Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008258.1 Hibiscus syriacus cultivar Beakdansim tig00110911_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: 1617810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:319000 original size:46 final size:45
Alignment explanation
Indices: 318886--319021 Score: 115
Period size: 46 Copynumber: 3.0 Consensus size: 45
318876 ATAATTTTAG
* *
318886 TATAAATATATAC-ATATATAATAATATAAAG-TTTATAT-A-TATA
1 TATAACTATA-ACTATAAATAAT-ATATAAAGTTTTATATAAGTATA
*
318929 TATAACTATAAGTATAAATAATATATAAAGTTTTAGTATAAGTATA
1 TATAACTATAACTATAAATAATATATAAAGTTTTA-TATAAGTATA
* *
318975 TAT-ACTATATACTAATAAA-ACTATAT-AAGTATTAAATATAAGTATA
1 TATAACTATA-ACT-ATAAATAATATATAAAGT-TT-TATATAAGTATA
319021 T
1 T
319022 GTACATAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
42 9 0.12
43 21 0.27
44 3 0.04
45 11 0.14
46 28 0.36
47 6 0.08
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (45 bp):
TATAACTATAACTATAAATAATATATAAAGTTTTATATAAGTATA
Found at i:319231 original size:23 final size:25
Alignment explanation
Indices: 319196--319241 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
319186 ATAATAAATA
*
319196 ATATATAATAAAGTGTAAATATATT
1 ATATATAATAAAGTATAAATATATT
*
319221 ATATAT-A-AAAGTATAATTATA
1 ATATATAATAAAGTATAAATATA
319242 AAGACTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 1 0.05
25 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (25 bp):
ATATATAATAAAGTATAAATATATT
Found at i:319272 original size:22 final size:22
Alignment explanation
Indices: 319247--319425 Score: 127
Period size: 22 Copynumber: 8.1 Consensus size: 22
319237 TTATAAAGAC
*
319247 TAAAGTATATAGGCATATAATA
1 TAAAGTATATAGGTATATAATA
*
319269 TAAAGTATATAAGTATATAATA
1 TAAAGTATATAGGTATATAATA
*
319291 TAAAATATATAAGTGT-TA-AATA
1 TAAAGTATAT-AG-GTATATAATA
*
319313 TAAAGTATATACGTATATATATA
1 TAAAGTATATAGGTATATA-ATA
* * * *
319336 TATATA-CATACACGTCTATAATAA
1 TA-A-AGTATATAGGTATATAAT-A
*
319360 TAAAGTATATAAGTAT-TAAATA
1 TAAAGTATATAGGTATAT-AATA
* *
319382 TAAAGTATATAAGTAAAT-ATA
1 TAAAGTATATAGGTATATAATA
* * *
319403 TAAACTATA-AAGTATATATTA
1 TAAAGTATATAGGTATATAATA
319424 TA
1 TA
319426 TACTTTATAT
Statistics
Matches: 128, Mismatches: 17, Indels: 25
0.75 0.10 0.15
Matches are distributed among these distances:
20 9 0.07
21 18 0.14
22 61 0.48
23 22 0.17
24 17 0.13
25 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (22 bp):
TAAAGTATATAGGTATATAATA
Found at i:319449 original size:20 final size:19
Alignment explanation
Indices: 319417--319456 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
319407 CTATAAAGTA
319417 TATATTATATACTTTATAT
1 TATATTATATACTTTATAT
*
319436 TATACTTATGTACTTTATAT
1 TATA-TTATATACTTTATAT
319456 T
1 T
319457 TAAACTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (19 bp):
TATATTATATACTTTATAT
Found at i:319488 original size:20 final size:19
Alignment explanation
Indices: 319465--319603 Score: 74
Period size: 20 Copynumber: 7.0 Consensus size: 19
319455 TTTAAACTAT
319465 ATAAACTATATAATTTATA
1 ATAAACTATATAATTTATA
319484 CATAATA-TATATAATTTATA
1 -ATAA-ACTATATAATTTATA
* *
319504 AT----TACATAATATATAA
1 ATAAACTATATAATTTAT-A
** *
319520 ATAAGTTGTATATATTTA-A
1 ATAAACTATATA-ATTTATA
319539 ATATAATTCATATATAATTTATAA
1 ATA-AA--C-TATATAATTTAT-A
319563 ATAAACTATATAATTCATATTA
1 ATAAACTATATAATT--TA-TA
*
319585 ATAAACTATATAGTTTATA
1 ATAAACTATATAATTTATA
319604 TATGATTCAA
Statistics
Matches: 94, Mismatches: 9, Indels: 33
0.69 0.07 0.24
Matches are distributed among these distances:
15 10 0.11
16 3 0.03
19 8 0.09
20 33 0.35
21 6 0.06
22 22 0.23
23 8 0.09
24 4 0.04
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAAACTATATAATTTATA
Found at i:319573 original size:22 final size:22
Alignment explanation
Indices: 319547--319605 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
319537 AAATATAATT
319547 CATATATAATT-TATAAATAAA
1 CATATATAATTATATAAATAAA
*
319568 C-TATATAATTCATATTAATAAA
1 CATATATAATT-ATATAAATAAA
*
319590 C-TATATAGTTTATATA
1 CATATATA-ATTATATA
319606 TGATTCAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.28
21 1 0.03
22 20 0.62
23 2 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
CATATATAATTATATAAATAAA
Found at i:319647 original size:11 final size:11
Alignment explanation
Indices: 319633--319673 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
319623 TATAAACTCT
319633 ATAGTTTATAC
1 ATAGTTTATAC
*
319644 ATAG--TATAT
1 ATAGTTTATAC
319653 ATAGTTTATAC
1 ATAGTTTATAC
*
319664 ATAATTTATA
1 ATAGTTTATA
319674 TAGTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (11 bp):
ATAGTTTATAC
Found at i:319657 original size:20 final size:20
Alignment explanation
Indices: 319632--319821 Score: 95
Period size: 20 Copynumber: 9.2 Consensus size: 20
319622 ATATAAACTC
*
319632 TATAGTTTATACATAGTATA
1 TATAGTTTATACATAATATA
*
319652 TATAGTTTATACATAATTTA
1 TATAGTTTATACATAATATA
319672 TATAGTATATATTA-ACTATATATA
1 TATAGT-T-TA-TACA-TA-ATATA
* * *
319696 TAAACTATATACATAATATA
1 TATAGTTTATACATAATATA
*
319716 TATAGTATATA-ATAATATAAA
1 TATAGTTTATACATAATAT--A
* * ** *
319737 TATAAACTATATAGTTTATATA
1 TAT--AGTTTATACATAATATA
* *
319759 TATAG-TTA-ATATACA-CTA
1 TATAGTTTATACATA-ATATA
*
319777 TATAGTTTATATAATAA-ACTA
1 TATAGTTTATA-CATAATA-TA
*
319798 TATAGTTTACACATAATATA
1 TATAGTTTATACATAATATA
319818 TATA
1 TATA
319822 ATTCATTATA
Statistics
Matches: 132, Mismatches: 21, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
18 9 0.07
19 13 0.10
20 51 0.39
21 25 0.19
22 10 0.08
23 11 0.08
24 13 0.10
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (20 bp):
TATAGTTTATACATAATATA
Found at i:319691 original size:11 final size:13
Alignment explanation
Indices: 319677--319749 Score: 65
Period size: 13 Copynumber: 5.3 Consensus size: 13
319667 ATTTATATAG
*
319677 TATATATTAACTA
1 TATATATAAACTA
319690 TATATATAAACTA
1 TATATATAAACTA
* *
319703 TATACATAATATATA
1 TATATATAA-A-CTA
*
319718 TAGTATATAATAATA
1 TA-TATATAA-ACTA
*
319733 TAAATATAAACTA
1 TATATATAAACTA
319746 TATA
1 TATA
319750 GTTTATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
13 26 0.52
14 7 0.14
15 9 0.18
16 8 0.16
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:319710 original size:44 final size:43
Alignment explanation
Indices: 319659--319764 Score: 149
Period size: 43 Copynumber: 2.4 Consensus size: 43
319649 ATATATAGTT
* * *
319659 TATACATAATTTATATAGTATATATTAACTATATATATAAACTA
1 TATACATAATATATATAGTATATAATAA-TATAAATATAAACTA
319703 TATACATAATATATATAGTATATAATAATATAAATATAAACTA
1 TATACATAATATATATAGTATATAATAATATAAATATAAACTA
** *
319746 TATAGTTTATATATATAGT
1 TATACATAATATATATAGT
319765 TAATATACAC
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
43 30 0.54
44 26 0.46
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (43 bp):
TATACATAATATATATAGTATATAATAATATAAATATAAACTA
Found at i:319757 original size:52 final size:49
Alignment explanation
Indices: 319701--319821 Score: 118
Period size: 52 Copynumber: 2.4 Consensus size: 49
319691 ATATATAAAC
*
319701 TATATACATAATATATATAGTATATAATAATATAAATATAAACTATATAGTT
1 TATATACATAATATATATACTATATAAT-ATATAAA-ATAAACTATATAG-T
* * * * * *
319753 TATATATATAGTTAATATACACTATATAGTTTATATAATAAACTATATAGT
1 TATATACATA-AT-ATATATACTATATAATATATAAAATAAACTATATAGT
*
319804 T-TACACATAATATATATA
1 TATATACATAATATATATA
319822 ATTCATTATA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
48 6 0.11
49 1 0.02
50 6 0.11
51 2 0.04
52 22 0.39
53 6 0.11
54 13 0.23
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (49 bp):
TATATACATAATATATATACTATATAATATATAAAATAAACTATATAGT
Found at i:319777 original size:31 final size:31
Alignment explanation
Indices: 319714--319789 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
319704 ATACATAATA
*
319714 TATATAGTATATA-ATAATATAAATATAAAC
1 TATATAGTTTATATATAATATAAATATAAAC
* *
319744 TATATAGTTTATATAT-ATAGTTAATATACAC
1 TATATAGTTTATATATAATA-TAAATATAAAC
319775 TATATAGTTTATATA
1 TATATAGTTTATATA
319790 ATAAACTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
30 15 0.37
31 26 0.63
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (31 bp):
TATATAGTTTATATATAATATAAATATAAAC
Found at i:319780 original size:2 final size:2
Alignment explanation
Indices: 319648--319762 Score: 53
Period size: 2 Copynumber: 57.0 Consensus size: 2
319638 TTATACATAG
* * *
319648 TA TA TA TA GTT TA TA CA TA -A TT TA TA TA GTA TA TA T- TA -A CTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* *
319690 TA TA TA TA AA CTA TA TA CA TA -A TA TA TA TA GTA TA TA -A TA -A
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
319731 TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
319763 GTTAATATAC
Statistics
Matches: 84, Mismatches: 16, Indels: 26
0.67 0.13 0.21
Matches are distributed among these distances:
1 6 0.07
2 69 0.82
3 9 0.11
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:319815 original size:23 final size:21
Alignment explanation
Indices: 319757--319808 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
319747 ATAGTTTATA
*
319757 TATATAG-TTA-AT-ATACAC
1 TATATAGTTTACATAATAAAC
*
319775 TATATAGTTTATATAATAAAC
1 TATATAGTTTACATAATAAAC
319796 TATATAGTTTACA
1 TATATAGTTTACA
319809 CATAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 7 0.24
19 3 0.10
20 2 0.07
21 17 0.59
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (21 bp):
TATATAGTTTACATAATAAAC
Found at i:322184 original size:192 final size:194
Alignment explanation
Indices: 321798--322185 Score: 703
Period size: 192 Copynumber: 2.0 Consensus size: 194
321788 CTCCGGTGAG
321798 TGCTTGAAAGGATGGAGATATTTGTTGAATTATCAATCCCAAGCTGCATTTCGGTTTGCCTTGAA
1 TGCTTGAAAGGATGGAGATATTTGTTGAATTATCAATCCCAAGCTGCATTTCGGTTTGCCTTGAA
321863 TGGGTGGTACGAGATCATGACTTTGCTTTGTGGGGTGTTGTGGAACCCACAAGCAAACCGTTGCT
66 TGGGTGGTACGAGA--ATGACTTTGCTTTGTGGGGTGTTGTGGAACCCACAAGCAAACCGTTGCT
*
321928 TCAGTGGGGATTTTGATTCAACCACCATCGTTGATATACATTTTCCCATCGTCTTTGAGTTTTGG
129 TCAATGGGGATTTTGATTCAACCACCATCGTTGATATACATTTTCCCATCGTCTTTGAGTTTTGG
321993 T
194 T
