Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019219.1 Corchorus olitorius cultivar O-4 contig19252, 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: 49957
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:821 original size:160 final size:160
Alignment explanation
Indices: 557--879 Score: 637
Period size: 160 Copynumber: 2.0 Consensus size: 160
547 TGATCTGCTG
557 TACTTCTGCGTTTGCAGATTATTGCATAGTCCATTGGAGCACTTGCTCATCGTTAGTATGGCATT
1 TACTTCTGCGTTTGCAGATTATTGCATAGTCCATTGGAGCACTTGCTCATCGTTAGTATGGCATT
622 CCTATTATACATCAAGGTATAATGGTGCCTTTGAATAAAAGTTGGAATGGGAATTCTTAATATGC
66 CCTATTATACATCAAGGTATAATGGTGCCTTTGAATAAAAGTTGGAATGGGAATTCTTAATATGC
687 AGTTAAAGGCACCACGATGCATTCCTATTA
131 AGTTAAAGGCACCACGATGCATTCCTATTA
717 TACTTCTGCGTTTGCAGATTATTGCATAGTCCATTGGAGCACTTGCTCATCGTTAGTATGGCATT
1 TACTTCTGCGTTTGCAGATTATTGCATAGTCCATTGGAGCACTTGCTCATCGTTAGTATGGCATT
782 CCTATTATACATCAAGGTATAATGGTGCCTTTGAATAAAAGTTGGAATGGGAATTCTTAATATGC
66 CCTATTATACATCAAGGTATAATGGTGCCTTTGAATAAAAGTTGGAATGGGAATTCTTAATATGC
*
847 AGTTAAAGGCACCATGATGCATTCCTATTA
131 AGTTAAAGGCACCACGATGCATTCCTATTA
877 TAC
1 TAC
880 ATCAAGGTAT
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (160 bp):
TACTTCTGCGTTTGCAGATTATTGCATAGTCCATTGGAGCACTTGCTCATCGTTAGTATGGCATT
CCTATTATACATCAAGGTATAATGGTGCCTTTGAATAAAAGTTGGAATGGGAATTCTTAATATGC
AGTTAAAGGCACCACGATGCATTCCTATTA
Found at i:986 original size:90 final size:89
Alignment explanation
Indices: 774--987 Score: 279
Period size: 88 Copynumber: 2.4 Consensus size: 89
764 CATCGTTAGT
* ** *
774 ATGGCATTCCTATTATACATCAAGGTATAATGGTGCCTTTGAATAAAAGTTGGAATGGGAATTCT
1 ATGGCATTCCTATTATACATCAAGGTATAATGGTGCATTCAAATAAAAGTTGGAACGGGAATTCT
* *
839 TAATATGCAGTTAAAGGCACCATG
66 TAATATGCAGTTAAAGGCACAAAG
* *
863 AT-GCATTCCTATTATACATCAAGGTATAATGGTGCATTCAAATAAAAGTTGGTAGCGGGAATTT
1 ATGGCATTCCTATTATACATCAAGGTATAATGGTGCATTCAAATAAAAGTTGG-AACGGGAATTC
* *
927 TTAATATGCTG-TAATAGGCGCAAAG
65 TTAATATGCAGTTAA-AGGCACAAAG
* * *
952 GTGGCATTCCTATTATACATAAAGGTATAGTGGTGC
1 ATGGCATTCCTATTATACATCAAGGTATAATGGTGC
988 CAAGTTGAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
88 50 0.46
89 28 0.26
90 31 0.28
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (89 bp):
ATGGCATTCCTATTATACATCAAGGTATAATGGTGCATTCAAATAAAAGTTGGAACGGGAATTCT
TAATATGCAGTTAAAGGCACAAAG
Found at i:1120 original size:49 final size:49
Alignment explanation
Indices: 1048--1150 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
1038 AACATGGACC
*
1048 CCCATAAAGGCTTATGCCCCGTTTCGCACTCCATTTCTTCTGATATATT
1 CCCATAAAGGCTTATGCCCCGTTTCCCACTCCATTTCTTCTGATATATT
1097 CCCATAAAGGCTTATGCCCCGTTTCCCACTCCATTTCTTCTGATATATT
1 CCCATAAAGGCTTATGCCCCGTTTCCCACTCCATTTCTTCTGATATATT
*
1146 TCCAT
1 CCCAT
1151 TTGGGATTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.20, C:0.32, G:0.11, T:0.37
