Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2753
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: 197694
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:140208 original size:78 final size:79
Alignment explanation
Indices: 140069--140274 Score: 263
Period size: 78 Copynumber: 2.6 Consensus size: 79
140059 TCATTCATGT
* * ** * *
140069 TTTTATTTCTAAGATATCGATTTTCCACCTTCAGGGATACTCCAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACAATCAGGGATACTCTAACCCCATTATTTTCGAGGGGA
* ** *
140134 TTCTTTAACCCCAG
66 TACTCCAACCCCAA
* *
140148 TTTTATTTCTAAAACATCGATTTTTCACAATC-GGGATACTCTAGCCCCATTATTTTCGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACAATCAGGGATACTCTAACCCCATTATTTTCGAGGGGA
140212 TACTCCAACCCCAA
66 TACTCCAACCCCAA
* *
140226 TTTTATTTCCAAAACATC-AGTTTTCCACAATCAAGGATACTCTAACCCC
1 TTTTATTTCTAAAACATCGA-TTTTCCACAATCAGGGATACTCTAACCCC
140275 GGCTTTATTT
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
77 1 0.01
78 67 0.61
79 41 0.38
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCGATTTTCCACAATCAGGGATACTCTAACCCCATTATTTTCGAGGGGA
TACTCCAACCCCAA
Found at i:140273 original size:51 final size:51
Alignment explanation
Indices: 140209--140323 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
140199 ATTTTCGAGG
*
140209 GGATACTCCAACCCCAATTTTATTTCCAAAACATCAG-TTTTCCACAATCAA
1 GGATACTCCAACCCCAACTTTATTTCCAAAACAT-AGATTTTCCACAATCAA
* ** * * * **
140260 GGATACTCTAACCCCGGCTTTATTTCTAAAATATTGATTTTCCACAATCGG
1 GGATACTCCAACCCCAACTTTATTTCCAAAACATAGATTTTCCACAATCAA
140311 GGATACTCCAACC
1 GGATACTCCAACC
140324 TCGTTATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCAACTTTATTTCCAAAACATAGATTTTCCACAATCAA
Found at i:140351 original size:78 final size:78
Alignment explanation
Indices: 140256--140429 Score: 219
Period size: 78 Copynumber: 2.2 Consensus size: 78
140246 TTTTCCACAA
* * *
140256 TCAA-GGATACTCTAACCCCGGCTT-TATTTCTAAAATATTGATTTTCCACAATCGGGGATACTC
1 TCAAGGGATACTCCAACCCCGG-TTCTATTTCTAAAACATCGATTTTCCACAATCGGGGATACTC
140319 CAAC-CTCGTTATTT
65 CAACTC-CGTTATTT
* * * * *
140333 TCAAGGGATACTCCAACCCCGGTTCTATTTCTAAAACATCGATTTTTCACCATTGTGGATACTCT
1 TCAAGGGATACTCCAACCCCGGTTCTATTTCTAAAACATCGATTTTCCACAATCGGGGATACTCC
140398 AACTCCGTTATTT
66 AACTCCGTTATTT
*
140411 TCGAAGAGATACTCCAACC
1 TC-AAGGGATACTCCAACC
140430 TCATTTTTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
77 6 0.07
78 62 0.74
79 16 0.19
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (78 bp):
TCAAGGGATACTCCAACCCCGGTTCTATTTCTAAAACATCGATTTTCCACAATCGGGGATACTCC
AACTCCGTTATTT
Found at i:140400 original size:129 final size:129
Alignment explanation
Indices: 140139--140372 Score: 326
Period size: 129 Copynumber: 1.8 Consensus size: 129
140129 GGGGATTCTT
* * * *
140139 TAACCCCAGTTTTATTTCTAAAACATCGATTTTTCACAATCGGGATACTCTAGCCCCATTATTTT
1 TAACCCCAGCTTTATTTCTAAAACATCGATTTTCCACAATCGGGATACTCCAACCCCATTATTTT
* *
140204 CGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAGTTTTCCACAATCAAGGATACTC
66 CGAAGGGATACTCCAACCCCAATTCTATTTCCAAAACATCAGTTTTCCACAATCAAGGATACTC
* * * * *
140268 TAACCCCGGCTTTATTTCTAAAATATTGATTTTCCACAATCGGGGATACTCCAACCTCGTTATTT
1 TAACCCCAGCTTTATTTCTAAAACATCGATTTTCCACAATC-GGGATACTCCAACCCCATTATTT
** *
140333 TC-AAGGGATACTCCAACCCCGGTTCTATTTCTAAAACATC
