Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold81
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: 1151237
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 79344 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:552627 original size:22 final size:19
Alignment explanation
Indices: 552612--552692 Score: 83
Period size: 20 Copynumber: 4.1 Consensus size: 19
552602 TAAACGATTG
552612 TCTCCTCCTTTATAAAAATT
1 TCTCC-CCTTTATAAAAATT
552632 TCTCCCCTTTTATAAAAATTT
1 TCTCCCC-TTTATAAAAA-TT
* **
552653 TCTCCCCCTTA-AACGATT
1 TCTCCCCTTTATAAAAATT
552671 ATCTCCTCCTTTATAAAAATT
1 -TCTCC-CCTTTATAAAAATT
552692 T
1 T
552693 TCTCAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.04
19 10 0.20
20 24 0.48
21 14 0.28
ACGTcount: A:0.28, C:0.27, G:0.01, T:0.43
Consensus pattern (19 bp):
TCTCCCCTTTATAAAAATT
Found at i:552704 original size:60 final size:60
Alignment explanation
Indices: 552592--552704 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
552582 AGAAAAAAAA
* ***
552592 TTCTCCCCCTTAAACGATTGTCTCCTCCTTTATAAAAATTTCTCCCCTTTTATAAAAATT
1 TTCTCCCCCTTAAACGATTATCTCCTCCTTTATAAAAATTTCTCCAAATTTATAAAAATT
552652 TTCTCCCCCTTAAACGATTATCTCCTCCTTTATAAAAATTT-TCTCAAATTTAT
1 TTCTCCCCCTTAAACGATTATCTCCTCCTTTATAAAAATTTCTC-CAAATTTAT
552705 TTTCACATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.42
Consensus pattern (60 bp):
TTCTCCCCCTTAAACGATTATCTCCTCCTTTATAAAAATTTCTCCAAATTTATAAAAATT
Found at i:554551 original size:13 final size:13
Alignment explanation
Indices: 554533--554557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
554523 AAATAGTACC
554533 CAATGTATCGATA
1 CAATGTATCGATA
554546 CAATGTATCGAT
1 CAATGTATCGAT
554558 TCATGTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:560535 original size:10 final size:10
Alignment explanation
Indices: 560520--560546 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
560510 TGATTTGAAA
560520 TTATAGCCGT
1 TTATAGCCGT
560530 TTATAGCCGT
1 TTATAGCCGT
560540 TTATAGC
1 TTATAGC
560547 TATGTATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (10 bp):
TTATAGCCGT
Found at i:560674 original size:19 final size:19
Alignment explanation
Indices: 560630--560685 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
560620 CTGCTAGTTT
**
560630 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
560650 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
560669 CATGTATCGATACAATG
1 CATGTATCGATACAATG
560686 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:560688 original size:13 final size:13
Alignment explanation
Indices: 560670--560696 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
560660 TACAATGAAC
560670 ATGTATCGATACA
1 ATGTATCGATACA
560683 ATGTATCGATACA
1 ATGTATCGATACA
560696 A
1 A
560697 AGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:560711 original size:33 final size:32
Alignment explanation
Indices: 560651--560715 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
560641 ACAATTGTCC
*
560651 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
560683 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
560716 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:567193 original size:24 final size:25
Alignment explanation
Indices: 567166--567213 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
567156 TAAATTTGAA
567166 TTTAAATTATTTTAT-TTTTAAAGT
1 TTTAAATTATTTTATATTTTAAAGT
* *
567190 TTTAATTTTTTTTATAATTTTAAA
1 TTTAAATTATTTTAT-ATTTTAAA
567214 ATACAAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
26 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTAAATTATTTTATATTTTAAAGT
Found at i:567715 original size:26 final size:26
Alignment explanation
Indices: 567659--567718 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
567649 AGTTTTAAAA
*
567659 TCAAAAATATTTTATTTTTAAAGATT
1 TCAAAAATATTTAATTTTTAAAGATT
* *
567685 T-AAAAAT-TTTAATTTTTTTAATATT
1 TCAAAAATATTTAA-TTTTTAAAGATT
567710 TCAAAAATA
1 TCAAAAATA
567719 AATCTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 7 0.25
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (26 bp):
TCAAAAATATTTAATTTTTAAAGATT
Found at i:569753 original size:23 final size:24
Alignment explanation
Indices: 569712--569760 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
569702 TTAGATTAAA
569712 TTTATTTAAGATTTGAATTATTTAT
1 TTTATTTAAGATTTGAATTA-TTAT
*
569737 TTTA-TTAA-ATTTTAATTATTAT
1 TTTATTTAAGATTTGAATTATTAT
569759 TT
1 TT
569761 AATAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 9 0.39
24 4 0.17
25 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTATTTAAGATTTGAATTATTAT
Found at i:570098 original size:12 final size:12
Alignment explanation
Indices: 570079--570108 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
570069 GATGGTTCAA
570079 AATCATTTTTTT
1 AATCATTTTTTT
*
570091 AGTCATTTTTTT
1 AATCATTTTTTT
570103 AATCAT
1 AATCAT
570109 CAATTTCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (12 bp):
AATCATTTTTTT
Found at i:574983 original size:2 final size:2
Alignment explanation
Indices: 574976--575004 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
574966 CTCATGAATC
574976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
575005 ACCAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:579721 original size:2 final size:2
Alignment explanation
Indices: 579714--579738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
579704 TAAAAACTGA
579714 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
579739 CATCACAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:583577 original size:13 final size:13
Alignment explanation
Indices: 583559--583615 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
583549 TTCAACAATT
583559 TGTATCGATACAA
1 TGTATCGATACAA
583572 TGTATCGATACATAA
1 TGTATCGATAC--AA
583587 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
583604 TGTATCAATACA
1 TGTATCGATACA
583616 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:583596 original size:19 final size:18
Alignment explanation
Indices: 583572--583634 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
583562 ATCGATACAA
583572 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
583591 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
583604 TGTATCAATACATAAGTTT
1 TGTATCGATACATAAG-TT
583623 TGTATCGATACA
1 TGTATCGATACA
583635 ATATATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:583599 original size:32 final size:32
Alignment explanation
Indices: 583558--583647 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
583548 TTTCAACAAT
583558 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
583590 TTGTATCGATACAATGTATCAATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
583622 TTGTATCGATACAATATATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
583648 AAGCTACTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:584668 original size:17 final size:17
Alignment explanation
Indices: 584646--584679 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
584636 ATAGCATGTC
584646 CAGTACCTTCATGAGTG
1 CAGTACCTTCATGAGTG
584663 CAGTACCTTCATGAGTG
1 CAGTACCTTCATGAGTG
584680 TTATTCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
CAGTACCTTCATGAGTG
Found at i:585462 original size:28 final size:28
Alignment explanation
Indices: 585422--585560 Score: 161
Period size: 28 Copynumber: 4.9 Consensus size: 28
585412 CCTCACCCTG
585422 TCAAAAGCCCACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
*
585450 TCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
** **
585480 TCCGAAGCCCACAAGTCAGTGGCATATTT
1 TCAAAAGCCCACAAGTCAGTGGCA-ACCT
* *
585509 TCCAAAGCCCACAAGCCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
585537 TCAAAAGTCCACAACTCCGTGGCA
1 TCAAAAGCCCACAAGTCAGTGGCA
585561 CATTTTTTCT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 47 0.51
29 23 0.25
30 23 0.25
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17
Consensus pattern (28 bp):
TCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:585532 original size:59 final size:58
Alignment explanation
Indices: 585426--585537 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 58
585416 ACCCTGTCAA
* *
585426 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCG
1 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGCCAGTGGCAACCTTTTCCG
** *
585484 AAGCCCACAAGTCAGTGGCATATTTTCCAAAGCCCACAAGCCAGTGGCAACCTT
1 AAGCCCACAAGTCAGTGGCA-ACCTTCAAAAGCCCACAAGCCAGTGGCAACCTT
585538 CAAAAGTCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 20 0.42
59 28 0.58
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (58 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGCCAGTGGCAACCTTTTCCG
Found at i:585569 original size:59 final size:58
Alignment explanation
