Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3247
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: 41621
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:6261 original size:75 final size:75
Alignment explanation
Indices: 6138--6288 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
6128 ACCTTGGATA
6138 AGTCTTCTCAGCTTTGTTTTAATTTCTCTATAGTAGAGGTGGAATAAACCTTTTACGCATAATCT
1 AGTCTTCTCAGCTTTGTTTTAATTTCTCTATAGTAGAGGTGGAATAAACCTTTTACGCATAATCT
6203 GTTTCAACTC
66 GTTTCAACTC
6213 AGTCTTCTCAGCTTTG-TTTAATTTCTCTATAGTAAGAGGTGGAATAAACCTTTTACGCATAATC
1 AGTCTTCTCAGCTTTGTTTTAATTTCTCTATAGT-AGAGGTGGAATAAACCTTTTACGCATAATC
6277 TGTTTCAACTC
65 TGTTTCAACTC
6288 A
1 A
6289 TCCCATGTCG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 17 0.23
75 58 0.77
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (75 bp):
AGTCTTCTCAGCTTTGTTTTAATTTCTCTATAGTAGAGGTGGAATAAACCTTTTACGCATAATCT
GTTTCAACTC
Found at i:9161 original size:326 final size:318
Alignment explanation
Indices: 8532--9168 Score: 948
Period size: 326 Copynumber: 2.0 Consensus size: 318
8522 CGTTGACGCG
* *
8532 CGTAATGGAGATCCAATGCGTTTTGGCCAAAGATTGGTTTCTTGACCAAGATTTCCAAGATTTGA
1 CGTAACGGAGATCCAATGCGTGTTGGCCAAAGATTGGTTTCTTGACCAAGATTTCCAAGATTTGA
*
8597 AATCTTGATTTCTGATTCTTGAAATCTCTCGAACAGCAAAATGGGCCAAATTCAGTTTCTTGATT
66 AATCTTGATTTCTGATTCTTGAAATCTCTCGAACAGCAAAATGGGCCAAATTCAGTTTCTTGAAT
*
8662 TTCTTGAAACAAGAAATGAATCTTGATTTTCTGTTCTTGTATGCATCTAAGCCTTGCTAACAAGC
131 TTCTTGAAACAAGAAATGAATCTTGATTTTCTGTTCTTGTATGCATCTAAGCCTTGCTAACAAAC
**
8727 TCTTGAATGGTCCCATTTAGTTTGGACTTCATTTGTCGGCCTTTGATCTCGTTATTGGCCTGTGC
196 TCTTGAATGGTCCCATTTAGTTTGGACCGCATTTGTCGGCCTTTGATCTCGTTATTGGCCTGTGC
* * *
8792 AATTTGAGCCATCACTCTTGGACTTGGATTGGCCTTTATGACTCGTATCATTGATGCT
261 AATCTGAGCCATCACTCTTGAACTTGGATTGGCCTTTATGACTCATATCATTGATGCT
8850 CGTAACGGAGATCCAATGCGTGTT-GCGC-AAGATTTGGTTTCTTGGACCAAGATTTCCAAGATT
1 CGTAACGGAGATCCAATGCGTGTTGGC-CAAAGA-TTGGTTTCTT-GACCAAGATTTCCAAGATT
* *
8913 TGAAATCTTGATTTTCTGA-TCTTGAAAAT-TCTTCGAACAGCATAATTGGCCAAGATTC-GTTT
63 TGAAATCTTGA-TTTCTGATTCTTG-AAATCTC-TCGAACAGCAAAATGGGCCAA-ATTCAGTTT
* *
8975 CTTGAATTTCTTGAAAACAAGAAGTGAATCTTGATTTTCTTTCTCTCGTGTATTGCATCTAAGGC
124 CTTGAATTTCTTG-AAACAAGAAATGAATCTTGATTTTCTGT-TCT--TGTA-TGCATCTAA-GC
9040 CTTGCTAACAAACTCTTGAATGGTCCCATTTAGTTTGGACCGCATTTGTCGGCCTTTGATCTCGT
183 CTTGCTAACAAACTCTTGAATGGTCCCATTTAGTTTGGACCGCATTTGTCGGCCTTTGATCTCGT
*
9105 TATTGGCCTTGTTGGCAA-CTGAGCCATCA-TCTTGAATTTGG-TTGGCCTTTATGACTCATATC
248 TATTGGCC-TG-T-GCAATCTGAGCCATCACTCTTGAACTTGGATTGGCCTTTATGACTCATATC
9167 AT
310 AT
9169 ATGGTTTAAG
Statistics
Matches: 289, Mismatches: 14, Indels: 24
0.88 0.04 0.07
Matches are distributed among these distances:
317 6 0.02
318 33 0.11
319 37 0.13
320 46 0.16
321 30 0.10
322 3 0.01
324 4 0.01
325 9 0.03
326 94 0.33
327 12 0.04
328 11 0.04
329 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (318 bp):
CGTAACGGAGATCCAATGCGTGTTGGCCAAAGATTGGTTTCTTGACCAAGATTTCCAAGATTTGA
AATCTTGATTTCTGATTCTTGAAATCTCTCGAACAGCAAAATGGGCCAAATTCAGTTTCTTGAAT
TTCTTGAAACAAGAAATGAATCTTGATTTTCTGTTCTTGTATGCATCTAAGCCTTGCTAACAAAC
TCTTGAATGGTCCCATTTAGTTTGGACCGCATTTGTCGGCCTTTGATCTCGTTATTGGCCTGTGC
AATCTGAGCCATCACTCTTGAACTTGGATTGGCCTTTATGACTCATATCATTGATGCT
Found at i:18799 original size:14 final size:14
Alignment explanation
Indices: 18769--18798 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18759 CAATTTTTCA
18769 TTCACTTTTTCTTT
1 TTCACTTTTTCTTT
18783 TTCATCTTTTTCTTT
1 TTCA-CTTTTTCTTT
18798 T
1 T
