Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008876.1 Hibiscus syriacus cultivar Beakdansim tig00112114_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: 1683876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:528078 original size:2 final size:2
Alignment explanation
Indices: 528071--528104 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
528061 ATATTAGATA
528071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
528105 ACAAATCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533006 original size:3 final size:3
Alignment explanation
Indices: 532998--533035 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
532988 TACTATTTAT
532998 TTA TTA TTA -TA GTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
533036 TATTTATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:533015 original size:12 final size:11
Alignment explanation
Indices: 532994--533031 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
532984 AATGTACTAT
532994 TTAT-TTATTA
1 TTATATTATTA
533004 TTATAGTTATTA
1 TTATA-TTATTA
533016 TTATTATTATTA
1 TTA-TATTATTA
533028 TTAT
1 TTAT
533032 TATTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 1 0.04
12 18 0.72
13 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
TTATATTATTA
Found at i:533501 original size:14 final size:14
Alignment explanation
Indices: 533455--533501 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
533445 CGTTGGGCAT
*
533455 CCGAAGCCATTCGA
1 CCGAGGCCATTCGA
* *
533469 CCGAGGGCATCCGA
1 CCGAGGCCATTCGA
533483 CCGAGGCCATTCGA
1 CCGAGGCCATTCGA
*
533497 GCGAG
1 CCGAG
533502 CTATGCGAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.23, C:0.34, G:0.32, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATTCGA
Found at i:533590 original size:29 final size:29
Alignment explanation
Indices: 533548--533624 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
533538 GAGGAGCAGA
533548 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
533577 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
533606 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
533625 TGCTGGGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:533795 original size:2 final size:2
Alignment explanation
Indices: 533788--533817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
533778 TACACTTGTT
533788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
533818 AGGTCATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:535694 original size:25 final size:24
Alignment explanation
Indices: 535646--535712 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
535636 ATAGCTGTGA
*
535646 TATATTTTAATATTTT-ATTTATT
1 TATATTTTAATATTTTAATTGATT
*
535669 TATATTTTAAAAATTTTAATTGATT
1 TATATTTT-AATATTTTAATTGATT
*
535694 TTTATTTTTAATATTTTAA
1 TATA-TTTTAATATTTTAA
535713 ATTTTGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.22
24 7 0.19
25 18 0.49
26 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (24 bp):
TATATTTTAATATTTTAATTGATT
Found at i:535695 original size:34 final size:32
Alignment explanation
Indices: 535649--535742 Score: 88
Period size: 32 Copynumber: 2.9 Consensus size: 32
535639 GCTGTGATAT
*
535649 ATTTTAATA-TTTTATTTATTTATATTTTAAAA
1 ATTTTAATATTTTTATTT-TTAATATTTTAAAA
535681 ATTTTAATTGATTTTTATTTTTAATATTTT--AA
1 ATTTTAA-T-ATTTTTATTTTTAATATTTTAAAA
*
535713 ATTTTGAATAATTTCTTAATTTTAAT-TTTT
1 ATTTT-AAT-ATTT-TTATTTTTAATATTTT
535743 CTTAAAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
32 23 0.43
33 13 0.24
34 10 0.19
35 8 0.15
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (32 bp):
ATTTTAATATTTTTATTTTTAATATTTTAAAA
Found at i:535716 original size:7 final size:8
Alignment explanation
Indices: 535647--535722 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 8
535637 TAGCTGTGAT
535647 ATATTTTA
1 ATATTTTA
535655 ATATTTT-
1 ATATTTTA
*
535662 AT-TTATTT
1 ATATT-TTA
535670 ATATTTTAA
1 ATATTTT-A
*
535679 AAATTTTA
1 ATATTTTA
*
535687 ATTGATTTTT
1 A-T-ATTTTA
535697 AT-TTTTA
1 ATATTTTA
535704 ATATTTTA
1 ATATTTTA
535712 A-ATTTTGA
1 ATATTTT-A
535720 ATA
1 ATA
535723 ATTTCTTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
6 2 0.04
7 15 0.28
8 21 0.39
9 10 0.19
10 6 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
ATATTTTA
Found at i:535747 original size:16 final size:15
Alignment explanation
Indices: 535649--535742 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 15
535639 GCTGTGATAT
535649 ATTTTAATA-TTTTA
1 ATTTTAATATTTTTA
* * *
535663 TTTATTTATATTTTAAAA
1 ATT-TTAATATTTT--TA
535681 ATTTTAATTGATTTTTA
1 ATTTTAA-T-ATTTTTA
* *
535698 TTTTTAATATTTTAA
1 ATTTTAATATTTTTA
535713 ATTTTGAATAATTTCTTA
1 ATTTT-AAT-ATTT-TTA
535731 ATTTTAAT-TTTT
1 ATTTTAATATTTT
535743 CTTAAAAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
14 3 0.05
15 18 0.30
16 7 0.11
17 17 0.28
18 11 0.18
19 5 0.08
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (15 bp):
ATTTTAATATTTTTA
Found at i:541120 original size:41 final size:42
Alignment explanation
Indices: 541053--541140 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 42
541043 ATGAAAATTT
* *
541053 TATTAATTAATGTTATCTATATATTCTTATAACAATCTATAA
1 TATTAATTAATATTATCTATATATTCTTAAAACAATCTATAA
* * *
541095 TATTAATT-ATATTATAC-ATATATTCTTAAAATATTTTATAA
1 TATTAATTAATATTAT-CTATATATTCTTAAAACAATCTATAA
541136 TATTA
1 TATTA
541141 TAAATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 31 0.77
42 9 0.22
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (42 bp):
TATTAATTAATATTATCTATATATTCTTAAAACAATCTATAA
Found at i:541139 original size:10 final size:10
Alignment explanation
Indices: 541114--541168 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
541104 TATTATACAT
*
541114 ATATTCTTAAA
1 ATATT-TTATA
541125 ATATTTTATA
1 ATATTTTATA
* *
541135 ATATTATAAA
1 ATATTTTATA
541145 TATATTCTTATA
1 -ATATT-TTATA
541157 ATATTTTATA
1 ATATTTTATA
541167 AT
1 AT
541169 TTATGATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
10 19 0.51
11 15 0.41
12 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (10 bp):
ATATTTTATA
Found at i:541140 original size:32 final size:32
Alignment explanation
Indices: 541103--541172 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
541093 AATATTAATT
*
541103 ATATTATACATATATTCTTAAAATATTTTATA
1 ATATTATAAATATATTCTTAAAATATTTTATA
*
541135 ATATTATAAATATATTCTTATAATATTTTATA
1 ATATTATAAATATATTCTTAAAATATTTTATA
541167 AT-TTAT
1 ATATTAT
541173 GATATAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATTATAAATATATTCTTAAAATATTTTATA
Found at i:541158 original size:22 final size:20
Alignment explanation
Indices: 541121--541161 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
541111 CATATATTCT
541121 TAAAATATTTTATAATATTA
1 TAAAATATTTTATAATATTA
541141 TAAATATATTCTTATAATATT
1 TAAA-ATATT-TTATAATATT
541162 TTATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATATTTTATAATATTA
Found at i:541684 original size:30 final size:30
Alignment explanation
Indices: 541649--541793 Score: 254
Period size: 30 Copynumber: 4.8 Consensus size: 30
541639 TCCGTCTTAA
*
541649 AAAAATGATCAAATTGCACGACTATTATAT
1 AAAAATGATCAAATTGCACGACTATTATAG
541679 AAAAATGATCAAATTGCACGACTATTATAG
1 AAAAATGATCAAATTGCACGACTATTATAG
541709 AAAAATGATCAAATTGCACGACTATTATAG
1 AAAAATGATCAAATTGCACGACTATTATAG
*
541739 AAAATTGATCAAATTGCACGACTATTATAG
1 AAAAATGATCAAATTGCACGACTATTATAG
* *
541769 AAAATTGATCAAATTGCATGACTAT
1 AAAAATGATCAAATTGCACGACTAT
541794 ATTGGTAAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 112 1.00
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (30 bp):
AAAAATGATCAAATTGCACGACTATTATAG
Found at i:542379 original size:13 final size:14
Alignment explanation
Indices: 542361--542396 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
542351 ACTCCACCAA
542361 TTACTTTTA-TTTG
1 TTACTTTTATTTTG
542374 TTACTTTTATTTTG
1 TTACTTTTATTTTG
542388 TTACTTTTA
1 TTACTTTTA
542397 CGGGTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (14 bp):
TTACTTTTATTTTG
Found at i:543455 original size:17 final size:18
Alignment explanation
Indices: 543432--543472 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
543422 AGTAATGCAA
543432 ATTATAATTA-AATAAAT
1 ATTATAATTATAATAAAT
* *
543449 TTTATAATTATACTAAAT
1 ATTATAATTATAATAAAT
543467 ATTATA
1 ATTATA
543473 TGAAAAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATAATTATAATAAAT
Found at i:549804 original size:21 final size:22
Alignment explanation
Indices: 549780--549834 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
549770 CGTTTGGATC
*
549780 TGTTTGGACCC-TCTGGGTTTT
1 TGTTTGGACCCGTATGGGTTTT
549801 TGTTTGGACCCGGGTATGGGTTTT