Indices: 585422--585566 Score: 159
Period size: 59 Copynumber: 2.5 Consensus size: 58
585412 CCTCACCCTG
* ** * * *
585422 TCAAAAGCCCACAAGTCAGTGGCA-ACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCAAAAGCCCACAACTCAGTGGCATATTTTCCAAAGCCCACAAGCCAGTGGCAACC-TT
** *
585480 TCCGAAGCCCACAAGTCAGTGGCATATTTTCCAAAGCCCACAAGCCAGTGGCAACC-T
1 TCAAAAGCCCACAACTCAGTGGCATATTTTCCAAAGCCCACAAGCCAGTGGCAACCTT
* * *
585537 TCAAAAGTCCACAACTCCGTGGCACATTTT
1 TCAAAAGCCCACAACTCAGTGGCATATTTT
585567 TTCTTTTTAA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 25 0.34
58 22 0.30
59 26 0.36
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.19
Consensus pattern (58 bp):
TCAAAAGCCCACAACTCAGTGGCATATTTTCCAAAGCCCACAAGCCAGTGGCAACCTT
Found at i:585623 original size:34 final size:34
Alignment explanation
Indices: 585545--585773 Score: 277
Period size: 34 Copynumber: 6.7 Consensus size: 34
585535 CTTCAAAAGT
* *
585545 CCACAACTCCGTGGCACAT-TTTTTCTTTTTAAAGC
1 CCACAACTCTGTGGCAC-TCTTTTTCCTTTT-AAGC
* *
585580 CCACAACTCTATGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGC
* *
585614 CCACAACTCTGTGACACT-TTTCTTCTTTTTAAAGC
1 CCACAACTCTGTGGCACTCTTT-TTCCTTTT-AAGC
*
585649 CCATAACTCTGTGGCACTCTTTTTCCTTTTAAGC
1 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGC
*
585683 CCACAACTCTGTGGCACTATTTTTCCTTTTAAGC
1 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGC
* *
585717 CCACAACT-TCGTGGTACTCTTTTTCCTTTTAAGT
1 CCACAACTCT-GTGGCACTCTTTTTCCTTTTAAGC
*
585751 CCACAACT-TCGTGGCACCCTTTT
1 CCACAACTCT-GTGGCACTCTTTT
585774 AAGCCCACAA
Statistics
Matches: 171, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
33 4 0.02
34 113 0.66
35 51 0.30
36 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.11, T:0.39
Consensus pattern (34 bp):
CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGC
Found at i:585640 original size:69 final size:68
Alignment explanation
Indices: 585541--585767 Score: 325
Period size: 69 Copynumber: 3.3 Consensus size: 68
585531 CAACCTTCAA
* *
585541 AAGTCCACAACTCCGTGGCACATTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTTCC
1 AAGTCCACAACTCTGTGGCAC-TTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
585606 TTTT
65 TTTT
* *
585610 AAGTCCACAACTCTGTGACACTTTTCTTCTTTTTAAAGCCCATAACTCTGTGGCACTCTTTTTCC
1 AAGTCCACAACTCTGTGGCACTTTT-TTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
585675 TTTT
65 TTTT
* * *
585679 AAGCCCACAACTCTGTGGCACTATTTTTCCTTTT-AAGCCCACAACT-TCGTGGTACTCTTTTTC
1 AAGTCCACAACTCTGTGGCACT-TTTTTCTTTTTAAAGCCCACAACTCT-GTGGCACTCTTTTTC
585742 CTTTT
64 CTTTT
585747 AAGTCCACAACT-TCGTGGCAC
1 AAGTCCACAACTCT-GTGGCAC
585768 CCTTTTAAGC
Statistics
Matches: 144, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
67 2 0.01
68 52 0.36
69 87 0.60
70 3 0.02
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.38
Consensus pattern (68 bp):
AAGTCCACAACTCTGTGGCACTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCT
TTT
Found at i:585781 original size:27 final size:28
Alignment explanation
Indices: 585741--585822 Score: 96
Period size: 27 Copynumber: 2.9 Consensus size: 28
585731 TACTCTTTTT
* *
585741 CCTTTTAAGTCCACAACTTC-GTGGCA-C
1 CCTTTTAAGCCCACAA-GTCGGTGGCATC
585768 CCTTTTAAGCCCACAAGTCGGTGGCATC
1 CCTTTTAAGCCCACAAGTCGGTGGCATC
* *
585796 CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCTTT-TAAGCCCACAAGTCGGTGGCA
585823 ACCTTCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.04
27 21 0.44
28 6 0.12
29 19 0.40
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (28 bp):
CCTTTTAAGCCCACAAGTCGGTGGCATC
Found at i:585810 original size:29 final size:27
Alignment explanation
Indices: 585761--585842 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
585751 CCACAACTTC
* *
585761 GTGGCACCCTTTTAAGCCCACAAGTCG
1 GTGGCACCCTTTAAAGCCCACAAGTCA
585788 GTGGCATCCCTTTCAAAGCCCACAAGTCA
1 GTGGCA-CCCTTT-AAAGCCCACAAGTCA
* * *
585817 GTGGCAACCTTCAAAAGCACACAAGT
1 GTGGCACCCTT-TAAAGCCCACAAGT
585843 TGATGCAACC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.13
28 22 0.47
29 19 0.40
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.20
Consensus pattern (27 bp):
GTGGCACCCTTTAAAGCCCACAAGTCA
Found at i:585827 original size:28 final size:29
Alignment explanation
Indices: 585774--585868 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
585764 GCACCCTTTT
* *
585774 AAGCCCACAAGTCGGTGGCATCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCA-ACCTTTCAA
585803 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* *
585831 AAGCACACAAGT-TGAT-GCAACCTTTTCAA
1 AAGCCCACAAGTCAG-TGGCAACC-TTTCAA
585860 AAGCCCACA
1 AAGCCCACA
585869 CAAGTTAGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
27 10 0.18
28 15 0.26
29 32 0.56
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:586183 original size:87 final size:87
Alignment explanation
Indices: 585895--586196 Score: 210
Period size: 87 Copynumber: 3.4 Consensus size: 87
585885 TCTTCTAAGT
* * * * * * *
585895 CCAATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCC
1 CCAATATCGCTGACCGTGAATCAGCATATTGGCACC-TTGTCTTTAAGA-CCAATGTCGCTAGCC
* * * *
585960 TTGAATCAGCATATTGACACCTTTAAGT
64 TCGAATCAGCACATCGACA-C---AAGC
** ** * * * * * * *
585988 CTGATATCATTGGCCTTGAATCAGCATATTAGCATC-GGCATCTTTAAGACCAATGTTGCTGGCC
1 CCAATATCGCTGACCGTGAATCAGCATATTGGCACCTTG--TCTTTAAGACCAATGTCGCTAGCC
* * * * *
586052 TTGAATTAGCACATTGGCATAAGC
64 TCGAATCAGCACATCGACACAAGC
** * * *
586076 CCAATATCGCTGACTTTGAATCGGCGTATTGGCACCTTGTCTTTAAGTCCAATGTCGCTAGCCTC
1 CCAATATCGCTGACCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTC
*
586141 GAATCAGCACATCGACACAAGT
66 GAATCAGCACATCGACACAAGC
* *
586163 CCAATATCGTTGGCCGTGAATCAGCATATTGGCA
1 CCAATATCGCTGACCGTGAATCAGCATATTGGCA
586197 TCTTTATCAC
Statistics
Matches: 163, Mismatches: 43, Indels: 12
0.75 0.20 0.06
Matches are distributed among these distances:
87 67 0.41
88 29 0.18
89 1 0.01
92 29 0.18
93 37 0.23
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (87 bp):
CCAATATCGCTGACCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTC
GAATCAGCACATCGACACAAGC
Found at i:591578 original size:20 final size:19
Alignment explanation
Indices: 591549--591623 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
591539 AAAAAGACAT
591549 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
591568 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
591589 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
591609 AATGTATCGATACAT
1 AATGTATCGATACAT
591624 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:591606 original size:40 final size:39
Alignment explanation
Indices: 591546--591623 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
591536 GGTAAAAAGA
*
591546 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
591585 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
591624 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:592292 original size:29 final size:29
Alignment explanation
Indices: 592181--592783 Score: 592
Period size: 28 Copynumber: 20.9 Consensus size: 29
592171 TTTTAAAAAT
* *
592181 GTGCCACTAACTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGACTTGTG--GGCTTTGAAAAGA
* * * *
592212 GTTACCACCGACACGTGTGGGTTTTGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTGAAAAGA
* * *
592244 GTTACTACTGGCTTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACTTGTGGGCTTTGAAAAGA
* *
592274 GTGTCACTGACTTATGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
592302 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
592331 -TGCCACTAACTTGTGGGCTTTGAAAA-A
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
592358 GTGCCACTGAGTTGTGGGC-TTGAAAA-A
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
592385 GTGCCACTGACTTGTGGGC-TTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* ** *
592412 GTTCCACTGACTCATGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * ** *
592440 GTGCTATTCACTCATGGACTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
592469 GTGCCACTGACTTGCGTGGGCTTT-AAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
*
592499 GTGCCACTGACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
592530 -TGCCACTGACTTGTGGGCTTT-AAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
592557 ATGCCACTGACTCGTGGGC-TTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
592584 GTGCCACTGACTTGCGTGGGCTTT-AAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* * *
592614 GTGCTACTAACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
592645 -TGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
592672 GTGCCATTGACTCGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
592700 GTGCTACTGACTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
