Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold219
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: 770726
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:130628 original size:18 final size:21
Alignment explanation
Indices: 130586--130630 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 21
130576 TGGCATTATC
130586 ATATGAT-GTTTAAGAATCCT
1 ATATGATAGTTTAAGAATCCT
130606 A-ATGATAG-TTAA-AAT-CT
1 ATATGATAGTTTAAGAATCCT
130623 ATATGATA
1 ATATGATA
130631 TACAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.13
18 9 0.39
19 9 0.39
20 2 0.09
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGATAGTTTAAGAATCCT
Found at i:135721 original size:68 final size:68
Alignment explanation
Indices: 135644--135772 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 68
135634 TGAGTTCAGT
* * *
135644 AACTAGTAATATTGAAGAACTTCCTAATATCTTATTCTTTCTATTATACTTTTGAAATTGAGTTC
1 AACTAGTAATATTGAAAAACTTCCTAATATCTTATTCATTCTATCATACTTTTGAAATTGAGTTC
135709 TAC
66 TAC
* * * *
135712 AACTCGTAATATTGAAAAACTTCTTAATCTCTTATTCATTCTATCATACTTTTGGAATTGA
1 AACTAGTAATATTGAAAAACTTCCTAATATCTTATTCATTCTATCATACTTTTGAAATTGA
135773 TTGGAGTTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (68 bp):
AACTAGTAATATTGAAAAACTTCCTAATATCTTATTCATTCTATCATACTTTTGAAATTGAGTTC
TAC
Found at i:137818 original size:185 final size:185
Alignment explanation
Indices: 137506--137888 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 185
137496 ACACACTTAT
137506 AAACTTTATTTATTTTAAAACTATTTGACAATATAACTTTGCCAAAATTTTCGTGCCATTGTTTA
1 AAACTTTATTTATTTTAAAACTATTTGACAATATAACTTTGCCAAAATTTTCGTGCCATTGTTTA
137571 GGAGCTTGTTTCAAGCTATACAATGACTTGACAAGTTTGTATATTTATTTTATTTTTCTTTAATA
66 GGAGCTTGTTTCAAGCTATACAATGACTTGACAAGTTTGTATATTTATTTTATTTTTCTTTAATA
137636 ATAAACTTCTCGGGTTATTGCATATAAACCTTTTCATCAAGATCACTATTTAGGA
131 ATAAACTTCTCGGGTTATTGCATATAAACCTTTTCATCAAGATCACTATTTAGGA
*
137691 AAACTTTATTTATTTTAAAGCTATTTGACAATATAACTTTGCCAAAATTTTCGTGCCATTGTTTA
1 AAACTTTATTTATTTTAAAACTATTTGACAATATAACTTTGCCAAAATTTTCGTGCCATTGTTTA
137756 GGAGCTTGTTTCAAGCTATACAATGACTTGACAAGTTTGTATATTTATTTTATTTTTCTTTAATA
66 GGAGCTTGTTTCAAGCTATACAATGACTTGACAAGTTTGTATATTTATTTTATTTTTCTTTAATA
137821 ATAAACTTCTCGGGTTATTGCATATAAACCTTTTCATCAAGATCACTATTTAGGA
131 ATAAACTTCTCGGGTTATTGCATATAAACCTTTTCATCAAGATCACTATTTAGGA
*
137876 AAACTTTCTTTAT
1 AAACTTTATTTAT
137889 ATCTATTTGA
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 196 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (185 bp):
AAACTTTATTTATTTTAAAACTATTTGACAATATAACTTTGCCAAAATTTTCGTGCCATTGTTTA
GGAGCTTGTTTCAAGCTATACAATGACTTGACAAGTTTGTATATTTATTTTATTTTTCTTTAATA
ATAAACTTCTCGGGTTATTGCATATAAACCTTTTCATCAAGATCACTATTTAGGA
Found at i:138589 original size:20 final size:20
Alignment explanation
Indices: 138564--138649 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
138554 TATTTCTATC
*
138564 GATACACATGAAAATGTATT
1 GATACACATGACAATGTATT
* * *
138584 GATACATATTG-CAATATATC
1 GATACACA-TGACAATGTATT
* *
138604 GATACATATTACAATGTATT
1 GATACACATGACAATGTATT
* *
138624 GATACACCTTG-CAATGTATC
1 GATACA-CATGACAATGTATT
138644 GATACA
1 GATACA
138650 TTATGTGAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 48 0.92
21 3 0.06
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
GATACACATGACAATGTATT
Found at i:138620 original size:40 final size:40
Alignment explanation
Indices: 138560--138650 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
138550 CCCTTATTTC
* *
138560 TATCGATACACATGAAAATGTATTGATACATATTGCAATA
1 TATCGATACATATGAAAATGTATTGATACACATTGCAATA
* * * *
138600 TATCGATACATATTACAATGTATTGATACACCTTGCAATG
1 TATCGATACATATGAAAATGTATTGATACACATTGCAATA
138640 TATCGATACAT
1 TATCGATACAT
138651 TATGTGAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (40 bp):
TATCGATACATATGAAAATGTATTGATACACATTGCAATA
Found at i:138743 original size:21 final size:22
Alignment explanation
Indices: 138715--138775 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
138705 ATACACATAT
138715 AGAAATGTATCGATACAATTCC
1 AGAAATGTATCGATACAATTCC
138737 A-AAATGTATCGATAC-A-TCC
1 AGAAATGTATCGATACAATTCC
* *
138756 AGAATTGTATCTATACAATT
1 AGAAATGTATCGATACAATT
138776 AGCCCAACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 15 0.44
22 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (22 bp):
AGAAATGTATCGATACAATTCC
Found at i:138766 original size:20 final size:21
Alignment explanation
Indices: 138715--138772 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
138705 ATACACATAT
138715 AGAAATGTATCGATACAATTCC
1 AGAAATGTATCGATAC-ATTCC
138737 A-AAATGTATCGATACA-TCC
1 AGAAATGTATCGATACATTCC
* *
138756 AGAATTGTATCTATACA
1 AGAAATGTATCGATACA
138773 ATTAGCCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 14 0.42
22 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (21 bp):
AGAAATGTATCGATACATTCC
Found at i:140677 original size:79 final size:79
Alignment explanation
Indices: 140588--140761 Score: 235
Period size: 79 Copynumber: 2.2 Consensus size: 79
140578 AATAGAATCA
* * * * *
140588 GGGTTTGAGTACTCCCGT-GAAAATAATGGGGTTGGAGTAT-CCTCAATTATGAGAAATTAATAT
1 GGGTTGGAGTA-TCCCCTCGAAAATAACGGGGTTAGAGTATCCCT-AATTATGAGAAATCAATAT
140651 TTTAGGAATAAAACCG
64 TTTAGGAATAAAACCG
* * *
140667 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCCCTGATTGTGAGAAATCAATATTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCTAATTATGAGAAATCAATATTT
*
140732 TAGGAATAAAACTG
66 TAGGAATAAAACCG
140746 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
140762 GATTGTGAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 5 0.06
79 76 0.90
80 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCTAATTATGAGAAATCAATATTT
TAGGAATAAAACCG
Found at i:140766 original size:51 final size:51
Alignment explanation
Indices: 140693--140812 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
140683 TCGGAAATAA
* * *
140693 CGGGGTTAGAGTATCCCTGATTGTGAGAAATCAATATTTTAGGAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAGAATAAAAC
*
140744 TGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAGAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAGAATAAAAC
140795 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
140813 TCGGAAATAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAAGAATAAAAC
Found at i:140830 original size:209 final size:210
Alignment explanation
Indices: 140426--140838 Score: 498
Period size: 209 Copynumber: 2.0 Consensus size: 210
140416 ACATCTCTCA
140426 ATGAGAAATTTAATATTTTAGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
1 ATGAGAAATTTAATATTTTAGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
* * ** *
140491 GGAGTATCCCCAATTGTGAAAAATCGATGATTTAGAAATAAGGCAAGGGTTGAAGTGTCCCCGAT
66 AGAGTATCCCCAATTGTGAAAAATCAATGATTTAGAAATAAAACAAGGGTTGAAGTATCCCCGAT
* * * * * *
140556 TATAGAAAATAGATGTTTCAAAAATAGAATCAGGGTTTGAGTACTCCCGTGAAAATAATGGGGTT
131 TATAGAAAATAGATATTTCAAAAATAAAACCAGGGTTGGAGTACTCCCCTGAAAATAACGGGGTT
140621 GGAGTATCCTCAATT
196 GGAGTATCCTCAATT
*
140636 ATGAGAAA-TTAATATTTTAG-GAATAA-AACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGG
1 ATGAGAAATTTAATATTTTAGAG-ATAATAA-CGGGGTTGGAGTATCCCCTCGAAAATAACGGGG
** * * ** *
140698 TTAGAGTATCCCTGATTGTGAGAAATCAAT-ATTTTAGGAATAAAACTGGGGTTGGAGTATCCCC
64 TTAGAGTATCCCCAATTGTGAAAAATCAATGA-TTTAGAAATAAAACAAGGGTTGAAGTATCCCC
* * * * * *
140762 GATTGT-GAGAAATCA-ATATTTTAAGAATAAAACCGGGGTTGGAGTA-TCCCCTCGGAAATACC
128 GATTATAGA-AAAT-AGATATTTCAAAAATAAAACCAGGGTTGGAGTACTCCCCT-GAAAATAAC
140824 GGGGTTGGAGTATCC
190 GGGGTTGGAGTATCC
140839 CTTCGGAAAT
Statistics
Matches: 172, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
208 11 0.06
209 152 0.88
210 9 0.05
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (210 bp):
ATGAGAAATTTAATATTTTAGAGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
AGAGTATCCCCAATTGTGAAAAATCAATGATTTAGAAATAAAACAAGGGTTGAAGTATCCCCGAT
TATAGAAAATAGATATTTCAAAAATAAAACCAGGGTTGGAGTACTCCCCTGAAAATAACGGGGTT
GGAGTATCCTCAATT
Found at i:140833 original size:28 final size:28
Alignment explanation
Indices: 140793--140860 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
140783 TAAGAATAAA
140793 ACCGGGGTTGGAGTATCCCCTCGGAAAT
1 ACCGGGGTTGGAGTATCCCCTCGGAAAT
*
140821 ACCGGGGTTGGAGTATCCCTTCGGAAAT
1 ACCGGGGTTGGAGTATCCCCTCGGAAAT
*
140849 AACGGGGTTGGA
1 ACCGGGGTTGGA
140861 AAATGCCACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (28 bp):
ACCGGGGTTGGAGTATCCCCTCGGAAAT
Found at i:141035 original size:62 final size:56
Alignment explanation
Indices: 140864--141263 Score: 508
Period size: 55 Copynumber: 7.0 Consensus size: 56
140854 GGTTGGAAAA
* * *
140864 TGCCACCAACTCGTGTGGGCTTTG-AAAGGCGTCCTGCTCTTTGAGGACTGGGAA-G
1 TGCCACCAACTTGTGTGGGCTTAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAGG
*
140919 TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAGAA-G
1 TGCCACCAACTTGTGTGGGC-TT---A-GAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAGG
* * *
140980 TGCCACCAACTCGTGTGGGCTTCGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTGGAGGG
1 TGCCACCAACTTGTGTGGGCTT-----AG-AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
* *
141042 TGCCACCAACTCGTGTGGGCTT-TAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
* *
141097 TGCCACCAACTTGTGTGGGCTTTG-AAAGGCGTCCTGCTCTTTGAGGATTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
*
141152 TGCCACCAACTTGTGTGGGCTTTG-AAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
* *
141207 TGCCACCAACTTGTGTGGGCTTTG-AAAGGCGTCCTGCTCTTTGAGGACTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
141262 TG
1 TG
141264 AAAAGAGAGA
Statistics
Matches: 317, Mismatches: 16, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
55 210 0.66
56 2 0.01
60 4 0.01
61 48 0.15
62 53 0.17
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (56 bp):
TGCCACCAACTTGTGTGGGCTTAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
