Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 379 of 410
Found at i:115336090 original size:14 final size:14
Alignment explanation
Indices: 115336071--115336113 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
115336061 ATTAAGTTCT
*
115336071 TGTGAATATGTATA
1 TGTGAATATATATA
115336085 TGTGAATATATATA
1 TGTGAATATATATA
*
115336099 TAT-ATATATATATA
1 TGTGA-ATATATATA
115336113 T
1 T
115336114 ATAATTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 1 0.04
14 25 0.96
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (14 bp):
TGTGAATATATATA
Found at i:115336097 original size:2 final size:2
Alignment explanation
Indices: 115336090--115336116 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115336080 GTATATGTGA
115336090 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
115336117 ATTGGAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115336516 original size:5 final size:5
Alignment explanation
Indices: 115336506--115336537 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
115336496 TTGTGTGTTC
115336506 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
115336538 TCAAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:115336525 original size:14 final size:14
Alignment explanation
Indices: 115336506--115336536 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
115336496 TTGTGTGTTC
115336506 TTTATTTTATTTTA
1 TTTATTTTATTTTA
115336520 TTTATTTTATTTTA
1 TTTATTTTATTTTA
115336534 TTT
1 TTT
115336537 TTCAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:115350567 original size:5 final size:5
Alignment explanation
Indices: 115350557--115350589 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
115350547 CTGTGTGTTC
115350557 TTTAT TTTAT TTTATT TTTAT TTTAT TTT-T TTT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTT
115350590 CACAGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTAT
Found at i:115350577 original size:11 final size:11
Alignment explanation
Indices: 115350557--115350586 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
115350547 CTGTGTGTTC
115350557 TTTA-TTTTAT
1 TTTATTTTTAT
115350567 TTTATTTTTAT
1 TTTATTTTTAT
115350578 TTTATTTTT
1 TTTATTTTT
115350587 TTTCACAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:115350578 original size:16 final size:15
Alignment explanation
Indices: 115350557--115350589 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
115350547 CTGTGTGTTC
115350557 TTTATTTTATTTTATT
1 TTTATTTTATTTT-TT
115350573 TTTATTTTATTTTTT
1 TTTATTTTATTTTTT
115350588 TT
1 TT
115350590 CACAGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTATTTTATTTTTT
Found at i:115352231 original size:16 final size:16
Alignment explanation
Indices: 115352207--115352240 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
115352197 TTGTGACGAG
*
115352207 GAAATATGCTCTTTGA
1 GAAAGATGCTCTTTGA
115352223 GAAAGATGCTCTTTGA
1 GAAAGATGCTCTTTGA
115352239 GA
1 GA
115352241 CAATGACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (16 bp):
GAAAGATGCTCTTTGA
Found at i:115353370 original size:27 final size:25
Alignment explanation
Indices: 115353287--115353399 Score: 82
Period size: 27 Copynumber: 4.2 Consensus size: 25
115353277 AGCATGGCTG
**
115353287 CCAGAACAGATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGGCAGAG-CA
*
115353313 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAG-AGCA
*
115353341 CCAGAACAAATATATGTGGCAGAGCGA
1 CCAGAACAGATA-ATGTGGCAGAGC-A
** *
115353368 CCAGGTCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAG-CA
115353396 CCAG
1 CCAG
115353400 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
26 8 0.11
27 32 0.46
28 28 0.40
29 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
CCAGAACAGATAATGTGGCAGAGCA
Found at i:115354835 original size:24 final size:24
Alignment explanation
Indices: 115354808--115354854 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
115354798 CTAGATTTCC
**
115354808 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
115354832 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
115354855 GTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:115361106 original size:27 final size:26
Alignment explanation
Indices: 115361071--115361182 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
115361061 AGCATGGCTG
* *
115361071 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
115361097 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
115361125 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
115361152 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
115361179 CCAG
1 CCAG
115361183 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:115361135 original size:54 final size:54
Alignment explanation
Indices: 115361071--115361182 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
115361061 AGCATGGCTG
*
115361071 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCA
* * * *
115361125 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
115361179 CCAG
1 CCAG
115361183 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
Found at i:115362626 original size:24 final size:24
Alignment explanation
Indices: 115362599--115362648 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
115362589 CTAGATTTCC
**
115362599 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
115362623 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
115362647 TC
1 TC
115362649 TTGACAGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:115368295 original size:5 final size:5
Alignment explanation
Indices: 115368285--115368353 Score: 63
Period size: 5 Copynumber: 13.6 Consensus size: 5
115368275 TATGTCTTTC
* *
115368285 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAG AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT AAAAT
115368332 AAAAT -AAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAA
115368354 GATAGGAGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 29 0.55
6 17 0.32
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:115368317 original size:17 final size:16
Alignment explanation
Indices: 115368295--115368350 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
115368285 AAAATAAAAT
115368295 AATAAAATTGAAATGAA
1 AATAAAATT-AAATGAA
* *
115368312 AATAAAAATCAAAAGAA
1 AAT-AAAATTAAATGAA
115368329 AATAAAA-TAAAT-AA
1 AATAAAATTAAATGAA
115368343 AATAAAAT
1 AATAAAAT
115368351 AAAGATAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.27
15 3 0.09
16 4 0.12
17 12 0.36
18 5 0.15
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (16 bp):
AATAAAATTAAATGAA
Found at i:115371234 original size:23 final size:25
Alignment explanation
Indices: 115371208--115371254 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
115371198 TATCATTCAT
*
115371208 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
115371231 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
115371255 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:115371575 original size:46 final size:46
Alignment explanation
Indices: 115371515--115372002 Score: 659
Period size: 46 Copynumber: 11.0 Consensus size: 46
115371505 TTTGACGTGA
* * * ** ** * *
115371515 TGCCATAGTGTCTTTCAACTATGGTCTTACTTATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
** * * *
115371561 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
115371607 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATAGT-AGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA-TCAGGT
* *
115371653 TGCCATGGTAACTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
115371699 TGCCATGGTTTCTTTCAACCATGGTCTTACACATCTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
115371745 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
115371791 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
115371837 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
115371875 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
115371921 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
115371959 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
115372003 AGAGAACACT
Statistics
Matches: 403, Mismatches: 21, Indels: 36
0.88 0.05 0.08
Matches are distributed among these distances:
38 66 0.16
39 2 0.00
40 6 0.01
41 2 0.00
43 2 0.00
44 6 0.01
45 3 0.01
46 315 0.78
47 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:115371883 original size:38 final size:38
Alignment explanation
Indices: 115371832--115371991 Score: 248
Period size: 38 Copynumber: 4.0 Consensus size: 38
115371822 CATTTCATAT
115371832 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
115371870 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
