Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 73
Found at i:501815 original size:19 final size:19
Alignment explanation
Indices: 501793--501923 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
501783 GGAAATTACT
501793 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
501812 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
501826 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
501845 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
501859 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
501878 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
501892 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
501911 ATCGCAACGCGAA
1 ATCGCAATGCGAA
501924 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:501835 original size:33 final size:33
Alignment explanation
Indices: 501793--501919 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
501783 GGAAATTACT
501793 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
501826 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
501858 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
501892 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
501920 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:501900 original size:66 final size:66
Alignment explanation
Indices: 501794--501926 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
501784 GAAATTACTA
*
501794 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
501859 T
66 T
*
501860 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
501925 T
66 T
501926 T
1 T
501927 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:501951 original size:14 final size:14
Alignment explanation
Indices: 501934--501990 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
501924 TTTAATTTCG
501934 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
501948 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
501967 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
501981 CGTTGCGATT
1 CGTTGCGATT
501991 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:501970 original size:33 final size:33
Alignment explanation
Indices: 501919--502008 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
501909 AAATCGCAAC
* *
501919 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
501952 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
501985 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
502009 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:501972 original size:19 final size:19
Alignment explanation
Indices: 501948--502008 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
501938 GCGATTCTCT
501948 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
501967 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
501981 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
502000 CATTGCGAT
1 CGTTGCGAT
502009 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:502134 original size:14 final size:14
Alignment explanation
Indices: 502115--502151 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
502105 CATCAATTAA
502115 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
502129 ACAAATCACCTTTT
1 ACAAATCAACTTTT
502143 ACAAATCAA
1 ACAAATCAA
502152 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:503509 original size:91 final size:90
Alignment explanation
Indices: 503334--503518 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
503324 ATTTCAAACT
*
503334 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
503399 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
503427 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
503491 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
503518 T
1 T
503519 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:505198 original size:20 final size:19
Alignment explanation
Indices: 505167--505288 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
505157 TCTTTTGGTT
505167 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
505186 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
505207 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
505226 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
505240 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
505259 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
505273 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
505289 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.26
20 29 0.37
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:505249 original size:33 final size:33
Alignment explanation
Indices: 505192--505288 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
505182 ACGAGATAAT
505192 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
505226 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
505259 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
505289 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:505321 original size:19 final size:19
Alignment explanation
Indices: 505289--505332 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
505279 AAAATCGCAA
*
505289 TGCGA-TTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
505307 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
505326 TGCGATT
1 TGCGATT
505333 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:505952 original size:20 final size:20
Alignment explanation
Indices: 505883--505976 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
505873 CGCTATATAA
* *
505883 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
505903 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
505924 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
505944 ATCGTATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
505964 ATCGCATTGCGAT
1 ATCGCATTGCGAT
505977 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.71
21 12 0.20
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:505995 original size:61 final size:61
Alignment explanation
Indices: 505883--505997 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
505873 CGCTATATAA
* * ** *
505883 ATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* * *
505944 ATCGTATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
505998 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:506087 original size:21 final size:21
Alignment explanation
Indices: 506047--506087 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
506037 ACTGTAGACC
**
506047 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
506068 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
506088 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:507681 original size:35 final size:35
Alignment explanation
Indices: 507632--507738 Score: 196
Period size: 35 Copynumber: 3.1 Consensus size: 35
507622 TTTAGAACGG
**
507632 GAAGCTTCGCCAAATAAATTTCAATCATCCTGAAA
1 GAAGCTTCATCAAATAAATTTCAATCATCCTGAAA
507667 GAAGCTTCATCAAATAAATTTCAATCATCCTGAAA
1 GAAGCTTCATCAAATAAATTTCAATCATCCTGAAA
507702 GAAGCTTCATCAAATAAATTTCAATCATCCTGAAA
1 GAAGCTTCATCAAATAAATTTCAATCATCCTGAAA
507737 GA
1 GA
507739 TCTCGAGGAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (35 bp):
GAAGCTTCATCAAATAAATTTCAATCATCCTGAAA
Found at i:508813 original size:20 final size:22
Alignment explanation
Indices: 508778--508821 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
508768 GCAATAAGAT
508778 TCCTTCGATATTTAATTATGCA
1 TCCTTCGATATTTAATTATGCA
508800 TCCTT-GAT-TTTAATTATGCA
1 TCCTTCGATATTTAATTATGCA
508820 TC
1 TC
508822 TTTTGGTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 3 0.14
22 5 0.23
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (22 bp):
TCCTTCGATATTTAATTATGCA
Found at i:513569 original size:23 final size:24
Alignment explanation
Indices: 513525--513571 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
513515 ATATATTTAT
*
513525 TATTTATGTAAATATTATTAAATA
1 TATTTATGTAAATATTACTAAATA
513549 TATTTATTGT-AA-ATTACTAAATA
1 TATTTA-TGTAAATATTACTAAATA
513572 AAAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 8 0.38
25 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTATGTAAATATTACTAAATA
Found at i:532955 original size:31 final size:31
Alignment explanation
Indices: 532917--532983 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
532907 AAGATCTGCA
532917 AATTGTCTACGTTCTTTACCATTATAAAAAC
1 AATTGTCTACGTTCTTTACCATTATAAAAAC
532948 AATTGTCTACGTTCTTTACCATTATAAAAAC
1 AATTGTCTACGTTCTTTACCATTATAAAAAC
*
532979 GATTG
1 AATTG
532984 AGTTGGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (31 bp):
AATTGTCTACGTTCTTTACCATTATAAAAAC
Found at i:534860 original size:22 final size:22
Alignment explanation
Indices: 534817--534860 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
