Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016902.1 Corchorus olitorius cultivar O-4 contig16935, 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: 50073
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:164 original size:22 final size:22
Alignment explanation
Indices: 115--166 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
105 CCTGTGTTTT
*
115 TTTTCTACATTTCTTTTTTAATC
1 TTTT-TACATTTCTCTTTTAATC
138 TTTTTACATTT-TCTTTTAATTTC
1 TTTTTACATTTCTCTTTTAA--TC
161 TTTTTA
1 TTTTTA
167 TCTTTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 7 0.27
23 12 0.46
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTACATTTCTCTTTTAATC
Found at i:8840 original size:10 final size:10
Alignment explanation
Indices: 8825--8853 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
8815 TATAACGTCT
8825 CTCTCTCTCC
1 CTCTCTCTCC
8835 CTCTCTCTCC
1 CTCTCTCTCC
8845 CTCTCTCTC
1 CTCTCTCTC
8854 TACACTGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (10 bp):
CTCTCTCTCC
Found at i:25101 original size:2 final size:2
Alignment explanation
Indices: 25094--25120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25084 TGAATTTGCT
25094 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
25121 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:26485 original size:72 final size:72
Alignment explanation
Indices: 26364--26506 Score: 241
Period size: 72 Copynumber: 2.0 Consensus size: 72
26354 AATTAGTTGC
* *
26364 TTATGCACAAATTCCTTGACGAAAGTGCAGAACTCGATAACTTGAGTATTTGGATTAATTTGGCT
1 TTATGCACAAATTCCTTGACGAAAGTGCAGAACTCAATAACTTGAGTATTTAGATTAATTTGGCT
*
26429 TCTTTTT
66 TATTTTT
* *
26436 TTATGCACAAATTCCTTGAGGAAAGTGCAGAACTCAATAACTTGTGTATTTAGATTAATTTGGCT
1 TTATGCACAAATTCCTTGACGAAAGTGCAGAACTCAATAACTTGAGTATTTAGATTAATTTGGCT
26501 TATTTT
66 TATTTT
26507 CTGCTACATC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (72 bp):
TTATGCACAAATTCCTTGACGAAAGTGCAGAACTCAATAACTTGAGTATTTAGATTAATTTGGCT
TATTTTT
Found at i:29388 original size:30 final size:27
Alignment explanation
Indices: 29335--29393 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
29325 AAAGGCACTG
29335 GATATCAACATATATTATACTACTACT
1 GATATCAACATATATTATACTACTACT
29362 GATATCAACATATATTATACTACTACT
1 GATATCAACATATATTATACTACTACT
29389 GATAT
1 GATAT
29394 AAAGCTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (27 bp):
GATATCAACATATATTATACTACTACT
Found at i:38429 original size:11 final size:11
Alignment explanation
Indices: 38413--38438 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38403 TGATTTTACA
38413 TAAGACTAGTT
1 TAAGACTAGTT
38424 TAAGACTAGTT
1 TAAGACTAGTT
38435 TAAG
1 TAAG
38439 CTTTCACGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (11 bp):
TAAGACTAGTT
Found at i:38513 original size:22 final size:22
Alignment explanation
Indices: 38481--38600 Score: 95
Period size: 22 Copynumber: 5.5 Consensus size: 22
38471 AGAATAGTTT
*
38481 TATGAAATTTTTATAATTACCC
1 TATGAAATTTTGATAATTACCC
* * *
38503 TATTAAATTTTGATAATCACGC
1 TATGAAATTTTGATAATTACCC
*
38525 TATGAAATTTTGATAATTA-TC
1 TATGAAATTTTGATAATTACCC
* *
38546 TATGATATTGTGATAA--ACTCC
1 TATGAAATTTTGATAATTAC-CC
* * *
38567 ATATGAATTTTTGATAACCTA-AC
1 -TATGAAATTTTGATAA-TTACCC
38590 TATGAAATTTT
1 TATGAAATTTT
38601 ACCTTCCTAT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.01
21 16 0.21
22 58 0.75
23 1 0.01
25 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATTACCC
Found at i:38631 original size:21 final size:21
Alignment explanation
Indices: 38568--38660 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
38558 ATAAACTCCA
* **
38568 TATGAATTTTTGATAACCTAAC
1 TATGAAATTTT-ATAACCTTCC
