Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014961.1 Corchorus olitorius cultivar O-4 contig14994, 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: 67765
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1147 original size:31 final size:32
Alignment explanation
Indices: 1112--1181 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1102 GGCAGGTTTA
* *
1112 GTTGAATCTGCTATTGT-AATT-TGTTTTCTTG
1 GTTGAATCTGATATTATAAATTCT-TTTTCTTG
1143 GTTGAATCTGATATTATAAATTCTTTTTCTTG
1 GTTGAATCTGATATTATAAATTCTTTTTCTTG
1175 GTTGAAT
1 GTTGAAT
1182 ATGTTCTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 15 0.43
32 19 0.54
33 1 0.03
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (32 bp):
GTTGAATCTGATATTATAAATTCTTTTTCTTG
Found at i:1603 original size:3 final size:3
Alignment explanation
Indices: 1595--1641 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1585 ATATGTGTAT
1595 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1642 TTTTTCATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1948 original size:2 final size:2
Alignment explanation
Indices: 1871--1932 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
1861 AGATGCATGC
* *
1871 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1913 AT TT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1933 AGTCTCCAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8701 original size:57 final size:56
Alignment explanation
Indices: 8622--8736 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 56
8612 TATCCGTTTC
*
8622 CTTTCACACAATAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAAAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
8678 CTTTCACACAACAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAA-AAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
8735 CT
1 CT
8737 ACAAAATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 11 0.19
57 46 0.81
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (56 bp):
CTTTCACACAAAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
Found at i:8861 original size:42 final size:42
Alignment explanation
Indices: 8802--8882 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
8792 TAAGGATCAG
*
8802 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
8844 GATTTGAATTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTC
8883 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (42 bp):
GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:26977 original size:21 final size:21
Alignment explanation
Indices: 26954--27045 Score: 125
Period size: 21 Copynumber: 4.4 Consensus size: 21
26944 TGCTAGGAGT
* *
26954 TCATTGGAGCAAGTTCAAAGT
1 TCATTGGAGCAAGTTCCAAGC
26975 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
26996 TCATTGGAG-AAGGTTCCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
*
27017 TCATTGGAG-AAGCTTTCAAGC
1 TCATTGGAGCAAG-TTCCAAGC
27038 TCATTGGA
1 TCATTGGA
27046 ATTGCCTAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
20 3 0.05
21 63 0.95
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:31806 original size:23 final size:24
Alignment explanation
Indices: 31762--31811 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
31752 CTCAAACCTT
*
31762 CTTAAGCCGCTTATCTTCTTCTTC
1 CTTAACCCGCTTATCTTCTTCTTC
31786 CTTAACCCAGCTT-TCTT-TTCTTC
1 CTTAACCC-GCTTATCTTCTTCTTC
31809 CTT
1 CTT
31812 CTTTCTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 11 0.46
25 4 0.17
ACGTcount: A:0.12, C:0.34, G:0.06, T:0.48
Consensus pattern (24 bp):
CTTAACCCGCTTATCTTCTTCTTC
Found at i:35784 original size:42 final size:42
Alignment explanation
Indices: 35704--35833 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 42
35694 CTCATAAAAT
* * * *
35704 CAACTTTTAATTCATTCTATATTTAGTTTTACCCTAATTAAA
1 CAACATTTAATTCATTCTATATTTACTTTCACCTTAATTAAA
* * *
35746 CTACATTTAATTCATTCTATGTTTACTTTCACATTAATTAAAA
1 CAACATTTAATTCATTCTATATTTACTTTCACCTTAATT-AAA
* * * * *
35789 AAACTTTTGATTCATTTTATATTTACTTTCACCTCAATTAAA
1 CAACATTTAATTCATTCTATATTTACTTTCACCTTAATTAAA
35831 CAA
1 CAA
35834 AAAATACAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 37 0.52
43 34 0.48
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (42 bp):
CAACATTTAATTCATTCTATATTTACTTTCACCTTAATTAAA
Found at i:35814 original size:43 final size:43
Alignment explanation
Indices: 35705--35835 Score: 147
Period size: 43 Copynumber: 3.0 Consensus size: 43
35695 TCATAAAATC
* * * *
35705 AACTTTTAATTCATTCTATATTTAGTTTTACCCTAATT-AAAC
1 AACTTTTAATTCATTCTATATTTACTTTCACCTTAATTAAAAA
* * * *
35747 TACATTTAATTCATTCTATGTTTACTTTCACATTAATTAAAAA
1 AACTTTTAATTCATTCTATATTTACTTTCACCTTAATTAAAAA
* * *
35790 AACTTTTGATTCATTTTATATTTACTTTCACCTCAATTAAACAA
1 AACTTTTAATTCATTCTATATTTACTTTCACCTTAATTAAA-AA
35834 AA
1 AA
35836 AATACAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 31 0.43
43 37 0.51
44 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.46