18799 CTCGCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCACTTTTTCTTT
Found at i:18841 original size:19 final size:20
Alignment explanation
Indices: 18817--18861 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
18807 CTTTTCATTC
*
18817 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
18836 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
18856 TCTTTT
1 TCTTTT
18862 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:21098 original size:10 final size:9
Alignment explanation
Indices: 21083--21146 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
21073 CCGTATACAA
21083 TTTTTTTCT
1 TTTTTTTCT
21092 TTTTTTTCT
1 TTTTTTTCT
21101 TTTTTTTCAAT
1 TTTTTTTC--T
* **
21112 TTTCTTTGA
1 TTTTTTTCT
*
21121 TTTTTTTAT
1 TTTTTTTCT
*
21130 TTTTTTTGAT
1 TTTTTTT-CT
21140 TTTTTTT
1 TTTTTTT
21147 TTAAAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
9 30 0.65
10 9 0.20
11 7 0.15
ACGTcount: A:0.08, C:0.06, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:21787 original size:20 final size:21
Alignment explanation
Indices: 21762--21806 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
21752 TTTTCCTTTG
21762 TTTTTTAATTAAGTTT-AAAT
1 TTTTTTAATTAAGTTTAAAAT
21782 TTTTTTAATTAAGTTTAAAAT
1 TTTTTTAATTAAGTTTAAAAT
21803 TTTT
1 TTTT
21807 AAGTTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTTTAATTAAGTTTAAAAT
Found at i:29573 original size:22 final size:22
Alignment explanation
Indices: 29541--29604 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
29531 TTGGTATTTA
29541 GGAA-TTGGTACGAAATGGTAT
1 GGAATTTGGTACGAAATGGTAT
*
29562 GGAATTTGGTACAAAATGGTAT
1 GGAATTTGGTACGAAATGGTAT
* *
29584 GGTATTTGGTACGAATTGGTA
1 GGAATTTGGTACGAAATGGTA
29605 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
21 4 0.11
22 34 0.89
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (22 bp):
GGAATTTGGTACGAAATGGTAT
Found at i:34599 original size:19 final size:18
Alignment explanation
Indices: 34563--34602 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34553 TTTCCACTCG
*
34563 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
34581 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
34600 TTT
1 TTT
34603 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:35701 original size:13 final size:12
Alignment explanation
Indices: 35654--35698 Score: 72
Period size: 13 Copynumber: 3.6 Consensus size: 12
35644 TAGCTCTCTC
35654 TTTTTCAAATTT
1 TTTTTCAAATTT
35666 TTTTTCAAATTTT
1 TTTTTCAAA-TTT
35679 TTTTTCACAATTT
1 TTTTTCA-AATTT
35692 TTTTTCA
1 TTTTTCA
35699 CAACTTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.29
13 20 0.65
14 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTCAAATTT
Found at i:38858 original size:19 final size:18
Alignment explanation
Indices: 38822--38861 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38812 TTTCCACTCG
*
38822 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
38840 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
38859 TTT
1 TTT
38862 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:39934 original size:13 final size:12
Alignment explanation
Indices: 39912--39955 Score: 79
Period size: 12 Copynumber: 3.6 Consensus size: 12
39902 TAGCTCTCTC
39912 TTTTTCAAATTT
1 TTTTTCAAATTT
39924 TTTTTCAAAATTT
1 TTTTTC-AAATTT
39937 TTTTTCAAATTT
1 TTTTTCAAATTT
39949 TTTTTCA
1 TTTTTCA
39956 CAACTTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 19 0.61
13 12 0.39
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTCAAATTT
Done.