Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012283.1 Corchorus olitorius cultivar O-4 contig12316, 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: 32717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:913 original size:333 final size:333
Alignment explanation
Indices: 9--1185 Score: 1604
Period size: 333 Copynumber: 3.6 Consensus size: 333
1 AAAATAAC
9 CTATAAGTGTTTTGGCCAAAGATTGT-G-AAAAA-CATTTCGGGTCAATTTTTGCAAAATTTTAG
1 CTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATC-TTTCGGGTCAATTTTTGCAAAATTTTAG
*
71 CCGAAATCGTGTACTAACCATCACAGTTTTTGGCT----A-----TCCGGAGCTCCGGCTAAGTT
65 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCTCCGGCTAAGTT
*
127 TTCAATGATTTTTGGCCCCGAGACTCCTTGACATATATATATATTCATCTAACCAAATCTCAGCC
130 TTCAATGATTTTTGGCCCCAAGACTCCTTGAC--ATATATATATTCATCTAACCAAATCTCAGCC
*
192 AAATTGGATTTACGGATTTGATTTTACGAGCATC-AA-CATGTTTCGATTTAATAAGAAATTAGT
193 AAATTGGATTTACGGATTTGATTTTACGAGCATCAAATCATGTTTCGATTTAATCAGAAATTAGT
* * * *
255 TCGCAAAGATATTGGAATATCGATATTAGAAGAGTGAAAAACCCTTCAATCTTTTTGGCGTTGAA
258 TCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAA
320 TTATACATATT
323 TTATACATATT
* * *
331 CTGTAAGTGTTTTGACCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGC
1 CTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
* * * ** * * *
396 CAAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGTGATATGGGGC-CTCGTCTTA-T
66 CGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACGCGTTCCGGAGCTC-CGGCTAAGT
* * *
459 ATTCTAATGATTTTTGGCCCCGAGACTCCTTGACATATATATATTCATCTAACCAAATCTCTGCC
129 TTTC-AATGATTTTTGGCCCCAAGACTCCTTGACATATATATATTCATCTAACCAAATCTCAGCC
* * * * * * * *
524 AAATTGGATTTAAGGATTTAATTGTACGGGCATTACATTCATGTTTCGATTTAATCAGAATTTAA
193 AAATTGGATTTACGGATTTGATTTTACGAGCATCA-AATCATGTTTCGATTTAATCAGAAATTAG
* *
589 TTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATGTTTTTGGCATTGA
257 TTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGA
* * *
654 GTTAAATATATT
322 ATTATACATATT
*
666 CTATAAGTGTTTTGGCCAAAGATTGTGG-AAAAA-CGTTTCGGGTCAATTTTTGCAAAATTTTTG
1 CTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATC-TTTCGGGTCAATTTTTGCAAAATTTTAG
*
729 CCGAAATCGTGTACTAACCATCACGGTATTTGGCTAAAAACGCGTTCCGGAGCTCCGGCTAAGTT
65 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCTCCGGCTAAGTT
* * * *
794 TTCAATGATATTTGGCCCCAAGACTACTTGACATATCTATATTCATCTAACCAAATCTAAGCCAA
130 TTCAATGATTTTTGGCCCCAAGACTCCTTGACATATATATATTCATCTAACCAAATCTCAGCCAA
859 ATTGGATTTACGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAGTT
195 ATTGGATTTACGGATTTGATTTTACGAGCATCA-AATCATGTTTCGATTTAATCAGAAATTAGTT
*
924 CGGAAAGATATAGGAAAATCGATATTAGAAGCGTTAAAAACCCTTCAATCTTTTTGGCGTTGAAT
259 CGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAAT
989 TATACATATT
324 TATACATATT
999 CTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
1 CTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
* * * * *
1064 CGAAATCATGTA-T-----T----GTTTTTGGCTAAAAACGCGTTCCAGG-TCGCCAGCTCAGTT
66 CGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGAGCTCCGGCTAAGTT
* * *
1118 TTCAATGATTTTTTGCCCCGAA-ACTCCTTGACATATCTATATTTATCTAACCAAATCTCAGCCA
130 TTCAATGATTTTTGGCCCC-AAGACTCCTTGACATATATATATTCATCTAACCAAATCTCAGCCA
1182 AATT
194 AATT
1186 TAATTTATGG
Statistics
Matches: 753, Mismatches: 77, Indels: 48
0.86 0.09 0.05
Matches are distributed among these distances:
322 24 0.03
323 1 0.00
324 148 0.20
325 14 0.02
328 1 0.00
329 1 0.00
332 59 0.08
333 242 0.32
334 145 0.19
335 118 0.16
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (333 bp):
CTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
CGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCTCCGGCTAAGTTT
TCAATGATTTTTGGCCCCAAGACTCCTTGACATATATATATTCATCTAACCAAATCTCAGCCAAA
TTGGATTTACGGATTTGATTTTACGAGCATCAAATCATGTTTCGATTTAATCAGAAATTAGTTCG
GAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTA
TACATATT
Found at i:4067 original size:21 final size:22
Alignment explanation
Indices: 4032--4082 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
4022 CGTAATTTCA
4032 TTTTTATAAATAAAAATTACATT
1 TTTTTA-AAATAAAAATTACATT
*
4055 TTTTTCAAAA-AAAAATCCACATT
1 TTTTT-AAAATAAAAAT-TACATT
4078 TTTTT
1 TTTTT
4083 TTGAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 6 0.24
23 18 0.72
24 1 0.04
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTTAAAATAAAAATTACATT
Found at i:4859 original size:2 final size:2
Alignment explanation
Indices: 4852--4896 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4842 AACCTTAAGC
4852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4894 AT A
1 AT A
4897 CACGATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19564 original size:18 final size:18
Alignment explanation
Indices: 19541--19583 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
19531 TTGGGTTTAG
19541 TCAGTTTCTTGAGTCAGT
1 TCAGTTTCTTGAGTCAGT
*
19559 TCAGTTTTTTTGAGTCAGT
1 TCAG-TTTCTTGAGTCAGT
19578 T-AGTTT
1 TCAGTTT
19584 GAGTATGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 6 0.26
19 14 0.61
ACGTcount: A:0.16, C:0.12, G:0.21, T:0.51
Consensus pattern (18 bp):
TCAGTTTCTTGAGTCAGT
Found at i:24594 original size:16 final size:16
Alignment explanation
Indices: 24573--24604 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24563 TGAAGGATTG
24573 TGGAGTATAGCTTCCT
1 TGGAGTATAGCTTCCT
24589 TGGAGTATAGCTTCCT
1 TGGAGTATAGCTTCCT
24605 GAAGGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
TGGAGTATAGCTTCCT
Found at i:27792 original size:28 final size:27
Alignment explanation
Indices: 27750--27804 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
27740 TTTTTATTTG
*
27750 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
27776 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
27805 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:32442 original size:18 final size:19
Alignment explanation
Indices: 32419--32454 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32409 AATGAGTTTG
*
32419 AAAAAAATG-AAGAAGTGA
1 AAAAAAAGGAAAGAAGTGA
32437 AAAAAAAGGAAAGAAGTG
1 AAAAAAAGGAAAGAAGTG
32455 GGACTTGGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (19 bp):
AAAAAAAGGAAAGAAGTGA
Done.