534807 AAAAATATTA
*
534817 TATCATAATTAAATTTTATAAT
1 TATCATAATTAAATATTATAAT
*
534839 TATCTTAATTAAAATATT-TAAT
1 TATCATAATT-AAATATTATAAT
534861 ATTTGTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TATCATAATTAAATATTATAAT
Found at i:535218 original size:22 final size:23
Alignment explanation
Indices: 535159--535221 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
535149 TAAGTCTGTC
535159 TGTATGACACATTTTCTTTTTCT
1 TGTATGACACATTTTCTTTTTCT
*
535182 T-TCATGGCACATTTT-TTTTGT-T
1 TGT-ATGACACATTTTCTTTT-TCT
*
535204 TGTATGACACGTTTTCTT
1 TGTATGACACATTTTCTT
535222 CTGCACATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (23 bp):
TGTATGACACATTTTCTTTTTCT
Found at i:535721 original size:21 final size:21
Alignment explanation
Indices: 535681--535719 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
535671 GTTGTAATTA
*
535681 TTTTAAAAAAAGTAGAAAATG
1 TTTTAAAAAAAGTAAAAAATG
535702 TTTTAAAAAAA-TAAAAAA
1 TTTTAAAAAAAGTAAAAAA
535720 ATCAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (21 bp):
TTTTAAAAAAAGTAAAAAATG
Found at i:535741 original size:16 final size:17
Alignment explanation
Indices: 535716--535804 Score: 65
Period size: 18 Copynumber: 5.1 Consensus size: 17
535706 AAAAAAATAA
535716 AAAAATCAAAGAAAAAT
1 AAAAATCAAAGAAAAAT
*
535733 AAAAA-CAAATAAAAA-
1 AAAAATCAAAGAAAAAT
* *
535748 AATAAATCAACGGCAAAAT
1 AA-AAATCAA-AGAAAAAT
* * *
535767 ATAAATAAAAAATATAAAT
1 AAAAATCAAAGA-A-AAAT
535786 AAAAATCAAAGGAAAAAT
1 AAAAATCAAA-GAAAAAT
535804 A
1 A
535805 TTAAATTTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
15 2 0.04
16 12 0.23
17 8 0.15
18 16 0.30
19 14 0.26
20 1 0.02
ACGTcount: A:0.73, C:0.07, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAATCAAAGAAAAAT
Found at i:535780 original size:13 final size:13
Alignment explanation
Indices: 535762--535790 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
535752 AATCAACGGC
535762 AAAATATAAATAA
1 AAAATATAAATAA
535775 AAAATATAAATAA
1 AAAATATAAATAA
535788 AAA
1 AAA
535791 TCAAAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATATAAATAA
Found at i:535780 original size:37 final size:36
Alignment explanation
Indices: 535706--535821 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 36
535696 AAAATGTTTT
*
535706 AAAAA-AATAAAAAAATCAAA-G-AAAA-ATAAA-A
1 AAAAATAAAAAAAAAATCAAAGGAAAAATATAAATA
* * *
535737 ACAAATAAAAAAATAAATCAACGGCAAAATATAAATA
1 AAAAATAAAAAAA-AAATCAAAGGAAAAATATAAATA
*
535774 AAAAATATAAATAAAAATCAAAGGAAAAATATTAAATTTA
1 AAAAATA-AAAAAAAAATCAAAGGAAAAATA-TAAA--TA
535814 AAAAATAA
1 AAAAATAA
535822 TAAAGGGAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
31 4 0.06
32 6 0.09
33 7 0.10
34 1 0.01
35 4 0.06
36 5 0.07
37 22 0.32
38 9 0.13
39 1 0.01
40 9 0.13
ACGTcount: A:0.73, C:0.05, G:0.04, T:0.17
Consensus pattern (36 bp):
AAAAATAAAAAAAAAATCAAAGGAAAAATATAAATA
Found at i:535825 original size:37 final size:34
Alignment explanation
Indices: 535705--535821 Score: 112
Period size: 34 Copynumber: 3.3 Consensus size: 34
535695 GAAAATGTTT
*
535705 TAAAAAAATAAAAAAATCAAA-GAAAAATAAAAA
1 TAAAAAAATAAAAAAATCAAAGGAAAAATATAAA
* * * *
535738 CAAATAAAA-AAATAAATCAACGGCAAAATATAAA
1 TAAA-AAAATAAAAAAATCAAAGGAAAAATATAAA
535772 TAAAAAATATAAATAAAAATCAAAGGAAAAATATTAAA
1 TAAAAAA-AT-AA-AAAAATCAAAGGAAAAATA-TAAA
*
535810 TTTAAAAAATAA
1 -TAAAAAAATAA
535822 TAAAGGGAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
33 16 0.24
34 18 0.27
36 2 0.03
37 18 0.27
38 6 0.09
39 6 0.09
ACGTcount: A:0.73, C:0.05, G:0.04, T:0.18
Consensus pattern (34 bp):
TAAAAAAATAAAAAAATCAAAGGAAAAATATAAA
Found at i:537825 original size:84 final size:83
Alignment explanation
Indices: 537713--538662 Score: 834
Period size: 84 Copynumber: 11.4 Consensus size: 83
537703 ATTTTATCGA
* * * * * *
537713 CAGATAGCCCTTCTTA-CCTTGAGCTATGCTGTAAA-GTATGTGCCCTGGAGCTGAGCATAGACG
1 CAGATAACCCTTC-TAGCCTTGAGTTATGCTGCAAATG-ATATGCCTTGGAGCTGAGCGTAGACG
* *
537776 AACTCAAAGGTTTTTGGTTGG
64 AACTCGAAGGTCTTTGG-TGG
* * * *
537797 CAGATAACTCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTCCGAAGCTGAGCCTA-ATCG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT-TGGAGCTGAGCGTAGA-CG
*
537861 AACTTGAAGGTCTTTGGTTGG
64 AACTCGAAGGTCTTTGG-TGG
* * * * * * * * *
537882 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTA-ATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGA-CGA
* *
537946 ACTCAAAGGTCTTTGTTGG
65 ACTCGAAGGTCTTTGGTGG
*
537965 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
* *
538030 CTCGAAGGTCTTTTAGTGA
66 CTCGAAGGTC-TTTGGTGG
* * * * * * *
538049 AAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATTATATGCCTTGGAGCTGAGCGTAGTCGAT
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
**
538114 CTCGAAGGTCTTTTGGTCA
66 CTCGAAGGTC-TTTGGTGG
* * * *
538133 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGA-GCCCTCGAAGCTGAGTGTA-ATC
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-ATG-CCTTGGAGCTGAGCGTAGA-C
*
538196 GAACTCGAGGGTCTTT-G-GG
63 GAACTCGAAGGTCTTTGGTGG
* * * * * **
538215 -AGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
538279 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGG-TGG
* * * * * * * *
538298 TAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCATAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
*
538363 CTCGAAGGTCTTTTGGTGA
66 CTCGAAGGTC-TTTGGTGG
** *** *
538382 CAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGCCCTCAAAGCTGAGTGTA-ATCG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGA-CG
*
538446 AACTCGAGGGTC-TT--TGG
64 AACTCGAAGGTCTTTGGTGG
* * * * * * ** **
538463 CAGATAGCCCTTCTCGACTTAAGCTATTCTATAAATGATATGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
* * *
538528 CTCGAAGATTTTTGTTGG
66 CTCGAAGGTCTTTGGTGG
* ** * * * * * * *
538546 CAAATAGTCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTTGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
* *
538611 CTTGAATGTC-TT--TGG
66 CTCGAAGGTCTTTGGTGG
*
538626 CAGATAACCCTTCTAGCCATGAGTTATGCTGCAAATG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
538663 TTTTCTTAAA
Statistics
Matches: 706, Mismatches: 138, Indels: 48
0.79 0.15 0.05
Matches are distributed among these distances:
80 85 0.12
81 75 0.11
82 2 0.00
83 134 0.19
84 285 0.40
85 125 0.18
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGACGAA
CTCGAAGGTCTTTGGTGG
Found at i:538264 original size:165 final size:165
Alignment explanation
Indices: 537713--538662 Score: 932
Period size: 165 Copynumber: 5.7 Consensus size: 165
537703 ATTTTATCGA
* * * * * * *
537713 CAGATAGCCCTTCTTA-CCTTGAGCTATGCTGTAAA-GTATGTGCCCTGGAGCTGAGCATAGACG
1 CAGATAGCCCTTC-TAGACTTAAGTTATGCTGCAAATG-ATGTGCCTTGGAGCTGAGCGTAGTCG
* * *
537776 AACTCAAAGGTTTTTGGTTGGCAGATAACTCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
64 AACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
* * * * *
537841 TCCGAAGCTGAGCCTAATCGAACTTGAAGGTCTTTGGTTGG
128 T-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-TGG
* * * * * *
537882 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
537947 CTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTG
66 CTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTG
*
538012 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGA
131 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GTGG
* * * * * *
538049 AAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATTATATGCCTTGGAGCTGAGCGTAGTCGAT
1 CAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
** *
538114 CTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGA-GCCC
66 CTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-ATG-CC
* * * * *
538178 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG-GG
128 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGG
* *
538215 -AGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * *
538279 CTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTT
66 CTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT
* * *
538344 GGAGCTGAGCATAGTCAAACTCGAAGGTCTTTTGGTGA
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GTGG
* * * ** * *** * *
538382 CAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGCCCTCAAAGCTGAGTGTAATCGA
1 CAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
* * * * * * * **
538447 ACTCGAGGGTC-TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTATAAATGATATGCCTT
65 ACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT
* * *
538509 GGAGCTGAGCGTAGTTGAACTCGAAGATTTTTGTTGG
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-TGG
* * * * * * * * *
538546 CAAATAGTCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTTGTCGAA
1 CAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