38590 TATGAAA-TTT-T-ACCTTCC
1 TATGAAATTTTATAACCTTCC
*
38608 TATGAAATTTTATAACCTTGC
1 TATGAAATTTTATAACCTTCC
** *
38629 TATGATTTTTTATAATCTTCC
1 TATGAAATTTTATAACCTTCC
*
38650 TATGAGATTTT
1 TATGAAATTTT
38661 GTTAATCTCC
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
18 12 0.21
19 4 0.07
20 1 0.02
21 35 0.60
22 6 0.10
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Found at i:38666 original size:22 final size:21
Alignment explanation
Indices: 38603--38682 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
38593 GAAATTTTAC
* * *
38603 CTTCCTATGAAATTTTATAAC
1 CTTCCTATGAGATTTTTTAAT
* *
38624 CTTGCTATGA-TTTTTTATAAT
1 CTTCCTATGAGATTTTT-TAAT
38645 CTTCCTATGAGATTTTGTTAAT
1 CTTCCTATGAGATTTT-TTAAT
*
38667 CTCCCTAT-A-ATTTTTT
1 CTTCCTATGAGATTTTTT
38683 GATACTATAG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 2 0.04
20 9 0.18
21 22 0.45
22 15 0.31
23 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (21 bp):
CTTCCTATGAGATTTTTTAAT
Found at i:38777 original size:42 final size:42
Alignment explanation
Indices: 38718--38810 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
38708 ATCTCTATTC
38718 GCAGATCGAGCTCGTCCACTCAGTCGTACAAACATATATAAT
1 GCAGATCGAGCTCGTCCACTCAGTCGTACAAACATATATAAT
38760 GCAGATCGAGCTCGTCCACTCAGTCGTACAAACATATATAAT
1 GCAGATCGAGCTCGTCCACTCAGTCGTACAAACATATATAAT
* *
38802 TCATATCGA
1 GCAGATCGA
38811 ACTCATCCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
GCAGATCGAGCTCGTCCACTCAGTCGTACAAACATATATAAT
Found at i:38887 original size:38 final size:36
Alignment explanation
Indices: 38809--38882 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
38799 AATTCATATC
*
38809 GAACTCATCCCTTTGATAGTATACTATATATAGAGA
1 GAACTCATCCATTTGATAGTATACTATATATAGAGA
38845 GAACTCATCCATTTGATAGTATACTATATATAGAGA
1 GAACTCATCCATTTGATAGTATACTATATATAGAGA
38881 GA
1 GA
38883 GAACTACTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (36 bp):
GAACTCATCCATTTGATAGTATACTATATATAGAGA
Found at i:39000 original size:35 final size:35
Alignment explanation
Indices: 38956--39025 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
38946 ACACCCAAAG
38956 ATCCCACTAACCACAGTATCTCCAAACACCGTAAT
1 ATCCCACTAACCACAGTATCTCCAAACACCGTAAT
* *
38991 ATCCTACTAACCTCAGTATCTCCAAACACCGTAAT
1 ATCCCACTAACCACAGTATCTCCAAACACCGTAAT
39026 TCCAATATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.36, G:0.06, T:0.23
Consensus pattern (35 bp):
ATCCCACTAACCACAGTATCTCCAAACACCGTAAT
Found at i:39949 original size:385 final size:385
Alignment explanation
Indices: 39239--40013 Score: 1435
Period size: 385 Copynumber: 2.0 Consensus size: 385
39229 AAAATATGAA
39239 ATTCACAATCTTGCAACGGTATAAATTATGAAATCACACAATATAATTAATTTATTTTATGTTTC
1 ATTCACAATCTTGCAACGGTATAAATTATGAAATCACACAATATAATTAATTTATTTTATGTTTC
39304 CAATAAAACAATGTTGAAAAAAGTGTTACGTAAGTTCGTAACTCAAATATCAAAGAAAACACTAA
66 CAATAAAACAATGTTGAAAAAAGTGTTACGTAAGTTCGTAACTCAAATATCAAAGAAAACACTAA
39369 ATTTAAAGGATTACGCAAGAATGCGACATGATAATCCAGACACCTTCACCCAAGACCTAAATTTC
131 ATTTAAAGGATTACGCAAGAATGCGACATGATAATCCAGACACCTTCACCCAAGACCTAAATTTC
39434 TTTCTCAATTTCAAACATACAACTTTTTTAATAAGAATAAAAGCAAACAATCATCAAAATTCGTA
196 TTTCTCAATTTCAAACATACAACTTTTTTAATAAGAATAAAAGCAAACAATCATCAAAATTCGTA
* *
39499 CATACGTTTAAAAACTCAACTCTTTTGAAAAATCGTTTTAAGAAATCATCAAACATAGTATTGAA
261 CATACGTTTAAAAACTCAACTCCTTTGAAAAATCGTTTTAAGAAATCATCAAACATAGCATTGAA
*
39564 AAAAAAATG-AAGAAAATAATTTACTCTTTTTTTGGCTTTTCTTTTGGCAATCTAATCCG
326 AAAAAAATGAAAAAAAATAATTTACTCTTTTTTTGGCTTTTCTTTTGGCAATCTAATCCG
39623 ATTCACAATCTTGCAACGGTATAAATTATGAAATCACACAATATAATTAATTTATTTTATGTTTC
1 ATTCACAATCTTGCAACGGTATAAATTATGAAATCACACAATATAATTAATTTATTTTATGTTTC
*
