Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 17
Found at i:466851 original size:37 final size:37
Alignment explanation
Indices: 466758--466855 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
466748 ATGCTTGTGG
* * * * *
466758 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* * *
466795 ATCATATTTTTAGGAGTTTGAATCATAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
466832 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
466856 CTAGTAGGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:467797 original size:106 final size:106
Alignment explanation
Indices: 467612--468887 Score: 1978
Period size: 106 Copynumber: 12.0 Consensus size: 106
467602 GCATTGTTCC
* * * ** *
467612 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAATCAGGAATTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
467677 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
467718 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
467783 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCATTTTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
467824 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
467889 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
467930 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
467995 TCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
468036 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
468101 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
468142 GAGTACAATATCTTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
468207 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
468248 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
468313 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
468354 GAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
468419 CCAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
468460 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
468525 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
468566 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
468631 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
468672 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
468736 ACCAGCGGTCCCTTTGTTGTGAAGTTGAACTTACGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
468778 GAGTCCAATATCTTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
468843 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
468884 GAGT
1 GAGT
468888 GGCACGATAT
Statistics
Matches: 1078, Mismatches: 90, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
105 1 0.00
106 1076 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:469878 original size:22 final size:22
Alignment explanation
Indices: 469852--469906 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
469842 TTGTGTTTGG
469852 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATAC
*
469874 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATAC
469896 TCAAAGGTTTG
1 TCAAAGGTTTG
469907 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATAC
Found at i:470541 original size:15 final size:16
Alignment explanation
Indices: 470523--470557 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
470513 TTCTTTTTGA
470523 TTTTTGTT-TTTTCTT
1 TTTTTGTTATTTTCTT
470538 TTTTT-TTATTTTCTT
1 TTTTTGTTATTTTCTT
470553 TTTTT
1 TTTTT
470558 TTGCTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTTGTTATTTTCTT
Found at i:470558 original size:15 final size:15
Alignment explanation
Indices: 470531--470559 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
470521 GATTTTTGTT
470531 TTTTCTTTTTTTTTA
1 TTTTCTTTTTTTTTA
470546 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
470560 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTA
Found at i:473978 original size:19 final size:19
Alignment explanation
Indices: 473945--473981 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
473935 TACAGATGAT
473945 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
473964 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
473982 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:475280 original size:13 final size:13
Alignment explanation
Indices: 475264--475307 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
475254 TATAATGAAA
475264 ATAAATAAATAAT
1 ATAAATAAATAAT
475277 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
475291 A-AAA-AAATATAT
1 ATAAATAAATA-AT
475303 ATAAA
1 ATAAA
475308 AATATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.18
12 3 0.11
13 12 0.43
14 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:475328 original size:22 final size:23
Alignment explanation
Indices: 475249--475317 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
475239 CAAAGAAACT
*
475249 AAAAATATA-ATGAAAATAA-ATA
1 AAAAATATATATAAAAATAATA-A
* *
475271 AATAATATAAAT-AAAATAATAA
1 AAAAATATATATAAAAATAATAA
475293 AAAAATATATATAAAAAT-ATAA
1 AAAAATATATATAAAAATAATAA
475315 AAA
1 AAA
475318 TGTATGTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 33 0.80
23 8 0.20
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (23 bp):
AAAAATATATATAAAAATAATAA
Found at i:475611 original size:19 final size:18
Alignment explanation
Indices: 475589--475633 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
475579 AAAATTTATA
475589 ATAAATAAATAAATAAAAT
1 ATAAATAAATAAAT-AAAT
* * *
475608 ATAATTAAATATATACAT
1 ATAAATAAATAAATAAAT
475626 ATAAATAA
1 ATAAATAA
475634 TAAGGGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATAAATAAATAAAT
Found at i:476122 original size:37 final size:37
Alignment explanation
Indices: 476029--476130 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
476019 ATGCTTGTGG
* * ** * *
476029 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
476066 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
476103 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
476131 TAGGATGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:480926 original size:22 final size:22
Alignment explanation
Indices: 480868--480927 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
480858 TCAGTTGTTA
*
480868 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTAAATCATG
480890 TAAC-CCTTGAAATTAAATCATG
1 TAACTCC-TGAAATTAAATCATG
*
480912 TAACTCCTGATATTAA
1 TAACTCCTGAAATTAA
480928 CATCTTGTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
TAACTCCTGAAATTAAATCATG
Found at i:481164 original size:6 final size:6
Alignment explanation
Indices: 481153--481212 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
481143 AGTATATGTG
* * *
481153 CCACGA CCACGA CCACGA CCACAA CCTCGA CCAC-A TCCACGA CCTC-A
1 CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA -CCACGA CCACGA
481200 TCCACGA CCACGA
1 -CCACGA CCACGA
481213 GCCGAGCCGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 2 0.05
6 40 0.91
7 2 0.05
ACGTcount: A:0.32, C:0.50, G:0.12, T:0.07
Consensus pattern (6 bp):
CCACGA
Found at i:481170 original size:12 final size:12
Alignment explanation
Indices: 481153--481210 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
481143 AGTATATGTG
481153 CCACGACCACGA-
1 CCACGACCAC-AT
*
481165 CCACGACCACAA
1 CCACGACCACAT
*
481177 CCTCGACCACAT
1 CCACGACCACAT
*
481189 CCACGACCTCAT
1 CCACGACCACAT
481201 CCACGACCAC
1 CCACGACCAC
481211 GAGCCGAGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 1 0.03
12 39 0.98
ACGTcount: A:0.31, C:0.52, G:0.10, T:0.07
Consensus pattern (12 bp):
CCACGACCACAT
Found at i:481211 original size:18 final size:18
Alignment explanation
Indices: 481153--481212 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
481143 AGTATATGTG
*
481153 CCACGACCACGACCACGA
1 CCACGACCTCGACCACGA
*
481171 CCACAACCTCGACCAC-A
1 CCACGACCTCGACCACGA
481188 TCCACGACCTC-ATCCACGA
1 -CCACGACCTCGA-CCACGA
481207 CCACGA
1 CCACGA
481213 GCCGAGCCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.06
18 33 0.92
19 1 0.03
ACGTcount: A:0.32, C:0.50, G:0.12, T:0.07
Consensus pattern (18 bp):
CCACGACCTCGACCACGA
Found at i:483750 original size:27 final size:27
Alignment explanation
Indices: 483719--483776 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
483709 TAGCTTCTTT
483719 AAAAGTTTTAAGATCCTCATCTAACAG
1 AAAAGTTTTAAGATCCTCATCTAACAG
*
483746 AAAAGTTTTAGGATCCTCATCTAACAG
1 AAAAGTTTTAAGATCCTCATCTAACAG
483773 AAAA
1 AAAA
483777 ATTTGAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (27 bp):
AAAAGTTTTAAGATCCTCATCTAACAG
Found at i:486684 original size:22 final size:22
Alignment explanation
Indices: 486652--486732 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
486642 TCAGCTGTTA
* *
486652 TAACTCTTGAAATTATATCATG
1 TAACTCCTAAAATTATATCATG
*
486674 TAACTCCTGAAATTATATCATG
1 TAACTCCTAAAATTATATCATG
* * *
486696 TAACACCCAAAATTAAATCATG
1 TAACTCCTAAAATTATATCATG
486718 TAACTCCTAAAATTA
1 TAACTCCTAAAATTA
486733 ACAACTTGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (22 bp):
TAACTCCTAAAATTATATCATG
Found at i:486992 original size:6 final size:6
Alignment explanation