321994 TGCTTGAAAGGATGGAGAT-TTTGTTGAATTTATCAATCCCAAGCTGCATTTCGGTTTGCCTTGA
1 TGCTTGAAAGGATGGAGATATTTGTTGAA-TTATCAATCCCAAGCTGCATTTCGGTTTGCCTTGA
322058 ATGGGTGGTACGAG-ATGACTTTGCTTTGTGGGGTGTTGTGGAACCCACAAGC-AACCGTTGCTT
65 ATGGGTGGTACGAGAATGACTTTGCTTTGTGGGGTGTTGTGGAACCCACAAGCAAACCGTTGCTT
322121 CAATGGGGATTTTGATTCAAACCA-CATCGTTGATATACATTTTCCCATCGTCTTTGAGTTTTGG
130 CAATGGGGATTTTGATTC-AACCACCATCGTTGATATACATTTTCCCATCGTCTTTGAGTTTTGG
322185 T
194 T
322186 GTGTCGACGA
Statistics
Matches: 189, Mismatches: 1, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
192 69 0.37
193 43 0.23
195 9 0.05
196 68 0.36
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (194 bp):
TGCTTGAAAGGATGGAGATATTTGTTGAATTATCAATCCCAAGCTGCATTTCGGTTTGCCTTGAA
TGGGTGGTACGAGAATGACTTTGCTTTGTGGGGTGTTGTGGAACCCACAAGCAAACCGTTGCTTC
AATGGGGATTTTGATTCAACCACCATCGTTGATATACATTTTCCCATCGTCTTTGAGTTTTGGT
Found at i:323743 original size:17 final size:19
Alignment explanation
Indices: 323716--323763 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
323706 TAGAAACTTA
323716 ATTTGATTAAAG-TATTTTT
1 ATTT-ATTAAAGATATTTTT
323735 -TTTATTAAAGCATATTTTT
1 ATTTATTAAAG-ATATTTTT
323754 ACTTTATTAA
1 A-TTTATTAA
323764 TGTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 7 0.28
21 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTATTAAAGATATTTTT
Found at i:326680 original size:20 final size:22
Alignment explanation
Indices: 326641--326683 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
326631 CAAAAATCAA
*
326641 TATATAAAAATATATATTATGT
1 TATATAAAAATACATATTATGT
326663 TATATAAAAAT-CAT-TTATGT
1 TATATAAAAATACATATTATGT
326683 T
1 T
326684 TATCAATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TATATAAAAATACATATTATGT
Found at i:334766 original size:3 final size:3
Alignment explanation
Indices: 334758--334843 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
334748 AAAATTCAAC
334758 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
334806 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
334844 TACATCAATC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:336335 original size:65 final size:65
Alignment explanation
Indices: 336197--336338 Score: 150
Period size: 65 Copynumber: 2.2 Consensus size: 65
336187 CACTAGGTGC
*
336197 ATTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCGATGCATA
1 ATTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAACTCTGAGTACATCGATGCATA
336262 G
65 G
* ** *
336263 -TAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCA-ATTTATTCCATG-GTACATCGATGC
1 AT-TGGTGCATCGATGCATCAAATGCATTCGATGTTTCATA-AAACT-C-TGAGTACATCGATGC
*
336323 ATGG
62 ATAG
336327 ATTGGTGCATCG
1 ATTGGTGCATCG
336339 GTTCATCACT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
62 1 0.02
63 6 0.09
64 16 0.25
65 40 0.62
66 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (65 bp):
ATTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAACTCTGAGTACATCGATGCATAG
Found at i:352315 original size:6 final size:6
Alignment explanation
Indices: 352304--352411 Score: 207
Period size: 6 Copynumber: 18.0 Consensus size: 6
352294 GATCAATACG
*
352304 TACACA TACACA TACACA TGCACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
352352 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
352400 TACACA TACACA
1 TACACA TACACA
352412 CATTACCATA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 100 1.00
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.17
Consensus pattern (6 bp):
TACACA
Found at i:367019 original size:41 final size:40
Alignment explanation
Indices: 366932--367038 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 40
366922 TTCTCAATTA
* * **
366932 CTAAGTCCTTCGGGCCATCTAAAAGTTTTCTGAGCCTAATG
1 CTAAGTCCTT-GGGCCATCTATAAGTCTTCTGAGCAGAATG
*
366973 CTAAGTCCTATGGGCCATCTATAAGTCTTCTGAGCAGGATG
1 CTAAGTCCT-TGGGCCATCTATAAGTCTTCTGAGCAGAATG
* **
367014 TTAAGTCCTCCAGGCCATCTATAAG
1 CTAAGTCCT-TGGGCCATCTATAAG
367039 ACCACTGGGC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 55 0.98
42 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (40 bp):
CTAAGTCCTTGGGCCATCTATAAGTCTTCTGAGCAGAATG
Found at i:371515 original size:5 final size:5
Alignment explanation
Indices: 371492--371537 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
371482 TTTAACTCAA
* * *
371492 TTTAT TTCAT TTAAG TTTAT TTTAT TTTAT TTTAT TTTCAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT
371538 CGTATGCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:390327 original size:16 final size:16
Alignment explanation
Indices: 390302--390333 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
390292 AAAAAAAATT
*
390302 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
390318 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
390334 CTTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:393491 original size:85 final size:85
Alignment explanation
Indices: 393382--393537 Score: 242
Period size: 85 Copynumber: 1.8 Consensus size: 85
393372 ATTTTAAACA
* *
393382 TTATATTTGTTTTAAGTATTTTAGTTTAAATAGGTTTT-AGTATTTCAATTAGGATTTAGGATAT
1 TTATATTTGTTTTAAGTATTTTAGTTTAAATA-GTTTTAAGTATTTCAATTAAGATTTAAGATAT
393446 TATTTTAAATATTATTTTATT
65 TATTTTAAATATTATTTTATT
* * * *
393467 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAAGATTTAAGATATT
1 TTATATTTGTTTTAAGTATTTTAGTTTAAATAGTTTTAAGTATTTCAATTAAGATTTAAGATATT
393532 ATTTTA
66 ATTTTA
393538 GGAATTATCT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
84 5 0.08
85 59 0.92
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.56
Consensus pattern (85 bp):
TTATATTTGTTTTAAGTATTTTAGTTTAAATAGTTTTAAGTATTTCAATTAAGATTTAAGATATT
ATTTTAAATATTATTTTATT
Found at i:399603 original size:21 final size:21
Alignment explanation
Indices: 399574--399617 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
399564 GTTTCATTAT
*
399574 AGGAATTCATGGCCTCGACAA
1 AGGAATTCATGGCCTCAACAA
* *
399595 AGGATTTCATGGCTTCAACAA
1 AGGAATTCATGGCCTCAACAA
399616 AG
1 AG
399618 ACCCTGATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (21 bp):
AGGAATTCATGGCCTCAACAA
Found at i:403900 original size:14 final size:15
Alignment explanation
Indices: 403881--403915 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
403871 TTATGCACTA
403881 TTTATTTAT-TTTAC
1 TTTATTTATGTTTAC
*
403895 TTTATTTATGTTTTC
1 TTTATTTATGTTTAC
403910 TTTATT
1 TTTATT
403916 GTAGGCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTATTTATGTTTAC
Found at i:418039 original size:6 final size:6
Alignment explanation
Indices: 418028--418072 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
418018 ACTAGAGTAC
418028 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAA
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAA
418073 CTTGAAGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:419038 original size:27 final size:27
Alignment explanation
Indices: 419019--419079 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
419009 AAAATATTTT
419019 ATATATAATTAATATAAAAAATATAAA
1 ATATATAATTAATATAAAAAATATAAA
*
419046 ATATTTAATTAATATAAAAAATATAAA
1 ATATATAATTAATATAAAAAATATAAA
419073 ATATATA
1 ATATATA
419080 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATATAATTAATATAAAAAATATAAA
Found at i:419070 original size:9 final size:9
Alignment explanation
Indices: 419029--419079 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
419019 ATATATAATT
419029 AATATAAAA
1 AATATAAAA
419038 AATATAAAA
1 AATATAAAA
* * **
419047 TATTTAATT
1 AATATAAAA
419056 AATATAAAA
1 AATATAAAA
419065 AATATAAAA
1 AATATAAAA
*
419074 TATATA
1 AATATA
419080 TATATATATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AATATAAAA
Found at i:419165 original size:22 final size:22
Alignment explanation
Indices: 419131--419179 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
419121 CCTTGCCCCG
* *
419131 ATCCCGAACCCAACCCGAAAAA
1 ATCCCGAAACCAACCCAAAAAA
*
419153 ATCCCTAAACCAACCCAAAAAA
1 ATCCCGAAACCAACCCAAAAAA
419175 ATCCC
1 ATCCC
419180 CGATACCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.41, G:0.04, T:0.08
Consensus pattern (22 bp):
ATCCCGAAACCAACCCAAAAAA
Found at i:426333 original size:17 final size:17
Alignment explanation
Indices: 426311--426346 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
426301 TTTAATCCTA
426311 TTCATGTTTATGAAATT
1 TTCATGTTTATGAAATT
426328 TTCATGTTTATGAAATT
1 TTCATGTTTATGAAATT
426345 TT
1 TT
426347 TGGCATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (17 bp):
TTCATGTTTATGAAATT
Found at i:427966 original size:19 final size:19
Alignment explanation
Indices: 427942--427988 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
427932 TGAGGTTACG
427942 AAAAGAAAAA-AAAAGAGAA
1 AAAAGAAAAAGAAAA-AGAA
427961 AAAAGAAAAAGAAAAAGAA
1 AAAAGAAAAAGAAAAAGAA
427980 AGAAAGAAA
1 A-AAAGAAA
427989 TAACACTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAAAGAA
Found at i:427969 original size:6 final size:6
Alignment explanation
Indices: 427942--427980 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
427932 TGAGGTTACG
427942 AAAAGA AAAA-A AAAGAGAA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAA-AG-A AAAAGA AAAAGA AAAAGA AA
427981 GAAAGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 2 0.07
8 4 0.13
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:427971 original size:15 final size:15
Alignment explanation
Indices: 427941--427984 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
427931 TTGAGGTTAC
427941 GAAAAGAAAA-AAAAA
1 GAAAA-AAAAGAAAAA
*
427956 GAGAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
427971 GAAAAAGAAAGAAA
1 GAAAAA-AAAGAAA
427985 GAAATAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 14 0.56
16 7 0.28
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:437762 original size:21 final size:22
Alignment explanation
Indices: 437732--437773 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
437722 TAAATGTCCA
437732 TCATTATTTA-TATTTACATTT
1 TCATTATTTATTATTTACATTT
* *
437753 TCATTCTTTATTCTTTACATT
1 TCATTATTTATTATTTACATT
