Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015076.1 Kokia drynarioides strain JFW-HI SEQ_130120, 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: 253429
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 328 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:903 original size:37 final size:37
Alignment explanation
Indices: 797--893 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
787 AAACGGTTAG
*
797 CTTCCAGATGAGATATTGAGAAGTGAACCAAATTCGT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGT
* * * * *
834 CTTTCTGATGATATACGGAGAAGTGAATCAAATTCGT
1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGT
*
871 CTTCCCGATGAGATACTGAGAAG
1 CTTCCAGATGAGATACTGAGAAG
894 AAGACCAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (37 bp):
CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGT
Found at i:1024 original size:194 final size:195
Alignment explanation
Indices: 695--1464 Score: 782
Period size: 194 Copynumber: 3.9 Consensus size: 195
685 TGAGATGCGA
** * * * *
695 AGAAGAAGACCAAATCAGGCCTACGCTCAAAGCAAGCAAAATCTTCGAACCCCAGCTTCTTGATG
1 AGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAG-TAAATCTTCGAACCCCAGCTTCCTGATG
* **
760 AGATACCGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTTCCAGATGAGATATTGAGAAGTGAA
65 AGACACCGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGATGAGATACGGAGAAGTGAA
* * * * *
824 CCAAATTCGTCTTTCTGATGATATACGGAGAAGTGAATCAAAT-TCGTCTTCCCGATGAGATACT
130 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATCAAATGTCATCTTCCCGATGAGATACT
888 G
195 G
*
889 AGAAGAAGACCAAATCAAGCCCACGCTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCCTGATG
1 AGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGT-AAATCTTCGAACCCCAGCTTCCTGATG
* * *
954 AGACACCGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTTTCAGATGAGATACTGAGGAGTGAA
65 AGACACCGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGATGAGATACGGAGAAGTGAA
* *
1018 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTTCT
130 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA-T----CAA---AT---GTCATCTTCCC
1083 GATGAGATACTG
184 GATGAGATACTG
* * * * * * * * *
1095 AGAAGAAGGCCAAACCAAACCCACGCAC-GA-TGAATAAACCTTCGAACCCCAGCTTCTTGATAA
1 AGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGTAAATCTTCGAACCCCAGCTTCCTGATGA
* ** * * * * *
1158 GATATTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACGGAAAAATTG-A
66 GACACCGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGATGAGATACGG-AGAAGTGAA
*
1222 TCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAAACTACGCAGTCATCTTCCC
130 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA-T----CAAA-T-----GTCATCTTCCC
*
1287 AATGAGATACTG
184 GATGAGATACTG
* * * * * * * *
1299 AGAAGAAGTCCAAATCAAACTCGCGCCCGATGTGAGTAAATCTTCGAA-CACAGCTTCCTGATGA
1 AGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGTAAATCTTCGAACCCCAGCTTCCTGATGA
* * *
1363 AACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCCA-ATGAGGTACGGAGAAGTGAA
66 GACACCGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTT-CCAGATGAGATACGGAGAAGTGAA
* *
1427 TCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAAT
130 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
1465 TGAAGCAAAC
Statistics
Matches: 489, Mismatches: 65, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
194 152 0.31
195 1 0.00
199 3 0.01
201 1 0.00
202 3 0.01
203 47 0.10
204 123 0.25
205 100 0.20
206 59 0.12
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (195 bp):
AGAAGAAGACCAAATCAAACCCACGCTCAAAGCGAGTAAATCTTCGAACCCCAGCTTCCTGATGA
GACACCGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGATGAGATACGGAGAAGTGAAC
CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATCAAATGTCATCTTCCCGATGAGATACTG
Found at i:1236 original size:204 final size:205
Alignment explanation
Indices: 870--1516 Score: 829
Period size: 205 Copynumber: 3.2 Consensus size: 205
860 ATCAAATTCG
* * * * *
870 TCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCAAAGCGAGTAAAATCTTC
1 TCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCAC-GAGTGAGT-AAATCTTC
* * *
935 GAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAAT-AAACGGTTAGCTTTCAGA
64 GAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGA
* * *
999 TGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAA
129 TGAGATACGGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAA
* * *
1064 GCGATGCGGTCA
194 ACGACGCAGTCA
* * * * *
1076 TCTTTCTGATGAGATACTGAGAAGAAGGCCAAACCAAACCCACGCACGA-TGAATAAACCTTCGA
1 TCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCACGAGTGAGTAAATCTTCGA
* * * * * *
1140 ACCCCAGCTTCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATG
66 ACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGATG
* * *
1205 AGATACGGAAAAATTG-ATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAAA
131 AGATACGG-AGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAA
*
1269 CTACGCAGTCA
195 CGACGCAGTCA
* * * * *
1280 TCTTCCCAATGAGATACTGAGAAGAAGTCCAAATCAAACTCGCGCCCGATGTGAGTAAATCTTCG
1 TCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCACGA-GTGAGTAAATCTTCG
*
1345 AA-CACAGCTTCCTGATGAA-ACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCCA-
65 AACCCCAGCTTCCTGAT-AAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTT-CCAG
* * *
1407 ATGAGGTACGGAGAAGTGAATCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAGCA
128 ATGAGATACGGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
*
1472 AACGACGCAATCA
193 AACGACGCAGTCA
* *
1485 TCTTCCGGATGAGATACTGGGAAGAAGGCCAA
1 TCTTCCCGATGAGATACTGAGAAGAAGGCCAA
1517 GTTAATGAAA
Statistics
Matches: 376, Mismatches: 58, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
203 47 0.12
204 126 0.34
205 144 0.38
206 59 0.16
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (205 bp):
TCTTCCCGATGAGATACTGAGAAGAAGGCCAAATCAAACCCACGCACGAGTGAGTAAATCTTCGA
ACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCAGATG
AGATACGGAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAAC
GACGCAGTCA
Found at i:2064 original size:29 final size:28
Alignment explanation
Indices: 2023--2290 Score: 194
Period size: 29 Copynumber: 9.4 Consensus size: 28
2013 CAGGCCCATT
2023 TTTTGACCCCGAACTTCCAAAAATCCCA
1 TTTTGACCCCGAACTTCCAAAAATCCCA
* * * *
2051 TTTTTGACCTCGAACCTTTCGAAAATTACCA
1 -TTTTGACCCCGAA-C-TTCCAAAAATCCCA
** *
2082 TTTT-A--CC---CTTTTAAAAATTACCA
1 TTTTGACCCCGAACTTCCAAAAA-TCCCA
*
2105 TTTT-ACCCTCGAACTTCCAAAAATTCCA
1 TTTTGACCC-CGAACTTCCAAAAATCCCA
*
2133 TTTTTTGACCCCGAACCTTCCAAAAATCTCA
1 --TTTTGACCCCGAA-CTTCCAAAAATCCCA
2164 TTTT-ACCCCCGAACTTCCAAAAATCCCA
1 TTTTGA-CCCCGAACTTCCAAAAATCCCA
* *
2192 TTTTGACCCCGAACCTTTCCAAAATTACCA
1 TTTTGACCCCGAA-C-TTCCAAAAATCCCA
*
2222 TTTT-ACCTTCGAACTTCCAAAAATCCCA
1 TTTTGACC-CCGAACTTCCAAAAATCCCA
** * *
2250 TTTTTGACTTCGAACCTTCCAAAACTACCA
1 -TTTTGACCCCGAA-CTTCCAAAAATCCCA
*
2280 TTTTGCCCCCG
1 TTTTGACCCCG
2291 TGCATCCAAA
Statistics
Matches: 193, Mismatches: 25, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
22 6 0.03
23 11 0.06
25 1 0.01
26 1 0.01
27 1 0.01
28 42 0.22
29 55 0.28
30 48 0.25
31 28 0.15
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (28 bp):
TTTTGACCCCGAACTTCCAAAAATCCCA
Found at i:2235 original size:58 final size:58
Alignment explanation
Indices: 2095--2283 Score: 274
Period size: 58 Copynumber: 3.2 Consensus size: 58
2085 TACCCTTTTA
*
2095 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTTGACCCCGAACCTTCC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACCTTCC
* *
2154 AAAAAT-CTCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACCTTTCC
1 AAAATTAC-CATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCC
* **
2212 AAAATTACCATTTTACCTTCGAACTTCCAAAAATCCCATTTTTGACTTCGAACCTTCC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
*
2270 AAAACTACCATTTT
1 AAAATTACCATTTT
2284 GCCCCCGTGC
Statistics
Matches: 117, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
57 15 0.13
58 55 0.47
59 47 0.40
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCC
Found at i:11531 original size:50 final size:50
Alignment explanation
Indices: 11468--11637 Score: 234
Period size: 50 Copynumber: 3.4 Consensus size: 50
11458 TCACAAAGAC
* **
11468 ACAA-AAGGGAAAGGTTTAGGTCACAACGGCGGACCGTGTACCTCAGAAG
1 ACAAGAAGGGAAAGGTTTAAGTCGTAACGGCGGACCGTGTACCTCAGAAG
* *
11517 ACAAGAAAGGAAAGGTTTAAGTCGTAACGGCGGACCATGTACCTCAGAAG
1 ACAAGAAGGGAAAGGTTTAAGTCGTAACGGCGGACCGTGTACCTCAGAAG
* * * * *
11567 ACAAGAAGGGAAAGGTTTAAATCGTAACAGCAGATCGTGTACCACAGAAG
1 ACAAGAAGGGAAAGGTTTAAGTCGTAACGGCGGACCGTGTACCTCAGAAG
*
11617 ACAAGAAGGGAAAGATTTAAG
1 ACAAGAAGGGAAAGGTTTAAG
11638 CCGCAACAGT
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
49 4 0.04
50 102 0.96
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.15
Consensus pattern (50 bp):
ACAAGAAGGGAAAGGTTTAAGTCGTAACGGCGGACCGTGTACCTCAGAAG
Found at i:11646 original size:50 final size:50
Alignment explanation
Indices: 11412--11693 Score: 230
Period size: 50 Copynumber: 5.6 Consensus size: 50
11402 TCAGTACCAT
* * * * * *
11412 GAAGACATGAAGGGAAAGATTTAAGACTGCAACAGCGGA-TATAGAATCACA
1 GAAGACAAGAAGGGAAAGGTTTAAGTC-GCAACAGCGGACCAT-GTACCACA
* * * * * *
11463 -AAGACACAAAAGGGAAAGGTTTAGGTCACAACGGCGGACCGTGTACCTCA
1 GAAGACA-AGAAGGGAAAGGTTTAAGTCGCAACAGCGGACCATGTACCACA
* * * *
11513 GAAGACAAGAAAGGAAAGGTTTAAGTCGTAACGGCGGACCATGTACCTCA
1 GAAGACAAGAAGGGAAAGGTTTAAGTCGCAACAGCGGACCATGTACCACA
* * * * *
11563 GAAGACAAGAAGGGAAAGGTTTAAATCGTAACAGCAGATCGTGTACCACA
1 GAAGACAAGAAGGGAAAGGTTTAAGTCGCAACAGCGGACCATGTACCACA
* * * *
11613 GAAGACAAGAAGGGAAAGATTTAAGCCGCAACAGTGAATCCA-GTACCAC-
1 GAAGACAAGAAGGGAAAGGTTTAAGTCGCAACAGCGGA-CCATGTACCACA
****
11662 GAAGGTTTGAAGGGGAAAGGTTTAAGTCGCAA
1 GAAGACAAGAA-GGGAAAGGTTTAAGTCGCAA
11694 TGGCGAACCC
Statistics
Matches: 186, Mismatches: 40, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
49 7 0.04
50 156 0.84
51 23 0.12
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.16
Consensus pattern (50 bp):
GAAGACAAGAAGGGAAAGGTTTAAGTCGCAACAGCGGACCATGTACCACA
Found at i:12566 original size:206 final size:206
Alignment explanation
Indices: 12203--13111 Score: 1408
Period size: 206 Copynumber: 4.4 Consensus size: 206
12193 AAATGGTTAG
* * *
12203 CTTCCTGATGAGATATAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
* * *
12268 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCAAACCCCAGCTTCCTGAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCTAGCTTCCTGAT
*
12333 GAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
131 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
12398 ACCAAATTCGT
196 ACCAAATTCGT
12409 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
** * *
12474 TGAGAAGAAGACCAAATCAAACCCACATTTGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCTAGCTTCCTGAT
* ** * * *
12539 GAGATATTGAGAATTAGGTCAAAGCAATTAAATGGTTAGCTTCCTGATGAGTTACTGAGAAGTGG
131 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
12604 ACCAAATTCGT
196 ACCAAATTCGT
* *
12615 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
* *
12680 TGAGAAGAAGACCAAATCAAACCCATGCTCGATATGAGCAAATCTTCGAAACCC-GGCTTCCTGA
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCG-AACCCTAGCTTCCTGA
* *
12744 TGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACTGAGAAGGG
130 TGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTG
12809 GACCAAATTCGT
195 GACCAAATTCGT
* * *
12821 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCAATGCGGTCATCTTCCTTACGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
* * *
12886 TAAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTTGAACCCTAGCTTCCTGAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCTAGCTTCCTGAT
* * *
12951 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACGGAGAAGTGA
131 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
*
13016 ACCAAATCCGT
196 ACCAAATTCGT
* * * * * * *
13027 CTTCCTGATGAAACACAGAAAAGTGAATT-AAGACAAGTGATGCGGTCATCTTCCTGATGAAATA
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAA-ACAAGCGATGCGGTCATCTTCCTGATGAGATA
* *
13091 CTAAGAAGTAGACCAAATCAA
65 CTGAGAAGAAGACCAAATCAA
13112 CTACACCAAA
Statistics
Matches: 644, Mismatches: 56, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
205 7 0.01
206 632 0.98
207 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATAC
TGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCTAGCTTCCTGAT
GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
ACCAAATTCGT
Found at i:13425 original size:6 final size:6
Alignment explanation
Indices: 13414--13495 Score: 66
Period size: 6 Copynumber: 14.0 Consensus size: 6
13404 CCCAACTCAT
* *
13414 TTTAAA TTTAAA TTT--A TTCTAGAA TTTAAA TTT-AA TTTAAG TTTAAG
1 TTTAAA TTTAAA TTTAAA TT-TA-AA TTTAAA TTTAAA TTTAAA TTTAAA
* *
13461 TTTATA TTTAAA TTTAAA ATT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
13496 AATGAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
4 5 0.08
5 7 0.11
6 42 0.68
7 5 0.08
8 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:13441 original size:18 final size:16
Alignment explanation
Indices: 13414--13495 Score: 83
Period size: 18 Copynumber: 4.8 Consensus size: 16