1 TGTTTGGACCC--GTATGGGTTTT
*
549825 GGTTTGGACC
1 TGTTTGGACC
549835 TGGGTCTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
24 18 0.62
ACGTcount: A:0.07, C:0.16, G:0.35, T:0.42
Consensus pattern (22 bp):
TGTTTGGACCCGTATGGGTTTT
Found at i:549829 original size:24 final size:24
Alignment explanation
Indices: 549793--549854 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
549783 TTGGACCCTC
*
549793 TGGGTTTTTGTTTGGACCCGGGTA
1 TGGGTTTTGGTTTGGACCCGGGTA
* *
549817 TGGGTTTTGGTTTGGACCTGGGTC
1 TGGGTTTTGGTTTGGACCCGGGTA
549841 TGGGTTTTGGTTTG
1 TGGGTTTTGGTTTG
549855 AACCGGTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.05, C:0.10, G:0.40, T:0.45
Consensus pattern (24 bp):
TGGGTTTTGGTTTGGACCCGGGTA
Found at i:549970 original size:5 final size:5
Alignment explanation
Indices: 549929--550017 Score: 63
Period size: 5 Copynumber: 16.4 Consensus size: 5
549919 TCAGGCCTGC
*
549929 AATAA AATATA AATGA AATAA AGATAAA AACTAA AATAA AATAAA AATAA
1 AATAA AATA-A AATAA AATAA A-AT-AA AA-TAA AATAA AAT-AA AATAA
* * *
549979 AAT-A GATAA AATAA GATAA GATAGAA AATAAA AATAA AA
1 AATAA AATAA AATAA AATAA -A-ATAA AAT-AA AATAA AA
550018 GAGTCGGGCG
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
4 3 0.04
5 35 0.52
6 22 0.33
7 7 0.10
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:550002 original size:19 final size:20
Alignment explanation
Indices: 549964--550017 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
549954 AAAAACTAAA
549964 ATAAAATAAAAATAAAATAG
1 ATAAAATAAAAATAAAATAG
* *
549984 ATAAAAT-AAGATAAGATAG
1 ATAAAATAAAAATAAAATAG
550003 --AAAATAAAAATAAAA
1 ATAAAATAAAAATAAAA
550018 GAGTCGGGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 10 0.34
20 7 0.24
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (20 bp):
ATAAAATAAAAATAAAATAG
Found at i:550008 original size:17 final size:16
Alignment explanation
Indices: 549929--550011 Score: 80
Period size: 17 Copynumber: 5.1 Consensus size: 16
549919 TCAGGCCTGC
* * *
549929 AATAAAATATAAATGA
1 AATAAGATAAAAATAA
549945 AATAAAGATAAAAACTAA
1 AAT-AAGATAAAAA-TAA
*
549963 AATAAAATAAAAATAA
1 AATAAGATAAAAATAA
549979 AAT-AGAT-AAAATAA
1 AATAAGATAAAAATAA
*
549993 GATAAGATAGAAAATAA
1 AATAAGATA-AAAATAA
550010 AA
1 AA
550012 ATAAAAGAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.16
15 7 0.13
16 9 0.16
17 25 0.45
18 5 0.09
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.19
Consensus pattern (16 bp):
AATAAGATAAAAATAA
Found at i:551126 original size:3 final size:3
Alignment explanation
Indices: 551118--551152 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
551108 CAAATAAATA
551118 AAT AAT AAT AAT AAT AAT AAT AACT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AA
551153 ATAAATAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:556392 original size:18 final size:18
Alignment explanation
Indices: 556371--556413 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
556361 CATATTTCTA
*
556371 TTATCTTGTTCATATGAT
1 TTATCTTGTTCATATCAT
556389 TTAT-TATGTTCATATCAT
1 TTATCT-TGTTCATATCAT
*
556407 ATATCTT
1 TTATCTT
556414 ATAACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.56
Consensus pattern (18 bp):
TTATCTTGTTCATATCAT
Found at i:559144 original size:20 final size:20
Alignment explanation
Indices: 559119--559169 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
559109 TTAATGAAGG
559119 CATGCATCGATGCACTACAC
1 CATGCATCGATGCACTACAC
559139 CATGCATCGATGCACTACAC
1 CATGCATCGATGCACTACAC
*
559159 CATGTATCGAT
1 CATGCATCGAT
559170 ACATCCCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (20 bp):
CATGCATCGATGCACTACAC
Found at i:563762 original size:20 final size:20
Alignment explanation
Indices: 563737--563787 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
563727 TTAATGAAGG
563737 CATGCATCGATGCACTACAC
1 CATGCATCGATGCACTACAC
563757 CATGCATCGATGCACTACAC
1 CATGCATCGATGCACTACAC
563777 CATGCATCGAT
1 CATGCATCGAT
563788 ACATCCCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (20 bp):
CATGCATCGATGCACTACAC
Found at i:568707 original size:29 final size:28
Alignment explanation
Indices: 568618--568691 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
568608 AAATAAAGTT
568618 AAAAATAAAATTCAATACTAGTATTGAA
1 AAAAATAAAATTCAATACTAGTATTGAA
568646 AAAAATAAAATTCAATACTAGTATTGAA
1 AAAAATAAAATTCAATACTAGTATTGAA
568674 AAAAATAAAATTTCAATA
1 AAAAATAAAA-TTCAATA
568692 GTATAAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 38 0.84
29 7 0.16
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAAATAAAATTCAATACTAGTATTGAA
Found at i:571193 original size:21 final size:22
Alignment explanation
Indices: 571159--571203 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
571149 TTCCTCACTT
*
571159 CTCACTCGTGTTTTTCT-TTCA
1 CTCACTCGTATTTTTCTCTTCA
* *
571180 CTCACTCTTATTTTTTTCTTCA
1 CTCACTCGTATTTTTCTCTTCA
571202 CT
1 CT
571204 TCTCTACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.11, C:0.29, G:0.04, T:0.56
Consensus pattern (22 bp):
CTCACTCGTATTTTTCTCTTCA
Found at i:575853 original size:21 final size:22
Alignment explanation
Indices: 575819--575863 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
575809 TTCCTCACTT
*
575819 CTCACTCGTGTTTTTCT-TTCA
1 CTCACTCGTATTTTTCTCTTCA
* *
575840 CTCACTCTTATTTTTTTCTTCA
1 CTCACTCGTATTTTTCTCTTCA
575862 CT
1 CT
575864 TCTCTACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.11, C:0.29, G:0.04, T:0.56
Consensus pattern (22 bp):
CTCACTCGTATTTTTCTCTTCA
Found at i:578040 original size:28 final size:27
Alignment explanation
Indices: 577992--578055 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
577982 TATTCTGTTA
577992 GGGTCGGGTTTTTTAAGTGTGATATCC
1 GGGTCGGGTTTTTTAAGTGTGATATCC
* *
578019 GGGTCGAGTTTTTTTAAGTGTGATATTC
1 GGGTCG-GGTTTTTTAAGTGTGATATCC
578047 GGGTCGGGT
1 GGGTCGGGT
578056 CGGGTCATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 8 0.24
28 25 0.76
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.41
Consensus pattern (27 bp):
GGGTCGGGTTTTTTAAGTGTGATATCC
Found at i:578662 original size:17 final size:18
Alignment explanation
Indices: 578640--578681 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
578630 AATTGTATTC
*
578640 CAATTCC-TGACAGATTT
1 CAATTCCTTCACAGATTT
578657 CAATTCCTTCACAGATTT
1 CAATTCCTTCACAGATTT
578675 CAATTCC
1 CAATTCC
578682 CTCAGAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (18 bp):
CAATTCCTTCACAGATTT
Found at i:580108 original size:21 final size:24
Alignment explanation
Indices: 580084--580126 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
580074 TTTTTTAAAG
580084 AAAAAT-TATTTA-AAT-TGATAT
1 AAAAATATATTTACAATATGATAT
580105 AAAAATATATTTACAATATGAT
1 AAAAATATATTTACAATATGAT
580127 TCAATGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 3 0.16
24 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (24 bp):
AAAAATATATTTACAATATGATAT
Found at i:580222 original size:27 final size:27
Alignment explanation
Indices: 580191--580244 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
580181 CTGAAGTTAA
580191 TTTTCTTTATTAGAATCCAATTAAAAG
1 TTTTCTTTATTAGAATCCAATTAAAAG
580218 TTTTCTTTATTAGAATCCAATTAAAAG
1 TTTTCTTTATTAGAATCCAATTAAAAG
580245 GGTTAGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (27 bp):
TTTTCTTTATTAGAATCCAATTAAAAG
Found at i:584319 original size:46 final size:46
Alignment explanation
Indices: 584178--584312 Score: 216
Period size: 46 Copynumber: 2.9 Consensus size: 46
584168 AAAAGTGATT
* ** * **
584178 TTTTTCCATAGCATTATTTCTGGCAGTTAATGCCTTTGGTGCATAC
1 TTTTTCCATGGCATTACATCTGGTAGTTGGTGCCTTTGGTGCATAC
584224 TTTTTCCATGGCATTACATCTGGTAGTTGGTGCCTTTGGTGCATAC
1 TTTTTCCATGGCATTACATCTGGTAGTTGGTGCCTTTGGTGCATAC
584270 TTTTTCCATGGCATTACATCTGGTAGTTGGTGCCTTTGGTGCA
1 TTTTTCCATGGCATTACATCTGGTAGTTGGTGCCTTTGGTGCA
584313 AGCTTTTCCC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (46 bp):
TTTTTCCATGGCATTACATCTGGTAGTTGGTGCCTTTGGTGCATAC
Found at i:588894 original size:44 final size:44
Alignment explanation
Indices: 588800--588890 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 44
588790 GAAATCTATT
* ** *
588800 TTAAATTGTTATTT-ATTTTTAAAGAGTTTTAAATAAATAATAA
1 TTAAATTATTATTTAATTTAAAAAGAGTTTTAAATAAATAAAAA
* *
588843 TTAAATTATTATTTAATTTAAAAAGA-TTTTTAATTAATAAAAA
1 TTAAATTATTATTTAATTTAAAAAGAGTTTTAAATAAATAAAAA
588886 TTAAA
1 TTAAA
588891 ATTAATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 32 0.78
44 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.47
Consensus pattern (44 bp):
TTAAATTATTATTTAATTTAAAAAGAGTTTTAAATAAATAAAAA
Found at i:599691 original size:24 final size:23
Alignment explanation
