Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011537.1 Kokia drynarioides strain JFW-HI SEQ_126523, whole genome shotgun sequence
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: 45054
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:467 original size:216 final size:210
Alignment explanation
Indices: 7--537 Score: 549
Period size: 211 Copynumber: 2.5 Consensus size: 210
1 CATTTG
* * * **
7 TGCTCGAAGGAATGGAT-AGTCTTGAATGCTTTAAGGAGCCGAAGCTCTA-AAAAAACTTGTAAA
1 TGCTCGAAGGAATGGATCA-TCTTGAATACTTTAAGGA-ACTAAG-T-TATAAAAAACCCGTAAA
* ** * **
70 AGTTTGACAAGTTTGTAAA-TTTAGCCAAGAACCAAGAGA-AATAATTTTTACGTAAATAAGTTT
62 AGTTTGACAAGTTCG-AAAGTTTAGTGAAGAACCAAGAGAGAATAATTTTCACAAAAATAAGTTT
* * * ** * * *
133 TTAATTCAAAGACTAAAAGGTGTTTATGAAACGATAAACTATTTAGACCAAATGATATATCCCGA
126 TTAATTCAAACACCAAAAGGTGTCTACAAAACAATAAAATATTTAGACCAAATGATATATCCCAA
*
198 GCATGGAATGTTCGAAAAAT
191 GCATGCAATGTTCGAAAAAT
* * *
218 TGCTCGAAGGAATGGATCGTATTAAATACTTTAAGGAACTACAGTTATAAAAGAACCCGTAAAAG
1 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACTA-AGTTATAAAA-AACCCGTAAAAG
* *
283 TTTGACAAGTTCGAAAGTTCAGTGAAAAACCAAGAGAGAAT-ATTTTCACACAAAAATAAGTTTT
64 TTTGACAAGTTCGAAAGTTTAGTGAAGAACCAAGAGAGAATAATTTT--CACAAAAATAAGTTTT
* * * * *
347 TAATTCAAACACCAATAGTTGTCTACAAAACAATAAAATGTTTAGACCAAATGATGCGATTTCCT
127 TAATTCAAACACCAAAAGGTGTCTACAAAACAATAAAATATTTAGACCAAATGAT---ATATCCC
412 AAGCATGCAATGCTT-GAAAAAT
189 AAGCATGCAATG-TTCGAAAAAT
434 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAA-TAAAAGTTA-AAAAAACCTCGTAAAA
1 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACT--AAGTTATAAAAAACC-CGTAAAA
* * *
497 GTGTGACAAGTTC-AAGAGTTTGGTGAAGAACCGAGAGAGAA
63 GTTTGACAAGTTCGAA-AGTTTAGTGAAGAACCAAGAGAGAA
538 AAAATTCTCA
Statistics
Matches: 266, Mismatches: 38, Indels: 28
0.80 0.11 0.08
Matches are distributed among these distances:
209 2 0.01
210 10 0.04
211 77 0.29
212 3 0.01
213 58 0.22
214 6 0.02
215 45 0.17
216 62 0.23
217 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (210 bp):
TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACTAAGTTATAAAAAACCCGTAAAAGTT
TGACAAGTTCGAAAGTTTAGTGAAGAACCAAGAGAGAATAATTTTCACAAAAATAAGTTTTTAAT
TCAAACACCAAAAGGTGTCTACAAAACAATAAAATATTTAGACCAAATGATATATCCCAAGCATG
CAATGTTCGAAAAAT
Found at i:8028 original size:34 final size:33
Alignment explanation
Indices: 7983--8046 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
7973 TATTCTGGAC
* * * *
7983 TTTCAAGTTTAATTTAATATTAAGTTTAAAACTA
1 TTTCAAATTTAACTAAAT-TTAAATTTAAAACTA
8017 TTTCAAATTTAACTAAATTTAAATTTAAAA
1 TTTCAAATTTAACTAAATTTAAATTTAAAA
8047 ATAAATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.42
34 15 0.58
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (33 bp):
TTTCAAATTTAACTAAATTTAAATTTAAAACTA
Found at i:8041 original size:6 final size:6
Alignment explanation
Indices: 8030--8119 Score: 71
Period size: 6 Copynumber: 15.7 Consensus size: 6
8020 CAAATTTAAC
** * * *
8030 TAAATT TAAATT TAAAAA TAAATC TAAATT TAAATT TAAA-A TAAAGT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** * *
8077 TAAATT TAAAAA TAAATT TAAACT T--ATT TAAACT T-AATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
8120 ATCAAAAGTT
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
4 3 0.05
5 8 0.12
6 53 0.83
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:8056 original size:24 final size:24
Alignment explanation
Indices: 8029--8086 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 24
8019 TCAAATTTAA
8029 CTAAATTTAAATTTAAAAATAAA-T
1 CTAAATTTAAATTT-AAAATAAAGT
8053 CTAAATTTAAATTTAAAATAAAGT
1 CTAAATTTAAATTTAAAATAAAGT
8077 -TAAATTTAAA
1 CTAAATTTAAA
8087 AATAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
CTAAATTTAAATTTAAAATAAAGT
Found at i:8083 original size:41 final size:41
Alignment explanation
Indices: 8016--8098 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
8006 GTTTAAAACT
* *
8016 ATTTCAAATTTAACTAAATTTAAATTTAAAAATAAATCTAA
1 ATTTCAAATTTAAATAAAGTTAAATTTAAAAATAAATCTAA
*
8057 ATTT-AAATTTAAAATAAAGTTAAATTTAAAAATAAATTTAA
1 ATTTCAAATTT-AAATAAAGTTAAATTTAAAAATAAATCTAA
8098 A
1 A
8099 CTTATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 6 0.16
41 32 0.84
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (41 bp):
ATTTCAAATTTAAATAAAGTTAAATTTAAAAATAAATCTAA
Found at i:8118 original size:11 final size:11
Alignment explanation
Indices: 8091--8119 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
8081 TTTAAAAATA
8091 AATTTAAACTT
1 AATTTAAACTT
8102 -ATTTAAACTT
1 AATTTAAACTT
8112 AATTTAAA
1 AATTTAAA
8120 ATCAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTAAACTT
Found at i:9026 original size:209 final size:209
Alignment explanation
Indices: 8423--10158 Score: 2232
Period size: 209 Copynumber: 8.3 Consensus size: 209
8413 TTTAGTGGTT
* * * * * * *
8423 TGGTGTCATTGATTTGGTCTACTTCTCAGTTTCTCATCAAGAAAATGACTGTATCATTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * *
8488 ATCCACTTCTTTGTGTCTCATCAGGAAGACAAATCTGGTTCACTTCTCTGTATCTCATCAAGAAG
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
* * * * * *
8553 GTAACCGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATTAAGAAGCTGGGGTTCAAAGATTT
131 CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
* *
8618 GCTAACTTTGAGCT
196 GCTCACTTTGAGCC
* * *
8632 TGGTTTCATTGGTTTGGTCTACTTCTTAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * *
8697 ATCCAC-T-TCTGTGTCAT-ATTAGGAAGAC-AGACCTGGTTCACTTCTCTGTATCTCATCAGGA
66 ATCCACTTCTCTGTGTC-TCATCAGGAAGACGA-ATCTGGTTCACTTCTCAGTATCTCATCAAGA
* * *
8758 AGGTAACCACTTTATTGCTTCGATCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGAT
129 AGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
8823 TTGCTCACTTTGAGCC
194 TTGCTCACTTTGAGCC
* * *
8839 TGGTTTCGTTGATTGGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * * *
8904 ATCGACTTCTCTGTGTCTCATCAGGAAGATGGACCTGGTTCACTTGTCAGTATCTCATCAGGAAG
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
* *
8969 CTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTT
131 CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
9034 GCTCACTTTGAGCC
196 GCTCACTTTGAGCC
* *
9048 TGGTTTCATTGATTTGGTCTACTTCTCAGTATTTCATCAAGAAGATGACCGCATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * *
9113 ATCCACTTCTCTATG--TCATCAGGAAGAC-AGATCTAGTTCACTTCTCAGTATCTCATCAGGAA
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGA-ATCTGGTTCACTTCTCAGTATCTCATCAAGAA
