Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4896.1
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: 40630
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.28
Warning! 4509 characters in sequence are not A, C, G, or T
Found at i:2333 original size:26 final size:26
Alignment explanation
Indices: 2302--2409 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
2292 TGAAATGTCC
* *
2302 ATCATGGACCATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2328 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
2354 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2380 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2406 ATCA
1 ATCA
2410 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2854 original size:30 final size:30
Alignment explanation
Indices: 2811--2871 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2801 TATAATAGCC
* *
2811 ATTAGGACTAAATTAAAACAAATATAAAAT
1 ATTAGGACCAAATTAAAACAAAAATAAAAT
* *
2841 ATTAGGGCCAAATTAAAATAAAAATAAAAT
1 ATTAGGACCAAATTAAAACAAAAATAAAAT
2871 A
1 A
2872 AATTGTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.25
Consensus pattern (30 bp):
ATTAGGACCAAATTAAAACAAAAATAAAAT
Found at i:4143 original size:44 final size:44
Alignment explanation
Indices: 4082--4463 Score: 539
Period size: 44 Copynumber: 8.7 Consensus size: 44
4072 AAACTTAGGA
* * *
4082 ACGCCAGATCTGTTATCTTCTATCTGCTCTCTGACAATACAGAG
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* *
4126 ATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAATACAGAG
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * *
4170 ACACTAAATCTGCTATCTTCGATCTGTTCTCTGACAATACAGAG
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * *
4214 ATGTCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAG
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * *
4258 ACTCCAAATCTGCTATCTTCAATCTACTCTTCTGACAATACAGAG
1 ACGCCAAATCTGCTATCTTCGATCTGCTC-TCTGACAATACAGAG
* * *
4303 ATGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGCG
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* * * *
4347 ACGCCAAATCTCCTATCTTCAATCTGCTCCCTAACAATACAGAG
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* *
4391 ACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAT
1 ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
*
4435 ACGCCAAGTCTGCTATCTTCGATCTGCTC
1 ACGCCAAATCTGCTATCTTCGATCTGCTC
4464 CTTGTAAACG
Statistics
Matches: 294, Mismatches: 43, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
44 255 0.87
45 39 0.13
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (44 bp):
ACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
Found at i:4333 original size:177 final size:176
Alignment explanation
Indices: 4082--4459 Score: 549
Period size: 177 Copynumber: 2.1 Consensus size: 176
4072 AAACTTAGGA
* * * *
4082 ACGCCAGATCTGTTATCTTCTATCTGCTCTCTGACAATACAGAGATGCCAAATCTACTATCTTCG
1 ACGCCAAATCTGCTATCTTCAATCTACTCTCTGACAATACAGAGATGCCAAATCTACTATCTTCG
* * * * * *
4147 ATCTGCTCTCTGACAATACAGAGACACTAAATCTGCTATCTTCGATCTGTTCTCTGACAATACAG
66 ATCTGCTCTCTGACAATACAGAGACACCAAATCTCCTATCTTCAATCTGCTCCCTAACAATACAG
* * *
4212 AGATGTCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAG
131 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* **
4258 ACTCCAAATCTGCTATCTTCAATCTACTCTTCTGACAATACAGAGATGCCAAATCTGTTATCTTC
1 ACGCCAAATCTGCTATCTTCAATCTACTC-TCTGACAATACAGAGATGCCAAATCTACTATCTTC
* *
4323 GATCTGCTCTCTGACAATACAGCGACGCCAAATCTCCTATCTTCAATCTGCTCCCTAACAATACA
65 GATCTGCTCTCTGACAATACAGAGACACCAAATCTCCTATCTTCAATCTGCTCCCTAACAATACA
* *
4388 GAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAT
130 GAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
* *
4435 ACGCCAAGTCTGCTATCTTCGATCT
1 ACGCCAAATCTGCTATCTTCAATCT
4460 GCTCCTTGTA
Statistics
Matches: 178, Mismatches: 23, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
176 24 0.13
177 154 0.87
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (176 bp):
ACGCCAAATCTGCTATCTTCAATCTACTCTCTGACAATACAGAGATGCCAAATCTACTATCTTCG
ATCTGCTCTCTGACAATACAGAGACACCAAATCTCCTATCTTCAATCTGCTCCCTAACAATACAG
AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAG
Found at i:4596 original size:44 final size:43
Alignment explanation
Indices: 4539--4621 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
4529 ATCTACTATG