538611 CTTGAATGTC-TT--TGGCAGATAACCCTTCTAGCCATGAGTTATGCTGCAAATG
66 CTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
538663 TTTTCTTAAA
Statistics
Matches: 653, Mismatches: 114, Indels: 34
0.82 0.14 0.04
Matches are distributed among these distances:
163 59 0.09
164 70 0.11
165 175 0.27
166 2 0.00
167 93 0.14
168 135 0.21
169 118 0.18
170 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
CAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGG
Found at i:538305 original size:249 final size:248
Alignment explanation
Indices: 537753--538662 Score: 1078
Period size: 249 Copynumber: 3.7 Consensus size: 248
537743 GTAAAGTATG
* * * * * * * * *
537753 TGCCCTGGAGCTGAGCATAGACGAACTCAAAGGTTTTTGGTTGGCAGATAACTCTTCTAGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * * * *
537818 AGTTATGCTGCAAATGATATGCCTCCGAAGCTGAGCCTAATCGAACTTGAAGGTCTTTGGTTGGC
66 AGTTATGCTGCAAATGATATGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGAC
* * * * * * * * *
537883 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGTTGTGCCTTTG-AGCTGAGTGTAATCGAA
129 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCCTCGAAGCTGAGTGTAATCGAA
* * * * * *
537947 CTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATA
194 CTCGAGGGTCTTTG--GG-AGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATA
* **
538005 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAG-TGAAAGATAACCCTTCTCGACTT
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTT
* * *
538069 AAGTTATGCTGCAAATTATATGCCTTGGAGCTGAGCGTAGTCGATCTCGAAGGTCTTTTGGTCAC
65 AAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGAC
*
538134 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCTCGAAGCTGAGTGTAATCGAA
129 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCCTCGAAGCTGAGTGTAATCGAA
*
538199 CTCGAGGGTCTTTGGGAGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATG
194 CTCGAGGGTCTTTGGGAGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATA
* *
538254 TGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * *
538319 AGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTTGGTGACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
** *
538384 GATAACCCTTCTAGCCTTGAGTTATGCTATAAATGAT-ATGCCCTCAAAGCTGAGTGTAATCGAA
130 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGA-GCCCTCGAAGCTGAGTGTAATCGAA
* * * **
538448 CTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTATAAATGATA
194 CTCGAGGGTCTTTGGGAGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATA
* * * * ** * * *
538503 TGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGAT-TTTTGTTGGCAAATAGTCCTTCTTGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * * * * *
538567 AGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTTGTCGAACTTGAATGTCTTT-G-G-CAG
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
*
538629 ATAACCCTTCTAGCCATGAGTTATGCTGCAAATG
131 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
538663 TTTTCTTAAA
Statistics
Matches: 575, Mismatches: 78, Indels: 18
0.86 0.12 0.03
Matches are distributed among these distances:
244 34 0.06
245 1 0.00
246 1 0.00
247 3 0.01
248 71 0.12
249 291 0.51
250 2 0.00
251 63 0.11
252 105 0.18
253 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (248 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGAGCCCTCGAAGCTGAGTGTAATCGAACT
CGAGGGTCTTTGGGAGATAGCCCTTCTAGACTTAAGTTATTCTGCAAATGATA
Found at i:540757 original size:23 final size:23
Alignment explanation
Indices: 540726--540816 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
540716 CACCACAGCT
* *
540726 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
*
540749 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGTAGTGCCG
* * *
540772 CATAGAATTGCACCGGAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
540795 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGTAGTGCC
540817 ATATAATGTC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCG
Found at i:542424 original size:19 final size:19
Alignment explanation
Indices: 542400--542436 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
542390 TTAAGGGGGG
542400 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
542419 TGCATCGATGCACTACTT
1 TGCATCGATGCACTACTT
542437 GCATTCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:547270 original size:32 final size:32
Alignment explanation
Indices: 547214--547274 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
547204 ATCAATGGCA
547214 AAATATAAATAAAAATAAAAGGAAAAAATATT
1 AAATATAAATAAAAATAAAAGGAAAAAATATT
* *
547246 AAATTTAAA-AAATAATAAAGGGAAAAAAT
1 AAATATAAATAAA-AATAAAAGGAAAAAAT
547275 GAAATATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.21
Consensus pattern (32 bp):
AAATATAAATAAAAATAAAAGGAAAAAATATT
Found at i:547271 original size:16 final size:16
Alignment explanation
Indices: 547227--547274 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
547217 TATAAATAAA
547227 AATAAAAGGAAAAAAT
1 AATAAAAGGAAAAAAT
* ***
547243 ATTAAATTTAAAAAAT
1 AATAAAAGGAAAAAAT
*
547259 AATAAAGGGAAAAAAT
1 AATAAAAGGAAAAAAT
547275 GAAATATGAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (16 bp):
AATAAAAGGAAAAAAT
Found at i:547416 original size:19 final size:20
Alignment explanation
Indices: 547369--547416 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
547359 GTGGCAAAAT
547369 GAAAAAATAACAGTAATAATA
1 GAAAAAA-AACAGTAATAATA
*
547390 -AATTAAAAACA-TAATAATA
1 GAA-AAAAAACAGTAATAATA
547409 GAAAAAAA
1 GAAAAAAA
547417 TGAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 12 0.52
20 8 0.35
21 3 0.13
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (20 bp):
GAAAAAAAACAGTAATAATA
Found at i:550448 original size:22 final size:20
Alignment explanation
Indices: 550399--550448 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
550389 AGAGTCCAAC
*
550399 AAAAA-AAT-TAAAAAAATT
1 AAAAACAATATAAAAAAATA
*
550417 AAAGACAATATAAAAAAATA
1 AAAAACAATATAAAAAAATA
550437 AGAAAACTAATA
1 A-AAAAC-AATA
550449 GTCACTGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 10 0.40
21 4 0.16
22 4 0.16
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (20 bp):
AAAAACAATATAAAAAAATA
Found at i:550696 original size:19 final size:18
Alignment explanation
Indices: 550652--550700 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
550642 ATATTTTTTG
550652 ATTTTTTAAAAATAAAAT
1 ATTTTTTAAAAATAAAAT
* * *
550670 ATTATTTATAAATATATAT
1 ATTTTTTAAAAATA-AAAT
550689 ATTTTTTAAAAA
1 ATTTTTTAAAAA
550701 ATCTGAATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTTTAAAAATAAAAT
Found at i:552072 original size:19 final size:19
Alignment explanation
Indices: 552031--552083 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
552021 ACTAGCCAAG
552031 AGTATCGATACTCTTATAGA
1 AGTATCGATACT-TTATAGA
* *
552051 AGTTTCGATACTTTATATA
1 AGTATCGATACTTTATAGA
*
552070 AGTACCGATACTTT
1 AGTATCGATACTTT
552084 TAAACATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (19 bp):
AGTATCGATACTTTATAGA
Found at i:553740 original size:2 final size:2
Alignment explanation
Indices: 553733--553767 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
553723 ATATAATTAA
553733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
553768 CATCAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:556049 original size:4 final size:4
Alignment explanation
Indices: 556040--556066 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
556030 CAATGCATGT
556040 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
556067 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:556098 original size:13 final size:13
Alignment explanation
Indices: 556080--556104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
556070 AGTTGAACAG
556080 TCTTCATATGCAC
1 TCTTCATATGCAC
556093 TCTTCATATGCA
1 TCTTCATATGCA
556105 ATTCCACAAA
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:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (13 bp):
TCTTCATATGCAC
Found at i:563368 original size:18 final size:17
Alignment explanation
Indices: 563314--563362 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
563304 TTGGACCCTT
* *
563314 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
563332 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
563350 AGTGCATTCGATG
1 AGTGCA-TCGATG
563363 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:563446 original size:64 final size:64
Alignment explanation
Indices: 563334--563492 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 64
563324 TGCACTAAGA
* *
563334 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-G
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGG-TAG
* * *
563398 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCA-AAATAGCCACAGTGCATCGATGCATGGTAG