* * * * * * *
9175 GCTAACCATTTTATTGCTTCAACTTGCTTCTCAATATCTCATCAGGAAGTTGAGGTTCGATGATT
130 GCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
*
9240 TGCTCACTTTGAACC
195 TGCTCACTTTGAGCC
* * * * **
9255 TGGTTTCATTGATTTGGCCTACTTCTCAATATCTCATCAGGAAGATGACAGCCTCACTTGTTTCA
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * * * * *
9320 ATCCGCTTCTCCGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAAAAAG
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
* * * * *
9385 CTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGATGCTGGGGTTCGAAGATTC
131 CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
*
9450 GCTCGCTTTGAGCC
196 GCTCACTTTGAGCC
* * * *
9464 TGATTTCTTTGATTTGGTCTGCTGCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * *
9529 ATCCACTTCTCTGTGTCTCATGAGGAAGACGAACCTGGTTCACTTATCTGTATCTCATCAAGAAG
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
* * *
9594 GTAACACACTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATT
131 CTAAC-CACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
* *
9659 TGCTTACTTGGAGCC
195 TGCTCACTTTGAGCC
* * *
9674 TGGTTTCGTAGATTTGGTCTACTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
** * * * * * * *
9739 ATTGACTTCTTTATATCTCATCAAGAAGATGGATCTGGTTCACTTCTTC-GTATCTCATCAGGAA
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTCACTTC-TCAGTATCTCATCAAGAA
* * * * *
9803 GGTAA-CAGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTTGGGTTCTATGAT
130 GCTAACCA-CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
*
9867 TTGCTCACTTTGAGCT
194 TTGCTCACTTTGAGCC
* * * **
9883 TTGTTTCATTGATTTGGTCTACTTCTCAGTATCTTATCAGGAAGATGACCGCATCGCTTGTTTCA
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
** * * * *
9948 ATCTGCTTCTCTGTATCTCATCAGGAAGATGAATTTGG-TCTACTTCTCAGTATCTCATCAAGAT
66 ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTC-ACTTCTCAGTATCTCATCAAGAA
* * * *
10012 GCTAACCATTTTATTGCTTCGACCTTCTTCTCAATATCTCATCAGGAAGCTAGGGATTTCGAAGA
130 GCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGG-GTTCGAAGA
*
10077 TTTGTTCACTTTGAGCC
193 TTTGCTCACTTTGAGCC
* *
10094 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCGCTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
10159 GCTAATCGTA
Statistics
Matches: 1328, Mismatches: 181, Indels: 34
0.86 0.12 0.02
Matches are distributed among these distances:
206 1 0.00
207 365 0.27
208 10 0.01
209 686 0.52
210 183 0.14
211 83 0.06
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (209 bp):
TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
ATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
GCTCACTTTGAGCC
Found at i:9785 original size:419 final size:418
Alignment explanation
Indices: 8423--10158 Score: 2234
Period size: 416 Copynumber: 4.2 Consensus size: 418
8413 TTTAGTGGTT
* * * * * * *
8423 TGGTGTCATTGATTTGGTCTACTTCTCAGTTTCTCATCAAGAAAATGACTGTATCATTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * * *
8488 ATCCACTTCTTTGTGTCTCATCAGGAAGACAAATCTGGTTCACTTCTCTGTATCTCATCAAGAAG
66 ATCGACTTCTCTGTATCTCATCAAGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
* * * * * *
8553 GTAACCGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATTAAGAAGCTGGGGTTCAAAGATTT
131 CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
* * * * *
8618 GCTAACTTTGAGCTTGGTTTCATTGGTTTGGTCTACTTCTTAGTATCTCATCAGAAAGATGACCG
196 GCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG
* *
8683 CATCACTTGTTTTGATCCAC-T-TCTGTGTCAT-ATTAGGAAGACAGACCTGGTTCACTTCTCTG
261 CATCACTTGTTTTGATCCACTTCTCTGTGTC-TCATCAGGAAGACAGACCTGGTTCACTTCTCAG
* * * * * * *
8745 TATCTCATCAGGAAGGTAACCACTTTATTGCTTCGATCTGCTTCTCAGTATCTCATCAAGAAGCT
325 TATCTCATCAAGAAGCTAACCACTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGTT
8810 GGGGTTCGAAGATTTGCTCACTTTGAGCC
390 GGGGTTCGAAGATTTGCTCACTTTGAGCC
* * *
8839 TGGTTTCGTTGATTGGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * * * *
8904 ATCGACTTCTCTGTGTCTCATCAGGAAGATGGACCTGGTTCACTTGTCAGTATCTCATCAGGAAG
66 ATCGACTTCTCTGTATCTCATCAAGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
* *
8969 CTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTT
131 CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
* *
9034 GCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATTTCATCAAGAAGATGACCG
196 GCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG
* * *
9099 CATCACTTGTTTTGATCCACTTCTCTATG--TCATCAGGAAGACAGATCTAGTTCACTTCTCAGT
261 CATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAGACCTGGTTCACTTCTCAGT
* * *
9162 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACTTGCTTCTCAATATCTCATCAGGAAGTTG
326 ATCTCATCAAGAAGCTAACCACTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGTTG
* * *
9227 AGGTTCGATGATTTGCTCACTTTGAACC
391 GGGTTCGAAGATTTGCTCACTTTGAGCC
* * * * **
9255 TGGTTTCATTGATTTGGCCTACTTCTCAATATCTCATCAGGAAGATGACAGCCTCACTTGTTTCA
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * *
9320 ATCCG-CTTCTCCGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAAAAA
66 AT-CGACTTCTCTGTATCTCATCAAGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAA
* * * *
9384 GCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGATGCTGGGGTTCGAAGATT
130 GCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
* * * * * *
9449 CGCTCGCTTTGAGCCTGATTTCTTTGATTTGGTCTGCTGCTCAGTATCTCATCAGGAAGATGACC
195 TGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACC
* * *
9514 GCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATGAGGAAGAC-GAACCTGGTTCACTTATCT
260 GCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAG-ACCTGGTTCACTTCTCA
* *
9578 GTATCTCATCAAGAAGGTAACACACTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAG
324 GTATCTCATCAAGAAGCTAAC-CACTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAG
* *
9643 TTGGGGTTCGAAGATTTGCTTACTTGGAGCC
388 TTGGGGTTCGAAGATTTGCTCACTTTGAGCC
* * *
9674 TGGTTTCGTAGATTTGGTCTACTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
* * * * * *
9739 ATTGACTTCTTTATATCTCATCAAGAAGATGGATCTGGTTCACTTCTTC-GTATCTCATCAGGAA
66 ATCGACTTCTCTGTATCTCATCAAGAAGACGAATCTGGTTCACTTC-TCAGTATCTCATCAAGAA
* * * * *
9803 GGTAA-CAGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTTGGGTTCTATGAT
130 GCTAACCA-CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
* * *
9867 TTGCTCACTTTGAGCTTTGTTTCATTGATTTGGTCTACTTCTCAGTATCTTATCAGGAAGATGAC