65 TCGAAGGGATACTCCAACCCCAATTCTATTTCCAAAACATC
140373 GATTTTTCAC
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
129 69 0.77
130 21 0.23
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (129 bp):
TAACCCCAGCTTTATTTCTAAAACATCGATTTTCCACAATCGGGATACTCCAACCCCATTATTTT
CGAAGGGATACTCCAACCCCAATTCTATTTCCAAAACATCAGTTTTCCACAATCAAGGATACTC
Found at i:152282 original size:8 final size:8
Alignment explanation
Indices: 152269--152294 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
152259 ACCAAACTTC
152269 AACTTGAA
1 AACTTGAA
152277 AACTTGAA
1 AACTTGAA
152285 AACTTGAA
1 AACTTGAA
152293 AA
1 AA
152295 GAAAGCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AACTTGAA
Found at i:153040 original size:21 final size:22
Alignment explanation
Indices: 153002--153042 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
152992 CCTTTTTCTC
*
153002 TTTATTTTTATTTGATTATTTA
1 TTTATTTTAATTTGATTATTTA
153024 TTTATTTTAATTT-ATTATT
1 TTTATTTTAATTTGATTATT
153043 GTGTTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTTTAATTTGATTATTTA
Found at i:153049 original size:21 final size:22
Alignment explanation
Indices: 153003--153051 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
152993 CTTTTTCTCT
* *
153003 TTATTTTTATTTGATTATTTAT
1 TTATTTTAATTTGATTATTTAG
153025 TTATTTTAATTT-ATTATTGT-G
1 TTATTTTAATTTGATTATT-TAG
153046 TTATTT
1 TTATTT
153052 CTATTGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (22 bp):
TTATTTTAATTTGATTATTTAG
Found at i:153133 original size:111 final size:109
Alignment explanation
Indices: 152988--153202 Score: 360
Period size: 111 Copynumber: 2.0 Consensus size: 109
152978 AAGGGATAAA
152988 TTTACCTTTTTCTCTTTATTTTTATTTGATTATTTATTTATTTTAATTTATTATTGTGTTATTTC
1 TTTACCTTTTTCTCTTTATTTTTATTTGATTATTTATTTATTTTAATTTATTATTGTGTTATTTC
*
153053 TATTGGAAAAACTAATCAAATATGTTGC-AAAATTTTTTAAAAT
66 TATTGGAAAAACTAATCAAATATGTAGCAAAAATTTTTTAAAAT
* *
153096 TTTACCTTTTTCTCTTTTTTCTTTTTATTTGATTATTTGTTTATTTTAATTTATTATTGTGTTAT
1 TTTACCTTTTTCTC---TTTATTTTTATTTGATTATTTATTTATTTTAATTTATTATTGTGTTAT
*
153161 TTCTATTGGAAAAACTAATGAAATATGTAGCAAAAATTTTTT
63 TTCTATTGGAAAAACTAATCAAATATGTAGCAAAAATTTTTT
153203 TTTTTTAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
108 14 0.14
111 75 0.76
112 10 0.10
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (109 bp):
TTTACCTTTTTCTCTTTATTTTTATTTGATTATTTATTTATTTTAATTTATTATTGTGTTATTTC
TATTGGAAAAACTAATCAAATATGTAGCAAAAATTTTTTAAAAT
Found at i:153143 original size:21 final size:20
Alignment explanation
Indices: 153118--153167 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
153108 TCTTTTTTCT
153118 TTTTATTTGATTATT-TGTTTA
1 TTTTATTT-ATTATTGTG-TTA
153139 TTTTAATTTATTATTGTGTTA
1 TTTT-ATTTATTATTGTGTTA
153160 TTTCTATT
1 TTT-TATT
153168 GGAAAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.70
Consensus pattern (20 bp):
TTTTATTTATTATTGTGTTA
Found at i:161115 original size:20 final size:20
Alignment explanation
Indices: 161090--161215 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
161080 TTTTTACCCA
161090 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
161110 AATGTATCGATACATTCTATCTTTTACCC
1 AATGTATCGAT--A--C-AT-TTTT---C
*
161139 AGATGTCTCGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
* * * *