115371915 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
115371954 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
115371992 TTTCATATCA
Statistics
Matches: 114, Mismatches: 0, Indels: 16
0.88 0.00 0.12
Matches are distributed among these distances:
38 71 0.62
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 33 0.29
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:115371927 original size:84 final size:84
Alignment explanation
Indices: 115371786--115372002 Score: 434
Period size: 84 Copynumber: 2.6 Consensus size: 84
115371776 CATCTCATAT
115371786 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
115371851 TCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACA
115371870 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
115371935 TCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACA
115371954 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
115372003 AGAGAACACT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 133 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (84 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
TCAACCATGGTCTTACACA
Found at i:115373680 original size:59 final size:59
Alignment explanation
Indices: 115373610--115373727 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
115373600 TTTTCAAAGT
*
115373610 TAGTCTACTGCTGCTGTCTAAACTGTTTTTGTGCAAGCTATTAATTACCATGTTATAAC
1 TAGTCTACTGCTGCTGTCCAAACTGTTTTTGTGCAAGCTATTAATTACCATGTTATAAC
115373669 TAGTCTACTGCTGCTGTCCAAACTGTTTTTGTGCAAGCTATTAATTACCATGTTATAAC
1 TAGTCTACTGCTGCTGTCCAAACTGTTTTTGTGCAAGCTATTAATTACCATGTTATAAC
115373728 ACCCTTATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (59 bp):
TAGTCTACTGCTGCTGTCCAAACTGTTTTTGTGCAAGCTATTAATTACCATGTTATAAC
Found at i:115377836 original size:46 final size:46
Alignment explanation
Indices: 115377786--115377961 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
115377776 TGGTTGAGCA
115377786 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
115377832 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
115377877 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
115377925 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
115377962 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:115377942 original size:93 final size:93
Alignment explanation
Indices: 115377783--115377954 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
115377773 GGATGGTTGA
* *
115377783 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
115377848 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
115377876 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
115377941 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
115377955 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:115388602 original size:22 final size:21
Alignment explanation
Indices: 115388565--115388607 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
115388555 AATAATAACG
*
115388565 ATATATAAACATATAA-ATGT
1 ATATATAAAAATATAATATGT
115388585 ATATATTAAAAATAATAATATGT
1 ATATA-TAAAAAT-ATAATATGT
115388608 GTACGTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 4 0.21
23 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
ATATATAAAAATATAATATGT
Found at i:115388881 original size:23 final size:23
Alignment explanation
Indices: 115388855--115388903 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
115388845 TAACATATAT
115388855 ATATATA-TACATATATAATGAAA
1 ATATATACTAC-TATATAATGAAA
* * *
115388878 ATATGTACTACTATGTAATGATA
1 ATATATACTACTATATAATGAAA
115388901 ATA
1 ATA
115388904 GAAATACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (23 bp):
ATATATACTACTATATAATGAAA
Found at i:115389896 original size:46 final size:46
Alignment explanation
Indices: 115389717--115389898 Score: 249
Period size: 46 Copynumber: 4.0 Consensus size: 46
115389707 TTTGACATGA
* * * * * *
115389717 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
115389763 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
115389809 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
115389855 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
115389899 AGAGCACACT
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 4 0.03
46 118 0.97
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:115392050 original size:11 final size:11
Alignment explanation
Indices: 115392034--115392085 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
115392024 TATACTAAAT
115392034 AAATAATAATA
1 AAATAATAATA
*
115392045 AAATAAT-ATT
1 AAATAATAATA
* *
115392055 AAATATCTCATA
1 AAATA-ATAATA
*
115392067 AAATATTAATA
1 AAATAATAATA
115392078 AAATAATA
1 AAATAATA
115392086 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:115403011 original size:2 final size:2
Alignment explanation
Indices: 115403004--115403053 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
115402994 CAGTGTTAAA
*
115403004 AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
115403046 AG AG AG AG
1 AG AG AG AG
115403054 CTTAATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:115403513 original size:7 final size:7
Alignment explanation
Indices: 115403503--115403530 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
115403493 TTATAATTTT
115403503 AAATTAA
1 AAATTAA
115403510 AAATTAA
1 AAATTAA
115403517 AAATTAA
1 AAATTAA
115403524 AAATTAA
1 AAATTAA
115403531 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATTAA
Found at i:115417207 original size:46 final size:46
Alignment explanation
Indices: 115417150--115417323 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
115417140 TGGTTGAGCA
*
115417150 TCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
115417196 TTCGAACTCGTTAAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
115417241 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
115417289 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTAT
115417324 AGGCGGGTTA
Statistics
Matches: 103, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 6 0.06
46 55 0.53
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:115417306 original size:93 final size:93
Alignment explanation
Indices: 115417147--115417317 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
115417137 GGATGGTTGA
* * *
115417147 GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTAAGT
1 GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTAAGT
115417212 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
** *
115417240 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTAAG
115417304 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
115417318 ACTTATAGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 3 0.04
93 68 0.96
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAAATCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTAAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:115423941 original size:18 final size:18
Alignment explanation
Indices: 115423828--115424019 Score: 82
Period size: 18 Copynumber: 10.1 Consensus size: 18
115423818 AGCAATTAAT
*
115423828 CAATCAGTAATATTCATTAA
1 CAATCAGT--TATTCAGTAA
* *
115423848 CAATCAGTCAATCAG-AA
1 CAATCAGTTATTCAGTAA
* *
115423865 CAATTATTTATTCAGTAA
1 CAATCAGTTATTCAGTAA
*
115423883 CAGA-CAGTTATTCGGTAA
1 CA-ATCAGTTATTCAGTAA
* * **
115423901 CAATAAATTATTCAAAAA
1 CAATCAGTTATTCAGTAA
*
115423919 TAATCAGTTATTCAGTATCAA
1 CAATCAGTTATTCAG--T-AA
* *
115423940 TCAATTGATCGGTTATCCAGTAA
1 -C-A---ATCAGTTATTCAGTAA
* *
115423963 CAGTCAATTATTCAGTAA
1 CAATCAGTTATTCAGTAA
* * *
115423981 AAATCAGATATACAGTAA
1 CAATCAGTTATTCAGTAA
* *
115423999 CAATTAAATTATTCAGTAA
1 CAA-TCAGTTATTCAGTAA
115424018 CA
1 CA
115424020 GTCGATCTTT
Statistics
Matches: 123, Mismatches: 37, Indels: 25
0.66 0.20 0.14
Matches are distributed among these distances:
17 14 0.11
18 68 0.55
19 14 0.11
20 8 0.07
21 3 0.02
22 1 0.01
23 3 0.02
24 1 0.01
26 11 0.09
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (18 bp):
CAATCAGTTATTCAGTAA
Found at i:115424214 original size:6 final size:6
Alignment explanation
Indices: 115424203--115424233 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
115424193 AATTCGAAAT
*
115424203 AGTAAC AGTAAC GGTAAC AGTAAC AGTAAC A
1 AGTAAC AGTAAC AGTAAC AGTAAC AGTAAC A
115424234 ACATCCGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AGTAAC
Found at i:115426959 original size:12 final size:11
Alignment explanation
Indices: 115426937--115426975 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
115426927 TTGAATAGGT
115426937 AATTGGTATTG
1 AATTGGTATTG
115426948 AATTGAGTATTG
1 AATTG-GTATTG
*
115426960 AATTTG-ATTG
1 AATTGGTATTG
115426970 AATTGG
1 AATTGG
115426976 ATATGGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.44