592729 GTGCCACCGACCTGTGGGCTTTGAAATGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
592758 GTGCCACTGACTCGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
592784 GGGATGAACA
Statistics
Matches: 482, Mismatches: 69, Indels: 44
0.81 0.12 0.07
Matches are distributed among these distances:
27 76 0.16
28 170 0.35
29 97 0.20
30 93 0.19
31 16 0.03
32 24 0.05
34 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:592606 original size:115 final size:112
Alignment explanation
Indices: 592250--592784 Score: 612
Period size: 115 Copynumber: 4.7 Consensus size: 112
592240 AAGAGTTACT
* * *
592250 ACTGGCTTGTGGGCTTTGAAAAGAGTGTCACTGACTTATGGGCTTTGAAAAGG-TGCCACTGACT
1 ACTGACTTGTGGGCTTT-AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
* * * *
592314 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGTGCC
64 TGTGGGCTTTGAAAGAATGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
* * * *
592363 ACTGAGTTGTGGGCTTGAAAA-AGTGCCACTGACTTGTGGGC-TTGAAAAGG-TTCCACTGACTC
1 ACTGACTTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTT
* ** * * * * *
592425 ATGGGCTTTGAAAGGGTGCTATTCACTCATGGACTTTGAAAAGAGTGCC
65 GTGGGCTTTGAAAGAATGCCACTGACTCGTGGGCTTTGAAAAG-GTGCC
*
592474 ACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCACTGA
1 ACTGACTT--GTGGGCTTTAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGATGCCACTGA
*
592539 CTTGTGGGCTTTAAAAGAATGCCACTGACTCGTGGGC-TTGAAAAGGTGCC
62 CTTGTGGGCTTTGAAAGAATGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
* * *
592589 ACTGACTTGCGTGGGCTTTAAAAGGGTGCTACTAACTTGCGTGGGCTTTGAAAGGATGCCACTGA
1 ACTGACTT--GTGGGCTTTAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGATGCCACTGA
* * * *
592654 CTTGTGGGCTTTGAAAGAGTGCCATTGACTCGTGGGCTTTGAAAGGGTGCT
62 CTTGTGGGCTTTGAAAGAATGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
* * * *
592705 ACTGACTTATGGGCTTTGAAAAGAGTGCCACCGACCTGTGGGCTTTGAAATGAGTGCCACTGACT
1 ACTGACTTGTGGGCTTT-AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
*
592770 CGTGGGCTTTGAAAG
64 TGTGGGCTTTGAAAG
592785 GGATGAACAT
Statistics
Matches: 366, Mismatches: 45, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
110 53 0.14
111 30 0.08
112 4 0.01
113 41 0.11
114 46 0.13
115 116 0.32
116 38 0.10
117 38 0.10
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (112 bp):
ACTGACTTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
TGGGCTTTGAAAGAATGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
Found at i:593464 original size:13 final size:13
Alignment explanation
Indices: 593446--593470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593436 CATAAAGTGT
593446 TGTATCGATACAA
1 TGTATCGATACAA
593459 TGTATCGATACA
1 TGTATCGATACA
593471 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:593468 original size:33 final size:33
Alignment explanation
Indices: 593426--593492 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
593416 TTCAACGATT
593426 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
593459 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
593492 T
1 T
593493 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:593551 original size:13 final size:13
Alignment explanation
Indices: 593533--593557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593523 ATTACTCAAA
593533 TGTATCGATACAT
1 TGTATCGATACAT
593546 TGTATCGATACA
1 TGTATCGATACA
593558 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:593622 original size:52 final size:52
Alignment explanation
Indices: 593566--593694 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
593556 CACTGATCTT
* *
593566 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
593618 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
593670 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
593695 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:597593 original size:14 final size:13
Alignment explanation
Indices: 597574--597637 Score: 62
Period size: 13 Copynumber: 4.9 Consensus size: 13
597564 GACCCCTTTC
597574 TTTTTTTTTTGCTA
1 TTTTTTTTTTG-TA
*
597588 -TTTTTTTCT-TA
1 TTTTTTTTTTGTA
*
597599 GTTTTTTTTTTGTT
1 -TTTTTTTTTTGTA
597613 TTATTTTTTTTGT-
1 TT-TTTTTTTTGTA
597626 TTTTTTTTTTGT
1 TTTTTTTTTTGT
597638 GTAAAGGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 2 0.05
12 10 0.23
13 20 0.47
14 11 0.26
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTGTA
Found at i:597637 original size:26 final size:25
Alignment explanation
Indices: 597574--597634 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
597564 GACCCCTTTC
597574 TTTTTTTTTTGCTATTTTTTTCTTAG
1 TTTTTTTTTTG-TATTTTTTTCTTAG
* *
597600 TTTTTTTTTTGT-TTTATTTTTTTTG
1 TTTTTTTTTTGTATTT-TTTTCTTAG
597625 TTTTTTTTTT
1 TTTTTTTTTT
597635 TGTGTAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 3 0.09
25 18 0.56
26 11 0.34
ACGTcount: A:0.05, C:0.03, G:0.07, T:0.85
Consensus pattern (25 bp):
TTTTTTTTTTGTATTTTTTTCTTAG
Found at i:611641 original size:20 final size:19
Alignment explanation
Indices: 611616--611690 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
611606 AAAAAGACAT
611616 AATATATCGATACATTGAA
1 AATATATCGATACATTGAA
*
611635 GAATATATCGATACATTCATA
1 -AATATATCGATACATTGA-A
* * *
611656 CATGTATCGATATATTGAAA
1 AATATATCGATACATTG-AA
*
611676 AATGTATCGATACAT
1 AATATATCGATACAT
611691 CTGGGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
AATATATCGATACATTGAA
Found at i:612735 original size:20 final size:20
Alignment explanation
Indices: 612710--612787 Score: 97
Period size: 20 Copynumber: 3.9 Consensus size: 20
612700 GTTAAAAGAC
612710 AGAATGTATCGATACATCGA
1 AGAATGTATCGATACATCGA
612730 AGAATGTATCGATACATTC-A
1 AGAATGTATCGATACA-TCGA
* *
612750 TA-CATGTGTCGATACATCGA
1 -AGAATGTATCGATACATCGA
*
612770 AAAATGTATCGATACATC
1 AGAATGTATCGATACATC
612788 TGGCTACTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.06
20 44 0.88
21 3 0.06
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
AGAATGTATCGATACATCGA
Found at i:614787 original size:2 final size:2
Alignment explanation
Indices: 614782--614842 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
614772 CTTAGGTGTG
614782 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
* * * *
614824 CA TG TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
614843 TGTTTGATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:614952 original size:22 final size:23
Alignment explanation
Indices: 614910--614952 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
614900 TTAGTTCGTT
* *
614910 AAAAATTAAAAGTTACGAATGAA
1 AAAAATTAAAAATAACGAATGAA
614933 AAAAATTAAAAATAAC-AATG
1 AAAAATTAAAAATAACGAATG
614953 TTGGTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (23 bp):
AAAAATTAAAAATAACGAATGAA
Found at i:616644 original size:16 final size:17
Alignment explanation
Indices: 616623--616669 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
616613 GTCATGATTG
616623 TATTTAAAGTATTTT-A
1 TATTTAAAGTATTTTAA
616639 TATTTATAAAG-ATTTTAA
1 TA-TT-TAAAGTATTTTAA
616657 TATTTAAA-TATTT
1 TATTTAAAGTATTT
616670 CATAGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 10 0.37
17 9 0.33
18 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
TATTTAAAGTATTTTAA
Found at i:616655 original size:17 final size:19
Alignment explanation
Indices: 616627--616662 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
616617 TGATTGTATT
616627 TAAAGTATTTT-ATATTTA
1 TAAAGTATTTTAATATTTA
616645 TAAAG-ATTTTAATATTTA
1 TAAAGTATTTTAATATTTA
616663 AATATTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TAAAGTATTTTAATATTTA
Found at i:618120 original size:42 final size:41
Alignment explanation
Indices: 618051--618131 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
618041 ATTATAAGTA
618051 TATTTGATATATAATAAATTTATATAAATTTTGATATATTACT
1 TATTTGATATATAATAAATTTATATAAA-TTT-ATATATTACT
*
618094 TATTTG-TAT-TATATAAATTTTTATAAATTTATATATTA
1 TATTTGATATATA-ATAAATTTATATAAATTTATATATTA
618132 ATAAGGTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
40 8 0.22
41 5 0.14
42 17 0.47
43 6 0.17
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (41 bp):
TATTTGATATATAATAAATTTATATAAATTTATATATTACT
Found at i:618142 original size:42 final size:42
Alignment explanation
Indices: 618064--618145 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
618054 TTGATATATA
* *
618064 ATAAATTTATATAAATTTTGATATATTACTTATTTGTATTAT
1 ATAAATTTATATAAATTTTGATATATTAATAATTTGTATTAT
*
618106 ATAAATTTTTATAAA-TTT-ATATATTAATAAGGTTTGTATT
1 ATAAATTTATATAAATTTTGATATATTAATAA--TTTGTATT
618146 TGATGCACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 10 0.29
41 3 0.09
42 22 0.63
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (42 bp):
ATAAATTTATATAAATTTTGATATATTAATAATTTGTATTAT
Found at i:619191 original size:16 final size:17
