Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009075.1 Hibiscus syriacus cultivar Beakdansim tig00112508_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: 1223780
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:165498 original size:23 final size:24
Alignment explanation
Indices: 165437--165498 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 24
165427 AAAAAGAAAA
*
165437 AATAATAAGTAATAAATAAATAAAT
1 AATAATAA-AAATAAATAAATAAAT
*
165462 AAAAAGGTAGAAAATAAATAAATAAAT
1 AATAA--TA-AAAATAAATAAATAAAT
165489 -ATAATAAAAA
1 AATAATAAAAA
165499 ATTCCAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 4 0.13
24 2 0.06
25 4 0.13
26 3 0.10
27 17 0.55
28 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (24 bp):
AATAATAAAAATAAATAAATAAAT
Found at i:165535 original size:28 final size:28
Alignment explanation
Indices: 165511--165565 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
165501 TCCAAAACTA
*
165511 TATAATATATATATATTTTTTAAAAAAT
1 TATAAAATATATATATTTTTTAAAAAAT
* *
165539 TCTAAAATATATATA-TTTTAAAAAAAT
1 TATAAAATATATATATTTTTTAAAAAAT
165566 AATTTTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAAAATATATATATTTTTTAAAAAAT
Found at i:165574 original size:32 final size:31
Alignment explanation
Indices: 165517--165602 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 31
165507 ACTATATAAT
**
165517 ATATATATATTTTTTAAAA-AA--TTCTAAA
1 ATATATATATTTTAAAAAATAATTTTCTAAA
165545 ATATATATATTTTAAAAAAATAATTTTCTAAA
1 ATATATATATTTT-AAAAAATAATTTTCTAAA
*
165577 CTATATATATTTTAAAAAATAATTTT
1 ATATATATATTTTAAAAAATAATTTT
165603 TAGAACTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
28 13 0.25
29 4 0.08
30 2 0.04
31 13 0.25
32 19 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
ATATATATATTTTAAAAAATAATTTTCTAAA
Found at i:165597 original size:31 final size:31
Alignment explanation
Indices: 165518--165614 Score: 121
Period size: 31 Copynumber: 3.2 Consensus size: 31
165508 CTATATAATA
** *
165518 TATATATATTTTTTAAAA-AA--TTCTAAAA
1 TATATATATTTTAAAAAATAATTTTCTAAAC
165546 TATATATATTTTAAAAAAATAATTTTCTAAAC
1 TATATATATTTT-AAAAAATAATTTTCTAAAC
165578 TATATATATTTTAAAAAATAATTTT-TAGAAC
1 TATATATATTTTAAAAAATAATTTTCTA-AAC
165609 TATATA
1 TATATA
165615 ATATATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
28 12 0.20
29 4 0.07
30 4 0.07
31 22 0.36
32 19 0.31
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (31 bp):
TATATATATTTTAAAAAATAATTTTCTAAAC
Found at i:165659 original size:37 final size:38
Alignment explanation
Indices: 165609--165902 Score: 217
Period size: 37 Copynumber: 7.4 Consensus size: 38
165599 TTTTTAGAAC
165609 TATATA-ATATATATTTTCAAAATTGTTTTAAAAACTA
1 TATATATATATATATTTTCAAAATTGTTTTAAAAACTA
*
165646 TATAT-TATATATATTTTCAAAAATGTTTTAAAAACTA
1 TATATATATATATATTTTCAAAATTGTTTTAAAAACTA
* *
165683 TATAATATACATATATGTTTTAAAA-TGTTTTAAAAACTATA
1 TAT-ATATATATATAT-TTTCAAAATTGTTTTAAAAAC--TA
***** *
165724 TATATATATATATATATGTGTGTGTGTGTGTTTTCAAAATGTTTTAAAATA
1 TATATATATATATAT-T-T-TCAAAAT-TGTTTT---AA------AAACTA
* *
165775 CTATATATTATATATATTTT-TAAATTGTTTAAAAAACTA
1 -TATATA-TATATATATTTTCAAAATTGTTTTAAAAACTA
* *
165814 TATAATATACATATGTTTTCAAAA-TGTTTTAAAAACTA
1 TAT-ATATATATATATTTTCAAAATTGTTTTAAAAACTA
*
165852 TTTAT-TATATATATTTTCAAAA-TG-TTTAAAAACTA
1 TATATATATATATATTTTCAAAATTGTTTTAAAAACTA
165887 TAATATATATATATAT
1 T-ATATATATATATAT
165903 ATATATATAT
Statistics
Matches: 208, Mismatches: 24, Indels: 50
0.74 0.09 0.18
Matches are distributed among these distances:
35 12 0.06
36 20 0.10
37 49 0.24
38 30 0.14
39 31 0.15
40 19 0.09
41 6 0.03
42 1 0.00
44 6 0.03
45 2 0.01
47 2 0.01
48 5 0.02
49 2 0.01
50 1 0.00
51 3 0.01
52 7 0.03
53 12 0.06
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (38 bp):
TATATATATATATATTTTCAAAATTGTTTTAAAAACTA
Found at i:165770 original size:131 final size:130
Alignment explanation
Indices: 165622--165865 Score: 395
Period size: 131 Copynumber: 1.9 Consensus size: 130
165612 ATAATATATA
*
165622 TTTTCAAAATTGTTTTAAAA-ACTATATATTATATATATTTTCAAAAATGTTTTAAAAACTATAT
1 TTTTCAAAATTGTTTTAAAATACTATATATTATATATATTTT-AAAAATGTTTAAAAAACTATAT
165686 AATATACATATATGTTTT-AAAATGTTTTAAAAACTATATATATATATATATATATGTGTGTGTG
65 AATATAC--ATATGTTTTCAAAATGTTTTAAAAACTATATAT-TATATATATATATGTGTGTGTG
165750 TGTG
127 TGTG
* *
165754 TTTTCAAAA-TGTTTTAAAATACTATATATTATATATATTTTTAAATTGTTTAAAAAACTATATA
1 TTTTCAAAATTGTTTTAAAATACTATATATTATATATATTTTAAAAATGTTTAAAAAACTATATA
*
165818 ATATACATATGTTTTCAAAATGTTTTAAAAACTATTTATTATATATAT
66 ATATACATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATAT
165866 TTTCAAAATG
Statistics
Matches: 106, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
129 18 0.17
130 22 0.21
131 36 0.34
132 30 0.28
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (130 bp):
TTTTCAAAATTGTTTTAAAATACTATATATTATATATATTTTAAAAATGTTTAAAAAACTATATA
ATATACATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATATATATGTGTGTGTGTGTG
Found at i:165848 original size:38 final size:38
Alignment explanation
Indices: 165752--165902 Score: 186
Period size: 36 Copynumber: 4.0 Consensus size: 38
165742 TGTGTGTGTG
*
165752 TGTTTTCAAAATGTTTTAAAATACTATATATTATATATA
1 TGTTTTCAAAATGTTTTAAAA-ACTATATAATATATATA
* * *
165791 T-TTTT-AAATTGTTTAAAAAACTATATAATATACATA
1 TGTTTTCAAAATGTTTTAAAAACTATATAATATATATA
*
165827 TGTTTTCAAAATGTTTTAAAAACTAT-TTAT-TATATA
1 TGTTTTCAAAATGTTTTAAAAACTATATAATATATATA
*
165863 TATTTTCAAAATG-TTTAAAAACTATAATATATATATATA
1 TGTTTTCAAAATGTTTTAAAAACTAT-ATA-ATATATATA
165902 T
1 T
165903 ATATATATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
35 12 0.12
36 33 0.34
37 20 0.21
38 23 0.24
39 8 0.08
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (38 bp):
TGTTTTCAAAATGTTTTAAAAACTATATAATATATATA
Found at i:165896 original size:2 final size:2
Alignment explanation
Indices: 165885--165919 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
165875 GTTTAAAAAC
165885 TA TA -A 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 TA TA
165920 ATAAGAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:166670 original size:84 final size:84
Alignment explanation
Indices: 166584--167639 Score: 1494
Period size: 84 Copynumber: 12.6 Consensus size: 84
166574 AGTGTAATCA
* * * * * * * * *
166584 AACTTGAAGGTCTTCGGTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
* * * *
166649 TTTGAGCTGAGTGTAATCA
66 TTGGAGCTGAGCGTAGTCG
* * *
166668 AACTCGAAGGTCTTTGATTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
*
166733 TTTGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * *
166752 AACTCAAAGGTCTTTTGG-TGGCAGATAGCCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGC
1 AACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
166816 CTTGGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCG
*
166836 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
166901 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
166920 AACTCGAAGGTCTTTTGG-TGGCAAATAGCCTTTCTAGCCTTGAGCTATGCTACAAATGATGTGC
1 AACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
*
166984 CTTGGAGCTGAGCGTAGTCT
65 CTTGGAGCTGAGCGTAGTCG
*
167004 AACTCGAAGGTCTTTGGCTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
*
167069 TTGGAGCTGAGCGTAATCG
66 TTGGAGCTGAGCGTAGTCG
* * *
167088 AACTCGAAGGTCTTTTGG-TGGCAGATATCCCTTCTAGCCTTGAGATATGCTGCAAATGATGTGC
1 AACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
*
167152 CTTGGAGCTGAGCGTAATCG
65 CTTGGAGCTGAGCGTAGTCG
* *
167172 AACTCGAATGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
167237 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * * *
167256 AACTCGAAGGTATTTTGG-TGGAAGGTAGCCCTTCTAGCCTTCAGCTATGCTGCAAATGATGTGC
1 AACTCGAAGGT-CTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
* *
167320 CTTGGAGCTGAACGTAGTCA
65 CTTGGAGCTGAGCGTAGTCG
* *
167340 AACTCGAAGGTCTTTGGTTGGAAGAAAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
167405 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * *
167424 AACTCGAAGGTCTTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGC
1 AACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
*
167488 CTTGGAGCTGAGCGTAATCG
65 CTTGGAGCTGAGCGTAGTCG
*
167508 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCCGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
*
167573 TTGGAGCTGAGCGTGGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * *
167592 AACTCGAAGGTC-TTGGCTGACAGATAACCATTCTCGCCTTGAGTTATG
1 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
167640 TTGCCGATAG
Statistics
Matches: 872, Mismatches: 90, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
83 57 0.07
84 791 0.91
85 24 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
TTGGAGCTGAGCGTAGTCG
Found at i:166804 original size:168 final size:168
Alignment explanation
Indices: 166604--167639 Score: 1662
Period size: 168 Copynumber: 6.2 Consensus size: 168
166594 TCTTCGGTTA
* * * * * *
166604 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
* * *
166669 ACTCGAAGGTCTTTGATTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
* *
166734 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* *
166772 GCAGATAGCCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
*
166837 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
166902 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* * * * *
166940 GCAAATAGCCTTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCTA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
*
167005 ACTCGAAGGTCTTTGGCTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
*
167070 TGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* *
167108 GCAGATATCCCTTCTAGCCTTGAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
* *
167173 ACTCGAATGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
*
167238 TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* * * * * *
167276 GAAGGTAGCCCTTCTAGCCTTCAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
* *
167341 ACTCGAAGGTCTTTGGTTGGAAGAAAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
167406 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* *
167444 GCAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
*
167509 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCCGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
*
167574 TGGAGCTGAGCGTGGTCGAACTCGAAGGTC--TTGGCTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TG
* * * * *
167611 ACAGATAACCATTCTCGCCTTGAGTTATG
1 GCAGATAGCCCTTCTAGCCTTGAGCTATG
167640 TTGCCGATAG
Statistics
Matches: 804, Mismatches: 63, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
166 4 0.00
167 27 0.03
168 773 0.96
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (168 bp):
GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
Found at i:168618 original size:23 final size:23
Alignment explanation
Indices: 168592--168637 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