Consensus pattern (11 bp):
AATTGGTATTG
Found at i:115428565 original size:22 final size:23
Alignment explanation
Indices: 115428540--115428585 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
115428530 CAACCAAATC
115428540 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
115428562 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
115428585 A
1 A
115428586 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:115428591 original size:23 final size:23
Alignment explanation
Indices: 115428547--115428591 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
115428537 ATCAATTCAA
*
115428547 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
115428570 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
115428592 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:115430289 original size:35 final size:31
Alignment explanation
Indices: 115430250--115430319 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 31
115430240 ATATACATAT
* *
115430250 AATAAAATACATGTATTGATAATATATATGATAAG
1 AATAAAATAAATGTA---ATAATATACAT-ATAAG
115430285 AATAAAATAAATGTAATAATATACATATAAG
1 AATAAAATAAATGTAATAATATACATATAAG
115430316 AATA
1 AATA
115430320 TAAAATCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.27
32 10 0.30
35 14 0.42
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (31 bp):
AATAAAATAAATGTAATAATATACATATAAG
Found at i:115430662 original size:14 final size:15
Alignment explanation
Indices: 115430637--115430677 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
115430627 GGTGTTCAAA
115430637 ATATATACATAACAT
1 ATATATACATAACAT
*
115430652 A-ATATATATAA-AT
1 ATATATACATAACAT
115430665 ATATATACATAAC
1 ATATATACATAAC
115430678 GTAGTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.14
14 18 0.82
15 1 0.05
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATATACATAACAT
Found at i:115436571 original size:37 final size:37
Alignment explanation
Indices: 115436521--115436606 Score: 154
Period size: 37 Copynumber: 2.3 Consensus size: 37
115436511 TTATTACGAA
115436521 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
115436558 GTCTTACCTGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
115436595 GTCTCACCCGGA
1 GTCTTACCCGGA
115436607 ATATATTTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:115436706 original size:48 final size:48
Alignment explanation
Indices: 115436651--115437042 Score: 739
Period size: 48 Copynumber: 8.2 Consensus size: 48
115436641 TGTTACAACA
*
115436651 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
115436699 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
115436747 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
115436795 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
115436843 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
115436891 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
115436939 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
* *
115436987 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
115437035 TTCACATT
1 TTCACATT
115437043 CATCACATCG
Statistics
Matches: 337, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 337 1.00
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
Found at i:115437089 original size:47 final size:47
Alignment explanation
Indices: 115437034--115437175 Score: 239
Period size: 47 Copynumber: 3.0 Consensus size: 47
115437024 CACACATATG
*
115437034 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
115437081 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACAC
*
115437130 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
115437176 TCTCCTACAT
Statistics
Matches: 89, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
47 45 0.51
49 44 0.49
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
Found at i:115437143 original size:49 final size:49
Alignment explanation
Indices: 115437035--115437173 Score: 237
Period size: 49 Copynumber: 2.9 Consensus size: 49
115437025 ACACATATGT
* *
115437035 TTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTCT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
*
115437082 TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACC
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
115437131 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
115437174 CATCTCCTAC
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
47 35 0.41
49 51 0.59
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACC
Found at i:115443416 original size:78 final size:77
Alignment explanation
Indices: 115443262--115443416 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 77
115443252 CCGAAGCAAT
* * * *
115443262 TGCAACGTTTCATTGAACTGTTTCTAGGAACTACTATGGTCATCATACAGAAGAATCAATGGATC
1 TGCAAAGTTTCATTGAACTGTTCCTAGGAACTACCATGGCCATCATACAGAAGAATCAATGGATC
*
115443327 AGATGACTGATG
66 AGACGACTGATG
** * * *
115443339 TGCAAAGTTTCATTGGTCTGTTCCTAGGAAGCTACCATGGCCTTCATACAGGATAATCAATGGAT
1 TGCAAAGTTTCATTGAACTGTTCCTAGGAA-CTACCATGGCCATCATACAGAAGAATCAATGGAT
*
115443404 CAGACGATTGATG
65 CAGACGACTGATG
115443417 CTTGCCATGG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
77 26 0.39
78 40 0.61
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (77 bp):
TGCAAAGTTTCATTGAACTGTTCCTAGGAACTACCATGGCCATCATACAGAAGAATCAATGGATC
AGACGACTGATG
Found at i:115445768 original size:15 final size:16
Alignment explanation
Indices: 115445750--115445779 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
115445740 TGTTAATATT
115445750 ATTTTATTA-AATTTA
1 ATTTTATTACAATTTA
115445765 ATTTTATTACAATTT
1 ATTTTATTACAATTT
115445780 TTTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTATTACAATTTA
Found at i:115451318 original size:46 final size:44
Alignment explanation
Indices: 115451214--115451321 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
115451204 TGTCTTTGAC
** * * *
115451214 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
115451258 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
115451304 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
115451322 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:115457809 original size:78 final size:77
Alignment explanation
Indices: 115457678--115457826 Score: 226
Period size: 78 Copynumber: 1.9 Consensus size: 77
115457668 CGATTGCGAC
* * **
115457678 GTTTCATTGAACTATTTCTAGGAACTACTATGGTCATCATACAGGAGAATCAATGGATCAGGTGA
1 GTTTCATTGAACTATTTCTAGGAACTACCATGGCCATCATACAGGAGAATCAATGGATCAGACGA
115457743 TTGATGTGCAAA
66 TTGATGTGCAAA
* * *
115457755 GTTTCATTGGACTGTTTCTAGGAAGCTACCATGGCCATCATACAGGATAATCAATGGATCAGACG
1 GTTTCATTGAACTATTTCTAGGAA-CTACCATGGCCATCATACAGGAGAATCAATGGATCAGACG
115457820 ATTGATG
65 ATTGATG
115457827 CTTGCCATGG
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
77 22 0.34
78 42 0.66
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (77 bp):
GTTTCATTGAACTATTTCTAGGAACTACCATGGCCATCATACAGGAGAATCAATGGATCAGACGA
TTGATGTGCAAA
Found at i:115461015 original size:30 final size:30
Alignment explanation
Indices: 115460966--115461024 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
115460956 CTTAACAAGT
115460966 AAATACCTCTAAAACAATAACAAAATTAAC
1 AAATACCTCTAAAACAATAACAAAATTAAC
* * *
115460996 AAATGCCTTTAAAATAATAACAAAATTAA
1 AAATACCTCTAAAACAATAACAAAATTAA
115461025 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (30 bp):
AAATACCTCTAAAACAATAACAAAATTAAC
Found at i:115461986 original size:20 final size:20
Alignment explanation
Indices: 115461961--115461999 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
115461951 GAGATTATGC
115461961 CATATCAATACCACAATTTT
1 CATATCAATACCACAATTTT
115461981 CATATCAATACCACAATTT
1 CATATCAATACCACAATTT
115462000 GAGTACCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (20 bp):
CATATCAATACCACAATTTT
Found at i:115463083 original size:21 final size:23
Alignment explanation
Indices: 115463059--115463101 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
115463049 GAAAGATAAG
115463059 TTTAA-TCAATA-TAATAAAAGC
1 TTTAACTCAATATTAATAAAAGC
115463080 TTTAACGTCAATATTAATAAAA
1 TTTAAC-TCAATATTAATAAAA
115463102 TATCATGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTAACTCAATATTAATAAAAGC
Found at i:115465948 original size:31 final size:31
Alignment explanation
Indices: 115465889--115465944 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
115465879 TTTTTATTTT
115465889 TAAAATATTTAAAATTATTAATATATTAATA
1 TAAAATATTTAAAATTATTAATATATTAATA
*
115465920 TAAAATA-TTATAATT-TTAA-ATATTA
1 TAAAATATTTAAAATTATTAATATATTA
115465945 TTAAACATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 4 0.17
30 7 0.29
31 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAAATATTTAAAATTATTAATATATTAATA