Alignment explanation
Indices: 619160--619194 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
619150 AATAATTAAA
619160 AATATAATAGGTAAAAT
1 AATATAATAGGTAAAAT
*
619177 AATATAA-ATGTAAAAT
1 AATATAATAGGTAAAAT
619193 AA
1 AA
619195 ATTGATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
AATATAATAGGTAAAAT
Found at i:619228 original size:16 final size:16
Alignment explanation
Indices: 619203--619248 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
619193 AAATTGATGA
*
619203 ATAATTTAAATTTTTT
1 ATAATATAAATTTTTT
619219 ATAATATAAATTATTTT
1 ATAATATAAATT-TTTT
619236 -T-ATATTAAATTTT
1 ATAATA-TAAATTTT
619249 ATACAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 18 0.67
17 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATAATATAAATTTTTT
Found at i:619269 original size:32 final size:32
Alignment explanation
Indices: 619208--619269 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
619198 GATGAATAAT
* * *
619208 TTAAATTTTTTATAATATAAATTATTTTTATA
1 TTAAATTTTATACAATATAAATAATTTTTATA
619240 TTAAATTTTATACAA-ATAAATAATATTTTA
1 TTAAATTTTATACAATATAAATAAT-TTTTA
619270 AATATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (32 bp):
TTAAATTTTATACAATATAAATAATTTTTATA
Found at i:619566 original size:14 final size:14
Alignment explanation
Indices: 619547--619576 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
619537 ATAATACTTC
619547 AATATTAAAAAATT
1 AATATTAAAAAATT
619561 AATATTAAAAAATT
1 AATATTAAAAAATT
619575 AA
1 AA
619577 ATAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATTAAAAAATT
Found at i:620249 original size:29 final size:29
Alignment explanation
Indices: 620186--620249 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
620176 AACATTTTTT
* *
620186 TATTATTTAATTTTTTATTTTACATCATA
1 TATTATTTAATTTTTTATATTACATAATA
* *
620215 TTTTATTT-ATTTTTTATATTATATAATTA
1 TATTATTTAATTTTTTATATTACATAA-TA
620244 TATTAT
1 TATTAT
620250 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (29 bp):
TATTATTTAATTTTTTATATTACATAATA
Found at i:620555 original size:10 final size:10
Alignment explanation
Indices: 620530--620569 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
620520 CATTAGATTT
620530 TTTTAAAAAAA
1 TTTT-AAAAAA
620541 TTTTTAAAAAA
1 -TTTTAAAAAA
620552 TTTTAAAAAA
1 TTTTAAAAAA
620562 TTTTAAAA
1 TTTTAAAA
620570 GATAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 6 0.21
12 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:620669 original size:27 final size:28
Alignment explanation
Indices: 620639--620691 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
620629 TATATTACAT
*
620639 AAATTAT-TTATATTTTAAAAATTATAA
1 AAATTATATAATATTTTAAAAATTATAA
*
620666 AAATTATATAATATTTTAAATATTAT
1 AAATTATATAATATTTTAAAAATTAT
620692 TATGATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATTATATAATATTTTAAAAATTATAA
Found at i:620690 original size:28 final size:27
Alignment explanation
Indices: 620630--620691 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
620620 ATTAAATATT
* * *
620630 ATATTACATAAATTATTTATATTTTAA
1 ATATTATAAAAATTATTAATATTTTAA
*
620657 AAATTATAAAAATTATATAATATTTTAA
1 ATATTATAAAAATTAT-TAATATTTTAA
620685 ATATTAT
1 ATATTAT
620692 TATGATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTATAAAAATTATTAATATTTTAA
Found at i:623899 original size:25 final size:24
Alignment explanation
Indices: 623871--623921 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
623861 TATTAATGTA
623871 TTCGTA-ATATGTTTATATTATTTTT
1 TTCGTATATAT-TTTA-ATTATTTTT
623896 TTCGTATTATATTTTAATTATTTTT
1 TTCGTA-TATATTTTAATTATTTTT
623921 T
1 T
623922 ATATTGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 16 0.67
26 4 0.17
27 4 0.17
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (24 bp):
TTCGTATATATTTTAATTATTTTT
Found at i:624195 original size:23 final size:21
Alignment explanation
Indices: 624141--624204 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
624131 ACACAATTAT
624141 AATATATTTAAT-AATTAAAA
1 AATATATTTAATAAATTAAAA
624161 AATAGTA--TAATAAATATAAAA
1 AATA-TATTTAATAAAT-TAAAA
624182 AATATATTTAAATATAATTAAAA
1 AATATATTT-AATA-AATTAAAA
624205 CATGTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
19 4 0.11
20 9 0.24
21 11 0.30
22 1 0.03
23 9 0.24
24 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATATATTTAATAAATTAAAA
Found at i:626859 original size:132 final size:131
Alignment explanation
Indices: 626615--626954 Score: 351
Period size: 132 Copynumber: 2.6 Consensus size: 131
626605 TGCATAACCT
* * * *
626615 AATCGAGTTAGGTTTCAGTTTCAATCGAAAACCCTTTTGTTTTACTCTATAAGTTGATCCACTTT
1 AATCGAGTTAAGTTTTAGTTTCAATTGAAAACCTTTTTGTTTTACTCT-TAAGTTGATCCA-TTT
* * * * * * * *
626680 -AAAATTATTTTGAAAGCAAGCAAACATAATTTTAAAATATAAAAATTTAAGAGTAATTACATAA
64 GAAAATTGTTTTGAAAACAAACAAACATAATTTCAAAACATAAAAATTTAAAAATAAATACATAA
626744 ATC
129 ATC
* * *
626747 AATCGAGTTAAGTTTTAGCTTCAATTAAAAACCTTTTTGTTTTACTCTCTAAGTTGATTCATTTG
1 AATCGAGTTAAGTTTTAGTTTCAATTGAAAACCTTTTTGTTTTACTCT-TAAGTTGATCCATTTG
* * * * * * *
626812 AAAATTGTTTTTAAAATAAACAAATATAATTTCGAAACGTAATAATTTAAAAATAAATATATAAA
65 AAAATTGTTTTGAAAACAAACAAACATAATTTCAAAACATAAAAATTTAAAAATAAATACATAAA
626877 TC
130 TC
* * * * * ** *
626879 AATCAAATCATA-TTTTAATTTCAATTGAAAATCTTTTAATTTTAGTCTTGAAGTTGATCCATTT
1 AATCGAGTTA-AGTTTTAGTTTCAATTGAAAACCTTTTTGTTTTACTCTT-AAGTTGATCCATTT
626943 GAAAATTGTTTT
64 GAAAATTGTTTT
626955 AGAAGCAACC
Statistics
Matches: 171, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
131 4 0.02
132 166 0.97
133 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (131 bp):
AATCGAGTTAAGTTTTAGTTTCAATTGAAAACCTTTTTGTTTTACTCTTAAGTTGATCCATTTGA
AAATTGTTTTGAAAACAAACAAACATAATTTCAAAACATAAAAATTTAAAAATAAATACATAAAT
C
Found at i:627333 original size:26 final size:26
Alignment explanation
Indices: 627294--627349 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
627284 AAAATATTTA
627294 TTTATATTTGTATA-A-AATTAATTAAT
1 TTTATATTTGTATATATAATT-ATT-AT
627320 TTTATAATTT-TATATATAATTATTAT
1 TTTAT-ATTTGTATATATAATTATTAT
627346 TTTA
1 TTTA
627350 ATAAATTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 15 0.56
27 8 0.30
28 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTATATTTGTATATATAATTATTAT
Found at i:627424 original size:27 final size:26
Alignment explanation
Indices: 627393--627462 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
627383 CTTTGTCAGG
627393 AATTTTTTTAATTTATTTAATAATTAA
1 AATTTTTTTAATTTATTTAATAATT-A
* ** * *
627420 AATTTTTTAAATCAAATAAATAATTA
1 AATTTTTTTAATTTATTTAATAATTA
*
627446 TA-TTTTTTAATTTATTT
1 AATTTTTTTAATTTATTT
627463 GAAATTTGAA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
25 10 0.31
26 2 0.06
27 20 0.62
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTTTTTTAATTTATTTAATAATTA
Found at i:627467 original size:27 final size:27
Alignment explanation
Indices: 627396--627467 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
627386 TGTCAGGAAT
627396 TTTTTTAATTTATTT-AATAATTAAAA
1 TTTTTTAATTTATTTAAATAATTAAAA
* * ** *
627422 TTTTTTAAATCAAATAAATAATT-ATA
1 TTTTTTAATTTATTTAAATAATTAAAA
627448 TTTTTTAATTTATTTGAAAT
1 TTTTTTAATTTATTT-AAAT
627468 TTGAAGTGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
26 24 0.69
27 11 0.31
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
TTTTTTAATTTATTTAAATAATTAAAA
Found at i:628605 original size:27 final size:27
Alignment explanation
Indices: 628567--628646 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
628557 AATCAACAAT
* *
628567 ATAATACATATTTTATGTAATAATTAA
1 ATAATAAATATTTTATATAATAATTAA
* *
628594 ATAATAAATA-TTTATTTTAATAATTTA
1 ATAATAAATATTTTA-TATAATAATTAA
*
628621 TTAAT-AAT-TTTTATAATAATAATTAA
1 ATAATAAATATTTTAT-ATAATAATTAA
628647 TATTTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
25 1 0.02
26 20 0.45
27 23 0.52
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
ATAATAAATATTTTATATAATAATTAA
Found at i:629153 original size:15 final size:15
Alignment explanation
Indices: 629133--629177 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
629123 AAAAATATAT
629133 TTATTTAATTTTTAA
1 TTATTTAATTTTTAA
*
629148 TTATTTTATTTTTAA
1 TTATTTAATTTTTAA
*
629163 TTATTTAATTATTAA
1 TTATTTAATTTTTAA
629178 ATATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTAATTTTTAA
Found at i:629171 original size:8 final size:8
Alignment explanation
Indices: 629133--629175 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
629123 AAAAATATAT
629133 TTATTTAA
1 TTATTTAA
629141 TT-TTTAA
1 TTATTTAA
*
629148 TTATTTTA
1 TTATTTAA
629156 TT-TTTAA
1 TTATTTAA
629163 TTATTTAA
1 TTATTTAA
629171 TTATT
1 TTATT
629176 AAATATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTATTTAA
Found at i:629327 original size:3 final size:3
Alignment explanation
