Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014536.1 Corchorus olitorius cultivar O-4 contig14569, 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: 39361
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:307 original size:28 final size:28
Alignment explanation
Indices: 191--435 Score: 235
Period size: 28 Copynumber: 8.6 Consensus size: 28
181 GTATGCAAAA
* *
191 AAAATGATCAAAATGCCCCTGGA--CGC
1 AAAATGACCAAAATGCCCCTGGATGTGC
* * *
217 GAAATGACCAAAATGCCCCTAGATGAGC
1 AAAATGACCAAAATGCCCCTGGATGTGC
* * *
245 AAAAATGA-CAGAAATGCCCCTAGATGGGTA
1 -AAAATGACCA-AAATGCCCCTGGATGTG-C
*
275 AAAATGACCAAAATGCCCTTGGATGTGC
1 AAAATGACCAAAATGCCCCTGGATGTGC
* * * *
303 AAAATGACCGAAATGCCCCTAGATGGGTA
1 AAAATGACCAAAATGCCCCTGGATGTG-C
*
332 AAAATGACCAAAATGCCCTTGGATGTGC
1 AAAATGACCAAAATGCCCCTGGATGTGC
* * *
360 AAAATGACCGAAATGCCCCTAGATATGC
1 AAAATGACCAAAATGCCCCTGGATGTGC
* *
388 GTAAAATGACCAAAATGCCCTTGGATGCGC
1 --AAAATGACCAAAATGCCCCTGGATGTGC
*
418 AAAATGATCAAAATGCCC
1 AAAATGACCAAAATGCCC
436 TTGGGTTCGC
Statistics
Matches: 179, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
26 20 0.11
28 68 0.38
29 66 0.37
30 25 0.14
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATGTGC
Found at i:326 original size:57 final size:57
Alignment explanation
Indices: 218--435 Score: 330
Period size: 57 Copynumber: 3.8 Consensus size: 57
208 CCTGGACGCG
* * * *
218 AAATGACCAAAATGCCCCTAGATGAGCAAAAATGACAGAAATGCCCCTAGATGGGTAA
1 AAATGACCAAAATGCCCTTGGATGTGC-AAAATGACCGAAATGCCCCTAGATGGGTAA
276 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGATGGGTAA
1 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGATGGGTAA
*
333 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGATATGCGT-A
1 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAG--ATGGGTAA
* * *
391 AAATGACCAAAATGCCCTTGGATGCGCAAAATGATCAAAATGCCC
1 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCC
436 TTGGGTTCGC
Statistics
Matches: 150, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
57 78 0.52
58 67 0.45
59 5 0.03
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (57 bp):
AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGATGGGTAA
Found at i:436 original size:28 final size:28
Alignment explanation
Indices: 191--449 Score: 227
Period size: 29 Copynumber: 9.1 Consensus size: 28
181 GTATGCAAAA
* *
191 AAAATGATCAAAATGCCCCTGGA--CGC
1 AAAATGACCAAAATGCCCTTGGATGCGC
* * * *
217 GAAATGACCAAAATGCCCCTAGATGAGC
1 AAAATGACCAAAATGCCCTTGGATGCGC
* * * *
245 AAAAATGA-CAGAAATGCCCCTAGATGGGTA
1 -AAAATGACCA-AAATGCCCTTGGATGCG-C
*
275 AAAATGACCAAAATGCCCTTGGATGTGC
1 AAAATGACCAAAATGCCCTTGGATGCGC
* * * * *
303 AAAATGACCGAAATGCCCCTAGATGGGTA
1 AAAATGACCAAAATGCCCTTGGATGCG-C
*
332 AAAATGACCAAAATGCCCTTGGATGTGC
1 AAAATGACCAAAATGCCCTTGGATGCGC
* * * *
360 AAAATGACCGAAATGCCCCTAGATATGCGT
1 AAAATGACCAAAATG-CCCTTG-GATGCGC
390 AAAATGACCAAAATGCCCTTGGATGCGC
1 AAAATGACCAAAATGCCCTTGGATGCGC
* * *
418 AAAATGATCAAAATGCCCTTGGGTTCGC
1 AAAATGACCAAAATGCCCTTGGATGCGC
446 AAAA
1 AAAA
450 ATGTCAATTA
Statistics
Matches: 191, Mismatches: 33, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
26 20 0.10
28 75 0.39
29 76 0.40
30 20 0.10
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCTTGGATGCGC
Found at i:960 original size:58 final size:58
Alignment explanation
Indices: 727--944 Score: 341
Period size: 58 Copynumber: 3.8 Consensus size: 58
717 TTTTATTATT
* *
727 AAAACTTTCTAACAGAGACCTCGAATAGGATTTTAAAACAAGA-TATGA-TTTGAATTG
1 AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATTA-GATTTTGAATTG
* *
784 AAAACTCTCTAACAGAGACCTCGACCAGGATTTTAAAACAAGATCAGATTTTGAATTG
1 AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATTAGATTTTGAATTG
* *
842 AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAGATAAGATTAGATTTTGAATTG
