Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014942.1 Corchorus olitorius cultivar O-4 contig14975, 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: 6689
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1696 original size:48 final size:47
Alignment explanation
Indices: 1572--1715 Score: 162
Period size: 48 Copynumber: 3.0 Consensus size: 47
1562 TGCCAATAGG
* **
1572 CCTAAAATTCGAAAGCTAACTATCACGACTTTTGGGGTGTTAAAAATGA
1 CCTAAAA-TCCAAAGCTAACTATCACGACTTTT-GGGTGCCAAAAATGA
* * * **
1621 CATACAATCTAAAGGCTAACTGCCACGACTTTTGGGTGCCAAAAATGA
1 CCTAAAATCCAAA-GCTAACTATCACGACTTTTGGGTGCCAAAAATGA
* *
1669 CCTAAAATCCAAAGACTATCTATCACGACTTTTAGGTGCCAAAAATG
1 CCTAAAATCCAAAG-CTAACTATCACGACTTTTGGGTGCCAAAAATG
1716 GAATGGCTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
47 1 0.01
48 56 0.71
49 22 0.28
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (47 bp):
CCTAAAATCCAAAGCTAACTATCACGACTTTTGGGTGCCAAAAATGA
Found at i:5126 original size:334 final size:334
Alignment explanation
Indices: 2429--6400 Score: 5387
Period size: 335 Copynumber: 12.0 Consensus size: 334
2419 GCCGAAATTG
** * *
2429 CGGTTTTTGGCTGAAAACGCGTTTCGGAACCTTGACTCAGTTTTGCATGCTTTTTGGCAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* *
2494 CTCCTCGAAATATCTGTATTCATCTAACAAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* * ** * *
2559 ACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATAAATTG-AG-AAAAAGATGGAAAAACGA
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAA-ATGGAAAAACGA
* * **
2622 TATTAGAAGCGTGAAAAGCATTAAAAT-TATTTTGGCGTTGAATTATATGATTTTTCTGAGTATT
195 TATTAGAAGCGTGAAAAACACTAAAATAT-TTTTGGAATTGAATTATATGATTTTTCTGAGTATT
** **
2686 GTGGCAAAAAAATTGGGGAAAAAAATTTTCGGGTCAGGCTTTTGCAAAA-TTTAGCCGAAATCGT
259 GTGGC-AAAAAATTGGGG-AAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGT
2750 G---T-ACCATCA
322 GTACTAACCATCA
* * * *
2759 CTGTTTTTGGCTAAAAACGCGTTTCGGGGACCTGGCTCAGCTTTT-CATGATTTTTGGCAGAAAG
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAG-TTTTGCATGATTTTTGGCAGAAAG
* * * *
2823 TCTCCTCGAAATATCTGTATTCATCTAACCAAATGTCAGCCACGTTGGATTTACAGATTTCTTTT
65 ACTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTT
* * *
2888 TACGAGTATTTGAATATTGTTTCGATTTAATTAGAAATGTATTGTGGCA-AAAATGGAAAAACGA
130 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGA
* * *
2952 TATTAGAAGCGTGAAAAATC-CTAAAATATTTTTGGACTTGAATTATATGATTTTTTTTAGTATT
195 TATTAGAAGCGTGAAAAA-CACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATT
* * *
3016 GTGGCAAAAAATTGGGGAGAATCATTTCGGGTCAGTTTTTTGTAAAATTTTAGCCGAAATCGTGT
259 GTGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGT
3081 ACTAACCATCA
324 ACTAACCATCA
* * *
3092 CGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGT
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* * *
3157 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTAGATTTACGGATTTATTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* * *
3222 ACGAGTATTTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTTGCAGAAAATGGAAAAACGAT
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
* * *
3287 ATTAGAAGCGTGAAGAACCCCTTAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTG
196 ATTAGAAGCGTGAA-AAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTG
* * *
3352 TGACAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATATTAGCGGAAATCGTGTA
260 TGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTA
*
3417 CTAAGCATCA
325 CTAACCATCA
* *
3427 CGGTTTTTGGCTGAAAACGCGTTTTGGGGCCCTGACTCAGTTTTGCATGATTTTTGGTAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* *
3492 CT-TCTC-AAATATCTGTATTCATCTAACCAAATCTCAGCCGCGATGGATTTACAGATTTGTTTT