13404 CCCAACTCAT
13414 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
13430 TTCTAGAATTTAAATTTAA
1 TT-TA-AATTTAAATTT-A
* *
13449 TTTAAGTTTAAGTTTATA
1 TTTAAATTTAA-ATT-TA
*
13467 TTTAAATTTAAAATTA
1 TTTAAATTTAAATTTA
13483 TTATAAATTTAAA
1 TT-TAAATTTAAA
13496 AATGAATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
16 6 0.11
17 19 0.35
18 26 0.47
19 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:13453 original size:35 final size:34
Alignment explanation
Indices: 13414--13495 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
13404 CCCAACTCAT
*
13414 TTTAAATTTAAATTTAT-TCTAGAATTTAAATTTAA
1 TTTAAATTTAAATTTATATCTA-AATTTAAAATT-A
* * *
13449 TTTAAGTTTAAGTTTATATTTAAATTTAAAATTA
1 TTTAAATTTAAATTTATATCTAAATTTAAAATTA
13483 TTATAAATTTAAA
1 TT-TAAATTTAAA
13496 AATGAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 3 0.08
35 33 0.85
36 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
TTTAAATTTAAATTTATATCTAAATTTAAAATTA
Found at i:14201 original size:3 final size:3
Alignment explanation
Indices: 14195--14247 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
14185 AATGTGATAT
14195 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14243 TAA TA
1 TAA TA
14248 TTTTTAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15357 original size:29 final size:29
Alignment explanation
Indices: 15325--15545 Score: 166
Period size: 29 Copynumber: 7.6 Consensus size: 29
15315 AAACTTCACC
*
15325 AAAATTATATTTTTACCCTAAACTTTTCA
1 AAAATTACATTTTTACCCTAAACTTTTCA
** *
15354 AAAATTACATTTTTACCCCGAAC-TTTCC
1 AAAATTACATTTTTACCCTAAACTTTTCA
* * * *
15382 AAAATTCCCTTTTAACCCTAAACTTTCCA
1 AAAATTACATTTTTACCCTAAACTTTTCA
*
15411 AAAATTACATTTTTACCCTAGAAC-TTTCT
1 AAAATTACATTTTTACCCTA-AACTTTTCA
* * *
15440 AAAATTCCATTTTGACCCT-GA-TTTGTCCA
1 AAAATTACATTTTTACCCTAAACTTT-T-CA
*
15469 AAAATTACCA-TTTTACCCTCAAAC-TTCCA
1 AAAATTA-CATTTTTACCCT-AAACTTTTCA
* * ** *
15498 AAAATTCCATTTTTAACCTCGATTTTTCCA
1 AAAATTACATTTTTACCCTAAACTTTT-CA
* *
15528 AAAATTATAATTTTACCC
1 AAAATTACATTTTTACCC
15546 CCAGATGTCT
Statistics
Matches: 146, Mismatches: 34, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
27 3 0.02
28 26 0.18
29 93 0.64
30 21 0.14
31 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTAAACTTTTCA
Found at i:15469 original size:58 final size:58
Alignment explanation
Indices: 15333--15545 Score: 213
Period size: 58 Copynumber: 3.7 Consensus size: 58
15323 CCAAAATTAT
* * * *
15333 ATTTTTACCCTAAACTTTT-CAAAAATTACATTTTTACCC-CGAACTTTCCAAAATTCC
1 ATTTTAACCCTAGA-TTTTCCAAAAATTACATTTTTACCCTAGAACTTTCAAAAATTCC
* * * *
15390 CTTTTAACCCTAAACTTTCCAAAAATTACATTTTTACCCTAGAACTTTCTAAAATTCC
1 ATTTTAACCCTAGATTTTCCAAAAATTACATTTTTACCCTAGAACTTTCAAAAATTCC
* *
15448 ATTTTGACCCT-GATTTGTCCAAAAATTACCA-TTTTACCCTCA-AACTTCCAAAAATTCC
1 ATTTTAACCCTAGATTT-TCCAAAAATTA-CATTTTTACCCT-AGAACTTTCAAAAATTCC
* * *
15506 ATTTTTAA-CCTCGATTTTTCCAAAAATTATAATTTTACCC
1 A-TTTTAACCCTAGA-TTTTCCAAAAATTACATTTTTACCC
15546 CCAGATGTCT
Statistics
Matches: 134, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
56 3 0.02
57 35 0.26
58 64 0.48
59 29 0.22
60 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (58 bp):
ATTTTAACCCTAGATTTTCCAAAAATTACATTTTTACCCTAGAACTTTCAAAAATTCC
Found at i:15570 original size:59 final size:58
Alignment explanation
Indices: 15348--15579 Score: 181
Period size: 58 Copynumber: 4.0 Consensus size: 58
15338 TACCCTAAAC
* * * * * *
15348 TTTT-CAAAAATTACATTTTTACCCCGA-ACTTTCCAAAATTCC-CTTTTAACC-CTAAA
1 TTTTCCAAAAATTACAATTTTACCCCCAGAC-TTCTAAAATTCCATTTTTAACCTC-GAT
* * * * *
15404 CTTTCCAAAAATTACATTTTTA-CCCTAGAACTTTCTAAAATTCCATTTTGACCCT-GAT
1 TTTTCCAAAAATTACAATTTTACCCCCAG-AC-TTCTAAAATTCCATTTTTAACCTCGAT
* * * * *
15462 TTGTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAT
1 TTTTCCAAAAATTACAATTTTACCCCCAGACTT-CTAAAATTCCATTTTTAACCTCGAT
* *
15521 TTTTCCAAAAATTATAATTTTACCCCCAGA-TGTCTAAAATTTCATTTTTTTAACCTCGA
1 TTTTCCAAAAATTACAATTTTACCCCCAGACT-TCTAAAATTCCA--TTTTTAACCTCGA
15580 ACTTTCCCAA
Statistics
Matches: 140, Mismatches: 25, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
56 7 0.05
57 19 0.14
58 63 0.45
59 38 0.27
60 13 0.09
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTTCCAAAAATTACAATTTTACCCCCAGACTTCTAAAATTCCATTTTTAACCTCGAT
Found at i:15620 original size:60 final size:60
Alignment explanation
Indices: 15465--15621 Score: 135
Period size: 60 Copynumber: 2.6 Consensus size: 60
15455 CCCTGATTTG
** * * * **
15465 TCCAAAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCA--TTTTTAACCTCGATTTT
1 TCCAAAAATTATAATTTTACCCCCAGA-TGTCC-AAAATTTCATTTTTTTAACCTCGAACTT
*
15524 TCCAAAAATTATAATTTTACCCCCAGATGTCTAAAATTTCATTTTTTTAACCTCGAACTT
1 TCCAAAAATTATAATTTTACCCCCAGATGTCCAAAATTTCATTTTTTTAACCTCGAACTT
* * * *
15584 TCCCAACATTACT-ATTTTGCCCTC-GAGTGTCCAAAATT
1 TCCAAAAATTA-TAATTTTACCCCCAGA-TGTCCAAAATT
15622 GCCATTTTGC
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
58 9 0.11
59 27 0.34
60 43 0.54
61 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
TCCAAAAATTATAATTTTACCCCCAGATGTCCAAAATTTCATTTTTTTAACCTCGAACTT
Found at i:15656 original size:29 final size:28
Alignment explanation
Indices: 15597--15658 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
15587 CAACATTACT
* * *
15597 ATTTTGCCCTCGAGTGTCCAAAATTGCC
1 ATTTTGCCCTCAAGTATCCAAAAATGCC
15625 ATTTTGCCCCTCAAGTATCCAAAAAT-CAC
1 ATTTTG-CCCTCAAGTATCCAAAAATGC-C
15654 ATTTT
1 ATTTT
15659 CAAACCCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (28 bp):
ATTTTGCCCTCAAGTATCCAAAAATGCC
Found at i:16582 original size:3 final size:3
Alignment explanation
Indices: 16574--16604 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16564 TGAAAGAAAA
16574 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
16605 GGGTTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:17345 original size:23 final size:23
Alignment explanation
Indices: 17302--17345 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17292 CAATTTCTAT
* *
17302 TAAATTATAATTATTTTTAAATA
1 TAAATTATAATAATTTATAAATA
17325 TAAATTA-AATAATTTGATAAA
1 TAAATTATAATAATTT-ATAAA
17346 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATTATAATAATTTATAAATA
Found at i:20567 original size:17 final size:17
Alignment explanation
Indices: 20544--20671 Score: 150
Period size: 17 Copynumber: 7.4 Consensus size: 17
20534 AATCAACTTT
20544 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
20562 -TTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAA
*
20578 TTTAAATTTGTTTTTAAA
1 TTTAAATTT-ATTTTAAA
*
20596 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* * *
20613 TTTAAGTTTAATTTAAG
1 TTTAAATTTATTTTAAA
20630 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
20648 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
20665 TTTAAAT
1 TTTAAAT
20672 AAATAAAAGT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.01
17 63 0.68
18 29 0.31
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:20601 original size:35 final size:34
Alignment explanation
Indices: 20544--20671 Score: 150
Period size: 35 Copynumber: 3.7 Consensus size: 34
20534 AATCAACTTT
*
20544 TTTAAATTTATTTTAAGA-TTAAATTTATTCTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTTAAA
* *
20578 TTTAAATTTGTTTTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTT-ATTTTAAATTTAAATTTATTTTAAA
* * *
20613 TTTAAGTTTAATTTAAGTTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTA-TTTTAAA
* *
20648 TTTAAAATTATTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
20672 AAATAAAAGT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
34 24 0.31
35 54 0.69
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:20610 original size:52 final size:52
Alignment explanation
Indices: 20544--20671 Score: 170
Period size: 52 Copynumber: 2.5 Consensus size: 52
20534 AATCAACTTT
*
20544 TTTAAATTTATTTTAAGA-TTAAATTT-ATTCTAAATTTAAATTTGTTTTTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATT-TAAATTTAAATTTATTTTTAAA
* * *
20596 TTTAAATTTGTTTTAAATTTAAGTTTAATTTAAGTTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAATTTAAATTTATTTTTAAA
* *
20648 TTTAAAATTATTATAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
20672 AAATAAAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 1 0.02
52 62 0.94
53 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (52 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAATTTAAATTTATTTTTAAA
Found at i:20625 original size:11 final size:12
Alignment explanation
Indices: 20555--20652 Score: 71
Period size: 12 Copynumber: 8.4 Consensus size: 12
20545 TTAAATTTAT
*
20555 TTTAAGATTAAA
1 TTTAAGTTTAAA
20567 TTT-A-TTCTAAA
1 TTTAAGTT-TAAA
* ***
20578 TTTAAATTTGTT
1 TTTAAGTTTAAA
*
20590 TTTAAATTTAAA
1 TTTAAGTTTAAA
20602 TTT--GTTTTAAA
1 TTTAAG-TTTAAA
20613 TTTAAGTTT-AA
1 TTTAAGTTTAAA
20624 TTTAAGTTTAAA
1 TTTAAGTTTAAA
**
20636 TTTATTTTTAAA
1 TTTAAGTTTAAA
20648 TTTAA
1 TTTAA
20653 AATTATTATA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
10 1 0.01
11 28 0.41
12 36 0.53
13 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (12 bp):
TTTAAGTTTAAA
Found at i:22164 original size:30 final size:30
Alignment explanation
Indices: 22119--22299 Score: 240
Period size: 30 Copynumber: 6.1 Consensus size: 30
22109 AATAGCTCGA
*
22119 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG
** *
22149 GGGCCAAAACATAATTTT-GAAAAGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG
*
22178 GGGTTAAAACATAATTTTGGAAAAGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG
*
22208 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG
* * *
22238 GGG-TAAATTATAATTTTGGAAAAGATAAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG
* * *
22267 GTGTTAAAATGTAATTTTGGAAATGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG
22297 GGG
1 GGG
22300 CCTCTTGAGC
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 51 0.39
30 79 0.61
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
GGGTTAAAATATAATTTTGGAAAAGTTTAG
Found at i:22185 original size:59 final size:60
Alignment explanation
Indices: 22119--22299 Score: 213
Period size: 59 Copynumber: 3.0 Consensus size: 60
22109 AATAGCTCGA
*
22119 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCCAAAACATAATTTT-GAAAAGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGCCAAAACATAATTTTGGAAAAGTTTAG
* ** **
22178 GGGTTAAAACATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGCCAAAACATAATTTTGGAAAAGTTTAG
* * * * ** ** *
22238 GGG-TAAATTATAATTTTGGAAAAGATAAGGTGTTAAAATGTAATTTTGGAAATGTTTAG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGCCAAAACATAATTTTGGAAAAGTTTAG
22297 GGG
1 GGG
22300 CCTCTTGAGC
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
59 95 0.87
60 14 0.13
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (60 bp):
GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGCCAAAACATAATTTTGGAAAAGTTTAG
Found at i:22230 original size:89 final size:89
Alignment explanation
Indices: 22119--22299 Score: 265
Period size: 89 Copynumber: 2.0 Consensus size: 89
22109 AATAGCTCGA
* *
22119 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCCAAAACATAATTTT-GAAAAGTTTAGGGGTT
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGG-CAAAACATAATTTTGGAAAAGATAAGGGGTT
22183 AAAACATAATTTTGGAAAAGTTTAG
65 AAAACATAATTTTGGAAAAGTTTAG
* ** *
22208 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTAAATTATAATTTTGGAAAAGATAAGGTGTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCAAAACATAATTTTGGAAAAGATAAGGGGTTA
** *
22273 AAATGTAATTTTGGAAATGTTTAG
66 AAACATAATTTTGGAAAAGTTTAG
22297 GGG
1 GGG
22300 CCTCTTGAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 11 0.13
89 71 0.87
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (89 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGCAAAACATAATTTTGGAAAAGATAAGGGGTTA
AAACATAATTTTGGAAAAGTTTAG
Found at i:23860 original size:3 final size:3
Alignment explanation
Indices: 23831--23883 Score: 72
Period size: 3 Copynumber: 17.0 Consensus size: 3
23821 TTGCCATTTT
23831 TAA TAA GTAA TAA -ATA TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TA-A TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
23878 TAA TAA
1 TAA TAA
23884 AGGAGAATCG
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 38 0.83
4 7 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25355 original size:59 final size:60
Alignment explanation
Indices: 25015--25485 Score: 343
Period size: 59 Copynumber: 8.1 Consensus size: 60
25005 CCCAAAAGGT
* * * * *
25015 CCCT-AAACTATCCAAAAATCATATTTGACCCCT-AAACTTT-CTAAAATATACA-TTTTGA
1 CCCTCAAACT-TCCAAAAATTACATTTTACCCCTCAAACTTTCCAAAAAT-TACATTTTTTA
*
25073 CCCCTCAAACTTTCCAAAAATTACATTTTGACCCCT-AAACTTTCTAAAAA-TACCA--TTTTA
1 -CCCTCAAAC-TTCCAAAAATTACATTTT-ACCCCTCAAACTTTCCAAAAATTA-CATTTTTTA
*
25133 CCCTAAAACTTCCAAAAATTACATTTTTGA-CCC-CAAACTTTCCAAAAATT--ATGTTTTTA
1 CCCTCAAACTTCCAAAAATTACA-TTTT-ACCCCTCAAACTTTCCAAAAATTACAT-TTTTTA
*
25192 CCCTCGAACTTCCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAAATTACA-TTTTTA
1 CCCTCAAACTTCCAAAAATTA-CATTTTACCCCTCAAACTTTCCAAAAATTACATTTTTTA
* * * *
25251 -CCTCGAACTTCCAAAAATTACCATTTTA-CCCTCGAAC-TTCTAAAAATTGCATTTTTTA
