Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008857.1 Hibiscus syriacus cultivar Beakdansim tig00112079_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: 530231
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:201027 original size:20 final size:20
Alignment explanation
Indices: 200990--201032 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
200980 AATCCACCAC
200990 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
201010 ATGCATCTATATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
201030 ATG
1 ATG
201033 GGCCTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:210812 original size:20 final size:20
Alignment explanation
Indices: 210775--210817 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
210765 AATCCACCAC
210775 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
210795 ATGCATCTATATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
210815 ATG
1 ATG
210818 GGCCTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:212501 original size:64 final size:63
Alignment explanation
Indices: 212396--212546 Score: 207
Period size: 64 Copynumber: 2.4 Consensus size: 63
212386 CACCAATTCA
* * * **
212396 AATGCATTTTTTGCATTGATACACTTACATGCATCGATGTACTCAAG-TT-TTATGAAAACATCG
1 AATGCATTTTATGCATCGATGCACAGACATGCATCGATGTACTCAAGCTTGTT-TG-AAACATCG
*
212459 AATGCATTTTATGCATCGATGCACAGACCATGCATCGATGTACTCAGGCTTGTTTGAAACATCG
1 AATGCATTTTATGCATCGATGCACAGA-CATGCATCGATGTACTCAAGCTTGTTTGAAACATCG
212523 AATGCATTTTATGCATCGATGCAC
1 AATGCATTTTATGCATCGATGCAC
212547 CCTTAGTGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
63 22 0.28
64 51 0.65
65 4 0.05
66 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (63 bp):
AATGCATTTTATGCATCGATGCACAGACATGCATCGATGTACTCAAGCTTGTTTGAAACATCG
Found at i:217625 original size:21 final size:22
Alignment explanation
Indices: 217599--217696 Score: 83
Period size: 21 Copynumber: 4.4 Consensus size: 22
217589 TTGTGCATAA
217599 TGCATCGATACACT-ATGAAGG
1 TGCATCGATACACTCATGAAGG
* * *
217620 TGCATCGATGCATCCCTATGAATG
1 TGCATCGATACA-CTC-ATGAAGG
*
217644 TGCATCGATACA-TCATGAAGA
1 TGCATCGATACACTCATGAAGG
* * * *
217665 TGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT-CATGAAGG
217688 TGCATCGAT
1 TGCATCGAT
217697 GCATAATGCC
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 26 0.44
22 3 0.05
23 13 0.22
24 17 0.29
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (22 bp):
TGCATCGATACACTCATGAAGG
Found at i:217646 original size:24 final size:24
Alignment explanation
Indices: 217611--217700 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 24
217601 CATCGATACA
*
217611 CTATGAAGGTGCATCGATGCATCC
1 CTATGAATGTGCATCGATGCATCC
*
217635 CTATGAATGTGCATCGATACAT--
1 CTATGAATGTGCATCGATGCATCC
*
217657 C-ATGAA-GATGCACCGATGCA-CTC
1 CTATGAATG-TGCATCGATGCATC-C
217680 CT-TGAATGTGCATCGATGCAT
1 CTATGAATGTGCATCGATGCAT
217701 AATGCCATGC
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 15 0.28
22 1 0.02
23 16 0.30
24 21 0.39
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
CTATGAATGTGCATCGATGCATCC
Found at i:217663 original size:45 final size:43
Alignment explanation
Indices: 217599--217722 Score: 137
Period size: 45 Copynumber: 2.8 Consensus size: 43
217589 TTGTGCATAA
217599 TGCATCGATACA-CTATGAAGGTGCATCGATGCATCCCTATGAATG
1 TGCATCGATACATC-ATGAA-GTGCATCGATGCATCCCT-TGAATG
*
217644 TGCATCGATACATCATGAAGATGCACCGATGCA-CTCCTTGAATG
1 TGCATCGATACATCATGAAG-TGCATCGATGCATC-CCTTGAATG
* * *
217688 TGCATCGATGCATAATGCCA-TGCATCGATGCATCC
1 TGCATCGATACATCATG-AAGTGCATCGATGCATCC
217723 GTCGGGTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
43 12 0.17
44 24 0.35
45 32 0.46
46 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (43 bp):
TGCATCGATACATCATGAAGTGCATCGATGCATCCCTTGAATG
Found at i:218380 original size:20 final size:20
Alignment explanation
Indices: 218355--218393 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
218345 TTCAATGCAC
218355 CGATGCA-CTGATGCACTCAT
1 CGATGCATC-GATGCACTCAT
218375 CGATGCATCGATGCACTCA
1 CGATGCATCGATGCACTCA
218394 CCAATTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.23
Consensus pattern (20 bp):
CGATGCATCGATGCACTCAT
Found at i:218466 original size:63 final size:64
Alignment explanation
Indices: 218399--218550 Score: 229
Period size: 64 Copynumber: 2.4 Consensus size: 64
218389 ACTCACCAAT
* *
218399 TCGAATGCATTTTTTGCATCGATGCACTTA-CATGCATCGATGCACTCA-GGTT-TTATGAAAAC
1 TCGAATGCATTTTTTGCATCGATGCACATACCATGCATCGATGCACTCATGCTTGTT-TG-AAAC
218461 A
64 A
*
218462 TCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCATGCTTGTTTGAAACA
1 TCGAATGCATTTTTTGCATCGATGCACATACCATGCATCGATGCACTCATGCTTGTTTGAAACA
218526 TCGAATGCATTTTTATGCATCGATG
1 TCGAATGCATTTTT-TGCATCGATG
218551 GACCCTTAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
63 28 0.35
64 36 0.44
65 15 0.19
66 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (64 bp):
TCGAATGCATTTTTTGCATCGATGCACATACCATGCATCGATGCACTCATGCTTGTTTGAAACA
Found at i:218570 original size:65 final size:64
Alignment explanation
Indices: 218399--218573 Score: 179
Period size: 65 Copynumber: 2.7 Consensus size: 64
218389 ACTCACCAAT
* *
218399 TCGAATGCATTTTT-TGCATCGAT-G-CACTTACATGCATCGATGCACTCAGGTTTTATGAAAAC
1 TCGAATGCATTTTTATGCATCGATGGACCCTT--ATGCATCGATGCACTCAGCTTTTATGAAAAC
218461 A
64 A
*
218462 TCGAATGCA-TTTTATGCATCGATGCACATACC--ATGCATCGATGCACTCATGCTTGTT-TG-A
1 TCGAATGCATTTTTATGCATCGATGGAC---CCTTATGCATCGATGCACTCA-GCTT-TTATGAA
218522 AACA
61 AACA
218526 TCGAATGCATTTTTATGCATCGATGGACCCTTAGTGCA-CTGATGCACT
1 TCGAATGCATTTTTATGCATCGATGGACCCTTA-TGCATC-GATGCACT
218574 AAGTGTTCCA
Statistics
Matches: 95, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
62 6 0.06
63 18 0.19
64 33 0.35
65 35 0.37
66 2 0.02
68 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (64 bp):
TCGAATGCATTTTTATGCATCGATGGACCCTTATGCATCGATGCACTCAGCTTTTATGAAAACA
Found at i:218665 original size:21 final size:21
Alignment explanation
Indices: 218613--218668 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
218603 TTTACACTTG
*
218613 ATGCATCGATACACCTTGACT
1 ATGCATCGATGCACCTTGACT
*
218634 ATGCATTGATGCACCTTGACT
1 ATGCATCGATGCACCTTGACT
218655 ATGCATCGATGCAC
1 ATGCATCGATGCAC
218669 ACACACTCCC
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:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCACCTTGACT
Found at i:220262 original size:17 final size:18
Alignment explanation
Indices: 220221--220279 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
220211 CATGACAGAG
* *
220221 CTTCTCTTTTTCTTC-AC
1 CTTCCCTTTATCTTCTAC
* *
220238 CTT-TCTTTGTCTTCTAC
1 CTTCCCTTTATCTTCTAC
*
220255 C-TCCCTTTATCTTCTTC
1 CTTCCCTTTATCTTCTAC
220272 CTTCCCTT
1 CTTCCCTT
220280 CAAGTGGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 11 0.31
17 18 0.51
18 6 0.17
ACGTcount: A:0.05, C:0.37, G:0.02, T:0.56
Consensus pattern (18 bp):
CTTCCCTTTATCTTCTAC
Found at i:221820 original size:19 final size:19
Alignment explanation
Indices: 221796--221835 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
221786 AATCGGAGTC
*
221796 TATAAATCGGATGATCTCT
1 TATAAACCGGATGATCTCT
221815 TATAAACCGGATGATCTCT
1 TATAAACCGGATGATCTCT
221834 TA
1 TA
221836 CTTACTAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
TATAAACCGGATGATCTCT
Found at i:227893 original size:18 final size:19
Alignment explanation
Indices: 227856--227899 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
227846 GGCTAAATTA
*
227856 AAATAAATTAAAATTAAAT
1 AAATAAATCAAAATTAAAT
*
227875 AACTAAATCAAAA-TAAAT
1 AAATAAATCAAAATTAAAT
227893 AAATAAA
1 AAATAAA
227900 GATTAGTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATAAATCAAAATTAAAT
Found at i:229856 original size:13 final size:15
Alignment explanation
Indices: 229824--229857 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
229814 CATTTATATT
229824 TTTTAAGTATTTTAA
1 TTTTAAGTATTTTAA
229839 TTTTAA-TATTTT-A
1 TTTTAAGTATTTTAA
229852 TTTTAA
1 TTTTAA
229858 CATAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTAAGTATTTTAA
Found at i:230199 original size:13 final size:14
Alignment explanation
Indices: 230174--230202 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
230164 TTTTTTATAG
230174 AACATTTTAATTTT
1 AACATTTTAATTTT
230188 AACATTTT-ATTTT
1 AACATTTTAATTTT
230201 AA
1 AA
230203 AATAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AACATTTTAATTTT
Found at i:231213 original size:32 final size:32
Alignment explanation
Indices: 231172--231241 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
231162 GTTGTGGGCA
* * * *
231172 TCATCTTCAATCTCTTACATATCACACTCCTT
1 TCATCTTCAATCTCTTACACAACAAACTCATT
231204 TCATCTTCAATCTCTTACACAACAAACTCATT
1 TCATCTTCAATCTCTTACACAACAAACTCATT
231236 TCATCT
1 TCATCT
231242 AACTAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.39
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAACAAACTCATT
