Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019093.1 Corchorus olitorius cultivar O-4 contig19126, 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: 18621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4011 original size:15 final size:16
Alignment explanation
Indices: 3991--4026 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3981 CGACTCTGGT
3991 CTTGTTGTGG-TGTTG
1 CTTGTTGTGGCTGTTG
4006 CTTGTTGTGGCTGTTG
1 CTTGTTGTGGCTGTTG
4022 -TTGTT
1 CTTGTT
4027 TGTTTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.00, C:0.08, G:0.36, T:0.56
Consensus pattern (16 bp):
CTTGTTGTGGCTGTTG
Found at i:6232 original size:24 final size:25
Alignment explanation
Indices: 6204--6251 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6194 AGAAACAATA
*
6204 AAAATAAATAAACAAGA-AAATAAT
1 AAAATAAAGAAACAAGATAAATAAT
* *
6228 AAAATTAAGCAACAAGATAAATAA
1 AAAATAAAGAAACAAGATAAATAA
6252 ATACTCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAACAAGATAAATAAT
Found at i:14652 original size:24 final size:24
Alignment explanation
Indices: 14616--14661 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
14606 CCCCCCATGA
14616 CCCATTCACAAAATTATTTCACGC
1 CCCATTCACAAAATTATTTCACGC
*
14640 CCCATTCATAAAATTATTTCAC
1 CCCATTCACAAAATTATTTCAC
14662 ATGTGTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (24 bp):
CCCATTCACAAAATTATTTCACGC
Found at i:14774 original size:12 final size:12
Alignment explanation
Indices: 14757--14783 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
14747 AAGTAGTCAA
14757 AATAAATTAACC
1 AATAAATTAACC
14769 AATAAATTAACC
1 AATAAATTAACC
14781 AAT
1 AAT
14784 GATATGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAATTAACC
Found at i:17874 original size:334 final size:330
Alignment explanation
Indices: 16876--18524 Score: 1076
Period size: 334 Copynumber: 4.9 Consensus size: 330
16866 AAATACCCAT
* * * *
16876 AATATATATAATTCAACTCCAAAAA-ATATTAGAGGACTTTTCACGCTTTTAATACCGTTTTTCA
1 AATATATATAATTCAACGCCAAAAAGAT-TGA-AGGACTTTTCACGCTTCTAATACCGTTTTTCC
** ** * *
16940 TATTTTTCTAAATTAAAATCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCTT
64 TATTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCT
* * * **
17005 TAAATACAATGTGGCTGAGATTTGATTAGATGAATATATATATTTCAATGAGTCTCAATGCCAAA
129 TAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATA-TTCAAGGAGTCTTAGCGCCAAA
** * *
17070 AATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAAAAAAAAAAAAAAAA
193 AATCATGCAAAACTGACCCGGGG-CCAGGAACGCGTTTTTAGC-----------AAAAAAAAAAA
* * * *
17135 CCGTGATGGTTAGTACACGATTTCGCCTTAAAATTTTACAAAAAAAGACC-ACAAAATTTTTCCT
246 TCGTGAT-GTT-G--CACGATTTCGGC-TAAAATTTTGCAAAAAATGACCGA-AAAATTTTTCCT
* * *
17199 CAA-TTTTTGGCTAAA-AT-ACTAATGA
305 CAATTTTTTGTCCAAATATCA-TAA-AA
* * * * * * * * *
17224 AATATATATAATTTAACGCCAAGAAGATTGGAGGACGTTTCACGTTTTTCATATCGTTTTTCGTA
1 AATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATACCGTTTTTCCT-
* * * *
17289 ATTTTTTCTGAATTCATTTCTAATTTAATCGAAATAAGATTTAAATGCTCGTAAAAACAAATCCT
65 A-TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCT
* * * *
17354 TAAATGCAATGTGTCTGAGATTTGATTAGATGAATATGGATATCTCAAGTAGTCTTAGCGCCAAA
129 TAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATAT-TCAAGGAGTCTTAGCGCCAAA
* * ** *
17419 AATCATGCAAAACTAACCCAGGGCCTTCGAACGCAG-TTTTAGC-----CAAAAATCGTGATGAT
193 AATCATGCAAAACTGACCCGGGGCC-AGGAACGC-GTTTTTAGCAAAAAAAAAAATCGTGATG--
* * * * * *
17478 TATTACACGAATTCGGCTAAAATTTTGCAAAAAATGACCAGAAAGATATTTCCTTAAATTTTTTT
254 --TTGCACGATTTCGGCTAAAATTTTGCAAAAAATGACC-GAAAAATTTTTCC-TCAATTTTTTG
17543 TCCAAATTATCATAAAA
315 TCCAAA-TATCATAAAA
* * * * **