Indices: 599664--599709 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
599654 CAAGTGAGAG
*
599664 ATTGTTGAAAATTCGGTGCAAATA
1 ATTGTTGAAAATT-GGCGCAAATA
599688 ATTGTTGAAAATTGGCGCAAAT
1 ATTGTTGAAAATTGGCGCAAAT
599710 CACATGCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTGTTGAAAATTGGCGCAAATA
Found at i:600376 original size:57 final size:57
Alignment explanation
Indices: 600288--600397 Score: 193
Period size: 57 Copynumber: 1.9 Consensus size: 57
600278 AGTCTACATG
* *
600288 TACTTCATATTGATATGATATTATATCTTACATGTCACCTCAATAAATAACTTAATT
1 TACTTCATATTGATATGATATTATATCTTACAAGCCACCTCAATAAATAACTTAATT
*
600345 TACTTCGTATTGATATGATATTATATCTTACAAGCCACCTCAATAAATAACTT
1 TACTTCATATTGATATGATATTATATCTTACAAGCCACCTCAATAAATAACTT
600398 TAAATAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.40
Consensus pattern (57 bp):
TACTTCATATTGATATGATATTATATCTTACAAGCCACCTCAATAAATAACTTAATT
Found at i:603916 original size:20 final size:20
Alignment explanation
Indices: 603822--604190 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
603812 GATTTTCCAT
* ** *
603822 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
603842 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
603862 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
603882 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
603902 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
603922 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
603942 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
603962 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
603982 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
604002 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
604022 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
604042 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
604062 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
604082 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
604102 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
604122 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
604142 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
604162 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
604182 AATCACAAC
1 AATCGCAAC
604191 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:604903 original size:24 final size:24
Alignment explanation
Indices: 604864--604910 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
604854 AAATTTGGTC
604864 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
604888 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
604911 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:605099 original size:12 final size:12
Alignment explanation
Indices: 605082--605106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
605072 ATATAATCCT
605082 GAAGAAGAAAAA
1 GAAGAAGAAAAA
605094 GAAGAAGAAAAA
1 GAAGAAGAAAAA
605106 G
1 G
605107 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:607422 original size:19 final size:19
Alignment explanation
Indices: 607400--607686 Score: 311
Period size: 19 Copynumber: 16.4 Consensus size: 19
607390 ACGGAAATAC
*
607400 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
607419 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
607433 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
607453 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
607467 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
607486 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
607505 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
607519 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
607538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
607557 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
607571 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
607590 AATCGCAATACGAAATG-A
1 AATCGCAATGCGAAATGAA
607608 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
607627 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
607646 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
607660 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
607679 AATCGCAA
1 AATCGCAA
607687 CGAGATAATC
Statistics
Matches: 228, Mismatches: 13, Indels: 54
0.77 0.04 0.18
Matches are distributed among these distances:
14 45 0.20
15 4 0.02
16 16 0.07
17 15 0.07
18 22 0.10
19 113 0.50
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:607487 original size:33 final size:33
Alignment explanation
Indices: 607400--607634 Score: 196
Period size: 33 Copynumber: 6.8 Consensus size: 33
607390 ACGGAAATAC
* *
607400 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
607433 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
607467 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
607505 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
607538 AATCGCAATGCGAAATGAAAATCG-AACCGACAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAA
* *
607571 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACGAGA--A
607608 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
607635 TGCGAAATGA
Statistics
Matches: 172, Mismatches: 13, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
33 79 0.46
34 31 0.18
35 11 0.06
36 6 0.03
37 28 0.16
38 17 0.10
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:607515 original size:52 final size:53
Alignment explanation
Indices: 607428--607653 Score: 325
Period size: 52 Copynumber: 4.2 Consensus size: 53
607418 AAATCCCAAC
607428 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
607481 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* *
607533 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* * * *
607585 ATTAAAATCGCAATACGAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GAGAATCGCAATGCGAA
607641 ATGAAAATCGCAA
1 ATGAAAATCGCAA
607654 CGAAAGAATC
Statistics
Matches: 159, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
51 8 0.05
52 105 0.66
53 18 0.11
55 1 0.01
56 27 0.17
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
Found at i:607669 original size:33 final size:34
Alignment explanation
Indices: 607467--607708 Score: 214
Period size: 33 Copynumber: 6.9 Consensus size: 34
607457 GCAACGAGAG
607467 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAA-G--AATCGCAATGCGAAATGAA
*
607505 AATCGCAA-CGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
**
607538 AATCGCAATGCGAAATGAA----AAT-CGAACCGACA
1 AATCGCAA-GCGAAA-GAATCGCAATGCGAAATGA-A
* *
607570 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATG-A
1 -AATCGCAA-GCG-AA--AGAATCGCAATGCGAAATGAA
607608 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAA-G--AATCGCAATGCGAAATGAA
607646 AATCGCAA-CGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
* *
607679 AATCGCAA-CGAGATAATCGCAATGCGAAAT
1 AATCGCAAGCGAAAGAATCGCAATGCGAAAT
607709 TATAAACGCA
Statistics
Matches: 176, Mismatches: 11, Indels: 39
0.78 0.05 0.17
Matches are distributed among these distances:
31 6 0.03
32 4 0.02
33 86 0.49
34 3 0.02
35 8 0.05
36 15 0.09
37 28 0.16
38 18 0.10
39 3 0.02
40 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (34 bp):
AATCGCAAGCGAAAGAATCGCAATGCGAAATGAA
Found at i:607685 original size:52 final size:54
Alignment explanation
Indices: 607428--607686 Score: 269
Period size: 52 Copynumber: 4.9 Consensus size: 54
607418 AAATCCCAAC
*
607428 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG--A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAA-GC-GAAATG-AAATCGCAATCGAAATGAAAATCGCAATGCGAA
*
607481 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG--A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCGAAATG-AAATCGCAATCGAAATGAAAATCGCAATGCGAA
* *
607533 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACAT---AATCGCAATGCGAA
1 ATGAAAATCGCAA-GCGAAATG-AAATCGCAATCGAAATGAAAATCGCAATGCGAA
* *
607585 ATTAAAATCGCAATACGAAATGAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCGAAATGAAATCGCAAT-CGAAATGAAAATCGCAATGCGAA
607641 ATGAAAATCGCAA-CGAAA-G-AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAAGCGAAATGAAATCGCAAT-CGAAATGAAAATCGCAA
607687 CGAGATAATC
Statistics
Matches: 192, Mismatches: 5, Indels: 19
0.89 0.02 0.09
Matches are distributed among these distances:
51 8 0.04
52 130 0.68
53 22 0.11
54 6 0.03
56 26 0.14
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (54 bp):
ATGAAAATCGCAAGCGAAATGAAATCGCAATCGAAATGAAAATCGCAATGCGAA
Found at i:607821 original size:19 final size:19
Alignment explanation
Indices: 607715--607813 Score: 133
Period size: 20 Copynumber: 5.6 Consensus size: 19
607705 AAATTATAAA
