Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002663.1 Hibiscus syriacus cultivar Beakdansim tig00005465_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: 975815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 4
Found at i:2812 original size:21 final size:21
Alignment explanation
Indices: 2786--2846 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
2776 TCCAGCAATT
2786 AGTGAATTCCAAGACCATATC
1 AGTGAATTCCAAGACCATATC
2807 AGTGAATATCC-AG--CA-ATC
1 AGTGAAT-TCCAAGACCATATC
2825 AGTGAATTCCAAGACCATATC
1 AGTGAATTCCAAGACCATATC
2846 A
1 A
2847 TCAAAAATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 3 0.09
18 12 0.34
19 2 0.06
20 2 0.06
21 13 0.37
22 3 0.09
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
AGTGAATTCCAAGACCATATC
Found at i:2827 original size:18 final size:17
Alignment explanation
Indices: 2776--2835 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 17
2766 ATCGGTGATA
*
2776 TCCAGCAATTAGTGAAT
1 TCCAGCAATCAGTGAAT
2793 TCCAAGACCATATCAGTGAAT
1 TCC-AG--CA-ATCAGTGAAT
2814 ATCCAGCAATCAGTGAAT
1 -TCCAGCAATCAGTGAAT
2832 TCCA
1 TCCA
2836 AGACCATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
17 7 0.19
18 12 0.32
19 2 0.05
20 2 0.05
21 11 0.30
22 3 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (17 bp):
TCCAGCAATCAGTGAAT
Found at i:21390 original size:9 final size:9
Alignment explanation
Indices: 21378--21415 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
21368 AAAAAAAAGG
21378 AAATGAAAA
1 AAATGAAAA
21387 AAATG--AA
1 AAATGAAAA
21394 AAATGAAAA
1 AAATGAAAA
*
21403 AAAAGAAAA
1 AAATGAAAA
21412 AAAT
1 AAAT
21416 AAATAAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAATGAAAA
Found at i:21412 original size:16 final size:16
Alignment explanation
Indices: 21356--21412 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
21346 TATTATACTT
21356 AAAAAAA-AAAAA--A
1 AAAAAAAGAAAAATGA
*
21369 AAAAAAAG-GAAATGA
1 AAAAAAAGAAAAATGA
*
21384 AAAAAATGAAAAATGA
1 AAAAAAAGAAAAATGA
21400 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
21413 AATAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 10 0.28
15 8 0.22
16 18 0.50
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAAAAAGAAAAATGA
Found at i:22553 original size:44 final size:44
Alignment explanation
Indices: 22505--22648 Score: 157
Period size: 44 Copynumber: 3.2 Consensus size: 44
22495 CCAGATCTCT
22505 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
* * * * * ** * *
22549 TCATCACGTAGGAACCATGTTATCACCTTTA-GATGGCCAGATC-TCT
1 TCATCACGTAAGAGCC--G-TGTCAACATTAGGATAACCAG-CCGTCC
22595 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
22639 TCATCACGTA
1 TCATCACGTA
22649 GGAACCGAGT
Statistics
Matches: 76, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
43 9 0.12
44 34 0.45
46 24 0.32
47 9 0.12
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (44 bp):
TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
Found at i:22605 original size:90 final size:93
Alignment explanation
Indices: 22493--22711 Score: 347
Period size: 90 Copynumber: 2.4 Consensus size: 93
22483 TCATCCCCTG
22493 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
22558 AGGAACC-ATGTTATCA-CCTT-T-AGAT
66 AGGAACCGA-GTTATCACCCTTCTAAGAT
*
22583 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
22648 AGGAACCGAGTTATCACCCTTCCTAAAGAT
66 AGGAACCGAGTTATCACCCTT-CT-AAGAT
* * *
22678 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
22712 CCCTTAGACG
Statistics
Matches: 118, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
90 78 0.66
91 5 0.04
93 1 0.01
95 34 0.29
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (93 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
AGGAACCGAGTTATCACCCTTCTAAGAT
Found at i:31424 original size:3 final size:3
Alignment explanation
Indices: 31418--31466 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
31408 CGAGTTTTGA
31418 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31466 A
1 A
31467 GTTGTTTCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:31622 original size:14 final size:14
Alignment explanation
Indices: 31603--31629 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31593 TGGCAAGGAC
31603 TAATTTCTTATTTT
1 TAATTTCTTATTTT
31617 TAATTTCTTATTT
1 TAATTTCTTATTT
31630 ATAGAACTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TAATTTCTTATTTT
Found at i:31622 original size:44 final size:44
Alignment explanation
Indices: 31566--31649 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
31556 TTATGATTAA
31566 TTATTTTTAATTTCTTATTTATAGAACTGGCAAGGACTAATTTC
1 TTATTTTTAATTTCTTATTTATAGAACTGGCAAGGACTAATTTC
31610 TTATTTTTAATTTCTTATTTATAGAACTGGCAAGGACTAA
1 TTATTTTTAATTTCTTATTTATAGAACTGGCAAGGACTAA
31650 GTTGTGGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (44 bp):
TTATTTTTAATTTCTTATTTATAGAACTGGCAAGGACTAATTTC
Found at i:33929 original size:21 final size:21
Alignment explanation
Indices: 33905--33965 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
33895 AACTTTGAAA
33905 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
33926 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
33940 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
33961 AAATG
1 AAATG
33966 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:33986 original size:36 final size:36
Alignment explanation
Indices: 33897--34015 Score: 188
Period size: 35 Copynumber: 3.3 Consensus size: 36
33887 TGGTAACCAA
33897 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
33934 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
33969 CTTTGAAAAATAGTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
34005 -GTTGAAAAATG
1 CTTTGAAAAATG
34016 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
35 44 0.57
36 28 0.36
37 5 0.06
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:38584 original size:19 final size:18
Alignment explanation
Indices: 38529--38585 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
38519 AAAAAATGGT
38529 TTTCAAATTTTGGTAAATG
1 TTTCAAA-TTTGGTAAATG
*
38548 TTTC---TTT-GAAAATGG
1 TTTCAAATTTGGTAAAT-G
38563 TTTCAAAGTTTGGTAAATG
1 TTTCAAA-TTTGGTAAATG
38582 TTTC
1 TTTC
38586 TTTGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 5 0.17
15 8 0.27
19 12 0.40
20 5 0.17
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (18 bp):
TTTCAAATTTGGTAAATG
Found at i:38613 original size:37 final size:36
Alignment explanation
Indices: 38514--38631 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 36
38504 TGGTAACCAA
* *
38514 CTTTGAAAAAATGGTTTTCAAATTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
38551 CTTTG-AAAAT-GGTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
38585 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
38622 -GTTGAAAAAT
1 CTTTGAAAAAT
38632 GATAATGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
34 27 0.36
35 10 0.14
36 10 0.14
37 27 0.36
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:39752 original size:18 final size:18
Alignment explanation
Indices: 39729--39798 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
39719 TATTTATGAG
39729 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
* *
39747 GGAATTGGAATATGTAAA
1 GGAATTGGAATCTGTGAA
* *
39765 TGAATTGAAATCTGTAGAAAA
1 GGAATTGGAATCTGT-G--AA
39786 TGGAATTGGAATC
1 -GGAATTGGAATC
39799 CAATTTCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 28 0.70
21 2 0.05
22 10 0.25
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:41095 original size:7 final size:7
Alignment explanation
Indices: 41083--41112 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
41073 TGTGTTGTTG
41083 ACTGATA
1 ACTGATA
41090 ACTGATA
1 ACTGATA
41097 ACTGATA
1 ACTGATA
41104 ACTGATA
1 ACTGATA
41111 AC
1 AC
41113 AGAAATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (7 bp):
ACTGATA
Found at i:41455 original size:197 final size:194
Alignment explanation
Indices: 41122--41508 Score: 668
Period size: 197 Copynumber: 2.0 Consensus size: 194
41112 CAGAAATGAA
*
41122 GTGATCTTATTATTATATATGTACCATAGGTTTAATTAATTATATATATATATATTTTGAAAATT
1 GTGATCTTATTATTATATATGTACCATAGGTTTAATTAATTATATATATATATATTTTGAAAAAT
41187 TGATTTATATATATATTAATAATGAGTGTTGTTTTCTGAAGCATTAGCAGCCGACAAGGGTCAAA
66 TGA-TTATATATATATTAATAATGAGTGTTGTTTTCTGAAGCATTAGCAGCCGACAAGGGTCAAA
* *
41252 TCTTTGCAGTTGTAAGATGAAAGACCACTTCCAATGGTACATTTTGCAGTAATTTATAGCATGGT
130 TCTTTGCAGTAGTAAGATGAAAGACCACTTCCAATGATACATTTTGCAGTAATTTATAGCATGGT
* * *
41317 GTGATCTTATTATTATATATGTACCATAGGTTTAATTAATTATATATTAATGTTTTTTTTTTGAA
1 GTGATCTTATTATTATATATGTACCATAGGTTTAATTAATTATATA-T-A--TATATATTTTGAA
41382 AAATTGA-TATATATATATTAATAATGAGTGTTGTTTTCTGAAGCATTAGCAGCCGACAAGGGTC
62 AAATTGATTATATATATATTAATAATGAGTGTTGTTTTCTGAAGCATTAGCAGCCGACAAGGGTC
41446 AAATCTTTGCAGTAGTAAGATGAAAGACCACTTCCAATGATACATTTTGCAGTAATTTATAGC
127 AAATCTTTGCAGTAGTAAGATGAAAGACCACTTCCAATGATACATTTTGCAGTAATTTATAGC
41509 TTTGGATAGT
Statistics
Matches: 182, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
195 46 0.25
196 1 0.01
197 119 0.65
199 16 0.09
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (194 bp):
GTGATCTTATTATTATATATGTACCATAGGTTTAATTAATTATATATATATATATTTTGAAAAAT
TGATTATATATATATTAATAATGAGTGTTGTTTTCTGAAGCATTAGCAGCCGACAAGGGTCAAAT