168582 AAGAACCAAG
*
168592 ATAAA-CTTAAATATACCATTAAA
1 ATAAAGCTTAAACAT-CCATTAAA
*
168615 ATAAAGTTTAAACATCCATTAAA
1 ATAAAGCTTAAACATCCATTAAA
168638 CCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAGCTTAAACATCCATTAAA
Found at i:180890 original size:100 final size:98
Alignment explanation
Indices: 180663--180922 Score: 360
Period size: 100 Copynumber: 2.6 Consensus size: 98
180653 GGCTAGCTGA
** * * * *
180663 ATCCATAAAGCTAGGGCGTTTAACCAATTACTCTAGAGGGACATCTCAA-TATCATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAACT-TTATTGTATAGAT
180727 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
65 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
180761 ATCCATAAAGCCGGGGCGTTTAACTAATTGCTATAGAGGTACAACTCAAGCTTTATTGTATAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-CTTTATTGTATAGAT
* * *
180826 ATTATGATCACCTTTATCAGGCTTAGCTTAATCTT
65 ATTATAATCACCTTTATCAGGC-TAGCTGAATATT
*
180861 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAATCTTTATTGTATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-CTTTATTGTATA
180923 TTATAATATT
Statistics
Matches: 142, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
98 42 0.30
99 32 0.23
100 68 0.48
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (98 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAACTTTATTGTATAGATA
TTATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:184726 original size:3 final size:3
Alignment explanation
Indices: 184720--184747 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
184710 AATCAAGACA
184720 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
184748 TGGAAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:187733 original size:16 final size:16
Alignment explanation
Indices: 187703--187733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
187693 AATATTGAAA
*
187703 CTTGAACTCGAAAAAG
1 CTTGAACTCAAAAAAG
187719 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
187734 AATTTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:189620 original size:8 final size:8
Alignment explanation
Indices: 189594--189710 Score: 77
Period size: 8 Copynumber: 15.1 Consensus size: 8
189584 TTTAATCTTC
189594 TATATACA
1 TATATACA
*
189602 TACAT--A
1 TATATACA
189608 TATATACA
1 TATATACA
*
189616 TATATATA
1 TATATACA
*
189624 TATATATA
1 TATATACA
189632 TATATACA
1 TATATACA
**
189640 TGCAT-CA
1 TATATACA
*
189647 TAAATACA
1 TATATACA
*
189655 T-CATACA
1 TATATACA
189662 TATATACA
1 TATATACA
*
189670 TGA-ATCATA
1 T-ATAT-ACA
189679 TATATACA
1 TATATACA
*
189687 TATCTA-A
1 TATATACA
189694 GTATA-ACA
1 -TATATACA
189702 TATATACA
1 TATATACA
189710 T
1 T
189711 GCATCTTACG
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
6 5 0.06
7 17 0.20
8 57 0.67
9 6 0.07
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.37
Consensus pattern (8 bp):
TATATACA
Found at i:189679 original size:15 final size:15
Alignment explanation
Indices: 189594--189682 Score: 77
Period size: 15 Copynumber: 6.4 Consensus size: 15
189584 TTTAATCTTC
*
189594 TATATACATACAT-A
1 TATATACATGCATCA
189608 TATATACAT--AT-A
1 TATATACATGCATCA
*
189620 TATATATAT--AT-A
1 TATATACATGCATCA
189632 TATATACATGCATCA
1 TATATACATGCATCA
*
189647 TAAATACAT-CATACA
1 TATATACATGCAT-CA
*
189662 TATATACATGAATCA
1 TATATACATGCATCA
189677 TATATA
1 TATATA
189683 TACATATCTA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
12 22 0.34
14 14 0.22
15 27 0.42
16 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.37
Consensus pattern (15 bp):
TATATACATGCATCA
Found at i:190015 original size:29 final size:28
Alignment explanation
Indices: 189982--190074 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
189972 TTCCTTTTAT
* *
189982 ATATATACACATGCATCATACATCCATGC
1 ATATATATACATGCATCATACATACAT-C
* *
190011 ATATATTTTCATGCATCATACATACATC
1 ATATATATACATGCATCATACATACATC
* *
190039 ATACATATACATACATACATACATACATAC
1 ATATATATACATGCAT-CATACATACAT-C
190069 ATATAT
1 ATATAT
190075 GAATATACTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
28 13 0.25
29 34 0.64
30 6 0.11
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (28 bp):
ATATATATACATGCATCATACATACATC
Found at i:190036 original size:4 final size:4
Alignment explanation
Indices: 190027--190071 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
190017 TTTCATGCAT
190027 CATA CATA CAT- CATA CAT- -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
190072 TATGAATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 33 0.87
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:192104 original size:38 final size:38
Alignment explanation
Indices: 192053--192128 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
192043 ATTAAAGTGT
192053 CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
1 CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
*
192091 CAAGGGTATAATTGATTTTGGGACACTTCGATTTATGC
1 CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
192129 ATGTTTTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.36
Consensus pattern (38 bp):
CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
Found at i:207483 original size:20 final size:20
Alignment explanation
Indices: 207458--207576 Score: 103
Period size: 20 Copynumber: 5.3 Consensus size: 20
207448 TAACTAAAAT
207458 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
207478 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
207504 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
207524 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
207550 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
207570 GCATGAA
1 GCATGAA
207577 TGAAATTAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
20 36 0.44
21 6 0.07
22 2 0.02
24 2 0.02
25 6 0.07
26 29 0.36
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:207516 original size:26 final size:26
Alignment explanation
Indices: 207446--207563 Score: 125
Period size: 26 Copynumber: 5.0 Consensus size: 26
207436 AAAACGAATT
207446 CATAACTAAAATGCATGAAAGGATG-
1 CATAACTAAAATGCATGAAAGGATGC
*
207471 CAT---T--AAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGC
*
207492 CATAACTAAAATGCATGAAATGATG-
1 CATAACTAAAATGCATGAAAGGATGC
*
207517 CAT---T--AAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGC
207538 CATAACTAAAATGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGC
207564 ATTAAGGCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
20 29 0.39
21 6 0.08
22 2 0.03
24 2 0.03
25 6 0.08
26 30 0.40
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (26 bp):
CATAACTAAAATGCATGAAAGGATGC
Found at i:207517 original size:46 final size:46
Alignment explanation
Indices: 207446--207576 Score: 253
Period size: 46 Copynumber: 2.8 Consensus size: 46
207436 AAAACGAATT
207446 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
207492 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
207538 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAA
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAA
207577 TGAAATTAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:213525 original size:7 final size:7
Alignment explanation
Indices: 213496--213578 Score: 62
Period size: 7 Copynumber: 12.0 Consensus size: 7
213486 ACCATTTATT
213496 AACCAATA
1 AACC-ATA
213504 AACCAT-
1 AACCATA
*
213510 -ACTATA
1 AACCATA
213516 AACCATA
1 AACCATA
*
213523 AACTATA
1 AACCATA
* *
213530 GACAATA
1 AACCATA
213537 AACCATA
1 AACCATA
*
213544 AACTATA
1 AACCATA
* *
213551 GACAATA
1 AACCATA
213558 AACCATA
1 AACCATA
* *
213565 GACTATA
1 AACCATA
213572 AACCATA
1 AACCATA
213579 GCCTAATATA
Statistics
Matches: 57, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
5 4 0.07
7 49 0.86
8 4 0.07
ACGTcount: A:0.55, C:0.22, G:0.04, T:0.19
Consensus pattern (7 bp):
AACCATA
Found at i:213539 original size:21 final size:21
Alignment explanation
Indices: 213513--213571 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
213503 AAACCATACT
213513 ATAAACCATAAACTATAGACA
1 ATAAACCATAAACTATAGACA
213534 ATAAACCATAAACTATAGACA
1 ATAAACCATAAACTATAGACA
*
213555 ATAAACCATAGACTATA
1 ATAAACCATAAACTATA
213572 AACCATAGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.20
Consensus pattern (21 bp):
ATAAACCATAAACTATAGACA
Found at i:213579 original size:14 final size:14
Alignment explanation
Indices: 213501--213579 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
213491 TTATTAACCA
213501 ATAAACCAT--ACT
1 ATAAACCATAGACT
*
213513 ATAAACCATAAACT
1 ATAAACCATAGACT
* * * *
213527 ATAGACAATAAACC
1 ATAAACCATAGACT
* *
213541 ATAAACTATAGACA
1 ATAAACCATAGACT
213555 ATAAACCATAGACT
1 ATAAACCATAGACT
213569 ATAAACCATAG
1 ATAAACCATAG
213580 CCTAATATAG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
12 9 0.16
14 47 0.84
ACGTcount: A:0.54, C:0.20, G:0.05, T:0.20
Consensus pattern (14 bp):
ATAAACCATAGACT
Found at i:213767 original size:39 final size:40
Alignment explanation
Indices: 213636--213784 Score: 237
Period size: 40 Copynumber: 3.8 Consensus size: 40
213626 ACCGTAGTGC
* *
213636 TACACATAAGGTTGTGCCCACCATATACACGGAAGTGCAT
1 TACACATAAGGTCGTGCCCACCATATACACGGAAATGCAT
* *
213676 TACACATAAGGTCGTGCCCACCATATACACTGAAATACAT
1 TACACATAAGGTCGTGCCCACCATATACACGGAAATGCAT
*
213716 TACACATAAGGTCGTGCCCACCATATACAC-CAAATGCAT
1 TACACATAAGGTCGTGCCCACCATATACACGGAAATGCAT
*
213755 TACACATAAGGTCATGCCCACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
213785 TTAGTGTCCT
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 36 0.35
40 66 0.65
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACGGAAATGCAT
Found at i:213800 original size:79 final size:80
Alignment explanation
Indices: 213636--213785 Score: 257
Period size: 79 Copynumber: 1.9 Consensus size: 80
213626 ACCGTAGTGC
* * * *
213636 TACACATAAGGTTGTGCCCACCATATACACGGAAGTGCATTACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATATACACGCAAATGCATTACACATAAGGTCATGCCCACCATA
213701 TACACTGAAATACAT
66 TACACTGAAATACAT
213716 TACACATAAGGTCGTGCCCACCATATACAC-CAAATGCATTACACATAAGGTCATGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATATACACGCAAATGCATTACACATAAGGTCATGCCCACCATA
213780 TACACT
66 TACACT
213786 TAGTGTCCTT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 37 0.56
80 29 0.44
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (80 bp):
TACACATAAGGTCGTGCCCACCATATACACGCAAATGCATTACACATAAGGTCATGCCCACCATA
TACACTGAAATACAT
Found at i:215400 original size:30 final size:32
Alignment explanation
Indices: 215361--215419 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
215351 TAATCACCAT
215361 TAAACTAAGACACCT-AACCTTATCATCTTCC
1 TAAACTAAGACACCTCAACCTTATCATCTTCC
215392 TAAA-TAAGACACCTCAACCTTATCATCT
1 TAAACTAAGACACCTCAACCTTATCATCT
215420 CCCATTAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (32 bp):
TAAACTAAGACACCTCAACCTTATCATCTTCC
Found at i:217029 original size:46 final size:46
Alignment explanation
Indices: 216962--217172 Score: 350
