Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007824.1 Hibiscus syriacus cultivar Beakdansim tig00110162_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: 895964
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 4
Found at i:470995 original size:64 final size:64
Alignment explanation
Indices: 470927--471103 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
470917 TAAAATAAAT
* *
470927 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA-A
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAAT-ACA
* * * *
470991 ACATCGAATGCAA-TCGGTGCATCAATGCATAAGGAGTGCATCGATGCATCCCAGTAATAATACT
1 ACATCGAATGCAATTC-ATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACA
* ** * * *
471055 ACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
471104 ACCTTCATTA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.03
64 91 0.96
65 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (64 bp):
ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACA
Found at i:471557 original size:30 final size:31
Alignment explanation
Indices: 471512--471722 Score: 278
Period size: 30 Copynumber: 7.0 Consensus size: 31
471502 AGGGTCGAGG
*
471512 GTTTA-CTATGTTTCTTCGGGATATATGGAC-
1 GTTTACCTATG-TTCTTCGGGACATATGGACT
471542 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
471573 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
471604 G-TTA-CTATGTTCTTCGGGA-ACATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
**
471632 GTTTACCTATG-TCTTCGGGACATACAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
471662 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
471692 ATTTACCTA-GGTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
471722 G
1 G
471723 GTCCTTCGGG
Statistics
Matches: 162, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
28 9 0.06
29 33 0.20
30 77 0.48
31 43 0.27
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:471667 original size:89 final size:90
Alignment explanation
Indices: 471514--471691 Score: 290
Period size: 89 Copynumber: 2.0 Consensus size: 90
471504 GGTCGAGGGT
* **
471514 TTACTATGTTTCTTCGGGATATATGGACGTTTACCTATGTTCTTCGGGACATATGGACTGTTTAC
1 TTACTATGTTTCTTCGGGATACATGGACGTTTACCTATGTTCTTCGGGACATACAGACTGTTTAC
471579 CTATGTTCTTCGGGACATATGGACTG
66 CTATGTTCTTC-GGACATATGGACTG
471605 TTACTATG-TTCTTCGGGA-ACATGGACTGTTTACCTATG-TCTTCGGGACATACAGACTGTTTA
1 TTACTATGTTTCTTCGGGATACATGGAC-GTTTACCTATGTTCTTCGGGACATACAGACTGTTTA
471667 CCTATGTTCTTCGGACATATGGACT
65 CCTATGTTCTTCGGACATATGGACT
471692 ATTTACCTAG
Statistics
Matches: 83, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
88 13 0.16
89 41 0.49
90 21 0.25
91 8 0.10
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (90 bp):
TTACTATGTTTCTTCGGGATACATGGACGTTTACCTATGTTCTTCGGGACATACAGACTGTTTAC
CTATGTTCTTCGGACATATGGACTG
Found at i:471707 original size:89 final size:90
Alignment explanation
Indices: 471514--471722 Score: 275
Period size: 89 Copynumber: 2.3 Consensus size: 90
471504 GGTCGAGGGT
* * **
471514 TTACTATGTTTCTTCGGGATATATGGAC-GTTTACCTATGTTCTTCGGGACATATGGACTGTTTA
1 TTACTATG-GTCTTCGGGA-ACATGGACTGTTTACCTATGTTCTTCGGGACATACAGACTGTTTA
471578 CCTATGTTCTTCGGGACATATGGACTG
64 CCTATGTTCTTCGGGACATATGGACTG
*
471605 TTACTATGTTCTTCGGGAACATGGACTGTTTACCTATG-TCTTCGGGACATACAGACTGTTTACC
1 TTACTATGGTCTTCGGGAACATGGACTGTTTACCTATGTTCTTCGGGACATACAGACTGTTTACC
*
471669 TATGTTCTTC-GGACATATGGACTAT
66 TATGTTCTTCGGGACATATGGACT-G
471694 TTACCTA-GGTCTTC-GGAATCTATGGACTG
1 TTA-CTATGGTCTTCGGGAA-C-ATGGACTG
471723 GTCCTTCGGG
Statistics
Matches: 108, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
88 17 0.16
89 51 0.47
90 32 0.30
91 8 0.07
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (90 bp):
TTACTATGGTCTTCGGGAACATGGACTGTTTACCTATGTTCTTCGGGACATACAGACTGTTTACC
TATGTTCTTCGGGACATATGGACTG
Found at i:478536 original size:20 final size:20
Alignment explanation
Indices: 478511--478553 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
478501 ATGACTTGAT
*
478511 TATATATATGTCATA-TGAAA
1 TATATACATG-CATATTGAAA
478531 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
478551 TAT
1 TAT
478554 CATGATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (20 bp):
TATATACATGCATATTGAAA
Found at i:493424 original size:50 final size:52
Alignment explanation
Indices: 493369--493466 Score: 157
Period size: 50 Copynumber: 1.9 Consensus size: 52
493359 ATATATGCTG
493369 GCAAAATAACTGAGCAATAA-TATCA-TC-TTTGCATCACATCTGACAATCAT
1 GCAAAATAACTGAGCAA-AAGTATCATTCTTTTGCATCACATCTGACAATCAT
*
493419 GCAAAATAACTGAGCAAAAGTATTATTCTTTTGCATCACATCTGACAA
1 GCAAAATAACTGAGCAAAAGTATCATTCTTTTGCATCACATCTGACAA
493467 CTTCATAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 2 0.05
50 21 0.48
51 2 0.05
52 19 0.43
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (52 bp):
GCAAAATAACTGAGCAAAAGTATCATTCTTTTGCATCACATCTGACAATCAT
Found at i:501367 original size:7 final size:7
Alignment explanation
Indices: 501355--501387 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
501345 ATAATATATT
501355 ATAATAA
1 ATAATAA
501362 ATAATAA
1 ATAATAA
501369 ATAATAA
1 ATAATAA
501376 AT-ATAA
1 ATAATAA
501382 ATAATA
1 ATAATA
501388 TGTATGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAATAA
Found at i:501570 original size:39 final size:38
Alignment explanation
Indices: 501475--501613 Score: 138
Period size: 40 Copynumber: 3.6 Consensus size: 38
501465 AAAATATTTT
* * *
501475 AAAACTATATATTATATGTTTTCAAAAATACGTTTTC--
1 AAAATTATATATTATATGTTTCCAAAAA-CCGTTTTCTG
* *
501512 AAAATCTATATTATATATATGTTTCCGAAAACCGTTTTTTG
1 AAAAT-TATA-TAT-TATATGTTTCCAAAAACCGTTTTCTG
*
501553 AAAAATTATATATTATATTGTTTTCAAAAACCGTTTTCTG
1 -AAAATTATATATTATA-TGTTTCCAAAAACCGTTTTCTG
* *
501593 AAAACTATATACTATATGTTT
1 AAAATTATATATTATATGTTT
501614 TTCAAAAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
37 4 0.05
38 9 0.11
39 27 0.32
40 36 0.42
41 4 0.05
42 5 0.06
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (38 bp):
AAAATTATATATTATATGTTTCCAAAAACCGTTTTCTG
Found at i:501660 original size:38 final size:36
Alignment explanation
Indices: 501429--501686 Score: 234
Period size: 39 Copynumber: 6.8 Consensus size: 36
501419 TATATTTAAA
* *
501429 AAAAACATTTT-AAAAACTATATACTATATGTTTTC
1 AAAAATATTTTCAAAAACTATATATTATATGTTTTC
501464 AAAAATATTTT--AAAACTATATATTATATGTTTTC
1 AAAAATATTTTCAAAAACTATATATTATATGTTTTC
* *
501498 AAAAATACGTTTTCAAAATCTATATTATATATATGTTTCC
1 AAAAATA--TTTTCAAAAACTATA-TAT-TATATGTTTTC
* * * *
501538 GAAAACCGTTTTTTGAAAAATTATATATTATATTGTTTTC
1 -AAAA--ATATTTTCAAAAACTATATATTATA-TGTTTTC
** * *
501578 AAAAACCGTTTTCTGAAAACTATATACTATATGTTTTTC
1 AAAAA-TATTTTC-AAAAACTATATATTATATG-TTTTC
*
501617 AAAAATATTTTCAAAAAAACTATATATTATATGTTTTT
1 AAAAATATTTTC--AAAAACTATATATTATATGTTTTC
*
501655 AAAAATATGTTTTCAAAAACTATATTTTATAT
1 AAAAATA--TTTTCAAAAACTATATATTATAT
501687 ATATATATAT
Statistics
Matches: 183, Mismatches: 24, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
34 29 0.16
35 10 0.05
36 4 0.02
38 47 0.26
39 52 0.28
40 24 0.13
41 16 0.09
43 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (36 bp):
AAAAATATTTTCAAAAACTATATATTATATGTTTTC
Found at i:501689 original size:2 final size:2
Alignment explanation
Indices: 501682--501724 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
501672 AACTATATTT
501682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
501724 T
1 T
501725 TTCCAAAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:501831 original size:37 final size:38
Alignment explanation
Indices: 501547--501831 Score: 109
Period size: 39 Copynumber: 7.4 Consensus size: 38
501537 CGAAAACCGT
* * *
501547 TTTTTGAAAAATTATATATTATAT-TGTTTTCAAAAACC
1 TTTTTCAAAAATTATATATTATATAT-TTTTAAAAAATC
* * * * * *
501585 GTTTTCTGAAAACTATATACTATATGTTTTTCAAAAAT-
1 TTTTTC-AAAAATTATATATTATATATTTTTAAAAAATC
* * *
501623 ATTTTCAAAAAAACTATATATTATATGTTTTTAAAAATAT-
1 TTTTTC--AAAAATTATATATTATATATTTTTAAAAA-ATC
* * * * * * * *
501663 GTTTTCAAAAACTATATTTTATATATATAT-ATATATA
1 TTTTTCAAAAATTATATATTATATATTTTTAAAAAATC
* * * * ** * *
501700 TATAT-ATATA-TATATATATATATATTTCCAAAACCCATT
1 TTTTTCAAAAATTATATAT-TATATATTTTTAAAA--AATC
* * *
501739 TTTTTAAAAAAACTATATATTATATTTTTTTAAAAAATC
1 TTTTT-CAAAAATTATATATTATATATTTTTAAAAAATC
* *
501778 GTTTTTTAAAAATTATATATTATATATTTTT-CAAAAT-
1 -TTTTTCAAAAATTATATATTATATATTTTTAAAAAATC
*
501815 TATTTTCAAAATTTATA
1 T-TTTTCAAAAATTATA
501832 CTATATTATT
Statistics
Matches: 188, Mismatches: 45, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
35 6 0.03
36 14 0.07
37 19 0.10
38 34 0.18
39 80 0.43
40 13 0.07
41 15 0.08
42 7 0.04
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (38 bp):
TTTTTCAAAAATTATATATTATATATTTTTAAAAAATC
Found at i:504883 original size:313 final size:311
Alignment explanation
Indices: 504309--504899 Score: 1004
Period size: 313 Copynumber: 1.9 Consensus size: 311
504299 TTTATCCACA
* * * *
504309 CCAAAAAAAAAAGGCTATTGTCAACAGTAAAACCAATAAAAATTTAATAGCAGCTTCGTCATGGC
1 CCAAAAAAAAAAAGCTATTGTCAACAGAAAAACCAATAAAAAATTAATAGCAGCTTCATCATGGC
* *
504374 CTAGGCCTTGGGGCAGCGTTGGATCAATTGGCCAATTGTTTGTAGGATTAAGACTAACCACTCCA
66 CTAGGCCTTGGGGCAGCGTTGAATCAATTGGACAATTGTTTGTAGGATTAAGACTAACCACTCCA
* *
504439 AACTCCAGAGTCCGGAGGTGCAAATCCTTGAGTTCTGCTATTTTGCAACCAATTATATTTGGCTA
131 AACTCCAGAGTCCGGAGGTACAAATCCTTGAGTTCTGCTATTTTACAACCAATTATATTTGGCTA
*
504504 CAATAATTACTAGATAAATGATAGGGTAGATCATGGAAAAAATTAACTACTAAAACAAACGGTGG
196 CAATAATTACTAGATAAATGATAGGGTAGACCATGGAAAAAATTAACTACTAAAACAAACGGTGG
*
504569 ACCAGAGCAAAATATCTATAAATCGATTACCAGTGGTTAATCCACACACACC
261 ACCAAAG-AAAATATCTATAAATCGATTACCAGTGGTTAATCCACACACACC
504621 CCAAAAAAAAAACAGCTATTGTCAACAGAAAAACCAATAAAAAATTAATAGCAGCTTCATCATGG
1 CCAAAAAAAAAA-AGCTATTGTCAACAGAAAAACCAATAAAAAATTAATAGCAGCTTCATCATGG
* *
504686 CTTAGGCCTTGGGGCAGCGTTGAATCAATTGGACAATTGTTTGTAGGATTAAGACTAATCACTCC
65 CCTAGGCCTTGGGGCAGCGTTGAATCAATTGGACAATTGTTTGTAGGATTAAGACTAACCACTCC
* *
