Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3804
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: 31397
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2249 original size:23 final size:22
Alignment explanation
Indices: 2197--2249 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2187 TCCACGTCTT
*
2197 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
2219 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
2242 TTTCTTTT
1 TTTCTTTT
2250 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:7244 original size:20 final size:20
Alignment explanation
Indices: 7221--7267 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7211 GGGTTAAGAT
*
7221 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
7241 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
7261 TGAGCTG
1 TGAGCTG
7268 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:8428 original size:17 final size:18
Alignment explanation
Indices: 8406--8442 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
8396 TGGAATAAAC
8406 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
8423 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
8441 TT
1 TT
8443 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:11787 original size:13 final size:12
Alignment explanation
Indices: 11771--11831 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 12
11761 AAAAAAAATC
11771 AAAAAAAATTCGA
1 AAAAAAAATT-GA
11784 AAAAAAATTGATTGAA
1 AAAAAAA---ATTG-A
*
11800 AAAAAAAATTTCA
1 AAAAAAAA-TTGA
*
11813 AAAAAAAAGTGA
1 AAAAAAAATTGA
11825 AAAAAAA
1 AAAAAAA
11832 TCGAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
12 9 0.22
13 17 0.43
14 2 0.05
15 1 0.03
16 11 0.28
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:11842 original size:15 final size:15
Alignment explanation
Indices: 11824--11877 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
11814 AAAAAAAGTG
11824 AAAAAAAATCGAGCAA
1 AAAAAAAATCGAGC-A
*
11840 AAAAAAAAAC-AG-A
1 AAAAAAAATCGAGCA
*
11853 AAAAAAAGGT-GAGCA
1 AAAAAAA-ATCGAGCA
11868 AAAAAAAATC
1 AAAAAAAATC
11878 AAGTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
13 8 0.27
14 3 0.10
15 10 0.33
16 9 0.30
ACGTcount: A:0.72, C:0.09, G:0.13, T:0.06
Consensus pattern (15 bp):
AAAAAAAATCGAGCA
Found at i:11844 original size:29 final size:28
Alignment explanation
Indices: 11812--11875 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
11802 AAAAAATTTC
**
11812 AAAAAAAAAGTGAAAAAAAA-TCGAGCAA
1 AAAAAAAAACAGAAAAAAAAGT-GAGCAA
11840 AAAAAAAAACAGAAAAAAAAGGTGAGCAA
1 AAAAAAAAACAGAAAAAAAA-GTGAGCAA
11869 AAAAAAA
1 AAAAAAA
11876 TCAAGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 18 0.56
29 13 0.41
30 1 0.03
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.05
Consensus pattern (28 bp):
AAAAAAAAACAGAAAAAAAAGTGAGCAA
Found at i:13728 original size:20 final size:20
Alignment explanation
Indices: 13682--13728 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13672 AGCTCGTTTC
*
13682 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13702 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13722 CAGCTCA
1 CAGCTCA
13729 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15161 original size:11 final size:13
Alignment explanation
Indices: 15131--15178 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
15121 TGAAACGTGA
*
15131 AAAAAAAAATTTG
1 AAAAAAAAATTCG
15144 ATTAAAAAAAA-TC-
1 A--AAAAAAAATTCG
15157 AAAAAAAAATTCG
1 AAAAAAAAATTCG
15170 AAAAAAAAA
1 AAAAAAAAA
15179 GAAAGACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 11 0.37
14 1 0.03
15 8 0.27
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:16376 original size:48 final size:47
Alignment explanation
Indices: 16297--16402 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
16287 GAGTGTCATG
*
16297 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
16345 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
16393 GAAAAAGAAA
1 GAAAAAGAAA
16403 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:20563 original size:17 final size:18
Alignment explanation
Indices: 20541--20577 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20531 TGGAATAAAC
20541 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
20558 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
20576 TT
1 TT
20578 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:22469 original size:30 final size:30
Alignment explanation
Indices: 22374--22470 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
22364 AGCTCACTCC
*
22374 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
22404 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
22434 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
22464 TAGCTCA
1 TAGCTCA
22471 TTTTTGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:23360 original size:22 final size:20
Alignment explanation
Indices: 23328--23376 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
23318 GCCAAATTTA
23328 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
23351 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
23371 TGAACA
1 TGAACA
23377 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:24124 original size:10 final size:10
Alignment explanation
Indices: 24109--24140 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
24099 GTTATACAAG
24109 TCAAAAAAAA
1 TCAAAAAAAA
24119 TCAAAAAAAA
1 TCAAAAAAAA
24129 TTCAAAAAAAA
1 -TCAAAAAAAA
24140 T
1 T
24141 TCGAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (10 bp):
TCAAAAAAAA
Found at i:24147 original size:10 final size:11
Alignment explanation
Indices: 24109--24152 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
24099 GTTATACAAG
24109 TCAAAAAAAA-
1 TCAAAAAAAAT
24119 TCAAAAAAAAT
1 TCAAAAAAAAT
24130 TCAAAAAAAAT
1 TCAAAAAAAAT
24141 TCGAAAAGAAAA
1 TC-AAAA-AAAA
24153 AAAAATCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.32
11 13 0.42
12 4 0.13
13 4 0.13
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.14
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:24164 original size:18 final size:17
Alignment explanation
Indices: 24132--24169 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
24122 AAAAAAATTC
24132 AAAAAAAATTCGAAAAGA
1 AAAAAAAATTCGAAAA-A
24150 AAAAAAAA-TCTGAAAAA
1 AAAAAAAATTC-GAAAAA
24167 AAA
1 AAA
24170 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAAATTCGAAAAA
Found at i:25232 original size:30 final size:31
Alignment explanation
Indices: 25169--25239 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
25159 TTTGAAAAGC
* *
25169 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
25199 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
25229 AAAAAGAAATT
1 AAAAAGAAATT
25240 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:27422 original size:30 final size:30
Alignment explanation
Indices: 27327--27423 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
27317 AGCTCACTCC
* *
27327 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
27357 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
* *
27387 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
27417 TAGCTCA
1 TAGCTCA
27424 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Done.