Found at i:115466063 original size:13 final size:13
Alignment explanation
Indices: 115466046--115466089 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
115466036 ATTTAAATTT
115466046 TATTTTAATAATAA
1 TATTTTAA-AATAA
115466060 -ATTTTAAAAATAA
1 TATTTT-AAAATAA
*
115466073 TAATTTAAAATAA
1 TATTTTAAAATAA
115466086 TATT
1 TATT
115466090 CTTCACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATTTTAAAATAA
Found at i:115468549 original size:21 final size:21
Alignment explanation
Indices: 115468523--115468565 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
115468513 GGCCGTGTAA
115468523 CTCATTGTTTGGATTTTGGGT
1 CTCATTGTTTGGATTTTGGGT
*
115468544 CTCATTGTTTGGATTTTTGGT
1 CTCATTGTTTGGATTTTGGGT
115468565 C
1 C
115468566 AACGGGCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (21 bp):
CTCATTGTTTGGATTTTGGGT
Found at i:115471054 original size:30 final size:30
Alignment explanation
Indices: 115470871--115471056 Score: 291
Period size: 30 Copynumber: 6.2 Consensus size: 30
115470861 AGTTAGGCCA
*
115470871 TTTGGGCCACCAAATGGACCGCCTTCGCCT
1 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
* * *
115470901 TTTCGGTCACCCAGTGGACCGCCTTCGCCT
1 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
* **
115470931 TTTCGTTCACCAAGTGGACCGCCTTCGCCT
1 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
*
115470961 TTTGGGCCACCGAGTGGACCGCCTTCGCCT
1 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
*
115470991 TTTCGGCCACCAAGTGGACCGCCTTCGCCT
1 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
115471021 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
1 TTTGGGCCACCAAGTGGACCGCCTTCGCCT
115471051 TTTGGG
1 TTTGGG
115471057 ACTAGACCAC
Statistics
Matches: 143, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 143 1.00
ACGTcount: A:0.12, C:0.37, G:0.25, T:0.26
Consensus pattern (30 bp):
TTTGGGCCACCAAGTGGACCGCCTTCGCCT
Found at i:115519188 original size:5 final size:5
Alignment explanation
Indices: 115519180--115519205 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
115519170 ATTAAAAAAT
115519180 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
115519206 GGAGGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:115523182 original size:46 final size:44
Alignment explanation
Indices: 115523094--115523185 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
115523084 TACAACATCG
*
115523094 TTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTCCA
1 TTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTCCA
* ***
115523138 TTCCATTCAACTAAACAGTTGAATTACTTATTACAGCTCTATTCCA
1 TTCCATTCAACCAAACACAAGAA-TAC-TATTACAGCTCTATTCCA
115523184 TT
1 TT
115523186 ACAGCTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 19 0.46
45 3 0.07
46 19 0.46
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (44 bp):
TTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTCCA
Found at i:115523188 original size:16 final size:16
Alignment explanation
Indices: 115523167--115523222 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
115523157 TGAATTACTT
115523167 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
115523183 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
115523199 ATTACAG-TCCTATTCC
1 ATTACAGCT-CTATTCC
115523215 ATTACAGC
1 ATTACAGC
115523223 CAACCAAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 1 0.03
16 35 0.97
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:115528217 original size:19 final size:18
Alignment explanation
Indices: 115528180--115528222 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
115528170 AAGAAATCAA
*
115528180 TAAATATATTTAGATATG
1 TAAATATATTTAAATATG
*
115528198 TAAATATTTGTTAAATATG
1 TAAATATAT-TTAAATATG
115528217 TAAATA
1 TAAATA
115528223 ATATATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (18 bp):
TAAATATATTTAAATATG
Found at i:115531479 original size:118 final size:115
Alignment explanation
Indices: 115531329--115531693 Score: 401
Period size: 118 Copynumber: 3.0 Consensus size: 115
115531319 GTTTGGAAGG
* * *
115531329 TTGGGAGGTCGTGCCCAATCGTG-TTGGGCTTCAATTTTCCATTCGGCTAAAATATGGAATATTT
1 TTGGGA-GTTGTGCCCAATCGTGCTT-GGCTTCAATTTTCCATTCGGCTAAAATACGGAATATCT
*
115531393 TTTGGAAATTTTGTCCATATTTTTTAAAAAATTAAAATGAGGCAATATTTCGTAT
64 TTTGGAAATTTAGTCCAT-TTTTTT--AAAATTAAAATGAGGCAATATTTCGTAT
* *
115531448 TTGGGAGTTGTGCCCAATCGTGCTTGGCTTCAATTTTCCATTCAGCTAAAATACGGAATATCCTT
1 TTGGGAGTTGTGCCCAATCGTGCTTGGCTTCAATTTTCCATTCGGCTAAAATACGGAATATCTTT
* *
115531513 TGGAAATTTCGTCCATTTTTTTTTAAAATTAAAATGAGGCAATATTTTGTATTT
66 TGGAAATTTAGTCCA--TTTTTTTAAAATTAAAATGAGGCAATATTTCGTA--T
* * * *
115531567 AGGGAGTTGGGGAGTTGTGCCCAATCGTGCTGGGCTTCAATTTTCCATCCGACTAAAATACAGAA
1 ------TT-GGGAGTTGTGCCCAATCGTGCTTGGCTTCAATTTTCCATTCGGCTAAAATACGGAA
* * * * *
115531632 TATACTTTT-GAAGTTTAATCCATGTTTTCTCAAATTAAAATGAGGCAATGTTTCGTAT
59 TAT-CTTTTGGAAATTTAGTCCAT-TTTTTTAAAATTAAAATGAGGCAATATTTCGTAT
115531690 TTGG
1 TTGG
115531694 AAATTCAATA
Statistics
Matches: 212, Mismatches: 20, Indels: 31
0.81 0.08 0.12
Matches are distributed among these distances:
116 2 0.01
117 28 0.13
118 65 0.31
119 15 0.07
120 1 0.00
123 1 0.00
124 1 0.00
125 31 0.15
126 64 0.30
127 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (115 bp):
TTGGGAGTTGTGCCCAATCGTGCTTGGCTTCAATTTTCCATTCGGCTAAAATACGGAATATCTTT
TGGAAATTTAGTCCATTTTTTTAAAATTAAAATGAGGCAATATTTCGTAT
Found at i:115531623 original size:126 final size:123
Alignment explanation
Indices: 115531246--115531694 Score: 500
Period size: 126 Copynumber: 3.6 Consensus size: 123
115531236 TTTCGTTCAG
* * * *
115531246 CTAAAATACGCAATATCCTTTGAAAATTTTGTCCAATTTTTTTTTAAAAAATTAAAACGATGCAA
1 CTAAAATACGGAATATCCTTTGGAAATTTTGTCC-ATTTTTTTTT--AAAATTAAAATGAGGCAA
* * * *
115531311 TATTTCGTGTTTGGAAGGTTGGGAGGTCGTGCCCAATCGTGTTGGGCTTCAATTTTCCATTCGG
63 TATTTCGTATTTGG-A-GTTGGGA-GTTGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCGA
* ** **
115531375 CTAAAATATGGAATATTTTTTGGAAATTTTGTCCATATTTTTTAAAAAATTAAAATGAGGCAATA
1 CTAAAATACGGAATATCCTTTGGAAATTTTGTCCAT-TTTTTTTTAAAATTAAAATGAGGCAATA
*
115531440 TTTCGTA--T----TTGGGAGTTGTGCCCAATCGTGCTTGGCTTCAATTTTCCATTC-A
65 TTTCGTATTTGGAGTTGGGAGTTGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCGA
*
115531492 GCTAAAATACGGAATATCCTTTGGAAATTTCGTCCATTTTTTTTTAAAATTAAAATGAGGCAATA
1 -CTAAAATACGGAATATCCTTTGGAAATTTTGTCCATTTTTTTTTAAAATTAAAATGAGGCAATA
* *
115531557 TTTTGTATTTAGGGAGTTGGGGAGTTGTGCCCAATCGTGCTGGGCTTCAATTTTCCATCCGA
65 TTTCGTATTT--GGAGTT-GGGAGTTGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCGA
* * * * ** * * * *
115531619 CTAAAATACAGAATATACTTTTGAAGTTTAATCCA-TGTTTTCTCAAATTAAAATGAGGCAATGT
1 CTAAAATACGGAATATCCTTTGGAAATTTTGTCCATTTTTTTTTAAAATTAAAATGAGGCAATAT
115531683 TTCGTATTTGGA
66 TTCGTATTTGGA
115531695 AATTCAATAA
Statistics
Matches: 274, Mismatches: 34, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
117 32 0.12
118 66 0.24
119 7 0.03
123 3 0.01
125 36 0.13
126 68 0.25
127 25 0.09
128 2 0.01
129 35 0.13
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (123 bp):
CTAAAATACGGAATATCCTTTGGAAATTTTGTCCATTTTTTTTTAAAATTAAAATGAGGCAATAT
TTCGTATTTGGAGTTGGGAGTTGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCGA
Found at i:115531723 original size:125 final size:126
Alignment explanation
Indices: 115531460--115531734 Score: 286
Period size: 125 Copynumber: 2.2 Consensus size: 126
115531450 GGGAGTTGTG
* * * * **
115531460 CCCAATCGTGCTTGGCTTCAATTTTCCATTCAGCTAAAATACGGAATATCCTTTGGAAATTTCGT
1 CCCAATCGTGCTGGGCTTCAATTTTCCATCCAGCTAAAATACAGAATATACTTTGGAAATTTAAT
* * * * * ** * * * *
115531525 CCATTTTTTTTTAAAATTAAAATGAGGCAATATTTTGTATTTAGGGAGTTGGGGAGTTGTG
66 CCATTGTTTTCTAAAATTAAAATGAGGCAATATTTCGTATTTAGGAAATTAAGAAATCGTA
* *
115531586 CCCAATCGTGCTGGGCTTCAATTTTCCATCC-GACTAAAATACAGAATATACTTTTGAAGTTTAA
1 CCCAATCGTGCTGGGCTTCAATTTTCCATCCAG-CTAAAATACAGAATATACTTTGGAAATTTAA
* * *
115531650 TCCA-TGTTTTCTCAAATTAAAATGAGGCAATGTTTCGTATTT-GGAAATTCAATAAATCGTA
65 TCCATTGTTTTCTAAAATTAAAATGAGGCAATATTTCGTATTTAGGAAATT-AAGAAATCGTA
* * *
115531711 CCCAATTGTGCTGGGTTTCGATTT
1 CCCAATCGTGCTGGGCTTCAATTT
115531735 ACCGTTTGGG
Statistics
Matches: 122, Mismatches: 25, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
124 5 0.04
125 59 0.48
126 58 0.48
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (126 bp):
CCCAATCGTGCTGGGCTTCAATTTTCCATCCAGCTAAAATACAGAATATACTTTGGAAATTTAAT
CCATTGTTTTCTAAAATTAAAATGAGGCAATATTTCGTATTTAGGAAATTAAGAAATCGTA
Found at i:115533469 original size:12 final size:11
Alignment explanation
Indices: 115533449--115533479 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
115533439 GTATTCCAAA
115533449 TTTTTTTTTAT