CTTTGCAGTAGTAAGATGAAAGACCACTTCCAATGATACATTTTGCAGTAATTTATAGCATGGT
Found at i:42122 original size:15 final size:15
Alignment explanation
Indices: 42102--42141 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
42092 CCGGATGTTA
42102 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
42117 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
42132 CGGGTACCCG
1 CGGGTACCCG
42142 ATACCCGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:42334 original size:19 final size:19
Alignment explanation
Indices: 42272--42334 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
42262 AAAATACAAA
*
42272 ATATAATAATCCA-TA-AT
1 ATATAATAATTCATTATAT
42289 ATA-AATAATTCATTATAT
1 ATATAATAATTCATTATAT
*
42307 -TTTATATAATT-ATATATAT
1 ATATA-ATAATTCAT-TATAT
42326 ATATAATAA
1 ATATAATAA
42335 AAATAAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 8 0.22
17 6 0.16
18 5 0.14
19 15 0.41
20 3 0.08
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAATAATTCATTATAT
Found at i:43820 original size:15 final size:16
Alignment explanation
Indices: 43791--43823 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
43781 ATCTCACAAG
*
43791 ATTAATATTTGTAAAT
1 ATTAATATTTCTAAAT
43807 ATTAA-ATTTCTAAAT
1 ATTAATATTTCTAAAT
43822 AT
1 AT
43824 ATATTCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTAATATTTCTAAAT
Found at i:44080 original size:13 final size:13
Alignment explanation
Indices: 44035--44082 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
44025 ATATAAACAA
*
44035 TTAATCAAATCAA
1 TTAATCAAATCAG
**
44048 TTTTTCAAATCAG
1 TTAATCAAATCAG
*
44061 CTAATCAAATCAG
1 TTAATCAAATCAG
*
44074 TTGATCAAA
1 TTAATCAAA
44083 CCGGCTACTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (13 bp):
TTAATCAAATCAG
Found at i:44089 original size:26 final size:26
Alignment explanation
Indices: 44036--44089 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
44026 TATAAACAAT
** *
44036 TAATCAAATCAATTTTTCAAATCAGC
1 TAATCAAATCAATTGATCAAACCAGC
* *
44062 TAATCAAATCAGTTGATCAAACCGGC
1 TAATCAAATCAATTGATCAAACCAGC
44088 TA
1 TA
44090 CTAGAATCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (26 bp):
TAATCAAATCAATTGATCAAACCAGC
Found at i:48554 original size:13 final size:14
Alignment explanation
Indices: 48530--48558 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
48520 ACAAAAACTC
48530 AATGAAAGAACTAA
1 AATGAAAGAACTAA
48544 AATGAAA-AACTAA
1 AATGAAAGAACTAA
48557 AA
1 AA
48559 CTTTACCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (14 bp):
AATGAAAGAACTAA
Found at i:49502 original size:26 final size:27
Alignment explanation
Indices: 49451--49507 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
49441 ACGAAAAAGA
49451 GGGAAACCCCACATGGTATTAAATTACAG
1 GGGAAACCCCACA--GTATTAAATTACAG
*
49480 GGGAAACCCCAC-GTATTAAATTATAG
1 GGGAAACCCCACAGTATTAAATTACAG
49506 GG
1 GG
49508 CAAAATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.56
29 12 0.44
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (27 bp):
GGGAAACCCCACAGTATTAAATTACAG
Found at i:54492 original size:32 final size:32
Alignment explanation
Indices: 54451--54518 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
54441 TTCATTAGTC
*
54451 AGTTAAATTGCTCTATCATACTGGATCTGTAT
1 AGTTAAATTGCTCTATCACACTGGATCTGTAT
*
54483 AGTTAAATTGCTTTATCACACTGGATCTGTAT
1 AGTTAAATTGCTCTATCACACTGGATCTGTAT
54515 AGTT
1 AGTT
54519 TTTTTAACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (32 bp):
AGTTAAATTGCTCTATCACACTGGATCTGTAT
Found at i:60202 original size:2 final size:2
Alignment explanation
Indices: 60197--60222 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60187 AGATAATTGT
60197 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
60223 CCAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66934 original size:28 final size:28
Alignment explanation
Indices: 66894--66951 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
66884 GTTTTTCTCA
66894 TTTTCCTGTGTTTGATAGCCGGAAAATG
1 TTTTCCTGTGTTTGATAGCCGGAAAATG
66922 TTTTCCTGTGTTTGATAGCCGGAAAATG
1 TTTTCCTGTGTTTGATAGCCGGAAAATG
66950 TT
1 TT
66952 CTCCGGGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (28 bp):
TTTTCCTGTGTTTGATAGCCGGAAAATG
Found at i:76703 original size:19 final size:19
Alignment explanation
Indices: 76679--76757 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 19
76669 TCGATTTTGA
76679 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
76698 AAAATGTGTTGCGAGAGCTT
1 AAAATGTGTTGCGATAG-TT
* *
76718 GAAAAACGTGTTGTTGTGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
*
76742 AAAAAGTGTTGCGATA
1 AAAATGTGTTGCGATA
76758 ATGAAAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
19 25 0.52
20 3 0.06
22 8 0.17
24 3 0.06
25 9 0.19
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:76762 original size:19 final size:19
Alignment explanation
Indices: 76729--76765 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
76719 AAAAACGTGT
* *
76729 TGTTGTGATAGTGAAAAAG
1 TGTTGCGATAATGAAAAAG
76748 TGTTGCGATAATGAAAAA
1 TGTTGCGATAATGAAAAA
76766 TCCAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.30
Consensus pattern (19 bp):
TGTTGCGATAATGAAAAAG
Found at i:77240 original size:40 final size:40
Alignment explanation
Indices: 77185--77263 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
77175 GATTTTAGAA
* *
77185 GACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTC
77225 GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTT
1 GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTT
77264 TGAACATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTC
Found at i:77325 original size:21 final size:19
Alignment explanation
Indices: 77271--77360 Score: 72
Period size: 19 Copynumber: 4.5 Consensus size: 19
77261 CTTTGAACAT
**
77271 GAACTTCGACTATCGCAAC
1 GAACTTCGAAAATCGCAAC
* *
77290 GAATTTAGAAAATCGCAACGC
1 GAACTTCGAAAATCGCAA--C
**
77311 GAACTTCGACTATCGCAAC
1 GAACTTCGAAAATCGCAAC
* *
77330 GAATTTGGAAAATCGCAACGC
1 GAACTTCGAAAATCGCAA--C
77351 GAACTTCGAA
1 GAACTTCGAA
77361 CCTGAACTTA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 29 0.55
21 24 0.45
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (19 bp):
GAACTTCGAAAATCGCAAC
Found at i:77326 original size:40 final size:40
Alignment explanation
Indices: 77271--77359 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
77261 CTTTGAACAT
77271 GAACTTCGACTATCGCAACGAATTTAGAAAATCGCAACGC
1 GAACTTCGACTATCGCAACGAATTTAGAAAATCGCAACGC
*
77311 GAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGC
1 GAACTTCGACTATCGCAACGAATTTAGAAAATCGCAACGC
77351 GAACTTCGA
1 GAACTTCGA
77360 ACCTGAACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
GAACTTCGACTATCGCAACGAATTTAGAAAATCGCAACGC
Found at i:77344 original size:93 final size:93
Alignment explanation
Indices: 77184--77454 Score: 407
Period size: 93 Copynumber: 2.9 Consensus size: 93
77174 CGATTTTAGA
* *
77184 AGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGAAAAA
1 AGACTATCGCAACGAATTTAGAAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAAA
*
77249 TCGCAACGCGAACTTTGAACATGAACTT
66 TCGCAACGCGAACTTCGAACATGAACTT
* *
77277 CGACTATCGCAACGAATTTAGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAA
1 AGACTATCGCAACGAATTTAGAAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAAA
*
77342 TCGCAACGCGAACTTCGAACCTGAACTT
66 TCGCAACGCGAACTTCGAACATGAACTT
* * *** * *
77370 AGACTATCGCAACGCGAACTTCGGCTATCTCAACGTGAACTTGGACTATCGCAACGAATTTGGAA
1 AGACTATCGCAA--CGAATTTAGAAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAA
77435 AATCGCAACGCGAACTTCGA
64 AATCGCAACGCGAACTTCGA
77455 CTATCGCAAC
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
93 98 0.61
95 63 0.39
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (93 bp):
AGACTATCGCAACGAATTTAGAAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAAA
TCGCAACGCGAACTTCGAACATGAACTT
Found at i:77390 original size:21 final size:21
Alignment explanation
Indices: 77364--77486 Score: 144
Period size: 21 Copynumber: 6.0 Consensus size: 21
77354 CTTCGAACCT
*
77364 GAACTTAGACTATCGCAACGC
1 GAACTTGGACTATCGCAACGC
* *
77385 GAACTTCGG-CTATCTCAACGT
1 GAACTT-GGACTATCGCAACGC
77406 GAACTTGGACTATCGCAA--C
1 GAACTTGGACTATCGCAACGC
* **
77425 GAATTTGGAAAATCGCAACGC
1 GAACTTGGACTATCGCAACGC
* *
77446 GAACTTCGACTATCGCAACGT
1 GAACTTGGACTATCGCAACGC
77467 GAACTTGGACTATCGCAACG
1 GAACTTGGACTATCGCAACG
77487 AATTTGGACT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.18
20 2 0.02
21 66 0.79
22 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
GAACTTGGACTATCGCAACGC
Found at i:77470 original size:61 final size:61
Alignment explanation
Indices: 77375--77494 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 61
77365 AACTTAGACT
* *
77375 ATCGCAACGCGAACTTCGGCTATCTCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
77436 ATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGA
77495 CTAACGTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (61 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:77510 original size:35 final size:36
Alignment explanation
Indices: 77429--77541 Score: 93
Period size: 35 Copynumber: 3.0 Consensus size: 36
77419 CGCAACGAAT
* *
77429 TTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAAC
1 TTGGAAAATCGCAAC-CGAACTTGGAC--T---AACGTAAAC