607715 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
607734 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
607754 CGCATTGCGA--TTC---T
1 CGCATTGCGATTTTCATTT
607768 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
607785 CGCATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
607803 CGCATTGCGAT
1 CGCATTGCGAT
607814 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 17
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.08
14 6 0.08
17 6 0.08
18 18 0.25
19 16 0.23
20 19 0.27
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:607938 original size:14 final size:14
Alignment explanation
Indices: 607919--607955 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
607909 CATCAATTAC
607919 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
607933 ACAAATCATCTTTT
1 ACAAATCAACTTTT
607947 ACAAATCAA
1 ACAAATCAA
607956 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:609925 original size:14 final size:14
Alignment explanation
Indices: 609906--609961 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
609896 GCGAAATGAA
*
609906 AATCGCAACGACAG
1 AATCGCAACGAAAG
609920 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
609937 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
609952 AATCGCAACG
1 AATCGCAACG
609962 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:609946 original size:32 final size:33
Alignment explanation
Indices: 609887--609978 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
609877 GCGAAACCAA
*
609887 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
609920 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
609952 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
609979 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:609976 original size:19 final size:19
Alignment explanation
Indices: 609850--609983 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
609840 TAGTTTACTT
* *
609850 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
609870 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
609889 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
609908 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
609922 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
609940 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
609954 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
609973 TCGCAATGCGA
1 TCGCAACGCGA
609984 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:610001 original size:19 final size:19
Alignment explanation
Indices: 609979--610107 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
609969 AAAATCGCAA
609979 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
609998 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
610012 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
610031 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
610045 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
610064 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
610083 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
610103 TGCGA
1 TGCGA
610108 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:610021 original size:33 final size:33
Alignment explanation
Indices: 609979--610070 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
609969 AAAATCGCAA
609979 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
610012 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
610045 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
610071 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:610416 original size:91 final size:93
Alignment explanation
Indices: 610151--610434 Score: 531
Period size: 92 Copynumber: 3.1 Consensus size: 93
610141 TTGAATGGAT
610151 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
610216 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
610244 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
610308 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
610336 AAATTTACTTTCAACC-AAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
610399 GGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
610427 -AATTTACT
1 AAATTTACT
610435 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
90 23 0.12
91 58 0.31
92 69 0.37
93 39 0.21
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:612143 original size:14 final size:14
Alignment explanation
Indices: 612124--612213 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
612114 TTGAAATGAA
612124 AATCGCAACGAGAG
1 AATCGCAACGAGAG
612138 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
612155 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
612171 AATCGCAACGCGAAATGG
1 AATCGCAA--CGAGA--G
612189 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
612204 AATCGCAACG
1 AATCGCAACG
612214 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 26 0.41
15 1 0.02
16 10 0.16
17 10 0.16
18 1 0.02
19 16 0.25
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:612161 original size:33 final size:33
Alignment explanation
Indices: 612116--612230 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
612106 TCTTTTGGTT
612116 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
612149 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
612182 GAAATGGAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
612215 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
612231 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:612162 original size:19 final size:18
Alignment explanation
Indices: 612123--612235 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
612113 GTTGAAATGA
612123 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
612138 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
612155 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
612171 -AATCGCAACGCGAAATGG
1 AAATCGCAACGCGAGAT-G
612189 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
612204 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
612221 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
612236 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 14 0.18
17 11 0.14
18 1 0.01
19 28 0.35
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:612266 original size:14 final size:14
Alignment explanation
Indices: 612247--612301 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
612237 TTTGGTTTCG
612247 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
612261 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
612280 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
612294 CGTTGCGA
1 CGTTGCGA
612302 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:612463 original size:33 final size:33
Alignment explanation
Indices: 612421--612490 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
612411 AATACTAACT
*
612421 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
612454 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
612487 TGAA
1 TGAA
612491 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:612721 original size:21 final size:22
Alignment explanation
Indices: 612670--612723 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
612660 TGGTTGTGAG
**
612670 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
612692 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
612713 GGATTTCTTCG
1 GGATTTCTTCG
612724 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:612895 original size:20 final size:20
Alignment explanation
Indices: 612870--613063 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
612860 CTTTAAATAT
612870 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
612890 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
612912 -TCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
612931 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
612951 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
612971 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
612991 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
613011 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
613031 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
613051 CGCGTTGCGATTT
1 CGCGTTGCGATTT
613064 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.88
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:613057 original size:60 final size:60
Alignment explanation
Indices: 612870--613063 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
612860 CTTTAAATAT
** *
612870 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
612931 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
612991 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