Period size: 46 Copynumber: 4.6 Consensus size: 46
216952 TAAAACGAAT
216962 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
217008 TCATAACTAAAAAGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * *
217054 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATG
1 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
217100 TCATAACTAAAATGCATGAAATGATGCATTAAGGAATGAAAGGATG
1 TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * *
217146 CCATAACTAAAATGCATAAAAGGATGC
1 TCATAACTAAAATGCATGAAATGATGC
217173 CATAACTAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 153 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
TCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
Found at i:217033 original size:26 final size:25
Alignment explanation
Indices: 216963--217246 Score: 213
Period size: 26 Copynumber: 12.1 Consensus size: 25
216953 AAAACGAATT
*
216963 CATAACTAAAATGCATGAAATGATG
1 CATAACTAAAATGCATGAAAGGATG
*
216988 CAT---T--AAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
* *
217008 TCATAACTAAAAAGCATGAAATGATG
1 -CATAACTAAAATGCATGAAAGGATG
*
217034 CAT---T--AAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
217054 CCATAACTAAAATGCATGAAAGGATG
1 -CATAACTAAAATGCATGAAAGGATG
* *
217080 CAT---T--AAGGCATGAAAGAATG
1 CATAACTAAAATGCATGAAAGGATG
*
217100 TCATAACTAAAATGCATGAAATGATG
1 -CATAACTAAAATGCATGAAAGGATG
* *
217126 CAT---T--AAGGAATGAAAGGATG
1 CATAACTAAAATGCATGAAAGGATG
*
217146 CCATAACTAAAATGCATAAAAGGATG
1 -CATAACTAAAATGCATGAAAGGATG
217172 CCATAACTAAAATGCATGAAAGGATG
1 -CATAACTAAAATGCATGAAAGGATG
* *
217198 CAT---T--AAGGCATGAAAGAATG
1 CATAACTAAAATGCATGAAAGGATG
*
217218 ACATAACTAAAATGCATGAAAGAATG
1 -CATAACTAAAATGCATGAAAGGATG
217244 CAT
1 CAT
217247 TAAGGCATGA
Statistics
Matches: 207, Mismatches: 22, Indels: 60
0.72 0.08 0.21
Matches are distributed among these distances:
20 69 0.33
21 15 0.07
22 5 0.02
24 5 0.02
25 18 0.09
26 95 0.46
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (25 bp):
CATAACTAAAATGCATGAAAGGATG
Found at i:217184 original size:118 final size:118
Alignment explanation
Indices: 217041--217269 Score: 415
Period size: 118 Copynumber: 1.9 Consensus size: 118
217031 ATGCATTAAG
* *
217041 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGTCATAA
1 GCATAAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGACATAA
217106 CTAAAATGCATGAAATG-ATGCATTAAGGAATGAAAGGATGCCATAACTAAAAT
66 CTAAAATGCATGAAA-GAATGCATTAAGGAATGAAAGGATGCCATAACTAAAAT
217159 GCATAAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGACATAA
1 GCATAAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGACATAA
*
217224 CTAAAATGCATGAAAGAATGCATTAAGGCATGAAAGGATGCCATAA
66 CTAAAATGCATGAAAGAATGCATTAAGGAATGAAAGGATGCCATAA
217270 ATGAAATTAA
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
117 1 0.01
118 106 0.99
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.20
Consensus pattern (118 bp):
GCATAAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGACATAA
CTAAAATGCATGAAAGAATGCATTAAGGAATGAAAGGATGCCATAACTAAAAT
Found at i:217283 original size:46 final size:46
Alignment explanation
Indices: 217159--217269 Score: 186
Period size: 46 Copynumber: 2.4 Consensus size: 46
217149 TAACTAAAAT
* *
217159 GCATAAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAG
* *
217205 GCATGAAAGAATGACATAACTAAAATGCATGAAAGAATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAG
217251 GCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAA
217270 ATGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.19
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAG
Found at i:222559 original size:11 final size:11
Alignment explanation
Indices: 222543--222573 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
222533 TAAAAACAGT
222543 AAATAAAATGA
1 AAATAAAATGA
222554 AAATAAAATGA
1 AAATAAAATGA
*
222565 AAAGAAAAT
1 AAATAAAAT
222574 AATCCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (11 bp):
AAATAAAATGA
Found at i:222562 original size:16 final size:16
Alignment explanation
Indices: 222543--222575 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
222533 TAAAAACAGT
222543 AAAT-AAAATGAAAATA
1 AAATGAAAA-GAAAATA
222559 AAATGAAAAGAAAATA
1 AAATGAAAAGAAAATA
222575 A
1 A
222576 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATGAAAAGAAAATA
Found at i:223094 original size:24 final size:24
Alignment explanation
Indices: 223050--223099 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
223040 ATAAAGAACC
*
223050 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
223074 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
223098 AA
1 AA
223100 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:232267 original size:24 final size:24
Alignment explanation
Indices: 232223--232272 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
232213 ATAAAGAACC
*
232223 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
232247 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
232271 AA
1 AA
232273 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:233602 original size:35 final size:35
Alignment explanation
Indices: 233556--233625 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
233546 AATACTCATG
* *
233556 GGGTATCGATACTGAA-GTGGTAGTATTGGTACCAT
1 GGGTATCGATAC-CAATGGGGTAGTATTGGTACCAT
* *
233591 GGGTATTGATACCAATGGGGTGGTATTGGTACCAT
1 GGGTATCGATACCAATGGGGTAGTATTGGTACCAT
233626 TTCTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.31
Consensus pattern (35 bp):
GGGTATCGATACCAATGGGGTAGTATTGGTACCAT
Found at i:236920 original size:183 final size:182
Alignment explanation
Indices: 236610--236966 Score: 482
Period size: 183 Copynumber: 2.0 Consensus size: 182
236600 AAGTTTCCAA
* * * * * *
236610 TTTGTAGTACCTTTAAGATACTTAGGTAGGCGTCTCATCATGGTTCAATGTTCACCACTTGGACT
1 TTTGTAGTACCTTTAAGATACTTAAGTAAGCGTATCATCATAGTCCAATGTTCACCACTTAGACT
* * * * * ** *
236675 ATGAGTATATCTACTTAATCTACTCACAATATAGACAATATCTAGCAGAGTGTAGTTCATTAATA
66 ATGAATATATCTACTTAATATACTCACAACATAGACAATATATAGCAGAGTATACCTCATTAAGA
* *
236740 AAATAAGGCTCCAT-ATGGTTTTAACATACTTTTTTTTGGGAAACACTACTTCC
131 AAATAAGGCT-CATGATAGTTTTAACATAC-TTTTGTTGGGAAACACTACTTCC
** *
236793 TTTGTAGTACCTTTAAGATACTTAAGTAAGCGTATCATTGTAGTCCAATGTTCACCACTTAGATT
1 TTTGTAGTACCTTTAAGATACTTAAGTAAGCGTATCATCATAGTCCAATGTTCACCACTTAGACT
* * *
236858 ATGAATATATCTACTTAATATACTCACAACATAGGCAATATATGGCAGAGTATACCTCATTAAGC
66 ATGAATATATCTACTTAATATACTCACAACATAGACAATATATAGCAGAGTATACCTCATTAAGA
*
236923 ACATAAGGCTCATGATAGTTTTAACATACTTTTGTTGGGAAACA
131 AAATAAGGCTCATGATAGTTTTAACATACTTTTGTTGGGAAACA
236967 TTATTTCTTT
Statistics
Matches: 150, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
182 17 0.11
183 133 0.89
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (182 bp):
TTTGTAGTACCTTTAAGATACTTAAGTAAGCGTATCATCATAGTCCAATGTTCACCACTTAGACT
ATGAATATATCTACTTAATATACTCACAACATAGACAATATATAGCAGAGTATACCTCATTAAGA
AAATAAGGCTCATGATAGTTTTAACATACTTTTGTTGGGAAACACTACTTCC
Found at i:238835 original size:43 final size:43
Alignment explanation
Indices: 238787--238971 Score: 192
Period size: 43 Copynumber: 4.3 Consensus size: 43
238777 ACCAGATCTT
* * * * * *
238787 TTGCGGTGCTTGTGGGAAAAATGCCGCAAAATCTCAAGACATA
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACATA
* * * * *
238830 TTGCGGTGTTTGTGTAAAAAAACGCTGCTAAATCTCAATACTTA
1 TTGCGGCGTTTGTG-GAAAAAACGCCGCTAAATCTCAACACATA
* *
238874 TTGCGGCGTTTGTGGAAAAAACGTCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACATA
* * * *
238917 TTGCGGCGTTTGTTGG-AAAAGCGTCGCTAAATATCAACACCTA
1 TTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACATA
238960 TTGCGGCGTTTG
1 TTGCGGCGTTTG
238972 AACACCGCTA
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
43 86 0.69
44 38 0.31
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACATA
Found at i:238894 original size:87 final size:86
Alignment explanation
Indices: 238787--238971 Score: 210
Period size: 87 Copynumber: 2.1 Consensus size: 86
238777 ACCAGATCTT
* * * * * *
238787 TTGCGGTGCTTGTGGGAAAAATGCCGCAAAATCTCAAGACATATTGCGGTGTTTGTGTAAAAAAA
1 TTGCGGCGTTTGTGGAAAAAACGCCGCAAAATCTCAACACATATTGCGGCGTTTGT-TAAAAAAA
* * *
238852 CG-CTGCTAAATCTCAATACTTA
65 CGTC-GCTAAATATCAACACCTA
* * * ** *
238874 TTGCGGCGTTTGTGGAAAAAACGTCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGAAAAGC
1 TTGCGGCGTTTGTGGAAAAAACGCCGCAAAATCTCAACACATATTGCGGCGTTTGTTAAAAAAAC
238939 GTCGCTAAATATCAACACCTA
66 GTCGCTAAATATCAACACCTA
238960 TTGCGGCGTTTG
1 TTGCGGCGTTTG
238972 AACACCGCTA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
86 34 0.41
87 48 0.59
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (86 bp):
TTGCGGCGTTTGTGGAAAAAACGCCGCAAAATCTCAACACATATTGCGGCGTTTGTTAAAAAAAC
GTCGCTAAATATCAACACCTA
Found at i:246928 original size:19 final size:21
Alignment explanation
Indices: 246886--246928 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
246876 CAAAATATTT
*
246886 TATATATTCTAAAATCTGGTA
1 TATATATTCTAAAATCTGGAA
*
246907 TATATA-TC-AAAATCTTGAA
1 TATATATTCTAAAATCTGGAA
246926 TAT
1 TAT
246929 CATAACCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
TATATATTCTAAAATCTGGAA
Found at i:247714 original size:75 final size:75
Alignment explanation
Indices: 247626--247779 Score: 290
Period size: 75 Copynumber: 2.1 Consensus size: 75
247616 GACTGATATG
* *
247626 GACCCGAACCCGAGATTGACCTGGTAAATAACTGGTATTACCTGACTTGTTTTCAACCTAACCTG
1 GACCCGAACCCGAGATTGACCTGGTAAATAACTGGGATTACCTGACTTGTTTTCAACCTAACATG
247691 TTTCTAACCT
66 TTTCTAACCT
247701 GACCCGAACCCGAGATTGACCTGGTAAATAACTGGGATTACCTGACTTGTTTTCAACCTAACATG
1 GACCCGAACCCGAGATTGACCTGGTAAATAACTGGGATTACCTGACTTGTTTTCAACCTAACATG
247766 TTTCTAACCT
66 TTTCTAACCT
247776 GACC
1 GACC
247780 TGTAAATGAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (75 bp):
GACCCGAACCCGAGATTGACCTGGTAAATAACTGGGATTACCTGACTTGTTTTCAACCTAACATG
TTTCTAACCT
Found at i:248088 original size:23 final size:24
Alignment explanation
Indices: 248050--248099 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
248040 ATGCAAAGGA
*
248050 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
248074 AAATT-ATATAATTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
248097 AAA
1 AAA
248100 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATTAATATAATTTAATTTATAT
Found at i:248276 original size:7 final size:7
Alignment explanation
Indices: 248264--248356 Score: 100
Period size: 7 Copynumber: 13.3 Consensus size: 7
248254 TCCATTTATA
248264 TTATGGT
1 TTATGGT
248271 TTATGGT
1 TTATGGT
248278 TTA-GTGT
1 TTATG-GT
248285 TTATGGT
1 TTATGGT
**
248292 TTAAAGT
1 TTATGGT
248299 TTATGGT
1 TTATGGT
248306 TTATGGT
1 TTATGGT
248313 TTATGGT
1 TTATGGT
248320 TTA-GTGT
1 TTATG-GT
248327 TTATGGT
1 TTATGGT
**
248334 TTAAAGT
1 TTATGGT
*
248341 TTAGGGT
1 TTATGGT
*
248348 TTAGGGT
1 TTATGGT
248355 TT
1 TT
248357 CTATAAACTA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
6 2 0.03
7 70 0.95
8 2 0.03
