Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007807.1 Hibiscus syriacus cultivar Beakdansim tig00110126_pilon, 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: 2195110
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 9
Found at i:165886 original size:19 final size:19
Alignment explanation
Indices: 165864--166018 Score: 94
Period size: 19 Copynumber: 8.3 Consensus size: 19
165854 CTATATTTTA
*
165864 TTTATTTCATTTTTTTGTC
1 TTTATTTCATTTTTTTATC
*
165883 TTTATTTTTTATTCTTTTTAT-
1 TTTA--TTTCATT-TTTTTATC
**
165904 TTTATTTTGTTTATTTTAT-
1 TTTATTTCATTT-TTTTATC
* *
165923 TTTGTTT-ATTTTATT-TC
1 TTTATTTCATTTTTTTATC
*
165940 TTTATTTTATTTTTGTT-TC
1 TTTATTTCATTTTT-TTATC
*
165959 TTTATTTTCATTTTGTTCAT-
1 TTTA-TTTCATTTT-TTTATC
* *
165979 TTTATTT-A-CTTTTAATC
1 TTTATTTCATTTTTTTATC
165996 TTTATTTCATTTTTTT-TC
1 TTTATTTCATTTTTTTATC
166014 TTTAT
1 TTTAT
166019 CTTTGTACTT
Statistics
Matches: 109, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.05
17 18 0.17
18 18 0.17
19 37 0.34
20 13 0.12
21 12 0.11
22 6 0.06
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTATTTCATTTTTTTATC
Found at i:167651 original size:28 final size:28
Alignment explanation
Indices: 167599--167652 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
167589 TTGGCCGTAA
*
167599 GTCGCCTGCACTCCGGGTGACCTTATAG
1 GTCGCCTGCACTCCGGGCGACCTTATAG
*
167627 GTCGCCATGCACTCCTGGCGA-CTTAT
1 GTCGCC-TGCACTCCGGGCGACCTTAT
167653 CCTTGCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (28 bp):
GTCGCCTGCACTCCGGGCGACCTTATAG
Found at i:168243 original size:16 final size:17
Alignment explanation
Indices: 168222--168263 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
168212 GGCTGGGGAG
168222 ATTAGGTTTAGA-TTA-A
1 ATTAGGTTTA-ACTTATA
168238 ATTAGG-TTAACTTATA
1 ATTAGGTTTAACTTATA
168254 ATTAGGTTTA
1 ATTAGGTTTA
168264 TATGGTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 6 0.26
16 13 0.57
17 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (17 bp):
ATTAGGTTTAACTTATA
Found at i:169055 original size:37 final size:37
Alignment explanation
Indices: 168982--169056 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
168972 GTTGGAAAAT
* *
168982 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
169019 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
169056 A
1 A
169057 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:183241 original size:69 final size:69
Alignment explanation
Indices: 183142--183322 Score: 240
Period size: 69 Copynumber: 2.6 Consensus size: 69
183132 TGATTATAAC
* * * * *
183142 AATAA-TATGATTAGGTGCTCTCGTGTGAGTCACTCTAATCTTTTGGGGCTCCCGTACGAGTCAC
1 AATAATTATGATTAGGTGCTCTCTTGTGAGTCACTTTAATCCTTCGAGGCTCCCGTACGAGTCAC
**
183206 CCTG
66 CCAA
* *
183210 AATAATTATGATTATGTGCTCTCATTG-GAGTCACTTTAATCCTTCGAGGCTCTCGTACGAGTCA
1 AATAATTATGATTAGGTGCTCTC-TTGTGAGTCACTTTAATCCTTCGAGGCTCCCGTACGAGTCA
183274 CCCAA
65 CCCAA
* *
183279 AATGATTATGATTAGGTGCTCCCTTGTGAGTCACTTTAATCCTT
1 AATAATTATGATTAGGTGCTCTCTTGTGAGTCACTTTAATCCTT
183323 TAAAGCTCCT
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
68 8 0.08
69 88 0.90
70 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (69 bp):
AATAATTATGATTAGGTGCTCTCTTGTGAGTCACTTTAATCCTTCGAGGCTCCCGTACGAGTCAC
CCAA
Found at i:183342 original size:69 final size:69
Alignment explanation
Indices: 183142--183437 Score: 228
Period size: 69 Copynumber: 4.3 Consensus size: 69
183132 TGATTATAAC
* * **
183142 AATAA-TATGATTAGGTGCTCTCGTGTGAGTCACTCTAATCTTTTGGGGCTCC-CGTACGAGTCA
1 AATAATTATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTAAGGCTCCTCGTAC-AGTCA
**
183205 CCCTG
65 CCCAA
* * * * **
183210 AATAATTATGATTATGTGCTCTCAT-TGGAGTCACTTTAATCCTTCGAGGCT-CTCGTACGAGTC
1 AATAATTATGATTAGGTGCTCCCGTGT-GAGTCACTCTAATCCTTTAAGGCTCCTCGTAC-AGTC
183273 ACCCAA
64 ACCCAA
* * * * *
183279 AATGATTATGATTAGGTGCTCCCTTGTGAGTCACTTTAATCCTTTAAAGCTCCTATGTA-AGTCA
1 AATAATTATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTAAGGCTCCT-CGTACAGTCA
183343 -CCAGA
65 CCCA-A
* * * * * * * * *
183348 AAAAATTATGATTAGGTACTTCGGTGTGAGTCACTCTAATCTTTTAGGGAT-CTCATACGAGTTA
1 AATAATTATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTAAGGCTCCTCGTAC-AGTCA
183412 CCCAA
65 CCCAA
* * *
183417 AGTGATTATTATTAGGTGCTC
1 AATAATTATGATTAGGTGCTC
183438 TTGTGCAAGT
Statistics
Matches: 182, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
67 2 0.01
68 12 0.07
69 159 0.87
70 6 0.03
71 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (69 bp):
AATAATTATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTAAGGCTCCTCGTACAGTCAC
CCAA
Found at i:183541 original size:19 final size:19
Alignment explanation
Indices: 183517--183702 Score: 126
Period size: 19 Copynumber: 9.6 Consensus size: 19
183507 CTGTGCGAGT
183517 CAACCTAAAATCTGTTTTC
1 CAACCTAAAATCTGTTTTC
* *
183536 CAACCT-AAATTTAGGTTTC
1 CAACCTAAAATCT-GTTTTC
**
183555 CAACCTAAAATCAATTTTC
1 CAACCTAAAATCTGTTTTC
**
183574 CAACCTAAAATCAATTTTC
1 CAACCTAAAATCTGTTTTC
*
183593 CAACCTAAAAGT-TGTTTTTA
1 CAACCTAAAA-TCTG-TTTTC
* * *
183613 CAAACTAAAAT-AGAGTTTC
1 CAACCTAAAATCTG-TTTTC
* * *
183632 CAACCTAAAACCTTTTTTTTT
1 CAACCTAAAA--TCTGTTTTC
* *
183653 TAACCTAAAATCAGTTTTC
1 CAACCTAAAATCTGTTTTC
* *
183672 CAACCTAAAATGTATTTTTC
1 CAACCTAAAATCT-GTTTTC
*
183692 CAAACTAAAAT
1 CAACCTAAAAT
183703 TAGAATTCTA
Statistics
Matches: 130, Mismatches: 29, Indels: 15
0.75 0.17 0.09
Matches are distributed among these distances:
18 5 0.04
19 79 0.61
20 33 0.25
21 13 0.10
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (19 bp):
CAACCTAAAATCTGTTTTC
Found at i:183632 original size:39 final size:38
Alignment explanation
Indices: 183517--183723 Score: 163
Period size: 39 Copynumber: 5.3 Consensus size: 38
183507 CTGTGCGAGT
* *
183517 CAACCTAAAATCT-GTTTTCCAACCTAAATTTAG-GTTTC
1 CAACCTAAAAT-TATTTTTCCAACCTAAA-ATAGAGTTTC
* * *
183555 CAACCTAAAATCAATTTTCCAACCTAAAATCA-ATTTTC
1 CAACCTAAAATTATTTTTCCAACCTAAAAT-AGAGTTTC
* * *
183593 CAACCTAAAAGTTGTTTTTACAAACTAAAATAGAGTTTC
1 CAACCTAAAA-TTATTTTTCCAACCTAAAATAGAGTTTC
* ** *
183632 CAACCTAAAACCTTTTTTTTTTAACCTAAAATCAG-TTTTC
1 CAACCTAAAA--TTATTTTTCCAACCTAAAAT-AGAGTTTC
* *
183672 CAACCTAAAATGTATTTTTCCAAACTAAAATTAGA-ATTC
1 CAACCTAAAAT-TATTTTTCCAACCTAAAA-TAGAGTTTC
*
183711 TAACCTAAAATTA
1 CAACCTAAAATTA
183724 GGTTTCCATG
Statistics
Matches: 137, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
37 1 0.01
38 44 0.32
39 59 0.43
40 31 0.23
41 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (38 bp):
CAACCTAAAATTATTTTTCCAACCTAAAATAGAGTTTC
Found at i:183674 original size:79 final size:79
Alignment explanation
Indices: 183575--183720 Score: 215
Period size: 79 Copynumber: 1.8 Consensus size: 79
183565 TCAATTTTCC
* *
183575 AACCTAAAATCAATTTTCCAACCTAAAA-GTTGTTTTTACAAACTAAAA-TAGAGTTTCCAACCT
1 AACCTAAAATCAATTTTCCAACCTAAAATG-TATTTTTACAAACTAAAATTAGA-ATTCCAACCT
183638 AAAACCTTTTTTTTTT
64 AAAACCTTTTTTTTTT
* * *
183654 AACCTAAAATCAGTTTTCCAACCTAAAATGTATTTTTCCAAACTAAAATTAGAATTCTAACCTAA
1 AACCTAAAATCAATTTTCCAACCTAAAATGTATTTTTACAAACTAAAATTAGAATTCCAACCTAA
183719 AA
66 AA
183721 TTAGGTTTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
79 55 0.92
80 5 0.08
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (79 bp):
AACCTAAAATCAATTTTCCAACCTAAAATGTATTTTTACAAACTAAAATTAGAATTCCAACCTAA
AACCTTTTTTTTTT
Found at i:185066 original size:3 final size:3
Alignment explanation
Indices: 185058--185096 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
185048 ATGTTTTTAA
*
185058 TAT TAT TAT TAG TAT TA- TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
185097 CAGGTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:187264 original size:131 final size:131
Alignment explanation
Indices: 187030--187290 Score: 380
Period size: 131 Copynumber: 2.0 Consensus size: 131
187020 AAATAGTAAC
* * * * *
187030 ACTCGAATCGATATTGATTTTTAAGATAGAATAGTGATATCTCTTCATTTCGATTAGAGTAATAA
1 ACTCGAACCAATATTGAATTTTAAGAGAGAATAATGATATCTCTTCATTTCGATTAGAGTAATAA
* * * * * *
187095 ATGATTGTTTTAAGGCGTGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATCATTTT
66 ATGACTGCTTTAAGACATGAGAGGTCATTTATTCTCGATTGGAAATAATTACATATTATCATTTT
187160 A
131 A
*
187161 ACTCGAACCAATATTGAATTTTAAGAG-GAAATAATGATATCTCTTCATTTCGATTGGAGTAATA
1 ACTCGAACCAATATTGAATTTTAAGAGAG-AATAATGATATCTCTTCATTTCGATTAGAGTAATA
* *
187225 AATGACTGCTTTAAGACATGAGAGTTCATTTATTCTCGATTGGAAATAATTACATATTATCGTTT
65 AATGACTGCTTTAAGACATGAGAGGTCATTTATTCTCGATTGGAAATAATTACATATTATCATTT
187290 T
130 T
187291 TCTCTTAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
130 1 0.01
131 114 0.99
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
ACTCGAACCAATATTGAATTTTAAGAGAGAATAATGATATCTCTTCATTTCGATTAGAGTAATAA
ATGACTGCTTTAAGACATGAGAGGTCATTTATTCTCGATTGGAAATAATTACATATTATCATTTT
A
Found at i:193378 original size:2 final size:2
Alignment explanation
Indices: 193367--193409 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
193357 TTAAGGCAGT
193367 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193408 TA
1 TA
193410 CAATAAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:195153 original size:42 final size:41
Alignment explanation
Indices: 195085--195188 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
195075 AGTAAGTCAA
** * *
195085 TCGGGTCAT-TAGTAAGTCTTTGGAGCATGATGATTAAATCCT
1 TCGGGTCATCTA-TAAACCTTTCGAGCAAGATGA-TAAATCCT
*
195127 TCGGGTCATCTATAAACCTTTCGAGCAAGATGATAAGTCCT
1 TCGGGTCATCTATAAACCTTTCGAGCAAGATGATAAATCCT
* *
195168 TCGAGTCATCAATAAGACCTT
1 TCGGGTCATCTATAA-ACCTT
195189 CGGGCAGGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 20 0.38
42 31 0.58
43 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
TCGGGTCATCTATAAACCTTTCGAGCAAGATGATAAATCCT
Found at i:195177 original size:41 final size:43
Alignment explanation
Indices: 195102--195188 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 43
195092 ATTAGTAAGT
* * * *
195102 CTTTGGAGCATGATGATTAAATCCTTCGGGTCATCTATAA-AC
1 CTTTCGAGCAAGATGATTAAATCCTTCGAGTCATCAATAAGAC
*
195144 CTTTCGAGCAAGATGA-TAAGTCCTTCGAGTCATCAATAAGAC
1 CTTTCGAGCAAGATGATTAAATCCTTCGAGTCATCAATAAGAC
195186 CTT
1 CTT
195189 CGGGCAGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTCGAGCAAGATGATTAAATCCTTCGAGTCATCAATAAGAC
Found at i:195615 original size:246 final size:244
Alignment explanation
Indices: 195076--195779 Score: 968
Period size: 246 Copynumber: 2.9 Consensus size: 244
195066 TTCTTACTTA
** * * ** * *
195076 GTAAGTCAATCGGGTCATTAGTAAGTCTTTGGAGCATGATGATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGACATCAGTAAGTCTTTCAAGCATGATGAGTAAATCCTTCGAGTCATCTATA
* * * * *
195141 AACCTTTCGAGCAAGATGATAAGTCCTTCGAGTCATCAATAAGACCTTCGGGCAGGATGTTTTCA
66 AGCCTTTCGAGCAAGATGATAAGT-CTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
*
195206 CATGTTTTTTG-AAAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGT
130 CATGTTTTTCGAAAAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGT
* ** *