161160 AATGTATCAATACATGTATG
1 AATGTATCGATACATTTTTC
*
161180 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
*
161200 AATGTATTGATACATT
1 AATGTATCGATACATT
161216 CCATCTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
20 55 0.65
21 2 0.02
22 1 0.01
24 5 0.06
25 4 0.05
26 5 0.06
28 1 0.01
29 2 0.02
30 9 0.11
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:168121 original size:22 final size:23
Alignment explanation
Indices: 168051--168122 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 23
168041 TCAAAATGAC
*
168051 AAAAAAAG-GTCAAAAGCAAAAGT
1 AAAAAAAGTG-CAAAAGCAAAACT
* * *
168074 ACAAAATA-TG-AAAAGGAAAACA
1 A-AAAAAAGTGCAAAAGCAAAACT
168096 AAAAAAAGTGCAAAAGCAAAA-T
1 AAAAAAAGTGCAAAAGCAAAACT
168118 AAAAA
1 AAAAA
168123 GGGAACAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
21 5 0.13
22 17 0.45
23 10 0.26
24 6 0.16
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.08
Consensus pattern (23 bp):
AAAAAAAGTGCAAAAGCAAAACT
Found at i:169449 original size:27 final size:27
Alignment explanation
Indices: 169412--169531 Score: 168
Period size: 27 Copynumber: 4.4 Consensus size: 27
169402 TTTCTTTTCA
*
169412 AAGTCCACAACTTCGTGGTATCCTTTT
1 AAGTCCACAACTTCGTGGCATCCTTTT
* *
169439 AAGTCCACAACTCCGTGGCATCCTTTCA
1 AAGTCCACAACTTCGTGGCATCCTTT-T
169467 AAGTCCACAACTTCGTGGCATCCTTTT
1 AAGTCCACAACTTCGTGGCATCCTTTT
* *
169494 AAGTCCATAACTTCGTGGTATCCTTTTT
1 AAGTCCACAACTTCGTGGCATCC-TTTT
*
169522 AAGCCCACAA
1 AAGTCCACAA
169532 GTAAGTGGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 45 0.55
28 37 0.45
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (27 bp):
AAGTCCACAACTTCGTGGCATCCTTTT
Found at i:169475 original size:55 final size:55
Alignment explanation
Indices: 169407--169519 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
169397 TGGCATTTCT
*
169407 TTTCAAAGTCCACAACTTCGTGGTATCCTTTTAAGTCCACAACTCCGTGGCATCC
1 TTTCAAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* * *
169462 TTTCAAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCATAACTTCGTGGTATCC
1 TTTCAAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
169517 TTT
1 TTT
169520 TTAAGCCCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (55 bp):
TTTCAAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
Found at i:169540 original size:55 final size:55
Alignment explanation
Indices: 169407--169588 Score: 157
Period size: 55 Copynumber: 3.3 Consensus size: 55
169397 TGGCATTTCT
* ** *
169407 TTTCAAAGTCCACAACTTCGTGGTATCCTTTTAAGTCCACAACTCCGTGGCATCC
1 TTTCAAAGCCCACAACTAAGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
* ** * * *
169462 TTTCAAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCATAACTTCGTGGTATCC
1 TTTCAAAGCCCACAACTAAGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
** * * ** * * * *
169517 TTTTTAAGCCCACAAGTAAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCAACCC
1 TTTCAAAGCCCACAACTAAGTGGCATCCTT-TTAAGTCCACAACTCCGTGGC-ATCC
169574 ATTTCAAAGCCCACA
1 -TTTCAAAGCCCACA
169589 CAAGTTGGTG
Statistics
Matches: 102, Mismatches: 22, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
55 74 0.73
56 13 0.13
57 3 0.03
58 12 0.12
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (55 bp):
TTTCAAAGCCCACAACTAAGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