Found at i:233836 original size:78 final size:79
Alignment explanation
Indices: 233754--233920 Score: 239
Period size: 78 Copynumber: 2.1 Consensus size: 79
233744 TGCCAAATCT
* * * * *
233754 TTTTTTTTTTTTCAAATTTGTTAAAAA-TTCTAAAAGTTTTATATTATTTTTAACTTTGAAATTT
1 TTTTTTATTTTTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
*
233818 TAAAATTTTTAATA
66 TAAAAATTTTAATA
***
233832 -TTTTTAAAATTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
1 TTTTTTATTTTTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
233896 TAAAAATTTTAATA
66 TAAAAATTTTAATA
233910 TTTTTTATTTT
1 TTTTTTATTTT
233921 ATTAACTACA
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
77 21 0.28
78 47 0.63
79 7 0.09
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (79 bp):
TTTTTTATTTTTCAAATTTATTAAAAATTTCTAAAAATTTGATATTATTTTTAACTTCGAAATTT
TAAAAATTTTAATA
Found at i:233848 original size:32 final size:34
Alignment explanation
Indices: 233778--233849 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
233768 AATTTGTTAA
* * ** *
233778 AAATTCTAAAAGTTTTATATTATTTTTAACTTTG
1 AAATTTTAAAAGTTTTATAATATTTTTAAAATTC
233812 AAATTTTAAAA-TTTT-TAATATTTTTAAAATTC
1 AAATTTTAAAAGTTTTATAATATTTTTAAAATTC
233844 AAATTT
1 AAATTT
233850 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 19 0.58
33 4 0.12
34 10 0.30
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (34 bp):
AAATTTTAAAAGTTTTATAATATTTTTAAAATTC
Found at i:236530 original size:21 final size:21
Alignment explanation
Indices: 236504--236548 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
236494 GATTTCTGGG
* *
236504 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
236525 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
236546 CAA
1 CAA
236549 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:237152 original size:18 final size:18
Alignment explanation
Indices: 237129--237163 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
237119 CTAGGAGATT
237129 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
237147 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
237164 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:237249 original size:21 final size:22
Alignment explanation
Indices: 237220--237263 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
237210 GTTGTATGAT
237220 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
237241 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
237263 A
1 A
237264 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:238221 original size:149 final size:149
Alignment explanation
Indices: 238041--238344 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
238031 GAGTCGAGGG
238041 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
238106 ACTTGATCCCTAGAATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGAATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
238171 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
238190 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
238255 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGAATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
238320 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
238339 TCTACG
1 TCTACG
238345 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGAATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:238367 original size:23 final size:23
Alignment explanation
Indices: 238323--238367 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
238313 ATCATTATAT
*
238323 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* * *
238346 GGCACTTCGGTGTATTTATACG
1 GGCACTACGGTGCAATTATACG
238368 AGCTGTTGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:250416 original size:31 final size:31
Alignment explanation
Indices: 250381--250454 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
250371 TTCAAAATCA
250381 TACCTAACATTT-ACTTTTTATTTCATTTTAG
1 TACCTAA-ATTTAACTTTTTATTTCATTTTAG
** *
250412 TACCTCATTTTTAACTTTTTGTTTCATTTTAG
1 TACCT-AAATTTAACTTTTTATTTCATTTTAG
250444 TACCTAAATTT
1 TACCTAAATTT
250455 TTAATGTCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.55
Consensus pattern (31 bp):
TACCTAAATTTAACTTTTTATTTCATTTTAG
Found at i:250437 original size:32 final size:33
Alignment explanation
Indices: 250393--250458 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
250383 CCTAACATTT
*
250393 ACTTTTTATTTCATTTTAGTACCT-CATTTTTA
1 ACTTTTTATTTCATTTTAGTACCTAAATTTTTA
*
250425 ACTTTTTGTTTCATTTTAGTACCTAAATTTTTA
1 ACTTTTTATTTCATTTTAGTACCTAAATTTTTA
250458 A
1 A
250459 TGTCTGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.58
Consensus pattern (33 bp):
ACTTTTTATTTCATTTTAGTACCTAAATTTTTA
Found at i:252668 original size:422 final size:422
Alignment explanation
Indices: 251884--252732 Score: 1671
Period size: 422 Copynumber: 2.0 Consensus size: 422
251874 TTTTATTGTA
251884 ATTTTAGTAGTTAAAGATTACATGGTAGATTTATTTAATAAAATAAATATTTATTTTAGGTAAGA
1 ATTTTAGTAGTTAAAGATTACATGGTAGATTTATTTAATAAAATAAATATTTATTTTAGGTAAGA
251949 TCAATACAAGTTATTGGTAACCAAGTATATAAATAGAGATTGTGTTTTAGTTTTTATGATTATGG
66 TCAATACAAGTTATTGGTAACCAAGTATATAAATAGAGATTGTGTTTTAGTTTTTATGATTATGG
252014 AAGAGGTAATTATTTTGGAGATATATAATTCTTTTAGGGTTCTATGCAATTTTTGGGTTTACATT
131 AAGAGGTAATTATTTTGGAGATATATAATTCTTTTAGGGTTCTATGCAATTTTTGGGTTTACATT
252079 GTAGAGATAATTTTGTAGGGATGTTGAAAGAGTATTGTAGGATATATCAAGTTTTGATATATATA
196 GTAGAGATAATTTTGTAGGGATGTTGAAAGAGTATTGTAGGATATATCAAGTTTTGATATATATA
*
252144 CCAGGTGTTAGGATACATGTGGTATCATGTATTTGTACTCTTTGTATTCTTTATGTTTGTAATGA
261 CCAGGTGTTAGGATACATGTGGTATCATGTATTTGTACTCTTTGTATTCTTTACGTTTGTAATGA
252209 ATTATTATTCATCTTACCCGTAAAGATAGGTAATATCGAACCACGTTAAATATTGCATCTTGTTT
326 ATTATTATTCATCTTACCCGTAAAGATAGGTAATATCGAACCACGTTAAATATTGCATCTTGTTT
*
252274 ATGTCTTATTTTATGTTGATATCACTTTGATT
391 ATGTCTTATTTTATGTTGATATAACTTTGATT
252306 ATTTTAGTAGTTAAAGATTACATGGTAGATTTATTTAATAAAATAAATATTTATTTTAGGTAAGA
1 ATTTTAGTAGTTAAAGATTACATGGTAGATTTATTTAATAAAATAAATATTTATTTTAGGTAAGA
252371 TCAATACAAGTTATTGGTAACCAAGTATATAAATAGAGATTGTGTTTTAGTTTTTATGATTATGG
66 TCAATACAAGTTATTGGTAACCAAGTATATAAATAGAGATTGTGTTTTAGTTTTTATGATTATGG
252436 AAGAGGTAATTATTTTGGAGATATATAATTCTTTTAGGGTTCTATGCAATTTTTGGGTTTACATT
131 AAGAGGTAATTATTTTGGAGATATATAATTCTTTTAGGGTTCTATGCAATTTTTGGGTTTACATT
252501 GTAGAGATAATTTTGTAGGGATGTTGAAAGAGTATTGTAGGATATATCAAGTTTTGATATATATA
196 GTAGAGATAATTTTGTAGGGATGTTGAAAGAGTATTGTAGGATATATCAAGTTTTGATATATATA
252566 CCAGGTGTTAGGATACATGTGGTATCATGTATTTGTACTCTTTGTATTCTTTACGTTTGTAATGA
261 CCAGGTGTTAGGATACATGTGGTATCATGTATTTGTACTCTTTGTATTCTTTACGTTTGTAATGA
*
252631 ATTATTATTCATCTTACCCGTAATGATAGGTAATATCGAACCACGTTAAATATTGCATCTTGTTT
326 ATTATTATTCATCTTACCCGTAAAGATAGGTAATATCGAACCACGTTAAATATTGCATCTTGTTT
252696 ATGTCTTATTTTATGTTGATATAACTTTGATT
391 ATGTCTTATTTTATGTTGATATAACTTTGATT
252728 ATTTT
1 ATTTT
252733 TTCGATCTCA
Statistics
Matches: 424, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
422 424 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (422 bp):
ATTTTAGTAGTTAAAGATTACATGGTAGATTTATTTAATAAAATAAATATTTATTTTAGGTAAGA
TCAATACAAGTTATTGGTAACCAAGTATATAAATAGAGATTGTGTTTTAGTTTTTATGATTATGG
AAGAGGTAATTATTTTGGAGATATATAATTCTTTTAGGGTTCTATGCAATTTTTGGGTTTACATT
GTAGAGATAATTTTGTAGGGATGTTGAAAGAGTATTGTAGGATATATCAAGTTTTGATATATATA
CCAGGTGTTAGGATACATGTGGTATCATGTATTTGTACTCTTTGTATTCTTTACGTTTGTAATGA
ATTATTATTCATCTTACCCGTAAAGATAGGTAATATCGAACCACGTTAAATATTGCATCTTGTTT
ATGTCTTATTTTATGTTGATATAACTTTGATT
Found at i:253897 original size:22 final size:22
Alignment explanation
Indices: 253849--253899 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
253839 ATAATTGTTT
* **
253849 ATTTAAATATCTACAATTGTTT
1 ATTTAAATATCTACAATTATAA
253871 ATTTAAATATCTACAA-TATAA
1 ATTTAAATATCTACAATTATAA
253892 AGTTTAAA
1 A-TTTAAA
253900 AACCTTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTTAAATATCTACAATTATAA
Found at i:253897 original size:26 final size:22
Alignment explanation
Indices: 253841--253887 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
253831 GGAAATATAT
253841 AATTGTTTATTTAAATATCTAC
1 AATTGTTTATTTAAATATCTAC
253863 AATTGTTTATTTAAATATCTAC
1 AATTGTTTATTTAAATATCTAC
253885 AAT
1 AAT
253888 ATAAAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTGTTTATTTAAATATCTAC
Found at i:255296 original size:228 final size:225
Alignment explanation
Indices: 254894--255375 Score: 817
Period size: 228 Copynumber: 2.1 Consensus size: 225
254884 GTAAATTATC
* * *
254894 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
254959 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
*
255024 TGTGTAAATGAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTG
131 TGTGTAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC-ATT-AAAAAAATTG
255089 AAACATAAATTACATAACTTTCAAAAAAGTATA
194 AAACATAAATTACATAACTTTC-AAAAAGTATA
* *
255122 TATCATTTTTATAAAAGTGTCCATATTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
