Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3535
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: 61742
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:6140 original size:22 final size:22
Alignment explanation
Indices: 6115--6206 Score: 98
Period size: 22 Copynumber: 4.0 Consensus size: 22
6105 TGCACTAATG
6115 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
6137 AACAGAGAGCAC-AAATGTGCTA
1 AACAGAGAGCACTAAA-GTGCTA
*
6159 AACAGAGAGCACTGACA-TGCTA
1 AACAGAGAGCACT-AAAGTGCTA
* *
6181 GTAATCAGAGAGCACCAACGTGCTA
1 --AA-CAGAGAGCACTAAAGTGCTA
6206 A
1 A
6207 TAATCAGAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
21 3 0.05
22 35 0.59
23 1 0.02
24 5 0.08
25 15 0.25
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:6192 original size:25 final size:25
Alignment explanation
Indices: 6161--6217 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
6151 ATGTGCTAAA
** *
6161 CAGAGAGCACTGACATGCTAGTAAT
1 CAGAGAGCACCAACATGCTAATAAT
*
6186 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACATGCTAATAAT
6211 CAGAGAG
1 CAGAGAG
6218 GGCGCTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACATGCTAATAAT
Found at i:7102 original size:16 final size:18
Alignment explanation
Indices: 7081--7125 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 18
7071 CGTGGCTTCC
7081 TTCTTTTTC-TTTTT-CT
1 TTCTTTTTCATTTTTGCT
7097 TTCTTTTTCATTTTTGCT
1 TTCTTTTTCATTTTTGCT
7115 TCTCTATTTTC
1 T-TCT-TTTTC
7126 GTTTCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.36
17 5 0.20
18 3 0.12
19 3 0.12
20 5 0.20
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (18 bp):
TTCTTTTTCATTTTTGCT
Found at i:7163 original size:5 final size:5
Alignment explanation
Indices: 7155--7234 Score: 94
Period size: 5 Copynumber: 16.0 Consensus size: 5
7145 TTCCTTTCTT
* *
7155 TATAA TATAA TATAA TATAA T-TAC T-TATT TATTAA GT-TAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATA-A TA-TAA -TATAA TATAA
7200 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
7235 AAATATCTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
4 6 0.09
5 58 0.87
7 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:18279 original size:135 final size:138
Alignment explanation
Indices: 18037--18539 Score: 473
Period size: 144 Copynumber: 3.6 Consensus size: 138
18027 AGCTATTCAG
* * *
18037 CTAACTCAAATAAATGAAGGCTGTGAACATAACTCAACTAACCTTTAAACATTAGCT-GGTAGCG
1 CTAACTCAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTTAAACATTAACTAGG-AGCG
* * *
18101 TAGGTCCACGAGCTATGTCGAAGTTTATCAGCTGGGAGGGTAGGTT-A-G-CC-AGAGTTGCGAG
65 TAGGTCCACGAGCTGTGTCGAAGTTTATTAGCTGGGAGCGTAGGTTAATGTCCGA-AGTTGCGAG
18162 CTTAA-CTCAA
129 CTTAACCT-AA
* *
18172 CTAACTCAAATAAATGAAGGTTGAGAGCATAACTCAACTAACCTTTAAACATTAACTAGGAGCGC
1 CTAACTCAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTTAAACATTAACTAGGAGCGT
* * * *
18237 AGGTCCATGAGTTGTGTCGAAGTTTATTAGCTGAGAGCGTAGGTTTGTAAGTTGTTTCGAAGTTG
66 AGGTCCACGAGCTGTGTCGAAGTTTATTAGCTGGGAGCGTAGG--T-TAA--TG-TCCGAAGTTG
*
18302 CGAGCTTAACCTAG
125 CGAGCTTAACCTAA
* * * * *
18316 CTAACTAAAATAAATGAATGTTGTGAGCATAACTCATCTAACCTTTAAACATCAACTAGGACCGT
1 CTAACTCAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTTAAACATTAACTAGGAGCGT
* * * ** *
18381 AAGTCCACGAGCTGTGTC-AGAGTTTATTAGCTGGGAGCGTAGGTTTGTGAGTTTTTTTGGAGTT
66 AGGTCCACGAGCTGTGTCGA-AGTTTATTAGCTGGGAGCGTAGG--T-T-A--ATGTCCGAAGTT
*
18445 GTGAGCTTAA-CTCAA
124 GCGAGCTTAACCT-AA
** * * * * * * *
18460 CTAACAAAAATAAATAAAGGCTGTAAGCATAACTCAGCTAAGCTTTAAACATCAACTAGGAGCAT
1 CTAACTCAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTTAAACATTAACTAGGAGCGT
* *
18525 AGGTCCGCAAGCTGT
66 AGGTCCACGAGCTGT
18540 TTCAGAGTTG
Statistics
Matches: 309, Mismatches: 42, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
135 94 0.30
136 2 0.01
137 1 0.00
138 1 0.00
139 1 0.00
142 1 0.00
143 3 0.01
144 201 0.65
145 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (138 bp):
CTAACTCAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTTAAACATTAACTAGGAGCGT
AGGTCCACGAGCTGTGTCGAAGTTTATTAGCTGGGAGCGTAGGTTAATGTCCGAAGTTGCGAGCT
TAACCTAA
Found at i:18413 original size:144 final size:144
Alignment explanation
Indices: 18153--18548 Score: 517
Period size: 144 Copynumber: 2.8 Consensus size: 144
18143 GGTTAGCCAG
* *
18153 AGTTGCGAGCTTAACTCAACTAACTCAAATAAATGAAGGTTGAGAGCATAACTCAACTAACCTTT
1 AGTTGCGAGCTTAACTCAACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTT
* * * *
18218 AAACATTAACTAGGAGCGCAGGTCCATGAGTTGTGTC-GAAGTTTATTAGCTGAGAGCGTAGGTT
66 AAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAG-AGTTTATTAGCTGAGAGCGTAGGTT
18282 TGTAAGTTGTTTCGA
130 TGTAAGTTGTTTCGA
* * *
18297 AGTTGCGAGCTTAAC-CTAGCTAACTAAAATAAATGAATGTTGTGAGCATAACTCATCTAACCTT
1 AGTTGCGAGCTTAACTC-AACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTT
* * *
18361 TAAACATCAACTAGGACCGTAAGTCCACGAGCTGTGTCAGAGTTTATTAGCTGGGAGCGTAGGTT
65 TAAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAGAGTTTATTAGCTGAGAGCGTAGGTT
* * * *
18426 TGTGAGTTTTTTTGG
130 TGTAAGTTGTTTCGA
* * * * * * *
18441 AGTTGTGAGCTTAACTCAACTAACAAAAATAAATAAAGGCTGTAAGCATAACTCAGCTAAGCTTT
1 AGTTGCGAGCTTAACTCAACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTT
* * * *
18506 AAACATCAACTAGGAGCATAGGTCCGCAAGCTGTTTCAGAGTT
66 AAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAGAGTT
18549 GCAAGCTTAA
Statistics
Matches: 218, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
143 1 0.00
144 215 0.99
145 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (144 bp):
AGTTGCGAGCTTAACTCAACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTT
AAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAGAGTTTATTAGCTGAGAGCGTAGGTTT
GTAAGTTGTTTCGA
Found at i:24900 original size:62 final size:57
Alignment explanation
Indices: 24824--24971 Score: 172
Period size: 57 Copynumber: 2.5 Consensus size: 57
24814 AATTGACGGT
*
24824 AAAAAGGATCTAGCCCGGATGGGTGATCCTATCCTAATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC--T--TAATATAGCCCTCCCGAAGAATATGTG-G
* *
24887 AAAAAGATCTAGCCCGGACGAGTGAT-CTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCTTAATATAGCCCTCCCGAAGAATATGTGG
* * *
24943 AAAATGGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
24972 GAATTAGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 5 0.07
57 44 0.58
58 1 0.01
59 1 0.01
61 1 0.01
62 19 0.25
63 5 0.07