Found at i:141150 original size:26 final size:26
Alignment explanation
Indices: 141118--141206 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
141108 TGTGTGGGCT
141118 TTGAAAGGCGTCCTGCTCTTTGAGGA
1 TTGAAAGGCGTCCTGCTCTTTGAGGA
* ** * * *
141144 TTGAAAGGTG-CCACCAACTTGTGTGGGCT
1 TTGAAAGGCGTCCTGC-TCTT-TG-AGG-A
141173 TTGAAAGGCGTCCTGCTCTTTGAGGA
1 TTGAAAGGCGTCCTGCTCTTTGAGGA
*
141199 CTGAAAGG
1 TTGAAAGG
141207 TGCCACCAAC
Statistics
Matches: 45, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 19 0.42
27 4 0.09
28 4 0.09
29 12 0.27
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (26 bp):
TTGAAAGGCGTCCTGCTCTTTGAGGA
Found at i:141343 original size:61 final size:60
Alignment explanation
Indices: 141274--141567 Score: 369
Period size: 61 Copynumber: 5.0 Consensus size: 60
141264 AAAAGAGAGA
141274 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAG
* *
141335 GCATCCTGCTCTTTCAGGACTGAGAA-GTGCCACCAACTCGTGTGGGCTTT----G-AAAG
1 GCATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAG
* * ** * *
141390 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTCGTGTGGGCTTT----G-AAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAG
*
141445 GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAG
* *
141505 GCATCCTGCTCTTTGAGGACTGGAAGGTACCACCAACTTGTGTGGGCTTTTAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGC-TTTAAAGGAAAAG
141566 GC
1 GC
141568 GTAAGGAGAG
Statistics
Matches: 208, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
54 26 0.12
55 71 0.34
56 1 0.00
59 1 0.00
60 24 0.12
61 78 0.38
62 7 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (60 bp):
GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAG
Found at i:141391 original size:265 final size:258
Alignment explanation
Indices: 141018--141499 Score: 770
Period size: 265 Copynumber: 1.8 Consensus size: 258
141008 GAAAAAGGCG
* * *
141018 TCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCATCCTGCTCTT
* * *
141083 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA-TTG
66 TCAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGG
* *
141147 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCA
131 AAA-ATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCA
*
141212 CCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGAAAAGAGAGAGCA
194 CCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGAAAAGAGAGAGCA
*
141277 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGCTTT------AAAAGGCATCCT
141342 GCTCTTTCAGGACTGAGAA-GTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
60 GCTCTTTCAGGACTGA-AAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
*
141406 GGACTGGAAAATGCCACTAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGG
124 GGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGG
141471 TGCCACCAACTTGTGTGGGCTTTAAAAGG
189 TGCCACCAACTTGTGTGGGCTTTAAAAGG
141500 AAAAGGCATC
Statistics
Matches: 204, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
259 44 0.22
264 33 0.16
265 120 0.59
266 7 0.03
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (258 bp):
TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCATCCTGCTCTT
TCAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGG
AAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACC
AACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGAAAAGAGAGAGCA
Found at i:141395 original size:210 final size:203
Alignment explanation
Indices: 141073--141472 Score: 626
Period size: 210 Copynumber: 1.9 Consensus size: 203
141063 TTAAAAGGCG
*
141073 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTT
* * *
141138 TGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-G
66 TCAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGG
* *
141202 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGAAA
131 AAA-ATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGAAA
141267 AGAGAGAGCA
194 AGAGAGAGCA
141277 TCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCATCC
141341 TGCTCTTTCAGGACTGAGAA-GTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
59 TGCTCTTTCAGGACTGA-AAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
*
141405 AGGACTGGAAAATGCCACTAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAG
123 AGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAG
141470 GTG
188 GTG
141473 CCACCAACTT
Statistics
Matches: 180, Mismatches: 7, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
203 1 0.01
204 45 0.25
209 8 0.04
210 120 0.67
211 6 0.03
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (203 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTT
TCAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGG
AAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGAAAAG
AGAGAGCA
Found at i:141421 original size:55 final size:54
Alignment explanation
Indices: 141274--141560 Score: 315
Period size: 55 Copynumber: 5.0 Consensus size: 54
141264 AAAAGAGAGA
*
141274 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAG
* *
141335 GCATCCTGCTCTTTCAGGACTGAGAAGTGCCACCAACTCGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACTGA-AAGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * * *
141390 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTCGTGTGGGCTTTGAAAG
1 GCATCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
*
141445 GCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-----G-AAAG
* * *
141505 GCATCCTGCTCTTTGAGGACTGGAAGGTACCACCAACTTGTGTGGGCTTTTAAAG
1 GCATCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
141560 G
1 G
141561 AAAAGGCGTA
Statistics
Matches: 201, Mismatches: 14, Indels: 28
0.83 0.06 0.12
Matches are distributed among these distances:
53 3 0.01
54 21 0.10
55 78 0.39
56 3 0.01
59 1 0.00
60 26 0.13
61 67 0.33
62 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (54 bp):
GCATCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:149100 original size:2 final size:2
Alignment explanation
Indices: 149093--149118 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
149083 CGCTTCCTAA
149093 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
149119 CAACTACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:154026 original size:16 final size:16
Alignment explanation
Indices: 154007--154047 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
153997 AATAAATTAT
154007 ATTTAAAATGATACAA
1 ATTTAAAATGATACAA
*
154023 ATTTGAAAA-GATTCAA
1 ATTT-AAAATGATACAA
154039 ATTTAAAAT
1 ATTTAAAAT
154048 TATCTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTTAAAATGATACAA
Found at i:154062 original size:17 final size:17
Alignment explanation
Indices: 154040--154121 Score: 57
Period size: 16 Copynumber: 5.0 Consensus size: 17
154030 AAGATTCAAA
154040 TTTAAAATTATCTAAAT
1 TTTAAAATTATCTAAAT
154057 TTTAAAAATT-T-TAAAT
1 TTT-AAAATTATCTAAAT
* *
154073 TTTTAAA-TATTTAAAT
1 TTTAAAATTATCTAAAT
** * *
154089 TAAAAAATAATTTAAA-
1 TTTAAAATTATCTAAAT
154105 TTT-AAATTAATCTAAAT
1 TTTAAAATT-ATCTAAAT
154122 AAAAAAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.02
15 8 0.16
16 24 0.48
17 11 0.22
18 6 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAATTATCTAAAT
Found at i:154073 original size:32 final size:32
Alignment explanation
Indices: 154007--154130 Score: 87
Period size: 32 Copynumber: 3.8 Consensus size: 32
153997 AATAAATTAT
* * *
154007 ATTTAAAATGATAC-AAATTTGAAAAGA-TTCAA
1 ATTTAAAATTAT-CTAAATTT-AAAAAATTTTAA
*
154039 ATTTAAAATTATCTAAATTTTAAAAATTTTAA
1 ATTTAAAATTATCTAAATTTAAAAAATTTTAA
* *
154071 ATTTTTAAA-TATTTAAA-TTAAAAAATAATTTAA
1 A-TTTAAAATTATCTAAATTTAAAAAAT--TTTAA
**
154104 ATTT-AAATTAATCTAAATAAAAAAAAT
1 ATTTAAAATT-ATCTAAATTTAAAAAAT
154131 AATACGATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
31 16 0.22
32 33 0.45
33 18 0.24
34 7 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTTAAAATTATCTAAATTTAAAAAATTTTAA
Found at i:154422 original size:13 final size:13
Alignment explanation
Indices: 154399--154432 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
154389 AAAGATTAAC
154399 ATAAAATTAAAATA
1 ATAAAA-TAAAATA
154413 ATAAAATAAAATA
1 ATAAAATAAAATA
154426 A-AAAATA
1 ATAAAATA
154433 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAAATAAAATA
Found at i:154845 original size:16 final size:16
Alignment explanation
Indices: 154809--154845 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
154799 TGTCCTATTT
154809 AAAAA-AATTTAAATA
1 AAAAATAATTTAAATA
154824 AAAAATAATTTAAATA
1 AAAAATAATTTAAATA
154840 AAAAAT
1 AAAAAT
154846 TTATATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATAATTTAAATA
Found at i:154857 original size:29 final size:29
Alignment explanation
Indices: 154810--154865 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
154800 GTCCTATTTA
*
154810 AAAAAATTTAAATAAAAAATAATTTAAAT
1 AAAAAATTTAAATAAAAAATAAATTAAAT
* **
154839 AAAAAATTTATATTGAAAATAAATTAA
1 AAAAAATTTAAATAAAAAATAAATTAA
154866 GCTTTGATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAATTTAAATAAAAAATAAATTAAAT
Found at i:156337 original size:5 final size:5
Alignment explanation
Indices: 156329--156402 Score: 57
Period size: 5 Copynumber: 15.4 Consensus size: 5
156319 TTGGATTCAA
* * *
156329 TAAAT TAAAT CTGAAT TAAAT TAAAA TAAAT T--TT TAAA- -AAAT TAAAT
1 TAAAT TAAAT -TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
* * *
156376 TAAAT TAATT TAATT TAATT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TA
156403 TTATTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
3 5 0.09
5 47 0.84
6 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (5 bp):
TAAAT
Found at i:156425 original size:35 final size:32
Alignment explanation
Indices: 156386--156456 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 32
156376 TAAATTAATT
*
156386 TAATTTAATTTAAATTATTATTTAAAAAATAAAAA