255187 TTAATATTGTTAAATTTAAATTCT-AATAATATTTTAT-AAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
*
255250 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACATTAAATAAATTG
130 TTGTGTAAA-TAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACATTAAAAAAATTG
255315 AAACATAAATTACATAACTTTCAAAAAGTATA
194 AAACATAAATTACATAACTTTCAAAAAGTATA
255347 TATCATTTTTA-AAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
255376 AAAAGTAGGT
Statistics
Matches: 242, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
224 17 0.07
225 21 0.09
226 31 0.13
227 37 0.15
228 89 0.37
229 47 0.19
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (225 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACATTAAAAAAATTGAA
ACATAAATTACATAACTTTCAAAAAGTATA
Found at i:255677 original size:20 final size:19
Alignment explanation
Indices: 255654--255700 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
255644 CGATATACCA
255654 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
255674 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
255694 GGTAAAA
1 GGTAAAA
255701 CGTTACCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:255796 original size:181 final size:182
Alignment explanation
Indices: 255442--255914 Score: 671
Period size: 181 Copynumber: 2.6 Consensus size: 182
255432 GATCCAAATT
* * * *
255442 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * * *
255506 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCAGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * * *
255571 CGTGAATTTAAAAGAGAATCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
255624 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
255689 AAACCGGTAAAACGTTACCAGATATATTAAAAGTGTTGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCAGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
255753 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * *
255805 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
255870 AAACCGATAAAATGATACCAGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCAGATATATTAAAAGTGTCGATACTTT
255915 CGTAAGTACG
Statistics
Matches: 260, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
181 165 0.63
182 95 0.37
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCAGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:255858 original size:20 final size:19
Alignment explanation
Indices: 255835--255881 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
255825 CGATATAACA
255835 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
255855 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
255875 GATAAAA
1 GGTAAAA
255882 TGATACCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:255883 original size:17 final size:20
Alignment explanation
Indices: 255844--255886 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
255834 AGGTAAAAAT
255844 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGGTATCAAA
255864 ATGATAAAACC-G-AT-AAA
1 ATGATAAAACCGGTATCAAA
255881 ATGATA
1 ATGATA
255887 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 1 0.04
20 11 0.48
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (20 bp):
ATGATAAAACCGGTATCAAA
Found at i:258113 original size:21 final size:20
Alignment explanation
Indices: 258086--258137 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
258076 AAGACAATCA
* *
258086 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAG-AACTCGAG
* *
258107 CGAGTCGTAGAGAACTCGAG
1 AGAGTCGAAGAGAACTCGAG
258127 AGAGTCGAAGA
1 AGAGTCGAAGA
258138 TACACTGAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.38, C:0.13, G:0.33, T:0.15
Consensus pattern (20 bp):
AGAGTCGAAGAGAACTCGAG
Found at i:260056 original size:19 final size:19
Alignment explanation
Indices: 260032--260080 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
260022 AATGTAGGGT
260032 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
260051 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
260070 TATTTTTGTAT
1 TAATTTTGTAT
260081 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:260942 original size:199 final size:199
Alignment explanation
Indices: 260189--261147 Score: 1737
Period size: 199 Copynumber: 4.8 Consensus size: 199
260179 GGCAAATTTA
* * *
260189 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
*
260254 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
260319 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTTCCAGAATGAATGGAAAACAGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTT-TTTTCCAGAATGAATGGAAAACAGG
260384 GTGCAC
194 GTGCAC
*
260390 CCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
260453 GTAATATGTAATTTTTAAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
260518 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATGGAAAACAGGG
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATGGAAAACAGGG
260583 TGCAC
195 TGCAC
*
260588 CCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
260653 GTAATATGTAATTTTTCAATCTAACC-GTACAATTATACC-GTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
260716 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
260781 GCAC
196 GCAC
*
260785 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATTATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
260850 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
260915 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
260980 GCAC
196 GCAC
260984 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
261049 GTAATATGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
261114 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
261148 CTAATTTAAA
Statistics
Matches: 734, Mismatches: 19, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
197 124 0.17
198 227 0.31
199 297 0.40
200 69 0.09
201 17 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
GCAC
Found at i:261028 original size:396 final size:397
Alignment explanation
Indices: 260189--261147 Score: 1726
Period size: 396 Copynumber: 2.4 Consensus size: 397
260179 GGCAAATTTA
* * *
260189 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
*
260254 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACC-GTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
260319 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTTCCAGAATGAATGGAAAACAGG
129 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTTCCAGAATGAATGGAAAACAGG
*
260384 GTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGTA
194 GTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
* *
260449 TAATGTAATATGTAATTTTTAAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTC
259 TAATGTAATATGTAATTTTTAAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTC
260514 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATGGAAAAC
324 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATGGAAAAC
260579 AGGGTGCAC
389 AGGGTGCAC
*
260588 CCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
260653 GTAATATGTAATTTTTCAATCTAACCGTACAATTATACC-GTTTTATGAGATAATATGTATAAAT
66 GTAATATGTAATTTTTCAATCTAACCGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
260717 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTT-TTTTCCAGAATGAATGGAAAACAGGGT
131 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTTCCAGAATGAATGGAAAACAGGGT
*
260781 GCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATTATCGAACCCAAAAGTA
196 GCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
*
260846 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTC
259 TAATGTAATATGTAATTTTTAAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTC
260911 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATGGAAAAC
324 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATGGAAAAC
260975 AGGGTGCAC
389 AGGGTGCAC
260984 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
261049 GTAATATGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAA-CCGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
261114 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
130 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
261148 CTAATTTAAA
Statistics
Matches: 538, Mismatches: 18, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
395 48 0.09
396 183 0.34
397 164 0.30
398 97 0.18
399 46 0.09
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (397 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTTCCAGAATGAATGGAAAACAGGGT
GCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTAAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTA
AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATGGAAAACAG
GGTGCAC
Found at i:262620 original size:18 final size:18
Alignment explanation
Indices: 262599--262660 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
262589 AGCGGTCGCA
262599 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
