Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2543
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: 160039
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
File 2 of 2
Found at i:146172 original size:13 final size:13
Alignment explanation
Indices: 146154--146178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
146144 ACAATGGACA
146154 TGTATCGATACAT
1 TGTATCGATACAT
146167 TGTATCGATACA
1 TGTATCGATACA
146179 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:146195 original size:33 final size:32
Alignment explanation
Indices: 146135--146199 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
146125 CAATTGTGTA
* * *
146135 TGTATCGATACAATGGACATGTATCGATACAT
1 TGTATCGATACAAAGCAAATGTATCGATACAT
146167 TGTATCGATACAAAGCATAATGTATCGATACAT
1 TGTATCGATACAAAGCA-AATGTATCGATACAT
146200 CTGGATGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGCAAATGTATCGATACAT
Found at i:147462 original size:58 final size:57
Alignment explanation
Indices: 147247--147496 Score: 153
Period size: 58 Copynumber: 4.3 Consensus size: 57
147237 AAATATCCCA
* * * *** * *
147247 AAAATGTATGAAATTACATAATAGTCCCTAAAACATAGAAAATGACTAAAATGATTTT
1 AAAATGCATGAAATTACATAATAGTTCAT-ATTTATGGAAAATGACTAAAATGGTTTT
* * ** * * * ** * * *
147305 -AAATGCATGAAATTACATAAAAGTGCATAAAATGTGGCAAATTACTTTAGTGGCTCT
1 AAAATGCATGAAATTACATAATAGTTCAT-ATTTATGGAAAATGACTAAAATGGTTTT
* * * *
147362 AAGATGCATGAAGTTACATAATAGTTC-TCAATTCATGGAAAATGACTACAATGGTTTT
1 AAAATGCATGAAATTACATAATAGTTCAT--ATTTATGGAAAATGACTAAAATGGTTTT
* * * *** *
147420 AAAATGCATGAAATTACATAATAGTTCATATGTTATGAAAAATAAATAAAATGACATA
1 AAAATGCATGAAATTACATAATAGTTCATAT-TTATGGAAAATGACTAAAATGGTTTT
*
147478 AAAATGCATGAAATGACAT
1 AAAATGCATGAAATTACAT
147497 TAAAGTCCCC
Statistics
Matches: 146, Mismatches: 42, Indels: 8
0.74 0.21 0.04
Matches are distributed among these distances:
57 45 0.31
58 100 0.68
59 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (57 bp):
AAAATGCATGAAATTACATAATAGTTCATATTTATGGAAAATGACTAAAATGGTTTT
Found at i:147482 original size:20 final size:20
Alignment explanation
Indices: 147457--147496 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
147447 ATATGTTATG
147457 AAAAATAAATAAAATGACAT
1 AAAAATAAATAAAATGACAT
** *
147477 AAAAATGCATGAAATGACAT
1 AAAAATAAATAAAATGACAT
147497 TAAAGTCCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (20 bp):
AAAAATAAATAAAATGACAT
Found at i:148329 original size:15 final size:15
Alignment explanation
Indices: 148309--148340 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
148299 CACTACCACC
148309 AATTTCTTAACAACA
1 AATTTCTTAACAACA
148324 AATTTCTTAACAACA
1 AATTTCTTAACAACA
148339 AA
1 AA
148341 CTTATGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTTCTTAACAACA
Found at i:150221 original size:49 final size:50
Alignment explanation
Indices: 150153--150252 Score: 166
Period size: 49 Copynumber: 2.0 Consensus size: 50
150143 TATAATAAGG
* *
150153 TTAGTTTTATGCATGGATGTTCTTTTTTTATTTGACGAAAC-ATATACGT
1 TTAGTTTTATGCATAGATGTTCTTTTCTTATTTGACGAAACGATATACGT
150202 TTAGTTTTATGCATAGATGTTCTTTTCTTATTTGACGAAACGTATATACGT
1 TTAGTTTTATGCATAGATGTTCTTTTCTTATTTGACGAAACG-ATATACGT
150253 ATTTGATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 39 0.83
51 8 0.17
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (50 bp):
TTAGTTTTATGCATAGATGTTCTTTTCTTATTTGACGAAACGATATACGT
Found at i:154556 original size:23 final size:24
Alignment explanation
Indices: 154508--154557 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
154498 TTTAAAAAAG
154508 TTAATTTTTTTAAAAATATCAATT
1 TTAATTTTTTTAAAAATATCAATT
*
154532 TTAATTTTTTTAAAAAT-TCATTT
1 TTAATTTTTTTAAAAATATCAATT
154555 TTA
1 TTA
154558 TCAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAATTTTTTTAAAAATATCAATT
Found at i:155691 original size:14 final size:14
Alignment explanation
Indices: 155674--155701 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
