Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007985.1 Hibiscus syriacus cultivar Beakdansim tig00110430_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: 2235968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2014526 original size:15 final size:15
Alignment explanation
Indices: 2014506--2014541 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2014496 CGCCCCACAT
*
2014506 CCGCCCCGCATCCGC
1 CCGCCCCACATCCGC
*
2014521 CCGCCCCACATCGGC
1 CCGCCCCACATCCGC
2014536 CCGCCC
1 CCGCCC
2014542 AGCTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.67, G:0.19, T:0.06
Consensus pattern (15 bp):
CCGCCCCACATCCGC
Found at i:2018758 original size:149 final size:148
Alignment explanation
Indices: 2018483--2019206 Score: 931
Period size: 149 Copynumber: 4.9 Consensus size: 148
2018473 CAGGGTGTTA
* * *
2018483 TAATATCACGCCGAGCACTTCAACGTTGAGAGTAGGCAGGGGGGACAGAGTACATGCCGAGCGCT
1 TAATATCACGCCGAGCGCTTCAACGTTTAGAGTAGGCA-GGGAGACAGAGTACATGCCGAGCGCT
2018548 TCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCG
65 TCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCG
*
2018613 GGTGAAACAAGATGTGCCT
130 GGTGAAATAAGATGTGCCT
*
2018632 TAATGTCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAGAGGAGACAGAGTACATGCCGAGCGCT
1 TAATATCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAG-GGAGACAGAGTACATGCCGAGCGCT
* *
2018697 TCCAGAGGGAAGTAGGCAGGATGACCTGGTCTTACGCCAAGCGCTCTAACGTGTGGAGTAGGCCG
65 TCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCG
2018762 GGTGAAATAAGATGTGCCT
130 GGTGAAATAAGATGTGCCT
* * *
2018781 TAATGTCACGCCGAGCGCTTCAACGTTGAGAGTAGGCAGAGGAGACAGAGTGCATGCCGAGCGCT
1 TAATATCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAG-GGAGACAGAGTACATGCCGAGCGCT
* * * *
2018846 TCCAAAGGGGAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCTCTAACGTATGGAGTAGG-C-
65 TCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCG
*
2018909 AG-G------G-TGT-CC-
130 GGTGAAATAAGATGTGCCT
* * * * * * *
2018918 CAGAT-TCACGCCGAGC-ATCTCAACGTGTAGGGTAAGCAGGGTAGACAGAGTTCATGCCTAGCG
1 TA-ATATCACGCCGAGCGCT-TCAACGTTTAGAGTAGGCAGGG-AGACAGAGTACATGCCGAGCG
* * *
2018981 CTTCTAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAACGTGTGGAGTAGGT
63 CTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGC
* * *
2019046 TGGGTGAAATATA-ATGCGCTT
128 CGGGTGAAATA-AGATGTGCCT
* * * * * * *
2019067 TAATATCAGGTCGAGCGCCTCAACGTGTGGGGTAGGCAGGGTAGACAGAGTTCATGCCGAGCGCT
1 TAATATCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAGGG-AGACAGAGTACATGCCGAGCGCT
*
2019132 TCCAGAGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGC-CTTAACGTGTGGAGTAGGCC
65 TCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTC-TAACGTGTGGAGTAGGCC
2019196 GGGTGAAATAA
129 GGGTGAAATAA
2019207 AATGATTTAG
Statistics
Matches: 509, Mismatches: 46, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
136 3 0.01
137 105 0.21
138 4 0.01
139 4 0.01
140 2 0.00
146 1 0.00
147 3 0.01
148 7 0.01
149 380 0.75
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.20
Consensus pattern (148 bp):
TAATATCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAGGGAGACAGAGTACATGCCGAGCGCTT
CCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGG
GTGAAATAAGATGTGCCT
Found at i:2019001 original size:286 final size:279
Alignment explanation
Indices: 2018220--2019200 Score: 1101
Period size: 286 Copynumber: 3.4 Consensus size: 279
2018210 TAAGGAATTT
* * * * * *
2018220 CGCCGAGCGCTTCAACATTAAGAGTTGGAAGGGGGACAGAGTTCATGCCGAGCGCTTCCAGTGGG
1 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* * * * *
2018285 GAGTAGGCCGGATGACCTGATCTTACGCCGGGCGCTCTAATGTATGGGGTAGGCAGGGTATTCCT
66 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGGCAGGGT-GTCCT
* * * * * *
2018350 ATTTTCACGCCGAGCGCTTCACCGTTAAGAGTTGGAAGGGGGATAGAGTTCATGCCGAGCGCTTC
130 A-ATTCACGCCGAGCGCTTCAACGTT-AGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTC
* * * * *
2018415 -CAGGGGAGTAGGCAGGATGACTTGATCTTACGCCGGGCGCTCTAACGTGTGGAGTAGGCAGG-G
193 AGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCGGGTG
*
2018478 ---T--G-T-T--ATAATATCA
258 AAATAAGATGTGCTTAATATCA
* * *
2018491 CGCCGAGCACTTCAACGTTGAGAGTAGGCAGGGGGGACAGAGTACATGCCGAGCGCTTCCAGAGG
1 CGCCGAGCGCTTCAACGTTGAGAGTAGGCA-GGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* * *
2018556 GGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAAC
65 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGG-C-AG-G----
*
2018621 AAGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTTAGAGTAGGCAGAGGAGACAGAGTACA
123 --G-TGT-CC-TAAT-TCACGCCGAGCGCTTCAACG-TTAGAGTAGGCAG-GGAGACAGAGTTCA
* *
2018686 TGCCGAGCGCTTCCAGAGGGAAGTAGGCAGGATGACCTGGTCTTACGCCAAGCGCTCTAACGTGT
180 TGCCGAGCGCTT-CAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGT
*
2018751 GGAGTAGGCCGGGTGAAATAAGATGTGCCTTAATGTCA
244 GGAGTAGG-CGGGTGAAATAAGATGTG-CTTAATATCA
* *
2018789 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGAGGAGACAGAGTGCATGCCGAGCGCTTCCAAAGG
1 CGCCGAGCGCTTCAACGTTGAGAGTAGGCAG-GGAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* *
2018854 GGAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCTCTAACGTATGGAGTAGGCAGGGTGTCCC
65 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGGCAGGGTGTCCT
* * * *
2018919 AGATTCACGCCGAGC-ATCTCAACGTGTAGGGTAAGCAGGGTAGACAGAGTTCATGCCTAGCGCT
130 A-ATTCACGCCGAGCGCT-TCAACGT-TAGAGTAGGCAGGG-AGACAGAGTTCATGCCGAGCGCT
* *
2018983 TCTAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAACGTGTGGAGTAGGTTG
191 TC-AGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGG-CG
*
2019048 GGTGAAATATA-ATGCGCTTTAATATCA
254 GGTGAAATA-AGATGTGC-TTAATATCA
* * * *
2019075 GGTCGAGCGCCTCAACGTGTG-GGGTAGGCAGGGTAGACAGAGTTCATGCCGAGCGCTTCCAGAG
1 CGCCGAGCGCTTCAACGT-TGAGAGTAGGCAGGG-AGACAGAGTTCATGCCGAGCGCTTCCAGAG
* *
2019139 GGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGC-CTTAACGTGTGGAGTAGGCCGGGTG
64 GGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTC-TAACGTATGGAGTAGGCAGGGTG
2019201 AAATAAAATG
Statistics
Matches: 608, Mismatches: 61, Indels: 67
0.83 0.08 0.09
Matches are distributed among these distances:
271 25 0.04
272 80 0.13
273 1 0.00
274 1 0.00
275 1 0.00
281 2 0.00
282 4 0.01
283 30 0.05
284 25 0.04
285 10 0.02
286 289 0.48
287 10 0.02
288 4 0.01
289 1 0.00
291 1 0.00
293 1 0.00
294 1 0.00
295 2 0.00
296 1 0.00
297 2 0.00
298 117 0.19
ACGTcount: A:0.23, C:0.22, G:0.35, T:0.20
Consensus pattern (279 bp):
CGCCGAGCGCTTCAACGTTGAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGGCAGGGTGTCCTA
ATTCACGCCGAGCGCTTCAACGTTAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCAGA
GGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCGGGTGAAA
TAAGATGTGCTTAATATCA
Found at i:2019053 original size:435 final size:427
Alignment explanation
Indices: 2018220--2019207 Score: 1298
Period size: 435 Copynumber: 2.3 Consensus size: 427
2018210 TAAGGAATTT
* * * * * *
2018220 CGCCGAGCGCTTCAACATTAAGAGTTGGAAGGGGGACAGAGTTCATGCCGAGCGCTTCCAGTGGG
1 CGCCGAGCGCTTCAACGTTTAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
* * * * * *
2018285 GAGTAGGCCGGATGACCTGATCTTACGCCGGGCGCTCTAATGTATGGGGTAGG-CAGG-G---T-
66 GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAATA
* * * * * * *
2018344 -ATTCCTATTTTCACGCCGAGCGCTTCACCGTTAAGAGTTGGAAGGGGGATAGAGTTCATGCCGA
131 AATTCCTAATGTCACGCCGAGCGCTTCAACGTTAAGAGTAGGAAGGGAGACAGAGTGCATGCCGA
* * *
2018408 GCGCTTCCAGGGGAGTAGGCAGGATGACTTGATCTTACGCCGGGCGCTCTAACGTGTGGAGTAGG
196 GCGCTTCCAGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGG
* * * *
2018473 CAGGGTGTTATAATATCACGCCGAGCACTTCAACGTTGAGAGTAGGCAGGGGGGACAGAGTACAT
261 CAGGGTGTCACAATATCACGCCGAGCACTTCAACGTTGAGAGTAAGCAGGGGAGACAGAGTACAT
*
2018538 GCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCTCTAACGTGTG
326 GCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAACGTGTG
* *
2018603 GAGTAGGCCGGGTGAAACA-AGATGTGCCTTAATGTCA
391 GAGTAGGCCGGGTGAAACATA-ATGCGCCTTAATATCA
*
2018640 CGCCGAGCGCTTCAACGTTTAGAGTAGGCAGAGGAGACAGAGTACATGCCGAGCGCTTCCAGAGG
1 CGCCGAGCGCTTCAACGTTTAGAGTAGGCAG-GGAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
* * *
2018705 GAAGTAGGCAGGATGACCTGGTCTTACGCCAAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAAT
65 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAAT
* *
2018770 AAGATGTGCCTTAATGTCACGCCGAGCGCTTCAACGTTGAGAGTAGGCAGAGGAGACAGAGTGCA
130 AA-AT-T-CC-TAATGTCACGCCGAGCGCTTCAACGTTAAGAGTAGGAAG-GGAGACAGAGTGCA
*
2018835 TGCCGAGCGCTTCCAAAGGGGAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCTCTAACGTAT
190 TGCCGAGCGCTTCC--AGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTAT
* * *
2018900 GGAGTAGGCAGGGTGTCCCAGAT-TCACGCCGAGCA-TCTCAACG-TGTAGGGTAAGCAGGGTAG
253 GGAGTAGGCAGGGTGTCACA-ATATCACGCCGAGCACT-TCAACGTTG-AGAGTAAGCAGGGGAG
* * *
2018962 ACAGAGTTCATGCCTAGCGCTTCTAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGC
315 ACAGAGTACATGCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGC
** * *
2019027 CCTAACGTGTGGAGTAGGTTGGGTGAAATATAATGCGCTTTAATATCA
380 CCTAACGTGTGGAGTAGGCCGGGTGAAACATAATGCGCCTTAATATCA
* * * * * *
2019075 GGTCGAGCGCCTCAACGTGTGGGGTAGGCAGGGTAGACAGAGTTCATGCCGAGCGCTTCCAGAGG
1 CGCCGAGCGCTTCAACGTTTAGAGTAGGCAGGG-AGACAGAGTTCATGCCGAGCGCTTCCAGAGG
2019140 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGC-CTTAACGTGTGGAGTAGGCCGGGTGAAA
65 GGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTC-TAACGTGTGGAGTAGGCCGGGTGAAA
2019204 TAAA
129 TAAA
2019208 ATGATTTAGG
Statistics
Matches: 491, Mismatches: 56, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
420 27 0.05
421 76 0.15
422 3 0.01
423 1 0.00
426 1 0.00
429 2 0.00
430 1 0.00
431 2 0.00
432 33 0.07
433 25 0.05
434 7 0.01
435 310 0.63
436 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.20
Consensus pattern (427 bp):
CGCCGAGCGCTTCAACGTTTAGAGTAGGCAGGGAGACAGAGTTCATGCCGAGCGCTTCCAGAGGG
GAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTGTGGAGTAGGCCGGGTGAAATA
AATTCCTAATGTCACGCCGAGCGCTTCAACGTTAAGAGTAGGAAGGGAGACAGAGTGCATGCCGA
GCGCTTCCAGGGGAGTAGGCAGGATGACCTGATCTTACGCCGAGCGCTCTAACGTATGGAGTAGG
CAGGGTGTCACAATATCACGCCGAGCACTTCAACGTTGAGAGTAAGCAGGGGAGACAGAGTACAT
GCCGAGCGCTTCCAGAGGGGAGTAGGCAGGATGACCTGGTCTTACGCCGAGCGCCCTAACGTGTG
GAGTAGGCCGGGTGAAACATAATGCGCCTTAATATCA
Found at i:2022630 original size:20 final size:22
Alignment explanation
Indices: 2022591--2022631 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2022581 TTAGATCTCT
*
2022591 ATTTTTATTGAATAATATTTAA
1 ATTTTTATTAAATAATATTTAA
2022613 ATTTTTA-TAAAT-ATATTTA
1 ATTTTTATTAAATAATATTTA
2022632 TTTTGAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTTTATTAAATAATATTTAA
Found at i:2024711 original size:11 final size:11
Alignment explanation
Indices: 2024674--2024716 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2024664 AAATATTGTA
*
2024674 TTTTAATTAAA
1 TTTTAATTAAT
* *
2024685 TTATATTTAGAT
1 TTTTAATTA-AT
2024697 TTTTAATTAAT
1 TTTTAATTAAT
2024708 TTTTAATTA
1 TTTTAATTA
2024717 TATATTTAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:2024724 original size:23 final size:23
Alignment explanation
Indices: 2024675--2024724 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
2024665 AATATTGTAT
* *
2024675 TTTAATTAAATTATATTTAGATT
1 TTTAATTAAATTATAATTAGATA
* * *
2024698 TTTAATTAATTTTTAATTATATA
1 TTTAATTAAATTATAATTAGATA
2024721 TTTA
1 TTTA
2024725 GTACTTTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTAATTAAATTATAATTAGATA
Found at i:2032859 original size:59 final size:60
Alignment explanation
Indices: 2032731--2032881 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 60
2032721 TTTAAATTGG
* * * * * *
2032731 TCCCTAAACTTTTAAATATTTTATTTTAATCCCTAAAATATGACTATCATTCTAAATTAG
1 TCCCTAAACTTTTAAACATTTCAATTTCATCCCTAAAATATGACTATCATTATAAATTAC
* * *
2032791 TCCTTAAACTTTTAAACATTTCAATTTCATCCC-AAACTATGACCT-TCATTATAAATTTC
1 TCCCTAAACTTTTAAACATTTCAATTTCATCCCTAAAATATGA-CTATCATTATAAATTAC
*
2032850 TCCCCAAACTTTTCAAACA-TTCTAATTTCATC
1 TCCCTAAACTTTT-AAACATTTC-AATTTCATC
2032882 TCAATTATAC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 33 0.43
60 44 0.57
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (60 bp):
TCCCTAAACTTTTAAACATTTCAATTTCATCCCTAAAATATGACTATCATTATAAATTAC
Found at i:2035572 original size:39 final size:39
Alignment explanation
Indices: 2035505--2035581 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
2035495 TACATCAATG
*
2035505 ATTCCATCATCTATACGAACCTTGAAGTGTCTGCAAACA
1 ATTCCATCATCTATACGAACCTTAAAGTGTCTGCAAACA
* * *
2035544 ATTCCATCATCTTTAGGCAA-CTTAAAGTGTTTGCAAAC
1 ATTCCATCATCTATACG-AACCTTAAAGTGTCTGCAAAC
2035582 CTTGGATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (39 bp):
ATTCCATCATCTATACGAACCTTAAAGTGTCTGCAAACA
Found at i:2036269 original size:12 final size:13
Alignment explanation
Indices: 2036240--2036264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2036230 ATGACAGAAT
2036240 AAAGAAATTTTTG
1 AAAGAAATTTTTG
2036253 AAAGAAATTTTT
1 AAAGAAATTTTT
2036265 TAAGAGCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AAAGAAATTTTTG
Found at i:2050254 original size:11 final size:12
Alignment explanation
Indices: 2050230--2050258 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2050220 AATCACGGGG
2050230 AAAAAATCATTT
1 AAAAAATCATTT
2050242 AAAAAATCA-TT
1 AAAAAATCATTT
2050253 AAAAAA
1 AAAAAA
2050259 GACTGTCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATCATTT
Found at i:2066386 original size:20 final size:20
Alignment explanation
Indices: 2066361--2066398 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2066351 ATCTTATTCT
2066361 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
2066381 CTGGTAATTTTACATTCC
1 CTGGTAATCTTACATTCC
2066399 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2070734 original size:13 final size:13
Alignment explanation
Indices: 2070716--2070741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2070706 CTTATAAGAG
2070716 TTTTAAAATTTTA
1 TTTTAAAATTTTA
2070729 TTTTAAAATTTTA
1 TTTTAAAATTTTA
2070742 AACTTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAAATTTTA
Found at i:2078087 original size:15 final size:14
Alignment explanation
Indices: 2078055--2078146 Score: 75
Period size: 15 Copynumber: 6.4 Consensus size: 14
2078045 ATTTATATGA
*
2078055 AAAATACAAGAAATT
1 AAAATACAATAAA-T
2078070 AAAATACAATAACAT
1 AAAATACAATAA-AT
* *
2078085 AAAATATAATATTAAA
1 AAAATACAATA--AAT
2078101 AAAATACAATAACAT
1 AAAATACAATAA-AT
2078116 AAAATACAAT--AT
1 AAAATACAATAAAT
2078128 CAAAA-A-AATAAAT
1 -AAAATACAATAAAT
2078141 AAAATA
1 AAAATA
2078147 ACATCAAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
11 3 0.05
12 7 0.11
13 7 0.11
14 1 0.02
15 33 0.52
16 12 0.19
17 1 0.02
ACGTcount: A:0.70, C:0.08, G:0.01, T:0.22
Consensus pattern (14 bp):
AAAATACAATAAAT
Found at i:2078107 original size:31 final size:31
Alignment explanation
Indices: 2078070--2078147 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
2078060 ACAAGAAATT
* *
2078070 AAAATACAATAACATAAAATATAATATTAAA
1 AAAATACAATAACATAAAATACAATATCAAA
2078101 AAAATACAATAACATAAAATACAATATCAAA
1 AAAATACAATAACATAAAATACAATATCAAA
*
2078132 AAAATA-AATAAAATAA
1 AAAATACAATAACATAA
2078148 CATCAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 9 0.20
31 35 0.80
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (31 bp):
AAAATACAATAACATAAAATACAATATCAAA
Found at i:2079689 original size:22 final size:24
Alignment explanation
Indices: 2079656--2079706 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
2079646 ATAAATTGCA
2079656 CCGAAGTGCCACAT-AGAA-TGTC
1 CCGAAGTGCCACATAAGAATTGTC
*
2079678 CCGAAG-GACCACGTAAGAATTGTC
1 CCGAAGTG-CCACATAAGAATTGTC
2079702 CCGAA
1 CCGAA
2079707 TGATCGTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 1 0.04
22 11 0.44
23 4 0.16
24 9 0.36
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (24 bp):
CCGAAGTGCCACATAAGAATTGTC
Found at i:2079858 original size:14 final size:15
Alignment explanation
Indices: 2079795--2079861 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
2079785 TTTACACATT
*
2079795 TCACATAGTTCAATA
1 TCACATAGATCAATA
*
2079810 TCACATAGAT-TATA
1 TCACATAGATCAATA
* *
2079824 TCTCAT-GTTCATATAA
1 TCACATAGATCA-AT-A
2079840 TCACATAGATC-ATA
1 TCACATAGATCAATA
2079854 TCACATAG
1 TCACATAG
2079862 CTTATATAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 2 0.05
14 17 0.41
15 13 0.32
16 6 0.15
17 3 0.07