* * * *
563462 GTGCATCAATGGATGAAATGCATTCAATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
563493 CAATTTATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 1 0.01
64 80 0.95
65 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAG
Found at i:564214 original size:14 final size:15
Alignment explanation
Indices: 564195--564223 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
564185 TCAAGCATTT
564195 AACAATCCA-AAACA
1 AACAATCCATAAACA
564209 AACAATCCATAAACA
1 AACAATCCATAAACA
564224 TAAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AACAATCCATAAACA
Found at i:566164 original size:23 final size:22
Alignment explanation
Indices: 566134--566213 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
566124 GCATGGCCTT
566134 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
566156 CGTGCATCGGTGTACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* * *
566178 GTGTATCGATACAAATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
566200 ATGCATCGATGCAC
1 GTGCATCGATGCAC
566214 TGTTAGGTGT
Statistics
Matches: 41, Mismatches: 15, Indels: 3
0.69 0.25 0.05
Matches are distributed among these distances:
21 12 0.29
22 14 0.34
23 15 0.37
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:572103 original size:64 final size:64
Alignment explanation
Indices: 572021--572158 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 64
572011 CTAAGAGTGT
* *
572021 ATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT-GGTG
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCACAGTGCATCGATGCATGG-TAGGTG
572084 C
64 C
* * * *
572085 ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTCAGTGTATCGATGCATGGTATGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCACAGTGCATCGATGCATGGTAGGTGC
572149 ATCGATGCAT
1 ATCGATGCAT
572159 GAATTGGTGC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.02
64 62 0.94
65 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (64 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCACAGTGCATCGATGCATGGTAGGTGC
Found at i:577803 original size:21 final size:21
Alignment explanation
Indices: 577754--577805 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
577744 ATTGGGAAAC
*
577754 CTATTGAGGACCCTAAGAAGA
1 CTATTGATGACCCTAAGAAGA
577775 CTATTGATGACCCTAAGAAGA
1 CTATTGATGACCCTAAGAAGA
577796 CTATTGATGA
1 CTATTGATGA
577806 AGAGGCTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (21 bp):
CTATTGATGACCCTAAGAAGA
Found at i:580571 original size:17 final size:17
Alignment explanation
Indices: 580549--580589 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
580539 TGTTACCTTT
580549 ATGTTGTGACATTCATG
1 ATGTTGTGACATTCATG
*
580566 ATGTTGTGACATTCCTG
1 ATGTTGTGACATTCATG
580583 ATGTTGT
1 ATGTTGT
580590 AGATATTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (17 bp):
ATGTTGTGACATTCATG
Found at i:581214 original size:33 final size:33
Alignment explanation
Indices: 581172--581246 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
581162 TTGCCCAGTC
*
581172 CACTGCATCGAGAGGTGAGTGTCACTATGTGAG
1 CACTGCATCGAGAGGTGAGTGGCACTATGTGAG
*
581205 CACTGCATCGAGAGGTGAGTGGCACTGTGTGAG
1 CACTGCATCGAGAGGTGAGTGGCACTATGTGAG
581238 CACTGCATC
1 CACTGCATC
581247 AGTGGTTACG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (33 bp):
CACTGCATCGAGAGGTGAGTGGCACTATGTGAG
Found at i:585769 original size:23 final size:23
Alignment explanation
Indices: 585743--585788 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
585733 AAAAAAAATT
585743 CGGGTAT-TCGGGTACCCGACATA
1 CGGGTATCT-GGGTACCCGACATA
585766 CGGGTATCTGGGTACCCGACATA
1 CGGGTATCTGGGTACCCGACATA
585789 TAGGTACCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (23 bp):
CGGGTATCTGGGTACCCGACATA
Found at i:593049 original size:17 final size:17
Alignment explanation
Indices: 593000--593055 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
592990 TTTTTTAGAC
593000 TAGAAATTAATAG-CC-
1 TAGAAATTAATAGACCA
* *
593015 TAGATATGTTATTAGACCA
1 TAGA-A-ATTAATAGACCA
593034 TAGAAATTAATAGACCAA
1 TAGAAATTAATAGACC-A
593052 TAGA
1 TAGA
593056 TATATGGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 15 0.47
18 8 0.25
19 4 0.12
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (17 bp):
TAGAAATTAATAGACCA
Found at i:594805 original size:15 final size:15
Alignment explanation
Indices: 594773--594830 Score: 80
Period size: 15 Copynumber: 3.7 Consensus size: 15
594763 AGAGTCTCTT
594773 AATCATTCAGACTGCTA
1 AATCATTCAG--TGCTA
*
594790 AATCATTCGGTGCTA
1 AATCATTCAGTGCTA
*
594805 AAACATTCAGTGCTA
1 AATCATTCAGTGCTA
594820 AATCATTCAGT
1 AATCATTCAGT
594831 TTTAACAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
15 28 0.76
17 9 0.24
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (15 bp):
AATCATTCAGTGCTA
Found at i:602477 original size:14 final size:14
Alignment explanation
Indices: 602458--602495 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
602448 TTATAAATAC
602458 CCTAAAGTTTAATG
1 CCTAAAGTTTAATG
602472 CCTAAAGTTTAATG
1 CCTAAAGTTTAATG
*
602486 ACTAAAGTTT
1 CCTAAAGTTT
602496 GTAATTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (14 bp):
CCTAAAGTTTAATG
Found at i:604966 original size:17 final size:17
Alignment explanation
Indices: 604944--604984 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
604934 CATTACTTTA
604944 GGTATCCGAAATTTTCG
1 GGTATCCGAAATTTTCG
604961 GGTATCCGAAATTTTCG
1 GGTATCCGAAATTTTCG
*
604978 GATATCC
1 GGTATCC
604985 AAAAATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (17 bp):
GGTATCCGAAATTTTCG
Found at i:605177 original size:30 final size:30
Alignment explanation
Indices: 605127--605191 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
605117 TAAAATTTAT
* * *
605127 TTTGAGGATTAAATTGAAATTTTAACTAAA
1 TTTGGGGATCAAAGTGAAATTTTAACTAAA
**
605157 TTTGGGGATCAAAGTGAAATTTTATTTAAA
1 TTTGGGGATCAAAGTGAAATTTTAACTAAA
605187 TTTGG
1 TTTGG
605192 ATTCAAATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (30 bp):
TTTGGGGATCAAAGTGAAATTTTAACTAAA
Found at i:610072 original size:123 final size:123
Alignment explanation
Indices: 609903--610191 Score: 517
Period size: 123 Copynumber: 2.4 Consensus size: 123
609893 TAACTACGTA
* * *
609903 TTTAGTACCTAAACTATCA-ATTTGGTCTATTTTAGTACCTAAACTTTTATTTTTTCCAAAATCA
1 TTTAGTACATAAACTATCAGTTTTGGTCTGTTTTAGTACCTAAACTTTTATTTTTTCCAAAATCA
609967 TACATAACGTTTAGTTTTTGTTTCATTTTAGTACCCCCACTGTTAAAAACTTAACGCG
66 TACATAACGTTTAGTTTTTGTTTCATTTTAGTACCCCCACTGTTAAAAACTTAACGCG
*
610025 TTTAGTACATAAACTATCAGTTTTGATCTGTTTTAGTACCTAAACTTTTATTTTTTCCAAAATCA
1 TTTAGTACATAAACTATCAGTTTTGGTCTGTTTTAGTACCTAAACTTTTATTTTTTCCAAAATCA
* *
610090 TACCTAATGTTTAGTTTTTGTTTCATTTTAGTACCCCCACTGTTAAAAACTTAACGCG
66 TACATAACGTTTAGTTTTTGTTTCATTTTAGTACCCCCACTGTTAAAAACTTAACGCG
610148 TTTAGTACATAAACTATCAGTTTTGGTCTGTTTTAGTACCTAAA
1 TTTAGTACATAAACTATCAGTTTTGGTCTGTTTTAGTACCTAAA
610192 TATTTTTTTA
Statistics
Matches: 159, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
122 18 0.11
123 141 0.89
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (123 bp):
TTTAGTACATAAACTATCAGTTTTGGTCTGTTTTAGTACCTAAACTTTTATTTTTTCCAAAATCA
TACATAACGTTTAGTTTTTGTTTCATTTTAGTACCCCCACTGTTAAAAACTTAACGCG
Found at i:612606 original size:32 final size:32
Alignment explanation
Indices: 612535--612617 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
612525 CTTTTGGTAT
* *
612535 TCGGGTCGGTTTTTTTAAAAAAAAAATTCAGGA
1 TCGGGTTGGATTTTTT-AAAAAAAAATTCAGGA
* * * *
612568 TC-GGTTGGATTTTTTAAAAAACATTTCGGGG
1 TCGGGTTGGATTTTTTAAAAAAAAATTCAGGA
*
612599 TCGGGTTGGGTTTTTTAAA
1 TCGGGTTGGATTTTTTAAA
612618 GTTTGATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 14 0.33
32 26 0.62
33 2 0.05
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (32 bp):
TCGGGTTGGATTTTTTAAAAAAAAATTCAGGA
Found at i:612643 original size:33 final size:33
Alignment explanation
Indices: 612596--612850 Score: 200
Period size: 33 Copynumber: 7.5 Consensus size: 33
612586 AAACATTTCG
* *
612596 GGGTCGGGTTGGGTTTTTTAAAGTTTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
*
612629 GGGTTGGGTCGGGTTTTTGT-AAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTT-TAAAGTGTGATATTC
***
612662 GGGTCGGGTTCAGGTCGGGTTTTTTTCAAA--AAAAT-TTC
1 GGGTC--G----GGTCGGG-TTTTTT-AAAGTGTGATATTC
* * * * *
612700 GGGATCAGGTCGGATTTTTTTAAAATTTCGGGT-TT-
1 GGG-TCGGGTCGG-GTTTTTTAAAGTGT--GATATTC
612735 GGGTCGGGTCGGGGTTTTTT-AAGTGTGATATTC
1 GGGTCGGGTC-GGGTTTTTTAAAGTGTGATATTC
*
612768 GGGTCGGGTCGGGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
* *
612801 GGGACGGGTCAGGTTTTTTAAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
612834 GGGTCGGGTTCGGGTTT
1 GGGTCGGG-TCGGGTTT
612851 AGGGTGAAAA
Statistics