504751 AAATTTCAGAGTCCAGG-GGTACAAATCCTTGAGTTCTGCTATTTTACAACCAATTATATTTGGC
130 AAACTCCAGAGTCC-GGAGGTACAAATCCTTGAGTTCTGCTATTTTACAACCAATTATATTTGGC
* *
504815 TACAATAATTACTAGATAAATTATAGGGTAGACCATGGAAAAAATTAACTACTAAAACAAATGGT
194 TACAATAATTACTAGATAAATGATAGGGTAGACCATGGAAAAAATTAACTACTAAAACAAACGGT
504880 GGACCAAAGAAAATATCTAT
259 GGACCAAAGAAAATATCTAT
504900 CAACTAATTA
Statistics
Matches: 261, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
312 23 0.09
313 236 0.90
314 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (311 bp):
CCAAAAAAAAAAAGCTATTGTCAACAGAAAAACCAATAAAAAATTAATAGCAGCTTCATCATGGC
CTAGGCCTTGGGGCAGCGTTGAATCAATTGGACAATTGTTTGTAGGATTAAGACTAACCACTCCA
AACTCCAGAGTCCGGAGGTACAAATCCTTGAGTTCTGCTATTTTACAACCAATTATATTTGGCTA
CAATAATTACTAGATAAATGATAGGGTAGACCATGGAAAAAATTAACTACTAAAACAAACGGTGG
ACCAAAGAAAATATCTATAAATCGATTACCAGTGGTTAATCCACACACACC
Found at i:510287 original size:46 final size:46
Alignment explanation
Indices: 510220--510311 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
510210 AACGGATCAG
510220 ACGAATATTAGCAATAATCTAAACTGAATTCAAAATTCAAAGATAA
1 ACGAATATTAGCAATAATCTAAACTGAATTCAAAATTCAAAGATAA
*
510266 ACGAATATTAGCAATAATCTAAACTGAATTCAGAATTCAAAGATAA
1 ACGAATATTAGCAATAATCTAAACTGAATTCAAAATTCAAAGATAA
510312 TGTTGGCAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (46 bp):
ACGAATATTAGCAATAATCTAAACTGAATTCAAAATTCAAAGATAA
Found at i:512514 original size:26 final size:25
Alignment explanation
Indices: 512471--512523 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
512461 GTATATATAG
*
512471 ATATTATTTTTAATTATTTAATAAAA
1 ATATTATTTTTAAATATTTAA-AAAA
512497 ATATT-TTTTTCAAATATTTAAAAAA
1 ATATTATTTTT-AAATATTTAAAAAA
512522 AT
1 AT
512524 TAAAACGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTATTTTTAAATATTTAAAAAA
Found at i:519713 original size:2 final size:2
Alignment explanation
Indices: 519660--519697 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
519650 CTAATAGAGT
519660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519698 ACGTTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:520651 original size:23 final size:21
Alignment explanation
Indices: 520610--520658 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
520600 AAAGAACCGA
520610 AAAACATGCCAAAAACATAAG
1 AAAACATGCCAAAAACATAAG
* *
520631 AAAACATGTCATAAAAGCATATG
1 AAAACATGCCA-AAAA-CATAAG
520654 AAAAC
1 AAAAC
520659 GTACAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 4 0.17
23 10 0.42
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAACATGCCAAAAACATAAG
Found at i:521211 original size:22 final size:22
Alignment explanation
Indices: 521183--521224 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
521173 TCTAATTTAT
521183 TCTATTTATAATTGTTAGAAAC
1 TCTATTTATAATTGTTAGAAAC
521205 TCTATTTATAATTGTTAGAA
1 TCTATTTATAATTGTTAGAA
521225 TGACATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (22 bp):
TCTATTTATAATTGTTAGAAAC
Found at i:528614 original size:3 final size:3
Alignment explanation
Indices: 528606--528644 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
528596 TTTTTCACTA
*
528606 TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
528645 AATTAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:528616 original size:22 final size:20
Alignment explanation
Indices: 528591--528641 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
528581 TAGTGTAGAC
*
528591 ATTAATTTTTCACTATATTATT
1 ATTAATTATT-ACTATA-TATT
*
528613 ATT-ATTATTATTATATATT
1 ATTAATTATTACTATATATT
528632 ATTAA-TATTA
1 ATTAATTATTA
528642 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 12 0.46
20 6 0.23
21 5 0.19
22 3 0.12
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTAATTATTACTATATATT
Found at i:528645 original size:9 final size:9
Alignment explanation
Indices: 528609--528649 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
528599 TTCACTATAT
*
528609 TATTATTAT
1 TATTATTAA
528618 TATTATTATA
1 TATTATTA-A
528628 TATTATTAA
1 TATTATTAA
528637 TATTATTAA
1 TATTATTAA
528646 -ATTA
1 TATTA
528650 AATATTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 4 0.13
9 18 0.60
10 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:530120 original size:4 final size:4
Alignment explanation
Indices: 530111--530135 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
530101 AATATAGTAT
530111 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
530136 GTTTTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:530190 original size:19 final size:17
Alignment explanation
Indices: 530166--530202 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
530156 CATGAAATAC
530166 AATATTATATTTTTATAAT
1 AATATT-TATTTTTA-AAT
530185 AATATTTATTTTTAAAT
1 AATATTTATTTTTAAAT
530202 A
1 A
530203 TCAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTTATTTTTAAAT
Found at i:530572 original size:2 final size:2
Alignment explanation
Indices: 530536--530561 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
530526 ATAAATATCT
530536 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
530562 AATTAATATA
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:531115 original size:28 final size:28
Alignment explanation
Indices: 531056--531113 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
531046 TAATTCTTTC
531056 TTTTCATAATTTTTATATATACTTATTA
1 TTTTCATAATTTTTATATATACTTATTA
* *
531084 TTTTCATAATATTTATATGTA--TATTA
1 TTTTCATAATTTTTATATATACTTATTA
531110 TTTT
1 TTTT
531114 TTTATTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 9 0.32
28 19 0.68
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTCATAATTTTTATATATACTTATTA
Found at i:533539 original size:12 final size:13
Alignment explanation
Indices: 533522--533550 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
533512 ACATTCACAT
533522 ATTTACA-TTTGC
1 ATTTACATTTTGC
533534 ATTTACATTTTGC
1 ATTTACATTTTGC
533547 ATTT
1 ATTT
533551 TTTTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:536822 original size:32 final size:32
Alignment explanation
Indices: 536786--536847 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
536776 GTCAGACACA
* *
536786 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTATACAAGATGAGCATAACAACG
536818 AGAAGTATCTATACAAGATGAGCATAACAA
1 AGAAGTATCTATACAAGATGAGCATAACAA
536848 TCATTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTATACAAGATGAGCATAACAACG
Found at i:541461 original size:45 final size:45
Alignment explanation
Indices: 541363--542044 Score: 1060
Period size: 46 Copynumber: 15.0 Consensus size: 45
541353 CTATTTCCCA
541363 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCATAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCA-AAACCTTCGGGT
*
541409 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
541454 CATCTGTAAGTCCTTCAATGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
541499 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
541544 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
541589 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
541635 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAATCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAACCTTCGGGT
* *
541681 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
541727 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* **
541772 CATCTGTAAGCCCTTCAAGT-CATGATATTTTCAAAAACCTTCAAGT
1 CATCTGTAAGCCCTTC-AGTGCATGATGTTTTC-AAAACCTTCGGGT
*
541818 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
541864 CATCTGTAAGCCCTTCAGTGCATGATGTTATTAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTT-TTCAAAACCTTCGGGT
* *
541910 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
541955 CATCTGTAAGCCCTTCAGTGTATGATATTATCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
542001 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
542045 AGTTTTTTGA
Statistics
Matches: 589, Mismatches: 39, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
45 270 0.46
46 314 0.53
47 5 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:541761 original size:183 final size:183
Alignment explanation
Indices: 541363--542044 Score: 1122
Period size: 183 Copynumber: 3.7 Consensus size: 183
541353 CTATTTCCCA
* *
541363 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCATAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCA-AAACCTTCGGGTCATCTGTAAGCCCTTCAGT
* * * *
541428 GCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAATGCATGATG-TTTTCAAAAC
65 GCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAAC
* * *
541491 CTCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTTGGGT
130 CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
541544 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* *
541609 CATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAATC
66 CATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAACC
541674 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
131 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
541727 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTC-AGT
** * *
541792 -CATGATATTTTCAAAAACCTTCAAGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAAC
65 GCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAAC
* *
541856 CTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATTAAAAACCTTCGGGT
130 CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
541910 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* *
541975 TATGATATTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTT-AAAACC
66 CATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAACC
542039 TTCGGG
131 TTCGGG
542045 AGTTTTTTGA
Statistics
Matches: 470, Mismatches: 26, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
180 43 0.09
181 70 0.15
182 61 0.13
183 293 0.62
184 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (183 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAACC
TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
