Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1400
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: 45015
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:2636 original size:260 final size:258
Alignment explanation
Indices: 2175--2690 Score: 1014
Period size: 260 Copynumber: 2.0 Consensus size: 258
2165 GAGTTTACCA
2175 AATTTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATAC
1 AATTTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATAC
2240 TCCTCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATT
66 TCCTCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATT
2305 GTTCACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAA
131 GTTCACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAA
2370 CCCTTCATAACATACTCATAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCTAG
196 CCCTTCATAACATACTC--AAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCTAG
2435 AATTTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATAC
1 AATTTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATAC
2500 TCCTCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATT
66 TCCTCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATT
2565 GTTCACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAA
131 GTTCACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAA
2630 CCCTTCATAACATACTCAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCT
196 CCCTTCATAACATACTCAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCT
2691 TAAAATGCAA
Statistics
Matches: 256, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
258 44 0.17
260 212 0.83
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (258 bp):
AATTTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATAC
TCCTCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATT
GTTCACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAA
CCCTTCATAACATACTCAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCTAG
Found at i:5166 original size:15 final size:15
Alignment explanation
Indices: 5146--5181 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
5136 TTAATAGCAA
5146 TAAAAATGTAAAGCT
1 TAAAAATGTAAAGCT
5161 TAAAAATGTAAAGCT
1 TAAAAATGTAAAGCT
5176 TAAAAA
1 TAAAAA
5182 AGTGAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (15 bp):
TAAAAATGTAAAGCT
Found at i:12401 original size:2 final size:2
Alignment explanation
Indices: 12394--12429 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12384 GGTTTCCATG
12394 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12430 CGCACAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21291 original size:28 final size:28
Alignment explanation
Indices: 21232--21301 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
21222 CCACCCATTT
21232 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
21260 -TTTGTCAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
*
21287 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
21302 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:23317 original size:13 final size:15
Alignment explanation
Indices: 23284--23319 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
23274 TTAAAAAAAT
23284 TTAAAATATAATTAA
1 TTAAAATATAATTAA
23299 TT-AAATA-AATT-A
1 TTAAAATATAATTAA
23311 TTAAAATAT
1 TTAAAATAT
23320 GTTGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 5 0.26
15 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATATAATTAA
Found at i:25267 original size:28 final size:29
Alignment explanation
Indices: 25195--25255 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
25185 CACATAACAA
* *
25195 AAAATAAAAACATTTTGATAAATTATTTT
1 AAAATAAAAATATTTTGATAAATTAATTT
25224 AAAATAAAAATATTTTGAT-AATTAATTT
1 AAAATAAAAATATTTTGATAAATTAATTT
25252 AAAA
1 AAAA
25256 AAATGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATAAAAATATTTTGATAAATTAATTT
Found at i:25491 original size:2 final size:2
Alignment explanation
Indices: 25481--25514 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
25471 TCTCTTTTTC
*
25481 TA TA T- TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25515 CTTTATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:25559 original size:45 final size:45
Alignment explanation
Indices: 25507--25596 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
25497 ATATATATAT
*
25507 ATATATATCTTTATGTTTGGATTAAATTTACTTTTCCTAGACTTA
1 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
25552 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
