Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold980
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: 39306
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1273 original size:3 final size:3
Alignment explanation
Indices: 1265--1318 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1255 AAGGGCTCAA
* * * *
1265 ATT ATT ATT ATC ATT ATC ATT ACT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
1311 ATT ATT AT
1 ATT ATT AT
1319 CTTTTTTTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1884 original size:149 final size:149
Alignment explanation
Indices: 1645--1960 Score: 394
Period size: 151 Copynumber: 2.1 Consensus size: 149
1635 GATCTTGGGA
*
1645 ATTTTTTT--AAAAAAAGGGAAAGTTTAGATTTTAAAAATAAAAAAAAAATATTTTTTTAGTCAT
1 ATTTTTTTAAAAAAAAAGAGAAAGTTTAGATTTT----ATAAAAAAAAAATATTTTTTTAGTCAT
* *
1708 TTCAAAGGAAATTTTAAAATTTTAAAACAAAGTTATGAT-TTTTTTAACTATTTCGAAATAAAAG
62 TTCAAAGGAAAATTTAAAATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAA-
1772 CTTTGA-TTTTAAAAAAAATAAT-
126 CTTTGATTTTTAAAAAAAATAATG
* *
1794 ATTTTTTTAAAAAAAAAGAGAAAGTTTAGATTTT-TGAAATAAAAATATGTTTTTTAGTCAGTTT
1 ATTTTTTTAAAAAAAAAGAGAAAGTTTAGATTTTATAAAAAAAAAATAT-TTTTTTAGTCA-TTT
* * *
1858 -TAAGGAAAAATTTAAATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAAC
64 CAAAGG-AAAATTTAAA-ATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAAC
* * *
1922 TTTGATTTTTAAAGAAAGTAGTG
127 TTTGATTTTTAAAAAAAATAATG
*
1945 ATTTTTTTAAAGAAAA
1 ATTTTTTTAAAAAAAA
1961 CTTTGATTCT
Statistics
Matches: 146, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
146 12 0.08
147 15 0.10
148 12 0.08
149 33 0.23
150 36 0.25
151 38 0.26
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (149 bp):
ATTTTTTTAAAAAAAAAGAGAAAGTTTAGATTTTATAAAAAAAAAATATTTTTTTAGTCATTTCA
AAGGAAAATTTAAAATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTG
ATTTTTAAAAAAAATAATG
Found at i:1967 original size:21 final size:21
Alignment explanation
Indices: 1917--1968 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1907 ATTTCGAAAT
1917 AAAACTTTGA--TTTTTAAAG
1 AAAACTTTGATTTTTTTAAAG
* *
1936 -AAAGTAGTGATTTTTTTAAAG
1 AAAACT-TTGATTTTTTTAAAG
1957 AAAACTTTGATT
1 AAAACTTTGATT
1969 CTACAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
21 14 0.56
22 4 0.16
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (21 bp):
AAAACTTTGATTTTTTTAAAG
Found at i:9967 original size:20 final size:20
Alignment explanation
Indices: 9910--9976 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
9900 GCAAGTTAAG
*
9910 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
* * *** *
9930 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTGA
9950 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
9970 ATGAGCT
1 ATGAGCT
9977 TGAAGTAGAG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTGA
Found at i:14123 original size:20 final size:20
Alignment explanation
Indices: 14066--14132 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
14056 GCAAGCTAAG
*
14066 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
* * *** *
14086 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTGA
14106 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
14126 ATGAGCT
1 ATGAGCT
14133 TGAAGTAGAG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTGA
Found at i:26117 original size:48 final size:48
Alignment explanation
Indices: 26058--26151 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