** * *
77471 TTGGACTATCGCAA-CGAATTTGGACTAACGTAAAT
1 TTGGAAAATCGCAACCGAACTTGGACTAACGTAAAC
*
77506 TTGGAAAATCGCAACGCGAACTTGGACTATCGTAAA
1 TTGGAAAATCGCAAC-CGAACTTGGACTAACGTAAA
77542 ATCACGTTGC
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
35 19 0.32
37 18 0.31
38 1 0.02
40 9 0.15
42 12 0.20
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (36 bp):
TTGGAAAATCGCAACCGAACTTGGACTAACGTAAAC
Found at i:85305 original size:36 final size:36
Alignment explanation
Indices: 85258--85329 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
85248 TGGTGATTGT
85258 TTGCAGTAATATGTTCTGAAAAGTTATAGCTTCCAC
1 TTGCAGTAATATGTTCTGAAAAGTTATAGCTTCCAC
85294 TTGCAGTAATATGTTCTGAAAAGTTATAGCTTCCAC
1 TTGCAGTAATATGTTCTGAAAAGTTATAGCTTCCAC
85330 CAGAGACCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (36 bp):
TTGCAGTAATATGTTCTGAAAAGTTATAGCTTCCAC
Found at i:109983 original size:5 final size:5
Alignment explanation
Indices: 109973--110014 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
109963 GGGTCACTTA
109973 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CC
1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CC
110015 AGGACCATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCTC
Found at i:119180 original size:23 final size:23
Alignment explanation
Indices: 119154--119206 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
119144 AGGGTAGATC
119154 AAAAGATTGAATTCAAGAAGCTT
1 AAAAGATTGAATTCAAGAAGCTT
119177 AAAAGATTGAATTCAAGAAGCTT
1 AAAAGATTGAATTCAAGAAGCTT
119200 AAAAGAT
1 AAAAGAT
119207 CTGATATGAT
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:0.51, C:0.08, G:0.17, T:0.25
Consensus pattern (23 bp):
AAAAGATTGAATTCAAGAAGCTT
Found at i:119593 original size:22 final size:22
Alignment explanation
Indices: 119567--119609 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
119557 TAATAAATTA
119567 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
119589 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
119610 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:119618 original size:22 final size:22
Alignment explanation
Indices: 119569--119617 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
119559 ATAAATTATT
**
119569 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
119591 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
119614 TAAA
1 TAAA
119618 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:119661 original size:80 final size:80
Alignment explanation
Indices: 119572--119722 Score: 302
Period size: 80 Copynumber: 1.9 Consensus size: 80
119562 AATTATTTAA
119572 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
119637 CCATACAACTACAAT
66 CCATACAACTACAAT
119652 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
119717 CCATAC
66 CCATAC
119723 TAATAAATTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:119698 original size:22 final size:23
Alignment explanation
Indices: 119623--119697 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
119613 ATAAATTATT
119623 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
119645 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
119671 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
119694 TAAA
1 TAAA
119698 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:119713 original size:112 final size:112
Alignment explanation
Indices: 119589--119829 Score: 464
Period size: 112 Copynumber: 2.2 Consensus size: 112
119579 CAATCCATAT
*
119589 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAAAA
119654 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
66 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
*
119701 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAAAA
119766 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
66 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
119813 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
119830 TATAAAACTA
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 127 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (112 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAAAA
TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:119785 original size:80 final size:80
Alignment explanation
Indices: 119701--119990 Score: 440
Period size: 80 Copynumber: 3.5 Consensus size: 80
119691 TAATAAATTA
119701 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAAAA
119766 TAAATCAATCCATAT
66 TAAATCAATCCATAT
* *
119781 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA-TCTATAAAACTACAATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTC-ATACAACTACAAAA
*
119845 ATAAATCAATCAATAT
65 ATAAATCAATCCATAT
* * *
119861 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAGCAATTCATACTAA-TAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAC-AACT--A-CA
119925 TTTAAAATAAATCAATCCATAT
62 ---AAAATAAATCAATCCATAT
119947 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
119991 TATTTTAAAA
Statistics
Matches: 190, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
79 2 0.01
80 123 0.65
81 4 0.02
82 1 0.01
83 1 0.01
86 59 0.31
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (80 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAAAA
TAAATCAATCCATAT
Found at i:119803 original size:192 final size:192
Alignment explanation
Indices: 119570--119945 Score: 689
Period size: 192 Copynumber: 2.0 Consensus size: 192
119560 TAAATTATTT
119570 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
119635 ATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
66 ATCCATAAAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATT
* *
119700 ATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACA
131 ATTTAAAATAAAGCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
119762 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
119827 ATCTATAAAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATTCATACTAATAAATT
66 ATCCATAAAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATT
*
119892 ATTTAAAATAAAGCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATA
131 ATTTAAAATAAAGCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
119946 TTTTAAAATA
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 177 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (192 bp):
AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
ATCCATAAAACTACAATAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATT
ATTTAAAATAAAGCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
Found at i:119810 original size:22 final size:22
Alignment explanation
Indices: 119735--119809 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
119725 ATAAATTATT
* *
119735 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
119757 CTACAAAAATAAATCAATCCATATTT
1 -T---AAAATAAATCAATCCATATAA
119783 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
119806 TAAA
1 TAAA
119810 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 18 0.43
23 6 0.14
25 1 0.02
26 17 0.40
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:119887 original size:18 final size:18
Alignment explanation
Indices: 119866--119922 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
119856 AATATTTTAA
119866 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
119884 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
*
119898 AATAAAGCAATTCATACT
1 AATAAATCAATTCATACT
119916 AATAAAT
1 AATAAAT
119923 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 6 0.21
15 5 0.17
17 5 0.17
18 13 0.45
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:119897 original size:112 final size:112
Alignment explanation
Indices: 119589--119945 Score: 413
Period size: 112 Copynumber: 3.2 Consensus size: 112
119579 CAATCCATAT
* * * * *
119589 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACAAATAAATTATATAAAATAAATCAATTCATACAAATACAAAAA
**
119654 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
66 TAAATCAATAAATATTTTAAAATAAATCAATCCATACTAATAAATTA
* * *
119701 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAAAA
1 TTTAAAATAAATCAATCCATACAAATAAATTATATAAAATAAATCAATTCATACAAATACAAAAA
**
119766 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
66 TAAATCAATAAATATTTTAAAATAAATCAATCCATACTAATAAATTA
* * **
119813 TTTAAAATAAATCAATCTATA-AAACTACAA-TA-AT-AAATCAATCAATATTTTA-AAATA-AA
1 TTTAAAATAAATCAATCCATACAAA-TA-AATTATATAAAATAAATCAAT-TCATACAAATACAA
* ** * *
119872 TCAATTCATACTAATAAAT-TATTTAAAATAAAGCAATTCATACTAATAAATTA
63 -AAATAAAT-C-AATAAATAT-TTTAAAATAAATCAATCCATACTAATAAATTA
119925 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
119946 TTTTAAAATA
Statistics
Matches: 221, Mismatches: 17, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
109 2 0.01
110 20 0.09
111 8 0.04
112 189 0.86
113 2 0.01
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (112 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATATAAAATAAATCAATTCATACAAATACAAAAA
TAAATCAATAAATATTTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:119951 original size:22 final size:22
Alignment explanation
Indices: 119925--120027 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
119915 TAATAAATTA
119925 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
119947 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
