Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023879.1 Corchorus olitorius cultivar O-4 contig23912, 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: 4275
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:2259 original size:335 final size:333
Alignment explanation
Indices: 20--3832 Score: 5245
Period size: 334 Copynumber: 11.4 Consensus size: 333
10 CGAAATCGTG
* ** * *
20 TCACGATTTTTGGCTAAAATTGCGTTTCGGGGCCCTGACTTAGTTTTGCATGATTTTTGGCAGAA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAA
* * ** * * * **
85 AGACTTCTTGAAATATCTATATTCATCTAATAAAATCTCTCAACCACAATGCATTTACGGATTAA
66 AGACTCCTCGAAATATCTATATTCATCTAACCAAA--TCTCAGCCACATTGGATTTACGGATTTG
* * * * *
150 TTTTTACAAGTATCTGGATCTTGTTTCGATTTATTTAGAAATAAATTCAGAAAAAAAAGGAAAAA
129 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAA
* * *
215 CGATATTAAAAGCGTGAAAAACCCTAAAATAGTTTTGGCGATGAATTATATGATTTTTCTGAATA
194 CGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTA
* *
280 TTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTTTTTTGCAAAATTTTAGCTGAAATC
259 TTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAG--TTTTTTGCAAAATTTTAGCCGAAATC
345 GTGTACTAACAAACA
322 GTGTACTAAC---CA
*
360 TCACGGCTTTTTGGCTAAAAATGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
1 TCACGG-TTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
* * * * *
425 AAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCAACCACATTTGATATATGGATTTGT
65 AAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
* ** * * * *
490 TTTTACGAGCATCTAAATCTTGTTAAGATTTAATTAGAAATAAATTAAAAAAAAAATGAAAAAAT
130 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAAC
* * *
555 GGTATTAGAAGCATGAAAAACCCTAAAATA-TTGTTGGCTTTGAATTATATGATTTTT-TAGAGT
195 GATATTAGAAGCGTGAAAAACCCTAAAATAGTT-TTGGCGTTGAATTATATGATTTTTCT-GAGT
* * *
618 ATTGTGGCAAAAAATTGGTGAAATACTTTTCGGGTCAGTTTTTTGCAAAATTCTAGCCGAAATCG
258 ATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
*
683 AGTACTAACCA
323 TGTACTAACCA
* * * * * *
694 TCAC-GATTTTGGCTAAAAACGTGTTTCGGGACCATGGCTAAGTTTTGTATGATTTTTGGCAGAA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAA
* * * *
758 AGACTCCTCGAAATATCTATATTTATCTAATCAAATCTCTCAGCCACAATGCATTTACGGATTTG
66 AGACTCCTCGAAATATCTATATTCATCTAACCAAA--TCTCAGCCACATTGGATTTACGGATTTG
*
823 TTTTTACGACCATCTGAATCTTGTTAT-GATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAA
129 TTTTTACGAGCATCTGAATCTTGTT-TCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAA
* *
887 ACGATATTTGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTCTGAGT
193 ACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGT
* *
952 ATTGAGGCAAAAAATTGGTGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
258 ATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
*
1017 TGTACTGACCA
323 TGTACTAACCA
* *
1028 TCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCT-ATCTCAGTTTTGCATGATTTTTGGCAGA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGA-CTCAGTTTTGCATGATTTTTGGCAGA
* * * * *
1092 ATGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGCATTTACGGATTT
65 AAGACTCCTCGAAATATCTATATTCATCTAACCAAA--TCTCAGCCACATTGGATTTACGGATTT
* * *
1157 ATTTTTTA--AGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAATGCAAA
128 -GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAA
* * * * * * * *
1219 AACGATATTTGAAGCGTGAAAAATCCTAAAACAGTATTGGGGATGAATTATATAATTTTT-TCAA
192 AACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCT-GA
* * *
1283 GTATTGTGGCAAAAAATTGGGGAAAAACTTTTCCGGTCTGTTTTTTGTAAAATTTTAGCCGAAAT
256 GTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAT
1348 CGTGTAC--A-CA
321 CGTGTACTAACCA
** * *
1358 TCACGGTTTTTTACTAAAAACGTGTTTCGGGGCCCTAACTCAGTTTTGCATAATTTTTGGCA-AA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAA
* *
1422 TAGAATCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
66 -AGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
* * * *
1487 TTTTACGAGCATTTGGATCATGTTTCGATTTAATTAGAAATAAATTCAGAAAAATATGGAAAAAC
130 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAAC
* * * * *
1552 GAAATTAAAAGCGTGAAAAAAACCTAAAATA-TTGTTGGTGTTGAATTATATGATTTTTCAGAGT
195 GATATTAGAAGCGTG-AAAAACCCTAAAATAGTT-TTGGCGTTGAATTATATGATTTTTCTGAGT
* * * * *
1616 ATTGTCGCTAAAAATTGAGTAAAAACATTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
258 ATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
1681 TGTACTAACCA
323 TGTACTAACCA
* * * * * *
1692 TCAC-GTTTTTGGCTAAAAACGCGTTTCGGGACCATGGCTAAGTTTTGTATGATTTTTGGCAGAA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAA
* * * *
1756 AGACTCCT-GAAAATATCTATATTTATCTAATCAAATCTCTCAGCCACAATGCATTTACGGATTT
66 AGACTCCTCG-AAATATCTATATTCATCTAACCAAA--TCTCAGCCACATTGGATTTACGGATTT
* * *
1820 ATTTTTACAAGTATCTGAATCTT-TTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAA
128 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAA
* *
1884 ACGATATTAGAAGCGTGAAAAACACTAAAATAGTATTGGCGTTGAATTATATGATTTTTCTGAGT
193 ACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGT
* * *
1949 ATTGTGGCAAAAAATTGGGGAAAAACTTTTCAGGTCTGTTTTTTTGCAAAATTTTAGCTGAAATC
258 ATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCCGAAATC
2014 GTGTACTAACCA
322 GTGTACTAACCA
*
2026 TCACGGTTTTTTGGCTAAAAACGTGTTTCGGGGGCCTGACTCAGTTTTGCATGATTTTTGGCAGA
1 TCACGG-TTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
* *
2091 AAGAATCCTCGATATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
65 AAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
* * *
2156 TTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAAATTTAGGAAAAAATGGAAAAAC
130 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAAC
* ** * * *
2221 GATATCAGAAGCGTGAAAAATACTAAAATAGTATTGGCGTTGAGTTATATGATTTTTCTAAGTAT
195 GATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTAT
** * *
2286 TGTGGCAAAATTTTGGGGAAAAACATTTT-GGGTCTGTTTTTTGCAAAATTTTAGCTGAAATCGT
260 TGTGGCAAAAAATTGGGGAAAAAC-TTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGT
*
2350 GTACTTAATCA
324 GTAC-TAACCA
*
2361 TCACGGTTTTTTGGCTAAAAACGTGTTTCAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
1 TCACGG-TTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
* * *
2426 AAGAATCCTCGATATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTACGGATTTGT
65 AAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
* * * *
2491 TTTTACGAGTATCTGACTATTGTTTCGATTTAATTAGAAATAAATTCATAAAAAAAAAATGGAAA
130 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC---AGAAAAAAATGG-AA
*
2556 AAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCATTGAATTATATGATTTTTCTGA
191 AAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGA
* * *
2621 GTATTATGGCAAGAAATTGGGGAAAAACTTTTCGGGTCAGTATTTTGCAAAATTTTAGCCGAAAT
256 GTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAT
*
2686 CGTG---T-ACGA
321 CGTGTACTAACCA
* * * *
2695 TCACGG-TTTTGGTTTAAAACGCGTTTC-GGGCCATGACTCAGTTTTGCATGATTTTTGGCAGAA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAA
* *
2758 AGCCTCATCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA-TTACGGATTTGTT
66 AGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGTT
*
2822 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAATTCAGAAAAAAATGGAAAAACG
131 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACG
* * *
2887 ATATTAGAAGCGTGGAAAACCCTAAAATAGTTTTGGCATTGAATTATATGATTTTTTTCGAGTAT
196 ATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCT-GAGTAT
* * *
2952 TGTGGCAAAAAATTGGGAAAAAACTTTACGGGTCAGTTTTTTGGAAAATTTTAGCCGAAATCGTG
260 TGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTG
*
3017 TACAAACCA
325 TACTAACCA
* *
3026 TCACGGTTGTTTGGCTAGAAACGTCTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
1 TCACGGTT-TTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
* * *
3091 AAGAATCCTCGATATATC-ATTATTCATCTAACCAAATCTCAACCACATTGGATTTACGGATTTG
65 AAGACTCCTCGAAATATCTA-TATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTG
*
3155 TTTTTACGAGAATCTGAATCTTGTTAT-GATTTAATTAGAAATAAATTCAGAAAAAAAAATGGAA
129 TTTTTACGAGCATCTGAATCTTGTT-TCGATTTAATTAGAAATAAATTCAG--AAAAAAATGGAA
* * * * * *
3219 AACCGATATTAGAACCGTGATAAACCGTAAAATAGTTTTTGCGATGAATTATATGATTTTTCTGA
191 AAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGA
* *
3284 GTATTGAGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAGT
256 GTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAAT
3349 CGTGTACTAACCA
321 CGTGTACTAACCA
* * * * *
3362 TCACAGTTTTTTGCCTAGAAACGTCTTTCGGGACCCTGACTCAGTTTTGCATGATTTTTGGCAGA
1 TCAC-GGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGA
* * *
3427 AAGAATCCTCGAAATATCTATATTCATTTAACCAAATCTCAACCACATTGGATTTACGGATTTGT
65 AAGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGT
3492 TTTTACGAGCATCTGAATCTTGTTAT-GATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAA
130 TTTTACGAGCATCTGAATCTTGTT-TCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAA
* *
3556 CGATATTTGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTA
194 CGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTA
* *
3621 TTGAGGCAAAAAATTGGTGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGT
259 TTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGT
3686 GTACTAACCA
324 GTACTAACCA
* * *
3696 TCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCT-AGCTCAGTTTTACATGATTTTTGGCAGA
1 TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGA-CTCAGTTTTGCATGATTTTTGGCAGA
* * * * *
3760 ATGACTTCTCGAAATATCTATATTCATCTAATCAAATCCCTCAGCCACAATGCATTTACGGATTT
65 AAGACTCCTCGAAATATCTATATTCATCTAACCAAAT--CTCAGCCACATTGGATTTACGGATTT
*
3825 ATTTTTAC
128 GTTTTTAC
3833 AAGTATTGTG
Statistics
Matches: 3103, Mismatches: 311, Indels: 123
0.88 0.09 0.03
Matches are distributed among these distances:
326 63 0.02
327 82 0.03
328 25 0.01
329 40 0.01
330 168 0.05
331 191 0.06
332 106 0.03
333 382 0.12
334 670 0.22
335 550 0.18
336 333 0.11
337 104 0.03
338 17 0.01
339 279 0.09
340 5 0.00
341 88 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (333 bp):
TCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAA
AGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGTT
TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACG
ATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
GTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGT
ACTAACCA
Done.