Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007308.1 Corchorus capsularis cultivar CVL-1 contig07329, 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: 8111
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:3119 original size:13 final size:13
Alignment explanation
Indices: 3101--3142 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3091 CATTCAATTC
*
3101 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
3114 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
3127 AAA-AAGAAAGAAA
1 AAAGAA-AAAGAAA
3140 AAA
1 AAA
3143 CTCAGCCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 2 0.07
13 25 0.93
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:3125 original size:19 final size:19
Alignment explanation
Indices: 3101--3141 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3091 CATTCAATTC
*
3101 AAAGAAAAGGAAA-AAAGAA
1 AAAGAAAA-AAAAGAAAGAA
3120 AAAGAAAAAAAAGAAAGAA
1 AAAGAAAAAAAAGAAAGAA
3139 AAA
1 AAA
3142 ACTCAGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAAAAGAAAGAA
Found at i:4071 original size:51 final size:50
Alignment explanation
Indices: 4012--4114 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 50
4002 GAAGTTTTAT
* *
4012 AATAAGATTGCATTCCATTTACGAGTTCAATATCAAAATTCGATTTTCTAA
1 AATAAGATTGCATTCCATTTACGAGTCCAAGATCAAAATTCGATTTTC-AA
** *
4063 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTACGAGTCCAAGATCAAAATTCGATTTTCAA
4113 AA
1 AA
4115 GGCATTTTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 4 0.09
51 43 0.91
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTACGAGTCCAAGATCAAAATTCGATTTTCAA
Found at i:6509 original size:42 final size:42
Alignment explanation
Indices: 6452--6682 Score: 417
Period size: 42 Copynumber: 5.5 Consensus size: 42
6442 AACGGAGTGC
6452 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
6494 TGAAATGCAGGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
* *
6536 TGAAATGCAAATTTTGAATTTTGACTTTTGAAGAATGAACCC
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
6578 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
6620 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATTAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
6662 TGAAATGCAGGTTTTGAATTT
1 TGAAATGCAAGTTTTGAATTT
6683 CGAACCATGA
Statistics
Matches: 181, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 181 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (42 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
Found at i:6688 original size:28 final size:28
Alignment explanation
Indices: 6657--6710 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
6647 TTGAAGAATT
* *
6657 AACCGTGAAATGCAGGTTTTGAATTTCG
1 AACCATGAAATGCAGATTTTGAATTTCG
* *
6685 AACCATGAGATGCTGATTTTGAATTT
1 AACCATGAAATGCAGATTTTGAATTT
6711 TGATTTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (28 bp):
AACCATGAAATGCAGATTTTGAATTTCG
Found at i:6710 original size:154 final size:148
Alignment explanation
Indices: 6546--6982 Score: 512
Period size: 154 Copynumber: 2.9 Consensus size: 148
6536 TGAAATGCAA
* *
6546 ATTTTGAATTTTGACTTTTGAAGAATGAACCCTGAAATGCAAGTTTTGAATTTTGACTTTT-GAA
1 ATTTTGAATTTTGA-TTTT---GAATGAA--CTGAAATGCAAATTTTGAACTTTGA-TTTTCGAA
* * * *
6610 GAATGAACCGTGAAATGCAAGTTTTGAATTTTGA-CTTTTGAAGAATTAACCGTGAAATGCAGGT
59 GAATGAAACGTGAAATGCAAGTTTTGAATTTTGATTTTTTGAAGAATAAACCATG-AATGCAGGT
6674 TTTGAATTTCGAACCATGAGATGCTG
123 TTTGAATTTCGAACCATGAGATGCTG
* *
6700 ATTTTGAATTTTGATTTTTGAAT-CA-GGAAATGCAAATTTTGAACTTTGATTTTCGAAGAATAG
1 ATTTTGAATTTTGA-TTTTGAATGAACTGAAATGCAAATTTTGAACTTTGATTTTCGAAGAAT-G
*
6763 AATAC-TGAAATGTAAGTTTTGAATTTTGATTTTTTTTTTTTGAAGAATAAACCATGAATGCAGG
64 AA-ACGTGAAATGCAAGTTTTGAATTTTGA------TTTTTTGAAGAATAAACCATGAATGCAGG
