Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold11714.1
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: 2627
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Found at i:633 original size:36 final size:36
Alignment explanation
Indices: 593--708 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
583 TACCATCATG
593 ATCAAACAGATTGAGAGTTTCACATGAAAACTCTTT
1 ATCAAACAGATTGAGAGTTTCACATGAAAACTCTTT
* * * * * ** ***
629 ATCAAACATGATTAAAAAATTT-TCATTACCA-TCACG
1 ATCAAACA-GATT-GAGAGTTTCACATGAAAACTCTTT
* *
665 ATCAAACAGATTGAGCGTTTCACATGAAAGCTCTTT
1 ATCAAACAGATTGAGAGTTTCACATGAAAACTCTTT
701 ATCAAACA
1 ATCAAACA
709 TGATCAGATT
Statistics
Matches: 54, Mismatches: 22, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
34 4 0.07
35 8 0.15
36 28 0.52
37 9 0.17
38 5 0.09
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (36 bp):
ATCAAACAGATTGAGAGTTTCACATGAAAACTCTTT
Found at i:648 original size:72 final size:72
Alignment explanation
Indices: 568--712 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
558 ACACTAAGAG
*
568 TTAAAAAATTTTCATTACCATCATGATCAAACAGATTGAGAGTTTCACATGAAAACTCTTTATCA
1 TTAAAAAATTTTCATTACCATCACGATCAAACAGATTGAGAGTTTCACATGAAAACTCTTTATCA
633 AACATGA
66 AACATGA
* *
640 TTAAAAAATTTTCATTACCATCACGATCAAACAGATTGAGCGTTTCACATGAAAGCTCTTTATCA
1 TTAAAAAATTTTCATTACCATCACGATCAAACAGATTGAGAGTTTCACATGAAAACTCTTTATCA
705 AACATGA
66 AACATGA
712 T
1 T
713 CAGATTTTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (72 bp):
TTAAAAAATTTTCATTACCATCACGATCAAACAGATTGAGAGTTTCACATGAAAACTCTTTATCA
AACATGA
Found at i:1180 original size:19 final size:18
Alignment explanation
Indices: 1144--1183 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1134 TTTCCACTCG
*
1144 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
1162 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
1181 TTT
1 TTT
1184 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:2260 original size:16 final size:17
Alignment explanation
Indices: 2239--2279 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
2229 AAACTAGCTC
2239 TCTTTTTTTTTTCA-AA
1 TCTTTTTTTTTTCACAA
2255 TC-TTTTTTTTTCACAA
1 TCTTTTTTTTTTCACAA
2271 T-TTTTTTTT
1 TCTTTTTTTT
2280 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TCTTTTTTTTTTCACAA
Found at i:2262 original size:13 final size:12
Alignment explanation
Indices: 2243--2294 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 12
2233 TAGCTCTCTT
2243 TTTTTTTTCAAA
1 TTTTTTTTCAAA
2255 TCTTTTTTTTTCACAA
1 ---TTTTTTTTCA-AA
2271 TTTTTTTTTCAAAA
1 -TTTTTTTTC-AAA
2285 TTTTTTTTCA
1 TTTTTTTTCA
2295 CAACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 12 0.34
15 11 0.31
16 2 0.06
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:2262 original size:14 final size:13
Alignment explanation
Indices: 2242--2294 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 13
2232 CTAGCTCTCT
2242 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
2255 TCTTTTTTTTTCACAA
1 --TTTTTTTTTCA-AA
2271 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
*
2284 ATTTTTTTTCA
1 TTTTTTTTTCA
2295 CAACTTGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 12 0.33
14 11 0.31
15 11 0.31
16 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:2262 original size:15 final size:14
Alignment explanation
Indices: 2241--2292 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
2231 ACTAGCTCTC
2241 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
2255 TCTTTTTTTTTCACAA
1 T-TTTTTTTTTCA-AA
2271 -TTTTTTTTTCAAAA
1 TTTTTTTTTTC-AAA
2285 TTTTTTTT
1 TTTTTTTT
2293 CACAACTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 13 0.38
15 19 0.56
16 2 0.06
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:2352 original size:12 final size:12
Alignment explanation
Indices: 2335--2383 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
2325 TGGAAACTAG
2335 TTTTTTTTTCGA
1 TTTTTTTTTCGA
*
2347 TTTTTTTTTTGAA
1 TTTTTTTTTCG-A
2360 TTTTTTTTTCGA
1 TTTTTTTTTCGA
* *
2372 GTTTTTTCTCGA
1 TTTTTTTTTCGA
2384 GAAACTACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTCGA
Found at i:2353 original size:13 final size:13
Alignment explanation
Indices: 2335--2378 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
2325 TGGAAACTAG
2335 TTTTTTTTTCGAT
1 TTTTTTTTTCGAT
*
2348 TTTTTTTTT-GAA
1 TTTTTTTTTCGAT
2360 TTTTTTTTTCGAGT
1 TTTTTTTTTCGA-T
2374 TTTTT
1 TTTTT
2379 CTCGAGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 11 0.41
14 5 0.19
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCGAT
Done.