Found at i:542289 original size:9 final size:9
Alignment explanation
Indices: 542251--542293 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
542241 ATTTTTCACT
542251 ATATTATTA
1 ATATTATTA
*
542260 TTATTATATA
1 ATATTAT-TA
542270 TATATTATTA
1 -ATATTATTA
542280 ATATTATTA
1 ATATTATTA
542289 A-ATTA
1 ATATTA
542294 AATATTACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 4 0.13
9 16 0.53
10 4 0.13
11 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTATTA
Found at i:543597 original size:17 final size:19
Alignment explanation
Indices: 543561--543597 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
543551 CATGAAATAC
543561 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
543580 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
543597 A
1 A
543598 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:549221 original size:16 final size:17
Alignment explanation
Indices: 549200--549242 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
549190 AAGAAATTTA
549200 TTTTTAT-GTTATTATT
1 TTTTTATAGTTATTATT
549216 TTTTTAAATAGTTATTATT
1 TTTTT--ATAGTTATTATT
549235 TTTTTATA
1 TTTTTATA
549243 TTAATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 3 0.12
18 2 0.08
19 14 0.58
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTTATAGTTATTATT
Found at i:549234 original size:33 final size:34
Alignment explanation
Indices: 549197--549302 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 34
549187 GGTAAGAAAT
* * *
549197 TTATTTTTATGTT-AT-TATTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
549230 TTATTTTTTTATATTAATATATTTATGTAAATATTA
1 TTA--TTTTTATATTAATATATTTATGTAAATATTA
* * *
549266 TTATTTTTAT-TAAAATAATATTTATATAATTATTA
1 TTATTTTTATAT-TAAT-ATATTTATGTAAATATTA
549301 TT
1 TT
549303 TATTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
33 4 0.07
34 10 0.16
35 27 0.44
36 8 0.13
37 12 0.20
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:549265 original size:20 final size:19
Alignment explanation
Indices: 549240--549279 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
549230 TTATTTTTTT
549240 ATATTAATATATTTATGTAA
1 ATATTAATATATTTAT-TAA
* *
549260 ATATTATTATTTTTATTAA
1 ATATTAATATATTTATTAA
549279 A
1 A
549280 ATAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTAATATATTTATTAA
Found at i:549282 original size:20 final size:18
Alignment explanation
Indices: 549208--549279 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 18
549198 TATTTTTATG
549208 TTATTATTTTTTTAAATA
1 TTATTATTTTTTTAAATA
549226 GTTATTATTTTTTT--ATA
1 -TTATTATTTTTTTAAATA
* *
549243 TTAATATATTTATGTAAATA
1 TT-AT-TATTTTTTTAAATA
549263 TTATTATTTTTATTAAA
1 TTATTATTTTT-TTAAA
549280 ATAATATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.05
17 5 0.11
18 13 0.30
19 19 0.43
20 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATTTTTTTAAATA
Found at i:549287 original size:20 final size:18
Alignment explanation
Indices: 549209--549287 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 18
549199 ATTTTTATGT
*
549209 TATTATTTTTTTAAATAGT
1 TATTATTTTTTTAAATA-A
*
549228 TATTATTTTTTTATATTAA
1 TATTATTTTTTTA-AATAA
* * *
549247 TA-TATTTATGTAAATAT
1 TATTATTTTTTTAAATAA
549264 TATTATTTTTATTAAAATAA
1 TATTATTTTT-TT-AAATAA
549284 TATT
1 TATT
549288 TATATAATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 5 0.11
18 14 0.30
19 16 0.34
20 12 0.26
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTATTTTTTTAAATAA
Found at i:549287 original size:35 final size:35
Alignment explanation
Indices: 549220--549302 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
549210 ATTATTTTTT
*
549220 TAAATAGTTATTATTTTTTTATATTAATATATTTATG
1 TAAATA-TTATTATTTTTTTATA-TAATATATTTATA
549257 TAAATATTATTATTTTTATTA-A-AATAATATTTATA
1 TAAATATTATTATTTTT-TTATATAAT-ATATTTATA
*
549292 TAATTATTATT
1 TAAATATTATT
549303 TATTAGAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 3 0.07
35 18 0.43
36 12 0.29
37 9 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (35 bp):
TAAATATTATTATTTTTTTATATAATATATTTATA
Found at i:549507 original size:16 final size:16
Alignment explanation
Indices: 549488--549519 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
549478 GAATTTATAT
*
549488 TAATTTATATTTTTTA
1 TAATTTATATTATTTA
549504 TAATTTATATTATTTA
1 TAATTTATATTATTTA
549520 GGTATTGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTATATTATTTA
Found at i:556204 original size:2 final size:2
Alignment explanation
Indices: 556199--556253 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
556189 TTTTTATTCT
556199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
556241 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
556254 TAATTATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:556630 original size:21 final size:21
Alignment explanation
Indices: 556605--556645 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
556595 TATTTATTTT
556605 TATAT-TAAATACTATATTACA
1 TATATATAAATA-TATATTACA
*
556626 TATATATATATATATATTAC
1 TATATATAAATATATATTAC
556646 CTAACATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATATAAATATATATTACA
Found at i:556853 original size:33 final size:34
Alignment explanation
Indices: 556799--556870 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
556789 TAGGATTGTT
*
556799 TTATTATTGTTATTATTATTTATTCTCTTATCTA
1 TTATTATTATTATTATTATTTATTCTCTTATCTA
556833 TTATTATTATT-TTATTATTTATTCTCTTATCTA
1 TTATTATTATTATTATTATTTATTCTCTTATCTA
556866 TTATT
1 TTATT
556871 TTTTTAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 27 0.73
34 10 0.27
ACGTcount: A:0.24, C:0.08, G:0.01, T:0.67
Consensus pattern (34 bp):
TTATTATTATTATTATTATTTATTCTCTTATCTA
Found at i:556963 original size:6 final size:6
Alignment explanation
Indices: 556954--557028 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
556944 TATTTATTTA
* * * * * *
556954 TTTTCT TTTT-T CCTTTCT TTTCCTT TTTTGT TTTTGT TTTTGT TTTT-G
1 TTTTCT TTTTCT -TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT
557002 TTTTCT TTTTCT TTTTCT ATTTTCT TT
1 TTTTCT TTTTCT TTTTCT -TTTTCT TT
557029 ATTTTCTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 5 0.09
6 41 0.72
7 11 0.19
ACGTcount: A:0.01, C:0.13, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:557011 original size:12 final size:11
Alignment explanation
Indices: 556954--557061 Score: 56
Period size: 12 Copynumber: 9.2 Consensus size: 11
556944 TATTTATTTA
556954 TTTTCTTTTTT
1 TTTTCTTTTTT
*
556965 CCTTTCTTTTCCTT
1 -TTTTCTTTT--TT
*
556979 TTTTGTTTTTGT
1 TTTTCTTTTT-T
* *
556991 TTTTGTTTTTG
1 TTTTCTTTTTT
557002 TTTTCTTTTTCT
1 TTTTCTTTTT-T
*
557014 TTTTCTATTTT
1 TTTTCTTTTTT
* *
557025 CTTTATTTTCTT
1 TTTTCTTTT-TT
*
557037 TTATT-TATTTTA
1 TT-TTCT-TTTTT
*
557049 TTTACTTTTTT
1 TTTTCTTTTTT
557060 TT
1 TT
557062 ATTTTGTCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
11 24 0.32
12 36 0.49
13 12 0.16
14 2 0.03
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:557011 original size:18 final size:18
Alignment explanation
Indices: 556954--557028 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
556944 TATTTATTTA
**
556954 TTTTCTTTTTTCCTTTCT
1 TTTTCTTTTTTGTTTTCT
*
556972 TTTCCTTTTTTGTTTT-T
1 TTTTCTTTTTTGTTTTCT
556989 GTTTT-TGTTTTTGTTTTCT
1 -TTTTCT-TTTTTGTTTTCT
*
557008 TTTTCTTTTTCTATTTTCT
1 TTTTCTTTTT-TGTTTTCT
557027 TT
1 TT
557029 ATTTTCTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 2 0.04
18 34 0.72
19 11 0.23
ACGTcount: A:0.01, C:0.13, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTGTTTTCT
Found at i:557033 original size:9 final size:9
Alignment explanation
Indices: 557019--557135 Score: 52
Period size: 9 Copynumber: 13.1 Consensus size: 9
557009 TTTCTTTTTC
557019 TATTTTCTT
1 TATTTTCTT
557028 TATTTTCTTT
1 TATTTTC-TT
557038 TATTTAT-TT
1 TATTT-TCTT
*
557047 TATTTAC--
1 TATTTTCTT
557054 T-TTTT-TT
1 TATTTTCTT
*
557061 TATTTTGTCT
1 TATTTTCT-T
557071 TATTTT-TT
1 TATTTTCTT
*
557079 GCTATATT-TT
1 --TATTTTCTT
*
557089 AATTTTCTT
1 TATTTTCTT
557098 GTATTTTCTT
1 -TATTTTCTT
*
557108 TATTTTATT
1 TATTTTCTT
**
557117 CGTTTTCATT
1 TATTTTC-TT
557127 T-TTTTCTT
1 TATTTTCTT
557135 T
1 T
557136 TCCTCTTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
6 3 0.04
7 2 0.02
8 12 0.14
9 35 0.42
10 31 0.37
11 1 0.01
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (9 bp):
TATTTTCTT
Found at i:557041 original size:19 final size:19
Alignment explanation
Indices: 556997--557061 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
556987 TTGTTTTTGT
*
556997 TTTTGTTTTCTTT-TTCTT-
1 TTTTATTTTCTTTATT-TTC
557015 TTTCTATTTTCTTTATTTTC
1 TTT-TATTTTCTTTATTTTC
*
557035 TTTTATTTAT-TTTATTTAC
1 TTTTATTT-TCTTTATTTTC
557054 TTTT-TTTT
1 TTTTATTTT
557062 ATTTTGTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 1 0.02
18 6 0.15
19 28 0.68
20 6 0.15
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTATTTTCTTTATTTTC
Found at i:557061 original size:23 final size:23
Alignment explanation
Indices: 556997--557065 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
556987 TTGTTTTTGT
* *
556997 TTTTGTTTTCTTTTTCTTT-TTCTA
1 TTTTATTTACTTTTT-TTTATT-TA
*
557021 TTTTCTTTA-TTTTCTTTTATTTA
1 TTTTATTTACTTTT-TTTTATTTA
557044 TTTTATTTACTTTTTTTTATTT
1 TTTTATTTACTTTTTTTTATTT
557066 TGTCTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 25 0.64
24 14 0.36
ACGTcount: A:0.10, C:0.09, G:0.01, T:0.80
Consensus pattern (23 bp):
TTTTATTTACTTTTTTTTATTTA
Found at i:557078 original size:19 final size:19
Alignment explanation
Indices: 557026--557066 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
557016 TTCTATTTTC
* *
557026 TTTATTTTCTTTTATTTAT
1 TTTATTTACTTTTTTTTAT
557045 TTTATTTACTTTTTTTTAT
1 TTTATTTACTTTTTTTTAT
557064 TTT
1 TTT
557067 GTCTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTATTTACTTTTTTTTAT
Found at i:560133 original size:12 final size:12
Alignment explanation