Indices: 486981--487017 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
486971 GACACATATT
*
486981 ACCACG ACCACG ACCATG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
487018 GTCAAGCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.46, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:492147 original size:22 final size:22
Alignment explanation
Indices: 492090--492147 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
492080 TCAACTATTA
* * *
492090 TAACTTCTGAAAATATATCATG
1 TAACTACTGAAATTAAATCATG
*
492112 TAACTCCTGAAATTAAATCATG
1 TAACTACTGAAATTAAATCATG
*
492134 TAACTACTGTAATT
1 TAACTACTGAAATT
492148 TCAGATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (22 bp):
TAACTACTGAAATTAAATCATG
Found at i:495041 original size:6 final size:6
Alignment explanation
Indices: 495030--495060 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
495020 GACACATATT
495030 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
495061 GTCAAGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:504348 original size:16 final size:17
Alignment explanation
Indices: 504329--504371 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
504319 AATATTATAT
504329 GTAATCATAATTAAT-A
1 GTAATCATAATTAATAA
* *
504345 GTAATAATTATTAATAA
1 GTAATCATAATTAATAA
504362 GTAACTCATA
1 GTAA-TCATA
504372 TATAATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 5 0.24
18 3 0.14
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (17 bp):
GTAATCATAATTAATAA
Found at i:504400 original size:2 final size:2
Alignment explanation
Indices: 504395--504459 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
504385 ACACACACAC
504395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
504437 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
504460 ATAAAAATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:506836 original size:21 final size:24
Alignment explanation
Indices: 506789--506843 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
506779 CCGTTGTATG
*
506789 GTATCGATACTACTCTATATAGTA
1 GTATCGATACTACTCTATATAGCA
*
506813 GTATCGATACTCCT-TA-ATA-CA
1 GTATCGATACTACTCTATATAGCA
506834 GTATCGATAC
1 GTATCGATAC
506844 CGGTGTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
23 2 0.07
24 13 0.45
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (24 bp):
GTATCGATACTACTCTATATAGCA
Found at i:513126 original size:28 final size:27
Alignment explanation
Indices: 513095--513148 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
513085 TATATTATTA
*
513095 TTTTT-ACAAAACTATATTATTATTTTTG
1 TTTTTCACAAAAAT-TATTATT-TTTTTG
513123 TTTTTCACAAAAATTATTATTTTTTT
1 TTTTTCACAAAAATTATTATTTTTTT
513149 CTTTGTAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 12 0.50
29 7 0.29
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTTCACAAAAATTATTATTTTTTTG
Found at i:514828 original size:13 final size:13
Alignment explanation
Indices: 514810--514836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
514800 TTTTTTTAAG
514810 TTTTCAAAGAAAA
1 TTTTCAAAGAAAA
514823 TTTTCAAAGAAAA
1 TTTTCAAAGAAAA
514836 T
1 T
514837 CTTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
TTTTCAAAGAAAA
Found at i:515240 original size:20 final size:20
Alignment explanation
Indices: 515215--515290 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
515205 TGTTAATATA
515215 GTAGTACCGATACTACATGT
1 GTAGTACCGATACTACATGT
*
515235 GTAGTACCGATACTACAGGT
1 GTAGTACCGATACTACATGT
*
515255 GTAGTACCAATACTACATGT
1 GTAGTACCGATACTACATGT
515275 GTAGTACCGATACTAC
1 GTAGTACCGATACTAC
515291 TCCTTTGGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (20 bp):
GTAGTACCGATACTACATGT
Found at i:516153 original size:12 final size:11
Alignment explanation
Indices: 516122--516155 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
516112 CTCTATTTTC
516122 TTTTTTTTCTT
1 TTTTTTTTCTT
516133 TTTCTTTTTCTT
1 TTT-TTTTTCTT
516145 TTCTTTTTTCT
1 TT-TTTTTTCT
516156 CCAAGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 17 0.81
13 1 0.05
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:517050 original size:16 final size:16
Alignment explanation
Indices: 517029--517071 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
517019 ACGTGGTTTC
517029 AAAGAAAAAGAGTGGA
1 AAAGAAAAAGAGTGGA
*
517045 AAAGAAAGAGAGTGGA
1 AAAGAAAAAGAGTGGA
517061 AAAGAAAAAGA
1 AAAGAAAAAGA
517072 TGGGGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (16 bp):
AAAGAAAAAGAGTGGA
Found at i:518299 original size:5 final size:5
Alignment explanation
Indices: 518289--518315 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
518279 TAACGGAATC
518289 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TT
518316 CAAACTCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:520090 original size:30 final size:31
Alignment explanation
Indices: 520018--520091 Score: 78
Period size: 35 Copynumber: 2.3 Consensus size: 31
520008 TCCCTCGATA
*
520018 ACCCCCTCCTCGAGTTATCTTTCCAATTATGTTCCC
1 ACCCCCT-CTCGAGTTATCATTCCAATTATG----C
*
520054 ACCCCCTCTCTAGTTATCATTCCAATTATG-
1 ACCCCCTCTCGAGTTATCATTCCAATTATGC
520084 ACCCCCTC
1 ACCCCCTC
520092 GATTGTCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 8 0.22
35 21 0.58
36 7 0.19
ACGTcount: A:0.19, C:0.41, G:0.07, T:0.34
Consensus pattern (31 bp):
ACCCCCTCTCGAGTTATCATTCCAATTATGC
Found at i:520224 original size:30 final size:30
Alignment explanation
Indices: 520188--520253 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
520178 CTAGTTAATA
*
520188 GCAATATATTCAGAAGAATGTTGCAAAAAG
1 GCAATATATTCAGAAGAATGTCGCAAAAAG
520218 GCAATATATTCAGAAGAATGTCGCAAAAAG
1 GCAATATATTCAGAAGAATGTCGCAAAAAG
520248 GCAATA
1 GCAATA
520254 CATAGCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (30 bp):
GCAATATATTCAGAAGAATGTCGCAAAAAG
Found at i:523271 original size:2 final size:2
Alignment explanation
Indices: 523264--523322 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
523254 AAAAGAAGAA
523264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
523306 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
523323 GAAACCATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:523378 original size:62 final size:62
Alignment explanation
Indices: 523312--523436 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
523302 ATATATATAT
523312 ATATATATATAGAAACCATTATATGAAGACCAGAAATCTACTCAAGCTGGAATTCTAGGAGC
1 ATATATATATAGAAACCATTATATGAAGACCAGAAATCTACTCAAGCTGGAATTCTAGGAGC
* *
523374 ATATATATATATAAACCGTTATATGAAGACCAGAAATCTACTCAAGCTGGAATTCTAGGAGC
1 ATATATATATAGAAACCATTATATGAAGACCAGAAATCTACTCAAGCTGGAATTCTAGGAGC
523436 A
1 A
523437 ACACCAGAGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (62 bp):
ATATATATATAGAAACCATTATATGAAGACCAGAAATCTACTCAAGCTGGAATTCTAGGAGC
Found at i:524078 original size:100 final size:100
Alignment explanation
Indices: 523882--524066 Score: 352
Period size: 100 Copynumber: 1.9 Consensus size: 100
523872 TCCTAAACGG
*
523882 AAGAGACCCTTGAGAAAACAGAACAAAGACAATCTAGAAAGGCTGGCTAAATTAAATCAATATGT
1 AAGAGACCCTTGAGAAAACAGAAAAAAGACAATCTAGAAAGGCTGGCTAAATTAAATCAATATGT
523947 TGCTAAATTGTGCCAGAGACAGGACAGTAGGGACA
66 TGCTAAATTGTGCCAGAGACAGGACAGTAGGGACA
*
523982 AAGAGACCCTTGAGAAAACAGAAAAAAGACAATCTAGAAAGGCTGGCTAAATTAGATCAATATGT
1 AAGAGACCCTTGAGAAAACAGAAAAAAGACAATCTAGAAAGGCTGGCTAAATTAAATCAATATGT
524047 TGCTAAATTGTGCCAGAGAC
66 TGCTAAATTGTGCCAGAGAC
524067 GGAAGAATAG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (100 bp):
AAGAGACCCTTGAGAAAACAGAAAAAAGACAATCTAGAAAGGCTGGCTAAATTAAATCAATATGT
TGCTAAATTGTGCCAGAGACAGGACAGTAGGGACA
Found at i:528314 original size:16 final size:16
Alignment explanation
Indices: 528293--528336 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
528283 TGTTAAGATT
528293 TTTTTAAAAAAAATTG
1 TTTTTAAAAAAAATTG
* * *
528309 TTTTTAAATAATATTT
1 TTTTTAAAAAAAATTG
528325 TATTTTAAAAAA
1 T-TTTTAAAAAA
528337 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTTTAAAAAAAATTG
Found at i:550918 original size:30 final size:31
Alignment explanation
Indices: 550882--550939 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
550872 AGAGTCGAGG
* *
550882 GTTACCTATTTCCTTCGGG-TATATGGACAT
1 GTTACCTATGTCCTTCGGGACATATGGACAT
550912 GTTACCTATGTCCTTCGGGACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
550940 TAGGTCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGGGACATATGGACAT
Found at i:555394 original size:19 final size:19
Alignment explanation
Indices: 555345--555387 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
555335 ATACAAAAAG
555345 GGTATCGATACCCAGACTT
1 GGTATCGATACCCAGACTT
555364 GGTATCGATACCCAGACTT
1 GGTATCGATACCCAGACTT
555383 GGTAT
1 GGTAT
555388 TTATACCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCCAGACTT
Found at i:556136 original size:31 final size:31
Alignment explanation
Indices: 556098--556162 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
556088 AAGAGTCGAG
*
556098 GGTTACCTATTTCCTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
*
556129 GGTTACCTATGTCCTTCGGGACATATGGATA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