66 CTCT-TCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTT
** * *
3555 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAGAAATAAATTG-AG-AAAAAGATGGAAAA
130 TACGAGCATCTGAATCTTGTTTCGATTTAATT---AGAAATGTATTGTGGCAGAAA-ATGGAAAA
* * * **
3618 ACGATATTAGAAGCGTGAAAAGCATTAAAATTTTTTTGGCGTTGAATTATATGATTTTTCTGAGT
191 ACGATATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGT
* * *
3683 ATTGTGGCAAAAAATTAGGGAAAATCTTTTCGGGTCAGTTTTTTGGAAAATTTTAACCGAAATCG
256 ATTGTGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
3748 TGTACTAACCATCA
321 TGTACTAACCATCA
* * *
3762 CGATTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACACAGTTTTGCATTATTTTTGGCAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* * *
3827 -TCCTTCGAAATATCTATATTCATCTAACCAAATCTCAGCCACGTTGGATTTACGGATTTATTTT
66 CT-CTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTT
* * *
3891 TACTAGTA-CTTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACA
130 TACGAGCATC-TGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACG
*
3955 ATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGAATTGAATTATATGATTTTTCT--G-A--
194 ATATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATT
* ***
4015 GT--------ATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGGAAAATTTTATATGAAATCGTGT
259 GTGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGT
*
4072 ACTAACCTTCA
324 ACTAACCATCA
4083 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* * *
4148 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTGAGCAAGGTTGGATTTACAGATTTGTTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* *
4213 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATAGAAAAACAAT
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
* * * *
4278 ATAAGAAGCGTGAAAAACCCTAAAATATTTTTGGAATTAAATTATATGATTTTTTTGAGTATTGT
196 ATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTGT
** *
4343 GATAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGGAAAATTTTAGCCGAAATCGTG---
261 GGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
4405 ---------
326 TAACCATCA
* * * *
4405 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTAAGTTTTGCATAATTTTTGGTAGAAAGT
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* *
4470 CTCCTCGAAATATCTGTATTCATCTAACCAAATCTTAGCCACGTTGGATTTACAGATTTGTTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* * ** ** *
4535 ACGAGCATCTGAGTCCTGTTTCGATTTAATTA-AGAATAAATTCG-GAAAAAAAATATGGAAAAA
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGA-AATGTATT-GTG-GCAGAAA-ATGGAAAAA
* * * **
4598 CAATATTAAAAGCGTGAAAAACATTAAAA-ATTTTTTGGCGTTGAATTATATGATATTTT-TGAG
192 CGATATTAGAAGCGTGAAAAACACTAAAATA-TTTTTGGAATTGAATTATATGAT-TTTTCTGAG
* * *
4661 TATTGTGGCAAAAGATTGGGGAAAAACTTTTCGGGTCGGTATTTTTGCAAAATTTTAGCCGAAAT
255 TATTGTGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGT-TTTTTGCAAAATTTTAGCCGAAAT
*
4726 CGTGTACTAACCATAA
319 CGTGTACTAACCATCA
* * *
4742 CGGTTTTTGGTTAAAAATGCGCTTT-GGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAG
1 CGGTTTTTGGCTGAAAACGCG-TTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAG
* * * * *
4806 ACTCTTCGAAATATCTGTATTCATTTAACTAAATCTCAGCCACGTTAGATTTACGGATTTATTTT
65 ACTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTT
* * * * *
4871 TACTAGTATTTGAATCTTCTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGAAAAAACGA
130 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGA
* * *
4936 TATTAAAAGCGTGAAAACCCCTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTG
195 TATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTG
* * *
5001 TGGCAAAAAATTGGGGAAAATCTTTTCGGGTCATTTTTTTGCAAAATTTTACCCAAAATCGTGTA
260 TGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTA
5066 CTAACCATCA