*
6827 TTTTGAATTTTGAACCATGAGATGCTG
122 TTTTGAATTTCGAACCATGAGATGCTG
6854 ATTTTGAATTTTGATTTTTGAAT-AA-TGAAATGCAAATTTTGAACTTTGATTTTCGAAGAAT-A
1 ATTTTGAATTTTGA-TTTTGAATGAACTGAAATGCAAATTTTGAACTTTGATTTTCGAAGAATGA
** *
6916 GATTGCTGAAATGCAAGTTTTGAATTTTGATTTTTTTGAAGAATAAACCATGAATGCAAGTTTTG
65 -AACG-TGAAATGCAAGTTTTGAATTTTGA-TTTTTTGAAGAATAAACCATGAATGCAGGTTTTG
6981 AA
127 AA
6983 ATTTGATTTT
Statistics
Matches: 253, Mismatches: 17, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
146 4 0.02
147 28 0.11
148 26 0.10
149 37 0.15
150 1 0.00
151 4 0.02
152 1 0.00
153 1 0.00
154 134 0.53
155 17 0.07
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (148 bp):
ATTTTGAATTTTGATTTTGAATGAACTGAAATGCAAATTTTGAACTTTGATTTTCGAAGAATGAA
ACGTGAAATGCAAGTTTTGAATTTTGATTTTTTGAAGAATAAACCATGAATGCAGGTTTTGAATT
TCGAACCATGAGATGCTG
Found at i:6712 original size:35 final size:35
Alignment explanation
Indices: 6673--6756 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
6663 GAAATGCAGG
* * * **
6673 TTTTGAATTTCGAACCATGAGATGCTGATTTTGAA
1 TTTTGATTTTCGAACCAGGAAATGCAAATTTTGAA
* *
6708 TTTTGATTTTTGAATCAGGAAATGCAAATTTTGAA
1 TTTTGATTTTCGAACCAGGAAATGCAAATTTTGAA
*
6743 CTTTGATTTTCGAA
1 TTTTGATTTTCGAA
6757 GAATAGAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (35 bp):
TTTTGATTTTCGAACCAGGAAATGCAAATTTTGAA
Found at i:6842 original size:27 final size:28
Alignment explanation
Indices: 6812--6867 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
6802 TTGAAGAATA
*
6812 AACCATGA-ATGCAGGTTTTGAATTTTG
1 AACCATGAGATGCAGATTTTGAATTTTG
*
6839 AACCATGAGATGCTGATTTTGAATTTTG
1 AACCATGAGATGCAGATTTTGAATTTTG
6867 A
1 A
6868 TTTTTGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (28 bp):
AACCATGAGATGCAGATTTTGAATTTTG
Found at i:6873 original size:35 final size:35
Alignment explanation
Indices: 6827--6906 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
6817 TGAATGCAGG
* * * **
6827 TTTTGAATTTTGAACCATGAGATGCTGATTTTGAA
1 TTTTGATTTTTGAACAATGAAATGCAAATTTTGAA
*
6862 TTTTGATTTTTGAATAATGAAATGCAAATTTTGAA
1 TTTTGATTTTTGAACAATGAAATGCAAATTTTGAA
*
6897 CTTTGATTTT
1 TTTTGATTTT
6907 CGAAGAATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.47
Consensus pattern (35 bp):
TTTTGATTTTTGAACAATGAAATGCAAATTTTGAA
Found at i:7045 original size:154 final size:149
Alignment explanation
Indices: 6529--7037 Score: 462
Period size: 154 Copynumber: 3.3 Consensus size: 149
6519 TTTTGAAGAA
* *
6529 TGAACCGTGA-AATGCAAATTTTGAATTTTGACTTTTGAAGAATGAACCCTGAAATGCAAGTTTT
1 TGAACCATGAGAA-GCAAA-TTTGAATTTTGACTTTT---GAA-GAA---TGAAATGCAAATTTT
* * *
6593 GAATTTTGACTTTT-GAAGAAT-GAA-CCGTGAAATGCAAGTTTTGAATTTTGA---CTTTTGAA
57 GAACTTTGA-TTTTCGAAGAATAGAATAC-TGAAATGCAAGTTTTGAATTTTGATTTTTTTTGAA
* * *
6652 GAATTAACCGTGAAATGCAGGTTTTG-AATT
120 GAATAAACCATG-AATGCAAGTTTTGAAATT
* * * * ** *
6682 TCGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATCAGGAAATGCAAATTTTGAACTTT
1 T-GAACCATGAGAAGC-AAATTTGAATTTTGACTTTTGAAGAATGAAATGCAAATTTTGAACTTT
*
6747 GATTTTCGAAGAATAGAATACTGAAATGTAAGTTTTGAATTTTGATTTTTTTTTTTTGAAGAATA
64 GATTTTCGAAGAATAGAATACTGAAATGCAAGTTTTGAATTTTGA----TTTTTTTTGAAGAATA
* *
6812 AACCATGAATGCAGGTTTTGAATTT
125 AACCATGAATGCAAGTTTTGAAATT
* * * * *
6837 TGAACCATGAGATGCTGATTTTGAATTTTGATTTTTGAATAATGAAATGCAAATTTTGAACTTTG
1 TGAACCATGAGAAGC-AAATTTGAATTTTGACTTTTGAAGAATGAAATGCAAATTTTGAACTTTG
* *
6902 ATTTTCGAAGAATAGATTGCTGAAATGCAAGTTTTGAATTTTGA-TTTTTTTGAAGAATAAACCA
65 ATTTTCGAAGAATAGAATACTGAAATGCAAGTTTTGAATTTTGATTTTTTTTGAAGAATAAACCA
6966 TGAATGCAAGTTTTGAAATT
130 TGAATGCAAGTTTTGAAATT
**** *
6986 TGATTTTTGAGCCAAG-AAATTTGAATTTTGAAGACTTTTGAAGAGTGAAATG
1 TGAACCATGAG--AAGCAAATTTGAATTTT---GACTTTTGAAGAATGAAATG
7038 TTGAAATTCT
Statistics