556160 GGT
1 GGT
556163 CTTTTGGGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGGACATATGGACA
Found at i:565186 original size:43 final size:41
Alignment explanation
Indices: 565072--565281 Score: 161
Period size: 43 Copynumber: 4.9 Consensus size: 41
565062 TGTTTAGGTA
* * * * *
565072 TTGATATTTAGCGGTGTTTTGCAGAAAAATGCCGCAATAGGTG
1 TTGATATTTAGCGGCGTTTT-C-TACAAACGCCGCAATAGATG
* * * **
565115 TTGATATTTAACGGCGTTTGGCAGACAAACGCCGCAATAGGCG
1 TTGATATTTAGCGGCGTTT-TC-TACAAACGCCGCAATAGATG
* * *
565158 TTGATGTTTAGCGGCGTTTTCTTCACAAACGCTGCAGTAGATG
1 TTGATATTTAGCGGCGTTTTC-T-ACAAACGCCGCAATAGATG
* * * *
565201 TTTATTTTTATCGGCGTTTTTCATACAAACGCCGTAGA-AGATG
1 TTGATATTTAGCGGCG-TTTTC-TACAAACGCCGCA-ATAGATG
*
565244 TTGATATTTAGCGGCGTTTTCCTACAAACGCTGCAATA
1 TTGATATTTAGCGGCGTTTT-CTACAAACGCCGCAATA
565282 TGTCTTGAGA
Statistics
Matches: 134, Mismatches: 27, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.01
42 17 0.13
43 110 0.82
44 6 0.04
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
TTGATATTTAGCGGCGTTTTCTACAAACGCCGCAATAGATG
Found at i:565229 original size:86 final size:85
Alignment explanation
Indices: 565121--565278 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 85
565111 GGTGTTGATA
* * *
565121 TTTAACGGCGTTTGGCAGACAAACGCCGCA-ATAGGCGTTGATGTTTAGCGGCGTTTTCTTCACA
1 TTTAACGGCGTTTGGCAGACAAACGCCGCAGA-AGACGTTGATATTTAGCGGCGTTTTCCT-ACA
565185 AACGCTGCAGTAGATGTTTATT
64 AACGCTGCAGTAGATGTTTATT
* ** * * *
565207 TTTATCGGCGTTTTTCATACAAACGCCGTAGAAGATGTTGATATTTAGCGGCGTTTTCCTACAAA
1 TTTAACGGCGTTTGGCAGACAAACGCCGCAGAAGACGTTGATATTTAGCGGCGTTTTCCTACAAA
565272 CGCTGCA
66 CGCTGCA
565279 ATATGTCTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 12 0.19
86 49 0.79
87 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (85 bp):
TTTAACGGCGTTTGGCAGACAAACGCCGCAGAAGACGTTGATATTTAGCGGCGTTTTCCTACAAA
CGCTGCAGTAGATGTTTATT
Found at i:565685 original size:21 final size:21
Alignment explanation
Indices: 565661--565714 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
565651 ATATATTACT
* *
565661 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCACTGCC
* *
565682 TCTCTGTGTGCTGCCACTGCT
1 TCTCTCTGTGCTGCCACTGCC
*
565703 TCTCTCTCTGCT
1 TCTCTCTGTGCT
565715 TCCGCTACTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.39, G:0.19, T:0.41
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCACTGCC
Found at i:573658 original size:81 final size:82
Alignment explanation
Indices: 573569--573875 Score: 394
Period size: 81 Copynumber: 3.8 Consensus size: 82
573559 AAATCAATTA
* * *
573569 CGGCGTTTACAGAAAAATGCCACT-AATGTACGACCCAT-TTGCGGCGTTTCTTGTAAAACGCCA
1 CGGCGTTTATATAAAAACGCCACTAAAT-TACGACCCATATTGCGGCGTTTCTTGTAAAACGCCA
573632 CTATAAACAACTCTATTG
65 CTATAAACAACTCTATTG
573650 CGGCGTTTATATAAAAACGCCACT-AATGTACGACCCAT-TTGCGGCGTTTCTTGTAAAACGCCA
1 CGGCGTTTATATAAAAACGCCACTAAAT-TACGACCCATATTGCGGCGTTTCTTGTAAAACGCCA
573713 CTATAAACAACTCTATTG
65 CTATAAACAACTCTATTG
* * * * * *
573731 CGGCGTTTATATAAAAACGCCGCTAAATTACTACTC-TATTGTGGTGTTT-TTTTAGAAAACGCC
1 CGGCGTTTATATAAAAACGCCACTAAATTACGACCCATATTGCGGCGTTTCTTGT--AAAACGCC
*
573794 ACTATAAACGACTCTATTG
64 ACTATAAACAACTCTATTG
* * * *
573813 CGGCGTTTATATAAAAACGCCGCTAAATTACCA-CCATATTGCGGCGTTTGTTGAAAAAACGCC
1 CGGCGTTTATATAAAAACGCCACTAAATTACGACCCATATTGCGGCGTTTCTTG-TAAAACGCC
573876 GCTAAAGTTT
Statistics
Matches: 203, Mismatches: 16, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
80 4 0.02
81 117 0.58
82 80 0.39
83 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (82 bp):
CGGCGTTTATATAAAAACGCCACTAAATTACGACCCATATTGCGGCGTTTCTTGTAAAACGCCAC
TATAAACAACTCTATTG
Found at i:573808 original size:41 final size:40
Alignment explanation
Indices: 573623--573833 Score: 230
Period size: 41 Copynumber: 5.2 Consensus size: 40
573613 CGTTTCTTGT
573623 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
** * * * *
573663 AAAACGCCACTAATGTACGAC-CCATTTGCGGCGTTTCT-TGT
1 AAAACGCCACT-ATAAACAACTCTA-TTGCGGCGTTTATAT-A
573704 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
* * * * * *
573744 AAAACGCCGCTA-AATTACTACTCTATTGTGGTGTTTTTTTA
1 AAAACGCCACTATAA--ACAACTCTATTGCGGCGTTTATATA
*
573785 GAAAACGCCACTATAAACGACTCTATTGCGGCGTTTATATA
1 -AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
573826 AAAACGCC
1 AAAACGCC
573834 GCTAAATTAC
Statistics
Matches: 138, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
39 2 0.01
40 51 0.37
41 72 0.52
42 11 0.08
43 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (40 bp):
AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
Found at i:573856 original size:41 final size:41
Alignment explanation
Indices: 573569--573861 Score: 225
Period size: 41 Copynumber: 7.2 Consensus size: 41
573559 AAATCAATTA
* * * *
573569 CGGCGTTTACAGAAAAATGCCACT-AATGTACGAC-CCATTTG
1 CGGCGTTTATATAAAAACGCCACTAAAT-TACGACTCTA-TTG
* * *
573610 CGGCGTTTCT-TGTAAAACGCCACTATAA--ACAACTCTATTG
1 CGGCGTTTATAT-AAAAACGCCACTA-AATTACGACTCTATTG
*
573650 CGGCGTTTATATAAAAACGCCACT-AATGTACGAC-CCATTTG
1 CGGCGTTTATATAAAAACGCCACTAAAT-TACGACTCTA-TTG
* * *
573691 CGGCGTTTCT-TGTAAAACGCCACTATAA--ACAACTCTATTG
1 CGGCGTTTATAT-AAAAACGCCACTA-AATTACGACTCTATTG
* *
573731 CGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTATTG
1 CGGCGTTTATATAAAAACGCCACTAAATTACGACTCTATTG
* * * *
573772 TGGTGTTTTTTTAGAAAACGCCACTATAA--ACGACTCTATTG
1 CGGCGTTTATATA-AAAACGCCACTA-AATTACGACTCTATTG
* *
573813 CGGCGTTTATATAAAAACGCCGCTAAATTACCAC-CATATTG
1 CGGCGTTTATATAAAAACGCCACTAAATTACGACTC-TATTG
573854 CGGCGTTT
1 CGGCGTTT
573862 GTTGAAAAAA
Statistics
Matches: 200, Mismatches: 31, Indels: 42
0.73 0.11 0.15
Matches are distributed among these distances:
38 2 0.01
39 4 0.02
40 69 0.34
41 108 0.54
42 11 0.05
43 6 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (41 bp):
CGGCGTTTATATAAAAACGCCACTAAATTACGACTCTATTG
Found at i:577167 original size:21 final size:21
Alignment explanation
Indices: 577125--577167 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
577115 TTTATGGGCT
* *
577125 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
577146 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
577167 A
1 A
577168 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:577640 original size:29 final size:30
Alignment explanation
Indices: 577577--577645 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
577567 TTATATGAAT
* *
577577 TATGGGATAAAGGTATGGAAAATGAAATGTT
1 TATGCGATAAAGGTATGG-AAATGAAATGTC
* **
577608 TATGTGATAAAGGTATGG-AATGTTATGTC
1 TATGCGATAAAGGTATGGAAATGAAATGTC
577637 TATGCGATA
1 TATGCGATA
577646 TAAATTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
TATGCGATAAAGGTATGGAAATGAAATGTC
Found at i:583422 original size:21 final size:21
Alignment explanation
Indices: 583380--583422 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
583370 TTTCTAGGCT
* *
583380 AGGGGAATCGGGACCCATTCA
1 AGGGGAATCGAGACCCACTCA
* *
583401 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGAGACCCACTCA
583422 A
1 A
583423 ATGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.14
Consensus pattern (21 bp):
AGGGGAATCGAGACCCACTCA
Found at i:583822 original size:29 final size:30
Alignment explanation
Indices: 583759--583827 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
583749 TTATATGAAT
* *
583759 TATGGGATAAAGGTATGGAAAATGAAATGTT
1 TATGCGATAAAGGTATGG-AAATGAAATGTC
* **
583790 TATGTGATAAAGGTATGG-AATGTTATGTC
1 TATGCGATAAAGGTATGGAAATGAAATGTC
583819 TATGCGATA
1 TATGCGATA
583828 TAAATTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
TATGCGATAAAGGTATGGAAATGAAATGTC
Found at i:584051 original size:24 final size:25
Alignment explanation
Indices: 584024--584074 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
584014 GTGGTCCTTT
*
584024 GGGAAAAAT-TCTACGCGGTTCTTC
1 GGGAAAAATCTCTACGCGGTACTTC
*
584048 GGGACAAATCTCTACGCGGTACTTC
1 GGGAAAAATCTCTACGCGGTACTTC
584073 GG
1 GG
584075 TGCAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (25 bp):
GGGAAAAATCTCTACGCGGTACTTC
Found at i:596785 original size:15 final size:15
Alignment explanation
Indices: 596765--596804 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
596755 TGGAGGTCAC
596765 AGAGGATGGTTGAGT
1 AGAGGATGGTTGAGT
596780 AGAGGATGGTTGAGT
1 AGAGGATGGTTGAGT
596795 AGAGGATGGT
1 AGAGGATGGT
596805 GGAAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (15 bp):
AGAGGATGGTTGAGT
Found at i:601935 original size:21 final size:20
Alignment explanation
Indices: 601911--601950 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
601901 AATATACGTG
601911 AGTACCGATACTAAGCCTTTC
1 AGTACCGATACTAA-CCTTTC
* *
601932 AGTATCGGTACTAACCTTT
1 AGTACCGATACTAACCTTT
601951 GGGTATTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (20 bp):
AGTACCGATACTAACCTTTC
Found at i:601956 original size:20 final size:20
Alignment explanation
Indices: 601919--601984 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
601909 TGAGTACCGA
**
601919 TACTAAGCCTTTCAGTATCGG
1 TACTAA-CCTTTGGGTATCGG
*
601940 TACTAACCTTTGGGTATTGG