Found at i:169600 original size:32 final size:32
Alignment explanation
Indices: 169527--169861 Score: 344
Period size: 32 Copynumber: 11.0 Consensus size: 32
169517 TTTTTAAGCC
** *
169527 CACAAGTAAGTGGC-ACCC-TTCCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
169555 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
169587 CACAAGTTGGTGGCAACCCATTTCAAAGCCTA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
169619 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * **
169649 CATAAGTCAGTGGC-A-TTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
169679 CACAAGTCGGTGGCAACTCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
169711 CACAAGTTGGTGGCAACCCATTTC-AAGCCTA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
**
169742 CACAAGTTAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
169774 CATAAGTCGGTGGCAACCCATTTCAAA-ACC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
169804 CATAAGTCGGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
169832 CACAAGTCAGTGGC-A-CCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
169862 TAAGTCAGTG
Statistics
Matches: 265, Mismatches: 30, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
28 55 0.21
29 10 0.04
30 45 0.17
31 35 0.13
32 120 0.45
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.20
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:169684 original size:92 final size:92
Alignment explanation
Indices: 169522--169861 Score: 410
Period size: 92 Copynumber: 3.7 Consensus size: 92
169512 TATCCTTTTT
** *
169522 AAGCC-CACAAGTAAGTGGCACCC-TTCCAAAGCCCACAAGTCAGTGGCAACCCATTTCAAAGCC
1 AAGCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACAAGTCAGTGGCAACCCATTTCAAAGCC
*
169585 CACACAAGTTGGTGGCAACCCATTTCA
66 CACACAAGTCGGTGGCAACCCATTTCA
* **
169612 AAGCCTACACAAGTCGGTGGCAACCCATTTCAAAGCCCATAAGTCAGTGGC-A-TTATTTCAAAG
1 AAGCC-ACACAAGTCGGTGGC-ACCCATTTCAAAGCCCACAAGTCAGTGGCAACCCATTTCAAAG
* *
169675 CCCACACAAGTCGGTGGCAACTCATTTGA
64 CCCACACAAGTCGGTGGCAACCCATTTCA
* *
169704 AAGCCCACACAAGTTGGTGGCAACCCATTTC-AAGCCTACACAAGTTAGTGGCAACCCATTTCAA
1 AAG-CCACACAAGTCGGTGGC-ACCCATTTCAAAGCC--CACAAGTCAGTGGCAACCCATTTCAA
*
169768 AGCCCACATAAGTCGGTGGCAACCCATTTCA
62 AGCCCACACAAGTCGGTGGCAACCCATTTCA
* * * * *
169799 AAACC-CATAAGTCGGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGC-A-CCTTTTCAAAGCC
1 AAGCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACAAGTCAGTGGCAACCCATTTCAAAGCC
169860 CA
66 CA
169862 TAAGTCAGTG
Statistics
Matches: 216, Mismatches: 24, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
88 14 0.06
89 1 0.00
90 18 0.08
91 10 0.05
92 80 0.37
93 31 0.14
94 25 0.12
95 37 0.17
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.20
Consensus pattern (92 bp):
AAGCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACAAGTCAGTGGCAACCCATTTCAAAGCC
CACACAAGTCGGTGGCAACCCATTTCA
Found at i:169755 original size:155 final size:156
Alignment explanation
Indices: 169555--169874 Score: 467
Period size: 155 Copynumber: 2.1 Consensus size: 156
169545 TTCCAAAGCC
* *
169555 CACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCTAC
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCAC
*
169620 ACAAGTCGGTGGCAACCCATTTCAAAGCCCATAAGTCAGTGGCAT-TATTTCAAAGCCCACACAA