194 TTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGAC
* ** ** * * **
9932 CGCATCGCTTGTTTCAATCTGCTTCTCTGTATCTCATCAGGAAGA-TGAATTTGG-TCTACTTCT
259 CGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAG-ACCTGGTTC-ACTTCT
* * * *
9995 CAGTATCTCATCAAGATGCTAACCATTTTATTGCTTCGACCTTCTTCTCAATATCTCATCAGGAA
322 CAGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAA
* * *
10060 GCTAGGGATTTCGAAGATTTGTTCACTTTGAGCC
387 G-TTGGG-GTTCGAAGATTTGCTCACTTTGAGCC
* *
10094 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCGCTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
10159 GCTAATCGTA
Statistics
Matches: 1141, Mismatches: 164, Indels: 26
0.86 0.12 0.02
Matches are distributed among these distances:
415 1 0.00
416 608 0.53
417 4 0.00
418 93 0.08
419 351 0.31
420 84 0.07
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (418 bp):
TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTG
ATCGACTTCTCTGTATCTCATCAAGAAGACGAATCTGGTTCACTTCTCAGTATCTCATCAAGAAG
CTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
GCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG
CATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAGACCTGGTTCACTTCTCAGT
ATCTCATCAAGAAGCTAACCACTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGTTG
GGGTTCGAAGATTTGCTCACTTTGAGCC
Found at i:23808 original size:29 final size:29
Alignment explanation
Indices: 23776--23912 Score: 134
Period size: 29 Copynumber: 4.7 Consensus size: 29
23766 GGATGCCCGG
*
23776 GGATAAAATGGTAATTTTTAGAGGTTCGA
1 GGATAAAATGGTAATTTTTAGACGTTCGA
* * **
23805 GGATAAAACGGTATTTTTTAGACACTCGA
1 GGATAAAATGGTAATTTTTAGACGTTCGA
* *
23834 GGATGAAAATGGTAATTTTTAGATGTTCAA
1 GGAT-AAAATGGTAATTTTTAGACGTTCGA
* *
23864 GGTTAAAATGGTAA-TTTTAGACACTTCGA
1 GGATAAAATGGTAATTTTTAGAC-GTTCGA
* *
23893 GGGA-AAAACGATAATTTTTA
1 -GGATAAAATGGTAATTTTTA
23913 AAAAATTCAA
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
28 7 0.08
29 50 0.58
30 29 0.34
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (29 bp):
GGATAAAATGGTAATTTTTAGACGTTCGA
Found at i:23852 original size:59 final size:58
Alignment explanation
Indices: 23776--23912 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 58
23766 GGATGCCCGG
* *
23776 GGATAAAATGGTAATTTTTAGAGGTTCGAGGATAAAACGGTATTTTTTAGACAC-TCGA
1 GGATAAAATGGTAATTTTTAGAGGTTCAAGGATAAAACGGTA-ATTTTAGACACTTCGA
* * *
23834 GGATGAAAATGGTAATTTTTAGATGTTCAAGGTTAAAATGGTAATTTTAGACACTTCGA
1 GGAT-AAAATGGTAATTTTTAGAGGTTCAAGGATAAAACGGTAATTTTAGACACTTCGA
* *
23893 GGGA-AAAACGATAATTTTTA
1 -GGATAAAATGGTAATTTTTA
23913 AAAAATTCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 28 0.41
59 38 0.55
60 3 0.04
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (58 bp):
GGATAAAATGGTAATTTTTAGAGGTTCAAGGATAAAACGGTAATTTTAGACACTTCGA
Found at i:24020 original size:88 final size:87
Alignment explanation
Indices: 23779--24057 Score: 235
Period size: 88 Copynumber: 3.2 Consensus size: 87
23769 TGCCCGGGGA
** * * * *
23779 TAAAATGGTAATTTTTAGAGGTTCGAGGATAAAACGGTATTTTTTAGACACTCGAGGATGAAAAT
1 TAAAATGGTAATTTTTAGACATTCGAGGGTAAAACGGTATTTTTTAGAAATTCGAGGTTGAAAAT
* *
23844 GGTAATTTTTAGATGTTCAAGGT
66 -GTAATTTTTAGAAGATCAAGGT
* * * * * **
23867 TAAAATGGTAA-TTTTAGACACTTCGAGGGAAAAACGATAATTTTTAAAAAATTCAAGGTCAAAA
1 TAAAATGGTAATTTTTAGACA-TTCGAGGGTAAAACGGT-ATTTTTTAGAAATTCGAGGTTGAAA
*
23931 AT-TATATTTTTGGAAGATCAAGAG-
64 ATGTA-ATTTTTAGAAGATCAAG-GT
* * * * *
23955 TAAAATGGTAATTTTTGGATATTCGAGGGTAAAATGGTATTTTTTGGATAATTCGGGGTTGAAAA
1 TAAAATGGTAATTTTTAGACATTCGAGGGTAAAACGGTATTTTTTAGA-AATTCGAGGTTGAAAA
* * *
24020 TGGAA-TTTTAGAA-ATTTAAGGG
65 TGTAATTTTTAGAAGA-TCAAGGT
*
24042 TAAAATGGTATTTTTT
1 TAAAATGGTAATTTTT
24058 TGAAAAGTTA
Statistics
Matches: 150, Mismatches: 32, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
86 2 0.01
87 42 0.28
88 78 0.52
89 28 0.19
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (87 bp):
TAAAATGGTAATTTTTAGACATTCGAGGGTAAAACGGTATTTTTTAGAAATTCGAGGTTGAAAAT
GTAATTTTTAGAAGATCAAGGT
Found at i:24062 original size:29 final size:29
Alignment explanation
Indices: 23936--24277 Score: 194
Period size: 29 Copynumber: 11.7 Consensus size: 29
23926 CAAAAATTAT
* *
23936 ATTTTTGGAAGA-TCAAGAGTAAAATGGTA
1 ATTTTTGGAA-ATTTAAGGGTAAAATGGTA
* **
23965 ATTTTTGGATATTCGAGGGTAAAATGGTA
1 ATTTTTGGAAATTTAAGGGTAAAATGGTA
* **
23994 TTTTTTGGATAA-TTCGGGGTTGAAAATGG-A
1 ATTTTTGGA-AATTTAAGGG-T-AAAATGGTA
*
24024 A-TTTTAGAAATTTAAGGGTAAAATGGTA
1 ATTTTTGGAAATTTAAGGGTAAAATGGTA
* * * *
24052 TTTTTTTGAAAAGTTAGGGGTCAAAAATGG-A
1 -ATTTTTGGAAATTTAAGGGT--AAAATGGTA
*
24083 ATTTTTGGAAAGTTT-AGGGTTAAAA-AG-A
1 ATTTTTGGAAA-TTTAAGGG-TAAAATGGTA
*
24111 GTTTTTGGAAATTTAAGGGT-AAATGGTA
1 ATTTTTGGAAATTTAAGGGTAAAATGGTA
* * *
24139 ATTTTTGAAAAGTTTAA-GGTCAAAAT-TTG
1 ATTTTTGGAAA-TTTAAGGGT-AAAATGGTA
*
24168 ATTTTTGGAAAGTTTAGGGGTGAAAAT-GTA
1 ATTTTTGGAAA-TTTAAGGGT-AAAATGGTA
* *
24198 ATTTTTTAGAAGTTT-AGGGTATAAA-GTGTA
1 A-TTTTTGGAAATTTAAGGGTA-AAATG-GTA
*
24228 ATTTTTGGAAAGTTTAAGTGTTAAAAT-GTA
1 ATTTTTGGAAA-TTTAAG-GGTAAAATGGTA
*
24258 ATTTTTAGAAAGTTT-AGGGT
1 ATTTTTGGAAA-TTTAAGGGT
24278 CAAACTAAGA
Statistics
Matches: 245, Mismatches: 41, Indels: 55
0.72 0.12 0.16
Matches are distributed among these distances:
26 3 0.01
27 12 0.05
28 37 0.15
29 89 0.36
30 70 0.29
31 24 0.10
32 10 0.04
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.39
Consensus pattern (29 bp):
ATTTTTGGAAATTTAAGGGTAAAATGGTA
Found at i:24095 original size:30 final size:29
Alignment explanation
Indices: 23956--24277 Score: 177
Period size: 30 Copynumber: 11.0 Consensus size: 29
23946 GATCAAGAGT
* *
23956 AAAATGGTAATTTTTGGATA-TTCGAGGGT-
1 AAAATGG-AATTTTTGGAAAGTT-TAGGGTA
* ** *
23985 AAAATGGTATTTTTTGGATAA-TTCGGGGTTG
1 AAAATGG-AATTTTTGGA-AAGTTTAGGG-TA
*
24016 AAAATGGAA-TTTTAGAAA-TTTAAGGGT-
1 AAAATGGAATTTTTGGAAAGTTT-AGGGTA
* *
24043 AAAATGGTATTTTTTTGAAAAG-TTAGGGGTCA
1 AAAATGG-A-ATTTTTGGAAAGTTTA-GGGT-A
24075 AAAATGGAATTTTTGGAAAGTTTAGGGTTA
1 AAAATGGAATTTTTGGAAAGTTTAGGG-TA
*
24105 AAAA--GAGTTTTTGGAAA-TTTAAGGGT-
1 AAAATGGAATTTTTGGAAAGTTT-AGGGTA
* *
24131 -AAATGGTAATTTTTGAAAAGTTTAAGGTCA
1 AAAATGG-AATTTTTGGAAAGTTTAGGGT-A
* * *
24161 AAATTTG-ATTTTTGGAAAGTTTAGGGGTG
1 AAAATGGAATTTTTGGAAAGTTTA-GGGTA
* *
24190 AAAATGTAATTTTT-TAGAAGTTTAGGGTA
1 AAAATGGAATTTTTGGA-AAGTTTAGGGTA
* * * *
24219 TAAAGTGTAATTTTTGGAAAGTTTAAGTGTT
1 -AAAATGGAATTTTTGGAAAGTTT-AGGGTA
* *
24250 AAAATGTAATTTTTAGAAAGTTTAGGGT