Indices: 560079--560134 Score: 67
Period size: 13 Copynumber: 4.4 Consensus size: 12
560069 ATCAAAAAGG
560079 AAAAAGAGAAAA
1 AAAAAGAGAAAA
560091 AACAAAGAGAAAA
1 AA-AAAGAGAAAA
*
560104 ACAAAGAGAAAATA
1 AAAAAGAG-AAA-A
*
560118 AAAAAGAGAAAC
1 AAAAAGAGAAAA
560130 AAAAA
1 AAAAA
560135 CAAAAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
12 13 0.34
13 17 0.45
14 8 0.21
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:560145 original size:12 final size:13
Alignment explanation
Indices: 560081--560128 Score: 71
Period size: 12 Copynumber: 3.7 Consensus size: 13
560071 CAAAAAGGAA
560081 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
560094 AAAGAG-AAAAAC
1 AAAGAGAAAAAAC
*
560106 AAAGAGAAAATAAA
1 AAAGAGAAAA-AAC
560120 AAAGAGAAA
1 AAAGAGAAA
560129 CAAAAACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 12 0.38
13 9 0.28
14 11 0.34
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:561290 original size:32 final size:32
Alignment explanation
Indices: 561204--561290 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
561194 GAACATTGGG
* * * *
561204 GGCATCTTTGAAGATTTAACATAAAATATTGT
1 GGCATATTTGGAGATTCAACATCAAATATTGT
*
561236 GGCATTTTTGGAGATTCAACATCAAATATTAG-
1 GGCATATTTGGAGATTCAACATCAAATATT-GT
*
561268 GGCATATTTGGGGATTCAACATC
1 GGCATATTTGGAGATTCAACATC
561291 CTGATGCGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
GGCATATTTGGAGATTCAACATCAAATATTGT
Found at i:562007 original size:110 final size:110
Alignment explanation
Indices: 561814--562214 Score: 631
Period size: 110 Copynumber: 3.6 Consensus size: 110
561804 AGAAAAGCTT
*
561814 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTAAATTTCAACTTCACAACGAAGGATATTG
1 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
* *
561879 GACTCGAGGCAACACAAGCTCAACTTCACAGCGAAGGGGCGACTG
66 GACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGACTG
* * * * *
561924 ACTGTCAACAAACAACTTTTCAATTTCATTAAGAGCCAATTTCAACTTCACAGCGAAAGATATTG
1 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
* *
561989 GACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCAACTA
66 GACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGACTG
*
562034 ACTGTCAAGAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
1 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
* * *
562099 GACTCGAGACAACACAAGCTCAGCTTCACAGTGAAAGGGCGATTG
66 GACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGACTG
* * *
562144 ACTGTCAACAAACAACTTTCCGAGTCTCGTTCAGAGTCAATTTCAACTTCACAACGAAGGATATT
1 ACTGTCAACAAACAACTTTTC-AGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT
*
562209 GAACTC
65 GGACTC
562215 AAAGCGACAT
Statistics
Matches: 264, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
110 218 0.83
111 46 0.17
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (110 bp):
ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
GACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGACTG
Found at i:562322 original size:55 final size:58
Alignment explanation
Indices: 562183--562339 Score: 158
Period size: 55 Copynumber: 2.7 Consensus size: 58
562173 TTCAGAGTCA
** * * *
562183 ATTTCAACTTCACAACGAAGGATATTGAACTCAAAGCGACATAATTTGTTTGAAATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAACTCAAAAC-ACATAATTTGCTCGAAATTGG
* * * * * *
562242 ATTTTAACTCCACGACGGAGGATATCCAACTCAAAAC-CA-ACTTT-CTCGAGATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAACTCAAAACACATAATTTGCTCGAAATTGG
* *
562297 ATTTCAACTTCACAACGAATGATATCCAACCCAAAACAACATA
1 ATTTCAACTTCACAACGAAGGATATCCAACTCAAAAC-ACATA
562340 CAATACTTGG
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
55 39 0.50
56 4 0.05
57 4 0.05
58 1 0.01
59 30 0.38
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (58 bp):
ATTTCAACTTCACAACGAAGGATATCCAACTCAAAACACATAATTTGCTCGAAATTGG
Found at i:562689 original size:21 final size:21
Alignment explanation
Indices: 562664--562733 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
562654 TGAGACAGTT
562664 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
562685 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
*
562702 -C-CTTAAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
562721 TCTATTGAGACAA
1 TCTCTTGAAACAA
562734 TTTCCCTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 6 0.16
16 3 0.08
17 2 0.05
18 4 0.11
19 2 0.05
20 3 0.08
21 17 0.46
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:562696 original size:36 final size:36
Alignment explanation
Indices: 562649--562851 Score: 172
Period size: 36 Copynumber: 5.8 Consensus size: 36
562639 AAGGTTTATT
*
562649 TCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
* *
562685 TCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
* * *
562721 TCTATTGAGACAATTTCCCTTGAAACAAA------A
1 TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
* * * **
562751 TCT-TTGA-ATATGTTTTACATT-AAACAAATTTCATC
1 TCTCTTGAGACA-G-TTTCCCTTGAAACAAATTTTGTC
* ** * *
562786 TCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTC
562823 TCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTTGAGACAGTTTCCCTTGAAACAAA
562852 ATCTTTGAAT
Statistics
Matches: 130, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
28 2 0.02
29 11 0.08
30 9 0.07
35 7 0.05
36 70 0.54
37 31 0.24
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
Found at i:562746 original size:72 final size:73
Alignment explanation
Indices: 562609--562749 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 73
562599 ACAAGGGGTC
* * * *
562609 GTCTCACTTGAGACTAATTTACTCAAAACAAAGGTTTATTTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCACTTGAGACTAATTTACTCAAAACAAAGGTTTATCTCTATTGAGACAATTTCCCTTGAAA
562674 CAAATTTT
66 CAAATTTT
* * * * *
562682 GTCTCTCTTGAGAC-AATTTCCCTTAAAACAAA-TTTTGTCTCTATTGAGACAATTTCCCTTGAA
1 GTCTCACTTGAGACTAATTT-ACTCAAAACAAAGGTTTATCTCTATTGAGACAATTTCCCTTGAA
562745 ACAAA
65 ACAAA
562750 ATCTTTGAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 35 0.60
73 23 0.40
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (73 bp):
GTCTCACTTGAGACTAATTTACTCAAAACAAAGGTTTATCTCTATTGAGACAATTTCCCTTGAAA
CAAATTTT
Found at i:562846 original size:102 final size:102
Alignment explanation
Indices: 562668--562953 Score: 378
Period size: 102 Copynumber: 2.8 Consensus size: 102
562658 ACAGTTTCTC
** * *** ** * *
562668 TTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTAAAAC-AAATTTTGTCTCTATTGAGAC
1 TTGAAACAAATTTCATCTCCCTTGAGACAATTTATTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
*
562732 AATTTCCCTTGAAACAAAATCTTTGAATATGTTTTACA
66 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT-CA
* *
562770 TT-AAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCATCTCCCTTGAGACAATTTATTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
*
562834 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
66 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCA
** * *
562871 TTGAAACAAATTTTGTCTCCCTTGAGACAATTTATTTTGGAACTAAGTTTTGTCTCTCTAGACAC
1 TTGAAACAAATTTCATCTCCCTTGAGACAATTTATTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
*
562936 AGTTTCTCTTGAAACAAA
66 AGTTTCCCTTGAAACAAA
562954 TTTTGTCTCT
Statistics
Matches: 163, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
101 35 0.21
102 128 0.79
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (102 bp):
TTGAAACAAATTTCATCTCCCTTGAGACAATTTATTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCA
Found at i:562992 original size:73 final size:73
Alignment explanation
Indices: 562866--563024 Score: 230
Period size: 73 Copynumber: 2.2 Consensus size: 73
562856 TTGAATATGT
** * *
562866 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAATTTATTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAAGTTTTGTCTCTCT
562930 AGACACAG
66 AGACACAG
* * *
562938 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAAGTTTTGTCTCTCT
* *
563003 TGAGACAG
66 AGACACAG
563011 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
563025 CCAATCTTTG
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 4 0.05
73 73 0.95
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTACCTTGAAACAAAGTTTTGTCTCTCT
AGACACAG
Found at i:563004 original size:37 final size:36
Alignment explanation
Indices: 562866--563024 Score: 212
Period size: 37 Copynumber: 4.4 Consensus size: 36
562856 TTGAATATGT
* *
562866 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * * * *
562901 TTTATTTTGGAACTAAGTTTTGTCTCTCTAGACACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
562938 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
562974 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
563011 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
563025 CCAATCTTTG
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
35 3 0.03
36 41 0.39
37 61 0.58
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:563081 original size:67 final size:66
Alignment explanation
Indices: 562973--563120 Score: 208
Period size: 67 Copynumber: 2.2 Consensus size: 66
562963 TCTTGAGACA
* * ** * *
562973 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAATCTTTGAAT
1 GTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-AAAAACCTTTGAAA
563038 AT
65 AT
*
563040 GTTTCTCTTGAAATAAAATTTTGTCT-TCCTTGAGACAGTTTCTCTTGAAAAAAAACCTTTGAAA
1 GTTTCTCTTGAAACAAAATTTTGTCTCT-CTTGAGACAGTTTCTCTTGAAAAAAAACCTTTGAAA
563104 AT
65 AT
563106 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
563121 CCAAAAGACC
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
66 27 0.38
67 45 0.62
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAACCTTTGAAAA
T
Found at i:565231 original size:11 final size:10
Alignment explanation
Indices: 565199--565244 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
565189 CTATTATTTT
565199 TATTTTTAT-
1 TATTTTTATA
565208 TATTTTTATA
1 TATTTTTATA
*
565218 TATTTTTCTCA
1 TATTTTTAT-A
*
565229 TATTTTTAGA
1 TATTTTTATA
565239 TATTTT
1 TATTTT