119970 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
*
119994 TTTAAAATAAATCAATCCATGT
1 TTTAAAATAAATCAATCCATAT
*
120016 TTTATAATAAAT
1 TTTAAAATAAAT
120028 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 34 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:119999 original size:15 final size:15
Alignment explanation
Indices: 119970--120057 Score: 88
Period size: 15 Copynumber: 5.5 Consensus size: 15
119960 AATCCATACT
119970 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
119984 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
119999 AATAAATCAATCCATGTTTTAT
1 AATAAAT---T--A--TTTTAA
120021 AATAAATTATTTTAA
1 AATAAATTATTTTAA
120036 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
120051 ACTAAAT
1 AATAAAT
120058 AACCTTATTA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
14 9 0.14
15 38 0.60
17 1 0.02
18 1 0.02
19 1 0.02
20 1 0.02
22 12 0.19
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:121481 original size:3 final size:3
Alignment explanation
Indices: 121473--121574 Score: 143
Period size: 3 Copynumber: 33.7 Consensus size: 3
121463 TTTTTATCCA
*
121473 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * *
121519 TAA TAT TAT TA- TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TTT TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
121567 TAT TAT TA
1 TAT TAT TA
121575 AATATATTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.02
3 80 0.91
4 6 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:127349 original size:18 final size:18
Alignment explanation
Indices: 127313--127357 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
127303 CTATTTCAAG
*
127313 TTCAATTTA--TTTGAGA
1 TTCAATTTATTTTTGAAA
127329 TTCAATTTATTTTTGAAA
1 TTCAATTTATTTTTGAAA
127347 TTCAATTTATT
1 TTCAATTTATT
127358 CTTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
18 17 0.65
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:128288 original size:83 final size:82
Alignment explanation
Indices: 128102--128445 Score: 521
Period size: 83 Copynumber: 4.2 Consensus size: 82
128092 ACATTAAATG
* * * *
128102 GAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGACCTGGTT-TAGCA
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTATA-CA
128166 GAACAAGCATTGAATTTA
65 GAACAAGCATTGAATTTA
* *
128184 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATATAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTATACAG
128249 AACCAAGCATTGAATTTA
66 AA-CAAGCATTGAATTTA
* *
128267 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATATAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTATACAG
*
128332 AACCAAGCATTGAATTTG
66 AA-CAAGCATTGAATTTA
* **
128350 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTATACAG
*
128415 AACAATCATTGAATTT-
66 AACAAGCATTGAATTTA
128431 GAAAGATGAATTTGC
1 G-AAGATGAATTTGC
128446 TCATAGTAAA
Statistics
Matches: 246, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.00
82 84 0.34
83 161 0.65
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (82 bp):
GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTATACAG
AACAAGCATTGAATTTA
Found at i:128427 original size:165 final size:164
Alignment explanation
Indices: 128102--128445 Score: 521
Period size: 165 Copynumber: 2.1 Consensus size: 164
128092 ACATTAAATG
* *
128102 GAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGACCTGGTTTAGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGACCTGATTTAGCAG
128167 AACAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 AACAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * *
128232 TTGATCTGATTATATAGAACCAAGCATTGAATTT
131 CTGATCTGATTAGACAGAACCAAGCATTGAATTT
* * * *
128266 AGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATA-T
1 -GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGACCTGATT-TAGC
*
128330 AGAACCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
64 AGAA-CAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* * *
128395 TATCTGATCTGGTTGGACAGAA-CAATCATTGAATTT
128 TATCTGATCTGATTAGACAGAACCAAGCATTGAATTT
128431 GAAAGATGAATTTGC
1 G-AAGATGAATTTGC
128446 TCATAGTAAA
Statistics
Matches: 163, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
164 1 0.01
165 84 0.52
166 78 0.48
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (164 bp):
GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGACCTGATTTAGCAG
AACAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTAGACAGAACCAAGCATTGAATTT
Found at i:129256 original size:113 final size:113
Alignment explanation
Indices: 129058--129507 Score: 731
Period size: 113 Copynumber: 4.0 Consensus size: 113
129048 TAGCAAAGAT
* * *
129058 TTGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTGGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
129123 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * *
129171 TTGAATCCGTCATTGGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTGGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
129236 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* *
129284 TTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTGGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
129349 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * * * *
129397 CTGAATCCATCATTTGG-TGAATCATCATTGCCAGAGAAAGTTCATGAATGAAAAGAACTCATCT
1 TTGAATCCATCA-TTGGATGGATCAGCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCT
**
129461 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
129508 GTTTGATATT
Statistics
Matches: 316, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
113 251 0.79
114 65 0.21
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TTGAATCCATCATTGGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
Found at i:129803 original size:3 final size:3
Alignment explanation
Indices: 129795--129895 Score: 129
Period size: 3 Copynumber: 34.7 Consensus size: 3
129785 TTTTTATCCA
* * *
129795 TAT TAT TAT TA- TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
129842 TAT TAT TA- TAT TAT TAT T-T TA- TAT TAT TAT TAT TAT TAT TTT TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
129888 TAT TAT TA
1 TAT TAT TA
129896 AATATATTAC
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
2 8 0.09
3 74 0.87
4 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:135516 original size:20 final size:20
Alignment explanation
Indices: 135491--135541 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
135481 ATAATTATAT
135491 CTTTGTGACATGTTCTTTGC
1 CTTTGTGACATGTTCTTTGC
135511 CTTTGTGACATGTTCTTTGC
1 CTTTGTGACATGTTCTTTGC
135531 CTTTGTGACAT
1 CTTTGTGACAT
135542 ATTTATCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.49
Consensus pattern (20 bp):
CTTTGTGACATGTTCTTTGC
Found at i:135579 original size:23 final size:23
Alignment explanation
Indices: 135531--135580 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
135521 TGTTCTTTGC
*
135531 CTTTGTGACATATTTATCTATGT
1 CTTTGTGACATATTTATCTATAT
* * *
135554 CTTTGTGACATGTTTTTCTCTAT
1 CTTTGTGACATATTTATCTATAT
135577 CTTT
1 CTTT
135581 TGGCAGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (23 bp):
CTTTGTGACATATTTATCTATAT
Found at i:136612 original size:15 final size:14
Alignment explanation
Indices: 136592--136636 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 14
136582 GGACATGAAC
136592 AATAAAAATAAAATT
1 AATAAAAATAAAA-T
136607 AATAAAAATAATAAT
1 AATAAAAATAA-AAT
136622 AATACTAAAATAAAA
1 AATA--AAAATAAAA
136637 AAAATGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 16 0.59
16 4 0.15
17 7 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAATAAAAT
Found at i:136700 original size:38 final size:39
Alignment explanation
Indices: 136658--136748 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 39
136648 TATAATAATA
*
136658 AAAAATATTTTTCAAAAACCTATA-TA-ATATATATTTTC
1 AAAAATA-TTTTCAAAAACATATATTATATATATATTTTC
** * *
136696 AAAAATATTTT-AAAATTATATATTATATATATTTTTTT
1 AAAAATATTTTCAAAAACATATATTATATATATATTTTC
136734 AAAAATATTTTCAAA
1 AAAAATATTTTCAAA
136749 CTCATAGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 8 0.18
37 6 0.13
38 28 0.62
39 3 0.07
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (39 bp):
AAAAATATTTTCAAAAACATATATTATATATATATTTTC
Found at i:136831 original size:38 final size:36
Alignment explanation
Indices: 136776--136871 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 36
136766 GTTTTGAAAT
*
136776 TATATGTTATATGTTTTCAAAAATGACTTCAAAAAC
1 TATATATTATATGTTTTCAAAAATGACTTCAAAAAC
**
136812 TATATAATATATATGTTTTCAAAAATGTTTTCAAAAAC
1 TATAT-AT-TATATGTTTTCAAAAATGACTTCAAAAAC
*
136850 TATATATTATATATTTTCAAAA
1 TATATATTATATGTTTTCAAAA
136872 TGTTTTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
36 19 0.35
37 3 0.06
38 32 0.59
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (36 bp):
TATATATTATATGTTTTCAAAAATGACTTCAAAAAC
Found at i:136841 original size:12 final size:12
Alignment explanation
Indices: 136824--136848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
136814 TATAATATAT
136824 ATGTTTTCAAAA
1 ATGTTTTCAAAA
136836 ATGTTTTCAAAA
1 ATGTTTTCAAAA
136848 A
1 A
136849 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:136886 original size:38 final size:36
Alignment explanation
Indices: 136806--136914 Score: 105
Period size: 41 Copynumber: 2.8 Consensus size: 36