1 AAAATGGAATTTTTGGAAAGTTTAGGGT
24278 CAAACTAAGA
Statistics
Matches: 232, Mismatches: 34, Indels: 54
0.73 0.11 0.17
Matches are distributed among these distances:
25 3 0.01
27 12 0.05
28 36 0.16
29 61 0.26
30 92 0.40
31 21 0.09
32 7 0.03
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.39
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAGTTTAGGGTA
Found at i:25556 original size:16 final size:16
Alignment explanation
Indices: 25532--25571 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
25522 TTATTAAAAC
*
25532 ATTATTTAATAAATTT
1 ATTAATTAATAAATTT
*
25548 ATTAATTAATATATTT
1 ATTAATTAATAAATTT
25564 ATTAATTA
1 ATTAATTA
25572 TACCTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTAATTAATAAATTT
Found at i:26742 original size:216 final size:216
Alignment explanation
Indices: 26355--28950 Score: 3162
Period size: 216 Copynumber: 12.0 Consensus size: 216
26345 CAACATTCAG
* * *
26355 AAAATAGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCCAAGTTATAAAAGAACTCAT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * *
26420 AAAAGTTTGACGAGTTC-GAATGCTT-GGCCAAGAAACAAGAGAGAAACAATTCTCATGTAAATA
66 AAAAGTTTGACAAGTTCGGAA-G-TTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * * *
26483 AGATTTTAATTCAAAGACCAAAAGTCGTTTACAAAATGACAAACTATTTTGACAAAATGATGCGA
129 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* *
26548 TTTCTAGAGCATGAAATGTTCGA
194 TTTCTCGAGCATGGAATGTTCGA
* * *
26571 AAAATTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCAT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * *
26636 AAAAGTGTGACAAGTTCGGAAGTTCGGCCAAAAACCAAGAGAAAAATC-ATTCTCACGTAAATAA
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAA-CAATTCTCACGTAAATAA
** * * * * *
26700 GTTTTTAATTCAAAGAATAAAAGTTGTTTACAAAACGACAAACTATTTAGACAAAATGTTGTGAT
130 GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
26765 TTCCCGAGCATGGAGTGTTCTG-
195 TTCTCGAGCATGGAATGTTC-GA
* * * * * * * * *
26787 ATAATTGCTCGAAAGAACGCATCATCTTGAATACTTTAAGAAATCGAAGTTATTAAAGAAGTCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * *
26852 AAAAGTATGACAAGTTCGGAAGTTCGACCAAGAACCAAGAGAGAAACAATTCTCAAGTAAATAAG
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * ** *
26917 TTTTTAATTCAAACACTAAAAGTTG-TTACAAAAAAACAAACTATTTAGGCCAAATGATGCGATT
131 TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
26981 TACT-GAGCATGGAATGTTCGA
196 T-CTCGAGCATGGAATGTTCGA
* ** * * *
27002 AAAATTGCTCGAAAGAATGGATCGTCTAAAATACTTTAAGGAGCTGAAGTTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* ** * *
27067 AAAAGTTTGGCAAGTTCGGAAGTTCATCCAAGAAACAAGAGAGAAACAATTCTCATGTAAATAAG
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * *
27132 TTTTTAATTCAAGGACCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGATT
131 TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
27197 TCTCGAGCATGGAATGTTCGA
196 TCTCGAGCATGGAATGTTCGA
* * * * * * * *
27218 AAAATTACTAGAAGGAATGGATCGTCTTCAATACTTTAAGGAGCCAAAGTTATTAAAGAGCTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * * *
27283 AAAAGTTTGACAAGTTCTGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTTTTACGTAAATAAG
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * *
27348 TTTTTAATT-AGAAGACCAAAACTTGTATACAAAATGACAGACTATTTAGACCAAATAATGCGAT
131 TTTTTAATTCA-AAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
*
27412 TTCTCGAGCATGTAATGTTCGA
195 TTCTCGAGCATGGAATGTTCGA
* * *
27434 AAAATTGCTGGAAGGAATGAATCGTCTTGTATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * * * * *
27499 AAAAGTTTGTCAACTTCGGAAGTTTGGCCAAGAATCAAGAGAGAAATAATACTCACGTAAATAAG
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * *
27564 TTTTTTATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTACACCAAAAGATGTGATT
131 TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
*
27629 TC-CTGAGCATGGAATGTTCGT
196 TCTC-GAGCATGGAATGTTCGA
* * * * * *
27650 AAAATTGCTGGAAGGAATAGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* *
27715 AAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-A-AGAGAAACAATTCTCACGTAAATAAG
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * *
27778 TTTTTAATTCAAAGACCAAAACTTGTATACAAAATGATAAATTATTTAGACCAAATAATGCAATT
131 TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
*
27843 TCTCGAACATGGAATGTTCGA
196 TCTCGAGCATGGAATGTTCGA
* * * * *
27864 AAAATTGCTCGAAAGAATGAATCGTCTTGAATAATTTGAGGAACCGAAGTTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * * * * *
27929 AAAAGATTGAC-AGTTCGAAAGTTTGACCAAGAACCAAGAGAGAAACAATACTCACGTAAATATG
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
** * * *
27993 TTTTTAATTCAAAGAAAAAAAGTAGTTTACAAAACGACAAACTATTTAGACCAAATGATGCGATT
131 TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* * *
28058 TCTTGAGCATGGAATGCTCAA
196 TCTCGAGCATGGAATGTTCGA
** * * ** *
28079 AAAATTAATCGATGGAATGGATTGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAAGTCG-
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * * *
28143 AATAAGTTTGACAAGTTC-AAATGTTCAGCCAAGAACTAAGAGAGAAA-AATTTCTCACGAAAAT
66 AA-AAGTTTGACAAGTTCGGAA-GTTCGGCCAAGAACCAAGAGAGAAACAA-TTCTCACGTAAAT
* * * *
28206 AAGTTTTTAATTCAACGACCAATAGTTGTTTACAAAATGACAAAACAATTTAGACCAAATGATGC
128 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC-AAACTATTTAGACCAAATGATGC
* * * *
28271 CATTTCCCGAGCATGTAATGTTTGA
192 GATTTCTCGAGCATGGAATGTTCGA
* * * * *
28296 AAAATTGCTCGAAGGAATTGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * ** * * * *
28361 -AAAGTGTCACAAGTTCGGAAGTTCGGTGAAGAACCGAGAGAGACACTATTCTCACGTAAATAAA
66 AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * *
28425 ATTATAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATTTTGACC-AATGATGCGATT
131 TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* * *
28489 TCCCAAGCATGGAATGTT-AA
196 TCTCGAGCATGGAATGTTCGA
* * * * * * *
28509 GAAAATTGTTCAAAGGTATGGATCATCTAT-AATACTTTAAGGAACCAAAGTTATAGAAGAACTT
1 -AAAATTGCTCGAAGGAATGGATCGTCT-TGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
* * * *
28573 GTAAAAGTTTGGA-AAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCATGTAAAT
64 GTAAAAGTTT-GACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
*
28637 AAGTTTTTAATTCAAGGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
128 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* *
28702 ATTTCCCGAGCATGGAATGCTCGA
193 ATTTCTCGAGCATGGAATGTTCGA
* * * * *
28726 AAAATTGCTAGAAGGAATGGATTGCCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