1 TTTTTTTTTAT
115533460 TTTATTTTTTAT
1 TTT-TTTTTTAT
115533472 TTTTTTTT
1 TTTTTTTT
115533480 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:115535659 original size:15 final size:14
Alignment explanation
Indices: 115535641--115535671 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
115535631 TTAATTTATT
115535641 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
115535656 TAATAATAATCTAA
1 TAATAATAATCTAA
115535670 TA
1 TA
115535672 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:115535682 original size:21 final size:20
Alignment explanation
Indices: 115535658--115535726 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
115535648 AATGCTAATA
115535658 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
115535679 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
115535698 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
115535719 ATAATAAT
1 ATAATAAT
115535727 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:115542038 original size:11 final size:9
Alignment explanation
Indices: 115542008--115542050 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
115541998 TTTTAAGTAT
115542008 TATATATATG
1 TATAT-TATG
115542018 TATA-TATG
1 TATATTATG
115542026 TATACTTTATG
1 TATA--TTATG
115542037 TATATTATG
1 TATATTATG
115542046 TATAT
1 TATAT
115542051 ATTTTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.27
9 10 0.33
10 4 0.13
11 8 0.27
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (9 bp):
TATATTATG
Found at i:115542544 original size:18 final size:18
Alignment explanation
Indices: 115542523--115542564 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
115542513 ATATTCTTAC
115542523 TATTATCATTACTATAT-T
1 TATTATCATTACTA-ATGT
*
115542541 TATTATCATTATTAATGT
1 TATTATCATTACTAATGT
115542559 TATTAT
1 TATTAT
115542565 TTTTATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTATCATTACTAATGT
Found at i:115548530 original size:42 final size:41
Alignment explanation
Indices: 115548483--115548651 Score: 123
Period size: 41 Copynumber: 4.1 Consensus size: 41
115548473 GCAAAAATTG
*
115548483 TAAAACACAAAGCAATAGCGGC-ATTGTTGTCAAAACGCCGC
1 TAAAA-ACAGAGCAATAGCGGCGATTGTTGTCAAAACGCCGC
* * * * *
115548524 TAAAAACTGAGCAATAGTGGCGTTTTTTGTTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGATTGTTGTCAAAACGCCGC
* * * *
115548565 TAAAAAACAGAGCATTAGTGGCGCTT-TTGGT-GAAACGCCGC
1 T-AAAAACAGAGCAATAGCGGCGATTGTT-GTCAAAACGCCGC
* * * * *
115548606 TAAAGACCAGAGCATTAGTGGCGCTT-TTGGT-GAAACGCCGC
1 TAAA-AACAGAGCAATAGCGGCGATTGTT-GTCAAAACGCCGC
115548647 TAAAA
1 TAAAA
115548652 GTCATGTAAC
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 17 0.15
41 73 0.65
42 23 0.20
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (41 bp):
TAAAAACAGAGCAATAGCGGCGATTGTTGTCAAAACGCCGC
Found at i:115548559 original size:41 final size:40
Alignment explanation
Indices: 115548514--115548651 Score: 186
Period size: 41 Copynumber: 3.4 Consensus size: 40
115548504 CATTGTTGTC
* * * *
115548514 AAAACGCCGCTAAAAACTGAGCAATAGTGGCGTTTTTTGTT
1 AAAACGCCGCTAAAAACAGAGCATTAGTGGCG-CTTTTGGT
115548555 AAAACGCCGCTAAAAAACAGAGCATTAGTGGCGCTTTTGGT
1 AAAACGCCGCT-AAAAACAGAGCATTAGTGGCGCTTTTGGT
* *
115548596 GAAACGCCGCTAAAGACCAGAGCATTAGTGGCGCTTTTGGT
1 AAAACGCCGCTAAA-AACAGAGCATTAGTGGCGCTTTTGGT
*
115548637 GAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
115548652 GTCATGTAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
40 4 0.04
41 66 0.74
42 19 0.21
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACAGAGCATTAGTGGCGCTTTTGGT
Found at i:115548927 original size:14 final size:14
Alignment explanation
Indices: 115548878--115548930 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
115548868 TCAAATCATA
*
115548878 AACCCTTAAAACTCC
1 AACCCTT-AAACCCC
*
115548893 AACCCCTAAACCCC
1 AACCCTTAAACCCC
115548907 AACCCTTAAACCCC
1 AACCCTTAAACCCC
*
115548921 AAGCCTTAAA
1 AACCCTTAAA
115548931 ACTAACCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 28 0.82
15 6 0.18
ACGTcount: A:0.40, C:0.43, G:0.02, T:0.15
Consensus pattern (14 bp):
AACCCTTAAACCCC
Found at i:115548981 original size:14 final size:14
Alignment explanation
Indices: 115548940--115549022 Score: 69
Period size: 14 Copynumber: 5.8 Consensus size: 14
115548930 AACTAACCTC
115548940 TAAACCCATAAACTA
1 TAAACCC-TAAACTA
* * * *
115548955 TAGATCGTGAACTA
1 TAAACCCTAAACTA
115548969 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
115548983 TAAACCATAAA-TCA
1 TAAACCCTAAACT-A
* *
115548997 TAAACTCTTAAACTG
1 TAAAC-CCTAAACTA
115549012 TAAACCCTAAA
1 TAAACCCTAAA
115549023 ATCTAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
13 1 0.02
14 37 0.70
15 14 0.26
16 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:115549015 original size:29 final size:28
Alignment explanation
Indices: 115548968--115549022 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
115548958 ATCGTGAACT
115548968 ATAAACCCTAAACTATAAACCATAAATC
1 ATAAACCCTAAACTATAAACCATAAATC
* * *
115548996 ATAAACTCTTAAACTGTAAACCCTAAA
1 ATAAAC-CCTAAACTATAAACCATAAA
115549023 ATCTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.24
Consensus pattern (28 bp):
ATAAACCCTAAACTATAAACCATAAATC
Found at i:115549117 original size:21 final size:21
Alignment explanation
Indices: 115549068--115549110 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
115549058 ATATATGTTC
* *
115549068 ATGGTCTAGGATTTAGGGTTT
1 ATGGTTTAAGATTTAGGGTTT
115549089 ATGGTTTAAGATTTAGGGTTT
1 ATGGTTTAAGATTTAGGGTTT
115549110 A
1 A
115549111 ATTTTTAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.44
Consensus pattern (21 bp):
ATGGTTTAAGATTTAGGGTTT
Found at i:115549526 original size:25 final size:24
Alignment explanation
Indices: 115549498--115549558 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
115549488 TATGTAAATT
* *
115549498 TAAAAATTATAAAATATTAAAAAAA
1 TAAAAATTAAAAAAAATT-AAAAAA
* *
115549523 TAAAATTTAAAAAAAATTAAAAAT
1 TAAAAATTAAAAAAAATTAAAAAA
115549547 TAAAAATTAAAA
1 TAAAAATTAAAA
115549559 TTAAAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAATTAAAAAAAATTAAAAAA
Found at i:115549533 original size:7 final size:7
Alignment explanation
Indices: 115549493--115549611 Score: 75
Period size: 7 Copynumber: 16.9 Consensus size: 7
115549483 TTTTATATGT
115549493 AAATTTAA
1 AAATTT-A
115549501 AAATTATA
1 AAATT-TA
115549509 AAATATTAA
1 AAAT-TT-A
**
115549518 AAAAATA
1 AAATTTA
115549525 AAATTTA
1 AAATTTA
115549532 AAA---A
1 AAATTTA
115549536 AAA-TTA
1 AAATTTA
*
115549542 AAAATTA
1 AAATTTA
*
115549549 AAAATTA
1 AAATTTA
*
115549556 AAATTAA
1 AAATTTA
115549563 AAATTTA
1 AAATTTA
115549570 AAATTTA
1 AAATTTA
**
115549577 AAATAAA
1 AAATTTA
*
115549584 AAACTTAA
1 AAA-TTTA
115549592 AAATTTA
1 AAATTTA
*
115549599 ATATTTA
1 AAATTTA
*
115549606 ATATTT
1 AAATTT
115549612 TAATCCATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
4 4 0.04
6 4 0.04
7 60 0.65
8 18 0.20
9 6 0.07
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (7 bp):
AAATTTA
Found at i:115549726 original size:17 final size:18
Alignment explanation
Indices: 115549690--115549728 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
115549680 TTTTGAAAGA
*
115549690 AAAAATAAAAAAAATGTT
1 AAAAATAAAAAAAATATT
115549708 AAAAATAAAAAAAA-ATT
1 AAAAATAAAAAAAATATT
115549725 AAAA
1 AAAA
115549729 TTGAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAATAAAAAAAATATT
Found at i:115550126 original size:9 final size:9
Alignment explanation
Indices: 115550085--115550127 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
115550075 TCCTTCCCCC
115550085 CTTTTCTTTT
1 CTTTT-TTTT
115550095 CTTTTTTTT
1 CTTTTTTTT
*
115550104 TTTTTTTTT
1 CTTTTTTTT
*
115550113 GCTTTGTTTT
1 -CTTTTTTTT
115550123 CTTTT
1 CTTTT
115550128 CAAACATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.84
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:115554006 original size:19 final size:21
Alignment explanation
Indices: 115553978--115554025 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
115553968 TTATTATTTA
115553978 TTTTAGTTTTGATTCTAA-AT
1 TTTTAGTTTTGATTCTAATAT
* *
115553998 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTCTAATAT
115554018 TTTTAGTT
1 TTTTAGTT
115554026 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTCTAATAT
Found at i:115554219 original size:43 final size:43
Alignment explanation
Indices: 115554148--115554254 Score: 178
Period size: 43 Copynumber: 2.5 Consensus size: 43
115554138 TTTTTAAATT
* *
115554148 TCATTACCTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGG
1 TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
*
115554191 TCATGACCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