66 ACAAGTCGGTGGCAACCCATTTCAAAACCCATAAGTCAGTGGCATCT-TTTCAAAGCCCACACAA
169684 GTCGGTGGCAACTCATTTGAAAGCCCA
130 GTCGGTGGCAACTCATTTGAAAGCCCA
** *
169711 CACAAGTTGGTGGCAACCCATTTC-AAGCCTACACAAGTTAGTGGCAACCCATTTCAAAGCCCAC
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCAC
* *
169775 ATAAGTCGGTGGCAACCCATTTCAAAACCCATAAGTCGGTGGCATCTTTTCAAAG-CC-CACAAG
66 ACAAGTCGGTGGCAACCCATTTCAAAACCCATAAGTCAGTGGCATCTTTTCAAAGCCCACACAAG
* * *
169838 TCAGTGGC-AC-CTTTTCAAAG-CC-
131 TCGGTGGCAACTCATTTGAAAGCCCA
*
169860 CATAAGTCAGTGGCA
1 CACAAGTCAGTGGCA
169875 TCCTTTGAAA
Statistics
Matches: 149, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
149 12 0.08
150 2 0.01
151 8 0.05
152 2 0.01
153 13 0.09
154 2 0.01
155 87 0.58
156 23 0.15
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (156 bp):
CACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCAC
ACAAGTCGGTGGCAACCCATTTCAAAACCCATAAGTCAGTGGCATCTTTTCAAAGCCCACACAAG
TCGGTGGCAACTCATTTGAAAGCCCA
Found at i:170090 original size:30 final size:28
Alignment explanation
Indices: 169404--170106 Score: 388
Period size: 28 Copynumber: 24.2 Consensus size: 28
169394 CAATGGCATT
* * *
169404 TCTTTTCAAAGTCCACAACTTC-GTGGTA
1 TCTTTTCAAAGCCCACAA-GTCAGTGGCA
* * *
169432 TCCTTTT--AAGTCCACAACTCCGTGGCA
1 T-CTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
169459 TCCTTTCAAAGTCCACAACTTC-GTGGCA
1 TCTTTTCAAAGCCCACAA-GTCAGTGGCA
* * * *
169487 TCCTTTT--AAGTCCATAACTTC-GTGGTA
1 T-CTTTTCAAAGCCCACAA-GTCAGTGGCA
* *
169514 TCCTTTT-TAAGCCCACAAGTAAGTGGCA
1 T-CTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
169542 CCCTTCCAAAGCCCACAAGTCAGTGGCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGC-A
* * **
169571 CCCATTTCAAAGCCCACACAAGTTGGTGGCAA
1 -TCTTTTCAAAG-CC-CACAAGTCAGTGGC-A
* * *
169603 CCCATTTCAAAGCCTACACAAGTCGGTGGCAA
1 -TCTTTTCAAAGCC--CACAAGTCAGTGGC-A
* * *
169635 CCCATTTCAAAGCCCATAAGTCAGTGGCA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
169664 T-TATTTCAAAGCCCACACAAGTCGGTGGCAA
1 TCT-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* * **
169695 CTCATTTGAAAGCCCACACAAGTTGGTGGCAA
1 -TCTTTTCAAAG-CC-CACAAGTCAGTGGC-A
* * *
169727 CCCATTTC-AAGCCTACACAAGTTAGTGGCAA
1 -TCTTTTCAAAGCC--CACAAGTCAGTGGC-A
* * *
169758 CCCATTTCAAAGCCCACATAAGTCGGTGGCAA
1 -TCTTTTCAAAGCCCAC--AAGTCAGTGGC-A
* * * * *
169790 CCCATTTCAAAACCCATAAGTCGGTGGCA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGCA
169819 TCTTTTCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
169847 CCTTTTCAAAGCCCATAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
169875 TCCTTTGAAAGTCCATAAATC-GATGGCA
1 TCTTTTCAAAGCCCACAAGTCAG-TGGCA
* **
169903 TCTTTTCAAAGCCCATAAGTTGGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
169931 TCTTTTCAAAGCCCACAAGTCAATGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
169959 TCTTTTCCAAGCCCATAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
169987 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
** *
170015 T-TTTTCCAAAGTTCACGAGTCAGTGGCA
1 TCTTTT-CAAAGCCCACAAGTCAGTGGCA
*
170043 TCTTTTCAAAGCCCACAAGTCAGTGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
170071 TCTCTTT-AAAGCTCACACAAGTTAGTGGCA
1 TCT-TTTCAAAGC-C-CACAAGTCAGTGGCA
*
170101 CCTTTT
1 TCTTTT
170107 TTTAAAAGCC
Statistics
Matches: 568, Mismatches: 76, Indels: 61