* * * *
28791 AAAAGTTTGACAAGTTC-TACAGTTCAGCCAAGAAACAGGAGAGAAACAATTCTCACGTAAATAA
66 AAAAGTTTGACAAGTTCGGA-AGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * * * *
28855 GTCTTTAATTCAAAGACTAGAACTTGTATACAAAATGACAAACTATTTAGACCAAATAATGCGAT
130 GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
28920 TTGTCGAGCATGGAATATTCGA
195 TTCTCGAGCATGGAATGTTCGA
*
28942 AAATTTGCT
1 AAAATTGCT
28951 GGAATACTTT
Statistics
Matches: 2040, Mismatches: 308, Indels: 64
0.85 0.13 0.03
Matches are distributed among these distances:
213 23 0.01
214 249 0.12
215 463 0.23
216 1200 0.59
217 105 0.05
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (216 bp):
AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
AAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
TTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
TCTCGAGCATGGAATGTTCGA
Found at i:27165 original size:431 final size:429
Alignment explanation
Indices: 26354--29383 Score: 3274
Period size: 431 Copynumber: 7.1 Consensus size: 429
26344 CCAACATTCA
* * *
26354 GAAAATAGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCCAAGTTATAAAAGAACTCA
1 GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
* * * *
26419 TAAAAGTTTGACGAGTTC-GAATGCTT-GGCCAAGAAACAAGAGAGAAACAATTCTCATGTAAAT
66 TAAAAGTTTGACAAGTTCGGAA-G-TTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
* * * * *
26482 AAGATTTTAATTCAAAGACCAAAAGTCGTTTACAAAATGACAAACTATTTTGACAAAATGATGCG
129 AAGTTTTTAATTCAAAGACCAAAACTTG-TTACAAAATGACAAACTATTTAGACCAAATGATGCG
* *
26547 ATTTCTAGAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGG
193 ATTTCT-GAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG
* * *
26612 AATCGAAGTTATAAAAGAACTCATAAAAGTGTGACAAGTTCGGAAGTTCGGCCAA-AAACCAAGA
257 AATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAGCCAAGAAA-CAAGA
* * *
26676 GAAAAATC-ATTCTCACGTAAATAAGTTTTTAATTCAAAGA-ATAAAAGTTGTTTACAAAACGAC
321 GAGAAA-CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACA-AAAACTTGTTTACAAAATGAC
* * * *
26739 AAACTATTTAGACAAAATGTTGTGATTTCCCGAGCATGGAGTGTTC
384 AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* * * * * * * * * *
26785 TGATAATTGCTCGAAAGAACGCATCATCTTGAATACTTTAAGAAATCGAAGTTATTAAAGAAGTC
1 -GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
* * *
26850 GTAAAAGTATGACAAGTTCGGAAGTTCGACCAAGAACCAAGAGAGAAACAATTCTCAAGTAAATA
65 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * ** *
26915 AGTTTTTAATTCAAACACTAAAAGTTGTTACAAAAAAACAAACTATTTAGGCCAAATGATGCGAT
130 AGTTTTTAATTCAAAGACCAAAACTTGTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* **
26980 TTACTGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTAAAATACTTTAAGG-A
195 TT-CTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * *
27044 GCTGAAGTTATAAAAGAACTTGTAAAAGTTTGGCAAGTTCGGAAGTTCATCCAAGAAACAAGAGA
259 TC-GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAGCCAAGAAACAAGAGA
* * * *
27109 GAAACAATTCTCATGTAAATAAGTTTTTAATTCAAGGACCAAAACTTGTTTACAAAATGAAAAAC
323 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAAC
* *
27174 TATTTAAACCAAATGATGCGATTTCTCGAGCATGGAATGTTC
388 TATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* * * * * * *
27216 GAAAAATTACTAGAAGGAATGGATCGTCTTCAATACTTTAAGGAGCCAAAGTTATTAAAGAGCTT
1 G-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
* * *
27281 GTAAAAGTTTGACAAGTTCTGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTTTTACGTAAATA
65 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* *
27346 AGTTTTTAATT-AGAAGACCAAAACTTGTATACAAAATGACAGACTATTTAGACCAAATAATGCG
130 AGTTTTTAATTCA-AAGACCAAAACTTGT-TACAAAATGACAAACTATTTAGACCAAATGATGCG
* * * *
27410 ATTTCTCGAGCATGTAATGTTCGAAAAATTGCTGGAAGGAATGAATCGTCTTGTATACTTTAAGG
193 ATTTCT-GAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG
* * * ** *
27475 AACCGAAGTTATAAAAGAACTCGTAAAAGTTTGTCAACTTCGGAAGTTTGGCCAAGAATCAAGAG
257 AATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAGCCAAGAAACAAGAG
* * * * *
27540 AGAAATAATACTCACGTAAATAAGTTTTTTATTCAAAGACCAAAACTTGTTTACAAAATGAAAAA
322 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAA
* * * *
27605 CTATTTACACCAAAAGATGTGATTTCCTGAGCATGGAATGTTC
387 CTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* * * * *
27648 GTAAAATTGCTGGAAGGAATAGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTT
1 G-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
*
27713 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-A-AGAGAAACAATTCTCACGTAAATA
65 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
27776 AGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGATAAATTATTTAGACCAAATAATGCAA
130 AGTTTTTAATTCAAAGACCAAAACTTGT-TACAAAATGACAAACTATTTAGACCAAATGATGCGA
* * * * *
27841 TTTCTCGAACATGGAATGTTCGAAAAATTGCTCGAAAGAATGAATCGTCTTGAATAATTTGAGGA
194 TTTCT-GAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * * * *
27906 ACCGAAGTTATAAAAGAACTTGTAAAAGATTGAC-AGTTCGAAAGTT-TGACCAAGAACCAAGAG
258 ATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAG-CCAAGAAACAAGAG
* * * * * *
27969 AGAAACAATACTCACGTAAATATGTTTTTAATTCAAAGAAAAAAAGTAGTTTACAAAACGACAAA
322 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAA
** *
28034 CTATTTAGACCAAATGATGCGATTTCTTGAGCATGGAATGCTC
387 CTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* ** * * * *
28077 AAAAAATTAATCGATGGAATGGATTGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAAGTC
1 -GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
* * *
28142 G-AATAAGTTTGACAAGTTC-AAATGTTCAG-CCAAGAACTAAGAGAGAAA-AATTTCTCACGAA
65 GTAA-AAGTTTGACAAGTTCGGAA-GTTC-GTCCAAGAACCAAGAGAGAAACAA-TTCTCACGTA
* * * *
28203 AATAAGTTTTTAATTCAACGACCAATAGTTGTTTACAAAATGACAAAACAATTTAGACCAAATGA
126 AATAAGTTTTTAATTCAAAGACCAAAACTTG-TTACAAAATGAC-AAACTATTTAGACCAAATGA
* * * * * *
28268 TGCCATTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGAATTGATCGTTTTGAATACTTT
189 TGCGATTT-CTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTT
* * * * * ** * *
28333 AAGGAATCAAAGTTATAAAAGAACTTGT-AAAGTGTCACAAGTTCGGAAGTTCGGTGAAGAACCG
253 AAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAGCCAAGAAACA
* * ** * *
28397 AGAGAGACACTATTCTCACGTAAATAAAATTATAATTCAAAGACAAAAAGTTGTTTACAAAATGA
318 AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGA
* * *
28462 CAAACTATTTTGACC-AATGATGCGATTTCCCAAGCATGGAATGTTAA
383 CAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT-C
