Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1958
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: 17477
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2319 original size:20 final size:20
Alignment explanation
Indices: 2296--2368 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2286 ACAATTCAAA
2296 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2316 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2337 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2357 GTATCGATACAT
1 GTATCGATACAT
2369 AAAAAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2347 original size:41 final size:40
Alignment explanation
Indices: 2296--2388 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 40
2286 ACAATTCAAA
2296 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAT
*
2337 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
2377 GTATCGATACAT
1 GTATCGATACAT
2389 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 19 0.37
41 32 0.63
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (40 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
Found at i:2379 original size:20 final size:19
Alignment explanation
Indices: 2315--2388 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
2305 CATGTTGCAA
2315 TGTATCGATACATGAAAAAG
1 TGTATCGATACAT-AAAAAG
***
2335 ATGTATCGATACATGTTGCAA-
1 -TGTATCGATACA--TAAAAAG
2356 TGTATCGATACATAAAAAG
1 TGTATCGATACATAAAAAG
2375 TTGTATCGATACAT
1 -TGTATCGATACAT
2389 TTCTTGGCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 3 0.07
20 25 0.58
21 12 0.28
22 2 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (19 bp):
TGTATCGATACATAAAAAG
Found at i:2445 original size:13 final size:13
Alignment explanation
Indices: 2427--2452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2417 TACATTAAGT
2427 ATGTATCGATACA
1 ATGTATCGATACA
2440 ATGTATCGATACA
1 ATGTATCGATACA
2453 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
Found at i:8637 original size:20 final size:21
Alignment explanation
Indices: 8558--8636 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
8548 AATGTCCAAA
*
8558 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
8578 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
8603 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
8623 TTGTATCGATACAT
1 ATGTATCGATACAT
8637 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:8641 original size:13 final size:13
Alignment explanation
Indices: 8623--8661 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
8613 ACATTTTTCT
8623 TTGTATCGATACA
1 TTGTATCGATACA
8636 TTGTATCGATACA
1 TTGTATCGATACA
*
8649 CTGTATCGATACA
1 TTGTATCGATACA
8662 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:10507 original size:53 final size:53
Alignment explanation
Indices: 10445--10551 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
10435 AGTGCAAATA
*
10445 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGGGGG
1 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGAGGG
10498 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGAGGG
1 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGAGGG
10551 A
1 A
10552 GATAAAGGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.34
Consensus pattern (53 bp):
AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGAGGG
Found at i:11182 original size:20 final size:20
Alignment explanation
Indices: 11159--11231 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
11149 ACAATTCAAA
11159 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
11179 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
11200 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
11220 GTATCGATACAT
1 GTATCGATACAT
11232 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:11203 original size:21 final size:21
Alignment explanation
Indices: 11177--11252 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
11167 ACATGTTGCA
11177 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
11198 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
11218 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
11239 TTGTATCGATACAT
1 ATGTATCGATACAT
11253 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:11210 original size:41 final size:41
Alignment explanation
Indices: 11159--11252 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
11149 ACAATTCAAA
*
11159 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
11200 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
11241 GTATCGATACAT
1 GTATCGATACAT
11253 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:11309 original size:13 final size:13
Alignment explanation
Indices: 11291--11316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11281 TACATTAAGT
11291 ATGTATCGATACA
1 ATGTATCGATACA
11304 ATGTATCGATACA
1 ATGTATCGATACA
11317 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
Found at i:12462 original size:20 final size:20
Alignment explanation
Indices: 12437--12490 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
12427 GTTTGAAGTA
* *
12437 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATGTACC
*
12457 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTACC
12477 ATGTATCGATACAA
1 ATGTATCGATACAA
12491 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:17302 original size:22 final size:20
Alignment explanation
Indices: 17257--17303 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
17247 TTGCAATTCA
**
17257 ATTATTTTCTTTTTTAATTC
1 ATTATTTTCTTTTTTAACAC
17277 -TTATTTTCTTTTTTTAAGCAC
1 ATTATTTTC-TTTTTTAA-CAC
17298 ATTATT
1 ATTATT
17304 CTCTAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 1 0.05
22 5 0.23
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTATTTTCTTTTTTAACAC
Done.