Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1256
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: 18436
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3061 original size:81 final size:82
Alignment explanation
Indices: 2892--3111 Score: 270
Period size: 81 Copynumber: 2.7 Consensus size: 82
2882 AAAAGGAGTA
* * * *
2892 CATCCTGCTCTTCGAGGGACAAA-AAAAAAG-AATAAAATGCGTCCTACTCTTTGAAGACAAAGG
1 CATCCTGCTCTTTGA-GGACAAAGGAAAAAGAAATAAAGTGCGTCCTGCTCTTTG-AGACAAAGG
*
2955 AAAATAAGGAAATTAAGTG
64 AAAATAAGGAAATAAAGTG
** *
2974 TGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGCGTCCTGCTCTTTGAGACAATGG
1 CATCCTGCTCTTTGAGGACAAAGGA-AAAA-GAAATAAAGTGCGTCCTGCTCTTTGAGACAAAGG
3039 -AAA-AA-GAAATAAAGTG
64 AAAATAAGGAAATAAAGTG
* *
3055 CATCCTGCTCTTTGAGGACAAAGTGAAAAAGAAATAAAGTGCATCCTGCTTTTTGAG
1 CATCCTGCTCTTTGAGGACAAAG-GAAAAAGAAATAAAGTGCGTCCTGCTCTTTGAG
3112 GACTAAAAGA
Statistics
Matches: 121, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
80 25 0.21
81 42 0.35
82 17 0.14
83 7 0.06
84 9 0.07
85 21 0.17
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (82 bp):
CATCCTGCTCTTTGAGGACAAAGGAAAAAGAAATAAAGTGCGTCCTGCTCTTTGAGACAAAGGAA
AATAAGGAAATAAAGTG
Found at i:3094 original size:41 final size:40
Alignment explanation
Indices: 2892--3114 Score: 254
Period size: 41 Copynumber: 5.5 Consensus size: 40
2882 AAAAGGAGTA
* * *
2892 CATCCTGCTCTTCGAGGGACAAA-AAAAAAG-AATAAAATG
1 CATCCTGCTCTTTGA-GGACAAAGGAAAAAGAAATAAAGTG
* * * *
2931 CGTCCTACTCTTTGAAGACAAAGGAAAATAAGGAAATTAAGTG
1 CATCCTGCTCTTTGAGGACAAAGG-AAA-AA-GAAATAAAGTG
**
2974 TGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTG
1 CATCCTGCTCTTTGAGGACAAAGGA-AAAA-GAAATAAAGTG
* *
3016 CGTCCTGCTCTTTGA-GACAATGGAAAAAGAAATAAAGTG
1 CATCCTGCTCTTTGAGGACAAAGGAAAAAGAAATAAAGTG
3055 CATCCTGCTCTTTGAGGACAAAGTGAAAAAGAAATAAAGTG
1 CATCCTGCTCTTTGAGGACAAAG-GAAAAAGAAATAAAGTG
*
3096 CATCCTGCTTTTTGAGGAC
1 CATCCTGCTCTTTGAGGAC
3115 TAAAAGATGT
Statistics
Matches: 160, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
38 6 0.04
39 37 0.23
40 13 0.08
41 45 0.28
42 29 0.18
43 30 0.19
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (40 bp):
CATCCTGCTCTTTGAGGACAAAGGAAAAAGAAATAAAGTG
Found at i:3246 original size:61 final size:60
Alignment explanation
Indices: 3106--3481 Score: 443
Period size: 61 Copynumber: 6.2 Consensus size: 60
3096 CATCCTGCTT
* * * * * * *
3106 TTTGAGGACTAAAAGATGTCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGTGTCCTGCAC
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-----GAAAAGCGTCCTACTC
**
3171 TTT-AGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGAGAAAGCGTCCTACTC
1 TTTGA-GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGCGTCCTACTC
* *
3232 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGTGTCCTACTC
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCGTCCTACTC
* * * *
3293 TTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCATCCTGCTC
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCCTACTC
** * *
3352 TTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATACTACTC
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCGTCCTACTC
* * * *
3413 TTTGAGGACTAGAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGG-AAAGTGTCATACTC
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCCTACTC
3472 TTTGAGGACT
1 TTTGAGGACT
3482 GAATGGATAA
Statistics
Matches: 276, Mismatches: 29, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
59 35 0.13
60 78 0.28
61 124 0.45
62 1 0.00
64 1 0.00
65 37 0.13
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (60 bp):
TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCCTACTC
Found at i:3372 original size:120 final size:121