1 TACTAACCTTTGGGTATCGG
* *
601960 TACTAACCTATGGGTATCGA
1 TACTAACCTTTGGGTATCGG
601980 TACTA
1 TACTA
601985 CTGACTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 33 0.85
21 6 0.15
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
TACTAACCTTTGGGTATCGG
Found at i:602044 original size:20 final size:21
Alignment explanation
Indices: 602016--602056 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
602006 AAAAAGGGCT
602016 AGTACCGATAC-TCTAGTTTG
1 AGTACCGATACTTCTAGTTTG
*
602036 AGTATCGATACTTCTAGTTTG
1 AGTACCGATACTTCTAGTTTG
602057 TGGTATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (21 bp):
AGTACCGATACTTCTAGTTTG
Found at i:602070 original size:22 final size:21
Alignment explanation
Indices: 602027--602070 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
602017 GTACCGATAC
* *
602027 TCTAGTTTGAGTATCGATACT
1 TCTAGTTTGAGTATCAAAACT
*
602048 TCTAGTTTGTGGTATCAAAACT
1 TCTAGTTTG-AGTATCAAAACT
602070 T
1 T
602071 TCCTGAGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (21 bp):
TCTAGTTTGAGTATCAAAACT
Found at i:603291 original size:21 final size:21
Alignment explanation
Indices: 603257--603389 Score: 97
Period size: 21 Copynumber: 6.4 Consensus size: 21
603247 CCGTTACAAT
*
603257 ATCTTTTT-TGTTAACATCAC
1 ATCTTTTTATATTAACATCAC
* *
603277 ATCTTTTTGTATTAACATTAC
1 ATCTTTTTATATTAACATCAC
* * *
603298 ATCTCTTCATATTAACATCAT
1 ATCTTTTTATATTAACATCAC
* * * *
603319 ATCTCTTCATGTTAATATCAC
1 ATCTTTTTATATTAACATCAC
* * *
603340 ATATTTTTATATTAACTTCGC
1 ATCTTTTTATATTAACATCAC
* * * *
603361 ATCTCTTCATGTTAACATCAT
1 ATCTTTTTATATTAACATCAC
*
603382 ATATTTTT
1 ATCTTTTT
603390 CTGTTACATT
Statistics
Matches: 85, Mismatches: 27, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
20 8 0.09
21 77 0.91
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.49
Consensus pattern (21 bp):
ATCTTTTTATATTAACATCAC
Found at i:603352 original size:42 final size:42
Alignment explanation
Indices: 603267--603389 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
603257 ATCTTTTTTG
* ** * * * * *
603267 TTAACATCACATCTTTTTGTATTAACATTACATCTCTTCATA
1 TTAACATCACATCTCTTCATGTTAACATCACATATTTTTATA
* *
603309 TTAACATCATATCTCTTCATGTTAATATCACATATTTTTATA
1 TTAACATCACATCTCTTCATGTTAACATCACATATTTTTATA
* * *
603351 TTAACTTCGCATCTCTTCATGTTAACATCATATATTTTT
1 TTAACATCACATCTCTTCATGTTAACATCACATATTTTT
603390 CTGTTACATT
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (42 bp):
TTAACATCACATCTCTTCATGTTAACATCACATATTTTTATA
Found at i:603364 original size:63 final size:63
Alignment explanation
Indices: 603265--603383 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
603255 ATATCTTTTT
* *
603265 TGTTAACATCACATCTTTTTGTATTAACATTACATCTCTTCATATTAACATCATATCTCTTCA
1 TGTTAACATCACATATTTTTATATTAACATTACATCTCTTCATATTAACATCATATCTCTTCA
* * *
603328 TGTTAATATCACATATTTTTATATTAAC-TTCGCATCTCTTCATGTTAACATCATAT
1 TGTTAACATCACATATTTTTATATTAACATT-ACATCTCTTCATATTAACATCATAT
603384 ATTTTTCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.45
Consensus pattern (63 bp):
TGTTAACATCACATATTTTTATATTAACATTACATCTCTTCATATTAACATCATATCTCTTCA
Found at i:603395 original size:63 final size:62
Alignment explanation
Indices: 603255--603420 Score: 176
Period size: 63 Copynumber: 2.6 Consensus size: 62
603245 GGCCGTTACA
* *
603255 ATATCTTTTT-TGTTAACATCACATCTTTTTGTATTAACATTACATCTCTTCATATTAACATC
1 ATAT-TTTTTCTGTTAACATCACATATTTTTATATTAACATTACATCTCTTCATATTAACATC
* * * * *
603317 ATATCTCTTCATGTTAATATCACATATTTTTATATTAAC-TTCGCATCTCTTCATGTTAACATC
1 ATATTTTTTC-TGTTAACATCACATATTTTTATATTAACATT-ACATCTCTTCATATTAACATC
* * *
603380 ATATATTTTTCTGTT-ACATTATATATTTTTTATATTTACAT
1 ATAT-TTTTTCTGTTAACATCACATA-TTTTTATATTAACAT
603421 CCTATCAATG
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
61 3 0.04
62 13 0.15
63 64 0.75
64 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.51
Consensus pattern (62 bp):
ATATTTTTTCTGTTAACATCACATATTTTTATATTAACATTACATCTCTTCATATTAACATC
Found at i:603410 original size:21 final size:21
Alignment explanation
Indices: 603370--603409 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
603360 CATCTCTTCA
603370 TGTTAACATCATATATTTTTC
1 TGTTAACATCATATATTTTTC
*
603391 TGTT-ACATTATATATTTTT
1 TGTTAACATCATATATTTTT
603410 TATATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
TGTTAACATCATATATTTTTC
Found at i:607485 original size:16 final size:17
Alignment explanation
Indices: 607443--607488 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
607433 TTTTACAAAT
*
607443 ATAATATAAAATACAAG
1 ATAAAATAAAATACAAG
607460 ATAAAATAAAATA-AAG
1 ATAAAATAAAATACAAG
607476 -TAAGAATAAAATA
1 ATAA-AATAAAATA
607489 TATAAAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 3 0.11
16 12 0.44
17 12 0.44
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (17 bp):
ATAAAATAAAATACAAG
Found at i:607579 original size:19 final size:18
Alignment explanation
Indices: 607530--607580 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
607520 ATAAATTGTA
*
607530 AAAATTATATAAAA--AT
1 AAAATTATTTAAAATTAT
*
607546 AAAATTACTTCAAAATTAT
1 AAAATTA-TTTAAAATTAT
607565 AAAAGTTATTTAAAAT
1 AAAA-TTATTTAAAAT
607581 GTAAAGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.25
17 5 0.18
19 13 0.46
20 3 0.11
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATTATTTAAAATTAT
Found at i:607633 original size:41 final size:41
Alignment explanation
Indices: 607587--607674 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 41
607577 AAATGTAAAG
* *
607587 TAATTATTTGAAAAGT-ATAACTATTATAAAATTGTAAAAAA
1 TAATTATTT-AAAAATCATAAATATTATAAAATTGTAAAAAA
607628 TAATTATTTAAAAATCATAAATATTATAAAATTGTAAAAAA
1 TAATTATTTAAAAATCATAAATATTATAAAATTGTAAAAAA
*
607669 AAATTA
1 TAATTA
607675 CACTTACACG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 5 0.12
41 38 0.88
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (41 bp):
TAATTATTTAAAAATCATAAATATTATAAAATTGTAAAAAA
Found at i:610072 original size:19 final size:18
Alignment explanation
Indices: 610050--610094 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
610040 AGATAAGCGA
*
610050 TATAAATTATATGTTATGG
1 TATAAATTATATGATAT-G
**
610069 TATAGGTTATATGATATG
1 TATAAATTATATGATATG
610087 TATAAATT
1 TATAAATT
610095 CAAGATATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (18 bp):
TATAAATTATATGATATG
Found at i:614855 original size:3 final size:3
Alignment explanation
Indices: 614776--614842 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
614766 TTCATTTGAA
* * *
614776 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT AAT TAT TAT AAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
614820 TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
614843 ATAAATATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:617022 original size:30 final size:29
Alignment explanation
Indices: 616972--617034 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
616962 TAATTCTTTC
*
616972 TTTTCAAAAATTTGTATATATACT-TATTA
1 TTTTCAAAAATTTATATATATA-TATATTA
*
617001 TTTTCATAATATTTATATATATATATATTA
1 TTTTCA-AAAATTTATATATATATATATTA
617031 TTTT
1 TTTT
617035 ATTAATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTCAAAAATTTATATATATATATATTA
Found at i:620343 original size:15 final size:15
Alignment explanation
Indices: 620323--620354 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
620313 GATCAATACC
620323 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
620338 TTTTGCATACATTCA
1 TTTTGCATACATGCA
620353 TT
1 TT
620355 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:624163 original size:8 final size:9
Alignment explanation
Indices: 624136--624166 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
624126 AAATGGCAAT
624136 CATTCTTTA
1 CATTCTTTA
624145 CATTCTTTA
1 CATTCTTTA
624154 CATT-TTTA
1 CATTCTTTA
624162 CATTC
1 CATTC
624167 ATTATTTTTC
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:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:628101 original size:18 final size:18
Alignment explanation
Indices: 628075--628118 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
628065 TTCCAAGTTT
* *
628075 ATTTTTTTTTTAAATTCA
1 ATTTATTTTTGAAATTCA
628093 ATTTATTTTTGAAATTCA
1 ATTTATTTTTGAAATTCA
628111 ATTTATTT
1 ATTTATTT
628119 AATATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTATTTTTGAAATTCA
Found at i:629474 original size:113 final size:113
Alignment explanation
Indices: 629267--630318 Score: 625
Period size: 123 Copynumber: 8.8 Consensus size: 113
629257 GATTCGAATC
*
629267 CATCATTCGATGGATCAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
629332 AGAAGAAGTTCATAATGTGAATAACTTGTTTAACCTTTTGCTCAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGCTCAAATT
*
629380 CATCACTT-GATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAATAACTCATCTGAAGAAGG
1 CATCA-TTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * **
629444 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTT-AAACCTTTTGCTCAAATT
* *
629494 CATCATTCGATGGATCAACTTTTCTAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * **
629558 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTAT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC-TCA-AAT-T
*** * * *
629609 CA-CAGAAGAAGATAGATCAACATCAACTTTTCCAGAGA-AGTTCATAATAAGAAGAACTCGTCT
1 CATC---ATTCGATGGATC-A-A-C-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
* * * **
629672 ---GAA-GAAG-A-AA-TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTAT
57 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC-TCA-AAT-T
** * *
629725 CA-CAGAATGAGATAGATCAATATCAACTTTTCCAGAGA-AGTTCATAATGAGAAAAACTCATCT
1 CATC---ATTCGATGGATC-A-A-C-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
* * * **
629788 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTAT
57 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC-TCA-AAT-T
*** * *
629848 CA-CAGAAGGAGATAGATCAACATCAACTTTTCCAGAGA-AGTTCATAATAAGAAGAACTCATCT
1 CATC---ATTCGATGGATC-A-A-C-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
* * * **
629911 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTAT
57 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC-TCA-AAT-T
*** * *
629971 CA-CAGAAGAAGATAGATCAACATCAACTTTTCCAGAGA-AGTTCATAATAAGAAGAACTCATCT
1 CATC---ATTCGATGGATC-A-A-C-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
* * * * * **
630034 AAAGAATGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTAT
57 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC-TCA-AAT-T
*** * * *
630094 CA-CAAAAAGAGATAGATCAACATCAACTTTTCCAGAGA-AGTTCATAATGAAAAGAACTCATCC
1 CATC---ATTCGATGGATC-A-A-C-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
* * * **
630157 GAAG-AGGTAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTAT
57 GAAGAAGG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGC-TCA-AAT-T
* *** *
630217 CATAGAAGGAGATAGATCAACATCAACTTTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTG
1 CAT--CATTCGATGGATC-A-A-C-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTG
630281 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
58 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
630319 TAATTTTTTT
Statistics
Matches: 856, Mismatches: 56, Indels: 44
0.90 0.06 0.05
Matches are distributed among these distances:
112 9 0.01
113 150 0.18
114 43 0.05
115 3 0.00
116 99 0.12
117 10 0.01
118 2 0.00
119 8 0.01
120 8 0.01
121 1 0.00
122 4 0.00
123 516 0.60
124 3 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGCTCAAATT
Found at i:629655 original size:123 final size:123
Alignment explanation
Indices: 629507--630318 Score: 1374
Period size: 123 Copynumber: 6.7 Consensus size: 123
629497 CATTCGATGG
*
629507 ATCAACTTTTCTAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
629572 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
* *
629630 ATCAACTTTTCCAGAGAAGTTCATAATAAGAAGAACTCGTCT---GAA-GAAG-A-AA-TTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
629688 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAATG-AGATAGATCAAT
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAA-GAAGATAGATCAAC
*
629746 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
629811 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
*
629869 ATCAACTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
629934 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
* * *
629992 ATCAACTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
630057 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACA-AAAAGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGA-AGATAGATCAAC
* *
630115 ATCAACTTTTCCAGAGAAGTTCATAATGAAAAGAACTCATCCGAAG-AGGTAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AAGAAGAAGTTCAT
* *
630179 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCATAGAAGGAGATAGATCAAC
65 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
630238 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
630303 ATGAGAAGAACTTGTT
66 ATGAGAAGAGCTTGTT
630319 TAATTTTTTT
Statistics
Matches: 650, Mismatches: 26, Indels: 26
0.93 0.04 0.04
Matches are distributed among these distances:
116 99 0.15
117 3 0.00
118 1 0.00
119 7 0.01
120 7 0.01
121 1 0.00
122 8 0.01
123 519 0.80
124 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
Found at i:629988 original size:246 final size:245
Alignment explanation
Indices: 629280--630318 Score: 1424
Period size: 246 Copynumber: 4.3 Consensus size: 245
629270 CATTCGATGG
* *
629280 ATCAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * ** *
629345 AATGTGAATAACTTGTTTAACCTTTTGC-TCAAAT-TCATCAC-----TTGATGGATC-A-A-C-
65 AATGAGAAGAACTTGTTCAACCTTTTGCAT-GACTCT-ATCACAGAAGGAGATAGATCAACATCA
* * *
629399 A--TTTCCAGAGAGAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
128 ACTTTTCCAGAGA-AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
** ** * * * **
629462 AGAAGAATTTGTTCAAACCTTTTGTTTGA--AT-TCATC-----A-TTCGAT--GG
192 AGAAGAGCTTGTTC-AACCTTTTGCATGACTCTATCA-CAGAAGAGATAGATCAAC
*
629507 ATCAACTTTTCTAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
629572 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAACATCAACT
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
*
629637 TTTCCAGAGAAGTTCATAATAAGAAGAACTCGTCT---GAA-GAAG-A-AA-TTCATAATGAGAA
131 TTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
*
629695 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAATGAGATAGATCAAT
196 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAA-GAGATAGATCAAC
*
629746 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
629811 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
629876 TTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
131 TTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
629941 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAAC
196 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAG-AGATAGATCAAC
* * *
629992 ATCAACTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * *
630057 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGATCAACATCAACT
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
*
630122 TTTCCAGAGAAGTTCATAATGAA-AAGAACTCATCCGAAG-AGGTAAGAAGAAGTTCATAATGAG
131 TTTCCAGAGAAGTTCATAAT-AAGAAGAACTCATCTGAAGAAGG-AAGAAGAAGTTCATAATGAG
*
630185 AAGAGCTTGTTCAACCTTTTGCATGACTCTATCATAGAAGGAGATAGATCAAC
194 AAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAA-GAGATAGATCAAC
630238 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
630303 ATGAGAAGAACTTGTT
66 ATGAGAAGAACTTGTT
630319 TAATTTTTTT
Statistics
Matches: 735, Mismatches: 41, Indels: 53
0.89 0.05 0.06
Matches are distributed among these distances:
226 79 0.11
227 16 0.02
228 12 0.02
229 21 0.03
230 4 0.01
231 11 0.01
232 5 0.01
233 4 0.01
234 1 0.00
235 1 0.00
236 23 0.03
237 14 0.02
239 160 0.22
242 3 0.00
243 4 0.01
244 1 0.00
245 6 0.01
246 367 0.50
247 3 0.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (245 bp):
ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
TTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAGATAGATCAAC
Found at i:630209 original size:369 final size:362
Alignment explanation
Indices: 629393--630318 Score: 1448
Period size: 369 Copynumber: 2.6 Consensus size: 362
629383 CACTTGATGG
* * * *
629393 ATCAACATTTCCAGAGAGAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGA-AGTTCATAATGAGAAAAACTCATCCGAAGAAGGAAGAAGAAGTTCAT
** ** * * * **
629458 AATGAGAAGAATTTGTTCAAACCTTTTGTTTGA--AT-TCATC------A-TTCGAT--GGATCA
65 AATGAGAAGAGCTTGTTC-AACCTTTTGCATGACTCTATCA-CAGAAGGAGATAGATCAACATCA
*
629511 ACTTTTCTAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
128 ACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
629576 GAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAACATCAACTTTTC
193 GAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAACATCAACTTTTC
*
629641 CAGAGAAGTTCATAATAAGAAGAACTCGTCTGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCA
258 CAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCA
* * *
629706 ACCTTTTGCATGACTCTATCACAGAATGAGATAGATCAAT
323 ACCTTTTGCATGACTCTATCACAAAAAGAGATAGATCAAC
*
629746 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAAAACTCATCCGAAGAAGGAAGAAGAAGTTCATA
629811 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
*
629876 TTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
131 TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
*
629941 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAACATCAACTTTTCCAG
196 GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAACATCAACTTTTCCAG
630006 AGAAGTTCATAATAAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATAATGAGAAGAGCTTG
261 AGAAGTTCATAATAAGAAGAACTCATCT---GAA-GAAG-A-AA-TTCATAATGAGAAGAGCTTG
630071 TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGATCAAC
319 TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGATCAAC
630115 ATCAACTTTTCCAGAGAAGTTCATAATGA-AAAGAACTCATCCGAAG-AGGTAAGAAGAAGTTCA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAA-AACTCATCCGAAGAAGG-AAGAAGAAGTTCA
*
630178 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCATAGAAGGAGATAGATCAACATCAA