Matches: 178, Mismatches: 23, Indels: 41
0.74 0.10 0.17
Matches are distributed among these distances:
31 2 0.01
32 14 0.08
33 108 0.61
34 20 0.11
35 6 0.03
36 3 0.02
38 6 0.03
39 12 0.07
40 5 0.03
41 2 0.01
ACGTcount: A:0.15, C:0.09, G:0.35, T:0.40
Consensus pattern (33 bp):
GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
Found at i:621634 original size:3 final size:3
Alignment explanation
Indices: 621626--621765 Score: 271
Period size: 3 Copynumber: 46.7 Consensus size: 3
621616 TCTGATTCTT
*
621626 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
621674 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
621722 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
621766 GTGAATCGGA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 135 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:622226 original size:30 final size:30
Alignment explanation
Indices: 622192--622310 Score: 105
Period size: 30 Copynumber: 4.0 Consensus size: 30
622182 ATATTATCGT
*
622192 ATCTTTCTATCACTATGATGACATAGACAC
1 ATCTTTCTATCACTATGATGACATGGACAC
** *
622222 ATCTTTCTATTGCTATGATGTCATGGACAC
1 ATCTTTCTATCACTATGATGACATGGACAC
* * * * *
622252 CTCTTTTTATTAC-AGTGATGACTTGGACAT
1 ATCTTTCTATCACTA-TGATGACATGGACAC
* * * *
622282 ATCTTTCTGTCACTGTAATAACATGGACA
1 ATCTTTCTATCACTATGATGACATGGACA
622311 AAATGACGTT
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
29 1 0.01
30 68 0.99
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (30 bp):
ATCTTTCTATCACTATGATGACATGGACAC
Found at i:624827 original size:27 final size:27
Alignment explanation
Indices: 624797--624851 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
624787 ATTGCATCAG
624797 CTGTAGTTTAGCTTGCATGAATCCTTA
1 CTGTAGTTTAGCTTGCATGAATCCTTA
*
624824 CTGTAGTTTTGCTTGCATGAATCCTTA
1 CTGTAGTTTAGCTTGCATGAATCCTTA
624851 C
1 C
624852 CATGTCTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (27 bp):
CTGTAGTTTAGCTTGCATGAATCCTTA
Found at i:626552 original size:2 final size:2
Alignment explanation
Indices: 626545--626571 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
626535 AACGAAAATG
626545 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
626572 AGAAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:627008 original size:19 final size:19
Alignment explanation
Indices: 626939--627008 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 19
626929 AGAATTTTAG
* *
626939 ATTAGTAAAATTAGGATTAA
1 ATTA-TAAAATAAAGATTAA
* *
626959 ATTAAATAACAACTAAAGTTTAC
1 ATT--ATAA-AA-TAAAGATTAA
*
626982 ATTCTAAAATAAAGATTAA
1 ATTATAAAATAAAGATTAA
627001 ATTATAAA
1 ATTATAAA
627009 TTCTTAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
19 15 0.39
20 5 0.13
21 6 0.16
22 3 0.08
23 9 0.24
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (19 bp):
ATTATAAAATAAAGATTAA
Found at i:627335 original size:122 final size:120
Alignment explanation
Indices: 627186--627538 Score: 492
Period size: 122 Copynumber: 2.9 Consensus size: 120
627176 TTTAGGATAA
*
627186 ACTAGAAATGTTATTATTTTTTTAACATTTCTGGTAAAGCGCTACCTAAATCATTATATTTT-TA
1 ACTAGAAATGTTATTA-TTTTTTAACATTTCCGGTAAAGCGCTACCTAAATCATTAT-TTTTCTA
* * * *
627250 CTGGAAATGTTAATATTAGAAGTTACCTAAAACATTATTTTTCTACCGGAAAGGCGCT
64 CTGAAAATGTTAATATT-GGAGCTACCTAAAACATTATTTTTCTACCAGAAAGGCGCT
*
627308 ACTAGAAATGTTATTAGTTTTTTAACATTTCCGATAAAGCGCTACCTAAATCATTATTTTTCTAC
1 ACTAGAAATGTTATTA-TTTTTTAACATTTCCGGTAAAGCGCTACCTAAATCATTATTTTTCTAC
* *
627373 TGAAAATGTTAATATTGGCGCTACCTAAAACATTATTTTTCTACCAGAAATGCGCT
65 TGAAAATGTTAATATTGGAGCTACCTAAAACATTATTTTTCTACCAGAAAGGCGCT
** * * * *
627429 ACCGGAAATGTTATTATTTTTTAGCATTTCCAGTAAAACGCTACCTAAAACATTATTTTTTCTAC
1 ACTAGAAATGTTATTATTTTTTAACATTTCCGGTAAAGCGCTACCTAAATCATTA-TTTTTCTAC
* * *
627494 CGAAAATGTTAATATTGGGTGCTACCTAAAACATTGTTTTTCTAC
65 TGAAAATGTTAATATT-GGAGCTACCTAAAACATTATTTTTCTAC
627539 TAGATTTTTT
Statistics
Matches: 209, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
120 34 0.16
121 77 0.37
122 98 0.47
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (120 bp):
ACTAGAAATGTTATTATTTTTTAACATTTCCGGTAAAGCGCTACCTAAATCATTATTTTTCTACT
GAAAATGTTAATATTGGAGCTACCTAAAACATTATTTTTCTACCAGAAAGGCGCT
Found at i:627815 original size:26 final size:25
Alignment explanation
Indices: 627779--627831 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
627769 TAGAAATAAT
*
627779 AATGTTTTAGGTAATTTTTTACCAGA
1 AATGTTATAGGTAATTTTTTACC-GA
627805 AATGTTATAGGTAATTTTTTACCGA
1 AATGTTATAGGTAATTTTTTACCGA
627830 AA
1 AA
627832 ACGTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
AATGTTATAGGTAATTTTTTACCGA
Found at i:627837 original size:26 final size:26
Alignment explanation
Indices: 627786--627837 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
627776 AATAATGTTT
*
627786 TAGGTAATTTTTTACCAGAAATGTTA
1 TAGGTAATTTTTTACCAGAAACGTTA
627812 TAGGTAATTTTTTACC-GAAAACGTTA
1 TAGGTAATTTTTTACCAG-AAACGTTA
627838 AAAAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (26 bp):
TAGGTAATTTTTTACCAGAAACGTTA
Found at i:629905 original size:2 final size:2
Alignment explanation
Indices: 629898--629923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
629888 AAGATTAAGA
629898 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
629924 TAATTATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:630014 original size:15 final size:15
Alignment explanation
Indices: 629993--630032 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
629983 TTTAATGGTT
629993 ATTTAATTCAAAATA
1 ATTTAATTCAAAATA
*
630008 TTTTAATTCAAAATA
1 ATTTAATTCAAAATA
*
630023 ATTAAATTCA
1 ATTTAATTCA
630033 GATTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAATTCAAAATA
Found at i:633703 original size:15 final size:15
Alignment explanation
Indices: 633685--633713 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
633675 TTTCTAATAA
633685 ATTTTTTAAAAAAAC
1 ATTTTTTAAAAAAAC
633700 ATTTTTTAAAAAAA
1 ATTTTTTAAAAAAA
633714 ATTGAAGATT
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:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTTTAAAAAAAC
Found at i:633886 original size:2 final size:2
Alignment explanation
Indices: 633881--633912 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
633871 TATATACTGC
633881 TA 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 TA
633913 GCTTATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:636908 original size:6 final size:6
Alignment explanation
Indices: 636897--636927 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
636887 TGGATTGGGA
636897 GTGATG GTGATG GTGATG GTGATG GTGATG G
1 GTGATG GTGATG GTGATG GTGATG GTGATG G
636928 GGAAGTAGAG
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:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GTGATG
Found at i:639606 original size:60 final size:59
Alignment explanation
Indices: 639502--639642 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 59
639492 CTCTCATTTC
* *
639502 AAATTAATCCTTAAGCTTTTAAACATTTCAATTGCATCCTCAAACTAT-GATACTCAGTCT
1 AAATTAGTCCTTAA-CTTTTAAACATTTCAATTGCATCCTCAAACTATAAATA-TCAGTCT
* * ** *
639562 AAATTAGTCCTTGAACTTTTGAACATTTCAGTTTTATTCC-CAAACTATAAATATCATTCT
1 AAATTAGTCCTT-AACTTTTAAACATTTCAATTGCA-TCCTCAAACTATAAATATCAGTCT
* *
639622 AAATTGGTCCCTAAACTTTTA
1 AAATTAGT-CCTTAACTTTTA
639643 GATCTTCTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
60 56 0.84
61 11 0.16
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (59 bp):
AAATTAGTCCTTAACTTTTAAACATTTCAATTGCATCCTCAAACTATAAATATCAGTCT
Found at i:642395 original size:75 final size:75
Alignment explanation
Indices: 642272--642424 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
642262 TCAAATTTAT
642272 AATAATTTTTTGGCCACACATCACATATCATGTTATTTCGAATTAGTATATGTTCTAAATACTCT
1 AATAATTTTTTGGCCACACATCACATATCATGTTATTTCGAATTAGTATATGTTCTAAATACTCT
642337 TACATTAGAC
66 TACATTAGAC
642347 AATAATTTTTTGGCCACACATCACATATCATGTTATTTCGAATTAGTATATGTTCTAAATACTCT
1 AATAATTTTTTGGCCACACATCACATATCATGTTATTTCGAATTAGTATATGTTCTAAATACTCT
642412 TACATTAGAC
66 TACATTAGAC
642422 AAT
1 AAT
642425 GAACGGCCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (75 bp):
AATAATTTTTTGGCCACACATCACATATCATGTTATTTCGAATTAGTATATGTTCTAAATACTCT
TACATTAGAC
Found at i:644979 original size:23 final size:23
Alignment explanation
Indices: 644953--645000 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
644943 ATAAAGTACA
*
644953 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
644976 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
644999 AT
1 AT
645001 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:645401 original size:21 final size:20
Alignment explanation
Indices: 645376--645430 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
