Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1009
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: 54056
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:18043 original size:10 final size:10
Alignment explanation
Indices: 18028--18072 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
18018 AATTGTAGAT
18028 TCAAAAAAAA
1 TCAAAAAAAA
18038 TCAAAAAAAAA
1 TC-AAAAAAAA
*
18049 TCGAAAAAAA
1 TCAAAAAAAA
*
18059 TTAAAAAAAA
1 TCAAAAAAAA
18069 -CAAA
1 TCAAA
18073 TTTTTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 3 0.10
10 17 0.57
11 10 0.33
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (10 bp):
TCAAAAAAAA
Found at i:18046 original size:11 final size:11
Alignment explanation
Indices: 18030--18068 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
18020 TTGTAGATTC
18030 AAAAAAAATCA
1 AAAAAAAATCA
18041 AAAAAAAATC-
1 AAAAAAAATCA
* *
18051 GAAAAAAATTA
1 AAAAAAAATCA
18062 AAAAAAA
1 AAAAAAA
18069 CAAATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:21495 original size:52 final size:51
Alignment explanation
Indices: 21380--21497 Score: 143
Period size: 50 Copynumber: 2.3 Consensus size: 51
21370 TAATAAAGTT
21380 ATGCATTATGTAACT-TCCATGCTAGTTAAGTATGCATCATAAATAATGAC
1 ATGCATTATGTAACTCTCCATGCTAGTTAAGTATGCATCATAAATAATGAC
* * *
21430 ATGCATTATGTAACTCT-CATGTTAGTTTAAGTCTGCATCATTAAATTAA-GTC
1 ATGCATTATGTAACTCTCCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
* *
21482 TTGCATTAAGTAACTC
1 ATGCATTATGTAACTC
21498 ATTTGTTCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
50 22 0.37
51 14 0.24
52 20 0.34
53 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (51 bp):
ATGCATTATGTAACTCTCCATGCTAGTTAAGTATGCATCATAAATAATGAC
Found at i:24212 original size:21 final size:23
Alignment explanation
Indices: 24167--24213 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
24157 TCACCTGCAA
* *
24167 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
24190 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
24211 TAA
1 TAA
24214 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:29601 original size:46 final size:46
Alignment explanation
Indices: 29548--29641 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
29538 CAAAGAAAAG
* *
29548 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAAACTTGGTATATGATGA
29594 ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
29640 AC
1 AC
29642 GCCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAAACTTGGTATATGATGA
Found at i:31446 original size:20 final size:20
Alignment explanation
Indices: 31400--31446 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31390 AGCTCGTTTC
*
31400 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
31420 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31440 CAGCTCA
1 CAGCTCA
31447 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:35132 original size:19 final size:18
Alignment explanation
Indices: 35096--35135 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35086 TTTCCACTCG
*
35096 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
35114 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
35133 TTT
1 TTT
35136 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:36207 original size:15 final size:14
Alignment explanation
Indices: 36187--36222 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
36177 TAGCTTCTTC
36187 TTTTTTTTCACGAAT
1 TTTTTTTTCAC-AAT
36202 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
36216 TTTTTTT
1 TTTTTTT
36223 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:36278 original size:10 final size:10
Alignment explanation
Indices: 36263--36300 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
36253 TGGAAACCTT
36263 TTTTTTTGAA
1 TTTTTTTGAA
36273 TTTTTTTTGAA
1 -TTTTTTTGAA
36284 TTTTTTTGAA
1 TTTTTTTGAA
36294 TTTTTTT
1 TTTTTTT
36301 TCGAGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:36278 original size:11 final size:11
Alignment explanation
Indices: 36262--36316 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
36252 ATGGAAACCT
36262 TTTTTTTTGAA
1 TTTTTTTTGAA
36273 TTTTTTTTGAA
1 TTTTTTTTGAA
36284 -TTTTTTTGAA
1 TTTTTTTTGAA
*
36294 TTTTTTTTCGAG
1 TTTTTTTT-GAA
36306 TTGTTTTTTGA
1 TT-TTTTTTGA
36317 GAAACTACTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
10 10 0.25
11 18 0.45
12 6 0.15
13 6 0.15
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:36278 original size:12 final size:12
Alignment explanation
Indices: 36261--36316 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
36251 AATGGAAACC
36261 TTTTTTTTTGAA
1 TTTTTTTTTGAA
36273 -TTTTTTTTGAA
1 TTTTTTTTTGAA
36284 --TTTTTTTGAA
1 TTTTTTTTTGAA
* *
36294 TTTTTTTTCGAG
1 TTTTTTTTTGAA
*
36306 TTGTTTTTTGA
1 TTTTTTTTTGA
36317 GAAACTACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 10 0.26
11 11 0.29
12 17 0.45
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:38126 original size:19 final size:19
Alignment explanation
Indices: 38082--38119 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
38072 TTGTAGGACA
38082 AAGGAAAGTAGGCTTGAAT
1 AAGGAAAGTAGGCTTGAAT
38101 AAGGAAAGTAGGCTTGAAT