195270 AAGATAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
195 AAGAAAAAAATTTCCAAAGTTTCTTACCTAGTAAACTAATTCCAAAATTG
* *
195320 GTAAGTCCTTCGGGACATCAGTAAGTCTTTCCAGCATGATGAGTAAATCCTTTGAGTCATCTATA
1 GTAAGTCCTTCGGGACATCAGTAAGTCTTTCAAGCATGATGAGTAAATCCTTCGAGTCATCTATA
195385 AGCCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
66 AGCCTTTCGAGCAAGATGATAAGTC-TTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
*
195450 CATGTTTTTCGAAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGT
130 CATGTTTTTCGAAAAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGT
* *
195515 AAGAAAACAAATTTTCAATGTTTCTTACCTAGTAAACTAATTCCAAAATTG
195 AAGAAAA-AAATTTCCAAAGTTTCTTACCTAGTAAACTAATTCCAAAATTG
**
195566 GTAAGTCCTTC-GGACCATCAGTAAGTCTTTCAAGCATGATGAGTAAATCCTTCCCGTCATCTAT
1 GTAAGTCCTTCGGGA-CATCAGTAAGTCTTTCAAGCATGATGAGTAAATCCTTCGAGTCATCTAT
*
195630 AAGCCTTTCGAGCAAGATGATAAGTGCTTCGGGCCATCCATAAGACCTTCAGGC-AGATGTTTTC
65 AAGCCTTTCGAGCAAGATGATAAGT-CTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTC
* *
195694 ACATG-TTTTC---------CGAAAAGTTTCTCATTTAAATATGAAAATT-AAAGTTTTTAAAAA
129 ACATGTTTTTCGAAAAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAA-TTTTTGAAAA
** * *
195748 GTAAGAAAACGATTTCCAAATTTTCGTACCTA
193 GTAAGAAAAAAATTTCCAAAGTTTCTTACCTA
195780 AACGATTTCC
Statistics
Matches: 418, Mismatches: 36, Indels: 22
0.88 0.08 0.05
Matches are distributed among these distances:
234 20 0.05
235 46 0.11
243 1 0.00
244 129 0.31
245 76 0.18
246 145 0.35
247 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (244 bp):
GTAAGTCCTTCGGGACATCAGTAAGTCTTTCAAGCATGATGAGTAAATCCTTCGAGTCATCTATA
AGCCTTTCGAGCAAGATGATAAGTCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAC
ATGTTTTTCGAAAAAATGAGAAAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTA
AGAAAAAAATTTCCAAAGTTTCTTACCTAGTAAACTAATTCCAAAATTG
Found at i:195788 original size:25 final size:25
Alignment explanation
Indices: 195754--195804 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
195744 AAAAGTAAGA
*
195754 AAACGATTTCCAAATTTTCGTACCT
1 AAACGATTTCCAAAGTTTCGTACCT
*
195779 AAACGATTTCCAAAGTTTCTTACCT
1 AAACGATTTCCAAAGTTTCGTACCT
195804 A
1 A
195805 GTAAACTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (25 bp):
AAACGATTTCCAAAGTTTCGTACCT
Found at i:196611 original size:13 final size:11
Alignment explanation
Indices: 196578--196609 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
196568 CCAAGCACGC
*
196578 AAAGAGGATAT
1 AAAGAGGAGAT
196589 AAAGAGGAGAT
1 AAAGAGGAGAT
196600 AAAGAGGAGA
1 AAAGAGGAGA
196610 GAGAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.34, T:0.09
Consensus pattern (11 bp):
AAAGAGGAGAT
Found at i:196679 original size:13 final size:12
Alignment explanation
Indices: 196642--196680 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
196632 TTGGGTTTTG
196642 AAAAA-AGGGAA
1 AAAAAGAGGGAA
196653 AAAAAGAGGGAA
1 AAAAAGAGGGAA
196665 AAATAAG-GGGAA
1 AAA-AAGAGGGAA
196677 AAAA
1 AAAA
196681 GAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.23
12 17 0.65
13 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (12 bp):
AAAAAGAGGGAA
Found at i:198419 original size:131 final size:131
Alignment explanation
Indices: 198157--198412 Score: 343
Period size: 131 Copynumber: 2.0 Consensus size: 131
198147 AAAATAGTAA
* * * * *
198157 CACTTGAATCGATATTGATTTTTAAGACAAAATAGTGATATCTATTCATATCGATTAGAGTAATA
1 CACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTATTCATATCAATTAGAATAATA
* * * * *
198222 AATGGATGCTTTAAGGCATGAGAGGTCATTTATTCTCGAATGGAAATCATTATATATTATCATTT
66 AATGGATACTTTAAGGCACGAGAGGCCATTTATTCTCGAATGGAAATAATTAGATATTATCATTT
198287 T
131 T
** * * * *
198288 CACTCGAATCAATATTGAATTTTAAGATGAAATAGTGATATCTCTTTATTTCAATTGGAATAATA
1 CACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTATTCATATCAATTAGAATAATA
*
198353 AAT-GACTACTTTAAGGCACGAGAGGCCATTTATTCTCGATTGGAAATAATTAGATATTAT
66 AATGGA-TACTTTAAGGCACGAGAGGCCATTTATTCTCGAATGGAAATAATTAGATATTAT
198413 TGTTTTCTCT
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
130 2 0.02
131 105 0.98
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (131 bp):
CACTCGAATCAATATTGAATTTTAAGACAAAATAGTGATATCTATTCATATCAATTAGAATAATA
AATGGATACTTTAAGGCACGAGAGGCCATTTATTCTCGAATGGAAATAATTAGATATTATCATTT
T
Found at i:203104 original size:20 final size:21
Alignment explanation
Indices: 203079--203143 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
203069 TTAGAAAATG
203079 GCAACAAAGAA-GTCAAATTC
1 GCAACAAAGAATGTCAAATTC
** *
203099 GCAACACTGAATTTCAAATTC
1 GCAACAAAGAATGTCAAATTC
* *
203120 GCAAC--TGAATTTCAAATTC
1 GCAACAAAGAATGTCAAATTC
203139 GCAAC
1 GCAAC
203144 TCGATTTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
20 9 0.22
21 13 0.32
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
GCAACAAAGAATGTCAAATTC
Found at i:203150 original size:19 final size:20
Alignment explanation
Indices: 203091--203182 Score: 98
Period size: 19 Copynumber: 4.7 Consensus size: 20
203081 AACAAAGAAG
*
203091 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACTC-GAATT
203112 TCAAATTCGCAACT-GAATT
1 TCAAATTCGCAACTCGAATT
*
203131 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACTCGAATT
** * *
203151 TTGAATTCACAACACGAATT
1 TCAAATTCGCAACTCGAATT
*
203171 T-AATTTCGCAAC
1 TCAAATTCGCAAC
203183 AGGTTTTAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 27 0.45
20 20 0.33
21 13 0.22
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (20 bp):
TCAAATTCGCAACTCGAATT
Found at i:203358 original size:14 final size:15
Alignment explanation
Indices: 203339--203376 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
203329 TCCCCATCTC
203339 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
203353 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
203369 TAATTTTT
1 TAATTTTT
203377 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:204145 original size:24 final size:24
Alignment explanation
Indices: 204118--204171 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
204108 GTATTCAAAA
*
204118 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGATCAATACCCGGAC
* *
204142 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
204166 TTTGAT
1 TTTGAT
204172 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:206690 original size:20 final size:20
Alignment explanation
Indices: 206665--206732 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
206655 GTTTTCCTTG
206665 AATTCGCATCGCGAAAGTCA
1 AATTCGCATCGCGAAAGTCA
* *
206685 AATTCGCATTGCGATAGTCA
1 AATTCGCATCGCGAAAGTCA
* *
206705 AATTCGCAACACGAAAGTCA
1 AATTCGCATCGCGAAAGTCA
206725 AATTCGCA
1 AATTCGCA
206733 ACGCAATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
AATTCGCATCGCGAAAGTCA
Found at i:206833 original size:20 final size:20
Alignment explanation
Indices: 206808--206876 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
206798 TCGCAACGCA
206808 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCACGTTGCG
* *
206828 AATTTGACTTTAACGTTGCA
1 AATTTGACTTTCACGTTGCG
* *
206848 AATTTGAGTTTCGCGTTGCG
1 AATTTGACTTTCACGTTGCG
206868 AATTTGACT
1 AATTTGACT
206877 ATCGTAACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (20 bp):
AATTTGACTTTCACGTTGCG
Found at i:207057 original size:64 final size:64
Alignment explanation
Indices: 206978--207135 Score: 289
Period size: 64 Copynumber: 2.5 Consensus size: 64
206968 TTGAATAAAC
206978 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
* *
207042 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
207106 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
207136 ATTCAATTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
64 87 0.96
65 4 0.04
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:208526 original size:21 final size:21
Alignment explanation
Indices: 208500--208597 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
208490 GTGAATCGAG
* * *
208500 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
208521 CTCTTGAATGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
208542 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
208563 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
208584 CTCTTGAACGATGA
1 CTCTTGAACGATGA
208598 CAGGTGCATC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:210755 original size:20 final size:20
Alignment explanation
Indices: 210732--210784 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
210722 AAACTTAAGT
*
210732 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
210752 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
210772 TCGCAACGCGAAA
1 TCGCAACGCGAAA
210785 CTAAATTCGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:210807 original size:14 final size:14
Alignment explanation
Indices: 210790--210820 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
210780 CGAAACTAAA
210790 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
*
210804 TTCGTGTTGCGATT
1 TTCGCGTTGCGATT
210818 TTC
1 TTC
210821 ATTTTCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.48
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:210846 original size:20 final size:20
Alignment explanation
Indices: 210803--210847 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
210793 GCGTTGCGAT
* * * *
210803 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCGAATTTAAG
210823 TTTCATGTTGCGAATTTAAG
1 TTTCATGTTGCGAATTTAAG
210843 TTTCA
1 TTTCA
210848 AAAACTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGAATTTAAG
Found at i:211198 original size:22 final size:22
Alignment explanation
Indices: 211172--211218 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
211162 GATGGAGATA
211172 GACGGATTTCGTCAGAGATGAG
1 GACGGATTTCGTCAGAGATGAG
* *
211194 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCAGAGATGAG
211216 GAC
1 GAC
211219 AGATGTCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCAGAGATGAG
Found at i:211370 original size:20 final size:20
Alignment explanation
Indices: 211345--211447 Score: 170
Period size: 20 Copynumber: 5.2 Consensus size: 20
211335 ATAAACGCGC
211345 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
211365 TTTGACTTCTGTGTTGTGAA
1 TTTGACTTCTGTGTTGCGAA
*
211385 TTTGACTTCTGTGTTGTGAA
1 TTTGACTTCTGTGTTGCGAA
* *
211405 TTTGACTTATGTGTTGCAAA
1 TTTGACTTCTGTGTTGCGAA
211425 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
211445 TTT
1 TTT
211448 ATAAAATCGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:220275 original size:51 final size:51
Alignment explanation
Indices: 220156--220276 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 51
220146 AAATGCAAAA
* * *
220156 AGTGACCAAAATGCATAAAACAGATGAACAATAGCCAAATCAGAACTAAAC
1 AGTGAACAAAATGCATAAAACAGAAGAACAATAGCCAAATCAGAAATAAAC
** * * * * * *
220207 AGTGAGTAGATTACATAAAATAGAAGAACAATAGCTAAATCAGAAATAAAT
1 AGTGAACAAAATGCATAAAACAGAAGAACAATAGCCAAATCAGAAATAAAC
*
220258 AGTGAACAAAAGGCATAAA
1 AGTGAACAAAATGCATAAA
220277 TTGAAAGTAT