Indices: 629319--629354 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
629309 ACATGTTTAG
629319 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
629355 CGGTTACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:629480 original size:3 final size:3
Alignment explanation
Indices: 629472--629505 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
629462 AGGAAAGTAA
629472 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
629506 ATTAATTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:629569 original size:2 final size:2
Alignment explanation
Indices: 629537--629589 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
629527 TAAATAAATT
* * *
629537 TA TA -A TA TA TT TA TA AA TA T- TA TA CA 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
629577 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
629590 GTTTGAAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:636483 original size:20 final size:20
Alignment explanation
Indices: 636425--636485 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
636415 ATTATTTATT
*
636425 ATATTTAATA-TTTATTT-A
1 ATATTTAAAATTTTATTTAA
* *
636443 A-CTTTAAAATTATTTTTTAA
1 ATATTTAAAATT-TTATTTAA
636463 ATATTTAAAATTTTATTTAA
1 ATATTTAAAATTTTATTTAA
636483 ATA
1 ATA
636486 AACTGTTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 6 0.18
18 2 0.06
19 5 0.15
20 12 0.35
21 9 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTAAAATTTTATTTAA
Found at i:636783 original size:16 final size:15
Alignment explanation
Indices: 636748--636793 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
636738 TTAATTTTAA
636748 AATA-TTTATATATT
1 AATATTTTATATATT
636762 AATATTTTATCATA-T
1 AATATTTTAT-ATATT
*
636777 AATTATTTTTTATATT
1 AA-TATTTTATATATT
636793 A
1 A
636794 TATCCGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 11 0.41
16 12 0.44
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTTATATATT
Found at i:639791 original size:19 final size:19
Alignment explanation
Indices: 639759--639814 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
639749 TTTCTCTTTT
*
639759 TTTCTTTAAAAATATATTA
1 TTTCTATAAAAATATATTA
* *
639778 TTTTTATTAAAATATATT-
1 TTTCTATAAAAATATATTA
*
639796 TTTCTATAAAAAGATATTA
1 TTTCTATAAAAATATATTA
639815 AAAAAACCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTCTATAAAAATATATTA
Found at i:639805 original size:17 final size:17
Alignment explanation
Indices: 639757--639806 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
639747 ACTTTCTCTT
*
639757 TTTTTCTTTAAAAATATA
1 TTTTTCTAT-AAAATATA
*
639775 TTATTTTTATTAAAATATA
1 TT-TTTCTA-TAAAATATA
639794 TTTTTCTATAAAA
1 TTTTTCTATAAAA
639807 AGATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 14 0.52
20 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTCTATAAAATATA
Found at i:640359 original size:17 final size:18
Alignment explanation
Indices: 640337--640385 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
640327 GTTTGACCTG
640337 AATTATAATTTAAA-ATT
1 AATTATAATTTAAATATT
*
640354 AATTATAAAATATAAATATT
1 AATTAT--AATTTAAATATT
640374 AA-TATAATTTAA
1 AATTATAATTTAA
640386 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 12 0.44
19 10 0.37
20 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTATAATTTAAATATT
Found at i:640745 original size:31 final size:31
Alignment explanation
Indices: 640684--640746 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
640674 AATAAATTAA
* *
640684 ATTGAATAAAATTTTAAAATTAATCAAATCG
1 ATTGAATAAAATTTCAAAATTAATAAAATCG
640715 ATTGAA-AAATATTTCAAAATTAA-AATAATCG
1 ATTGAATAAA-ATTTCAAAATTAATAA-AATCG
640746 A
1 A
640747 ATCAAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (31 bp):
ATTGAATAAAATTTCAAAATTAATAAAATCG
Found at i:640889 original size:30 final size:27
Alignment explanation
Indices: 640821--640882 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
640811 TTATATTGTT
* *
640821 ATATAATATA-ATATAAATTATATATA
1 ATATAATATATTTTTAAATTATATATA
*
640847 ATATTATATATTTTTAAATTATTATATAA
1 ATATAATATATTTTTAAATTA-TATAT-A
640876 ATATAAT
1 ATATAAT
640883 TTTATTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.31
27 8 0.28
28 5 0.17
29 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATAATATATTTTTAAATTATATATA
Found at i:641393 original size:16 final size:16
Alignment explanation
Indices: 641374--641414 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
641364 TTATAAAATT
**
641374 TTCGGGTCATTTTGGG
1 TTCGGGTCATTTCAGG
641390 TTCGGGTCATTTCAGG
1 TTCGGGTCATTTCAGG
641406 TTCGGGTCA
1 TTCGGGTCA
641415 ATCGAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.17, G:0.34, T:0.39
Consensus pattern (16 bp):
TTCGGGTCATTTCAGG
Found at i:641463 original size:53 final size:53
Alignment explanation
Indices: 641387--641490 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
641377 GGGTCATTTT
*
641387 GGGTTCGGGTCATTTCAGGTTCGGGTCAATCGAGTTTAACAC-TCGGGTTAATC
1 GGGTTCGGGTCATTTCAGATTCGGGTCAATCGAGTTTAAC-CTTCGGGTTAATC
* * * *
641440 GGGTTCGGGTCA-TTCTGTATTCGGGTTAATTGGGTTTAACCTTCGGGTTAA
1 GGGTTCGGGTCATTTCAG-ATTCGGGTCAATCGAGTTTAACCTTCGGGTTAA
641491 ATTAGGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
52 5 0.11
53 39 0.89
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.36
Consensus pattern (53 bp):
GGGTTCGGGTCATTTCAGATTCGGGTCAATCGAGTTTAACCTTCGGGTTAATC
Found at i:641484 original size:22 final size:23
Alignment explanation
Indices: 641459--641501 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
641449 TCATTCTGTA
*
641459 TTCGGGTT-AATTGGGTTTAACC
1 TTCGGGTTAAATTAGGTTTAACC
641481 TTCGGGTTAAATTAGGTTTAA
1 TTCGGGTTAAATTAGGTTTAA
641502 GTCATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (23 bp):
TTCGGGTTAAATTAGGTTTAACC
Found at i:642698 original size:2 final size:2
Alignment explanation
Indices: 642691--642723 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
642681 ACCAAGCTTT
642691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
642724 CAATAAGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:642993 original size:2 final size:2
Alignment explanation
Indices: 642980--643013 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
642970 TGATGTTTAC
*
642980 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
643014 TCAAAGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:643204 original size:24 final size:24
Alignment explanation
Indices: 643175--643249 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
643165 TTCAATTATT
643175 ATTTAAATAAAAAAATTTATTTAA
1 ATTTAAATAAAAAAATTTATTTAA
* * *
643199 ATTTAATTATAAAAA--TATATAA
1 ATTTAAATAAAAAAATTTATTTAA
*
643221 ATATTAATATAAAATAATTT-TTT-A
1 AT-TTAA-ATAAAAAAATTTATTTAA
643245 ATTTA
1 ATTTA
643250 TTTAGTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
22 8 0.20
23 7 0.17
24 22 0.55
25 2 0.05
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTAAATAAAAAAATTTATTTAA
Found at i:644903 original size:25 final size:25
Alignment explanation
Indices: 644870--644936 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
644860 ATCTTTTATT
644870 TTAT-TTTATATATAATATAAAAAA
1 TTATATTTATATATAATATAAAAAA
**
644894 TTATATTTATATAATAAT-TTTAAAA
1 TTATATTTATAT-ATAATATAAAAAA
*
644919 -TATA-TAATATATAATATA
1 TTATATTTATATATAATATA
644937 TAGTTATTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 5 0.14
23 6 0.17
24 8 0.22
25 12 0.33
26 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATATTTATATATAATATAAAAAA
Found at i:645082 original size:27 final size:27
Alignment explanation
Indices: 645047--645098 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
645037 ATATTTTTTA
*
645047 ATCAGTTTAA-TAATTTTTAAAAATTCG
1 ATCAATTTAATTAA-TTTTAAAAATTCG
645074 ATCAATTTAATTAATTTTAAAAATT
1 ATCAATTTAATTAATTTTAAAAATT
645099 ATAAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
ATCAATTTAATTAATTTTAAAAATTCG
Found at i:645477 original size:15 final size:16
Alignment explanation
Indices: 645459--645488 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
645449 TTGAGAAATA
645459 AAAATTTGAT-ATTTT
1 AAAATTTGATCATTTT
645474 AAAATTTGATCATTT
1 AAAATTTGATCATTT
645489 AACTACCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (16 bp):
AAAATTTGATCATTTT
Found at i:645734 original size:24 final size:24
Alignment explanation
Indices: 645689--645734 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
645679 AATATTTATA
* * *
645689 TAATAAAAAATTTTTATTTAAATT
1 TAATAAAAAATATTAATATAAATT
*
645713 TAATTAAAAATATTAATATAAA
1 TAATAAAAAATATTAATATAAA
645735 AATAATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAAAAAATATTAATATAAATT
Found at i:645805 original size:18 final size:17
Alignment explanation
Indices: 645751--645806 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