565245 ATTTATGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 9 0.28
10 15 0.47
11 8 0.25
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (10 bp):
TATTTTTATA
Found at i:565598 original size:12 final size:12
Alignment explanation
Indices: 565581--565673 Score: 51
Period size: 12 Copynumber: 7.2 Consensus size: 12
565571 GTTAGGATTG
565581 TTTTTTTATTATT
1 TTTTTTTATTA-T
*
565594 TTTTTTCCTCTTAT
1 TTTTTT--TATTAT
* *
565608 CTATTATTATTAT
1 -TTTTTTTATTAT
* *
565621 TATTATTATTAT
1 TTTTTTTATTAT
* *
565633 TATTATTATTAT
1 TTTTTTTATTAT
*
565645 TATTTTATATATAT
1 T-TTTTTTAT-TAT
565659 TTTTATTTATTAT
1 TTTT-TTTATTAT
565672 TT
1 TT
565674 ATTATTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
12 25 0.38
13 24 0.36
14 9 0.14
15 8 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTTATTAT
Found at i:565615 original size:3 final size:3
Alignment explanation
Indices: 565604--565679 Score: 93
Period size: 3 Copynumber: 24.7 Consensus size: 3
565594 TTTTTTCCTC
565604 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
565649 TTA -TA TATA TTT TTA TTTA TTA TTTA TTA TT
1 TTA TTA T-TA TTA TTA -TTA TTA -TTA TTA TT
565680 TTTTACTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.06
3 49 0.75
4 12 0.18
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:565780 original size:1 final size:1
Alignment explanation
Indices: 565770--565835 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
565760 TATTTATTTA
* * * * * * * * *
565770 TTTTTATTTTTCTTTTTTTATTTTTATTTTTATTTTTCTTTATTTTTTTTATTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
565835 T
1 T
565836 GTTGTATTTT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:565791 original size:20 final size:20
Alignment explanation
Indices: 565758--565873 Score: 105
Period size: 20 Copynumber: 5.7 Consensus size: 20
565748 CTCTGTCGTA
*
565758 TTTATTTATTTATTTTTATT
1 TTTATTTTTTTATTTTTATT
*
565778 TTTCTTTTTTTATTTTTATT
1 TTTATTTTTTTATTTTTATT
*
565798 TTTATTTTTCTT-TATTT-TT
1 TTTATTTTT-TTATTTTTATT
565817 TTTATTTTTTTATTTTT-TT
1 TTTATTTTTTTATTTTTATT
* *
565836 GTTGTATTTTATTTGTCTTGTATT
1 -TT-TATTTT-TTTAT-TTTTATT
565860 TTT-TTTATTTTATT
1 TTTATTT-TTTTATT
565874 CATTTTCATT
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.03
19 17 0.21
20 33 0.41
21 15 0.19
22 6 0.08
23 5 0.06
24 2 0.03
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (20 bp):
TTTATTTTTTTATTTTTATT
Found at i:565795 original size:26 final size:26
Alignment explanation
Indices: 565766--565849 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
565756 TATTTATTTA
565766 TTTATTTTTATTTTTCTTTTTTTATT
1 TTTATTTTTATTTTTCTTTTTTTATT
*
565792 TTTATTTTTATTTTTCTTTATTT-TT
1 TTTATTTTTATTTTTCTTTTTTTATT
565817 TTTATTTTT-TTATTT-TTTTGTTGTA-T
1 TTTATTTTTATT-TTTCTTTT-TT-TATT
565843 TTTATTT
1 TTTATTT
565850 GTCTTGTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.10
25 16 0.31
26 31 0.60
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (26 bp):
TTTATTTTTATTTTTCTTTTTTTATT
Found at i:565821 original size:45 final size:45
Alignment explanation
Indices: 565762--565879 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 45
565752 GTCGTATTTA
*
565762 TTTATTTATTTTTATTTTTCTT-TTTTTATT-TT-TATTTTTATTTTTC
1 TTTATTT-TTTTTATTTTT-TTATTTTT-TTGTTGTA-TTTTATTTGTC
565808 TTTATTTTTTTTATTTTTTTATTTTTTTGTTGTATTTTATTTGTC
1 TTTATTTTTTTTATTTTTTTATTTTTTTGTTGTATTTTATTTGTC
*
565853 TTGTATTTTTTTTATTTTATTCATTTT
1 TT-TATTTTTTTTATTTT-TTTATTTT
565880 CATTTTTTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
44 4 0.06
45 30 0.46
46 24 0.37
47 7 0.11
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (45 bp):
TTTATTTTTTTTATTTTTTTATTTTTTTGTTGTATTTTATTTGTC
Found at i:565833 original size:6 final size:6
Alignment explanation
Indices: 565766--565825 Score: 66
Period size: 6 Copynumber: 9.5 Consensus size: 6
565756 TATTTATTTA
* * *
565766 TTTATT TTTATTT TTCTTTT TTTATT TTTATT TTTATT TTTCTT TATTTTT
1 TTTATT TTTA-TT TT-TATT TTTATT TTTATT TTTATT TTTATT T-TTATT
565817 TTTATT TTT
1 TTTATT TTT
565826 TTATTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
6 32 0.70
7 13 0.28
8 1 0.02
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:575499 original size:15 final size:16
Alignment explanation
Indices: 575479--575508 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
575469 AATATTTTAA
575479 AATTTAAA-ATCAAAT
1 AATTTAAATATCAAAT
575494 AATTTAAATATCAAA
1 AATTTAAATATCAAA
575509 ACTCAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTTAAATATCAAAT
Found at i:575692 original size:17 final size:16
Alignment explanation
Indices: 575662--575705 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
575652 TCTCCTTCGT
*
575662 ATAAAAAAT-TTATTGA
1 ATAAAAAATAATATT-A
575678 ATAAAAAATAATATTA
1 ATAAAAAATAATATTA
575694 ATAAAATAATAA
1 ATAAAA-AATAA
575706 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAAAAAATAATATTA
Found at i:575716 original size:21 final size:21
Alignment explanation
Indices: 575677--575717 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
575667 AAATTTATTG
* *
575677 AATAAAAAATAATATTAATAA
1 AATAAAAAATAAAAATAATAA
*
575698 AATAATAAATAAAAATAATA
1 AATAAAAAATAAAAATAATA
575718 GTTCTCGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAAAATAAAAATAATAA
Found at i:581046 original size:7 final size:7
Alignment explanation
Indices: 581025--581081 Score: 78
Period size: 7 Copynumber: 8.0 Consensus size: 7
581015 ATCATTCATT
581025 AACCAATA
1 AACC-ATA
581033 AACCATA
1 AACCATA
*
581040 AATCATA
1 AACCATA
581047 AACCATA
1 AACCATA
* *
581054 TACTATA
1 AACCATA
581061 AACCATA
1 AACCATA
581068 AACCATA
1 AACCATA
581075 AACCATA
1 AACCATA
581082 GCCCCATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
7 39 0.91
8 4 0.09
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCATA
Found at i:587092 original size:21 final size:21
Alignment explanation
Indices: 587068--587118 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
587058 ACATATAATT
587068 ATAAATTATCTAAAATAAAAG
1 ATAAATTATCTAAAATAAAAG
*
587089 ATAAATTATTTAAAATAAAAG
1 ATAAATTATCTAAAATAAAAG
587110 ATAAATTAT
1 ATAAATTAT
587119 ATCAATATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
ATAAATTATCTAAAATAAAAG
Found at i:591697 original size:36 final size:36
Alignment explanation
Indices: 591642--591780 Score: 224
Period size: 36 Copynumber: 3.9 Consensus size: 36
591632 AGTTGAGTAT
*
591642 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
* * *
591678 TATCAGCTTTGGTATATTCGTGTATCAATGTTATTA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
* *
591714 TATCAGCTTTCGTACATTCGTGTATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
591750 TATCAACTTTGGTACATTCGTGTATCAATGT
1 TATCAACTTTGGTACATTCGTGTATCAATGT
591781 CCAGCACTGT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (36 bp):
TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:595126 original size:25 final size:25
Alignment explanation
Indices: 595098--595155 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
595088 CTAATGCAAA
*
595098 AAGGTAAAGTGGTAGCCTATGCTTC
1 AAGGCAAAGTGGTAGCCTATGCTTC
595123 AAGGCAAAGTGGTAGCCTATGCTTC
1 AAGGCAAAGTGGTAGCCTATGCTTC
595148 AAGGCAAA
1 AAGGCAAA
595156 TAAAGGCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (25 bp):
AAGGCAAAGTGGTAGCCTATGCTTC
Found at i:599207 original size:36 final size:36
Alignment explanation
Indices: 599155--599329 Score: 296
Period size: 36 Copynumber: 4.9 Consensus size: 36
599145 AGTTGAGTAT
* *
599155 TATCAGCTTTGATACATTAGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
599191 TATCAGCTTTGGTACATTTGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
599227 TATCAGCTTTCGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
599263 TATCAGCTTTCGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
599299 TATTAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
599330 CCAACACCGT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 133 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:605961 original size:15 final size:15
Alignment explanation
Indices: 605937--605970 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
605927 CCGTAGGACC
605937 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
605952 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
605967 ACTA
1 ACTA
605971 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:606095 original size:29 final size:29
Alignment explanation
Indices: 606057--606135 Score: 142
Period size: 29 Copynumber: 2.7 Consensus size: 29
606047 TCATATGTTT
606057 ATGTA-CTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
606085 ATGTAGCTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
606114 ATGTAGCTCATGTCATGTTCTC
1 ATGTAGCTCATGTCAT-TTCTC
606136 ATATCACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.10
29 39 0.80
30 5 0.10
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
ATGTAGCTCATGTCATTTCTCTTGTGATC
Found at i:606581 original size:64 final size:63
Alignment explanation
Indices: 606512--606665 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 63
606502 TAATAAAGGT
* *
606512 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGA
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
606575 G
63 G
* * * *
606576 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
606639 AGTGCATCGATGCACTACCTGTGCATC
1 A-TGCATCGATGCACTACTTGTGCATC
606666 AATACACCTT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
63 4 0.05
64 63 0.83
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:612900 original size:15 final size:15
Alignment explanation
Indices: 612876--612909 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
612866 CCATAGGACC
612876 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
612891 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
612906 ACTA
1 ACTA
612910 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:613036 original size:29 final size:29
Alignment explanation