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.17
Consensus pattern (51 bp):
AGTGAACAAAATGCATAAAACAGAAGAACAATAGCCAAATCAGAAATAAAC
Found at i:222714 original size:101 final size:103
Alignment explanation
Indices: 222577--222787 Score: 250
Period size: 101 Copynumber: 2.1 Consensus size: 103
222567 AAGAGATGCT
* * * *
222577 ATCTCAGGTGAGATAAATTTTTGTTTCGAGGAAAACAATTTCAAAATTTTCGTTTCAAGGGAAAA
1 ATCTCAAGTGAGATAAATTTTTGTTTCAAGGAAAACAATTTCAAAATTTGCGCTTCAAGGG-AAA
**
222642 CTATCTCAAGCGAGA-CAAAATTTGTTTTTAGA-AAATA
65 CTATCTCAAGCGAGATCAAAATTTGTTTGGAGAGAAATA
* ** * *
222679 ATCTCAAGTGAGATCAA-TTTTGTTTCAAGTG-AAACAATTTTGAAATTTGGGCTTCATGGGAAA
1 ATCTCAAGTGAGATAAATTTTTGTTTCAAG-GAAAACAATTTCAAAATTTGCGCTTCAAGGGAAA
* * *
222742 CTGTCTCAAGCGAGATGAAACTTTGTTTGGAGAGAAATA
65 CTATCTCAAGCGAGATCAAAATTTGTTTGGAGAGAAATA
222781 ATCTCAA
1 ATCTCAA
222788 AGGTTTATGT
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
100 17 0.18
101 47 0.51
102 28 0.30
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (103 bp):
ATCTCAAGTGAGATAAATTTTTGTTTCAAGGAAAACAATTTCAAAATTTGCGCTTCAAGGGAAAC
TATCTCAAGCGAGATCAAAATTTGTTTGGAGAGAAATA
Found at i:222718 original size:20 final size:21
Alignment explanation
Indices: 222682--222720 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
222672 GAAAATAATC
*
222682 TCAAGTGAGATCAATTTTGTT
1 TCAAGTGAGAACAATTTTGTT
222703 TCAAGTGA-AACAATTTTG
1 TCAAGTGAGAACAATTTTG
222721 AAATTTGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (21 bp):
TCAAGTGAGAACAATTTTGTT
Found at i:222873 original size:168 final size:167
Alignment explanation
Indices: 222597--222959 Score: 509
Period size: 168 Copynumber: 2.2 Consensus size: 167
222587 AGATAAATTT
* * * * *
222597 TTGTTTCGAG-GAAAACAATTTCAAA-ATTT-TCGTTTCAAGGGAAAACTATCTCAAGCGAGACA
1 TTGTTTCGAGAG-AAACAATCTCAAAGGTTTAT-GTTTCAAGAG-AAATTGTCTCAAGCGAGACA
* * * *
222659 AAATTTGTTTTTAGAAAATAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTTGAAA
63 AAATTTGTATTTAGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTCTGAAA
* * *
222724 TTTGGGCTTCATGGGAAACTGTCTCAAGCGAGATGAAACT
128 TTTGGGCTTCAAGGGAAACTATCTCAAGCGAGATGAAACA
* *
222764 TTGTTTGGAGAGAAATAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAA
1 TTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGCGAGAC-AAA
222829 ATTT-TATTTAGGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTCTGAAAT
65 ATTTGTATTTA-GAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTCTGAAAT
* *
222893 TTGGGCTTTAAGGGAAATTATCTCAAGCGAGATGAAACA
129 TTGGGCTTCAAGGGAAACTATCTCAAGCGAGATGAAACA
222932 TTGTTTCGAGAGAAACAATCTCAAAGGT
1 TTGTTTCGAGAGAAACAATCTCAAAGGT
222960 GACATACAAT
Statistics
Matches: 173, Mismatches: 18, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
167 42 0.24
168 130 0.75
169 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (167 bp):
TTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAA
TTTGTATTTAGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTCTGAAATTT
GGGCTTCAAGGGAAACTATCTCAAGCGAGATGAAACA
Found at i:230422 original size:6 final size:6
Alignment explanation
Indices: 230391--230420 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
230381 TATTCTTTCC
*
230391 TTTATT TTTATT TTTATT TTTATT CTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT
230421 CTGTTTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:247954 original size:5 final size:4
Alignment explanation
Indices: 247933--248176 Score: 53
Period size: 4 Copynumber: 60.8 Consensus size: 4
247923 AAAAGGCAAG
* * *
247933 AAAT AAAT AAAT AAATT AAATT AAAAT GAAG AAA- AAAC AAATT AAAT
1 AAAT AAAT AAAT AAA-T AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT
* * * * * *
247980 AAA- AGAT AAGAT AAAG AAAGT AAAG ATA- AAAT -AGT AAGT AAAAT AAA-
1 AAAT AAAT AA-AT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
* * * * * * * *
248027 ATAT AAAA AAAT AAAA AAAT AAAG AAAT AAAG AAAT AAAG AAAA ATAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
*
248076 AAA- AAAT ATAT AAAT AAA- ATAAT -AAT AAA- AAAGT -AA- AAAT AATAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT AAAT AA-AT
* * * * * * *
248121 ATAT ATAT ATAT ATAAT AAAA AAAT AAA- AAAT AGTAT ATAT ATAT AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
*
248170 TAAT AAA
1 AAAT AAA
248177 ACTGATAATA
Statistics
Matches: 180, Mismatches: 36, Indels: 48
0.68 0.14 0.18
Matches are distributed among these distances:
3 26 0.14
4 119 0.66
5 32 0.18
6 3 0.02
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:248048 original size:16 final size:16
Alignment explanation
Indices: 248019--248106 Score: 70
Period size: 16 Copynumber: 5.2 Consensus size: 16
248009 AATAGTAAGT
*
248019 AAAAT-AAAATATAAA
1 AAAATAAAAAAATAAA
248034 AAAATAAAAAAATAAA
1 AAAATAAAAAAATAAA
* *
248050 GAAATAAAGAAATAAAGA
1 AAAATAAAAAAAT-AA-A
*
248068 AAAATAAGAAAAAATATA
1 AAAAT-A-AAAAAATAAA
* *
248086 TAAATAAAATAATAATA
1 AAAATAAAAAAATAA-A
248103 AAAA
1 AAAA
248107 AGTAAAAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.09
16 27 0.47
17 7 0.12
18 10 0.18
19 2 0.04
20 6 0.11
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAAATAAA
Found at i:248100 original size:36 final size:35
Alignment explanation
Indices: 248020--248235 Score: 149
Period size: 36 Copynumber: 5.9 Consensus size: 35
248010 ATAGTAAGTA
*
248020 AAATAAAAT-AT-AAAAAAATAAAAAAATA-A-AG
1 AAATAAAATAATAAAAAAAATAAAAAAATATATAT
248051 AAATAAAGA-AATAAAGAAAAATAAGAAAAA-ATATAT
1 AAATAAA-ATAATAAA-AAAAATAA-AAAAATATATAT
248087 AAATAAAATAATAATAAAAAAGTAAAAATAATATATAT
1 AAATAAAATAATAA-AAAAAA-TAAAAA-AATATATAT
* *
248125 ATATATATATAAT-AAAAAAATAAAAAATAGTATATAT
1 AAATA-AAATAATAAAAAAAATAAAAAA-A-TATATAT
* * *
248162 ATATAAATTAATAAAACTGATAATAAAAAATAATATATAT
1 AAATAAAATAATAAAA---AAAAT-AAAAA-AATATATAT
* * * *
248202 ATATATATATAATCTAAAAAAATAAAAATATATA
1 AAATA-AAATAAT-AAAAAAAATAAAAAAATATA
248236 CTAAAGTAAA
Statistics
Matches: 151, Mismatches: 11, Indels: 40
0.75 0.05 0.20
Matches are distributed among these distances:
31 7 0.05
32 3 0.02
33 2 0.01
34 9 0.06
35 8 0.05
36 33 0.22
37 32 0.21
38 16 0.11
39 10 0.07
40 16 0.11
41 11 0.07
42 4 0.03
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (35 bp):
AAATAAAATAATAAAAAAAATAAAAAAATATATAT
Found at i:248100 original size:44 final size:42
Alignment explanation
Indices: 248024--248153 Score: 111
Period size: 44 Copynumber: 2.9 Consensus size: 42
248014 TAAGTAAAAT
* *
248024 AAAATATAAAAAAATAAAAAAATAAAGAAATAAAGAAATAAAG-A
1 AAAATA-AAAAAAATATATAAATAAA-AAATAAA-AAATAAAGTA
*
248068 AAAATAAGAAAAAATATATAAATAAAATAATAATAAA-AAAGTA
1 AAAATAA-AAAAAATATATAAATAAAA-AATAAAAAATAAAGTA
*
248111 AAAATAATATATATATATATATATAATAAAAAAATAAAAAATA
1 AAAATAA-A-A-A-AAATATATA-AAT-AAAAAATAAAAAATA
248154 GTATATATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.06
43 14 0.20
44 28 0.39
45 1 0.01
46 8 0.11
47 11 0.15
48 5 0.07
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (42 bp):
AAAATAAAAAAAATATATAAATAAAAAATAAAAAATAAAGTA
Found at i:248164 original size:79 final size:78
Alignment explanation
Indices: 248081--248229 Score: 205
Period size: 77 Copynumber: 1.9 Consensus size: 78
248071 ATAAGAAAAA
248081 ATATATAAATAAAATAATAA-TAAAAA-AGTAAAAATAATATATATATATATATATAA-TAAAAA
1 ATATATAAAT-AAATAA-AACTAAAAATA--AAAAATAATATATATATATATATATAACTAAAAA
248143 AATAAAAAATAGTATAT
62 AATAAAAAATAGTATAT
* * *
248160 ATATATAAATTAATAAAACTGATAATAAAAAATAATATATATATATATATATAATCTAAAAAAAT
1 ATATATAAATAAATAAAACTAAAAATAAAAAATAATATATATATATATATATAA-CTAAAAAAAT
248225 AAAAA
65 AAAAA
248230 TATATACTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
77 29 0.46
78 9 0.14
79 25 0.40
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (78 bp):
ATATATAAATAAATAAAACTAAAAATAAAAAATAATATATATATATATATATAACTAAAAAAATA
AAAAATAGTATAT
Found at i:248363 original size:14 final size:14
Alignment explanation
Indices: 248344--248389 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
248334 AAATGTGCGT
248344 ATAAATAAAATTAA
1 ATAAATAAAATTAA
*
248358 ATAAATAAAATAATA
1 ATAAATAAAATTA-A
*
248373 ATAATTAAAATGTAA
1 ATAAATAAAAT-TAA
248388 AT
1 AT
248390 GTAAGAGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.44
15 14 0.52
16 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAAATAAAATTAA
Found at i:249382 original size:39 final size:36
Alignment explanation
Indices: 249328--249418 Score: 128
Period size: 39 Copynumber: 2.4 Consensus size: 36
249318 CAAGGGTTTG
*
249328 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT-T-T-T
* *
249367 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
249403 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
249419 TATCTCAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 17 0.35
37 1 0.02
38 1 0.02
39 30 0.61
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:249444 original size:36 final size:36
Alignment explanation
Indices: 249404--249637 Score: 205
Period size: 36 Copynumber: 6.6 Consensus size: 36
249394 TTTTTTTTTG
*
249404 TGTTTCAAGAGAAACTATCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
249440 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * * **
249477 AG-TTCTAAAAGAAACTGTCTCAAGAGAGATGAAATT
1 TGTTTC-AAGAGAAACTATCTCAAGAGAGACAAAATT
** * ** *
249513 TGTTTCAAG-GAAAAGATATTTA-A-AG----ATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
249542 TGTTTCAAGGGAAACTTTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
249578 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAA-AATT
* *
249615 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTATCTCAA
249638 AACTCATTTT
Statistics
Matches: 162, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
29 12 0.07
30 7 0.04
31 1 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 7 0.04
36 73 0.45
37 57 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
Found at i:249567 original size:102 final size:102
Alignment explanation
Indices: 249438--249624 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
249428 AGGGACAAAA
*
249438 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAG-TTCTAAAAGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTTC-AAAAGAAACTATCTCAAGA
*
249502 GAGATGAA-A-TTTGTTTCAAGGAAAAGATATTTAAAGAT
64 GAGA-CAAGATTTTGTTTCAAGGAAAAGATATTTAAAGAT
** * * **
249540 TTTGTTTCAAGGGAAACTTTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAAGAAACTATCTCAAGAGA
249605 GACAAGATTTTGTTTCAAGG
66 GACAAGATTTTGTTTCAAGG
249625 GAAACTGTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 2 0.03
101 24 0.32
102 48 0.65
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAAAGAAACTATCTCAAGAGA
GACAAGATTTTGTTTCAAGGAAAAGATATTTAAAGAT
Found at i:249753 original size:37 final size:38
Alignment explanation
Indices: 249702--249775 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
249692 TCAAGGTTTA
* *
249702 TGTTTCAAGAGAAACTATCTCATGGGAGA-AAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTT
*
249739 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAATT
249776 AATTTCAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (38 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAATTT
Found at i:249782 original size:37 final size:37
Alignment explanation
Indices: 249704--249789 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
249694 AAGGTTTATG
* * * **
249704 TTTCAAGAGAAACTATCTCATGGGAGAAAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTTAA
249741 TTTCAAGGGAAACTATCTCAAGAGAGACAAAAA-TTAA
1 TTTCAAGGGAAACTATCTCAAGAGAGA-AAAAATTTAA
*
249778 TTTCAAAGGAAA
1 TTTCAAGGGAAA
249790 TGTTTTCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 37 0.88
38 5 0.12
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (37 bp):
TTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTTAA
Found at i:249798 original size:103 final size:103
Alignment explanation
Indices: 249675--249915 Score: 340
Period size: 103 Copynumber: 2.3 Consensus size: 103
249665 ATATTGTGTG
* * *
249675 TTTCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCATGGGAGA-AAAAATTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAATTT
* *
249739 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAATTAA
66 TGTTTCAAGGGAAACTACCCCAAGAGAGA-AAAAATTAA
* * *
249778 TTTCAAAGGAAATGTTTTCAATGTTTCTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAATTT
* * * * *
249843 TGTTTTAAGGTAAACTACCCCAAGCGAGATAAAATTTA
66 TGTTTCAAGGGAAACTACCCCAAGAGAGAAAAAATTAA
*
249881 TTTCAAGGGAAATATTTTCAATGTTTATGTTTCAA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAA
249916 AGGAGACAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
103 89 0.74
104 32 0.26
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (103 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAATTT
TGTTTCAAGGGAAACTACCCCAAGAGAGAAAAAATTAA
Found at i:249945 original size:87 final size:88
Alignment explanation
Indices: 249824--250002 Score: 279
Period size: 87 Copynumber: 2.0 Consensus size: 88
249814 AGAAACTGTC
* * * *
249824 TCAAGGGAGACAAAAATTTTGTTTTAAGGTAAACTACCCCAAGCGAGATAAAATTTATTTCAAGG
1 TCAAAGGAGACAAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGG
249889 GAAATATTTTCAATGTTTATGTT
66 GAAATATTTTCAATGTTTATGTT
* * *
249912 TCAAAGGAGAC-AAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGG
1 TCAAAGGAGACAAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGG
*
249976 GAAATGTTTTCAATGTTTATGTT
66 GAAATATTTTCAATGTTTATGTT
249999 TCAA
1 TCAA
250003 GAGAAATTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 73 0.88
88 10 0.12
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (88 bp):
TCAAAGGAGACAAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGG
GAAATATTTTCAATGTTTATGTT
Found at i:250578 original size:106 final size:106
Alignment explanation
Indices: 250259--250581 Score: 421
Period size: 106 Copynumber: 3.0 Consensus size: 106
250249 TGTATTGTTC
* * * * * **
250259 CGAGTCCAATATCCTCCACCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * * * * *
250324 GTTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ATAAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
250365 CCAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * *
250430 ATAAGTCGTCTCTTCGTTGTGAAGTTGAACTTTTGTTGTCT
66 ATAAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
250471 CGAGTCCAATATCATTCGCTGTGAAGTTGAACTTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* *
250536 ACAAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ATAAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
250577 CGAGT
1 CGAGT
250582 GGCACGATAT
Statistics
Matches: 186, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 186 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
ATAAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:251246 original size:31 final size:32
Alignment explanation
Indices: 251176--251269 Score: 136
Period size: 31 Copynumber: 2.9 Consensus size: 32
251166 ATTCCCAAAG
*
251176 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* * *
251208 ATACCCCAACATTCGATGTTAAATCT-AAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
251239 ATGCCCCAACATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
251270 GATGCCCTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 27 0.51
32 23 0.43
33 3 0.06
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:252375 original size:14 final size:13
Alignment explanation
Indices: 252358--252415 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
252348 TGTTTCTTTA
*
252358 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
252371 TTTTTATTTTCTCT
1 TTTTT-TTTTCTCT
**
252385 TTGCTTTTT-TCT
1 TTTTTTTTTCTCT
*
252397 TCTTTTTTTCTCT
1 TTTTTTTTTCTCT
252410 TTTTTT
1 TTTTTT
252416 CCTTTTTGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 9 0.25
13 17 0.47
14 10 0.28
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:252378 original size:19 final size:19
Alignment explanation
Indices: 252354--252414 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
252344 CATTTGTTTC
*
252354 TTTATTTTTGTTTCTCTTT
1 TTTATTTTTCTTTCTCTTT
*
252373 TTTATTTTCTCTTT-GCTTT
1 TTTATTTT-TCTTTCTCTTT
* *
252392 TTTCTTCTTTTTTTCTCTTT
1 TTTATT-TTTCTTTCTCTTT
252412 TTT
1 TTT
252415 TCCTTTTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 21 0.62
20 13 0.38
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTATTTTTCTTTCTCTTT
Found at i:252415 original size:10 final size:10
Alignment explanation
Indices: 252389--252427 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
252379 TTCTCTTTGC
252389 TTTTTTCTTCT
1 TTTTTTC-TCT
252400 TTTTTTCTCT
1 TTTTTTCTCT
252410 TTTTTTC-CT
1 TTTTTTCTCT
252419 TTTTGTTCT
1 TTTT-TTCT
252428 GATTGAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.23
10 13 0.50
11 7 0.27
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:253808 original size:64 final size:59
Alignment explanation
Indices: 253679--253805 Score: 191
Period size: 65 Copynumber: 2.1 Consensus size: 59
253669 CATTGATCCA
253679 AAAACATGTCTTATTAAAATAATCTCATTGGGACAAAGTTTTTATCTTTTAGAGACAAT
1 AAAACATGTCTTATTAAAATAATCTCATTGGGACAAAGTTTTTATCTTTTAGAGACAAT
*
253738 AAAACATGTCTGTATTATAAATAATCTTTATTGGGACAAAAGTGTTTTATCTTTTAAGAGACAAT
1 AAAACATGTCT-TATTA-AAATAATC-TCATTGGGAC-AAAGT-TTTTATCTTTT-AGAGACAAT
253803 AAA
1 AAA
253806 CATATTTAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
59 11 0.18
60 5 0.08
61 8 0.13
62 9 0.15
63 5 0.08
64 11 0.18
65 12 0.20
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (59 bp):
AAAACATGTCTTATTAAAATAATCTCATTGGGACAAAGTTTTTATCTTTTAGAGACAAT
Found at i:254607 original size:20 final size:19
Alignment explanation
Indices: 254574--254626 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 19
254564 AAAGAAGAAG
254574 AAAAAAATATATAAATAAACA
1 AAAAAAATA-ATAAATAAA-A
254595 AAAAAAATAAT-AATAAAA
1 AAAAAAATAATAAATAAAA
254613 AAGTAAAAATAATA
1 AA--AAAAATAATA
254627 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 6 0.21
20 11 0.38
21 9 0.31
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAAAATAATAAATAAAA
Found at i:255518 original size:35 final size:36
Alignment explanation
Indices: 255468--255551 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
255458 ATACTTGATC
* *
255468 CATTTTCTCTCTTTTCCCT-TTTTT-TCTTTTTTTT
1 CATTTTCTTTTTTTTCCCTGTTTTTCTCTTTTTTTT
*
255502 CAATTTTCTTTTTTTTCTCTGTTTTTCTCTTTTTTTT
1 C-ATTTTCTTTTTTTTCCCTGTTTTTCTCTTTTTTTT
*
255539 C-TCTTCTTTTTTT
1 CATTTTCTTTTTTT
255552 CTTTGTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
34 1 0.02
35 26 0.60
36 5 0.12
37 11 0.26
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.75
Consensus pattern (36 bp):
CATTTTCTTTTTTTTCCCTGTTTTTCTCTTTTTTTT
Found at i:255535 original size:9 final size:9
Alignment explanation
Indices: 255470--255536 Score: 64
Period size: 9 Copynumber: 7.4 Consensus size: 9
255460 ACTTGATCCA
*
255470 TTTTCTCTC
1 TTTTCTCTT
*
255479 TTTTCCCTT
1 TTTTCTCTT
255488 TTTT-TCTT
1 TTTTCTCTT
* **
255496 TTTTTTCAA
1 TTTTCTCTT
*
255505 TTTTCTTTT
1 TTTTCTCTT
255514 TTTTCTCTGT
1 TTTTCTCT-T
255524 TTTTCTCTT
1 TTTTCTCTT
255533 TTTT
1 TTTT
255537 TTCTCTTCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
8 7 0.15
9 30 0.65
10 9 0.20
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:255543 original size:11 final size:11
Alignment explanation
Indices: 255508--255555 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
255498 TTTTCAATTT
255508 TCTTTTTTTTC
1 TCTTTTTTTTC
*
255519 TC-TGTTTTTC
1 TCTTTTTTTTC
255529 TCTTTTTTTTC
1 TCTTTTTTTTC
255540 TCTTCTTTTTT-
1 TCTT-TTTTTTC
255551 TCTTT
1 TCTTT
255556 GTATTCTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 10 0.30
11 17 0.52
12 6 0.18
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (11 bp):
TCTTTTTTTTC
Found at i:266891 original size:18 final size:18
Alignment explanation
Indices: 266868--266976 Score: 137
Period size: 18 Copynumber: 6.1 Consensus size: 18
266858 CAGGCCACTA
* *
266868 AAGCAGAAGAGTCTGCTG
1 AAGCAGAAGAGCCCGCTG
* *
266886 AAGCAGAAGAGTCTGCTG
1 AAGCAGAAGAGCCCGCTG
*
266904 AAGCAGAAGAGTCCGCTG
1 AAGCAGAAGAGCCCGCTG
**
266922 AAGCAGAAGAGCCCATTG
1 AAGCAGAAGAGCCCGCTG
*
266940 AAGCAGAAGAACCCGCTG
1 AAGCAGAAGAGCCCGCTG
*
266958 AAGCAGAAGAGCCTGCTG
1 AAGCAGAAGAGCCCGCTG
266976 A
1 A
266977 TCCAGTCCAT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.36, C:0.21, G:0.31, T:0.12
Consensus pattern (18 bp):
AAGCAGAAGAGCCCGCTG
Found at i:266915 original size:36 final size:36
Alignment explanation
Indices: 266868--266976 Score: 155
Period size: 36 Copynumber: 3.0 Consensus size: 36
266858 CAGGCCACTA
* *
266868 AAGCAGAAGAGTCTGCTGAAGCAGAAGAGTCTGCTG
1 AAGCAGAAGAGTCCGCTGAAGCAGAAGAGCCTGCTG
***
266904 AAGCAGAAGAGTCCGCTGAAGCAGAAGAGCCCATTG
1 AAGCAGAAGAGTCCGCTGAAGCAGAAGAGCCTGCTG
**
266940 AAGCAGAAGAACCCGCTGAAGCAGAAGAGCCTGCTG
1 AAGCAGAAGAGTCCGCTGAAGCAGAAGAGCCTGCTG
266976 A
1 A
266977 TCCAGTCCAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.36, C:0.21, G:0.31, T:0.12
Consensus pattern (36 bp):
AAGCAGAAGAGTCCGCTGAAGCAGAAGAGCCTGCTG
Found at i:271000 original size:22 final size:22
Alignment explanation
Indices: 270973--271023 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
270963 TTTAAAAGAC
*
270973 AAAATTTGGTCTGCATTTACCA
1 AAAATTTGATCTGCATTTACCA
270995 AAAATTTGATCTGCATTTACCA
1 AAAATTTGATCTGCATTTACCA
271017 AAAATTT
1 AAAATTT
271024 ATTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
AAAATTTGATCTGCATTTACCA
Found at i:271205 original size:79 final size:79
Alignment explanation
Indices: 271074--271231 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
271064 ATAAGCACCC
271074 CCATAACACCCAAAATTAGTACCTAATCGCTTATACATTGTCGTAAATGGTGGACATCATAAATT
1 CCATAACACCCAAAATTAGTACCTAATCGCTTATACATTGTCGTAAATGGTGGACATCATAAATT
271139 CAAATCAATATTTA
66 CAAATCAATATTTA
271153 CCATAACACCCAAAATTAGTACCTAATCGCTTATACATTGTCGTAAATGGTGGACATCATAAATT
1 CCATAACACCCAAAATTAGTACCTAATCGCTTATACATTGTCGTAAATGGTGGACATCATAAATT
271218 CAAATCAATATTTA
66 CAAATCAATATTTA