437774 CATTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (22 bp):
TCATTATTTATTATTTACATTT
Found at i:441268 original size:24 final size:25
Alignment explanation
Indices: 441236--441298 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
441226 AATATGCTTG
* *
441236 AAGAAGAAAAAAAG-AACAAATAAA
1 AAGATGAAAAAAAGAAAAAAATAAA
*
441260 AAGATGAAAAAATGAAAAAAATAAA
1 AAGATGAAAAAAAGAAAAAAATAAA
441285 AAGAAATGAAAAAA
1 AAG--ATGAAAAAA
441299 TGAATAGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.36
25 12 0.36
27 9 0.27
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.08
Consensus pattern (25 bp):
AAGATGAAAAAAAGAAAAAAATAAA
Found at i:441269 original size:8 final size:8
Alignment explanation
Indices: 441241--441302 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
441231 GCTTGAAGAA
*
441241 GAAAAAAA
1 GAAAAAAT
*
441249 GAACAAAT
1 GAAAAAAT
441257 -AAAAAGAT
1 GAAAAA-AT
441265 GAAAAAAT
1 GAAAAAAT
441273 GAAAAAAAT
1 G-AAAAAAT
*
441282 AAAAAGAAAT
1 -GAAA-AAAT
441292 GAAAAAAT
1 GAAAAAAT
441300 GAA
1 GAA
441303 TAGAGAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.09
8 18 0.41
9 18 0.41
10 4 0.09
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.10
Consensus pattern (8 bp):
GAAAAAAT
Found at i:441301 original size:27 final size:25
Alignment explanation
Indices: 441236--441302 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 25
441226 AATATGCTTG
* * *
441236 AAGAAGAAAAAAAG-AACAAATAAA
1 AAGATGAAAAAATGAAAAAAATAAA
441260 AAGATGAAAAAATGAAAAAAATAAA
1 AAGATGAAAAAATGAAAAAAATAAA
441285 AAGAAATGAAAAAATGAA
1 AAG--ATGAAAAAATGAA
441303 TAGAGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.32
25 12 0.32
27 13 0.35
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.09
Consensus pattern (25 bp):
AAGATGAAAAAATGAAAAAAATAAA
Found at i:442601 original size:240 final size:239
Alignment explanation
Indices: 442177--442975 Score: 978
Period size: 240 Copynumber: 3.3 Consensus size: 239
442167 GGAGGTGAAC
* ** *
442177 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACATAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAAGAAGTTCATA
*
442242 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCAAATCAGTGACACCTCGCTTG
65 ATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGGCATTTCAAATCAGTGACACCTCGCTTG
*
442307 AGGGATTGACATTTTCAAAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAA
130 AGGGATTGACATTTTCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAA
*
442372 TGAGAATAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGAT
195 TGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGAT-GAT
* * * *
442418 CAACATTTCCAATGGAGAGTTCATACTGAAAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAA
1 CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
* *
442483 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGTATTTCAAATCAGTGACACCTCGCTTGA
66 TGAGAAGAACTTGTTCGACCTATCACTCGATTCACGGCATTTCAAATCAGTGACACCTCGCTTGA
* *
442548 GGGATTGACATTTTCAAAAGAGTTCATAATGAGAAAAACTCGTCCTAAAGGAGAAAGTTCATGAT
131 GGGATTGACATTTTCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAAT
*
442613 GAGAAGAACTTGTTCCTTTCAAGTCCATCATAGAAAGAGATAGAT
196 GAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGAT-GAT
* * * * *
442658 CGACATTTACAATGAAGAGTTTATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTTATAA
1 CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
* * * * * * * *
442723 TGAGAAGAACTTGTTCAACTTCGCATCAACAT--TTTCAATGGAGAATTCATAATGAGAAGA-AC
66 TGAGAAGAACTTGTTCGAC--C-TATC-AC-TCGATTC-ACGG-CATTTCA-AATCAG-TGACAC
** * * * *
442785 TCATC-C--GAAAGA--GAGA-----GAATGAATTCATAATGAGAAGAACTCGTCCTAAAGGAGA
122 -C-TCGCTTGAGGGATTGACATTTTCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGA
* * * * *
442840 AAGTTCATAATGAAAAGAACTTGTTCCTTTCAAGTCCACCACAAAAATAGGTGACT
185 AAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGA-T
* * *
442896 CAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCC-ACGAGAGAGAATAAGTTCATAA
1 CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
442960 TGAGAAGAACTTGTTC
66 TGAGAAGAACTTGTTC
442976 AATCCAACGA
Statistics
Matches: 495, Mismatches: 51, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
237 36 0.07
238 119 0.24
240 261 0.53
241 41 0.08
242 1 0.00
243 9 0.02
244 5 0.01
245 10 0.02
246 7 0.01
247 4 0.01
248 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (239 bp):
CAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCGACCTATCACTCGATTCACGGCATTTCAAATCAGTGACACCTCGCTTGA
GGGATTGACATTTTCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAAT
GAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGAT
Found at i:442814 original size:40 final size:37
Alignment explanation
Indices: 442764--442860 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 37
442754 TTTTCAATGG
442764 AGAATTCATAATGAGAAGAACTCATCCGAAAGAGAGAGA
1 AGAATTCATAATGAGAAGAACTCATCCGAAAG-GAGA-A
* *
442803 ATGAATTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 A-GAATTCATAATGAGAAGAACTCATCCGAAAGGAGAA
*
442841 AG--TTCATAATGAAAAGAACT
1 AGAATTCATAATGAGAAGAACT
442861 TGTTCCTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
35 17 0.31
37 1 0.02
38 2 0.04
39 5 0.09
40 29 0.54
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (37 bp):
AGAATTCATAATGAGAAGAACTCATCCGAAAGGAGAA
Found at i:443119 original size:3 final size:3
Alignment explanation
Indices: 443104--443178 Score: 134
Period size: 3 Copynumber: 25.3 Consensus size: 3
443094 GGTTAAAGAA
*
443104 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
443151 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
443179 TTGTGCAGGC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 1 0.01
3 68 0.99
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:452283 original size:27 final size:26
Alignment explanation
Indices: 452252--452318 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
452242 TTAATGACCA
* *
452252 TTTTAAGTTCTTCTTAATCTTTAATCC
1 TTTTAA-TTCTTCTTAACCATTAATCC
* *
452279 TTTTAATTTCTTTTTAACCATTATTCC
1 TTTTAA-TTCTTCTTAACCATTAATCC
452306 TTTTAATT-TTCTT
1 TTTTAATTCTTCTT
452319 TAAATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 4 0.12
26 2 0.06
27 28 0.82
ACGTcount: A:0.21, C:0.16, G:0.01, T:0.61
Consensus pattern (26 bp):
TTTTAATTCTTCTTAACCATTAATCC
Found at i:462453 original size:21 final size:21
Alignment explanation
Indices: 462429--462468 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
462419 ATATTAATCT
*
462429 TAATAGTAGTATTGATACTAA
1 TAATAGAAGTATTGATACTAA
*
462450 TAATAGAAGTGTTGATACT
1 TAATAGAAGTATTGATACT
462469 TAAGATTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (21 bp):
TAATAGAAGTATTGATACTAA
Found at i:474586 original size:24 final size:24
Alignment explanation
Indices: 474559--474618 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
474549 ATCAAAATGT
*
474559 AGGTCAAGTATTGGATAAGAATCC
1 AGGTCAAGTATTCGATAAGAATCC
* * *
474583 AGGTAAAGTATCCGATCAGAATCC
1 AGGTCAAGTATTCGATAAGAATCC
*
474607 AGGTCAGGTATT
1 AGGTCAAGTATT
474619 ATAATATAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (24 bp):
AGGTCAAGTATTCGATAAGAATCC
Found at i:475778 original size:18 final size:18
Alignment explanation
Indices: 475757--475791 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
475747 TTCTATCCGG
*
475757 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
475775 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
475792 TTCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:480750 original size:16 final size:16
Alignment explanation
Indices: 480729--480759 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
480719 TAGTGTGAGT
480729 TATCCGTAATAGGAGC
1 TATCCGTAATAGGAGC
480745 TATCCGTAATAGGAG
1 TATCCGTAATAGGAG
480760 TTATGGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (16 bp):
TATCCGTAATAGGAGC
Found at i:486391 original size:51 final size:51
Alignment explanation
Indices: 486336--486475 Score: 153
Period size: 51 Copynumber: 2.8 Consensus size: 51
486326 GCTCTATGTC
* *
486336 CCGCGCTATATACTGATTTGGC-GCCACGTGGGGTATAGCGCGCCCCCTG-T
1 CCGCGCTATAT-CTGATTTGGCTGACACGTGGGGTATAGCGCGACCCCTGAT
** *
486386 ACCGCGCTATATGCTGACATGGCTTACACGT-GGGTATAGCGCGACCCCTGAT
1 -CCGCGCTATAT-CTGATTTGGCTGACACGTGGGGTATAGCGCGACCCCTGAT
* **
486438 CCGCACTATATCTG-TTTATCTGACACGTGGGGTATAGC
1 CCGCGCTATATCTGATTTGGCTGACACGTGGGGTATAGC
486476 ACGGTACAGG
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
49 9 0.12
50 12 0.16
51 47 0.64
52 6 0.08
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.26
Consensus pattern (51 bp):
CCGCGCTATATCTGATTTGGCTGACACGTGGGGTATAGCGCGACCCCTGAT
Found at i:486591 original size:12 final size:10
Alignment explanation
Indices: 486562--486589 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
486552 ATCACACCAT
486562 ATTCTCTCAA
1 ATTCTCTCAA
486572 ATTCTCTCAA
1 ATTCTCTCAA
486582 ATTCTCTC
1 ATTCTCTC
486590 TCTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTCTCTCAA
Found at i:488903 original size:29 final size:29
Alignment explanation
Indices: 488860--488940 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
488850 CTCACCTAAC
488860 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
488890 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
488919 TAAATGATGTAAGCAATGACAT
1 TAAATGATGTAAGCAATGACAT
488941 AAATTTAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:491632 original size:16 final size:16
Alignment explanation
Indices: 491588--491633 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
491578 TTTACAATAC
491588 ATAT-TATTTA-TATA
1 ATATATATTTATTATA
491602 ATATATAATTT-TTATA
1 ATATAT-ATTTATTATA
*
491618 ATCTATATTTATTATA
1 ATATATATTTATTATA
491634 TTAAATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 18 0.67
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATATTTATTATA
Found at i:492618 original size:12 final size:12
Alignment explanation
Indices: 492596--492642 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
492586 ATACTATTTT
492596 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
492609 TTATTTTTAAAA
