Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2950
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: 85266
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4846 original size:15 final size:15
Alignment explanation
Indices: 4826--4880 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
4816 ACTCTCCTCA
*
4826 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
4841 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
4856 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
4870 TTCTTTT-TCTC
1 TTCTTTTCTCTC
4881 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:6997 original size:13 final size:14
Alignment explanation
Indices: 6976--7011 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6966 TGTTTTTTTT
6976 ATTTCTTTTTTC-AA
1 ATTT-TTTTTTCGAA
6990 ATTTTTTTTTCGAA
1 ATTTTTTTTTCGAA
7004 ATTTTTTT
1 ATTTTTTT
7012 ACAATCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.69
Consensus pattern (14 bp):
ATTTTTTTTTCGAA
Found at i:9228 original size:20 final size:20
Alignment explanation
Indices: 9205--9251 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9195 GGGTTAAGAT
*
9205 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
9225 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
9245 TGAGCTG
1 TGAGCTG
9252 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:10387 original size:52 final size:52
Alignment explanation
Indices: 10273--10373 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
10263 TAAGGAAACG
* *
10273 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
10325 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
10374 TATGTGCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:18883 original size:21 final size:21
Alignment explanation
Indices: 18857--18910 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
18847 TTGGTATTTG
* *
18857 GGAATTGGTTCGAAATAGTAT
1 GGAATTGGTACAAAATAGTAT
*
18878 GGAATTGGTACAAAATGGTAT
1 GGAATTGGTACAAAATAGTAT
*
18899 GGTATTTGGTAC
1 GG-AATTGGTAC
18911 GAATTGGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACAAAATAGTAT
Found at i:18910 original size:22 final size:22
Alignment explanation
Indices: 18859--18924 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
18849 GGTATTTGGG
* * *
18859 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACAAAATGGTATGGT
18880 AATTGGTACAAAATGGTATGGT
1 AATTGGTACAAAATGGTATGGT
* * *
18902 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACAAAATGGT-ATGGT
18925 TCAAAGAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (22 bp):
AATTGGTACAAAATGGTATGGT
Found at i:26200 original size:24 final size:25
Alignment explanation
Indices: 26147--26200 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
26137 AACAAATTCT
* *
26147 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
26172 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
26195 TTTTTT
1 TTTTTT
26201 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:28466 original size:15 final size:14
Alignment explanation
Indices: 28437--28465 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28427 CTAGACCGTA
28437 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
28451 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
28465 T
1 T
28466 TTTTTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:28466 original size:19 final size:18
Alignment explanation
Indices: 28442--28482 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28432 CCGTATGCAA
*
28442 TTTTTTTTTTGCAATTTT
1 TTTTTTTTTTTCAATTTT
*
28460 TTTTTTTTTTTCGATTTT
1 TTTTTTTTTTTCAATTTT
28478 TTTTT
1 TTTTT
28483 CAAAACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTCAATTTT
Found at i:31890 original size:22 final size:22
Alignment explanation
Indices: 31839--31904 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
31829 GGTATTTGGG
* *
31839 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
31860 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
31882 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
31905 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:34766 original size:52 final size:52
Alignment explanation
Indices: 34683--34783 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
34673 ATAAGAAACG
* * *
34683 TAATGGACAGTAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
*
34735 TAATAGACAGCAGCTTAAGACCTTATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
34784 TATGTGCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:38830 original size:21 final size:21
Alignment explanation
Indices: 38804--38847 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38794 TTTGGTATTG
38804 GGAATTGGCT-CAAAATGGTAT
1 GGAATTGG-TACAAAATGGTAT
*
38825 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACAAAATGGTAT
38846 GG
1 GG
38848 TTATTTGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.32, C:0.07, G:0.34, T:0.27
Consensus pattern (21 bp):
GGAATTGGTACAAAATGGTAT
Found at i:38859 original size:23 final size:23
Alignment explanation
Indices: 38816--38873 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
38806 AATTGGCTCA
38816 AAATGGTATGG--AATTGGTACG
1 AAATGGTATGGTTAATTGGTACG
*
38837 AAATGGTATGGTTATTTGGTACG
1 AAATGGTATGGTTAATTGGTACG
*
38860 AATTGGTAATGGTT
1 AAATGGT-ATGGTT
38874 CAAAGAGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 11 0.34
23 15 0.47
24 6 0.19
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.36
Consensus pattern (23 bp):
AAATGGTATGGTTAATTGGTACG
Found at i:46875 original size:22 final size:22
Alignment explanation
Indices: 46847--46890 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46837 TTTTGAACCA
46847 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
46869 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
46891 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:47217 original size:11 final size:11
Alignment explanation
Indices: 47201--47228 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
47191 AGGAGTTCGA
47201 AAAAAAAATTG
1 AAAAAAAATTG
47212 AAAAAAAATTG
1 AAAAAAAATTG
47223 AAAAAA
1 AAAAAA
47229 TTGCATACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:51800 original size:21 final size:21
Alignment explanation
Indices: 51755--51817 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
51745 TTTGAACCAT
* *
51755 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
51777 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
51798 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
51818 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:52241 original size:12 final size:12
Alignment explanation
Indices: 52224--52248 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52214 TTTCACTCTT
52224 CTCTTTTTCAAA
1 CTCTTTTTCAAA
52236 CTCTTTTTCAAA
1 CTCTTTTTCAAA
52248 C
1 C
52249 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:53272 original size:30 final size:28
Alignment explanation
Indices: 53215--53276 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 28
53205 TTTAACTTGA
*
53215 TTTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCA-CTTTTTTTACTTTT-T
53245 TTTTTTTTGCTCGA-TTTTTTTCACTTTTT
1 TTTTTTTTGCTC-ACTTTTTTT-ACTTTTT
53274 TTT
1 TTT
53277 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 11 0.38
30 17 0.59
31 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (28 bp):
TTTTTTTTGCTCACTTTTTTTACTTTTT
Found at i:53274 original size:12 final size:12
Alignment explanation
Indices: 53259--53326 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 12
53249 TTTTGCTCGA
*
53259 TTTTTTTC-ACT
1 TTTTTTTCAATT
*
53270 TTTTTTTGAATT
1 TTTTTTTCAATT
53282 TTTTTTTCAATCAAT
1 TTTTTTTCAAT---T
53297 TTTTTTTCGAATT
1 TTTTTTTC-AATT
*
53310 TTTTTTT-GATT
1 TTTTTTTCAATT
53321 TTTTTT
1 TTTTTT
53327 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
11 16 0.33
12 12 0.25
13 8 0.17
15 9 0.19
16 3 0.06
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:58212 original size:17 final size:18
Alignment explanation
Indices: 58190--58230 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
58180 CATTTCTTTT
58190 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
58207 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
58225 T-TTTTG
1 TCTTTTG
58231 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:69186 original size:21 final size:23
Alignment explanation
Indices: 69141--69187 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
69131 TCACCTGTAA
* *
69141 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
69164 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
69185 TAA
1 TAA
69188 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:81383 original size:4 final size:4
Alignment explanation
Indices: 81374--81405 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
81364 TTAAACTAAG
81374 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
81406 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:85160 original size:5 final size:4
Alignment explanation
Indices: 85126--85159 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
85116 TTAAACTAAG
85126 TAAA TAAA TAAA TAAA TAAA TAAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA T-AAA T-AAA TAAA
85160 ACTTTACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 20 0.69
5 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Done.