* * * * * *
28509 GAAAATTGTTCAAAGGTATGGATCATCTAT-AATACTTTAAGGAACCAAAGTTATAGAAGAACTT
1 GAAAATTGCTCGAAGGAATGGATCGTCT-TGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
* * *
28573 GTAAAAGTTTGGA-AAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCATGTAAAT
65 GTAAAAGTTT-GACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
*
28637 AAGTTTTTAATTCAAGGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
129 AAGTTTTTAATTCAAAGACCAAAACTTG-TTACAAAATGACAAACTATTTAGACCAAATGATGCG
* * * * *
28702 ATTTCCCGAGCATGGAATGCTCGAAAAATTGCTAGAAGGAATGGATTGCCTTGAATACTTTAAGG
193 ATTT-CTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG
* * *
28767 AATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTC-TACAGTTCAGCCAAGAAACAGGA
257 AATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGA-AGTTCAGCCAAGAAACAAGA
* * * *
28831 GAGAAACAATTCTCACGTAAATAAGTCTTTAATTCAAAGACTAGAACTTGTATACAAAATGACAA
321 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAA
* **
28896 ACTATTTAGACCAAATAATGCGATTTGTCGAGCATGGAA---T-
386 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
* * * *
28936 ----A-T--TCGAA--AAT---TTG-CTGGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCG
1 GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
* * * * * ** *
28988 TAAAAGTCTGACAAGTTCGGAAGTTCGGCCAATAATCAAGAGTCA-AAAAAATAATCATGTAAAT
66 TAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAG--AGAAACAATTCTCACGTAAAT
* *
29052 AAGTTTTTAATTCAAATACCAAAATTTGTGTACAAAATGACAAACTATTTAGACCAAATGATGCG
129 AAGTTTTTAATTCAAAGACCAAAACTTGT-TACAAAATGACAAACTATTTAGACCAAATGATGCG
* * *
29117 ATTTCCTGAGCATGGAATGTTCAAAAAATTGTTGGAAGGAATGGA-----TTG--T--TTT----
193 ATTT-CTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG
* * * *
29169 --TC---------CAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTT-TGTCCAAGAACCAAGA
257 AATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAG-CCAAGAAACAAGA
** * * * * *
29222 GAGAAACAATTCTCACAAAAATAAGTTATTAATTCATAA-ACCAAAACTGGTATACAAAATGATA
321 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA-AAGACAAAAACTTGTTTACAAAATGACA
* * * * * ** *
29286 AACTATTTA-AACAGAATAATGAGATTTCTCAATAATGGAATGTTTG
385 AACTATTTAGACCA-AATGATGCGATTTCCCGAGCATGGAATG-TTC
* * *
29332 GAAAATTGCTCAAAGGAATGGATCGTCTTGGATACTTTAAGGAACCGAAGTT
1 GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTT
29384 CGGCCAAGAG
Statistics
Matches: 2220, Mismatches: 315, Indels: 149
0.83 0.12 0.06
Matches are distributed among these distances:
390 4 0.00
391 124 0.06
392 3 0.00
395 1 0.00
400 3 0.00
401 1 0.00
403 4 0.00
405 3 0.00
406 3 0.00
408 3 0.00
409 23 0.01
410 3 0.00
413 2 0.00
414 68 0.03
415 117 0.05
416 1 0.00
418 2 0.00
420 4 0.00
422 1 0.00
423 1 0.00
428 6 0.00
429 198 0.09
430 281 0.13
431 681 0.31
432 676 0.30
433 7 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (429 bp):
GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
TAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACCAAAACTTGTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
TCTGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATC
GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAGCCAAGAAACAAGAGAGAA
ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTAT
TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
Found at i:28705 original size:647 final size:649
Alignment explanation
Indices: 26355--29383 Score: 3283
Period size: 647 Copynumber: 4.7 Consensus size: 649
26345 CAACATTCAG
* * * * **
26355 AAAATAGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCCAAGTTATAAAAGAACTCAT
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
* * *
26420 AAAAGTTTGACGAGTTC-GAATGCTT-GGCCAAGAAACAAGAGAGAAACAATTCTCATGTAAATA
66 AAAAGTTTGACAAGTTCGGAA-G-TTCGTCCAAGAAACAAGAGAGAAACAATTCTCACGTAAATA
* * * *
26483 AGATTTTAATTCAAAGACCAAAAGTCGTTTACAAAATGACAAACTATTTTGACAAAATGATGCGA
129 AGATTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* *
26548 TTT-CTAGAGCATGAAATGTTCGAAAAATTGCTCG-AAGGAATGAATCGTCTTGAATACTTTAAG
194 TTTCCCA-AGCATGGAATGTTCGAAAAATTGCTCGAAAGGAATGAATCGTCTTGAATACTTTAAG
* * ** * * *
26611 GAATCGAAGTTATAAAAGAACTCATAAAAGTGTGACAAGTTCGGAAGTTCGGCCAAAAACCAAGA
258 GAACCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGA
* * *
26676 GAAAAATC-ATTCTCACGTAAATAAGTTTTTAATTCAAAGAATAAAAGTTGTTTACAAAACGACA
323 GAGAAA-CAATTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAACGACA
* * * * * * *
26740 AACTATTTAGACAAAATGTTGTGATTTCCCGAGCATGGAGTGTTCTG-ATAATTGCTCGAAAGAA
387 AACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGCTC-GAAAAATTGCTCGAAGGAA
* * * * * *
26804 CGCATCATCTTGAATACTTTAAGAAATCGAAGTTATTAAAGAAGTCGTAAAAGTATGACAAGTTC
451 TGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTC
* * * *
26869 GGAAGTTC-GACCAAGAACCAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAATTCAAACAC
516 GAAAGTTCAG-CCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * ** * * *
26933 TAAAAGTTG-TTACAAAAAAACAAACTATTTAGGCCAAATGATGCGATTTACTGAGCATGGAATG
580 CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATG
26997 TTCGA
645 TTCGA
* * *
27002 AAAATTGCTCGAAAGAATGGATCGTCTAAAATACTTTAAGG-AGCTGAAGTTATAAAAGAACTTG
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAAGC-AAAGTTATAAAAGAACTTG
* * *
27066 TAAAAGTTTGGCAAGTTCGGAAGTTCATCCAAGAAACAAGAGAGAAACAATTCTCATGTAAATAA
65 TAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAACAAGAGAGAAACAATTCTCACGTAAATAA
* * * *
27131 GTTTTTAATTCAAGGACCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGAT
130 GATTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * * *
27196 TTCTCGAGCATGGAATGTTCGAAAAATTACTAG-AAGGAATGGATCGTCTTCAATACTTTAAGGA
195 TTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAAGGAATGAATCGTCTTGAATACTTTAAGGA
* * * *
27260 GCCAAAGTTATTAAAGAGCTTGTAAAAGTTTGACAAGTTCTGAAGTTCGTCCAAGAACCAAGAGA
260 ACCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGA
* * * * * *
27325 GAAACAATTTTTACGTAAATAAGTTTTTAATT-AGAAGACCAAAACTTGTATACAAAATGACAGA
325 GAAACAATTCTCACGTAAATAAGTTTTTAATTCA-AAGAACAAAACTTGTTTACAAAACGACAAA
* * * * * *
27389 CTATTTAGACCAAATAATGCGATTTCTCGAGCATGTAATGTTCGAAAAATTGCTGGAAGGAATGA
389 CTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGCTCGAAAAATTGCTCGAAGGAATGG
* * * * * *
27454 ATCGTCTTGTATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGTCAACTTCGGA
454 ATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCGAA
** * * *
27519 AGTTTGGCCAAGAA-TCAAGAGAGAAATAATACTCACGTAAATAAGTTTTTTATTCAAAGACCAA
519 AGTTCAGCCAAGAACT-AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * * * *
27583 AACTTGTTTACAAAATGAAAAACTATTTACACCAAAAGATGTGATTTCCTGAGCATGGAATGTTC
583 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTC
*
27648 GT
648 GA
* *
27650 AAAATTGCTGGAAGGAATAGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
* *
27715 AAAAGTTTGACAAGTTCGAAAGTTCGTCCAAG-AACCA-AGAGAAACAATTCTCACGTAAATAAG
66 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAACAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * * *
27778 TTTTTAATTCAAAGACCAAAACTTGTATACAAAATGATAAATTATTTAGACCAAATAATGCAATT
131 ATTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* * *
27843 TCTCGAA-CATGGAATGTTCGAAAAATTGCTCGAAA-GAATGAATCGTCTTGAATAATTTGAGGA
196 TC-CCAAGCATGGAATGTTCGAAAAATTGCTCGAAAGGAATGAATCGTCTTGAATACTTTAAGGA
* * * * *
27906 ACCGAAGTTATAAAAGAACTTGTAAAAGATTGAC-AGTTCGAAAGTTTGACCAAGAACCAAGAGA
260 ACCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGA
* * * * *
27970 GAAACAATACTCACGTAAATATGTTTTTAATTCAAAGAAAAAAAGTAGTTTACAAAACGACAAAC
325 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAACGACAAAC
** * ** *
28035 TATTTAGACCAAATGATGCGATTTCTTGAGCATGGAATGCTCAAAAAATTAATCGATGGAATGGA
390 TATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGCTCGAAAAATTGCTCGAAGGAATGGA
* *
28100 TTGTCTTGAATACTTTAAGGAA-CAAAAGTTATAAAAGAAGTCG-AATAAGTTTGACAAGTTC-A
455 TCGTCTTGAATACTTTAAGGAATC-GAAGTTATAAAAGAAGTCGTAA-AAGTTTGACAAGTTCGA
* *
28162 AATGTTCAGCCAAGAACTAAGAGAGAAA-AATTTCTCACGAAAATAAGTTTTTAATTCAACGACC
518 AA-GTTCAGCCAAGAACTAAGAGAGAAACAA-TTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * * *
28226 AATAGTTGTTTACAAAATGACAAAACAATTTAGACCAAATGATGCCATTTCCCGAGCATGTAATG
581 AAAACTTGTTTACAAAATGAC-AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATG
*
28291 TTTGA
645 TTCGA
* * * *
28296 AAAATTGCTCGAAGGAATTGATCGTTTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
* * * * * * *
28361 -AAAGTGTCACAAGTTCGGAAGTTCGGT-GAAGAACCGAGAGAGACACTATTCTCACGTAAATAA
66 AAAAGTTTGACAAGTTCGGAAGTTC-GTCCAAGAAACAAGAGAGAAACAATTCTCACGTAAATAA
* * * * *
28424 AATTATAATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTATTTTGACC-AATGATGCGAT
130 GATTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * *
28488 TTCCCAAGCATGGAATGTT-AAGAAAATTGTTC-AAAGGTATGGATCATCTAT-AATACTTTAAG
195 TTCCCAAGCATGGAATGTTCGA-AAAATTGCTCGAAAGGAATGAATCGTCT-TGAATACTTTAAG
* *
28550 GAACCAAAGTTATAGAAGAACTTGTAAAAGTTTGGA-AAGTTTGGAAGTTCGTCCAAGAACCAAG
258 GAACCAAAGTTATAAAAGAACTTGTAAAAGTTT-GACAAGTTCGGAAGTTCGTCCAAGAACCAAG
* * * * *
28614 AGAGAAATAATTCTCATGTAAATAAGTTTTTAATTCAAGGACCAAAACTTGTTTACAAAATGACA
322 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAACGACA
*
28679 AACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGCTCGAAAAATTGCTAGAAGGAAT
387 AACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGCTCGAAAAATTGCTCGAAGGAAT
* * *
28744 GGATTGCCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCT
452 GGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCG
* * * *
28809 ACAGTTCAGCCAAGAAAC-AGGAGAGAAACAATTCTCACGTAAATAAGTCTTTAATTCAAAGACT
517 AAAGTTCAGCCAAG-AACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * ** *
28873 AGAACTTGTATACAAAATGACAAACTATTTAGACCAAATAATGCGATTTGTCGAGCATGGAATAT
581 AAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
28938 TCG-
646 TCGA
* * * *
28941 AAAATT--T-----G-CT-G---G-----AATACTTTAAGGAATCGAAGTTATAAAAGAACTCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
* * * * * ** *
28989 AAAAGTCTGACAAGTTCGGAAGTTCGGCCAATAATCAAGAGTCA-AAAAAATAATCATGTAAATA
66 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAACAAGAG--AGAAACAATTCTCACGTAAATA
* * * *
29053 AGTTTTTAATTCAAATACCAAAATTTGTGTACAAAATGACAAACTATTTAGACCAAATGATGCGA
129 AGATTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
** * * * *
29118 TTTCCTGAGCATGGAATGTTCAAAAAATTG-TTGGAAGGAATG----G-ATTG--T--TTT----
194 TTTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAAGGAATGAATCGTCTTGAATACTTTAAGG
* * * *
29169 -TCC----------AAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTTGTCCAAGAACCAAGAG
259 AACCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAG
** * * * * * *
29223 AGAAACAATTCTCACAAAAATAAGTTATTAATTCATAA-ACCAAAACTGGTATACAAAATGATAA
324 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCA-AAGAACAAAACTTGTTTACAAAACGACAA
* * * * * ** * * * *
29287 ACTATTTA-AACAGAATAATGAGATTTCTCAATAATGGAATGTTTGGAAAATTGCTCAAAGGAAT
388 ACTATTTAGACCA-AATGATGCGATTTCCCGAGCATGGAATGCTCGAAAAATTGCTCGAAGGAAT
* *
29351 GGATCGTCTTGGATACTTTAAGGAACCGAAGTT
452 GGATCGTCTTGAATACTTTAAGGAATCGAAGTT
29384 CGGCCAAGAG
Statistics
Matches: 2032, Mismatches: 305, Indels: 130
0.82 0.12 0.05
Matches are distributed among these distances:
606 5 0.00
607 174 0.09
608 1 0.00
617 2 0.00
622 3 0.00
624 1 0.00
625 1 0.00
626 1 0.00
628 35 0.02
629 31 0.02
630 61 0.03
631 43 0.02
632 2 0.00
633 1 0.00
636 1 0.00
637 1 0.00
638 1 0.00
643 1 0.00
644 7 0.00
645 288 0.14
646 394 0.19
647 825 0.41
648 150 0.07
649 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (649 bp):
AAAATTGCTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAAGCAAAGTTATAAAAGAACTTGT
AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAACAAGAGAGAAACAATTCTCACGTAAATAAG
ATTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
TCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAAGGAATGAATCGTCTTGAATACTTTAAGGAA
CCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAG
AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAACGACAAACT
ATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGCTCGAAAAATTGCTCGAAGGAATGGAT
CGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCGAAAG
TTCAGCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAC
TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA
Found at i:29118 original size:199 final size:198
Alignment explanation
Indices: 28754--29313 Score: 549
Period size: 199 Copynumber: 2.9 Consensus size: 198
28744 GGATTGCCTT
* * *
28754 GAATACTTTAAGGAATCGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCTACAGTTCAGC
1 GAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTCTGACAAGTTCGACAGTTCAGC
* * ** * *
28819 CAAGAAACAGGAGAGAAACAATTCTCACGTAAATAAGTCTTTAATTCAAAGACTAGAACTTGTAT