645366 GATAGACACT
645376 TTACAATATAACCATTACCTA
1 TTACAATATAACCA-TACCTA
*
645397 TTACATTATATAAACGATACCTA
1 TTACA--ATAT-AACCATACCTA
*
645420 TTACATTATAA
1 TTACAATATAA
645431 AGGGCTACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 8 0.28
23 15 0.52
24 4 0.14
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (20 bp):
TTACAATATAACCATACCTA
Found at i:645442 original size:22 final size:23
Alignment explanation
Indices: 645391--645452 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
645381 ATATAACCAT
645391 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
645414 TACCTATTACATTATA-AAGGGC
1 TACCTATTACATTATATAAACGA
*
645436 TACCTATTACATCATAT
1 TACCTATTACATTATAT
645453 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:648074 original size:33 final size:33
Alignment explanation
Indices: 648028--648093 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
648018 CATCTTAATA
*
648028 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
648061 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
648094 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:648159 original size:21 final size:22
Alignment explanation
Indices: 648133--648173 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
648123 ATGCCTCTCG
648133 AGTTTCTCTACGACT-TGATCA
1 AGTTTCTCTACGACTCTGATCA
*
648154 AGTTTCTCTTCGACTCTGAT
1 AGTTTCTCTACGACTCTGAT
648174 TGTCTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (22 bp):
AGTTTCTCTACGACTCTGATCA
Found at i:650206 original size:23 final size:23
Alignment explanation
Indices: 650180--650226 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
650170 TATTTTCAGA
*
650180 GGATAT-TTAGCTTATATTTCATC
1 GGATATGTTA-CTTATATTTAATC
*
650203 GGATATGTTATTTATATTTAATC
1 GGATATGTTACTTATATTTAATC
650226 G
1 G
650227 ATACAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (23 bp):
GGATATGTTACTTATATTTAATC
Found at i:650418 original size:20 final size:18
Alignment explanation
Indices: 650364--650409 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
650354 TCCGGTATCA
650364 TTTTACCGTTTTATCATT
1 TTTTACCGTTTTATCATT
*
650382 TTGATACCGGTTTTATCATAT
1 TT-TTACC-GTTTTATCAT-T
650403 TTTTACC
1 TTTTACC
650410 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 4 0.17
20 14 0.61
21 3 0.13
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (18 bp):
TTTTACCGTTTTATCATT
Found at i:650552 original size:20 final size:20
Alignment explanation
Indices: 650526--650571 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
650516 ACACTTTTAA
*
650526 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTGTTATCATATT
650545 TGTTACCGGTGTTATCATATT
1 T-TTACCGGTGTTATCATATT
650566 TTTACC
1 TTTACC
650572 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (20 bp):
TTTACCGGTGTTATCATATT
Found at i:651021 original size:217 final size:216
Alignment explanation
Indices: 650637--651061 Score: 691
Period size: 217 Copynumber: 2.0 Consensus size: 216
650627 TTAAAACTGC
*
650637 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
650702 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAATATTATT
66 TTAATTTAATAATTTAATTTACACAAAA-TTTATTTGATTGTTTTGATATTTTATAAATATTATT
650767 AGAATTTAAATTTAACAATATAACCAAATATATAATAAATATGTTTTCAACA-GAAATAAGTATG
130 AGAATTTAAATTTAACAATATAACCAAATATATAAT-AATAT-TTTTC-ACAGGAAATAAGTATG
650831 GACAC-TTTATAAAATGATATACTT
192 GACACTTTTATAAAATGATATACTT
650855 TTTTGAAAGTTATGTAATTTATGTTTCAA-TT-TTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
650918 ATTAATTTAATAATTTCATTTACACAAAA-TTATTTGATTGTTTTGATATTTTATAAAATATTAT
65 ATTAATTTAATAATTTAATTTACACAAAATTTATTTGATTGTTTTGATATTTTAT-AAATATTAT
* *
650982 TAGATTTTAAATTTAACAATATTAACTAAGATA-ATAATAATATTTTTCACAGTGAAATAAGTAT
129 TAGAATTTAAATTTAACAATA-TAACCAA-ATATATAATAATATTTTTCACAG-GAAATAAGTAT
651046 GGACACTTTTATAAAA
191 GGACACTTTTATAAAA
651062 AGGATAGATA
Statistics
Matches: 196, Mismatches: 4, Indels: 15
0.91 0.02 0.07
Matches are distributed among these distances:
214 3 0.02
215 30 0.15
216 51 0.26
217 79 0.40
218 9 0.05
219 24 0.12
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.46
Consensus pattern (216 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAATTTATTTGATTGTTTTGATATTTTATAAATATTATTA
GAATTTAAATTTAACAATATAACCAAATATATAATAATATTTTTCACAGGAAATAAGTATGGACA
CTTTTATAAAATGATATACTT
Found at i:652060 original size:17 final size:18
Alignment explanation
Indices: 652024--652064 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
652014 ATATTATGTA
*
652024 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
652042 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
652059 TTTACT
1 TTTACT
652065 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:653746 original size:18 final size:18
Alignment explanation
Indices: 653719--653754 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
653709 ACAGCAGCCA
* *
653719 CCGCAGCCATTTATGATG
1 CCGCAACCATATATGATG
653737 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
653755 TAGCCGCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:654259 original size:24 final size:24
Alignment explanation
Indices: 654232--654307 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
654222 TTTATTATAT
654232 TTGTATTTACTTTATTTTGTTAAA
1 TTGTATTTACTTTATTTTGTTAAA
** * * *
654256 TTGTATTTTTTTTATTATTTTTCAT
1 TTGTATTTACTTTATT-TTGTTAAA
* *
654281 TTAATACTTACTTTATTTTGTTAAA
1 TT-GTATTTACTTTATTTTGTTAAA
654306 TT
1 TT
654308 TGTTGGACTT
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
24 14 0.37
25 14 0.37
26 10 0.26
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (24 bp):
TTGTATTTACTTTATTTTGTTAAA
Found at i:659455 original size:21 final size:20
Alignment explanation
Indices: 659409--659456 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
659399 TTTTTGGTTG
* *
659409 AATTTTAATCAATTAATTTT
1 AATTTTAATAAATTAATTAT
* *
659429 ATTTTTAATTAAATTTATTAT
1 AATTTTAA-TAAATTAATTAT
659450 AATTTTA
1 AATTTTA
659457 TAATTTTGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTTAATAAATTAATTAT
Found at i:666224 original size:32 final size:31
Alignment explanation
Indices: 666188--666250 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
666178 CAAAAATAAT
666188 AAATGGGTCACTAACGTTATCAATTTATAACA
1 AAAT-GGTCACTAACGTTATCAATTTATAACA
** *
666220 AAATGGTTGCTAACGTTATCAATTTGTAACA
1 AAATGGTCACTAACGTTATCAATTTATAACA
666251 GAACAATCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (31 bp):
AAATGGTCACTAACGTTATCAATTTATAACA
Found at i:666888 original size:30 final size:31
Alignment explanation
Indices: 666852--666917 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
666842 ATACCGGTGG
*
666852 AGTGATCATTTTATTACAAAT-GATAACGTT
1 AGTGATCATTTTATTACAAATCAATAACGTT
* *
666882 AGTGATCATTTTGTTACAAATCAATAATGTT
1 AGTGATCATTTTATTACAAATCAATAACGTT
666913 AGTGA
1 AGTGA
666918 CTAATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (31 bp):
AGTGATCATTTTATTACAAATCAATAACGTT
Found at i:668612 original size:31 final size:30
Alignment explanation
Indices: 668566--668652 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
668556 TTCGATAATA
*
668566 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
668597 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
668628 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
668653 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:669270 original size:27 final size:26
Alignment explanation
Indices: 669235--669307 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
669225 GTCCCCGTGA
*
669235 TTTT-CTAAGTTT-TTATATAAAATTTT
1 TTTTACTAAGTTTATTATAT--AATATT
*
669261 TTTTACTAAGTTTAATTGTATAATATT
1 TTTTACTAAGTTT-ATTATATAATATT
*
669288 TTTTACTAAGTTTAATATAT
1 TTTTACTAAGTTTATTATAT
669308 TTTTTCAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 9 0.22
27 26 0.65
29 5 0.12
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (26 bp):
TTTTACTAAGTTTATTATATAATATT
Found at i:669401 original size:11 final size:10
Alignment explanation
Indices: 669381--669460 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
669371 AGTTTAAAAA
*
669381 ATTATAAAAT
1 ATTATTAAAT
669391 ACTTATTAAAT
1 A-TTATTAAAT
669402 -TTATTAAAAT
1 ATTATT-AAAT
*
669412 ATTATAAAATT
1 ATTATTAAA-T
*
669423 ATTAATAAAT
1 ATTATTAAAT
669433 -TTATCTAAAT
1 ATTAT-TAAAT
* *
669443 ACTATAAAAT
1 ATTATTAAAT
669453 AATTATTA
1 -ATTATTA
669461 TATTATCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
10 18 0.33
11 28 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:669416 original size:31 final size:30
Alignment explanation
Indices: 669374--669460 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
669364 TCAATAAAGT
*
669374 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
