Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023541.1 Corchorus olitorius cultivar O-4 contig23574, 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: 53174
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1117 original size:51 final size:51
Alignment explanation
Indices: 1041--1142 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
1031 ATTTATTATC
*
1041 CACAAAAATAAACCAAAAGACTATTCTTTAGAAGTCTAAATTAGGTTAGGG
1 CACAAAAATAAACCAAAAAACTATTCTTTAGAAGTCTAAATTAGGTTAGGG
1092 CACAAAAATAAACCAAAAAACTATTCTTTAGAAGTCTAAATTAGGTTAGGG
1 CACAAAAATAAACCAAAAAACTATTCTTTAGAAGTCTAAATTAGGTTAGGG
1143 TTTGAAGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (51 bp):
CACAAAAATAAACCAAAAAACTATTCTTTAGAAGTCTAAATTAGGTTAGGG
Found at i:4630 original size:2 final size:2
Alignment explanation
Indices: 4615--4661 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
4605 GCTCACTAGC
* *
4615 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4657 TA TA T
1 TA TA T
4662 CTTTCCCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5119 original size:4 final size:4
Alignment explanation
Indices: 5110--5148 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
5100 AAATGCATAT
5110 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
5149 ATATTCCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:8221 original size:10 final size:10
Alignment explanation
Indices: 8206--8236 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
8196 CGTTTTATTC
8206 AAATATCCAT
1 AAATATCCAT
*
8216 AAATATCCGT
1 AAATATCCAT
8226 AAATATCCAT
1 AAATATCCAT
8236 A
1 A
8237 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATATCCAT
Found at i:9440 original size:31 final size:31
Alignment explanation
Indices: 9405--9478 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
9395 TTCTGTTTTG
* * *
9405 AGTCTCAAATTGATCAATTTTTGAAATGTTT
1 AGTCTCAAATTGAGCAACTTTTGAAAGGTTT
9436 AGTCTCAAATTGAGCAACTTTTGAAAGGTTT
1 AGTCTCAAATTGAGCAACTTTTGAAAGGTTT
*
9467 AGGCTCAAATTG
1 AGTCTCAAATTG
9479 GTAATTTGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (31 bp):
AGTCTCAAATTGAGCAACTTTTGAAAGGTTT
Found at i:9849 original size:75 final size:77
Alignment explanation
Indices: 9715--9862 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 77
9705 AAACCTCTAT
* *
9715 AAATATAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGCTTACTAATGTATCGAGTGT
1 AAATATAATAATGTTGGGACCATGAAAAAATATTAATTTAGAGAGCTTACTAATGTATCGAGTAT
9780 TAATTTATATGG
66 TAATTTATATGG
** * * * *
9792 AAAT-TAATAATGTT-GGATTATGAAAAAATATTAATTTAGAGAGGTTATTGATTTATCGAGTAT
1 AAATATAATAATGTTGGGACCATGAAAAAATATTAATTTAGAGAGCTTACTAATGTATCGAGTAT
9855 TAATTTAT
66 TAATTTAT
9863 GGAGGTTATA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 49 0.78
76 10 0.16
77 4 0.06
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (77 bp):
AAATATAATAATGTTGGGACCATGAAAAAATATTAATTTAGAGAGCTTACTAATGTATCGAGTAT
TAATTTATATGG
Found at i:15586 original size:12 final size:12
Alignment explanation
Indices: 15571--15604 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15561 AGAATTTTGA
15571 TTCTTTTTTTCT
1 TTCTTTTTTTCT
*
15583 TTCTTATTTTCT
1 TTCTTTTTTTCT
*
15595 TCCTTTTTTT
1 TTCTTTTTTT
15605 TTTTGGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTTTTTTCT
Found at i:27751 original size:6 final size:6
Alignment explanation
Indices: 27740--27772 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