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.34
Consensus pattern (15 bp):
TCACATAGATCAATA
Found at i:2079860 original size:44 final size:44
Alignment explanation
Indices: 2079795--2079931 Score: 145
Period size: 44 Copynumber: 3.1 Consensus size: 44
2079785 TTTACACATT
2079795 TCACATAGTTCAATATCACATAGATTATATCTCATGTTCATATAA
1 TCACATAGTTC-ATATCACATAGATTATATCTCATGTTCATATAA
* * ** * *
2079840 TCACATAGATCATATCACATAGCTTATATAACATTTTCATATAT
1 TCACATAGTTCATATCACATAGATTATATCTCATGTTCATATAA
*
2079884 TCACGTAGTTCAGTATCACAT-GATTTATATCAT-ATGTTC-TCATAA
1 TCACATAGTTCA-TATCACATAGA-TTATATC-TCATGTTCAT-ATAA
2079929 TCA
1 TCA
2079932 TGTAAACATG
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
44 40 0.53
45 35 0.47
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (44 bp):
TCACATAGTTCATATCACATAGATTATATCTCATGTTCATATAA
Found at i:2079868 original size:14 final size:14
Alignment explanation
Indices: 2079807--2079873 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
2079797 ACATAGTTCA
2079807 ATATCACATAGATT
1 ATATCACATAGATT
* *
2079821 ATATCTCAT-GTTCAT
1 ATATCACATAGAT--T
*
2079836 ATAATCACATAGATC
1 AT-ATCACATAGATT
*
2079851 ATATCACATAGCTT
1 ATATCACATAGATT
*
2079865 ATATAACAT
1 ATATCACAT
2079874 TTTCATATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 2 0.05
14 26 0.63
15 5 0.12
16 6 0.15
17 2 0.05
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (14 bp):
ATATCACATAGATT
Found at i:2081927 original size:25 final size:25
Alignment explanation
Indices: 2081873--2081928 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
2081863 TTATAAGAAC
2081873 TAAAATTAAATAAAATGTTAATAAA
1 TAAAATTAAATAAAATGTTAATAAA
* * * *
2081898 CAAAATTAATTCAAAT-TTGAATATA
1 TAAAATTAAATAAAATGTT-AATAAA
2081923 TAAAAT
1 TAAAAT
2081929 GATATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (25 bp):
TAAAATTAAATAAAATGTTAATAAA
Found at i:2083595 original size:4 final size:4
Alignment explanation
Indices: 2083588--2083624 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
2083578 TAAAGTAAGT
2083588 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
2083625 CATTATGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:2087747 original size:30 final size:31
Alignment explanation
Indices: 2087689--2087747 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
2087679 TATTGATGTG
* *
2087689 ATATATGTCATATCATTATTTATGTATATATT
1 ATATATGTCATATCAATATTGA-GTATATATT
*
2087721 ATATGTGTCATATCAATATTGA-TATAT
1 ATATATGTCATATCAATATTGAGTATAT
2087748 GTCACATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
32 19 0.79
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (31 bp):
ATATATGTCATATCAATATTGAGTATATATT
Found at i:2087851 original size:32 final size:34
Alignment explanation
Indices: 2087775--2087857 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 34
2087765 AATATATAGT
** *
2087775 ATGTAATACATCATCACTTATATACACATGGTAT
1 ATGTAATATGTCATCACTTATATACACATGGTAC
* *
2087809 AT-TTAT-TGTCATCACTTATGTACACAT-G-AC
1 ATGTAATATGTCATCACTTATATACACATGGTAC
2087839 ATGTAATATGTCATCACTT
1 ATGTAATATGTCATCACTT
2087858 TGAATACGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 3 0.07
31 4 0.10
32 29 0.71
33 3 0.07
34 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (34 bp):
ATGTAATATGTCATCACTTATATACACATGGTAC
Found at i:2088743 original size:30 final size:30
Alignment explanation
Indices: 2088709--2088769 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2088699 CAGTTTTTGA
* *
2088709 TAGAAGTGGTCATGATTATACTATGATTTC
1 TAGAAGTGGTCAAGATTATACGATGATTTC
*
2088739 TAGAAGTTGTCAAGATTATACGATGATTTC
1 TAGAAGTGGTCAAGATTATACGATGATTTC
2088769 T
1 T
2088770 GTCCAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (30 bp):
TAGAAGTGGTCAAGATTATACGATGATTTC
Found at i:2096061 original size:13 final size:13
Alignment explanation
Indices: 2096017--2096067 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2096007 AATGTAAAAT
2096017 TATGACATAGAAG
1 TATGACATAGAAG
* * *
2096030 TATAACCACA-AAT
1 TATGA-CATAGAAG
2096043 TATGACATAGAAG
1 TATGACATAGAAG
2096056 TATGACATAGAA
1 TATGACATAGAA
2096068 TGTAAAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
TATGACATAGAAG
Found at i:2099996 original size:16 final size:18
Alignment explanation
Indices: 2099965--2099999 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2099955 TATACATATC
2099965 ATATAAAATTATAATTTT
1 ATATAAAATTATAATTTT
2099983 ATAT-AAATTA-AATTTT
1 ATATAAAATTATAATTTT
2099999 A
1 A
2100000 ATTGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAAAATTATAATTTT
Found at i:2109359 original size:2 final size:2
Alignment explanation
Indices: 2109352--2109380 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2109342 ATGAACACAA
2109352 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 A
2109381 GCTTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2111646 original size:22 final size:19
Alignment explanation
Indices: 2111589--2111647 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 19
2111579 TTTTATTTTG
2111589 ACTATTTTAATGTTATCAA
1 ACTATTTTAATGTTATCAA
* *
2111608 TCT-TTTTAATAG-AATCATTTA
1 ACTATTTTAAT-GTTATCA---A
2111629 ACTATTTTAATGTTATCAA
1 ACTATTTTAATGTTATCAA
2111648 TCAAGTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
18 11 0.37
19 4 0.13
21 4 0.13
22 11 0.37
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (19 bp):
ACTATTTTAATGTTATCAA
Found at i:2113779 original size:59 final size:59
Alignment explanation
Indices: 2113670--2113819 Score: 156
Period size: 59 Copynumber: 2.5 Consensus size: 59
2113660 AGGGTTATAG
* * * * * * * * *
2113670 TTTAAGGATGAATTTAGAATGTTCAAAAGTTTAGGGATCAATTTATAATGTGAATCATAA
1 TTTAAGAATGAAATTAAAATATT-AAAAATTTGGGGGTCAATTAACAATGTGAATCATAA
* * * *
2113730 TTTAGGGATGGAATTAAAATATTAAAAATTTGGGGGTCAATTAACAATGTGAATTATAA
1 TTTAAGAATGAAATTAAAATATTAAAAATTTGGGGGTCAATTAACAATGTGAATCATAA
* *
2113789 TTTAAGAATGAAATTATAATATTTAAAATTT
1 TTTAAGAATGAAATTAAAATATTAAAAATTT
2113820 TAAGAACCAA
Statistics
Matches: 74, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
59 56 0.76
60 18 0.24
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (59 bp):
TTTAAGAATGAAATTAAAATATTAAAAATTTGGGGGTCAATTAACAATGTGAATCATAA
Found at i:2113798 original size:20 final size:19
Alignment explanation
Indices: 2113770--2113808 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2113760 TGGGGGTCAA
*
2113770 TTAACAATGTGAATTATAAT
1 TTAACAATG-AAATTATAAT
*
2113790 TTAAGAATGAAATTATAAT
1 TTAACAATGAAATTATAAT
2113809 ATTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (19 bp):
TTAACAATGAAATTATAAT
Found at i:2116651 original size:34 final size:33
Alignment explanation
Indices: 2116570--2116697 Score: 238
Period size: 33 Copynumber: 3.8 Consensus size: 33
2116560 GGAAATTACT
*
2116570 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
2116603 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
2116636 ATCGCAAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGC-AATGCGAAATGAAAATCGCAACGAGGGA
2116670 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2116698 CGAATTTAAT
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
33 60 0.65
34 33 0.35
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
Found at i:2116663 original size:67 final size:66
Alignment explanation
Indices: 2116570--2116697 Score: 238
Period size: 67 Copynumber: 1.9 Consensus size: 66
2116560 GGAAATTACT
2116570 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGGG
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGGG
2116635 A
66 A
*
2116636 ATCGCAAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGC-AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACG
2116698 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
66 5 0.08
67 55 0.92
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGGG
A
Found at i:2116719 original size:19 final size:20
Alignment explanation
Indices: 2116697--2116739 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2116687 AAATCGCAAC
2116697 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2116716 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2116736 GCGA
1 GCGA