1 CCCTCAAACTTCCAAAAATTA-CATTTTACCCCTCAAACTTTCCAAAAATTACATTTTTTA
* * * *
25309 -CCTCAAACTTTCCAAAAATTACATTTTACCCCTCGAAC-ATCGAAAAATTAC-TATTTTA
1 CCCTCAAAC-TTCCAAAAATTACATTTTACCCCTCAAACTTTCCAAAAATTACATTTTTTA
* * * * * **
25367 CCCTCAAA-TGTCC-AAAATCACCTTTTTACCCC-CAAGC-GTCTAAAAATTAC-CGTTTTA
1 CCCTCAAACT-TCCAAAAATTA-CATTTTACCCCTCAAACTTTCCAAAAATTACATTTTTTA
* * * * * *
25424 CCCTCGAACCT-CTAAAATTACCATTTTATCCC-CAAA-TGTCAAAAAATTACA-TTTTTA
1 CCCTCAAACTTCCAAAAATTA-CATTTTACCCCTCAAACTTTCCAAAAATTACATTTTTTA
25481 CCCTC
1 CCCTC
25486 GAGTGTCCAA
Statistics
Matches: 351, Mismatches: 34, Indels: 56
0.80 0.08 0.13
Matches are distributed among these distances:
56 2 0.01
57 91 0.26
58 101 0.29
59 110 0.31
60 26 0.07
61 17 0.05
62 4 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (60 bp):
CCCTCAAACTTCCAAAAATTACATTTTACCCCTCAAACTTTCCAAAAATTACATTTTTTA
Found at i:25470 original size:86 final size:85
Alignment explanation
Indices: 25232--25543 Score: 301
Period size: 86 Copynumber: 3.6 Consensus size: 85
25222 CCCTAAACTT
** * *
25232 TCCAAAAATTACATTTTTA-CCTCGAACTTCCAAAAATTACCATTTTACCCTCGAACT-TCTAAA
1 TCCAAAAATTACCGTTTTACCCTCGAACCT-CAAAAATTACCATTTTACCCTC-AAATGTC-AAA
** * * *
25295 AATTGCATTTTTTA-CCTCAAACTT
63 AATCACA-TTTTTACCCCCAAGC-G
* * * *
25319 TCCAAAAATTA-CATTTTACCCCTCGAACATCGAAAAATTACTATTTTACCCTCAAATGTCCAAA
1 TCCAAAAATTACCGTTTTA-CCCTCGAACCTC-AAAAATTACCATTTTACCCTCAAATGTCAAAA
*
25383 ATCACCTTTTTACCCCCAAGCG
64 ATCACATTTTTACCCCCAAGCG
* *
25405 TCTAAAAATTACCGTTTTACCCTCGAACCTCTAAAATTACCATTTTATCCC-CAAATGTCAAAAA
1 TCCAAAAATTACCGTTTTACCCTCGAACCTCAAAAATTACCATTTTA-CCCTCAAATGTC-AAAA
* * * *
25469 ATTACATTTTTACCCTCGAGTG
64 ATCACATTTTTACCCCCAAGCG
* *
25491 TCCAAAATTTACCGTTTTATCCTCGAACCTCCAAAAATTACCATTTTACCCTC
1 TCCAAAAATTACCGTTTTACCCTCGAACCT-CAAAAATTACCATTTTACCCTC
25544 GGGCATCCGA
Statistics
Matches: 188, Mismatches: 27, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
85 22 0.12
86 85 0.45
87 50 0.27
88 31 0.16
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (85 bp):
TCCAAAAATTACCGTTTTACCCTCGAACCTCAAAAATTACCATTTTACCCTCAAATGTCAAAAAT
CACATTTTTACCCCCAAGCG
Found at i:25544 original size:29 final size:29
Alignment explanation
Indices: 25057--25544 Score: 341
Period size: 29 Copynumber: 16.7 Consensus size: 29
25047 TAAACTTTCT
*
25057 AAAATATA-CATTTTGACCCCTCAAACTTTCCA
1 AAAAT-TACCATTTT-A-CCCTCGAAC-TTCCA
* *
25089 AAAATTA-CATTTTGACCC-CTAAACTTTCTA
1 AAAATTACCATTTT-ACCCTC-GAAC-TTCCA
**
25119 AAAA-TACCATTTTACCCTAAAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
*
25147 AAAATTA-CATTTTTGACCC-CAAACTTTCCA
1 AAAATTACCA-TTTT-ACCCTCGAAC-TTCCA
***
25177 AAAATTATGTTTTTACCCTCGAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
*
25206 AAAATTACCATTTTACCC-CTAAACTTTCCA
1 AAAATTACCATTTTACCCTC-GAAC-TTCCA
25236 AAAATTA-CATTTTTA-CCTCGAACTTCCA
1 AAAATTACCA-TTTTACCCTCGAACTTCCA
*
25264 AAAATTACCATTTTACCCTCGAACTTCTA
1 AAAATTACCATTTTACCCTCGAACTTCCA
* *
25293 AAAATT-GCATTTTTTA-CCTCAAACTTTCCA
1 AAAATTACCA--TTTTACCCTCGAAC-TTCCA
* *
25323 AAAATTA-CATTTTACCCCTCGAACATCGA
1 AAAATTACCATTTTA-CCCTCGAACTTCCA
* *
25352 AAAATTACTATTTTACCCTC-AAATGTCC-
1 AAAATTACCATTTTACCCTCGAACT-TCCA
* * * * *
25380 AAAATCACCTTTTTACCC-CCAAGCGTCTA
1 AAAATTACCATTTTACCCTCGAA-CTTCCA
* * *
25409 AAAATTACCGTTTTACCCTCGAACCT-CT
1 AAAATTACCATTTTACCCTCGAACTTCCA
* *
25437 AAAATTACCATTTTATCCC-C-AAATGTCAA
1 AAAATTACCATTTTA-CCCTCGAACT-TCCA
*
25466 AAAATTA-CATTTTTACCCTCG-AGTGTCCA
1 AAAATTACCA-TTTTACCCTCGAACT-TCCA
* * * *
25495 AAATTTACCGTTTTATCCTCGAACCTCCA
1 AAAATTACCATTTTACCCTCGAACTTCCA
25524 AAAATTACCATTTTACCCTCG
1 AAAATTACCATTTTACCCTCG
25545 GGCATCCGAA
Statistics
Matches: 371, Mismatches: 50, Indels: 73
0.75 0.10 0.15
Matches are distributed among these distances:
27 3 0.01
28 77 0.21
29 177 0.48
30 99 0.27
31 10 0.03
32 5 0.01
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACTTCCA
Found at i:29153 original size:39 final size:39
Alignment explanation
Indices: 29094--29244 Score: 176
Period size: 39 Copynumber: 3.9 Consensus size: 39
29084 GTTATCAAAT
* *
29094 TACTGAACTGACAGTGACACTGTAAACACTGCAATAAGC
1 TACTGAACTGGCAATGACACTGTAAACACTGCAATAAGC
* * * * *
29133 TACTGAATTGGCAGTAACACTGTAAACACTACAATATGC
1 TACTGAACTGGCAATGACACTGTAAACACTGCAATAAGC
* * * *
29172 TACTGAACTAGCAATGACACTATAAACACTGCAACACGC
1 TACTGAACTGGCAATGACACTGTAAACACTGCAATAAGC
* * *
29211 AACTGAACTGGCAATGATACTGAAAACACTGCAA
1 TACTGAACTGGCAATGACACTGTAAACACTGCAA
29245 AGGAATACTG
Statistics
Matches: 94, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (39 bp):
TACTGAACTGGCAATGACACTGTAAACACTGCAATAAGC
Found at i:29781 original size:15 final size:14
Alignment explanation
Indices: 29736--29783 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
29726 TGCAAAGACA
29736 AAAGACAGAAAAACAC
1 AAAGA-AGAAAAA-AC
29752 AGAA-AAGAAAAAAC
1 A-AAGAAGAAAAAAC
29766 AAAGAAGAAAAGAAC
1 AAAGAAGAAAA-AAC
29781 AAA
1 AAA
29784 TATGTAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
15 13 0.45
16 2 0.07
17 2 0.07
ACGTcount: A:0.75, C:0.10, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAAAAC
Found at i:30052 original size:52 final size:54
Alignment explanation
Indices: 29982--30091 Score: 156
Period size: 52 Copynumber: 2.1 Consensus size: 54
29972 ATATAGACAT
*
29982 ATATCTTGATTTTATTTTTATTATGTTCTT-T-TATACACGTATG-A-ATATATAA
1 ATATCTTGATTTCATTTTTATTAT-TT-TTATATATACACGTATGTACATATATAA
*
30034 ATATCTTGATTTCATTTTTATTATTTTTATATATACACGTATGTACATATATAC
1 ATATCTTGATTTCATTTTTATTATTTTTATATATACACGTATGTACATATATAA
30088 ATAT
1 ATAT
30092 ATATATATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
50 2 0.04
51 3 0.06
52 35 0.67
53 1 0.02
54 11 0.21
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (54 bp):
ATATCTTGATTTCATTTTTATTATTTTTATATATACACGTATGTACATATATAA
Found at i:34359 original size:30 final size:30
Alignment explanation
Indices: 34341--34486 Score: 231
Period size: 30 Copynumber: 4.9 Consensus size: 30
34331 CCCTGTTTTG
* *
34341 TTCAAAAATTATATTTTAACCCATAAACTT
1 TTCAAAAATTATATTTTAACCCCTAAAATT
*
34371 TTCAAAAATTATATTTCAACCCCTAAAATT
1 TTCAAAAATTATATTTTAACCCCTAAAATT
34401 TTCAAAAATTATATTTTAACCCCTAAAATT
1 TTCAAAAATTATATTTTAACCCCTAAAATT
*
34431 TTCAAAAATTATATTTTAACCCCTAAACTT
1 TTCAAAAATTATATTTTAACCCCTAAAATT
**
34461 TTTTAAAATTATATTTTAA-CCCTAAA
1 TTCAAAAATTATATTTTAACCCCTAAA
34487 CTCTCTAGAA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 7 0.06
30 102 0.94
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (30 bp):
TTCAAAAATTATATTTTAACCCCTAAAATT
Found at i:34512 original size:90 final size:90
Alignment explanation
Indices: 34341--34515 Score: 237
Period size: 90 Copynumber: 2.0 Consensus size: 90
34331 CCCTGTTTTG
*
34341 TTCAAAAATTATATTTTAACCCATAAACTTTTCAAAAATTATATTTCAACCCCTAAAATTTTCAA
1 TTCAAAAATTATATTTTAACCCATAAACTTTTCAAAAATTATATTTCAACCCCTAAAATTCTCAA
*
34406 AAATTATATTTTAACCCCTAAAATT
66 AAATTACATTTTAACCCCTAAAATT
* ** * *
34431 TTCAAAAATTATATTTTAACCCCTAAACTTTTTTAAAATTATATTTTAA-CCCT-AAACTCTCTA
1 TTCAAAAATTATATTTTAACCCATAAACTTTTCAAAAATTATATTTCAACCCCTAAAATTCTC-A
* * *
34494 GAAATTGCATTTTAAACCCTAA
65 AAAATTACATTTTAACCCCTAA
34516 GCTTTCCAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
88 6 0.08
89 23 0.31
90 45 0.61
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.39
Consensus pattern (90 bp):
TTCAAAAATTATATTTTAACCCATAAACTTTTCAAAAATTATATTTCAACCCCTAAAATTCTCAA
AAATTACATTTTAACCCCTAAAATT
Found at i:46483 original size:49 final size:49
Alignment explanation
Indices: 46358--46795 Score: 318
Period size: 49 Copynumber: 8.9 Consensus size: 49
46348 TACCATAAAG
* *
46358 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-GAA
1 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAGAA
* * * *
46406 GATAAT-AGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAA
1 -A-CATGA-AGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAGAA
* *
46457 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-AGTACCATGAAGAT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTAGTACC-T-CAGAA
* * * * *
46508 A-ATGGAGGGAAAGGTTTAAGTCACAAC-AGCGAACCTTGTACCTCAGAA
1 ACATGAAGGGAAAGATTTAAGCCGCAACGA-CGAACCTAGTACCTCAGAA
* * * * *
46556 GCATGAAGGGAAAGATTTGAGCCGCAAC-AGCGAATCGAGTACCAC-GAA
1 ACATGAAGGGAAAGATTTAAGCCGCAACGA-CGAACCTAGTACCTCAGAA
* * * * * * ** *
46604 GATAATGGAGAGAAAGGTTTAAGTCGTAACGGTGAACCTTGTACCTCAGAA
1 -A-CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAGAA
* * * * * *
46655 GCATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGAT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTC--AGAA
* * * * * * *
46706 ACA--AAGGAAAAGGTTTAAGTCGTAATGGCGAACCTTGTACCTCAGAA
1 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAGAA
* * *
46753 GCATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACC
1 ACATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACC
46796 ACAAAGACAT
Statistics
Matches: 294, Mismatches: 77, Indels: 36
0.72 0.19 0.09
Matches are distributed among these distances:
47 5 0.02
48 6 0.02
49 166 0.56
50 102 0.35
51 15 0.05
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (49 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAGAA
Found at i:46529 original size:99 final size:99
Alignment explanation
Indices: 46359--46802 Score: 653
Period size: 99 Copynumber: 4.5 Consensus size: 99
46349 ACCATAAAGA
*
46359 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATAGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAAGGT
*
46424 TTAAGTCGCAACGACGAACCTTGTACCTCAGAAA
66 TTAAGTCGCAACGACGAACCTTGTACCTCAGAAG
* *
46458 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCATGAAGATAATGGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAAGGT
*
46523 TTAAGTCACAAC-AGCGAACCTTGTACCTCAGAAG
66 TTAAGTCGCAACGA-CGAACCTTGTACCTCAGAAG
* * *
46557 CATGAAGGGAAAGATTTGAGCCGCAAC-AGCGAATCGAGTACCACGAAGATAATGGAGAGAAAGG
1 CATGAAGGGAAAGATTTAAGCCGCAACGA-CGAATCTAGTACCACGAAGATAATGGAGGGAAAGG
* **
46621 TTTAAGTCGTAACGGTGAACCTTGTACCTCAGAAG
65 TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAG
* * * *
46656 CATGAAGGGAAAGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATACA--AAGGAAAAGG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATA-ATGGAGGGAAAGG
* * *
46719 TTTAAGTCGTAATGGCGAACCTTGTACCTCAGAAG
65 TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAG
* *
46754 CATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACAAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGA
46803 CATTGAAGCC
Statistics
Matches: 314, Mismatches: 26, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
98 87 0.28
99 226 0.72
100 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (99 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAAGGT
TTAAGTCGCAACGACGAACCTTGTACCTCAGAAG
Found at i:48611 original size:30 final size:29
Alignment explanation
Indices: 48593--48805 Score: 202
Period size: 30 Copynumber: 7.2 Consensus size: 29
48583 CCCTATTTTG
*
48593 TTCAAAAATTATATTTTAACCCCTAGACTT
1 TTCAAAAATTATATTTTAA-CCCTAAACTT
* * *
48623 TTCAAAAATTATATTTTTACCCTCGAGCTT
1 TTCAAAAATTATATTTTAACCCT-AAACTT
*
48653 TTCAAAATTTATATTTTAACCTCTAAACTT
1 TTCAAAAATTATATTTTAACC-CTAAACTT
48683 TTC-AAAATTATATTTTAACCCCTAAACTT
1 TTCAAAAATTATATTTTAA-CCCTAAACTT
*
48712 TTCAAAAATTATATTTTGACCCTAAA-TT
1 TTCAAAAATTATATTTTAACCCTAAACTT
* * *
48740 CTAT-AAAAAATACATTTTGACCCCTAAA-TT
1 -T-TCAAAAATTATATTTT-AACCCTAAACTT
* *
48770 TTCCAAAAATTAAATTTTGATCCC-AAACTT
1 TT-CAAAAATTATATTTT-AACCCTAAACTT
*
48800 TCCAAA
1 TTCAAA
48806 TTTACTTTTT
Statistics
Matches: 155, Mismatches: 18, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.02
29 57 0.37
30 93 0.60
31 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (29 bp):
TTCAAAAATTATATTTTAACCCTAAACTT
Found at i:48757 original size:59 final size:59
Alignment explanation
Indices: 48593--48789 Score: 186
Period size: 59 Copynumber: 3.3 Consensus size: 59
48583 CCCTATTTTG
* * * * * * * *
48593 TTCAAAAATTATATTTTAACCCCTAGACTTTTCAAAAATTATATTTTTA-CCCTCGAGCTT
1 TTCAAAAATTATATTTTGACCTCTAAACTTTT-AAAAAATACATTTTAACCCCT-AAACTT
* * * * *
48653 TTCAAAATTTATATTTTAACCTCTAAACTTTTCAAAATTATATTTTAACCCCTAAACTT
1 TTCAAAAATTATATTTTGACCTCTAAACTTTTAAAAAATACATTTTAACCCCTAAACTT
*
48712 TTCAAAAATTATATTTTGACC-CTAAA-TTCTATAAAAAATACATTTTGACCCCTAAA-TT
1 TTCAAAAATTATATTTTGACCTCTAAACTT-T-TAAAAAATACATTTTAACCCCTAAACTT
*
48770 TTCCAAAAATTAAATTTTGA
1 TT-CAAAAATTATATTTTGA
48790 TCCCAAACTT
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
57 2 0.02
58 10 0.08
59 74 0.62
60 33 0.28
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (59 bp):
TTCAAAAATTATATTTTGACCTCTAAACTTTTAAAAAATACATTTTAACCCCTAAACTT
Found at i:59138 original size:12 final size:12
Alignment explanation
Indices: 59118--59150 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
59108 ATATAAAAAT
*
59118 AAATAAAAATTA
1 AAATTAAAATTA
59130 AAATTAAAATTA
1 AAATTAAAATTA
59142 AAATTAAAA
1 AAATTAAAA
59151 CTAAGAGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATTAAAATTA
Found at i:64740 original size:22 final size:22
Alignment explanation
Indices: 64686--64746 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