66 CAAGAAACAAGAGAGAAAAAATAATCACGTAAATAAGTCTTTAATTCAAAGACCAAAACTTGTAT
* * *
28884 ACAAAATGACAAACTATTTAGACCAAATAATGCGATTT-GTCGAGCATGGAATATTCGAAAATTT
131 ACAAAATGACAAACTATTTAGACCAAATAATGCGATTTCCT-GAGCATGGAATATTCAAAAAATT
28948 GCTG
195 GCTG
*
28952 GAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTCTGACAAGTTCGGA-AGTTCGG
1 GAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTCTGACAAGTTC-GACAGTTCAG
* * * * * *
29016 CCAATAATCAAGAGTCA-AAAAAATAATCATGTAAATAAGTTTTTAATTCAAATACCAAAATTTG
65 CCAAGAAACAAGAG--AGAAAAAATAATCACGTAAATAAGTCTTTAATTCAAAGACCAAAACTTG
* * *
29080 TGTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAAAAAA
128 TATACAAAATGACAAACTATTTAGACCAAATAATGCGATTTCCTGAGCATGGAATATTCAAAAAA
*
29145 TTGTTG
193 TTGCTG
* * * ** *
29151 G--------AAGGAATGGATTGTTTTTCCAAGAACTCGTAAAAGTTTGACAAGTTCAGA-AGTT-
1 GAATACTTTAAGGAATCGA-AG-TTATAAAAGAACTCGTAAAAGTCTGACAAGTTC-GACAGTTC
* * * ** **
29206 TGTCCAAGAACCAAGAGAGAAACAATTCTCACAAAAATAAGT-TATTAATTCATAA-ACCAAAAC
63 AG-CCAAGAAACAAGAGAGAAAAAATAATCACGTAAATAAGTCT-TTAATTCA-AAGACCAAAAC
* * * *
29269 TGGTATACAAAATGATAAACTATTTA-AACAGAATAATGAGATTTC
125 TTGTATACAAAATGACAAACTATTTAGACCA-AATAATGCGATTTC
29314 TCAATAATGG
Statistics
Matches: 305, Mismatches: 46, Indels: 28
0.80 0.12 0.07
Matches are distributed among these distances:
191 14 0.05
192 69 0.23
193 49 0.16
198 69 0.23
199 102 0.33
200 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (198 bp):
GAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTCTGACAAGTTCGACAGTTCAGC
CAAGAAACAAGAGAGAAAAAATAATCACGTAAATAAGTCTTTAATTCAAAGACCAAAACTTGTAT
ACAAAATGACAAACTATTTAGACCAAATAATGCGATTTCCTGAGCATGGAATATTCAAAAAATTG
CTG
Found at i:29326 original size:192 final size:192
Alignment explanation
Indices: 28979--29329 Score: 422
Period size: 192 Copynumber: 1.8 Consensus size: 192
28969 GAAGTTATAA
* * *
28979 AAGAACTCGTAAAAGTCTGACAAGTTCGGAAGTTCGGCCAATAATCAAGAGTCAAAAAAATAATC
1 AAGAACTCGTAAAAGTCTGACAAGTTCAGAAGTTCGGCCAAGAACCAAGAG-CAAAAAAATAATC
*** * * * * *
29044 ATGTAAATAAGTTTTTAATTCAAATACCAAAATTTGTGTACAAAATGACAAACTATTTAGACCAA
65 ACAAAAATAAGTTATTAATTCAAATACCAAAACTGGTATACAAAATGACAAACTATTTAGAACAA
* * * *
29109 ATGATGCGATTTCCTGAGCATGGAATGTTCAAAAAATTGTTGGAAGGAATGGATTGTTTTTCC
130 ATAATGAGATTTCCTAAGAATGGAATGTTCAAAAAATTGTTGGAAGGAATGGATTGTTTTTCC
* * * * **
29172 AAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTTGTCCAAGAACCAAGAG-AGAAACAATTCTC
1 AAGAACTCGTAAAAGTCTGACAAGTTCAGAAGTTCGGCCAAGAACCAAGAGCA-AAAAAATAATC
*
29236 ACAAAAATAAGTTATTAATTCATAA-ACCAAAACTGGTATACAAAATGATAAACTATTTA-AACA
65 ACAAAAATAAGTTATTAATTCA-AATACCAAAACTGGTATACAAAATGACAAACTATTTAGAACA
*
29299 GAATAATGAGATTT-CTCAATAATGGAATGTT
129 -AATAATGAGATTTCCT-AAGAATGGAATGTT
29330 TGGAAAATTG
Statistics
Matches: 131, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
191 6 0.05
192 78 0.60
193 47 0.36
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (192 bp):
AAGAACTCGTAAAAGTCTGACAAGTTCAGAAGTTCGGCCAAGAACCAAGAGCAAAAAAATAATCA
CAAAAATAAGTTATTAATTCAAATACCAAAACTGGTATACAAAATGACAAACTATTTAGAACAAA
TAATGAGATTTCCTAAGAATGGAATGTTCAAAAAATTGTTGGAAGGAATGGATTGTTTTTCC
Found at i:31895 original size:80 final size:80
Alignment explanation
Indices: 31770--31919 Score: 248
Period size: 80 Copynumber: 1.9 Consensus size: 80
31760 ACTAATTTTA
*
31770 TTTTAACTATTGTAGGGAAATCAATGAGTCATGTCCCTTCATTAGGATCTGATGTAGTTGAAAAG
1 TTTTAACTATTGTAGGGAAACCAATGAGTCATGTCCCTTCATTAGGATCTGATGTAGTTGAAAAG
31835 GCATGGCAATTTCAT
66 GCATGGCAATTTCAT
* * *
31850 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATG-CCTCTTCATTAGGATTTGATGTAGTTGAAAA
1 TTTTAACTATTGTAGGGAAACCAATGAGTCATGTCC-CTTCATTAGGATCTGATGTAGTTGAAAA
31914 GGCATG
65 GGCATG
31920 ATATTTCTCC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
79 2 0.03
80 63 0.97
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (80 bp):
TTTTAACTATTGTAGGGAAACCAATGAGTCATGTCCCTTCATTAGGATCTGATGTAGTTGAAAAG
GCATGGCAATTTCAT
Found at i:34523 original size:23 final size:23
Alignment explanation
Indices: 34485--34529 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34475 CATATACATA
*
34485 ATTTGAAATCTGTATTAAAGGTC
1 ATTTGAAATCTCTATTAAAGGTC
* *
34508 ATTTGAAATTTCTATTAGAGGT
1 ATTTGAAATCTCTATTAAAGGT
34530 ACTAAGGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (23 bp):
ATTTGAAATCTCTATTAAAGGTC
Found at i:39087 original size:19 final size:20
Alignment explanation
Indices: 39054--39091 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39044 GAATATTTTT
*
39054 TATTTTTTTTATTTTTCTCA
1 TATTTTTCTTATTTTTCTCA
39074 TATTTTTCTT-TTTTTCTC
1 TATTTTTCTTATTTTTCTC
39092 GACTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTCTTATTTTTCTCA
Found at i:39495 original size:128 final size:128
Alignment explanation
Indices: 39333--39592 Score: 493
Period size: 128 Copynumber: 2.0 Consensus size: 128
39323 ATGAAAGCGG
39333 AAGAGGATCGTAAAGTTGTCAAGTCGCGGATCTACCCTAAAGCTCTAGACAAATGTAGTCTAAAA
1 AAGAGGATCGTAAAGTTGTCAAGTCGCGGATCTACCCTAAAGCTCTAGACAAATGTAGTCTAAAA
*
39398 CGAAAANAAAGAAAGACAGATTAATTGATAAGAAAAATAATCAAACGAAATTAAAACGAAAGA
66 CGAAAACAAAGAAAGACAGATTAATTGATAAGAAAAATAATCAAACGAAATTAAAACGAAAGA
*
39461 AAGAGGATCGTCAAGTTGTCAAGTCGCGGATCTACCCTAAAGCTCTAGACAAATGTAGTCTAAAA
1 AAGAGGATCGTAAAGTTGTCAAGTCGCGGATCTACCCTAAAGCTCTAGACAAATGTAGTCTAAAA
*
39526 CGAAAACAAAGAAAGACAGATTAATTGATAAGAAGAATAATCAAACGAAATTAAAACGAAAGA
66 CGAAAACAAAGAAAGACAGATTAATTGATAAGAAAAATAATCAAACGAAATTAAAACGAAAGA
39589 AAGA
1 AAGA
39593 TGAATGGCTA
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (128 bp):
AAGAGGATCGTAAAGTTGTCAAGTCGCGGATCTACCCTAAAGCTCTAGACAAATGTAGTCTAAAA
CGAAAACAAAGAAAGACAGATTAATTGATAAGAAAAATAATCAAACGAAATTAAAACGAAAGA
Found at i:43758 original size:19 final size:20
Alignment explanation
Indices: 43721--43758 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43711 AATACTCGAA
*
43721 TTTTTTCTTCTTTCGATTCT
1 TTTTTTCTTCTTTCAATTCT
*
43741 TTTTTTCTT-TTTTAATTC
1 TTTTTTCTTCTTTCAATTC
43759 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTTCTTCTTTCAATTCT
Found at i:43849 original size:20 final size:20
Alignment explanation
Indices: 43809--43851 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
43799 TTTTTCAATA
* **
43809 TTTCGATTTTTTTTCTTTTT
1 TTTCGAATTTTTTTCACTTT
43829 TTTCGAATTTTTTTCACTTT
1 TTTCGAATTTTTTTCACTTT
43849 TTT
1 TTT
43852 TGAAATACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTCGAATTTTTTTCACTTT
Done.