2116740 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2116724 original size:14 final size:14
Alignment explanation
Indices: 2116725--2116758 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2116715 TGCGATTTTC
2116725 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
2116739 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
2116753 ATTTTC
1 ATTTTC
2116759 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2116896 original size:14 final size:14
Alignment explanation
Indices: 2116877--2116913 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2116867 CATCAATTAA
2116877 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2116891 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2116905 ACAAATCAA
1 ACAAATCAA
2116914 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2118538 original size:19 final size:19
Alignment explanation
Indices: 2118421--2118600 Score: 173
Period size: 19 Copynumber: 9.8 Consensus size: 19
2118411 TCTTTTGGTT
*
2118421 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2118440 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2118460 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2118478 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2118494 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2118512 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2118527 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2118547 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2118566 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2118585 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2118601 TGCGCTTTTG
Statistics
Matches: 134, Mismatches: 14, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 58 0.43
20 45 0.34
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2118559 original size:39 final size:38
Alignment explanation
Indices: 2118421--2118600 Score: 173
Period size: 33 Copynumber: 4.9 Consensus size: 38
2118411 TCTTTTGGTT
* *
2118421 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
2118460 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
2118494 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
2118527 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
2118566 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
2118601 TGCGCTTTTG
Statistics
Matches: 122, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
33 42 0.34
34 16 0.13
35 2 0.02
38 20 0.16
39 28 0.23
40 14 0.11
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:2119243 original size:20 final size:20
Alignment explanation
Indices: 2119158--2119251 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
2119148 CGCTAAGTAA
*
2119158 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
2119178 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
2119198 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
2119219 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
2119239 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2119252 TTTCCTAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:2119270 original size:41 final size:41
Alignment explanation
Indices: 2119183--2119313 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 41
2119173 TCAGTATCGT
* * * * *
2119183 GTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATTATCGC
1 GTTGCGATAGTAAGTATCGCATTGCGATTTTCCTAAT-TCGC
* *
2119224 ATTGCGATAGTCAGTATCGCATTGCGATTTTCCTAATTCGC
1 GTTGCGATAGTAAGTATCGCATTGCGATTTTCCTAATTCGC
* ** * *
2119265 GTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAATTCGC
1 GTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCTAATTCGC
2119306 GTTGCGAT
1 GTTGCGAT
2119314 TTACTTATTC
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 68 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
GTTGCGATAGTAAGTATCGCATTGCGATTTTCCTAATTCGC
Found at i:2119284 original size:20 final size:20
Alignment explanation
Indices: 2119240--2119332 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
2119230 ATAGTCAGTA
*
2119240 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTACTAAT
* *
2119261 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
2119281 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
2119302 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
2119322 TCGCATTGCGA
1 TCGCATTGCGA
2119333 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 33 0.56
21 26 0.44
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:2119314 original size:41 final size:41
Alignment explanation
Indices: 2119240--2119335 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
2119230 ATAGTCAGTA
* *
2119240 TCGCATTGCGATTTTCCTAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2119281 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2119322 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2119336 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2133950 original size:20 final size:19
Alignment explanation
Indices: 2133903--2133941 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2133893 ATGACCAACA
*
2133903 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
2133922 AAATCGCAACGTGATCTCT
1 AAATCGCAACGCGATCTCT
2133941 A
1 A
2133942 GCATCGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2134274 original size:22 final size:22
Alignment explanation
Indices: 2134249--2134291 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2134239 GGCGACATCC
2134249 GTCCCCATCTCCGACGAAATCT
1 GTCCCCATCTCCGACGAAATCT
*
2134271 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
2134292 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCT
Found at i:2134720 original size:20 final size:20
Alignment explanation
Indices: 2134676--2134750 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
2134666 GCGATTTTAG
* *
2134676 TTTCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
2134696 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
2134716 TTTCGTGTTCGCGATTTTCAT
1 TTTCGCGTT-GCGATAGTCAT
*
2134737 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
2134751 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2134751 original size:20 final size:20
Alignment explanation
Indices: 2134697--2134753 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
2134687 GATAGTCAAA
* **
2134697 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2134717 TTCGTGTTCGCGATTTTCATT
1 TTCGTGTT-GCGATTTTCATT
2134738 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
2134754 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2134760 original size:20 final size:21
Alignment explanation
Indices: 2134716--2134760 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2134706 CGATAGTCAT
* *
2134716 TTTCGTGTTCGCGATTTTCAT
1 TTTCGTGTTCGCGATTTTAAG
2134737 TTTCGTGTT-GCGATTTTAAG
1 TTTCGTGTTCGCGATTTTAAG
2134757 TTTC
1 TTTC
2134761 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.11, C:0.16, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTCGTGTTCGCGATTTTAAG
Found at i:2136365 original size:21 final size:21
Alignment explanation
Indices: 2136341--2136387 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2136331 TGGTGTATGG
* * *
2136341 CGTGATGAGGTATCTACTTTA
1 CGTGATGAGGTAGCGACTCTA
*
2136362 CGTGGTGAGGTAGCGACTCTA
1 CGTGATGAGGTAGCGACTCTA
2136383 CGTGA
1 CGTGA
2136388 GATGATAGCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTAGCGACTCTA
Found at i:2136736 original size:19 final size:20
Alignment explanation
Indices: 2136679--2136736 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
2136669 GCAACGCGAA
*
2136679 TTTAGTTTCGCGTTACGA-T
1 TTTAGTTTCGCGTTGCGATT
*
2136698 TTTAGTTTCGCGTTGTGATT
1 TTTAGTTTCGCGTTGCGATT
*
2136718 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCGTTGCGATT
2136737 ATCTTGTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 29 0.85
20 5 0.15
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.52
Consensus pattern (20 bp):
TTTAGTTTCGCGTTGCGATT
Found at i:2136770 original size:20 final size:20
Alignment explanation
Indices: 2136742--2136809 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
2136732 CGATTATCTT
* *
2136742 GTTGAGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
