Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017893.1 Corchorus olitorius cultivar O-4 contig17926, 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: 6319
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:2707 original size:31 final size:31
Alignment explanation
Indices: 2666--2833 Score: 118
Period size: 31 Copynumber: 5.5 Consensus size: 31
2656 TTTTGATGTC
2666 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
* ** * *
2697 AGGCCTTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
*
2726 GGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
2757 AGGCCCTTATTTG-GTCAAATT---AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTGGCAAACGTT
* * *
2785 CGGACCCTTATTTGAGCATTTTGACAAACATT
1 AGG-CCCTTATTTGAGCATTTTGGCAAACGTT
*
2817 AAGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
2834 ATTAGCCTAA
Statistics
Matches: 101, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
28 11 0.11
29 30 0.30
30 4 0.04
31 47 0.47
32 9 0.09
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:2735 original size:29 final size:28
Alignment explanation
Indices: 2698--2798 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 28
2688 GCAAACGTTA
*
2698 GGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGG-CAAATTAAAAGATCG
** * **
2727 GGCCCTTATTTGAGCATTTTGGCAAACG-TTA
1 GGCCCTTATTTG-GCAAATT---AAAAGATCG
2758 GGCCCTTATTTGGTCAAATTAAAAGATCG
1 GGCCCTTATTTGG-CAAATTAAAAGATCG
*
2787 GACCCTTATTTG
1 GGCCCTTATTTG
2799 AGCATTTTGA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
28 4 0.07
29 27 0.50
30 2 0.04
31 17 0.31
32 4 0.07
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (28 bp):
GGCCCTTATTTGGCAAATTAAAAGATCG
Found at i:2740 original size:60 final size:60
Alignment explanation
Indices: 2667--2829 Score: 272
Period size: 60 Copynumber: 2.7 Consensus size: 60
2657 TTTGATGTCA
*
2667 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
2727 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * * *
2787 GACCCTTATTTGAGCATTTTGACAAACATTAAGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
2830 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:5127 original size:329 final size:330
Alignment explanation
Indices: 3704--5342 Score: 1507
Period size: 329 Copynumber: 5.0 Consensus size: 330
3694 AAAAACCGTT
* * * *
3704 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCAT-AAAAATATATAATTC
* ** * * * ** * *
3769 GACATCGAAATGATTGAAGGGGTTTTAACGCTTCTAATATTGTTTTTC----------CGAATTA
65 AACGCCAAAAAGATTGGAGGATTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTTCGAATTA
* * * * ** *
3824 ATTTTTAATGAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATTGTTAAATCTAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * *
3889 TGAGATTTGGTTAGATGAATATAGATATTTCAAGG-GATCTTGGCACCAAAAATCAAGTAAAATT
195 TGAGATTTGGTTAGATGAATATAGATATTTTAAGGAG-TCTTGGCACCAAAAATCATGCAAAACT
* * * * *
3953 GAGCCG-GGTCCTGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTTGGCT-A
259 GAGCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG-TAGTACACGATTTCGGCTAA
4016 AATTTTGC
323 AATTTTGC
* * * *
4024 AAAAATTGACCCGAAAGATTTTTCCTCTATTTCTAGCGAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCAT-AAAAATATATAATTC
* * * ** * * *
4089 GACGCCAAAAAAAACT-GAAAACCTTTTTCACGCTTCTAATATCGTTTTCCCTATTTTATTTCCA
65 AACGCC-AAAAAGATTGGAGGA--TTTTTCACGCTTCTAATATCGTTTTTCATATTTT-TTT-CG
* * ** *