136796 AAATGACTTC
* *
136806 AAAAACTATATAATATATATGTTTTCAAAAATGTTTT-C
1 AAAAACTATAT-AT-TATATATTTTC-AAAATGTTTTAA
136844 AAAAACTATATATTATATATTTTCAAAATGTTTTTTTAAAA
1 AAAAACTATATATTATATATTTTCAAAATG---TTTT--AA
136885 AAAAAC-ATATATTATATAGTTTTCAAAATG
1 AAAAACTATATATTATATA-TTTTCAAAATG
136915 ATTTCAAACT
Statistics
Matches: 62, Mismatches: 2, Indels: 11
0.83 0.03 0.15
Matches are distributed among these distances:
35 6 0.10
36 10 0.16
37 2 0.03
38 15 0.24
40 12 0.19
41 17 0.27
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAAACTATATATTATATATTTTCAAAATGTTTTAA
Found at i:137807 original size:85 final size:83
Alignment explanation
Indices: 137481--138343 Score: 822
Period size: 85 Copynumber: 10.5 Consensus size: 83
137471 ATGATTTTAT
* * * * * * * * **
137481 TGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAAC
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
** *
137546 CGAACTCGGGGGTCTTTCT
66 CGAACTCGAAGGTCTTT-G
* * * *
137565 TGACGGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
**
137630 CGAACTCGGGGGTCTTTG
66 CGAACTCGAAGGTCTTTG
* * * * * *
137648 -G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
*
137710 CGAACTCAAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTT-G
* * * * * *
137730 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
137795 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTT-G
* * *
137815 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
*
137880 CGAACTCAAAGGTCTTTTG
66 CGAACTCGAAGGTC-TTTG
* * * * * * * * *
137899 TTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TGA-CAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAG
* **
137964 TCGAACTTGGGGGTCTTTG
65 TCGAACTCGAAGGTCTTTG
* * * * * *
137983 -GA-AGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
138045 CGAACTCGAAGGTCTTTG
66 CGAACTCGAAGGTCTTTG
* * * *
138063 -G-CAGATAGCCC-T-T---CTTAAGCTATTCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
* **
138121 CGAACTTGGGGGTCTTCTGG
66 CGAACTCGAAGGTCTT-T-G
* * *
138141 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
* **
138206 CAAACTCGGGGGTCTTTG
66 CGAACTCGAAGGTCTTTG
* * * * * *
138224 -G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
* *
138286 CGAACTCAAAGGTCTTGG
66 CGAACTCGAAGGTCTTTG
* * *
138304 TGGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 T-GACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAAT
138344 AGTTTGTTTA
Statistics
Matches: 657, Mismatches: 102, Indels: 41
0.82 0.13 0.05
Matches are distributed among these distances:
75 25 0.04
76 28 0.04
77 1 0.00
78 2 0.00
79 2 0.00
80 107 0.16
81 110 0.17
82 5 0.01
83 34 0.05
84 112 0.17
85 231 0.35
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (83 bp):
TGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTG
Found at i:138219 original size:241 final size:240
Alignment explanation
Indices: 137592--138321 Score: 856
Period size: 241 Copynumber: 3.0 Consensus size: 240
137582 AGCCTTGAGT
*
137592 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGGGGGTCTTTG-G-CAGATA
1 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGGGGGTCTTTGTGACAGATA
* * * * * **
137655 GCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAA
66 ACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGG
* * * * * * * * * * *
137719 AGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAG
131 GGGTC-TTT-G-GA-AGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAG
* * * * *
137784 CTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
191 CTGAGCGTAGTCGAACTCGAAGGTC-TTTGG-G-CAGATAGCCC-T-T---CTTAAGC
* *** *
137842 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGA
1 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGGGGGTC-TTTGTGA-CAGA
* * * *
137907 TAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTT
64 TAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTC
*
137972 GGGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTG
129 GGGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTG
138037 AGCGTAGTCGAACTCGAAGGTCTTT-GGCAGATAGCCCTTCTTAAGC
194 AGCGTAGTCGAACTCGAAGGTCTTTGGGCAGATAGCCCTTCTTAAGC
* * * *
138083 TATTCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTCTGGTGACAGA
1 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGGGGGTCTT-T-GTGACAGA
* * * * *
138148 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCAAACTC
64 TAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTC
*
138213 GGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTG
129 GGGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTG
*
138278 AGCGTAGTCGAACTCAAAGGTCTTGGTGGGCAGATAGCCCTTCT
194 AGCGTAGTCGAACTCGAAGGTCTT--TGGGCAGATAGCCCTTCT
138322 GGCCTTGAGC
Statistics
Matches: 419, Mismatches: 51, Indels: 26
0.84 0.10 0.05
Matches are distributed among these distances:
240 2 0.00
241 196 0.47
242 3 0.01
243 1 0.00
244 17 0.04
245 1 0.00
246 9 0.02
247 1 0.00
248 1 0.00
249 3 0.01
250 78 0.19
251 37 0.09
252 2 0.00
253 1 0.00
254 42 0.10
255 25 0.06
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (240 bp):
TATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGGGGGTCTTTGTGACAGATA
ACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGG
GGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAG
CGTAGTCGAACTCGAAGGTCTTTGGGCAGATAGCCCTTCTTAAGC
Found at i:141713 original size:18 final size:19
Alignment explanation
Indices: 141672--141716 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
141662 AGTTAATGTG
141672 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
141691 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
141709 AATGCAAA
1 AATGCAAA
141717 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:144074 original size:38 final size:39
Alignment explanation
Indices: 144027--144118 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 39
144017 ATAATAATAA
*
144027 AAAATATATTTTTCAAAAACCTATA-TA-ATATATATTTTC
1 AAAA-ATA-TTTTCAAAAACATATATTATATATATATTTTC
** * *
144066 AAAAATATTTT-AAAATTATATATTATATATATTTTTTT
1 AAAAATATTTTCAAAAACATATATTATATATATATTTTC
144104 AAAAATATTTTCAAA
1 AAAAATATTTTCAAA
144119 CTCATAGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 8 0.18
37 6 0.13
38 24 0.53
39 7 0.16
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (39 bp):
AAAAATATTTTCAAAAACATATATTATATATATATTTTC
Found at i:144201 original size:38 final size:36
Alignment explanation
Indices: 144146--144241 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 36
144136 GTTTTGAAAT
*
144146 TATATGTTATATGTTTTCAAAAATGACTTCAAAAAC
1 TATATATTATATGTTTTCAAAAATGACTTCAAAAAC
**
144182 TATATAATATATATGTTTTCAAAAATGTTTTCAAAAAC
1 TATAT-AT-TATATGTTTTCAAAAATGACTTCAAAAAC
*
144220 TATATATTATATATTTTCAAAA
1 TATATATTATATGTTTTCAAAA
144242 TGTTTTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
36 19 0.35
37 3 0.06
38 32 0.59
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (36 bp):
TATATATTATATGTTTTCAAAAATGACTTCAAAAAC
Found at i:144211 original size:12 final size:12
Alignment explanation
Indices: 144194--144218 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
144184 TATAATATAT
144194 ATGTTTTCAAAA
1 ATGTTTTCAAAA
144206 ATGTTTTCAAAA
1 ATGTTTTCAAAA
144218 A
1 A
144219 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:144256 original size:38 final size:36
Alignment explanation
Indices: 144176--144285 Score: 98
Period size: 42 Copynumber: 2.8 Consensus size: 36
144166 AAATGACTTC
* *
144176 AAAAACTATATAATATATATGTTTTCAAAAATGTTTT-C
1 AAAAACTATAT-AT-TATATATTTTC-AAAATGTTTTAA
144214 AAAAACTATATATTATATATTTTCAAAATGTTTTTTTAAAAA
1 AAAAACTATATATTATATATTTTCAAAATG---TTTT---AA
144256 AAAAAC-ATATATTATATAGTTTTCAAAATG
1 AAAAACTATATATTATATA-TTTTCAAAATG
144286 ATTTCAAACT
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
35 6 0.10
36 10 0.16
37 2 0.03
38 15 0.24
41 12 0.19
42 17 0.27
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAAACTATATATTATATATTTTCAAAATGTTTTAA
Found at i:159369 original size:190 final size:188
Alignment explanation
Indices: 159042--159419 Score: 607
Period size: 190 Copynumber: 2.0 Consensus size: 188
159032 TGAGGTTGAT
159042 AATTGTTTGCACTCAATTGGTTATTGCCCCCCCCCCATTTTCTAAGGCATCATTAGGCCAACCTG
1 AATTGTTTGCACTCAATTGGTTATT--CCCCCCCCCATTTTCTAAGGCATCATTAGGCCAACCTG
* *
159107 CCAGATCAGTTCGTCTACAGAAGCATAATCAATGTTTATCTAGATAAAAACAAATGCTTTGGATA
64 CCAGATCAGTTCGTCTACAAAAGCATAATCAATGTTTATCTAGATAAAAACAAATACTTTGGATA
159172 AACTTGCATTGATTTTCTCATCATTTCTTTGAGCTCCTATAACAAATAAGATCATGTATG
129 AACTTGCATTGATTTTCTCATCATTTCTTTGAGCTCCTATAACAAATAAGATCATGTATG
* **
159232 AATTGTTTGCACTCAATTGGTTCTT-TTCCCCCCATTTTCTAAGGCATCATTAGGCCAACCTGCC
1 AATTGTTTGCACTCAATTGGTTATTCCCCCCCCCATTTTCTAAGGCATCATTAGGCCAACCTGCC
* *
159296 AGATCATGAGTTTGTCTACAAAAGCATAATCAATGTTTATCTAGATTAAAACAAGA-ACTTTGGA
66 AGATC---AGTTCGTCTACAAAAGCATAATCAATGTTTATCTAGATAAAAACAA-ATACTTTGGA
* *
159360 TACACTTGCATTGATTTTCTCATCGTTTCTTTGAGCTCCTATAACAAATAAGATCATGTA
127 TAAACTTGCATTGATTTTCTCATCATTTCTTTGAGCTCCTATAACAAATAAGATCATGTA
159420 GGAACTACGA
Statistics
Matches: 175, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
187 42 0.24
190 132 0.75
191 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (188 bp):
AATTGTTTGCACTCAATTGGTTATTCCCCCCCCCATTTTCTAAGGCATCATTAGGCCAACCTGCC