2136762 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
*
2136782 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGC
2136802 GTTGCGAT
1 GTTGCGAT
2136810 TTTAAGTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:2138263 original size:20 final size:20
Alignment explanation
Indices: 2138240--2138303 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
2138230 AACACTAAAC
*
2138240 TCAAAATGGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
2138260 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
2138280 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
2138300 TCAA
1 TCAA
2138304 TTCGCGTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:2138370 original size:20 final size:20
Alignment explanation
Indices: 2138342--2138398 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
2138332 ATGATTTTCT
* *
2138342 CGTTACGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
2138362 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
2138382 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
2138399 CGTTGCGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:2138949 original size:15 final size:14
Alignment explanation
Indices: 2138913--2138949 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2138903 TACCATGGCA
2138913 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2138927 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2138941 TTATTCTTC
1 TT-TTCTTC
2138950 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:2140036 original size:20 final size:20
Alignment explanation
Indices: 2140011--2140051 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2140001 TTGAAATTCA
2140011 GTGTTGCGACAGTCAGAATC
1 GTGTTGCGACAGTCAGAATC
**
2140031 GTGTTGCGATTGTCAGAATC
1 GTGTTGCGACAGTCAGAATC
2140051 G
1 G
2140052 CATTGCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (20 bp):
GTGTTGCGACAGTCAGAATC
Found at i:2140057 original size:20 final size:20
Alignment explanation
Indices: 2140022--2140182 Score: 94
Period size: 20 Copynumber: 7.9 Consensus size: 20
2140012 TGTTGCGACA
*
2140022 GTCAGAATCGTGTTGCGATT
1 GTCAGAATCGCGTTGCGATT
*
2140042 GTCAGAATCGCATTGCGATTAT
1 GTCAGAATCGCGTTGCGA-T-T
** * * *
2140064 GT-ATTATCGCATTACGATA
1 GTCAGAATCGCGTTGCGATT
*
2140083 GTCAGAATCGTGTTGCGATTAT
1 GTCAGAATCGCGTTGCGA-T-T
** *
2140105 GT-ATTATCGCGTTGCGATA
1 GTCAGAATCGCGTTGCGATT
*
2140124 GTCAGAATCCCGTTGCGATT
1 GTCAGAATCGCGTTGCGATT
* * *
2140144 -TACATATTCGCATTGCGATT
1 GT-CAGAATCGCGTTGCGATT
* *
2140164 TTCTAAAATCGCGTTGCGA
1 GTC-AGAATCGCGTTGCGA
2140183 ATCTGGAAAC
Statistics
Matches: 105, Mismatches: 27, Indels: 17
0.70 0.18 0.11
Matches are distributed among these distances:
19 5 0.05
20 56 0.53
21 39 0.37
22 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
GTCAGAATCGCGTTGCGATT
Found at i:2140074 original size:21 final size:21
Alignment explanation
Indices: 2140048--2140122 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
2140038 GATTGTCAGA
2140048 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* **
2140069 ATCGCATTACGA-TA-GTCAGA
1 ATCGCATTGCGATTATGT-ATT
**
2140089 ATCGTGTTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
*
2140110 ATCGCGTTGCGAT
1 ATCGCATTGCGAT
2140123 AGTCAGAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 26 0.62
22 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:2140088 original size:41 final size:41
Alignment explanation
Indices: 2140037--2140143 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
2140027 AATCGTGTTG
* *
2140037 CGATTGTCAGAATCGCATTGCGATTATGTATTATCGCATTA
1 CGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCATTA
* * *
2140078 CGATAGTCAGAATCGTGTTGCGATTATGTATTATCGCGTTG
1 CGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCATTA
*
2140119 CGATAGTCAGAATCCCGTTGCGATT
1 CGATAGTCAGAATCGCGTTGCGATT
2140144 TACATATTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
CGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCATTA
Found at i:2141867 original size:26 final size:27
Alignment explanation
Indices: 2141816--2141867 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2141806 CTAACTGCTT
* *
2141816 AATACATGTGCATATTTCTTTAACAGC
1 AATACACGTGCATAGTTCTTTAACAGC
2141843 AATACACGTGCAT-GTTCTTTAACAG
1 AATACACGTGCATAGTTCTTTAACAG
2141868 TCTAACAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (27 bp):
AATACACGTGCATAGTTCTTTAACAGC
Found at i:2143230 original size:21 final size:20
Alignment explanation
Indices: 2143198--2143240 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2143188 CTTAAACTAT
*
2143198 TTTTATATATTTAAATTAAA
1 TTTTATAGATTTAAATTAAA
* *
2143218 TTTTATGAGATTTTATTTAAA
1 TTTTAT-AGATTTAAATTAAA
2143239 TT
1 TT
2143241 AATGTCATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTATAGATTTAAATTAAA
Found at i:2145820 original size:28 final size:28
Alignment explanation
Indices: 2145788--2145956 Score: 257
Period size: 28 Copynumber: 6.0 Consensus size: 28
2145778 CCGTCGTTAC
* * *
2145788 TTTCAAGTACTGACTCGATGACATAATG
1 TTTCAAGCACTAAGTCGATGACATAATG
*
2145816 TTTCAAGCACTAAGTCGACGACATAATG
1 TTTCAAGCACTAAGTCGATGACATAATG
2145844 TTTCAAGCACTAAGTCGATGACATAATG
1 TTTCAAGCACTAAGTCGATGACATAATG
2145872 TTTCAAGCACTAAGTCGATGACATAATG
1 TTTCAAGCACTAAGTCGATGACATAATG
*
2145900 TTTCAAGCACTAAGTCGACGACATAATG
1 TTTCAAGCACTAAGTCGATGACATAATG
* * * *
2145928 TTTTAAGCAATAACTCAATGACATAATG
1 TTTCAAGCACTAAGTCGATGACATAATG
2145956 T
1 T
2145957 AAACTAAGAG
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 130 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (28 bp):
TTTCAAGCACTAAGTCGATGACATAATG
Found at i:2151529 original size:28 final size:28
Alignment explanation
Indices: 2151487--2151542 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2151477 AGAGATCTTG
2151487 CTAAGCATACATAGCATAATGCAACCTT
1 CTAAGCATACATAGCATAATGCAACCTT
**
2151515 CTAAGCATATGTAGCATAATGCAACCTT
1 CTAAGCATACATAGCATAATGCAACCTT
2151543 GAATAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (28 bp):
CTAAGCATACATAGCATAATGCAACCTT
Found at i:2152047 original size:127 final size:123
Alignment explanation
Indices: 2151814--2152102 Score: 463
Period size: 127 Copynumber: 2.3 Consensus size: 123
2151804 AAGCATTGGG
* * * * *
2151814 TTCCCATAAGTTACAATT-ATTATCTATATCGGTAATTATGCTTTTATTTAAATACCTCCGTAGG
1 TTCCCATAAGTTGC-ATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTCCGTAGG
*
2151878 TCGTCAGGTCCTCCGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
65 TCGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
*
2151937 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTCTGTAGGT
1 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTC----CGT
2152002 AGGTCGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
62 AGGTCGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
2152064 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAG
1 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAG
2152103 TGGTCCATAA
Statistics
Matches: 154, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
122 3 0.02
123 49 0.32
127 102 0.66
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (123 bp):
TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTCCGTAGGT
CGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
Found at i:2155339 original size:36 final size:36
Alignment explanation
Indices: 2155292--2155366 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
2155282 CCACAACTGA
*
2155292 ACCAGAAGGCTTAACTGGAGTTGCCTTCATTTCAAC
1 ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
2155328 ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
1 ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
2155364 ACC
1 ACC
2155367 TTCAAGCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (36 bp):
ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
Found at i:2156748 original size:2 final size:2
Alignment explanation
Indices: 2156741--2156765 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2156731 TTATTATAGA
2156741 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 A
2156766 ATTTTGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2162625 original size:95 final size:92
