Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015158.1 Corchorus olitorius cultivar O-4 contig15191, 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: 9535
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1006 original size:332 final size:331
Alignment explanation
Indices: 1--1659 Score: 1522
Period size: 332 Copynumber: 5.0 Consensus size: 331
* * * * * * * *
1 AATCCTTTTGGTGTTAAATTATA-TATATTTTATGAGTATTTATAGC-AAAAATTGACAGAAAAC
1 AATCTTTTTGGCGTTGAATTATATTATTTTTTATGAGTA-TTGTGGCTAAAAATTGA-GGAAAAA
* * * ** * * * *
64 TTTTTTGGGTCACTTTTTACAAAATTTTAGCTGAAATCGTATACTAATCATCATAGTTTTTTTGG
64 TATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAC----CATCATGGGTTTTTTGG
* * ** * *
129 CTAAGAACGCGTTTCGGAACCC-CGGTTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
125 CTAAAAACGCGTTCCGGGGCCCTAGG-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-AA
* * * **
193 ATATCTATATTTATCTAATCAAATCTTAGCCACATTCAATTTAAGGATTTGTTTTTACGAG----
188 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGATTC
* * * * *
254 -G---C-----TCGATTTAATTAGAAATTAATTCTCAGAAAATATA--AAAAATGATATTAAAAG
253 TGAATCTTGTTTCGATTTAATTAGAAATTAATTTTGA-AAAAAATAGGAAAAACGATATTAGAAG
* * *
308 CGTGAAGAGTCCTCC
317 CGTGAAAAGCCCTTC
* * * * * * *
323 AATATTTTTGGCTTTTAATTATA-TATATTCTATAAGTATTGTGGCTAAAAATGGAGGAAAAATA
1 AATCTTTTTGGCGTTGAATTATATTATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATA
* * * * ** *
387 TTTTGGGTCAATTTTTGGAAAATATTAGCCGAAATCGTGTACTAT-AACGGTTTTTTGGCTAGAA
66 TTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACCATCATGGGTTTTTTGGCTAAAA
** * * * * * *
451 ACGCGTTTTGGGGCCCCAGGTCAGTTTTGCATGATTTTTAGTGGCAACATTCCTTGAAATATCTA
131 ACGCGTTCCGGGGCCCTAGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-AAATATCTA
* *
516 TATTCATCTAACCAAATCTTAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATT-TGAATC
195 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG-ATTCTGAATC
* * * ** *
580 ATGTTTCAATTTAATTAGACATTAA-TTTGAAAACAAATAGGAAAAGTGATATTAGAAGCGTGAG
259 TTGTTTCGATTTAATTAGAAATTAATTTTGAAAA-AAATAGGAAAAACGATATTAGAAGCGTGAA
*
644 AAGCCCTTT
323 AAGCCCTTC
* *
653 AATCTTTTTGGCGTGGAATTATATT-TTTTTTATGAGTATTGTGGCTAAAAATTGAGAAAAAATA
1 AATCTTTTTGGCGTTGAATTATATTATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATA
* * * * *
717 TTTCAGATCAATTTTTGTAAAATTTTAGCCGAAATTGTGTACCATCTTGGTTGTTTTTTTGCTAA
66 TTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACCATCATGG--GTTTTTTGGCTAA
* * *
782 AAAAGCGTTCCGGGGCTCTAGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-AATATAT
129 AAACGCGTTCCGGGGCCCTAGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTAAATATCT
* * * * * *
846 ATATTCATCTAACCAAATCTCAGCCGCATTGTATTTAAGAATTTGTTTGTACGAGTTTCTAAATC
194 ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGATTCTGAATC
* *
911 TTGTTTTGATTTAATCAGAAATTAATTTTGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAA
259 TTGTTTCGATTTAATTAGAAATTAATTTTGAAA-AAAATAGGAAAAACGATATTAGAAGCGTG-A
*
976 AAAG-CTTTC
322 AAAGCCCTTC
* * ** * *
985 AATTTTTTTGGCGTTGAATTAT-TTATTTTTTATGAGTATTTTCACTAGAAATTGAGGAAAAATC
1 AATCTTTTTGGCGTTGAATTATATTATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATA
* * *
1049 TTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCA-CGG-TTTTCGGCT
66 TTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTG---T-ACCATCATGGGTTTTTTGGCT
* * * *
1111 AAAAACGCGTTCCGGGACCCTA-CTCAGTTTTGCATGATTTTTGGTGTCAAGACTCCTTGAAATA
127 AAAAACGCGTTCCGGGGCCCTAGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-AAATA
* * * *
1175 TTTATATTCATCTAACCAAATCTCAGCCCCATTAGATTTAAGGATTTATTTTTACGAGCATT-TG
191 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG-ATTCTG
* * *
