Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1815
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: 178430
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:166756 original size:21 final size:20
Alignment explanation
Indices: 166690--166766 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
166680 AAAAGACTAG
* *
166690 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTAAAA
* * * *
166710 AATATATCGATATATTCATAC
1 AATGTATCGATACATT-AAAA
*
166731 CATGTATCGATACATTAAAAA
1 AATGTATCGATACATT-AAAA
166752 AATGTATCGATACAT
1 AATGTATCGATACAT
166767 CTGGGTACGT
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 14 0.32
21 30 0.68
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:167708 original size:28 final size:28
Alignment explanation
Indices: 167647--168367 Score: 911
Period size: 28 Copynumber: 25.5 Consensus size: 28
167637 CACCGACTCG
* * *
167647 TGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
167677 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
167705 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
167733 TGTGGGCTTTGAAAAGAGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
167762 TGTTGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
167790 TATGGGCTTTAAAAGGATGCCATTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
167818 TGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
167846 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
167875 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
167903 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
167931 TGTGGACTTTGAAAAGAGTGTCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
167960 TGTTGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
167988 TGTGGGCTTTGAAAGGATGCTACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
168016 TATGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
168044 TGTTGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
168072 TATGAGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
168100 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
168128 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
168156 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACT
*
168185 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*** *
168213 TGTGGGCTTTGAAAAAATGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
168241 TGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
168270 TGTAGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
168298 TGTGAGCTTTAAAAAGAGTGCCACTAACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
** * *
168327 TGTAAGCTTTGAAAGGGTGCCATTGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
168355 TATTGGCTTTGAA
1 TGTGGGCTTTGAA
168368 GAGATGAACG
Statistics
Matches: 601, Mismatches: 84, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
28 436 0.73
29 154 0.26
30 11 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:167779 original size:85 final size:85
Alignment explanation
Indices: 167647--168367 Score: 939
Period size: 85 Copynumber: 8.5 Consensus size: 85
167637 CACCGACTCG
* *
167647 TGTGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
167712 TTTGAAAGGATGCCACTGACT
65 TTTGAAAGGATGCCACTAACT
* * *
167733 TGTGGGCTTTGAAAAGAGTGCCATTGACTTGTTGGCTTTGAAAGGGTGCCACTGACTTATGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
167798 TTAAAAGGATGCCATTAACT
66 TTGAAAGGATGCCACTAACT
*
167818 TGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
167882 TTTGAAAGGGTGCCACTAACT
65 TTTGAAAGGATGCCACTAACT
* * * * *
167903 TGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGACTTTGAAAAGAGTGTCACTGACTTGTTGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
* *
167967 TTTGAAAGGGTGCCACTGACT
65 TTTGAAAGGATGCCACTAACT
* * * * * *
167988 TGTGGGCTTTGAAAGGA-TGCTACTAACTTATGGGCTTTGAAAGAGTGCCACTGACTTGTTGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
168052 TTGAAAGGGTGCCACTGACT
66 TTGAAAGGATGCCACTAACT
* * *
168072 TATGAGCTTTGAAAAGA-TGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
*
168136 TTGAAAGGGTGCCACTAACT
66 TTGAAAGGATGCCACTAACT
* *
168156 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
** * *
168221 TTGAAAAAATGCCATTGACT
66 TTGAAAGGATGCCACTAACT
* * * *
168241 TGTGGGCTTTGAAAAAAGTGCCACTGACTTGTAGGCTTTGAAAGGGTGCCACTAACTTGTGAGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
168306 TTAAAAAGAGTGCCACTAACT
66 TTGAAAGGA-TGCCACTAACT
** * * * * *
168327 TGTAAGCTTTG-AAAGGGTGCCATTGAGTTATTGGCTTTGAA
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAA
168368 GAGATGAACG
Statistics
Matches: 568, Mismatches: 63, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
84 153 0.27
85 379 0.67
86 36 0.06
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
TTGAAAGGATGCCACTAACT
Found at i:167811 original size:113 final size:113
Alignment explanation
Indices: 167615--168367 Score: 931
Period size: 113 Copynumber: 6.6 Consensus size: 113
167605 CATTAACTTG
* * * * * *
167615 TGTGGGCCTTGAAAAGAGTTACCACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACTGGCTTGT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGT
*
167680 GGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
61 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
167733 TGTGGGCTTTGAAAAGAGTGCCATTGACTTGTTGGCTTTGAAAGGGTGCCACTGACTTATGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* * *
167798 TTAAAAGGATGCCATTAACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
*
167846 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* * *
167911 TTGAAAGGATGCCACTGACTTGTGGACTTTGAAAAGAGTGTCACTGACT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * * * *
167960 TGTTGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCTACTAACTTATGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
168024 TTGAAA-GAGTGCCACTGACTTGTTGGCTTTGAAAGGGTGCCACTGACT
66 TTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
168072 TATGAGCTTTGAAAAGA-TGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
* *
168136 TTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACT
66 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *** *
168185 TGTGGGCTTTG-AAAGGGTGCCATTGACTTGTGGGCTTTGAAAAAATGCCATTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
** * * *
168249 TTGAAAAAAGTGCCACTGACTTGTAGGCTTTGAAAGGGTGCCACTAACT
66 TTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * ** * * * *
168298 TGTGAGCTTTAAAAAGAGTGCCACTAACTTGTAAGCTTTGAAAGGGTGCCATTGAGTTATTGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
168363 TTGAA
66 TTGAA
168368 GAGATGAACG
Statistics
Matches: 552, Mismatches: 73, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
