Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011759.1 Corchorus olitorius cultivar O-4 contig11792, 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, 894
Length: 1490
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Found at i:616 original size:154 final size:154
Alignment explanation
Indices: 1--1487 Score: 2076
Period size: 154 Copynumber: 9.6 Consensus size: 154
* * * *
1 TGAGTTAAAAACTTCATAGTGGACTAATCTCAGCAAAATGATTATAGTTAGCCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* * * * * *
66 AAACAAAAGCATCGAGGGTTGCCAAATCGATGACGATTCGAATCGAAACTAATGGCCCCCGGA-A
66 AAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCC-GATA
*
130 GGCCTAAAATAACAAGTGTTCCAAA
130 GGCCCAAAATAACAAGTGTTCCAAA
* * *
155 TGAGTTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGCCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* * * **
220 AAAGAAAAGCATCGACGGGTTGCCAAATCGATGACGATTCAAAACGTCACTAATGGGTCTTGATA
66 AAAGAAAAGCATCGA-GGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATA
*
285 CGCCCAAAATAACAAGTGTTCCAAA
130 GGCCCAAAATAACAAGTGTTCCAAA
* * *
310 GGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* *
375 AAAGAAAAGCATCGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
66 AAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
440 GCCCAAAATAACAAGTGTTCCAAA
131 GCCCAAAATAACAAGTGTTCCAAA
*
464 TGAGCTAAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA-ATAT
1 TGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA-AT
* *
528 GGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGA-ACTAAT-GGCCCCGA
64 GGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGA
* *
591 AAGGCCTAAAATAACAAGTGTTCCAAA
128 TAGGCCCAAAATAACAAGTGTTCCAAA
* * *
618 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* * * *
683 AAAG-AAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAG
66 AAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
*
747 GCCCAAAATAACAATTAGTTCCAAA
131 GCCCAAAATAACAAGT-GTTCCAAA
* * *
772 TGAGCTAAAAACTTCACTGTGGGA-TAATCTCACGAAAATGATAATAGTTAGGCCATAAACAATG
1 TGAGCTAAAAACTTCACAGT-GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
* * *
836 GAAAGAAAAGCATTGA-GGTTTCTACAAATCGAAGACGATTCGAAAACGACACTAATCGTGACCC
65 GAAAGAAAAGCATCGAGGGTTGC--CAAATCGAAGACGATTC-AAAACGACACTAAT-G-GGCCC
900 CGATAGGCCCAAAATAACAAGTGTTCCAAA
125 CGATAGGCCCAAAATAACAAGTGTTCCAAA
*
930 TGACGACTAAAAACTTCACAAGTGGACTAATCTCAACCAAAATGATTTTAGTTAGGCCATAAACA
1 TGA-G-CTAAAAACTTCAC-AGTGGACTAATCTC-ACCAAAATGATTATAGTTAGGCCATAAACA
* * *
995 ATTGGAAAGAAAAGCATTGA-GGTTACCAAATCGAAGACGATTCATAACGACACTAATGGGCCCC
62 A-TGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGG-CCC
*
1059 CGATAGGCACAAAATAACAAGTG-TCCAAA
125 CGATAGGCCCAAAATAACAAGTGTTCCAAA
* * *
1088 TGACCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
** * * * *
1153 AAAGAAAAGCATTTA-GGTTTCTAAATCGAAGGCGATTCAGAACGACACTAATGGGCCCCGATAG
66 AAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
1217 GCCCAAAATAACAAGTGTTCCAAA
131 GCCCAAAATAACAAGTGTTCCAAA
*
1241 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* * * * * * ** *
1306 AAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTG
66 AAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
*
1371 GCACAAAATAACAAGTGTTCCAAA
131 GCCCAAAATAACAAGTGTTCCAAA
*** *
1395 TGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAAGTGATTATAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
*
1460 AAACAAAAGCATCGAGGGTTGCCAAATC
66 AAAGAAAAGCATCGAGGGTTGCCAAATC
1488 TAA
Statistics
Matches: 1207, Mismatches: 101, Indels: 50
0.89 0.07 0.04
Matches are distributed among these distances:
151 2 0.00
152 65 0.05
153 213 0.18
154 441 0.37
155 262 0.22
156 31 0.03
157 13 0.01
158 22 0.02
159 52 0.04
160 29 0.02
161 26 0.02
162 28 0.02
163 23 0.02
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
AAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAA
Found at i:823 original size:307 final size:308
Alignment explanation
Indices: 1--1487 Score: 2123