64 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAA
630243 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
129 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
630308 AAGAACTTGTT
194 AAGAACTTGTT
630319 TAATTTTTTT
Statistics
Matches: 529, Mismatches: 23, Indels: 26
0.92 0.04 0.04
Matches are distributed among these distances:
351 12 0.02
352 61 0.12
353 18 0.03
354 3 0.01
359 1 0.00
360 4 0.01
362 161 0.30
365 3 0.01
366 4 0.01
367 1 0.00
368 8 0.02
369 253 0.48
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (362 bp):
ATCAACTTTTCCAGAGAAGTTCATAATGAGAAAAACTCATCCGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAACATCAACTTTTCCAG
AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCAACC
TTTTGCATGACTCTATCACAAAAAGAGATAGATCAAC
Found at i:630631 original size:3 final size:3
Alignment explanation
Indices: 630625--630708 Score: 64
Period size: 3 Copynumber: 27.7 Consensus size: 3
630615 TTCATTTGAA
* * *
630625 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT AAT TAT TAT AAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
630669 AAT AAT TAT TAT TAT TAT TAAT AAA TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT -TAT TA
630709 CATGCCAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.04
3 59 0.87
4 6 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:632283 original size:18 final size:19
Alignment explanation
Indices: 632262--632297 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
632252 TTTAAATAAG
*
632262 ATAT-TATTTTTATAAATT
1 ATATCTATTTTAATAAATT
632280 ATATCTATTTTAATAAAT
1 ATATCTATTTTAATAAAT
632298 GCTTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATCTATTTTAATAAATT
Found at i:634067 original size:18 final size:18
Alignment explanation
Indices: 634044--634078 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
634034 ACTCTATTGA
*
634044 TCCAGTTGAGGACTCTCT
1 TCCAGTTGAAGACTCTCT
634062 TCCAGTTGAAGACTCTC
1 TCCAGTTGAAGACTCTC
634079 ACCCATCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (18 bp):
TCCAGTTGAAGACTCTCT
Found at i:638747 original size:18 final size:18
Alignment explanation
Indices: 638724--638812 Score: 151
Period size: 18 Copynumber: 4.9 Consensus size: 18
638714 GAGGGATTAC
*
638724 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
638742 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
638760 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
638778 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
638796 AATGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
638813 AATATTCAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:648593 original size:31 final size:31
Alignment explanation
Indices: 648555--648626 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
648545 ACTACGTAAA
*
648555 TGGTCACTTGCATTATGGTATTATTCAA-TTT
1 TGGTCACTTGCATTATCGTATTATT-AAGTTT
*
648586 TGGTCACTTGCGTTATCGTATTATTAAGTTT
1 TGGTCACTTGCATTATCGTATTATTAAGTTT
*
648617 TGATCACTTG
1 TGGTCACTTG
648627 GATGTTGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (31 bp):
TGGTCACTTGCATTATCGTATTATTAAGTTT
Found at i:654781 original size:14 final size:14
Alignment explanation
Indices: 654746--654783 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
654736 TTAAATTTTT
654746 TAAAAAAAATGTTA
1 TAAAAAAAATGTTA
*
654760 TATAAAAAATGTTA
1 TAAAAAAAATGTTA
654774 -AAAGAAAAAT
1 TAAA-AAAAAT
654784 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (14 bp):
TAAAAAAAATGTTA
Found at i:654782 original size:67 final size:65
Alignment explanation
Indices: 654711--654853 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 65
654701 TTAAATTTAA
* *
654711 AAAAAATAAATCAAA-GAATGAA-ATATTAAATTTTTTAAAA-AAAATGTTATATAAAAAATGTT
1 AAAAAATAAAT-AAATG-ATGAATATATTAAATTTTATAAAAGAAAA--ATA-ATAAAAAATGTT
654773 AAAAG
61 AAAAG
*
654778 AAAAATTAAAATAAATGATGAATATATTAAATTTTATAAAAGAAAAATAATAAAAAATGTTAAAA
1 AAAAAAT-AAATAAATGATGAATATATTAAATTTTATAAAAGAAAAATAATAAAAAATGTTAAAA
654843 G
65 G
654844 AAAAAATAAA
1 AAAAAATAAA
654854 AATAAAACAA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
65 3 0.04
66 23 0.34
67 16 0.24
68 22 0.32
69 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (65 bp):
AAAAAATAAATAAATGATGAATATATTAAATTTTATAAAAGAAAAATAATAAAAAATGTTAAAAG
Found at i:654832 original size:66 final size:67
Alignment explanation
Indices: 654728--654859 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
654718 AAATCAAAGA
* * *
654728 ATGAAATATTAAATTTTTTAAAAAAAATGTTATATAAAAAATGTTAAAAG-AAAAATTAAAATAA
1 ATGAAATATTAAATTTTATAAAAAAAA-GATATATAAAAAATGTTAAAAGAAAAAATAAAAATAA
654792 ATG
65 ATG
654795 ATGAATATATTAAATTTTATAAAAGAAAA-ATA-ATAAAAAATGTTAAAAGAAAAAATAAAAATA
1 ATGAA-ATATTAAATTTTATAAAA-AAAAGATATATAAAAAATGTTAAAAGAAAAAATAAAAATA
654858 AA
64 AA
654860 ACAAAATAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
66 17 0.29
67 21 0.36
68 17 0.29
69 4 0.07
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (67 bp):
ATGAAATATTAAATTTTATAAAAAAAAGATATATAAAAAATGTTAAAAGAAAAAATAAAAATAAA
TG
Found at i:654854 original size:6 final size:5
Alignment explanation
Indices: 654846--654879 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
654836 GTTAAAAGAA
*
654846 AAAAT AAAAAT AAAAC AAAAT AAAAT AAAAT AAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAA
654880 GAGGTGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:654993 original size:5 final size:5
Alignment explanation
Indices: 654970--655029 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
654960 AAAACAATGG
*
654970 TAAAA TAAAA GGTATAA TAAAA TAAAA TAAAA TAAAA TAAAAGA TAAAA
1 TAAAA TAAAA --TAAAA TAAAA TAAAA TAAAA TAAAA T-AAA-A TAAAA
655019 T--AA TAAAA TAA
1 TAAAA TAAAA TAA
655030 TAAATAATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 3 0.06
5 32 0.68
6 6 0.13
7 6 0.13
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:655036 original size:32 final size:32
Alignment explanation
Indices: 654970--655029 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
654960 AAAACAATGG
654970 TAAAATAAAAGGTATAATAAAATAAAATAAAA
1 TAAAATAAAAGGTATAATAAAATAAAATAAAA
655002 TAAAATAAAA-G-ATAA-AATAATAAAATAA
1 TAAAATAAAAGGTATAATAA-AATAAAATAA
655030 TAAATAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.07
30 14 0.52
31 1 0.04
32 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (32 bp):
TAAAATAAAAGGTATAATAAAATAAAATAAAA
Found at i:655113 original size:18 final size:18
Alignment explanation
Indices: 655078--655120 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
655068 GTTGTTTTTA
*
655078 AAATAAAAGATATGAATT
1 AAATAAAAGAAATGAATT
655096 AAATAAAAGAAAAT-AATT
1 AAATAAAAG-AAATGAATT
*
655114 TAATAAA
1 AAATAAA
655121 TAATATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
AAATAAAAGAAATGAATT
Found at i:661390 original size:16 final size:16
Alignment explanation
Indices: 661371--661401 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
661361 AAAATGTTTA
*
661371 AAAAGAAAATAAAAAT
1 AAAACAAAATAAAAAT
661387 AAAACAAAATAAAAA
1 AAAACAAAATAAAAA
661402 AAGAGGTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAACAAAATAAAAAT
Found at i:661390 original size:26 final size:26
Alignment explanation
Indices: 661336--661390 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
661326 AGAAAATATT
*
661336 AAATTTTAGAAAAGAAAAATAATAAA
1 AAATTTTAGAAAAGAAAAATAAAAAA
661362 AAATGTTTA-AAAAG-AAAATAAAAATA
1 AAAT-TTTAGAAAAGAAAAATAAAAA-A
661388 AAA
1 AAA
661391 CAAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 9 0.35
26 13 0.50
27 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (26 bp):
AAATTTTAGAAAAGAAAAATAAAAAA
Found at i:662218 original size:12 final size:13
Alignment explanation
Indices: 662201--662229 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
662191 AAAGATAAAA
662201 TAAAATAATAT-T
1 TAAAATAATATCT
662213 TAAAATAATATCT
1 TAAAATAATATCT
662226 TAAA
1 TAAA
662230 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:662799 original size:114 final size:114
Alignment explanation
Indices: 662598--662821 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 114
662588 ATATCACATA
*
662598 AACTTCCTTCATAATGAATAAAATATCTTATTTGGTACAATAATAATTTCAAATGATAGAGAATC
1 AACTTCCTTCATAATGAATAAAATATCTTATCTGGTACAATAATAATTTCAAATGATAGAGAATC
* * * *
662663 TTAACTATTCATATCTTTTTCTTTTCAGAGAATTATCATTTCAAATTAG
66 TTAACTATTCACATCTTCTTCTTTTCAGAGAAATATCATATCAAATTAG
662712 AACTTCCTTCATAATGAATAAAATATCTTATCTGGTACAATAATAATTTCAAATGATAGAGAATC
1 AACTTCCTTCATAATGAATAAAATATCTTATCTGGTACAATAATAATTTCAAATGATAGAGAATC
* * *
662777 TTAATTATTCACA-CATTCTTCTTTTTAGTGAAATATCATATCAAA
66 TTAACTATTCACATC-TTCTTCTTTTCAGAGAAATATCATATCAAA
662822 CCAAAATTTT
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 100 0.99
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.40
Consensus pattern (114 bp):
AACTTCCTTCATAATGAATAAAATATCTTATCTGGTACAATAATAATTTCAAATGATAGAGAATC
TTAACTATTCACATCTTCTTCTTTTCAGAGAAATATCATATCAAATTAG
Found at i:665362 original size:18 final size:18