1 TAATTTAATTTAAA-TA-TAATT-AAAAATAAAAA
* *
156421 TAATTTTATTTAAATATAATTATAAATAAAAA
1 TAATTTAATTTAAATATAATTAAAAATAAAAA
156453 TAAT
1 TAAT
156457 AAAATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.42
33 4 0.12
34 2 0.06
35 13 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAATTTAATTTAAATATAATTAAAAATAAAAA
Found at i:156450 original size:16 final size:16
Alignment explanation
Indices: 156412--156456 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
156402 ATTATTTAAA
*
156412 AAATAAAAATAATTTT
1 AAATAAAAATAATTAT
** *
156428 ATTTAAATATAATTAT
1 AAATAAAAATAATTAT
156444 AAATAAAAATAAT
1 AAATAAAAATAAT
156457 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAAAAATAATTAT
Found at i:156458 original size:35 final size:34
Alignment explanation
Indices: 156386--156480 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 34
156376 TAAATTAATT
* *
156386 TAATTTAATTTAAATTATTATTTAAAAAATAAAAA
1 TAATTTTATTTAAA-TATAATTTAAAAAATAAAAA
156421 TAATTTTATTTAAATATAATTATAAATAAA-AATAATA
1 TAATTTTATTTAAATATAATT-TAAA-AAATAA-AA-A
* *
156458 AAATTTTATTATAAAAATAATTT
1 TAATTTTATT-TAAATATAATTT
156481 TGATATTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
34 6 0.12
35 19 0.37
36 5 0.10
37 11 0.22
38 10 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
TAATTTTATTTAAATATAATTTAAAAAATAAAAA
Found at i:161381 original size:125 final size:125
Alignment explanation
Indices: 161159--161413 Score: 510
Period size: 125 Copynumber: 2.0 Consensus size: 125
161149 ACAAATTGTT
161159 TGGCAATGCAGTTTGACAGAGCTTACCTAACATCATGAATCATTGAAAAAGCATTGCATGATAAT
1 TGGCAATGCAGTTTGACAGAGCTTACCTAACATCATGAATCATTGAAAAAGCATTGCATGATAAT
161224 TTGGAACAATTAGCCAAGGTGCATCATTACATGAAGAGCTGTGAAGCTACTAAGAAAGGG
66 TTGGAACAATTAGCCAAGGTGCATCATTACATGAAGAGCTGTGAAGCTACTAAGAAAGGG
161284 TGGCAATGCAGTTTGACAGAGCTTACCTAACATCATGAATCATTGAAAAAGCATTGCATGATAAT
1 TGGCAATGCAGTTTGACAGAGCTTACCTAACATCATGAATCATTGAAAAAGCATTGCATGATAAT
161349 TTGGAACAATTAGCCAAGGTGCATCATTACATGAAGAGCTGTGAAGCTACTAAGAAAGGG
66 TTGGAACAATTAGCCAAGGTGCATCATTACATGAAGAGCTGTGAAGCTACTAAGAAAGGG
161409 TGGCA
1 TGGCA
161414 TGATTCTTAG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 130 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (125 bp):
TGGCAATGCAGTTTGACAGAGCTTACCTAACATCATGAATCATTGAAAAAGCATTGCATGATAAT
TTGGAACAATTAGCCAAGGTGCATCATTACATGAAGAGCTGTGAAGCTACTAAGAAAGGG
Found at i:162993 original size:31 final size:31
Alignment explanation
Indices: 162951--163010 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
162941 TTTTTATTTG
162951 ATTAAAATTTATCAT-TAAATTTTAATTTTTA
1 ATTAAAATTTATC-TCTAAATTTTAATTTTTA
* *
162982 ATTAAATTTTATCTCTCAATTTTAATTTT
1 ATTAAAATTTATCTCTAAATTTTAATTTT
163011 AAATGATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAAAATTTATCTCTAAATTTTAATTTTTA
Found at i:163378 original size:5 final size:6
Alignment explanation
Indices: 163361--163386 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
163351 ATTCTTTTGT
163361 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
163387 TTGGCAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:166483 original size:78 final size:78
Alignment explanation
Indices: 166354--166515 Score: 315
Period size: 78 Copynumber: 2.1 Consensus size: 78
166344 GCTGTCATCT
166354 CTTTTTCAATCAAAAGAGGGTGGACCTGAGTTGCTTTTTCCTTCCACCTTTGTGCATATTGTCGA
1 CTTTTTCAATCAAAAGAGGGTGGACCTGAGTTGCTTTTTCCTTCCACCTTTGTGCATATTGTCGA
166419 AAGCTCTCGGAAG
66 AAGCTCTCGGAAG
*
166432 CTTTTTCAATCAAAAGAGGGTGGACTTGAGTTGCTTTTTCCTTCCACCTTTGTGCATATTGTCGA
1 CTTTTTCAATCAAAAGAGGGTGGACCTGAGTTGCTTTTTCCTTCCACCTTTGTGCATATTGTCGA
166497 AAGCTCTCGGAAG
66 AAGCTCTCGGAAG
166510 CTTTTT
1 CTTTTT
166516 TTCCATATTC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (78 bp):
CTTTTTCAATCAAAAGAGGGTGGACCTGAGTTGCTTTTTCCTTCCACCTTTGTGCATATTGTCGA
AAGCTCTCGGAAG
Found at i:172360 original size:162 final size:163
Alignment explanation
Indices: 172002--172383 Score: 424
Period size: 164 Copynumber: 2.3 Consensus size: 163
171992 ACGGGGTTGG
** * * * *
172002 AGTATCCTTGAAAATAGAAAATTTAATTTTTTTATAG-GTAAACCAAGGGTTGGAGTATCCACTT
1 AGTATCCCCGAAAATAGAAAATTTGATTTTTTT-TAGAGTAAAACAA-GGTTAGAGTATCCACTA
* * * *
172066 GAAGCTAGCAAGGTTAGAGTATCCTTAAAAATGGAAAATTTGATTTTTTTTTACAGGTAAAAATG
64 GAAGATAGCAAGGTTAGAGTATCCTCAAAAATAGAAAATTTGATTTTTTTTTACAAGTAAAAATG
* * *
172131 GGGTTGAAGTATCTTCTCGGAATTGGCAGGGTTAA
129 GAGTTGAAGTATCTTCTCGAAATAGGCAGGGTTAA
* *
172166 AGTATCCCCGAAAATAGAAATTTTGATTTTTTTTAGAGATAAAAC-AGGATTAGAGTATCCCCTC
1 AGTATCCCCGAAAATAGAAAATTTGATTTTTTTTAGAG-TAAAACAAGG-TTAGAGTATCCACT-
* *
172230 AG-AGATAGTAAGGTTAGGGTATCCTCAAAAATAGAAAATTTGA-TTTTTTTTA-AAGTAAAAAC
63 AGAAGATAGCAAGGTTAGAGTATCCTCAAAAATAGAAAATTTGATTTTTTTTTACAAGTAAAAA-
*
172292 T-GAGTT-AGAGTATCCCTT-T-GAAATAGGCAGGGTTAG
127 TGGAGTTGA-AGTAT--CTTCTCGAAATAGGCAGGGTTAA
*
172328 AGTATCTCCGAAAATAGAAAATTTGA-TTTTTTTAGAGGTAAAAACAAGGTTAGAGT
1 AGTATCCCCGAAAATAGAAAATTTGATTTTTTTTAGA-GT-AAAACAAGGTTAGAGT
172384 TTCTTCTCGA
Statistics
Matches: 187, Mismatches: 20, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
161 12 0.06
162 68 0.36
163 19 0.10
164 82 0.44
165 6 0.03
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (163 bp):
AGTATCCCCGAAAATAGAAAATTTGATTTTTTTTAGAGTAAAACAAGGTTAGAGTATCCACTAGA
AGATAGCAAGGTTAGAGTATCCTCAAAAATAGAAAATTTGATTTTTTTTTACAAGTAAAAATGGA
GTTGAAGTATCTTCTCGAAATAGGCAGGGTTAA
Found at i:172405 original size:162 final size:159
Alignment explanation
Indices: 171995--172547 Score: 491
Period size: 162 Copynumber: 3.4 Consensus size: 159
171985 AAAGATGACG
* * * * * *
171995 GGGTTGGAGTATCCTTGAAAATAGAAAATTTAATTTTTTTATAGGTAAACCAAGGGTTGGAGTAT
1 GGGTTAGAGTATCC-CGAAAATAGAAAATTTGATTTTTTTAGAGGTAAAACAA-GGTTAGAGTAT
* * * * *
172060 CCACTTGAAGCTAGCAAGGTTAGAGTATCCTTAAAAATGGAAAATTTGATTTTTTTTTACAGGTA
64 CCACTCGAAGATAGTAAGGTTAGGGTATCCTTAAAAATAGAAAATTTGA-TTTTTTTTACAGGTA
* *
172125 AAAA-TGGGGTTGAAGTAT-CTTCTCGGAATTGGCA
128 AAAACT-GAGTTG-AGTATCCTTCT--GAAATGGCA
* * *
172159 GGGTTAAAGTATCCCCGAAAATAGAAATTTTGATTTTTTTTAGAGATAAAAC-AGGATTAGAGTA
1 GGGTTAGAGTAT-CCCGAAAATAGAAAATTTGA-TTTTTTTAGAGGTAAAACAAGG-TTAGAGTA
* * *
172223 TCCCCTC-AGAGATAGTAAGGTTAGGGTATCCTCAAAAATAGAAAATTTGATTTTTTTTA-AAGT
63 TCCACTCGA-AGATAGTAAGGTTAGGGTATCCTTAAAAATAGAAAATTTGATTTTTTTTACAGGT
172286 AAAAACTGAGTTAGAGTATCCCTT-TGAAATAGGCA
127 AAAAACTGAGTT-GAGTAT-CCTTCTGAAAT-GGCA
*
172321 GGGTTAGAGTATCTCCGAAAATAGAAAATTTGATTTTTTTAGAGGTAAAAACAAGGTTAGAGTTT
1 GGGTTAGAGTATC-CCGAAAATAGAAAATTTGATTTTTTTAGAGGT-AAAACAAGGTTAGAGTAT
** * * * * * * * *
172386 CTTCTCGAAAATGGTAAGGTT-GGAGTATCATTGAAAACA-AAATAATT-A-ATTTTTTAGAGGT
64 CCACTCGAAGATAGTAAGGTTAGG-GTATCCTTAAAAATAGAAA-ATTTGATTTTTTTTACAGGT
* * *
172447 AAAAAC-GAGGTTGGAATATCTCTTCAGAGATGGC-
127 AAAAACTGA-GTT-GAGTATC-CTTCTGAAATGGCA
* * *
172481 GGGATTAGAGTATCCCAAAAATAGAAAATTTGATTTTTTTATAGGTAAAAACAAGGTTGGAGTAT
1 GGG-TTAGAGTATCCCGAAAATAGAAAATTTGATTTTTTTAGAGGT-AAAACAAGGTTAGAGTAT
172546 CC
64 CC
172548 TTTCGAAGGA
Statistics
Matches: 326, Mismatches: 43, Indels: 44
0.79 0.10 0.11
Matches are distributed among these distances:
160 61 0.19
161 56 0.17
162 96 0.29
163 19 0.06
164 77 0.24
165 17 0.05
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.33
Consensus pattern (159 bp):
GGGTTAGAGTATCCCGAAAATAGAAAATTTGATTTTTTTAGAGGTAAAACAAGGTTAGAGTATCC
ACTCGAAGATAGTAAGGTTAGGGTATCCTTAAAAATAGAAAATTTGATTTTTTTTACAGGTAAAA
ACTGAGTTGAGTATCCTTCTGAAATGGCA
Found at i:172519 original size:80 final size:79
Alignment explanation
Indices: 171931--172547 Score: 350
Period size: 81 Copynumber: 7.6 Consensus size: 79
171921 GAGTATCTTT
* * * * * * *
171931 GAAAAT-GAAAATTTTAATTTTTTAGAGGTAAAAATG-GGATAGAAGTATCCCCTCAAAGATGAC
1 GAAAATAGAAAATTTGATTTTTTTAGAGGTAAAAACGAGGTTAG-AGTATCCCTTCAGAGATGGC
* *
171994 GGGGTTGGAGTATCCTT
65 -GGGTTAGAGTATCC-C
* * * * * *
172011 GAAAATAGAAAATTTAATTTTTTTATAGGTAAACCAA-G-GGTTGGAGTATCCACTTGA-AGCTA
1 GAAAATAGAAAATTTGATTTTTTTAGAGGTAAA--AACGAGGTTAGAGTATCC-CTTCAGAGATG
* *
172073 GCAAGGTTAGAGTATCCTT
63 GC-GGGTTAGAGTATCC-C
* * * * * * *
172092 AAAAATGGAAAATTTGATTTTTTTTTACAGGTAAAAATGGGGTT-GAAGTAT-CTTCTCGGA-AT
1 GAAAATAGAAAATTTGA--TTTTTTTAGAGGTAAAAACGAGGTTAG-AGTATCCCT-TCAGAGA-
*
172154 TGGCAGGGTTAAAGTATCCCC
61 TGGC-GGGTTAGAGTAT-CCC
* * *
172175 GAAAATAGAAATTTTGATTTTTTTTAGAGAT-AAAAC-AGGATTAGAGTATCCCCTCAGAGATAG
1 GAAAATAGAAAATTTGA-TTTTTTTAGAGGTAAAAACGAGG-TTAGAGTATCCCTTCAGAGAT-G
*** *
172238 TAAGGTTAGGGTATCCTC
63 GCGGGTTAGAGTATCC-C
* * * *
172256 AAAAATAGAAAATTTGATTTTTTTTA-AAGTAAAAACTGA-GTTAGAGTATCCCTT-TGAAATAG
1 GAAAATAGAAAATTTGA-TTTTTTTAGAGGTAAAAAC-GAGGTTAGAGTATCCCTTCAGAGAT-G
172318 GCAGGGTTAGAGTATCTCC
63 GC-GGGTTAGAGTATC-CC
* * * *
172337 GAAAATAGAAAATTTGATTTTTTTAGAGGTAAAAACAAGGTTAGAGT-T-TCTTCTCGAAAATGG
1 GAAAATAGAAAATTTGATTTTTTTAGAGGTAAAAACGAGGTTAGAGTATCCCTTC-AG-AGATGG
** * **
172400 TAAGGTTGGAGTATCATT
64 -CGGGTTAGAGTATC-CC
* * * * * *
172418 GAAAACA-AAATAATT-AATTTTTTAGAGGTAAAAACGAGGTTGGAATATCTCTTCAGAGATGGC
1 GAAAATAGAAA-ATTTGATTTTTTTAGAGGTAAAAACGAGGTTAGAGTATCCCTTCAGAGATGGC
172481 GGGATTAGAGTATCCC
65 GGG-TTAGAGTATCCC
* * * *
172497 AAAAATAGAAAATTTGATTTTTTTATAGGTAAAAACAAGGTTGGAGTATCC
1 GAAAATAGAAAATTTGATTTTTTTAGAGGTAAAAACGAGGTTAGAGTATCC
172548 TTTCGAAGGA
Statistics
Matches: 418, Mismatches: 83, Indels: 72
0.73 0.14 0.13
Matches are distributed among these distances:
79 13 0.03
80 105 0.25
81 203 0.49
82 39 0.09
83 56 0.13
84 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (79 bp):
GAAAATAGAAAATTTGATTTTTTTAGAGGTAAAAACGAGGTTAGAGTATCCCTTCAGAGATGGCG
GGTTAGAGTATCCC
Found at i:177368 original size:33 final size:32
Alignment explanation
Indices: 177308--177371 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
177298 TAATTTAGTG
*
177308 TGTATCGATACTAAGAACATGTATCGATACAA
1 TGTATCGATACAAAGAACATGTATCGATACAA
* *
177340 TGTATGGATACAAAGCAATATGTATCGATACA
