Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2498
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: 42374
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:1068 original size:31 final size:29
Alignment explanation
Indices: 1033--1091 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
1023 CTCCGCCATC
* *
1033 TAGTGCTTACACTAGAATCATACTCGCACAT
1 TAGTGCTAACAATAG-ATCA-ACTCGCACAT
*
1064 TAGTGCTAACAATAGTTCAACTCGCACA
1 TAGTGCTAACAATAGATCAACTCGCACA
1092 CATATTAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 3 0.12
31 13 0.52
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (29 bp):
TAGTGCTAACAATAGATCAACTCGCACAT
Found at i:1103 original size:33 final size:31
Alignment explanation
Indices: 1062--1123 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 31
1052 ATACTCGCAC
1062 ATTAGTGCTAACAATAGTTCAAC-TCGCACACAT
1 ATTAGTGCTAAC-ATAG-TCAACATCG-ACACAT
*
1095 ATTAGTGCTGACATAGTCAACATCGACAC
1 ATTAGTGCTAACATAGTCAACATCGACAC
1124 TTAGGCTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 9 0.33
32 7 0.26
33 11 0.41
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (31 bp):
ATTAGTGCTAACATAGTCAACATCGACACAT
Found at i:14225 original size:27 final size:26
Alignment explanation
Indices: 14195--14255 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
14185 ATTTACTAAA
14195 ATACCCCTAAGTATG-AAAATTACCATT
1 ATACCCCT-AG-ATGCAAAATTACCATT
*
14222 ATACCCCTAGGTGCAAAATTACCATT
1 ATACCCCTAGATGCAAAATTACCATT
14248 ATACCCCT
1 ATACCCCT
14256 TGGGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 2 0.06
26 22 0.69
27 8 0.25
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCATT
Found at i:14402 original size:27 final size:28
Alignment explanation
Indices: 14364--14471 Score: 123
Period size: 27 Copynumber: 4.0 Consensus size: 28
14354 GAGGAAGCGT
*
14364 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGACTCTGCCACAAATATCTGTA
* *
14391 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGACTCTGCCACAAATATCTGTA
* *
14419 TCTAGTGACTCTGCCA-TAATATCTGTA
1 TCTGGTGACTCTGCCACAAATATCTGTA
* **
14446 TTTGGTGACTCTTTCAC-AATATCTGT
1 TCTGGTGACTCTGCCACAAATATCTGT
14472 TCTCACAGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 56 0.80
28 14 0.20
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (28 bp):
TCTGGTGACTCTGCCACAAATATCTGTA
Found at i:14470 original size:54 final size:55
Alignment explanation
Indices: 14363--14472 Score: 134
Period size: 55 Copynumber: 2.0 Consensus size: 55
14353 GGAGGAAGCG
* * *
14363 TTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTAGTGACTCTGCCACAAATATCTGATCTGGTGACTCTGCCACAAATATCTGT
* * **
14418 TTCTAGTGACTCTGCCA-TAATATCTGTATTTGGTGACTCTTTCAC-AATATCTGT
1 TTCTAGTGACTCTGCCACAAATATCTG-ATCTGGTGACTCTGCCACAAATATCTGT
14472 T
1 T
14473 CTCACAGCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
54 18 0.38
55 29 0.62
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (55 bp):
TTCTAGTGACTCTGCCACAAATATCTGATCTGGTGACTCTGCCACAAATATCTGT
Found at i:17728 original size:8 final size:8
Alignment explanation
Indices: 17715--17753 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
17705 CTAGATCGGC
17715 AAAAGCCG
1 AAAAGCCG
*
17723 AAAAGCCA
1 AAAAGCCG
17731 AAAAGCCG
1 AAAAGCCG
17739 AAATA-CCG
1 AAA-AGCCG
17747 AAAAGCC
1 AAAAGCC
17754 AACATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.54, C:0.26, G:0.18, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:18238 original size:27 final size:28
Alignment explanation
Indices: 18163--18256 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 28
18153 GAGGGAGTGT
* * *
18163 TCTGGTGGCTCTGTCACAAATATTTG-A
1 TCTGGTGGCTCTGCCAAAAATATCTGTA
* *
18190 TATGGTGGCTCTGCCAAAAATATCTGTT
1 TCTGGTGGCTCTGCCAAAAATATCTGTA
* *
18218 TCTGGTGGCTTTGCC-ATAATATCTGTA
1 TCTGGTGGCTCTGCCAAAAATATCTGTA
*
18245 TCTGGTGACTCT
1 TCTGGTGGCTCT
18257 ATCACAATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 42 0.76
28 13 0.24
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCAAAAATATCTGTA
Found at i:18265 original size:27 final size:26
Alignment explanation
Indices: 18208--18275 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
18198 CTCTGCCAAA
* * * *
18208 AATATCTGTTTCTGGTGGCTTTGCCAT
1 AATATCTG-TTCTGGTGACTCTACCAC
*
18235 AATATCTGTATCTGGTGACTCTATCAC
1 AATATCTGT-TCTGGTGACTCTACCAC
*
18262 AATATATGTTCTGG
1 AATATCTGTTCTGG
18276 CAGCCATGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (26 bp):
AATATCTGTTCTGGTGACTCTACCAC
Found at i:20994 original size:43 final size:43
Alignment explanation
Indices: 20933--21017 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
20923 GTCTAAAAAG
20933 TACAGGGACTATTTTACAAGTTTCTCTTCCTCGATTTTTTACA
1 TACAGGGACTATTTTACAAGTTTCTCTTCCTCGATTTTTTACA
20976 TACAGGGACTATTTTACAAGTTTCTCTTCCTCGATTTTTTAC
1 TACAGGGACTATTTTACAAGTTTCTCTTCCTCGATTTTTTAC
21018 TCGTTCTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (43 bp):
TACAGGGACTATTTTACAAGTTTCTCTTCCTCGATTTTTTACA
Found at i:28763 original size:39 final size:39
Alignment explanation
Indices: 28713--28959 Score: 311
Period size: 39 Copynumber: 6.3 Consensus size: 39
28703 CAAGACTTTA
* *
28713 AGCCCGGATATAATACCAGCA-GAAAGCCTGCGGGACTTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGAC-TT
* *
28752 AGCCCGGATATAATACCAGCAC-AAAGCCTGCGGGACTTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGAC-TT
* * * *
28791 AGCCCAGATAAAACACCAGCACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
* *
28830 AACCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
* *
28869 AGCCCGGATATAACACCAGCGC-AAATGCCTTTGGGACTT
1 AGCCCGGATATAACACCAGCACGAAA-GCCTTCGGGACTT
* *
28908 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
*
28947 AGCCCGGGTATAA
1 AGCCCGGATATAA
28960 TTCTCCATTA
Statistics
Matches: 185, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
38 2 0.01
39 170 0.92
40 13 0.07
ACGTcount: A:0.30, C:0.29, G:0.23, T:0.18
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
Found at i:30144 original size:35 final size:35
Alignment explanation
Indices: 30098--30168 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
30088 ACATAAAAAT
30098 TTTACCTATGCATAACATTACTCATATTCCAATAC
1 TTTACCTATGCATAACATTACTCATATTCCAATAC
30133 TTTACCTATGCATAACATTACTCATATTCCAATAC
1 TTTACCTATGCATAACATTACTCATATTCCAATAC
30168 T
1 T
30169 CATATTATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (35 bp):
TTTACCTATGCATAACATTACTCATATTCCAATAC
Done.