39688 CAATAGAACAATGTTGAAAAAAAGTGTTACGTAAGTTCGTAACTCAAATATCAAAGAAAACACTA
66 CAATAAAACAATGTTG-AAAAAAGTGTTACGTAAGTTCGTAACTCAAATATCAAAGAAAACACTA
39753 AATTTAAAGGATTACGCAAGAATGCGACATGATAATCCAGACACCTTCACCCAAGACCTAAATTT
130 AATTTAAAGGATTACGCAAGAATGCGACATGATAATCCAGACACCTTCACCCAAGACCTAAATTT
* * *
39818 CTTTCTCAATTTCAAACATAGAATTTTTTTAATGAGAATAAAAGCAAACAATCATCAAAATTCGT
195 CTTTCTCAATTTCAAACATACAACTTTTTTAATAAGAATAAAAGCAAACAATCATCAAAATTCGT
*
39883 ACATACGTTTAAAAATTCAACTCCTTTGAAAAATCGTTTTAAGAAATCATCAAACATAGCATTGA
260 ACATACGTTTAAAAACTCAACTCCTTTGAAAAATCGTTTTAAGAAATCATCAAACATAGCATTGA
*
39948 AAAAAAAATGAAAAAAAAAATAATTTACTCTTTTTTTGGCTTTTCTTTTGGCAATCTAATTCG
325 AAAAAAAATG--AAAAAAAATAATTTACTCTTTTTTTGGCTTTTCTTTTGGCAATCTAATCCG
40011 ATT
1 ATT
40014 TAGCTCATAT
Statistics
Matches: 378, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
384 80 0.21
385 247 0.65
388 51 0.13
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (385 bp):
ATTCACAATCTTGCAACGGTATAAATTATGAAATCACACAATATAATTAATTTATTTTATGTTTC
CAATAAAACAATGTTGAAAAAAGTGTTACGTAAGTTCGTAACTCAAATATCAAAGAAAACACTAA
ATTTAAAGGATTACGCAAGAATGCGACATGATAATCCAGACACCTTCACCCAAGACCTAAATTTC
TTTCTCAATTTCAAACATACAACTTTTTTAATAAGAATAAAAGCAAACAATCATCAAAATTCGTA
CATACGTTTAAAAACTCAACTCCTTTGAAAAATCGTTTTAAGAAATCATCAAACATAGCATTGAA
AAAAAAATGAAAAAAAATAATTTACTCTTTTTTTGGCTTTTCTTTTGGCAATCTAATCCG
Found at i:40076 original size:45 final size:45
Alignment explanation
Indices: 40012--40097 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
40002 TCTAATTCGA
*
40012 TTTAGCTCATATAGTATGATTATACATTTATAAATTCAACTCCGG
1 TTTAGCTCATATAGTATGATTATACATTTAAAAATTCAACTCCGG
* *
40057 TTTAGTTCTTATAGTATGATTATACATTTAAAAATTCAACT
1 TTTAGCTCATATAGTATGATTATACATTTAAAAATTCAACT
40098 GCTTCGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (45 bp):
TTTAGCTCATATAGTATGATTATACATTTAAAAATTCAACTCCGG
Found at i:41468 original size:22 final size:22
Alignment explanation
Indices: 41396--41468 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 22
41386 TTGTAGGAGA
* *
41396 GAAAATATGTCAACTCCGTAAG
1 GAAAATTTATCAACTCCGTAAG
* * **
41418 GAAAATTTATATAATTTTGTAA-
1 GAAAATTTAT-CAACTCCGTAAG
41440 G--AA-TTATCAACTCCGTAAG
1 GAAAATTTATCAACTCCGTAAG
41459 GAAAATTTAT
1 GAAAATTTAT
41469 AAATGCAATC
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
18 7 0.19
19 5 0.14
20 2 0.06
21 2 0.06
22 13 0.36
23 7 0.19
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (22 bp):
GAAAATTTATCAACTCCGTAAG
Found at i:42897 original size:3 final size:3
Alignment explanation
Indices: 42889--42997 Score: 209
Period size: 3 Copynumber: 36.0 Consensus size: 3
42879 TCTTACTCAA
42889 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42985 ATT ATT ATAT ATT
1 ATT ATT AT-T ATT
42998 TCTAACTACT
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 102 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:45239 original size:51 final size:50
Alignment explanation
Indices: 45138--45240 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
45128 GTTCTTCATA
* *
45138 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
* * *
45188 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGT
45239 TT
1 TT
45241 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
Found at i:47752 original size:21 final size:21
Alignment explanation
Indices: 47719--47758 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47709 CAACAAAGAG
* * *
47719 GGAGGTGCTTCCTTCCTCCTA
1 GGAGATGCCTCCTACCTCCTA
47740 GGAGATGCCTCCTACCTCC
1 GGAGATGCCTCCTACCTCC
47759 CAAGAGGCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.23, T:0.28
Consensus pattern (21 bp):
GGAGATGCCTCCTACCTCCTA
Done.