271232 AAGTGTGATC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (79 bp):
CCATAACACCCAAAATTAGTACCTAATCGCTTATACATTGTCGTAAATGGTGGACATCATAAATT
CAAATCAATATTTA
Found at i:273193 original size:2 final size:2
Alignment explanation
Indices: 273186--273215 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
273176 AAGTAAAAAT
273186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
273216 AAGTTTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:274040 original size:13 final size:13
Alignment explanation
Indices: 274022--274048 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
274012 AAATTTTAAA
274022 GATATTTGAGATT
1 GATATTTGAGATT
274035 GATATTTGAGATT
1 GATATTTGAGATT
274048 G
1 G
274049 GTGATAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (13 bp):
GATATTTGAGATT
Found at i:276529 original size:2 final size:2
Alignment explanation
Indices: 276446--276510 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
276436 CTTAACGTTC
*
276446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276488 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
276511 ATTATGTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:277710 original size:54 final size:54
Alignment explanation
Indices: 277667--277986 Score: 426
Period size: 54 Copynumber: 5.9 Consensus size: 54
277657 TCGATACGAC
* * * ** * * *
277667 AATTCACAAACTCATTATGAATTACATGGGGTGCACACATAGTGTCAATACGGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
* * * * *
277721 AATTCATAAACTAATTATGAATTTCTTAAGTTGTACTCACAGTGTCAATACAGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
*
277775 AATTCATAAACTCATTATGAATTTCTTAAGTTACACACACAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
* * * **
277829 AATTCATAAACTCATCATGAATTTCTTAAATAGCACACACAGTGCCAATACAAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
* * *
277883 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAATGCCAATACGAA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
277937 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACA-TCGCCAATA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGT-GCCAATA
277987 TAGTAAATGC
Statistics
Matches: 235, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.00
54 234 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (54 bp):
AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
Found at i:279220 original size:16 final size:16
Alignment explanation
Indices: 279184--279241 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
279174 ATTTATTCAA
279184 TTAAATCCTCCAAATTT
1 TTAAATCCTCCAAA-TT
*
279201 TTAAATCCTTCAAATT
1 TTAAATCCTCCAAATT
279217 TTAAATCCTCCAAATT
1 TTAAATCCTCCAAATT
279233 TTAAATCCT
1 TTAAATCCT
279242 TTCATTATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
16 26 0.67
17 13 0.33
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATCCTCCAAATT
Found at i:284462 original size:54 final size:54
Alignment explanation
Indices: 284140--284460 Score: 507
Period size: 54 Copynumber: 5.9 Consensus size: 54
284130 TCGATACGGT
* * * ** *
284140 AATTCACAAACTCATTATGAATTACGTGGGGTGCACACATAGTGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGA
* * *
284194 AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACAATGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGA
* * *
284248 AATTTATAAACTCATTATGAATTTCTTAAGTTACACACATAGTGCCAATACATA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGA
* *
284302 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAATGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGA
*
284356 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGA
284410 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC
1 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC
284461 GGTAAATACA
Statistics
Matches: 244, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 244 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (54 bp):
AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGA
Found at i:287465 original size:40 final size:42
Alignment explanation
Indices: 287421--287507 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 42
287411 AATTATTAAA
287421 ATATTTAAATATTTAT-TAATATTT-TCAA-A-AATATAATATT
1 ATATTTAAATATTTATATAATATTTAT-AATATAATAT-ATATT
** *
287461 ATATTTTTATATTTATATATTATTTATAATATAATATATATT
1 ATATTTAAATATTTATATAATATTTATAATATAATATATATT
287503 ATATT
1 ATATT
287508 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 14 0.35
41 9 0.22
42 12 0.30
43 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (42 bp):
ATATTTAAATATTTATATAATATTTATAATATAATATATATT
Found at i:287528 original size:5 final size:5
Alignment explanation
Indices: 287451--287512 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
287441 ATTTTCAAAA
* *
287451 ATATA ATATT ATATT -T-TT ATATT -TA-T ATATT AT-TT ATAAT ATAATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT-AT-T
287498 ATATT ATATT ATATT
1 ATATT ATATT ATATT
287513 TTAAAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
3 3 0.06
4 10 0.21
5 28 0.60
6 3 0.06
7 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:287670 original size:24 final size:24
Alignment explanation
Indices: 287638--287690 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
287628 ATAATCTAGT
287638 AATAT-TTTAATAAAAATACTTAA
1 AATATATTTAATAAAAATACTTAA
* **
287661 AATATATTTAATAATAATTTTTAA
1 AATATATTTAATAAAAATACTTAA
287685 AATATA
1 AATATA
287691 ATATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AATATATTTAATAAAAATACTTAA
Found at i:287735 original size:28 final size:28
Alignment explanation
Indices: 287682--287735 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
287672 TAATAATTTT
*
287682 TAAAATATAATATATTTTTTACTTTAAA
1 TAAAATAAAATATATTTTTTACTTTAAA
*
287710 TAAAATAAAATTTATATTTTTA-TTTA
1 TAAAATAAAATATAT-TTTTTACTTTA
287736 TTCAGATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TAAAATAAAATATATTTTTTACTTTAAA
Found at i:287845 original size:21 final size:22
Alignment explanation
Indices: 287820--287865 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
287810 TTATTCTAAT
*
287820 ATTTTAAAAAT-AATGATATTA
1 ATTTTAAAAATAAATAATATTA
* *
287841 ATTTTTATAATAAATAATATTA
1 ATTTTAAAAATAAATAATATTA
287863 ATT
1 ATT
287866 ATTATATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTAAAAATAAATAATATTA
Found at i:287878 original size:22 final size:22
Alignment explanation
Indices: 287830--287878 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
287820 ATTTTAAAAA
* *
287830 TAATGATATTAATTTTTATAAT
1 TAATAATATTAATTATTATAAT
* *
287852 AAATAATATTAATTATTATATT
1 TAATAATATTAATTATTATAAT
287874 TAATA
1 TAATA
287879 TTTATAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATAATATTAATTATTATAAT
Found at i:288372 original size:12 final size:12
Alignment explanation
Indices: 288357--288390 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
288347 TTATTTTATA
288357 TAAAAAATATTT
1 TAAAAAATATTT
288369 TAAAAAATATTT
1 TAAAAAATATTT
*
288381 CAATAAAATA
1 TAA-AAAATA
288391 AATGGACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:288606 original size:386 final size:378
Alignment explanation
Indices: 287903--288666 Score: 1408
Period size: 386 Copynumber: 2.0 Consensus size: 378
287893 TCTTAAAAAA
287903 TTCACAACTAATGAAAAATTATTGCACAACCTCTTTCAGACATCGTAAAACATTTTAAAAAATAT
1 TTCACAACTAATGAAAAATTATTGCACAACCTCTTTCAGACATCGTAAAACATTTTAAAAAATAT
287968 AATTTATTTTATATAAAAAATATTTTAAAAATATTTCAAATAAATAATGGACCTTAAAATAAATA
66 AATTTATTTTATATAAAAAATATTTTAAAAATATTTCAAATAAATAATGGACCTTAAAATAAATA
288033 AAACCAATTTTTAAATCAAATCAAAGTTTATCCCCATAATTGAAAGTTGTATTTACTCGAAACAC
131 AAACCAATTTTTAAATCAAATCAAAGTTTATCCCCATAATTGAAAGTTGTATTTACTCGAAACAC
288098 TAGAGGCCCAAACTCAAATTGGAAATGGGAAGTGGTATGGGCAGAGGCCTTTTCTCTTTCATTCG
196 TAGAGGCCCAAACTCAAATTGGAAATGGGAAGTGGTATGGGCAGAGGCCTTTTCTCTTTCATTCG
288163 GACCGATAAAAGAAAGTGAAAAGAAAAGAGAGTACAGTCCTTGGCTCAAACTCACAC-TCTCTCT
261 GACCGATAAAAGAAAGTGAAAAGAAAAGAGAGTACAGTCCTTGGCTCAAACTCACACTTCTCTCT
288227 TTCTCGGGACATAT-TTCCTCTTTAAATTCTTCCATAAACCTAAAACGCACAC
326 TTCTCGGGACATATATTCCTCTTTAAATTCTTCCATAAACCTAAAACGCACAC
288279 TTCACAACTAATGAAAAATTATTGCACAACCTCTTTCAGACATCGTAAAACATTTTAAAAAATAT
1 TTCACAACTAATGAAAAATTATTGCACAACCTCTTTCAGACATCGTAAAACATTTTAAAAAATAT
288344 AATTTATTTTATATAAAAAATATTTTAAAAAATATTTC-AATAAAATAAATGGACCTTAAAATAA
66 AATTTATTTTATATAAAAAATATTTT-AAAAATATTTCAAAT-AAAT-AATGGACCTTAAAATAA
288408 ATAAAAAATACCAATTTTTTAAATCAAATCAAAGTTTATTCCCCATAATTGAAAGTTGTATTTAC
128 AT---AAA-ACCAA-TTTTTAAATCAAATCAAAGTTTA-TCCCCATAATTGAAAGTTGTATTTAC
288473 TCGAAATACACTAGAGGCCCAAACTCAAATTGGAAATGGGAAGTGGTATGGGCAGAGGCCTTTTC
187 TCG-AA-ACACTAGAGGCCCAAACTCAAATTGGAAATGGGAAGTGGTATGGGCAGAGGCCTTTTC
288538 TCTTTCATTCGGACCGATAAAAGAAAGTGAAAAGAAAAGAGAGTACAGTCCTTGGCTCAAACTCA
250 TCTTTCATTCGGACCGATAAAAGAAAGTGAAAAGAAAAGAGAGTACAGTCCTTGGCTCAAACTCA
288603 CACTTCTCTCTTTCTCGGGACATATATTCCTCTTTAAATTCTTCCATAAACCTAAAACGCACAC
315 CACTTCTCTCTTTCTCGGGACATATATTCCTCTTTAAATTCTTCCATAAACCTAAAACGCACAC
288667 ACAATTTTCA
Statistics
Matches: 375, Mismatches: 0, Indels: 14
0.96 0.00 0.04
Matches are distributed among these distances:
376 94 0.25
377 15 0.04
378 19 0.05
381 3 0.01
382 5 0.01
383 23 0.06
384 29 0.08
385 2 0.01
386 126 0.34
387 21 0.06
388 38 0.10
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (378 bp):
TTCACAACTAATGAAAAATTATTGCACAACCTCTTTCAGACATCGTAAAACATTTTAAAAAATAT
AATTTATTTTATATAAAAAATATTTTAAAAATATTTCAAATAAATAATGGACCTTAAAATAAATA
AAACCAATTTTTAAATCAAATCAAAGTTTATCCCCATAATTGAAAGTTGTATTTACTCGAAACAC
TAGAGGCCCAAACTCAAATTGGAAATGGGAAGTGGTATGGGCAGAGGCCTTTTCTCTTTCATTCG
GACCGATAAAAGAAAGTGAAAAGAAAAGAGAGTACAGTCCTTGGCTCAAACTCACACTTCTCTCT
TTCTCGGGACATATATTCCTCTTTAAATTCTTCCATAAACCTAAAACGCACAC
Found at i:299398 original size:82 final size:82
Alignment explanation
Indices: 299261--299427 Score: 280
Period size: 82 Copynumber: 2.0 Consensus size: 82
299251 TTGGCGCAGT
* ** *
299261 AGGGGATCCTAAAGGCTTTACGACCTACAAAGCCGGCGTCGATGGAGGAGGACGATTGGGAAGAA
1 AGGGGATCCTAAAGGCTCTACGACCTACAAAGCCAACGTCGATGGAGGAGGACGATTGAGAAGAA
*
299326 TTGCAACAGTGAGCGGC
66 TTGCAACAGCGAGCGGC
*
299343 AGGGGATCCTGAAGGCTCTACGACCTACAAAGCCAACGTCGATGGAGGAGGACGATTGAGAAGAA
1 AGGGGATCCTAAAGGCTCTACGACCTACAAAGCCAACGTCGATGGAGGAGGACGATTGAGAAGAA
299408 TTGCAACAGCGAGCGGC
66 TTGCAACAGCGAGCGGC
299425 AGG
1 AGG
299428 AACCATACGA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.14
Consensus pattern (82 bp):
AGGGGATCCTAAAGGCTCTACGACCTACAAAGCCAACGTCGATGGAGGAGGACGATTGAGAAGAA
TTGCAACAGCGAGCGGC
Found at i:300158 original size:30 final size:30
Alignment explanation
Indices: 300110--300169 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
300100 CAATTTAAGG
*
300110 CAAAATGGTTTTTAGACTTAAATTGACTTTA
1 CAAAATGGTTTTTAGACTT-AATTGAATTTA
*
300141 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATGGTTTTTAGACTTAATTGAATTTA
300170 TTTAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGGTTTTTAGACTTAATTGAATTTA