1 TTATTTTTAAAA
492621 TTA-TTTTAAAA
1 TTATTTTTAAAA
492632 TATATTTTTAA
1 T-TATTTTTAA
492643 GGTGTTCGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.28
12 13 0.41
13 10 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:493963 original size:16 final size:17
Alignment explanation
Indices: 493942--493976 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
493932 CTCCCCCTTA
493942 CTTT-AACACTTCTCCC
1 CTTTAAACACTTCTCCC
493958 CTTTAAAACACTTCTCCC
1 CTTT-AAACACTTCTCCC
493976 C
1 C
493977 CTTTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
18 13 0.76
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (17 bp):
CTTTAAACACTTCTCCC
Found at i:495819 original size:23 final size:24
Alignment explanation
Indices: 495787--495850 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
495777 TGATTCCCTC
495787 AAGGAGGGAATCGGTTCCCATTCA
1 AAGGAGGGAATCGGTTCCCATTCA
*
495811 AAGGA-GGAATCGGTTCCCCTTC-
1 AAGGAGGGAATCGGTTCCCATTCA
* *
495833 AAGG-GGGTATCGATTCCC
1 AAGGAGGGAATCGGTTCCC
495851 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 15 0.42
23 16 0.44
24 5 0.14
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (24 bp):
AAGGAGGGAATCGGTTCCCATTCA
Found at i:495844 original size:22 final size:22
Alignment explanation
Indices: 495769--495850 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
495759 ATAACCCATT
* *
495769 GGGGGTATTGATT-CCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
495789 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
* *
495813 GGAGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
495835 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
495851 TCTGCCCTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.04
21 8 0.16
22 17 0.35
23 18 0.37
24 4 0.08
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:504648 original size:9 final size:9
Alignment explanation
Indices: 504624--504654 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
504614 GATATAATAA
504624 TAATATTAT
1 TAATATTAT
504633 T-ATATTAT
1 TAATATTAT
504641 TAATATTAT
1 TAATATTAT
504650 TAATA
1 TAATA
504655 CTGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATATTAT
Found at i:505113 original size:21 final size:21
Alignment explanation
Indices: 505059--505118 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
505049 CGTCCGAATT
*
505059 ACCCGCGATGGCCTCAATAGC
1 ACCCGCGATGGCCGCAATAGC
** ** *
505080 GTCCATGACGGCCGCAATAGC
1 ACCCGCGATGGCCGCAATAGC
505101 ACCCGCGATGGCCGCAAT
1 ACCCGCGATGGCCGCAAT
505119 CACGGAAAAT
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.37, G:0.27, T:0.13
Consensus pattern (21 bp):
ACCCGCGATGGCCGCAATAGC
Found at i:506962 original size:20 final size:20
Alignment explanation
Indices: 506929--506996 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
506919 TCCTAATTCA
* *
506929 CAATGTGAATACGTAAATGG
1 CAATGCGAATACGTAAATCG
*
506949 CAATGCGACA-ACGTAAATTG
1 CAATGCGA-ATACGTAAATCG
506969 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
506989 CAATGCGA
1 CAATGCGA
506997 TTTACATAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:507199 original size:22 final size:22
Alignment explanation
Indices: 507174--507239 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
507164 GGCGACATCC
507174 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
507196 GTCCCCATCTCCGTCGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
507218 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
507240 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:507664 original size:20 final size:20
Alignment explanation
Indices: 507576--507665 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
507566 GCGATTCTTT
507576 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
507595 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
** * *
507615 CGTTGCGATAGTCTTTTTCA
1 CGTTGCGATTTTCATTTTCG
*
507635 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
507655 TGTTGCGATTT
1 CGTTGCGATTT
507666 AAAGTTTCAG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
19 12 0.21
20 46 0.79
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:507673 original size:20 final size:20
Alignment explanation
Indices: 507630--507674 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
507620 CGATAGTCTT
** *
507630 TTTCATGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTAAAG
*
507650 TTTCGTGTTGCGATTTAAAG
1 TTTCATGTTGCGATTTAAAG
507670 TTTCA
1 TTTCA
507675 GAAACTACTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTAAAG
Found at i:509579 original size:20 final size:20
Alignment explanation
Indices: 509554--509732 Score: 143
Period size: 20 Copynumber: 9.6 Consensus size: 20
509544 AGAATAGTTT
509554 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
509574 ACTATCGCAATGAGAAAATG
1 ACTATCGCAATGCGAAAATG
*
509594 ACTATCGCAAT--G-AGA-G
1 ACTATCGCAATGCGAAAATG
* *
509610 A--ATCACAATGCG-AAATA
1 ACTATCGCAATGCGAAAATG
**
509627 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
509643 A--ATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
509661 TCTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
509681 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
**
509701 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
509721 ACTATCGCAATG
1 ACTATCGCAATG
509733 AAAGAATCGC
Statistics
Matches: 130, Mismatches: 15, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 14 0.11
16 8 0.06
17 7 0.05
18 3 0.02
19 6 0.05
20 92 0.71
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:509802 original size:20 final size:20
Alignment explanation
Indices: 509775--509862 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
509765 GCGATTCTCT
**
509775 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
509795 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
509815 CGTTGCGATAATCATTTTCA
1 CGTTGCGATAGTCATTTTCG
509835 CGTTGCGATAGTCATTTT-G
1 CGTTGCGATAGTCATTTTCG
509854 CGTTGCGAT
1 CGTTGCGAT
509863 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 9 0.15
20 51 0.85
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:509873 original size:39 final size:40
Alignment explanation
Indices: 509797--509873 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
509787 CAAATTCGCA
* *
509797 TTGCGATAGTCATTTTCGCGTTGCGATAATCATTTTCACG
1 TTGCGATAGTCATTTTCGCGTTGCGATAATAAGTTTCACG
**
509837 TTGCGATAGTCATTTT-GCGTTGCGATTTTAAGTTTCA
1 TTGCGATAGTCATTTTCGCGTTGCGATAATAAGTTTCA
509874 GATTCTATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (40 bp):
TTGCGATAGTCATTTTCGCGTTGCGATAATAAGTTTCACG
Found at i:510416 original size:41 final size:41
Alignment explanation
Indices: 510341--510433 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
510331 AGCCCGACTC
** * *
510341 ACCTGTCATCGTTCAAGAGTCCTCCCCTATCGTTCAAGAGG
1 ACCTGTCATCCCTCAAGAGTCCTCCCCCACCGTTCAAGAGG
*
510382 ACCTGTCATCCCTCAAGAGTCC-CCTCCCACCGTTCATGAGG
1 ACCTGTCATCCCTCAAGAGTCCTCC-CCCACCGTTCAAGAGG
*
510423 CCACTGTCATC
1 AC-CTGTCATC
510434 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.05
41 34 0.77
42 8 0.18
ACGTcount: A:0.20, C:0.38, G:0.17, T:0.25
Consensus pattern (41 bp):
ACCTGTCATCCCTCAAGAGTCCTCCCCCACCGTTCAAGAGG
Found at i:511999 original size:14 final size:14
Alignment explanation
Indices: 511980--512033 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
511970 GGAAATGACT
511980 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
511994 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
512013 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
512027 ATCGCAA
1 ATCGCAA
512034 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:512048 original size:34 final size:33
Alignment explanation
Indices: 511960--512055 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
511950 AAAACAGACT
* **
511960 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
511994 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
512027 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
512056 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:512051 original size:20 final size:19
Alignment explanation
Indices: 511993--512060 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
511983 GCAACGAGAG
511993 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
512012 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
512026 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
512046 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
512061 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:512111 original size:14 final size:14
Alignment explanation
Indices: 512092--512146 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
512082 CATTTTCGCA
512092 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
512106 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
512123 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
512139 TTGCGATT
1 TTGCGATT
512147 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:512127 original size:33 final size:33
Alignment explanation
Indices: 512070--512164 Score: 181
Period size: 33 Copynumber: 2.8 Consensus size: 33
512060 ACTAAATTCG
512070 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
512104 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
512137 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
512165 AGTCAATTCC
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:512183 original size:20 final size:20
Alignment explanation
Indices: 512158--512230 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
512148 TCATTTCGCA
512158 TTGCGATAGTCAATTCCGCG
1 TTGCGATAGTCAATTCCGCG
* *
512178 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCAATTCCGCG
512198 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCA-ATTCCGCG
512218 TTGCGATAGTCAA
1 TTGCGATAGTCAA
512231 ATGAATGTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 1 0.02
20 45 0.94
21 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAATTCCGCG
Found at i:514678 original size:24 final size:24
Alignment explanation