27730 ATTTGAGAAA
27740 TAATTG TAATTG TAATTG TAATTG TAATTG TAA
1 TAATTG TAATTG TAATTG TAATTG TAATTG TAA
27773 GAGAAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (6 bp):
TAATTG
Found at i:27939 original size:16 final size:16
Alignment explanation
Indices: 27914--27945 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27904 CCTTCATTTC
*
27914 ATTTCTCTCTACTTGT
1 ATTTCACTCTACTTGT
27930 ATTTCACTCTACTTGT
1 ATTTCACTCTACTTGT
27946 TTGTTCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTCACTCTACTTGT
Found at i:28638 original size:27 final size:27
Alignment explanation
Indices: 28602--28670 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
28592 AATTAAAATC
28602 ATATATATTAGGTTTTTTTTGGTGAAT
1 ATATATATTAGGTTTTTTTTGGTGAAT
28629 ATATATATTAGGTTTTTTTTGGTGAAT
1 ATATATATTAGGTTTTTTTTGGTGAAT
28656 ATATATATTAGGTTT
1 ATATATATTAGGTTT
28671 CAAATACAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (27 bp):
ATATATATTAGGTTTTTTTTGGTGAAT
Found at i:29716 original size:27 final size:27
Alignment explanation
Indices: 29686--29748 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
29676 TGAGATTGAC
*
29686 CTTGTACACTTATGGCAGGACTTGGTA
1 CTTGTACACTTATGGCAGGAATTGGTA
* *
29713 CTTGTACACTTGTGGCAGGAATTGGTG
1 CTTGTACACTTATGGCAGGAATTGGTA
*
29740 CTTGGACAC
1 CTTGTACAC
29749 CAATTGCAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.32
Consensus pattern (27 bp):
CTTGTACACTTATGGCAGGAATTGGTA
Found at i:30113 original size:132 final size:132
Alignment explanation
Indices: 29871--30150 Score: 479
Period size: 132 Copynumber: 2.1 Consensus size: 132
29861 GGGATACGAC
* * *
29871 ACAGATGAGGATGAAGTTTGTGGATAAGCAGGGGCTGAGACACCTTGGTCAATGCTGGGATATGC
1 ACAGATGAGGATGGAGCTTGTGGATAAGCAGGGGCGGAGACACCTTGGTCAATGCTGGGATATGC
29936 TGCAGATGGAGATGATCTAGATGGTAGGGACACAGGGACATGGACAATTTGGTCATTGATATAAG
66 TGCAGATGGAGATGATCTAGATGGTAGGGACACAGGGACATGGACAATTTGGTCATTGATATAAG
30001 AT
131 AT
* * *
30003 ACAGCTGAGGATGGAGCTTGTGGATAAGCAGGGGCGGAGACACCTTGGTCAATGCTTGGATATGT
1 ACAGATGAGGATGGAGCTTGTGGATAAGCAGGGGCGGAGACACCTTGGTCAATGCTGGGATATGC
* *
30068 TGCAGATGGAGATGATCTAGGTGGTCGGGACACAGGGACATGGACAATTTGGTCATTGATATAAG
66 TGCAGATGGAGATGATCTAGATGGTAGGGACACAGGGACATGGACAATTTGGTCATTGATATAAG
30133 AT
131 AT
*
30135 ACAGATGATGATGGAG
1 ACAGATGAGGATGGAG
30151 GAATAGAGGT
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 138 1.00
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.24
Consensus pattern (132 bp):
ACAGATGAGGATGGAGCTTGTGGATAAGCAGGGGCGGAGACACCTTGGTCAATGCTGGGATATGC
TGCAGATGGAGATGATCTAGATGGTAGGGACACAGGGACATGGACAATTTGGTCATTGATATAAG
AT
Found at i:36279 original size:17 final size:17
Alignment explanation
Indices: 36253--36286 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36243 CAAGAGTATG
* *
36253 ATAAATAAATGTACAAC
1 ATAAACAAATATACAAC
36270 ATAAACAAATATACAAC
1 ATAAACAAATATACAAC
36287 CCGTTGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.21
Consensus pattern (17 bp):
ATAAACAAATATACAAC
Found at i:42697 original size:17 final size:17
Alignment explanation
Indices: 42677--42709 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42667 TTAAAAGTGA
42677 AATTA-AATTAAACTAAC
1 AATTAGAATT-AACTAAC
42694 AATTAGAATTAACTAA
1 AATTAGAATTAACTAA
42710 GAAAGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (17 bp):
AATTAGAATTAACTAAC
Done.