325 CTAACCATCA
* * * * *
5076 TGGTTTTTCGCTGAAAACGCATTTCGGAGCCCTGACTCAGTTTTGCATGATTTTTGGTAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* *
5141 CTCCTC-AAATATCTGTATTCATCTAACCAAATCTCAGCCACGATGGATTTACAGATTTGTTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* * ** * *
5205 ACGAACATCTGAATCTTGTTGCGATTTAATTAGAAGAAATAAATTG-AG-AAAAAGATGGAAAAA
131 ACGAGCATCTGAATCTTGTTTCGATTTAATT---AGAAATGTATTGTGGCAGAAA-ATGGAAAAA
* * * * * *
5268 CGATATTAGAAGCGTGAAAAGCATTAAAATTTTTTTGGAGTTGAATTATTTGATTTTTCAGAGTA
192 CGATATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTA
* * * *
5333 TTGTGGCAAAAAATTGGGGAAAATCTTTTCGGTTTAGTTTTTTGGAAAATTTTAACCGAAATCGT
257 TTGTGGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGT
5398 GTACTAACCATCA
322 GTACTAACCATCA
* *
5411 CGGTTTTTGGCTGAAAACGCGTTTCGGCGCCCTGACTCAGTTTTGCATAATTTTTGGCAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* * * * *
5476 CTCTTCGAAATATCTGTATTCATTTAACAAAATCTCAGCCACATTGGATTTACGGATTTATTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* * *
5541 -CTAGTATTTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
* * *
5605 ATTAGAAGCGTGTAAAACCCTAAAATATTTTTCGAATTGAATTATATGATTTTTCTGAGTATTGT
196 ATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTGT
* *
5670 GGCAAAAAATTGGGGAAAATCTTTTCGGGTCATTTTTTTGCAAAATTTTAGCCAAAATCGTGTAC
261 GGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
*
5735 GAACCATCA
326 TAACCATCA
*
5744 CGGTTTTTGGCTGAAAACGCGTTTCGGAGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* * * *
5809 CTCCTC-AAATATCTGTATTCATCTAACCAAATCTCAGTCACGATAGATTTACAGATTTGTTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* ** * *
5873 ACGAGCATCTGAATCATGTTTCGATTTAATTA-AGAATAAATT-CGG-AAAAAGATGGAAAAACG
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGA-AATGTATTGTGGCAGAAA-ATGGAAAAACG
* * * *
5935 ATATTAGAAGCGTCAAAAACATTAAAAT-TTTTTCGGCATTGAATTATATGATTTTTCTAAGTAT
194 ATATTAGAAGCGTGAAAAACACTAAAATATTTTT-GGAATTGAATTATATGATTTTTCTGAGTAT
5999 TGTGGCAAAAAATTGGGGGAAAA-CTTTTCGGGTCAGTTTTTTTGCAAAATTTTAGCCGAAATCG
258 TGTGGCAAAAAATT-GGGGAAAATCTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCCGAAATCG
*
6063 TGTACTAACCATAA
321 TGTACTAACCATCA
* * * * *
6077 CGGTTTTTGGTTAAAAATGCGTTTTGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAAA
1 CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
* * *
6142 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAACCACGTTGGATTTACGGATTTATTTTT
66 CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
* * *
6207 ACTAGTATTTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
131 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
*
6272 ATTAGAAGCGTGAAAAACACTAAAATAATTTTGGAATTGAATTATATGATTTTTCTGAGTATTGT
196 ATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTGT
* * *
6337 GGTAAAAGATTGGGGAAAATCTTTTCGGGTCAATTTTTTTGCAAAATTTTAGCC-ACAATCGTGT
261 GGCAAAAAATTGGGGAAAATCTTTTCGGGTC-AGTTTTTTGCAAAATTTTAGCCGA-AATCGTGT
6401 TTCTTTCTCT
Statistics
Matches: 3220, Mismatches: 336, Indels: 167
0.86 0.09 0.04
Matches are distributed among these distances:
321 294 0.09
322 161 0.05
323 7 0.00
324 93 0.03
325 31 0.01
326 2 0.00
328 23 0.01
329 30 0.01
330 220 0.07
331 20 0.01
332 158 0.05
333 608 0.19
334 431 0.13
335 797 0.25
336 186 0.06
337 155 0.05
338 4 0.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (334 bp):
CGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGA
CTCTTCGAAATATCTGTATTCATCTAACCAAATCTCAGCCACGTTGGATTTACAGATTTGTTTTT
ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGCAGAAAATGGAAAAACGAT
ATTAGAAGCGTGAAAAACACTAAAATATTTTTGGAATTGAATTATATGATTTTTCTGAGTATTGT
GGCAAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
TAACCATCA
Done.