669405 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
669436 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
669461 TATTATCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:669419 original size:19 final size:21
Alignment explanation
Indices: 669378--669427 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
669368 TAAAGTTTAA
669378 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAATACTTATT
*
669398 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
669417 AAAATTATTAA
1 AAAATTATTAA
669428 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:670348 original size:16 final size:16
Alignment explanation
Indices: 670327--670360 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
670317 AGGGCCACTT
670327 ATCTTTTCATGCTCAA
1 ATCTTTTCATGCTCAA
670343 ATCTTTTCATGCTCAA
1 ATCTTTTCATGCTCAA
670359 AT
1 AT
670361 TGCTCAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (16 bp):
ATCTTTTCATGCTCAA
Found at i:670549 original size:17 final size:17
Alignment explanation
Indices: 670513--670551 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
670503 CGACCCTATA
*
670513 TAAAATAATAACTTAAT
1 TAAAATAATAACTAAAT
670530 TAAAATAATAA-TAAATT
1 TAAAATAATAACTAAA-T
670547 TAAAA
1 TAAAA
670552 ATATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATAATAACTAAAT
Found at i:680289 original size:21 final size:21
Alignment explanation
Indices: 680252--680291 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
680242 AAAAAAATAA
*
680252 AAAATATATATGTAAATATGT
1 AAAATATATATGAAAATATGT
680273 AAAATAT-TATAGAAAATAT
1 AAAATATATAT-GAAAATAT
680292 ATTAGGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAATATATATGAAAATATGT
Found at i:680487 original size:18 final size:15
Alignment explanation
Indices: 680450--680508 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 15
680440 CCATAATAGT
680450 AATAATAAAAGAATA
1 AATAATAAAAGAATA
*
680465 TATAATAAAACGAAATTA
1 AATAATAAAA-G-AA-TA
*
680483 AATAATAAAAAAAGTA
1 AATAATAAAAGAA-TA
680499 AATAAATAAA
1 AAT-AATAAA
680509 TAAAATTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 9 0.25
16 8 0.22
17 8 0.22
18 11 0.31
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (15 bp):
AATAATAAAAGAATA
Found at i:683747 original size:20 final size:19
Alignment explanation
Indices: 683724--683762 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
683714 TTTCTCTTGT
683724 TCTTGTTCTTGTTCTTTTTC
1 TCTTGTTCTT-TTCTTTTTC
* *
683744 TCTTTTTCTTTTTTTTTTC
1 TCTTGTTCTTTTCTTTTTC
683763 AATTTAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (19 bp):
TCTTGTTCTTTTCTTTTTC
Found at i:683818 original size:16 final size:14
Alignment explanation
Indices: 683799--683851 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
683789 ACCCTAAATG
*
683799 TTTTTCTCTTTTTT
1 TTTTTTTCTTTTTT
683813 ATTTTTTTCCTTTTTT
1 -TTTTTTT-CTTTTTT
683829 TCTTTTTTCTTTTTT
1 T-TTTTTTCTTTTTT
*
683844 CTTTTTTC
1 TTTTTTTC
683852 AACTTAGGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 7 0.21
15 14 0.41
16 13 0.38
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:683826 original size:9 final size:8
Alignment explanation
Indices: 683799--683850 Score: 63
Period size: 7 Copynumber: 6.5 Consensus size: 8
683789 ACCCTAAATG
683799 TTTTTCTCT
1 TTTTTCT-T
*
683808 TTTTTATT
1 TTTTTCTT
683816 TTTTTCCTT
1 TTTTT-CTT
683825 TTTTTC-T
1 TTTTTCTT
683832 TTTTTC-T
1 TTTTTCTT
683839 TTTTTCTT
1 TTTTTCTT
683847 TTTT
1 TTTT
683851 CAACTTAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 14 0.36
8 12 0.31
9 13 0.33
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:690988 original size:26 final size:28
Alignment explanation
Indices: 690947--690998 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
690937 ATGAATGTAA
690947 AAACATGGAAAATATAAAATAAAAAAAC
1 AAACATGGAAAATATAAAATAAAAAAAC
*
690975 AAACAT-G-AAATATAAAATACAAAA
1 AAACATGGAAAATATAAAATAAAAAA
690999 TATGCAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 1 0.04
28 6 0.26
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (28 bp):
AAACATGGAAAATATAAAATAAAAAAAC
Found at i:694250 original size:39 final size:37
Alignment explanation
Indices: 694204--694304 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 37
694194 ATAATTAATA
694204 AAAAAAACGAATGAAATAAATAAAAAGTAATA-TAAAAT
1 AAAAAAACGAATGAAATAAATAAAAA-TAA-AGTAAAAT
* *
694242 AAAGAAAACCAATGAAATAAA-AAAAATAAAGTAAAGGT
1 AAA-AAAACGAATGAAATAAATAAAAATAAAGTAAA-AT
*
694280 AAAAAAATGAAT-ACAATAAATAAAA
1 AAAAAAACGAATGA-AATAAATAAAA
694305 TGAATAAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
36 2 0.04
37 20 0.37
38 16 0.30
39 16 0.30
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (37 bp):
AAAAAAACGAATGAAATAAATAAAAATAAAGTAAAAT
Found at i:694320 original size:18 final size:18
Alignment explanation
Indices: 694200--694313 Score: 68
Period size: 18 Copynumber: 6.1 Consensus size: 18
694190 GAAAATAATT
* * *
694200 AATAAAAAAAACGAATGA
1 AATAAATAAAATGAATAA
*
694218 AATAAATAAAAAGTAATATAA
1 AATAAAT-AAAA-TGA-ATAA
* ** *
694239 AATAAAGAAAACCAATGA
1 AATAAATAAAATGAATAA
* *
694257 AATAAAAAAAATAAAGTAA
1 AATAAATAAAATGAA-TAA
* *
694276 AGGTAAA-AAAATGAATAC
1 A-ATAAATAAAATGAATAA
694294 AATAAATAAAATGAATAA
1 AATAAATAAAATGAATAA
694312 AA
1 AA
694314 CTAATAATCA
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
17 4 0.05
18 36 0.49
19 15 0.21
20 9 0.12
21 9 0.12
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.17
Consensus pattern (18 bp):
AATAAATAAAATGAATAA
Found at i:694430 original size:21 final size:21
Alignment explanation
Indices: 694393--694432 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
694383 ACAAAAATAA
*
694393 AAAATATATATGTAAATATGT
1 AAAATATATATGAAAATATGT
694414 AAAATAT-TATAGAAAATAT
1 AAAATATATAT-GAAAATAT
694433 AATAGGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAATATATATGAAAATATGT
Found at i:694639 original size:21 final size:21
Alignment explanation
Indices: 694608--694655 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
694598 ATAATAAAAG
*
694608 AATATATAATAAAACA-TAATTA
1 AATA-ATAATAAAA-AGTAAATA
694630 AATAATAATAAAAAGTAAATA
1 AATAATAATAAAAAGTAAATA
694651 AATAA
1 AATAA
694656 AATTAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAATAATAAAAAGTAAATA
Found at i:694662 original size:14 final size:17
Alignment explanation
Indices: 694596--694667 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 17
694586 ACCATAATAG
* *
694596 TAATAATAAAAGAATATA
1 TAATAATAAAA-ATTAAA
694614 TAATAA-AACATAATTAAA
1 TAATAATAA-A-AATTAAA
*
694632 TAATAATAAAAAGTAAA
1 TAATAATAAAAATTAAA
694649 T-A-AAT-AAAATTAAA
1 TAATAATAAAAATTAAA
694663 GTAAT
1 -TAAT
694668 TGATTTCAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
14 8 0.18
15 4 0.09
16 2 0.05
17 9 0.20
18 18 0.41
19 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (17 bp):
TAATAATAAAAATTAAA
Found at i:704685 original size:47 final size:47
Alignment explanation
Indices: 704589--704689 Score: 150
Period size: 47 Copynumber: 2.1 Consensus size: 47
704579 TTTAAACAAT
* * *
704589 TTTTCAGAGAACGGGCGAAATATTGGTGCATTATCATCTTCAGTGAC
1 TTTTCAGAGAACGAGCGAAATAGTGGTGCATTATCATCTTCAGTAAC
*
704636 TTTTCAGAGAACGAGTGAAATAGTGGTGCATTATCATCTTCA-TCAAC
1 TTTTCAGAGAACGAGCGAAATAGTGGTGCATTATCATCTTCAGT-AAC
704683 TTTTCAG
1 TTTTCAG
704690 TGATATATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 1 0.02
47 48 0.98
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (47 bp):
TTTTCAGAGAACGAGCGAAATAGTGGTGCATTATCATCTTCAGTAAC
Found at i:711928 original size:18 final size:18
Alignment explanation
Indices: 711905--711939 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
711895 CTAGGAGATT
711905 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
711923 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
711940 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:713248 original size:23 final size:23
Alignment explanation
Indices: 713215--713259 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
713205 ATCATTATAT
*
713215 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
713238 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
713260 AGCTGTGGTG
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:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:714390 original size:28 final size:25
Alignment explanation
Indices: 714359--714416 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
714349 TAATACATAC
*
714359 ATTTTATCTATATA-TATATATATATT
1 ATTTTAT-TATAAATTATATATAT-TT
714385 ATATTT-TTATAAATTATATATATTT
1 AT-TTTATTATAAATTATATATATTT
714410 ATTTTAT
1 ATTTTAT
714417 GATATATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 3 0.11
25 10 0.36
26 12 0.43