Indices: 612994--613074 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
612984 TTTCATATGT
612994 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
613022 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
613051 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
613075 ATATCACAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:622622 original size:42 final size:41
Alignment explanation
Indices: 622574--622690 Score: 105
Period size: 41 Copynumber: 2.8 Consensus size: 41
622564 GTGTTTTTCA
622574 AACAAACGCTGTAATAGAGTGGTAATTTAGCGGCGTTTATAGC
1 AACAAACGC-GTAATAGAGTGGTAATTTAGCGGCGTTTAT-GC
* * * * * *
622617 -TCAAACGACGCAATAGAGTTGT--TTATAGTGGCGTTTCTTC
1 AACAAACG-CGTAATAGAGTGGTAATT-TAGCGGCGTTTATGC
*
622657 AACAAACGCCATAATAGAGTGGTAATTTAGCGGC
1 AACAAACG-CGTAATAGAGTGGTAATTTAGCGGC
622691 ATTTTTATAC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
40 3 0.05
41 28 0.49
42 23 0.40
43 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (41 bp):
AACAAACGCGTAATAGAGTGGTAATTTAGCGGCGTTTATGC
Found at i:622622 original size:81 final size:81
Alignment explanation
Indices: 622517--622690 Score: 185
Period size: 83 Copynumber: 2.1 Consensus size: 81
622507 AAATTTAAGC
*
622517 ATTTAGCGGCGTTTACAATACAAACGCCACAAAATGA-TTCTTTAGCAGT-GTTT-TTCAAACAA
1 ATTTAGCGGCGTTTACAATACAAACGACACAAAA-GAGTTCTTTA-CAGTGGTTTCTTC-AACAA
**
622579 ACGCTGTAATAGAGTGGTA
63 ACGCCATAATAGAGTGGTA
* * * * * *
622598 ATTTAGCGGCGTTTATAGCT-CAAACGACGCAATAGAGTTGTTTATAGTGGCGTTTCTTCAACAA
1 ATTTAGCGGCGTTTACA-ATACAAACGACACAAAAGAGTTCTTTACAGT-G-GTTTCTTCAACAA
622662 ACGCCATAATAGAGTGGTA
63 ACGCCATAATAGAGTGGTA
622681 ATTTAGCGGC
1 ATTTAGCGGC
622691 ATTTTTATAC
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
80 5 0.06
81 33 0.42
82 1 0.01
83 36 0.46
84 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (81 bp):
ATTTAGCGGCGTTTACAATACAAACGACACAAAAGAGTTCTTTACAGTGGTTTCTTCAACAAACG
CCATAATAGAGTGGTA
Found at i:622663 original size:41 final size:39
Alignment explanation
Indices: 622557--622819 Score: 102
Period size: 41 Copynumber: 6.4 Consensus size: 39
622547 AAAATGATTC
* * * *
622557 TTTAGCAGTGTTTTTCAAACAAACG-CTGTAATAGAGTGGT
1 TTTAGCGGCGTTTTTC-AACAAACGAC-GCAATAGAGTTGT
* *
622597 AATTTAGCGGCGTTTAT-AGCTCAAACGACGCAATAGAGTTGT
1 --TTTAGCGGCGTTTTTCA--ACAAACGACGCAATAGAGTTGT
* * ** *
622639 TTATAGTGGCGTTTCTTCAACAAACGCCATAATAGAGTGGT
1 TT-TAGCGGCGTTT-TTCAACAAACGACGCAATAGAGTTGT
* * * *
622680 AATTTAGCGGCATTTTT-ATACAAACGCCGCGATAGTGTTGTT
1 --TTTAGCGGCGTTTTTCA-ACAAACGACGCAATAGAGTTG-T
* * * * * **
622722 TTTAGAGTCATTTGTTCAACAAACGACGCTATTGAGAAGT
1 TTTAGCGGCGTTT-TTCAACAAACGACGCAATAGAGTTGT
* * *
622762 AATTTAGCGGCGTTTATCAAACAAACGTCGCAAAAG-GTTTGT
1 --TTTAGCGGCGTTTTTC-AACAAACGACGCAATAGAG-TTGT
*
622804 TTATAGTGGCGTTTTT
1 TT-TAGCGGCGTTTTT
622820 GCAAAAAAAA
Statistics
Matches: 164, Mismatches: 40, Indels: 35
0.69 0.17 0.15
Matches are distributed among these distances:
40 18 0.11
41 76 0.46
42 66 0.40
43 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (39 bp):
TTTAGCGGCGTTTTTCAACAAACGACGCAATAGAGTTGT
Found at i:622679 original size:83 final size:78
Alignment explanation
Indices: 622566--622819 Score: 231
Period size: 83 Copynumber: 3.1 Consensus size: 78
622556 CTTTAGCAGT
*
622566 GTTTTTCAAACAAACGCTGTAATAGAGTGGTAATTTAGCGGCGTTTATAGCTCAAACGACGCAAT
1 GTTTTTC-AACAAACGC-CTAATAGAGTGGTAATTTAGCGGCGTTTATA--TCAAACGACGCAAT
622631 AGAGTTGTTTATAGTGGC
62 AG-GTTGTTTATAGTGGC
* * * *
622649 GTTTCTTCAACAAACGCCATAATAGAGTGGTAATTTAGCGGCATTTTTATACAAACGCCGCGATA
1 GTTT-TTCAACAAACGCC-TAATAGAGTGGTAATTTAGCGGCGTTTATAT-CAAACGACGCAATA
* * *
622714 GTGTTGTTTTTAGAGTC
63 G-GTTGTTTATAGTGGC
* * ** * *
622731 ATTTGTTCAACAAACGACGCT-ATTGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGTCGCAA
1 GTTT-TTCAACAAACG-C-CTAATAGAGTGGTAATTTAGCGGCGTTTAT--ATCAAACGACGCAA
*
622795 AAGGTTTGTTTATAGTGGC
61 TAGG-TTGTTTATAGTGGC
622814 GTTTTT
1 GTTTTT
622820 GCAAAAAAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 17
0.77 0.13 0.09
Matches are distributed among these distances:
81 1 0.01
82 64 0.46
83 69 0.50
84 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (78 bp):
GTTTTTCAACAAACGCCTAATAGAGTGGTAATTTAGCGGCGTTTATATCAAACGACGCAATAGGT
TGTTTATAGTGGC
Found at i:623210 original size:42 final size:42
Alignment explanation
Indices: 623126--623226 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
623116 GTTTATAAAA
* * * *
623126 AAACGCCGCAATAGTTTTGTCATTTAATGGCGTTTCTTTAAT
1 AAACGCCGCAGTAGTTTTGTCATCTAAGGGCATTTCTTTAAT
* *
623168 AAACGCCGCAGTAGTTTTGTCCTCTAGGGGCATTT-TTGTAAT
1 AAACGCCGCAGTAGTTTTGTCATCTAAGGGCATTTCTT-TAAT
* *
623210 AAACACCGCAGAAGTTT
1 AAACGCCGCAGTAGTTT
623227 CATTAATCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
41 2 0.04
42 48 0.96
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
AAACGCCGCAGTAGTTTTGTCATCTAAGGGCATTTCTTTAAT
Found at i:623323 original size:25 final size:25
Alignment explanation
Indices: 623295--623343 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
623285 TAACTCCTGT
*
623295 GATACTATCTCCCCCCTTTCACAGC
1 GATACCATCTCCCCCCTTTCACAGC
*
623320 GATACCATTTCCCCCCTTTCACAG
1 GATACCATCTCCCCCCTTTCACAG
623344 ACATTTACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.43, G:0.08, T:0.29
Consensus pattern (25 bp):
GATACCATCTCCCCCCTTTCACAGC
Found at i:631682 original size:21 final size:21
Alignment explanation
Indices: 631664--631747 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
631654 ATGAAGCAAG
*
631664 GGAAGCAGAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGC
* **
631685 AGAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
631706 GGAAGCAGAGAAAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
631727 GGCAGCACAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
631748 ATATCAGTAG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.40, C:0.20, G:0.38, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:632304 original size:42 final size:42
Alignment explanation
Indices: 632159--632324 Score: 208
Period size: 43 Copynumber: 3.9 Consensus size: 42
632149 CGTTTTTAGC
* * * *
632159 AAAAACGCCGCAAAAAATCAATACCTATTGCGGCGTTTGTGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGAGTTTGTG-G
* *
632202 AAAAACGTCGCAAAACATCAAAACCTACTGC-GACGTTTGTGG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGA-GTTTGTGG
* *
632244 AAAAAACGCCGCAAAACATCAACATCTACTGCGGAGTTTATGG
1 -AAAAACGCCGCAAAACATCAACACCTACTGCGGAGTTTGTGG
* *
632287 AAAAACGCCGCATAACATCAACACCTACTGCGGCGTTT
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGAGTTT
632325 CTAAATATCA
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
42 37 0.34
43 69 0.64
44 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (42 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGGAGTTTGTGG
Found at i:632317 original size:85 final size:86
Alignment explanation
Indices: 632159--632324 Score: 235
Period size: 85 Copynumber: 1.9 Consensus size: 86
632149 CGTTTTTAGC
* * * * *
632159 AAAAACGCCGCAAAAAATCAATACCTATTGCGGCGTTTGTGAGAAAAACGTCGCAAAACATCAAA
1 AAAAACGCCGCAAAAAATCAACACCTACTGCGGAGTTTATGAGAAAAACGCCGCAAAACATCAAA
632224 ACCTACTGCGACGTTTGTGGA
66 ACCTACTGCGACGTTTGTGGA
* * * *
632245 AAAAACGCCGCAAAACATCAACATCTACTGCGGAGTTTATG-GAAAAACGCCGCATAACATCAAC
1 AAAAACGCCGCAAAAAATCAACACCTACTGCGGAGTTTATGAGAAAAACGCCGCAAAACATCAAA
*
632309 ACCTACTGCGGCGTTT
66 ACCTACTGCGACGTTT
632325 CTAAATATCA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
85 35 0.50
86 35 0.50
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (86 bp):
AAAAACGCCGCAAAAAATCAACACCTACTGCGGAGTTTATGAGAAAAACGCCGCAAAACATCAAA
ACCTACTGCGACGTTTGTGGA
Found at i:632386 original size:43 final size:43
Alignment explanation
Indices: 632325--632481 Score: 226
Period size: 43 Copynumber: 3.7 Consensus size: 43
632315 TGCGGCGTTT
* * * * * *
632325 CTAAATATCATA-ACCTATTGCAGCGTTTATCTTAAAAACGCTG
1 CTAAATATCA-ACACCTATTGCGGCGTTTGTGTGACAAACGCCG
632368 CTAAATATCAACACCTATTGCGGCGTTTGTGTGACAAACGCCG
1 CTAAATATCAACACCTATTGCGGCGTTTGTGTGACAAACGCCG
*
632411 CTAAATATCAACACCTATTGTGGCGTTTGTGTGACAAACGCCG
1 CTAAATATCAACACCTATTGCGGCGTTTGTGTGACAAACGCCG
*
632454 CTAAATATCAATACCTATTGCGGCGTTT
1 CTAAATATCAACACCTATTGCGGCGTTT
632482 TTTGTTTAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 1 0.01
43 103 0.99
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
CTAAATATCAACACCTATTGCGGCGTTTGTGTGACAAACGCCG
Found at i:636896 original size:15 final size:16
Alignment explanation
Indices: 636862--636902 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
636852 TTTCTTCTAT
636862 ATATTGA-TATTTTAAA
1 ATATTGATTA-TTTAAA
*
636878 ATATT-ATTATTTAAT
1 ATATTGATTATTTAAA
636893 ATATTGATTA
1 ATATTGATTA
636903 AAATTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATATTGATTATTTAAA
Found at i:638148 original size:79 final size:79
Alignment explanation
Indices: 638017--638212 Score: 313
Period size: 79 Copynumber: 2.5 Consensus size: 79
638007 ACTTACGCAA
* * *
638017 ACTCTAAGGTGCTTATGCTTATCAAATGATCAATCTTTCACACTGGAACATGAAAACTTCTCGAC
1 ACTCTAAGGCGCTTATGCTTATAAAATGATCAATCTTTCACACTGGAACATGAAAACTTCTCAAC
638082 ACATGGGTACATGC
66 ACATGGGTACATGC
*
638096 ACTCTAAGGCGCTTACGCTTATAAAATGATCAATCTTTCAC-CTTGGAACATGAAAACTTCTCAA
1 ACTCTAAGGCGCTTATGCTTATAAAATGATCAATCTTTCACAC-TGGAACATGAAAACTTCTCAA
638160 CACATGGGTACATGC
65 CACATGGGTACATGC
* * *
638175 ACTCTAAGGCACTTATGCTTGTAAAATGATCAAGCTTT
1 ACTCTAAGGCGCTTATGCTTATAAAATGATCAATCTTT
638213 TGTTGAAATT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
78 1 0.01
79 107 0.99
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (79 bp):
ACTCTAAGGCGCTTATGCTTATAAAATGATCAATCTTTCACACTGGAACATGAAAACTTCTCAAC
ACATGGGTACATGC
Found at i:638285 original size:21 final size:21
Alignment explanation
Indices: 638261--638321 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
638251 AACTTTGAAA
638261 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