262617 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
262635 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
262653 GAAGATGA
1 GAAGATGA
262661 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:262623 original size:6 final size:6
Alignment explanation
Indices: 262599--262690 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
262589 AGCGGTCGCA
* * * * * *
262599 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
262647 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
262691 TGATCAAACA
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:262634 original size:3 final size:3
Alignment explanation
Indices: 262614--262694 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
262604 TGAAGCTGAC
* * * * * ** *
262614 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
262662 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
262695 CAAACAAGTA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:262653 original size:36 final size:36
Alignment explanation
Indices: 262602--262678 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
262592 GGTCGCAGAA
*
262602 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
262638 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
262674 GATGA
1 GATGA
262679 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:262694 original size:12 final size:12
Alignment explanation
Indices: 262602--262690 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
262592 GGTCGCAGAA
*
262602 GATGAAGCTGAC
1 GATGAAGATGAC
262614 GATGAAGATGAC
1 GATGAAGATGAC
*
262626 GATGATGATGAC
1 GATGAAGATGAC
* *
262638 GATGAAGCTGGC
1 GATGAAGATGAC
*
262650 GATGAAGATGAT
1 GATGAAGATGAC
* * *
262662 GACGATGATGAT
1 GATGAAGATGAC
* *
262674 GATGATGATGAA
1 GATGAAGATGAC
262686 GATGA
1 GATGA
262691 TGATCAAACA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:262694 original size:18 final size:18
Alignment explanation
Indices: 262599--262690 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
262589 AGCGGTCGCA
*
262599 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
262617 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
262635 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
262653 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
262671 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
262689 GA
1 GA
262691 TGATCAAACA
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:265867 original size:25 final size:25
Alignment explanation
Indices: 265839--265903 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
265829 TTATCATTAA
265839 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
265864 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
265889 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
265904 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:266278 original size:23 final size:23
Alignment explanation
Indices: 266247--266319 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
266237 ATAGGTAAAC
*
266247 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
266270 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
266293 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
266316 ATAT
1 ATAT
266320 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:267076 original size:38 final size:37
Alignment explanation
Indices: 267034--267115 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 37
267024 TCCGATGCTC
* *
267034 ATCAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAATCC-AAGCTCATATGATGCCAAGCAAAAAGAA
* *
267072 ATCAAAATTCAATCTCATATGATGCCAAGCAAAAAGAA
1 ATC-AAATCCAAGCTCATATGATGCCAAGCAAAAAGAA
267110 ATCAAA
1 ATCAAA
267116 ATCTACAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 3 0.08
38 31 0.79
39 5 0.13
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (37 bp):
ATCAAATCCAAGCTCATATGATGCCAAGCAAAAAGAA
Found at i:267568 original size:23 final size:23
Alignment explanation
Indices: 267537--267609 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
267527 ATAGGTAAAC
*
267537 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
267560 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
267583 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
267606 ATAT
1 ATAT
267610 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:268566 original size:2 final size:2
Alignment explanation
Indices: 268559--268588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
268549 CCCATTTATG
268559 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
268589 TAATAAATTA
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):
AT
Found at i:269284 original size:31 final size:31
Alignment explanation
Indices: 269246--269316 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
269236 CGTTAAAATT
269246 AAGTGCCTAACGTTTACATCGGAGCAATTTC
1 AAGTGCCTAACGTTTACATCGGAGCAATTTC
* *
269277 AAGTGCCTAATGTTTACATCGGAGCACTTTC
1 AAGTGCCTAACGTTTACATCGGAGCAATTTC
269308 AAGTGCCTA
1 AAGTGCCTA
269317 GACTGTAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (31 bp):
AAGTGCCTAACGTTTACATCGGAGCAATTTC
Found at i:270801 original size:21 final size:19
Alignment explanation
Indices: 270751--270801 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
270741 ACTATGATTG
*
270751 TATATGATTAT-ATAAAAT
1 TATATTATTATGATAAAAT
* *
270769 TATAATAATATGATATAAAT
1 TATATTATTATGATA-AAAT
270789 TAATATTATTATG
1 T-ATATTATTATG
270802 GGTAAATATG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 8 0.32
19 3 0.12
20 5 0.20
21 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
TATATTATTATGATAAAAT
Found at i:275078 original size:2 final size:2
Alignment explanation
Indices: 275071--275095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
275061 TCTCAATCAA
275071 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
275096 TATCTACTTA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:275772 original size:2 final size:2
Alignment explanation
Indices: 275765--275790 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
275755 TCCTGCTCTT
275765 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
275791 AAGGGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278834 original size:19 final size:19
Alignment explanation
Indices: 278810--278859 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
278800 TTGTATTAAT
*
278810 AATTAAAATGAGGGTAAAA
1 AATTAAAATAAGGGTAAAA
* * *
278829 AATTAAGAATAATGGTCACA
1 AATTAA-AATAAGGGTAAAA
278849 AATTAAAATAA
1 AATTAAAATAA
278860 AATAACACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.58, C:0.04, G:0.14, T:0.24
Consensus pattern (19 bp):
AATTAAAATAAGGGTAAAA
Found at i:287171 original size:21 final size:21
Alignment explanation
Indices: 287147--287186 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
287137 AATTACTATC
287147 AATA-AAAAGAGTTTATTTTTT
1 AATATAAAAGA-TTTATTTTTT
*
287168 AATATAAAATATTTATTTT
1 AATATAAAAGATTTATTTT
287187 AATTCTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
AATATAAAAGATTTATTTTTT
Found at i:288026 original size:16 final size:18
Alignment explanation
Indices: 288005--288038 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
287995 TTGTAAAATT
288005 ATTTAAAT-TAA-TATTC
1 ATTTAAATATAATTATTC
288021 ATTTAAATATAATTATTC
1 ATTTAAATATAATTATTC
288039 TATTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAATATAATTATTC
Found at i:289782 original size:20 final size:20
Alignment explanation
Indices: 289741--289787 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
289731 AACGATTTTC
* *
289741 TTTTG-AAAGCAAAATTAGA
1 TTTTGAAAAGCAAAATAAAA
*
289760 TTTTGAAAATCAAAATAAAA
1 TTTTGAAAAGCAAAATAAAA
289780 TTTT-AAAA
1 TTTTGAAAA
289788 AATGATTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATAAAA
Found at i:291502 original size:21 final size:21
Alignment explanation
Indices: 291444--291508 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 21
291434 GTAAGTTTTA
* *
291444 GATCGGTCCCTTTAT-AAAAG
1 GATCGATCCCTCTATGAAAAG
* * * *
291464 GATAGAT-CCTCAAGGAAAAT
1 GATCGATCCCTCTATGAAAAG
291484 GATCGATCCCTCTATGAAAAG
1 GATCGATCCCTCTATGAAAAG
291505 GATC
1 GATC
291509 AATCTTTTTC
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
21 14 0.42
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
GATCGATCCCTCTATGAAAAG
Found at i:292786 original size:14 final size:16
Alignment explanation
Indices: 292745--292789 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
292735 CTTATTTTAT
292745 AATTATACCTAATACA
1 AATTATACCTAATACA
* *
292761 ATTTATAACTAA-A-A
1 AATTATACCTAATACA
292775 AATTATACCTAATAC
1 AATTATACCTAATAC
292790 GAAAAGTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTATACCTAATACA
Found at i:293152 original size:2 final size:2
Alignment explanation
Indices: 293145--293179 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
293135 ATCCTAACTC
293145 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 A