27 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTATTATAAATTATATATATTT
Found at i:716406 original size:3 final size:3
Alignment explanation
Indices: 716398--716429 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
716388 TTCAAAAAGA
716398 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
716430 TCCACGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:720705 original size:121 final size:118
Alignment explanation
Indices: 720438--720957 Score: 384
Period size: 121 Copynumber: 4.3 Consensus size: 118
720428 AGAGTATTAA
* * * * * * ** *
720438 CTAAACTATTAGTTTGGGCATGTTTTAGTA-TTAAATTTTAAATTTTTTTAAAATCATATTTAAT
1 CTAAACTATCAGTTT-TGTATGTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCATACCTAAC
* * * * *** *
720502 GTTTAGTTTTCATCTCATTTTAATAC-CCATTGTTAAAAACTTAATGTGTTTAGTAT
65 G-TTAGTTTTCATTTCATTTTAGTACACC-CT-TTAAAAATTTAACCCGTTTAGTAC
* * *** * *
720558 TTAAATTATCAGTTTTGGTCCATTTTAGTACATAAACTTTTAATTTTTTCGAAAA-CATACCTAA
1 CTAAACTATCAGTTTT-GTATGTTTTAGTACCTAAACTTTAAATTTTTTC-AAAATCATACCTAA
*
720622 CGTTAGTTTTCGTTTCATTTTAGTGACACGCCTTTAAAAATTTAACCCGTTTAGTAC
64 CGTTAGTTTTCATTTCATTTTAGT-ACAC-CCTTTAAAAATTTAACCCGTTTAGTAC
* * * * * *
720679 CTAAACTATCAATTTTAGTTTGTTTTAGTACCTAAACTTTAAATTGTTTCAAAATCGTACGTAAT
1 CTAAACTATCAGTTTT-GTATGTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCATACCTAAC
* ** **
720744 GCTTAGTTTTCATTTTATTTTAGT--ACCCTACAACAAAATCTTAACGTGTTTAGTAC
65 G-TTAGTTTTCATTTCATTTTAGTACACCCT-TTA-AAAAT-TTAACCCGTTTAGTAC
* * * * * * *
720800 CTAAATTGTCGGTTTTGATCTATTTTAGTACCTAAACTTTCAATTTTTTCAAAATTATACCTAAC
1 CTAAACTATCAGTTTTG-TATGTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCATACCTAAC
* * * * * *
720865 ATCTAGTTTTTATTTCATTTTAGTACCACCACCGTTAAAAACTTAACTCGTTTAGCAC
65 GT-TAGTTTTCATTTCATTTTAGTA-CA-C-CCTTTAAAAATTTAACCCGTTTAGTAC
*
720923 CTAAACTATCAGTTTTGGTATGTTTTAGTATCTAA
1 CTAAACTATCAGTTTT-GTATGTTTTAGTACCTAA
720958 TTTTTTTCTT
Statistics
Matches: 310, Mismatches: 71, Indels: 35
0.75 0.17 0.08
Matches are distributed among these distances:
118 3 0.01
119 3 0.01
120 51 0.16
121 176 0.57
122 26 0.08
123 41 0.13
124 6 0.02
125 2 0.01
126 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (118 bp):
CTAAACTATCAGTTTTGTATGTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCATACCTAACG
TTAGTTTTCATTTCATTTTAGTACACCCTTTAAAAATTTAACCCGTTTAGTAC
Found at i:724109 original size:31 final size:31
Alignment explanation
Indices: 724047--724106 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
724037 TTTGCTTGAA
* *
724047 TTTAGGTGTTAAATTGATATTTTATCTAAAT
1 TTTAGGTGTTAAAATGATATTTTACCTAAAT
724078 TTTAGG-GTTAAAATGATATTTTACCTAAA
1 TTTAGGTGTTAAAATGATATTTTACCTAAA
724107 ATTCATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (31 bp):
TTTAGGTGTTAAAATGATATTTTACCTAAAT
Found at i:724243 original size:20 final size:20
Alignment explanation
Indices: 724218--724273 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
724208 TAATGACTTA
*
724218 ATAATCAAAATATAATAAGC
1 ATAATCAAAATATAATAAAC
724238 ATAATCAAAATATAA-AAAC
1 ATAATCAAAATATAATAAAC
724257 AT-ATCAATAATA-AATAA
1 ATAATCAA-AATATAATAA
724274 TCAAAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 7 0.21
19 11 0.33
20 15 0.45
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (20 bp):
ATAATCAAAATATAATAAAC
Found at i:729652 original size:3 final size:3
Alignment explanation
Indices: 729644--729704 Score: 86
Period size: 3 Copynumber: 19.0 Consensus size: 3
729634 CACAAAAATT
729644 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TATA TAAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA-A T-AA
729693 TAA TAA TAA TAA
1 TAA TAA TAA TAA
729705 AAAAGACCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 43 0.80
4 10 0.19
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:734300 original size:23 final size:23
Alignment explanation
Indices: 734259--734312 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
734249 AGAGTATCAT
734259 TAATTTA-ATTTAAAATTTTAAA
1 TAATTTATATTTAAAATTTTAAA
* * *
734281 TAATTTATCTTTAAATTTTTAAT
1 TAATTTATATTTAAAATTTTAAA
734304 TAATTTATA
1 TAATTTATA
734313 ATTATACTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATTTATATTTAAAATTTTAAA
Found at i:735075 original size:21 final size:19
Alignment explanation
Indices: 735050--735088 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
735040 TTTAAAATTT
735050 TGAAAATTTATTATTATTATA
1 TGAAAA-TTATT-TTATTATA
735071 TGAAAATTATTTTATTAT
1 TGAAAATTATTTTATTAT
735089 TTAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TGAAAATTATTTTATTATA
Found at i:742761 original size:3 final size:3
Alignment explanation
Indices: 742753--742777 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
742743 CTCCCCACTC
742753 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
742778 TAGCAACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:743111 original size:21 final size:21
Alignment explanation
Indices: 743054--743117 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
743044 CAGTGATATA
743054 TGAAATGGTTGTGGTGCCATC
1 TGAAATGGTTGTGGTGCCATC
* ** *
743075 TGAAACGACTGCGGTGCCATC
1 TGAAATGGTTGTGGTGCCATC
743096 TGAAATGGTTGTGGTGCCATC
1 TGAAATGGTTGTGGTGCCATC
743117 T
1 T
743118 AAACTGCTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (21 bp):
TGAAATGGTTGTGGTGCCATC
Found at i:746566 original size:15 final size:15
Alignment explanation
Indices: 746546--746693 Score: 181
Period size: 15 Copynumber: 9.5 Consensus size: 15
746536 TAATAAGGTT
746546 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
746561 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
746576 ATTGATTATAAAATA
1 ATTTATTTTAAAATA
746591 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
746606 ATTGATTATAAAATA
1 ATTTATTTTAAAATA
746621 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
746636 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
746655 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
746673 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
746687 ATTTATT
1 ATTTATT
746694 AGTGTGGATT
Statistics
Matches: 115, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
14 14 0.12
15 80 0.70
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 7 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:746692 original size:51 final size:48
Alignment explanation
Indices: 746561--747000 Score: 177
Period size: 54 Copynumber: 8.5 Consensus size: 48
746551 TTTTAAAATA
* * * *
746561 ATTTATTTTAAAATAATTGATTATAAAATAATTTATTTTAAAAT-AATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTA--TTAATATGGATTG
746610 A-TTA---TAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTA-T-T--AATATGGATTG
* *
746658 ATTTATTTTAAAATAATTTA-TTTAAAATAATTTATTAGTGTGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAATATGGATTG
* *
746705 ATTTATTTTAAAATATTGATTGATTTATTTT-AAATAATTTATTAGTATAGATTG
1 ATTTATTTT-AAA-A-T-A---ATTTATTTTAAAATAATTTATTAATATGGATTG
* * * *
746759 ATTTATTGTTGTAGTTGTATGGATTGATTTATTTT-AAATAATTTATTAGTATGAATTG
1 ATTTA-T-TT-TA-----A---AATAATTTATTTTAAAATAATTTATTAATATGGATTG
* * *
746817 ATTTATTTTAAAATATAGATTGATTTATTTTTTAAAA-AA-ATATTAGTATGAATTG
1 ATTTATTTT-AAA-AT--A---ATTTA--TTTTAAAATAATTTATTAATATGGATTG
* *
746872 ATTTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAGTATAGATTG
1 ATTTATTTT-AAA-AT--A---ATTTATTTTAAAATAATTTATTAATATGGATTG
* * * *
746926 ATTTATTTT-AAATAATTTATTAGTATCAATTGATTTTTTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATT--T-TAAAAT-A-ATTTATT--AATATGGATTG
746980 ATTTATTTT-AAATAATTTATT
1 ATTTATTTTAAAATAATTTATT
747001 AGTATAGATT
Statistics
Matches: 320, Mismatches: 24, Indels: 89
0.74 0.06 0.21
Matches are distributed among these distances:
44 2 0.01
45 26 0.08
46 7 0.02
47 22 0.07
48 13 0.04
49 9 0.03
50 5 0.02
51 19 0.06
52 22 0.07
53 6 0.02
54 88 0.28
55 46 0.14
56 12 0.04
57 5 0.02
58 35 0.11
61 1 0.00
62 1 0.00
64 1 0.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (48 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAATATGGATTG
Found at i:746726 original size:69 final size:67
Alignment explanation
Indices: 746591--746748 Score: 212
Period size: 69 Copynumber: 2.3 Consensus size: 67
746581 TTATAAAATA
*
746591 ATTTATTTTAAAATAATTGATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
746656 TG
66 TG
** * * * *
746658 ATTTATTTTAAAATAATTTATT-TAAAATAATTTATTAGTGTGGATTGATTTATTTTAAAATATT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATG
746722 GATTG
63 GATTG
746727 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
746749 GTATAGATTG
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
66 14 0.17
67 21 0.26
68 13 0.16
69 32 0.40
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
TG
Done.