17560 AATA-ATATAATTCTACGCCAAAAATATTGAAGGATTTTTTACGCTTCTAATATAGTTTTTCCTA
1 AATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATACCGTTTTTCCTA
* * *
17624 CTATTTCCGAATTAATTTCTAATTAAATCGAAAGAAGATTTAGATGCTCATAAAAACAAATCCTT
66 -TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTT
* * * *
17689 AAATCCAATGTGGCTGAGATCTT-ATTAGTTTAATATAGATAGTTCAAGGAGTCTTGGCGCCAAA
130 AAATACAATGTGGCTGAGAT-TTGATTAGATGAATATAGATA-TTCAAGGAGTCTTAGCGCCAAA
* *
17753 AATCATGCAATACTGACCCGGGGTCCAGGAACGCGTTTTTAGCAAAAAAAAAAATCGTGATGCTG
193 AATCATGCAAAACTGACCCGGGG-CCAGGAACGCGTTTTTAGCAAAAAAAAAAATCGTGATGTTG
* * *
17818 CACGATTTCGGCTAATATTTTGCAAAAAATGACGCGAAATATTTTTCCTCAATTTTTAGT-CACA
257 CACGATTTCGGCTAAAATTTTGCAAAAAATGAC-CGAAAAATTTTTCCTCAATTTTTTGTCCA-A
*
17882 ATACTCAT--GA
320 ATA-TCATAAAA
* **
17892 AA-ATATATAA-TCGAACGCCAAAAAGATTGAAGGGCTTTTCATACTTCTAATACCGTTTTTCCT
1 AATATATATAATTC-AACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATACCGTTTTTCCT
** * * * * *
17955 ATTTTTCCGAATTAATTTCTAATTAAAAAGAAACATGATTCAAATGCT--T--------AT--AT
65 ATTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTT
* * * * * * **
18008 -AA-ACAA--TAGCTGGGATTTGGTTAGATGAATATAGACATTTCCAGGATTCTCGGCGCCAAAA
130 AAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATA-TTCAAGGAGTCTTAGCGCCAAAA
* * **** * *** *
18069 ATCATTCAAATCTGA-AATAGGCCACGGAACGCGTTTTTAGC--CAAAAACCGT-GATGATTATT
194 ATCATGCAAAACTGACCCGGGGCCA-GGAACGCGTTTTTAGCAAAAAAAAAAATCG-TGA-TGTT
* * * * * *
18130 ACACGATTTCAGCTAAACA-TTTGCAAAAATTGACCCGAAAGATATTTCCTCAA-TTTTTATCCA
256 GCACGATTTCGGCTAAA-ATTTTGCAAAAAATGA-CCGAAAAATTTTTCCTCAATTTTTTGTCCA
18193 TAATAGTCAT-AAA
319 -AATA-TCATAAAA
* * * *
18206 AATATA-A-AATTCAACGCCAAAAAGATTGAAGGACTTTTGACGCTTTTAATATCGTTTTTCATA
1 AATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATACCGTTTTTCCTA
** * * ** * *
18269 TTTTT-TTAATTAATTTCTAATTAAATTGAAACATTATTCAGATGCTTGTTAAAAACAAAAAAAA
66 TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCG-TAAAAAC-------A
* * * * * * *
18333 AAT-CTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGTTATTTCAAGGAGTGTTGGT
123 AATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATA-TTCAAGGAGTCTTAGC
* * * * * * * * * *
18397 GCTAAAAATCATGCAAAATTGAGCTGGTGTCCCGAAACGCATTTTTAGC-----CAAAAACCGTG
187 GCCAAAAATCATGCAAAACTGACCCGG-GGCCAGGAACGCGTTTTTAGCAAAAAAAAAAATCGTG
* * * *
18457 ATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAATATAACCCGAAAAAATTTTTCTTCAATT
251 AT-GTT-G--CACGATTTCGGCTAAAATTTTGCAAAAAATGA-CCG-AAAAATTTTTCCTCAATT
18522 TTT
310 TTT
18525 GGATAAAATA
Statistics
Matches: 1029, Mismatches: 198, Indels: 158
0.74 0.14 0.11
Matches are distributed among these distances:
311 1 0.00
312 49 0.05
313 109 0.11
314 28 0.03
315 58 0.06
317 3 0.00
318 2 0.00
319 1 0.00
321 2 0.00
329 1 0.00
330 2 0.00
331 44 0.04
332 75 0.07
333 45 0.04
334 163 0.16
335 158 0.15
336 51 0.05
337 21 0.02
338 5 0.00
339 13 0.01
347 28 0.03
348 27 0.03
349 142 0.14
350 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (330 bp):
AATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATACCGTTTTTCCTA
TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTA
AATACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTCAAGGAGTCTTAGCGCCAAAAAT
CATGCAAAACTGACCCGGGGCCAGGAACGCGTTTTTAGCAAAAAAAAAAATCGTGATGTTGCACG
ATTTCGGCTAAAATTTTGCAAAAAATGACCGAAAAATTTTTCCTCAATTTTTTGTCCAAATATCA
TAAAA
Found at i:18548 original size:2 final size:2
Alignment explanation
Indices: 18541--18565 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18531 AATACTCCAA
18541 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18566 ATTTAACGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.