645741 TTTTAATATT
* *
645751 ATTTTAAAAATAAAATAG
1 ATTTTAAAAA-AAATTAA
* *
645769 ATTTTTAAACAAATTAA
1 ATTTTAAAAAAAATTAA
645786 ATTTTAAAAAAAATTTAA
1 ATTTTAAAAAAAA-TTAA
645804 ATT
1 ATT
645807 ATAATTCAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTTTAAAAAAAATTAA
Found at i:649686 original size:200 final size:200
Alignment explanation
Indices: 649343--649741 Score: 789
Period size: 200 Copynumber: 2.0 Consensus size: 200
649333 GGGTTTTGCC
649343 TGCTTCGAACTCCGACGATTATTATAGTAACCATCTTTTAGTTGTTTATAACCAGCATAGTTACA
1 TGCTTCGAACTCCGACGATTATTATAGTAACCATCTTTTAGTTGTTTATAACCAGCATAGTTACA
649408 AGTGTTACTTCTTAATGAAACTAACATAAGTGCACCTATCAAACAAGAAAGTGATTCCGTAGGTT
66 AGTGTTACTTCTTAATGAAACTAACATAAGTGCACCTATCAAACAAGAAAGTGATTCCGTAGGTT
649473 TTGACTTTGACTGCTTCGAACTCATATGGAGTATGAATAGCGATGTTGTTCCGGCTCTTCATTTT
131 TTGACTTTGACTGCTTCGAACTCATATGGAGTATGAATAGCGATGTTGTTCCGGCTCTTCATTTT
649538 TTTTT
196 TTTTT
649543 TGCTTCGAACTCCGACGATTATTATAGTAACCATCTTTTAGTTGTTTATAACCAGCATAGTTACA
1 TGCTTCGAACTCCGACGATTATTATAGTAACCATCTTTTAGTTGTTTATAACCAGCATAGTTACA
649608 AGTGTTACTTCTTAATGAAACTAACATAAGTGCACCTATCAAACAAGAAAGTGATTCCGTAGGTT
66 AGTGTTACTTCTTAATGAAACTAACATAAGTGCACCTATCAAACAAGAAAGTGATTCCGTAGGTT
*
649673 TTGACTTTGACTGCTTCGAACTCATATGGAGTATGAATAGCGATGTTGTTTCGGCTCTTCATTTT
131 TTGACTTTGACTGCTTCGAACTCATATGGAGTATGAATAGCGATGTTGTTCCGGCTCTTCATTTT
649738 TTTT
196 TTTT
649742 GGTTAAAGCT
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 198 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (200 bp):
TGCTTCGAACTCCGACGATTATTATAGTAACCATCTTTTAGTTGTTTATAACCAGCATAGTTACA
AGTGTTACTTCTTAATGAAACTAACATAAGTGCACCTATCAAACAAGAAAGTGATTCCGTAGGTT
TTGACTTTGACTGCTTCGAACTCATATGGAGTATGAATAGCGATGTTGTTCCGGCTCTTCATTTT
TTTTT
Found at i:654364 original size:96 final size:95
Alignment explanation
Indices: 653772--654416 Score: 622
Period size: 92 Copynumber: 6.9 Consensus size: 95
653762 GACAATAGAA
* * * * * * * * * *
653772 GCATCATAAGAGCTTAATAAACTTGATCAACAAAGACCATTAACATGCTGAAGAGACAAG-AAAG
1 GCATCATAAGAGCATACTAAACTTAATCAACAAACACAATCAAGATGCTAAAGAGAAAAGAAAAC
* * *
653836 AAGCATACCACGAGCTATGAGGATTATCTT
66 AAGTATACCACGAGCTACGGGGATTATCTT
* * * * * **
653866 GCGTCATAAGAGCATACTAAACTTTAA--AAC-AACATAACCAAGATGTTAAAGAG-ACAGAGGA
1 GCATCATAAGAGCATACTAAAC-TTAATCAACAAACACAATCAAGATGCTAAAGAGAAAAGAAAA
*
653927 CAAGTATACCAGGAGCTACGGGGATTATCTT
65 CAAGTATACCACGAGCTACGGGGATTATCTT
** * * *
653958 GTGTCATAAGAGCATACTAAACTTAATTAACAAACACAATCAAGATCCTAAAGAG-ACAGAAAAC
1 GCATCATAAGAGCATACTAAACTTAATCAACAAACACAATCAAGATGCTAAAGAGAAAAGAAAAC
* *
654022 AAGTATACCAC-A--AACAGGGA-TATCTT
66 AAGTATACCACGAGCTACGGGGATTATCTT
* * * *
654048 GCATCATAAGAGCATGCTATACTTAATTAACAAACACAATCAAGATGCT-AA-A-CAAAGAAAAC
1 GCATCATAAGAGCATACTAAACTTAATCAACAAACACAATCAAGATGCTAAAGAGAAAAGAAAAC
* * * *
654110 AAGCATGCCTCAAGCTACGGGGATTATCTT
66 AAGTATACCACGAGCTACGGGGATTATCTT
** * * *
654140 GTGTCATAAGTGCATACTAAACTTAATTAACAAACACAATCAAGATGCTAAATAGACAAAGAAAA
1 GCATCATAAGAGCATACTAAACTTAATCAACAAACACAATCAAGATGCTAAAGAGA-AAAGAAAA
*
654205 CAAGTATA-CACGAGCTATGGGGATTATCTT
65 CAAGTATACCACGAGCTACGGGGATTATCTT
* *
654235 GCATCATAAGTA-CATACTAAACTTAATCCACAAACACAATTAAGATGCTAAAGAGAAAAAGAAA
1 GCATCATAAG-AGCATACTAAACTTAATCAACAAACACAATCAAGATGCTAAAGAG-AAAAGAAA
* * *
654299 ACAAGTATACAATGAGCTACAGGGATTATCTT
64 ACAAGTATACCACGAGCTACGGGGATTATCTT
* * * * *
654331 GCATCATAAAAGCAAATTAAACTTAATCAACAAACA-AAACTAAG-TAGCTAAAGAGATGAAGAA
1 GCATCATAAGAGCATACTAAACTTAATCAACAAACACAATC-AAGAT-GCTAAAGAGA-AAAGAA
* *
654394 AACAAGTATACCTCAAGCTACGG
63 AACAAGTATACCACGAGCTACGG
654417 ATCAATACTA
Statistics
Matches: 454, Mismatches: 76, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
88 17 0.04
89 3 0.01
90 50 0.11
91 18 0.04
92 113 0.25
93 9 0.02
94 56 0.12
95 90 0.20
96 98 0.22
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (95 bp):
GCATCATAAGAGCATACTAAACTTAATCAACAAACACAATCAAGATGCTAAAGAGAAAAGAAAAC
AAGTATACCACGAGCTACGGGGATTATCTT
Found at i:654584 original size:171 final size:173
Alignment explanation
Indices: 654248--654585 Score: 420
Period size: 171 Copynumber: 2.0 Consensus size: 173
654238 TCATAAGTAC
*
654248 ATACTAAACTTAATCCACAAACACAATTAAGATGCTAAAGAGAAAAAGAAAACAAGTATACAATG
1 ATACTAAACTTAATCCACAAACACAATCAAGATGCTAAAGAGAAAAAGAAAACAAGTATACAATG
* *
654313 AGCTACAGGGATTATCTTGCATCATAAAAGCAAATTAAACTTAATCAACAAACAAAACTAAGTAG
66 AGCTACAGGGATTATCTTGCATCATAAAAGCAAAATAAACTTAATCAACAAACAAAACCAAGTAG
* *
654378 CTAAAGAGATGAAGAAAACAAGTATACCTCAAGCTACGGATCA
131 CTAAAGAGAAGAAGAAAACAAGTATACCACAAGCTACGGATCA
* * ** *
654421 ATACTAAACTTAAT-TAGCAAACACAGTCAAGATGCTAAAGAGATGAAGAAAACAAGTA-CCAA-
1 ATACTAAACTTAATCCA-CAAACACAATCAAGATGCTAAAGAGAAAAAGAAAACAAGTATACAAT
* * * * * * *
654483 GATCTA-TGAGGATTATCTT-CTCTCATAAGAG-AATAATAAACTTAATTAACAAATACAACCAA
65 GAGCTACAG-GGATTATCTTGC-ATCATAAAAGCAA-AATAAACTTAATCAACAAACAAAACCAA
*
654545 G-ATGCTAAAGAGAAGAAGAAAACTAGTATACCACAAGCTAC
127 GTA-GCTAAAGAGAAGAAGAAAACAAGTATACCACAAGCTAC
654586 AGAGATTATC
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
170 5 0.04
171 82 0.58
172 4 0.03
173 51 0.36
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (173 bp):
ATACTAAACTTAATCCACAAACACAATCAAGATGCTAAAGAGAAAAAGAAAACAAGTATACAATG
AGCTACAGGGATTATCTTGCATCATAAAAGCAAAATAAACTTAATCAACAAACAAAACCAAGTAG
CTAAAGAGAAGAAGAAAACAAGTATACCACAAGCTACGGATCA
Found at i:654624 original size:96 final size:94
Alignment explanation
Indices: 654416--654633 Score: 262
Period size: 94 Copynumber: 2.3 Consensus size: 94
654406 TCAAGCTACG
* ** *
654416 GATCAATACTAAACTTAATTAGCAAACACAGTCAAGATGCTAAAGAGATGAAGAAAACAAGTACC
1 GATC-ATACTAAACTTAATTAACAAACACAACCAAGATGCTAAAGAGAAGAAGAAAACAAGTACC
* *
654481 AAGATCTATGAGGATTATCTTCTCTCATAA
65 AAGAGCTAAGAGGATTATCTTCTCTCATAA
** * * *
654511 GAGAATAATAAACTTAATTAACAAATACAACCAAGATGCTAAAGAGAAGAAGAAAACTAGTATAC
1 GATCATACTAAACTTAATTAACAAACACAACCAAGATGCTAAAGAGAAGAAGAAAACAAG--TAC
654576 CACA-AGCTACAGA-GATTATCTTGCT-TCATAA
64 CA-AGAGCTA-AGAGGATTATCTT-CTCTCATAA
654607 GATCATACTAAACTTAATTAACAAACA
1 GATCATACTAAACTTAATTAACAAACA
654634 TGATGCTAAT
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
94 49 0.48
95 2 0.02
96 47 0.46
97 5 0.05
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (94 bp):
GATCATACTAAACTTAATTAACAAACACAACCAAGATGCTAAAGAGAAGAAGAAAACAAGTACCA
AGAGCTAAGAGGATTATCTTCTCTCATAA
Found at i:655689 original size:2 final size:2
Alignment explanation
Indices: 655673--655727 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
655663 TTAAATGAAA
*
655673 AG AG AG AT AG A- 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 AG
655714 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
655728 CTTACTGAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:656429 original size:11 final size:11
Alignment explanation
Indices: 656413--656453 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
656403 AATGGATAAA
656413 ATTAATTTTAT
1 ATTAATTTTAT
656424 ATTAATTTTAT
1 ATTAATTTTAT
*
656435 AATT--TTTTTT
1 -ATTAATTTTAT
656445 ATTAATTTT
1 ATTAATTTT
656454 CTTTAAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.12
10 5 0.19
11 15 0.58
12 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:659297 original size:28 final size:28
Alignment explanation
Indices: 659266--659322 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
659256 CATCGTAATG
*
659266 TAAAAATATTATTATATATAATA-ATTTT
1 TAAAAATATTATTATA-AAAATATATTTT
659294 TAAAAATATTATTATAAAAATATATTTT
1 TAAAAATATTATTATAAAAATATATTTT
659322 T
1 T
659323 TATAAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAAAATATTATTATAAAAATATATTTT
Found at i:666495 original size:16 final size:16
Alignment explanation
Indices: 666465--666519 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
666455 ATTTTATTAA
666465 ATATTTA-TTATATTTG
1 ATATTTATTTA-ATTTG
*
666481 ATATTTATTTAATTTT
1 ATATTTATTTAATTTG
* *
666497 AAATTTATTTATTTTG
1 ATATTTATTTAATTTG
666513 ATATTTA
1 ATATTTA
666520 AAAATTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 30 0.91
17 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
ATATTTATTTAATTTG
Found at i:667051 original size:16 final size:16
Alignment explanation
Indices: 667026--667057 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
667016 ATATAAATAC
*
667026 ATTATTGAGTTTTGAT
1 ATTATCGAGTTTTGAT
667042 ATTATCGAGTTTTGAT
1 ATTATCGAGTTTTGAT
667058 TGTTTTGGGG
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:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (16 bp):
ATTATCGAGTTTTGAT
Found at i:668267 original size:28 final size:28
Alignment explanation
Indices: 668210--668267 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
668200 TAGTATCTCC
* *
668210 ATGCATTATTATCATGACTTACATGTTT
1 ATGCATTATTATCATGAATTACATGATT