Matches: 304, Mismatches: 33, Indels: 39
0.81 0.09 0.10
Matches are distributed among these distances:
146 4 0.01
147 28 0.09
148 26 0.09
149 57 0.19
150 1 0.00
151 5 0.02
152 17 0.06
153 1 0.00
154 142 0.47
155 23 0.08
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (149 bp):
TGAACCATGAGAAGCAAATTTGAATTTTGACTTTTGAAGAATGAAATGCAAATTTTGAACTTTGA
TTTTCGAAGAATAGAATACTGAAATGCAAGTTTTGAATTTTGATTTTTTTTGAAGAATAAACCAT
GAATGCAAGTTTTGAAATT
Found at i:7184 original size:37 final size:37
Alignment explanation
Indices: 7143--7505 Score: 301
Period size: 37 Copynumber: 9.8 Consensus size: 37
7133 TTGTTTTCGA
*
7143 ACACCTAAACAGGGATCATT-AACAAGATTTTGATGAG
1 ACACCTAAACAGGGATC-TTAAACAAGATTTTGATAAG
* *
7180 ACACCTAAATAGGGA-CTTTAAATAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATC-TTAAACAA-GATTTTGATAAG
* * * * * * *
7217 AAACCTAAACAGGCATCTTGAAGAAGGTTTTGATGAC
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
** * *
7254 ACACCTAAACAGATACCTTAAATAAAGATTTTGATAAG
1 ACACCTAAACAGGGATCTTAAA-CAAGATTTTGATAAG
* * * * *
7292 AAATCTAAATAGGAATCTTGAACAAGATTTTGAT--G
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
*
7327 ACACCTAAACAGGGATCTTAAACAAGGA-TTTAATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATAAG
* * * *
7364 AAACCTAAACAGGAATCTTGAACAAGATTTTGATGAG
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
* *
7401 ACACCTAAACAGGGACCTTAAAGAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATAAG
* * * *
7438 AAATCTAAACAGGTATCTTGAACAAGATTTTGATGAA-
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGAT-AAG
* * *
7475 ACACCTAAACAGAGACCTTAAATAAGGATTT
1 ACACCTAAACAGGGATCTTAAACAA-GATTT
7506 GTCATGAAAA
Statistics
Matches: 254, Mismatches: 59, Indels: 25
0.75 0.17 0.07
Matches are distributed among these distances:
35 26 0.10
36 10 0.04
37 180 0.71
38 38 0.15
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (37 bp):
ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
Found at i:7275 original size:74 final size:74
Alignment explanation
Indices: 7145--7506 Score: 505
Period size: 74 Copynumber: 4.9 Consensus size: 74
7135 GTTTTCGAAC
* * *
7145 ACCTAAACAGGGATCATT-AACAAGATTTTGATGAGACACCTAAATAGGGACTTTAAATAAGGAT
1 ACCTAAACAGGAATC-TTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
7209 TTGATAAGAA
65 TTGATAAGAA
* * * * ** *
7219 ACCTAAACAGGCATCTTGAAGAAGGTTTTGATGACACACCTAAACAGATACCTTAAATAAAGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-T
7284 TTGATAAGAA
65 TTGATAAGAA
* * * *
7294 ATCTAAATAGGAATCTTGAACAAGATTTTGAT--GACACCTAAACAGGGATCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
*
7357 TAATAAGAA
66 TGATAAGAA
*
7366 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAAGAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
7431 TGATAAGAA
66 TGATAAGAA
* * * *
7440 ATCTAAACAGGTATCTTGAACAAGATTTTGATGAAACACCTAAACAGAGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
7505 TG
66 TG
7507 TCATGAAAAA
Statistics
Matches: 253, Mismatches: 31, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
72 40 0.16
73 25 0.10
74 150 0.59
75 38 0.15
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
TGATAAGAA
Found at i:7982 original size:69 final size:69
Alignment explanation
Indices: 7903--8111 Score: 346
Period size: 69 Copynumber: 3.0 Consensus size: 69
7893 GTCAGTTCGA
7903 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
7968 GCGG
66 GCGG
* * **
7972 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
*
8037 AGGGG
65 AGCGG
*
8042 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
8107 ACGG
66 GCGG
8111 C
1 C
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
69 64 0.50
70 63 0.50
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GCGG
Done.