Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold142
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1252394
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.30
Warning! 144568 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:4595 original size:8 final size:8
Alignment explanation
Indices: 4580--4613 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4570 CCGTCAGTTC
4580 GTCCGTCT
1 GTCCGTCT
*
4588 GTCTGTCT
1 GTCCGTCT
*
4596 GTCCGTCC
1 GTCCGTCT
4604 GTCCGTCT
1 GTCCGTCT
4612 GT
1 GT
4614 AAAGGTTTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.38
Consensus pattern (8 bp):
GTCCGTCT
Found at i:4599 original size:16 final size:16
Alignment explanation
Indices: 4567--4613 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4557 CGTTAACCTT
*
4567 CGTCCGTCAGT-TCGTC
1 CGTCCGTCCGTCT-GTC
* *
4583 CGTCTGTCTGTCTGTC
1 CGTCCGTCCGTCTGTC
4599 CGTCCGTCCGTCTGT
1 CGTCCGTCCGTCTGT
4614 AAAGGTTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.02, C:0.36, G:0.26, T:0.36
Consensus pattern (16 bp):
CGTCCGTCCGTCTGTC
Found at i:38372 original size:15 final size:15
Alignment explanation
Indices: 38340--38371 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
38330 TTTTAATACA
38340 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTTCTT
38355 TTTCTTTTTTTT-TT
1 TTTCTTTTTTTTCTT
38369 TTT
1 TTT
38372 TAGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:44840 original size:12 final size:11
Alignment explanation
Indices: 44820--44850 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
44810 CGTTCCTTAA
44820 AAAAAACAAAC
1 AAAAAACAAAC
44831 AAACAAACAAAC
1 AAA-AAACAAAC
44843 AAAAAACA
1 AAAAAACA
44851 GCTTATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAC
Found at i:44876 original size:18 final size:18
Alignment explanation
Indices: 44853--44888 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
44843 AAAAAACAGC
44853 TTATTGTAATG-ACAAATT
1 TTATTGT-ATGAACAAATT
44871 TTATTGTATGAACAAATT
1 TTATTGTATGAACAAATT
44889 ACAGTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (18 bp):
TTATTGTATGAACAAATT
Found at i:45556 original size:21 final size:21
Alignment explanation
Indices: 45530--45621 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
45520 TACTGCCATC
*
45530 ACTTGTCAGATAATCATGTCG
1 ACTTGTCAGATAATGATGTCG
**
45551 ACTTGTCAGATCTTGATGGT-G
1 ACTTGTCAGATAATGAT-GTCG
* * *
45572 ACGTGTCAGATAATTATGTTG
1 ACTTGTCAGATAATGATGTCG
**
45593 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATGATGTCG
45614 ACTTGTCA
1 ACTTGTCA
45622 CTTATTCACA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (21 bp):
ACTTGTCAGATAATGATGTCG
Found at i:45621 original size:42 final size:42
Alignment explanation
Indices: 45530--45621 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
45520 TACTGCCATC
45530 ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGGTG
1 ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGGTG
* * *
45572 ACGTGTCAGATAATTATGTTGACTTGTCAGATCTTGAT-GTCG
1 ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGGT-G
45614 ACTTGTCA
1 ACTTGTCA
45622 CTTATTCACA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (42 bp):
ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGGTG
Found at i:45846 original size:21 final size:21
Alignment explanation
Indices: 45682--45856 Score: 165
Period size: 21 Copynumber: 8.4 Consensus size: 21
45672 TTTGTTCAAT
* *
45682 CAAGTTGACAT-ATTTTCTGA
1 CAAGTCGACATAATTATCTGA
* ***
45702 CAAGTCAACATAAGGCTCTGA
1 CAAGTCGACATAATTATCTGA
*
45723 CAAGTCGACAAAATTATCTGA
1 CAAGTCGACATAATTATCTGA
*
45744 CAAGTCGACATAATCATCTGA
1 CAAGTCGACATAATTATCTGA
* *
45765 CAAGTCGACATAATTATTTGG
1 CAAGTCGACATAATTATCTGA
** *
45786 CAAGTCGACATCTTTATTTGA