668238 ATGCATT-TT-TCATGAATATACTATGATT
1 ATGCATTATTATCATGAAT-TAC-ATGATT
668266 AT
1 AT
668268 CGCGACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 7 0.27
27 5 0.19
28 14 0.54
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (28 bp):
ATGCATTATTATCATGAATTACATGATT
Found at i:668957 original size:172 final size:173
Alignment explanation
Indices: 668634--668970 Score: 380
Period size: 172 Copynumber: 1.9 Consensus size: 173
668624 GCATATTTTT
* *
668634 TGTCATTTAAGTCATTTTTCATAATATAAAGACTTTGATGTAATTTTACAAATTTTAATGTCATT
1 TGTCATTTAAGTCATTTTTCATAATATAAAGACTTTGA-GTAATTTCACAAATTTTAATATCATT
* ** * *
668699 TAAGTAATTCTCCATGACTTAAGGACTCAAATTTAATATTATGAATTTTTTTGTCATTTAGATTA
65 TAAGTAATTCTCCATGACTTAAGAACTCAAATGCAATATTATGAATTTTATTGTCATTTAGATCA
**
668764 TTTTCAATAATCTAGAGACTTTGATATAATTTTATAAATATTGA
130 TAATCAATAATCTAGAGACTTTGATATAATTTTATAAATATTGA
* * *
668808 TGTCATTTAAGTCATTTTTCATAATCTAGAA-ACTTTG-GTAATTTCATAAATTTTAATATTA-T
1 TGTCATTTAAGTCATTTTTCATAATATA-AAGACTTTGAGTAATTTCACAAATTTTAATATCATT
* * * * *** *
668870 TAAGGTTATTTTCGATGACTTAAGAATTTTGATGCAATTTTATGAATTTTGATT-TCATTTAGAT
65 TAA-GTAATTCTCCATGACTTAAGAACTCAAATGCAATATTATGAATTTT-ATTGTCATTTAGAT
* *
668934 CATGAATC-ATGATCT-GAAGACTTTGATGTAATTTTAT
128 CAT-AATCAATAATCTAG-AGACTTTGATATAATTTTAT
668971 GAATTTTTTA
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
171 5 0.04
172 92 0.68
173 4 0.03
174 33 0.24
175 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (173 bp):
TGTCATTTAAGTCATTTTTCATAATATAAAGACTTTGAGTAATTTCACAAATTTTAATATCATTT
AAGTAATTCTCCATGACTTAAGAACTCAAATGCAATATTATGAATTTTATTGTCATTTAGATCAT
AATCAATAATCTAGAGACTTTGATATAATTTTATAAATATTGA
Found at i:670037 original size:24 final size:23
Alignment explanation
Indices: 670005--670064 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
669995 ATTTTTATTT
670005 AAATTTAAT-TAAAAATATATCTA
1 AAATTTAATATAAAAATA-ATCTA
* *
670028 AAATATTAATATAAAATTAATTTA
1 AAAT-TTAATATAAAAATAATCTA
670052 AAATTTTAATATA
1 AAA-TTTAATATA
670065 TTTTGAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.12
24 20 0.62
25 8 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTTAATATAAAAATAATCTA
Found at i:675089 original size:26 final size:24
Alignment explanation
Indices: 675054--675101 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
675044 ACTTGTATGA
675054 AAATTAATTTAAAAAGACTAACTTGG
1 AAATTAATTT-AAAA-ACTAACTTGG
*
675080 AAATTAATTTCAAAACTAACTT
1 AAATTAATTTAAAAACTAACTT
675102 CGATTTGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATTAATTTAAAAACTAACTTGG
Found at i:677587 original size:15 final size:14
Alignment explanation
Indices: 677569--677639 Score: 55
Period size: 15 Copynumber: 5.4 Consensus size: 14
677559 ATGCGATAAA
*
677569 AAATTTAATAATATT
1 AAATATAATAATA-T
*
677584 AAATATAATTATAT
1 AAATATAATAATAT
677598 AAATATAAT-ATA-
1 AAATATAATAATAT
*
677610 AAA-ATAAAAATAT
1 AAATATAATAATAT
*
677623 TAA-A-AAT-ATAT
1 AAATATAATAATAT
677634 AAATAT
1 AAATAT
677640 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 10 0.22
12 9 0.20
13 6 0.13
14 10 0.22
15 11 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATAATAATAT
Found at i:677609 original size:19 final size:18
Alignment explanation
Indices: 677585--677639 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
677575 AATAATATTA
677585 AATATAATTATATAAATAT
1 AATATAA-TATATAAATAT
* *
677604 AATATAAAAATAAAAATATT
1 AATAT-AATATATAAATA-T
677624 AA-A-AATATATAAATAT
1 AATATAATATATAAATAT
677640 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
19 14 0.47
20 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATATATAAATAT
Found at i:677622 original size:25 final size:26
Alignment explanation
Indices: 677575--677636 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
677565 TAAAAAATTT
* * *
677575 AATAATAT-TAAATATAATTATATAAA
1 AATAATATAAAAATAAAAATAT-TAAA
*
677601 TATAATATAAAAATAAAAATATTAAA
1 AATAATATAAAAATAAAAATATTAAA
677627 AAT-ATATAAA
1 AATAATATAAA
677637 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 7 0.23
26 13 0.43
27 10 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AATAATATAAAAATAAAAATATTAAA
Found at i:677644 original size:19 final size:19
Alignment explanation
Indices: 677593--677646 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
677583 TAAATATAAT
*
677593 TATATAAATATAATATAAAAA
1 TATATAAATAT--TTTAAAAA
677614 TA-A-AAATA--TTAAAAA
1 TATATAAATATTTTAAAAA
677629 TATATAAATATTTTAAAA
1 TATATAAATATTTTAAAA
677647 TTTATATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 5 0.18
19 11 0.39
20 1 0.04
21 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TATATAAATATTTTAAAAA
Found at i:677677 original size:32 final size:32
Alignment explanation
Indices: 677641--677764 Score: 115
Period size: 32 Copynumber: 3.7 Consensus size: 32
677631 TATAAATATT
677641 TTAAAATTTATATAATATAAATTATTAATTTA
1 TTAAAATTTATATAATATAAATTATTAATTTA
* * *
677673 TTAAAATTTAAATTATTTAAATATGATATAAATATATA
1 TTAAAATTTATATAATATAAAT-T-AT-T-AAT-T-TA
** *
677711 TTTAAAATTTTATATAATATAAATTATTAACGTG
1 -TTAAAA-TTTATATAATATAAATTATTAATTTA
677745 TTAAAATTTATAT-ATATAAA
1 TTAAAATTTATATAATATAAA
677765 ATATCTTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
31 7 0.09
32 26 0.35
33 7 0.09
34 3 0.04
35 1 0.01
36 5 0.07
37 2 0.03
38 4 0.05
39 7 0.09
40 13 0.17
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (32 bp):
TTAAAATTTATATAATATAAATTATTAATTTA
Found at i:677687 original size:23 final size:22
Alignment explanation
Indices: 677645--677740 Score: 68
Period size: 23 Copynumber: 4.1 Consensus size: 22
677635 AATATTTTAA
*
677645 AATTTATATAATATAAATTATT
1 AATTTATAAAATATAAATTATT
*
677667 AATTTATTAAAATTTAAATTATTT
1 AATTTA-TAAAATATAAATTA-TT
* * *
677691 AAATATGATATAAATATATATT-TAA
1 -AAT-TTATA-AAATATAAATTAT-T
*
677716 AATTTTATATAATATAAATTATT
1 AA-TTTATAAAATATAAATTATT
677739 AA
1 AA
677741 CGTGTTAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
22 6 0.11
23 23 0.41
24 10 0.18
25 6 0.11
26 11 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
AATTTATAAAATATAAATTATT
Found at i:677706 original size:11 final size:10
Alignment explanation
Indices: 677593--677711 Score: 53
Period size: 11 Copynumber: 12.5 Consensus size: 10
677583 TAAATATAAT
677593 TATATAAATA
1 TATATAAATA
677603 TAATATAAA-A
1 T-ATATAAATA
677613 -ATA-AAA-A
1 TATATAAATA
*
677620 TAT-TAAAAA
1 TATATAAATA
677629 TATATAAATA
1 TATATAAATA
* *
677639 T-TTTAAAATT
1 TATAT-AAATA
677649 TATATAATATA
1 TATATAA-ATA
* * *
677660 AATTATTAATT
1 TA-TATAAATA
677671 TAT-TAAA-A
1 TATATAAATA
677679 T-T-TAAAT-
1 TATATAAATA
*
677686 TATTTAAATA
1 TATATAAATA
677696 TGATATAAATA
1 T-ATATAAATA
677707 TATAT
1 TATAT
677712 TTAAAATTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
7 10 0.12
8 10 0.12
9 14 0.17
10 21 0.25
11 24 0.29
12 4 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (10 bp):
TATATAAATA
Found at i:677767 original size:72 final size:70
Alignment explanation
Indices: 677628--677768 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 70
677618 AATATTAAAA
** *
677628 ATATATAAATATTTTAAAATTTATATAATATAAATTATTAATTTATTAAAATTTAAATTATTTAA
1 ATATATAAATATTTTAAAATTTATATAATATAAATTATTAACGTATTAAAATTTAAATTATTAAA
677693 ATATG
66 ATATG
* *
677698 ATATA-AATATATATTTAAAATTTTATATAATATAAATTATTAACGTGTTAAAATTTATA-TATA
1 ATATATAA-ATAT-TTTAAAA-TTTATATAATATAAATTATTAACGTATTAAAATTTAAATTAT-
677761 TAAAATAT
62 TAAAATAT
677769 CTTAAAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
69 2 0.03
70 9 0.15
71 10 0.16
72 41 0.66
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (70 bp):
ATATATAAATATTTTAAAATTTATATAATATAAATTATTAACGTATTAAAATTTAAATTATTAAA
ATATG
Found at i:677881 original size:20 final size:20
Alignment explanation
Indices: 677815--677882 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
677805 AACACGAATA
* *
677815 TATAAATTTTTTAAATCTAAT
1 TATAAATATTTTAAAT-AAAT
* *
677836 TA-AAAT-TTATT-ATTAAAA
1 TATAAATATT-TTAAATAAAT
677854 TATAAAATATTTTAAATAAAT
1 TAT-AAATATTTTAAATAAAT
677875 TATAAATA
1 TATAAATA
677883 AAAAATATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 17 0.46
21 12 0.32
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAAATATTTTAAATAAAT
Found at i:677914 original size:94 final size:94
Alignment explanation
Indices: 677758--677930 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 94
677748 AAATTTATAT
*
677758 ATATAAAATATCTTAAAAAAATTATAATAAATAAAATATATGAACATAACACGAATATATAAATT
1 ATATAAAATATCTTAAAAAAATTATAATAAATAAAATATACGAACATAACACGAATATATAAA-T
* *
677823 TTTTAAATCTAATTAAAATTTATTATTAAA
65 TATTAAATATAATTAAAATTTATTATTAAA
* * * *
677853 ATATAAAATATTTTAAATAAATTATAA-ATAA-AAAATATACGAATATAACATGAATATATAAAT
1 ATATAAAATATCTTAAAAAAATTATAATA-AATAAAATATACGAACATAACACGAATATATAAAT
