Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018129.1 Corchorus olitorius cultivar O-4 contig18162, 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: 5197
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:908 original size:332 final size:330
Alignment explanation
Indices: 5--855 Score: 1106
Period size: 331 Copynumber: 2.6 Consensus size: 330
1 CATG
* * *
5 AAAAAATNTATAATTCAACGCCTAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCGATTTTT
1 AAAAAATATATAATTCAACGCC-AAAAAGATTGGACGGCTTTTCACGCTTCTAAT-TC-ATTGTT
* * *
70 CATTTTTTTTCCTGAATT-AATATCT-AATTTAATCGAAACAAGATTTCAGATGCTCGTAAAATC
63 -A-TTTTTTT-CTGAATTAAAT-TCTAAATTAAATCGAAACAAGA-TTCAAATGCTCGTAAAAAC
* * * * * *
133 AAATCCTTAAATCCATCATTGCTGAGATTTGGTCAGATGAAAATAGATATTTCAAGGAGTCTTGG
123 AAATCCTAAAATCCATCATTGCTGAGATTTGGTTAGAGGAAAATAGATATTCCAAGGAATCTTTG
* * * * * *
198 CGCCAAAAATCATGCAAAACTTAGTTGGGCCGCCAGAACGCGTTTTT-AGG-CTAAAACAATGAT
188 CGGCAAAAAT-A-GCAAAACTGAGTTGGGCCACCAAAACACGTTTTTGTGGCCTAAAACAATGAT
* * *
261 CGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTT
251 CGTTAATACACGATCTCGGCTAAAATTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAATTTTT
*
326 TCCCAGAATACTCTT
316 TCCCAGAATACTCAT
* * *
341 AAAAAATATATAATTCAACGCCAAAAATATTGGACGGCTTTTCACGTTTCTAATTTCATTTTTAT
1 AAAAAATATATAATTCAACGCCAAAAAGATTGGACGGCTTTTCACGCTTCTAA-TTCATTGTTAT
*
406 TTTTTTCTGAATTAAATTCTAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
65 TTTTTTCTGAATTAAATTCTAAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
* * * * * *
471 TAGATCCATCGTTGCTGAGATTTGGTTAGAGGAATATGGATATTTCAAGGAATCTTTGCGGCAAA
130 AAAATCCATCATTGCTGAGATTTGGTTAGAGGAAAATAGATATTCCAAGGAATCTTTGCGGCAAA
* * ** *
536 AATTATGCAAAACTGAGTTGGGCCCCCAAAACGCGTTTTTGTGGCCTAAAACCGTGATGGTTAAT
195 AA-TA-GCAAAACTGAGTTGGGCCACCAAAACACGTTTTTGTGGCCTAAAACAATGATCGTTAAT
*
601 ACACGATCTCGGCTAAAATTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAA-TTTTTCTCAGA
258 ACACGATCTCGGCTAAAATTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAATTTTTTCCCAGA
665 ATACTCAT
323 ATACTCAT
* * *
673 AAAAAATATATAATTCAATGCCAAAAAGATTGGACGTCTTTTCATGCTTCTAA-T-ATTGTT-TT
1 AAAAAATATATAATTCAACGCCAAAAAGATTGGACGGCTTTTCACGCTTCTAATTCATTGTTATT
* *
735 TTTTTCTGAATTAATTTCTAAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAAGAAATCCTA
66 TTTTTCTGAATTAAATTCTAAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT-
* * *
800 AAAATCCATCATTGTTGAGATTTGGTTAGATGAAAATAGATATTCCAAGGATTCTT
130 AAAATCCATCATTGCTGAGATTTGGTTAGAGGAAAATAGATATTCCAAGGAATCTT
856 GGTAATCGAT
Statistics
Matches: 463, Mismatches: 45, Indels: 21
0.88 0.09 0.04
Matches are distributed among these distances:
328 63 0.14
329 52 0.11
330 1 0.00
331 126 0.27
332 95 0.21
333 68 0.15
334 6 0.01
335 30 0.06
336 22 0.05
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (330 bp):
AAAAAATATATAATTCAACGCCAAAAAGATTGGACGGCTTTTCACGCTTCTAATTCATTGTTATT
TTTTTCTGAATTAAATTCTAAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTA
AAATCCATCATTGCTGAGATTTGGTTAGAGGAAAATAGATATTCCAAGGAATCTTTGCGGCAAAA
ATAGCAAAACTGAGTTGGGCCACCAAAACACGTTTTTGTGGCCTAAAACAATGATCGTTAATACA
CGATCTCGGCTAAAATTTTGCAAAAATGGACCCGAAAGATTTTTCCTCAATTTTTTCCCAGAATA
CTCAT
Found at i:4794 original size:330 final size:327
Alignment explanation
Indices: 2692--5183 Score: 3154