0.81 0.11 0.09
Matches are distributed among these distances:
26 6 0.01
27 50 0.09
28 268 0.47
29 28 0.05
30 64 0.11
31 32 0.06
32 120 0.21
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (28 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:170342 original size:48 final size:49
Alignment explanation
Indices: 170210--170332 Score: 221
Period size: 49 Copynumber: 2.5 Consensus size: 49
170200 GGCACCTTTA
170210 TTAGCTCAATGTCGTTGGCCTTGAATCAACACATTGTCCACTTTTGCCC
1 TTAGCTCAATGTCGTTGGCCTTGAATCAACACATTGTCCACTTTTGCCC
*
170259 TTAGCTCAATGTCGCTGGCCTTGAATCAACACATTGTCCACTTTT-CCC
1 TTAGCTCAATGTCGTTGGCCTTGAATCAACACATTGTCCACTTTTGCCC
*
170307 TTAGCTCGATGTCGTTGGCCTTGAAT
1 TTAGCTCAATGTCGTTGGCCTTGAAT
170333 TGGCACATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
48 27 0.38
49 44 0.62
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.35
Consensus pattern (49 bp):
TTAGCTCAATGTCGTTGGCCTTGAATCAACACATTGTCCACTTTTGCCC
Found at i:171937 original size:20 final size:21
Alignment explanation
Indices: 171905--171943 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
171895 AGCCTTTGAC
*
171905 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAATATGTTT
171926 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
171944 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:176966 original size:433 final size:433
Alignment explanation
Indices: 176160--177028 Score: 1623
Period size: 433 Copynumber: 2.0 Consensus size: 433
176150 TGCATTCACG
*
176160 GGATTATATCGAAATGATTTCAAGTTGAAACTATTGAAACCAATGTCAAGTCAAAATGTAGGTAG
1 GGATTATATCGAAATGATTTCAAGTCGAAACTATTGAAACCAATGTCAAGTCAAAATGTAGGTAG
176225 CAAAGTACCGATTTCAAGCATCGTGAGGAGGTTCGTATCTCTTTACGTGTAATCAACTCCCAAAC
66 CAAAGTACCGATTTCAAGCATCGTGAGGAGGTTCGTATCTCTTTACGTGTAATCAACTCCCAAAC
*
176290 CCAACCGACGAGTCTCTTAATTACGTAGACCATGGGATTGATGTCTCGAGTTTCATAACTTAAGA
131 CCAACCGACGAGTCTCTTAATTACGTAGACCATGGGATTAATGTCTCGAGTTTCATAACTTAAGA
176355 CATGGCTTTCAATAGGCATTCGATCATGCCTAGCCCAAAATGATCGGTGGCGACTCCAAAATTTC
196 CATGGCTTTCAATAGGCATTCGATCATGCCTAGCCCAAAATGATCGGTGGCGACTCCAAAATTTC
*
176420 AGTCACTTCGTGGTGACCATCGAGGATCAGTTAGATGGGCGATTCATTTATCAATCTTCCCTTTT
261 AGTCACTTCGTAGTGACCATCGAGGATCAGTTAGATGGGCGATTCATTTATCAATCTTCCCTTTT
176485 TCAACACATACCTCTTACCATGCCATAGAAATCCCCAATCACGAGGGATATTAAGTCGAGCACAC
326 TCAACACATACCTCTTACCATGCCATAGAAATCCCCAATCACGAGGGATATTAAGTCGAGCACAC
*
176550 CTTATTTGGCCTATCGCAGGGGGTCGAGCCCATGTCGCGACAA
391 CTCATTTGGCCTATCGCAGGGGGTCGAGCCCATGTCGCGACAA
176593 GGATTATATCGAAATGATTTCAAGTCGAAACTATTGAAACCAATGTCAAGTCAAAATGTAGGTAG
1 GGATTATATCGAAATGATTTCAAGTCGAAACTATTGAAACCAATGTCAAGTCAAAATGTAGGTAG
*
176658 TAAAGTACCGATTTCAAGCATCGTGAGGAGGTTCGTATCTCTTTACGTGTAATCAACTCCCAAAC
66 CAAAGTACCGATTTCAAGCATCGTGAGGAGGTTCGTATCTCTTTACGTGTAATCAACTCCCAAAC
* *
176723 CCAACTGACGAGTCTCTTAATTACGTAGACCATGGGATTAATGTCTCGAGTTTCCTAACTTAAGA
131 CCAACCGACGAGTCTCTTAATTACGTAGACCATGGGATTAATGTCTCGAGTTTCATAACTTAAGA
176788 CATGGCTTTCAATAGGCATTCGATCATGCCTAGCCCAAAATGATCGGTGGCGACTCCAAAATTTC
196 CATGGCTTTCAATAGGCATTCGATCATGCCTAGCCCAAAATGATCGGTGGCGACTCCAAAATTTC
* *
176853 -GATCACTTCGTAGTGACCGTCGAGGATCGGTTAGATGGGCGATTCATTTATCAATCTTCCCTTT
261 AG-TCACTTCGTAGTGACCATCGAGGATCAGTTAGATGGGCGATTCATTTATCAATCTTCCCTTT
*