Alignment explanation
Indices: 2162504--2162783 Score: 287
Period size: 95 Copynumber: 2.9 Consensus size: 92
2162494 ATAGTGTAAT
* * * * *
2162504 AATAATTATAACTTAACCGTTAAAAATAAAATATGTGCAACATATTACGTTAAACTAGCTATTGG
1 AATATTTACAACTTAACCGTT-AAAATAAAATA-GCGCAACTTATTGCGTTAAACTAGCTATT-G
*
2162569 TTTGTTTAAATGTATATAATGTAACA-CTAA
63 TTTGTTTAAATGTATATAATGTAA-AGATAA
*
2162599 AATATTTACAACTTAACCAGTTAAAATAAAATAGGCGTAACTTA-TGCGTTAAACTAGCTATCTG
1 AATATTTACAACTTAACC-GTTAAAATAAAATA-GCGCAACTTATTGCGTTAAACTAGCTAT-TG
2162663 -TTGTTTAAATGTATAATTATAATGTAAATGATAA
63 TTTGTTTAAATG--T-A-TATAATGTAAA-GATAA
* *
2162697 AATATTTACAACTAAACCGGTTTAAAATAAAATAGACGCTACTTATTGCGTTAAACTAGCTACTT
1 AATATTTACAACTTAACC-G-TTAAAATAAAATAG-CGCAACTTATTGCGTTAAACTAGCTA-TT
* *
2162762 ATTTGTTTAAAGGTATAATAAT
62 GTTTGTTTAAATGTAT-ATAAT
2162784 AATGTAAACG
Statistics
Matches: 157, Mismatches: 14, Indels: 25
0.80 0.07 0.13
Matches are distributed among these distances:
93 11 0.07
94 17 0.11
95 36 0.23
96 5 0.03
97 11 0.07
98 28 0.18
99 21 0.13
100 17 0.11
101 11 0.07
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (92 bp):
AATATTTACAACTTAACCGTTAAAATAAAATAGCGCAACTTATTGCGTTAAACTAGCTATTGTTT
GTTTAAATGTATATAATGTAAAGATAA
Found at i:2162783 original size:98 final size:94
Alignment explanation
Indices: 2162546--2162783 Score: 277
Period size: 98 Copynumber: 2.4 Consensus size: 94
2162536 ATGTGCAACA
* *
2162546 TATTACGTTAAACTAGCTATTGGTTTGTTTAAATGTAT-ATAATGTAACACTAAAATATTTACAA
1 TATTGCGTTAAACTAGCTATT--TTTGTTTAAATGTATAATAATGTAACAATAAAATATTTACAA
* *
2162610 CTTAACCAGTTAAAATAAAATAGGCGTAACT
64 CTAAACCAGTTAAAATAAAATAGACGTAACT
*
2162641 TA-TGCGTTAAACTAGCTATCTGTTGTTTAAATGTATAATTATAATGTAA-ATGATAAAATATTT
1 TATTGCGTTAAACTAGCTAT-TTTTGTTTAAATGTAT-A--ATAATGTAACA--ATAAAATATTT
*
2162704 ACAACTAAACCGGTTTAAAATAAAATAGACGCT-ACT
60 ACAACTAAACCAG-TTAAAATAAAATAGACG-TAACT
*
2162740 TATTGCGTTAAACTAGCTACTTATTTGTTTAAAGGTATAATAAT
1 TATTGCGTTAAACTAGCTA-TT-TTTGTTTAAATGTATAATAAT
2162784 AATGTAAACG
Statistics
Matches: 123, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
93 14 0.11
94 16 0.13
95 3 0.02
96 1 0.01
97 9 0.07
98 26 0.21
99 21 0.17
100 19 0.15
101 14 0.11
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (94 bp):
TATTGCGTTAAACTAGCTATTTTTGTTTAAATGTATAATAATGTAACAATAAAATATTTACAACT
AAACCAGTTAAAATAAAATAGACGTAACT
Found at i:2162786 original size:101 final size:98
Alignment explanation
Indices: 2162596--2162791 Score: 279
Period size: 101 Copynumber: 2.0 Consensus size: 98
2162586 AATGTAACAC
* *
2162596 TAAAATATTTACAACTTAACCAGTTAAAATAAAATAGGCGTAACTTATGCGTTAAACTAGCTATC
1 TAAAATATTTACAACTAAACCAGTTAAAATAAAATAGACGTAACTTATGCGTTAAACTAGCTATC
* *
2162661 TGTTGTTTAAATGTATAATTATAATGTAAATGA
66 TGTTGTTTAAAGGTATAATAATAATGTAAATGA
*
2162694 TAAAATATTTACAACTAAACCGGTTTAAAATAAAATAGACGCT-ACTTATTGCGTTAAACTAGCT
1 TAAAATATTTACAACTAAACCAG-TTAAAATAAAATAGACG-TAACTTA-TGCGTTAAACTAGCT
*
2162758 A-CTTATTTGTTTAAAGGTATAATAATAATGTAAA
63 ATC-T-GTTGTTTAAAGGTATAATAATAATGTAAA
2162792 CGGTAAATAA
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
98 21 0.24
99 22 0.25
100 18 0.21
101 26 0.30
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (98 bp):
TAAAATATTTACAACTAAACCAGTTAAAATAAAATAGACGTAACTTATGCGTTAAACTAGCTATC
TGTTGTTTAAAGGTATAATAATAATGTAAATGA
Found at i:2162875 original size:75 final size:76
Alignment explanation
Indices: 2162719--2162875 Score: 237
Period size: 75 Copynumber: 2.1 Consensus size: 76
2162709 TAAACCGGTT
* * * * * *
2162719 TAAAATAAAATAGACGCTACTTATTGCGTTAAACTAGCTACTTATTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGGTATAATAAT
2162784 AATGTAAACGG
66 AATGTAAACGG
*
2162795 T-AAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTT-TTTAAAGTTATAATAAT
1 TAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGGTATAATAAT
2162858 AATGTAAACGG
66 AATGTAAACGG
2162869 TAAAATA
1 TAAAATA
2162876 TTTACAACTA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 28 0.38
75 44 0.60
76 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (76 bp):
TAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGGTATAATAAT
AATGTAAACGG
Found at i:2162961 original size:97 final size:98
Alignment explanation
Indices: 2162815--2162996 Score: 287
Period size: 97 Copynumber: 1.9 Consensus size: 98
2162805 AGACGCGACC
* *
2162815 TATTACGTTAAACTAACTAATGATTTTTTAAAGTTATAATAATAATGTAAACGGTAAAATATTTA
1 TATTACGTTAAACTAACTAACGATTTTTTAAAGGTATAATAATAATGTAAACGGTAAAATATTTA
*
2162880 CAAC-TAACCGTTTAAAATAAATATGCGCTACA
66 CAACTTAACCATTTAAAATAAATATGCGCTACA
* * *
2162912 TATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTAT-ATAATAATGTAAACGGTAAAATATTT
1 TATTACGTTAAACTAACTAACGATTT-TTTAAAGGTATAATAATAATGTAAACGGTAAAATATTT
2162976 ACAACTTAACCATTTAAAATA
65 ACAACTTAACCATTTAAAATA
2162997 TTTTTTTATA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
97 53 0.69
98 24 0.31
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (98 bp):
TATTACGTTAAACTAACTAACGATTTTTTAAAGGTATAATAATAATGTAAACGGTAAAATATTTA
CAACTTAACCATTTAAAATAAATATGCGCTACA
Found at i:2164842 original size:2 final size:2
Alignment explanation
Indices: 2164835--2164867 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2164825 TGATTTTTAA
2164835 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2164868 TCAAAGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2165176 original size:123 final size:124
Alignment explanation
Indices: 2165039--2165264 Score: 445
Period size: 124 Copynumber: 1.8 Consensus size: 124
2165029 TCCTTTAAGG
2165039 TATACATCAACTTCCCATCTTCATTTTATCC-TTTCCATGGCTTTATCTTCTAGCTTTTTATATG
1 TATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTTTTTATATG
2165103 TGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTTGATGTTAGCTAGCTTAAGGTA
66 TGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTTGATGTTAGCTAGCTTAAGGTA
2165162 TATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTTTTTATATG
1 TATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTTTTTATATG
2165227 TGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTT
66 TGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTT
2165265 ATCGAGGAAA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 31 0.30
124 71 0.70
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (124 bp):
TATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTTTTTATATG
TGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTTGATGTTAGCTAGCTTAAGGTA
Found at i:2167397 original size:2 final size:2
Alignment explanation
Indices: 2167390--2167414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2167380 TGCTCAACAG
2167390 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2167415 GTCGTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2175699 original size:26 final size:26
Alignment explanation
Indices: 2175670--2175721 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2175660 GGTGGAAATA
* *
2175670 TATATTAATAATATTTTT-TATAGAAT
1 TATATAAATAAAATTTTTATAT-GAAT
2175696 TATATAAATAAAATTTTTATATGAAT
1 TATATAAATAAAATTTTTATATGAAT
2175722 ATTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TATATAAATAAAATTTTTATATGAAT
Found at i:2175731 original size:26 final size:24
Alignment explanation
Indices: 2175671--2175733 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
2175661 GTGGAAATAT
*
2175671 ATATTAATAAT--ATTTTTTATAG
1 ATATTAATAATAAAATTTTTATAG
2175693 A-ATTATATAAATAAAATTTTTATATG
1 ATATTA-AT-AATAAAATTTTTATA-G
2175719 AATATTAATAATAAA
1 -ATATTAATAATAAA
2175734 TGAATAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
21 4 0.12
22 3 0.09
23 3 0.09
25 9 0.27
26 7 0.21
27 3 0.09
28 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (24 bp):
ATATTAATAATAAAATTTTTATAG
Found at i:2175873 original size:20 final size:20
Alignment explanation
Indices: 2175848--2175885 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2175838 TTTGGTTCAC
2175848 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTATCAGTG
2175868 GGAATGTAAGATTATCAG
1 GGAATGTAAGATTATCAG
2175886 GAAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:2177308 original size:19 final size:19
Alignment explanation
Indices: 2177277--2177331 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