Period size: 325 Copynumber: 7.6 Consensus size: 327
2682 TCGACTAAAA
* * * * * *
2692 TTTTTCTGAACTAATTTCTACTTAAATCGAAACAATATTCAGATGCTCGTAAAAATAAATCCATA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * *
2757 AATCCAAT-G-TGTTTGAGATTTGCTGT-GATGAAAATAGATATTTCAAGGAGTCTTGCCACCAA
66 AATCC-ATCGTTG-CTGAGATTTGGT-TAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAA
* * * * * *
2819 ACATCATGCAAAATTGAGACGGG--GCCTAGAAT-GCGTTTTTAGCCAAAAACAGTGATGCTCAT
128 AAATCATGCAAAACTGAGTCGGGCCGCC-A-AATCGCGTTTTTAGCCTAAAACCGTGATG---GT
* * * ** * * * *
2881 TAGTACACAATTTCGGCTAAAAATGTGCGTAAATTAACCAGAATA-TTTTTTCCTCAATTTTTGG
188 TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA-AGATTTTTCCTCAATTTTT-C
** * * * * *
2945 CCTTAGTACTCATTAAAAAATATATAATTCCACGCCAAAAATATTGGAGGGCATTTCACGCTTCC
251 CCAGAATACTCA-T-AAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCT
*
3010 AATATCATTTTTATTT
314 AATATC-GTTTT-TTT
* *
3026 TTTTTCCAGAATTAATTTCAAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTT-CTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * *
3091 AATTCCATCGTTGCAGAGATTTGGTTAGATGAATATGGATATCTCAAGGAATCTTGGCGCCAAAA
65 AAATCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAA
* * * * *
3156 ATCATGCAAAACTGAGTCAGGCCCCCAAAACGCATTTTTAGCCTAAAACCATGATGGTT--TACA
130 ATCATGCAAAACTGAGTCGGGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACA
** *
3219 CGATTTCAACTAAAATTTTGCAAAAAATTGACCCAAAAGATTTTTCCTCAATTTTTCCCAGAATA
195 CGATTTCGGCTAAAATTTTGC-AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCCCAGAATA
* * *
3284 CTCCTAAAAAATATATAATTCAACGCCACAAAGATTGGAGGGTTTTTCACGCTTCTAATATCGTT
259 CTCAT-AAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCGTT
3349 TTTCTT
323 TTT-TT
* *
3355 TTTTTCTAAATTAATTTCTAATTTTATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
3420 AATCCATCGTTG-TAGAGATTTGGTTAGATGAATATGGATATCTCAAGGAATCTTGGCGCCAAAA
66 AATCCATCGTTGCT-GAGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAA
* *
3484 ATCATGCAAAACTGAGTCGGGCC-CCTAAAACGCGTTTTTAGCCTAAAACCATGATGGTTAGTAC
130 ATCATGCAAAACTGAGTCGGGCCGCC-AAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTAC
* *
3548 ATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTCTTACCAGAAT
194 ACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTT-TTCCCAGAAT
* * * * *
3613 ACTCCTAAAAAATATATAATTCAACGTCAAAAAGATTGGAGGGTTTTTAACACTTCTAATATCG-
258 ACTCAT-AAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCGT
*
3677 --TATT
322 TTTTTT
3681 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* ** * * *
3746 ATTCCATCAATGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCATGGCGCCAACAA
66 AATCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAAA
* * * **
3811 TCATGCAAAACTTCA-TCGGGCCGCCAGATCGCGTATTTAGCCTAAAACCGTGATAATTAGTACA
131 TCATGCAAAAC-TGAGTCGGGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACA
* *
3875 CGATTTAGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTTCCCATAATA
195 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA-TTTTTCCCAGAATA
* * *
3940 CTCATATAAAATATATAATTCAACGCCAAAAAGAATGGAGGACTTTTCACGCTTCTAATAACG--
259 CTCATA-AAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCGTT
4003 --TTT
323 TTTTT
* *
4006 TTTTTCTGAATTAATTTCTAATTTAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCGTA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * *
4071 ATTCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCATGGCACCAAAAA
66 AATCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAAA
* * * *
4136 TCATGCAAAACTTAGTCGGGCCGCCAGATCGCATATTTAGCCTAAAACCGTGATGGTTAGTACAC
131 TCATGCAAAACTGAGTCGGGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACAC
* *
4201 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTTCCCTGAATAC
196 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA-TTTTTCCCAGAATAC
* *
4266 TCATATAAAATATATAATTCAACGCCAAAAAGAATGGAGGGCTTTTCACGCTTCTAATAACG---
260 TCATA-AAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCGTTT
4328 -TTT
324 TTTT
4331 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
4396 ATTCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCATGGCGCCAAAAA
66 AATCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAAA
* *
4461 TCATGCAAAACAT-AGTCGGGCCGCCAGATCGCGTATTTAGCCTAAAACCGTGATGGTTAGTACA
131 TCATGCAAAAC-TGAGTCGGGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACA
*
4525 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTCCCTCAATTGTTTCCCAGAATA
195 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT-TTTCCCAGAATA
* * *
4590 CACATAAAATTATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATGTCGTTT
259 CTCATAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCG-TT
4655 TTCTTT
323 TT-TTT
4661 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
** * * *
4726 AATCCATCGTTGGAGAGATTTTGTTAGATGAATATGGAT-TTCTCAAGGAATCTTGGCGCCAAAA
66 AATCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATT-TCAAGGAATCTTGGCGCCAAAA
* * * * * *
4790 ATCATGCAAAACAT-AGTCGAGCCCCCCAAAACGTGTTTTTAGCCTAAAAACGTGATGGTTAGTG
130 ATCATGCAAAAC-TGAGTCG-GGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTA
* *
4854 CACGATTTCGGCTAAAATTTTTC-AAAATTGACCCGAAAGATTTTTCCTCAATTTTTTTCTCAGA
193 CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA--TTTTTCCCAGA
* *
4918 ATACTTATAAGAAATATATAATTCAACG-CAATAAAGATTGGAGGGTTTTTCACGCTTCTAATAT
256 ATACTCATAA-AAATATATAATTCAACGCCAA-AAAGATTGGAGGGCTTTTCACGCTTCTAATAT
*
4982 CAGTTTTCATT
319 C-GTTTT-TTT
* *
4993 TTTTT-AGAATTAATTTTTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * *
5057 AATCCATCGTTGC-GTAGATTTCGTTTGATGAATATGGAAATCTCAAGAAATATTGGCGCCAAAA
66 AATCCATCGTTGCTG-AGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAA
* * * * * * *
5121 ATCATGCAAAACTGACTCGGGCCGCCAAATCGCATTATTATCCAAAAACTGTGATGATTAGTA
130 ATCATGCAAAACTGAGTCGGGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTA
5184 AAACGATTAA
Statistics
Matches: 1944, Mismatches: 175, Indels: 82
0.88 0.08 0.04
Matches are distributed among these distances:
324 56 0.03
325 562 0.29
326 281 0.14
327 11 0.01
328 172 0.09
329 44 0.02
330 344 0.18
331 232 0.12
332 88 0.05
333 3 0.00
334 8 0.00
335 117 0.06
336 24 0.01
337 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (327 bp):
TTTTTCTGAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
AATCCATCGTTGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAATCTTGGCGCCAAAAA
TCATGCAAAACTGAGTCGGGCCGCCAAATCGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACAC
GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCCCAGAATACT
CATAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCGTTTTT
TT
Done.