613051 CGCGTTGCGATTT
1 CGCGTTGCGATTT
613064 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:613080 original size:21 final size:20
Alignment explanation
Indices: 613056--613132 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
613046 ATATTCGCGT
613056 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
613077 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
613097 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
613119 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
613133 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:613143 original size:20 final size:20
Alignment explanation
Indices: 613118--613169 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
613108 AAGAATCGCG
*
613118 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
613138 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
613158 TTGCGATTCTGG
1 TTGCGATTCTGG
613170 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:613312 original size:12 final size:12
Alignment explanation
Indices: 613295--613356 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
613285 TCTCTCTCTC
*
613295 TATATATATATA
1 TATATATATATG
613307 TATATACTATATG
1 TATATA-TATATG
* *
613320 --TGTGTATATG
1 TATATATATATG
*
613330 TATATGTATATG
1 TATATATATATG
*
613342 TATATGTATATG
1 TATATATATATG
613354 TAT
1 TAT
613357 GTGTTTGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
10 6 0.14
11 2 0.05
12 30 0.70
13 5 0.12
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:613331 original size:6 final size:6
Alignment explanation
Indices: 613322--613356 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
613312 ACTATATGTG
613322 TGTATA TGTATA TGTATA TGTATA TGTATA TGTAT
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTAT
613357 GTGTTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (6 bp):
TGTATA
Found at i:613373 original size:5 final size:5
Alignment explanation
Indices: 613359--613391 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
613349 ATATGTATGT
*
613359 GTTTG ATTTG GTTTG GTTTG GTTTG GTTTG GTT
1 GTTTG GTTTG GTTTG GTTTG GTTTG GTTTG GTT
613392 ATGAAGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.36, T:0.61
Consensus pattern (5 bp):
GTTTG
Found at i:616109 original size:18 final size:18
Alignment explanation
Indices: 616086--616128 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
616076 GGGAATATTC
*
616086 TTTTAAAGAAGGTTTTTT
1 TTTTAAAGAAGATTTTTT
* *
616104 TTTTAAATAATATTTTTT
1 TTTTAAAGAAGATTTTTT
616122 TTTTAAA
1 TTTTAAA
616129 TATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
TTTTAAAGAAGATTTTTT
Found at i:616129 original size:18 final size:16
Alignment explanation
Indices: 616098--616138 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 16
616088 TTAAAGAAGG
616098 TTTTTTTTTTAAATAAT
1 TTTTTTTTTTAAAT-AT
616115 ATTTTTTTTTTAAATAT
1 -TTTTTTTTTTAAATAT
616132 TTTTTTT
1 TTTTTTT
616139 AAATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 14 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTTAAATAT
Found at i:616134 original size:13 final size:13
Alignment explanation
Indices: 616118--616144 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
616108 AAATAATATT
616118 TTTTTTTTAAATA
1 TTTTTTTTAAATA
616131 TTTTTTTTAAATA
1 TTTTTTTTAAATA
616144 T
1 T
616145 AAATATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTTAAATA
Found at i:616895 original size:26 final size:26
Alignment explanation
Indices: 616866--616919 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
616856 GTCCATGTTA
* *
616866 GAGAGCAAACTTATGAATTTTTAAGT
1 GAGAGCAAACTTATAAAATTTTAAGT
* *
616892 GAGAGCGAACTTGTAAAATTTTAAGT
1 GAGAGCAAACTTATAAAATTTTAAGT
616918 GA
1 GA
616920 CGAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.31
Consensus pattern (26 bp):
GAGAGCAAACTTATAAAATTTTAAGT
Found at i:617196 original size:14 final size:14
Alignment explanation
Indices: 617171--617207 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
617161 TTTTTACCTG
617171 TAAATC-TAAATTA
1 TAAATCTTAAATTA
617184 TAAATCTTAAATTA
1 TAAATCTTAAATTA
*
617198 TAAATTTTAA
1 TAAATCTTAA
617208 TGTTTAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATCTTAAATTA
Found at i:634427 original size:17 final size:16
Alignment explanation
Indices: 634407--634456 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
634397 CTTTTATACT
634407 TTTTATAATTTTTAATA
1 TTTTAT-ATTTTTAATA
*
634424 TTTTAT-TTTTAAATA
1 TTTTATATTTTTAATA
*
634439 TTTTAGATTTTTTAATA
1 TTTTATA-TTTTTAATA
634456 T
1 T
634457 AAAAGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTATATTTTTAATA
Found at i:634433 original size:14 final size:15
Alignment explanation
Indices: 634414--634443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
634404 ACTTTTTATA
634414 ATTTTT-AATATTTT
1 ATTTTTAAATATTTT
634428 ATTTTTAAATATTTT
1 ATTTTTAAATATTTT
634443 A
1 A
634444 GATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTAAATATTTT
Found at i:634434 original size:32 final size:32
Alignment explanation
Indices: 634389--634457 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
634379 GTGTGTATAT
* *
634389 ATATATTACTTTTATACT-TTTTATAATTTTTA
1 ATATATTACTTTTA-AATATTTTAGAATTTTTA
* * *
634421 ATATTTTATTTTTAAATATTTTAGATTTTTTA
1 ATATATTACTTTTAAATATTTTAGAATTTTTA
634453 ATATA
1 ATATA
634458 AAAGATAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (32 bp):
ATATATTACTTTTAAATATTTTAGAATTTTTA
Found at i:636164 original size:37 final size:38
Alignment explanation
Indices: 636085--636171 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
636075 TTCACCCTAA
*
636085 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACACG
* *
636124 ACCCGACTCGACCCGAATATCACACTT-AAAAAACATG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACACG
636161 ACCCGACCCGA
1 ACCCGACCCGA
636172 ACAAAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 18 0.41
38 21 0.48
39 5 0.11
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.11
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACACG
Found at i:636363 original size:27 final size:26
Alignment explanation
Indices: 636331--636398 Score: 73
Period size: 33 Copynumber: 2.3 Consensus size: 26
636321 CCTAAATCCG
636331 AACCCGACCGAATATCACACTTAAAAA
1 AACCCGACCGAATATCACACTT-AAAA
636358 AACCCGACCTGACCCGAATATCACACTTAAAA
1 AA--C--CC-GA-CCGAATATCACACTTAAAA
636390 AACCCGACC
1 AACCCGACC
636399 CGACCCGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
26 2 0.06
27 4 0.11
28 2 0.06
29 1 0.03
30 1 0.03
31 2 0.06
32 8 0.23
33 15 0.43
ACGTcount: A:0.43, C:0.35, G:0.09, T:0.13
Consensus pattern (26 bp):
AACCCGACCGAATATCACACTTAAAA
Found at i:636395 original size:32 final size:33
Alignment explanation
Indices: 636332--636407 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 33
636322 CTAAATCCGA
636332 ACCCGA-CCGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
636364 ACCTGACCCGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
636396 ACCCGACCCGAA
1 ACCCGACCCGAA
636408 CAAAATAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 26 0.63
33 15 0.37
ACGTcount: A:0.41, C:0.37, G:0.11, T:0.12
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:636414 original size:235 final size:243
Alignment explanation
Indices: 636043--636610 Score: 832
Period size: 235 Copynumber: 2.3 Consensus size: 243
636033 TATAAGGTAA
* * *
636043 AATTATATTTTTTTTCGGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACCCGACCCGAATATCA
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTCACCCTAAATCCGAACCCGACCCGAATATCA
*
636108 CACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACATGACCCGACCCGAA
66 CACTTAAAAAAACCCGA-CC-ACTCGACCCGAATATCACACTTAAAAAACACGACCCGACCCGAA
* *
636173 CAAAATAAACTTTCATCCGACCCGACCCGAATATATGAATTAG-A-AA-CCGACCCGAAATAATA
129 CAAAATAAACTTTCATCCGACCAGACCCGAATATATGAATTAGAACAACCCAACCCGAAATAATA
*
636235 AAAAATTATTTTTATTTAAT-AAAACATTGACTTAATCCGA-CCAACCCG
194 AAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCAACCCG
636283 AATTATATATATTTTCGGGTCGGTCC-GTTTTTTCCCACCCTAAATCCGAACCCGA-CCGAATAT
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTT--CACCCTAAATCCGAACCCGACCCGAATAT
*
636346 CACACTTAAAAAAACCCGA-C-CT-GACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAA
64 CACACTTAAAAAAACCCGACCACTCGACCCGAATATCACACTTAAAAAACACGACCCGACCCGAA
*
636408 CAAAATAAAGTTTCATCCGACCAGACCCGAATATATGAATTAGAAATCCAACCCAACCCGAAATA
129 CAAAATAAACTTTCATCCGACCAGACCCGAATATATGAATTAG-AA--CAACCCAACCCGAAATA
* *
636473 ATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTG
191 ATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCAACCCG
* *