1 AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATTAGATTTTGAATTG
* *
900 AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAGATAAGATT
1 AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATT
945 TTGTTTTAAA
Statistics
Matches: 151, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
57 42 0.28
58 109 0.72
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (58 bp):
AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATTAGATTTTGAATTG
Found at i:17664 original size:29 final size:28
Alignment explanation
Indices: 17622--17792 Score: 173
Period size: 29 Copynumber: 5.8 Consensus size: 28
17612 ATAAAAGACC
*
17622 AAAATGACCAAAATGCCACTGGATATGCT
1 AAAATGACCAAAATGCC-CTGGATATGCA
**
17651 AAAATGACCAAAATGCTCCTAAATATGCA
1 AAAATGACCAAAATGC-CCTGGATATGCA
* *
17680 AAAATGACCAAAATGCCCTCGGATGTAC-
1 AAAATGACCAAAATGCCCT-GGATATGCA
**
17708 AAAATGACCCAAAATGCCCCTAAATATGCTA
1 AAAATGA-CCAAAATG-CCCTGGATATGC-A
* *
17739 AAAATGACCAAAATGCCCTCGGATGTACAA
1 AAAATGACCAAAATGCCCT-GGATATGC-A
17769 AAAATGACCAAAATGCCTCTGGAT
1 AAAATGACCAAAATGCC-CTGGAT
17793 TCACAAAAGG
Statistics
Matches: 118, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
28 10 0.08
29 60 0.51
30 39 0.33
31 9 0.08
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCTGGATATGCA
Found at i:17720 original size:58 final size:59
Alignment explanation
Indices: 17622--17785 Score: 244
Period size: 58 Copynumber: 2.8 Consensus size: 59
17612 ATAAAAGACC
* * * *
17622 AAAATGACCAAAATGCCACT-GGATATGCTAAAATGACCAAAATGCTCCTAAATATGC-A
1 AAAATGACCAAAATGCC-CTCGGATGTACAAAAATGACCAAAATGCCCCTAAATATGCTA
17680 AAAATGACCAAAATGCCCTCGGATGTAC-AAAATGACCCAAAATGCCCCTAAATATGCTA
1 AAAATGACCAAAATGCCCTCGGATGTACAAAAATGA-CCAAAATGCCCCTAAATATGCTA
17739 AAAATGACCAAAATGCCCTCGGATGTACAAAAAATGACCAAAATGCC
1 AAAATGACCAAAATGCCCTCGGATGTAC-AAAAATGACCAAAATGCC
17786 TCTGGATTCA
Statistics
Matches: 98, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
57 9 0.09
58 43 0.44
59 29 0.30
60 10 0.10
61 7 0.07
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (59 bp):
AAAATGACCAAAATGCCCTCGGATGTACAAAAATGACCAAAATGCCCCTAAATATGCTA
Found at i:23869 original size:30 final size:30
Alignment explanation
Indices: 23813--23871 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
23803 AATGTCACCG
* *
23813 GATATTTGTCGATATATCCGTGTATCCGTC
1 GATATTTATCGATATATCCGTATATCCGTC
*
23843 GATATTTATCGATATCT-CGATATATCCGT
1 GATATTTATCGATATATCCG-TATATCCGT
23872 AAATATCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (30 bp):
GATATTTATCGATATATCCGTATATCCGTC
Found at i:24118 original size:27 final size:28
Alignment explanation
Indices: 24080--24153 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
24070 GGTCATTTAG
24080 GGGGCATTTTGGTCATTTTTGCA-TTCA
1 GGGGCATTTTGGTCATTTTTGCAGTTCA
24107 GGGGCATTTTGGTCA-TTTTGCATGTTCA
1 GGGGCATTTTGGTCATTTTTGCA-GTTCA
24135 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
24154 AAGTTCACAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
26 7 0.16
27 15 0.34
28 19 0.43
29 3 0.07
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTTGCAGTTCA
Found at i:30700 original size:12 final size:13
Alignment explanation
Indices: 30683--30716 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
30673 TCGATACCTT
30683 GATATATCCG-TC
1 GATATATCCGTTC
30695 GATATATCCGTTC
1 GATATATCCGTTC
30708 GATATATCC
1 GATATATCC
30717 ATGGATACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (13 bp):
GATATATCCGTTC
Found at i:30853 original size:13 final size:13
Alignment explanation
Indices: 30837--30862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30827 TAATTTTATT
30837 TTATAATAATATA
1 TTATAATAATATA
30850 TTATAATAATATA
1 TTATAATAATATA
30863 CTTAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTATAATAATATA
Done.