Indices: 514644--514693 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
514634 CTGAAAAATC
514644 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
514668 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
514692 AT
1 AT
514694 TAAATTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:515568 original size:20 final size:20
Alignment explanation
Indices: 515543--515605 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
515533 TAAGTATTGT
*
515543 GATAGTTAGAATCTCGTTGC
1 GATAGTCAGAATCTCGTTGC
515563 GATAGTCAGAATCTCGTTGC
1 GATAGTCAGAATCTCGTTGC
* *
515583 GATAGTCAGATTCGCGTTGC
1 GATAGTCAGAATCTCGTTGC
515603 GAT
1 GAT
515606 TTACATATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (20 bp):
GATAGTCAGAATCTCGTTGC
Found at i:515615 original size:20 final size:20
Alignment explanation
Indices: 515592--515724 Score: 212
Period size: 20 Copynumber: 6.7 Consensus size: 20
515582 CGATAGTCAG
* *
515592 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
515612 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
515632 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
515652 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
515672 TTTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
515692 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
515712 ATTCGCATTGCGA
1 ATTCGCATTGCGA
515725 ATTAGGAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 103 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:515745 original size:21 final size:21
Alignment explanation
Indices: 515721--515766 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
515711 TATTCGCATT
515721 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
515742 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
515763 GCGA
1 GCGA
515767 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:515787 original size:41 final size:40
Alignment explanation
Indices: 515742--515829 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
515732 AAATCGCAAC
*
515742 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAGA-ATCGCGTT
1 GCGAATTTGGAAAAT-G-ATATGCGATA-CCAGAGATCGCGTT
* * *
515783 GCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
515823 GCGAATT
1 GCGAATT
515830 ATCGATCGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 5 0.12
40 22 0.55
41 13 0.32
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (40 bp):
GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
Found at i:517927 original size:64 final size:65
Alignment explanation
Indices: 517858--518045 Score: 190
Period size: 65 Copynumber: 2.9 Consensus size: 65
517848 GGCTGTCCAA
517858 GTGCATCAGTGCAT-AAATCAACTTCGATGTTTCAA-AATAGC-CAGAGTGCATCGATGCATGGC
1 GTGCATCAGTGCATAAAATCAA-TTCGATGTTTCAATAATA-CACAGAGTGCATCGATGCATGGC
517920 TT
64 TT
* * * *
517922 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATAGAGTGCATCGATGCAT-GATA
1 GTGCATCAGTGCATAAAATCAATTCGATGTTTCAATAATACACAGAGTGCATCGATGCATGGCT-
517986 T
65 T
* * * * * * * *
517987 GTGCATCGGTACACAAAAGCTATTCGATG-TTCAATTAAAACA-AGGGTGCATTGATGCAT
1 GTGCATCAGTGCATAAAATCAATTCGATGTTTCAA-TAATACACAGAGTGCATCGATGCAT
518046 TGATTTATGA
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
64 47 0.44
65 60 0.56
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (65 bp):
GTGCATCAGTGCATAAAATCAATTCGATGTTTCAATAATACACAGAGTGCATCGATGCATGGCTT
Found at i:517979 original size:65 final size:64
Alignment explanation
Indices: 517858--518017 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
517848 GGCTGTCCAA
* *
517858 GTGCATCAGTGCAT-AAATCAACTTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-
1 GTGCATCGGTGCATAAAATCAA-TTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCAT-GATA
517921 T
64 T
* *
517922 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATA-CATAGAGTGCATCGATGCATGATA
1 GTGCATCGGTGCATAAAATCAATTCGATGTTTCAA-AATAGC-CAGAGTGCATCGATGCATGATA
517986 T
64 T
* * * *
517987 GTGCATCGGTACACAAAAGCTATTCGATGTT
1 GTGCATCGGTGCATAAAATCAATTCGATGTT
518018 CAATTAAAAC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 28 0.33
65 56 0.67
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (64 bp):
GTGCATCGGTGCATAAAATCAATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGATAT
Found at i:520575 original size:43 final size:45
Alignment explanation
Indices: 520527--520623 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
520517 GGCAGTGTGC
* *
520527 ATCGATGCACATTC-AA-GTAGTG-ATCGGTGCATCTTCAT-GATGT
1 ATCGATGCACATTCAAAGGTAG-GCATCGATGCACCTTCATAG-TGT
520570 ATCGATGCACATTCAAAGGTAGGCATCGATGCACCTTCATAGTGT
1 ATCGATGCACATTCAAAGGTAGGCATCGATGCACCTTCATAGTGT
520615 ATCGATGCA
1 ATCGATGCA
520624 TTATGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
43 14 0.29
44 3 0.06
45 30 0.62
46 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (45 bp):
ATCGATGCACATTCAAAGGTAGGCATCGATGCACCTTCATAGTGT
Found at i:520584 original size:21 final size:22
Alignment explanation
Indices: 520527--520623 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 22
520517 GGCAGTGTGC
520527 ATCGATGCACATTCAAGTAGTG
1 ATCGATGCACATTCAAGTAGTG
* *
520549 ATCGGTGCATC-TTCATG-A-TG
1 ATCGATGCA-CATTCAAGTAGTG
520569 TATCGATGCACATTCAAAGGTAG-G
1 -ATCGATGCACATTC-AA-GTAGTG
*
520593 CATCGATGCACCTTC-A-TAGTG
1 -ATCGATGCACATTCAAGTAGTG
520614 TATCGATGCA
1 -ATCGATGCA
520624 TTATGCACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
20 6 0.10
21 22 0.37
22 15 0.25
23 2 0.03
24 15 0.25
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (22 bp):
ATCGATGCACATTCAAGTAGTG
Found at i:526441 original size:64 final size:64
Alignment explanation
Indices: 526372--526495 Score: 148
Period size: 65 Copynumber: 1.9 Consensus size: 64
526362 GGCTGTCCAA
* *
526372 GTGCATC-GATGCAT-AAATCAGCTTTGATGTTTCAA-AATAGCCA-GAGTGCATCGATGCATGG
1 GTGCATCAG-TGCATAAAATCA-ATTCGATGTTTCAATAATA--CAGGAGTGCATCGATGCATGG
526433 CTT
62 CTT
*
526436 GTGCATCAGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCAT
1 GTGCATCAGTGCATAAAATCAATTCGATGTTTCAATAATACA-GGAGTGCATCGATGCAT
526496 TGATTTATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
63 2 0.04
64 23 0.44
65 27 0.52
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCAGTGCATAAAATCAATTCGATGTTTCAATAATACAGGAGTGCATCGATGCATGGCTT
Found at i:534945 original size:20 final size:22
Alignment explanation
Indices: 534920--534979 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
534910 TTTCCAAAAT
534920 TAAATCCTTCGGGTCATCA-G-
1 TAAATCCTTCGGGTCATCATGA
* * *
534940 TAAATCTTTCGAG-CATGATGA
1 TAAATCCTTCGGGTCATCATGA
534961 TTAAATCCTTCGGGTCATC
1 -TAAATCCTTCGGGTCATC
534980 TATAAGTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
22 11 0.37
23 3 0.10
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (22 bp):
TAAATCCTTCGGGTCATCATGA
Found at i:535070 original size:188 final size:192
Alignment explanation
Indices: 534843--535203 Score: 525
Period size: 191 Copynumber: 1.9 Consensus size: 192
534833 AAAATAAGAG
* * *
534843 GTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAAA
1 GTTTATCATTCAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCCAGTAAAA
* **
534908 TATTTCCAAAA-TTA-AA-TCCTTCGGGTCATCAGTAAATCTTTCGAGCATGATGA-TTAAATCC
66 TATTTCCAAAATTTATAAGTCATTCGGGAAATCAGTAAATCTTTCGAGCATGAT-ACTTAAATCC
* * *
534969 TTCGGGTCATCTATAAGTATTTCGAGCAAGATAATAAGCCCTTCGGGCATATATATGAGAAAT
130 TTCGAGTCATCAATAAGCATTTCGAGCAAGATAATAAGCCCTTCGGGCATATATATGAGAAAT
* * *
535032 GTTTATCATTTAAATCTG-AAATTGAAATTTTTGAAAAGTATGAAAGGTTTCTTACCCAGTAAAC
1 GTTTATCATTCAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCCAGTAAAA
* *
535096 TATTTCCAAAATTTATAAGTTATTCGGGAAATCAGTAAGTCTTTCGAGCATGATACTTAAATCCT
66 TATTTCCAAAATTTATAAGTCATTCGGGAAATCAGTAAATCTTTCGAGCATGATACTTAAATCCT
* * *
535161 TCGAGTCATCAATAAGCCTTTCGAGCAAGATGATAAGTCCTTC
131 TCGAGTCATCAATAAGCATTTCGAGCAAGATAATAAGCCCTTC
535204 AGGCCATCCA
Statistics
Matches: 151, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
188 54 0.36
189 18 0.12
190 3 0.02
191 76 0.50
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (192 bp):
GTTTATCATTCAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCCAGTAAAA
TATTTCCAAAATTTATAAGTCATTCGGGAAATCAGTAAATCTTTCGAGCATGATACTTAAATCCT
TCGAGTCATCAATAAGCATTTCGAGCAAGATAATAAGCCCTTCGGGCATATATATGAGAAAT
Found at i:535460 original size:37 final size:37
Alignment explanation
Indices: 535405--535822 Score: 218
Period size: 37 Copynumber: 11.0 Consensus size: 37
535395 CCGGACCATC
* *
535405 TTAAGCCTTCATCAAAGAGTAGTGAAGCAAATTAATA
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
* *
535442 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATC
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
* *
535479 TTAAGCCTTCATCGAAGAGTAGTGAATCAAATCCATCA
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAAT-A
* * * * ** * * *
535517 GTAAGCCTTTTGAGCAT-GACGATTAAGTCG--TCCGAGCCATC
1 TTAAGCC--TT---CATCGAAGAGT-AGT-GAAGCAAATCAATA
* *
535558 TTAAGCCTTCA-CTGAAAAGTAGTGAAGCAAATCCATCA
1 TTAAGCCTTCATC-GAAGAGTAGTGAAGCAAATCAAT-A
* * * * * *** **** * *
535596 GTAAGTCTTCTGAGCATGACGATTAAGT-CCTCCGGGCCATC
1 TTAAGCCTTC--ATC--GAAGAGT-AGTGAAGCAAATCAATA
* *
535637 TTAAGCCTTCA-CTGAAGAGTAGTGAAACAAATCAATC
1 TTAAGCCTTCATC-GAAGAGTAGTGAAGCAAATCAATA
* * * *
535674 TTAAGCCTTTACCGAAGAGTAGTGAATCAAATCAATT
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
* *
535711 TTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATC
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
* * * *
535748 TTAAGCCTTCATCAAAAAGTACTGAAGCAAATCAATC
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
* * * * *
535785 TTAAACCTCCACCGAAGAGTGGTGAAGCAAATCGATA
1 TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
535822 T
1 T
535823 CGAGTCTGAC
Statistics
Matches: 293, Mismatches: 68, Indels: 40
0.73 0.17 0.10
Matches are distributed among these distances:
35 1 0.00
36 8 0.03
37 215 0.73
38 16 0.05
39 3 0.01
40 3 0.01
41 15 0.05
42 22 0.08
43 9 0.03
44 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (37 bp):
TTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATA
Found at i:535579 original size:79 final size:79
Alignment explanation
Indices: 535476--535683 Score: 312
Period size: 79 Copynumber: 2.6 Consensus size: 79
535466 AAGCAAATCA
*
535476 ATCTTAAGCCTTCA-TCGAAGAGTAGTGAATCAAATCCATCAGTAAGCCTTTTGAGCATGACGAT
1 ATCTTAAGCCTTCACT-GAAGAGTAGTGAAACAAATCCATCAGTAAGCCTTTTGAGCATGACGAT
*
535540 TAAGTCGTCCGAGCC
65 TAAGTCCTCCGAGCC
* * * *
535555 ATCTTAAGCCTTCACTGAAAAGTAGTGAAGCAAATCCATCAGTAAGTCTTCTGAGCATGACGATT
1 ATCTTAAGCCTTCACTGAAGAGTAGTGAAACAAATCCATCAGTAAGCCTTTTGAGCATGACGATT
*
535620 AAGTCCTCCGGGCC
66 AAGTCCTCCGAGCC
* *
535634 ATCTTAAGCCTTCACTGAAGAGTAGTGAAACAAATCAATC-TTAAGCCTTT
1 ATCTTAAGCCTTCACTGAAGAGTAGTGAAACAAATCCATCAGTAAGCCTTT
535684 ACCGAAGAGT
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
78 7 0.06
79 108 0.93
80 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (79 bp):
ATCTTAAGCCTTCACTGAAGAGTAGTGAAACAAATCCATCAGTAAGCCTTTTGAGCATGACGATT
AAGTCCTCCGAGCC
Found at i:535731 original size:74 final size:74
Alignment explanation
Indices: 535634--535817 Score: 260
Period size: 74 Copynumber: 2.5 Consensus size: 74
535624 CCTCCGGGCC
* * * * * *
535634 ATCTTAAGCCTTCACTGAAGAGTAGTGAAACAAATCAATCTTAAGCCTTTACCGAAGAGTAGTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAAAGTACTGA
*
535699 ATCAAATCA
66 AGCAAATCA
* *
535708 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCATCAAAAAGTACTGA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAAAGTACTGA
535773 AGCAAATCA
66 AGCAAATCA
* * *
535782 ATCTTAAACCTCCACCGAAGAGTGGTGAAGCAAATC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
535818 GATATCGAGT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 97 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (74 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAAAGTACTGA
AGCAAATCA
Found at i:542262 original size:53 final size:53
Alignment explanation
Indices: 542182--542287 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
542172 TACATATATT
542182 TTACTCTATTTGTATGTTTGCCGTGTTGGAATCAAACCCAATGGGTGTGTCGG
1 TTACTCTATTTGTATGTTTGCCGTGTTGGAATCAAACCCAATGGGTGTGTCGG
542235 TTACTCTATTTGTATGTTTGCCGTGTTGGAATCAAACCCAATGGGTGTGTCGG
1 TTACTCTATTTGTATGTTTGCCGTGTTGGAATCAAACCCAATGGGTGTGTCGG
542288 CAAAGATGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (53 bp):
TTACTCTATTTGTATGTTTGCCGTGTTGGAATCAAACCCAATGGGTGTGTCGG
Found at i:542870 original size:198 final size:199
Alignment explanation
Indices: 542532--542926 Score: 783
Period size: 198 Copynumber: 2.0 Consensus size: 199
542522 ACATGATTGT
542532 TGATAAGATAATTTTTTTAATATTTTTCAATGATAATGTGATATAACATTATGATGACATGTTAA
1 TGATAAGATAATTTTTTTAATATTTTTCAATGATAATGTGATATAACATTATGATGACATGTTAA
542597 TTCACTGTTAGTTTCTTTCAAAATCATACCTAATGTTCTAAATATTCTCAATTATTTAACAATAA
66 TTCACTGTTAGTTTCTTTCAAAATCATACCTAATGTTCTAAATATTCTCAATTATTTAACAATAA
542662 AAGCTTAAACA-CTTTGCAGTCTCTGGTGCTCGAACCTGGACATCTAGGATAACAACTATCTCCT
131 AAGCTTAAACACCTTTGCAGTCTCTGGTGCTCGAACCTGGACATCTAGGATAACAACTATCTCCT
542726 TATG
196 TATG
542730 TGATAAGATAATTTTTTTAATATTTTTCAATGATAATGTGATATAACATTATGATGACATGTTAA
1 TGATAAGATAATTTTTTTAATATTTTTCAATGATAATGTGATATAACATTATGATGACATGTTAA
542795 TTCACTGTTAGTTTCTTTCAAAATCATACCTAATGTTCTAAATATTCTCAATTATTTAACAATAA
66 TTCACTGTTAGTTTCTTTCAAAATCATACCTAATGTTCTAAATATTCTCAATTATTTAACAATAA
542860 AAGCTTAAACACCTTTGCAGTCTCTGGTGCTCGAACCTGGACATCTAGGATAACAACTATCTCCT
131 AAGCTTAAACACCTTTGCAGTCTCTGGTGCTCGAACCTGGACATCTAGGATAACAACTATCTCCT
542925 TA
196 TA
542927 ACAACATAGG
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
198 141 0.72
199 55 0.28
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (199 bp):
TGATAAGATAATTTTTTTAATATTTTTCAATGATAATGTGATATAACATTATGATGACATGTTAA
TTCACTGTTAGTTTCTTTCAAAATCATACCTAATGTTCTAAATATTCTCAATTATTTAACAATAA
AAGCTTAAACACCTTTGCAGTCTCTGGTGCTCGAACCTGGACATCTAGGATAACAACTATCTCCT
TATG
Found at i:546596 original size:16 final size:16
Alignment explanation
Indices: 546564--546608 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
546554 CGCGTGAGGC
*
546564 TTAATTTA-TTTATGT
1 TTAATTTAGTTTAGGT
546579 TTAATTTAGTTTAGGT
1 TTAATTTAGTTTAGGT
546595 TTAATTT-GTTTAGG
1 TTAATTTAGTTTAGG
546609 AATTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (16 bp):
TTAATTTAGTTTAGGT
Found at i:548803 original size:238 final size:236
Alignment explanation
Indices: 548355--548833 Score: 899
Period size: 238 Copynumber: 2.0 Consensus size: 236
548345 TTTAGTATGT
548355 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
1 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
548420 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATAGACACCATAACAAGAGGTTCTCA
66 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATAGACACCATAACAAGAGGTTCTCA
548485 TAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAAAC
131 TAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAAAC
548550 CTCCAAAGAAGAACTCAAAATAGAAAATATGATGAGGACTAAC
196 CTCCAAAGAAGAACTCAAAATAG-AAA-ATGATGAGGACTAAC
548593 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
1 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
*
548658 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATCTGGACACCATAACAAGAGGTTCT
66 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCA--TAGACACCATAACAAGAGGTTCT
548723 CAT-ACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
129 CATAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
548787 ACCTCCAAAG-AGAACTCAAAATAGAAAATGATGAGGACTAAC
194 ACCTCCAAAGAAGAACTCAAAATAGAAAATGATGAGGACTAAC
548829 CCTCT
1 CCTCT
548834 GAAAATGATA
Statistics
Matches: 238, Mismatches: 1, Indels: 6
0.97 0.00 0.02
Matches are distributed among these distances:
236 20 0.08
237 3 0.01
238 119 0.50
239 71 0.30
240 25 0.11
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (236 bp):
CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATAGACACCATAACAAGAGGTTCTCA
TAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAAAC
CTCCAAAGAAGAACTCAAAATAGAAAATGATGAGGACTAAC
Found at i:552903 original size:16 final size:16
Alignment explanation
Indices: 552882--552912 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
552872 AATCATAATC
552882 AAACCTTAAATCATCA
1 AAACCTTAAATCATCA
552898 AAACCTTAAATCATC
1 AAACCTTAAATCATC
552913 TTCATCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
AAACCTTAAATCATCA
Found at i:557784 original size:13 final size:13
Alignment explanation
Indices: 557766--557794 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
557756 CTTAAGGAAC
557766 CGAAAGTCTAACT
1 CGAAAGTCTAACT
557779 CGAAAGTCTAACT
1 CGAAAGTCTAACT
557792 CGA
1 CGA
557795 TGAGTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (13 bp):
CGAAAGTCTAACT
Found at i:569502 original size:31 final size:29
Alignment explanation
Indices: 569465--569536 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
569455 GGGACTAATT
* *
569465 TTTTTAAATTAATTCCAGAGACTAAATTGAA
1 TTTTT-AATTAATT-CAGAGACCAAAGTGAA
* *
569496 TTTTTAATTAAATTTAGGGACCAAAGTGAA
1 TTTTTAATT-AATTCAGAGACCAAAGTGAA
569526 TTTTTAATTAA
1 TTTTTAATTAA
569537 ATTTGAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.06
30 25 0.69
31 9 0.25
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (29 bp):
TTTTTAATTAATTCAGAGACCAAAGTGAA
Found at i:570246 original size:18 final size:18
Alignment explanation
Indices: 570201--570252 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
570191 AAATAAGTCA
* *
570201 ACCATTTACCGTTGACCG
1 ACCATTGACTGTTGACCG
570219 ACCATTGACTGTTGACCG
1 ACCATTGACTGTTGACCG
* *
570237 ACCGTTGACTATTGAC
1 ACCATTGACTGTTGAC
570253 AACTGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (18 bp):
ACCATTGACTGTTGACCG
Found at i:574113 original size:299 final size:300
Alignment explanation
Indices: 573684--574282 Score: 1166
Period size: 299 Copynumber: 2.0 Consensus size: 300
573674 CTTCAAATCC
573684 AAGCATCCAAAAGCATAATCAAACATTCTAATAATATATTTAAACATTACTCTACAACCTCATAC
1 AAGCATCCAAAAGCATAATCAAACATTCTAATAATATATTTAAACATTACTCTACAACCTCATAC
573749 AATTTCCATTTCAAAATCACATTTCCTTCTTTTTACAATTTGGCCCATTAACCTGTACAATCTTC
66 AATTTCCATTTCAAAATCACATTTCCTTCTTTTTACAATTTGGCCCATTAACCTGTACAATCTTC
573814 CAAATTGGTCCAAACAACTTTATAATTCTTGCATAATCATCCATTCATCATGTCTAACTTTAAAA
131 CAAATTGGTCCAAACAACTTTATAATTCTTGCATAATCATCCATTCATCATGTCTAACTTTAAAA
573879 TAATTTTTCACAAAATTTTCCCTATTTAATTCAT-TTGGCCTATTATAACAAGTCACCTAAGGCT
196 TAATTTTTCACAAAATTTTCCCTATTTAATTCATCTTGGCCTATTATAACAAGTCACCTAAGGCT
573943 TGATTTCCAACTTGA-TCAAGCATGAATTCAACTTCCAAA
261 TGATTTCCAACTTGATTCAAGCATGAATTCAACTTCCAAA
573982 AAGCATCCAAAAGCATAATCAAACATTCTAATAATATATTTAAACATTACTCTACAACCTCATAC
1 AAGCATCCAAAAGCATAATCAAACATTCTAATAATATATTTAAACATTACTCTACAACCTCATA-
*
574047 CAATTTCCATTTCAAAATCACATTTCCTTCTTTTTACAATTTGGCCCATTAACCTTTACAATCTT
65 CAATTTCCATTTCAAAATCACATTTCCTTCTTTTTACAATTTGGCCCATTAACCTGTACAATCTT
574112 CCAAATTGGTCCAAACAACTTTATAATTCTTGCATAATCATCCATTCATCATGTCTAACTTTAAA
130 CCAAATTGGTCCAAACAACTTTATAATTCTTGCATAATCATCCATTCATCATGTCTAACTTTAAA
574177 ATAATTTTTCACAAAATTTTCCCTATTTAATTCATCTTGGCCTATTATAACAAGTCACCTAAGGC
195 ATAATTTTTCACAAAATTTTCCCTATTTAATTCATCTTGGCCTATTATAACAAGTCACCTAAGGC
574242 TTGATTTCCAACTTGATTCAAGCATGAATTCAACTTCCAAA
260 TTGATTTCCAACTTGATTCAAGCATGAATTCAACTTCCAAA
574283 TATCATTTCC
Statistics
Matches: 297, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
298 64 0.22
299 164 0.55
300 45 0.15
301 24 0.08
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (300 bp):
AAGCATCCAAAAGCATAATCAAACATTCTAATAATATATTTAAACATTACTCTACAACCTCATAC
AATTTCCATTTCAAAATCACATTTCCTTCTTTTTACAATTTGGCCCATTAACCTGTACAATCTTC
CAAATTGGTCCAAACAACTTTATAATTCTTGCATAATCATCCATTCATCATGTCTAACTTTAAAA
TAATTTTTCACAAAATTTTCCCTATTTAATTCATCTTGGCCTATTATAACAAGTCACCTAAGGCT
TGATTTCCAACTTGATTCAAGCATGAATTCAACTTCCAAA
Found at i:574529 original size:2 final size:2
Alignment explanation
Indices: 574522--574557 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
574512 GGAAAACATG
574522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
574558 AATTCTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:574702 original size:181 final size:182