155664 GATAAAGTGT
155674 TTGAAAAAAAAAAA
1 TTGAAAAAAAAAAA
155688 TTGAAAAAAAAAAA
1 TTGAAAAAAAAAAA
155702 AAAATTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
TTGAAAAAAAAAAA
Found at i:155784 original size:19 final size:19
Alignment explanation
Indices: 155760--155827 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
155750 AATTCAACAA
155760 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
155779 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
155794 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
155811 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
155828 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:155799 original size:13 final size:13
Alignment explanation
Indices: 155781--155805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155771 ACATAAGTTT
155781 TGTATCGATACAA
1 TGTATCGATACAA
155794 TGTATCGATACA
1 TGTATCGATACA
155806 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:155803 original size:32 final size:32
Alignment explanation
Indices: 155762--155824 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
155752 TTCAACAATT
*
155762 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
155794 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
155825 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:155885 original size:13 final size:13
Alignment explanation
Indices: 155867--155892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
155857 CATTTTTCTG
155867 TGTATCGATACAT
1 TGTATCGATACAT
155880 TGTATCGATACAT
1 TGTATCGATACAT
155893 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:155889 original size:33 final size:33
Alignment explanation
Indices: 155847--155913 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
155837 GCCGAGGAAA
***
155847 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
155880 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
155913 T
1 T
155914 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:158481 original size:80 final size:82
Alignment explanation
Indices: 158311--158489 Score: 281
Period size: 80 Copynumber: 2.2 Consensus size: 82
158301 ATTTTCTATA
*
158311 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
158376 TCCAACCCCGTTATTTC
66 TCCAACCCCGTTATTTC
*** * *
158393 CGAGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
*
158456 TCCAACCTCGTTATTTC
66 TCCAACCCCGTTATTTC
158473 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
158490 CCCGTTACTT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 45 0.52
81 13 0.15
82 29 0.33
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (82 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
TCCAACCCCGTTATTTC
Found at i:158482 original size:28 final size:28
Alignment explanation
Indices: 158450--158521 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
158440 TCACAGTCGA
* * **
158450 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
158478 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
158506 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
158522 GCTTTGTTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:158614 original size:79 final size:80
Alignment explanation
Indices: 158476--158630 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 80
158466 TTATTTCATC
* *
158476 GGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTGTTCCCAAAATATT
1 GGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGGCTTTGTTCCCAAAACATT
*
158541 -GATTTCTCATAATT
66 AAATTTCTCATAATT
* **
158555 GGGGATACTCCAACCCCGTTATTTTTGAGAGGATACTCCAACCCC-G-TTAT-TATCTCCAAAAC
1 GGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGGCTT-TGT-TC-CCAAAAC
158617 ATTAAATTTCTCAT
63 ATTAAATTTCTCAT
158631 CGGGAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
77 3 0.05
78 4 0.06
79 50 0.76
80 9 0.14
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGGCTTTGTTCCCAAAACATT
AAATTTCTCATAATT
Done.