638282 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
638296 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
638317 AAATG
1 AAATG
638322 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:638299 original size:35 final size:36
Alignment explanation
Indices: 638253--638353 Score: 168
Period size: 35 Copynumber: 2.8 Consensus size: 36
638243 TGGTAACCAA
638253 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
638290 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
638325 CTTTGAAAAATAGTTTTTCAAAGTTTGGT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGT
638354 GAAAAATGAT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
35 35 0.57
36 5 0.08
37 21 0.34
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:642825 original size:14 final size:14
Alignment explanation
Indices: 642806--642837 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
642796 TTTGAAAAAA
642806 TGGTTTTCAAAGTT
1 TGGTTTTCAAAGTT
642820 TGGTTTTCAAAGTT
1 TGGTTTTCAAAGTT
642834 TGGT
1 TGGT
642838 AAATGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (14 bp):
TGGTTTTCAAAGTT
Found at i:642908 original size:37 final size:35
Alignment explanation
Indices: 642820--642925 Score: 151
Period size: 35 Copynumber: 3.0 Consensus size: 35
642810 TTTCAAAGTT
642820 TGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAA
1 TGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAA
*
642855 TGGTTTTCAAAGTTTGGTAAATGTTTTTTTGGAAAA
1 TGGTTTTCAAAGTTTGGTAAATGTTTCTTT-GAAAA
* * *
642891 TAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGAAAA
1 T-GGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAA
642926 ATGATAATGG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
35 34 0.52
36 8 0.12
37 23 0.35
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (35 bp):
TGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAA
Found at i:651294 original size:114 final size:113
Alignment explanation
Indices: 651094--651853 Score: 618
Period size: 113 Copynumber: 6.6 Consensus size: 113
651084 TAATATTTAA
*
651094 AAATGATAGAGAATCTTAACTATTCACATTA-TTTCTTTTCAGTGATATATCA-TCTCAAATAAA
1 AAATGATAGA-AATCTTAACTATTCACATCATTTTCTTTTCAGTGATATATCACT-TCAAAT-AA
* * * *
651157 AAATTTATTTCATATTGAATGAAAAATCTTTTTCGGTAGAACAATAATTTC
63 GAACTTATTTCATATTGAATGAAAAATCTTTTTCGGTACAATAATAATTTC
* * *
651208 AAATGACAGATAATCTCAACTATTCACATCATTTTCTTTTCAGTGA-ATTATCACTTCAAATCAG
1 AAATGATAGA-AATCTTAACTATTCACATCATTTTCTTTTCAGTGATA-TATCACTTCAAATAAG
* * * *
651272 AACTTATTTCATATTGAATGAAAAATCTTATCCGATACAATAATAATTTT
64 AACTTATTTCATATTGAATGAAAAATCTTTTTCGGTACAATAATAATTTC
* * * * * *
651322 AAATGATAG-AGTCTTAACTATTCATAACATTTTTATTTTCAGTGATATATAACCTT-AAATTAG
1 AAATGATAGAAATCTTAACTATTCACATCA-TTTTCTTTTCAGTGATATATCA-CTTCAAATAAG
* *
651385 AACTTATTTCATACTGAAT-AAACAATC-TTTTCAAGTACAATAATAATTTC
64 AACTTATTTCATATTGAATGAAA-AATCTTTTTC-GGTACAATAATAATTTC
* * * *
651435 AAATAATAATTTCAAGTGATAAAGAATCTTAACTATTTACGTTATTTTCTTTTCAGTGA-ATTAT
1 --------A----AA-TGATAGA-AATCTTAACTATTCACATCATTTTCTTTTCAGTGATA-TAT
* * **
651499 CAATTCAAATAAGAACTTATTTCATATTGAATGAAAAATC-TTATCATTCACAATAATAATTTC
51 CACTTCAAATAAGAACTTATTTCATATTGAATGAAAAATCTTTTTCGGT-ACAATAATAATTTC
* * * *
651562 AAATGACAGAGAATCTTAACTATTCA-AT-TTCTTTCTTTTCAATGATATATCACCTCAAATAAG
1 AAATGATAGA-AATCTTAACTATTCACATCAT-TTTCTTTTCAGTGATATATCACTTCAAATAAG
** * *
651625 AACTTATTTCATATTGAATGGAAAAAGATTTCTT--ATACAATAATAAATTC
64 AACTTATTTCATATTGAAT-GAAAAATCTTT-TTCGGTACAATAATAATTTC
* * * *
651675 AAATGGAAATG-AATCTTAACTATTCA-AGTCATTTTCTTTTCAATAATATATCACCTT--AATC
1 AAAT-GATA-GAAATCTTAACTATTCACA-TCATTTTCTTTTCAGTGATATATCA-CTTCAAATA
* * * *
651736 AGAACTTATTTTATATTGAAAGAAAAATCTTATTCGCTACAATAATAATTTC
62 AGAACTTATTTCATATTGAATGAAAAATCTTTTTCGGTACAATAATAATTTC
* *** * * * * *
651788 AAATGATAGAGAATCTTAACTACTCGTGTCCTTTTCTTTTTAGTGATCTATCACCTCAAATCAGA
1 AAATGATAGA-AATCTTAACTATTCACATCATTTTCTTTTCAGTGATATATCACTTCAAATAAGA
651853 A
65 A
651854 TTTGATTAAA
Statistics
Matches: 526, Mismatches: 76, Indels: 88
0.76 0.11 0.13
Matches are distributed among these distances:
111 3 0.01
112 36 0.07
113 213 0.40
114 144 0.27
115 33 0.06
116 2 0.00
119 1 0.00
121 1 0.00
125 2 0.00
126 10 0.02
127 64 0.12
128 17 0.03
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (113 bp):
AAATGATAGAAATCTTAACTATTCACATCATTTTCTTTTCAGTGATATATCACTTCAAATAAGAA
CTTATTTCATATTGAATGAAAAATCTTTTTCGGTACAATAATAATTTC
Found at i:651424 original size:113 final size:111
Alignment explanation
Indices: 651094--651438 Score: 342
Period size: 114 Copynumber: 3.0 Consensus size: 111
651084 TAATATTTAA
* * *
651094 AAATGATAGAGAATCTTAACTATTC--ACATTATTTCTTTTCAGTGATATATCATCTCAAATAAA
1 AAATGATAGAG--TCTTAACTATTCAAACATT-TTTCTTTTCAGTGATATATAACCTTAAAT-AA
* * * * *
651157 AAATTTATTTCATATTGAATGAAAAATCTTTTTCGGTAGAACAATAATTTC
62 GAACTTATTTCATATTGAATGAAAAATC-TTTTCAGTACAATAATAATTTC
* * * * * *
651208 AAATGACAGATAATCTCAACTATTCACATCA-TTTTCTTTTCAGTGA-AT-TATCACTTCAAATC
1 AAATGATAG--AGTCTTAACTATTCA-AACATTTTTCTTTTCAGTGATATATAAC-CTT-AAATA
* * *
651270 AGAACTTATTTCATATTGAATGAAAAATCTTATCCGATACAATAATAATTTT
61 AGAACTTATTTCATATTGAATGAAAAATCTTTTCAG-TACAATAATAATTTC
* *
651322 AAATGATAGAGTCTTAACTATTCATAACATTTTTATTTTCAGTGATATATAACCTTAAATTAGAA
1 AAATGATAGAGTCTTAACTATTCA-AACATTTTTCTTTTCAGTGATATATAACCTTAAATAAGAA
*
651387 CTTATTTCATACTGAAT-AAACAATCTTTTCAAGTACAATAATAATTTC
65 CTTATTTCATATTGAATGAAA-AATCTTTTC-AGTACAATAATAATTTC
651435 AAAT
1 AAAT
651439 AATAATTTCA
Statistics
Matches: 190, Mismatches: 28, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
112 19 0.10
113 70 0.37
114 76 0.40
115 21 0.11
116 2 0.01
117 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (111 bp):
AAATGATAGAGTCTTAACTATTCAAACATTTTTCTTTTCAGTGATATATAACCTTAAATAAGAAC
TTATTTCATATTGAATGAAAAATCTTTTCAGTACAATAATAATTTC
Found at i:651456 original size:16 final size:13
Alignment explanation
Indices: 651423--651449 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
651413 TTTCAAGTAC
651423 AATAATAATTTCA
1 AATAATAATTTCA
651436 AATAATAATTTCA
1 AATAATAATTTCA
651449 A
1 A
651450 GTGATAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AATAATAATTTCA
Found at i:651629 original size:240 final size:239
Alignment explanation
Indices: 651199--651809 Score: 640
Period size: 240 Copynumber: 2.6 Consensus size: 239
651189 TCGGTAGAAC
* * *
651199 AATAATTTCAAATGACAGATAATCTCAACTATTCACATCATTTTCTTTTCAGTGAATTATCACTT
1 AATAATTTCAAATGACAAAGAATCTCAACTATTCACATCATTTTCTTTTCAGTGAATTATCAATT
* * *
651264 CAAATCAGAACTTATTTCATATTGAATGAAAAATCTTATCCGATACAATAATAATTTTAAATGAT
66 CAAATAAGAACTTATTTCATATTGAATGAAAAATCTTATCCGATACAATAATAATTTCAAATGAC
* * *
651329 AGAGTCTTAACTATTCATAACATTTTTATTTTCAGTGATATATAACCTTAAATTAGAACTTATTT
131 AGAGTCTTAACTATTCA-AACATTTTTATTTTCAATGATATATAACCTCAAATAAGAACTTATTT
651394 CATACTGAATAAACAATCTTTTCAAGTACAATAATAATTTCAAAT
195 CATACTGAATAAACAATCTTTTCAAGTACAATAATAATTTCAAAT
* * * * * *
651439 AATAATTTCAAGTGATAAAGAATCTTAACTATTTACGTTATTTTCTTTTCAGTGAATTATCAATT
1 AATAATTTCAAATGACAAAGAATCTCAACTATTCACATCATTTTCTTTTCAGTGAATTATCAATT
651504 CAAATAAGAACTTATTTCATATTGAATGAAAAATCTTAT-C-ATTCACAATAATAATTTCAAATG
66 CAAATAAGAACTTATTTCATATTGAATGAAAAATCTTATCCGA-T-ACAATAATAATTTCAAATG
* * *
651567 ACAGAGAATCTTAACTATTC-AA-TTTCTTTCTTTTCAATGATATATCACCTCAAATAAGAACTT
129 ACAGAG--TCTTAACTATTCAAACATT-TTTATTTTCAATGATATATAACCTCAAATAAGAACTT
* **
651630 ATTTCATATTGAATGGAAA-AA-GATTTC---T----T-AT-A---C-AAT
191 ATTTCATACTGAAT--AAACAATCTTTTCAAGTACAATAATAATTTCAAAT
* * * *
651666 AATAAATTCAAATGGA-AATGAATCTTAACTATTCA-AGTCATTTTCTTTTCAAT-AATATATCA
1 AATAATTTCAAAT-GACAAAGAATCTCAACTATTCACA-TCATTTTCTTTTCAGTGAAT-TATCA
* * * * * *
651728 CCTT--AATCAGAACTTATTTTATATTGAAAGAAAAATCTTATTCGCTACAATAATAATTTCAAA
63 -ATTCAAATAAGAACTTATTTCATATTGAATGAAAAATCTTATCCGATACAATAATAATTTCAAA
*
651791 TGATAGAGAATCTTAACTA
127 TGACAGAG--TCTTAACTA
651810 CTCGTGTCCT
Statistics
Matches: 324, Mismatches: 34, Indels: 40
0.81 0.09 0.10
Matches are distributed among these distances:
226 72 0.22
227 52 0.16
228 5 0.02
231 1 0.00
232 2 0.01
233 1 0.00
237 1 0.00
238 1 0.00
239 4 0.01
240 168 0.52
241 2 0.01
242 15 0.05
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (239 bp):
AATAATTTCAAATGACAAAGAATCTCAACTATTCACATCATTTTCTTTTCAGTGAATTATCAATT
CAAATAAGAACTTATTTCATATTGAATGAAAAATCTTATCCGATACAATAATAATTTCAAATGAC
AGAGTCTTAACTATTCAAACATTTTTATTTTCAATGATATATAACCTCAAATAAGAACTTATTTC
ATACTGAATAAACAATCTTTTCAAGTACAATAATAATTTCAAAT
Found at i:663512 original size:29 final size:29
Alignment explanation
Indices: 663470--663539 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
663460 AACTTTGGTA
*
663470 AAGGACCACATTAGGTGCAAAAGAAAGTT
1 AAGGGCCACATTAGGTGCAAAAGAAAGTT
663499 AAGGGCCACATTAGGTGCAAAAGAAAGTT
1 AAGGGCCACATTAGGTGCAAAAGAAAGTT
*
663528 GAGGGCCACATT
1 AAGGGCCACATT
663540 GATTTTTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.17
Consensus pattern (29 bp):
AAGGGCCACATTAGGTGCAAAAGAAAGTT
Found at i:671639 original size:33 final size:33
Alignment explanation
Indices: 671564--671644 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
671554 ACACCTCCCT
**
671564 CACCACTTCCAAAACCTCCCCCACCACCAAAAC
1 CACCACTTCCACCACCTCCCCCACCACCAAAAC
* * * *
671597 CGCCGCTTCCACCACCTCCCCCACCTCCAAATC
1 CACCACTTCCACCACCTCCCCCACCACCAAAAC
*
671630 CACCACTTCCTCCAC
1 CACCACTTCCACCAC
671645 TGCCCATACC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.26, C:0.58, G:0.02, T:0.14
Consensus pattern (33 bp):
CACCACTTCCACCACCTCCCCCACCACCAAAAC
Found at i:674722 original size:21 final size:21
Alignment explanation
Indices: 674681--674725 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
674671 TTTTCATTTT
* *
674681 AATTTATTTTTTATTTGTAAA
1 AATTAATTTTTTATATGTAAA
674702 AATTAATTTTTTAATAT-TAAA
1 AATTAATTTTTT-ATATGTAAA
674723 AAT
1 AAT
674726 AGTCACGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTAATTTTTTATATGTAAA
Found at i:677981 original size:21 final size:22