64676 TCAAATATCC
*
64686 GTATCTGATAAGCTCTGCATCT
1 GTATCTGATATGCTCTGCATCT
*
64708 GTATCTGATATGTTCTGCAT-T
1 GTATCTGATATGCTCTGCATCT
*
64729 AGTATCTGATATACTCTG
1 -GTATCTGATATGCTCTG
64747 TTTCTATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (22 bp):
GTATCTGATATGCTCTGCATCT
Found at i:66703 original size:20 final size:20
Alignment explanation
Indices: 66678--66715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
66668 TTTTCAATTT
*
66678 TTTTAATATTTTAATTAAAA
1 TTTTAATAATTTAATTAAAA
*
66698 TTTTAATAATTTATTTAA
1 TTTTAATAATTTAATTAA
66716 TTAAATCGTT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAATAATTTAATTAAAA
Found at i:70701 original size:39 final size:39
Alignment explanation
Indices: 70617--70724 Score: 162
Period size: 39 Copynumber: 2.7 Consensus size: 39
70607 GACTTCAATT
* *
70617 TGCCCAATGATCGGGGTAAGAGATTAGATGATGGCTGCAATC
1 TGCCCCATGATCGGGGTAAGAGATT-G--GATGGCTGCAACC
70659 TGCCCCATGATCGGGGTAAGAGATTGGATGGCTGCAACC
1 TGCCCCATGATCGGGGTAAGAGATTGGATGGCTGCAACC
*
70698 TGCCCCATGATCGAGGTAAGAGATTGG
1 TGCCCCATGATCGGGGTAAGAGATTGG
70725 TTGTCTTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
39 38 0.60
41 1 0.02
42 24 0.38
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (39 bp):
TGCCCCATGATCGGGGTAAGAGATTGGATGGCTGCAACC
Found at i:70818 original size:77 final size:77
Alignment explanation
Indices: 70569--70969 Score: 364
Period size: 77 Copynumber: 5.1 Consensus size: 77
70559 GGTGATGTAA
* * * * ** * * *
70569 CTTCAATCTACCCTCTGATTAGGGTAAAAGACCGGAATGACTTCAATTTGCCCAATGATCGGGGT
1 CTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGG-ATG-CTTCAATCTGCCCCATGATCGAGGT
*
70634 AAGAGATTAGATGATGG
64 AAGAGATTAG-T--TGT
* *** *** * * *
70651 CTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTGCAACCTGCCCCATGATCGAGGTA
1 CTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGAGGTA
*
70716 AGAGATTGGTTGT
65 AGAGATTAGTTGT
* *
70729 CTTCAATTTGCCTTTTGATTAAGGTAAAAGATTGGATGCTTCAATCTACCCCATGA-C-AGGGTA
1 CTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGA-GGTA
70792 AGAGATTAGTGTGT
65 AGAGATTAGT-TGT
* * * *
70806 CCTCAATCTGCCTTTTGATTAAGGTAAAAGATTGAATGCTTCAATTTGCTCCATGATCG-GTGTA
1 CTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGAG-GTA
*
70870 AGAGATT-GCATGT
65 AGAGATTAG-TTGT
* * *
70883 CTTCAATCTGCCTTCTGATTAAGGTAAGAGA-TGGAATTCTTCAATCTGCCCCATGATCGAGGTA
1 CTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGG-ATGCTTCAATCTGCCCCATGATCGAGGTA
* *
70947 AAAGATTAGATG-
65 AGAGATTAGTTGT
70959 CTTCAATCTGC
1 CTTCAATCTGC
70970 TCCATAGTCA
Statistics
Matches: 265, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
75 1 0.00
76 27 0.10
77 135 0.51
78 43 0.16
80 1 0.00
81 31 0.12
82 27 0.10
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (77 bp):
CTTCAATCTGCCTTTTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAA
GAGATTAGTTGT
Found at i:71106 original size:115 final size:115
Alignment explanation
Indices: 70827--71112 Score: 339
Period size: 115 Copynumber: 2.5 Consensus size: 115
70817 CTTTTGATTA
* * *
70827 AGGTAAAAGATTGAATGCTTCAATTTGCTCCATGA-TCGGTGTAAGAGATTGCATGTCTTCAATC
1 AGGTAAAAGATTGGATGCTTCAATCTGCTCCATGATTAGG-GTAAGAGATTGCATGTCTTCAATC
* * *
70891 TGCCTTCTGATTAAGGTAAGAGATGGAATTCTTCAATCTGCCCCATGATCG
65 TGCCTTCTAATTAAGGTAAAAGATGGAATGCTTCAATCTGCCCCATGATCG
* * * * *
70942 AGGTAAAAGATTAGATGCTTCAATCTGCTCCAT-AGTCAGAGCAAGAGATTGTC-TGTCTTTAAT
1 AGGTAAAAGATTGGATGCTTCAATCTGCTCCATGA-TTAGGGTAAGAGATTG-CATGTCTTCAAT
* *
71005 CTGTCTTCTAATTAAGGTAAAAGATTGG-ATGCTTCAATTTGCCCCATGATCG
64 CTGCCTTCTAATTAAGGTAAAAGA-TGGAATGCTTCAATCTGCCCCATGATCG
* * * *
71057 GGGTAAAAGACTGGATGCTTCAATCTG-TCCCATGATTAGGGTAAAAGATTGGATGT
1 AGGTAAAAGATTGGATGCTTCAATCTGCT-CCATGATTAGGGTAAGAGATTGCATGT
71113 TGATTTAATC
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
114 2 0.01
115 135 0.94
116 6 0.04
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (115 bp):
AGGTAAAAGATTGGATGCTTCAATCTGCTCCATGATTAGGGTAAGAGATTGCATGTCTTCAATCT
GCCTTCTAATTAAGGTAAAAGATGGAATGCTTCAATCTGCCCCATGATCG
Found at i:71140 original size:41 final size:39
Alignment explanation
Indices: 70590--71223 Score: 238
Period size: 38 Copynumber: 16.2 Consensus size: 39
70580 CCTCTGATTA
** * *
70590 GGGTAAAAGACCGGAATGACTTCAATTTG-CCCAATGATCG
1 GGGTAAAAGATTGGATTG-CTTCAATCTGTCCC-ATGATCG
* * * *
70630 GGGTAAGAGATTAGATGATGGCTGCAATCTGCCCCATGATCG
1 GGGTAAAAGATT-G--GATTGCTTCAATCTGTCCCATGATCG
* * * * *
70672 GGGTAAGAGATTGGATGGCTGCAACCTGCCCCATGATCG
1 GGGTAAAAGATTGGATTGCTTCAATCTGTCCCATGATCG
* * * ** **
70711 AGGTAAGAGATTGG-TTGTCTTCAATTTG-CCTTTTGATTA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGTCC-CATGATCG
* ** *
70750 AGGTAAAAGATTGGA-TGCTTCAATCTACCCCATGA-CA
1 GGGTAAAAGATTGGATTGCTTCAATCTGTCCCATGATCG
* * * ** **
70787 GGGTAAGAGATTAG-TGTGTCCTCAATCTG-CCTTTTGATTA
1 GGGTAAAAGATTGGAT-TG-CTTCAATCTGTCC-CATGATCG
* * *
70827 AGGTAAAAGATT-GAATGCTTCAATTTG-CTCCATGATCG
1 GGGTAAAAGATTGGATTGCTTCAATCTGTC-CCATGATCG
* * * **
70865 GTGTAAGAGATTGCA-TGTCTTCAATCTG-CCTTC-TGATTA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGTCC--CATGATCG
* * *
70904 AGGTAAGAGA-TGGAATT-CTTCAATCTGCCCCATGATCG
1 GGGTAAAAGATTGG-ATTGCTTCAATCTGTCCCATGATCG
* * *
70942 AGGTAAAAGATTAGA-TGCTTCAATCTG-CTCCAT-AGTCA
1 GGGTAAAAGATTGGATTGCTTCAATCTGTC-CCATGA-TCG
* * * * * * **
70980 GAGCAAGAGATT-G-TCTGTCTTTAATCTGTCTTC-TAATTA
1 GGGTAAAAGATTGGAT-TG-CTTCAATCTGTC-CCATGATCG
* * *
71019 AGGTAAAAGATTGGA-TGCTTCAATTTGCCCCATGATCG
1 GGGTAAAAGATTGGATTGCTTCAATCTGTCCCATGATCG
* **
71057 GGGTAAAAGACTGGA-TGCTTCAATCTGTCCCATGATTA
1 GGGTAAAAGATTGGATTGCTTCAATCTGTCCCATGATCG
* *
71095 GGGTAAAAGATTGGATGTTGATTTAATCTG-CCTCATGATCG
1 GGGTAAAAGATTGGA--TTGCTTCAATCTGTCC-CATGATCG
* * **
71136 GGGTAAAAGATTGG-TGTGTCTTTAATCTG-CCCTCTGATTA
1 GGGTAAAAGATTGGAT-TG-CTTCAATCTGTCCC-ATGATCG
*
71176 GGGTAAAAGGTTGGATATTAGCTTCAATCTGTCCCATGATCG
1 GGGTAAAAGATTGG--ATT-GCTTCAATCTGTCCCATGATCG
71218 GGGTAA
1 GGGTAA
71224 GAGACCTGTA
Statistics
Matches: 454, Mismatches: 93, Indels: 92
0.71 0.15 0.14
Matches are distributed among these distances:
37 18 0.04
38 155 0.34
39 134 0.30
40 57 0.13
41 32 0.07
42 47 0.10
43 11 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (39 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGTCCCATGATCG
Found at i:71181 original size:81 final size:79
Alignment explanation
Indices: 70943--71223 Score: 256
Period size: 77 Copynumber: 3.6 Consensus size: 79
70933 CCATGATCGA
* * * * * *
70943 GGTAAAAGATTAGA--TGCTTCAATCTGCTCCAT-AGTCAGAGCAAGAGATT-GTCTGTCTTTAA
1 GGTAAAAGATTGGATTTGCTTCAATCTGC-CCATGA-TCGGGGTAAAAGATTGGTATGTCTTTAA
* * * *
71004 TCTGTCTTCTAATTAA
64 TCTGCCCTCTGATTAG
* * *
71020 GGTAAAAGATTGGA--TGCTTCAATTTGCCCCATGATCGGGGTAAAAGACTGG-ATG-CTTCAAT
1 GGTAAAAGATTGGATTTGCTTCAATCTG-CCCATGATCGGGGTAAAAGATTGGTATGTCTTTAAT
*
71081 CTGTCCC-ATGATTAG
65 CTG-CCCTCTGATTAG
* * *
71096 GGTAAAAGATTGGATGTTGATTTAATCTGCCTCATGATCGGGGTAAAAGATTGGTGTGTCTTTAA
1 GGTAAAAGATTGGAT-TTGCTTCAATCTGCC-CATGATCGGGGTAAAAGATTGGTATGTCTTTAA
71161 TCTGCCCTCTGATTAG
64 TCTGCCCTCTGATTAG
*
71177 GGTAAAAGGTTGGATATTAGCTTCAATCTGTCCCATGATCGGGGTAA
1 GGTAAAAGATTGGAT-TT-GCTTCAATCTG-CCCATGATCGGGGTAA
71224 GAGACCTGTA
Statistics
Matches: 166, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
76 28 0.17
77 41 0.25
78 5 0.03
79 30 0.18
80 5 0.03
81 32 0.19
82 23 0.14
83 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (79 bp):
GGTAAAAGATTGGATTTGCTTCAATCTGCCCATGATCGGGGTAAAAGATTGGTATGTCTTTAATC
TGCCCTCTGATTAG
Found at i:83196 original size:13 final size:13
Alignment explanation
Indices: 83176--83206 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
83166 CTTTAAATTC
83176 TATT-TTTAGGAT
1 TATTATTTAGGAT
83188 TATTATTTAGGAT
1 TATTATTTAGGAT
83201 TATTAT
1 TATTAT
83207 GATATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (13 bp):
TATTATTTAGGAT
Found at i:91587 original size:12 final size:12
Alignment explanation
Indices: 91570--91596 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
91560 ATATAGGGCA
91570 AATTACAAAATT
1 AATTACAAAATT
91582 AATTACAAAATT
1 AATTACAAAATT
91594 AAT
1 AAT
91597 CACTTATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTACAAAATT
Found at i:94094 original size:18 final size:18
Alignment explanation
Indices: 94063--94103 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
94053 TAACACGTTA
94063 ATAAATAATTTAAAATTT
1 ATAAATAATTTAAAATTT
94081 ATAAA-AATTCTAAAATTT
1 ATAAATAATT-TAAAATTT
94099 -TAAAT
1 ATAAAT
94104 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAATAATTTAAAATTT
Found at i:94119 original size:25 final size:25
Alignment explanation
Indices: 94069--94120 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
94059 GTTAATAAAT
*
94069 AATTTAAAATTTATAAAAATTCTAA
1 AATTTAAAATTTATAAAAATACTAA
*
94094 AATTTTAAATTT-TAAAAATACATAA
1 AATTTAAAATTTATAAAAATAC-TAA
94119 AA
1 AA
94121 ATAGAAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AATTTAAAATTTATAAAAATACTAA
Found at i:96368 original size:21 final size:22
Alignment explanation
Indices: 96324--96374 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
96314 CCCGAATCAG
*
96324 TTGTTTTGTTGTTGTTTCACTA
1 TTGTTTTGTTATTGTTTCACTA
96346 TT-TTTTGTTATTGTTTCGA-TA
1 TTGTTTTGTTATTGTTTC-ACTA
96367 TTGTTTTG
1 TTGTTTTG
96375 CTACCATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.67
Consensus pattern (22 bp):
TTGTTTTGTTATTGTTTCACTA
Found at i:96795 original size:40 final size:40
Alignment explanation
Indices: 96713--96795 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
96703 AAATATAAAC
* *
96713 CTAAAATTTTATATCGATCTAACCCGATCCATTATTAGAT
1 CTAAAATTTTATATCGATCTAACCCGATCCATTATCAAAT
*
96753 CTAAAATTTTATATCGATTTAACCCGATCCATTATCAAAT
1 CTAAAATTTTATATCGATCTAACCCGATCCATTATCAAAT
96793 CTA
1 CTA
96796 CATCAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.37
Consensus pattern (40 bp):
CTAAAATTTTATATCGATCTAACCCGATCCATTATCAAAT
Found at i:115710 original size:22 final size:21
Alignment explanation
Indices: 115682--115749 Score: 93
Period size: 22 Copynumber: 3.2 Consensus size: 21
115672 TGATGCTATT
* *
115682 TTTTTTATTGTTTTGATTGCTG
1 TTTTTTACTGTTTTG-TTGTTG
115704 TTTTTTACTGTTTTG-TGTTG
1 TTTTTTACTGTTTTGTTGTTG
115724 TTTTTTACTGTTTTGGTTGTTG
1 TTTTTTACTGTTTT-GTTGTTG
115746 TTTT
1 TTTT
115750 CGTGTTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.43
21 1 0.02
22 23 0.55
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (21 bp):
TTTTTTACTGTTTTGTTGTTG
Found at i:115747 original size:12 final size:12
Alignment explanation
Indices: 115732--115847 Score: 71
Period size: 12 Copynumber: 10.1 Consensus size: 12
115722 TGTTTTTTAC
*
115732 TGTTTTGGTTGT
1 TGTTTTTGTTGT
*
115744 TGTTTTCG-TGT
1 TGTTTTTGTTGT
115755 TGTTTTTGTTGT
1 TGTTTTTGTTGT
*
115767 TATTTTTGTTG-
1 TGTTTTTGTTGT
* *
115778 -CTATTT-TTGT
1 TGTTTTTGTTGT
**
115788 TGTTTTTAATGT
1 TGTTTTTGTTGT
115800 TG-TTTTGTTGT
1 TGTTTTTGTTGT
* * **
115811 TATTTTTGCTAC
1 TGTTTTTGTTGT
* *
115823 TATTTTAGTTGT
1 TGTTTTTGTTGT
*
115835 TATTTTTGTTGT
1 TGTTTTTGTTGT
115847 T
1 T
115848 TGGATGTTAT
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 22 0.28
12 51 0.64
ACGTcount: A:0.08, C:0.03, G:0.20, T:0.69
Consensus pattern (12 bp):
TGTTTTTGTTGT
Found at i:115755 original size:20 final size:20
Alignment explanation
Indices: 115682--115749 Score: 84
Period size: 20 Copynumber: 3.3 Consensus size: 20
115672 TGATGCTATT
* *
115682 TTTTTTATTGTTTTGATTGCTG
1 TTTTTTACTGTTTTG--TGTTG
115704 TTTTTTACTGTTTTGTGTTG
1 TTTTTTACTGTTTTGTGTTG
115724 TTTTTTACTGTTTTG-GTTG
1 TTTTTTACTGTTTTGTGTTG
115743 TTGTTTT
1 TT-TTTT
115750 CGTGTTGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.14
20 23 0.53
22 14 0.33
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (20 bp):
TTTTTTACTGTTTTGTGTTG
Found at i:115788 original size:44 final size:43
Alignment explanation
Indices: 115740--115861 Score: 136
Period size: 44 Copynumber: 2.8 Consensus size: 43
115730 ACTGTTTTGG
** * *
115740 TTGTTGTTTTCGTGTTGTTTTTGTTGTTATTTTTGTTGCTATTT
1 TTGTTGTTTTAATGTTG-TTTTGTTGTTATTTTTGCTACTATTT
115784 TTGTTGTTTTTAATGTTGTTTTGTTGTTATTTTTGCTACTATTT
1 TTGTTG-TTTTAATGTTGTTTTGTTGTTATTTTTGCTACTATTT
* ** * *
115828 TAGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 TTGTTGTT-TTAATGTTGTTTTGTTGTTATTTTT
115862 ATGCGTTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.03
44 56 0.84
45 9 0.13
ACGTcount: A:0.09, C:0.03, G:0.19, T:0.69
Consensus pattern (43 bp):
TTGTTGTTTTAATGTTGTTTTGTTGTTATTTTTGCTACTATTT
Found at i:115792 original size:56 final size:56
Alignment explanation
Indices: 115732--115848 Score: 137
Period size: 56 Copynumber: 2.1 Consensus size: 56
115722 TGTTTTTTAC
** * * ** *
115732 TGTTTTGGTTGTTGTTTTCG-TGTTGTTTTTGTTGTTATTTTTGTTGCTATTTTTGT
1 TGTTTTGAATGTTGTTTT-GTTGTTATTTTTGCTACTATTTTAGTTGCTATTTTTGT
* *
115788 TGTTTTTAATGTTGTTTTGTTGTTATTTTTGCTACTATTTTAGTTGTTATTTTTGT
1 TGTTTTGAATGTTGTTTTGTTGTTATTTTTGCTACTATTTTAGTTGCTATTTTTGT
115844 TGTTT
1 TGTTT
115849 GGATGTTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 1 0.02
56 50 0.98
ACGTcount: A:0.08, C:0.03, G:0.20, T:0.69
Consensus pattern (56 bp):
TGTTTTGAATGTTGTTTTGTTGTTATTTTTGCTACTATTTTAGTTGCTATTTTTGT