Alignment explanation
Indices: 3090--3461 Score: 489
Period size: 120 Copynumber: 3.0 Consensus size: 121
3080 AAAAAGAAAT
* * *
3090 AAAGTGCATCCTGCTTTTTGAGGACTA-AAAGATGTCACCAACTTGTGTGGGCTTTAAAAGAAAA
1 AAAG-GCATCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * *
3154 AGGAAAGTGTCCTGCACTTT-AGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGG
64 A-G---GTGTCCTACTCTTTGA-GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
* * * ** *
3216 AGAAAGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA
1 A-AAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* *
3281 GGTGTCCTACTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
65 GGTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
3337 AAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
** * *
3402 GCATACTACTCTTTGAGGACTAGAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGG
66 GTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
3458 AAAG
1 AAAG
3462 TGTCATACTC
Statistics
Matches: 216, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
120 76 0.35
121 67 0.31
122 17 0.08
123 1 0.00
125 1 0.00
126 50 0.23
127 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (121 bp):
AAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
GTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:3434 original size:181 final size:183
Alignment explanation
Indices: 3106--3484 Score: 545
Period size: 181 Copynumber: 2.1 Consensus size: 183
3096 CATCCTGCTT
* *
3106 TTTGAGGACTAAAAGATGTCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGTGTCCTGCAC
1 TTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAA--GTCCTGCAC
** ** * *
3171 TTTAGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGAGAAAGCGTCCTACTCTTTG
64 TTTAGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATACTACTCTTTG
*
3236 AGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGTGTCCTACTC
129 AGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG-AAA-GTGTCATACTC
* * *
3293 TTTGAGGACTGAAAG-TGCCACCAACTTGTGTGGGCTTTAAAAG-GAAAGG-CA-TCCTGCTCTT
1 TTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGTCCTGCACTT
3354 T-GAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCATACTACTCTTTG
66 TAG-GGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAA-GCATACTACTCTTTG
*
3417 AGGACTAGAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGAAAGTGTCATACTC
129 AGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGTGTCATACTC
3472 TTTGAGGACTGAA
1 TTTGAGGACTGAA
3485 TGGATAAAAG
Statistics
Matches: 177, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
179 23 0.13
180 7 0.04
181 100 0.56
184 1 0.01
185 5 0.03
186 27 0.15
187 14 0.08
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (183 bp):
TTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGTCCTGCACTT
TAGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATACTACTCTTTGAG
GACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGTGTCATACTC
Found at i:4475 original size:10 final size:10
Alignment explanation
Indices: 4450--4510 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
4440 CTTAAGCATG
*
4450 TTCTTTTCTT
1 TTCTTTTTTT
*
4460 TACTTTTTTT
1 TTCTTTTTTT
4470 TTCTTTTTTT
1 TTCTTTTTTT
*
4480 CTCTTTTTATT
1 TTCTTTTT-TT
*
4491 TTTTTGTTTTT
1 TTCTT-TTTTT
*
4502 TTGTTTTTT
1 TTCTTTTTT
4511 AGAAAAAGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 28 0.67
11 11 0.26
12 3 0.07
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:4510 original size:9 final size:8
Alignment explanation
Indices: 4465--4510 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
4455 TTCTTTACTT
*
4465 TTTTTTTC
1 TTTTTTTG
*
4473 TTTTTTTC
1 TTTTTTTG
* *
4481 TCTTTTTA