AGATCAGTTCGTCTACAAAAGCATAATCAATGTTTATCTAGATAAAAACAAATACTTTGGATAAA
CTTGCATTGATTTTCTCATCATTTCTTTGAGCTCCTATAACAAATAAGATCATGTATG
Found at i:159811 original size:136 final size:137
Alignment explanation
Indices: 159439--159994 Score: 915
Period size: 136 Copynumber: 4.0 Consensus size: 137
159429 ATATTCAGTG
* *
159439 CTCAGTGCACAACACTGCAAATGCGCACGCACACCAAAATCTCAAGCTACATCGTATAACTTAAC
1 CTCAGTGCACAACACTGCAAAT--GCA--CACACCAAAATCTCAAACTACATCGTATAACTTCAC
*
159504 AAATTAAGTTGATGTTCATCACTAGTTTCAAGTATTATTATTTATGCGTACACCAAACAGTATGT
62 AACTTAAGTTGATGTTCATCACTAGTTTCAAGTATTATTATTTATGCGTA-ACCAAACAGTATGT
159569 GGATCCATAATA
126 GGATCCATAATA
*
159581 CTCAGTGCACAACACTTCAAATGCACACACCAAAATCTCAAACTACATCGTATAACTTCACAACT
1 CTCAGTGCACAACACTGCAAATGCACACACCAAAATCTCAAACTACATCGTATAACTTCACAACT
*
159646 TAAGTTGATGTTGATCACTAGTTTCAAGTATATTATTATTTATGCGT-A-CAAACAGTATGTGGA
66 TAAGTTGATGTTCATCACTAGTTTCAAG--TATTATTATTTATGCGTAACCAAACAGTATGTGGA
159709 TCCATAATA
129 TCCATAATA
*
159718 CTCGGTGCACAACACTGCAAATGCACACACC-AAATCTCAAACTACATCGTATAACTTCACAACT
1 CTCAGTGCACAACACTGCAAATGCACACACCAAAATCTCAAACTACATCGTATAACTTCACAACT
*
159782 TAAGTTGATGTTGATCACTAGTTTCAAGTATTATTATTTATGCGTACACCAAACAGTATGTGGAT
66 TAAGTTGATGTTCATCACTAGTTTCAAGTATTATTATTTATGCGTA-ACCAAACAGTATGTGGAT
159847 CCATAATA
130 CCATAATA
*
159855 CTCAGTGCACAACACTGCAAATG--CACACCAAAATCTCAAACTACATCGTACAACTTCACAACT
1 CTCAGTGCACAACACTGCAAATGCACACACCAAAATCTCAAACTACATCGTATAACTTCACAACT
*
159918 TAAGTTGATGATCATCACTAGTTTCAAGTATTATTATTTATGCGTACACCAAACAGTATGTGGAT
66 TAAGTTGATGTTCATCACTAGTTTCAAGTATTATTATTTATGCGTA-ACCAAACAGTATGTGGAT
159983 CCATAATA
130 CCATAATA
159991 CTCA
1 CTCA
159995 CCGTCCTAGT
Statistics
Matches: 397, Mismatches: 11, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
134 17 0.04
135 6 0.02
136 169 0.43
137 99 0.25
138 65 0.16
140 20 0.05
142 21 0.05
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (137 bp):
CTCAGTGCACAACACTGCAAATGCACACACCAAAATCTCAAACTACATCGTATAACTTCACAACT
TAAGTTGATGTTCATCACTAGTTTCAAGTATTATTATTTATGCGTAACCAAACAGTATGTGGATC
CATAATA
Found at i:162504 original size:31 final size:29
Alignment explanation
Indices: 162459--162561 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 29
162449 AATATTTCAG
*
162459 TTAT-AAATAGTTATTAGATTTATCAATTTA
1 TTATAAAATAATTATTA-ATTTAT-AATTTA
* *
162489 TTATAAAATATTTATTAATTTTATTAA-TTG
1 TTATAAAATAATTATTAA-TTTA-TAATTTA
*
162519 TTATAAAATAATTATTAAATTATATATTTTA
1 TTATAAAATAATTATT-AATT-TATAATTTA
*
162550 TTATAATATAAT
1 TTATAAAATAAT
162562 AATCATTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
30 26 0.43
31 34 0.56
32 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (29 bp):
TTATAAAATAATTATTAATTTATAATTTA
Found at i:164109 original size:20 final size:20
Alignment explanation
Indices: 164071--164110 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
164061 TAATCCTATT
* **
164071 CACTGGTAATCTTTTATTCC
1 CACTGATAATCTTACATTCC
164091 CACTGATAATCTTACATTCC
1 CACTGATAATCTTACATTCC
164111 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.07, T:0.40
Consensus pattern (20 bp):
CACTGATAATCTTACATTCC
Found at i:165244 original size:15 final size:15
Alignment explanation
Indices: 165224--165268 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
165214 AATTGATTTT
165224 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
**
165239 CTGGAATTTGAATT-
1 CTGGAAAATGAATTA
165253 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
165268 C
1 C
165269 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (15 bp):
CTGGAAAATGAATTA
Found at i:165258 original size:14 final size:14
Alignment explanation
Indices: 165222--165266 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
165212 ATAATTGATT
165222 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
**
165236 TTACTGGAATTTGAA
1 TT-CTGGAAAATGAA
165251 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
165265 TT
1 TT
165267 ACATTTCTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:165600 original size:23 final size:23
Alignment explanation
Indices: 165551--165601 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
165541 GTGTTAAATT
**
165551 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
165574 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
165597 ATATT
1 ATATT
165602 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:165613 original size:19 final size:19
Alignment explanation
Indices: 165589--165659 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
165579 TTAAATATCT
*
165589 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
165608 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
165627 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
165647 TTATTAAATATAT
1 TTATTAAA-ATAT
165660 AAAAAATTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:165641 original size:29 final size:30
Alignment explanation
Indices: 165609--165744 Score: 106
Period size: 29 Copynumber: 4.6 Consensus size: 30
165599 ATTATTAGAT
165609 TATTATATTA-ATATTAAATATATAAATAA
1 TATTATATTATATATTAAATATATAAATAA
* *
165638 TATTAT-TCAT-TATTAAATATATAAAAAA
1 TATTATATTATATATTAAATATATAAATAA
* *
165666 TTATTATA-TATTTATTAAA-ATAAAAAT-A
1 -TATTATATTATATATTAAATATATAAATAA
* * * *
165694 TAATATATTATATTATTATA-ATATAATTGAT
1 TATTATATTATA-TATTAAATATATAAAT-AA
*
165725 TATTTTATTATAATATTAAA
1 TATTATATTAT-ATATTAAA
165745 AACATTATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
27 6 0.07
28 23 0.27
29 32 0.38
30 7 0.08
31 15 0.18
32 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TATTATATTATATATTAAATATATAAATAA
Found at i:165658 original size:28 final size:30
Alignment explanation
Indices: 165583--165718 Score: 99
Period size: 29 Copynumber: 4.6 Consensus size: 30
165573 TATATTTTAA
* * *
165583 ATATCTTTATTAAA-ATATTATTAGATTATT
1 ATATATTTATTAAATATATAAATA-ATTATT
*
165613 ATAT-TAATATTAAATATATAAATAA-TATT
1 ATATAT-TTATTAAATATATAAATAATTATT
*
165642 AT-TCA-TTATTAAATATATAAAAAATTATT
1 ATAT-ATTTATTAAATATATAAATAATTATT
* *
165671 ATATATTTATTAAA-ATAAAAAT-A-TAAT
1 ATATATTTATTAAATATATAAATAATTATT
165698 ATATTATATTATTATAATATA
1 ATA-TAT-TTATTA-AATATA
165719 ATTGATTATT
Statistics
Matches: 87, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
27 6 0.07
28 22 0.25
29 26 0.30
30 23 0.26
31 10 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
ATATATTTATTAAATATATAAATAATTATT
Found at i:165663 original size:66 final size:60
Alignment explanation
Indices: 165593--165718 Score: 146
Period size: 66 Copynumber: 2.0 Consensus size: 60
165583 ATATCTTTAT
* * *
165593 TAAAATATTATTAGATTATTATATTAATATTAAATATATAAATAATATTATTCATTATTA-AATA
1 TAAAAAATTATTAGA-TATT-TATTAA-AATAAAAATAT-AAT-ATATTA-T-ATTATTATAATA
165657 TA
59 TA
*
165659 TAAAAAATTATTATATATTTATTAAAATAAAAATATAATATATTATATTATTATAATATA
1 TAAAAAATTATTAGATATTTATTAAAATAAAAATATAATATATTATATTATTATAATATA
165719 ATTGATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
59 7 0.13
60 7 0.13
61 6 0.11
62 3 0.05
63 9 0.16
64 6 0.11
65 4 0.07
66 13 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (60 bp):
TAAAAAATTATTAGATATTTATTAAAATAAAAATATAATATATTATATTATTATAATATA
Found at i:165706 original size:30 final size:28
Alignment explanation
Indices: 165610--165719 Score: 91
Period size: 28 Copynumber: 3.8 Consensus size: 28
165600 TTATTAGATT
* *
165610 ATTATATTAATATTAAATATATAAATAAT-
1 ATTATA-TATTATTAAA-ATATAAAAAATA
*
165639 ATTAT-TCATTATTAAATATATAAAAAATT
1 ATTATAT-ATTATTAAA-ATATAAAAAATA
*
165668 ATTATATATTTATTAAAATA-AAAATATA
1 ATTATATA-TTATTAAAATATAAAAAATA
*
165696 ATATATTATATTATTATAATATAA
1 AT-TA-TATATTATTAAAATATAA
165720 TTGATTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.01
28 27 0.39
29 26 0.38
30 15 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTATATATTATTAAAATATAAAAAATA
Found at i:165716 original size:23 final size:23
Alignment explanation
Indices: 165690--165740 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
165680 TTAAAATAAA
165690 AATATAATAT-ATTATATTATTAT
1 AATATAAT-TGATTATATTATTAT
*
165713 AATATAATTGATTATTTTATTAT
1 AATATAATTGATTATATTATTAT
165736 AATAT
1 AATAT
165741 TAAAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATATAATTGATTATATTATTAT
Found at i:165726 original size:18 final size:19
Alignment explanation
Indices: 165692--165738 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
165682 AAAATAAAAA
*
165692 TATAATAT-ATTATATTAT
1 TATAATATAATTAGATTAT
165710 TATAATATAATT-GATTAT
1 TATAATATAATTAGATTAT
* *
165728 TTTATTATAAT
1 TATAATATAAT
165739 ATTAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TATAATATAATTAGATTAT
Found at i:165758 original size:22 final size:22
Alignment explanation
Indices: 165730--165773 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
165720 TTGATTATTT
165730 TATTATAATATTAAAAACATTA
1 TATTATAATATTAAAAACATTA
* * *
165752 TATTATATTATTACAAATATTA
1 TATTATAATATTAAAAACATTA
165774 ATAAATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATAATATTAAAAACATTA
Found at i:166312 original size:43 final size:44
Alignment explanation
Indices: 166265--166401 Score: 133
Period size: 43 Copynumber: 3.2 Consensus size: 44
166255 TTACAACATA
*
166265 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCATACAAACGCCGCAATAGGTATTGATATT
*
166308 TAGCGGCG-TTTATCATTA-AAACGCCGCAATAGGTTTTGATATT