Period size: 307 Copynumber: 4.8 Consensus size: 308
* * *
1 TGAGTTAAAAACTTCATAGTGGACTAATCTCA-GCAAAATGATTATAGTTAGCCCATAAACAATG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACG-AAAATGATTATAGTTAGGCCATAAACAATG
* * * * * * * * *
65 GAAACAAAAGCATCGAGGGTTGCCAAATCGATGACGATTCGAATCGAAACTAATGGCCCCCGGA-
65 GAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCC-GAT
* * *
129 AGGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCAGCAAAAT
129 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* *
194 GATTATAGTTAGCCCATAAACAATGGAAAGAAAAGCATCGACGGGTTGCCAAATCGATGACGATT
194 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGA-GGGTTGCCAAATCGAAGACGATT
* * ** *
259 CAAAACGTCACTAATGGGTCTTGATACGCCCAAAATAACAAGTGTTCCAAA
258 CAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
310 GGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
* *
375 AAAGAAAAGCATCGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
66 AAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
*
440 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAACTTCACAATGGACTAATCTCACCAAAATG
131 GCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATG
* *
505 ATTATAGTTAGGCCATAAA-ATATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTC
195 ATTATAGTTAGGCCATAAACA-ATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTC
* *
569 AAAACGGA-ACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAA
259 AAAAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
618 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAAGAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
* *
683 AAAG-AAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAG
66 AAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
* * *
747 GCCCAAAATAACAATTAGTTCCAAATGAGCTAAAAACTTCACTGTGGGA-TAATCTCACGAAAAT
131 GCCCAAAATAACAAGT-GTTCCAAATGAGCTAAAAACTTCACAGT-GGACTAATCTCACCAAAAT
* * *
811 GATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCTACAAATCGAAGACGAT
194 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGC--CAAATCGAAGACGAT
*
875 TCGAAAACGACACTAATCGTGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
257 TC-AAAACGACACTAAT-G-GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* *
930 TGACGACTAAAAACTTCACAAGTGGACTAATCTCAACCAAAATGATTTTAGTTAGGCCATAAACA
1 TGA-G-CTAAAAACTTCAC-AGTGGACTAATCTC-ACGAAAATGATTATAGTTAGGCCATAAACA
*
995 ATTGGAAAGAAAAGCATTGAGG-TTACCAAATCGAAGACGATTCATAACGACACTAATGGGCCCC
62 A-TGGAAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGACACTAATGGG-CCC
* * *
1059 CGATAGGCACAAAATAACAAGTG-TCCAAATGACCTAAAAACTTTACAGTGGACTAATCTCACCA
125 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
* ** * * *
1123 AAATGATTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTTA-GGTTTCTAAATCGAAGGCG
190 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACG
*
1187 ATTCAGAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
255 ATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
1241 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
* * * ** *
1306 AAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATTG
66 AAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
* *** *
1371 GCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAAAAGACTAATCTCACCAAAGTGA
131 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
1436 TTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATC
196 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATC
1488 TAA
Statistics
Matches: 1068, Mismatches: 84, Indels: 53
0.89 0.07 0.04
Matches are distributed among these distances:
306 47 0.04
307 275 0.26
308 158 0.15
309 198 0.19
310 71 0.07
311 37 0.03
312 36 0.03
313 14 0.01
314 28 0.03
315 17 0.02
316 108 0.10
317 44 0.04
318 35 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (308 bp):
TGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
AAAGAAAAGCATTGAGGTTTACCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAA
AACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
Done.