1 AAGGAAAGTAGGCTTGAAT
38120 CAAGAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.32, T:0.21
Consensus pattern (19 bp):
AAGGAAAGTAGGCTTGAAT
Found at i:38240 original size:15 final size:15
Alignment explanation
Indices: 38220--38273 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
38210 CTTCTTCTTC
38220 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAA--T
*
38237 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
38252 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
38267 TTTTTTT
1 TTTTTTT
38274 TCAACTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 22 0.63
17 13 0.37
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:38241 original size:16 final size:16
Alignment explanation
Indices: 38220--38276 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
38210 CTTCTTCTTC
38220 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAA-TT
38237 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
38252 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
38268 TTTTTTTCA
1 TTTTTTTCA
38277 ACTTGATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.33
16 15 0.38
17 11 0.28
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:38242 original size:17 final size:17
Alignment explanation
Indices: 38220--38274 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
38210 CTTCTTCTTC
38220 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAATTT
38237 TTTTTTTCACG-AA-TT
1 TTTTTTTCACGAAATTT
38252 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAATTT
38269 TTTTTT
1 TTTTTT
38275 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.36
16 4 0.11
17 19 0.53
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTTTTCACGAAATTT
Found at i:38332 original size:13 final size:13
Alignment explanation
Indices: 38314--38375 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
38304 ATGGAAACCA
38314 AATTTTTTTTTTC
1 AATTTTTTTTTTC
38327 AA-TTTTTTTTTC
1 AATTTTTTTTTTC
*
38339 AATCTTTTTTTTTG
1 AAT-TTTTTTTTTC
**
38353 AATTTTTTTTTGA
1 AATTTTTTTTTTC
38366 AATTTTTTTT
1 AATTTTTTTT
38376 GAAGAAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
12 12 0.27
13 20 0.45
14 12 0.27
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTTC
Found at i:38334 original size:12 final size:12
Alignment explanation
Indices: 38317--38375 Score: 73
Period size: 12 Copynumber: 4.7 Consensus size: 12
38307 GAAACCAAAT
38317 TTTTTTTTTCAA
1 TTTTTTTTTCAA
38329 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
38341 TCTTTTTTTTTGAA
1 --TTTTTTTTTCAA
*
38355 TTTTTTTTTGAAA
1 TTTTTTTTT-CAA
38368 TTTTTTTT
1 TTTTTTTT
38376 GAAGAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
12 21 0.50
13 10 0.24
14 11 0.26
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:38335 original size:14 final size:14
Alignment explanation
Indices: 38316--38363 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
38306 GGAAACCAAA
38316 TTTTTTTTTTCAA-
1 TTTTTTTTTTCAAT
38329 -TTTTTTTTTCAAT
1 TTTTTTTTTTCAAT
* *
38342 CTTTTTTTTTGAAT
1 TTTTTTTTTTCAAT
38356 TTTTTTTT
1 TTTTTTTT
38364 GAAATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
12 12 0.39
14 19 0.61
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTCAAT
Found at i:39404 original size:21 final size:23
Alignment explanation
Indices: 39360--39406 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
39350 TCACCTGCAA
*
39360 TAAACACATTAAAATGAGCTTAT
1 TAAACACATTAAAATCAGCTTAT
39383 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39404 TAA
1 TAA
39407 TCATAACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 1 0.04
23 14 0.61
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:47567 original size:6 final size:6
Alignment explanation
Indices: 47558--47608 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
47548 AAACAGCATG
* * *
47558 AGAAAA AGAAAA AGAAAA AGAAAG TGAAAA AGAAAT AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
47606 AGA
1 AGA
47609 GTGCGAGCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
AGAAAA
Found at i:47599 original size:24 final size:24
Alignment explanation
Indices: 47559--47604 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
47549 AACAGCATGA
47559 GAAAAAGAAAAAGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAAAAGAAAGT
*
47583 GAAAAAGAAATAGAAAAAGAAA
1 GAAAAAGAAAAAGAAAAAGAAA
47605 AAGAGTGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAAAGT
Found at i:48008 original size:22 final size:22
Alignment explanation
Indices: 47978--48021 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47968 TTTGGTATTT
47978 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
48000 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
48022 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:52237 original size:17 final size:17
Alignment explanation
Indices: 52215--52262 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
52205 TTTCATTCTC
52215 TTTTTTGAATTTTCTTT
1 TTTTTTGAATTTTCTTT
* *
52232 TTTTTTCATTTTTCTTT
1 TTTTTTGAATTTTCTTT
* *
52249 TCTTTTGTATTTTC
1 TTTTTTGAATTTTC
52263 GCTCTTTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTTGAATTTTCTTT
Done.