Found at i:300277 original size:21 final size:21
Alignment explanation
Indices: 300251--300306 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
300241 GGTGTCAAAG
300251 TGCATCCATGCACCCCTGCAC
1 TGCATCCATGCACCCCTGCAC
* *
300272 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCACCCCTGCAC
300293 TGCATCCATGCACC
1 TGCATCCATGCACC
300307 TGCACTAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.21
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAC
Found at i:300334 original size:42 final size:40
Alignment explanation
Indices: 300249--300347 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 40
300239 AGGGTGTCAA
* *
300249 AGTGCATCCATGCACCCCTGCACTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA--CCTGCACTGCATCCACGCATCCATGC
*
300291 AGTGCATCCATGCACCTGCACTAGTGCATCGACGCA-CCATGC
1 AGTGCATCCATGCACCTGCAC---TGCATCCACGCATCCATGC
300333 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
300348 TCAAACACCG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 7 0.14
42 34 0.67
43 10 0.20
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.20
Consensus pattern (40 bp):
AGTGCATCCATGCACCTGCACTGCATCCACGCATCCATGC
Found at i:300397 original size:20 final size:20
Alignment explanation
Indices: 300372--300440 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
300362 CAATTAGTGA
*
300372 ATCGATGCATCCTACTGTGC
1 ATCGATGCATCCTGCTGTGC
*
300392 ATCGATGCATCCTGCTGTAC
1 ATCGATGCATCCTGCTGTGC
*
300412 ATCGATGCATCCTGGTGTGC
1 ATCGATGCATCCTGCTGTGC
*
300432 ATCCATGCA
1 ATCGATGCA
300441 CGAAGGCTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (20 bp):
ATCGATGCATCCTGCTGTGC
Found at i:300582 original size:21 final size:21
Alignment explanation
Indices: 300553--300592 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
300543 TTTGAGTAGA
300553 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
300575 AAAA-CATCCTCAACGGCT
1 AAAATCATCCCCAACGGCT
300593 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:301673 original size:19 final size:20
Alignment explanation
Indices: 301649--301696 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
301639 AATGATTTTC
*
301649 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
301668 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
301688 TTTTGAAAA
1 TTTTGAAAA
301697 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:302996 original size:34 final size:30
Alignment explanation
Indices: 302958--303026 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
302948 TTGATATAAC
302958 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA-G-AAAAT-GTTTTTGGACTT-AATTG
302992 AATTT-AGAAAATGTTTTTGGACTTAATTG
1 AATTTAAGAAAATGTTTTTGGACTTAATTG
303021 AATTTA
1 AATTTA
303027 TTCAAAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 5 0.15
32 1 0.03
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (30 bp):
AATTTAAGAAAATGTTTTTGGACTTAATTG
Found at i:303008 original size:30 final size:30
Alignment explanation
Indices: 302968--303026 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
302958 AATTTAAGGC
302968 AAAATGGTTTTTGGACTTGAATTGAATTTAG
1 AAAATGGTTTTTGGACTT-AATTGAATTTAG
302999 AAAAT-GTTTTTGGACTTAATTGAATTTA
1 AAAATGGTTTTTGGACTTAATTGAATTTA
303027 TTCAAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (30 bp):
AAAATGGTTTTTGGACTTAATTGAATTTAG
Found at i:303132 original size:21 final size:21
Alignment explanation
Indices: 303106--303158 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
303096 AGGGTGTCAA
*
303106 AGTGCATCCATACA-CCCTTGC
1 AGTGCATCCATACATCCC-TAC
303127 AGTGCATCCATACATCCCTAC
1 AGTGCATCCATACATCCCTAC
303148 AGTGCATCCAT
1 AGTGCATCCAT
303159 GCACTTGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.26, C:0.36, G:0.13, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATACATCCCTAC
Found at i:303176 original size:22 final size:19
Alignment explanation
Indices: 303106--303205 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 19
303096 AGGGTGTCAA
* *
303106 AGTGCATCCATACACCCTTGC
1 AGTGCATCCATGCA--CTTAC
* *
303127 AGTGCATCCATACATCCCTAC
1 AGTGCATCCATGCA--CTTAC
303148 AGTGCATCCATGCACTTGCAC
1 AGTGCATCCATGCACTT--AC
* *
303169 TAGTGCATCGATGCACCATAC
1 -AGTGCATCCATGCA-CTTAC
303190 AGTGCATCCATGCACT
1 AGTGCATCCATGCACT
303206 CAAACACCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
19 3 0.05
20 13 0.20
21 35 0.53
22 13 0.20
23 2 0.03
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (19 bp):
AGTGCATCCATGCACTTAC
Found at i:303250 original size:20 final size:20
Alignment explanation
Indices: 303225--303358 Score: 189
Period size: 20 Copynumber: 6.7 Consensus size: 20
303215 AATGCAATTA
*
303225 GTGCATTGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
303245 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
303265 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
**
303285 GTGCATCGATGCATCAAGGT-T
1 GTGCATCGATGCATC--CTTCT
*
303306 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
303326 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
303346 GTGCATCCATGCA
1 GTGCATCGATGCA
303359 CGAAGGCTAC
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
20 87 0.84
21 16 0.15
22 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:303318 original size:61 final size:61
Alignment explanation
Indices: 303244--303358 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
303234 TGCATCCTTC
* * *
303244 TGTGCATCGATGCATCCTTCTGTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGT
1 TGTGCATCGATGCATCCTGCTGTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGT
303305 TGTGCATCGATGCATCCTGCTGTGCATCGATGCATCCTGCTGTGCATCCATGCA
1 TGTGCATCGATGCATCCTGCTGTGCATCGATGCATCCTGCTGTGCATCCATGCA
303359 CGAAGGCTAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.31
Consensus pattern (61 bp):
TGTGCATCGATGCATCCTGCTGTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGT
Found at i:307465 original size:35 final size:35
Alignment explanation
Indices: 307417--307488 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
307407 TAAACTAAAA
* *
307417 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
1 AATAAGTCCATTCACCAAGTGAAATGAATTATTAT
*
307452 AATAAGTCTATTCACCAAGTGAAATGAATTATTAT
1 AATAAGTCCATTCACCAAGTGAAATGAATTATTAT
307487 AA
1 AA
307489 ATAGCATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (35 bp):
AATAAGTCCATTCACCAAGTGAAATGAATTATTAT
Found at i:309849 original size:19 final size:19
Alignment explanation
Indices: 309822--309864 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
309812 TTGTTGATCC
*
309822 TTTCATATGTGAAATGTCA
1 TTTCCTATGTGAAATGTCA
* *
309841 TTTCCTATGTGAATTGTCC
1 TTTCCTATGTGAAATGTCA
309860 TTTCC
1 TTTCC
309865 AACCAACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.47
Consensus pattern (19 bp):
TTTCCTATGTGAAATGTCA
Found at i:312268 original size:21 final size:22
Alignment explanation
Indices: 312238--312283 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
312228 TGTTGTGTCC
**
312238 TTTTGATGAAAGGGTTTAATCT
1 TTTTGATGAAAGGAATTAATCT
312260 TTTTG-TGAAAGGAATTAATCT
1 TTTTGATGAAAGGAATTAATCT
312281 TTT
1 TTT
312284 CAAAAAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (22 bp):
TTTTGATGAAAGGAATTAATCT
Found at i:312388 original size:35 final size:35
Alignment explanation
Indices: 312342--312410 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
312332 ACTAAAAAAA
* *
312342 TAAGTTTATTCACTAAGTGACATGACTTATTATAT
1 TAAGTTTATTCACCAAGTGACATAACTTATTATAT
*
312377 TAAGTTTATTCACCAAGTGACATAATTTATTATA
1 TAAGTTTATTCACCAAGTGACATAACTTATTATA
312411 AATATCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (35 bp):
TAAGTTTATTCACCAAGTGACATAACTTATTATAT
Found at i:322622 original size:3 final size:3
Alignment explanation
Indices: 322614--322664 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
322604 ATTTATATAT
* * * *
322614 TTA TTA TTA TTA TTA TCA TTA TTTA TAA TTA TTA TTG TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
322660 TTA TT
1 TTA TT
322665 TAATATTACA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:322646 original size:28 final size:30
Alignment explanation
Indices: 322604--322671 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
322594 TACCCATTTT
322604 ATTTATATATTTATTATTATTATT-ATCATT
1 ATTTATATATTTATTATTATTATTAAT-ATT
*
322634 ATTTATA-A-TTATTATTGTTATTAATATT
1 ATTTATATATTTATTATTATTATTAATATT
322662 ATTTA-ATATT
1 ATTTATATATT
322672 ACAAAGCCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 22 0.65
29 4 0.12
30 7 0.21
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
ATTTATATATTTATTATTATTATTAATATT
Found at i:323250 original size:16 final size:16
Alignment explanation
Indices: 323213--323251 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
323203 GGAGCAACCA
323213 ACAGCAAACCCAAAGC
1 ACAGCAAACCCAAAGC
*
323229 AGAGCAAACCCACAA-C
1 ACAGCAAACCCA-AAGC
323245 ACAGCAA
1 ACAGCAA
323252 CCAAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.51, C:0.36, G:0.13, T:0.00
Consensus pattern (16 bp):
ACAGCAAACCCAAAGC
Found at i:330318 original size:17 final size:19
Alignment explanation
Indices: 330296--330332 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
330286 TCTTATACTC
330296 ATCCAGCAAA-AAA-AAAA
1 ATCCAGCAAAGAAAGAAAA
330313 ATCCAGCAAAGAAAGAAAA
1 ATCCAGCAAAGAAAGAAAA
330332 A
1 A
330333 AAGAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.68, C:0.16, G:0.11, T:0.05
Consensus pattern (19 bp):
ATCCAGCAAAGAAAGAAAA
Found at i:330348 original size:10 final size:8
Alignment explanation
Indices: 330324--330392 Score: 59
Period size: 8 Copynumber: 8.2 Consensus size: 8
330314 TCCAGCAAAG
330324 AAAGAAAA
1 AAAGAAAA
330332 AAAG-AAA
1 AAAGAAAA
330339 AAAGATGAAA
1 AAAGA--AAA
*
330349 AAGGAAAA
1 AAAGAAAA
*
330357 ATGAGAAAA
1 A-AAGAAAA
330366 AGAAGAAAA
1 A-AAGAAAA
*
330375 AAAGGAAA
1 AAAGAAAA
*
330383 GAAGAAAA
1 AAAGAAAA
330391 AA
1 AA
330393 GGGGAGAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
7 7 0.15
8 21 0.44
9 13 0.27
10 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:330349 original size:9 final size:8
Alignment explanation
Indices: 330324--330393 Score: 56
Period size: 9 Copynumber: 8.5 Consensus size: 8
330314 TCCAGCAAAG
*
330324 AAAGAAAA
1 AAAGAGAA
330332 AAAGA-AA
1 AAAGAGAA
330339 AAAGATGAA
1 AAAGA-GAA
330348 AAAG-GAA
1 AAAGAGAA
330355 AAATGAGAA
1 AAA-GAGAA
330364 AAAGAAGAA
1 AAAG-AGAA
*
330373 AAAAAGGAA
1 AAAGA-GAA
330382 AGAAGA-AA
1 A-AAGAGAA
330390 AAAG
1 AAAG
330394 GGGAGAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
7 16 0.30
8 11 0.21
9 23 0.43
10 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (8 bp):
AAAGAGAA
Found at i:330351 original size:16 final size:15
Alignment explanation
Indices: 330324--330393 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 15
330314 TCCAGCAAAG
*
330324 AAAGAAAAAAAGAAA
1 AAAGAGAAAAAGAAA
330339 AAAGATGAAAAAGGAAA
1 AAAGA-GAAAAA-GAAA
*
330356 AATGAGAAAAAGAAGAA
1 AAAGAGAAAAAG-A-AA
*