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (7 bp):
TTATGGT
Found at i:248288 original size:21 final size:21
Alignment explanation
Indices: 248264--248356 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
248254 TCCATTTATA
**
248264 TTATGGTTTATGGTTTAGTGT
1 TTATGGTTTAAAGTTTAGTGT
248285 TTATGGTTTAAAGTTTA-TGGT
1 TTATGGTTTAAAGTTTAGT-GT
**
248306 TTATGGTTTATGGTTTAGTGT
1 TTATGGTTTAAAGTTTAGTGT
*
248327 TTATGGTTTAAAGTTTAGGGT
1 TTATGGTTTAAAGTTTAGTGT
*
248348 TTAGGGTTT
1 TTATGGTTT
248357 CTATAAACTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (21 bp):
TTATGGTTTAAAGTTTAGTGT
Found at i:248454 original size:20 final size:21
Alignment explanation
Indices: 248431--248482 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
248421 TAATTTATTT
248431 TATATAGTTTATTATATA-TA
1 TATATAGTTTATTATATACTA
248451 TATATAGTTTA-TATATACTA
1 TATATAGTTTATTATATACTA
* *
248471 TACATGGTTTAT
1 TATATAGTTTAT
248483 ACATACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (21 bp):
TATATAGTTTATTATATACTA
Found at i:248483 original size:20 final size:20
Alignment explanation
Indices: 248434--248488 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
248424 TTTATTTTAT
*
248434 ATAGTTTATTATATA-TATAT
1 ATAGTTTA-TATATACTATAC
248454 ATAGTTTATATATACTATAC
1 ATAGTTTATATATACTATAC
* *
248474 ATGGTTTATACATAC
1 ATAGTTTATATATAC
248489 ATATTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (20 bp):
ATAGTTTATATATACTATAC
Found at i:248537 original size:15 final size:15
Alignment explanation
Indices: 248491--248545 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
248481 ATACATACAT
*
248491 ATTATATAAA-ATTA
1 ATTATATAAATATAA
*
248505 TTTA-ATAAATTAATAA
1 ATTATATAAA-T-ATAA
*
248521 ATTATTTAAATATAA
1 ATTATATAAATATAA
248536 ATTATATAAA
1 ATTATATAAA
248546 ACATGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.16
14 3 0.09
15 13 0.41
16 7 0.22
17 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATATAAATATAA
Found at i:248840 original size:7 final size:7
Alignment explanation
Indices: 248817--248874 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
248807 TCCATTTACA
248817 TTAGGGT
1 TTAGGGT
* *
248824 TTATGAT
1 TTAGGGT
*
248831 TTAGTGT
1 TTAGGGT
*
248838 TTAGTGT
1 TTAGGGT
***
248845 TTATAAT
1 TTAGGGT
248852 TTAGGGT
1 TTAGGGT
248859 TTAGGGT
1 TTAGGGT
248866 TTAGGGT
1 TTAGGGT
248873 TT
1 TT
248875 CTATAAACTA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (7 bp):
TTAGGGT
Found at i:248846 original size:21 final size:21
Alignment explanation
Indices: 248817--248868 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
248807 TCCATTTACA
* *
248817 TTAGGGTTTATGATTTAGTGT
1 TTAGGGTTTATAATTTAGGGT
*
248838 TTAGTGTTTATAATTTAGGGT
1 TTAGGGTTTATAATTTAGGGT
248859 TTAGGGTTTA
1 TTAGGGTTTA
248869 GGGTTTCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTATAATTTAGGGT
Found at i:249013 original size:20 final size:20
Alignment explanation
Indices: 248952--249021 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
248942 TAAACTTTAT
248952 ATAGTTTATATATA-TAT--
1 ATAGTTTATATATACTATAC
* *
248969 ATA-TATATATATA-TATAT
1 ATAGTTTATATATACTATAC
248987 ATAGTTTATATATACTATAC
1 ATAGTTTATATATACTATAC
*
249007 ATGGTTTATATATAC
1 ATAGTTTATATATAC
249022 ATATTATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
16 12 0.27
17 3 0.07
18 3 0.07
19 9 0.20
20 18 0.40
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (20 bp):
ATAGTTTATATATACTATAC
Found at i:249020 original size:2 final size:2
Alignment explanation
Indices: 248958--249005 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
248948 TTATATAGTT
*
248958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
249001 CTA TA
1 -TA TA
249006 CATGGTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:249891 original size:21 final size:21
Alignment explanation
Indices: 249867--249912 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
249857 AGTACTTATG
*
249867 GTTTAA-AGTTTAGGGTTTAGA
1 GTTTAAGA-TTTAAGGTTTAGA
*
249888 GTTTATGATTTAAGGTTTAGA
1 GTTTAAGATTTAAGGTTTAGA
249909 GTTT
1 GTTT
249913 TTATAAACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (21 bp):
GTTTAAGATTTAAGGTTTAGA
Found at i:250065 original size:2 final size:2
Alignment explanation
Indices: 249997--250046 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
249987 TTATATAGTT
249997 TA TA TA TA TA 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 TA TA TA TA TA
250039 TA TA TA TA
1 TA TA TA TA
250047 GTGTATACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:250601 original size:18 final size:19
Alignment explanation
Indices: 250551--250632 Score: 82
Period size: 18 Copynumber: 4.5 Consensus size: 19
250541 AAATAAAATC
*
250551 AATTCTCAATTTCCCTCCAA
1 AATTCTCAATTTCCCT-CTA
* *
250571 AATTTTCTA-TTCCCTCTA
1 AATTCTCAATTTCCCTCTA
*
250589 AATT-TCAATTTCCTTCTA
1 AATTCTCAATTTCCCTCTA
250607 AATTCTCAATTT--CTCTA
1 AATTCTCAATTTCCCTCTA
*
250624 TATTCTCAA
1 AATTCTCAA
250633 AATTAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 15 0.28
18 18 0.34
19 13 0.25
20 7 0.13
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTCTCAATTTCCCTCTA
Found at i:250628 original size:17 final size:18
Alignment explanation
Indices: 250551--250632 Score: 78
Period size: 17 Copynumber: 4.5 Consensus size: 18
250541 AAATAAAATC
*
250551 AATTCTCAATTTCCCTCCAA
1 AATTCTCAATTT-CCT-CTA
* * *
250571 AATTTTCTATTCCCTCTA
1 AATTCTCAATTTCCTCTA
250589 AATT-TCAATTTCCTTCTA
1 AATTCTCAATTTCC-TCTA
250607 AATTCTCAATTT-CTCTA
1 AATTCTCAATTTCCTCTA
*
250624 TATTCTCAA
1 AATTCTCAA
250633 AATTAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 19 0.36
18 15 0.28
19 10 0.19
20 9 0.17
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTCTCAATTTCCTCTA
Found at i:250725 original size:2 final size:2
Alignment explanation
Indices: 250718--250958 Score: 109
Period size: 2 Copynumber: 122.0 Consensus size: 2
250708 ACTTTGAATA
250718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
250760 AT AT AT -T AT AT ACT AT AT AT -T TT AT AGT TT AT A- AC AT AT ACT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * * * * *
250802 -T TT TT AGT TT AT AC AT AT AGT -T AC AT AT AT AGT TT AT AT AT
1 AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
* * *
250843 AGT -T CAT AT AA AC AT A- AT TT AT AT AT AT A- ACT -T AT A- AT
1 A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
250881 A- AT -T AT AGT TT AT A- AT AT AA AT AT AGT AT AT AT AT AT AGT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
* *
250921 TT AT AT AT AA ACT -T AT AT -T AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250959 TTTTTTCAAT
Statistics
Matches: 184, Mismatches: 26, Indels: 58
0.69 0.10 0.22
Matches are distributed among these distances:
1 16 0.09
2 155 0.84
3 13 0.07
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252760 original size:6 final size:6
Alignment explanation
Indices: 252712--252757 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
252702 CCAAGATTTT
* *
252712 TATACA TATACA TATACA TATACA TATACA TATATA TATATA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
252758 TATTATACAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (6 bp):
TATACA
Found at i:252863 original size:76 final size:74
Alignment explanation
Indices: 252779--253038 Score: 269
Period size: 76 Copynumber: 3.4 Consensus size: 74
252769 TTTTAAAATA
*
252779 ATTTTGAAAACTTATATAATATATAGTCTTTTTTAAAAGCGTTTTGAAAATATATATAATATATG
1 ATTTTGAAAACTTATATAATATATAGT-TTTTTTAAAA-CATTTTGAAAATATATATAATATATG
252844 ATTTCTAAAAC
64 ATTTCTAAAAC
* *
252855 ATTTTGAAAAATTATATATATTATATAG--TTTTTAAAATATTTTGAAAATAAATATATAATATA
1 ATTTTGAAAACTTATATA-A-TATATAGTTTTTTTAAAACATTTTGAAAAT--ATATATAATATA
*
252918 TGGGTTTTCT--AAC
62 T--GATTTCTAAAAC
* * *
252931 ATTTTGAAAACATATATATTATATAGGTTTTTTT-AAACATTTTGGAAATAAATATATAATATAT
1 ATTTTGAAAACTTATATAATATATA-GTTTTTTTAAAACATTTT-GAAA-ATATATATAATATAT
* * *
252995 GGTTTTTAAAGC
63 GATTTCTAAAAC
*
253007 ATTTTGAAAACATATATATATTATATAGTTTT
1 ATTTTGAAAAC-T-TATATAATATATAGTTTT
253039 AAAATATTTT
Statistics
Matches: 156, Mismatches: 13, Indels: 29
0.79 0.07 0.15
Matches are distributed among these distances:
74 21 0.13
75 10 0.06
76 83 0.53
77 15 0.10
78 27 0.17
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (74 bp):
ATTTTGAAAACTTATATAATATATAGTTTTTTTAAAACATTTTGAAAATATATATAATATATGAT
TTCTAAAAC
Found at i:252871 original size:38 final size:37
Alignment explanation
Indices: 252751--253089 Score: 233
Period size: 38 Copynumber: 8.9 Consensus size: 37
252741 ATATATATAT
* * *
252751 ATATATATATTATA-CAGTTTTTAAAATAATTTTGAAAA
1 ATATATATAATATATGA-TTTTTAAAA-CATTTTGAAAA
* * *
252789 CT-TATATAATATATAGTCTTTTTTAAAAGCGTTTTG-AAA
1 ATATATATAATATAT-G--ATTTTTAAAA-CATTTTGAAAA
*
252828 ATATATATAATATATGATTTCTAAAACATTTTGAAAA
1 ATATATATAATATATGATTTTTAAAACATTTTGAAAA
* *
252865 ATTATATATATTATAT-AGTTTTTAAAATATTTTGAAAA
1 A-TATATATAATATATGA-TTTTTAAAACATTTTGAAAA
* ** **
252903 TAAATATATAATATATGGGTTTTCTAACATTTTGAAAA
1 -ATATATATAATATATGATTTTTAAAACATTTTGAAAA
* * * *
252941 CATATATATTATATAGGTTTTTTTAAACATTTTGGAAATA
1 -ATATATATAATATATGATTTTTAAAACATTTT-GAAA-A
* *
252981 A-ATATATAATATATGGTTTTTAAAGCATTTTGAAAA
1 ATATATATAATATATGATTTTTAAAACATTTTGAAAA
* * * *
253017 CATATATATATTATAT-AGTTTTAAAATATTTTTTGGAAA
1 -ATATATATAATATATGATTTTTAAAACA--TTTTGAAAA
* *
253056 ATATAT-TATATCATATGGTTTTGAAAAACATTTT
1 ATATATATA-AT-ATATGATTTT-TAAAACATTTT
253090 TTTTAAAATC
Statistics
Matches: 236, Mismatches: 45, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
36 7 0.03
37 38 0.16
38 129 0.55
39 27 0.11
40 30 0.13
41 5 0.02
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATGATTTTTAAAACATTTTGAAAA
Found at i:252947 original size:114 final size:115
Alignment explanation
Indices: 252751--253034 Score: 296
Period size: 114 Copynumber: 2.5 Consensus size: 115
252741 ATATATATAT
* * *
252751 ATATATATATTATACAGTTTTTAAAATAATTTTGAAAACT--TATATAATATATAGTCTTTTTTA
1 ATATATATATTATATAGTTTTTAAAAT-ATTTTGAAAA-TAATATATAATATATAGGCTTTTCT-
* *
252814 AAAGCGTTTTGAAAATATATATAATATATGATTTCTAAAACATTTT-GAAA-A
63 AAAGCATTTTGAAAATATATATAATATAGGATTTCTAAAACATTTTGGAAATA
*
252865 ATTATATATATTATATAGTTTTTAAAATATTTTGAAAATAAATATATAATATAT-GGGTTTTCT-
1 A-TATATATATTATATAGTTTTTAAAATATTTTGAAAAT-AATATATAATATATAGGCTTTTCTA
* * * *
252928 AA-CATTTTGAAAACATATATATTATATAGGTTTTTTTAAACATTTTGGAAATA
64 AAGCATTTTG-AAA-ATATATATAATATAGGATTTCTAAAACATTTTGGAAATA
* * ** * *
252981 A-ATATATAATATATGGTTTTTAAAGCATTTTGAAAACATATATATATTATATAG
1 ATATATATATTATATAGTTTTTAAAATATTTTGAAAATA-ATATATAATATATAG
253035 TTTTAAAATA
Statistics
Matches: 144, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
112 6 0.04
113 7 0.05
114 81 0.56
115 36 0.25
116 14 0.10
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (115 bp):
ATATATATATTATATAGTTTTTAAAATATTTTGAAAATAATATATAATATATAGGCTTTTCTAAA
GCATTTTGAAAATATATATAATATAGGATTTCTAAAACATTTTGGAAATA