636526 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCATAAATTCGAATCCGACCCGACCCGA
1 AATTATATATATTTTCGGGTCGGTCCGG-TTTTTTCACCCTAAATCCG-A----ACCCGACCCGA
636591 ATATCACACTTAAAAAAACC
60 ATATCACACTTAAAAAAACC
636611 TGATTAAAGG
Statistics
Matches: 297, Mismatches: 13, Indels: 27
0.88 0.04 0.08
Matches are distributed among these distances:
235 79 0.27
236 2 0.01
237 1 0.00
238 1 0.00
239 7 0.02
240 53 0.18
241 54 0.18
242 19 0.06
243 43 0.14
244 2 0.01
245 6 0.02
248 6 0.02
249 24 0.08
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (243 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTCACCCTAAATCCGAACCCGACCCGAATATCA
CACTTAAAAAAACCCGACCACTCGACCCGAATATCACACTTAAAAAACACGACCCGACCCGAACA
AAATAAACTTTCATCCGACCAGACCCGAATATATGAATTAGAACAACCCAACCCGAAATAATAAA
AAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCAACCCG
Found at i:643757 original size:28 final size:28
Alignment explanation
Indices: 643712--643768 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
643702 GTCTCTGTTT
* *
643712 ATATTATATCGTCAAGTCATTGCTTGAA
1 ATATTATATCATCAAGTCAGTGCTTGAA
* * *
643740 ATATTATGTCATCGAGTCAGTGTTTGAA
1 ATATTATATCATCAAGTCAGTGCTTGAA
643768 A
1 A
643769 GCAACAGCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (28 bp):
ATATTATATCATCAAGTCAGTGCTTGAA
Found at i:659256 original size:156 final size:157
Alignment explanation
Indices: 658972--659283 Score: 617
Period size: 156 Copynumber: 2.0 Consensus size: 157
658962 TAAAACTTGT
658972 AGATAAATATTTTATGTTCCTACCTGAAGATAAATACAAATGCGGTGTAGTCTGTTTAGATTCCA
1 AGATAAATATTTTATGTTCCTACCTGAAGATAAATACAAATGCGGTGTAGTCTGTTTAGATTCCA
659037 ATAACCTCCTTGCAATAACCTGCAGAATGAACACAAATGCAGTAAAAAGAAAGAATCAAAGTTCT
66 ATAACCTCCTTGCAATAACCTGCAGAATGAACACAAATGCAGTAAAAAGAAAGAATCAAAGTTCT
659102 CCATTAACTCATTAAA-CATATAAAAA
131 CCATTAACTCATTAAACCATATAAAAA
659128 AGATAAATATTTTATGTTCCTACCTGAAGATAAATACAAATGCGGTGTAGTCTGTTTAGATTCCA
1 AGATAAATATTTTATGTTCCTACCTGAAGATAAATACAAATGCGGTGTAGTCTGTTTAGATTCCA
659193 ATAACCTCCTTGCAATAACCTGCAGAATGAACACAAATGCAGTAAAAAGAAAGAATCAAAGTTCT
66 ATAACCTCCTTGCAATAACCTGCAGAATGAACACAAATGCAGTAAAAAGAAAGAATCAAAGTTCT
659258 CCATTAACTCATTAAACCATATAAAA
131 CCATTAACTCATTAAACCATATAAAA
659284 CAACATACTT
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 146 0.94
157 9 0.06
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (157 bp):
AGATAAATATTTTATGTTCCTACCTGAAGATAAATACAAATGCGGTGTAGTCTGTTTAGATTCCA
ATAACCTCCTTGCAATAACCTGCAGAATGAACACAAATGCAGTAAAAAGAAAGAATCAAAGTTCT
CCATTAACTCATTAAACCATATAAAAA
Found at i:664554 original size:112 final size:112
Alignment explanation
Indices: 664357--664581 Score: 441
Period size: 112 Copynumber: 2.0 Consensus size: 112
664347 ATATTGTTTC
*
664357 TGATTAATAAAATATAGATGACTCTTACTTCAACATATACCAAAAATTTGTGGAAGTTTACCAGT
1 TGATTAATAAAATATAGATGACTCTTACTTCAACATATACAAAAAATTTGTGGAAGTTTACCAGT
664422 AAATAGCTCTTTGCGTAGATAAATATCCATGACTAGCATTTAAGACA
66 AAATAGCTCTTTGCGTAGATAAATATCCATGACTAGCATTTAAGACA
664469 TGATTAATAAAATATAGATGACTCTTACTTCAACATATACAAAAAATTTGTGGAAGTTTACCAGT
1 TGATTAATAAAATATAGATGACTCTTACTTCAACATATACAAAAAATTTGTGGAAGTTTACCAGT
664534 AAATAGCTCTTTGCGTAGATAAATATCCATGACTAGCATTTAAGACA
66 AAATAGCTCTTTGCGTAGATAAATATCCATGACTAGCATTTAAGACA
664581 T
1 T
664582 AAGTCCAGTG
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (112 bp):
TGATTAATAAAATATAGATGACTCTTACTTCAACATATACAAAAAATTTGTGGAAGTTTACCAGT
AAATAGCTCTTTGCGTAGATAAATATCCATGACTAGCATTTAAGACA
Found at i:670323 original size:302 final size:299
Alignment explanation
Indices: 669708--670521 Score: 1078
Period size: 302 Copynumber: 2.7 Consensus size: 299
669698 AATTTCTACA
* * * * *
669708 ATGTTCGTCGAACGTGGATGTGCACTTTTAACAATGACCACCATCAAATTAATTTATAAAACGTT
1 ATGTTCGTCGAGCGTGGATGAGCACTGTTAACGATGACCACCATTAAATTAATTTATAAAA-GTT
* * * *
669773 AAATTATAAAGTACTAAACATATTATTATAAATTAGTTAAAAATCTAAACGTATTTTAATTAAAA
65 AAATTATAAAGTACTAAACGTATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAATTAAAA
* ** *
669838 TATAATATTTATAAAGTATTAGTTTTTAGGATAAATTATACCATTGACCACCTAACTATTTATCT
130 TACAATATTTATAAAACATTAGTTTTTA-GATAAACTATACCATTGACCACCTAACTATTTATCT
* * *
669903 TTTTTACTTTAACCACCAATTTTTCAAGTTTATCAATCGGATCATCTAATTATTTAAATATTGTA
194 TTTTTACTTTAACAACCAATTTTTCAAGTTTATCAATCGGACCACCTAATTATTTAAATATTGTA
* * *
669968 AATTAAGACACATGTCCTTAAATATTAATGGAGAATATGAC
259 AATCAAGACACATGTCCTTAAATATTAACGGAGAAGATGAC
* * * *
670009 ACGTACGTCGAGCGTGGATGAGCACCGTTAACGATGATCACCATTAAAATTAATTTATAAAATGT
1 ATGTTCGTCGAGCGTGGATGAGCACTGTTAACGATGACCACCATT-AAATTAATTTATAAAA-GT
*
670074 TAAATTATAAAGTACTAAACGTATAATTATAAATTAGTTAAAAATATAAATGTAATTTAATTAAA
64 TAAATTATAAAGTACTAAACGTATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAATTAAA
* * *
670139 ATACAATATTTATAAAACATTAGTTTTTAGAATAAACTATACCATTGACCATCTAATTATTTACC
129 ATACAATATTTATAAAACATTAGTTTTTAG-ATAAACTATACCATTGACCACCTAACTATTTATC
* * * * * *
670204 CTTTTTACTTTAACAATCGATTTTTCAATTTTGTCAATCGGACCACCTGATTATTTAAATATTGT
193 TTTTTTACTTTAACAACCAATTTTTCAAGTTTATCAATCGGACCACCTAATTATTTAAATATTGT
* *
670269 CAATCAA-ACCACATGTCGTTAAATATTAACGGAGAAGATGAC
258 AAATCAAGA-CACATGTCCTTAAATATTAACGGAGAAGATGAC
* * *
670311 ATGTTTGTCGAGCGTGGATGAGCATTGTTAACGATGACCACCATTAAATCAATTTATAAACA-TT
1 ATGTTCGTCGAGCGTGGATGAGCACTGTTAACGATGACCACCATTAAATTAATTTATAAA-AGTT
* ** * *
670375 AAATTAAAAAAAAACTAAATGTATAATTATAAATTAGTTAAAAATCTAAATATAATTTAATTAAA
65 AAATT-ATAAAGTACTAAACGTATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAATT---
*
670440 ATACAATACAATATTTATAAAACATTAG-TTTTATGATAAACTAT-CCATTAACCACCTAACTAT
126 A-A-AATACAATATTTATAAAACATTAGTTTTTA-GATAAACTATACCATTGACCACCTAACTAT
670503 TTATCTTTTTTACTTTAAC
188 TTATCTTTTTTACTTTAAC
670522 CACTATTTTT
Statistics
Matches: 448, Mismatches: 54, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
300 7 0.02
301 102 0.23
302 265 0.59
304 34 0.08
305 15 0.03
306 25 0.06
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (299 bp):
ATGTTCGTCGAGCGTGGATGAGCACTGTTAACGATGACCACCATTAAATTAATTTATAAAAGTTA
AATTATAAAGTACTAAACGTATAATTATAAATTAGTTAAAAATCTAAATGTAATTTAATTAAAAT
ACAATATTTATAAAACATTAGTTTTTAGATAAACTATACCATTGACCACCTAACTATTTATCTTT
TTTACTTTAACAACCAATTTTTCAAGTTTATCAATCGGACCACCTAATTATTTAAATATTGTAAA
TCAAGACACATGTCCTTAAATATTAACGGAGAAGATGAC
Found at i:670588 original size:56 final size:55
Alignment explanation
Indices: 670485--670595 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 55
670475 ATAAACTATC
* * * *
670485 CATTAACCACCTAACTATTTATCTTTTTTACTTTAACCACTATTTTTTTCAATTTT
1 CATTAACCACCTAACTATTTACCCTTTTTACTTTAACAACGA-TTTTTTCAATTTT
* * *
670541 CATTGACCATCTAATTATTTACCCTTTTTACTTTAACAATCGA-TTTTTCAATTTT
1 CATTAACCACCTAACTATTTACCCTTTTTACTTTAACAA-CGATTTTTTCAATTTT
670596 GTCAATCGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
55 12 0.26
56 33 0.70
57 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.02, T:0.50
Consensus pattern (55 bp):
CATTAACCACCTAACTATTTACCCTTTTTACTTTAACAACGATTTTTTCAATTTT
Found at i:672796 original size:19 final size:19
Alignment explanation
Indices: 672774--672813 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
672764 TTGGTTTGGT
*
672774 TAATTTTATTAATTTTATA
1 TAATTTTATTAATTGTATA
* *
672793 TAATTTTGTTCATTGTATA
1 TAATTTTATTAATTGTATA
672812 TA
1 TA
672814 TATATAGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
TAATTTTATTAATTGTATA
Found at i:693636 original size:19 final size:19
Alignment explanation
Indices: 693614--693701 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 19
693604 AAATATTAAA
*
693614 AATATTATTATATATATAT
1 AATATTAATATATATATAT
* * *
693633 AATATTAATAAATTTAATTT
1 AATATTAATATATAT-ATAT
693653 AA-ATTAATATATATATAT
1 AATATTAATATATATATAT
693671 AATATT--TATATAT-T-T
1 AATATTAATATATATATAT
693686 AAT-TTAA-ATATATATA
1 AATATTAATATATATATA
693702 CTCGGCCCGA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.04
15 10 0.18
16 2 0.04
17 7 0.12
18 5 0.09
19 25 0.45
20 5 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTAATATATATATAT
Found at i:693664 original size:38 final size:38
Alignment explanation
Indices: 693617--693701 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
693607 TATTAAAAAT
*
693617 ATTATTATATATATATAATATTAATAAATTTAATTTAA
1 ATTAATATATATATATAATATTAATAAATTTAATTTAA
* *
693655 ATTAATATATATATATAATATTTATATATTTAATTTAA
1 ATTAATATATATATATAATATTAATAAATTTAATTTAA
693693 A-T-ATATATA
1 ATTAATATATA
693702 CTCGGCCCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 7 0.16
37 1 0.02
38 36 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTAATATATATATATAATATTAATAAATTTAATTTAA
Found at i:703138 original size:21 final size:21
Alignment explanation
Indices: 703099--703138 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