1 TGTATCGATACAAAG-AACATGTATCGATACA
177372 TTTAGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAA
Found at i:180416 original size:257 final size:257
Alignment explanation
Indices: 179960--180466 Score: 924
Period size: 257 Copynumber: 2.0 Consensus size: 257
179950 ATCAAAGTCT
* * * * *
179960 TGGACTTGTTTTAATCATAATTTCATACCTGAAAACTAAATTTGCCCTAAGATTGTAGTGTCAAT
1 TGGACTTGTTTTAATCATAATTCCAGACCTGAAAACTAAATTTACCCTAAGATTATAGTGCCAAT
180025 TTAATGAAAATCTTAAATCCAAGCCAATCCTCATTGATTGAGGCTACCTTGAACTTAACTTGGGA
66 TTAATGAAAATCTTAAATCCAAGCCAATCCTCATTGATTGAGGCTACCTTGAACTTAACTTGGGA
180090 AGGTGTTTGAAAATCTGCTTTAAGGCAAACAAGTATGATGATCATGCAAGAACATGATGAACAAC
131 AGGTGTTTGAAAATCTGCTTTAAGGCAAACAAGTATGATGATCATGCAAGAACATGATGAACAAC
* *
180155 ATTCATGGAGGTGCTAGAGATGCTATAAATGCATGAAGCATAGTAAAAATGCATGGAGGTGC
196 ATTCATGGAGGTGCTAGACATACTATAAATGCATGAAGCATAGTAAAAATGCATGGAGGTGC
*
180217 TGGACTTGTTTTAATTATAATTCCAGACCTGAAAACTAAATTTACCCTAAGATTATAGTGCCAAT
1 TGGACTTGTTTTAATCATAATTCCAGACCTGAAAACTAAATTTACCCTAAGATTATAGTGCCAAT
*
180282 TTAATGAAAATCTTAAATCCAAGCTAATCCTCATTGATTGAGGCTACCTTGAACTTAACTTGGGA
66 TTAATGAAAATCTTAAATCCAAGCCAATCCTCATTGATTGAGGCTACCTTGAACTTAACTTGGGA
180347 AGGTGTTTGAAAATCTGCTTTAAGGCAAACAAGTATGATGATCATGCAAGAACATGATGAACAAC
131 AGGTGTTTGAAAATCTGCTTTAAGGCAAACAAGTATGATGATCATGCAAGAACATGATGAACAAC
*
180412 ATTCATGGAGGTGCTGGACATACTATAAATGCATGAAGCATAGTAAAAATGCATG
196 ATTCATGGAGGTGCTAGACATACTATAAATGCATGAAGCATAGTAAAAATGCATG
180467 ATCAAGGTTT
Statistics
Matches: 240, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
257 240 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (257 bp):
TGGACTTGTTTTAATCATAATTCCAGACCTGAAAACTAAATTTACCCTAAGATTATAGTGCCAAT
TTAATGAAAATCTTAAATCCAAGCCAATCCTCATTGATTGAGGCTACCTTGAACTTAACTTGGGA
AGGTGTTTGAAAATCTGCTTTAAGGCAAACAAGTATGATGATCATGCAAGAACATGATGAACAAC
ATTCATGGAGGTGCTAGACATACTATAAATGCATGAAGCATAGTAAAAATGCATGGAGGTGC
Found at i:183651 original size:116 final size:117
Alignment explanation
Indices: 183525--183749 Score: 307
Period size: 116 Copynumber: 1.9 Consensus size: 117
183515 TTATTAATTT
* * * ***
183525 ATTTAAATTAATAAATATTTAAAAATAGAGT-TCATATGATATT-AAT-ACTTTATGGTTAATAA
1 ATTTAAATTAATAAATATTTAAAAATAAAGTCT-AAATAAT-TTAAATGACTTTAAAATTAAT--
183587 AAAATTTTC-TATTTAAATATGTAA-TTTAATTAATTTATTTAAATTTGAATTTAA
62 AAAATTTTCTTATTTAAATATGTAATTTTAATTAATTTATTTAAATTTGAATTTAA
*
183641 ATTTAAATTAATAAATATTTAAAAATAAAGTCTAAATAATTTAAATGACTTTAAAATTAATAAAC
1 ATTTAAATTAATAAATATTTAAAAATAAAGTCTAAATAATTTAAATGACTTTAAAATTAATAAAA
*
183706 TTTTCTTATTTAAATATGTAATTTTTATTAATTTATTTAAATTT
66 TTTTCTTATTTAAATATGTAATTTTAATTAATTTATTTAAATTT
183750 AAATGGGCTA
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
115 10 0.10
116 53 0.55
117 33 0.34
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (117 bp):
ATTTAAATTAATAAATATTTAAAAATAAAGTCTAAATAATTTAAATGACTTTAAAATTAATAAAA
TTTTCTTATTTAAATATGTAATTTTAATTAATTTATTTAAATTTGAATTTAA
Found at i:184653 original size:22 final size:23
Alignment explanation
Indices: 184610--184653 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
184600 AAAAAATTTA
**
184610 AATAATTAGTAAATTATGAATAT
1 AATAATTAGTAAAAGATGAATAT
*
184633 AATAA-TAGTAAAAGATTAATA
1 AATAATTAGTAAAAGATGAATA
184654 ACATAACAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
AATAATTAGTAAAAGATGAATAT
Found at i:184659 original size:22 final size:22
Alignment explanation
Indices: 184634--184702 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
184624 TATGAATATA
*
184634 ATAATAGTAAAAGATTAATAAC
1 ATAAAAGTAAAAGATTAATAAC
*
184656 ATAACAAGTATCAA-ATTAATAAC
1 ATAA-AAGTA-AAAGATTAATAAC
* *
184679 ATAAAAATAAATGATTAATAAC
1 ATAAAAGTAAAAGATTAATAAC
184701 AT
1 AT
184703 GTAAAAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 19 0.49
23 17 0.44
24 2 0.05
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (22 bp):
ATAAAAGTAAAAGATTAATAAC
Found at i:184718 original size:25 final size:22
Alignment explanation
Indices: 184670--184715 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
184660 CAAGTATCAA
184670 ATTAATAACATAAAAATAAATG
1 ATTAATAACATAAAAATAAATG
**
184692 ATTAATAACATGTAAA-AAATG
1 ATTAATAACATAAAAATAAATG
184713 ATT
1 ATT
184716 GATCATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (22 bp):
ATTAATAACATAAAAATAAATG
Found at i:186661 original size:24 final size:24
Alignment explanation
Indices: 186625--186674 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
186615 AAAATTATTA
186625 ATAAAATTTTATTTT-AATAAATT
1 ATAAAATTTTATTTTAAATAAATT
* *
186648 ATAATATTTATATTTTAAATAATTT
1 ATAAAATTT-TATTTTAAATAAATT
186673 AT
1 AT
186675 GTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 6 0.26
25 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAAAATTTTATTTTAAATAAATT
Found at i:187391 original size:2 final size:2
Alignment explanation
Indices: 187384--187409 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
187374 CTACAGGATG
187384 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
187410 GTTACATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:192558 original size:33 final size:33
Alignment explanation
Indices: 192518--192580 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
192508 ATTGGTATAA
*
192518 TTTTA-TTTAAATTATTGTTAAATAATAATAATT
1 TTTTATTTTAAATTATT-ATAAATAATAATAATT
* *
192551 TTTTATTTTAATTTATTATAAATATTAATA
1 TTTTATTTTAAATTATTATAAATAATAATA
192581 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 16 0.62
34 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
TTTTATTTTAAATTATTATAAATAATAATAATT
Found at i:198057 original size:20 final size:19
Alignment explanation
Indices: 198034--198116 Score: 63
Period size: 20 Copynumber: 4.6 Consensus size: 19
198024 ATATCCAGAT
198034 GTATCGATACATTTTGCTTA
1 GTATCGATACA-TTTGCTTA
* *
198054 GTATTGATGCA-TTG--T-
1 GTATCGATACATTTGCTTA
198069 --ATCGATACATATTGCTTA
1 GTATCGATACAT-TTGCTTA
*
198087 GTATCGATACATGTT-CTTT
1 GTATCGATACAT-TTGCTTA
198106 GTATCGATACA
1 GTATCGATACA
198117 CCATAAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
13 7 0.14
15 3 0.06
16 1 0.02
17 1 0.02
18 3 0.06
19 14 0.28
20 21 0.42
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (19 bp):
GTATCGATACATTTGCTTA
Found at i:198111 original size:19 final size:20
Alignment explanation
Indices: 198065--198116 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
198055 TATTGATGCA
198065 TTGTATCGATACATATTGCT
1 TTGTATCGATACATATTGCT
* *
198085 TAGTATCGATACATGTT-CT
1 TTGTATCGATACATATTGCT
198104 TTGTATCGATACA
1 TTGTATCGATACA
198117 CCATAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATATTGCT
Found at i:198814 original size:31 final size:31
Alignment explanation
Indices: 198731--198852 Score: 138
Period size: 31 Copynumber: 3.9 Consensus size: 31
198721 AAGGAGAAAT
* *
198731 GTTCTATCTCAGCTTGTGAAAAGATAGTGAAGAG
1 GTTCTATCTTAGCCTGTGAAAAGATAG-G--GAG
* *
198765 GTTCTATTTTATCCTGTGAAAAGATAGGGAG
1 GTTCTATCTTAGCCTGTGAAAAGATAGGGAG
* *
198796 GTTCCATCTTAGCTTGTGAAAAGATAGGGAG
1 GTTCTATCTTAGCCTGTGAAAAGATAGGGAG
* *
198827 ATTCTATCTTAGCCT-TCAAAAGATAG
1 GTTCTATCTTAGCCTGTGAAAAGATAG
198853 TGCTGTAAGG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
30 10 0.13
31 42 0.55
33 1 0.01
34 23 0.30
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (31 bp):
GTTCTATCTTAGCCTGTGAAAAGATAGGGAG
Found at i:200481 original size:21 final size:20
Alignment explanation
Indices: 200430--200481 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
200420 AAGTGAACTA
* *
200430 GAAGAGAAAATAAATGAGTT
1 GAAGAAAAAAGAAATGAGTT
*
200450 GAAAAAGAAAAGAAATGAGTT
1 GAAGAA-AAAAGAAATGAGTT
200471 GCAAGAAAAAA
1 G-AAGAAAAAA
200482 TGATGAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.23, T:0.13
Consensus pattern (20 bp):
GAAGAAAAAAGAAATGAGTT
Found at i:202820 original size:32 final size:32
Alignment explanation
Indices: 202784--202850 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
202774 TCATAATGAG
*
202784 TCAGATTTCATGCCAATATCAAATGCCAGACT
1 TCAGACTTCATGCCAATATCAAATGCCAGACT
*
202816 TCAGACTTCATGCCAATATCAAATGCTAGACT
1 TCAGACTTCATGCCAATATCAAATGCCAGACT
202848 TCA
1 TCA
202851 AAATTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (32 bp):
TCAGACTTCATGCCAATATCAAATGCCAGACT
Found at i:203857 original size:19 final size:18
Alignment explanation
Indices: 203829--203891 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
203819 AAATCGTAAC
*
203829 TGTATTGATACATAAGTGT
1 TGTATCGATACATAAGT-T
203848 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
203861 TGTATCGATATATAAGTTT
1 TGTATCGATACATAAG-TT
203880 TGTATCGATACA
1 TGTATCGATACA
203892 ATGTATCGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:203876 original size:32 final size:32
Alignment explanation
Indices: 203829--203899 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
203819 AAATCGTAAC
*
203829 TGTATTGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
203861 TGTATCGATATATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
203893 TGTATCG
1 TGTATCG
203900 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:209896 original size:30 final size:30
Alignment explanation
Indices: 209862--209959 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
209852 TATATCGATA
209862 CATTGAGTCCAACGGCTAGAATTTCAAATG
1 CATTGAGTCCAACGGCTAGAATTTCAAATG
* ** * *
209892 CATTGTA-TCGATAC-ATTATGAATTAT-ATCGATA
1 CATTG-AGTCCA-ACGGCTA-GAATT-TCA--AATG
209925 CATTGAGTCCAACGGCTAGAATTTCAAATG
1 CATTGAGTCCAACGGCTAGAATTTCAAATG
209955 CATTG
1 CATTG
209960 TATCGATACA
Statistics
Matches: 49, Mismatches: 10, Indels: 18
0.64 0.13 0.23
Matches are distributed among these distances:
30 17 0.35
31 10 0.20
32 10 0.20
33 12 0.24
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (30 bp):
CATTGAGTCCAACGGCTAGAATTTCAAATG
Found at i:209908 original size:63 final size:63
Alignment explanation