Consensus pattern (43 bp):
AACTTTTAATTCATTCTATATTTACTTTCACCTTAATTAAAAA
Found at i:38754 original size:21 final size:21
Alignment explanation
Indices: 38728--38768 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38718 TGGAACCCTT
38728 TTGGATTCAAGTGGTACAAAA
1 TTGGATTCAAGTGGTACAAAA
* *
38749 TTGGATTTAAGTGGTTCAAA
1 TTGGATTCAAGTGGTACAAA
38769 TTAGGGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
TTGGATTCAAGTGGTACAAAA
Found at i:38820 original size:22 final size:23
Alignment explanation
Indices: 38771--38820 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
38761 GGTTCAAATT
*
38771 AGGGTTCTGTTTCACCCTTTTCC
1 AGGGTTCAGTTTCACCCTTTTCC
* *
38794 A-GGTTCAGTTTGACCC-TTTGC
1 AGGGTTCAGTTTCACCCTTTTCC
38815 AGGGTT
1 AGGGTT
38821 GAGACAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 5 0.22
22 17 0.74
23 1 0.04
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (23 bp):
AGGGTTCAGTTTCACCCTTTTCC
Found at i:55996 original size:20 final size:20
Alignment explanation
Indices: 55971--56008 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55961 TTTGGTTAGG
**
55971 GGTGATCTTTGATCACCTGT
1 GGTGATCTCAGATCACCTGT
55991 GGTGATCTCAGATCACCT
1 GGTGATCTCAGATCACCT
56009 TGTTTGGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (20 bp):
GGTGATCTCAGATCACCTGT
Found at i:56121 original size:53 final size:53
Alignment explanation
Indices: 55989--56124 Score: 202
Period size: 53 Copynumber: 2.6 Consensus size: 53
55979 TTGATCACCT
* * *
55989 GTGGTGATCTCAGATCACCTTGTTTGGTTGGGGTCACTTGTTGGTGATCTTGG
1 GTGGTGATCTCAGATCACCCTGTTTGGTTAGGATCACTTGTTGGTGATCTTGG
*
56042 GTGGTGATCTCAGATCAACCTGTTTGGTTAGGATCACTTGTTGGTGATCTTGG
1 GTGGTGATCTCAGATCACCCTGTTTGGTTAGGATCACTTGTTGGTGATCTTGG
**
56095 GTGGTGAT-TACAGATCACCCCATTTGGTTA
1 GTGGTGATCT-CAGATCACCCTGTTTGGTTA
56125 CATATTTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
52 1 0.01
53 74 0.99
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (53 bp):
GTGGTGATCTCAGATCACCCTGTTTGGTTAGGATCACTTGTTGGTGATCTTGG
Found at i:57256 original size:25 final size:24
Alignment explanation
Indices: 57220--57266 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
57210 TCCTTCTATT
57220 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
57243 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
57267 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:57745 original size:21 final size:21
Alignment explanation
Indices: 57719--57759 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57709 TTTAAACCCT
57719 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
57740 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
57760 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:64824 original size:131 final size:132
Alignment explanation
Indices: 64618--64879 Score: 379
Period size: 131 Copynumber: 2.0 Consensus size: 132
64608 TTGTTTAAAT
*
64618 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAAATATAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAAATATAATATCCGTATAACT
* * * *
64683 ATTTATTTTTTACCATTTTACTATTTTAATT-AGAAACTTATATATATTAGAATTTTTTAAATAT
66 ATTTATTTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
64747 AC
131 AC
* * * *
64749 TTTTATAGTTTTTA-TTAACTAAAAACTCTATTTTTTATTTTA-TTAAATCTAATATCCGTATAC
1 TTTTATAG-TTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTTAAATATAATATCCGTATAA
*
64812 CTATTT-TATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAA
64 CTATTTAT-TTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAA
64876 TATA
128 TATA
64880 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
130 1 0.01
131 70 0.60
132 46 0.39
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (132 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAAATATAATATCCGTATAACT
ATTTATTTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
AC
Found at i:66030 original size:2 final size:2
Alignment explanation
Indices: 66025--66064 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
66015 TAGTAATGTA
66025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
66065 CCTTCAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:66101 original size:15 final size:15
Alignment explanation
Indices: 66058--66102 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
66048 TATATATCAT
* *
66058 AATATATCCTTCAAA
1 AATATATTCTTAAAA
*
66073 AATAAATTCTTTAAAA
1 AATATATTC-TTAAAA
66089 AATATATTCTTAAA
1 AATATATTCTTAAA
66103 TACCTTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATTCTTAAAA
Found at i:66887 original size:22 final size:22
Alignment explanation
Indices: 66847--66888 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
66837 ATTTATAATA
* *
66847 TTCTTTGGTCATCCGGGTTAAC
1 TTCTTAGGTCATCCAGGTTAAC
*
66869 TTCTTAGGTCATTCAGGTTA
1 TTCTTAGGTCATCCAGGTTA
66889 CGGATTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (22 bp):
TTCTTAGGTCATCCAGGTTAAC
Done.