Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019665.1 Corchorus olitorius cultivar O-4 contig19698, 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: 27741
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:758 original size:12 final size:12
Alignment explanation
Indices: 741--775 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
731 GGAGTAGAGG
741 TCGCTTACCAGC
1 TCGCTTACCAGC
*
753 TCGCTTACCAAC
1 TCGCTTACCAGC
*
765 TCGATTACCAG
1 TCGCTTACCAG
776 ATCATATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (12 bp):
TCGCTTACCAGC
Found at i:16290 original size:126 final size:121
Alignment explanation
Indices: 16113--16364 Score: 380
Period size: 126 Copynumber: 2.0 Consensus size: 121
16103 AATAAAGAAT
* * *
16113 GAAATTCTAATGAGAATTTTTTTTCTATCCGGTATCCAGAGTTTTGCCCTGACTAATTCGGATTC
1 GAAATTCTAATGAGAATTTTTTTTCTATCCGGTATCCAGAGCTTTGCCCTGACTAATCCGAATTC
*
16178 GATCC-GCGTCGCACACCTGATTATGCTGGGTGAGTCTCCCAACAGGGGCAGCTGCG
66 GA-CCAGCGTCGCACACCTGATTATGCTGGGTGAGTCTCCCAACAGGCGCAGCTGCG
16234 GAAATTCTAATGAGAATTTTTTTTCTATCCCATCCGGTATCCAGAGCTTTGCCCTGACTAATCCG
1 GAAATTCTAATGAGAATTTTTTTTC--T---ATCCGGTATCCAGAGCTTTGCCCTGACTAATCCG
* * *
16299 AATTCGACCAGCGTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAACAGGCGCAGCTGCG
61 AATTCGACCAGCGTCGCACACCTGATTATGCTGGGTGAGTCTCCCAACAGGCGCAGCTGCG
16360 GAAAT
1 GAAAT
16365 GAGAATGGGA
Statistics
Matches: 118, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
121 25 0.21
123 1 0.01
125 2 0.02
126 90 0.76
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (121 bp):
GAAATTCTAATGAGAATTTTTTTTCTATCCGGTATCCAGAGCTTTGCCCTGACTAATCCGAATTC
GACCAGCGTCGCACACCTGATTATGCTGGGTGAGTCTCCCAACAGGCGCAGCTGCG
Found at i:26837 original size:333 final size:332
Alignment explanation
Indices: 25898--27650 Score: 2356
Period size: 333 Copynumber: 5.3 Consensus size: 332
25888 ACGGAGGGAG
* * * *
25898 TAGAAATTTAATCGGAAAAAGTAGAAAAAATGATATTAGAAGCGTAAAAAAGCCTTCAATATTTT
1 TAGAAATTTATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAA-CCTTCAATATTTT
** * *
25963 TGGTCTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTTAGGAAATATCTTTCGGGT
65 TGGAGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAAAAATCTTTCGGGT
26028 CAATTTTTGCAAAATTTT-------A--G-G-------CATCACGATTTTTTTGCTAAAAACGCG
130 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGA-TTTTTTGCTAAAAACGCG
* *
26076 TTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATTTATATTC
194 TTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTC
26141 ATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
259 ATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
26206 CAATTTAAT
324 CAATTTAAT
*
26215 TAGAAATTTATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGTAAAAAACTCTTCAATATTTT
1 TAGAAATTTATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAAC-CTTCAATATTTT
* * *
26280 TCGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAAATATCTTTCGGGT
65 TGGAGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAAAAATCTTTCGGGT
*
26345 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTT-CTAAAAACGTGT
130 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGT
* * * * *
26409 TCCGGGGCCCCGGCTCAGTTCTGTATGATTTTCGGCGTCGAGACTCCATCAAAAATCTATATTCA
195 TTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTCA
* * ** *
26474 TCTAGTCAAATCTCAGCCAAATTGCATTTAAGTTTTTGTTTTTACGAGCATCTGAATCTTGTTTC
260 TCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTC
*
26539 GATTTAAT
325 AATTTAAT
* * * * * * ** *
26547 TAGAAATTAATTCGGTTAAAATAAT-GAAAAAACGATATGAAAAGTGTGAAAGTCCTCCAATCA-
1 TAGAAATTTATTCGG--AAAA-AATAGGAAAAACGATATTAGAAGCGTAAAAAACCTTCAAT-AT
* *
26610 TTTTGGAG-TGAAATTATATATAT-TAC-ACGAGTATATT-AGGC-AAAAATTGAGGAAAAATTT
62 TTTTGGAGTTG-AATTATATATATCT-CTATGAGTAT-TTCA-GCTAAAAATTGAGGAAAAATCT
* * * * * *
26670 TTTGGATCATTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACTATAACGATTTTTTGCTAAA
123 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAA
*
26735 AACGCTTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCT
188 AACGCGTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCT
* *
26800 ATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATC
253 ATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATC
* *
26865 TTATTTCAACTTAAT
318 TTGTTTCAATTTAAT
* * *
26880 TAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTTGAAGCGTAAAAAAACCTTCAATATTTT
1 TAGAAATTTATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGT-AAAAAACCTTCAATATTTT
* * * *
26945 TGGCGTTGAAATATATATATCTCTATGAGTATTTCAGCTAAGAATTGA-G-----TCCTTC-GGT
65 TGGAGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAAAAATCTTTCGGGT
* * * *
27003 CAA-TTTTG-ATAAA-TTTAGTCTAAATTGTATACTAACCATCACGATTTCTTTGCTAAAAACGC
130 CAATTTTTGCA-AAATTTTAGCCGAAATCGTGTACTAACCATCACGATTT-TTTGCTAAAAACGC
* * * *
27065 GTTTCGGGGCCCCAACACAATTCTGCAGGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATT
193 GTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATT
*
27130 CATCTAATCAAATCTCAGCCGCATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
258 CATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
27195 TCAATTTAAT
323 TCAATTTAAT
* * * *
27205 TAGAAATTTTTTCGGAAAAAGTATGAAAAATGATATTAGAAGCGTAAAAAACCTTCAATATTTTT
1 TAGAAATTTATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAACCTTCAATATTTTT
* *
27270 GGCA-TTGAATTATATATATCTCTATGAGTACTTCAGCTAAAAATTG-TGAAAATATCTTTCGGG
66 GG-AGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAAAA-ATCTTTCGGG
27333 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTCTTTGCTAAAAACGC
129 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTT-TTTGCTAAAAACGC
* *
27398 GTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTCGGCGTCGAGACTCCTTCAAAAATCTATATT
193 GTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATT
* * * *
27463 CATATGATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGAATCTAAATCTTATT
258 CATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
27528 TCAATTTAAT
323 TCAATTTAAT
* * *
27538 TAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTAGAAGCGTAAAAAAAACCTTCAATAATT
1 TAGAAATTTATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGT--AAAAAACCTTCAATATTT
*
27603 TTGGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTG
64 TTGGAGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTG
27651 TGGGAATAAG
Statistics
Matches: 1260, Mismatches: 124, Indels: 86
0.86 0.08 0.06
Matches are distributed among these distances:
316 1 0.00
317 139 0.11
324 92 0.07
325 193 0.15
326 5 0.00
327 4 0.00
330 7 0.01
331 27 0.02
332 273 0.22
333 420 0.33
334 35 0.03
335 64 0.05
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (332 bp):
TAGAAATTTATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAACCTTCAATATTTTT
GGAGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAAAAATCTTTCGGGTC
AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTT
TCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTCAT
CTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCA
ATTTAAT
Found at i:27442 original size:658 final size:660
Alignment explanation
Indices: 25898--27650 Score: 2469
Period size: 658 Copynumber: 2.7 Consensus size: 660
25888 ACGGAGGGAG
*
25898 TAGAAATTTAATCGGAAAAAGTA-GAAAAAATGATATTAGAAGCGTAAAAAAGCCTTCAATATTT
1 TAGAAATTTATTCGGAAAAAGTATGAAAAAATGATATTAGAAGCGTAAAAAA-CCTTCAATATTT
*
25962 TTGGTC-TTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATT-TAGGAAATATCTTTCG
65 TTGG-CATTGAATTATATATATCTCTATGAGTA-TTCAGCTAAAAATTGT-GAAAATATCTTTCG
26025 GGTCAATTTTTGCAAAATTTT-------A--G-G-------CATCACGATTTTTTTGCTAAAAAC
127 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGA-TTTTTTGCTAAAAAC
* *
26073 GCGTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCATCGAGACTCCTTCAAATATTTATA
191 GCGTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATA
*
26138 TTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTG
256 TTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTA
*
26203 TTTCAATTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGT-AAAAAAC
321 TTTCAATTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTAGAAGCGTAAAAAAAC
*
26267 TCTTCAATATTTTTCGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGAA
386 -CTTCAATATTTTTGGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGG--
* *
26332 ATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTT
448 --ATCCTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGATTTTTT
* ** * * * *
26397 CTAAAAACGTGTTCCGGGGCCCCGGCTCAGTTCTGTATGATTTTCGGCGTCGAGACTCCATCAAA
511 CTAAAAACGCGTTCCGGGGCCCCAACACAATTCTGCAGGATTTTCGGCGTCGAGACTCCATCAAA
* **
26462 AATCTATATTCATCTAGTCAAATCTCAGCCAAATTGCATTTAAGTTTTTGTTTTTACGAGCATCT
576 AATCTATATTCATCTAATCAAATCTCAGCCAAATTGCATTTAAGGATTTGTTTTTACGAGCATCT
* *
26527 GAATCTTGTTTCGATTTAAT
641 AAATCTTGTTTCAATTTAAT
* * * * * * * ** *
26547 TAGAAATTAATTCGGTTAAAA-TAATGAAAAAACGATATGAAAAGTGTGAAAGTCCTCCAATCA-
1 TAGAAATTTATTCGG-AAAAAGT-ATGAAAAAATGATATTAGAAGCGTAAAAAACCTTCAAT-AT
* * * * *
26610 TTTTGG-AGTGAAATTATATATAT-TAC-ACGAGTATATTAGGC-AAAAATTGAGGAAAA-ATTT
63 TTTTGGCATTG-AATTATATATATCT-CTATGAGTAT-TCA-GCTAAAAATTG-TGAAAATATCT
* * * * * *
26670 TTTGGATCATTTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACTATAACGATTTTTTGCTAAA
123 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAA
*
26735 AACGCTTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCT
188 AACGCGTTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCT
* *
26800 ATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTATATC
253 ATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATC
* *
26865 TTATTTCAACTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTTGAAGCGTAAAAA
318 TTATTTCAATTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTAGAAGCGTAAAAA
* *
26930 AACCTTCAATATTTTTGGCGTTGAAATATATATATCTCTATGAGTATTTCAGCTAAGAATTGA-G
383 AACCTTCAATATTTTTGGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGG
* * *
26994 -TCCTTC-GGTCAA-TTTTG-ATAAA-TTTAGTCTAAATTGTATACTAACCATCACGATTTCTTT
448 ATCCTTCGGGTCAATTTTTGCA-AAATTTTAGCCGAAATCGTATACTAACCATCACGATTT-TTT
* *
27054 GCTAAAAACGCGTTTCGGGGCCCCAACACAATTCTGCAGGATTTTCGGCGTCGAGACTCCTTCAA
511 -CTAAAAACGCGTTCCGGGGCCCCAACACAATTCTGCAGGATTTTCGGCGTCGAGACTCCATCAA
* **
27119 ATATCTATATTCATCTAATCAAATCTCAGCCGCATTGCATTTAAGGATTTGTTTTTACGAGCATC
575 AAATCTATATTCATCTAATCAAATCTCAGCCAAATTGCATTTAAGGATTTGTTTTTACGAGCATC
27184 TAAATCTTGTTTCAATTTAAT
640 TAAATCTTGTTTCAATTTAAT
*
27205 TAGAAATTTTTTCGGAAAAAGTATG-AAAAATGATATTAGAAGCGTAAAAAACCTTCAATATTTT
1 TAGAAATTTATTCGGAAAAAGTATGAAAAAATGATATTAGAAGCGTAAAAAACCTTCAATATTTT
27269 TGGCATTGAATTATATATATCTCTATGAGTACTTCAGCTAAAAATTGTGAAAATATCTTTCGGGT
66 TGGCATTGAATTATATATATCTCTATGAGTA-TTCAGCTAAAAATTGTGAAAATATCTTTCGGGT
27334 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTCTTTGCTAAAAACGCG
130 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTT-TTTGCTAAAAACGCG
* *
27399 TTTCGGGGCCCCGACTCAGTTTTGCATGATTTTCGGCGTCGAGACTCCTTCAAAAATCTATATTC
194 TTTCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTC
* * *
27464 ATATGATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGAATCTAAATCTTATTT
259 ATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTT
27529 CAATTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTAGAAGCGTAAAAAAAACCT
324 CAATTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTAGAAGCGT-AAAAAAACCT
*
27594 TCAATAATTTTGGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTG
388 TCAATATTTTTGGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTG
27651 TGGGAATAAG
Statistics
Matches: 970, Mismatches: 92, Indels: 74
0.85 0.08 0.07
Matches are distributed among these distances:
648 1 0.00
649 56 0.06
650 37 0.04
651 22 0.02
655 1 0.00
656 84 0.09
657 91 0.09
658 344 0.35
659 70 0.07
664 1 0.00
665 250 0.26
666 13 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (660 bp):
TAGAAATTTATTCGGAAAAAGTATGAAAAAATGATATTAGAAGCGTAAAAAACCTTCAATATTTT
TGGCATTGAATTATATATATCTCTATGAGTATTCAGCTAAAAATTGTGAAAATATCTTTCGGGTC
AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTTGCTAAAAACGCGTT
TCGGGGCCCCGACTCAGTTCTGCATGATTTTCGGCGTCGAGACTCCTTCAAATATCTATATTCAT
CTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCA
ATTTAATTAGAAATTTATTCGGAAAAAGTAGGAAAAATGATATTAGAAGCGTAAAAAAACCTTCA
ATATTTTTGGCGTTGAATTATATATATCTCTATGAGTATTTCAGCTAAAAATTGAGGATCCTTCG
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGATTTTTTCTAAAAACGC
GTTCCGGGGCCCCAACACAATTCTGCAGGATTTTCGGCGTCGAGACTCCATCAAAAATCTATATT
CATCTAATCAAATCTCAGCCAAATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
TCAATTTAAT
Done.