Indices: 209830--209992 Score: 326
Period size: 63 Copynumber: 2.6 Consensus size: 63
209820 AACGGCTATA
209830 ATTGTATCGATACATTATGAATTATATCGATACATTGAGTCCAACGGCTAGAATTTCAAATGC
1 ATTGTATCGATACATTATGAATTATATCGATACATTGAGTCCAACGGCTAGAATTTCAAATGC
209893 ATTGTATCGATACATTATGAATTATATCGATACATTGAGTCCAACGGCTAGAATTTCAAATGC
1 ATTGTATCGATACATTATGAATTATATCGATACATTGAGTCCAACGGCTAGAATTTCAAATGC
209956 ATTGTATCGATACATTATGAATTATATCGATACATTG
1 ATTGTATCGATACATTATGAATTATATCGATACATTG
209993 GAGTGTGTAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 100 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (63 bp):
ATTGTATCGATACATTATGAATTATATCGATACATTGAGTCCAACGGCTAGAATTTCAAATGC
Found at i:210485 original size:31 final size:31
Alignment explanation
Indices: 210405--210529 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
210395 GATAGGGAGA
*
210405 AAGGTTCTATCTTAGCCTGTTAAAAGATAGTG
1 AAGGTTCTATCTTAGCCTGTAAAAAGATAG-G
* * *
210437 AAGATGTTCTATTTTAGCCCGTGAAAAGATAGG
1 AAG--GTTCTATCTTAGCCTGTAAAAAGATAGG
*
210470 AAGGTTCTATCTTAGCCTATAAAAAGATAGG
1 AAGGTTCTATCTTAGCCTGTAAAAAGATAGG
* * * *
210501 GAGGTTTTATCTTAGCAT-TCAAAAGATAG
1 AAGGTTCTATCTTAGCCTGTAAAAAGATAG
210530 TGTTGTAAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
30 10 0.12
31 39 0.49
32 3 0.04
33 4 0.05
34 24 0.30
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (31 bp):
AAGGTTCTATCTTAGCCTGTAAAAAGATAGG
Found at i:214660 original size:17 final size:18
Alignment explanation
Indices: 214640--214679 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
214630 ACACTTTTTA
214640 AATTATAATT-AAATAAT
1 AATTATAATTAAAATAAT
*
214657 AATTA-ATTTAAAATAAT
1 AATTATAATTAAAATAAT
214674 AATTAT
1 AATTAT
214680 TTGAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATAATTAAAATAAT
Found at i:215526 original size:17 final size:18
Alignment explanation
Indices: 215485--215528 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
215475 ATACTCAATT
*
215485 TAAAATTTAATTATTTATA
1 TAAAATTTAA-TATTTAAA
*
215504 TCAAATTTAA-ATTTAAA
1 TAAAATTTAATATTTAAA
215521 TAAAATTT
1 TAAAATTT
215529 TTTAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAATTTAATATTTAAA
Found at i:215564 original size:21 final size:20
Alignment explanation
Indices: 215540--215597 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
215530 TTAATATTAA
215540 TTTAAAATAATAAAAATATAT
1 TTTAAAATAAT-AAAATATAT
215561 TTTAAAATAATAAAATATA-
1 TTTAAAATAATAAAATATAT
* * *
215580 ATTAAATTTATAAAATAT
1 TTTAAAATAATAAAATAT
215598 TTAAGTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 15 0.44
20 8 0.24
21 11 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAAATAATAAAATATAT
Found at i:215632 original size:15 final size:15
Alignment explanation
Indices: 215571--215656 Score: 64
Period size: 15 Copynumber: 5.3 Consensus size: 15
215561 TTTAAAATAA
*
215571 TAAAATATAATTAAATT
1 TAAAA-ATATTTAAA-T
*
215588 TATAAAATATTTAAGT
1 TA-AAAATATTTAAAT
215604 TAAATATTAATATTTAAAT
1 T-AA-A--AATATTTAAAT
* *
215623 TTAAAATATTTAACT
1 TAAAAATATTTAAAT
*
215638 TAAAAATAATTAAAT
1 TAAAAATATTTAAAT
215653 TAAA
1 TAAA
215657 CTCGTAAGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
15 26 0.46
16 3 0.05
17 12 0.21
18 4 0.07
19 11 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
TAAAAATATTTAAAT
Found at i:215645 original size:36 final size:37
Alignment explanation
Indices: 215581--215650 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 37
215571 TAAAATATAA
*
215581 TTAAATTTATAAAATATTTAAGTTAAAT-ATTAATAT
1 TTAAATTTATAAAATATTTAACTTAAATAATTAATAT
215617 TTAAA-TT-TAAAATATTTAACTTAAAAATAATTAA
1 TTAAATTTATAAAATATTTAACTT--AAATAATTAA
215651 ATTAAACTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 14 0.47
35 2 0.07
36 9 0.30
37 5 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
TTAAATTTATAAAATATTTAACTTAAATAATTAATAT
Found at i:216593 original size:13 final size:13
Alignment explanation
Indices: 216575--216599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
216565 TGCTAACTTT
216575 CTTTTCTTTTTTC
1 CTTTTCTTTTTTC
216588 CTTTTCTTTTTT
1 CTTTTCTTTTTT
216600 TTTTGGTTGA
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTCTTTTTTC
Found at i:220293 original size:20 final size:20
Alignment explanation
Indices: 220268--220305 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
220258 AAAGGCTTGT
220268 AATCTATACGTTGTGGAGTC
1 AATCTATACGTTGTGGAGTC
220288 AATCTATACGTTGTGGAG
1 AATCTATACGTTGTGGAG
220306 CCTAACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (20 bp):
AATCTATACGTTGTGGAGTC
Found at i:222712 original size:2 final size:2
Alignment explanation
Indices: 222707--222743 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
222697 CTCAGCAACT
222707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
222744 TCTCTCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:223143 original size:13 final size:13
Alignment explanation
Indices: 223111--223149 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
223101 ACCTGATTAC
223111 AAATTAAATTAAA
1 AAATTAAATTAAA
** *
223124 ATTTTAATTTAAA
1 AAATTAAATTAAA
223137 AAATTAAATTAAA
1 AAATTAAATTAAA
223150 TTGAATATTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAAATTAAA
Found at i:223355 original size:22 final size:22
Alignment explanation
Indices: 223317--223358 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
223307 AAAAAAACAT
*
223317 AATAATATAATTAAACAATAGC
1 AATAATAAAATTAAACAATAGC
223339 AATAGATAAAATT-AACAATA
1 AATA-ATAAAATTAAACAATA
223359 ATAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (22 bp):
AATAATAAAATTAAACAATAGC
Found at i:223364 original size:22 final size:22
Alignment explanation
Indices: 223315--223368 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
223305 AAAAAAAAAC
*
223315 ATAATAATATAATTAAACAATA
1 ATAATAATAAAATTAAACAATA
**
223337 GCAATAGATAAAATT-AACAATA
1 ATAATA-ATAAAATTAAACAATA
223359 ATAAT-ATAAA
1 ATAATAATAAA
223369 TAAAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 5 0.19
22 14 0.54
23 7 0.27
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (22 bp):
ATAATAATAAAATTAAACAATA
Found at i:224237 original size:17 final size:17
Alignment explanation
Indices: 224215--224249 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
224205 GAGATAAAAT
*
224215 AAATAATTATATTAAAG
1 AAATAATCATATTAAAG
*
224232 AAATAATCATATTTAAG
1 AAATAATCATATTAAAG
224249 A
1 A
224250 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (17 bp):
AAATAATCATATTAAAG
Found at i:224685 original size:25 final size:29
Alignment explanation
Indices: 224652--224709 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
224642 TTTATGTTAA
224652 AAAT-TTATTT-A-TATAAATTAAAAATT
1 AAATATTATTTGAGTATAAATTAAAAATT
224678 AAATTATTATTTGAGTATAAATTAAAAATT
1 AAA-TATTATTTGAGTATAAATTAAAAATT
224708 AA
1 AA
224710 TAATTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 3 0.11
27 1 0.04
28 6 0.21
29 1 0.04
30 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
AAATATTATTTGAGTATAAATTAAAAATT
Found at i:225278 original size:14 final size:13
Alignment explanation
Indices: 225255--225297 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
225245 ATTTTGATAT
225255 TTTTATTTATTCATA
1 TTTTA-TTATT-ATA
225270 TTTTATTATTATTA
1 TTTTATTATTA-TA
*
225284 TTTTTTTATTATA
1 TTTTATTATTATA
225297 T
1 T
225298 CTTAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.15
14 17 0.65
15 5 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATTATTATA
Found at i:226851 original size:20 final size:20
Alignment explanation
Indices: 226818--226855 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
226808 TGCAAAAAAT
226818 ATAAAATATAAATTTTATAC
1 ATAAAATATAAATTTTATAC
* *
226838 ATAAATTATTAATTTTAT
1 ATAAAATATAAATTTTAT
226856 TCCCGATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAATATAAATTTTATAC
Found at i:232098 original size:13 final size:13
Alignment explanation
Indices: 232080--232105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232070 CAATTTTTTG
232080 TGTATCGATACAT
1 TGTATCGATACAT
232093 TGTATCGATACAT
1 TGTATCGATACAT
232106 ACTTGCTGTA
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:232170 original size:21 final size:21
Alignment explanation
Indices: 232144--232219 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
232134 CTGCCAAGAA
*
232144 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
232165 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
232185 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
232206 ATGTATCGATACAT
1 ATGTATCGATACAT
232220 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:232190 original size:20 final size:20
Alignment explanation
Indices: 232165--232237 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
232155 CATCTTTTTT
232165 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
232185 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
232206 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
232226 ATGTATCGATAC
1 ATGTATCGATAC
232238 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:232201 original size:41 final size:41
Alignment explanation
Indices: 232144--232237 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
232134 CTGCCAAGAA
*
232144 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
232185 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
232226 ATGTATCGATAC
1 ATGTATCGATAC
232238 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:232898 original size:33 final size:33
Alignment explanation
Indices: 232858--232922 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
232848 CCCGTTTATT
232858 AAAAAATCTCCCCCTTAATCAAGTAATTCATAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCATAA
232891 AAAAAATCTCCCCCTTAATCAAGTAATTCATA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCATA
232923 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (33 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCATAA
Found at i:234731 original size:13 final size:13
Alignment explanation
Indices: 234713--234751 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
234703 ATAATCACCT
*
234713 TGTATCGATACAG
1 TGTATCGATACAA
234726 TGTATCGATACAA
1 TGTATCGATACAA
234739 TGTATCGATACAA
1 TGTATCGATACAA
234752 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234762 original size:20 final size:20
Alignment explanation
Indices: 234737--234815 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
234727 GTATCGATAC
234737 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
234757 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
234782 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
234802 CATGTATCGATACA
1 AATGTATCGATACA
234816 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:236807 original size:15 final size:15
Alignment explanation
Indices: 236787--236817 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
236777 ATTTCGTTTG
*
236787 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
236802 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
236817 G
1 G
236818 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:240897 original size:13 final size:13
Alignment explanation
Indices: 240879--240904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
240869 CAATTTTTTA
240879 TGTATCGATACAT
1 TGTATCGATACAT
240892 TGTATCGATACAT
1 TGTATCGATACAT
240905 ACTTGCTGTA
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:240969 original size:21 final size:21
Alignment explanation
Indices: 240943--241018 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
240933 CTGCCAAGAA
*
240943 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
240964 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
240984 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
241005 ATGTATCGATACAT
1 ATGTATCGATACAT
241019 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:240989 original size:20 final size:20
Alignment explanation
Indices: 240964--241036 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
240954 CATCTTTTTT
240964 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
240984 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
241005 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
241025 ATGTATCGATAC
1 ATGTATCGATAC
241037 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:241000 original size:41 final size:41
Alignment explanation
Indices: 240943--241036 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
240933 CTGCCAAGAA
*
240943 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
240984 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
241025 ATGTATCGATAC
1 ATGTATCGATAC
241037 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:241749 original size:4 final size:4
Alignment explanation
Indices: 241732--241792 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
241722 TTGGCTTATA
* * * * *
241732 ACAT ACAT AAAT ACAT ACAT ACAT ACAT ATAC ATAT ACAT AAAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
241780 ACAT ACAT ACAT A
1 ACAT ACAT ACAT A
241793 TACATATACA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:241765 original size:6 final size:6
Alignment explanation
Indices: 241754--241824 Score: 70
Period size: 6 Copynumber: 11.5 Consensus size: 6
241744 ACATACATAC
* * *
241754 ATACAT ATACAT ATACAT AAATACAT ACATAC ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT --ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
241804 ATATAT ATATAT ATATAT ATA
1 ATACAT ATACAT ATACAT ATA
241825 TAGACGCACA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 50 0.89
8 6 0.11
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
ATACAT
Found at i:241771 original size:32 final size:32
Alignment explanation
Indices: 241734--241804 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
241724 GGCTTATAAC
241734 ATACATAAATACATACATACATACATATACAT
1 ATACATAAATACATACATACATACATATACAT
241766 ATACATAAATACATACATACATACATATACAT
1 ATACATAAATACATACATACATACATATACAT
241798 ATACATA
1 ATACATA
241805 TATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (32 bp):
ATACATAAATACATACATACATACATATACAT
Found at i:241807 original size:8 final size:8
Alignment explanation
Indices: 241734--241824 Score: 74
Period size: 8 Copynumber: 11.4 Consensus size: 8
241724 GGCTTATAAC
*
241734 ATACATAA
1 ATACATAT
*
241742 ATACATAC
1 ATACATAT
*
241750 ATACATAC
1 ATACATAT
* *
241758 ATATACAT
1 ATACATAT
*
241766 ATACATAA
1 ATACATAT
*
241774 ATACATAC
1 ATACATAT
*
241782 ATACATAC
1 ATACATAT
* *
241790 ATATACAT
1 ATACATAT
241798 ATACATAT
1 ATACATAT
*
241806 ATATATAT
1 ATACATAT
*
241814 ATATATAT
1 ATACATAT
241822 ATA
1 ATA
241825 TAGACGCACA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 69 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (8 bp):
ATACATAT
Found at i:241809 original size:4 final size:4
Alignment explanation
Indices: 241758--241826 Score: 57
Period size: 4 Copynumber: 17.2 Consensus size: 4
241748 ACATACATAC
* * * * * * * * *
241758 ATAT ACAT ATAC ATAA ATAC ATAC ATAC ATAC ATAT ACAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
241806 ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT A
241827 GACGCACACA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (4 bp):
ATAT
Found at i:242067 original size:31 final size:31
Alignment explanation
Indices: 242032--242093 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
242022 ACAAACTTAA
242032 TTTCTAAATTTTAACATTATCCTATATATAG
1 TTTCTAAATTTTAACATTATCCTATATATAG
242063 TTTCTAAATTTTAACATTATCCTATATATAG
1 TTTCTAAATTTTAACATTATCCTATATATAG
242094 AAGATACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCTAAATTTTAACATTATCCTATATATAG
Found at i:242185 original size:21 final size:22
Alignment explanation
Indices: 242161--242202 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
242151 ACCTGGAATG
242161 GATCAATCTTTT-TTATAAAAT
1 GATCAATCTTTTCTTATAAAAT
* *
242182 GATCTATCTTTTCTTGTAAAA
1 GATCAATCTTTTCTTATAAAA
242203 ATAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (22 bp):
GATCAATCTTTTCTTATAAAAT
Found at i:242363 original size:2 final size:2
Alignment explanation
Indices: 242269--242347 Score: 83
Period size: 2 Copynumber: 40.0 Consensus size: 2
242259 AATAAAAATG
* * *
242269 AT AT AT AT AT AT AA AT AT -T AT ACT -T AT AT GT AT AT AT AGT AA
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
*
242311 AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242348 TCGAAATGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
1 3 0.05
2 60 0.91
3 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:248638 original size:115 final size:116
Alignment explanation
Indices: 248431--248665 Score: 445
Period size: 115 Copynumber: 2.0 Consensus size: 116
248421 ATCAAGTGAT
248431 ACAAGGTTTTTCTTTATGTTAGTAGTATGACGAATAGTTATCAAGTAATGGATGAAGCCTAGGAG
1 ACAAGGTTTTTCTTTATGTTAGTAGTATGACGAATAGTTATCAAGTAATGGATGAAGCCTAGGAG
248496 ATGCAAATCTCTGATGCTTGGAATCTTCAATAATAGTGTACCCAT-TCGAC
66 ATGCAAATCTCTGATGCTTGGAATCTTCAATAATAGTGTACCCATGTCGAC
248546 ACAAGGTTTTTCTTTATGTTAGTAGTATGACGAATAGTTATCAAGTAATGGATGAAGCCTAGGAG
1 ACAAGGTTTTTCTTTATGTTAGTAGTATGACGAATAGTTATCAAGTAATGGATGAAGCCTAGGAG
* *
248611 ATGCAAATCTCTGATGCTTGGACTCTTCAATAATGGTGTACCCATGTCGAC
66 ATGCAAATCTCTGATGCTTGGAATCTTCAATAATAGTGTACCCATGTCGAC
248662 ACAA
1 ACAA
248666 CACAATCTTT
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
115 108 0.92
116 9 0.08
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (116 bp):
ACAAGGTTTTTCTTTATGTTAGTAGTATGACGAATAGTTATCAAGTAATGGATGAAGCCTAGGAG
ATGCAAATCTCTGATGCTTGGAATCTTCAATAATAGTGTACCCATGTCGAC
Found at i:255337 original size:20 final size:20
Alignment explanation
Indices: 255292--255345 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
255282 TAATATTATC
*
255292 TTTATATTAATATTAAAAAA
1 TTTATATAAATATTAAAAAA
* *
255312 TATTATATAAATTTTAAAATA
1 T-TTATATAAATATTAAAAAA
*
255333 TTTATATATATAT
1 TTTATATAAATAT
255346 ATATTATATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATATAAATATTAAAAAA
Found at i:255342 original size:2 final size:2
Alignment explanation
Indices: 255330--255382 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
255320 AAATTTTAAA
*
255330 AT AT TT AT AT AT AT AT AT AT -T AT AT CAT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
255371 AT AT AT AT AT AT
1 AT AT AT AT AT AT
255383 TAATTAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:256123 original size:14 final size:14
Alignment explanation
Indices: 256104--256133 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
256094 ATTTTATAAG
*
256104 TATTTTTAAATTTT
1 TATTTTTAAATATT
256118 TATTTTTAAATATT
1 TATTTTTAAATATT
256132 TA
1 TA
256134 ATATATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTAAATATT
Found at i:257646 original size:18 final size:17
Alignment explanation
Indices: 257622--257672 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
257612 GTTTTTTATC
*
257622 TTTTTTTTTTAATTTCA
1 TTTTTTTTTGAATTTCA
*
257639 TATTTTTTTTGAATTTCC
1 T-TTTTTTTTGAATTTCA
257657 TTTTTTTTTGGAATTT
1 TTTTTTTTT-GAATTT
257673 TATAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTTTTTTGAATTTCA
Found at i:258575 original size:19 final size:18
Alignment explanation
Indices: 258549--258587 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
258539 TCCTTCAAGG
* *
258549 TTATTTTCTTTTCTTTTT
1 TTATTTTCTTGTATTTTT
258567 TTATCTTTCTTGTATTTTT
1 TTAT-TTTCTTGTATTTTT
258586 TT
1 TT
258588 TTGTCTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.08, C:0.10, G:0.03, T:0.79
Consensus pattern (18 bp):
TTATTTTCTTGTATTTTT
Found at i:258628 original size:18 final size:17