293180 GATTCATACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:293546 original size:6 final size:6
Alignment explanation
Indices: 293537--293607 Score: 115
Period size: 6 Copynumber: 11.8 Consensus size: 6
293527 TAAACACTGA
* * *
293537 GCTGGA GCTGGG GCTGGA GCTGGG GCTGGG GCTGGA GCTGGG GCTGGG
1 GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG
293585 GCTGGG GCTGGG GCTGGG GCTGG
1 GCTGGG GCTGGG GCTGGG GCTGG
293608 TTATAGAGGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.04, C:0.17, G:0.62, T:0.17
Consensus pattern (6 bp):
GCTGGG
Found at i:293558 original size:18 final size:18
Alignment explanation
Indices: 293535--293607 Score: 128
Period size: 18 Copynumber: 4.1 Consensus size: 18
293525 CCTAAACACT
*
293535 GAGCTGGAGCTGGGGCTG
1 GAGCTGGGGCTGGGGCTG
293553 GAGCTGGGGCTGGGGCTG
1 GAGCTGGGGCTGGGGCTG
293571 GAGCTGGGGCTGGGGCTG
1 GAGCTGGGGCTGGGGCTG
*
293589 GGGCTGGGGCTGGGGCTG
1 GAGCTGGGGCTGGGGCTG
293607 G
1 G
293608 TTATAGAGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.62, T:0.16
Consensus pattern (18 bp):
GAGCTGGGGCTGGGGCTG
Found at i:300063 original size:19 final size:19
Alignment explanation
Indices: 300039--300076 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
300029 AGATGCTAAG
300039 TTACATATCAAATAACAAA
1 TTACATATCAAATAACAAA
300058 TTACATATCAAATAACAAA
1 TTACATATCAAATAACAAA
300077 GAAGATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (19 bp):
TTACATATCAAATAACAAA
Found at i:300084 original size:19 final size:19
Alignment explanation
Indices: 300041--300084 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
300031 ATGCTAAGTT
**
300041 ACATATCAAATAACAAATT
1 ACATATCAAATAACAAAGA
300060 ACATATCAAATAACAAAGA
1 ACATATCAAATAACAAAGA
*
300079 AGATAT
1 ACATAT
300085 AACACATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.23
Consensus pattern (19 bp):
ACATATCAAATAACAAAGA
Found at i:300828 original size:20 final size:20
Alignment explanation
Indices: 300783--300829 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
300773 GACCAACAAA
*
300783 ATCGCAATGCGATCGCTAAT
1 ATCGCAATGCGATCGCCAAT
* *
300803 -TCGCAATGCGATCTCCATT
1 ATCGCAATGCGATCGCCAAT
300822 ATCGCAAT
1 ATCGCAAT
300830 TCGCGTTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATCGCCAAT
Found at i:300880 original size:17 final size:18
Alignment explanation
Indices: 300842--300891 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
300832 GCGTTGCATT
300842 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATA---GGAAA
300863 TCGCG-TGCGATAGGAAA
1 TCGCGTTGCGATAGGAAA
300880 TCGCGTTGCGAT
1 TCGCGTTGCGAT
300892 GGTCTACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
20 7 0.25
21 5 0.18
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (18 bp):
TCGCGTTGCGATAGGAAA
Found at i:300947 original size:20 final size:20
Alignment explanation
Indices: 300922--300972 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
300912 TTTTCCCAAT
*
300922 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
300942 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
300962 TCGCAATGCGA
1 TCGCAATGCGA
300973 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:300984 original size:20 final size:20
Alignment explanation
Indices: 300961--301054 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
300951 GAATTGGGAA
300961 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
300981 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
301001 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
301022 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
301042 TTCGCAACGCGAT
1 ATCGCAATGCGAT
301055 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:301459 original size:19 final size:19
Alignment explanation
Indices: 301437--301601 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
301427 GAAACCAAAA
*
301437 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
301456 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
301475 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
301494 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
301508 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
301527 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
301541 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
301560 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
301580 ATCTCGTTGTGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
301600 TC
1 TC
301602 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
14 19 0.16
16 4 0.03
17 5 0.04
19 58 0.50
20 30 0.26
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:301497 original size:38 final size:33
Alignment explanation
Indices: 301442--301576 Score: 153
Period size: 33 Copynumber: 3.9 Consensus size: 33
301432 CAAAATCGCA
*
301442 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
*
301480 TTGTGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
301513 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
301546 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
301577 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 15 0.17
36 3 0.03
38 24 0.27
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:301531 original size:33 final size:33
Alignment explanation
Indices: 301489--301576 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
301479 GTTGTGATTT
301489 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
301522 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
301555 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
301577 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:303755 original size:21 final size:21
Alignment explanation
Indices: 303731--303879 Score: 54
Period size: 21 Copynumber: 7.1 Consensus size: 21
303721 TCATTCCTCG
303731 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
303752 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
303773 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
303794 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
303815 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
303836 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
303857 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
303878 AG
1 AG
303880 GCCCGATTCA
Statistics
Matches: 84, Mismatches: 37, Indels: 14
0.62 0.27 0.10
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 77 0.92
22 3 0.04
23 1 0.01
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:303756 original size:42 final size:42
Alignment explanation
Indices: 303704--303842 Score: 197
Period size: 42 Copynumber: 3.3 Consensus size: 42
303694 TCACTCCTAT
*
303704 CGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
* * * * * * *
303746 CGTTCAAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTAT
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
*
303788 CGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
303830 CGTTCAAGAGGCC
1 CGTTCAAGAGGCC
303843 ACTGTCATCG
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
Found at i:303860 original size:84 final size:84
Alignment explanation
Indices: 303676--303851 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
303666 CCCGACTCGC
*
303676 CTGTCATCCCTCAAGAGTTCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
303741 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
303760 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
303825 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
303844 CTGTCATC
1 CTGTCATC
303852 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:303867 original size:42 final size:41
Alignment explanation
Indices: 303676--303879 Score: 160
Period size: 42 Copynumber: 4.9 Consensus size: 41
303666 CCCGACTCGC
* * * * * * *
303676 CTGTCATCCCTCAAGAGTTCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAG-TCCCTCCCACCGTTCAAGAGGCCA
* *
303718 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
* * * * * *
303760 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCA
* *
303802 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
* *
303844 CTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAG
1 CTGTCATCCTTGAAGA-GTCCCTCCCACCGTTCAAG
303880 GCCCGATTCA
Statistics
Matches: 125, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
41 10 0.08
42 105 0.84
43 10 0.08
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (41 bp):
CTGTCATCCTTGAAGAGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:305242 original size:14 final size:14
Alignment explanation
Indices: 305223--305258 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
305213 ATTGTTTAAT
305223 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
305237 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
305251 TGATTTGT
1 TGATTTGT
305259 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:305389 original size:19 final size:20