Alignment explanation
Indices: 574364--574703 Score: 603
Period size: 182 Copynumber: 1.9 Consensus size: 182
574354 GGTTGACCAA
*
574364 ATATGATATATAAATTTCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
1 ATATAATATATAAATTTCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
*
574429 CAACACATCATAATAAAGCCTTAAATCATCAAAACTAACATCCCCATCATCCATCCAATTCAAGA
66 CAACACATCATAATAAAGCATTAAATCATCAAAACTAACATCCCCATCATCCATCCAATTCAAGA
574494 AATTAATGTTTTAAGCATGGAAAACATGATATATATATATATATATATATAT
131 AATTAATGTTTTAAGCATGGAAAACATGATATATATATATATATATATATAT
* *
574546 ATATAATATATAAA-TTCTAAATAGTTTCATTCCTCATACAAGCATGGAAATGATTGTCCAATAT
1 ATATAATATATAAATTTCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
*
574610 CAACAACATCATAATAAAGCATTAAATCATCAAAACTAACATCCCCTTCATCCATCCAATTCAAG
66 CAAC-ACATCATAATAAAGCATTAAATCATCAAAACTAACATCCCCATCATCCATCCAATTCAAG
*
574675 AACTTAATGTTTTAAGCATGG-AAACATGA
130 AAATTAATGTTTTAAGCATGGAAAACATGA
574704 ACTAATGGTA
Statistics
Matches: 151, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
181 60 0.40
182 91 0.60
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.31
Consensus pattern (182 bp):
ATATAATATATAAATTTCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
CAACACATCATAATAAAGCATTAAATCATCAAAACTAACATCCCCATCATCCATCCAATTCAAGA
AATTAATGTTTTAAGCATGGAAAACATGATATATATATATATATATATATAT
Found at i:575372 original size:15 final size:15
Alignment explanation
Indices: 575348--575383 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
575338 GGATTATGTA
*
575348 ACTTTTTAAAATTAC
1 ACTTTATAAAATTAC
575363 ACTTTATAAAATTAC
1 ACTTTATAAAATTAC
575378 ACTTTA
1 ACTTTA
575384 GTCCTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (15 bp):
ACTTTATAAAATTAC
Found at i:575564 original size:19 final size:19
Alignment explanation
Indices: 575542--575584 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
575532 ATTGTATCAG
575542 TACTC-GGGATAGGTATCGA
1 TACTCAGGG-TAGGTATCGA
*
575561 TACTCAAGGGTTGGTATCGA
1 TACTC-AGGGTAGGTATCGA
575581 TACT
1 TACT
575585 ATATGGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 13 0.62
21 3 0.14
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (19 bp):
TACTCAGGGTAGGTATCGA
Found at i:578436 original size:41 final size:41
Alignment explanation
Indices: 578322--578607 Score: 274
Period size: 41 Copynumber: 7.0 Consensus size: 41
578312 ACTGTAGTAG
* * * * *
578322 TTTTTATACAAATGCCGCTATAAACTAGTAATTTAGTGGCC
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* * * * * *
578363 TTTTTATATAACACG--TCTATATACTCATACTTTTGTGGCG
1 TTTTTATACAA-ACGCCGCTATAGACTCGTACTTTAGTGGCA
* * * **
578403 GTTTTATACAAACGCTGCTATAAACTCGTACTTTAGTGGTGT
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG-CA
* * *
578445 TTTTTACACAAATGCCGCTATAGACTCATACTTTAGTGGCA
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
578486 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* **
578527 TTTTTATACAAATGCCGCTATAGACTCGTACTTT-GTGGTG
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
* * * *
578567 TTTGTGTTTAGAAACGTCGCTATAGAC-CATACTTTAGTGGC
1 TTT-T-TATACAAACGCCGCTATAGACTCGTACTTTAGTGGC
578608 GTTTACATAA
Statistics
Matches: 201, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.01
40 34 0.17
41 108 0.54
42 56 0.28
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (41 bp):
TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCA
Found at i:578566 original size:123 final size:123
Alignment explanation
Indices: 578322--578607 Score: 339
Period size: 123 Copynumber: 2.3 Consensus size: 123
578312 ACTGTAGTAG
* * * * * *
578322 TTTTTATACAAATGCCGCTATAAACT-AGTAATTTAGTGGCCTTTTTATATAACACGTCTATATA
1 TTTTTATACAAATGCCGCTATAGACTCA-TACTTTAGTGGCATTTTTATACAACACGGCTATAGA
* * *
578386 CTCATACTTTTGTGGCGGTTTTATACAAACGCTGCTATAAACTCGTACTTTAGTGGTGT
65 CTCATACTTTAGTGGCAGTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGTGT
*
578445 TTTTTACACAAATGCCGCTATAGACTCATACTTTAGTGGCATTTTTATACAA-ACGCCGCTATAG
1 TTTTTATACAAATGCCGCTATAGACTCATACTTTAGTGGCATTTTTATACAACACG--GCTATAG
* * * *
578509 ACTCGTACTTTAGTGGCATTTTTATACAAATGCCGCTATAGACTCGTACTTT-GTGGTGT
64 ACTCATACTTTAGTGGCAGTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGTGT
* * *
578568 TTGTGTT-TAGAAACGTCGCTATAGAC-CATACTTTAGTGGC
1 TT-T-TTATACAAATGCCGCTATAGACTCATACTTTAGTGGC
578608 GTTTACATAA
Statistics
Matches: 140, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
122 3 0.02
123 68 0.49
124 67 0.48
125 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (123 bp):
TTTTTATACAAATGCCGCTATAGACTCATACTTTAGTGGCATTTTTATACAACACGGCTATAGAC
TCATACTTTAGTGGCAGTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGTGT
Found at i:578582 original size:83 final size:82
Alignment explanation
Indices: 578322--578607 Score: 285
Period size: 83 Copynumber: 3.5 Consensus size: 82
578312 ACTGTAGTAG
* * * * * * *
578322 TTTTTATACAAATGCCGCTATAAACTAGTAATTTAGTGGCCTTTTTATA-TAA--CACGTCTATA
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAATGC-CG-CTATA
* * *
578384 TACTCATACTTTTGTGGCG
64 GACTCATACTTTAGTGGCA
* * * **
578403 GTTTTATACAAACGCTGCTATAAACTCGTACTTTAGTGGTGTTTTTTACACAAATGCCGCTATAG
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG-CATTTTTACACAAATGCCGCTATAG
578468 ACTCATACTTTAGTGGCA
65 ACTCATACTTTAGTGGCA
*
578486 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATACAAATGCCGCTATAGA
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAATGCCGCTATAGA
* **
578551 CTCGTACTTT-GTGGTG
66 CTCATACTTTAGTGGCA
* * * *
578567 TTTGTGTTTAGAAACGTCGCTATAGAC-CATACTTTAGTGGC
1 TTT-T-TATACAAACGCCGCTATAGACTCGTACTTTAGTGGC
578608 GTTTACATAA
Statistics
Matches: 174, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
81 41 0.24
82 53 0.30
83 77 0.44
84 2 0.01
85 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (82 bp):
TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAATGCCGCTATAGA
CTCATACTTTAGTGGCA
Found at i:583684 original size:22 final size:22
Alignment explanation
Indices: 583667--583720 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
583657 GTTGACCACT
583667 GTTGACCAGGACTTTGACCGGC
1 GTTGACCAGGACTTTGACCGGC
**
583689 GTTGACCAAAACTTTGACCGGC
1 GTTGACCAGGACTTTGACCGGC
583711 GTTGACCAGG
1 GTTGACCAGG
583721 CATTGAACGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (22 bp):
GTTGACCAGGACTTTGACCGGC
Found at i:583685 original size:12 final size:11
Alignment explanation
Indices: 583648--583726 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 11
583638 GCATTAACCA
583648 TTGA-CAGGCG
1 TTGACCAGGCG
583658 TTGACCA--CTG
1 TTGACCAGGC-G
*
583668 TTGACCAGGACT
1 TTGACCAGG-CG
583680 TTGACC-GGCG
1 TTGACCAGGCG
** *
583690 TTGACCAAAACT
1 TTGACC-AGGCG
583702 TTGACC-GGCG
1 TTGACCAGGCG
*
583712 TTGACCAGGCA
1 TTGACCAGGCG
583723 TTGA
1 TTGA
583727 ACGACCTTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
9 1 0.02
10 26 0.50
11 11 0.21
12 13 0.25
13 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (11 bp):
TTGACCAGGCG
Found at i:586005 original size:24 final size:24
Alignment explanation
Indices: 585978--586089 Score: 130
Period size: 24 Copynumber: 5.0 Consensus size: 24
585968 TTCGATTTGA
585978 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
586002 A---T--TCTGAT-C-TGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
586019 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
586043 ATTCTAATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
586067 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
586090 AATAATGTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.12
18 1 0.01
19 6 0.08
20 1 0.01
21 1 0.01
22 6 0.08
23 1 0.01
24 49 0.66
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:586016 original size:17 final size:17
Alignment explanation
Indices: 585994--586030 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
585984 ATCTGATACT
585994 TGACATGGATTCTGATC
1 TGACATGGATTCTGATC
586011 TGACATGGATTCTGATC
1 TGACATGGATTCTGATC
586028 TGA
1 TGA
586031 TACTTGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (17 bp):
TGACATGGATTCTGATC
Found at i:590523 original size:24 final size:24
Alignment explanation
Indices: 590496--590614 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
590486 TTCGATTTGA
590496 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
590520 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
590544 ATTATGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
590568 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
590592 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
590615 AATTATGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 85 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:599446 original size:18 final size:18
Alignment explanation
Indices: 599423--599458 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
599413 TTATTTGTAC
599423 TTAACATTAGTATTATTA
1 TTAACATTAGTATTATTA
*
599441 TTAACATTATTATTATTA
1 TTAACATTAGTATTATTA
599459 AGTCCAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAACATTAGTATTATTA
Found at i:600865 original size:40 final size:40
Alignment explanation
Indices: 600821--600923 Score: 179
Period size: 40 Copynumber: 2.6 Consensus size: 40
600811 TCAGCTGTTA
600821 TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
1 TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
* *
600861 TTTTACTCATATTTTGATCCCTCTACAATGACATGGATTG
1 TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
*
600901 TTTTACTCCTATTTTGATAACTC
1 TTTTACTCCTATTTTGATCACTC
600924 AATTGAGAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (40 bp):
TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
Found at i:604722 original size:68 final size:68
Alignment explanation
Indices: 604613--604968 Score: 588
Period size: 68 Copynumber: 5.2 Consensus size: 68
604603 TAAAGGATTG
*
604613 TGAGGCCTAACTGTGCTTATGACA-AGAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTA
1 TGAGGCCTAACTGTGCTTATGACAGA-AAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTG
604677 CCTT
65 CCTT
* * *