Alignment explanation
Indices: 258605--258639 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
258595 TGTTATTAAC
*
258605 AAATTTTTGTTTTTTTTA
1 AAATTTTT-TTGTTTTTA
258623 AAATTTTTTTGTTTTTA
1 AAATTTTTTTGTTTTTA
258640 CCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
AAATTTTTTTGTTTTTA
Found at i:260314 original size:27 final size:28
Alignment explanation
Indices: 260253--260323 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
260243 AAACAAGCCT
*
260253 CCATATTTGACAAATC-CAAAAGAAACCA
1 CCATTTTTGACAAA-CACAAAAGAAACCA
* *
260281 CTATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
260308 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
260324 AATGGATGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:263192 original size:22 final size:23
Alignment explanation
Indices: 263160--263208 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
263150 AAACTCTAAT
*
263160 TATTTGTTAATTGTTAATAAACA
1 TATTTGTTAATTATTAATAAACA
**
263183 TATTT-TTAATTATTTGTAAACA
1 TATTTGTTAATTATTAATAAACA
263205 TATT
1 TATT
263209 CGATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (23 bp):
TATTTGTTAATTATTAATAAACA
Found at i:268317 original size:78 final size:78
Alignment explanation
Indices: 268040--268319 Score: 284
Period size: 79 Copynumber: 3.6 Consensus size: 78
268030 ATTTTTCATC
* * *
268040 TTGGGG-ATACTCTAACCCTAGTTTTATTTCTAAAATATCGATTTTCAACTATCGGGGATACTCT
1 TTGGGGAATACTCCAACCCTAGTTTTATTTCTAAAGTATCGATTTTCCACTATCGGGGATACTCT
*
268104 AACCCTATTATTT
66 AACCCCATTATTT
* ** * **
268117 TTGCGGAGATACTCCAACCCCGGTTTTATTGTCAAAACGT-T-GATTTTCCACCGTCGGGGATAC
1 TTGGGGA-ATACTCCAACCCTAGTTTTATT-TCTAAA-GTATCGATTTTCCACTATCGGGGATAC
*
268180 TCCAACCCCATTATTT
63 TCTAACCCCATTATTT
* *** * * * *
268196 TCGGGGGGGACTCCAACTCC-AATTTTATTTCTGAAA-CACCGA-TTTCCATTATCGGGGATACT
1 TTGGGGAATACTCCAAC-CCTAGTTTTATTTCT-AAAGTATCGATTTTCCACTATCGGGGATACT
268258 CTAACCCCATTATTT
64 CTAACCCCATTATTT
*
268273 TTGAGGGAATACTCCAACCCTGGTTTTATTTCTAAAGTATCGATTTT
1 TTG-GGGAATACTCCAACCCTAGTTTTATTTCTAAAGTATCGATTTT
268320 TCACAACATC
Statistics
Matches: 158, Mismatches: 33, Indels: 22
0.74 0.15 0.10
Matches are distributed among these distances:
77 45 0.28
78 45 0.28
79 61 0.39
80 6 0.04
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (78 bp):
TTGGGGAATACTCCAACCCTAGTTTTATTTCTAAAGTATCGATTTTCCACTATCGGGGATACTCT
AACCCCATTATTT
Found at i:281951 original size:19 final size:18
Alignment explanation
Indices: 281927--282021 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
281917 AGCGATACAT
281927 TGTATCGATACAATACTTA
1 TGTATCGATACAA-ACTTA
281946 TGTATCGATAC--A-TTA
1 TGTATCGATACAAACTTA
281961 --TATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
* *
281978 TATATTGATAC--A--T-
1 TGTATCGATACAAACTTA
281991 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
282010 TGTATCGATACA
1 TGTATCGATACA
282022 GTTACTTGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
13 18 0.30
14 1 0.02
15 3 0.05
16 4 0.07
17 3 0.05
18 1 0.02
19 31 0.51
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:281955 original size:32 final size:32
Alignment explanation
Indices: 281919--282021 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
281909 AGCTTCATAG
*
281919 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
281951 CGATACATTATATCGATACAACACTTATATAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
281983 TGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
282015 CGATACA
1 CGATACA
282022 GTTACTTGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:285518 original size:61 final size:61
Alignment explanation
Indices: 285365--285790 Score: 469
Period size: 61 Copynumber: 7.0 Consensus size: 61
285355 ACGCAGGACA
* * * * * ** * *
285365 TCTTTTCCTTTTAACGGCCACACAAGTTGGTAGCACCTTTTAGTCCTTGAAGAGTAGAACACT-
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAG--GA-TG
* * * * *
285428 TCTTTT-CTGTTAAAGCCTACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAACAGGATG
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGATG
* * * * * *
285488 CCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACTTTTCAATTCTCAAAAAGTAGGATG
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGATG
* * *
285549 TTTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTCATTTCTCAAAGAGCAGGATG
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGATG
* * * * *
285610 TCTTTTCCTTTTAAAGCCCACATAAATCGGTGGTACCTTTCAGTCCTCAAAGAGCAGGATG
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGATG
* * * * *
285671 CCTTTTCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAATTCTCAAAGTGCAAGATG
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGATG
* * * * *
285732 TCTTTTCCTTTCAAAGCTCACACAATTTGGTGGCACCTTTTAGTTCGCAAAGAGCAGGA
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGA
285791 CACTTCTTTT
Statistics
Matches: 303, Mismatches: 58, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
59 1 0.00
60 6 0.02
61 251 0.83
62 39 0.13
63 6 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (61 bp):
TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCTCAAAGAGCAGGATG
Found at i:285676 original size:183 final size:182
Alignment explanation
Indices: 285365--285800 Score: 541
Period size: 183 Copynumber: 2.4 Consensus size: 182
285355 ACGCAGGACA
* * * ** * *
285365 TCTTTTCCTTTTAACGGCCACACAAGTTGGTAGCACCTTTTAGTCCTTGAAGAGTAGAACACTTC
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTTAGTTCTCAAAGAGCAG--GACTTC
* * *
285430 TTTTCTGTTAAAGCCTACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAACAGGATGCCTTTTC
64 TTTTCTGTTAAAGCCCACACAAATCGGTGGCACATTTCAGTCCTCAAAGAACAGGATGCCTTTTC
* * * *
285495 CTTTTAAAGCCCATACAAGTTGGTGGCACTTTTCAATTCTCAAAAAGTAGGATG
129 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATTCTCAAAAAGCAAGATG
* * *
285549 TTTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTCATTTCTCAAAGAGCAGGA-TGTCT
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTTAGTTCTCAAAGAGCAGGACT-TCT
* * * * *
285613 TTTCCTTTTAAAGCCCACATAAATCGGTGGTACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTC
65 TTT-CTGTTAAAGCCCACACAAATCGGTGGCACATTTCAGTCCTCAAAGAACAGGATGCCTTTTC
* **
285678 CTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAATTCTCAAAGTGCAAGATG
129 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATTCTCAAAAAGCAAGATG
* * * * *
285732 TCTTTTCCTTTCAAAGCTCACACAATTTGGTGGCACCTTTTAGTTCGCAAAGAGCAGGACACTTC
1 TCTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTTAGTTCTCAAAGAGCAGG--ACTTC
285797 TTTT
64 TTTT
285801 TCTTTTTTTA
Statistics
Matches: 214, Mismatches: 33, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
181 1 0.00
182 7 0.03
183 150 0.70
184 48 0.22
185 7 0.03
186 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (182 bp):
TCTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTTAGTTCTCAAAGAGCAGGACTTCTT
TTCTGTTAAAGCCCACACAAATCGGTGGCACATTTCAGTCCTCAAAGAACAGGATGCCTTTTCCT
TTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATTCTCAAAAAGCAAGATG
Found at i:286447 original size:28 final size:27
Alignment explanation
Indices: 286408--286463 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
286398 GTATCGATAC
286408 ATTCTGGTTTTACCTAGATGCATCGAT
1 ATTCTGGTTTTACCTAGATGCATCGAT
*
286435 ATTCTAGGTTTTACCTAGATGTATCGAT
1 ATTCT-GGTTTTACCTAGATGCATCGAT
286463 A
1 A
286464 CATTTTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (27 bp):
ATTCTGGTTTTACCTAGATGCATCGAT
Found at i:286505 original size:49 final size:49
Alignment explanation
Indices: 286435--286588 Score: 168
Period size: 49 Copynumber: 3.1 Consensus size: 49
286425 ATGCATCGAT
* *
286435 ATTCTAGGTTTTACC-TAGATGTATCGATACATTTTTCATTGTATCGATAC
1 ATTCT-GGTTTTACCAT-GATGTATCGATACATTTCTCAATGTATCGATAC
* **
286485 ATTCTGGTGTTACCATGATGTATTAATACATTTCTCAATGTATCGATAC
1 ATTCTGGTTTTACCATGATGTATCGATACATTTCTCAATGTATCGATAC
* * * *
286534 ATTTTGAGTTTTAACCCA-GATTTATCGATACATTTCTCAATGTATTGATAA
1 ATTCTG-GTTTT-A-CCATGATGTATCGATACATTTCTCAATGTATCGATAC
286585 ATTC
1 ATTC
286589 AGGCATTTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
49 42 0.48
50 10 0.11
51 32 0.37
52 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (49 bp):
ATTCTGGTTTTACCATGATGTATCGATACATTTCTCAATGTATCGATAC
Found at i:289078 original size:79 final size:77
Alignment explanation
Indices: 288895--289177 Score: 296
Period size: 79 Copynumber: 3.6 Consensus size: 77
288885 TTTTCATCTT
* * * * * *
288895 GGGGATATTCTAACCCCAGTTTTATTTCTAAAATATTGATTTTTCACCATCGGGGATACTCTACC
1 GGGGATACTCTAA-CCCAGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAAC
* *
288960 CCGTTATTTTCGC
65 CTGTTATTTTCGA
** * * * *
288973 CAGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTTTCCACCATCGGGGATACTCCAAT
1 GGGGATACTCTAACCCAG-TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAA-
* **
289038 CCTATTATTTTTAA
64 CCTGTTATTTTCGA
* * * *
289052 GGGGATACTCTAACCCTAGTTTTATTTCTAAAACATCGATTTTCAATCATCAGGGATACTCTAAC
1 GGGGATACTCTAACCC-AGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAAC
289117 CTTGTTATTTTCGA
65 C-TGTTATTTTCGA
* **
289131 GGGGATACTCCAACTCCAGTTTTATTTCTAAATTATCGATTTTCCAC
1 GGGGATACTCTAAC-CCAGTTTTATTTCTAAAACATCGATTTTCCAC
289178 AACATCGATT
Statistics
Matches: 165, Mismatches: 35, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
77 4 0.02
78 49 0.30
79 109 0.66
80 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (77 bp):
GGGGATACTCTAACCCAGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACC
TGTTATTTTCGA
Found at i:289249 original size:95 final size:94
Alignment explanation
Indices: 289083--289271 Score: 240
Period size: 95 Copynumber: 2.0 Consensus size: 94
289073 TTATTTCTAA
* * *** *
289083 AACATCGATTTTCAATCATCAGGGATACTCTAACCTTGTTATTTTCGAGGGGATACTCCAACTCC
1 AACATCGATTTTCAATAATCAGGGATACTCCAACCCCCTTATTTTCGAAGGGATACTCCAAC-CC
*