1 TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
*
115554234 TCTTGACCTTTAGCGGCGTTT
1 TCATGACCTTTAGCGGCGTTT
115554255 TTTTAAATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (43 bp):
TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
Found at i:115564780 original size:20 final size:20
Alignment explanation
Indices: 115564741--115564780 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
115564731 GCAATTGTAT
*
115564741 GTGTTGAAATTATGATTTTA
1 GTGTTGAAATTATGAGTTTA
115564761 GTGTTGAAATT-TGAGGTTTA
1 GTGTTGAAATTATGA-GTTTA
115564781 ATTCATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (20 bp):
GTGTTGAAATTATGAGTTTA
Found at i:115564931 original size:30 final size:28
Alignment explanation
Indices: 115564896--115564971 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 28
115564886 CCTCTAAATT
115564896 AATAAAAGAATTAAATTAAATTAAATTGAA
1 AATAAAA-AATTAAATTAAATTAAATT-AA
**
115564926 AATAAAATAATTAAATTATGTTAAATTAA
1 AATAAAA-AATTAAATTAAATTAAATTAA
115564955 AATATAAAAATTAAATT
1 AATA-AAAAATTAAATT
115564972 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.36
30 27 0.64
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (28 bp):
AATAAAAAATTAAATTAAATTAAATTAA
Found at i:115564971 original size:5 final size:5
Alignment explanation
Indices: 115564904--115564955 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
115564894 TTAATAAAAG
* * **
115564904 AATTA AATTA AATTA AATTGA AAATA AAAT- AATTA AATTA TGTTA AATTA
1 AATTA AATTA AATTA AATT-A AATTA AATTA AATTA AATTA AATTA AATTA
115564954 AA
1 AA
115564956 ATATAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 3 0.08
5 32 0.82
6 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:115565633 original size:16 final size:15
Alignment explanation
Indices: 115565596--115565629 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
115565586 TTAATTATAC
115565596 TTTTATAATTAAATT
1 TTTTATAATTAAATT
115565611 TTTTATAA-TAATATT
1 TTTTATAATTAA-ATT
115565626 TTTT
1 TTTT
115565630 TATATTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATAATTAAATT
Found at i:115566221 original size:13 final size:13
Alignment explanation
Indices: 115566203--115566244 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
115566193 TTCGATTACT
115566203 TCAAAAGTTGTCA
1 TCAAAAGTTGTCA
* *
115566216 TCAAAA-TT-ACT
1 TCAAAAGTTGTCA
115566227 TCAAAAGTTGTCA
1 TCAAAAGTTGTCA
115566240 TCAAA
1 TCAAA
115566245 GCGTAGTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (13 bp):
TCAAAAGTTGTCA
Found at i:115566224 original size:24 final size:24
Alignment explanation
Indices: 115566197--115566244 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
115566187 GCTCAATTCG
115566197 ATTACTTCAAAAGTTGTCATCAAA
1 ATTACTTCAAAAGTTGTCATCAAA
115566221 ATTACTTCAAAAGTTGTCATCAAA
1 ATTACTTCAAAAGTTGTCATCAAA
115566245 GCGTAGTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (24 bp):
ATTACTTCAAAAGTTGTCATCAAA
Found at i:115566917 original size:16 final size:17
Alignment explanation
Indices: 115566898--115566962 Score: 70
Period size: 16 Copynumber: 4.1 Consensus size: 17
115566888 TTTATTTTTA
115566898 AATATTTAAA-ATTATT
1 AATATTTAAATATTATT
115566914 AATATATT-AATA-TATT
1 AATAT-TTAAATATTATT
*
115566930 AATA-TAAAATATTA-T
1 AATATTTAAATATTATT
115566945 AAT-TTTAAATATTATT
1 AATATTTAAATATTATT
115566961 AA
1 AA
115566963 ACATACATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
14 1 0.02
15 17 0.41
16 20 0.49
17 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTTAAATATTATT
Found at i:115567070 original size:13 final size:14
Alignment explanation
Indices: 115567052--115567093 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
115567042 TTTCAATTTT
115567052 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
115567065 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
115567080 ATTTTAAATAATAT
1 ATTTT-AATAATAT
115567094 TCTTCCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:115567078 original size:16 final size:16
Alignment explanation
Indices: 115567056--115567092 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
115567046 AATTTTATTT
115567056 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
115567073 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
115567088 TAATA
1 TAATA
115567093 TTCTTCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:115567175 original size:7 final size:7
Alignment explanation
Indices: 115567163--115567187 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
115567153 AGAGATGGAG
115567163 AGAACAA
1 AGAACAA
115567170 AGAACAA
1 AGAACAA
115567177 AGAACAA
1 AGAACAA
115567184 AGAA
1 AGAA
115567188 AATATGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (7 bp):
AGAACAA
Found at i:115567950 original size:18 final size:19
Alignment explanation
Indices: 115567905--115567956 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
115567895 AAAAATTTCC
*
115567905 CAAGAATTTTAATATGCTT
1 CAAGAATTTTAATATCCTT
* *
115567924 CTAGCATTTTAA-ATCCTT
1 CAAGAATTTTAATATCCTT
*
115567942 CAAGGATTTTAATAT
1 CAAGAATTTTAATAT
115567957 AAATTTTACT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (19 bp):
CAAGAATTTTAATATCCTT
Found at i:115571454 original size:33 final size:33
Alignment explanation
Indices: 115571406--115571468 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
115571396 AATTTAAAAC
* *
115571406 TTAGCCCCTGTACTTTTATTTTTAAGAATTTAG
1 TTAGCCCCTATACTTTTATTTTCAAGAATTTAG
* *
115571439 TTAGTCCCTATACTTTTGTTTTCAAGAATT
1 TTAGCCCCTATACTTTTATTTTCAAGAATT
115571469 AAGTCCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (33 bp):
TTAGCCCCTATACTTTTATTTTCAAGAATTTAG
Found at i:115572486 original size:25 final size:25
Alignment explanation
Indices: 115572458--115572507 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
115572448 CTCTCCATGG
115572458 GTTGAAAGGGTGGAAACATGTATGT
1 GTTGAAAGGGTGGAAACATGTATGT
115572483 GTTGAAAGGGTGGAAACATGTATGT
1 GTTGAAAGGGTGGAAACATGTATGT
115572508 ATGCATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (25 bp):
GTTGAAAGGGTGGAAACATGTATGT
Found at i:115578310 original size:25 final size:25
Alignment explanation
Indices: 115578273--115578321 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
115578263 GTCCAAATTC
**
115578273 AAAAAATTAAAAAATTTATAATTTT
1 AAAAAATTAAAAAAAATATAATTTT
* *
115578298 AAAAACTTGAAAAAAATATAATTT
1 AAAAAATTAAAAAAAATATAATTT
115578322 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAAAATTAAAAAAAATATAATTTT
Found at i:115578504 original size:16 final size:17
Alignment explanation
Indices: 115578472--115578510 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
115578462 GAAAATATAT
115578472 AAATAAAACATTTAAAA
1 AAATAAAACATTTAAAA
*
115578489 ATATAAAACA-TTAAAA
1 AAATAAAACATTTAAAA
115578505 AAATAA
1 AAATAA
115578511 TTGATCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACATTTAAAA
Found at i:115582139 original size:23 final size:24
Alignment explanation
Indices: 115582113--115582166 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
115582103 TAAATATATA
115582113 TAATTATA-TAAACAA-ATTATTAT
1 TAATTATATTAAACAATATT-TTAT
*
115582136 TAATTATATTTAAATAATATTTTAT
1 TAATTATA-TTAAACAATATTTTAT
115582161 TAATTA
1 TAATTA
115582167 GTAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 8 0.30
25 16 0.59
26 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTATATTAAACAATATTTTAT
Found at i:115595447 original size:2 final size:2
Alignment explanation
Indices: 115595440--115596052 Score: 998
Period size: 2 Copynumber: 312.5 Consensus size: 2
115595430 TATCTTCCAG
* * *
115595440 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CC CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * *
115595482 CT CT CT CT CC CT CT CT CT CT CT CC CT CT CC CT CT CT C- CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
115595523 CT C- CC CT CT CT CC CT CT CT CT C- CT CT CT CC CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
115595563 CT CC CT CT CT CT CC CT CT CT CT CT CT CT CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
115595605 CC CT CT C- CT -T CT CT CC CT CT CT CT CT CT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595645 CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595686 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595728 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595770 CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595811 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595852 CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595893 CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595933 CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115595974 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115596016 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