Alignment explanation
Indices: 665334--665374 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
665324 AATATTTTTA
665334 TTAGG-ATTTTATTTTCT
1 TTAGGTATTTTATTTTCT
665351 TTAGGTATTTTATTTTCT
1 TTAGGTATTTTATTTTCT
665369 TTAGGT
1 TTAGGT
665375 TTTCTCAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (18 bp):
TTAGGTATTTTATTTTCT
Found at i:671983 original size:13 final size:13
Alignment explanation
Indices: 671965--671994 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
671955 CTTTTTAATT
671965 TTTTTATTATTTA
1 TTTTTATTATTTA
671978 TTTTTATTATTTA
1 TTTTTATTATTTA
671991 TTTT
1 TTTT
671995 AATTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:682992 original size:12 final size:12
Alignment explanation
Indices: 682975--683007 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
682965 TTTTGAAATA
682975 TATATATATATG
1 TATATATATATG
682987 TATATATATATG
1 TATATATATATG
*
682999 TATGTATAT
1 TATATATAT
683008 GGATCGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:682993 original size:16 final size:16
Alignment explanation
Indices: 682972--683007 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
682962 GCATTTTGAA
682972 ATATATATATATATGT
1 ATATATATATATATGT
*
682988 ATATATATATGTATGT
1 ATATATATATATATGT
683004 ATAT
1 ATAT
683008 GGATCGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
ATATATATATATATGT
Found at i:683998 original size:14 final size:14
Alignment explanation
Indices: 683969--684023 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
683959 CGTTCGTGAA
683969 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
683985 CGTTCATTTA---T
1 CGTTCATTTATGTT
*
683996 -GTTCATTTATATT
1 CGTTCATTTATGTT
684009 CGTTCATTTATGTT
1 CGTTCATTTATGTT
684023 C
1 C
684024 AAACAGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 15 0.44
15 3 0.09
16 5 0.15
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.55
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:684687 original size:17 final size:18
Alignment explanation
Indices: 684675--684712 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
684665 AGTATTTTTA
684675 TTAAG-ATTTTATTTTCT
1 TTAAGTATTTTATTTTCT
*
684692 TTAGGTATTTTATTTTCT
1 TTAAGTATTTTATTTTCT
684710 TTA
1 TTA
684713 GTTTTTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (18 bp):
TTAAGTATTTTATTTTCT
Found at i:690609 original size:21 final size:22
Alignment explanation
Indices: 690574--690629 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
690564 ATTCTCGATT
*
690574 GTATCGATAC-TCCTTATTG-G
1 GTATCAATACTTCCTTATTGTG
* *
690594 GTATCAATATTTCCTTTTTGTG
1 GTATCAATACTTCCTTATTGTG
*
690616 GTATCGATACTTCC
1 GTATCAATACTTCC
690630 CTGATTATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 8 0.28
21 8 0.28
22 13 0.45
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (22 bp):
GTATCAATACTTCCTTATTGTG
Found at i:690707 original size:20 final size:19
Alignment explanation
Indices: 690684--690746 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
690674 CTTAGTATAC
690684 ATACCCCTACTAGAGTATCG
1 ATACCCCTACT-GAGTATCG
* *
690704 ATA-CTCTACCCTTAGTATCG
1 ATACCCCTA--CTGAGTATCG
*
690724 ATACTCCTA-TGAGTATCG
1 ATACCCCTACTGAGTATCG
690742 ATACC
1 ATACC
690747 AAAATGGCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 12 0.35
19 4 0.12
20 13 0.38
21 5 0.15
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.30
Consensus pattern (19 bp):
ATACCCCTACTGAGTATCG
Found at i:692499 original size:41 final size:39
Alignment explanation
Indices: 692454--692532 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 39
692444 TTACATTTGT
*
692454 AATGCTTGTAATATTAT-TACAATGTAAGAGTTAATGCTTGC
1 AATGCTTGTAATATAATGT--AATGTAAGAG-TAATGCTTGC
*
692495 AATGCTTGTAATATAATGTAATGTAGGAGTAATGCTTG
1 AATGCTTGTAATATAATGTAATGTAAGAGTAATGCTTG
692533 TAAGGATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 9 0.26
40 9 0.26
41 16 0.46
42 1 0.03
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (39 bp):
AATGCTTGTAATATAATGTAATGTAAGAGTAATGCTTGC
Found at i:692776 original size:32 final size:34
Alignment explanation
Indices: 692733--692814 Score: 114
Period size: 32 Copynumber: 2.4 Consensus size: 34
692723 TATATATATA
* *
692733 TTATAATGTAATGTAGGAGTTCATGCTTGTAAT-C
1 TTAT-ATGTAATGTAGGAGTTAATACTTGTAATGC
692767 TTAT-TGTAATGTAGGAGTTAATACTTGTAATGC
1 TTATATGTAATGTAGGAGTTAATACTTGTAATGC
692800 TTATAATGTAATGTA
1 TTAT-ATGTAATGTA
692815 ATGTATGAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 25 0.58
33 5 0.12
34 4 0.09
35 9 0.21
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.43
Consensus pattern (34 bp):
TTATATGTAATGTAGGAGTTAATACTTGTAATGC
Found at i:693448 original size:14 final size:14
Alignment explanation
Indices: 693424--693475 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
693414 TCGATTATAT
*
693424 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
*
693438 GTTCA--TAT-AT-
1 GTTCATTTATGTTC
693448 GTTCATTTATGTTC
1 GTTCATTTATGTTC
693462 GTTCATTTATGTTC
1 GTTCATTTATGTTC
693476 ATTTATGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 1 0.03
12 6 0.19
13 1 0.03
14 18 0.58
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:693451 original size:24 final size:24
Alignment explanation
Indices: 693410--693486 Score: 118
Period size: 24 Copynumber: 3.1 Consensus size: 24
693400 ACGTTTGTGA
*
693410 TCGTTCGATTATATGTTCGTTTATGT
1 TCGTTC-A-TATATGTTCATTTATGT
693436 TCGTTCATATATGTTCATTTATGT
1 TCGTTCATATATGTTCATTTATGT
*
693460 TCGTTCATTTATGTTCATTTATGT
1 TCGTTCATATATGTTCATTTATGT
693484 TCG
1 TCG
693487 AACAGATGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 42 0.86
25 1 0.02
26 6 0.12
ACGTcount: A:0.17, C:0.13, G:0.16, T:0.55
Consensus pattern (24 bp):
TCGTTCATATATGTTCATTTATGT
Found at i:693475 original size:10 final size:10
Alignment explanation
Indices: 693438--693485 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
693428 GTTTATGTTC
*
693438 GTTCATATAT
1 GTTCATTTAT
693448 GTTCATTTATGTT
1 GTTCATTTA---T
693461 CGTTCATTTAT
1 -GTTCATTTAT
693472 GTTCATTTAT
1 GTTCATTTAT
693482 GTTC
1 GTTC
693486 GAACAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:693898 original size:14 final size:16
Alignment explanation
Indices: 693858--693899 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
693848 AAAAAAAATT
* *
693858 TGTTCGTTTATGTTCG
1 TGTTCATTTATTTTCG
693874 TGTTCATTTATTTTCG
1 TGTTCATTTATTTTCG
693890 T-TT-ATTTATT
1 TGTTCATTTATT
693900 AAATGAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 7 0.29
15 2 0.08
16 15 0.62
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (16 bp):
TGTTCATTTATTTTCG
Found at i:695350 original size:30 final size:30
Alignment explanation
Indices: 695316--695433 Score: 129
Period size: 30 Copynumber: 4.0 Consensus size: 30
695306 AAAAAAGATT
*
695316 AAATAAGAATAAGATATATTTTTTAAGTTA
1 AAATAAGAATAATATATATTTTTTAAGTTA
*
695346 AAATAAGATTAA-ACTATATTTTTTAA--TA
1 AAATAAGAATAATA-TATATTTTTTAAGTTA
**
695374 AAATAA-AA-AATATATATTTAATAAGTTA
1 AAATAAGAATAATATATATTTTTTAAGTTA
* *
695402 AGATAAAAATAATATATATTTTTTAATGTTA
1 AAATAAGAATAATATATATTTTTTAA-GTTA
695433 A
1 A
695434 TAAGTGAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
26 12 0.16
27 2 0.03
28 15 0.20
29 3 0.04
30 37 0.50
31 5 0.07
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.41
Consensus pattern (30 bp):
AAATAAGAATAATATATATTTTTTAAGTTA
Found at i:697029 original size:4 final size:4
Alignment explanation
Indices: 697020--697049 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
697010 AAAACATGCA
*
697020 TATC TATC TATC TATC CATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TATC TA
697050 GGTAGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (4 bp):
TATC
Found at i:699486 original size:19 final size:19
Alignment explanation
Indices: 699462--699511 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
699452 AATGACCAAT
699462 AAAATCGCAATGAGAAATA
1 AAAATCGCAATGAGAAATA
699481 AAAATCGCAATGAGAAATA
1 AAAATCGCAATGAGAAATA
699500 AAAATCGCAATG
1 AAAATCGCAATG
699512 CGATCTCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGAGAAATA
Found at i:699612 original size:20 final size:21
Alignment explanation
Indices: 699564--699616 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
699554 GATTTTTCAG
*
699564 AATC-GCAACGCGAATATGAA
1 AATCAGCAACGCGAACATGAA
699584 AATCA-CAACGCGAACAT-ATA
1 AATCAGCAACGCGAACATGA-A
699604 AAT-AGCAACGCGA
1 AATCAGCAACGCGA
699617 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (21 bp):
AATCAGCAACGCGAACATGAA
Found at i:699649 original size:81 final size:80
Alignment explanation
Indices: 699564--699835 Score: 289
Period size: 81 Copynumber: 3.4 Consensus size: 80
699554 GATTTTTCAG
* * * * * * *
699564 AATCGCAACGCGAATATGAAAATCACAACGCGAACATATAAATAGCAACGCGATTC-TGACTATC
1 AATCGCAACGCGTATCTGTAAATCGCAATGCGAACATATAAATCGCAACGCGATTCGT-A-AATC
699628 GCAACGAGTATCCGTAA
64 GCAACGAGTATCCGTAA
* * * *
699645 AATCGCAACGCGTATCCGTAAATCGCAATGACAATACGTA-AAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGTATCTGTAAATCGCAATG-CGA-ACATATAAATCGCAACGCG-ATTCGTAAAT