330373 AAAAAGGAAAGAAGAAA
1 AAAGA-GAAA-AAGAAA
330390 AAAG
1 AAAG
330394 GGGAGAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 6 0.14
16 12 0.27
17 18 0.41
18 5 0.11
19 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAGAGAAAAAGAAA
Found at i:330355 original size:25 final size:24
Alignment explanation
Indices: 330327--330393 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 24
330317 AGCAAAGAAA
*
330327 GAAAAAAAGAAAAAAGATGAAAAAG
1 GAAAAAAAGAAAAAAGA-AAAAAAG
*
330352 GAAAAATGAGAAAAAGAAGAAAAAAAG
1 GAAAAA-AAG-AAAA-AAGAAAAAAAG
*
330379 G-AAAGAAGAAAAAAG
1 GAAAAAAAGAAAAAAG
330394 GGGAGAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 3 0.09
24 4 0.11
25 8 0.23
26 5 0.14
27 11 0.31
28 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (24 bp):
GAAAAAAAGAAAAAAGAAAAAAAG
Found at i:332709 original size:114 final size:114
Alignment explanation
Indices: 332505--332728 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 114
332495 GTGCCACGTT
332505 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
332570 CTTCGGTAGGAACCACAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 CTTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTG
332619 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
332684 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 CTTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAA
332729 CTGAATGATC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
CTTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTG
Found at i:335112 original size:39 final size:41
Alignment explanation
Indices: 335067--335153 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
335057 TAAAGAAAGC
* *
335067 ATAATAA-AAGTGAAATAAAA-TA-ATATATACAAATGTAAA
1 ATAATAAGAA-TGAAATAAAAGTATATATAAAAAAATGTAAA
335106 ATAATAAGAATGAAATAAAATGTATATATAAAAAAATGTAAA
1 ATAATAAGAATGAAATAAAA-GTATATATAAAAAAATGTAAA
*
335148 ACAATA
1 ATAATA
335154 GCGTATAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 17 0.41
40 2 0.05
41 2 0.05
42 20 0.49
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.25
Consensus pattern (41 bp):
ATAATAAGAATGAAATAAAAGTATATATAAAAAAATGTAAA
Found at i:335343 original size:2 final size:2
Alignment explanation
Indices: 335330--335362 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
335320 AAAATACAAA
*
335330 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
335363 GCATATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:346042 original size:2 final size:2
Alignment explanation
Indices: 346035--346071 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
346025 AAAATACAAA
346035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
346072 GCATATAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:346551 original size:20 final size:19
Alignment explanation
Indices: 346512--346551 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
346502 TGTGCCACCT
*
346512 CACCGCCGCCGTTGAACGG
1 CACCGCCGCCGTTCAACGG
*
346531 CACCGGCCGCCGTTCATCGG
1 CACC-GCCGCCGTTCAACGG
346551 C
1 C
346552 GACAAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.12, C:0.45, G:0.30, T:0.12
Consensus pattern (19 bp):
CACCGCCGCCGTTCAACGG
Found at i:348096 original size:22 final size:22
Alignment explanation
Indices: 348066--348113 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
348056 CTCTTCAAAG
*
348066 ATGATAGATTCCCTTTTAAAAA
1 ATGACAGATTCCCTTTTAAAAA
* * *
348088 ATGACAGATTCTCTTTTCAAAG
1 ATGACAGATTCCCTTTTAAAAA
348110 ATGA
1 ATGA
348114 AAGCTTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
ATGACAGATTCCCTTTTAAAAA
Found at i:348828 original size:113 final size:113
Alignment explanation
Indices: 348505--349344 Score: 1471
Period size: 113 Copynumber: 7.5 Consensus size: 113
348495 GCAAAGATTT
* * * * * *
348505 AAATCCATCATTCGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
348570 AAGGAAGAAGAACTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
348618 AAATCCATCATCTGATGGATCAACTTTTCCAGGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCATTTGATGGATCAGCTTTTCCA-GAGAAAGTTCATAATGAGAAGAACTCATCTGAA
348683 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
348732 AAATCCATAATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGTAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
348797 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
348845 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAT--G-AG-----ATCTGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
348902 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
348950 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
349015 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
349063 AAATCCATCATTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
349128 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
349176 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
349241 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
349289 AAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
349345 TGTTCAACTT
Statistics
Matches: 698, Mismatches: 20, Indels: 18
0.95 0.03 0.02
Matches are distributed among these distances:
105 102 0.15
107 1 0.00
108 2 0.00
110 2 0.00
111 1 0.00
113 483 0.69
114 107 0.15
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:349169 original size:331 final size:334
Alignment explanation
Indices: 348505--349344 Score: 1443
Period size: 331 Copynumber: 2.5 Consensus size: 334
348495 GCAAAGATTT
* * * * *
348505 AAATCCATCATTCGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAT-AGAAGAA-TC-T--GAAG
* *
348570 AAGGAAGAAGAACTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
61 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATG
348635 GATCAACTTTTCCAGGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
126 GATCAACTTTTCCA-GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
348700 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGA
190 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGA
* *
348765 GAAAGTTCATAATGAGTAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
255 AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
348830 TTCAACCTTTTGCTC
320 TTCAACCTTTTGCTC
348845 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAT-G-AG-ATCTGAAGAAGGA
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAGAAGAATCTGAAGAAGGA
348907 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
* *
348972 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
131 ACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* *
349037 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCTAGAAAAAGT
196 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGAAAAAGT
349102 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
261 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
349167 CTTTTGCTC
326 CTTTTGCTC
349176 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAT-AGAAG-A---ATCTGAAG
349241 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATG
61 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATG
349306 GATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
126 GATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
349345 TGTTCAACTT
Statistics
Matches: 477, Mismatches: 15, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
331 236 0.49
332 80 0.17
333 1 0.00
334 3 0.01
335 2 0.00
336 1 0.00
337 2 0.00
338 1 0.00
339 110 0.23
340 41 0.09
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (334 bp):
AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAGAAGAATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
ACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGAAAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
CTTTTGCTC
Found at i:349335 original size:444 final size:445
Alignment explanation
Indices: 348505--349338 Score: 1535
Period size: 444 Copynumber: 1.9 Consensus size: 445
348495 GCAAAGATTT
348505 AAATCCATCATTCGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAG
1 AAATCCATCATTCGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAG
*
348570 AAGGAAGAAGAACTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
348635 GATCAACTTTTCCAGGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
131 GATCAACTTTTCCAGGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
348700 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGA
196 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGA
*
348765 GAAAGTTCATAATGAGTAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
261 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* *
348830 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGA
326 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGA
348895 TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
391 TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * *
348950 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAG
*
349015 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATG
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
* *
349080 GATCAGCTTTTCTA-GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
131 GATCAACTTTTCCAGGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
*
349144 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGA
196 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGA
349209 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
261 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
349274 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGA
326 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGA
349339 AGAACTTGTT
Statistics
Matches: 375, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
444 241 0.64
445 134 0.36
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (445 bp):
AAATCCATCATTCGATGAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
GATCAACTTTTCCAGGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTCCAGA
GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGA
TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:349404 original size:186 final size:187
Alignment explanation
Indices: 349132--349526 Score: 503
Period size: 186 Copynumber: 2.1 Consensus size: 187
349122 CTGAAGAAGG
* * ** *
349132 AAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGAT
1 AAGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCAATCATCAGATGGAA
** * *
349196 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
65 CAGCAGTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAA
* * *
349261 TGAGAAGAATTTGTTCAACCTTTT-GCTCAAATCCATCATT-TGATGGATCAACTTTTCC
130 TGAGAAGAACTTGTTCAA-CTTTTCGCTCAAATCCATCATTCT-ATGGATCAACATTACC
* * *
349319 -AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTAATCACTCAG-TGGAA
1 AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCAATCA-TCAGATGGAA
** * *
349382 CAGCAGTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAA
65 CAGCAGTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAA
** *
349447 TGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCTATGGATCAACATTACC
130 TGAGAAGAACTTGTTCAACTTTTCGCTCAAATCCATCATTCTATGGATCAACATTACC
* *
349505 AAGAAGAAGTTTATAATGAGAA
1 AAGAAAAAGTTCATAATGAGAA
349527 CTCATCTGAA
Statistics
Matches: 179, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
185 8 0.04
186 149 0.83
187 22 0.12
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (187 bp):
AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCAATCATCAGATGGAAC
AGCAGTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAAT
GAGAAGAACTTGTTCAACTTTTCGCTCAAATCCATCATTCTATGGATCAACATTACC
Found at i:349822 original size:113 final size:114
Alignment explanation
Indices: 349319--349808 Score: 670
Period size: 113 Copynumber: 4.3 Consensus size: 114
349309 CAACTTTTCC
* * * * * *
349319 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTAATCACTC-AGTGGAAC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGA-TGGATC
* * * * *
349383 AGCAGTACC-AGTTAG-AGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
65 AACATTACCAAG-AAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
349432 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCTATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
*
349497 ACATTACCAAGAAGAAGTTTATAAT--G-AGAACTCATCTGAAGAAAGA
66 ACATTACCAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
349543 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
*
349608 ACATTACCAAGAAGAAGTTTATAATGAGAAGAACTCATCTGAAGAAAGA
66 ACATTACCAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * *
349657 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGACCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
* * * ** * * *
349722 GCATTGCCAGGGCG-AGTTCATAATAAGAAGAACTCATCTGAGGAAGGA
66 ACATTACCAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
349770 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
349809 GCATGATTCT
Statistics
Matches: 345, Mismatches: 25, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
111 107 0.31
112 1 0.00
113 129 0.37
114 108 0.31
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (114 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
ACATTACCAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
Found at i:350086 original size:8 final size:7
Alignment explanation
Indices: 350072--350113 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
350062 TTTACCCATT
350072 TTATTTA
1 TTATTTA
350079 TATATTTA
1 T-TATTTA
350087 TTA-TTA
1 TTATTTA
350093 TTATTATCA
1 TTATT-T-A
350102 TTATTTA
1 TTATTTA
350109 TTATT
1 TTATT
350114 AAATTTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.19
7 10 0.32
8 9 0.29
9 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:353565 original size:30 final size:30
Alignment explanation
Indices: 353529--353585 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
353519 TTTAAAAGAG
*
353529 TTTTACAATACT-AAGTTTTAAATAATTTTA
1 TTTTACAATACTGAA-ATTTAAATAATTTTA
353559 TTTTACAATACTGAAATTTAAATAATT
1 TTTTACAATACTGAAATTTAAATAATT
353586 CATATAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (30 bp):
TTTTACAATACTGAAATTTAAATAATTTTA
Found at i:353625 original size:22 final size:22
Alignment explanation
Indices: 353600--353646 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
353590 TAACTACAAT
353600 AATAAAT-TATTTAAAATAAATC
1 AATAAATAT-TTTAAAATAAATC
*
353622 AATATATATTTTAAAATAAATC
1 AATAAATATTTTAAAATAAATC
353644 AAT
1 AAT
353647 CAAACTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATATTTTAAAATAAATC
Found at i:353668 original size:54 final size:54
Alignment explanation
Indices: 353599--354804 Score: 781
Period size: 54 Copynumber: 21.8 Consensus size: 54
353589 ATAACTACAA
*
353599 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAAT-CAAAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
* * **
353652 TTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATA-
1 -TAATAAATTATTTAAAATAAATCAA-T-ATA-TATTTTAA-AATAAATCAATCCATAC
** * * * ** *
353710 TTTTAAAATAAATCAATCAATCCATACAA-ATAAATTATTTAAAATAAATCAATCCATAC
1 TAAT-AAATTATTTAA--AATAAAT-CAATATATA-T-TTTAAAATAAATCAATCCATAC
* *
353769 -AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
*
353817 AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATC-A---ATA-T-AT--A-T-TTTAAAATAAATCAATCCATAC
** * ** * ** *
353880 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATATATAT-TTTAAAATAAATCAATCCATAC
* * ** *
353935 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAAT--ATA-TATTTTAA-AATAAATCAATCCATA--C
* * * * *
353995 TAAAATAAATCAATTCATACAAAT-AA-AT-TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
**
354047 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
* * ** *
354101 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAA-T-ATA-TATTTTAA-AATAAATCAATCCATA--C
* * ** * * *
354161 TAAAATAAATCAATCCATACAAAT-AA-AT-TA-TTTAAAATAAATCAATTCATAC
1 T--AATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
** *
354213 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
* ** * *
354267 TAATAAATTATTTAAAATAAATCAATCCATACA-ACTACGATAATAAATCAATACATATT
1 TAATAAATTATTTAAAATAAATCAAT--ATATATTTTA--A-AATAAATCAATCCATA-C
* * ** * * * *
354326 TGAAAATAAATCAATCCATACAAAT-AA-AT-TA-TTTAAAGTAAATCAATCTATAC
1 T---AATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
**
354379 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
**
354433 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
* * **
354487 TAATAAATTATTTAAAATAAATCAATCTATAAAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAA--TAT-ATATTTTAA-AATAAATCAATCCATAC
** * **
354544 TTTTAAAATAAAT-AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT--AT----AT--A-T-TTTAAAATAAATCAATCCATAC
* * *
354607 -AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATAAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
* *
354655 AAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
** *
354709 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
** *
354763 TAATAAATTATTTAAAATAAATCAATCCATATTTTATAATAA
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAA
354805 TTTATTTTAA
Statistics
Matches: 907, Mismatches: 151, Indels: 188
0.73 0.12 0.15
Matches are distributed among these distances:
48 49 0.05
49 9 0.01
50 57 0.06
51 6 0.01
52 6 0.01
53 7 0.01
54 426 0.47
55 21 0.02
56 31 0.03
57 32 0.04
58 123 0.14
59 12 0.01
60 12 0.01
61 11 0.01
62 68 0.07
63 16 0.02
64 21 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
Found at i:353699 original size:26 final size:27
Alignment explanation
Indices: 353667--353991 Score: 126
Period size: 32 Copynumber: 11.6 Consensus size: 27
353657 AAATTATTTA
* *
353667 AAATAAATCAATTCATACAACTACAAT
1 AAATAAATCAATCCATACAACTAAAAT
***
353694 -AATAAATCAATCCATA-TTTTAAAAT
1 AAATAAATCAATCCATACAACTAAAAT
* *
353719 AAATCAATCAATCCATACAAATAAATTATTT
1 AAATAAATCAATCCATACAACTAAA--A--T
*
353750 AAAATAAATCAATCCATACAACTACAAT
1 -AAATAAATCAATCCATACAACTAAAAT
* ***
353778 -AATAAATCAAT-C-TA-TA-TTTTA-
1 AAATAAATCAATCCATACAACTAAAAT
*
353799 AAATAAATCAATCCATACAAATAAATTATTT
1 AAATAAATCAATCCATACAACTAAA--A--T
353830 AAAATAAATCAATCCATACTAA-TAAATTATTT
1 -AAATAAATCAATCCATAC-AACTAAA--A--T
***
353862 AAAATAAATCAATCCAT---A-TTTTA-
1 -AAATAAATCAATCCATACAACTAAAAT
353885 AAATAAATCAATCCATACTAA-TAAATTATTT
1 AAATAAATCAATCCATAC-AACTAAA--A--T
353916 AAAATAAATCAATCCATACTAA-TAAATTATTT
1 -AAATAAATCAATCCATAC-AACTAAA--A--T
*
353948 AAAATAAATCAATCCATACAACTACAAT
1 -AAATAAATCAATCCATACAACTAAAAT
353976 -AATAAATCAATCCATA
1 AAATAAATCAATCCATA
353992 TTTTAAAATA
Statistics
Matches: 241, Mismatches: 27, Indels: 61
0.73 0.08 0.19
Matches are distributed among these distances:
22 29 0.12
23 2 0.01
24 4 0.02
25 7 0.03
26 61 0.25
27 4 0.02
28 6 0.02
29 1 0.00
30 2 0.01
31 3 0.01
32 120 0.50
33 2 0.01
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATAAATCAATCCATACAACTAAAAT
Found at i:353768 original size:84 final size:80
Alignment explanation
Indices: 353614--354681 Score: 449
Period size: 80 Copynumber: 12.8 Consensus size: 80
353604 AATTATTTAA
** * *
353614 AATAAATCAATATATATTTTAAAATAAATCAAT-CAAACTTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC-AAATAAATTATTTAAAATAAATCAA
*
353678 TTCATACAACTACAAT
65 TCCATACAACTACAAT
353694 AATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAAT--A--AATCAATCCATACAAATAAATTATTTAAAATAAAT
353759 CAATCCATACAACTACAAT
62 CAATCCATACAACTACAAT
*
353778 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
*
353843 CCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
353862 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
*
353927 ATCCATACTAA-TAAATTATTT
64 ATCCATAC-AACTACA--A--T
*** * * * *
353948 AAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATC
1 --AATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATC
* * *
354006 AATTCATACAAATAAATTATTT
63 AATCCATACAACTACA--A--T
* * * ** * * *
354028 AAAATAAATCAATCCATA--CT--AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAAT---TA-TTTAAAATAA
354089 ATCAATCCATACTAA-TA-AATT
60 ATCAATCCATAC-AACTACAA-T
* * * * ** **
354110 ATTTAAAATAAAT-CA-ATTCATACAACTACAAT-AATAAAT-C-AATCCA-TATTTTAAAATAA
1 A-AT-AAATCAATCCATATT-TTA-AAATA-AATCAATCCATACAAATAAATTA-TTTAAAATAA
*
354169 ATCAATCCATACAAATA-AATT
60 ATCAATCCATACAACTACAA-T
* * * * * * ** * * *
354190 ATTTAAAATAAAT-CA-ATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
1 A-AT-AAATCAATCCATATT-TTA-AAATAAATCAATCCATACAAATAAAT---TA-TTTAAAAT
* *
354253 AAATCAATCTATACTAA-TAAATTATTT
58 AAATCAATCCATAC-AACTACA--A--T
*** * * * *
354280 AAAATAAATCAATCCATACAACTACGATAATAAATCAATACATATTTGAAAATAAATCAATCCAT
1 --AATAAATCAATCCATA-TTTTA--A-AATAAATCAATCCATA----CAAATAAAT-TAT--TT
* * *
354345 ACAAATAAAT-TAT--TTA-AAGTA-AAT
53 A-AAATAAATCAATCCATACAACTACAAT
** **
354369 CAATCTATACTAATAAAT-TATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAAT
1 -AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAAT
*
354423 CAATCCATACTAA-TAAATTATTT
62 CAATCCATAC-AACTACA--A--T
*
354446 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
* *
354511 ATCTATAAAACTACAAT
64 ATCCATACAACTACAAT
354528 AATAAATCAATCCATATTTTAAAATAAATAAATAAATCAATCCATACAAATAAATTATTTAAAAT
1 AATAAATCAATCCATA-TTT----T--A-AAATAAATCAATCCATACAAATAAATTATTTAAAAT
354593 AAATCAATCCATACAACTACAAT
58 AAATCAATCCATACAACTACAAT
* *
354616 AATAAATCAATCTATATTTTAAAATAAATAAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
354681 C
66 C
354682 TATATTTTAA
Statistics
Matches: 805, Mismatches: 86, Indels: 194
0.74 0.08 0.18
Matches are distributed among these distances:
68 8 0.01
69 4 0.00
71 3 0.00
72 2 0.00
73 3 0.00
74 1 0.00
75 4 0.00
76 30 0.04
77 6 0.01
78 7 0.01
79 7 0.01
80 245 0.30
81 10 0.01
82 21 0.03
83 3 0.00
84 81 0.10
85 11 0.01
86 199 0.25
87 18 0.02
88 76 0.09
89 5 0.01
90 14 0.02
91 4 0.00
92 4 0.00
93 3 0.00
94 13 0.02
95 3 0.00
96 1 0.00
97 4 0.00
98 15 0.02
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Done.