTTGGTTATATGAATATAAATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAA
192 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
* * * * * * * *
10619 CTGAG-CAGGGTCCCGGAACAG-GTTTTTAGCCGAAATCTGTGATGATTAGTATACGATTTCGGC
257 CTAAGCCGGGGCCCCGGAAC-GCGTTTTTAGCCAAAAACCGTGATG-GTAGTACACGATTTCGGC
10682 TAAAATTTTGC
320 TAAAATTTTGC
* * * *
10693 AAAAA-TGAGCCGAAAGATTTTTCCTCAAATTCTAGCAAAAATACTCATAAAAAAATATATAATT
1 AAAAATTGA-CCGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCAT-AAAAAATATATAATT
* * * *** * * *
10757 CAACGCCAAAAAAATTTAAATTCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAA
64 CAATGCCAAAAAGATTGAAGGGC-TTTTCACGCTTTTAATATCGTTTTTCATA-TTT-TTTCTAA
* * * * * ** ** *
10822 ATTAATTGCTGATTAAATCGAAATAAGATT-AGATACTTGTAAAAGTAAATATTTAAATACAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * * * * *
10886 TGACCGAGATTTGGTTAGATGAATATAGATATATTTTATGGAGTCCTGGCGCCAAAAGTCTTGCA
191 TGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCA
* * ** * **** *
10951 AAACTTACCCGGGGCCTTGGAACGCGTTTTTAG-CAAAAA----AAAAAAAG-A-GCG--TTCGG
254 AAACTAAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTCGG
11007 CTAAAATTTTGC
319 CTAAAATTTTGC
* * ** * * * *
11019 AAAAAATGTTCCGAATTATTTTT-CT-AATTTTTAGCCACAATACTCACAAAAAATATATAATTC
1 AAAAATTG-ACCGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATTC
* * ** * *
11082 AATGCCGAAAAGATTGAAGGGCTTCTCACGCTTCCAATATCGTTTTCCCTATTTTTT-TCAAATT
65 AATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT-AAATT
* * * *
11146 AATTTCTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAA-AAATCATTAAATCCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
11210 CTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-TTTGCAACCAAAAGTCATGCAAAAC
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGC-GCCAAAAATCATGCAAAAC
* * * * *
11274 TGA-CCCGGGCCCTGGAACGCGATTTTAGCAAAAAAAAAACCGTGAT-G--GTACACGATTTCGG
258 TAAGCCGGGGCCCCGGAACGCGTTTTTAGC----CAAAAACCGTGATGGTAGTACACGATTTCGG
* *
11335 CTAAAATCTTAC
319 CTAAAATTTTGC
* * * * * *
11347 AAAAATTGACCCG----A-TTTTCTTCAATTTTTAGCCACAATACTCACAAAATATATATAATTC
1 AAAAATTGA-CCGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATTC
* * ** *
11407 AACTG-AAAAAAGATTGGAGAACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCAAAATT
65 AA-TGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATT
* *
11470 AATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
11535 CTGAGATTTGATTAGATGAATACATATATTTCAAGGAGTCTCGACGCCAAAAATCATGCCAAACT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * * ** * *
11600 AAGTCGGGGCCCCGAAACACATTTTTAGGAAAAAACCGTGATGGT-GTACATGATTTCGGCTACA
259 AAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTCGGCTAAA
*
11664 ATTTTAC
324 ATTTTGC
* * * *
11671 AAAAAAATGACCTGAAAAATTTTTCCTTAATTTTTGGCAAAAATACTCATGAAATATATATAATT
1 -AAAAATTGACC-GAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATT
* ** * * **
11736 TAATGCCAAAAAGATTGGAA-GATTTTTCACCCTTTTCATATCGTTTTTTCATA-TTTTTCTAGG
64 CAATGCCAAAAAGATT-GAAGGGCTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTTCTAAA
* * * *
11799 TTAATGTCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCTTTAAATGCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * *** *
11864 GCCTAAGATTTGATTAGATAAATAT-GAATATCTCAAGGAGTCTTAATGCAAAAAATCATGCAAA
192 GGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * * * **
11928 ACTAA-CTCGGGGCTCTGGAACGCATTTTTAGCCAAAAATCGTGATGATTATTACATGATTTCAA
256 ACTAAGC-CGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG-GTAGTACACGATTTCGG
11992 CTAAAATTTTGC
319 CTAAAATTTTGC
* * * * *
12004 AAAAATTGACCCAAAAGATATTCCCTCAATTTCTGGCTAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCGAAAA-ATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATTC
* * * * * ** * **
12069 AATGCCAAAAATATTGAAGGGTTTTTTACACTTCTAATAT--TTTTTTTTACTTTTTCCGAATTA
65 AATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTA
* * * * * **
12132 ATTTGTAATTAAATCGAAACAAGATTTATATGCTCATAAAAACAAATCCTTAAATCCAATATATC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
12197 TGAGATTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
195 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTA
* * **** * * * *
12262 A-CCGGGGGCCCCGGAACGCATTTTTAGCAAAAAAAAAAGATCGTTTTGGTACACGATTTTGCCT
260 AGCC-GGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G--GTAGTACACGATTTCGGCT