1239 AATCTTGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAATAGGAATAAACAATATTAGAAGCG
255 AATCTTGTTTCGATTTAATTAGAAATTAATTTTGAAAAAAATAGGAA-AAACGATATTAGAAGCG
*
1303 TTAAAAGCCCTTC
319 TGAAAAGCCCTTC
*** * * * * *
1316 AATCTTTTTGATATCGAATTATATATATTTTTTATGAGTATTTTAGCAAAAAATTGAGGAAATAT
1 AATCTTTTTGGCGTTGAATTATAT-TATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAT
* *
1381 CTTTCGGGTCAATTTTT-TCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGG--TTTTGG
65 ATTTCGGGTCAATTTTTGT-AAAATTTTAGCCGAAATCGTG---T-ACCATCATGGGTTTTTTGG
* * * * * **
1443 CTAAAAACGCGTTACAGGG-CC-ACGACTATGTTTTGCATGATTTTTGGCACTGAGACTCCTTGA
125 CTAAAAACGCGTTCCGGGGCCCTAGGTC-A-GTTTTGCATGATTTTTGGCGCCAAGACTCCTT-A
* * * * *
1506 AATATCTTTATTCATCTAACCAAATCTCAGCGATATTGGATTTAAGGATTTGTTTTTATGTGCA-
187 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG-AT
** * *
1570 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATATGAAAAACGATATTAAAA
251 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTTGAAAAAAATAGGAAAAACGATATTAGAA
* * * *
1635 TCATGAAAAGTCCTCC
316 GCGTGAAAAGCCCTTC
1651 AATCTTTTT
1 AATCTTTTT
1660 TGGCATCTTT
Statistics
Matches: 1108, Mismatches: 183, Indels: 79
0.81 0.13 0.06
Matches are distributed among these distances:
316 115 0.10
317 4 0.00
321 48 0.04
322 39 0.04
324 1 0.00
327 3 0.00
328 7 0.01
329 18 0.02
330 166 0.15
331 168 0.15
332 194 0.18
333 124 0.11
334 53 0.05
335 155 0.14
336 13 0.01
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (331 bp):
AATCTTTTTGGCGTTGAATTATATTATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATA
TTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACCATCATGGGTTTTTTGGCTAAAA
ACGCGTTCCGGGGCCCTAGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTAAATATCTAT
ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGATTCTGAATCTT
GTTTCGATTTAATTAGAAATTAATTTTGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAG
CCCTTC
Found at i:3926 original size:33 final size:30
Alignment explanation
Indices: 3883--3970 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 30
3873 AATTACATAT
*
3883 TATTTTTAATAATATTTACTGTATATTAAATAAA
1 TATTTCTAATAATATTTAC---ATATT-AATAAA
3917 TA-TTCTAATAACTA-TTACATATTAATAAA
1 TATTTCTAATAA-TATTTACATATTAATAAA
*
3946 TATTTCTAATAAAATTTGA-ATATTA
1 TATTTCTAATAATATTT-ACATATTA
3971 TTTGAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
29 9 0.19
30 22 0.46
31 1 0.02
33 12 0.25
34 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (30 bp):
TATTTCTAATAATATTTACATATTAATAAA
Found at i:4066 original size:11 final size:11
Alignment explanation
Indices: 4021--4083 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
4011 AATCTTAATT
4021 AACGAAC-ATA
1 AACGAACAATA
* *
4031 AACGAGCTATA
1 AACGAACAATA
* *
4042 AACGAGCTATTA
1 AACGAAC-AATA
*
4054 AATGAACAATA
1 AACGAACAATA
*
4065 AACGAACACTA
1 AACGAACAATA
4076 AACGAACA
1 AACGAACA
4084 TTAATCGAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
10 6 0.14
11 30 0.70
12 7 0.16
ACGTcount: A:0.54, C:0.19, G:0.13, T:0.14
Consensus pattern (11 bp):
AACGAACAATA
Found at i:4739 original size:49 final size:50
Alignment explanation
Indices: 4667--4771 Score: 187
Period size: 49 Copynumber: 2.1 Consensus size: 50
4657 AAAAAATCTA
4667 TTGAA-TAGCGATGTTTGTCCCCCCAAAACGCCCCTATATATAGTGGCGT
1 TTGAATTAGCGATGTTTGTCCCCCCAAAACGCCCCTATATATAGTGGCGT
*
4716 TTGAATTA-CGATGTTTGTCCCCCCAAAACGCCTCTATATATAGTGGCGT
1 TTGAATTAGCGATGTTTGTCCCCCCAAAACGCCCCTATATATAGTGGCGT
4765 TTGAATT
1 TTGAATT
4772 GGACAAACGC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 52 0.96
50 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (50 bp):
TTGAATTAGCGATGTTTGTCCCCCCAAAACGCCCCTATATATAGTGGCGT
Done.