Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2700
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: 23028
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:167 original size:20 final size:22
Alignment explanation
Indices: 128--170 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
118 TCAAAGGTCA
128 AAACCCTAGAAAGCATCGATAC
1 AAACCCTAGAAAGCATCGATAC
*
150 AAACCC-AG-AAGTATCGATAC
1 AAACCCTAGAAAGCATCGATAC
170 A
1 A
171 TATTGCTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.47, C:0.26, G:0.14, T:0.14
Consensus pattern (22 bp):
AAACCCTAGAAAGCATCGATAC
Found at i:2708 original size:13 final size:13
Alignment explanation
Indices: 2690--2715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2680 ACAATTTTTG
2690 TGTATCGATACAT
1 TGTATCGATACAT
2703 TGTATCGATACAT
1 TGTATCGATACAT
2716 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2714 original size:32 final size:32
Alignment explanation
Indices: 2671--2733 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2661 TACAAGCCAA
*
2671 TGTATCAATACA-ATTTTTGTGTATCGATACAT
1 TGTATCAATACATA-CTTTGTGTATCGATACAT
*
2703 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCAATACATACTTTGTGTATCGATACA
2734 AGTTTAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCAATACATACTTTGTGTATCGATACAT
Found at i:4301 original size:19 final size:20
Alignment explanation
Indices: 4277--4327 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4267 ACAATTCATG
4277 ATGTATCGATACCAAG-AAC
1 ATGTATCGATACCAAGCAAC
* *
4296 ATGTATCGATACTAAGCAAT
1 ATGTATCGATACCAAGCAAC
4316 ATGTATCGATAC
1 ATGTATCGATAC
4328 ATCTGGGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACCAAGCAAC
Found at i:4321 original size:20 final size:19
Alignment explanation
Indices: 4256--4328 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
4246 CTGTCAATTT
*
4256 TATGTATCGATACAATTC-A
1 TATGTATCGATACAA-GCAA
4275 TGATGTATCGATACCAAG-AA
1 T-ATGTATCGATA-CAAGCAA
*
4295 CATGTATCGATACTAAGCAA
1 TATGTATCGATAC-AAGCAA
4315 TATGTATCGATACA
1 TATGTATCGATACA
4329 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.02
19 16 0.35
20 26 0.57
21 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
TATGTATCGATACAAGCAA
Found at i:10621 original size:17 final size:18
Alignment explanation
Indices: 10599--10632 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10589 AATTTGAAAA
10599 AAAAGAG-TTTGTTTTAT
1 AAAAGAGATTTGTTTTAT
*
10616 AAAAGAGATTTTTTTTA
1 AAAAGAGATTTGTTTTA
10633 GAAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
AAAAGAGATTTGTTTTAT
Found at i:11420 original size:43 final size:43
Alignment explanation
Indices: 11359--11456 Score: 196
Period size: 43 Copynumber: 2.3 Consensus size: 43
11349 ATGAAGAATG
11359 GTATCGATACATGAAACTAGCAGTAGCTACCTTATCACTTTTT
1 GTATCGATACATGAAACTAGCAGTAGCTACCTTATCACTTTTT
11402 GTATCGATACATGAAACTAGCAGTAGCTACCTTATCACTTTTT
1 GTATCGATACATGAAACTAGCAGTAGCTACCTTATCACTTTTT
11445 GTATCGATACAT
1 GTATCGATACAT
11457 AGGACTTGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (43 bp):
GTATCGATACATGAAACTAGCAGTAGCTACCTTATCACTTTTT
Found at i:14395 original size:21 final size:21
Alignment explanation
Indices: 14362--14411 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
14352 TTGCAAGTTG
*
14362 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
14384 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
14405 AAATAAA
1 AAATAAA
14412 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:16230 original size:15 final size:15
Alignment explanation
Indices: 16210--16240 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16200 TAAAAATGTC
*
16210 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
16225 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
16240 C
1 C
16241 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:18491 original size:20 final size:20
Alignment explanation
Indices: 18448--18494 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
18438 AAATCTTTTG
18448 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
18469 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
18489 CAAAAT
1 CAAAAT
18495 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:20880 original size:13 final size:13
Alignment explanation
Indices: 20862--20887 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20852 TACAGCAAGT
20862 ATGTATCGATACA
1 ATGTATCGATACA
20875 ATGTATCGATACA
1 ATGTATCGATACA
20888 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.