26048 AAGGTGGAAG
*
26058 TATGTGACAGTTTATCTGC-ATTAAT-GTGACACTGTTCACAATTTTGAT
1 TATGTGACAG-TTATCTGCGATT-ATGGTGACACTGTTCACAAATTTGAT
* * *
26106 TATGTGGCAGTTATCTGCGATTTTGGTGCCACTGTTCACAAATTTG
1 TATGTGACAGTTATCTGCGATTATGGTGACACTGTTCACAAATTTG
26152 GTGTGTTGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 9 0.22
48 31 0.77
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (48 bp):
TATGTGACAGTTATCTGCGATTATGGTGACACTGTTCACAAATTTGAT
Found at i:28165 original size:27 final size:27
Alignment explanation
Indices: 28106--28172 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
28096 CCTAAACTGA
*
28106 TATAAAATGGCTATTATGCCCCCACGT
1 TATAAAATGACTATTATGCCCCCACGT
** * * *
28133 GGTAAAATGACTGTTATGCCCCTATGT
1 TATAAAATGACTATTATGCCCCCACGT
28160 TATAAAATGACTA
1 TATAAAATGACTA
28173 CATGCTCTAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (27 bp):
TATAAAATGACTATTATGCCCCCACGT
Found at i:30317 original size:3 final size:3
Alignment explanation
Indices: 30309--30359 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
30299 AAGGGCTCAA
* * * *
30309 ATT ATT ATT ATC ATT ATC ATT ACT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
30355 ATT AT
1 ATT AT
30360 CTTTTTTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:30856 original size:147 final size:146
Alignment explanation
Indices: 30680--30961 Score: 401
Period size: 147 Copynumber: 1.9 Consensus size: 146
30670 GATCTTGGGA
*
30680 ATTTTTTTTAAAAAAGGGAAAGTTTAGATTTTAAAAATAAAAAAAAATATTTTTTAGTCA-TTTC
1 ATTTTTTTTAAAAAAGAGAAAGTTTAGATTTTAAAAAT--AAAAAAATATTTTTTAGTCAGTTT-
* *
30744 AAAGG-AAATTTTAAA-ATTTTAAAACAAAGTTATGAT-TTTTTTAACTATTTCGAAATAAAAGC
63 AAAGGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAA-C
30806 TTTGATTTTAAAAAAATAAT
127 TTTGATTTTAAAAAAATAAT
** * * *
30826 ATTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTGAAATAAAAATATGTTTTTTAGTCAGTTTTA
1 ATTTTTTTT-AAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAAAATATTTTTTAGTCAGTTTAA
* *
30891 AGGAAAAATTTAAATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAACTTT
65 AGGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTT
30956 GATTTT
130 GATTTT
30962 TAAAGAAAGT
Statistics
Matches: 121, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
145 22 0.18
146 21 0.17
147 55 0.45
148 23 0.19
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (146 bp):
ATTTTTTTTAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAAAATATTTTTTAGTCAGTTTAAA
GGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTG
ATTTTAAAAAAATAAT
Found at i:30998 original size:21 final size:21
Alignment explanation
Indices: 30948--30999 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
30938 ATTTCGAAAT
30948 AAAACTTTGA--TTTTTAAAG
1 AAAACTTTGATTTTTTTAAAG
* *
30967 -AAAGTAGTGATTTTTTTAAAG
1 AAAACT-TTGATTTTTTTAAAG
30988 AAAACTTTGATT
1 AAAACTTTGATT
31000 CTACAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
21 14 0.56
22 4 0.16
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (21 bp):
AAAACTTTGATTTTTTTAAAG
Found at i:31441 original size:25 final size:25
Alignment explanation
Indices: 31408--31458 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31398 TTTAGTCCCA
31408 AAATCAGCTATGTCATTTTGCTTCC
1 AAATCAGCTATGTCATTTTGCTTCC
31433 AAATCAGCTATGTCATTTTGCTTCC
1 AAATCAGCTATGTCATTTTGCTTCC
31458 A
1 A
31459 TCTTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (25 bp):
AAATCAGCTATGTCATTTTGCTTCC
Done.