Alignment explanation
Indices: 305365--305418 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
305355 AAAAAGTACT
305365 ATCGCAATGCGAAATG-AAA
1 ATCGCAATGCGAAATGAAAA
*
305384 ATCGCAACGCGAAATGAAAA
1 ATCGCAATGCGAAATGAAAA
305404 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
305419 TAAATTCGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAATGCGAAATGAAAA
Found at i:305469 original size:33 final size:32
Alignment explanation
Indices: 305427--305552 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
305417 ATTAAATTCG
305427 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
305460 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
305493 CGTTGCGA-TTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
305525 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
305553 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
30 3 0.04
32 25 0.30
33 53 0.63
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:305490 original size:71 final size:71
Alignment explanation
Indices: 305405--305572 Score: 240
Period size: 65 Copynumber: 2.4 Consensus size: 71
305395 AAATGAAAAA
*
305405 TCGCAATGCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATT
1 TCGCATTGCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATT
305470 TTCATT
66 TTCATT
*
305476 TCGCATTGCGAAATT--A---GCGTTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATT
305535 TTCATT
66 TTCATT
* * *
305541 TCGCATTGCGATAGTAATTTCCGCGTTGCGAT
1 TCGCATTGCGAAATTAAATT-CGCGTTGCGAT
305573 AGACATTAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 13
0.83 0.05 0.13
Matches are distributed among these distances:
65 52 0.61
66 9 0.11
69 1 0.01
71 23 0.27
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39
Consensus pattern (71 bp):
TCGCATTGCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATT
TTCATT
Found at i:307838 original size:12 final size:12
Alignment explanation
Indices: 307821--307845 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
307811 TCTTCGGGGA
307821 CTTTTTCTTCTT
1 CTTTTTCTTCTT
307833 CTTTTTCTTCTT
1 CTTTTTCTTCTT
307845 C
1 C
307846 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:308052 original size:23 final size:23
Alignment explanation
Indices: 308020--308064 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
308010 CTGAACATCA
308020 TCAAAATCCGAGTATTGACCAAT
1 TCAAAATCCGAGTATTGACCAAT
* *
308043 TCAAAGTCCGGGTATTGACCAA
1 TCAAAATCCGAGTATTGACCAA
308065 GATCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (23 bp):
TCAAAATCCGAGTATTGACCAAT
Found at i:308893 original size:33 final size:33
Alignment explanation
Indices: 308856--308975 Score: 129
Period size: 33 Copynumber: 3.7 Consensus size: 33
308846 TGACCATCGT
* *
308856 AATGCGAAATGCAAATCGCAACGATAGAATCAC
1 AATGCGAAATGAAAATCGCAACGAGAGAATCAC
** *
308889 AATGCGAAATGAAAAAGGCAACGAGAGAATCGC
1 AATGCGAAATGAAAATCGCAACGAGAGAATCAC
* *
308922 AATGCGAAATGAAAAT---AACGAGGGAATCGC
1 AATGCGAAATGAAAATCGCAACGAGAGAATCAC
* *
308952 AAAGCGAAAATTAAAATCGCAACG
1 AATGCG-AAATGAAAATCGCAACG
308976 CGATTTTAGT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.24
31 9 0.12
33 43 0.58
34 4 0.05
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (33 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCAC
Found at i:309022 original size:33 final size:34
Alignment explanation
Indices: 308975--309089 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 34
308965 AAATCGCAAC
* * *
308975 GCGATTTT-AGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
*
309008 GCGATTTTCA-TTTCGCATTGTGATTCTATCGTT
1 GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
* *
309041 GCGATTTTC-TTTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
**
309074 GCGATAGTCAGTTTCG
1 GCGATTTTCAGTTTCG
309090 TGTTGCGACA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 64 0.91
34 6 0.09
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (34 bp):
GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
Found at i:309063 original size:19 final size:18
Alignment explanation
Indices: 309006--309065 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
308996 GATTTTGTCG
309006 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTC-TTTCGCA
* *
309025 TTGTGA--TTCTATCG--
1 TTGCGATTTTCTTTCGCA
309039 TTGCGATTTTCTTTTCGCA
1 TTGCGATTTTC-TTTCGCA
309058 TTGCGATT
1 TTGCGATT
309066 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.50
Consensus pattern (18 bp):
TTGCGATTTTCTTTCGCA
Found at i:309600 original size:19 final size:20
Alignment explanation
Indices: 309542--309611 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
309532 ATTCATTTGA
309542 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
309562 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
309582 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
*
309601 CTATTGCAACG
1 CTATCGCAACG
309612 ACAAAATTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 16 0.33
20 33 0.67
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:309678 original size:19 final size:19
Alignment explanation
Indices: 309637--309701 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
309627 AAAATGAAAA
309637 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
309653 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
309670 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
309689 TCGCATTGCGATT
1 TCGCATTGCGATT
309702 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:309732 original size:20 final size:20
Alignment explanation
Indices: 309707--309745 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
309697 CGATTCTCTC
309707 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
309727 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
309746 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:311144 original size:19 final size:20
Alignment explanation
Indices: 311106--311155 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
311096 ATTCATTTGA
311106 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
311126 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
311145 CTATCGCAACG
1 CTATCGCAACG
311156 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:311222 original size:19 final size:19
Alignment explanation
Indices: 311181--311245 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
311171 GAAATGAAAA
311181 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
311197 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
311214 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
311233 TCGCATTGCGATT
1 TCGCATTGCGATT
311246 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:311276 original size:20 final size:20
Alignment explanation
Indices: 311251--311289 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
311241 CGATTCTCTC
311251 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
311271 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
311290 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:313314 original size:19 final size:20
Alignment explanation
Indices: 313259--313326 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
313249 AAAACTTAAA
**
313259 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
313279 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
313299 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
313318 ATCGCAACG
1 ATCGCAACG
313327 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:313334 original size:14 final size:14
Alignment explanation
Indices: 313315--313372 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
313305 ATGCGAAATG
313315 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
313329 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
313345 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
313361 AAAATCGCAACG
1 AAAATCGCAACG
313373 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:313357 original size:32 final size:33
Alignment explanation
Indices: 313299--313377 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
313289 GGAAATGGCT
313299 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
313332 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
313364 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
313378 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:313425 original size:14 final size:14
Alignment explanation
Indices: 313406--313463 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
313396 TTTCATTTCG
313406 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
313420 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
313436 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
313452 CGTTGCGATTTT
1 CGTTGCGATTTT
313464 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:313470 original size:33 final size:33
Alignment explanation
Indices: 313389--313474 Score: 156