Consensus pattern (49 bp):
CCCATAAAGGCTTATGCCCCGTTTCCCACTCCATTTCTTCTGATATATT
Found at i:8207 original size:33 final size:33
Alignment explanation
Indices: 8148--8212 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
8138 AGCTGTGGTT
*
8148 GCTCGTGACTAAGCCATGGCTCGGTCGCGAGCG
1 GCTCGTGACTAAGCCACGGCTCGGTCGCGAGCG
* * * *
8181 GCTCGTGACTGAGCCGCGGCTTGGTCGTGAGC
1 GCTCGTGACTAAGCCACGGCTCGGTCGCGAGC
8213 CGCGTGCGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.20
Consensus pattern (33 bp):
GCTCGTGACTAAGCCACGGCTCGGTCGCGAGCG
Found at i:8276 original size:39 final size:35
Alignment explanation
Indices: 8165--8289 Score: 105
Period size: 33 Copynumber: 3.6 Consensus size: 35
8155 ACTAAGCCAT
* * *
8165 GGCTCGGTCGCGAG-CG-GCTCGTGACTGAGCCGC
1 GGCTTGGTCGCAAGCCGCGCTCGCGACTGAGCCGC
** * *
8198 GGCTTGGTCGTGAGCCGCG-T-GCGACCGAGCCGT
1 GGCTTGGTCGCAAGCCGCGCTCGCGACTGAGCCGC
*
8231 GACTTGGTCGCAAGCCTTGGTCGCTCGCGACTGAGCCGC
1 GGCTTGGTCGCAAGCC---G-CGCTCGCGACTGAGCCGC
*
8270 GGCTTGGTGGCAAGCCGCGC
1 GGCTTGGTCGCAAGCCGCGC
8290 GCGACCAAGC
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
33 35 0.49
34 3 0.04
35 4 0.06
36 2 0.03
37 2 0.03
38 1 0.01
39 25 0.35
ACGTcount: A:0.10, C:0.32, G:0.40, T:0.18
Consensus pattern (35 bp):
GGCTTGGTCGCAAGCCGCGCTCGCGACTGAGCCGC
Found at i:19896 original size:30 final size:30
Alignment explanation
Indices: 19860--20020 Score: 97
Period size: 30 Copynumber: 5.3 Consensus size: 30
19850 CGGCGGCGGA
*
19860 GGCGGTGGAGGAGGGGGAGGGGGTGGTGGT
1 GGCGGTGGAGGAGGGGGAGGGGGTGGAGGT
* * *
19890 GGCGGTGGTGGAGGAGGAGGAGGAGGTGGTGGT
1 GGC---GGTGGAGGAGGGGGAGGGGGTGGAGGT
* *** ** * *
19923 GGCAGTTTTGGTTGGGGATGGGGTGGAGGC
1 GGCGGTGGAGGAGGGGGAGGGGGTGGAGGT
* * * *
19953 GGAGGTGGAGGTGGGGGAGGTGGTGGAGGA
1 GGCGGTGGAGGAGGGGGAGGGGGTGGAGGT
* * * * *
19983 GGCGGTGGTGGATGGGGATGGGGAGGAGGA
1 GGCGGTGGAGGAGGGGGAGGGGGTGGAGGT
*
20013 GGAGGTGG
1 GGCGGTGG
20021 TTGGTATAAA
Statistics
Matches: 98, Mismatches: 30, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
30 70 0.71
33 28 0.29
ACGTcount: A:0.14, C:0.03, G:0.67, T:0.16
Consensus pattern (30 bp):
GGCGGTGGAGGAGGGGGAGGGGGTGGAGGT
Found at i:19905 original size:33 final size:33
Alignment explanation
Indices: 19863--20021 Score: 119
Period size: 33 Copynumber: 4.7 Consensus size: 33
19853 CGGCGGAGGC
* *
19863 GGTGGAGGAGGGGGAGGGGGTGGTGGTGGCGGT
1 GGTGGAGGAGGAGGAGGAGGTGGTGGTGGCGGT
*
19896 GGTGGAGGAGGAGGAGGAGGTGGTGGTGGCAGTTTT
1 GGTGGAGGAGGAGGAGGAGGTGGTGGTGGC-G--GT
* * * *
19932 GGTTGG-GGATGG-GGTGGAGGCGGAGGTGGAGGT
1 GG-TGGAGGA-GGAGGAGGAGGTGGTGGTGGCGGT
* * * * *
19965 GGGGGAGGTGGTGGAGGAGGCGGTGGTGGATGG-
1 GGTGGAGGAGGAGGAGGAGGTGGTGGTGG-CGGT
19998 GGATGG-GGAGGAGGAGGAGGTGGT
1 GG-TGGAGGAGGAGGAGGAGGTGGT
20022 TGGTATAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
