Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2568
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: 25455
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Found at i:4278 original size:27 final size:27
Alignment explanation
Indices: 4248--4425 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
4238 ATATTGAGTC
* * * *
4248 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
4275 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
4302 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
4330 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
4357 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
4384 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
4411 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4426 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:4387 original size:82 final size:81
Alignment explanation
Indices: 4269--4424 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
4259 TGCTATATAA
* *
4269 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
4334 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
4351 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
4415 CACTTAGTGC
65 CACTTAGTGC
4425 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:12433 original size:27 final size:27
Alignment explanation
Indices: 12403--12580 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12393 ATATTGAGTC
* * * *
12403 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
12430 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12457 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
12485 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
12512 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
12539 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12566 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12581 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:12542 original size:82 final size:81
Alignment explanation
Indices: 12424--12579 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12414 TGCTATATAA
* *
12424 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
12489 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
12506 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
12570 CACTTAGTGC
65 CACTTAGTGC
12580 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17274 original size:50 final size:50
Alignment explanation
Indices: 17146--17436 Score: 296
Period size: 50 Copynumber: 5.7 Consensus size: 50
17136 TATAATAACA
* ** * * *
17146 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGT-GC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * **
17195 TACTAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
17245 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
** * * *
17295 TGCCAGCGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
**
17345 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
17401 TGCCAATGCCATGTCCCAGACATGGTCTTACTTGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
17437 TTCTCTTTAC
Statistics
Matches: 198, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
49 37 0.19
50 124 0.63
53 2 0.01
56 35 0.18
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:21790 original size:39 final size:40
Alignment explanation
Indices: 21631--21880 Score: 321
Period size: 40 Copynumber: 6.3 Consensus size: 40
21621 CATTTGAATG
* *
21631 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
21671 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
21711 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
21751 TTATCCGGGTTAAGACCCGAAGGCA-TTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
21790 TTATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
21829 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
21869 ATATCC-GGCTAA
1 ATATCCGGGCTAA
21881 ATTCCGAAGA
Statistics
Matches: 185, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
38 9 0.05
39 61 0.33
40 113 0.61
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:21843 original size:118 final size:120
Alignment explanation
Indices: 21631--21880 Score: 398
Period size: 118 Copynumber: 2.1 Consensus size: 120
21621 CATTTGAATG
*
21631 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
* *
21696 TTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
66 TTTGTGCGAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
21751 TTATCCGGGTTAAGACCCGAAGGC-ATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
* * * *
21814 TTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
66 TTTGTGCGAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
21869 ATATCC-GGCTAA
1 ATATCCGGGCTAA
21881 ATTCCGAAGA
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
117 5 0.04
118 63 0.53
119 30 0.25
120 21 0.18
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Done.