604681 TGAGGCCTAACTGTACTTATGGCAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGT
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
604746 CTT
66 CTT
* * *
604749 TGAGGCCTAACTGTGCTTATGACAGAAAGATGTCATATATGCCAGTTAGATGAAAGGCAAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
*
604814 TTT
66 CTT
* *
604817 TGAGGCCTAACTGTGCTTATGACAGAAATGTATCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
604882 CTT
66 CTT
* *
604885 TAAGGCCTAACTGTGCTTATGAGAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
604950 CTT
66 CTT
604953 TGAGGCCTAACTGTGC
1 TGAGGCCTAACTGTGC
604969 AATTGGTAGA
Statistics
Matches: 265, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
68 264 1.00
69 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (68 bp):
TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
CTT
Found at i:605094 original size:81 final size:81
Alignment explanation
Indices: 604957--605596 Score: 877
Period size: 81 Copynumber: 7.9 Consensus size: 81
604947 TGCCTTTGAG
* * *
604957 GCCTAACTGTGCAATTGGTAGAAAGGTACTAATTATTCCAGTTAGATGAACAGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
605022 GAGTAAAAGAATAATG
66 GAGTAAAAGAATAATA
* * * *
605038 GACTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCTA-TTAGATGAATGGTTTAATATCGT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCC-AGTTAGATGAACGGTTTAATACCGT
605102 TGAGTAAAAGAATAATA
65 TGAGTAAAAGAATAATA
* * * *
605119 GTCTAACTGTGCAACTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAATGTTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
605184 GAGTAAATGAATAATA
66 GAGTAAAAGAATAATA
* * ** ** * *
605200 GACTAACTGTGCAATTGATAGAAAGGTGTCAATTATGTTAGTTAGATGAACGTTTTAATATCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
605265 GAGTAAAAGAATAATG
66 GAGTAAAAGAATAATA
* *
605281 GCCTAACTGTGCAATTGGTAGAAAGATACCAATTATACCAGTTAGATGAACGGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
605346 GAGTAAAAGAATCATA
66 GAGTAAAAGAATAATA
* *
605362 GCCTAACTGTGCAATGGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
605427 GAGTAAAATAATAATA
66 GAGTAAAAGAATAATA
* * * * *
605443 GCCTAAATGTGCAATTGGTATAAAGGTACCAATTATGCCAATTAGATTAACAGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
* *
605508 GAGTAAAGGAATAATG
66 GAGTAAAAGAATAATA
* * * * * * *
605524 GCCTAACTATGCAATTGGTAGAAGGGTGCCAATTATGTCAGTTAGATGAACGGTTAAACACGGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
605589 GAGCAAAA
66 GAGTAAAA
605597 ACGAAAGGTT
Statistics
Matches: 490, Mismatches: 67, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 1 0.00
81 488 1.00
82 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (81 bp):
GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
GAGTAAAAGAATAATA
Found at i:605770 original size:2 final size:2
Alignment explanation
Indices: 605763--605787 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
605753 AGGGATGATA
605763 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
605788 ATAAGGTACA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:607101 original size:91 final size:91
Alignment explanation
Indices: 606991--607160 Score: 261
Period size: 91 Copynumber: 1.9 Consensus size: 91
606981 GTAAAGTTTG
* * * **
606991 ATAATTTCAATAATTATTTCTCTTTTAAATATATAAA-ATTATTTCAACTCAGATATTATTTTAT
1 ATAATTACAATAAATATTTCTCTTTTAAATATATAAATA-TATTTCAACTCAGAAAAGATTTTAT
* *
607055 CATATATATATATATTAATTGAGATTA
65 CATAAAAATATATATTAATTGAGATTA
607082 ATAATTACAATAAATATTTCTCTTTTAAATATATAAATATATTTCAACTCAGAAAAGATTTTATC
1 ATAATTACAATAAATATTTCTCTTTTAAATATATAAATATATTTCAACTCAGAAAAGATTTTATC
607147 ATAAAAATATATAT
66 ATAAAAATATATAT
607161 GTTAATAAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
91 70 0.99
92 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (91 bp):
ATAATTACAATAAATATTTCTCTTTTAAATATATAAATATATTTCAACTCAGAAAAGATTTTATC
ATAAAAATATATATTAATTGAGATTA
Found at i:607221 original size:80 final size:79
Alignment explanation
Indices: 607110--607270 Score: 214
Period size: 80 Copynumber: 2.0 Consensus size: 79
607100 TCTCTTTTAA
*
607110 ATATATAAATATATTTCAACTCAGAAAAGATTTTATCATAAAAATATATATGTTAATAAAGTTTG
1 ATATATAAATATATTTCAACTCAGAAAAGATTCTATCATAAAAATATATAT-TTAATAAAGTTTG
* * *
607175 ATATTTATAATATAT
65 ATAATTAGAATAAAT
* * ** ** *
607190 ATATATATATATATTTCAACTGAGATTAGATTCTATTTTATAAATATATATTTAATAAAGTTTGA
1 ATATATAAATATATTTCAACTCAGAAAAGATTCTATCATAAAAATATATATTTAATAAAGTTTGA
607255 TAATTAGAATAAAT
66 TAATTAGAATAAAT
607269 AT
1 AT
607271 CTCCTTTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
79 27 0.39
80 43 0.61
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (79 bp):
ATATATAAATATATTTCAACTCAGAAAAGATTCTATCATAAAAATATATATTTAATAAAGTTTGA
TAATTAGAATAAAT
Found at i:607316 original size:9 final size:9
Alignment explanation
Indices: 607302--607361 Score: 79
Period size: 9 Copynumber: 6.8 Consensus size: 9
607292 TTATATTTAC
607302 AATAATTAT
1 AATAATTAT
607311 AATAATTATT
1 AATAATTA-T
* *
607321 TATAGTTAT
1 AATAATTAT
607330 AATAATTAT
1 AATAATTAT
607339 AAT-ATTA-
1 AATAATTAT
607346 AATAATTAT
1 AATAATTAT
607355 AATAATT
1 AATAATT
607362 TTGTTTTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
7 3 0.07
8 8 0.18
9 26 0.59
10 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
AATAATTAT
Found at i:607321 original size:28 final size:28
Alignment explanation
Indices: 607289--607342 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
607279 TAAATATTTA
*
607289 TATTTATATTTACAATAATTATAATAAT
1 TATTTATAGTTACAATAATTATAATAAT
*
607317 TATTTATAGTTATAATAATTATAATA
1 TATTTATAGTTACAATAATTATAATA
607343 TTAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TATTTATAGTTACAATAATTATAATAAT
Found at i:607349 original size:16 final size:17
Alignment explanation
Indices: 607306--607358 Score: 72
Period size: 16 Copynumber: 3.1 Consensus size: 17
607296 ATTTACAATA
*
607306 ATTATAATAATTATTTAT
1 ATTATAATAATTA-TAAT
607324 AGTTATAATAATTATAAT
1 A-TTATAATAATTATAAT
607342 ATTA-AATAATTATAAT
1 ATTATAATAATTATAAT
607358 A
1 A
607359 ATTTTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 13 0.39
17 3 0.09
18 5 0.15
19 12 0.36
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTATAATAATTATAAT
Found at i:612622 original size:83 final size:82
Alignment explanation
Indices: 612531--612853 Score: 235
Period size: 82 Copynumber: 3.9 Consensus size: 82
612521 TTTAGCGGCG
*
612531 TTTTTTCAACAAACGCCATAATAGAGTGGTAATTTAGCGGCATTTGTAGCT-CAAACACCGGAAT
1 TTTTTTCAACAAACGCCATAATAGAGTAGTAATTTAGCGGCATTT-TAG-TACAAACACCGGAAT
612595 AGAGTTGTTTATAGTGGCA
64 AGAGTTGTTTATAGTGGCA
** * * * * ***
612614 TTTTTTCAACCTACGTCGTAATAGAGTAGTAATTTAGCGGCGTTTTTGTACAAATGTCGGAATAG
1 TTTTTTCAACAAACGCCATAATAGAGTAGTAATTTAGCGGCATTTTAGTACAAACACCGGAATAG
*
612679 GGTTGTTTATAGTGGCA
66 AGTTGTTTATAGTGGCA
* * * * * *** *
612696 TTTGTTCAACAAACGACGC-T-ATGGAGAAGTAATTTAGCGGCGTTTATCA-AACAAATGTCGTA
1 TTTTTTCAACAAACG-C-CATAATAGAGTAGTAATTTAGCGGCATTT-T-AGTACAAACACCGGA
* * *
612758 ATAGGGTTATTTATAGTGGCG
62 ATAGAGTTGTTTATAGTGGCA
* * * ** * * * * *
612779 TTTGTTCAAAAAATGCCGCAATAGAGTA-TAATTTAGCGGCGTTTGTAGCAAAAACGCCGCAATA
1 TTTTTTCAACAAACGCCATAATAGAGTAGTAATTTAGCGGCATTT-TAGTACAAACACCGGAATA
*
612843 -TGTTGTTTATA
65 GAGTTGTTTATA
612854 ATGGTGTTTT
Statistics
Matches: 197, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
81 12 0.06
82 94 0.48
83 90 0.46
84 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (82 bp):
TTTTTTCAACAAACGCCATAATAGAGTAGTAATTTAGCGGCATTTTAGTACAAACACCGGAATAG
AGTTGTTTATAGTGGCA
Found at i:612696 original size:82 final size:83
Alignment explanation
Indices: 612535--612822 Score: 307
Period size: 83 Copynumber: 3.5 Consensus size: 83
612525 GCGGCGTTTT
* * * * *** *
612535 TTCAACAAACGCCATAATAGAGTGGTAATTTAGCGGCATTTGTAGCT-CAAACACCGGAATAGAG
1 TTCAACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTATAG-TACAAATGTCGGAATAGGG
*
612599 TTGTTTATAGTGGCATTTT
65 TTGTTTATAGTGGCATTTG
** * *
612618 TTCAACCTACGTCGTAATAGAGTAGTAATTTAGCGGCGTTT-TTGTACAAATGTCGGAATAGGGT
1 TTCAACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTATAGTACAAATGTCGGAATAGGGT
612682 TGTTTATAGTGGCATTTG
66 TGTTTATAGTGGCATTTG
* * * * *
612700 TTCAACAAACGACGCT-ATGGAGAAGTAATTTAGCGGCGTTTATCA-AACAAATGTCGTAATAGG
1 TTCAACAAACGCCG-TAATAGAGTAGTAATTTAGCGGCGTTTAT-AGTACAAATGTCGGAATAGG
* *
612763 GTTATTTATAGTGGCGTTTG
64 GTTGTTTATAGTGGCATTTG
* * *
612783 TTCAAAAAATGCCGCAATAGAGTA-TAATTTAGCGGCGTTT
1 TTCAACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTT
612823 GTAGCAAAAA
Statistics
Matches: 172, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 83 0.48
83 88 0.51
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (83 bp):
TTCAACAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTATAGTACAAATGTCGGAATAGGGT
TGTTTATAGTGGCATTTG
Found at i:612708 original size:41 final size:40
Alignment explanation
Indices: 612589--612710 Score: 111
Period size: 41 Copynumber: 3.0 Consensus size: 40
612579 GCTCAAACAC
**
612589 CGGAATAGAGTTGTTTATAGTGGCATTTTTTCAACCTACGT
1 CGGAATAGAGTTGTTTATAGTGGCA-TTTTTCAACAAACGT
* * * * ** *
612630 CGTAATAGAGTAGTAATT-TAGCGGCGTTTTTGTACAAATGT
1 CGGAATAGAGTTGT--TTATAGTGGCATTTTTCAACAAACGT
*
612671 CGGAATAGGGTTGTTTATAGTGGCATTTGTTCAACAAACG
1 CGGAATAGAGTTGTTTATAGTGGCATTT-TTCAACAAACG
612711 ACGCTATGGA
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
39 2 0.03
40 9 0.15
41 41 0.68
42 6 0.10
43 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (40 bp):
CGGAATAGAGTTGTTTATAGTGGCATTTTTCAACAAACGT
Found at i:612793 original size:41 final size:40
Alignment explanation
Indices: 612725--612824 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 40
612715 TATGGAGAAG
*
612725 TAATTTAGCGGCGTTT-ATCAAACAAATGTCGTAATAGGGT
1 TAATTTAGCGGCGTTTGTTCAAA-AAATGTCGTAATAGGGT
* * * * *
612765 TATTTATAGTGGCGTTTGTTCAAAAAATGCCGCAATAGAGT
1 TAATT-TAGCGGCGTTTGTTCAAAAAATGTCGTAATAGGGT
612806 ATAATTTAGCGGCGTTTGT
1 -TAATTTAGCGGCGTTTGT
612825 AGCAAAAACG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.08
41 36 0.73
42 9 0.18
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (40 bp):
TAATTTAGCGGCGTTTGTTCAAAAAATGTCGTAATAGGGT
Done.