32 4 0.04
33 65 0.65
34 5 0.05
35 1 0.01
36 20 0.20
37 5 0.05
ACGTcount: A:0.14, C:0.03, G:0.67, T:0.17
Consensus pattern (33 bp):
GGTGGAGGAGGAGGAGGAGGTGGTGGTGGCGGT
Found at i:19960 original size:60 final size:60
Alignment explanation
Indices: 19884--20020 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 60
19874 GGGAGGGGGT
* * * * ** *
19884 GGTGGTGGCGGTGGTGGAGGAGGAGGAGGAGGTGGTGGTGGCAGTTTTGGTTGGGGATGG
1 GGTGGAGGCGGAGGTGGAGGAGGAGGAGGAGGTGGAGGAGGCAGTGGTGGATGGGGATGG
* * * *
19944 GGTGGAGGCGGAGGTGGAGGTGGGGGAGGTGGTGGAGGAGGCGGTGGTGGATGGGGATGG
1 GGTGGAGGCGGAGGTGGAGGAGGAGGAGGAGGTGGAGGAGGCAGTGGTGGATGGGGATGG
* *
20004 GGAGGAGGAGGAGGTGG
1 GGTGGAGGCGGAGGTGG
20021 TTGGTATAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.14, C:0.03, G:0.66, T:0.18
Consensus pattern (60 bp):
GGTGGAGGCGGAGGTGGAGGAGGAGGAGGAGGTGGAGGAGGCAGTGGTGGATGGGGATGG
Found at i:20021 original size:30 final size:29
Alignment explanation
Indices: 19935--20021 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
19925 CAGTTTTGGT
* *
19935 TGGGGATGGGGTGGAGGCGGAGGTGGAGG
1 TGGGGATGGGGTGGAGGAGGAGGTGGTGG
*
19964 TGGGGGA-GGTGGTGGAGGAGGCGGTGGTGG
1 T-GGGGATGG-GGTGGAGGAGGAGGTGGTGG
*
19994 ATGGGGATGGGGAGGAGGAGGAGGTGGT
1 -TGGGGATGGGGTGGAGGAGGAGGTGGT
20022 TGGTATAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
29 3 0.06
30 43 0.88
31 3 0.06
ACGTcount: A:0.15, C:0.02, G:0.68, T:0.15
Consensus pattern (29 bp):
TGGGGATGGGGTGGAGGAGGAGGTGGTGG
Found at i:22160 original size:20 final size:20
Alignment explanation
Indices: 22135--22172 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
22125 GTTCACCTTA
22135 ATTATTTGGAACAAAAAGTG
1 ATTATTTGGAACAAAAAGTG
22155 ATTATTTGGAACAAAAAG
1 ATTATTTGGAACAAAAAG
22173 CAGTGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (20 bp):
ATTATTTGGAACAAAAAGTG
Found at i:28091 original size:23 final size:23
Alignment explanation
Indices: 28059--28107 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28049 TATTTAGTAA
* *
28059 TTAAATATATATT-ATTTATTTTT
1 TTAAAAATATATTCA-TTATTTAT
28082 TTAAAAATATATTCATTATTTAT
1 TTAAAAATATATTCATTATTTAT
28105 TTA
1 TTA
28108 TTAATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAAAAATATATTCATTATTTAT
Found at i:28913 original size:2 final size:2
Alignment explanation
Indices: 28906--28940 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
28896 ATTGACTCGC
28906 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
28941 TATCAAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30189 original size:21 final size:21
Alignment explanation
Indices: 30165--30208 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
30155 TTGGAAAGAA
*
30165 AAATATTATTAAAAAATGTAT
1 AAATATTATTAAAAAATGAAT
*
30186 AAATATTATTAAGAAATGAAT
1 AAATATTATTAAAAAATGAAT