1 TTTTTTTG
4489 TTTTTTTG
1 TTTTTTTG
4497 TTTTTTTG
1 TTTTTTTG
4505 TTTTTT
1 TTTTTT
4511 AGAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.02, C:0.07, G:0.04, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:7451 original size:32 final size:31
Alignment explanation
Indices: 7327--7453 Score: 103
Period size: 32 Copynumber: 4.0 Consensus size: 31
7317 CCGGTGACAT
* * * * *
7327 TGGGTTTTAAAAGGGTTACCACCAACTTATG
1 TGGGCTTTAAAAGGGATGCCACCAACTTGTA
* * * * *
7358 TGGGCTTT-AGAGTAGGCTACCACCAACTTATG
1 TGGGCTTTAAAAG--GGATGCCACCAACTTGTA
* * *
7390 TGGGCTTTAGAAGGGTTGCCACCAGCTTGTA
1 TGGGCTTTAAAAGGGATGCCACCAACTTGTA
7421 TGGGCTTTAAAAGGAGATGCCACCAACTTGTA
1 TGGGCTTTAAAAGG-GATGCCACCAACTTGTA
7453 T
1 T
7454 AGTCTCTTGA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
30 3 0.04
31 33 0.42
32 41 0.52
33 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (31 bp):
TGGGCTTTAAAAGGGATGCCACCAACTTGTA
Found at i:8217 original size:20 final size:20
Alignment explanation
Indices: 8194--8259 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
8184 CACACCCAGA
8194 TGTATCGATACATGCTGCTT
1 TGTATCGATACATGCTGCTT
8214 TGTATCGATACA-------T
1 TGTATCGATACATGCTGCTT
8227 TGTATCGATACATGCTGCTT
1 TGTATCGATACATGCTGCTT
8247 TGTATCGATACAT
1 TGTATCGATACAT
8260 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGCTGCTT
Found at i:8231 original size:13 final size:13
Alignment explanation
Indices: 8213--8272 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
8203 ACATGCTGCT
8213 TTGTATCGATACA
1 TTGTATCGATACA
8226 TTGTATCGATACA
1 TTGTATCGATACA
* *
8239 -TG---C--TGCT
1 TTGTATCGATACA
8246 TTGTATCGATACA
1 TTGTATCGATACA
8259 TTGTATCGATACA
1 TTGTATCGATACA
8272 T
1 T
8273 ATTCATTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 1 0.03
11 1 0.03
12 2 0.05
13 29 0.78
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:8236 original size:33 final size:33
Alignment explanation
Indices: 8194--8291 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
8184 CACACCCAGA
8194 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATGCTGCTTTGTATCGATACAT
8227 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATGCTGCTTTGTATCGATACAT
* * *
8260 TGTATCGATACAT-ATTCATTGTATCGATACAT
1 TGTATCGATACATGCTGCTTTGTATCGATACAT
8292 GGACAAATTG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 16 0.26
33 46 0.74
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATGCTGCTTTGTATCGATACAT
Found at i:14197 original size:13 final size:13
Alignment explanation
Indices: 14179--14207 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
14169 ACAACATTCC
14179 TTGTATCGATACA
1 TTGTATCGATACA
14192 TTGTATCGATACA
1 TTGTATCGATACA
14205 TTG
1 TTG
14208 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:18296 original size:78 final size:78
Alignment explanation
Indices: 18200--18397 Score: 222
Period size: 78 Copynumber: 2.6 Consensus size: 78
18190 ACATTGGTAT
* * **
18200 TTGG-AATAAAACCAGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTAT
1 TTGGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTAT
*
18264 G-AAAATCGGTGCA
66 GAAAAATCAGTG-A
* * * * * * *
18277 TTGGAAATAAAATCGGGGTTAGAGTATCCCCTCTAAAATAATGAGGTTGGAGTATTCTCGATTGT
1 TTGGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTAT
* *
18342 GAAAAATTAGTGG
66 GAAAAATCAGTGA
* *
18355 TTGGAAATAAACT-GGGGTTGGAGTCTCCCCTCAAAAATAACGG
1 TTGGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGG
18398 TTGAACTATC
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
77 29 0.29
78 63 0.63
79 8 0.08
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (78 bp):
TTGGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTAT
GAAAAATCAGTGA
Done.