Period size: 32 Copynumber: 2.6 Consensus size: 33
313379 ACAAATCGCA
*
313389 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
313422 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
313454 TTGCGATTTTCATTTCGCATT
1 TTGCGATTTTCATTTCGCATT
313475 ATGATAGCCA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 31 0.61
33 20 0.39
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:313488 original size:19 final size:20
Alignment explanation
Indices: 313464--313507 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
313454 TTGCGATTTT
*
313464 CATTT-CGCATTATGATAGC
1 CATTTCCGCATTACGATAGC
* *
313483 CATTTCCGCGTTACGATAGT
1 CATTTCCGCATTACGATAGC
313503 CATTT
1 CATTT
313508 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTACGATAGC
Found at i:314020 original size:18 final size:18
Alignment explanation
Indices: 313994--314038 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
313984 GTCGATCAGA
*
313994 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
314012 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
314030 TGATGGCTC
1 TGATGGCTC
314039 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:315386 original size:20 final size:20
Alignment explanation
Indices: 315363--315410 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
315353 GAAAATGAAA
315363 ATCGCAACACGAAAATT-ACT
1 ATCGCAACACG-AAATTGACT
* *
315383 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAATTGACT
315403 ATCGCAAC
1 ATCGCAAC
315411 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (20 bp):
ATCGCAACACGAAATTGACT
Found at i:315700 original size:22 final size:22
Alignment explanation
Indices: 315673--315716 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
315663 GATGGAGATA
*
315673 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
315695 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
315717 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:315990 original size:20 final size:20
Alignment explanation
Indices: 315884--316018 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
315874 CGCTTTGAAA
*
315884 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
315905 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
315925 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
315945 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
315966 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
315986 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
316006 ATCGCATTGCGAT
1 ATCGCATTGCGAT
316019 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:315990 original size:61 final size:61
Alignment explanation
Indices: 315884--316021 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
315874 CGCTTTGAAA
* * * *
315884 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
315945 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
316006 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
316022 CCCAATTTGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:316037 original size:61 final size:61
Alignment explanation
Indices: 315884--316039 Score: 163
Period size: 61 Copynumber: 2.6 Consensus size: 61
315874 CGCTTTGAAA
* ** * * *
315884 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * *
315945 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
316006 ATCGCATTGCGATTTTCCCAATT-T-GCGTTGCGAT
1 ATCGCATTGCGATTTT--CAATTATCGCGTTGCGAT
316040 TTACTTATTC
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 75 0.95
62 1 0.01
63 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCAATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:316433 original size:31 final size:31
Alignment explanation
Indices: 316395--316462 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
316385 TCAAAAATCA
* * * *
316395 TAAGATTTGATTATTTTCATTTCGTTTTAAT
1 TAAGATTTGATCACTTTCATTTCATTTTAAC
* *
316426 TAAGATTTGGTCACTTTCGTTTCATTTTAAC
1 TAAGATTTGATCACTTTCATTTCATTTTAAC
316457 TAAGAT
1 TAAGAT
316463 GTAGTCACTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.51
Consensus pattern (31 bp):
TAAGATTTGATCACTTTCATTTCATTTTAAC
Found at i:316470 original size:31 final size:31
Alignment explanation
Indices: 316409--316471 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
316399 ATTTGATTAT
* * * *
316409 TTTCATTTCGTTTTAATTAAGATTTGGTCAC
1 TTTCATTTCATTTTAACTAAGATGTAGTCAC
*
316440 TTTCGTTTCATTTTAACTAAGATGTAGTCAC
1 TTTCATTTCATTTTAACTAAGATGTAGTCAC
316471 T
1 T
316472 GAAGGTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTCATTTCATTTTAACTAAGATGTAGTCAC
Found at i:316688 original size:31 final size:31
Alignment explanation
Indices: 316635--316712 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
316625 AATATATATA
* * * **
316635 TAAGTTTTGGTCAGTTATGTTATTGTTTTAT
1 TAAGTTTTAGTCACTTACGTTATCATTTTAT
*
316666 TAAGTTTTAGTAACTTACGTTATCATTTTAT
1 TAAGTTTTAGTCACTTACGTTATCATTTTAT
* *
316697 GAAGCTTTAGTCACTT
1 TAAGTTTTAGTCACTT
316713 GGACGTTGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.51
Consensus pattern (31 bp):
TAAGTTTTAGTCACTTACGTTATCATTTTAT
Found at i:317565 original size:31 final size:31
Alignment explanation
Indices: 317530--317607 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
317520 TTCAATGTCT
* *
317530 AAGTGACCAAAACTTAACAAATCGATAACGC
1 AAGTGACCAAAACTTAACAAAACAATAACGC
* *
317561 AAGTGACCAAAACTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAACAAAACAATAACGC
317592 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
317608 TGTTTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.18
Consensus pattern (31 bp):
AAGTGACCAAAACTTAACAAAACAATAACGC
Found at i:320490 original size:15 final size:15
Alignment explanation
Indices: 320451--320496 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
320441 ATGAAAACAC
320451 AAATAAG-AAAATAA
1 AAATAAGTAAAATAA
* *
320465 AAA-AGAATAAAGTAA
1 AAATA-AGTAAAATAA
320480 AAATAAGTAAAATAA
1 AAATAAGTAAAATAA
320495 AA
1 AA
320497 TATACAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 1 0.04
14 4 0.16
15 19 0.76
16 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (15 bp):
AAATAAGTAAAATAA
Found at i:321720 original size:2 final size:2
Alignment explanation
Indices: 321694--321772 Score: 128
Period size: 2 Copynumber: 41.0 Consensus size: 2
321684 ATAATAAATA
*
321694 AT AT AC AT A- AT AT A- AT AT A- 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
321733 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
321773 GTAACGCATA
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 69 0.96
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:322733 original size:85 final size:80
Alignment explanation
Indices: 322536--322771 Score: 283
Period size: 85 Copynumber: 2.9 Consensus size: 80
322526 TTGATGACAA
* * ** * * * *
322536 ATAACCCTTTTTGCCTTGAGTTATGCTATGAATGATGTGTCTTTGAGCTGAGTGGAATCAAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTC
* *
322601 GAAGGTCTTTGGCAG
66 AAAGGTCTTGGGCAG
*
322616 ATAACCCTTCTAGCCTTGAGTTATTCTACAAATGATGGTGCCTTTGAGCTGAGTGTAGTCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGAT-GTGCCTTTGAGCTGAGTGTAGTCGAACT
322681 CAAAGGTCTTGGGTTAACAG
65 CAAAGGTCTTGGG----CAG
* * * **
322701 ATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTC
322766 AAAGGT
66 AAAGGT
322772 TTTTTTGTTT
Statistics
Matches: 134, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 31 0.23
81 35 0.26
84 32 0.24
85 36 0.27
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (80 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTC
AAAGGTCTTGGGCAG
Found at i:322880 original size:38 final size:36
Alignment explanation
Indices: 322779--322880 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
322769 GGTTTTTTTG
* * * *
322779 TTTTAAGAGAAACTGTCTCATGGGAGACGAAATTTG
1 TTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
* *
322815 TTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
* *
322851 TTTTAAGAGAAAAGTAGTCTCAAGCGAGAC
1 TTTTAAGAG-AAACT-GTCTCAAGAGAGAC
322881 GACCCCTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 37 0.69
37 4 0.07
38 13 0.24
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:323363 original size:110 final size:110
Alignment explanation
Indices: 323128--323769 Score: 1008
Period size: 110 Copynumber: 5.9 Consensus size: 110
323118 GTATTATTTC
* * * **
323128 GAGTCCAATAT-CTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAAATGGGAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
* * *
323192 ACAGCCAG-CG-CCCATCGTTGTGAAGTTGAGCTTGTGTTGTCTT
66 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
*
323235 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-AAATAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA-AGTTGTTTGTT
**
323299 GACA-TACAGTCGCCCCTTTACTGTGAAGTTGAGCTTGTGTTGTCTT
65 GACAGT-CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
323345 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