677916 TATTAAATATAATTA
65 TATTAAATATAATTA
677931 TAATCTAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
93 14 0.20
94 29 0.41
95 27 0.39
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (94 bp):
ATATAAAATATCTTAAAAAAATTATAATAAATAAAATATACGAACATAACACGAATATATAAATT
ATTAAATATAATTAAAATTTATTATTAAA
Found at i:678011 original size:16 final size:15
Alignment explanation
Indices: 677986--678019 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
677976 AATGATATTT
677986 ATAATAAATATTAAA
1 ATAATAAATATTAAA
*
678001 ATAATTAAATATTATA
1 ATAA-TAAATATTAAA
678017 ATA
1 ATA
678020 TTTACTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATAAATATTAAA
Found at i:678230 original size:6 final size:6
Alignment explanation
Indices: 678219--678276 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
678209 TTTTAAATCA
* *
678219 TATATT TATA-T TATATT TATATA TATTATGT TATAAT TATATT TATA--
1 TATATT TATATT TATATT TATATT TA-TAT-T TATATT TATATT TATATT
678266 -ATATT TATATT
1 TATATT TATATT
678277 AATTTTGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 3 0.07
5 5 0.12
6 27 0.64
7 5 0.12
8 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:678245 original size:15 final size:15
Alignment explanation
Indices: 678225--678276 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
678215 ATCATATATT
678225 TATATTATATTTATA
1 TATATTATATTTATA
*
678240 TATA-T-TATGT-TA
1 TATATTATATTTATA
678252 TA-ATTATATTTATA
1 TATATTATATTTATA
678266 -ATATTTATATT
1 TATA-TTATATT
678277 AATTTTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
11 1 0.03
12 5 0.17
13 9 0.30
14 4 0.13
15 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATATTATATTTATA
Found at i:678252 original size:20 final size:19
Alignment explanation
Indices: 678218--678260 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
678208 TTTTTAAATC
*
678218 ATATATTTATATTATATTT
1 ATATATTTATATTATAATT
*
678237 ATATATATTATGTTATAATT
1 ATATAT-TTATATTATAATT
678257 ATAT
1 ATAT
678261 TTATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATATTTATATTATAATT
Found at i:678277 original size:20 final size:21
Alignment explanation
Indices: 678218--678281 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 21
678208 TTTTTAAATC
678218 ATATATTTATATTATATTTATAT
1 ATATATTTATATTATA-TT-TAT
678241 ATATTATGTTATAATTATATTTAT
1 ATA-TAT-TTAT-ATTATATTTAT
678265 A-ATATTTATATTA-ATTT
1 ATATATTTATATTATATTT
678282 TGATACGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 4 0.11
22 3 0.08
23 4 0.11
24 7 0.18
25 6 0.16
26 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATATTTATATTATATTTAT
Found at i:678377 original size:14 final size:15
Alignment explanation
Indices: 678353--678388 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
678343 TTATTACGTT
678353 ATATATATCATATTA
1 ATATATATCATATTA
*
678368 ATAT-TATCATATTT
1 ATATATATCATATTA
678382 ATATATA
1 ATATATA
678389 AGTTTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATCATATTA
Found at i:678845 original size:23 final size:23
Alignment explanation
Indices: 678819--678873 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
678809 ATTATTTAAC
678819 TAAATAATATTTAAAT-TTAATTA
1 TAAATAATATTTAAATATTAA-TA
*
678842 TAAAT--TATATAAATATTAATA
1 TAAATAATATTTAAATATTAATA
678863 TAAA-AATATTT
1 TAAATAATATTT
678874 TTTAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 14 0.52
22 8 0.30
23 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATAATATTTAAATATTAATA
Found at i:679673 original size:92 final size:92
Alignment explanation
Indices: 679577--679767 Score: 307
Period size: 92 Copynumber: 2.1 Consensus size: 92
679567 ATTAATATTT
* *
679577 TTATTTAATATATTAAAAATATAATTTTTTAAAAAGTTATGCATTTAAATTCTTTGTATATGATA
1 TTATTTAATATATTAAAAATATAATTTTTTAAAAAGTTATGCATTTAAATTCTCTGAATATGATA
679642 TTAAACTT-CTTCAAATTATTAAACTTG
66 TTAAACTTAC-TCAAATTATTAAACTTG
* *
679669 TTATTTGATATATTAAAAATATAATTTTTTTAAAAGTTATGCATTTAAATTCTCTGAATATGATA
1 TTATTTAATATATTAAAAATATAATTTTTTAAAAAGTTATGCATTTAAATTCTCTGAATATGATA
*
679734 TTAAATTTACTCAAATTATTAAACTTG
66 TTAAACTTACTCAAATTATTAAACTTG
679761 --ATTTAAT
1 TTATTTAAT
679768 GATTGTTATA
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
90 6 0.07
92 85 0.92
93 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (92 bp):
TTATTTAATATATTAAAAATATAATTTTTTAAAAAGTTATGCATTTAAATTCTCTGAATATGATA
TTAAACTTACTCAAATTATTAAACTTG
Found at i:679801 original size:92 final size:88
Alignment explanation
Indices: 679613--679801 Score: 195
Period size: 92 Copynumber: 2.1 Consensus size: 88
679603 TTTTAAAAAG
* *
679613 TTATGCATTTAAATTCTTTGTATATGATATTAAACTTCTTCAAATTATTAAACTTGTTATTTGAT
1 TTATGCATTTAAATTCTCTGAATATGATATTAAACTTCTTCAAATTATTAAACTTGTTATTTGAT
* * *
679678 ATATTAAAAATATAATTTTTTTAAAA
66 ATATGAAAAATAAAATTATTTT---A
*
679704 GTTATGCATTTAAATTCTCTGAATATGATATTAAATTTAC-TCAAATTATTAAACTTGATTTAAT
1 -TTATGCATTTAAATTCTCTGAATATGATATTAAACTT-CTTCAAATTATTAAACTTG--TT-AT
*
679768 GATTGTTATATGAAAAA-AAAATTAATTTT-
61 --TTGATATATGAAAAATAAAATT-ATTTTA
679797 TTATG
1 TTATG
679802 GTTATGCATT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
92 56 0.67
93 1 0.01
94 2 0.02
95 2 0.02
96 5 0.06
97 17 0.20
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.47
Consensus pattern (88 bp):
TTATGCATTTAAATTCTCTGAATATGATATTAAACTTCTTCAAATTATTAAACTTGTTATTTGAT
ATATGAAAAATAAAATTATTTTA
Found at i:682100 original size:6 final size:7
Alignment explanation
Indices: 682062--682148 Score: 57
Period size: 6 Copynumber: 13.4 Consensus size: 7
682052 GTATTCATGT
682062 TATATT-
1 TATATTA
682068 TAT-TTA
1 TATATTA
*
682074 TTTATT-
1 TATATTA
682080 TAT-TTA
1 TATATTA
682086 TATATTA
1 TATATTA
682093 TA-ATTA
1 TATATTA
682099 TAT-TTAA
1 TATATT-A
*
682106 AATATTA
1 TATATTA
*
682113 TATATAAA
1 TATAT-TA
682121 TATATT-
1 TATATTA
682127 TATATT-
1 TATATTA
*
682133 TTTATTA
1 TATATTA
682140 TAT-TTA
1 TATATTA
682146 TAT
1 TAT
682149 TAACATATTG
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
5 4 0.06
6 35 0.55
7 17 0.27
8 8 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TATATTA
Found at i:682114 original size:14 final size:15
Alignment explanation
Indices: 682095--682133 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
682085 ATATATTATA
682095 ATTATATTTAAA-AT
1 ATTATATTTAAATAT
*
682109 ATTATATATAAATAT
1 ATTATATTTAAATAT
682124 ATTTATATTT
1 A-TTATATTT
682134 TTATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 3 0.14
16 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATATTTAAATAT
Found at i:682131 original size:8 final size:8
Alignment explanation
Indices: 682062--682148 Score: 68
Period size: 8 Copynumber: 10.4 Consensus size: 8
682052 GTATTCATGT
682062 TATATTTA
1 TATATTTA
*
682070 TTTATTTA
1 TATATTTA
*
682078 TTTATTTA
1 TATATTTA
682086 TATATTATAA
1 TATATT-T-A
682096 TTATATTTA
1 -TATATTTA
*
682105 -AAATATTA
1 TATAT-TTA
**
682113 TATATAAA
1 TATATTTA
682121 TATATTTA
1 TATATTTA
*
682129 TATTTTTA
1 TATATTTA
682137 TTATATTTA
1 -TATATTTA
682146 TAT
1 TAT
682149 TAACATATTG
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
7 3 0.05
8 40 0.63
9 12 0.19
10 2 0.03
11 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATTTA
Found at i:682279 original size:16 final size:18
Alignment explanation
Indices: 682242--682279 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
682232 TATATATCTG
*
682242 TATTATATTCATAAATTT
1 TATTATATTCATAAATTA
682260 TATTATA-TCAT-AATTA
1 TATTATATTCATAAATTA
682276 TATT
1 TATT
682280 TAATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATATTCATAAATTA
Found at i:682293 original size:15 final size:14
Alignment explanation
Indices: 682244--682300 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
682234 TATATCTGTA
* *
682244 TTATATTCATAAAT
1 TTATATTTATATAT
*
682258 TT-TATTATATCATAA
1 TTATATT-TAT-ATAT
682273 TTATATTTAATATAT
1 TTATATTT-ATATAT
682288 TTATATTTATATA
1 TTATATTTATATA
682301 AATTTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.11
14 9 0.26
15 16 0.46
16 6 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATTTATATAT
Found at i:682343 original size:18 final size:17
Alignment explanation
Indices: 682252--682343 Score: 51
Period size: 16 Copynumber: 5.8 Consensus size: 17
682242 TATTATATTC
682252 ATAAATTTTAT-TATAT
1 ATAAATTTTATATATAT
*
682268 CAT-AA--TTATATTTA-
1 -ATAAATTTTATATATAT
* *
682282 ATATA-TTTATATTTAT
1 ATAAATTTTATATATAT
682298 ATAAATTTTA-ATATAT
1 ATAAATTTTATATATAT
*
682314 -T-AATTAGTTATA-CTAT
1 ATAAATT--TTATATATAT
682330 ATAAATTTTATATA
1 ATAAATTTTATATA
682344 ATTATATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
13 2 0.03
14 9 0.16
15 13 0.22
16 22 0.38
17 8 0.14
18 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (17 bp):
ATAAATTTTATATATAT
Done.