Found at i:253156 original size:17 final size:16
Alignment explanation
Indices: 253132--253171 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
253122 AAAATATTTT
253132 TTTATTTT-TTTATTTA
1 TTTATTTTATTTA-TTA
253148 TTCTATTTTATTTATTA
1 TT-TATTTTATTTATTA
253165 TTTATTT
1 TTTATTT
253172 GTTATCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTATTTATTA
Found at i:257486 original size:20 final size:19
Alignment explanation
Indices: 257461--257525 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
257451 ATCCAATCAG
*
257461 AACAAAAAGGAAAAAGAAAA
1 AACAAAAA-GAAAAACAAAA
*
257481 AACAAAGAGAAAAAC-AAA
1 AACAAAAAGAAAAACAAAA
*
257499 AA-TAAAAGAAAAGA-AAAGA
1 AACAAAAAGAAAA-ACAAA-A
257518 AACAAAAA
1 AACAAAAA
257526 CCAAGAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 8 0.22
18 8 0.22
19 9 0.25
20 11 0.31
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (19 bp):
AACAAAAAGAAAAACAAAA
Found at i:257499 original size:25 final size:25
Alignment explanation
Indices: 257471--257525 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
257461 AACAAAAAGG
*
257471 AAAAAGAAAAAACAAAGAGAA-AAAC
1 AAAAAGAAAAAA-AAAGAAAAGAAAC
* *
257496 AAAAATAAAAGAAAAGAAAAGAAAC
1 AAAAAGAAAAAAAAAGAAAAGAAAC
257521 AAAAA
1 AAAAA
257526 CCAAGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAGAAAAGAAAC
Found at i:257506 original size:19 final size:18
Alignment explanation
Indices: 257464--257507 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
257454 CAATCAGAAC
*
257464 AAAAAG-GAAAAAGAAAA
1 AAAAAGAGAAAAACAAAA
257481 AACAAAGAGAAAAACAAAA
1 AA-AAAGAGAAAAACAAAA
257500 ATAAAAGA
1 A-AAAAGA
257508 AAAGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 2 0.09
18 4 0.17
19 16 0.70
20 1 0.04
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAGAGAAAAACAAAA
Found at i:257524 original size:19 final size:18
Alignment explanation
Indices: 257472--257524 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
257462 ACAAAAAGGA
257472 AAAAG-AAAAAACAAAGAG
1 AAAAGAAAAAAACAAA-AG
* *
257490 AAAA-ACAAAAATAAAAG
1 AAAAGAAAAAAACAAAAG
257507 AAAAGAAAAGAAACAAAA
1 AAAAGAAAA-AAACAAAA
257525 ACCAAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 6 0.21
18 15 0.54
19 7 0.25
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAACAAAAG
Found at i:258482 original size:20 final size:20
Alignment explanation
Indices: 258457--258501 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
258447 GATATTGGGC
* *
258457 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
258477 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
258497 TATTG
1 TATTG
258502 AATAATGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.04, G:0.22, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:258572 original size:46 final size:45
Alignment explanation
Indices: 258505--258611 Score: 142
Period size: 46 Copynumber: 2.3 Consensus size: 45
258495 GTTATTGAAT
* * * * *
258505 AATGGCAAGTATATTGGTAAAATAAGTTTACGGGCTTATGATATTA
1 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGAGA-TA
*
258551 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGAGATA
258596 AATGGTAAGATATTTT
1 AATGGTAAG-TATTTT
258612 TATCTTATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 11 0.20
46 43 0.80
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (45 bp):
AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGAGATA
Found at i:265801 original size:33 final size:33
Alignment explanation
Indices: 265759--265825 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
265749 CCTAATATAG
265759 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
265792 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
265825 A
1 A
265826 GCACTACAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:265913 original size:20 final size:20
Alignment explanation
Indices: 265885--265928 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
265875 TATATTGGGC
* *
265885 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
265905 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
265925 TATT
1 TATT
265929 AAATAATGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.59
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:266531 original size:13 final size:13
Alignment explanation
Indices: 266511--266558 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
266501 CGATTCCCCC
266511 ACTGTTCACGGTT
1 ACTGTTCACGGTT
* *
266524 ATTGTTCACTGTT
1 ACTGTTCACGGTT
266537 ACTGTTCACGGGTT
1 ACTGTTCAC-GGTT
266551 -CTGTTCAC
1 ACTGTTCAC
266559 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 27 0.90
14 3 0.10
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (13 bp):
ACTGTTCACGGTT
Found at i:267242 original size:38 final size:37
Alignment explanation
Indices: 267200--267495 Score: 266
Period size: 38 Copynumber: 7.8 Consensus size: 37
267190 TACATATACA
*
267200 TATATATATTATACAGTTTTTAAATA-ATTTTGAAAACT
1 TATATATATTATATAGTTTTTAAA-ACATTTTGAAAA-T
*
267238 TATATA-A-TATATAGTCTTTTTTAAAAGCATTTTG-AAAG
1 TATATATATTATATAG---TTTTTAAAA-CATTTTGAAAAT
* * * *
267276 TATATATAATATATTGTTTCTAAAACATTTTGAAAAAG
1 TATATATATTATATAGTTTTTAAAACATTTTG-AAAAT
* *
267314 TATATATATTATATAGTTTTTAAAACAATTCGAAAAT
1 TATATATATTATATAGTTTTTAAAACATTTTGAAAAT
* *
267351 AAATATATAATATATTA-TTTTTAAAACATTTTGAAAA-
1 -TATATATATTATA-TAGTTTTTAAAACATTTTGAAAAT
*
267388 TATACATATTATATAGGTTTTTATAAACATTTTGAAAA-
1 TATATATATTATATA-GTTTTTA-AAACATTTTGAAAAT
* * * *
267426 TAAATATATAATATATGGTTTTAAAAGCATTTTGAAAACA
1 TATATATATTATATA-GTTTTTAAAA-CATTTTGAAAA-T
*
267466 TATATATATTATATAG-TTTTAAAATATTTT
1 TATATATATTATATAGTTTTTAAAACATTTT
267496 TTGGAAAATA
Statistics
Matches: 216, Mismatches: 25, Indels: 35
0.78 0.09 0.13
Matches are distributed among these distances:
35 2 0.01
36 23 0.11
37 27 0.12
38 124 0.57
39 15 0.07
40 25 0.12
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATATATTATATAGTTTTTAAAACATTTTGAAAAT
Found at i:267306 original size:76 final size:74
Alignment explanation
Indices: 267201--267495 Score: 323
Period size: 76 Copynumber: 3.9 Consensus size: 74
267191 ACATATACAT
* ** *
267201 ATATATATTATACAGTTTTTAAATA-ATTTTGAAAACT-TATATAATATATAGTCTTTTTTAAAA
1 ATATATAATATATTGTTTTTAAA-ACATTTTGAAAACTATATATATTATATAG---TTTTTAAAA
*
267264 GCATTTTGAAAGT-
62 -CATTTTGAAAATA
* * *
267277 ATATATAATATATTGTTTCTAAAACATTTTGAAAAAGTATATATATTATATAGTTTTTAAAACAA
1 ATATATAATATATTGTTTTTAAAACATTTTG-AAAACTATATATATTATATAGTTTTTAAAACAT
*
267342 TTCGAAAATAA
65 TTTGAAAAT-A
* *
267353 ATATATAATATATTATTTTTAAAACATTTTGAAAA-TATACATATTATATAGGTTTTTATAAACA
1 ATATATAATATATTGTTTTTAAAACATTTTGAAAACTATATATATTATATA-GTTTTTA-AAACA
267417 TTTTGAAAATAA
64 TTTTGAAAAT-A
* *
267429 ATATATAATATA-TGGTTTTAAAAGCATTTTGAAAACATATATATATTATATAG-TTTTAAAATA
1 ATATATAATATATTGTTTTTAAAA-CATTTTGAAAAC-TATATATATTATATAGTTTTTAAAACA
267492 TTTT
64 TTTT
267496 TTGGAAAATA
Statistics
Matches: 191, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
74 23 0.12
75 38 0.20
76 97 0.51
77 6 0.03
78 27 0.14
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (74 bp):
ATATATAATATATTGTTTTTAAAACATTTTGAAAACTATATATATTATATAGTTTTTAAAACATT
TTGAAAATA
Found at i:267332 original size:114 final size:114
Alignment explanation
Indices: 267199--267482 Score: 305
Period size: 114 Copynumber: 2.5 Consensus size: 114
267189 ATACATATAC
* *
267199 ATATATATATTATACAGTTTTTAAATAATTTTGAAAACT-TATATAATATATAGTCTTTTTTAAA
1 ATATATATATTATATAGTTTTTAAA-AATTTTGAAAACTATATATAATATATAGT-ATTTTTAAA
* * *
267263 AGCATTTTGAAAGTATATATAATATAT-TGTTTCTA-AAACATTTTGAAAA-
64 A-CATTTTGAAAATATACATAATATATAGGTTTCTATAAACATTTTGAAAAT
* *
267312 AGTATATATATTATATAGTTTTTAAAACAATTCGAAAA-TAAATATATAATATAT--TATTTTTA
1 A-TATATATATTATATAGTTTTTAAAA-ATTTTGAAAACT--ATATATAATATATAGTATTTTTA
* *
267374 AAACATTTTGAAAATATACATATTATATAGGTTTTTATAAACATTTTGAAAAT
62 AAACATTTTGAAAATATACATAATATATAGGTTTCTATAAACATTTTGAAAAT
* * * *
267427 AAATATATAATATAT-GGTTTTAAAAGCATTTTGAAAACATATATATATTATATAGT
1 ATATATATATTATATAGTTTTTAAAA--ATTTTGAAAAC-TATATATAATATATAGT
267483 TTTAAAATAT
Statistics
Matches: 143, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
112 22 0.15
113 27 0.19
114 79 0.55
115 1 0.01
116 14 0.10
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (114 bp):
ATATATATATTATATAGTTTTTAAAAATTTTGAAAACTATATATAATATATAGTATTTTTAAAAC
ATTTTGAAAATATACATAATATATAGGTTTCTATAAACATTTTGAAAAT
Found at i:267556 original size:21 final size:20
Alignment explanation
Indices: 267532--267571 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
267522 TTTTAAAAAA
*
267532 TATTTTTTATTTATTCTATTT
1 TATTTATTATTTATT-TATTT
267553 TATTTATTATTTATTTATT
1 TATTTATTATTTATTTATT
267572 AGTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTTATTATTTATTTATTT
Found at i:267565 original size:11 final size:11
Alignment explanation
Indices: 267532--267578 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
267522 TTTTAAAAAA
*
267532 TATTTTTTATT
1 TATTTATTATT
267543 TATTCTA-T-TT
1 TATT-TATTATT
267553 TATTTATTATT
1 TATTTATTATT
*
267564 TATTTATTAGT
1 TATTTATTATT
267575 TATT
1 TATT
267579 ATTTTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 7 0.23
11 21 0.68
12 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTTATTATT
Found at i:270040 original size:23 final size:23
Alignment explanation
Indices: 270010--270062 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
270000 GATTAGGGAT
270010 TTGATTGTGAAGATGTTAAAAGG
1 TTGATTGTGAAGATGTTAAAAGG
270033 TTGATTGTGAAGATGTTAAAAGG
1 TTGATTGTGAAGATGTTAAAAGG
270056 TTGATTG
1 TTGATTG
270063 AAAGTTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.30, T:0.38
Consensus pattern (23 bp):
TTGATTGTGAAGATGTTAAAAGG
Found at i:270288 original size:30 final size:30
Alignment explanation
Indices: 270223--270290 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
270213 ATAAGCCTTA
* * * *
270223 GAAAAATTTGGGGACCATTTTATAATTTTT
1 GAAAAGTTAGGGGACCAATTTATAAATTTT
270253 GAAAAGTTAGGGGACCAATTTA-ACAATTTT
1 GAAAAGTTAGGGGACCAATTTATA-AATTTT
270283 GAAAAGTT
1 GAAAAGTT
270291 GTTAATGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.35
Consensus pattern (30 bp):
GAAAAGTTAGGGGACCAATTTATAAATTTT
Found at i:270858 original size:24 final size:24
Alignment explanation
Indices: 270826--270874 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
270816 TGCATGACAT
*
270826 TGTACATAGATGTTTTATTCATCA
1 TGTACATAGATGTTTTATACATCA
270850 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
270874 T
1 T
270875 TTGGAAGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:271236 original size:40 final size:40
Alignment explanation
Indices: 271192--271421 Score: 415
Period size: 40 Copynumber: 5.8 Consensus size: 40
271182 AGGACACTAA
271192 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
271232 GTGTATATGGTGGGCACAACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
271272 GTGTATATGGTGGGCATGACCTTATGTGTAATACACTTTG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