115596053 GTCCTTTAAA
Statistics
Matches: 569, Mismatches: 30, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
1 12 0.02
2 557 0.98
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:115598261 original size:18 final size:19
Alignment explanation
Indices: 115598225--115598271 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
115598215 CCTGCAAAAG
115598225 AAAGCA-AAAAGAAGAAACA
1 AAAGCAGAAAAG-AGAAACA
115598244 AAAGCAGAAAAG-GAAACA
1 AAAGCAGAAAAGAGAAACA
**
115598262 GTAGCAGAAA
1 AAAGCAGAAA
115598272 CAGCAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.56
19 6 0.24
20 5 0.20
ACGTcount: A:0.66, C:0.11, G:0.21, T:0.02
Consensus pattern (19 bp):
AAAGCAGAAAAGAGAAACA
Found at i:115598481 original size:12 final size:12
Alignment explanation
Indices: 115598448--115598481 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
115598438 TGATCCTTTA
115598448 TTATTTTTTTCG
1 TTATTTTTTTCG
*
115598460 TTATTCTTTTTCT
1 TTATT-TTTTTCG
115598473 TTATTTTTT
1 TTATTTTTT
115598482 AAGGCTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (12 bp):
TTATTTTTTTCG
Found at i:115600383 original size:21 final size:18
Alignment explanation
Indices: 115600340--115600384 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
115600330 ATTAAAGTAT
115600340 ATACATAATATACATGAA
1 ATACATAATATACATGAA
115600358 A-ACATAATATAGCATTAGAA
1 ATACATAATATA-CA-T-GAA
115600378 ATACATA
1 ATACATA
115600385 TACATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 1 0.04
20 4 0.17
21 5 0.22
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (18 bp):
ATACATAATATACATGAA
Found at i:115600410 original size:25 final size:27
Alignment explanation
Indices: 115600359--115600411 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
115600349 ATACATGAAA
*
115600359 ACATAATATAGCATTAGAAATACATAT
1 ACATAATATAGCAATAGAAATACATAT
*
115600386 ACATAATATAG-AATA-AAATATATAT
1 ACATAATATAGCAATAGAAATACATAT
115600411 A
1 A
115600412 TATATAGCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 11 0.46
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.30
Consensus pattern (27 bp):
ACATAATATAGCAATAGAAATACATAT
Found at i:115601873 original size:3 final size:3
Alignment explanation
Indices: 115601849--115601902 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
115601839 AATATTCTTG
* * * *
115601849 TTA TTT TTA -TA TTA TTA GTA TTA TTA CTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
115601896 TCA TTA T
1 TTA TTA T
115601903 CATATATATA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:115601925 original size:13 final size:12
Alignment explanation
Indices: 115601904--115601938 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
115601894 TATCATTATC
115601904 ATATATATATGT
1 ATATATATATGT
*
115601916 TTAGTATATATGT
1 ATA-TATATATGT
115601929 ATATATATAT
1 ATATATATAT
115601939 TTTTTACGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
ATATATATATGT
Found at i:115602250 original size:20 final size:21
Alignment explanation
Indices: 115602225--115602295 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
115602215 GTTACATACG
*
115602225 TATATATTATGTGTATT-TTA
1 TATATATTATGTATATTATTA
115602245 TATATATTATGTATATTATTA
1 TATATATTATGTATATTATTA
* ** *
115602266 TCT-TATTATACATATTACGTA
1 TATATATTATGTATATTA-TTA
115602287 TATATATTA
1 TATATATTA
115602296 AATATCGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 28 0.67
21 9 0.21
22 5 0.12
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (21 bp):
TATATATTATGTATATTATTA
Found at i:115602257 original size:18 final size:19
Alignment explanation
Indices: 115602225--115602263 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
115602215 GTTACATACG
*
115602225 TATATATTATGTGTATTTTA
1 TATATATTA-GTGTATATTA
115602245 TATATATTA-TGTATATTA
1 TATATATTAGTGTATATTA
115602263 T
1 T
115602264 TATCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TATATATTAGTGTATATTA
Found at i:115602260 original size:29 final size:29
Alignment explanation
Indices: 115602227--115602295 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
115602217 TACATACGTA
* * *
115602227 TATATTATGTGTATT-TTATATATATTATG
1 TATATTAT-TATATTATTATACATATTACG
*
115602256 TATATTATTATCTTATTATACATATTACG
1 TATATTATTATATTATTATACATATTACG
115602285 TATATATATTA
1 TATAT-TATTA
115602296 AATATCGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.12
29 25 0.74
30 5 0.15
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (29 bp):
TATATTATTATATTATTATACATATTACG
Found at i:115602343 original size:23 final size:22
Alignment explanation
Indices: 115602327--115602373 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
115602317 TATATATGTA
*
115602327 TATATCTTTAATATATAAATAAG
1 TATATCTTT-ATATATATATAAG
*
115602350 TATATCTTTATATA-ATATTAG
1 TATATCTTTATATATATATAAG
115602371 TAT
1 TAT
115602374 TGTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
23 9 0.41
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TATATCTTTATATATATATAAG
Found at i:115603502 original size:15 final size:15
Alignment explanation
Indices: 115603480--115603513 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
115603470 TACCAATAAC
*
115603480 AATA-AATAATAGTA
1 AATATAATAATAGAA
115603494 AATATAATAATAGAA
1 AATATAATAATAGAA
115603509 AATAT
1 AATAT
115603514 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AATATAATAATAGAA
Found at i:115604169 original size:23 final size:23
Alignment explanation
Indices: 115604133--115604187 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
115604123 GTATATGTGC
115604133 ATAAAAAGAGAGAAAAA-AAATAAA
1 ATAAAAA-AGAGAAAAAGAAA-AAA
* *
115604157 ATAAAAAATAGAAAAAGAAAGAA
1 ATAAAAAAGAGAAAAAGAAAAAA
115604180 ATAAAAAA
1 ATAAAAAA
115604188 AATTCGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
ATAAAAAAGAGAAAAAGAAAAAA
Found at i:115604188 original size:24 final size:23
Alignment explanation
Indices: 115604133--115604188 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
115604123 GTATATGTGC
* *
115604133 ATAAAAAGAGAGAAAAAAAATAAA
1 ATAAAAAAAGAGAAAAAAAA-GAA
*
115604157 ATAAAAAATAGA-AAAAGAAAGAA
1 ATAAAAAA-AGAGAAAAAAAAGAA
115604180 ATAAAAAAA
1 ATAAAAAAA
115604189 ATTCGAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.04
23 10 0.36
24 14 0.50
25 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
ATAAAAAAAGAGAAAAAAAAGAA
Found at i:115605968 original size:253 final size:251
Alignment explanation
Indices: 115605400--115606092 Score: 1160
Period size: 253 Copynumber: 2.8 Consensus size: 251
115605390 TTTTTTTTTT
* * *
115605400 GGAA-TTTGAGAAATTGTGCTCTACGTGTT-GGTGTCGATTTATCATTTGACCAAATAACCGAAT
1 GGAATTTTGAGAAATTGTGCCCTACGTGTTGGGTGTCGATTTATCATTTGACCGAACAACCGAAT
* * *
115605463 ATCC-TTTTTAAATTTTAATGCATAAGCTTTGGAAATTACGAGATGATTTTGGTATCAAAGATTT
66 ATCCTTTTTTAAATTTCAATGCATAAGCTTTGGAAATTACGAGATGATTTTGGTATCGAAGGTTT
*
115605527 GAAATATTGTGTCCTACGTGCTGGATATGATATTTTATTTCTT-GAAACAAGAGAATCTTAATCG
131 GAAATATTGTGTCCTACGTGCTGGATGTGATATTTTATTTCTTCGAAACAAGAGAATCTTAATCG
*
115605591 TTCACACTATTGCATTTTTTTCCGAAATTTTTTAACGAGACAATATTTTGTGTTTG
196 TTCACACTATTGCATTTTTATCCGAAATTTTTTAACGAGACAATATTTTGTGTTTG
*
115605647 GGAATTTTGAGAAATTGTGCCCTACGTGTTGGGTGTCGATTTATCATTTGACCGAACAACTGAAT
1 GGAATTTTGAGAAATTGTGCCCTACGTGTTGGGTGTCGATTTATCATTTGACCGAACAACCGAAT
*
115605712 ATCCTTTTTTAAATTTCAATGCATAAGCTTTGGAAATTACGAGATGATTTTGGTATTGAAGGTTT
66 ATCCTTTTTTAAATTTCAATGCATAAGCTTTGGAAATTACGAGATGATTTTGGTATCGAAGGTTT
*
115605777 GAAATATTGTGTCCTACGTGCTGGATGTGATATTTTATTTCTTCGATACAAGAGAATCTTAATCG
131 GAAATATTGTGTCCTACGTGCTGGATGTGATATTTTATTTCTTCGAAACAAGAGAATCTTAATCG
* *
115605842 TTTCACACTATTTCATTTTTATCCGAAATTTTTTTAACGAGGCAATATTTTGTGTTTG
196 -TTCACACTATTGCATTTTTATCCGAAA-TTTTTTAACGAGACAATATTTTGTGTTTG
*
115605900 GGAATTTTGAGAAATTGTGCCCTACGTGTTGGGTGTTGATTTATCATTTGACCGAACAACCGAAT
1 GGAATTTTGAGAAATTGTGCCCTACGTGTTGGGTGTCGATTTATCATTTGACCGAACAACCGAAT
* *
115605965 ATCCTTTTTTAAATTTCAATGCATAAGTTTTGGAAATTATGAGATGATTTTGGTATCGAAGGTTT
66 ATCCTTTTTTAAATTTCAATGCATAAGCTTTGGAAATTACGAGATGATTTTGGTATCGAAGGTTT
* * * *
115606030 GAAATGTCGTGTCTTACGTGCTGGATGTGATATTTTATTTCTTCGAAACAAAAGAATCTTAAT
131 GAAATATTGTGTCCTACGTGCTGGATGTGATATTTTATTTCTTCGAAACAAGAGAATCTTAAT
115606093 ATCCACTTCA
Statistics
Matches: 417, Mismatches: 23, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
247 4 0.01
248 24 0.06
249 35 0.08
250 98 0.24
251 20 0.05
252 25 0.06
253 211 0.51
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (251 bp):
GGAATTTTGAGAAATTGTGCCCTACGTGTTGGGTGTCGATTTATCATTTGACCGAACAACCGAAT