30207 AA
1 AA
30209 CACACTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
AAATATTATTAAAAAATGAAT
Found at i:32876 original size:14 final size:14
Alignment explanation
Indices: 32857--32884 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32847 ATGTTTGATC
32857 TAATAATAATAAGT
1 TAATAATAATAAGT
32871 TAATAATAATAAGT
1 TAATAATAATAAGT
32885 ACTTATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TAATAATAATAAGT
Found at i:33840 original size:16 final size:16
Alignment explanation
Indices: 33815--33847 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33805 TCATCAACTG
*
33815 ATCAAGGCTAACTTAC
1 ATCAAAGCTAACTTAC
33831 ATCAAAGCTAACTTAC
1 ATCAAAGCTAACTTAC
33847 A
1 A
33848 GTGGTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (16 bp):
ATCAAAGCTAACTTAC
Found at i:39085 original size:29 final size:29
Alignment explanation
Indices: 39050--39107 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39040 TAGTTTTGTA
39050 GGTTTTGAAGGGTTTGTTTTGATTTTGGC
1 GGTTTTGAAGGGTTTGTTTTGATTTTGGC
39079 GGTTTTGAAGGGTTTGTTTTGATTTTGGC
1 GGTTTTGAAGGGTTTGTTTTGATTTTGGC
39108 AGACCAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.10, C:0.03, G:0.34, T:0.52
Consensus pattern (29 bp):
GGTTTTGAAGGGTTTGTTTTGATTTTGGC
Found at i:48096 original size:43 final size:45
Alignment explanation
Indices: 48048--48153 Score: 180
Period size: 47 Copynumber: 2.4 Consensus size: 45
48038 TTGTCCATGG
48048 TGTATTTGCTGCTTTC-TT-TTTTTTGTTCAAGGGTTCTATCTCC
1 TGTATTTGCTGCTTTCTTTCTTTTTTGTTCAAGGGTTCTATCTCC
48091 TGTATTTGCTGCTTTCTTTTTCTTTTTTGTTCAAGGGTTCTATCTCC
1 TGTATTTGCTGCTTTC--TTTCTTTTTTGTTCAAGGGTTCTATCTCC
48138 TGTATTTGCTGCTTTC
1 TGTATTTGCTGCTTTC
48154 ATTAATTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
43 16 0.27
46 2 0.03
47 41 0.69
ACGTcount: A:0.08, C:0.19, G:0.16, T:0.57
Consensus pattern (45 bp):
TGTATTTGCTGCTTTCTTTCTTTTTTGTTCAAGGGTTCTATCTCC
Found at i:49380 original size:13 final size:12
Alignment explanation
Indices: 49361--49408 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
49351 CTTTAAAGCA
49361 ATATATAATACT
1 ATATATAATACT
49373 ACTATAT-ATACTT
1 A-TATATAATAC-T
*
49386 ATATATTATACT
1 ATATATAATACT
49398 ATACTATAATA
1 ATA-TATAATA
49409 ATAATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 14 0.45
13 17 0.55
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATATAATACT
Found at i:49638 original size:21 final size:21
Alignment explanation
Indices: 49612--49654 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49602 GTAAAGGGTA
*
49612 TTACTAAATACCGCCCCTCTT
1 TTACTAAACACCGCCCCTCTT
**
49633 TTACTAGCCACCGCCCCTCTT
1 TTACTAAACACCGCCCCTCTT
49654 T
1 T
49655 GGACTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.42, G:0.07, T:0.33
Consensus pattern (21 bp):
TTACTAAACACCGCCCCTCTT
Done.