Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017770.1 Corchorus olitorius cultivar O-4 contig17803, 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: 8549
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:850 original size:3 final size:3
Alignment explanation
Indices: 838--876 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
828 CTAATAATAA
* *
838 TAT TAC TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
877 AAGAAGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:861 original size:15 final size:15
Alignment explanation
Indices: 838--872 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
828 CTAATAATAA
838 TATTACTATTATTAT
1 TATTACTATTATTAT
853 TATTACTATTATTAT
1 TATTACTATTATTAT
868 TATTA
1 TATTA
873 TTATAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTACTATTATTAT
Found at i:958 original size:15 final size:15
Alignment explanation
Indices: 938--966 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
928 ATACATCAAA
938 GTAAGTCTTGATTCG
1 GTAAGTCTTGATTCG
953 GTAAGTCTTGATTC
1 GTAAGTCTTGATTC
967 ATGAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (15 bp):
GTAAGTCTTGATTCG
Found at i:985 original size:15 final size:15
Alignment explanation
Indices: 967--1014 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
957 GTCTTGATTC
967 ATGAAATAATTTGGG
1 ATGAAATAATTTGGG
*
982 ATG-AA-AATCTT--C
1 ATGAAATAAT-TTGGG
994 ATGAAATAATTTGGG
1 ATGAAATAATTTGGG
1009 ATGAAA
1 ATGAAA
1015 ATCTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
12 3 0.12
13 7 0.27
14 7 0.27
15 9 0.35
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (15 bp):
ATGAAATAATTTGGG
Found at i:1002 original size:27 final size:27
Alignment explanation
Indices: 964--1019 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
954 TAAGTCTTGA
964 TTCATGAAATAATTTGGGATGAAAATC
1 TTCATGAAATAATTTGGGATGAAAATC
991 TTCATGAAATAATTTGGGATGAAAATC
1 TTCATGAAATAATTTGGGATGAAAATC
1018 TT
1 TT
1020 TCATTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (27 bp):
TTCATGAAATAATTTGGGATGAAAATC
Found at i:1169 original size:24 final size:24
Alignment explanation
Indices: 1137--1187 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1127 CTACTACTAA
*
1137 TAATTATTATAATAATAAGAA-GTT
1 TAATAATTATAATAATAA-AATGTT
*
1161 TAATAATTATAATGATAAAATGTT
1 TAATAATTATAATAATAAAATGTT
1185 TAA
1 TAA
1188 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAAATGTT
Found at i:1368 original size:6 final size:6
Alignment explanation
Indices: 1350--1390 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
1340 GTTTAGACTT
1350 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1391 GGGTAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:2728 original size:31 final size:30
Alignment explanation
Indices: 2671--2735 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
2661 CATCTGAAAA
*
2671 GGGCTTATTTAGCCTTTTTCAAGAGTTCAT
1 GGGCTTATTTAGCCTTTTTCAAGAGTTCAG
* ***
2701 GGGCTTATTTGGCCGTTTTTTGTGAGTTCAG
1 GGGCTTATTTAGCC-TTTTTCAAGAGTTCAG
2732 GGGC
1 GGGC
2736 CTTTTTGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.14, C:0.15, G:0.29, T:0.42
Consensus pattern (30 bp):
GGGCTTATTTAGCCTTTTTCAAGAGTTCAG
Found at i:4947 original size:48 final size:48
Alignment explanation
Indices: 4892--4984 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
4882 AACTCTTGTT
*
4892 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
* *
4940 TGATCAACCTTGTCATTTACTTTTCATCACCCTTGTTTTTACAAG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAG
4985 GTGTAATCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.45
Consensus pattern (48 bp):
TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
Found at i:4973 original size:23 final size:22
Alignment explanation