2177267 ACTTTAAAAT
*
2177277 TATAAGAAA-ATATAACAA
1 TATAAAAAATATATAACAA
*
2177295 TTTAAAAAATATATTAGACAA
1 TATAAAAAATATA-TA-ACAA
*
2177316 TATAAAAAATACATAA
1 TATAAAAAATATATAA
2177332 TGTAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 4 0.13
21 15 0.50
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (19 bp):
TATAAAAAATATATAACAA
Found at i:2178526 original size:19 final size:19
Alignment explanation
Indices: 2178502--2178538 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2178492 ATGATCAACA
*
2178502 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2178521 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2178539 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2178635 original size:21 final size:21
Alignment explanation
Indices: 2178611--2178687 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
2178601 ACTATCGCAA
2178611 TGCGATAGTCCAAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
*
2178632 TGCGATAGTCCGAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
* *
2178653 TGCGATAGTCCGAATTCGAGT
1 TGCGATAGTCCAAATTCGCGT
2178674 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
2178688 ATCATTGCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
TGCGATAGTCCAAATTCGCGT
Found at i:2178742 original size:21 final size:21
Alignment explanation
Indices: 2178690--2178882 Score: 159
Period size: 21 Copynumber: 9.4 Consensus size: 21
2178680 AGTCCAAAAT
*
2178690 CATTGCGATAACACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
**
2178711 TGTTGCGATAGCACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
*
2178732 CATTGCGATAGTC-C-GAATTC-G
1 CATTGCGATAG-CACTG--TTCAC
* *** *
2178753 CGTTGCGATAG---TGCAAAAT
1 CATTGCGATAGCACTG-TTCAC
*
2178772 CATTGCGATAGTACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
*
2178793 CGTTGCGATAGCACTGTTCA-
1 CATTGCGATAGCACTGTTCAC
* *
2178813 CATTGCGATAACACTGTTCAT
1 CATTGCGATAGCACTGTTCAC
* *
2178834 CATTGTGATAACACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
2178855 CATTGCGATAGCACTGTTCA-
1 CATTGCGATAGCACTGTTCAC
2178875 CATTGCGA
1 CATTGCGA
2178883 ATTTGCGATA
Statistics
Matches: 138, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
19 11 0.08
20 27 0.20
21 94 0.68
22 6 0.04
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (21 bp):
CATTGCGATAGCACTGTTCAC
Found at i:2178748 original size:82 final size:81
Alignment explanation
Indices: 2178652--2178822 Score: 288
Period size: 82 Copynumber: 2.1 Consensus size: 81
2178642 CGAATTCGCG
*
2178652 TTGCGATAGTCCGAATTCGAGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACTGTTGC
1 TTGCGATAGTCCGAATTCGAGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGC
2178717 GATAGCACTGTTCACCA
66 GATAGCACTGTTCA-CA
* * **
2178734 TTGCGATAGTCCGAATTCGCGTTGCGATAGTGCAAAATCATTGCGATAGTACTGTTCACCGTTGC
1 TTGCGATAGTCCGAATTCGAGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGC
2178799 GATAGCACTGTTCACA
66 GATAGCACTGTTCACA
2178815 TTGCGATA
1 TTGCGATA
2178823 ACACTGTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 10 0.12
82 74 0.88
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (81 bp):
TTGCGATAGTCCGAATTCGAGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGC
GATAGCACTGTTCACA
Found at i:2178879 original size:41 final size:41
Alignment explanation
Indices: 2178772--2178882 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 41
2178762 AGTGCAAAAT
* * *
2178772 CATTGCGATAGTACTGTTCACCGTTGCGATAGCACTGTTCA
1 CATTGCGATAGCACTGTTCACCATTGCGATAACACTGTTCA
* * *
2178813 CATTGCGATAACACTGTTCATCATTGTGATAACACTGTTCA
1 CATTGCGATAGCACTGTTCACCATTGCGATAACACTGTTCA
2178854 CCATTGCGATAGCACTGTTCA-CATTGCGA
1 -CATTGCGATAGCACTGTTCACCATTGCGA
2178883 ATTTGCGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 42 0.69
42 19 0.31
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (41 bp):
CATTGCGATAGCACTGTTCACCATTGCGATAACACTGTTCA
Found at i:2179136 original size:22 final size:22
Alignment explanation
Indices: 2179111--2179159 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2179101 CATTGAAAGG
2179111 AAAAAAAT-TACAAAAACAAGAT
1 AAAAAAATGTAC-AAAACAAGAT
** *
2179133 AAAAATTTGTACAAAATAAGAT
1 AAAAAAATGTACAAAACAAGAT
2179155 AAAAA
1 AAAAA
2179160 CTTGAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAAAATGTACAAAACAAGAT
Found at i:2179145 original size:23 final size:23
Alignment explanation
Indices: 2179119--2179168 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2179109 GGAAAAAAAT
*
2179119 TACAAAAACAAGATAAAAATTTG
1 TACAAAAACAAGATAAAAACTTG
*
2179142 TAC-AAAATAAGATAAAAACTTG
1 TACAAAAACAAGATAAAAACTTG
*
2179164 AACAA
1 TACAA
2179169 TTTTTGTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (23 bp):
TACAAAAACAAGATAAAAACTTG
Found at i:2179459 original size:16 final size:17
Alignment explanation
Indices: 2179430--2179481 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
2179420 ATCATAGCTA
*
2179430 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
2179447 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
2179462 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
2179480 AT
1 AT
2179482 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:2179683 original size:21 final size:21
Alignment explanation
Indices: 2179637--2179738 Score: 152
Period size: 21 Copynumber: 4.9 Consensus size: 21
2179627 AATTCGCAAT
*
2179637 GTGAACAGTGCTATTGCAAC-
1 GTGAACAGTGCTATCGCAACG
*
2179657 GTGAACAGTGCTATCGTAACG
1 GTGAACAGTGCTATCGCAACG
* *
2179678 GTGAACAGTGTTATCGCAATG
1 GTGAACAGTGCTATCGCAACG
*
2179699 GTGAACAGTGTTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
2179720 GTGAACAGTGCTATCGCAA
1 GTGAACAGTGCTATCGCAA
2179739 TGATTTTGGA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
20 18 0.24
21 56 0.76
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:2179754 original size:19 final size:20
Alignment explanation
Indices: 2179730--2179777 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2179720 GTGAACAGTG
* *
2179730 CTATCGCAA-TGATTTTGGA
1 CTATCGCAACCGAATTTGGA
2179749 CTATCGCAACGCGAATTTGGA
1 CTATCGCAAC-CGAATTTGGA
2179770 CTATCGCA
1 CTATCGCA
2179778 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
21 16 0.64
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (20 bp):
CTATCGCAACCGAATTTGGA
Found at i:2179854 original size:19 final size:19
Alignment explanation
Indices: 2179830--2179866 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2179820 TGGGATACTT
*
2179830 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2179849 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2179867 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2180172 original size:2 final size:2
Alignment explanation
Indices: 2180165--2180206 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2180155 TATTTTATGC
2180165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2180207 TTGACTATCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2180677 original size:34 final size:34
Alignment explanation
Indices: 2180612--2180688 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
2180602 TACTAGCTTA
***
2180612 AGGGGGCAAAGTATAATTAACCATTTAAAATGAG
1 AGGGGGCAAAGTATAATTAACCAGAGAAAATGAG
* * *
2180646 AGGGGGTAAAGTATAATTAGCCAGAGGAAATGAG
1 AGGGGGCAAAGTATAATTAACCAGAGAAAATGAG
*
2180680 A-TGGGCAAA
1 AGGGGGCAAA
2180689 ATCAAAATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 6 0.17
34 29 0.83
ACGTcount: A:0.43, C:0.08, G:0.30, T:0.19
Consensus pattern (34 bp):
AGGGGGCAAAGTATAATTAACCAGAGAAAATGAG
Found at i:2181392 original size:24 final size:24
Alignment explanation
Indices: 2181360--2181473 Score: 86
Period size: 24 Copynumber: 4.8 Consensus size: 24
2181350 CATTTAAATT
2181360 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
*** ** * *
2181384 ATAAACGAATGGATGTAAACAAAC
1 ATAAACGAACACAAATGAACGAAC
* *
2181408 AGAAACGGACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
* * * *
2181432 GTAAACGAACAC-AATAAATGAAT
1 ATAAACGAACACAAATGAACGAAC
* *
2181455 TTAAACGAACATAAATGAA
1 ATAAACGAACACAAATGAA
2181474 AATATATTTT
Statistics
Matches: 64, Mismatches: 25, Indels: 2
0.70 0.27 0.02
Matches are distributed among these distances:
23 18 0.28
24 46 0.72
ACGTcount: A:0.56, C:0.16, G:0.15, T:0.13
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:2181698 original size:14 final size:14
Alignment explanation
Indices: 2181681--2181738 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
2181671 ACGAGTGAAC
2181681 ATAAACGAACATAA
1 ATAAACGAACATAA
*
2181695 ATAAAC--A-A-AC
1 ATAAACGAACATAA
2181705 ATAAACGAACATAA
1 ATAAACGAACATAA
2181719 ATAAACGAACATAA
1 ATAAACGAACATAA
*
2181733 ACAAAC
1 ATAAAC
2181739 ATATTACCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 7 0.19
11 1 0.03
12 2 0.05
13 1 0.03
14 26 0.70
ACGTcount: A:0.66, C:0.17, G:0.05, T:0.12
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:2181705 original size:24 final size:24
Alignment explanation
Indices: 2181640--2181741 Score: 114
Period size: 24 Copynumber: 4.2 Consensus size: 24
2181630 GATTGTGATA
* *
2181640 AACATAAATGAACACACATAAACG
1 AACATAAATAAACAAACATAAACG
* ** ***
2181664 AAAATAAACGAGTGAACATAAACG
1 AACATAAATAAACAAACATAAACG
2181688 AACATAAATAAACAAACATAAACG
1 AACATAAATAAACAAACATAAACG
* *
2181712 AACATAAATAAACGAACATAAACA
1 AACATAAATAAACAAACATAAACG
2181736 AACATA
1 AACATA
2181742 TTACCGAACG
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.63, C:0.17, G:0.08, T:0.13
Consensus pattern (24 bp):
AACATAAATAAACAAACATAAACG
Found at i:2184388 original size:197 final size:197
Alignment explanation
Indices: 2184053--2184448 Score: 783
Period size: 197 Copynumber: 2.0 Consensus size: 197
2184043 AAGATTTTCT
2184053 TCCTTTCTTTCTCTCTGAATATTTGGGTTTTTTGTTCTAATTTGTGTAGTTCTGGATTTTTCATA
1 TCCTTTCTTTCTCTCTGAATATTTGGGTTTTTTGTTCTAATTTGTGTAGTTCTGGATTTTTCATA
*
2184118 GGTTCGGATGGGAATTTGCAAACACAGTAGAAACACAAGTTGATGATTTTCATGTCGCCAACTGT
66 GGTTCGGATGGGAATTTGCAAACACAGTAGAAACACAAGTTGATGACTTTCATGTCGCCAACTGT
2184183 TCGTGCAGCTTCAAATATCAGTTTTCCAAGAAAGAAAGTCTTAGGCGAAAGAAATGAATCTCCAG
131 TCGTGCAGCTTCAAATATCAGTTTTCCAAGAAAGAAAGTCTTAGGCGAAAGAAATGAATCTCCAG
2184248 GA
196 GA
2184250 TCCTTTCTTTCTCTCTGAATATTTGGGTTTTTTGTTCTAATTTGTGTAGTTCTGGATTTTTCATA
1 TCCTTTCTTTCTCTCTGAATATTTGGGTTTTTTGTTCTAATTTGTGTAGTTCTGGATTTTTCATA
2184315 GGTTCGGATGGGAATTTGCAAACACAGTAGAAACACAAGTTGATGACTTTCATGTCGCCAACTGT
66 GGTTCGGATGGGAATTTGCAAACACAGTAGAAACACAAGTTGATGACTTTCATGTCGCCAACTGT
2184380 TCGTGCAGCTTCAAATATCAGTTTTCCAAGAAAGAAAGTCTTAGGCGAAAGAAATGAATCTCCAG
131 TCGTGCAGCTTCAAATATCAGTTTTCCAAGAAAGAAAGTCTTAGGCGAAAGAAATGAATCTCCAG
2184445 GA
196 GA
2184447 TC
1 TC
2184449 AAATCCCACC
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
197 198 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (197 bp):
TCCTTTCTTTCTCTCTGAATATTTGGGTTTTTTGTTCTAATTTGTGTAGTTCTGGATTTTTCATA
GGTTCGGATGGGAATTTGCAAACACAGTAGAAACACAAGTTGATGACTTTCATGTCGCCAACTGT
TCGTGCAGCTTCAAATATCAGTTTTCCAAGAAAGAAAGTCTTAGGCGAAAGAAATGAATCTCCAG
GA
Found at i:2201544 original size:34 final size:34
Alignment explanation
Indices: 2201501--2201566 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
2201491 CGTCAAGTCC
2201501 AGTAAGGCCCTGAGCACACAGCCGAAGAGCCTGA
1 AGTAAGGCCCTGAGCACACAGCCGAAGAGCCTGA
*
2201535 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCT
1 AGTAAGGCCCTGAGCACACAGCCGAAGAGCCT
2201567 TCATGTATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.30, T:0.09
Consensus pattern (34 bp):
AGTAAGGCCCTGAGCACACAGCCGAAGAGCCTGA
Found at i:2201661 original size:24 final size:24
Alignment explanation
Indices: 2201634--2201757 Score: 90
Period size: 24 Copynumber: 5.2 Consensus size: 24
2201624 TATATCAAAA
2201634 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
2201658 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
2201682 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
2201706 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
2201730 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
2201754 ATCA
1 ATCA
2201758 TATCAGAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 6 0.07
24 83 0.91
25 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:2201762 original size:24 final size:24
Alignment explanation
Indices: 2201651--2201766 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
2201641 CATAAATCAG
* * *
2201651 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
2201675 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2201699 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2201723 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
2201747 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCAGATCAGAAT
2201767 TCAAATCGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2201782 original size:48 final size:47
Alignment explanation
Indices: 2201651--2201784 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 47
2201641 CATAAATCAG
* *
2201651 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAA
* * *
2201699 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAAGTCA-ATATCAGATCAGAATCCAA
* * *
2201747 GTCAAGTATCATATCAGAATTCAAATCGAAAATCAGAT
1 GTCAAGTATCATATCAGAATCCAAGTC-AATATCAGAT
2201785 AAAATATTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
48 73 0.97
49 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAATCCAAGTCAATATCAGATCAGAATCCAA
Found at i:2203542 original size:36 final size:36
Alignment explanation
Indices: 2203490--2203562 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2203480 GATAAATTAT
2203490 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
2203526 AATCTACATATTCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
2203562 A
1 A
2203563 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:2213728 original size:120 final size:120
Alignment explanation
Indices: 2213515--2213756 Score: 484
Period size: 120 Copynumber: 2.0 Consensus size: 120
2213505 ATCAAAATCA
2213515 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
1 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
2213580 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
66 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
2213635 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
1 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
2213700 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
66 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
2213755 CA
1 CA
2213757 ATAGGAAGGT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (120 bp):
CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
Found at i:2217566 original size:26 final size:26
Alignment explanation
Indices: 2217530--2217581 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2217520 TATATAAAAG
2217530 TTAAATTTGATTAAATTCGAGTATGT
1 TTAAATTTGATTAAATTCGAGTATGT
2217556 TTAAATTTGATTAAATTCGAGTATGT
1 TTAAATTTGATTAAATTCGAGTATGT
2217582 GAACTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (26 bp):
TTAAATTTGATTAAATTCGAGTATGT
Found at i:2219256 original size:16 final size:15
Alignment explanation
Indices: 2219231--2219260 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2219221 TGAGAGGCTG
2219231 AATTAAGCTTAACTA
1 AATTAAGCTTAACTA
2219246 AATTGAAGCTTAACT
1 AATT-AAGCTTAACT
2219261 GGTTTCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (15 bp):
AATTAAGCTTAACTA
Found at i:2227288 original size:43 final size:43
Alignment explanation
Indices: 2227227--2227315 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
2227217 AATCGGTATC
2227227 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
1 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
2227270 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
1 TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
2227313 TCT
1 TCT
2227316 CCTGAACTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (43 bp):
TCTTCACTGATTTGGCGGGAACACACTAAATACAATATTATGA
Found at i:2231046 original size:24 final size:24
Alignment explanation
Indices: 2230992--2231046 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2230982 AATGTGCCAT
*
2230992 GGATTTACGTAGATGAAACCATCA
1 GGATTTTCGTAGATGAAACCATCA
2231016 GGATTTTCGTAGATGAAACCATCA
1 GGATTTTCGTAGATGAAACCATCA
2231040 GGATTTT
1 GGATTTT
2231047 GTATGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (24 bp):
GGATTTTCGTAGATGAAACCATCA
Done.