Found at i:116848 original size:22 final size:23
Alignment explanation
Indices: 116802--116848 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
116792 TTTTTGTATA
**
116802 TTTATTTTTAGAAATTTAATTAT
1 TTTATTTTTAGAAATTTAAAGAT
*
116825 TTTATTTTTCG-AATTTAAAGAT
1 TTTATTTTTAGAAATTTAAAGAT
116847 TT
1 TT
116849 AGATTCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTATTTTTAGAAATTTAAAGAT
Found at i:119745 original size:26 final size:27
Alignment explanation
Indices: 119708--119759 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
119698 CCGTACTATG
119708 TTAATTATCCAATTTAATTTAATCCCT
1 TTAATTATCCAATTTAATTTAATCCCT
119735 TTAA-TATCCAATTTAATTTAATCCC
1 TTAATTATCCAATTTAATTTAATCCC
119760 ACTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (27 bp):
TTAATTATCCAATTTAATTTAATCCCT
Found at i:119765 original size:27 final size:26
Alignment explanation
Indices: 119708--119767 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 26
119698 CCGTACTATG
*
119708 TTAATTATCCAATTTAATTTAATCCCT
1 TTAA-TATCCAATTTAATTTAATCCCC
119735 TTAATATCCAATTTAATTTAATCCCAC
1 TTAATATCCAATTTAATTTAATCCC-C
119762 TTAATA
1 TTAATA
119768 ATTGACCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATATCCAATTTAATTTAATCCCC
Found at i:130588 original size:21 final size:21
Alignment explanation
Indices: 130562--130613 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
130552 GTTCATAGTA
*
130562 GTATCGGTAGTTTGAATACTT
1 GTATCGGTAGTATGAATACTT
130583 GTATCGGTAGTATGAATACTT
1 GTATCGGTAGTATGAATACTT
130604 GTATCGGTAG
1 GTATCGGTAG
130614 AAGTTGTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (21 bp):
GTATCGGTAGTATGAATACTT
Found at i:134304 original size:24 final size:24
Alignment explanation
Indices: 134258--134336 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
134248 CACAAACAGC
*
134258 AACAAAAATAACAACAAAAATAAT
1 AACAAAAACAACAACAAAAATAAT
*
134282 AACAAAAACAACAACAAAAATAAC
1 AACAAAAACAACAACAAAAATAAT
** * *
134306 AGTAAAAACAAC-ACTAAAATAGT
1 AACAAAAACAACAACAAAAATAAT
*
134329 AAAAAAAA
1 AACAAAAA
134337 GCACCAAAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 14 0.30
24 32 0.70
ACGTcount: A:0.73, C:0.14, G:0.03, T:0.10
Consensus pattern (24 bp):
AACAAAAACAACAACAAAAATAAT
Found at i:134306 original size:12 final size:12
Alignment explanation
Indices: 134213--134306 Score: 89
Period size: 12 Copynumber: 7.8 Consensus size: 12
134203 TCTAAATAAA
134213 AAAAATAACAAC
1 AAAAATAACAAC
* * * *
134225 CACAATAGCAGC
1 AAAAATAACAAC
**
134237 AAAAATAGTAAC
1 AAAAATAACAAC
* * *
134249 ACAAACAGCAAC
1 AAAAATAACAAC
134261 AAAAATAACAAC
1 AAAAATAACAAC
*
134273 AAAAATAATAAC
1 AAAAATAACAAC
*
134285 AAAAACAACAAC
1 AAAAATAACAAC
134297 AAAAATAACA
1 AAAAATAACA
134307 GTAAAAACAA
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 64 1.00
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:134313 original size:36 final size:36
Alignment explanation
Indices: 134207--134313 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
134197 ATAACATCTA
* * * * *
134207 AATAAAAAAAATAACAACCACAATAGCAGCAAAAAT
1 AATAACAAAAACAACAACAAAAATAACAGCAAAAAT
* * * *
134243 AGTAACACAAACAGCAACAAAAATAACAACAAAAAT
1 AATAACAAAAACAACAACAAAAATAACAGCAAAAAT
*
134279 AATAACAAAAACAACAACAAAAATAACAGTAAAAA
1 AATAACAAAAACAACAACAAAAATAACAGCAAAAA
134314 CAACACTAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (36 bp):
AATAACAAAAACAACAACAAAAATAACAGCAAAAAT
Found at i:134318 original size:21 final size:22
Alignment explanation
Indices: 134267--134306 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
134257 CAACAAAAAT
134267 AACAACAA-AAATAATAACAAA
1 AACAACAACAAATAATAACAAA
134288 AACAACAACAAA-AATAACA
1 AACAACAACAAATAATAACA
134307 GTAAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.07
Consensus pattern (22 bp):
AACAACAACAAATAATAACAAA
Found at i:134345 original size:21 final size:20
Alignment explanation
Indices: 134306--134345 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
134296 CAAAAATAAC
* *
134306 AGTAAAAACAACACTAAAAT
1 AGTAAAAAAAACACCAAAAT
134326 AGTAAAAAAAAGCACCAAAA
1 AGTAAAAAAAA-CACCAAAA
134346 CAATAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.10
Consensus pattern (20 bp):
AGTAAAAAAAACACCAAAAT
Found at i:138595 original size:30 final size:28
Alignment explanation
Indices: 138559--138628 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 28
138549 TAAATGATTT
138559 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTTT-AAATA
138589 TAAAATTATTAAAATTATTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTTAAATA
*
138617 -ATAATTATTAAA
1 TAAAATTATTAAA
138629 TAATGATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 11 0.28
28 5 0.13
29 6 0.15
30 17 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTAAATA
Found at i:139002 original size:158 final size:159
Alignment explanation
Indices: 138713--139028 Score: 535
Period size: 158 Copynumber: 2.0 Consensus size: 159
138703 TTTAAATCAC
* * *
138713 TAAAAATTTGAGTTTTTGAAATTTGAAAATTAGTGTTTCTAAAGGTTTACAGATTAACAAATGTT
1 TAAAAATTTGAGTTTTTGAAATTTGAAAATTAGTGTTTCTAAAGGCTTACAGATGAACAAAAGTT
* *
138778 ATGGAACAATGAGGAAGAAAAATATTTGTAACATCCAGGTTTTTAAGTTTGATTTTTAAAAATTT
66 ATGGAACAATGAGGAAGAAAAATATTTGTAACACCCAGGTTTTTAAGTTTGAATTTTAAAAATTT
*
138843 TCAGATTTCAAAAACTCAAATTTTATTTT
131 TCAGATTTCAAAAACCCAAATTTTATTTT
* *
138872 TAAAAATTTGGGTTTTTGAAATTTGAAAATTAGTGTTTTTAAAGGCTTACAGATGAACAAAAG-T
1 TAAAAATTTGAGTTTTTGAAATTTGAAAATTAGTGTTTCTAAAGGCTTACAGATGAACAAAAGTT
*
138936 ATGGAACAATGAGGAAGAAGAATATTTGTAACACCCAGGTTTTTAAGTTTGAATTTTAAAAATTT
66 ATGGAACAATGAGGAAGAAAAATATTTGTAACACCCAGGTTTTTAAGTTTGAATTTTAAAAATTT
*
139001 TCAGATTTCAATAACCCAAATTTTATTT
131 TCAGATTTCAAAAACCCAAATTTTATTT
139029 GGTGGATTAA
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
158 89 0.61
159 58 0.39
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (159 bp):
TAAAAATTTGAGTTTTTGAAATTTGAAAATTAGTGTTTCTAAAGGCTTACAGATGAACAAAAGTT
ATGGAACAATGAGGAAGAAAAATATTTGTAACACCCAGGTTTTTAAGTTTGAATTTTAAAAATTT
TCAGATTTCAAAAACCCAAATTTTATTTT
Found at i:148911 original size:65 final size:65
Alignment explanation
Indices: 148807--148941 Score: 234
Period size: 65 Copynumber: 2.1 Consensus size: 65
148797 ACTTCTACAT
*
148807 GGCATGACTTCATTTATAGTAGTGAAATTCATAGATCGATAAAAGGTAAATGATATCCTCTCATG
1 GGCATGACTTCATTTATAGTAGTGAAATTCATAGATCGATAAAAGATAAATGATATCCTCTCATG
* *
148872 GGCATGACTTCCTTTATAGTAGTGAAATTCATAGCTCGATAAAAGATAAATGATATCCTCTCATG
1 GGCATGACTTCATTTATAGTAGTGAAATTCATAGATCGATAAAAGATAAATGATATCCTCTCATG
*
148937 AGCAT
1 GGCAT
148942 TACATGGTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (65 bp):
GGCATGACTTCATTTATAGTAGTGAAATTCATAGATCGATAAAAGATAAATGATATCCTCTCATG
Found at i:154844 original size:21 final size:22
Alignment explanation
Indices: 154818--154861 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
154808 AACCAAATTC
154818 AAAATA-AAATCA-AAAAGAAAA
1 AAAATACAAAT-ATAAAAGAAAA
*
154839 AAAATACATATATAAAAGAAAA
1 AAAATACAAATATAAAAGAAAA
154861 A
1 A
154862 CAGAGCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAATACAAATATAAAAGAAAA
Found at i:155767 original size:17 final size:18
Alignment explanation
Indices: 155745--155784 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
155735 GATGTTTGTT
155745 AAAAATACTTTT-AAGAA
1 AAAAATACTTTTAAAGAA
*
155762 AAAAATATTTTTAAAGAA
1 AAAAATACTTTTAAAGAA
155780 AAAAA
1 AAAAA
155785 AAAAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAATACTTTTAAAGAA
Found at i:162175 original size:14 final size:14
Alignment explanation
Indices: 162158--162186 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
162148 TCCATTGGTT
162158 TTAAAAGATATTCA
1 TTAAAAGATATTCA
162172 TTAAAAGATATTCA
1 TTAAAAGATATTCA
162186 T
1 T
162187 AATGAGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TTAAAAGATATTCA
Found at i:163936 original size:16 final size:16
Alignment explanation
Indices: 163917--163961 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
163907 AAGGAAATGA
*
163917 AAAATGATAGTGAGAG
1 AAAACGATAGTGAGAG
* *
163933 AAAACGATGGTGAGGG
1 AAAACGATAGTGAGAG
*
163949 AAAACGATGGTGA
1 AAAACGATAGTGA
163962 AAATGAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.36, T:0.16
Consensus pattern (16 bp):
AAAACGATAGTGAGAG
Found at i:166015 original size:20 final size:20
Alignment explanation
Indices: 165992--166029 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
165982 ATAGAACTGT
*
165992 AGTTGTAACGGTAGAAGTGG
1 AGTTCTAACGGTAGAAGTGG
*
166012 AGTTCTACCGGTAGAAGT
1 AGTTCTAACGGTAGAAGT
166030 CTCACTAGAG
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:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (20 bp):
AGTTCTAACGGTAGAAGTGG
Found at i:174569 original size:23 final size:22
Alignment explanation
Indices: 174517--174579 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
174507 ATATTTAAAA
*
174517 TTTAATTTTATATTTTTATTTT
1 TTTAATTTAATATTTTTATTTT
*
174539 TATGAATTTAATATTTTTACTTTT
1 T-TTAATTTAATATTTTTA-TTTT
174563 TTTAATTTGAAT-TTTTT
1 TTTAATTT-AATATTTTT
174580 GGATAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 26 0.74
24 8 0.23
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (22 bp):
TTTAATTTAATATTTTTATTTT
Found at i:174827 original size:16 final size:15
Alignment explanation
Indices: 174767--174827 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
174757 AAGTCCGTCC
174767 ATATTATTTT-TTTTAA
1 ATATT-TTTTATTTT-A
*
174783 ATATATTTTATTTTA
1 ATATTTTTTATTTTA
* *
174798 ATATTTAATAATTTTA
1 ATATTT-TTTATTTTA
174814 TATATTTTTTATTT
1 -ATATTTTTTATTT
174828 ATTGAATTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 10 0.28
16 20 0.56
17 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTTTTTATTTTA
Found at i:175653 original size:16 final size:16
Alignment explanation
Indices: 175632--175669 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
175622 AAATTGATTG
*
175632 TTATAACGAAAT-ATTA
1 TTATAAC-AAATAACTA
175648 TTATAACAAATAACTA
1 TTATAACAAATAACTA
175664 TTATAA
1 TTATAA
175670 AAAAGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (16 bp):
TTATAACAAATAACTA
Found at i:177024 original size:57 final size:57
Alignment explanation
Indices: 176947--177080 Score: 139
Period size: 57 Copynumber: 2.4 Consensus size: 57
176937 TCCAAGTTCT
* * * * * * *
176947 AATATGAGAACAATTGTCAAATTTAAGGATTAATTTGAATA-AAAAAAATT-AAACCTC
1 AATATGAAAACAACTATCAAATTCAAGGACTAACTT-AA-ACAAAAAAATTCAAACCAC
* *
177004 AATAT-ATAAACAACTATCAAATTCAAGTACTAACTTAAACCAAAAAATTCAAACCAC
1 AATATGA-AAACAACTATCAAATTCAAGGACTAACTTAAACAAAAAAATTCAAACCAC
177061 AATATGAAAACAACTATCAA
1 AATATGAAAACAACTATCAA
177081 GTTAAAACCC
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 1 0.02
56 11 0.17
57 51 0.80
58 1 0.02
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (57 bp):
AATATGAAAACAACTATCAAATTCAAGGACTAACTTAAACAAAAAAATTCAAACCAC
Found at i:177833 original size:71 final size:71
Alignment explanation
Indices: 177712--177859 Score: 278
Period size: 71 Copynumber: 2.1 Consensus size: 71
177702 ACATTTTTAA
*
177712 CATATTCAACATAGTAATAATTAATTAACATAATTAACTCTTATATCTTAAGATAACAAGAACTC
1 CATAGTCAACATAGTAATAATTAATTAACATAATTAACTCTTATATCTTAAGATAACAAGAACTC
177777 ACAGTT
66 ACAGTT
*
177783 CATAGTCAACATATTAATAATTAATTAACATAATTAACTCTTATATCTTAAGATAACAAGAACTC
1 CATAGTCAACATAGTAATAATTAATTAACATAATTAACTCTTATATCTTAAGATAACAAGAACTC
177848 ACAGTT
66 ACAGTT
177854 CATAGT
1 CATAGT
177860 GGCACATCAC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.34
Consensus pattern (71 bp):
CATAGTCAACATAGTAATAATTAATTAACATAATTAACTCTTATATCTTAAGATAACAAGAACTC
ACAGTT
Found at i:181492 original size:22 final size:22
Alignment explanation
Indices: 181446--181492 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
181436 AAATGGTAGC
*
181446 AAAACAACAACATAACAGTAAT
1 AAAACAACAACATAACAATAAT
* * *
181468 AAAATAACAACGTAACAATAGT
1 AAAACAACAACATAACAATAAT
181490 AAA
1 AAA
181493 TAAAAGAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.64, C:0.15, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAACAACAACATAACAATAAT
Found at i:182734 original size:3 final size:3
Alignment explanation
Indices: 182726--182763 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
182716 TCCAGGCTTC
182726 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
182764 GGTGAGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:188010 original size:20 final size:20
Alignment explanation
Indices: 187976--188025 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
187966 TTAAATTAAG
187976 ATTATTTT-TTAATTTTATGT
1 ATTATTTTATTAA-TTTATGT
*
187996 ATTATTTTATT-ATTTATTT
1 ATTATTTTATTAATTTATGT
188015 ATTTATTTTAT
1 A-TTATTTTAT
188026 AAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 7 0.26
20 18 0.67
21 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
ATTATTTTATTAATTTATGT
Found at i:188157 original size:19 final size:16
Alignment explanation
Indices: 188120--188160 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
188110 AATCTATTAG
188120 AAAAAAAAATTTAAAA
1 AAAAAAAAATTTAAAA
188136 AAAACAAAAATTTATAATA
1 AAAA-AAAAATTTA-AA-A
188155 AAAAAA
1 AAAAAA