271312 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTTG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
*
271352 GTGTATATGGTGGGCACGACCTTATGTTTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
271392 GTGTATATGGTGGGCACGACCTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
271422 GCACTACGGT
Statistics
Matches: 182, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 182 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:273837 original size:32 final size:29
Alignment explanation
Indices: 273796--273857 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 29
273786 GACAGAGGAG
*
273796 AGTATCGATACTCTAGCTCGAGTATCGATACC
1 AGTATCGATACT-T-GCACGA-TATCGATACC
273828 AGTATCGATACTTGCACGATATCGATACC
1 AGTATCGATACTTGCACGATATCGATACC
273857 A
1 A
273858 AAAATAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.38
30 5 0.17
31 1 0.03
32 12 0.41
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (29 bp):
AGTATCGATACTTGCACGATATCGATACC
Found at i:273924 original size:20 final size:20
Alignment explanation
Indices: 273899--273951 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
273889 ACCATATAGG
273899 GAGTATCGGTACTCCATCCC
1 GAGTATCGGTACTCCATCCC
273919 GAGTATCGGTACTCCATCCC
1 GAGTATCGGTACTCCATCCC
273939 GAGTATCGGTACT
1 GAGTATCGGTACT
273952 ACTGCCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (20 bp):
GAGTATCGGTACTCCATCCC
Found at i:276149 original size:19 final size:19
Alignment explanation
Indices: 276127--276192 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
276117 CAGTCAATGG
276127 AAAAGTAAATGGTCAACAA
1 AAAAGTAAATGGTCAACAA
* * ***
276146 AAAAGTCAATGGTTAATGG
1 AAAAGTAAATGGTCAACAA
* * *
276165 ATAAGTCAATGATCAACAA
1 AAAAGTAAATGGTCAACAA
276184 AAAAGTAAA
1 AAAAGTAAA
276193 CGATCAATGG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.20
Consensus pattern (19 bp):
AAAAGTAAATGGTCAACAA
Found at i:276210 original size:38 final size:38
Alignment explanation
Indices: 276120--276202 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
276110 AATTCAACAG
* * * * * *
276120 TCAATGGAAAAGTAAATGGTCAACAAAAAAGTCAATGG
1 TCAATGGATAAGTCAATGATCAACAAAAAAGTAAACGA
*
276158 TTAATGGATAAGTCAATGATCAACAAAAAAGTAAACGA
1 TCAATGGATAAGTCAATGATCAACAAAAAAGTAAACGA
276196 TCAATGG
1 TCAATGG
276203 GTTAGTCAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.20
Consensus pattern (38 bp):
TCAATGGATAAGTCAATGATCAACAAAAAAGTAAACGA
Found at i:277353 original size:13 final size:13
Alignment explanation
Indices: 277337--277361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277327 TTAATATTAA
277337 AATAAAATAAAAT
1 AATAAAATAAAAT
277350 AATAAAATAAAA
1 AATAAAATAAAA
277362 CATAAGATAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:280453 original size:68 final size:68
Alignment explanation
Indices: 280339--280682 Score: 528
Period size: 68 Copynumber: 5.1 Consensus size: 68
280329 TTTTAGAAAA
* * *
280339 CACAATCCATGTGAATTAGATTACAACCATTGATAAAGAAATGAATCTTTCAATCTCAGCCATTC
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAAGGAATCTTTCAATCTCAGCCGTTC
280404 ATT
66 ATT
* * *
280407 CACAATCCATGTTAATTGTATTACAACCATTGATAAAGAAAGGAATCTTTCGATCTCAGCCGTTC
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAAGGAATCTTTCAATCTCAGCCGTTC
280472 ATT
66 ATT
* * * *
280475 CACAATCCATGTGAATTGGATTACAACCATTGATAAATAAAGAAATCTTTCGATCTCATCCGTTC
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAAGGAATCTTTCAATCTCAGCCGTTC
280540 ATT
66 ATT
* *
280543 TACAATCCATGTGAATTGGAATACAACCATTGATAAAGAAAGGAATCTTTCAATCTCAGCCGTTC
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAAGGAATCTTTCAATCTCAGCCGTTC
280608 ATT
66 ATT
* * *
280611 CATAATCCATGTGAATTGGATTACAACCATTGA-AAACGAAAAGAATCTTTCAATCTCATCCGTT
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAA-GAAAGGAATCTTTCAATCTCAGCCGTT
*
280675 CACT
65 CATT
280679 CACA
1 CACA
280683 TGTGCTTGCA
Statistics
Matches: 251, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
67 3 0.01
68 248 0.99
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (68 bp):
CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAAGGAATCTTTCAATCTCAGCCGTTC
ATT
Found at i:283034 original size:3 final size:3
Alignment explanation
Indices: 283026--283067 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
283016 AATTAATATA
*
283026 AAT AAT AAT AAAT AAT AAT ATT AAAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
283068 TTAACTCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 30 0.86
4 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:283044 original size:13 final size:13
Alignment explanation
Indices: 283026--283067 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
283016 AATTAATATA
283026 AATAATAATAAAT
1 AATAATAATAAAT
*
283039 AATAATATTAAAT
1 AATAATAATAAAT
283052 AATAATAAT-AAT
1 AATAATAATAAAT
283064 AATA
1 AATA
283068 TTAACTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:283069 original size:22 final size:23
Alignment explanation
Indices: 283019--283071 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
283009 TTTGTAAAAT
283019 TAATA-TAAATAATAATAAATAA
1 TAATATTAAATAATAATAAATAA
283041 TAATATTAAATAATAAT-AATAA
1 TAATATTAAATAATAATAAATAA
283063 TAATATTAA
1 TAATATTAA
283072 CTCGAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATATTAAATAATAATAAATAA
Found at i:283492 original size:134 final size:133
Alignment explanation
Indices: 283253--284677 Score: 1543
Period size: 134 Copynumber: 10.7 Consensus size: 133
283243 GTAATCAGAT
** * * * **
283253 CTCGA-AAAATTTTGATCCACTTCGTTACTCTTCATGGAAGATTGAATCGAACTCGATTTACTTC
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAA-TTGATTTGTTTC
** * * * * *
283317 GTTGTTCTTCAGAAATACCAAATTTGAAAGAA-AGAGAATCTGCTCCACTGCTCTTTAGGGGAGA
65 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGA-AGAATCTGCTCCACTACTCTTTAGGGGAGA
283381 TCAAA
129 TCAAA
** *
283386 CTCGAGAAAATTTTGATCCACTTCGTTGCTCTTCA-GGAAGATTGAATTGAACTTGATTTGTTTC
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAA-TTGATTTGTTTC
* * * *
283450 GCTCCTCTTCACGAAGACCAAATCTTGAAAGAAGAAGAATCTGCTCCACTACTTTTTAGGGGAGA
65 ACTGCTCTTCAGGAAGACCAAATC-TGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
*
283515 TCATA
129 TCAAA
* * *** * * * *
283520 -TACG-TAATATTTTGATCCACTTTGGTACTTTTCAGGGAACATTGAATCGAAATTAATTTGTTT
1 CT-CGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCG-AATTGATTTGTTT
* ** *
283583 CACTGCTCTTCAGGAAGA-CTAATCTGAAAGAAGAAGAATCAACTCCACTACTCTTTAGGGGACA
64 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
*
283647 TCAAG
129 TCAAA
* * * * * *
283652 CTTGATAAAAATTTGATCCACTTCATTGCTCTTCAGGGAAGATTGAATCGAATATAATTTGCTTC
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAAT-TGATTTGTTTC
** * * *
283717 GTTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAAAATCTGCTCCTCTACTCTTTATGGGAGAT
65 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGAT
* *
283782 TAGA
130 CAAA
* * * * *
283786 CACG-TAATATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCGTAATTGATTTGTTTA
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCG-AATTGATTTGTTTC
*
283850 ACTGCTCTTCAGGAAGACCAAATCTG--A-AAGAAGATTCTGCTCCACTACTCTTTAGGGGAGAT
65 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGAT
*
283912 CATA
130 CAAA
* * * *
283916 CACG-TAATATTTTGATCCTCTTCGA-TGCTCTTCAGGGAAGATTGAATCGTAATTGATTTGTTT
1 CTCGAGAAAATTTTGATCCACTTC-ACTGCTCTTCAGGGAAGATTGAATCG-AATTGATTTGTTT
*
283979 CACTGCTCTTCAGGAAGACCAAATCTGAAAG-AGAAAGAATCTACTCCACTACTCTTTAGGGGAG
64 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAG-AAGAATCTGCTCCACTACTCTTTAGGGGAG
284043 ATCAAA
128 ATCAAA
* * * * *
284049 TTCGAGAAAACTTTGATACACTTCACTGCTCTTCAGGGAAGATTGAATTAGAATCGATTTGTTTC
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAA-TCGAATTGATTTGTTTC
* * * *
284114 ACTGCTATTCAGGATGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTAGTGGAGAT
65 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGAT
284179 CATAA
130 CA-AA
* * * * ** *
284184 -TCGAGAAAACTTTGATCCACTTCACTGCTCTTCATGGAAGATTAAATAAGAATCAATTTGCTTC
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAAT-CGAATTGATTTGTTTC
* * * * *
284248 ACTTCTCTTTAGGAAGACCAAATATGAAAGAAGAAGAATATGCTCCACTACTCTTTAAGGGAGAT
65 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGAT
*
284313 CAGA
130 CAAA
* * * * *
284317 CTCGAGAAAACTTTGATCCACTTCACTCCTCTTCAGCGAAGATTGAATCAAAATCGATTTGCTTT
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATC-GAATTGATTTG-TTT
* * * *
284382 -ACTGCTCTTCAGGAATACCAAATCTGAAAAAAGAAGAATATGCTCCATTACTCTTTAGGGGAGA
64 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
*
284446 TCAGA
129 TCAAA
* * * *
284451 CTCGAGAAAAATTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATCTGCTTC
1 CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATC-GAATTGATTTGTTTC
* * *
284516 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGTTCCACTACTCTTTA-GGGATAT
65 ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGAT
*
284580 CAGA
130 CAAA
* * * * * * * * * *
284584 CTCAAG-AAATCTTTGATCTACTTCAATGATATTTATGAAAGATTGAATCGAACGTGGTTTGTTT
1 CTCGAGAAAAT-TTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAA-TTGATTTGTTT
* *
284648 CACTTCTCTTCAGGAAGACCAAATATGAAA
64 CACTGCTCTTCAGGAAGACCAAATCTGAAA
284678 ATCAATCATT
Statistics
Matches: 1116, Mismatches: 148, Indels: 56
0.85 0.11 0.04
Matches are distributed among these distances:
130 118 0.11
131 2 0.00
132 52 0.05
133 333 0.30
134 600 0.54
135 11 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (133 bp):
CTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAATTGATTTGTTTCA
CTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATC
AAA
Found at i:285318 original size:19 final size:19
Alignment explanation
Indices: 285294--285332 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
285284 TCTACTTCTC
285294 TTCATGAGAAAGTCAATAA
1 TTCATGAGAAAGTCAATAA
**
285313 TTCATGAGGGAGTCAATAA
1 TTCATGAGAAAGTCAATAA
285332 T
1 T
285333 AACAAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (19 bp):
TTCATGAGAAAGTCAATAA
Found at i:285386 original size:38 final size:38
Alignment explanation
Indices: 285313--285916 Score: 557
Period size: 38 Copynumber: 15.5 Consensus size: 38
285303 AAGTCAATAA
* * * * * *
285313 TTCATGAGGGAGTCAATAATAACAAAGGTTAACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
** * *
285351 TTCACGAGGAAACCAAGAATAAAAAATATCGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* * *
285389 TTCACGTGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
1 TTCACGAGGAAGTCAAGAATAA-A---AAAGATTGACTTCTC
* * * *
285431 TTCATGAGGGAGTCAATAATAATAAAGATTGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* * *
285469 TTCATGAGGAAGTAAAGAATAAAAAATATTGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* *
285507 TTCACGAGGAAGTCAAGAATAACGTTGAAAGATCT-ACTCCTC
1 TTCACGAGGAAGTCAAGAATAA----AAAAGAT-TGACTTCTC
* *
285549 TTCACGAGGGAGTCAAGAATAACAAAGATTGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