1 TAGCGGCGATTTATCA-TACAAACGCCGCAATAGGTATTGATATT
* ** * * *
166351 TAACGGC-ATTTGGCAGACAAACGCCGCAATA-GTCGTTGATGTT
1 TAGCGGCGATTTATCATACAAACGCCGCAATAGGT-ATTGATATT
166394 TAGCGGCG
1 TAGCGGCG
166402 TTTTTGAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 8 0.10
43 68 0.87
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TAGCGGCGATTTATCATACAAACGCCGCAATAGGTATTGATATT
Found at i:166870 original size:21 final size:21
Alignment explanation
Indices: 166846--166907 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
166836 ATATATTACT
*
166846 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
*
166867 TCTCTCTGTGCTGCCGCTGCT
1 TCTCTCTGTGCTGCCGCTGCC
* *
166888 TCTCTCTCTGCTTCCGCTGC
1 TCTCTCTGTGCTGCCGCTGC
166908 TGCTCTAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.00, C:0.42, G:0.19, T:0.39
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:166908 original size:21 final size:21
Alignment explanation
Indices: 166844--166952 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 21
166834 TGATATATTA
* * *
166844 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
166865 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
166886 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* ** *
166907 CTGCTCTAGCTACTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
166928 CTGCTCTTTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
166949 CTTC
1 CTTC
166953 ATTTTCCGCT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 1 0.01
21 72 0.99
ACGTcount: A:0.02, C:0.39, G:0.17, T:0.41
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:175262 original size:41 final size:41
Alignment explanation
Indices: 175195--175355 Score: 213
Period size: 41 Copynumber: 4.0 Consensus size: 41
175185 GTTTATACAA
175195 AAAAAACGCCACTATTGATTAT-ACTATT-CTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGC-GGCGTTTGTT
175235 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
175275 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGT-T
*
175318 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTG
175356 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 24 0.23
41 79 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:175315 original size:82 final size:81
Alignment explanation
Indices: 175196--175354 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 81
175186 TTTATACAAA
* * *
175196 AAAAACGCCACTATTGATTATACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
175260 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
175277 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
175342 TATTGCGGCGTTT
65 TATTGCGGCGTTT
175355 GAGGAATAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 18 0.25
82 53 0.74
83 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:175430 original size:42 final size:42
Alignment explanation
Indices: 175384--175537 Score: 143
Period size: 42 Copynumber: 3.7 Consensus size: 42
175374 ATGTGTAATA
* *
175384 TATTGAGGCGTTTGTGGTATAAACGCCACGAATTTACCACTC
1 TATTGAGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
* * * *
175426 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGAGGCGTTTGTGG-TATAAACGCCGC-AAATTTACCACTC
* * *
175467 TATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTGAGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
* * * * *
175509 TATTGCGGCATTTTTTGTAAAAACGCCGC
1 TATTGAGGCGTTTGTGGTATAAACGCCGC
175538 TATATGTCAA
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
41 33 0.37
42 57 0.63
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (42 bp):
TATTGAGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
Found at i:175554 original size:42 final size:42
Alignment explanation
Indices: 175341--175582 Score: 127
Period size: 42 Copynumber: 5.8 Consensus size: 42
175331 TTGATTATCA
* * * **
175341 CTATTGCGGCGTTTG-AGGAATAAACGACACTATATGTGTAA-T
1 CTATTGCGGCGTTTGTAGTAA-AAACGCCGCTA-ATGTACAACT
* * * * * * * *
175383 ATATTGAGGCGTTTGTGGTATAAACGCCACGAATTTACCACT
1 CTATTGCGGCGTTTGTAGTAAAAACGCCGCTAATGTACAACT
* * * * * *
175425 CTATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACT
1 CTATTGCGGCGTTTGTAG-TAAAAACGCCGC-TAATGTACAACT
* * * * * *
175466 CTATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACC
1 CTATTGCGGCGTTTGTAGTAAAAACGCCGCTAATGTACAACT
* * *
175508 CTATTGCGGCATTTTTTGTAAAAACGCCGCTATATGT-CAACT
1 CTATTGCGGCGTTTGTAGTAAAAACGCCGCTA-ATGTACAACT
* *
175550 CTATTGCAGCGTTTGTACTAAAAACGCCGCTAA
1 CTATTGCGGCGTTTGTAGTAAAAACGCCGCTAA
175583 AGTATCAATT
Statistics
Matches: 155, Mismatches: 37, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
41 38 0.25
42 112 0.72
43 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (42 bp):
CTATTGCGGCGTTTGTAGTAAAAACGCCGCTAATGTACAACT
Found at i:176636 original size:38 final size:40
Alignment explanation
Indices: 176587--176674 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 40
176577 GAAAATATTT
* * *
176587 TTTTTTTGGTCGAATC-GAGTCGGATGA-AGGATATATA-A
1 TTTTTTAGGTCGAATCAGAGTC-GATCAGAGGATACATATA
* *
176625 TTTTTTAGGTCGGATCAGATTCGATCAGAGGATACATATA
1 TTTTTTAGGTCGAATCAGAGTCGATCAGAGGATACATATA
176665 TTTTTTAGGT
1 TTTTTTAGGT
176675 TGATGCGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 18 0.43
39 13 0.31
40 11 0.26
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (40 bp):
TTTTTTAGGTCGAATCAGAGTCGATCAGAGGATACATATA
Found at i:177629 original size:28 final size:29
Alignment explanation
Indices: 177564--177630 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
177554 GATTGATTCA
177564 AATTATTATTTCAATTTAAAATTTAATTT
1 AATTATTATTTCAATTTAAAATTTAATTT
177593 AATTATTATTT-AGATTTAAAATTT-ATTT
1 AATTATTATTTCA-ATTTAAAATTTAATTT
**
177621 TTTTATTATT
1 AATTATTATT
177631 ACAAGTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
AATTATTATTTCAATTTAAAATTTAATTT
Found at i:178256 original size:3 final size:3
Alignment explanation
Indices: 178242--178332 Score: 146
Period size: 3 Copynumber: 30.3 Consensus size: 3
178232 TACCCATATC
* * *
178242 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
178290 ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
178333 AATATATTAA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:179755 original size:20 final size:21
Alignment explanation
Indices: 179726--179766 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
179716 TTTGTTTTTA
179726 TTTTATTATATGAATAAATAT
1 TTTTATTATATGAATAAATAT
**
179747 TTTTA-TATATTCATAAATAT
1 TTTTATTATATGAATAAATAT
179767 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTATTATATGAATAAATAT
Found at i:183880 original size:14 final size:15
Alignment explanation
Indices: 183850--183882 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
183840 TTATTATTTT
183850 ATTTATTAAGATAAA
1 ATTTATTAAGATAAA
*
183865 ATTTATTAA-TTAAA
1 ATTTATTAAGATAAA
183879 ATTT
1 ATTT
183883 GAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTATTAAGATAAA
Found at i:192589 original size:82 final size:82
Alignment explanation
Indices: 192299--192763 Score: 790
Period size: 82 Copynumber: 5.6 Consensus size: 82
192289 AAACATTAAA
*
192299 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
192364 AGAACCAATCATTGAATT
66 AGAA-CAATCATTGAGTT
** * *
192382 TAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAG
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-
*
192446 CAGAACCAATCATTGAATT
65 CAGAA-CAATCATTGAGTT
** *
192465 GGGAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
192529 CAGAACAATCATTGAGTT
65 CAGAACAATCATTGAGTT
192547 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
192612 AGAACAATCATTGAGTT
66 AGAACAATCATTGAGTT
192629 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
192694 AGAACAATCATTGAGTT
66 AGAACAATCATTGAGTT
192711 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
192764 GTTTGGTATG
Statistics
Matches: 362, Mismatches: 16, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.00
82 225 0.62
83 135 0.37
84 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (82 bp):
TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAACAATCATTGAGTT
Found at i:193805 original size:113 final size:113
Alignment explanation
Indices: 193607--194053 Score: 770
Period size: 113 Copynumber: 4.0 Consensus size: 113
193597 GCAAAGATTC
193607 GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
193672 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
193720 GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
193785 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
*
193833 GAATCCATCATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
193898 AAGGAAGAAGAAGTTCATAATTAGAAGAATTTGTTCAATCTTTTACCT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
* * * * * *
193946 GAATTCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
194010 AAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
194054 GCATAATTCT
Statistics
Matches: 321, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
112 69 0.21
113 252 0.79
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
GAATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
Found at i:194392 original size:3 final size:3
Alignment explanation
Indices: 194386--194509 Score: 230
Period size: 3 Copynumber: 41.3 Consensus size: 3
194376 CATTATCATC