112 101 0.18
113 315 0.57
114 101 0.18
115 10 0.02
117 8 0.01
118 17 0.03
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (113 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:169614 original size:12 final size:11
Alignment explanation
Indices: 169599--169645 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
169589 TTTTTTATTA
*
169599 TTTTTTCTTGG
1 TTTTTTCTTGT
169610 TTTTTTCTTGT
1 TTTTTTCTTGT
*
169621 TTTTTTGTT-T
1 TTTTTTCTTGT
169631 TTTTTT-TTGT
1 TTTTTTCTTGT
169641 TTTTT
1 TTTTT
169646 AGGTATGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 2 0.06
10 13 0.39
11 18 0.55
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTGT
Found at i:169633 original size:10 final size:10
Alignment explanation
Indices: 169588--169645 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
169578 TCCCTTTCGA
*
169588 TTTTTTTATTA
1 TTTTTTT-TTG
*
169599 TTTTTTCTTGG
1 TTTTTT-TTTG
*
169610 TTTTTTCTTG
1 TTTTTTTTTG
169620 TTTTTTTGTT-
1 TTTTTTT-TTG
169630 TTTTTTTTTG
1 TTTTTTTTTG
169640 TTTTTT
1 TTTTTT
169646 AGGTATGAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 2 0.05
10 21 0.54
11 15 0.38
12 1 0.03
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:174974 original size:52 final size:52
Alignment explanation
Indices: 174894--175013 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
174884 AAAAGTTGTT
*
174894 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
174946 TGCAGGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
174998 TGCATGTATCGATACA
1 TGCATGTATCGATACA
175014 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:175026 original size:52 final size:51
Alignment explanation
Indices: 174894--175033 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 51
174884 AAAAGTTGTT
174894 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
* * *
174946 TGCAGGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCC
*
174998 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
175034 ATGTATCGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:175040 original size:13 final size:13
Alignment explanation
Indices: 175022--175046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175012 CAAAGATCAG
175022 TGTATCGATACAA
1 TGTATCGATACAA
175035 TGTATCGATACA
1 TGTATCGATACA
175047 TTTGAGTAAT
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:175124 original size:33 final size:33
Alignment explanation
Indices: 175087--175153 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
175077 AGTAGCTTAA
175087 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
175120 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
175153 A
1 A
175154 AATCATTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:175127 original size:13 final size:13
Alignment explanation
Indices: 175109--175133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175099 CAAAAAAATA
175109 TGTATCGATACAT
1 TGTATCGATACAT
175122 TGTATCGATACA
1 TGTATCGATACA
175134 ACATTTTATG
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:175232 original size:21 final size:21
Alignment explanation
Indices: 175191--175232 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
175181 GTTGGGACCT
*
175191 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
175212 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
175233 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:176120 original size:171 final size:171
Alignment explanation
Indices: 175921--176315 Score: 691
Period size: 171 Copynumber: 2.3 Consensus size: 171
175911 TTTTAGAGAT
*
175921 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
175986 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAAGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAAGA
176051 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * *
176092 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
* *
176157 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAAGA
176222 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
176263 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
176316 GTGCCAATGT
Statistics
Matches: 212, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
171 168 0.79
172 4 0.02
174 40 0.19
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAAGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:176296 original size:52 final size:51
Alignment explanation
Indices: 176162--176459 Score: 328
Period size: 52 Copynumber: 5.9 Consensus size: 51
176152 GAAAAGTGAT
* * * * * *
176162 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* ** *
176216 AAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAA-G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
176269 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G-
1 AAA-GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
176316 ---GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GA
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
176363 AGA-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
176413 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAA-GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
176460 GTGCCAATGT
Statistics
Matches: 210, Mismatches: 23, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
43 37 0.18
44 2 0.01
45 1 0.00
46 1 0.00
48 1 0.00
49 42 0.20
50 5 0.02
51 2 0.01
52 73 0.35
53 5 0.02
54 4 0.02
55 37 0.18
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (51 bp):
AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:176334 original size:43 final size:47
Alignment explanation
Indices: 176230--176486 Score: 296
Period size: 52 Copynumber: 5.4 Consensus size: 47
176220 GATGTCAACG
*
176230 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G---A-GTGCCAATA
* *
176282 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G-GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGTGCCAATA
176325 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AG-TGCCAATA
*
176374 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G---A-GTGCCAATA
* *
176426 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G-GTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGTGCCAATA
176469 TGCTGATTCAAGGCCAGC
1 TGCTGATTCAAGGCCAGC
176487 ATAGGTCGAA
Statistics
Matches: 186, Mismatches: 9, Indels: 29
0.83 0.04 0.13
Matches are distributed among these distances:
43 63 0.34
44 2 0.01
45 1 0.01
46 1 0.01
48 3 0.02
49 42 0.23
50 3 0.02
51 4 0.02
52 66 0.35
53 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (47 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGTGCCAATA
Done.