** * * *
285587 TTCACGATAAAGTCAAGAATAACAAAGATTAACCTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* *
285625 TTCACGAGGAAGTCAAGAATAACGTTGAAAGATTGACTCCTC
1 TTCACGAGGAAGTCAAGAATAA----AAAAGATTGACTTCTC
* * *
285667 TTCACGAGGGAGTCAAGAATAACAAAGATTAACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* * *
285705 ATCACGAGGAAATCAAGAATAACAAA-ATTGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* * *
285742 TTCACGAGGAAGTAAAGAATAACATTGAAATATTGACTCCTC
1 TTCACGAGGAAGTCAAGAATAA-A---AAAGATTGACTTCTC
* * * *
285784 TTAATGAGGGAGTCAAGAATAACAAAGATTGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* *
285822 TTCACGAGGAATTCAAGAATAACAAAGATTGACTTCTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
* ** *
285860 TTCATGAGGAAGTCAAGAATAACGACGATTGAC-TCTTC
1 TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTC-TC
* *
285898 TTCATGAGGGAGTCAAGAA
1 TTCACGAGGAAGTCAAGAA
285917 AGACAATGAA
Statistics
Matches: 469, Mismatches: 77, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
37 32 0.07
38 310 0.66
39 1 0.00
41 3 0.01
42 122 0.26
43 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (38 bp):
TTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTCTC
Found at i:285465 original size:80 final size:76
Alignment explanation
Indices: 285313--285916 Score: 629
Period size: 80 Copynumber: 7.8 Consensus size: 76
285303 AAGTCAATAA
* * * * * ** * *
285313 TTCATGAGGGAGTCAATAATAACAAAGGTTAACTTCTCTTCACGAGGAAACCAAGAATAAAAAAT
1 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
285378 ATCGACTTCTC
66 ATTGACTTCTC
* * * * * * *
285389 TTCACGTGAAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCATGAGGGAGTCAATAATAAT
1 TTCACGAGGAAGTCAAGAATAAC----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
285454 AAAGATTGACTTCTC
62 AAAGATTGACTTCTC
* * * *
285469 TTCATGAGGAAGTAAAGAATAAAAAATATTGACTTCTCTTCACGAGGAAGTCAAGAATAACGTTG
1 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----
*
285534 AAAGATCT-ACTCCTC
62 AAAGAT-TGACTTCTC
* **
285549 TTCACGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGATAAAGTCAAGAATAACAAAG
1 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
285614 ATTAACCTCTC
66 ATTGACTTCTC
* *
285625 TTCACGAGGAAGTCAAGAATAACGTTGAAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAC
1 TTCACGAGGAAGTCAAGAATAAC----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
285690 AAAGATTAACTTCTC
62 AAAGATTGACTTCTC
* * *
285705 ATCACGAGGAAATCAAGAATAACAAA-ATTGACTTCTCTTCACGAGGAAGTAAAGAATAACATTG
1 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----
* *
285769 AAATATTGACTCCTC
62 AAAGATTGACTTCTC
* * * *
285784 TTAATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAATTCAAGAATAACAAAG
1 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
285849 ATTGACTTCTC
66 ATTGACTTCTC
* * * * *
285860 TTCATGAGGAAGTCAAGAATAACGACGATTGAC-TCTTCTTCATGAGGGAGTCAAGAA
1 TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAA
285917 AGACAATGAA
Statistics
Matches: 441, Mismatches: 67, Indels: 40
0.80 0.12 0.07
Matches are distributed among these distances:
75 34 0.08
76 146 0.33
79 33 0.07
80 227 0.51
81 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (76 bp):
TTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
ATTGACTTCTC
Found at i:285521 original size:118 final size:118
Alignment explanation
Indices: 285313--285916 Score: 853
Period size: 118 Copynumber: 5.2 Consensus size: 118
285303 AAGTCAATAA
* * * * * *
285313 TTCATGAGGGAGTCAATAATAACAAAGGTTAACTTCTCTTCACGAGGAAACCAAGAATAAAAAAT
1 TTCATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAATCAAGAATAACAAAG
* * *
285378 ATCGACTTCTCTTCACGTGAAAGTCAAGAATAACATTGAAAGATTGACTCCTC
66 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* * * * * * *
285431 TTCATGAGGGAGTCAATAATAATAAAGATTGACTTCTCTTCATGAGGAAGTAAAGAATAAAAAAT
1 TTCATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAATCAAGAATAACAAAG
*
285496 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACGTTGAAAGATCT-ACTCCTC
66 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGAT-TGACTCCTC
* *
285549 TTCACGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGA-TAAAGTCAAGAATAACAAA
1 TTCATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAA-TCAAGAATAACAAA
* * *
285613 GATTAACCTCTCTTCACGAGGAAGTCAAGAATAACGTTGAAAGATTGACTCCTC
65 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* * *
285667 TTCACGAGGGAGTCAAGAATAACAAAGATTAACTTCTCATCACGAGGAAATCAAGAATAACAAA-
1 TTCATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAATCAAGAATAACAAAG
* *
285731 ATTGACTTCTCTTCACGAGGAAGTAAAGAATAACATTGAAATATTGACTCCTC
66 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTC
* *
285784 TTAATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAATTCAAGAATAACAAAG
1 TTCATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAATCAAGAATAACAAAG
* * *
285849 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC---G-ACGATTGACTCTTC
66 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTC
285898 TTCATGAGGGAGTCAAGAA
1 TTCATGAGGGAGTCAAGAA
285917 AGACAATGAA
Statistics
Matches: 440, Mismatches: 41, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
114 29 0.07
115 1 0.00
117 110 0.25
118 296 0.67
119 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (118 bp):
TTCATGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAATCAAGAATAACAAAG
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTC
Found at i:286600 original size:21 final size:20
Alignment explanation
Indices: 286557--286624 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
286547 ACATCCTACC
286557 CGAAGGACTTACAGATGGCT
1 CGAAGGACTTACAGATGGCT
** *
286577 CGAAGGACTTATCATCTTGCT
1 CGAAGGACTTA-CAGATGGCT
* * * *
286598 CGAAAGACTGACAGATGACC
1 CGAAGGACTTACAGATGGCT
286618 CGAAGGA
1 CGAAGGA
286625 TTTAATCATC
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.19
Consensus pattern (20 bp):
CGAAGGACTTACAGATGGCT
Found at i:286624 original size:41 final size:41
Alignment explanation
Indices: 286557--286666 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 41
286547 ACATCCTACC
* *
286557 CGAAGGACTTACAGATGGCTCGAAGGACTT-ATCATCTTGCT
1 CGAAAGAC-TACAGATGGCCCGAAGGACTTAATCATCTTGCT
* *
286598 CGAAAGACTGACAGATGACCCGAAGGATTTAATCATCTTGCT
1 CGAAAGACT-ACAGATGGCCCGAAGGACTTAATCATCTTGCT
*
286640 CGAAAGACATACTGATGGCCCGAAGGA
1 CGAAAGAC-TACAGATGGCCCGAAGGA
286667 ATTACCAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.02
41 24 0.40
42 34 0.57
43 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (41 bp):
CGAAAGACTACAGATGGCCCGAAGGACTTAATCATCTTGCT
Found at i:286721 original size:287 final size:285
Alignment explanation
Indices: 286102--286958 Score: 1214
Period size: 287 Copynumber: 3.0 Consensus size: 285
286092 TGATGGTCCG
* * * *
286102 ATTTTGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCGCTGTCTTACTTTTCAAAATTTTCA
1 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
* * *
286167 TTTTAAGAAAATACTAAATGAGAAAATTTGGAAATTACTTTCTCATTATGGGAAACTTTGAAAAT
66 TTTTCAGAAAATACTAAATGAGAAACTTTGGAAA-TACTTTTTCATTATGGGAAACTTTGAAAAT
* * * *
286232 TGTTTTCCCATTTTTAAATTTATGTGAAAACATCATACCCGAAGGTCTTA-AGATGGCCCGGAGG
130 CGTTTTCCCATTTTCAAATTTATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGG
* * * * * *
286296 ACTTATCATCTTGCTCAAAAGACTGAAAAATAACCCGAATGATTTAATTATCATGCTCGAGAGAC
195 ACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGAC
* * *
286361 ATACTGATGGCACGAATGACTTATCA
260 ATACTGATGGCCCGAAGGACTTACCA
*
286387 ATTTGGGAGATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
1 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
** * *
286452 TTTTCTTAAAATATTAAATGAGAAACTTTGGAAATCACTTTTTCATTATGAGAAACTTTGAAAAT
66 TTTTCAGAAAATACTAAATGAGAAACTTTGGAAAT-ACTTTTTCATTATGGGAAACTTTGAAAAT
* * *
286517 CATTTTCCCATTTTCCAAATTTATGTGAAAACATCCTACCCGAAGGACTTACAGATGGCTCGAAG
130 CGTTTTCCCATTTT-CAAATTTATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAG
* *
286582 GACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCATCTTGCTCGAAAGA
194 GACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGA
*
286647 CATACTGATGGCCCGAAGGAATTACCA
259 CATACTGATGGCCCGAAGGACTTACCA
* * * * * *
286674 ATTTGGGAAATCGTTTAATGGGTAAGAAATTTTTGAAATCACTTTCTTACTTTTCAAAAATTTCA
1 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
*
286739 TTTTCAGAAAATACTAAATGAGAAACTTTGGAAAT-CGTTTTCATATTATGGGAAACTTTGAAAA
66 TTTTCAGAAAATACTAAATGAGAAACTTTGGAAATACTTTTTC--ATTATGGGAAACTTTGAAAA
* * * * *
286803 TCGCTTTCCCATTTTTCAAATTTATATGAAAACATCCTACCCGAAGGTTTTACGGATGGCCCAAA
129 TCGTTTTCCCA-TTTTCAAATTTATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAA
*
286868 GGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAG
193 GGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAG
* * * *
286933 ACTTAGTGATAGCCTGAAGGACTTAC
258 ACATACTGATGGCCCGAAGGACTTAC
286959 TAAGTAAGAA
Statistics
Matches: 507, Mismatches: 59, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
284 1 0.00
285 134 0.26
286 33 0.07
287 335 0.66
288 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (285 bp):
ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
TTTTCAGAAAATACTAAATGAGAAACTTTGGAAATACTTTTTCATTATGGGAAACTTTGAAAATC
GTTTTCCCATTTTCAAATTTATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGA
CTTATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACA
TACTGATGGCCCGAAGGACTTACCA
Found at i:286953 original size:42 final size:41
Alignment explanation
Indices: 286852--286937 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 41
286842 CCCGAAGGTT
* * * *
286852 TTACGGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGAC
1 TTACAGATGACCCGAAGGACTTATCATCATGCTCAAAAGAC
* *
286893 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGAC
1 TTACAGATGACCCGAAGGACTT-ATCATCATGCTCAAAAGAC
286935 TTA
1 TTA
286938 GTGATAGCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 18 0.47
42 20 0.53
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (41 bp):
TTACAGATGACCCGAAGGACTTATCATCATGCTCAAAAGAC
Found at i:292945 original size:5 final size:5
Alignment explanation
Indices: 292935--292966 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
292925 ATTTAATATA
292935 AAAAT AAAAT AAAAT AAAAT --AAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
292967 CATAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:292950 original size:18 final size:19
Alignment explanation
Indices: 292929--292977 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
292919 AATTATATTT
292929 AATATAAA-AATAAAATAA
1 AATATAAATAATAAAATAA
292947 AATA-AAATAATAAAATAA
1 AATATAAATAATAAAATAA
*
292965 AACATAAGATAAT
1 AATATAA-ATAAT
292978 CTCTCAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 17 0.63
19 2 0.07
20 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AATATAAATAATAAAATAA
Found at i:292958 original size:13 final size:13
Alignment explanation
Indices: 292942--292966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