1 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
25597 TGTGCTCCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (45 bp):
ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
Found at i:29546 original size:42 final size:42
Alignment explanation
Indices: 29499--29579 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
29489 ATCAAGAATG
*
29499 GGTTCAGATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
1 GGTTCAAATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
*
29541 GGTTCAAATTCTGGAGATTCAGGTTCGGACACATGGTCA
1 GGTTCAAATTCTGGAGATTCAGGTTCGAACACATGGTCA
29580 GGTTTGGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
GGTTCAAATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
Found at i:29565 original size:21 final size:21
Alignment explanation
Indices: 29499--29566 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29489 ATCAAGAATG
*
29499 GGTTCAGATTCTGGAGATTCA
1 GGTTCAAATTCTGGAGATTCA
* ** ** *
29520 GGTTCGAACACATGGTCAATC-
1 GGTTCAAATTC-TGGAGATTCA
29541 GGTTCAAATTCTGGAGATTCA
1 GGTTCAAATTCTGGAGATTCA
29562 GGTTC
1 GGTTC
29567 GGACACATGG
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
GGTTCAAATTCTGGAGATTCA
Found at i:29582 original size:18 final size:18
Alignment explanation
Indices: 29559--29594 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29549 TTCTGGAGAT
29559 TCAGGTTCGGACACATGG
1 TCAGGTTCGGACACATGG
*
29577 TCAGGTTTGGACACATGG
1 TCAGGTTCGGACACATGG
29595 CTCGGACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (18 bp):
TCAGGTTCGGACACATGG
Found at i:31404 original size:62 final size:62
Alignment explanation
Indices: 31307--31428 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
31297 CCAACTATCA
* * *
31307 AACAAAATCAATCAGTAATGAAGGCTAACTGAATGAAATAATTTAGCGATAAAAGCTGATCT
1 AACAAAATCAATCAGCAATGAAGGCTAACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
* *
31369 AACAAAATCAATCAGCACTGAAGGCTGACTGAATGAAATAAATCAGCGATAAAAGCTGAT
1 AACAAAATCAATCAGCAATGAAGGCTAACTGAATGAAATAAATCAGCGATAAAAGCTGAT
31429 TCAGAGAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (62 bp):
AACAAAATCAATCAGCAATGAAGGCTAACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
Found at i:31413 original size:31 final size:30
Alignment explanation
Indices: 31324--31415 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
31314 TCAATCAGTA
* * *
31324 ATGAAGGCTAACTGAATGAAATAATTTAGC
1 ATGAAGGCTGACTGAATGAAATAAATCAGC
* * ** *
31354 GATAAAAGCTGATCT-AACAAAATCAATCAGC
1 -ATGAAGGCTGA-CTGAATGAAATAAATCAGC
31385 ACTGAAGGCTGACTGAATGAAATAAATCAGC
1 A-TGAAGGCTGACTGAATGAAATAAATCAGC
31416 GATAAAAGCT
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
30 3 0.07
31 40 0.89
32 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (30 bp):
ATGAAGGCTGACTGAATGAAATAAATCAGC
Found at i:31427 original size:31 final size:31
Alignment explanation
Indices: 31334--31427 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
31324 ATGAAGGCTA
* *
31334 ACTGAATGAAATAATTTAGCGATAAAAGCTG
1 ACTGAATGAAATAAATCAGCGATAAAAGCTG
** * * *
31365 ATCT-AACAAAATCAATCAGC-ACTGAAGGCTG
1 A-CTGAATGAAATAAATCAGCGA-TAAAAGCTG
31396 ACTGAATGAAATAAATCAGCGATAAAAGCTG
1 ACTGAATGAAATAAATCAGCGATAAAAGCTG
31427 A
1 A
31428 TTCAGAGAGA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
30 3 0.06
31 41 0.87
32 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (31 bp):
ACTGAATGAAATAAATCAGCGATAAAAGCTG
Found at i:31482 original size:26 final size:25
Alignment explanation
Indices: 31437--31497 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
31427 ATTCAGAGAG
*
31437 AAAAGGAATCCCAAAATTTTTTTTTC
1 AAAA-GAATTCCAAAATTTTTTTTTC
31463 AAAAGAATTCCAAAATTTTTTTTTC
1 AAAAGAATTCCAAAATTTTTTTTTC
*
31488 AGAAGAATTC
1 AAAAGAATTC
31498 GAACCTATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (25 bp):
AAAAGAATTCCAAAATTTTTTTTTC
Found at i:44041 original size:58 final size:59
Alignment explanation
Indices: 43942--44059 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
43932 TTCCCCGGTT
* *
43942 ACAGGATCTGTTTATGCCCCCGCCAATACAGAAACAAGTAATTTCCAATTCTAAGACATA
1 ACAGGATCTGTTTATG-CCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
* *
44002 ACAGGATCTGTTTATG-CCTGCAAATACAGAAACAAGTAATTTCTAATTCCAAGACATA
1 ACAGGATCTGTTTATGCCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
44060 GCATGACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 38 0.70
60 16 0.30
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (59 bp):
ACAGGATCTGTTTATGCCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
Done.