*
12326 AATATTTTGC
321 AAAATTTTGC
* * * * * *
12336 GAAAATTGACCCGAAATA-TTTTCCTGAATTTTTAGTC-ACAATACTCATAAAAAATGTATAATT
1 AAAAATTGA-CCGAAAAATTTTTCCTCAATTTTT-GGCAAAAATACTCATAAAAAATATATAATT
* * * *
12399 CAATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCCTATTTTTTCTGAATT
64 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATT
* * * *
12464 AATTTCTAATTAAATTGAAACATGATTCAAATGCTTGT---AA-AAA--C---AAT---A----G
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* ** *
12513 CTGGGATTTGGCTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * *
12578 GAA-CC-TGGCCCCGGAATGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTA
259 -AAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG-GTAGTACACGATTTCGGCTA
*
12641 AAGTTTTGC
322 AAATTTTGC
* * * * * * *
12650 AAAAATTGACCCG-AAAGTTATTTCC-GAAATTTTAGCCACAATACTCATAGAAAATATATAATT
1 AAAAATTGA-CCGAAAAATT-TTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATT
* * * * * *
12713 CAACGCCAAAAATATTGAAGGGGTTTTCACGATTTTAATATCATTTTTCATATTTTTTCTGAATT
64 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATT
* * ** * *
12778 AATATCTAAATAAATCGAAACAAGATTCAGATGCAAGTAAAAACAAATCCTTAAATGCAATGCGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *
12843 CTAACATTTTATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * * * *
12908 GAGTCGGGACCCCGAAACGCGTTTTTATG-CAAAAACCATGAT--TA-T--ACGATTTTGGCTAA
259 AAGCCGGGGCCCCGGAACGCGTTTTTA-GCCAAAAACCGTGATGGTAGTACACGATTTCGGCTAA
12967 AATTTTGC
323 AATTTTGC
* *** * * *
12975 GAAAGA-TGACACGTAATTTTTTTTCCTCAATTTTTGG-ATAAAATACTGATTAAATATATATAA
1 -AAAAATTGAC-CG-AAAAATTTTTCCTCAATTTTTGGCA-AAAATACTCATAAAAAATATATAA
* * * * * * * *
13038 TTTAACGCCAAAAATATTGGAGGACTTTTCACGC-TTTAATTTCGTTTTTCTTATTTTTTTCAAA
62 TTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTAA
* * * **
13102 ATTAATTTTTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATTTTTAAATCCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * ** *
13167 TGGCTGAGATTTGATTAGATGGATATGGATATTTCAAAGAGGGTTGGCGTCAAAAATCATGCAAA
191 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * *
13232 ACTAAGCCGGGGTCCCGGAACGC-TTTGTTAGCCAAAAGCTGTAATGGTTATTACACGATTTCGA
256 ACTAAGCCGGGGCCCCGGAACGCGTTT-TTAGCCAAAAACCGTGATGG-TAGTACACGATTTCGG
*
13296 CTAAAATTTTGT
319 CTAAAATTTTGC
* * * * * *
13308 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTAGCTAAAATAGTCATAAAAGATATATAATTC
1 AAAAATTGAC-CGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATTC
** * ** * *
13373 AACACCAAAAAGATTAAAATGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGATTT
65 AATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTAAATT
* * * * *
13438 AATTTCTAATTAAATCGAAATAATATTCAGATGCTCGTAAAAAAAAATCCTTAAATGCAATGCGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * ** * * *
13503 CTAACATTTTATTAGATGAATATAGGTATTTTAAGGAGTCTCAGCGCCAAAAATTATGCTAAATT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * * * *
13568 GAGCCGAGGCCCCGGAATGCGTTTTTTGTCAAAAACCGTGATGGTTATTTAGTACACGATTTCGA
259 AAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG-----TAGTACACGATTTCGG
*
13633 CTAAAATTGTGC
319 CTAAAATTTTGC
* * * * *
13645 AAAAATTGACACGAAAGACTTTTGCTCAATTTTTGGCTAAAATACTTAT-AAAAATATATAATTC
1 AAAAATTGAC-CGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATTC
* * * ** *
13709 AACGCCAAAAAGATTGAAGGGCTTTTCACTCTTTTAATATCATAATTCTTATTTTTTCTAAATTA
65 AATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTA
* *
13774 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATTCTTAAATCCAATGT
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
13836 TATTGAGATT
Statistics
Matches: 2829, Mismatches: 524, Indels: 237
0.79 0.15 0.07
Matches are distributed among these distances:
313 3 0.00
314 155 0.05
315 6 0.00
316 28 0.01
317 62 0.02
318 31 0.01
319 31 0.01
320 1 0.00
321 71 0.03
322 27 0.01
323 39 0.01
324 112 0.04
325 199 0.07
326 78 0.03
327 222 0.08
328 29 0.01
329 52 0.02
330 350 0.12
331 462 0.16
332 243 0.09
333 339 0.12
334 39 0.01
335 108 0.04
336 74 0.03
337 68 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (330 bp):
AAAAATTGACCGAAAAATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAAAATATATAATTCA
ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAA
GCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAAT
TTTGC
Done.