292932 ATAAAAATAA
292942 AATAAAATAAAAT
1 AATAAAATAAAAT
292955 AATAAAATAAAA
1 AATAAAATAAAA
292967 CATAAGATAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:295198 original size:10 final size:10
Alignment explanation
Indices: 295189--295242 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
295179 TTTGTAAAAT
295189 TAAT-ATAAA
1 TAATAATAAA
295198 TAATAATAAA
1 TAATAATAAA
295208 TAATAAT-AA
1 TAATAATAAA
*
295217 CAATAATATAA
1 TAATAATA-AA
295228 TAATAAT-AA
1 TAATAATAAA
295237 TAATAA
1 TAATAA
295243 CTCGGTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 20 0.50
10 12 0.30
11 8 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
TAATAATAAA
Found at i:295204 original size:3 final size:3
Alignment explanation
Indices: 295196--295242 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
295186 AATTAATATA
*
295196 AAT AAT AAT AAAT AAT AAT AAC AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
295241 AA
1 AA
295243 CTCGGTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:295227 original size:17 final size:17
Alignment explanation
Indices: 295196--295241 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
295186 AATTAATATA
295196 AATAATAATAA-ATAAT
1 AATAATAATAATATAAT
*
295212 AATAACAATAATATAAT
1 AATAATAATAATATAAT
295229 AATAATAATAATA
1 AATAATAATAATA
295242 ACTCGGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATATAAT
Found at i:295298 original size:3 final size:3
Alignment explanation
Indices: 295286--295400 Score: 63
Period size: 3 Copynumber: 36.7 Consensus size: 3
295276 ATATATATAT
* *
295286 ATA ATAA ATA ATA ATA ATA TATA ATA ATA ATA TTA ATA TTA ATAA ATA
1 ATA AT-A ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * * * *
295334 CTA ATA CT- ATA GATA ACA ATA ATA ATTA AT- GTT GTA ATTA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA
* *
295380 ACA ATA CTA ATA ATA GATA AT
1 ATA ATA ATA ATA ATA -ATA AT
295401 GAACCTATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
2 2 0.02
3 63 0.73
4 21 0.24
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:295305 original size:22 final size:24
Alignment explanation
Indices: 295280--295339 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
295270 TAGTATATAT
295280 ATATATATAATAA-A-TAATAATA
1 ATATATATAATAATATTAATAATA
*
295302 ATATATAATAATAATATTAATATTA
1 ATATAT-ATAATAATATTAATAATA
*
295327 ATAAATACTAATA
1 ATATATA-TAATA
295340 CTATAGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 6 0.19
23 7 0.22
24 2 0.06
25 17 0.53
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATATAATAATATTAATAATA
Found at i:295305 original size:28 final size:27
Alignment explanation
Indices: 295274--295359 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
295264 CAATACTAGT
295274 ATATATATATATATAATAAATAATAATA
1 ATATATA-ATATATAATAAATAATAATA
*
295302 ATATATAATA-ATAATATTAATATTAATA
1 ATATATAATATATAATA--AATAATAATA
*
295330 A-ATACTAATACTATAGAT-AACAATAATA
1 ATATA-TAATA-TATA-ATAAATAATAATA
295358 AT
1 AT
295360 TAATGTTGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 6 0.12
27 6 0.12
28 31 0.65
30 3 0.06
31 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (27 bp):
ATATATAATATATAATAAATAATAATA
Found at i:299143 original size:19 final size:21
Alignment explanation
Indices: 299104--299143 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
299094 GTTAATAAAA
*
299104 TTGGTATAATTACACATTTTT
1 TTGGTATAATTACAAATTTTT
299125 TTGG-ATAATT-CAAATTTTT
1 TTGGTATAATTACAAATTTTT
299144 ATTATCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (21 bp):
TTGGTATAATTACAAATTTTT
Found at i:303018 original size:87 final size:87
Alignment explanation
Indices: 302905--303070 Score: 242
Period size: 87 Copynumber: 1.9 Consensus size: 87
302895 CCTTAGGAGT
* * *
302905 ATGATCTTGTTGTTCCTCGTCGAGTTCTTTGTTTTCCTTTGCATGTTCATCAACATTTACACTAA
1 ATGATCTTGATGTTCCTCGTCGAGTTCTTTGTTTTCATTTGCATATTCATCAACATTTACACTAA
302970 GTTCATTCACATCAGTAACAGA
66 GTTCATTCACATCAGTAACAGA
* * * * **
302992 ATGATCTTGATGTTCCTCTTCTAGTTCTTTGTTTTCATTTGTATATTCATCAGCATTTGTACTAA
1 ATGATCTTGATGTTCCTCGTCGAGTTCTTTGTTTTCATTTGCATATTCATCAACATTTACACTAA
*
303057 TTTCATTCACATCA
66 GTTCATTCACATCA
303071 TTAGAAGGGA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.45
Consensus pattern (87 bp):
ATGATCTTGATGTTCCTCGTCGAGTTCTTTGTTTTCATTTGCATATTCATCAACATTTACACTAA
GTTCATTCACATCAGTAACAGA
Found at i:306290 original size:15 final size:16
Alignment explanation
Indices: 306270--306305 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
306260 TTTTAAATTT
306270 AATATT-AAAAGTAAA
1 AATATTAAAAAGTAAA
*
306285 AATATTAAAAATTAAA
1 AATATTAAAAAGTAAA
306301 AATAT
1 AATAT
306306 ATAACAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATATTAAAAAGTAAA
Found at i:307140 original size:8 final size:8
Alignment explanation
Indices: 307122--307246 Score: 53
Period size: 8 Copynumber: 14.8 Consensus size: 8
307112 ATGTTTTTAA
307122 AATATTTTT
1 AATA-TTTT
307131 AATATTTT
1 AATATTTT
*
307139 AATAATTT
1 AATATTTT
*
307147 -ATAGCTTGTG
1 AATA--TT-TT
307157 ATATATTTT
1 A-ATATTTT
307166 AAATTATTTT
1 -AA-TATTTT
* *
307176 GAT-CTTT
1 AATATTTT
307183 AATATTTAT
1 AATATTT-T
307192 ATATATATATT
1 A-ATAT-T-TT
307203 AAT-TTTT
1 AATATTTT
307210 -AT-TTTT
1 AATATTTT
*
307216 AATATTTG
1 AATATTTT
307224 AATATTTT
1 AATATTTT
*
307232 TATATTTT
1 AATATTTT
307240 AAATATT
1 -AATATT
307247 AAATTTAATT
Statistics
Matches: 89, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
6 6 0.07
7 12 0.13
8 32 0.36
9 16 0.18
10 16 0.18
11 3 0.03
12 4 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (8 bp):
AATATTTT
Found at i:307244 original size:17 final size:17
Alignment explanation
Indices: 307209--307246 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
307199 TATTAATTTT
*
307209 TATTTTTAATATTTGAA
1 TATTTTTAATATTTAAA
307226 TATTTTT-ATATTTTAAA
1 TATTTTTAATA-TTTAAA
307243 TATT
1 TATT
307247 AAATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TATTTTTAATATTTAAA
Found at i:309785 original size:16 final size:16
Alignment explanation
Indices: 309752--309804 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
309742 TAAATAATCC
* *
309752 GACTTGTTATTGACCT
1 GACTTGATATTTACCT
* *
309768 GATTTGATATTTATCT
1 GACTTGATATTTACCT
309784 GACTTGATATTTACCT
1 GACTTGATATTTACCT
309800 GACTT
1 GACTT
309805 ATAAGTTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (16 bp):
GACTTGATATTTACCT
Found at i:310099 original size:11 final size:12
Alignment explanation
Indices: 310043--310101 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 12
310033 ATAATTAAAT
310043 ATTTATAAATTTA
1 ATTTAT-AATTTA
*
310056 ATTTAT--TTTT
1 ATTTATAATTTA
*
310066 ATGTAATAA-TTA
1 AT-TTATAATTTA
310078 ATTTATAATTTA
1 ATTTATAATTTA
310090 A-TTATAATTTA
1 ATTTATAATTTA
310101 A
1 A
310102 CATAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
10 5 0.13
11 19 0.50
12 8 0.21
13 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
ATTTATAATTTA
Found at i:310283 original size:45 final size:44
Alignment explanation
Indices: 310232--310379 Score: 165
Period size: 45 Copynumber: 3.2 Consensus size: 44
310222 ATTATATTTG
*
310232 AGAATTTAGAGAGAAATTGAGAAATTTTGGGACATTAGGAAATTA
1 AGAATTTAGAGAGAAATTGGGAAATTTTGGGA-ATTAGGAAATTA
* * *
310277 AGAATTTAGAGAGAAATCGGGAAACTTTGGAAAGTT-GAGAAATTA
1 AGAATTTAGAGAGAAATTGGGAAATTTTGGGAA-TTAG-GAAATTA
* *
310322 AGAATTTAGAG-GAAATTTGGGAAATTTTGAGAATATAGGGAAATTG
1 AGAATTTAGAGAGAAA-TTGGGAAATTTTGGGAAT-TA-GGAAATTA
310368 AGAAATTTAGAG
1 AG-AATTTAGAG
310380 GGAATAGATA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
44 7 0.08
45 62 0.71
46 8 0.09
47 10 0.11
ACGTcount: A:0.44, C:0.02, G:0.26, T:0.28
Consensus pattern (44 bp):
AGAATTTAGAGAGAAATTGGGAAATTTTGGGAATTAGGAAATTA
Found at i:310372 original size:27 final size:29
Alignment explanation
Indices: 310305--310375 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 29
310295 GGGAAACTTT
*
310305 GGAAAGTTGAGAAA--TTAAGAATTTAGA
1 GGAAAGTTGAGAAATTTTAAGAATATAGA
* * *
310332 GGAAATTTGGGAAATTTTGAGAATATAG-
1 GGAAAGTTGAGAAATTTTAAGAATATAGA
310360 GGAAA-TTGAGAAATTT
1 GGAAAGTTGAGAAATTT
310376 AGAGGGAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.59
28 5 0.14
29 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.30
Consensus pattern (29 bp):
GGAAAGTTGAGAAATTTTAAGAATATAGA
Found at i:310396 original size:90 final size:90
Alignment explanation
Indices: 310232--310401 Score: 204
Period size: 90 Copynumber: 1.9 Consensus size: 90
310222 ATTATATTTG
* * *
310232 AGAATTTAGAGAGAAATTGAGAAATTTTGGGACATTAGGAAATTAAGAATTTAGAGAGAAATCGG
1 AGAATTTAGAGAGAAATTGAGAAATTTTGAGACATTAGGAAATTAAGAATTTAGAGAGAAATAGA
310297 GAAACTTTGGAAAGTTGAGAAATTA
66 GAAACTTTGGAAAGTTGAGAAATTA
* * *
310322 AGAATTTAGAG-GAAATTTGGGAAATTTTGAGA-ATATAGGGAAATTGAGAAATTTAGAG-GGAA
1 AGAATTTAGAGAGAAA-TTGAGAAATTTTGAGACAT-TA-GGAAATTAAG-AATTTAGAGAGAAA
* *
310384 TAGATAAA-TTTGGGAAGT
62 TAGAGAAACTTTGGAAAGT
310402 GAGCGTCAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
89 6 0.09
90 36 0.53
91 17 0.25
92 9 0.13
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.28
Consensus pattern (90 bp):
AGAATTTAGAGAGAAATTGAGAAATTTTGAGACATTAGGAAATTAAGAATTTAGAGAGAAATAGA
GAAACTTTGGAAAGTTGAGAAATTA
Found at i:310744 original size:2 final size:2
Alignment explanation
Indices: 310739--310835 Score: 74
Period size: 2 Copynumber: 48.0 Consensus size: 2
310729 TATACATCAC
* * * *
310739 AT AT AT AT ACT -T AC AT AT ACT -T AT AT AT AC AT AT TT AT GT AT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
310781 AT ACT TT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
310824 AT AT AC AT AT AT
1 AT AT AT AT AT AT
310836 TATTTTTCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
1 3 0.04
2 67 0.91
3 4 0.05
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:310940 original size:16 final size:18
Alignment explanation
Indices: 310921--310957 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
310911 ACATAATTAC
310921 ACACACACAT-A-TATAT
1 ACACACACATAAGTATAT
310937 ACACACACATAAGTATAT
1 ACACACACATAAGTATAT
310955 ACA
1 ACA
310958 TGCATCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.22
Consensus pattern (18 bp):
ACACACACATAAGTATAT
Found at i:310999 original size:12 final size:12
Alignment explanation
Indices: 310984--311061 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 12
310974 ACATACATGC
*
310984 ATATATATTCTT
1 ATATATATACTT
310996 ATATATATACTT
1 ATATATATACTT
*
311008 ATACTATATAGTT
1 ATA-TATATACTT
*
311021 -TATATACTTACAT
1 ATATATA--TACTT
311034 AT-TATATAC--
1 ATATATATACTT
311043 A-A-ATATACTT
1 ATATATATACTT
311053 ATATATATA
1 ATATATATA
311062 TATTTGTACT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
8 6 0.11
9 1 0.02
10 1 0.02
11 8 0.15
12 21 0.40
13 15 0.28
14 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.47
Consensus pattern (12 bp):
ATATATATACTT
Done.