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCTTAATATAGCCCTCCCGAAGAATATGTGG
Found at i:25131 original size:67 final size:67
Alignment explanation
Indices: 25036--25170 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
25026 GTAATTGTCA
* * *
25036 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGAGAGTGTGCTC
1 TTGCAAGGGATTTAGCCTGGACTGGTAATCCAGCTGTAAGAAATGAAGTTCGCGAGAGTGTGCTC
25101 TC
66 TC
* * *
25103 TTGCAAGGGATTTAGCCTGGACTGGTAATCCAGTTGTAAGAAATGAAGTTTGCGGGAGTGTGCTC
1 TTGCAAGGGATTTAGCCTGGACTGGTAATCCAGCTGTAAGAAATGAAGTTCGCGAGAGTGTGCTC
25168 TC
66 TC
25170 T
1 T
25171 GAATTGGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (67 bp):
TTGCAAGGGATTTAGCCTGGACTGGTAATCCAGCTGTAAGAAATGAAGTTCGCGAGAGTGTGCTC
TC
Found at i:27632 original size:37 final size:35
Alignment explanation
Indices: 27591--27672 Score: 146
Period size: 37 Copynumber: 2.3 Consensus size: 35
27581 ATGAAATTCC
27591 TGAGTCAATTGTTTTTGATCAGGACAAAATTTTCTT
1 TGAGTCAATTGTTTTTGATCAGGACAAAATTTTC-T
27627 ATGAGTCAATTGTTTTTGATCAGGACAAAATTTTCT
1 -TGAGTCAATTGTTTTTGATCAGGACAAAATTTTCT
27663 TGAGTCAATT
1 TGAGTCAATT
27673 TTGGCAGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 10 0.22
36 1 0.02
37 34 0.76
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (35 bp):
TGAGTCAATTGTTTTTGATCAGGACAAAATTTTCT
Found at i:27658 original size:21 final size:21
Alignment explanation
Indices: 27597--27658 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
27587 TTCCTGAGTC
27597 AATTGTTTTTGATCAGGACAA
1 AATTGTTTTTGATCAGGACAA
* * *
27618 AATT-TTCTT-ATGA-GTC--
1 AATTGTTTTTGATCAGGACAA
27634 AATTGTTTTTGATCAGGACAA
1 AATTGTTTTTGATCAGGACAA
27655 AATT
1 AATT
27659 TTCTTGAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 5 0.17
19 5 0.17
20 4 0.13
21 8 0.27
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (21 bp):
AATTGTTTTTGATCAGGACAA
Found at i:36746 original size:17 final size:17
Alignment explanation
Indices: 36726--36774 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
36716 TAACTTATAT
36726 TTTTTTATATTTTCCTA
1 TTTTTTATATTTTCCTA
*
36743 -TTTTTATAGTTTTTCTA
1 TTTTTTATA-TTTTCCTA
36760 TTTTTATAATATTTT
1 TTTTT-T-ATATTTT
36775 AATAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 8 0.30
17 7 0.26
18 4 0.15
19 5 0.19
20 3 0.11
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTTTATATTTTCCTA
Found at i:44862 original size:22 final size:22
Alignment explanation
Indices: 44837--44928 Score: 98
Period size: 22 Copynumber: 4.0 Consensus size: 22
44827 TGCACTAATG
44837 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
44859 AACAGAGAGCAC-AAATGTGCTA
1 AACAGAGAGCACTAAA-GTGCTA
*
44881 AACAGAGAGCACTGACA-TGCTA
1 AACAGAGAGCACT-AAAGTGCTA
* *
44903 GTAATCAGAGAGCACCAACGTGCTA
1 --AA-CAGAGAGCACTAAAGTGCTA
44928 A
1 A
44929 TAATCAGAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
21 3 0.05
22 35 0.59
23 1 0.02
24 5 0.08
25 15 0.25
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:44914 original size:25 final size:25
Alignment explanation
Indices: 44883--44939 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
44873 ATGTGCTAAA
** *
44883 CAGAGAGCACTGACATGCTAGTAAT
1 CAGAGAGCACCAACATGCTAATAAT
*