* **
323410 ACAGTTAGTCGCCCCTTTACTGTGAAGTTGAGCTTGTGTTGTCTT
66 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * *
323455 GAGTCTAATATCATTCGCTGTGAAGTT-AAAATGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
323519 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
66 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * *
323564 GAGGCCAATATTCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
323629 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
66 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * *
323674 GAGTCCAATATCATTTGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
*
323739 ACAGTCAGTCTCCCCTTCGCTGTGAAGTTGA
66 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
323770 ACTACCACCA
Statistics
Matches: 495, Mismatches: 32, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
107 11 0.02
108 52 0.11
109 103 0.21
110 325 0.66
111 4 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (110 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:323544 original size:219 final size:218
Alignment explanation
Indices: 323128--323769 Score: 1006
Period size: 219 Copynumber: 2.9 Consensus size: 218
323118 GTATTATTTC
* * * **
323128 GAGTCCAATATCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAAATGGGAAGTTGTTTGTTGA
1 GAGTCCAATATCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
* * * *
323193 CAGCCAG-CGCCCATCGT-TGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCCTTCGCTGT
66 CAGTCAGTCGCCCCT-TTCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCATTCGCTGT
**
323256 GAAGTTGAAATTGACTCTGAATGAAACT-AAATAGTTGTTTGTTGACA-TACAGTCGCCCCTTTA
130 GAAGTTGAAATTGACTCTGAATGAAACTGAAA-AGTTGTTTGTTGACAGT-CAGTCGCCCCTTCG
323319 CTGTGAAGTTGAGCTTGTGTTGTCTT
193 CTGTGAAGTTGAGCTTGTGTTGTCTT
323345 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
1 GAGTCCAATAT-CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
*
323410 ACAGTTAGTCGCCCCTTTACTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCATTCGCTG
65 ACAGTCAGTCGCCCCTTT-CTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCATTCGCTG
*
323475 TGAAGTT-AAAATGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGC
129 TGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGC
323539 TGTGAAGTTGAGCTTGTGTTGTCTT
194 TGTGAAGTTGAGCTTGTGTTGTCTT
* *
323564 GAGGCCAATATTCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTG
1 GAGTCCAATA-TCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
* * * *
323629 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTTGCTA
65 ACAGTCAGTCGCCCCTT-TCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCATTCGCTG
*
323694 TGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCTCCCCTTCGC
129 TGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGC
323759 TGTGAAGTTGA
194 TGTGAAGTTGA
323770 ACTACCACCA
Statistics
Matches: 394, Mismatches: 22, Indels: 15
0.91 0.05 0.03
Matches are distributed among these distances:
217 11 0.03
218 55 0.14
219 206 0.52
220 122 0.31
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (218 bp):
GAGTCCAATATCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
CAGTCAGTCGCCCCTTTCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATATCATTCGCTGTG
AAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTG
TGAAGTTGAGCTTGTGTTGTCTT
Found at i:324835 original size:35 final size:35
Alignment explanation
Indices: 324789--324859 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
324779 CCAATTGCTC
324789 TAGAGGGACAACTCAAACTTTATTGTATATTATAA
1 TAGAGGGACAACTCAAACTTTATTGTATATTATAA
*
324824 TAGAGGGACAACTCAAGCTTTATTGTATATTATAA
1 TAGAGGGACAACTCAAACTTTATTGTATATTATAA
324859 T
1 T
324860 CACCTTTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (35 bp):
TAGAGGGACAACTCAAACTTTATTGTATATTATAA
Found at i:324891 original size:130 final size:133
Alignment explanation
Indices: 324691--324956 Score: 382
Period size: 130 Copynumber: 2.0 Consensus size: 133
324681 CCAATTGCTC
* * *
324691 TAGAGGGACAACTCAATATTATTGTATAGATATAATTATCACCTTTATCATGCTAGCTGAATATT
1 TAGAGGGACAACTCAATATTATTGTATA-ATATAATAATCACCTTTATCAGGCTAGCTAAATATT
* *
324756 ATCCATAAAGC-TGGGACGTTTAACCAATTGCTCTAGAGGGACAACTCAAACTTTATTGTATAT-
65 ATCCATAAAGCTTGGG-CATTTAACCAATTGCTCTAGAGAGACAACTCAAACTTTATTGTATATA
324819 TATAA
129 TATAA
*
324824 TAGAGGGACAACTCAAGCT-TTATTGTAT-AT-T-ATAATCACCTTTATCAGGCTAGCTAAATCT
1 TAGAGGGACAACTCAA--TATTATTGTATAATATAATAATCACCTTTATCAGGCTAGCTAAATAT
* *
324885 TATCCATAAAGCTTGGGCATTTAACCAATTGCTTTAGAGAGACAACTCAAGCTTTATTGTATATA
64 TATCCATAAAGCTTGGGCATTTAACCAATTGCTCTAGAGAGACAACTCAAACTTTATTGTATATA
324950 TATAA
129 TATAA
324955 TA
1 TA
324957 TTATAATATG
Statistics
Matches: 121, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
130 81 0.67
131 12 0.10
132 2 0.02
133 16 0.13
134 9 0.07
135 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (133 bp):
TAGAGGGACAACTCAATATTATTGTATAATATAATAATCACCTTTATCAGGCTAGCTAAATATTA
TCCATAAAGCTTGGGCATTTAACCAATTGCTCTAGAGAGACAACTCAAACTTTATTGTATATATA
TAA
Found at i:327454 original size:90 final size:91
Alignment explanation
Indices: 327301--327482 Score: 348
Period size: 90 Copynumber: 2.0 Consensus size: 91
327291 GACATATTGA
327301 CTAGTCTTCTGCCTTCGTCTGTCACCGATTGAATAACCTGTCGAACCGCTCCGGCTTCTCTAGAT
1 CTAGTCTTCTGCCTTCGTCTGTCACCGATTGAATAACCTGTCGAACCGCTCCGGCTTCTCTAGAT
327366 GAACC-GCAAATGTTGAGTTGCTTTT
66 GAACCAGCAAATGTTGAGTTGCTTTT
327391 CTAGTCTTCTGCCTTCGTCTGTCACCGATTGAATAACCTGTCGAACCGCTCCGGCTTCTCTAGAT
1 CTAGTCTTCTGCCTTCGTCTGTCACCGATTGAATAACCTGTCGAACCGCTCCGGCTTCTCTAGAT
327456 GAACCATGCAAATGTTGAGTTGCTTTT
66 GAACCA-GCAAATGTTGAGTTGCTTTT
327483 TGTACTGGCC
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
90 70 0.78
92 20 0.22
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (91 bp):
CTAGTCTTCTGCCTTCGTCTGTCACCGATTGAATAACCTGTCGAACCGCTCCGGCTTCTCTAGAT
GAACCAGCAAATGTTGAGTTGCTTTT
Found at i:329793 original size:2 final size:2
Alignment explanation
Indices: 329786--329818 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
329776 TACAAATTCC
329786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
329819 CTAACTCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338047 original size:21 final size:21
Alignment explanation
Indices: 338021--338076 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
338011 GGGAGCGTCA
338021 GTGCATCGATGCATACCCTAG
1 GTGCATCGATGCATACCCTAG
338042 GTGCATCGATGCATACCCTAG
1 GTGCATCGATGCATACCCTAG
*
338063 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
338077 CAGTGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATACCCTAG
Found at i:338264 original size:45 final size:46
Alignment explanation
Indices: 338179--338266 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
338169 AAATAGCCTG
* * *
338179 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATACATAAAATGCACTA
338225 AGTGCATCGATGCATGGT-ATGTGCATCGATACATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATACATAAAATGCA
338267 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATACATAAAATGCACTA
Found at i:339061 original size:64 final size:65
Alignment explanation
Indices: 338987--339143 Score: 178
Period size: 64 Copynumber: 2.4 Consensus size: 65
338977 CAATGAAGGT
* *
338987 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATACATTCGATGTTTCA-A-TATTAAGG
1 ATGCATCGATGCACTACTTGTGCATCGGTGCACT-AAATACATCCGATGTTT-ATATTATTAAGA
*
339049 GG
64 AG
** * * * *
339051 ATGCATCGATGCACGCCTTATGCATCGATGCACTAATTGCATCCGATGTTTATATTATTAAGAAG
1 ATGCATCGATGCACTACTTGTGCATCGGTGCACTAAATACATCCGATGTTTATATTATTAAGAAG
*
339116 -TACATCGATGCACTACTTGTGCATCGGT
1 ATGCATCGATGCACTACTTGTGCATCGGT
339144 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 1 0.01
64 66 0.87
65 9 0.12
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTGTGCATCGGTGCACTAAATACATCCGATGTTTATATTATTAAGAAG
Found at i:341626 original size:13 final size:13
Alignment explanation
Indices: 341608--341668 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
341598 AATAATATAC
*
341608 ATAATATATGTTT
1 ATAATATATATTT
341621 ATAATATATA--T
1 ATAATATATATTT
341632 AT-ATATATATCTT
1 ATAATATATAT-TT
*
341645 AT-ATATATATAT
1 ATAATATATATTT
341657 ATATATATATAT
1 ATA-ATATATAT
341669 AACGCATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 7 0.17
11 3 0.07
12 3 0.07
13 20 0.49
14 8 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (13 bp):
ATAATATATATTT
Found at i:341629 original size:2 final size:2
Alignment explanation
Indices: 341602--341669 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
341592 AATAAAAATA
* * *
341602 AT AT AC AT A- AT AT AT GT TT AT A- 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
*
341642 CT -T 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
341670 ACGCATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
1 3 0.05
2 54 0.95
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Done.