188161 CTCAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 4 0.18
19 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAAAAAATTTAAAA
Found at i:189531 original size:19 final size:19
Alignment explanation
Indices: 189495--189532 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
189485 AACTAGTTCG
**
189495 ATTAAAAAATTATTAAAAT
1 ATTAAAAAATTAAAAAAAT
189514 ATTAAAAAATTAAAAAAAT
1 ATTAAAAAATTAAAAAAAT
189533 GGTCGGTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTAAAAAATTAAAAAAAT
Found at i:189575 original size:20 final size:20
Alignment explanation
Indices: 189550--189602 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
189540 TCAATCACTT
189550 GTTCAACTGATTTTTAGTTA
1 GTTCAACTGATTTTTAGTTA
*
189570 GTTCAA-TCGAGTTTTTAGTTG
1 GTTCAACT-GA-TTTTTAGTTA
*
189591 GTTTAACTGATT
1 GTTCAACTGATT
189603 CGTACTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 10 0.36
21 16 0.57
22 1 0.04
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (20 bp):
GTTCAACTGATTTTTAGTTA
Found at i:191054 original size:18 final size:18
Alignment explanation
Indices: 191031--191076 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
191021 AAGAAATTAT
191031 CTACAAGTGA-GGTAAGTA
1 CTACAAGT-ATGGTAAGTA
191049 CTACAAGTATGGTAAGTA
1 CTACAAGTATGGTAAGTA
191067 CTACAAGTAT
1 CTACAAGTAT
191077 TAAAAGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (18 bp):
CTACAAGTATGGTAAGTA
Found at i:192118 original size:18 final size:18
Alignment explanation
Indices: 192095--192131 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
192085 TTTGTGATCA
192095 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
192113 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
192131 A
1 A
192132 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:194866 original size:18 final size:18
Alignment explanation
Indices: 194824--194866 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
194814 CCACAAAGGT
* *
194824 AGACGGAAACGTACCATA
1 AGACAGAAACGTACCACA
*
194842 AGACAGAAACGTGCCACA
1 AGACAGAAACGTACCACA
*
194860 AGGCAGA
1 AGACAGA
194867 GGAAAAACGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.26, T:0.07
Consensus pattern (18 bp):
AGACAGAAACGTACCACA
Found at i:202920 original size:28 final size:28
Alignment explanation
Indices: 202880--202941 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
202870 AGAATATGAC
202880 AATATCAAAATTTACAAAAAGTAAATTG
1 AATATCAAAATTTACAAAAAGTAAATTG
* * * *
202908 AATATGAAAATTTATAGAAAGTAATTTG
1 AATATCAAAATTTACAAAAAGTAAATTG
202936 AATATC
1 AATATC
202942 CGAATAAGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (28 bp):
AATATCAAAATTTACAAAAAGTAAATTG
Found at i:210532 original size:23 final size:24
Alignment explanation
Indices: 210505--210587 Score: 91
Period size: 23 Copynumber: 3.5 Consensus size: 24
210495 TTTAATGTTC
* *
210505 ACGAACATGATCATTTAAC-TTAA
1 ACGAACATGTTCATTGAACATTAA
*
210528 TCGAACATGTTCA-TGAACATTAA
1 ACGAACATGTTCATTGAACATTAA
210551 ACGAACATGTTCA-TGAACATATAA
1 ACGAACATGTTCATTGAACAT-TAA
**
210575 TTGAACATGTTCA
1 ACGAACATGTTCA
210588 CGAACAATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 4 0.08
23 34 0.65
24 14 0.27
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (24 bp):
ACGAACATGTTCATTGAACATTAA
Found at i:210547 original size:12 final size:12
Alignment explanation
Indices: 210524--210604 Score: 58
Period size: 12 Copynumber: 6.7 Consensus size: 12
210514 ATCATTTAAC
210524 TTAATCGAACATG
1 TTAAT-GAACATG
*
210537 TTCATGAACAT-
1 TTAATGAACATG
* *
210548 TAAACGAACATG
1 TTAATGAACATG
*
210560 TTCATGAACAT-
1 TTAATGAACATG
*
210571 ATAATTGAACATG
1 TTAA-TGAACATG
* *
210584 TTCACGAACAATG
1 TTAATGAAC-ATG
210597 TTAATGAA
1 TTAATGAA
210605 TAATAAACAA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
11 10 0.20
12 25 0.50
13 15 0.30
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (12 bp):
TTAATGAACATG
Found at i:214519 original size:45 final size:45
Alignment explanation
Indices: 214451--214540 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
214441 GAAGAATAGC
* *
214451 TGGTAAAGAATTTGTGTTATCTGGTCTTGGTTAATTTGCTCATCT
1 TGGTAAAGAAATTGTGTTATCTGGTCTTGATTAATTTGCTCATCT
* * *
214496 TGGTAATGAAATTGTGTTGTCTGGTGTTGATTAATTTGCTCATCT
1 TGGTAAAGAAATTGTGTTATCTGGTCTTGATTAATTTGCTCATCT
214541 CAATGGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (45 bp):
TGGTAAAGAAATTGTGTTATCTGGTCTTGATTAATTTGCTCATCT
Found at i:222988 original size:22 final size:22
Alignment explanation
Indices: 222954--223004 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
222944 CGAATATAAC
*
222954 ATCAGAAACTAGTATATACAAA
1 ATCACAAACTAGTATATACAAA
* *
222976 ATCACAAATTAGTATATATAAA
1 ATCACAAACTAGTATATACAAA
*
222998 ATTACAA
1 ATCACAA
223005 GTTTGAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (22 bp):
ATCACAAACTAGTATATACAAA
Found at i:223614 original size:34 final size:34
Alignment explanation
Indices: 223576--223693 Score: 182
Period size: 34 Copynumber: 3.5 Consensus size: 34
223566 AAAGTTAAGA
223576 AAGATGGAAGGTTAAAGATCAAGGGAGGTTAAAG
1 AAGATGGAAGGTTAAAGATCAAGGGAGGTTAAAG
*
223610 AAGATGGAAGGTTAAAGATCAAGAGAGGTTAAAG
1 AAGATGGAAGGTTAAAGATCAAGGGAGGTTAAAG
* * * *
223644 AAGATGGAAGGTTAAAGGTCAAAGAAAGTTAAAG
1 AAGATGGAAGGTTAAAGATCAAGGGAGGTTAAAG
*
223678 AAGATGAAAGGTTAAA
1 AAGATGGAAGGTTAAA
223694 AGATGAAATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 77 1.00
ACGTcount: A:0.48, C:0.03, G:0.31, T:0.18
Consensus pattern (34 bp):
AAGATGGAAGGTTAAAGATCAAGGGAGGTTAAAG
Found at i:223655 original size:17 final size:17
Alignment explanation
Indices: 223576--223693 Score: 94
Period size: 17 Copynumber: 6.9 Consensus size: 17
223566 AAAGTTAAGA
223576 AAGATGGAAGGTTAAAG
1 AAGATGGAAGGTTAAAG
** * *
223593 ATCAAGGGAGGTTAAAG
1 AAGATGGAAGGTTAAAG
223610 AAGATGGAAGGTTAAAG
1 AAGATGGAAGGTTAAAG
** *
223627 ATCA-AGAGAGGTTAAAG
1 AAGATGGA-AGGTTAAAG
223644 AAGATGGAAGGTTAAAG
1 AAGATGGAAGGTTAAAG
*** ** *
223661 GTCAAAGAAAGTTAAAG
1 AAGATGGAAGGTTAAAG
*
223678 AAGATGAAAGGTTAAA
1 AAGATGGAAGGTTAAA
223694 AGATGAAATG
Statistics
Matches: 72, Mismatches: 27, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
16 2 0.03
17 68 0.94
18 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.31, T:0.18
Consensus pattern (17 bp):
AAGATGGAAGGTTAAAG
Found at i:228464 original size:34 final size:34
Alignment explanation
Indices: 228410--228502 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
228400 AGAATATGAA
* *
228410 AAGTTAAGAAAGATGAAAGGTTAAAGATCAAGGG
1 AAGTTAAGGAAGATGAAAGGTTAAAGATCAAAGG
* * * *
228444 AGGTTATGGAAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGAAAGGTTAAAGATCAAAGG
228478 AAGTTAAGGAAGATGAAAGGTTAAA
1 AAGTTAAGGAAGATGAAAGGTTAAA
228503 CATCCGTAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.46, C:0.02, G:0.32, T:0.19
Consensus pattern (34 bp):
AAGTTAAGGAAGATGAAAGGTTAAAGATCAAAGG
Found at i:230683 original size:32 final size:29
Alignment explanation
Indices: 230616--230685 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
230606 TAACTTATAT
*
230616 TTAAAAATAAAAATTATAAATAAAAAATT
1 TTAAAAATAAAAATTATAAATAAAAAATA
**
230645 TCTAAAAATACAAAATATATATGTAAAAAAATA
1 T-TAAAAATA-AAAAT-TATAAAT-AAAAAATA
230678 TTAAAAAT
1 TTAAAAAT
230686 TTACAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 1 0.03
30 8 0.24
31 5 0.15
32 12 0.35
33 8 0.24
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (29 bp):
TTAAAAATAAAAATTATAAATAAAAAATA
Found at i:230912 original size:17 final size:17
Alignment explanation
Indices: 230890--230927 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
230880 GAGTGACTAG
230890 AATTCTTGT-TAAAATAA
1 AATTC-TGTATAAAATAA
230907 AATTCTGTAGTAAAATAA
1 AATTCTGTA-TAAAATAA
230925 AAT
1 AAT
230928 AAAAGTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 5 0.26
18 11 0.58
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (17 bp):
AATTCTGTATAAAATAA
Found at i:236514 original size:29 final size:29
Alignment explanation
Indices: 236473--237038 Score: 228
Period size: 29 Copynumber: 19.5 Consensus size: 29
236463 ACGGAGTCAA
*
236473 AAAAT-GTAATTTTTGGATGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTGAGGGT
* *
236501 AAAATGGTAATTTTTGGAAGTTCG-GGGC
1 AAAATGGTAATTTTTGGAAGTTTGAGGGT
* ** * *
236529 AAAAT-GTAA-TTTT-AAATGCCCTG-TGGA
1 AAAATGGTAATTTTTGGAA-G-TTTGAGGGT
* * * * * *
236556 AAAATGGTAATTTTGGGATGATCGCGGAT
1 AAAATGGTAATTTTTGGAAGTTTGAGGGT
* * ** * *
236585 AAAACGATAATTTTTGGACA-CCTGGGGGC
1 AAAATGGTAATTTTTGGA-AGTTTGAGGGT
* * * ***
236614 AAAATGATAATTTTTAGACGTCAAAGGGT
1 AAAATGGTAATTTTTGGAAGTTTGAGGGT
* *
236643 AAAATGGTAATTTTTGGATA-CTTAAGGGT
1 AAAATGGTAATTTTTGGA-AGTTTGAGGGT
* *
236672 AAAATGATAA-TTTTGAAAAGTTTG-GGGT
1 AAAATGGTAATTTTTG-GAAGTTTGAGGGT
** *
236700 AAAAAAT-GTAATTTTTGGGCAA--CCGAGAGT
1 --AAAATGGTAATTTTT-GG-AAGTTTGAGGGT
* *
236730 AAAATGGTAATTTTTGGAAAGTTTGATGTT
1 AAAATGGTAATTTTTGG-AAGTTTGAGGGT
* **
236760 AAAAAT-GTAATTTTTAGACA-TTCAAGGGT
1 -AAAATGGTAATTTTTGGA-AGTTTGAGGGT
*
236789 AAAATGGTAATTTTT-GAATGTTCGAGGGT
1 AAAATGGTAATTTTTGGAA-GTTTGAGGGT
* *
236818 AAAATAGTAATTTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGAGGGT
* **
236848 CAAAAT-GTAA-TTTTAGACA-TCCGAGGGT
1 -AAAATGGTAATTTTTGGA-AGTTTGAGGGT
* *
236876 AAAATGCTAATTTTTGGAAGTTCGAGAGGGAT
1 AAAATGGTAATTTTTGGAAGTT--TGAGGG-T
** * * *
236908 AAAAAAGTGATTTTTGGAAGTTCGA-GTT
1 AAAATGGTAATTTTTGGAAGTTTGAGGGT
*
236936 AAAAATGG-AATTTTTGAAAAGTTT-AGGGT
1 -AAAATGGTAATTTTTG-GAAGTTTGAGGGT
* *
236965 CTAAAT-GTAATTTTTGGAAAGTTTGAGGATT
1 -AAAATGGTAATTTTTGG-AAGTTTGAGG-GT
*
236996 AAAAT-GTAATTTTTGGAAAGTTTAAGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGAGGGT
*
237025 AAAAT-GTTATTTTT
1 AAAATGGTAATTTTT
237039 AAAAAATTCA
Statistics
Matches: 401, Mismatches: 94, Indels: 85
0.69 0.16 0.15
Matches are distributed among these distances:
25 2 0.00
26 5 0.01
27 18 0.04
28 65 0.16
29 201 0.50
30 70 0.17
31 21 0.05
32 19 0.05
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTTGAGGGT
Found at i:236787 original size:146 final size:147
Alignment explanation
Indices: 236614--236894 Score: 376
Period size: 146 Copynumber: 1.9 Consensus size: 147
236604 ACCTGGGGGC
*
236614 AAAATGATAATTTTTAGACGTCAAAGGGTAAAATGGTAATTTTTGGATACTT-AAGGGTAAAAT-
1 AAAATGATAATTTTTAGACGTCAAAGGGTAAAATGGTAATTTTTGAAT-CTTCAAGGGTAAAATA
* * *
236677 GATAA-TTTTGAAAAGTTT-GGGGTAAAAAATGTAATTTTTGGGCAACCGAGAGTAAAATGGTAA
65 G-TAATTTTTGAAAAGTTTGGGGGT-AAAAATGTAA-TTTTAGACAACCGAGAGTAAAATGCTAA
236740 TTTTTGGAAAGTTTGATGTTA
127 TTTTTGGAAAGTTTGATGTTA
* * *
236761 AAAATG-TAATTTTTAGACATTC-AAGGGTAAAATGGTAATTTTTGAATGTTCGAGGGTAAAATA
1 AAAATGATAATTTTTAGAC-GTCAAAGGGTAAAATGGTAATTTTTGAATCTTCAAGGGTAAAATA
* * * *
236824 GTAATTTTTGGAAAGTTTGGGGGTCAAAATGTAATTTTAGACATCCGAGGGTAAAATGCTAATTT
65 GTAATTTTTGAAAAGTTTGGGGGTAAAAATGTAATTTTAGACAACCGAGAGTAAAATGCTAATTT
236889 TTGGAA
130 TTGGAA
236895 GTTCGAGAGG
Statistics
Matches: 118, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
145 2 0.02
146 81 0.69
147 30 0.25
148 5 0.04
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (147 bp):
AAAATGATAATTTTTAGACGTCAAAGGGTAAAATGGTAATTTTTGAATCTTCAAGGGTAAAATAG
TAATTTTTGAAAAGTTTGGGGGTAAAAATGTAATTTTAGACAACCGAGAGTAAAATGCTAATTTT
TGGAAAGTTTGATGTTA
Found at i:236858 original size:59 final size:57
Alignment explanation
Indices: 236473--237038 Score: 272
Period size: 58 Copynumber: 9.8 Consensus size: 57
236463 ACGGAGTCAA
* *
236473 AAAATGTAATTTTTGG-ATGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTCG-GGGC
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTAAAAT-GTAATTTTTGGAAGTTCGAGGGT
** * * * * * * *
236529 AAAATGTAA-TTTT--AAATGCCCTG-TGGAAAAATGGTAATTTTGGGATGATCGCGGAT
1 AAAATGTAATTTTTGGAAA-G-TTTGAGGGTAAAAT-GTAATTTTTGGAAGTTCGAGGGT
* * ** * * * * *
236585 AAAACGATAATTTTTGGACA-CCTGGGGGCAAAATGATAATTTTTAGACG-TCAAAGGGT
1 AAAATG-TAATTTTTGGAAAGTTTGAGGGTAAAATG-TAATTTTTGGAAGTTC-GAGGGT
* * * * *
236643 AAAATGGTAATTTTTGGATA-CTTAAGGGTAAAATGATAA-TTTTGAAAAGTTTG-GGGT
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGTAAAATG-TAATTTTTG-GAAGTTCGAGGGT
* ** * * * *
236700 AAAAAATGTAATTTTTGGGCAA--CCGAGAGTAAAATGGTAATTTTTGGAAAGTTTGATGTT
1 --AAAATGTAATTTTT-GGAAAGTTTGAGGGTAAAAT-GTAATTTTTGG-AAGTTCGAGGGT
* * **
236760 AAAAATGTAATTTTTAGACA-TTCAAGGGTAAAATGGTAATTTTT-GAATGTTCGAGGGT
1 -AAAATGTAATTTTTGGAAAGTTTGAGGGTAAAAT-GTAATTTTTGGAA-GTTCGAGGGT
* * *
236818 AAAATAGTAATTTTTGGAAAGTTTGGGGGTCAAAATGTAA-TTTTAGACA-TCCGAGGGT
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGT-AAAATGTAATTTTTGGA-AGTTCGAGGGT
* * * *
236876 AAAATGCTAATTTTTGG-AAGTTCGAGAGGGATAAAAAAGTGATTTTTGGAAGTTCGA-GTT
1 AAAATG-TAATTTTTGGAAAGTT--TGAGGG-T-AAAATGTAATTTTTGGAAGTTCGAGGGT
* * * * *
236936 AAAAATGGAATTTTTGAAAAGTTT-AGGGTCTAAATGTAATTTTTGGAAAGTTTGAGGATT
1 -AAAATGTAATTTTTGGAAAGTTTGAGGGT-AAAATGTAATTTTTGG-AAGTTCGAGG-GT
* *
236996 AAAATGTAATTTTTGGAAAGTTTAAGGGTAAAATGTTATTTTT
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTAAAATGTAATTTTT
237039 AAAAAATTCA
Statistics
Matches: 395, Mismatches: 75, Indels: 77
0.72 0.14 0.14
Matches are distributed among these distances:
54 1 0.00
55 28 0.07
56 18 0.05
57 45 0.11
58 138 0.35