* *
699709 CGCAACGAGAATACGT-A
63 CGCAACGAGTATCCGTAA
* * * *
699726 AATCGCAACGCGTATCTGTAAATCGCAATGAGAATATATAAATCGCAACGACAATACGTAAAATC
1 AATCGCAACGCGTATCTGTAAATCGCAATGCGAACATATAAATCGCAACG-CGATTCGT-AAATC
*
699791 GCAACGCGTATCCGTAA
64 GCAACGAGTATCCGTAA
*
699808 AATCGCAACGCGTATCCGTAAATCGCAA
1 AATCGCAACGCGTATCTGTAAATCGCAA
699836 CGTGATTTTT
Statistics
Matches: 159, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
79 3 0.02
80 17 0.11
81 72 0.45
82 58 0.36
83 8 0.05
84 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATCTGTAAATCGCAATGCGAACATATAAATCGCAACGCGATTCGTAAATCGC
AACGAGTATCCGTAA
Found at i:699656 original size:41 final size:41
Alignment explanation
Indices: 699625--699837 Score: 272
Period size: 41 Copynumber: 5.2 Consensus size: 41
699615 GATTCTGACT
* *
699625 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
699666 ATCGCAATGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
699707 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
699747 ATCGCAATGAGAATA--TATAAATCGCAACGAC-AATACGTAAA
1 ATCGCAACGAGAATACGTA-AAATCGCAACG-CGTATCCGT-AA
* * *
699788 ATCGCAACGCGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
699829 ATCGCAACG
1 ATCGCAACG
699838 TGATTTTTAA
Statistics
Matches: 148, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
40 50 0.34
41 79 0.53
42 16 0.11
43 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:699669 original size:20 final size:20
Alignment explanation
Indices: 699625--699837 Score: 214
Period size: 20 Copynumber: 10.4 Consensus size: 20
699615 GATTCTGACT
*
699625 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
699646 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
699666 ATCGCAATGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
699687 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
699707 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
699727 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * ***
699747 ATCGCAATGAGAATATATAA
1 ATCGCAACGCGTATCCGTAA
* *
699767 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
699788 ATCGCAACGCGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
699809 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
699829 ATCGCAACG
1 ATCGCAACG
699838 TGATTTTTAA
Statistics
Matches: 161, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
20 91 0.57
21 70 0.43
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:700404 original size:21 final size:21
Alignment explanation
Indices: 700343--700421 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
700333 TTCTAAACTT
700343 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
*
700363 AAAATCGCAA-TACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
700383 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
700404 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
700422 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 28 0.56
21 22 0.44
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:700425 original size:14 final size:14
Alignment explanation
Indices: 700403--700467 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
700393 CGAGAGAAAT
700403 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
700417 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
700435 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
700450 GATAATCGCAACGC
1 GAAAATCGCAACGA
700464 GAAA
1 GAAA
700468 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:700439 original size:33 final size:33
Alignment explanation
Indices: 700398--700478 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
700388 CGCAACGAGA
700398 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
700431 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
700464 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
700479 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:700565 original size:20 final size:20
Alignment explanation
Indices: 700503--700558 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
700493 TCGCGTTGCG
700503 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
700523 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
700543 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
700559 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:702514 original size:95 final size:95
Alignment explanation
Indices: 702263--702496 Score: 398
Period size: 95 Copynumber: 2.5 Consensus size: 95
702253 TAGATTGCTT
* * *
702263 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
702328 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTATCTTTTGGTTGAA
* *
702358 AGTAAATTTGTTTGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
702423 ATTTGTC-TTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTATCTTTTGGTTGAA
*
702452 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACTGTGTATTC
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC
702497 ACGTTGCGAT
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 63 0.48
95 67 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (95 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGTTTTATCTTTTGGTTGAA
Found at i:704384 original size:14 final size:14
Alignment explanation
Indices: 704365--704398 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
704355 TGTTTAATTT
704365 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
*
704379 ATTTGTAAAAGTTG
1 ATTTGTAAAAGATG
704393 ATTTGT
1 ATTTGT
704399 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:704521 original size:19 final size:17
Alignment explanation
Indices: 704505--704555 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
704495 AAAAATGACT
704505 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
704524 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
704538 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
704555 A
1 A
704556 AATTGCAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:704547 original size:33 final size:33
Alignment explanation
Indices: 704505--704592 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
704495 AAAAATGACT
704505 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
704538 ATCGCAATGCGAAATGAAAATTGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
704571 ATCGTAAAGCAAAATGAAAATC
1 ATCGCAATGCGAAATGAAAATC
704593 TCAATGCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:704565 original size:19 final size:19
Alignment explanation
Indices: 704505--704565 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
704495 AAAAATGACT
704505 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
704524 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
704538 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
704557 ATTGCAATG
1 ATCGCAATG
704566 AGGGAATCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:704655 original size:33 final size:33
Alignment explanation
Indices: 704613--704793 Score: 193
Period size: 33 Copynumber: 5.3 Consensus size: 33
704603 TTTAGTTTCG
* * *
704613 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
704646 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
704679 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * *
704718 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
* *
704752 CGTTGCGATTTTCATTTCGTATAGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
704785 CGTTGCGAT
1 CGTTGCGAT
704794 AGTAATTTCC
Statistics
Matches: 126, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
33 78 0.62
34 16 0.13
35 3 0.02
38 2 0.02
39 15 0.12
40 12 0.10
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:704705 original size:19 final size:19
Alignment explanation
Indices: 704608--704770 Score: 124
Period size: 19 Copynumber: 9.3 Consensus size: 19
704598 GCAAATTTAG
704608 TTTCGCGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
704626 GTTTCGCGTTGCGA-TTT--
1 -TTTCGCGTTGCGATTTTCA
*
704643 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
704660 TTTCGCATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
704676 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* **
704693 TTTCGCATTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
704712 TTTCCGCGTTGCGATATTCA
1 TTT-CGCGTTGCGATTTTCA
704732 TATTCGCGTTGCGATTTTCA
1 T-TTCGCGTTGCGATTTTCA
704752 -----CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
704766 TTTCG
1 TTTCG
704771 TATAGCGATT
Statistics
Matches: 115, Mismatches: 12, Indels: 34
0.71 0.07 0.21
Matches are distributed among these distances:
14 31 0.27
15 3 0.03
16 5 0.04
17 5 0.04
18 3 0.03
19 36 0.31
20 30 0.26
21 2 0.02
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:704757 original size:14 final size:14
Alignment explanation
Indices: 704738--704765 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
704728 TTCATATTCG
704738 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
704752 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
704766 TTTCGTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Done.