194386 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
194434 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
194482 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
194510 AATATATTAA
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:195931 original size:20 final size:21
Alignment explanation
Indices: 195902--195942 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
195892 TTTATTTTTA
195902 TTTTATTATATGAATAAATAT
1 TTTTATTATATGAATAAATAT
**
195923 TTTTA-TATATTCATAAATAT
1 TTTTATTATATGAATAAATAT
195943 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTATTATATGAATAAATAT
Found at i:197154 original size:18 final size:16
Alignment explanation
Indices: 197125--197163 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
197115 ATATGATTTT
197125 TTTTATTAATTAATTA
1 TTTTATTAATTAATTA
*
197141 TTTTATTGATATTATTTA
1 TTTTATT-A-ATTAATTA
197159 TTTTA
1 TTTTA
197164 AAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTATTAATTAATTA
Found at i:197182 original size:27 final size:27
Alignment explanation
Indices: 197140--197199 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
197130 TTAATTAATT
*
197140 ATTTTATTGATATTA-TTTATTTTAAA
1 ATTTTATTGATATTATTTTATTTAAAA
*
197166 ATTTTATTTATATTTATTTTATTTAAAA
1 ATTTTATTGATA-TTATTTTATTTAAAA
197194 ATTTTA
1 ATTTTA
197200 CTTTGTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 11 0.37
27 3 0.10
28 16 0.53
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTTATTGATATTATTTTATTTAAAA
Found at i:204810 original size:29 final size:28
Alignment explanation
Indices: 204743--204811 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
204733 CAATCCAAAG
204743 AATAATCATTATTGTAAACTTTTTTTAA
1 AATAATCATTATTGTAAACTTTTTTTAA
*
204771 AAT-AT-ACTTATATGATATA-TTTTTTTAA
1 AATAATCA-TTAT-TG-TAAACTTTTTTTAA
204799 AATAATCATTATT
1 AATAATCATTATT
204812 TTTTTTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
28 18 0.51
29 9 0.26
30 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (28 bp):
AATAATCATTATTGTAAACTTTTTTTAA
Found at i:208358 original size:21 final size:23
Alignment explanation
Indices: 208294--208353 Score: 106
Period size: 21 Copynumber: 2.7 Consensus size: 23
208284 AAACTGTTTA
208294 GGGGGGAATCGGTTCCTCCTAT-
1 GGGGGGAATCGGTTCCTCCTATG
208316 -GGGGGAATCGGTTCCTCCTATG
1 GGGGGGAATCGGTTCCTCCTATG
208338 GGGGGGAATCGGTTCC
1 GGGGGGAATCGGTTCC
208354 CTATGAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.58
23 15 0.42
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.25
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCTCCTATG
Found at i:210976 original size:21 final size:21
Alignment explanation
Indices: 210950--210989 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
210940 CAGAACCCCA
*
210950 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
210971 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
210990 TCAAAGTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:213039 original size:12 final size:12
Alignment explanation
Indices: 213022--213046 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
213012 ATGATGATTC
213022 TCTAACGTCATT
1 TCTAACGTCATT
213034 TCTAACGTCATT
1 TCTAACGTCATT
213046 T
1 T
213047 GCTTGTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTAACGTCATT
Found at i:214881 original size:22 final size:21
Alignment explanation
Indices: 214839--214878 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
214829 GAGTTTGTTT
*
214839 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
214860 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
214879 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:221564 original size:31 final size:32
Alignment explanation
Indices: 221528--221591 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
221518 TTGAGTTTAA
* **
221528 AAATTTCTAATT-GAATTAAATATGATTATTT
1 AAATTTCTAATTAAAATTAAATACAATTATTT
*
221559 AAATTTCTATTTAAAATTAAATACAATTATTT
1 AAATTTCTAATTAAAATTAAATACAATTATTT
221591 A
1 A
221592 TAATGTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (32 bp):
AAATTTCTAATTAAAATTAAATACAATTATTT
Found at i:222404 original size:2 final size:2
Alignment explanation
Indices: 222397--222431 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
222387 ATTAATAACC
222397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222432 ACCCTTGCAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:226386 original size:2 final size:2
Alignment explanation
Indices: 226379--226427 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
226369 TAAAAGATGG
226379 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
226421 AT AT AT A
1 AT AT AT A
226428 AGAGTTGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:227064 original size:23 final size:21
Alignment explanation
Indices: 227021--227064 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
227011 TTTATCTTAA
* *
227021 CTTAAATATTTAAATTCTATT
1 CTTAAATATTTAAAATATATT
227042 CTTATAATATTTTAAAATATATT
1 CTTA-AATA-TTTAAAATATATT
227065 TTCAATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
CTTAAATATTTAAAATATATT
Found at i:227130 original size:13 final size:14
Alignment explanation
Indices: 227112--227140 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
227102 TTAAACCAAA
227112 AAATATATATT-TT
1 AAATATATATTCTT
227125 AAATATATATTCTT
1 AAATATATATTCTT
227139 AA
1 AA
227141 CTTAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATATTCTT
Found at i:227268 original size:123 final size:121
Alignment explanation
Indices: 227118--227471 Score: 570
Period size: 118 Copynumber: 2.9 Consensus size: 121
227108 CAAAAAATAT
*
227118 ATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCATGCTTTAAACCAAAAATATATA
1 ATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCATACTTTAAACCAAAAA-ATATA
* * *
227183 TATACAATAAATTAAGAAAAAATAATAAAAATACATATTTTTATAGTTAAGAATTTAA
65 TATTCGATAAATTAAGAAAAAATAAT-AAAATATATATTTTTATAGTTAAGAATTTAA
* *
227241 ATATTTTAAATATATAATCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAAAATATAT
1 ATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCATACTTTAAACCAAAAAATATAT
*
227306 ATTCGATAAATTAAG--AAAA-AATAAAATATATATTTTTATAGTTAAGATTTTAA
66 ATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
* *
227359 ATATTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATAT
1 ATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCATACTTTAAACCAAAAAATATAT
* *
227424 ATTTGATAAATTAAGAAATAATAATAAAATATATATTTTTATAGTTAA
66 ATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAA
227472 AAATCTAACA
Statistics
Matches: 215, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
118 104 0.48
119 3 0.01
120 7 0.03
121 26 0.12
122 19 0.09
123 56 0.26
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (121 bp):
ATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCATACTTTAAACCAAAAAATATAT
ATTCGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
Found at i:233169 original size:26 final size:25
Alignment explanation
Indices: 233140--233188 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
233130 TAGGGTCAAT
233140 TAATTTAATTTAGTATTTATATATGC
1 TAATTTAATTTAGTA-TTATATATGC
233166 TAATTTAATTTAGTATTATATAT
1 TAATTTAATTTAGTATTATATAT
233189 TTTACCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (25 bp):
TAATTTAATTTAGTATTATATATGC
Found at i:239993 original size:2 final size:2
Alignment explanation
Indices: 239986--240026 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
239976 TTAAAAATAA
239986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
240027 TAATAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:240030 original size:6 final size:7
Alignment explanation
Indices: 239985--240031 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 7
239975 ATTAAAAATA
239985 AATATAT
1 AATATAT
239992 -ATATAT
1 AATATAT
239998 ATATATAT
1 A-ATATAT
240006 ATATATAT
1 A-ATATAT
240014 ATATATAT
1 A-ATATAT
240022 AATAT-T
1 AATATAT
240028 AATA
1 AATA
240032 AATTTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 11 0.29
7 4 0.11
8 23 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AATATAT
Found at i:241812 original size:29 final size:29
Alignment explanation
Indices: 241780--241837 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
241770 TTGTTTAATA
241780 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
*
241809 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
241838 CAGTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.05, G:0.16, T:0.62
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:248589 original size:10 final size:11
Alignment explanation
Indices: 248566--248599 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
248556 AAAAACAAAA
248566 TTTCCGGATTT
1 TTTCCGGATTT
*
248577 TTTCCGGTTTT
1 TTTCCGGATTT
248588 TTTCCGG-TTT
1 TTTCCGGATTT
248598 TT
1 TT
248600 AGCCGGTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (11 bp):
TTTCCGGATTT
Found at i:248630 original size:17 final size:18
Alignment explanation
Indices: 248608--248641 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
248598 TTAGCCGGTC
248608 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
248625 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
248642 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Done.