289148 AGTTTTATTTCT-AAATTATCGATTTTCCAC
65 AGTTTTATTTCTCAAA-CATCGATTTTCCAC
*
289178 AACATCGATTTTTC-ATAATCAGGGATACTCCAACCCCCTTATTTTTGAAGGGATACTCCAA-CC
1 AACATCGA-TTTTCAATAATCAGGGATACTCCAACCCCCTTATTTTCGAAGGGATACTCCAACCC
289241 ATGATTTTATTTCTCAAACATCGATTTTCCA
65 A-G-TTTTATTTCTCAAACATCGATTTTCCA
289272 TCATTGGGGA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
93 3 0.04
94 1 0.01
95 70 0.85
96 8 0.10
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (94 bp):
AACATCGATTTTCAATAATCAGGGATACTCCAACCCCCTTATTTTCGAAGGGATACTCCAACCCA
GTTTTATTTCTCAAACATCGATTTTCCAC
Found at i:289343 original size:51 final size:51
Alignment explanation
Indices: 289227--289345 Score: 193
Period size: 51 Copynumber: 2.3 Consensus size: 51
289217 TATTTTTGAA
** *
289227 GGGATACTCCAACCATGATTTTATTTCTCAAACATCGATTTTCCATCATTG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCATCATTG
*
289278 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCATGATTG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCATCATTG
*
289329 GGGTTACTCCAACCCCG
1 GGGATACTCCAACCCCG
289346 TAACCCTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCATCATTG
Found at i:289542 original size:23 final size:22
Alignment explanation
Indices: 289511--289559 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
289501 CGTCCCTCCT
** *
289511 TTTTATGTATTTTTGTGTATTTA
1 TTTTATGTAAATTTGTCTA-TTA
*
289534 TTTTGTGTAAATTTGTCTATTA
1 TTTTATGTAAATTTGTCTATTA
289556 TTTT
1 TTTT
289560 CTTTTTTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.18, C:0.02, G:0.12, T:0.67
Consensus pattern (22 bp):
TTTTATGTAAATTTGTCTATTA
Found at i:290286 original size:24 final size:23
Alignment explanation
Indices: 290249--290294 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
290239 ACAACTATCG
*
290249 TTATTTTTAATTATATTATTAAAT
1 TTATTATTAATTAT-TTATTAAAT
* *
290273 TTATTATTATTTATTTTTTAAA
1 TTATTATTAATTATTTATTAAA
290295 AATAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTATTAATTATTTATTAAAT
Found at i:293802 original size:52 final size:51
Alignment explanation
Indices: 293684--293822 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 51
293674 TTTGGAATGA
** * * *
293684 AAATGTATTAATACATTTTTCATTATATCGATACATTCTAGGTTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTATAGGTTTTGACCC
* * *
293735 AAATGTATCGATACATTCTTCATTGTATTGATACATTATGGGTTTCTGACCT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTATAGGTTT-TGACCC
*
293787 AAATGTATCGATACATTCCTC-TATGTATCGATACAT
1 AAATGTATCGATACATTCTTCAT-TGTATCGATACAT
293823 GTGGGCAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
51 39 0.51
52 37 0.49
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (51 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTATAGGTTTTGACCC
Found at i:296308 original size:96 final size:96
Alignment explanation
Indices: 296183--296360 Score: 338
Period size: 96 Copynumber: 1.9 Consensus size: 96
296173 CATTCATCTG
*
296183 AGGGGATACTTTAAACTTGCTTTTAAACTTGTCAAGATTTAAATCTTAATTTTACACAAATTGTC
1 AGGGGATACTCTAAACTTGCTTTTAAACTTGTCAAGATTTAAATCTTAATTTTACACAAATTGTC
296248 ACTTTGGGGACACTCCAACCCTATTTATCCA
66 ACTTTGGGGACACTCCAACCCTATTTATCCA
296279 AGGGGATACTCTAAACTTGCTTTTAAACTTGTCAAGATTTAAATCTTAATTTTACACAAATTGTC
1 AGGGGATACTCTAAACTTGCTTTTAAACTTGTCAAGATTTAAATCTTAATTTTACACAAATTGTC
*
296344 ACTTTGGGGACATTCCA
66 ACTTTGGGGACACTCCA
296361 TTCACACTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (96 bp):
AGGGGATACTCTAAACTTGCTTTTAAACTTGTCAAGATTTAAATCTTAATTTTACACAAATTGTC
ACTTTGGGGACACTCCAACCCTATTTATCCA
Found at i:298695 original size:20 final size:20
Alignment explanation
Indices: 298670--298743 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
298660 TTTTACCCAG
*
298670 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * *
298690 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
298710 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
298730 ATGTATCGATACAT
1 ATGTATCGATACAT
298744 CTAGTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:298710 original size:71 final size:71
Alignment explanation
Indices: 298544--298726 Score: 260
Period size: 71 Copynumber: 2.5 Consensus size: 71
298534 TACCCAGATC
* * * * *
298544 TCAATGTATTGATACATTTATGAATGTATCGATACATTTTGTCTTTTTTACCCAGATGTTTTGAT
1 TCAATGTATCGATACA-TTATGAATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGAT
298609 ACATTTT
65 ACATTTT
**
298616 TCAATACATCGATACATTCATGAATGTATCGATACATTCTATC-TTTTTACCCAGATGTATCGAT
1 TCAATGTATCGATACATT-ATGAATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGAT
298680 ACATTTT
65 ACATTTT
*
298687 TTAATGTATCGATACATGTATGAATGTATCGATACATTCT
1 TCAATGTATCGATACAT-TATGAATGTATCGATACATTCT
298727 TCAATGTATC
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
71 63 0.64
72 36 0.36
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (71 bp):
TCAATGTATCGATACATTATGAATGTATCGATACATTCTATCTTTTTTACCCAGATGTATCGATA
CATTTT
Found at i:312657 original size:19 final size:19
Alignment explanation
Indices: 312629--312700 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
312619 CTTCGTACCC
312629 AAAAACAAAAAAACAAAAA
1 AAAAACAAAAAAACAAAAA
* * *
312648 AAAAAGAAAAAACCAAAAGC
1 AAAAACAAAAAAACAAAA-A
* *
312668 AAAAGCAAAAAAAAAAAACA
1 AAAAACAAAAAAACAAAA-A
312688 AACAAACAAAAAA
1 AA-AAACAAAAAA
312701 GGGGTCCAGA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 16 0.39
20 16 0.39
21 9 0.22
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAACAAAAA
Found at i:313909 original size:28 final size:29
Alignment explanation
Indices: 313883--314236 Score: 431
Period size: 28 Copynumber: 12.4 Consensus size: 29
313873 CGTTCATCTC
* * *
313883 TTCAAAGCGCACAGGTCAGTGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
313911 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
313939 TTCAAAGCCCACAAGTTAGTGGCAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
313967 TTCAAAGCCCACAAGTCAGTGACAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
313995 TTCAAAGCCCACAAGTTAGTGGCATCTC-
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* * * *
314023 TTCAAAAGACCATAAGTCAATGTCAT-CCT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCCT
*
314052 TTCAAAGCCCAAAAGTCAGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* * * *
314080 TTAAAAGCCTACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
314108 TTCAAAGCCCACAAGTCAGTGGCATACCCC
1 TTCAAAGCCCACAAGTCAGTGGCAT-CCCT
*
314138 TTCAAAGCCCACAAATCAGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
314166 TTCAAAGCCCACAAGTCGGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CCCT
*
314196 TTCAAAGCCCACAAGTCGGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
314224 TTCAAAGCCCACA
1 TTCAAAGCCCACA
314237 CAAGTCGGTA
Statistics
Matches: 283, Mismatches: 33, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
28 209 0.74
29 21 0.07
30 53 0.19
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCCT
Found at i:314173 original size:58 final size:56
Alignment explanation
Indices: 313883--314287 Score: 452
Period size: 56 Copynumber: 7.0 Consensus size: 56
313873 CGTTCATCTC
* * *
313883 TTCAAAGCGCACAGGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
313939 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * * *
313995 TTCAAAGCCCACAAGTTAGTGGCAT-CTCTTCAAAAGACCATAAGTCAATGTCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT-TTC-AAAGCCCACAAGTCAGTGGCACCCT
* * * * * *
314052 TTCAAAGCCCAAAAGTCAGTGGCACCCTTTAAAAGCCTACAAGTTAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
314108 TTCAAAGCCCACAAGTCAGTGGCATACCCCTTCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
314166 TTCAAAGCCCACAAGTCGGTGGCATACCCTTTCAAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* ** * *
314224 TTCAAAGCCCACACAAGTCGGTAGTAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGT-GGCA-TCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCT
314286 TT
1 TT
314288 TTTTAAAAAA
Statistics
Matches: 299, Mismatches: 39, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
55 2 0.01
56 118 0.39
57 45 0.15
58 88 0.29
59 2 0.01
60 20 0.07
61 4 0.01
62 20 0.07
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:315203 original size:20 final size:20
Alignment explanation
Indices: 315164--315214 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
315154 TACCCAGATA
* *
315164 TATCGATACATTTTTCAATG
1 TATCGATACATGTATCAATG
* *
315184 TGTCGATACATGTATGAATG
1 TATCGATACATGTATCAATG
*
315204 TATTGATACAT
1 TATCGATACAT
315215 TCTGTCTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (20 bp):
TATCGATACATGTATCAATG
Found at i:315261 original size:20 final size:20
Alignment explanation
Indices: 315233--315288 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
315223 TTTTACCTAA
*
315233 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTATC
* * *
315253 AATGCATCGATACATGTATG
1 AATGTATCGATACATTTATC
315273 AATGTATCGATACATT
1 AATGTATCGATACATT
315289 ATGTCTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTTATC
Found at i:315285 original size:73 final size:71
Alignment explanation
Indices: 315150--315318 Score: 239
Period size: 73 Copynumber: 2.4 Consensus size: 71
315140 AAAAGTCACA
* * * ** *
315150 TTTTTACCCAGATATATCGATACATTTTTCAATGTGTCGATACATGTATGAATGTATTGATACAT
1 TTTTTACCAAAATGTATCGATACATTTTTCAATGCATCGATACATGTATGAATGTATCGATACAT
*
315215 TCTGTC
66 TATGTC
315221 TCTTTTACCTAAAATGTATCGATACATTTTTCAATGCATCGATACATGTATGAATGTATCGATAC
1 T-TTTTACC-AAAATGTATCGATACATTTTTCAATGCATCGATACATGTATGAATGTATCGATAC
315286 ATTATGTC
64 ATTATGTC
* *
315294 TTTTTACCCAGATGTATCGATACAT
1 TTTTTACCAAAATGTATCGATACAT
315319 GTATGAATGT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 16 0.18
72 14 0.16
73 57 0.66
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (71 bp):
TTTTTACCAAAATGTATCGATACATTTTTCAATGCATCGATACATGTATGAATGTATCGATACAT
TATGTC
Done.