703089 ATATTAATTA
*
703099 AATAATTATGACTATTTTTCT
1 AATAATTATGACTACTTTTCT
703120 AATAATTATGATCT-CTTTT
1 AATAATTATGA-CTACTTTT
703139 AGGGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
AATAATTATGACTACTTTTCT
Found at i:703971 original size:21 final size:19
Alignment explanation
Indices: 703947--703987 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
703937 TTATTTGATA
*
703947 TATAAACATAATTTTAATAAT
1 TATAAAAAT-ATTTTAA-AAT
703968 TATAAAAATATTTTAAAAT
1 TATAAAAATATTTTAAAAT
703987 T
1 T
703988 TCAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAAAATATTTTAAAAT
Found at i:706536 original size:12 final size:12
Alignment explanation
Indices: 706519--706543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
706509 CTCCGTCCAT
706519 ATACTTATTCTC
1 ATACTTATTCTC
706531 ATACTTATTCTC
1 ATACTTATTCTC
706543 A
1 A
706544 GTGTTTCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
ATACTTATTCTC
Found at i:707879 original size:32 final size:31
Alignment explanation
Indices: 707811--707908 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 31
707801 TCTTCATCAA
* *
707811 AGTACTTGAAGTGTTTTTTTTATCAAATTA-
1 AGTACTTGAAGTGTTTTTTTTGTCAAAATAG
707841 AGTACTTGAAGTTGTTTTTTTTTGTCAAAATAG
1 AGTACTTGAAG-TG-TTTTTTTTGTCAAAATAG
* *
707874 A-TACTTAAAAGTATTTTTTTTGTCAAAATAG
1 AGTACTT-GAAGTGTTTTTTTTGTCAAAATAG
707905 -GTAC
1 AGTAC
707909 ATAAAATATT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.19
31 23 0.39
32 21 0.36
33 4 0.07
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (31 bp):
AGTACTTGAAGTGTTTTTTTTGTCAAAATAG
Found at i:707893 original size:30 final size:30
Alignment explanation
Indices: 707856--707918 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
707846 TTGAAGTTGT
*
707856 TTTTTTTTGTCAAAATAGATACTTAAAAGTA
1 TTTTTTTTGTCAAAATAGATACATAAAA-TA
*
707887 TTTTTTTTGTCAAAATAGGTACATAAAATA
1 TTTTTTTTGTCAAAATAGATACATAAAATA
707917 TT
1 TT
707919 CAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (30 bp):
TTTTTTTTGTCAAAATAGATACATAAAATA
Found at i:708201 original size:2 final size:2
Alignment explanation
Indices: 708196--708225 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
708186 CACATATTAC
708196 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
708226 TACAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:710933 original size:136 final size:136
Alignment explanation
Indices: 710677--710945 Score: 412
Period size: 136 Copynumber: 2.0 Consensus size: 136
710667 ATAATTTACT
* *
710677 AAGTATTTCATGATAAAATTTGATAACTCTCATCATCCAAAATTTATCTGAAATGTGCTGCAATC
1 AAGTATTTCATGATAAAAATTGATAACTCTCATCATCCAAAATCTATCTGAAATGTGCTGCAATC
* *** * * * *
710742 TCTTAACATGCATAAAAGTGTAGGTTGTAATATCAAATGAACACAACCATAGATAACGAATCATT
66 TCTTAACATGCATAAAAATGTAGGCCCTAATATCAAATAAACACAACCACAGATAACAAATCACT
710807 ATCACC
131 ATCACC
710813 AAGTATTTCATGATAAAAATTGATAACTCTCATCATCCAAAATCTATCTGAAATGTGCTGCAATC
1 AAGTATTTCATGATAAAAATTGATAACTCTCATCATCCAAAATCTATCTGAAATGTGCTGCAATC
* ** *
710878 TCTTAACATGCATAAAAATGTAGGCCCTAATATCAAATAAACGCGGCCACGGATAACAAATCACT
66 TCTTAACATGCATAAAAATGTAGGCCCTAATATCAAATAAACACAACCACAGATAACAAATCACT
710943 ATC
131 ATC
710946 GCTACGGAGA
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
136 119 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (136 bp):
AAGTATTTCATGATAAAAATTGATAACTCTCATCATCCAAAATCTATCTGAAATGTGCTGCAATC
TCTTAACATGCATAAAAATGTAGGCCCTAATATCAAATAAACACAACCACAGATAACAAATCACT
ATCACC
Found at i:712761 original size:14 final size:14
Alignment explanation
Indices: 712742--712771 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
712732 AATGTTGTTG
712742 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
712756 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
712770 AC
1 AC
712772 AATCAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTCTTTCTC
Found at i:717980 original size:20 final size:18
Alignment explanation
Indices: 717954--718008 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
717944 TGTGTTATTC
717954 TTTTGTTATTCATTTCCTT
1 TTTTGTTATTCATTT-CTT
*
717973 TCTTTGTTTTTCATGTTCTT
1 T-TTTGTTATTCAT-TTCTT
*
717993 TTATTGTTCTTCATTT
1 TT-TTGTTATTCATTT
718009 TTCTTTCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
20 25 0.81
21 2 0.06
ACGTcount: A:0.09, C:0.15, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTGTTATTCATTTCTT
Found at i:718325 original size:20 final size:20
Alignment explanation
Indices: 718289--718326 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
718279 TAGAAGAAAT
*
718289 GATGAGAAAGAAGGGGAATG
1 GATGAGAAAGAAAGGGAATG
718309 GATGAGAAA-ATAAGGGAA
1 GATGAGAAAGA-AAGGGAA
718327 ATCTGGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (20 bp):
GATGAGAAAGAAAGGGAATG
Found at i:718978 original size:13 final size:13
Alignment explanation
Indices: 718960--718984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
718950 AACTTTATAA
718960 AAATTTTAAAACT
1 AAATTTTAAAACT
718973 AAATTTTAAAAC
1 AAATTTTAAAAC
718985 GATGTCATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTTTAAAACT
Found at i:724296 original size:81 final size:81
Alignment explanation
Indices: 724161--724321 Score: 322
Period size: 81 Copynumber: 2.0 Consensus size: 81
724151 AATTTGATTA
724161 TAGAGTATATGATTTTGAAATTGACTATGCAAAAAATATATTAATATGGTTTCTTGAGATAGCAC
1 TAGAGTATATGATTTTGAAATTGACTATGCAAAAAATATATTAATATGGTTTCTTGAGATAGCAC
724226 TCCGAGAATACCCTGT
66 TCCGAGAATACCCTGT
724242 TAGAGTATATGATTTTGAAATTGACTATGCAAAAAATATATTAATATGGTTTCTTGAGATAGCAC
1 TAGAGTATATGATTTTGAAATTGACTATGCAAAAAATATATTAATATGGTTTCTTGAGATAGCAC
724307 TCCGAGAATACCCTG
66 TCCGAGAATACCCTG
724322 ATTTGATAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (81 bp):
TAGAGTATATGATTTTGAAATTGACTATGCAAAAAATATATTAATATGGTTTCTTGAGATAGCAC
TCCGAGAATACCCTGT
Found at i:728620 original size:88 final size:87
Alignment explanation
Indices: 728471--728645 Score: 341
Period size: 88 Copynumber: 2.0 Consensus size: 87
728461 GCAACTGAAA
728471 CGATCCAAAATTAGAAGAGAGTTAAACGTAATTTTGCAAGTATAGTAATAAGAAACAATTGACAA
1 CGATCCAAAATTAGAAGAGAGTTAAACGTAATTTTGCAAGTATAGTAATAAGAAACAATTGACAA
728536 CGAGTCTGGTTTAATTTGTAAGT
66 -GAGTCTGGTTTAATTTGTAAGT
728559 CGATCCAAAATTAGAAGAGAGTTAAACGTAATTTTGCAAGTATAGTAATAAGAAACAATTGACAA
1 CGATCCAAAATTAGAAGAGAGTTAAACGTAATTTTGCAAGTATAGTAATAAGAAACAATTGACAA
728624 GAGTCTGGTTTAATTTGTAAGT
66 GAGTCTGGTTTAATTTGTAAGT
728646 AGTTTGGATA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 22 0.25
88 65 0.75
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (87 bp):
CGATCCAAAATTAGAAGAGAGTTAAACGTAATTTTGCAAGTATAGTAATAAGAAACAATTGACAA
GAGTCTGGTTTAATTTGTAAGT
Found at i:733376 original size:26 final size:26
Alignment explanation
Indices: 733321--733376 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
733311 TCATGTCGAG
*
733321 TCAAAAGATCGATTTTTTGACTCTAG
1 TCAAAAGATCGATTTTTTGACTCTAA
*
733347 TCAAAAGATCGATTTTTCT-AGTCTAA
1 TCAAAAGATCGATTTTT-TGACTCTAA
733373 TCAA
1 TCAA
733377 GTTTTGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (26 bp):
TCAAAAGATCGATTTTTTGACTCTAA
Found at i:735193 original size:16 final size:16
Alignment explanation
Indices: 735172--735204 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
735162 GATTAAGCGC
735172 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
*
735188 TGAATGATTCAGATGT
1 TGAATGATTCAAATGT
735204 T
1 T
735205 ATGTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (16 bp):
TGAATGATTCAAATGT
Found at i:735490 original size:17 final size:18
Alignment explanation
Indices: 735452--735491 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
735442 AATAATTAAC
735452 CTAAAATAACTTTTAGAA
1 CTAAAATAACTTTTAGAA
735470 -TAAAAT-ACTTTTA-AA
1 CTAAAATAACTTTTAGAA
735485 TCTAAAA
1 -CTAAAA
735492 AAATTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.10
16 7 0.35
17 11 0.55
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (18 bp):
CTAAAATAACTTTTAGAA
Found at i:741141 original size:155 final size:156
Alignment explanation
Indices: 740852--741165 Score: 603
Period size: 156 Copynumber: 2.0 Consensus size: 156
740842 CGGGTCGGAT
740852 TTTTTATAAAAAATTCGGGTTCGGGTCGGGTTTAGGGTGAAAAAAATCCGACCCGACCCGACCCG
1 TTTTTATAAAAAATTCGGGTTCGGGTCGGGTTTAGGGTGAAAAAAATCCGACCCGACCCGACCCG
740917 AAAATATATATAATTTTATCCTATATATTTAGGGATAATTACAATAATATCCCTCCATATATAAT
66 AAAATATATATAATTTTATCCTATATATTTAGGGATAATTACAATAATATCCCTCCATATATAAT
740982 TTTTTTCAATTAAGTCA-AGTTTTCA
131 TTTTTTCAATTAAGTCACAGTTTTCA
741007 TTTTTATAAAAAATTCGGGTTCGGGTCGGGTTTAGGGTGAAAAAAATCCGACCCGACCCGACCCG
1 TTTTTATAAAAAATTCGGGTTCGGGTCGGGTTTAGGGTGAAAAAAATCCGACCCGACCCGACCCG