59 108 0.27
60 36 0.09
61 21 0.05
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGGTAAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:237059 original size:59 final size:58
Alignment explanation
Indices: 236638--237068 Score: 260
Period size: 59 Copynumber: 7.3 Consensus size: 58
236628 TAGACGTCAA
* * *
236638 AGGGTAAAATGGTAATTTTTGGATA-CTTAAGGGT-AAAATGATAA-TTTTGAAAAGTTTG
1 AGGGTAAAAT-GTAATTTTTGGAAAGTTTAAGGGTCAAAATG-TAATTTTTG-AAAGTTCG
* *** * *
236696 -GGGTAAAAAATGTAATTTTTGGGCAA--CCGAGAGT-AAAATGGTAATTTTTGGAAAGTTTG
1 AGGGT--AAAATGTAATTTTT-GGAAAGTTTAAGGGTCAAAAT-GTAATTTTT-GAAAGTTCG
* * * * * *
236755 ATGTTAAAAATGTAATTTTTAGACA-TTCAAGGGT-AAAATGGTAATTTTTGAATGTTCG
1 AGGGT-AAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAAT-GTAATTTTTGAAAGTTCG
** * * *
236813 AGGGTAAAATAGTAATTTTTGGAAAGTTTGGGGGTCAAAATGTAATTTTAGACA-TCCG
1 AGGGTAAAAT-GTAATTTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTTGAAAGTTCG
* * * * *
236871 AGGGTAAAATGCTAATTTTTGG-AAGTTCGAGAGGGATAAAAAAGTGATTTTTGGAAGTTCG
1 AGGGTAAAATG-TAATTTTTGGAAAGTT-TA-AGGG-TCAAAATGTAATTTTTGAAAGTTCG
* * * * *
236932 A-GTTAAAAATGGAATTTTTGAAAAGTTT-AGGGTCTAAATGTAATTTTTGGAAAGTTTG
1 AGGGT-AAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTT-GAAAGTTCG
* * * * *
236990 AGGATTAAAATGTAATTTTTGGAAAGTTTAAGGGT-AAAATGTTATTTTTAAAAAATTCA
1 AGG-GTAAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTT-GAAAGTTCG
*
237049 AGGGTCAAAATGTGATTTTT
1 AGGGT-AAAATGTAATTTTT
237069 AGAGAGTTCA
Statistics
Matches: 292, Mismatches: 58, Indels: 45
0.74 0.15 0.11
Matches are distributed among these distances:
57 27 0.09
58 81 0.28
59 130 0.45
60 39 0.13
61 15 0.05
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (58 bp):
AGGGTAAAATGTAATTTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTTGAAAGTTCG
Found at i:237079 original size:30 final size:29
Alignment explanation
Indices: 236637--237081 Score: 241
Period size: 29 Copynumber: 15.1 Consensus size: 29
236627 TTAGACGTCA
* *
236637 AAGGGTAAAATGGTAATTTTTGGATACTT-
1 AAGGGTAAAAT-GTAATTTTTGGAAAGTTC
*
236666 AAGGGTAAAATGATAA-TTTTGAAAAGTT-
1 AAGGGTAAAATG-TAATTTTTGGAAAGTTC
** * *
236694 TGGGGTAAAAAATGTAATTTTTGGGCAA--CC
1 AAGGGT--AAAATGTAATTTTT-GGAAAGTTC
* * *
236724 GAGAGTAAAATGGTAATTTTTGGAAAGTTT
1 AAGGGTAAAAT-GTAATTTTTGGAAAGTTC
* * * * *
236754 GATGTTAAAAATGTAATTTTTAGACA-TTC
1 AAGGGT-AAAATGTAATTTTTGGAAAGTTC
*
236783 AAGGGTAAAATGGTAATTTTT-GAATGTTC
1 AAGGGTAAAAT-GTAATTTTTGGAAAGTTC
* *
236812 GAGGGTAAAATAGTAATTTTTGGAAAGTTT
1 AAGGGTAAAAT-GTAATTTTTGGAAAGTTC
** * * *
236842 GGGGGTCAAAATGTAA-TTTTAGACA-TCC
1 AAGGGT-AAAATGTAATTTTTGGAAAGTTC
*
236870 GAGGGTAAAATGCTAATTTTTGG-AAGTTC
1 AAGGGTAAAATG-TAATTTTTGGAAAGTTC
* *
236899 GAGAGGGATAAAAAAGTGATTTTTGG-AAGTTC
1 -A-AGGG-T-AAAATGTAATTTTTGGAAAGTTC
* * * *
236931 GA-GTTAAAAATGGAATTTTTGAAAAGTT-
1 AAGGGT-AAAATGTAATTTTTGGAAAGTTC
* * *
236959 TAGGGTCTAAATGTAATTTTTGGAAAGTTT
1 AAGGGT-AAAATGTAATTTTTGGAAAGTTC
* * *
236989 GAGGATTAAAATGTAATTTTTGGAAAGTTT
1 AAGG-GTAAAATGTAATTTTTGGAAAGTTC
* ** *
237019 AAGGGTAAAATGTTATTTTTAAAAAATTC
1 AAGGGTAAAATGTAATTTTTGGAAAGTTC
* * *
237048 AAGGGTCAAAATGTGATTTTTAGAGAGTTC
1 AAGGGT-AAAATGTAATTTTTGGAAAGTTC
237078 AAGG
1 AAGG
237082 ACCTTCTGAG
Statistics
Matches: 323, Mismatches: 67, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
27 6 0.02
28 55 0.17
29 128 0.40
30 95 0.29
31 18 0.06
32 16 0.05
33 5 0.02
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
AAGGGTAAAATGTAATTTTTGGAAAGTTC
Found at i:238981 original size:17 final size:17
Alignment explanation
Indices: 238954--239048 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
238944 TTAAATTTTT
238954 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
238972 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* **
238989 ACTCT-AAATAAGCTTAA
1 A-TTTAAAATAAATTTAA
* * *
239006 ACTTACAATCAATTTAA
1 ATTTAAAATAAATTTAA
* * *
239023 ACTTAAAATGAATTAAA
1 ATTTAAAATAAATTTAA
239040 ATTTAAAAT
1 ATTTAAAAT
239049 CTAAAATTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
16 1 0.02
17 55 0.89
18 6 0.10
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:240383 original size:209 final size:209
Alignment explanation
Indices: 239430--240416 Score: 1288
Period size: 209 Copynumber: 4.7 Consensus size: 209
239420 TTCATCTCTC
* * *
239430 GGTTTACTTCTCTATATCTCATCAGAAAGGTAACCACTTTATTGCTTCGACTTGCTTCTCAGTAT
1 GGTTCACTTCTCTATATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTAT
* * *
239495 CTCATCAGGAAGCTGTGGTTCGAAGATTGGCTCACTTTGAG-TTTGGTTTCATTAATTTGGTCTA
66 CTCATCAGGAAGCTG-GGTTCGAAGATTTGCTCACTTTGAGCTCTGGTTTCATTGATTTGGTCTA
* * * * * *
239559 CTTCTCAGTATCTCATCAGGAAGATGACCGTATCACTTGTTTTGATCCATTTCTCTGTGTCTCAT
130 CTTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTAATCCACTTCTTTGTATCTCAT
*
239624 CAGGAAGACGGATTT
195 CAGGAAGACGGATCT
* *
239639 GGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTAT
1 GGTTCACTTCTCTATATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTAT
* * *
239704 CTCATTAGGAAGCTGAGGTTCGAATATTTGCTCACTCTGAGC-CTGGTTTCATTGATTTGGTCTA
66 CTCATCAGGAAGCTG-GGTTCGAAGATTTGCTCACTTTGAGCTCTGGTTTCATTGATTTGGTCTA
* *
239768 CTTCTCAGTATCTCATCAGGAAGAT--C-GCATCACTTATTTTAATCCGCTTCTTTGTATCTCAT
130 CTTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTAATCCACTTCTTTGTATCTCAT
239830 CAGGAAGACGGATCT
195 CAGGAAGACGGATCT
* * * * * *
239845 GGTTCACTTTTTTATATCTCATCAGGAAGGTAACTACTTTATCGCTTCGACTTGCTTCTCAATAT
1 GGTTCACTTCTCTATATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTAT
* *
239910 CTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG-TCTGGTTACATTTATTTGGTCTA
66 CTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACTTTGAGCTCTGGTTTCATTGATTTGGTCTA
*
239974 CTTCTCAGTATCTCATCAGGAAGATGA-TCGTATCACTTGTTTTAATCCGCTTCTACTTCTTTGT
130 CTTCTCAGTATCTCATCAGGAAGATGACT-GCATCACTTGTTTTAAT---C--C-ACTTCTTTGT
*
240038 ATCTCATCATGAAGACGGATCT
188 ATCTCATCAGGAAGACGGATCT
* * * * * *
240060 GGTTCACTTCTTTGTATCTCATCAGGAAGGAAACCGCTTTATTGCTTCAACATGCTTCTCAGTAT
1 GGTTCACTTCTCTATATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTAT
240125 CTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGC-CTGGTTTCATTGATTTGGTCTA
66 CTCATCAGGAAGCTGGG-TTCGAAGATTTGCTCACTTTGAGCTCTGGTTTCATTGATTTGGTCTA
* * * *
240189 CTTCTCAGTATTTCATCAGGAAGATGACTGCATCACTTGCTTTAATTCGCTTCTTTGTATCTCAT
130 CTTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTAATCCACTTCTTTGTATCTCAT
* *
240254 CAAGAAGACGGATTT
195 CAGGAAGACGGATCT
* * * * * *
240269 GGTTCACTTCTCTATATCTCATTAAGAAGATGACTATTTTATTGCTTCGACCTGCTTCTCAGTAT
1 GGTTCACTTCTCTATATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTAT
* * * * * * * * * *
240334 CTCATCAGAAAGCTGGATTCGAAGTTTTACTCACATCGAGCTTTGGTTTCATTGAGTTGGTATAT
66 CTCATCAGGAAGCTGGGTTCGAAGATTTGCTCACTTTGAGCTCTGGTTTCATTGATTTGGTCTAC
*
240399 TTCTCTGTATCTCATCAG
131 TTCTCAGTATCTCATCAG
240417 AAAGGTAACT
Statistics
Matches: 682, Mismatches: 79, Indels: 34
0.86 0.10 0.04
Matches are distributed among these distances:
206 181 0.27
207 2 0.00
208 20 0.03
209 288 0.42
210 1 0.00
212 1 0.00
214 4 0.01
215 184 0.27
216 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (209 bp):
GGTTCACTTCTCTATATCTCATCAGGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTAT
CTCATCAGGAAGCTGGGTTCGAAGATTTGCTCACTTTGAGCTCTGGTTTCATTGATTTGGTCTAC
TTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTAATCCACTTCTTTGTATCTCATC
AGGAAGACGGATCT
Found at i:240503 original size:123 final size:123
Alignment explanation
Indices: 240306--240549 Score: 339
Period size: 123 Copynumber: 2.0 Consensus size: 123
240296 AGATGACTAT
240306 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCACATC
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCACATC
* ** *
240371 GAGCTTTGGTTTCATTGAGTTGGTATATTTCTCTGTATCTCATCAGAAAGGTAACTGC
66 GAGCTTTGGTTTCATTGAGTTGGTATACTTCTAAGTATCTCATCAGAAAGATAACTGC
* * * *
240429 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAA-TATTTGCTCACT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCT-GGATTCGAAGT-TTTACTCACA
* * * * *
240493 TTGAGC-TTGGTTTCGTTGATTTGGTCTACTTCTAAGTATCTCATCAGGAAGATAACT
64 TCGAGCTTTGGTTTCATTGAGTTGGTATACTTCTAAGTATCTCATCAGAAAGATAACT
240550 ACATCACTTG
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
123 85 0.80
124 21 0.20
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (123 bp):
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCACATC
GAGCTTTGGTTTCATTGAGTTGGTATACTTCTAAGTATCTCATCAGAAAGATAACTGC
Found at i:240681 original size:332 final size:332
Alignment explanation
Indices: 240067--240748 Score: 1035
Period size: 332 Copynumber: 2.1 Consensus size: 332
240057 TCTGGTTCAC
* *
240067 TTCTTTGTATCTCATCAGGAAGGAAACCGCTTTATTGCTTCAACATGCTTCTCAGTATCTCATCA
1 TTCTCTGTATCTCATCAGAAAGGAAACCGCTTTATTGCTTCAACATGCTTCTCAGTATCTCATCA
*
240132 GGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAG
66 GGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTAAG
* * * * *
240197 TATTTCATCAGGAAGATGACTGCATCACTTGCTTTAATTCGCTTCTTTGTATCTCATCAAGAAGA
131 TATCTCATCAGGAAGATAACTACATCACTTGCTTTAATTCGCTTCTCTGAATCTCATCAAGAAGA
* * * * *
240262 CGGATTTGGTTCACTTCTCTATATCTCATTAAGAAGATGACTATTTTATTGCTTCGACCTGCTTC
196 CGAATCTGGTTCACTTCTCTATATCTCATCAAGAAGATAACCATTTTATTGCTTCGACCTGCTTC
** *
240327 TCAGTATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCACA-TCGAGCTTTGGTTTCATTGAGT
261 TCAACATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCA-AGTCGAGCTTTGGTTTCATTGAGC
240391 TGGTATAT
325 TGGTATAT
* * * *
240399 TTCTCTGTATCTCATCAGAAAGGTAACTGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCA
1 TTCTCTGTATCTCATCAGAAAGGAAACCGCTTTATTGCTTCAACATGCTTCTCAGTATCTCATCA
* * * *
240464 GGAAGCTGGGGTTCGAATATTTGCTCACTTTGAGCTTGGTTTCGTTGATTTGGTCTACTTCTAAG
66 GGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTAAG
*
240529 TATCTCATCAGGAAGATAACTACATCACTTGTTTTAA-TCTGCTTCTCTGAATCTCATCAAGAAG
131 TATCTCATCAGGAAGATAACTACATCACTTGCTTTAATTC-GCTTCTCTGAATCTCATCAAGAAG
* * *
240593 ACGAATCTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTT
195 ACGAATCTGGTTCACTTCTCTATATCTCATCAAGAAGATAACCATTTTATTGCTTCGACCTGCTT
* * * *
240658 CTTAACATCTCATCAGGAAGCTGGGTTCGAAGTTTTGCTCAAGTCGAGCTTTGGTTTCATTGAGC
260 CTCAACATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCAAGTCGAGCTTTGGTTTCATTGAGC
240723 TGGTATAT
325 TGGTATAT
*
240731 TTATCTGTATCTCATCAG
1 TTCTCTGTATCTCATCAG
240749 GAAGATGACC
Statistics
Matches: 315, Mismatches: 33, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
331 3 0.01
332 312 0.99
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (332 bp):
TTCTCTGTATCTCATCAGAAAGGAAACCGCTTTATTGCTTCAACATGCTTCTCAGTATCTCATCA
GGAAGCTGGGATTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTAAG
TATCTCATCAGGAAGATAACTACATCACTTGCTTTAATTCGCTTCTCTGAATCTCATCAAGAAGA
CGAATCTGGTTCACTTCTCTATATCTCATCAAGAAGATAACCATTTTATTGCTTCGACCTGCTTC
TCAACATCTCATCAGAAAGCTGGATTCGAAGTTTTACTCAAGTCGAGCTTTGGTTTCATTGAGCT
GGTATAT
Found at i:240768 original size:209 final size:209
Alignment explanation
Indices: 240399--240794 Score: 537
Period size: 209 Copynumber: 1.9 Consensus size: 209
240389 GTTGGTATAT
* ** **
240399 TTCTCTGTATCTCATCAGAAAGGTAACTGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCA
1 TTCTCTGTATCTCATCAGAAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAACATCTCATCA
** * * ** * *
240464 GGAAGCTGGGGTTCGAATATTTGCTCACTTTGAGCTTGGTTTCGTTGATTTGGTCTACTTCTAAG
66 GGAAGCTGGGGTTCGAATATTTGCTCAAGTCGAGCTTGGTTTCATTGAGCTGGTATACTTATAAG
*
240529 TATCTCATCAGGAAGATAACTACATCACTTGTTTTAA-TCTGCTTCTCTGAATCTCATCAAGAAG
131 TATCTCATCAGGAAGATAACCACATCACTTGTTTTAATTC-GCTTCTCTGAATCTCATCAAGAAG
240593 ACGAATCTGGTTCAC
195 ACGAATCTGGTTCAC
* * *
240608 TTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTTAACATCTCATCA
1 TTCTCTGTATCTCATCAGAAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAACATCTCATCA
* *
240673 GGAAGCT-GGGTTCGAAGT-TTTGCTCAAGTCGAGCTTTGGTTTCATTGAGCTGGTATATTTATC
66 GGAAGCTGGGGTTCGAA-TATTTGCTCAAGTCGAGC-TTGGTTTCATTGAGCTGGTATACTTATA
* * * *
240736 TGTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATTCGCTTCTCTGTATCTCAT
129 AGTATCTCATCAGGAAGATAACCACATCACTTGTTTTAATTCGCTTCTCTGAATCTCAT
240795 TTGGAAGCTG
Statistics
Matches: 161, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
208 22 0.14
209 137 0.85
210 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (209 bp):
TTCTCTGTATCTCATCAGAAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAACATCTCATCA
GGAAGCTGGGGTTCGAATATTTGCTCAAGTCGAGCTTGGTTTCATTGAGCTGGTATACTTATAAG
TATCTCATCAGGAAGATAACCACATCACTTGTTTTAATTCGCTTCTCTGAATCTCATCAAGAAGA
CGAATCTGGTTCAC
Found at i:240898 original size:172 final size:172
Alignment explanation
Indices: 240607--240973 Score: 540
Period size: 172 Copynumber: 2.1 Consensus size: 172
240597 ATCTGGTTCA
*
240607 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTTAACATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAACATCTCATC
* * * *
240672 AGGAAGCTGGGTTCGAAGTTTTGCTCAAGTCGAGCTTTGGTTTCATTGAGCTGGTATATTTATCT
66 AAGAAGCTGGGCTCGAAGTTTTGCTCAAGTCGAGCTTTGGTTTCATTAAGCTGGTATACTTATCT
* * * * *
240737 GTATCTCATCAGGAAGATGACCA-CCTCACTTGTTTTAATTCG