Alignment explanation
Indices: 677932--677982 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
677922 AATTTATCTT
677932 TTGAATATT-TCAAATTAAAAG
1 TTGAATATTATCAAATTAAAAG
* * *
677953 AT-ATTATTATCAACTT-AAAG
1 TTGAATATTATCAAATTAAAAG
677973 TTGAATATTA
1 TTGAATATTA
677983 AAAGACATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (22 bp):
TTGAATATTATCAAATTAAAAG
Found at i:678303 original size:6 final size:7
Alignment explanation
Indices: 678287--678311 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
678277 TCGATAGCTC
678287 AAAAATA
1 AAAAATA
678294 AAAAATA
1 AAAAATA
678301 AAAAATA
1 AAAAATA
678308 AAAA
1 AAAA
678312 GATTATTTTT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:680409 original size:35 final size:36
Alignment explanation
Indices: 680365--680433 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
680355 AACAATCTTT
*
680365 AATTTTATTCTAAACCCCAAATTCC-AAAATAATTC
1 AATTATATTCTAAACCCCAAATTCCAAAAATAATTC
*
680400 AATTATATTCTAAACCCTAAATTCCAAAAATAAT
1 AATTATATTCTAAACCCCAAATTCCAAAAATAAT
680434 CAAAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (36 bp):
AATTATATTCTAAACCCCAAATTCCAAAAATAATTC
Found at i:681010 original size:35 final size:35
Alignment explanation
Indices: 680964--681037 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
680954 ACAATATTAT
* *
680964 TTGAAGTATTTT-AGAATTTTGGGTTTAGAATGTAA
1 TTGAAGTATTTTGA-AATTTGGGGTTTAGAATGAAA
*
680999 TTGAATTATTTTGAAATTTGGGGTTTAGAATGAAA
1 TTGAAGTATTTTGAAATTTGGGGTTTAGAATGAAA
681034 TTGA
1 TTGA
681038 GGACTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (35 bp):
TTGAAGTATTTTGAAATTTGGGGTTTAGAATGAAA
Found at i:690884 original size:2 final size:2
Alignment explanation
Indices: 690877--690916 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
690867 ACATCTAGAT
690877 AG AG AG AG AG AG 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
690917 GACCAGTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:692066 original size:57 final size:57
Alignment explanation
Indices: 691978--692094 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
691968 TCAAAATAAG
691978 TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
1 TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
*
692035 TTGCAATAAAACTGAGAGTAGATCTAAAGCCATTATTGCATGCAATAAGATTGGCAC
1 TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
692092 TTG
1 TTG
692095 ATGTTGCTCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (57 bp):
TTGCAATAAAACTGAGAGTAGATCCAAAGCCATTATTGCATGCAATAAGATTGGCAC
Found at i:692783 original size:34 final size:33
Alignment explanation
Indices: 692707--692813 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
692697 GTGGTAAGAA
* *
692707 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
692741 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
692776 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
692810 ATTT
1 ATTT
692814 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:692795 original size:36 final size:34
Alignment explanation
Indices: 692740--692818 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
692730 TTTAAATAGT
*
692740 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
692772 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
692806 TATTATTTATTTA
1 TATTATTTTTTTA
692819 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:693667 original size:33 final size:34
Alignment explanation
Indices: 693608--693704 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
693598 AAATGTTTTT
*
693608 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
693642 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
693675 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
693705 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:693711 original size:34 final size:33
Alignment explanation
Indices: 693606--693711 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
693596 ATAAATGTTT
*
693606 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
693640 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
693672 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
693707 TTAAA
1 TTAAA
693712 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:694315 original size:126 final size:126
Alignment explanation
Indices: 694090--694442 Score: 697
Period size: 126 Copynumber: 2.8 Consensus size: 126
694080 TTTAAGTTAT
*
694090 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
694155 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
694216 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
694281 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
694342 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
694407 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
694443 CCGATTATAG
Statistics
Matches: 226, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 226 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:694523 original size:8 final size:8
Alignment explanation
Indices: 694510--694550 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
694500 TCACAATCTT
694510 TCAAATTC
1 TCAAATTC
694518 TCAAATTC
1 TCAAATTC
* *
694526 CCAAACTC
1 TCAAATTC
694534 T-AAATTC
1 TCAAATTC
694541 TCAAATTC
1 TCAAATTC
694549 TC
1 TC
694551 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:697556 original size:12 final size:12
Alignment explanation
Indices: 697539--697577 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
697529 AATACATAAA
697539 TATTTAATATAT
1 TATTTAATATAT
*
697551 TATTTAATATAA
1 TATTTAATATAT
697563 TATTTAATATTAT
1 TATTTAATA-TAT
697576 TA
1 TA
697578 GTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:703395 original size:116 final size:116
Alignment explanation
Indices: 703186--704287 Score: 1682
Period size: 116 Copynumber: 9.5 Consensus size: 116
703176 AAAACATTCT
* * *
703186 GCCCAGAGGTCTTATCATCTTGCATTGTAGGTCTTACAGATGACCCGGAGGTTTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
*
703251 AAGCTCCCGAAGGCTTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* * * *
703302 GCCCTGAGGTCTTATCATCTTGCATTGTAGGTCTTACAGATGATCCGAAGGATTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
*
703367 AAGCTCCCGAAGGTTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* * * ** *
703418 GCCCTGAGGTCTTATCATCTTGGATTGTAGATCTTACAGATGAATCGAAGGCTTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* * * ***
703483 AATCTCCCGAAGGATTTTTGAAAATATCCTGCACTACCGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* * *
703534 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATAACCCGAAGACTTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* * *
703599 AAGCTCTCGAAGGCTTTTTGAAAACATCATACACTGTAGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* * *
703650 GCCCTGAGGTTTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTAATTATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* * *
703715 AAGCTCCCGAAAGCTTTTTGAAAACATCTTGCGCTGTAGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* *
703766 GCCTTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGACTTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* *
703831 AAGCTCCCGAAGGATTTTTGAAAACATCCTACACTGTAGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* * *
703882 GCCCTGAGGTCTTATCATCTTACACTGTAGGTCTTACAGATTACCCGGAGGCTTTAAATATTAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* *
703947 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAAGTCTTATAGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* *
703998 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGATCTGGAGGCTTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* * ** **
704063 AAACTCTCGAAGGCTTTTTGAAAACATTATGCACTGTATATCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* *
704114 GCCTTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGAACCGGAGGCTTTAAATATCAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
* * * *
704179 AAGATCCCGAAGGCTTTTTGAAAATAACCTGCATTGTAGGTCTTATGGATG
66 AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
* *
704230 GCTCTGAGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAA
1 GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAA
704288 AACATCATGC
Statistics
Matches: 896, Mismatches: 90, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 896 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (116 bp):
GCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAA
AAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
Found at i:704985 original size:22 final size:22
Alignment explanation
Indices: 704960--705005 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
704950 AATAAAGCTT
*
704960 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
*
704982 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
705004 TC
1 TC
705006 TATGAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:705467 original size:54 final size:54
Alignment explanation
Indices: 705380--705535 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
705370 ATAATCACTG
* * * *
705380 GTTCATAAAATATTTAACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
*
705434 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
* *
705488 GTTCGTAAAATATTTGACAAGACATTCATTCTTTC-TAGTGGCTTCTGC
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCAT-GTGGCTTCTGC
705536 CCATATTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 92 0.99
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAAAT
Found at i:708323 original size:8 final size:8
Alignment explanation
Indices: 708310--708350 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
708300 CTCGATTCAA
708310 TTTTTTTC
1 TTTTTTTC
708318 TTTTTTTC
1 TTTTTTTC
708326 TTTTCTCTTC
1 TTTT-T-TTC
*
708336 TTTTTCTC
1 TTTTTTTC
708344 TTTTTTT
1 TTTTTTT
708351 TCTTATGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 20 0.69
9 2 0.07
10 7 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Done.