Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011824.1 Corchorus olitorius cultivar O-4 contig11857, 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: 23114
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:282 original size:154 final size:154
Alignment explanation
Indices: 1--1967 Score: 3251
Period size: 154 Copynumber: 12.8 Consensus size: 154
*
1 AGTGTTCCAAATGAGCCAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* *
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCGAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
* **
131 GGCCCCGATAGGCCCTTAATAACA
131 GACCCCGATAGGCCCAAAATAACA
* * * *
155 AGTGTTCCAAATGAGCTAAAAACTTTACAGTGGACCAATCTCGCCAAAATGATTATAGTTAGTCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * * **
220 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCCAATCGAAGAAGATTCAATACGTCACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * *
285 GGCCCTGATAAGCCCAAAATAAAA
131 GACCCCGATAGGCCCAAAATAACA
* *
309 AGTATTCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
374 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
439 GACCCCGATAGGCCAAAAATAACA
131 GACCCCGATAGGCCCAAAATAACA
*
463 AGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
*
528 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
593 GACCCCGATAGGCCCAAAATAAAAA
131 GACCCCGATAGGCCCAAAAT-AACA
*
618 AGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA--CC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* ** *
681 ATAAACAATGGAGAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
** *
746 GACCTTGATAGGCCAAAAATAACA
131 GACCCCGATAGGCCCAAAATAACA
* *
770 AGTATTCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
835 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT-
* *
900 GGA-CTCGATAGGCCAAAAATAACA
130 GGACCCCGATAGGCCCAAAATAACA
*
924 AGTGTTCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
** *
989 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
1054 GACCTCGATAGGCCCAAAATAACA
131 GACCCCGATAGGCCCAAAATAACA
1078 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1143 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
1208 GACCCCGATAGGCCAAAAATAACA
131 GACCCCGATAGGCCCAAAATAACA
*
1232 AGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * *
1297 ATAAACAAGGGAAAGAAAAGCATTGAGGTTGGCCAAATCGAAGACGATTCGAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
**
1362 GACCCCGATAGGCCCTTAATAACA
131 GACCCCGATAGGCCCAAAATAACA
*
1386 AGTGTTACAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
** *
1451 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
1516 GACCTCGATAGGCCCAAAATAACA
131 GACCCCGATAGGCCCAAAATAACA
1540 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * ** *
1605 ATAAACAATGGAAAGAAAAGCATTAAGGTTTTCCAAATCGAAGACGATTCAAAACGTCACAAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
1670 GACCTCGATAGGCCCAAAATAACA
131 GACCCCGATAGGCCCAAAATAACA
* *
1694 AGTGTTCCAAATGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGGTTATAGTTAGGCC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* *
1759 CTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACGGAACTAATG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
*
1824 GACCCCGATAGGCCCAAAATAAAAA
131 GACCCCGATAGGCCCAAAAT-AACA
* *
1849 AGTGTTCTAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTA--CC
1 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* *
1912 ATAAATAATGGAGAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
66 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
1968 TCACAAATGG
Statistics
Matches: 1699, Mismatches: 108, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
152 61 0.04
153 136 0.08
154 1377 0.81
155 125 0.07
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
GACCCCGATAGGCCCAAAATAACA
Found at i:3688 original size:16 final size:17
Alignment explanation
Indices: 3661--3692 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3651 AAAAATTGAA
3661 GAAAATTCAAAAAAAGG
1 GAAAATTCAAAAAAAGG
3678 GAAAA-TCAAAAAAAG
1 GAAAATTCAAAAAAAG
3693 AAAGTGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.06, G:0.16, T:0.09
Consensus pattern (17 bp):
GAAAATTCAAAAAAAGG
Found at i:3849 original size:40 final size:40
Alignment explanation
Indices: 3805--3885 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
3795 GAATGTTTTC
* * * *
3805 TTTTTGAGAACTCTAAGAGAAAATTTTTGGAAAATAAATG
1 TTTTTGAGAAATCCAAAAGAAAACTTTTGGAAAATAAATG
* *
3845 TTTTTTAGAAATCCAAAAGAAGACTTTTGGAAAATAAATG
1 TTTTTGAGAAATCCAAAAGAAAACTTTTGGAAAATAAATG
3885 T
1 T
3886 GTTTCTTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (40 bp):
TTTTTGAGAAATCCAAAAGAAAACTTTTGGAAAATAAATG
Found at i:13501 original size:50 final size:50
Alignment explanation
Indices: 13440--13575 Score: 245
Period size: 50 Copynumber: 2.7 Consensus size: 50
13430 CACCTTTGAT
* *
13440 AGATTGCCCTTGTGTTTCATGTGTTTAGGGGCTTTGTATGTTTGAGAGAG
1 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
*
13490 AGATTGCCCTTGTGTTAAATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
1 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
13540 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTG
1 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTG
13576 GTTATTGGGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.18, C:0.10, G:0.30, T:0.41
Consensus pattern (50 bp):
AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
Found at i:17706 original size:16 final size:16
Alignment explanation
Indices: 17687--17725 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17677 TGCTGTGAGG
17687 ACATTTTGCTGCGGCA
1 ACATTTTGCTGCGGCA
* *
17703 ACATTCTGCTGTGGCA
1 ACATTTTGCTGCGGCA
*
17719 ATATTTT
1 ACATTTT
17726 TCAGCAACGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (16 bp):
ACATTTTGCTGCGGCA
Done.