4153 AATTAATTTCTAATTAAATTGAAACAAGATTTAGAAACTCGTAAAAACAAATCCTTAAATACAAT
125 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* *
4218 GT-GCGTGAGATTTGATTAGATGAATATAGATATATTTTAAGGAGTCTTGGTACCAAAAATCATG
190 GTGGC-TGAGATTTGGTTAGATGAATATAG--ATATTTTAAGGAGTCTTGGCACCAAAAATCATG
* * * * *
4282 CAAAACTGA-CCGAGGATCCCGGAACTCGTTTTTAGCCAAAAAAACC--AAT-G--GTACACTAT
252 CAAAACTGAGCCGAGG-CCCCGAAACGCGTTTTTAGCC--AAAAACCGTGATGGTAGTACACGAT
*
4341 TTCGGCTAAAATTCTGC
314 TTCGGCTAAAATTTTGC
* * *
4358 AAAAATTGACAC-AAAATATTTTT-CTCAATTTTTTGCCACAATACTCATAAAAAATATATAATT
1 AAAAATTGACCCGAAAA-ATTTTTCCTCAATTTTTAGCCAAAATACTCAT-AAAAATATATAATT
* * * * *
4421 CAACGCCAAAAAGATTGAAGGGTTTCTCGCGCTTCTAATATCGTTTTTTC-TATTTTTTTCAAAT
64 CAACGCCAAAAAGATTGGAGGATTTTTCACGCTTCTAATATCG-TTTTTCATATTTTTTTCGAAT
* * * * * * * *
4485 TAATTGT-TATTTAAATCGAAACATGACTCAAATGCACATAAAAAGAAAACCTTAAATCCAAT-T
128 TAATT-TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * * *
4548 CGGTTAAGATTTGGTTAGA-GAATATAGATATTTTAAGGAGTTTTGCCACAAAAAATTATGCAAA
192 -GGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAA
* * ** * *
4612 ACTGACCCGGGGCCCTAAAACGCGTTTTTTGCAAAAAAAACCGTGAT-G--GTACACGATTTCGG
256 ACTGAGCCGAGGCCCCGAAACGCGTTTTTAGC--CAAAAACCGTGATGGTAGTACACGATTTCGG
*
4674 CTACAATTTTGC
319 CTAAAATTTTGC
* * * * ** * * * *
4686 AAAAATTGACCTGAAATATTTTTTTCGCAATTTTTCTCCACAATACTTAT-AGAATATATAATTA
1 AAAAATTGACCCGAAA-AATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTC
* * * *
4750 AACGCCAAAAAGATTGGAGGAATTTTCACGCTTTTAGTATCATTTTTCATATTTTTTT-GAATTA
65 AACGCCAAAAAGATTGGAGGATTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTTCGAATTA
* *
4814 ATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* ** * * * * *
4879 TGATATTTCATTAGATGAATATAAATATTTTAAGGAGTCTCGGCTCTAAAAAT-ATGCAAAACTA
195 TGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAACTG
*** * * * * *
4943 AGCCGAGGCCCCGAAACATATTTTTTGCCAAAAACCGTTATGGGTAGTACATGATTTAGCCTAAA
260 AGCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-GGTAGTACACGATTTCGGCTAAA
5008 ATTTTGC
324 ATTTTGC
* * * * *
5015 AAAAAATGACCCGAAAAATTTTTCCATCAATTTTTGGCTAAAATACTCAT-AATATATATAATTT
1 AAAAATTGACCCGAAAAATTTTTCC-TCAATTTTTAGCCAAAATACTCATAAAAATATATAATTC
* * * * * *
5079 AACGGCAAAAAGATTGGAGTATTTTTAACGCTTTTAATATTGTTTTTCATATTTTTTCCGAATTA
65 AACGCCAAAAAGATTGGAGGATTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTTCGAATTA
*
5144 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * *
5209 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT-TCTGCCAAAAATC-TAGAAAAAC
195 TGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGC-ACCAAAAATCAT-GCAAAAC
* * * *
5272 TAAGCCTG-GGCCCCGAACCGCGTTTTTGGCCAAAAACCGTGATGTTTAGTGTACACGATTTTCG
258 TGAGCC-GAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG-GTA--GTACACGA-TTTCG
5336 GCTAAAA
318 GCTAAAA
5343 ACTGATCCAA
Statistics
Matches: 1074, Mismatches: 189, Indels: 98
0.79 0.14 0.07
Matches are distributed among these distances:
320 65 0.06
321 5 0.00
322 23 0.02
325 11 0.01
326 59 0.05
327 111 0.10
328 139 0.13
329 189 0.18
330 139 0.13
331 68 0.06
332 13 0.01
333 68 0.06
334 115 0.11
335 3 0.00
336 38 0.04
337 22 0.02
339 6 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCA
ACGCCAAAAAGATTGGAGGATTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTTCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGA
GCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAAT
TTTGC
Done.