176917 TTCAACACATACCTCTTACCATGCCATAGAAATCCCCAATCACGAGGGATATTAAGTCGAGCACG
325 TTCAACACATACCTCTTACCATGCCATAGAAATCCCCAATCACGAGGGATATTAAGTCGAGCACA
*
176982 CCTCATTTGGCCTATCGGAGGGGGTCGAGCCCATGTCGCGACAA
390 CCTCATTTGGCCTATCGCAGGGGGTCGAGCCCATGTCGCGACAA
177026 GGA
1 GGA
177029 CCACACTTGG
Statistics
Matches: 424, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
432 1 0.00
433 423 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (433 bp):
GGATTATATCGAAATGATTTCAAGTCGAAACTATTGAAACCAATGTCAAGTCAAAATGTAGGTAG
CAAAGTACCGATTTCAAGCATCGTGAGGAGGTTCGTATCTCTTTACGTGTAATCAACTCCCAAAC
CCAACCGACGAGTCTCTTAATTACGTAGACCATGGGATTAATGTCTCGAGTTTCATAACTTAAGA
CATGGCTTTCAATAGGCATTCGATCATGCCTAGCCCAAAATGATCGGTGGCGACTCCAAAATTTC
AGTCACTTCGTAGTGACCATCGAGGATCAGTTAGATGGGCGATTCATTTATCAATCTTCCCTTTT
TCAACACATACCTCTTACCATGCCATAGAAATCCCCAATCACGAGGGATATTAAGTCGAGCACAC
CTCATTTGGCCTATCGCAGGGGGTCGAGCCCATGTCGCGACAA
Found at i:177357 original size:97 final size:95
Alignment explanation
Indices: 177081--177357 Score: 322
Period size: 97 Copynumber: 2.8 Consensus size: 95
177071 TTTGGAAATC
* *
177081 TAAATCTTATTTTTTGTTTAAATTGTCATCATCGGGGACACTCCAACCCCATTCCTTCGAGGGGA
1 TAAATCTTA-TTTTTGCTTAAATTGTCATCATCGGGGACACTCTAACCCCATTCC-TCGAGGGGA
* * * *
177146 TAGTCCAATCCCACTTTTAAACTCGTAAAGATT
64 TACTTC-ATCCCATTTTTAAACTCATAAAGATT
* * *
177179 TAAATTTTATTTTTACTTAAATTGTCATCATCGAGGACACTCTAACCCCATTCCTCCGAGGGGAT
1 TAAATCTTATTTTTGCTTAAATTGTCATCATCGGGGACACTCTAACCCCATTCCT-CGAGGGGAT
* * *
177244 ACTTTGA-CCCTGTTTTTAAACTCATCAAGATT
65 AC-TTCATCCC-ATTTTTAAACTCATAAAGATT
* * * * *
177276 TAAATCTTATTTTTGCTTAAATTATCATCATCGGGGAGACACTAACCCTATTCCTCAGAGGAGAT
1 TAAATCTTATTTTTGCTTAAATTGTCATCATCGGGGACACTCTAACCCCATTCCTC-GAGGGGAT
177341 ACTTCATCTCCATTTTT
65 ACTTCATC-CCATTTTT
177358 CAACCAAAAA
Statistics
Matches: 151, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
96 8 0.05
97 132 0.87
98 11 0.07
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (95 bp):
TAAATCTTATTTTTGCTTAAATTGTCATCATCGGGGACACTCTAACCCCATTCCTCGAGGGGATA
CTTCATCCCATTTTTAAACTCATAAAGATT
Found at i:181528 original size:19 final size:20
Alignment explanation
Indices: 181504--181555 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
181494 CTTAACTGTT
181504 TGTATCGATACAT-A-CAAGA
1 TGTATCGATACATGACCAA-A
181523 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
*
181543 TGTATCAATACAT
1 TGTATCGATACAT
181556 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 14 0.47
21 3 0.10
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:187706 original size:13 final size:13
Alignment explanation
Indices: 187688--187726 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
187678 CAGCATTCTC
187688 TGTATCGATACAT
1 TGTATCGATACAT
*
187701 TGTATCGATACAC
1 TGTATCGATACAT
187714 TGTATCGATACAT
1 TGTATCGATACAT
187727 GGCATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:196636 original size:16 final size:16
Alignment explanation
Indices: 196614--196650 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
196604 TGGCAATTGG
196614 AAAAAAAAAACA-AAA
1 AAAAAAAAAACAGAAA
196629 AGAAAAAAAAACAGAAA
1 A-AAAAAAAAACAGAAA
196646 AAAAA
1 AAAAA
196651 GTGAAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 15 0.75
17 4 0.20
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAGAAA
Done.