Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2451
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: 39017
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4234 original size:79 final size:81
Alignment explanation
Indices: 4100--4283 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
4090 TGAATGATGT
*
4100 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
4164 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * * ** *
4180 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAGTTCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
4243 GTGCGAGTTACTATAA
66 GTGCGAGATACTATAA
*
4259 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
4284 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
79 58 0.65
80 31 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATAA
Found at i:4290 original size:40 final size:40
Alignment explanation
Indices: 4099--4283 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
4089 TTGAATGATG
* * * *
4099 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
4139 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
4179 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
4218 TCCGGGTTAAGTTCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
4259 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
4284 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:4305 original size:79 final size:79
Alignment explanation
Indices: 4146--4316 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 79
4136 ATATCCGGAC
* ** **
4146 TAAGATCCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGT
1 TAAGTTCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGT
4211 TACTAAATCCGGGT
66 TACTAAATCCGGGT
* *
4225 TAAGTTCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGTTCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGA
* *
4289 G-TAGCTATATTC-GGT
64 GTTA-CTAAATCCGGGT
*
4304 TAAATTCCGAAGG
1 TAAGTTCCGAAGG
4317 TACGTGATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.03
79 53 0.67
80 24 0.30
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (79 bp):
TAAGTTCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGT
TACTAAATCCGGGT
Found at i:5987 original size:42 final size:42
Alignment explanation
Indices: 5940--6041 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
5930 TGAGTTTCCA
* * * *
5940 TTTAACCGTAATGGGTTTCCGTTCAACTCTTTTGAGCTTCAG
1 TTTAACCCTAATGGGTTTCCATTCAACACTTATGAGCTTCAG
** * *
5982 TTTAACCCTTGTGGGTTTCCATTCAGCACTTATGAGCTTCCG
1 TTTAACCCTAATGGGTTTCCATTCAACACTTATGAGCTTCAG
* *
6024 TTCAACCCTCATGGGTTT
1 TTTAACCCTAATGGGTTT
6042 TTTTTAGCAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (42 bp):
TTTAACCCTAATGGGTTTCCATTCAACACTTATGAGCTTCAG
Found at i:17212 original size:18 final size:18
Alignment explanation
Indices: 17191--17225 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17181 AATCATCCCT
17191 TAATCATCCCTCATTTCA
1 TAATCATCCCTCATTTCA
**
17209 TAATCATTTCTCATTTC
1 TAATCATCCCTCATTTC
17226 TCATTTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATCATCCCTCATTTCA
Found at i:18746 original size:21 final size:22
Alignment explanation
Indices: 18707--18747 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18697 CAATTTCTCA
* *
18707 ATCTAATATATATACTTCAATC
1 ATCTAAGATATATAATTCAATC
18729 ATCTAAGA-ATATAATTCAA
1 ATCTAAGATATATAATTCAA
18748 ATTACACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (22 bp):
ATCTAAGATATATAATTCAATC
Found at i:20915 original size:24 final size:24
Alignment explanation
Indices: 20900--20949 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
20890 AATTTATGTA
20900 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
** *
20924 AAATATATTATATTAATAAATACT
1 AAATATATTATGCTAATAAATGCT
20948 AA
1 AA
20950 CTCTTTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:21534 original size:31 final size:31
Alignment explanation
Indices: 21498--21560 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
21488 TTCATCTTTT
21498 TCAGTCATCCTATACGAGATTGAGGTGGGAA
1 TCAGTCATCCTATACGAGATTGAGGTGGGAA
*
21529 TCAGTCATCTTATACGAGATTGAGGTGGGAA
1 TCAGTCATCCTATACGAGATTGAGGTGGGAA
21560 T
1 T
21561 TATCTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (31 bp):
TCAGTCATCCTATACGAGATTGAGGTGGGAA
Found at i:28431 original size:39 final size:39
Alignment explanation
Indices: 28358--28475 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
28348 TAGCTCCTCG
* * *
28358 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCA
* *
28398 TTCAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCG
1 TTCAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCA
** * *
28437 CACAAAGGCCTTCGGGACTTAACCCGGAATTAATAACTC
1 TTC-AATGCCTTCGGGACTTAACCCGGAATTAGTAACTC
28476 GCACAAATAC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 28 0.42
40 38 0.58
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (39 bp):
TTCAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCA
Found at i:28453 original size:40 final size:38
Alignment explanation
Indices: 28404--28544 Score: 142
Period size: 40 Copynumber: 3.6 Consensus size: 38
28394 CTCATTCAAT
28404 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 GCCTTCGGGACTTAACCCGGAATTAGTA-CTCGCACAAA
*
28443 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
1 -GCCTTCGGGACTTAACCCGGAATTAGT-ACTCGCACAAA
* ** *
28483 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA
1 -GCCTTCGGGA-CTTAACCCGGAAT-TAGT-AC-TCGCACAAA
*
28524 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
28545 CAGCATTCAA
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
39 5 0.06
40 68 0.80
41 12 0.14
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (38 bp):
GCCTTCGGGACTTAACCCGGAATTAGTACTCGCACAAA
Found at i:36285 original size:39 final size:40
Alignment explanation
Indices: 36208--36354 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
36198 TAGCTCCTCG
* * *
36208 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
36248 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
36287 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
36327 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
36355 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:36365 original size:80 final size:80
Alignment explanation
Indices: 36254--36434 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
36244 CTCATTCAAT
* * *
36254 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
36317 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
36333 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
36397 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
36414 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
36435 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:36394 original size:40 final size:40
Alignment explanation
Indices: 36251--36434 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
36241 TAACTCATTC
* *
36251 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
36291 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
36331 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
36371 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
36412 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
36435 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Done.