131 ATATCTCATCAGGAAGAT-AACAGCCTCACTTATTTCAATCCG
** * *
240779 CTTCTCTGTATCTCATTTGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAACATCTCATC
* *
240844 AAGAGGCTGGGCTCGAAGTTTTGCTCACA-TCGAGCTTTGGTTTCATTAAGCTGGTATACTTCTC
66 AAGAAGCTGGGCTCGAAGTTTTGCTCA-AGTCGAGCTTTGGTTTCATTAAGCTGGTATACTTATC
* *
240908 TATATCTCATCAGGAAGCTAACAGCGTCACTTATTTCAATCCG
130 TATATCTCATCAGGAAGATAACAGCCTCACTTATTTCAATCCG
240951 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
240974 ATGAATTTGG
Statistics
Matches: 173, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
171 3 0.02
172 169 0.98
173 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (172 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAACATCTCATC
AAGAAGCTGGGCTCGAAGTTTTGCTCAAGTCGAGCTTTGGTTTCATTAAGCTGGTATACTTATCT
ATATCTCATCAGGAAGATAACAGCCTCACTTATTTCAATCCG
Found at i:241110 original size:381 final size:381
Alignment explanation
Indices: 240429--241175 Score: 1022
Period size: 381 Copynumber: 2.0 Consensus size: 381
240419 AGGTAACTGC
* * * *
240429 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAATATTTGCTCACTT
1 TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGCTCGAATATTTGCTCACAT
* * * ** *
240494 TGAGCTTGGTTTCGTTGATTTGGTCTACTTCTAAGTATCTCATCAGGAAGATAACTACATCACTT
66 CGAGCTTGGTTTCATTAAGCTGGTATACTTCTAAGTATCTCATCAGGAAGATAACTACATCACTT
* * * * *
240559 GTTTTAATCTGCTTCTCTGAATCTCATCAAGAAGACGAATCTGGTTCACTTCTCTGTATCTCATC
131 ATTTCAATCCGCTTCTCTGAATCTCATCAAGAAGACGAATCTGGTCCACTTCTCAGTATCTCATC
* * * *
240624 AGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTTAACATCTCATCAGGAAGCTGGGTTCGAA
196 AAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAACATCTCATCAAGAAGCTGGGATCGAA
* *
240689 GTTTTGCTCAAGTCGAGCTTTGGTTTCATTGAGCTGGTATATTTATCTGTATCTCATCAGGAAGA
261 GTTTTGCTCAAGTCGAGCTTTGGTTTCATTGAGCTGGTATACTTATCTGTATCTCATCAAGAAGA
*
240754 TGACCACCTCACTTGTTTTAATTCGCTTCTCTGTATCTCATTTGGAAGCTGACCAT
326 AGACCACCTCACTTGTTTTAATTCGCTTCTCTGTATCTCATTTGGAAGCTGACCAT
*
240810 TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAGGCT-GGGCTCGAAGT-TTTGCTCACA
1 TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGCTCGAA-TATTTGCTCACA
* * *
240873 TCGAGCTTTGGTTTCATTAAGCTGGTATACTTCTCTA-TATCTCATCAGGAAGCTAAC-AGCGTC
65 TCGAGC-TTGGTTTCATTAAGCTGGTATACTTCT-AAGTATCTCATCAGGAAGATAACTA-CATC
* * * *
240936 ACTTATTTCAATCCGCTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCT
127 ACTTATTTCAATCCGCTTCTCTGAATCTCATCAAGAAGACGAATCTGGTCCACTTCTCAGTATCT
* ** *
241001 CATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGTTAGGGA
192 CATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAACATCTCATCAAGAAGCT-GGGA
* * * *
241066 TCGAA-TTTTAGCTCATA-TTGAGCTTT-GTTTTATTGAGTTGGTATACTTCTCTGTATCTCATC
256 TCGAAGTTTT-GCTCA-AGTCGAGCTTTGGTTTCATTGAGCTGGTATACTTATCTGTATCTCATC
* *
241128 AAGAAGAAGATCGCCTCACTTGTTTTAATTCGCTTCTCTGTATCTCAT
319 AAGAAGAAGACCACCTCACTTGTTTTAATTCGCTTCTCTGTATCTCAT
241176 CAGGAAGACG
Statistics
Matches: 319, Mismatches: 40, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
380 23 0.07
381 273 0.86
382 22 0.07
383 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (381 bp):
TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGCTCGAATATTTGCTCACAT
CGAGCTTGGTTTCATTAAGCTGGTATACTTCTAAGTATCTCATCAGGAAGATAACTACATCACTT
ATTTCAATCCGCTTCTCTGAATCTCATCAAGAAGACGAATCTGGTCCACTTCTCAGTATCTCATC
AAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAACATCTCATCAAGAAGCTGGGATCGAA
GTTTTGCTCAAGTCGAGCTTTGGTTTCATTGAGCTGGTATACTTATCTGTATCTCATCAAGAAGA
AGACCACCTCACTTGTTTTAATTCGCTTCTCTGTATCTCATTTGGAAGCTGACCAT
Found at i:241164 original size:209 final size:209
Alignment explanation
Indices: 240779--241233 Score: 648
Period size: 209 Copynumber: 2.2 Consensus size: 209
240769 TTTTAATTCG
* *
240779 CTTCTCTGTATCTCATTTGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATTAGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* *
240844 AAGAGGCTGGGCTCGAAGTTTTGCTCACATCGAGCTTTGGTTTCATTAAGCTGGTATACTTCTCT
66 AAGAAGCTGGGATCGAAGTTTTGCTCACATCGAGCTTTGGTTTCATTAAGCTGGTATACTTCTCT
* * *
240909 ATATCTCATCAGGAAGCTAACAGCGTCACTTATTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
131 ATATCTCATCAAGAAGCAAACAGCCTCACTTATTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
*
240974 ATGAATTTGGTCCA
196 ACGAATTTGGTCCA
* * *
240988 CTTCTCAGTATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATTAGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* * * * * *
241053 AAGAAGTTAGGGATCGAA-TTTTAGCTCATATTGAGCTTT-GTTTTATTGAGTTGGTATACTTCT
66 AAGAAGCT-GGGATCGAAGTTTT-GCTCACATCGAGCTTTGGTTTCATTAAGCTGGTATACTTCT
* * * *
241116 CTGTATCTCATCAAGAAG-AAGATC-GCCTCACTTGTTTTAATTCGCTTCTCTGTATCTCATCAG
129 CTATATCTCATCAAGAAGCAA-A-CAGCCTCACTTATTTCAATCCGCTTCTCTGTATCTCATCAG
241179 GAAGACGAATTTGGTCCA
192 GAAGACGAATTTGGTCCA
*
241197 CTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATT
1 CTTCTCAGTATCTCATTAGGAAGCTGACCATTTTATT
241234 TTTTTGGATA
Statistics
Matches: 218, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
208 1 0.00
209 194 0.89
210 23 0.11
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (209 bp):
CTTCTCAGTATCTCATTAGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
AAGAAGCTGGGATCGAAGTTTTGCTCACATCGAGCTTTGGTTTCATTAAGCTGGTATACTTCTCT
ATATCTCATCAAGAAGCAAACAGCCTCACTTATTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
ACGAATTTGGTCCA
Found at i:241830 original size:49 final size:49
Alignment explanation
Indices: 241774--242012 Score: 184
Period size: 50 Copynumber: 4.8 Consensus size: 49
241764 GAGAGTCACT
* *
241774 GTTGTGGCCTCAACCTTTCCTTTTATATC-TTTATGGTA-TCGGGTTCGTC
1 GTTGTGGCCTCAACCTTTCCTTTCATATCTTTTA-GGTACT-GGGTTCGCC
** * * *
241823 GTTGTGGCCTCAACCTTTCCCATCACATCTTTTTAGGTA-TCGGATTCACC
1 GTTGTGGCCTCAACCTTTCCTTTCATATC-TTTTAGGTACT-GGGTTCGCC
* ** * *
241873 GTCGCAGCTTCAATCC-TTCCTTTCATATCTTTGT-GGTACTAGGTTCGCC
1 GTTGTGGCCTCAA-CCTTTCCTTTCATATCTTT-TAGGTACTGGGTTCGCC
** * *
241922 GTTACGGCCTCAACCTTT-CTCATCACATCTTCTTAGGTACTGGGTTCGCC
1 GTTGTGGCCTCAACCTTTCCT-TTCATATCTT-TTAGGTACTGGGTTCGCC
* *
241972 GTTATGGCCTCAACCTTTCCCTTTTATATCTTCTTAGGTAC
1 GTTGTGGCCTCAACCTTT-CCTTTCATATCTT-TTAGGTAC
242013 CGAATTCGTC
Statistics
Matches: 151, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
48 4 0.03
49 58 0.38
50 65 0.43
51 22 0.15
52 2 0.01
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.39
Consensus pattern (49 bp):
GTTGTGGCCTCAACCTTTCCTTTCATATCTTTTAGGTACTGGGTTCGCC
Found at i:242986 original size:22 final size:23
Alignment explanation
Indices: 242951--242994 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
242941 TCTCCTTTTC
*
242951 TTTTTCCTCTTTTTTTGTTCTTG
1 TTTTTCCTCTTTTTTTCTTCTTG
*
242974 TTTTTCTTC-TTTTTTCTTCTT
1 TTTTTCCTCTTTTTTTCTTCTT
242995 TATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (23 bp):
TTTTTCCTCTTTTTTTCTTCTTG
Found at i:242986 original size:32 final size:31
Alignment explanation
Indices: 242948--243042 Score: 88
Period size: 32 Copynumber: 3.0 Consensus size: 31
242938 AACTCTCCTT
*
242948 TTCTTTTTCCTCTTTTTTTGTTCT-TGTTTTTC
1 TTCTTTTTCCTCTTTTTTTATT-TAT-TTTTTC
* *
242980 TTCTTTTTTCTTCTTTATTTATTTATTTTTTC
1 TTC-TTTTTCCTCTTTTTTTATTTATTTTTTC
243012 TT-TTTCTTCTCTCTTTTTTTA-TTATCTTTTT
1 TTCTTT-TTC-CTCTTTTTTTATTTAT-TTTTT
243043 ATTTATTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
30 3 0.06
31 7 0.13
32 26 0.49
33 17 0.32
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (31 bp):
TTCTTTTTCCTCTTTTTTTATTTATTTTTTC
Found at i:243030 original size:22 final size:19
Alignment explanation
Indices: 242946--243031 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 19
242936 CGAACTCTCC
*
242946 TTTTCTTTTTCCTCTTTTTT
1 TTTTCTTTTT-TTCTTTTTT
*
242966 TGTTCTTGTTTTTCTTCTTTT
1 TTTTCTT-TTTTTCTT-TTTT
* * *
242987 TTCTTCTTTATTTATTTATT
1 TT-TTCTTTTTTTCTTTTTT
243007 TTTTCTTTTTCTTCTCTCTTTT
1 TTTTCTTTTT-TTCT-T-TTTT
243029 TTT
1 TTT
243032 ATTATCTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
19 7 0.14
20 18 0.35
21 15 0.29
22 11 0.22
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTTTTCTTTTTT
Found at i:243031 original size:43 final size:41
Alignment explanation
Indices: 242963--243056 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 41
242953 TTTCCTCTTT
* *
242963 TTTTGTTCTTGTTTTTCTTCTTTTTTCTTCT-TTATTTATTTA
1 TTTT-TTCTTGTTTTTCTTCTTTTTTATTATCTT-TTTATTTA
243005 TTTTTTCTT-TTTCTTCTCTCTTTTTTTATTATCTTTTTATTTA
1 TTTTTTCTTGTTT-TTCT-TC-TTTTTTATTATCTTTTTATTTA
243048 TTTATTTCT
1 TTT-TTTCT
243057 CTTTATCGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
40 3 0.07
41 9 0.20
42 6 0.13
43 20 0.44
44 7 0.16
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.77
Consensus pattern (41 bp):
TTTTTTCTTGTTTTTCTTCTTTTTTATTATCTTTTTATTTA
Found at i:243032 original size:28 final size:30
Alignment explanation
Indices: 242975--243039 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
242965 TTGTTCTTGT
*
242975 TTTTCTTCTTTTTTCTTCTTTATTTATTTA
1 TTTTCTTCTTTTTTCTTCTCTATTTATTTA
* *
243005 TTTT-TTC-TTTTTCTTCTCTCTTTTTTTA
1 TTTTCTTCTTTTTTCTTCTCTATTTATTTA
*
243033 TTATCTT
1 TTTTCTT
243040 TTTATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 21 0.70
29 5 0.17
30 4 0.13
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTCTTCTTTTTTCTTCTCTATTTATTTA
Found at i:248620 original size:87 final size:89
Alignment explanation
Indices: 248268--248867 Score: 342
Period size: 87 Copynumber: 6.8 Consensus size: 89
248258 TGCCTAAGGG
* * * * * *
248268 TAAAATGGTAATTTTCG-AAAG-TTCGAGG-CAAAAATGTAATGTTTAGA-AGCTCGAGGGAAAA
1 TAAAATGGTAATTTTTGAAAAGTTTAG-GGTCAAAAATGTAATTTTTGGACA-TTCGAGGGTAAA
* * * *
248329 ATGGTAATTTTAGGATGATCGAG-GG
64 ATGGTAATTTTTGAATGTTCGAGAGA
* * * * * *
248354 TAAAATGGTAATTTTTGGACACTTGAAGGGGT--AAAATGGTAATTGTTGGAC-GTCAGAGGGTA
1 TAAAATGGTAATTTTTGAAAAGTT-TA-GGGTCAAAAAT-GTAATTTTTGGACATTC-GAGGGTA
* *** * *
248416 AAATGGTAAATTTT-ACACACTC-AGGGGC
62 AAATGGTAATTTTTGA-ATGTTCGA-GAGA
* * *
248444 T-AAAT-GTAA-TTTTGAAAAGTTTAAGGTCAAAAATGTAATTTTTGGGCA-TCTAGGGGTAAAA
1 TAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGTAATTTTTGGACATTCGA-GGGTAAAA
* * *
248505 TGGTAA-TTTGGGATGTTCG-GGGA
65 TGGTAATTTTTGAATGTTCGAGAGA
* * * *
248528 TAAAATGGTAATTTTTGAAAAGTATGGGGTC-AAAATGTAATTTTTGGATATTCGAGGATAAAAT
1 TAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAAT
*
248592 GGTAATTTTTTAATGTTCGAGAG-
66 GGTAATTTTTGAATGTTCGAGAGA
*
248615 TAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGTAA-TTTTAGACATTCGAGGGTAAAAT
1 TAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAAT
*
248679 GGTAATTTTTGAAAGTTCGAGAGGGA
66 GGTAATTTTTGAATGTTCGAGA--GA
* * * * * **
248705 TAAAAAT-ATAATTTTTTG-ACA-TTCAGGGGT--AGAATGGTAATTTTTGAATGTTCGAGGGTA
1 T-AAAATGGTAA-TTTTTGAAAAGTTTA-GGGTCAAAAAT-GTAATTTTTGGACATTCGAGGGT-
* * *
248765 AAAATGG-AATTTTTGATAAGTT-TAG-GG
61 AAAATGGTAATTTTTGA-ATGTTCGAGAGA
* * * * **
248792 TCTAAAT-GTAATTTTTGAAAAGTTTAAAGGTC-AAAATATAATTTTTGGAAAATTTAAGGGTAA
1 T-AAAATGGTAATTTTTGAAAAGTTT-AGGGTCAAAAATGTAATTTTTGG-ACATTCGAGGGTAA
248855 TAAT-GTAATTTTT
63 -AATGGTAATTTTT
248868 AGAAAGTTTA
Statistics
Matches: 401, Mismatches: 72, Indels: 79
0.73 0.13 0.14
Matches are distributed among these distances:
84 4 0.01
85 14 0.03
86 84 0.21
87 125 0.31
88 45 0.11
89 68 0.17
90 38 0.09
91 23 0.06
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.34
Consensus pattern (89 bp):
TAAAATGGTAATTTTTGAAAAGTTTAGGGTCAAAAATGTAATTTTTGGACATTCGAGGGTAAAAT
GGTAATTTTTGAATGTTCGAGAGA
Found at i:248657 original size:30 final size:28
Alignment explanation
Indices: 248445--248898 Score: 180
Period size: 29 Copynumber: 15.5 Consensus size: 28
248435 CTCAGGGGCT
*
248445 AAATGTAA-TTTTGAAAAGTTTAAGGTCAA
1 AAATGTAATTTTTGAAAAGTTTAGGGT--A
*** *
248474 AAATGTAATTTTTGGGCA-TCTAGGGGTA
1 AAATGTAATTTTTGAAAAGTTTA-GGGTA
** * **
248502 AAATGGTAA--TTTGGGATGTTCGGGGATA
1 AAAT-GTAATTTTTGAAAAGTTTAGGG-TA
* *
248530 AAATGGTAATTTTTGAAAAGTATGGGGTCA
1 AAAT-GTAATTTTTGAAAAGTTTAGGGT-A
* * * *
248560 AAATGTAATTTTTGGATA-TTCGAGGATA
1 AAATGTAATTTTTGAAAAGTT-TAGGGTA
* * * *
248588 AAATGGTAATTTTT-TAATGTTCGAGAGTA
1 AAAT-GTAATTTTTGAAAAGTT-TAGGGTA
248617 AAATGGTAATTTTTGAAAAGTTTAGGGTCAA
1 AAAT-GTAATTTTTGAAAAGTTTAGGGT--A
* * *
248648 AAATGTAATTTTAG-ACA-TTCGAGGGTA
1 AAATGTAATTTTTGAAAAGTT-TAGGGTA
*
248675 AAATGGTAATTTTTG-AAAGTTCGAGAGGGATAA
1 AAAT-GTAATTTTTGAAAAGTT---TAGGG-T-A
* * *
248708 AAATATAATTTTTTG-ACA-TTCAGGGGTA
1 AAATGTAA-TTTTTGAAAAGTTTA-GGGTA
* * *
248736 GAATGGTAATTTTTG-AATGTTCGAGGGTAA
1 AAAT-GTAATTTTTGAAAAGTT-TAGGGT-A
* * *
248766 AAATGGAATTTTTGATAAGTTTAGGGTCT
1 AAATGTAATTTTTGAAAAGTTTAGGGT-A
*
248795 AAATGTAATTTTTGAAAAGTTTAAAGGTCA
1 AAATGTAATTTTTGAAAAGTTT-AGGGT-A
*
248825 AAATATAATTTTTGGAAAA-TTTAAGGGTA
1 AAATGTAATTTTT-GAAAAGTTT-AGGGTA
*
248854 ATAATGTAATTTTT-AGAAAGTTTAATGGTCA
1 A-AATGTAATTTTTGA-AAAGTTT-AGGGT-A
248885 AAATGTAATTTTTG
1 AAATGTAATTTTTG
248899 GAGAGTTCAG
Statistics
Matches: 331, Mismatches: 59, Indels: 68
0.72 0.13 0.15
Matches are distributed among these distances:
27 14 0.04
28 49 0.15
29 125 0.38
30 107 0.32
31 17 0.05
32 6 0.02
33 13 0.04
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (28 bp):
AAATGTAATTTTTGAAAAGTTTAGGGTA
Done.