* **
4539 TCTTCAATCTGCTCTCCGTCAAATATGGAGATGCCAAATCTGTT
1 TCTTCAATCTGCTCTCCGAC-AATACAGAGATGCCAAATCTGTT
* * *
4583 TCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATC
1 TCTTCAATCTGCTCTCCGACAATACAGAGATGCCAAATC
4622 AACTTAGATC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 17 0.52
44 16 0.48
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (43 bp):
TCTTCAATCTGCTCTCCGACAATACAGAGATGCCAAATCTGTT
Found at i:4886 original size:220 final size:220
Alignment explanation
Indices: 4450--4873 Score: 632
Period size: 220 Copynumber: 1.9 Consensus size: 220
4440 AAGTCTGCTA
* * *
4450 TCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTGCTTCGATGCAAAAA
1 TCTTCGACCTGCTCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGCAAAAA
* * * * *
4515 TATTCGAAGGTTAGATCTACTATGTCTTCAATCTGCTCTCCGTCAAATATGGAGATGCCAAATCT
66 CATCCGAAGGTTAGATCTACTATGTCTCCAATCTACTCTCCGTCAAATACGGAGATGCCAAATCT
* *
4580 GTTTCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCAACTTAGATCTTCTTCAGCGTAA
131 GTTTCTTCGATTTGCTCTCTGACAATACAAAGATGCCAAATCAACTTAGATCTACTTCAGCGTAA
*
4645 ACACGTGAAAGCCAAATCTGCTTTG
196 ACACCTGAAAGCCAAATCTGCTTTG
**
4670 TCTTCGACCTGCTCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAA
1 TCTTCGACCTGCTCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGCAAAAA
* * * * *
4735 CATCCGAAGGTTAGATCTGCTATGTCTCCGATCTACTCTCTGTCGAATACGGAGATGCCAAATTT
66 CATCCGAAGGTTAGATCTACTATGTCTCCAATCTACTCTCCGTCAAATACGGAGATGCCAAATCT
* * ** * *
4800 GTTTCTTCTATTTGTTCTCTGGTAATACAAAGATGCCAAATCATCTTGGATCTACTTCAGCGTAA
131 GTTTCTTCGATTTGCTCTCTGACAATACAAAGATGCCAAATCAACTTAGATCTACTTCAGCGTAA
4865 ACACCTGAA
196 ACACCTGAA
4874 GGTCAGATCT
Statistics
Matches: 180, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
220 180 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (220 bp):
TCTTCGACCTGCTCCTTGTAAACACAAGGATGCCAAATCATCTTGGATCTACTTCGATGCAAAAA
CATCCGAAGGTTAGATCTACTATGTCTCCAATCTACTCTCCGTCAAATACGGAGATGCCAAATCT
GTTTCTTCGATTTGCTCTCTGACAATACAAAGATGCCAAATCAACTTAGATCTACTTCAGCGTAA
ACACCTGAAAGCCAAATCTGCTTTG
Found at i:17054 original size:30 final size:30
Alignment explanation
Indices: 17011--17069 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
17001 TATAATAGCC
* *
17011 ATTAGGACTAAATTGAAACAAATATAAAAT
1 ATTAGGACCAAATTGAAACAAAAATAAAAT
* *
17041 ATTAGGGCCAAATTGAAATAAAAATAAAA
1 ATTAGGACCAAATTGAAACAAAAATAAAA
17070 CAAAATTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.24
Consensus pattern (30 bp):
ATTAGGACCAAATTGAAACAAAAATAAAAT
Found at i:18730 original size:18 final size:19
Alignment explanation
Indices: 18695--18732 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
18685 TATAGAAAAT
*
18695 ACAAAAAAGAAAAGAAACA
1 ACAAAAAACAAAAGAAACA
18714 ACAAAAAACAAAA-AAACA
1 ACAAAAAACAAAAGAAACA
18732 A
1 A
18733 AATTGATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (19 bp):
ACAAAAAACAAAAGAAACA
Found at i:18920 original size:15 final size:15
Alignment explanation
Indices: 18900--18930 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18890 ATATCTACTG
*
18900 AAATAGATGAATTAC
1 AAATAGACGAATTAC
18915 AAATAGACGAATTAC
1 AAATAGACGAATTAC
18930 A
1 A
18931 TACAACATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.23
Consensus pattern (15 bp):
AAATAGACGAATTAC
Found at i:20789 original size:18 final size:18
Alignment explanation
Indices: 20766--20801 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20756 TACAAAAATT
*
20766 AAAAAATGAAATTAAACA
1 AAAAAATAAAATTAAACA
20784 AAAAAATAAAATTAAACA
1 AAAAAATAAAATTAAACA
20802 GTCTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAATAAAATTAAACA
Found at i:22282 original size:29 final size:30
Alignment explanation
Indices: 22196--22312 Score: 96
Period size: 33 Copynumber: 3.7 Consensus size: 30
22186 TATATAAAAA
*
22196 ATTATTTATCGTATATTATTT-TATTATATAT
1 ATTATTTAT--TATGTTATTTATATTATATAT
*
22227 -TTATATTATTATGTTATGTTGTCTATTATATAT
1 ATTAT-TTATTATGTTA--TT-TATATTATATAT
*
22260 ATTATCTATTAT-TTATTTATATTTTATCATAT
1 ATTATTTATTATGTTATTTATA--TTAT-ATAT
*
22292 ATTATTTATTATGTTGTTTAT
1 ATTATTTATTATGTTATTTAT
22313 CTTTATCTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
29 9 0.13
30 6 0.08
31 10 0.14
32 19 0.27
33 23 0.32
34 4 0.06
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (30 bp):
ATTATTTATTATGTTATTTATATTATATAT
Done.