ATCCTTTTTTAAATTTCAATGCATAAGCTTTGGAAATTACGAGATGATTTTGGTATCGAAGGTTT
GAAATATTGTGTCCTACGTGCTGGATGTGATATTTTATTTCTTCGAAACAAGAGAATCTTAATCG
TTCACACTATTGCATTTTTATCCGAAATTTTTTAACGAGACAATATTTTGTGTTTG
Found at i:115606001 original size:131 final size:130
Alignment explanation
Indices: 115605614--115606002 Score: 328
Period size: 122 Copynumber: 3.0 Consensus size: 130
115605604 ATTTTTTTCC
*
115605614 GAAATTTTTTAACGAGACAATATTTTGTGTTTGGGAATTTTGAGAAATTGTGCCCTACGTGTTGG
1 GAAATTTTTTAACGAGGCAATATTTTGTGTTTGGGAATTTTGAGAAATTGTGCCCTACGTGTTGG
* * *
115605679 GTGTCGATTTATCATTTGACCGAACAACTGAATATCCTTTTTTAAATTTCAATGCATAAGCTTTG
66 GTGTTGATTTATCATTTGACCGAACAACAGAATATCCTTTTTTAAATTTCAATGCATAAGTTTTG
* *
115605744 GAAA----TT-ACGA-G--ATGATTTTG-GTATT--GAAGGTTTGA-AATATTGTGTCCTACGTG
1 GAAATTTTTTAACGAGGCAAT-ATTTTGTGT-TTGGGAA-TTTTGAGAA-ATTGTGCCCTACGTG
* * * *** * * ** * * * * * *
115605797 CTGGATG-TGATATT-TTATTTCTTCGATACAAGAGAATCTTAATCGTTTCACA-CT-ATTTCAT
62 TTGGGTGTTGAT-TTATCATTTGACCGA-ACAACAGAAT-ATCCT-TTTTTAAATTTCAATGCAT
* *
115605858 --TTTTATCC
123 AAGTTT-T-G
115605866 GAAATTTTTTTAACGAGGCAATATTTTGTGTTTGGGAATTTTGAGAAATTGTGCCCTACGTGTTG
1 GAAA-TTTTTTAACGAGGCAATATTTTGTGTTTGGGAATTTTGAGAAATTGTGCCCTACGTGTTG
*
115605931 GGTGTTGATTTATCATTTGACCGAACAACCGAATATCCTTTTTTAAATTTCAATGCATAAGTTTT
65 GGTGTTGATTTATCATTTGACCGAACAACAGAATATCCTTTTTTAAATTTCAATGCATAAGTTTT
115605996 G
130 G
115605997 GAAATT
1 GAAATT
115606003 ATGAGATGAT
Statistics
Matches: 185, Mismatches: 45, Indels: 58
0.64 0.16 0.20
Matches are distributed among these distances:
120 2 0.01
121 17 0.09
122 47 0.25
123 11 0.06
124 5 0.03
125 4 0.02
126 2 0.01
127 2 0.01
128 4 0.02
129 6 0.03
130 17 0.09
131 47 0.25
132 18 0.10
133 3 0.02
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (130 bp):
GAAATTTTTTAACGAGGCAATATTTTGTGTTTGGGAATTTTGAGAAATTGTGCCCTACGTGTTGG
GTGTTGATTTATCATTTGACCGAACAACAGAATATCCTTTTTTAAATTTCAATGCATAAGTTTTG
Found at i:115606575 original size:19 final size:19
Alignment explanation
Indices: 115606525--115606575 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
115606515 TTTTTATTTT
*
115606525 AATTTATCTTTCTTTTAAAA
1 AATTTAT-TTTTTTTTAAAA
* *
115606545 AATAATAATTTTTTTTAAAA
1 AAT-TTATTTTTTTTTAAAA
115606565 AATTTATTTTT
1 AATTTATTTTT
115606576 CAGTCATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.24
20 17 0.68
21 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTATTTTTTTTTAAAA
Found at i:115612886 original size:28 final size:28
Alignment explanation
Indices: 115612821--115612880 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
115612811 TTTAACATGG
* *
115612821 ATAAAATATAAA--AAATTTGAAATAAA
1 ATAATATATAAAGCAAATTTCAAATAAA
115612847 ATAATATATAAAGCAAATTTCAAAT-AA
1 ATAATATATAAAGCAAATTTCAAATAAA
115612874 ATAATAT
1 ATAATAT
115612881 GTTAAATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 11 0.37
27 9 0.30
28 10 0.33
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (28 bp):
ATAATATATAAAGCAAATTTCAAATAAA
Found at i:115613434 original size:3 final size:3
Alignment explanation
Indices: 115613426--115613473 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
115613416 GTTGCTCAAG
* *
115613426 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
115613474 GTAAATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:115615326 original size:28 final size:28
Alignment explanation
Indices: 115615295--115615350 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
115615285 ACATTGAGAG
115615295 TTAATTTTAAAATAATGAGAAAATATAA
1 TTAATTTTAAAATAATGAGAAAATATAA
115615323 TTAATTTTAAAATAATGAGAAAATATAA
1 TTAATTTTAAAATAATGAGAAAATATAA
115615351 AAATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (28 bp):
TTAATTTTAAAATAATGAGAAAATATAA
Found at i:115616085 original size:29 final size:29
Alignment explanation
Indices: 115616043--115616101 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
115616033 AAAATTCTAA
115616043 AATAGAATCCGAATTTTATTTGATGTTTT
1 AATAGAATCCGAATTTTATTTGATGTTTT
115616072 AATAGAATCCGAATTTTATTTGATGTTTT
1 AATAGAATCCGAATTTTATTTGATGTTTT
115616101 A
1 A
115616102 TATGTTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (29 bp):
AATAGAATCCGAATTTTATTTGATGTTTT
Found at i:115623055 original size:171 final size:171
Alignment explanation
Indices: 115622713--115623199 Score: 465
Period size: 171 Copynumber: 2.8 Consensus size: 171
115622703 ATAGAGTTTG
* * * * * *
115622713 TCAAAAATTAAAATATAGAGTTTAAATCTTAAATTTAAATGTAGTATAGGGATCAAAATTGAATT
1 TCAAAAATTAAAATATAGAGATTAAATCTCAAATTTAAACGTAGTATAAGGAACAAAATTGAAAT
* *
115622778 TTGACCATTGTTATATAACTTGAAAAAAA-TAGAGGGGTCAAATTTG-AAATTCAACCA--TTTA
66 TTGACCATTATTATATAA-TT-AAAAAAAGTAGAGGGATCAAATTTGAAAATT-AACCATTTTTA
* *
115622839 TAATGTCAAAAAAAAGGGAAAGGACACATGTTCTATTGAAAGGCCT
128 TAATGTCAAAAAAAA-GGAAA-GACACATGTCCTATCGAAAGGCCT
** *
115622885 T-AAAAATTAAAATATAGAGATTAAATCTCAAATTTGGACGTAGTATAAGGAACAAAATTAAAAT
1 TCAAAAATTAAAATATAGAGATTAAATCTCAAATTTAAACGTAGTATAAGGAACAAAATTGAAAT
* * * * * *
115622949 TTAACCATTTTTATATTATTTAAAAATGTAGAGGGATCAAATTTGAAAATTGACCATTTCTTATA
66 TTGACCATTATTATATAATTAAAAAAAGTAGAGGGATCAAATTTGAAAATTAACCATTT-TTATA
*
115623014 ATGTCAAATAAAAA-G-AA-AC-CGATGTGCCTTATCGGAAGGCCT
130 ATGTCAAA-AAAAAGGAAAGACAC-ATGT-CC-TATCGAAAGGCCT
* * * * * * * * ***
115623056 TCGATAATTAAAATATAGATATCAAAACTCAAACTTAAACATAATATAA-GAATTGTAATTGAAA
1 TCAAAAATTAAAATATAGAGATTAAATCTCAAATTTAAACGTAGTATAAGGAA-CAAAATTGAAA
* * *
115623120 TTTGACCATTATTATGTAATTCAAAAAAAGTAGAGAGATCAAATTT-AAAATTTAACCTTTTTTT
65 TTTGACCATTATTATATAATT-AAAAAAAGTAGAGGGATCAAATTTGAAAA-TTAACC-ATTTTT
115623184 ATAATGTCAAAAAAAA
127 ATAATGTCAAAAAAAA
115623200 AAGAGAAAGG
Statistics
Matches: 259, Mismatches: 42, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
168 1 0.00
169 11 0.04
170 23 0.09
171 91 0.35
172 73 0.28
173 52 0.20
174 8 0.03
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.32
Consensus pattern (171 bp):
TCAAAAATTAAAATATAGAGATTAAATCTCAAATTTAAACGTAGTATAAGGAACAAAATTGAAAT
TTGACCATTATTATATAATTAAAAAAAGTAGAGGGATCAAATTTGAAAATTAACCATTTTTATAA
TGTCAAAAAAAAGGAAAGACACATGTCCTATCGAAAGGCCT
Found at i:115623656 original size:20 final size:19
Alignment explanation
Indices: 115623615--115623658 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
115623605 AAAAAACATT
*
115623615 AAAAATATTTAAAACTATA
1 AAAAATATTTAAAACTAAA
115623634 AAAAATATTTTAAAA-TGAAA
1 AAAAATA-TTTAAAACT-AAA
115623654 AAAAA
1 AAAAA
115623659 AACTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATATTTAAAACTAAA
Found at i:115631263 original size:12 final size:13
Alignment explanation
Indices: 115631246--115631275 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
115631236 CCAATTTGTG
115631246 AAAAAT-AAAATA
1 AAAAATAAAAATA
115631258 AAAAATAAAAATA
1 AAAAATAAAAATA
115631271 AAAAA
1 AAAAA
115631276 CACAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:115633474 original size:27 final size:24
Alignment explanation
Indices: 115633444--115633511 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
115633434 AAAAATGACT
115633444 AAAAATTGTCCACTATAAAAACTATGG
1 AAAAATTGTCCA-T-TAAAAA-TATGG
*
115633471 AAAAATTG-CCATTTAAAATATGG
1 AAAAATTGTCCATTAAAAATATGG
*
115633494 AAAAATT-TCCATTTAAAA
1 AAAAATTGTCCATTAAAAA
115633512 CCATTCATTC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 22 0.56
24 5 0.13
25 1 0.03
26 3 0.08
27 8 0.21
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (24 bp):
AAAAATTGTCCATTAAAAATATGG
Found at i:115633498 original size:24 final size:24
Alignment explanation
Indices: 115633461--115633512 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
115633451 GTCCACTATA
115633461 AAAACTATGGAAAAATTGCCATTT
1 AAAACTATGGAAAAATTGCCATTT
*
115633485 AAAA-TATGGAAAAATTTCCATTT
1 AAAACTATGGAAAAATTGCCATTT
115633508 AAAAC
1 AAAAC
115633513 CATTCATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (24 bp):
AAAACTATGGAAAAATTGCCATTT
Found at i:115634948 original size:21 final size:21
Alignment explanation
Indices: 115634924--115634964 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
115634914 TTTTTTAAAA
115634924 ATAAAAATTAAATAA-AAATAG
1 ATAAAAATTAAA-AATAAATAG
*
115634945 ATAAAATTTAAAAATAAATA
1 ATAAAAATTAAAAATAAATA
115634965 AAATGAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAAAATTAAAAATAAATAG
Found at i:115634956 original size:17 final size:17
Alignment explanation
Indices: 115634936--115634968 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
115634926 AAAAATTAAA
*
115634936 TAAAAATAGATAAAATT
1 TAAAAATAAATAAAATT
115634953 TAAAAATAAATAAAAT
1 TAAAAATAAATAAAAT
115634969 GAGGGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAAAATAAATAAAATT
Done.