Indices: 4907--4981 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
4897 AACCCTATCT
*
4907 TTTACTTTTCATCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
* * *
4929 TTTACAAGTTGTGATCAACCTTGTCA
1 TTTAC---TTTTCATCACCCTTGT-A
*
4955 TTTACTTTTCATCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
4977 TTTAC
1 TTTAC
4982 AAGGTGTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 10 0.24
23 13 0.32
25 13 0.32
26 5 0.12
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (22 bp):
TTTACTTTTCATCACCCTTGTA
Found at i:6690 original size:49 final size:51
Alignment explanation
Indices: 6630--6763 Score: 200
Period size: 49 Copynumber: 2.6 Consensus size: 51
6620 GGATCTTTCC
*
6630 CTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTG-AA-AG
1 CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAGAG
* *
6679 CTAAATTGAACACTTTGAAAACTTGACGGAAACTTTCCCACTTTGAAAAGAG
1 CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTG-AAAGAG
* *
6731 CTAAATTGAACACTTCGAAAACCTGATGGGAAC
1 CTAAATTGAACACTTTGAAAACTTGATGGGAAC
6764 CGAACACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 42 0.56
51 2 0.03
52 31 0.41
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (51 bp):
CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAGAG
Found at i:6769 original size:27 final size:27
Alignment explanation
Indices: 6738--6790 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6728 GAGCTAAATT
*
6738 GAACACTTCGAAAACCTGATGGGAACC
1 GAACACTTCGAAAACATGATGGGAACC
*
6765 GAACACTTTGAAAACATGATGGGAAC
1 GAACACTTCGAAAACATGATGGGAAC
6791 TTTCCCACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (27 bp):
GAACACTTCGAAAACATGATGGGAACC
Found at i:6776 original size:79 final size:80
Alignment explanation
Indices: 6686--6843 Score: 228
Period size: 79 Copynumber: 2.0 Consensus size: 80
6676 AAGCTAAATT
* * **
6686 GAACACTTTGAAAACTTGACGGAAACTTTCCCACTTTG-AAAAGAGCTAAATTGAACACTTCGAA
1 GAACACTTTGAAAACATGACGGAAACTTTCCCACTTTGAAAAAGACCTAAATCAAACACTTCGAA
6750 AACCTGATGGGAACC
66 AACCTGATGGGAACC
* * * *
6765 GAACACTTTGAAAACATGATGGGAACTTTCCCACTTTGAAAAAGACCTTAATCAAACACTTTGAA
1 GAACACTTTGAAAACATGACGGAAACTTTCCCACTTTGAAAAAGACCTAAATCAAACACTTCGAA
*
6830 AACTTGATGGGAAC
66 AACCTGATGGGAAC
6844 TTTCCCACTT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
79 35 0.51
80 34 0.49
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (80 bp):
GAACACTTTGAAAACATGACGGAAACTTTCCCACTTTGAAAAAGACCTAAATCAAACACTTCGAA
AACCTGATGGGAACC
Found at i:6806 original size:28 final size:28
Alignment explanation
Indices: 6768--6860 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
6758 GGGAACCGAA
6768 CACTTTGAAAACATGATGGGAACTTTCC
1 CACTTTGAAAACATGATGGGAACTTTCC
**** ****
6796 CACTTTGAAAA-A-GACCTTAA-TCAAA
1 CACTTTGAAAACATGATGGGAACTTTCC
*
6821 CACTTTGAAAACTTGATGGGAACTTTCC
1 CACTTTGAAAACATGATGGGAACTTTCC
6849 CACTTTGAAAAC
1 CACTTTGAAAAC
6861 TTTGAAGGAA
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
25 12 0.27
26 4 0.09
27 5 0.11
28 24 0.53
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (28 bp):
CACTTTGAAAACATGATGGGAACTTTCC
Found at i:7235 original size:13 final size:13
Alignment explanation
Indices: 7213--7243 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7203 TTCTAAATAC
*
7213 ATGAATGCGAATG
1 ATGAAAGCGAATG
7226 ATGAAAGCGAATG
1 ATGAAAGCGAATG
7239 ATGAA
1 ATGAA
7244 TGCAATTCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (13 bp):
ATGAAAGCGAATG
Found at i:7602 original size:19 final size:20
Alignment explanation
Indices: 7578--7615 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
7568 TTAAATTTGA
7578 AAACTAAATTAA-TCTAATG
1 AAACTAAATTAATTCTAATG
*
7597 AAACTAATTTAATTCTAAT
1 AAACTAAATTAATTCTAAT
7616 TATTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (20 bp):
AAACTAAATTAATTCTAATG
Done.