44908 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACATGCTAATAAT
44933 CAGAGAG
1 CAGAGAG
44940 GGCGCTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACATGCTAATAAT
Found at i:45824 original size:16 final size:18
Alignment explanation
Indices: 45803--45847 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 18
45793 CGTGGCTTCC
45803 TTCTTTTTC-TTTTT-CT
1 TTCTTTTTCATTTTTGCT
45819 TTCTTTTTCATTTTTGCT
1 TTCTTTTTCATTTTTGCT
45837 TCTCTATTTTC
1 T-TCT-TTTTC
45848 GTTTCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.36
17 5 0.20
18 3 0.12
19 3 0.12
20 5 0.20
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (18 bp):
TTCTTTTTCATTTTTGCT
Found at i:45885 original size:5 final size:5
Alignment explanation
Indices: 45877--45961 Score: 104
Period size: 5 Copynumber: 17.0 Consensus size: 5
45867 TTCCTTTCTT
* *
45877 TATAA TATAA TATAA TATAA TATAA TATAA T-TAC T-TATT TATTAA GT-TAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TA-TAA -TATAA
45927 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
45962 AAATATCTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
4 6 0.08
5 63 0.88
7 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:57138 original size:144 final size:144
Alignment explanation
Indices: 56878--57273 Score: 517
Period size: 144 Copynumber: 2.8 Consensus size: 144
56868 GGTTAGCCAG
* *
56878 AGTTGCGAGCTTAACTCAACTAACTCAAATAAATGAAGGTTGAGAGCATAACTCAACTAACCTTT
1 AGTTGCGAGCTTAACTCAACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTT
* * * *
56943 AAACATTAACTAGGAGCGCAGGTCCATGAGTTGTGTC-GAAGTTTATTAGCTGAGAGCGTAGGTT
66 AAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAG-AGTTTATTAGCTGAGAGCGTAGGTT
57007 TGTAAGTTGTTTCGA
130 TGTAAGTTGTTTCGA
* * *
57022 AGTTGCGAGCTTAAC-CTAGCTAACTAAAATAAATGAATGTTGTGAGCATAACTCATCTAACCTT
1 AGTTGCGAGCTTAACTC-AACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTT
* * *
57086 TAAACATCAACTAGGACCGTAAGTCCACGAGCTGTGTCAGAGTTTATTAGCTGGGAGCGTAGGTT
65 TAAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAGAGTTTATTAGCTGAGAGCGTAGGTT
* * * *
57151 TGTGAGTTTTTTTGG
130 TGTAAGTTGTTTCGA
* * * * * * *
57166 AGTTGTGAGCTTAACTCAACTAACAAAAATAAATAAAGGCTGTAAGCATAACTCAGCTAAGCTTT
1 AGTTGCGAGCTTAACTCAACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTT
* * * *
57231 AAACATCAACTAGGAGCATAGGTCCGCAAGCTGTTTCAGAGTT
66 AAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAGAGTT
57274 GCAAGCTTAA
Statistics
Matches: 218, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
143 1 0.00
144 215 0.99
145 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (144 bp):
AGTTGCGAGCTTAACTCAACTAACTAAAATAAATGAAGGTTGTGAGCATAACTCAACTAACCTTT
AAACATCAACTAGGAGCGTAGGTCCACGAGCTGTGTCAGAGTTTATTAGCTGAGAGCGTAGGTTT
GTAAGTTGTTTCGA
Found at i:60718 original size:19 final size:17
Alignment explanation
Indices: 60676--60718 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
60666 TATGTAGCTA
60676 GGTTGTGTGCGTCACAC
1 GGTTGTGTGCGTCACAC
60693 GGTTGTGTGCGTCACAC
1 GGTTGTGTGCGTCACAC
*
60710 GGCTGTGTG
1 GGTTGTGTG
60719 ACAACCCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.09, C:0.21, G:0.40, T:0.30
Consensus pattern (17 bp):
GGTTGTGTGCGTCACAC
Done.