741072 AAAAATATATATAATTTTATCCTATATATTTAGGGATAATTACAATAATATCCCTCCATATATAA
66 -AAAATATATATAATTTTATCCTATATATTTAGGGATAATTACAATAATATCCCTCCATATATAA
*
741137 TTTTTTTCAATTAAGTCACTGTTTTCA
130 TTTTTTTCAATTAAGTCACAGTTTTCA
741164 TT
1 TT
741166 GAATAAAATT
Statistics
Matches: 156, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
155 65 0.42
156 82 0.53
157 9 0.06
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (156 bp):
TTTTTATAAAAAATTCGGGTTCGGGTCGGGTTTAGGGTGAAAAAAATCCGACCCGACCCGACCCG
AAAATATATATAATTTTATCCTATATATTTAGGGATAATTACAATAATATCCCTCCATATATAAT
TTTTTTCAATTAAGTCACAGTTTTCA
Found at i:741404 original size:29 final size:29
Alignment explanation
Indices: 741348--741409 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
741338 GCCATCCCTA
**
741348 CTACTAGGTCGCCATGCCTTCCGGGCGAC
1 CTACTAGGTCGCCATGCCTTCCCCGCGAC
* *
741377 CTACTAGGTCGCCATGTCTTCCCCGCGAG
1 CTACTAGGTCGCCATGCCTTCCCCGCGAC
741406 CTAC
1 CTAC
741410 AAGAGATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.23
Consensus pattern (29 bp):
CTACTAGGTCGCCATGCCTTCCCCGCGAC
Found at i:741508 original size:23 final size:23
Alignment explanation
Indices: 741457--741509 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
741447 ATCTGAGGCC
* *
741457 ATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGCGAGCTATGCGAGGGA
*
741480 AGCCGAGCGAGCTATGCGAGGGA
1 ATCCGAGCGAGCTATGCGAGGGA
741503 ATCCGAG
1 ATCCGAG
741510 GGCAACCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (23 bp):
ATCCGAGCGAGCTATGCGAGGGA
Found at i:741578 original size:29 final size:29
Alignment explanation
Indices: 741536--741598 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
741526 ATGTGTTGGG
*
741536 CCTACAAGGTCGCCCGG-AGTTCATGGCGA
1 CCTACAAGGTCGCCCGGAAG-GCATGGCGA
741565 CCTACAAGGTCGCCCGGAAGGCATGGCGA
1 CCTACAAGGTCGCCCGGAAGGCATGGCGA
741594 CCTAC
1 CCTAC
741599 GGCCAACACT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.14
Consensus pattern (29 bp):
CCTACAAGGTCGCCCGGAAGGCATGGCGA
Found at i:758300 original size:25 final size:26
Alignment explanation
Indices: 758259--758310 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
758249 GGAGATGAAT
*
758259 AACCTACAAAAAGAAAGTAAA-GAGA
1 AACCTACAAAAAGAAAGGAAAGGAGA
758284 AACCTAC-AAAAGAAAAGGAAAGGAGA
1 AACCTACAAAAAG-AAAGGAAAGGAGA
758310 A
1 A
758311 TGGTGTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 14 0.58
26 5 0.21
ACGTcount: A:0.63, C:0.12, G:0.19, T:0.06
Consensus pattern (26 bp):
AACCTACAAAAAGAAAGGAAAGGAGA
Found at i:760921 original size:23 final size:23
Alignment explanation
Indices: 760894--760937 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
760884 TTCCATGTAA
760894 TTATGTTTATGTCTTAATAGTAG
1 TTATGTTTATGTCTTAATAGTAG
760917 TTATGTTTATGTCTTAATAGT
1 TTATGTTTATGTCTTAATAGT
760938 TCCAATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (23 bp):
TTATGTTTATGTCTTAATAGTAG
Found at i:764039 original size:24 final size:24
Alignment explanation
Indices: 764007--764056 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
763997 TTAAAATCTC
764007 CAACCGTTAAATCAACACCGAATA
1 CAACCGTTAAATCAACACCGAATA
764031 CAACCGTTAAATCAACACCGAATA
1 CAACCGTTAAATCAACACCGAATA
764055 CA
1 CA
764057 TGTTACTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.08, T:0.16
Consensus pattern (24 bp):
CAACCGTTAAATCAACACCGAATA
Found at i:769443 original size:16 final size:17
Alignment explanation
Indices: 769424--769457 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
769414 CATTTAACAA
*
769424 AAATAA-AATTTGTTTT
1 AAATAATAATATGTTTT
769440 AAATAATAATATGTTTT
1 AAATAATAATATGTTTT
769457 A
1 A
769458 GGTAACAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATAATAATATGTTTT
Found at i:770651 original size:40 final size:40
Alignment explanation
Indices: 770596--770676 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
770586 CTTCCTAAAC
770596 CTAACACAGTGTTGAATAATGCAGAAGAACTTCAAGAATT
1 CTAACACAGTGTTGAATAATGCAGAAGAACTTCAAGAATT
770636 CTAACACAGTGTTGAATAATGCAGAAGAACTTCAAGAATT
1 CTAACACAGTGTTGAATAATGCAGAAGAACTTCAAGAATT
770676 C
1 C
770677 ATGTATGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (40 bp):
CTAACACAGTGTTGAATAATGCAGAAGAACTTCAAGAATT
Found at i:773452 original size:63 final size:63
Alignment explanation
Indices: 773323--773452 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 63
773313 GAAGGTCATC
* *
773323 TTCATCTTCATCACCAAAATCAACTTCAGCACGTTTTTCTTCATTAACATGCAAGACAGATTG
1 TTCATCTTCATCACCAAAATCAACTTCAGCACGTTTTTCTTCATTAACAAGCAAGACAGATAG
* * * * * * **
773386 TTCATCTTCCTCATCATAATGAACTTCAGCAC-TTTTTCCTTCATTAAGAAGCATGTGAGATAG
1 TTCATCTTCATCACCAAAATCAACTTCAGCACGTTTTT-CTTCATTAACAAGCAAGACAGATAG
773449 TTCA
1 TTCA
773453 CGATGGTCGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 5 0.09
63 51 0.91
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (63 bp):
TTCATCTTCATCACCAAAATCAACTTCAGCACGTTTTTCTTCATTAACAAGCAAGACAGATAG
Found at i:784668 original size:2 final size:2
Alignment explanation
Indices: 784661--784685 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
784651 CAACATACAT
784661 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
784686 CAGAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:786414 original size:23 final size:23
Alignment explanation
Indices: 786385--786429 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
786375 TAAACGAATA
*
786385 CTAAATGAACATTTTCGTGAACG
1 CTAAATGAACATGTTCGTGAACG
*
786408 CTAAATGAATATGTTCGTGAAC
1 CTAAATGAACATGTTCGTGAAC
786430 ATATAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (23 bp):
CTAAATGAACATGTTCGTGAACG
Found at i:786516 original size:44 final size:44
Alignment explanation
Indices: 786450--786536 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
786440 ACATGTTTGC
*
786450 AAACATTAAATGATATTGTTCGCGAACAAAAAATAAACGAACAA
1 AAACATTAAATGACATTGTTCGCGAACAAAAAATAAACGAACAA
786494 AAACATTAAATGAACATT-TTCGCGAACAAAAAATAAACGAACA
1 AAACATTAAATG-ACATTGTTCGCGAACAAAAAATAAACGAACA
786537 CGAATACCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (44 bp):
AAACATTAAATGACATTGTTCGCGAACAAAAAATAAACGAACAA
Found at i:791561 original size:13 final size:14
Alignment explanation
Indices: 791526--791564 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
791516 TTCGGAACTT
*
791526 TAACAACTC-AAAA
1 TAACAACTCTAATA
791539 TAACAACTCTAATA
1 TAACAACTCTAATA
791553 -AACAACTCTAAT
1 TAACAACTCTAAT
791565 TTTATGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
TAACAACTCTAATA
Found at i:791734 original size:23 final size:23
Alignment explanation
Indices: 791682--791743 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
791672 TTTTTTAGAC
* *
791682 ATAT-TTTTATATATATATATTT
1 ATATATTTTATAGATATAAATTT
*
791704 TTATATTTTATAGATA-AAATTT
1 ATATATTTTATAGATATAAATTT
*
791726 ATATAATTTTTTA-ATATA
1 ATAT-ATTTTATAGATATA
791744 TTTAGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATATATTTTATAGATATAAATTT
Found at i:793052 original size:21 final size:21
Alignment explanation
Indices: 793026--793065 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
793016 GACTATCGCA
793026 TTGCGATTTCCCAAATTCGAG
1 TTGCGATTTCCCAAATTCGAG
* *
793047 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
793066 CAACGCGAAT
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:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGAG
Found at i:793750 original size:33 final size:33
Alignment explanation
Indices: 793700--793900 Score: 195
Period size: 33 Copynumber: 5.8 Consensus size: 33
793690 CTTAATGTCT
*
793700 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
793734 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * * * *
793767 ATCACAACGCGAAACTAAAAATCACATCGCGGAAATGA
1 ATCGCAATGCGAAA-TGAAAATCGCA--AC-GAGA-GA
* * *
793805 CTACCGCAATGCTAAATGAAAATCGCAATGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
793840 ATCGCAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
793873 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
793901 CGAATTTAGT
Statistics
Matches: 134, Mismatches: 26, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
33 87 0.65
34 18 0.13
35 2 0.01
36 4 0.03
37 3 0.02
38 1 0.01
39 9 0.07
40 10 0.07
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:793915 original size:19 final size:19
Alignment explanation
Indices: 793893--793934 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
793883 GAAATGAAAA
793893 TCGCAACGCGAATTTAGTT
1 TCGCAACGCGAATTTAGTT
** *
793912 TCGCATTGCGATTTTAGTT
1 TCGCAACGCGAATTTAGTT
793931 TCGC
1 TCGC
793935 GTTGCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (19 bp):
TCGCAACGCGAATTTAGTT
Done.