1 CAAGTCGACATAATTATCTGA
**
45807 CAAGAAGACATAA-TATCTGA
1 CAAGTCGACATAATTATCTGA
* * *
45827 CAAGTCAACATCATTATCTGT
1 CAAGTCGACATAATTATCTGA
*
45848 TAAGTCGAC
1 CAAGTCGAC
45857 TTATAATATG
Statistics
Matches: 123, Mismatches: 30, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
20 24 0.20
21 99 0.80
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (21 bp):
CAAGTCGACATAATTATCTGA
Found at i:45948 original size:41 final size:41
Alignment explanation
Indices: 45903--45992 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
45893 TTCTGTCAAA
*
45903 TAATTATGTTAACTTGTAAGATCATTATGTCGACTTGTCAG
1 TAATTATGTCAACTTGTAAGATCATTATGTCGACTTGTCAG
* * * *
45944 TAATTTTGTCGACTTGTCAGATGATTATGTCGACTTGTCAG
1 TAATTATGTCAACTTGTAAGATCATTATGTCGACTTGTCAG
45985 -ATATTATG
1 TA-ATTATG
45993 ACAAGGTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (41 bp):
TAATTATGTCAACTTGTAAGATCATTATGTCGACTTGTCAG
Found at i:45955 original size:20 final size:21
Alignment explanation
Indices: 45896--45992 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
45886 TTATTTTTTC
* **
45896 TGTCAAATAATTATGTTAACT
1 TGTCAGATAATTATGTCGACT
* *
45917 TGTAAGATCATTATGTCGACT
1 TGTCAGATAATTATGTCGACT
*
45938 TGTCAG-TAATTTTGTCGACT
1 TGTCAGATAATTATGTCGACT
*
45958 TGTCAGATGATTATGTCGACT
1 TGTCAGATAATTATGTCGACT
45979 TGTCAGAT-ATTATG
1 TGTCAGATAATTATG
45993 ACAAGGTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 24 0.37
21 41 0.63
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (21 bp):
TGTCAGATAATTATGTCGACT
Found at i:46090 original size:21 final size:20
Alignment explanation
Indices: 46061--46161 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 20
46051 AGTCAATATG
* *
46061 ATAATTATCTGAAAAGTCATC
1 ATAAATATCTGACAAGTCA-C
*
46082 ATAAATATCTGACAAGTTGAC
1 ATAAATATCTGACAAG-TCAC
46103 ATAAATATCTGACAAGTCGAC
1 ATAAATATCTGACAAGTC-AC
*
46124 AT-AATCATTTGACAAGTCAGC
1 ATAAAT-ATCTGACAAGTCA-C
**
46145 ATATTTATCTGACAAGT
1 ATAAATATCTGACAAGT
46162 GGTGGCAGAC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.07
21 59 0.88
22 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (20 bp):
ATAAATATCTGACAAGTCAC
Found at i:47611 original size:21 final size:21
Alignment explanation
Indices: 47585--47959 Score: 448
Period size: 21 Copynumber: 17.9 Consensus size: 21
47575 ATATGCAAAC
* *
47585 TTTACAGATAAAAGTGTAAAT
1 TTTACAGATTAAAGTGTAAAA
**
47606 TTTACACTTTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
*
47627 TTTACAGATTTAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
* * *
47648 TTTACAGATAAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
** ** *
47669 TTTACACTTTAAAGTGCGAAT
1 TTTACAGATTAAAGTGTAAAA
**
47690 TTTACACTTTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
* * *
47711 TTTAAAGATTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
* *
47732 TTTACAGATTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
** * *
47753 TTTACACTTTAAAGTGTGAAT
1 TTTACAGATTAAAGTGTAAAA
* *
47774 TTTACAGATTAAAGTGTATAT
1 TTTACAGATTAAAGTGTAAAA
47795 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
47816 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
47837 TTTACAGATTAAAGT-TGAAAA
1 TTTACAGATTAAAGTGT-AAAA
*
47858 TTTACAGATTAAAGTGGAAAA
1 TTTACAGATTAAAGTGTAAAA
47879 TTTACAGATTAAAGT-TGAAAA
1 TTTACAGATTAAAGTGT-AAAA
47900 TTTACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
*
47921 TTAACAGATTAAAGTGTAAAA
1 TTTACAGATTAAAGTGTAAAA
**
47942 TTTACACTTTAAAGTGTA
1 TTTACAGATTAAAGTGTA
47960 GAATATAATA
Statistics
Matches: 312, Mismatches: 38, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
20 1 0.00
21 310 0.99
22 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (21 bp):
TTTACAGATTAAAGTGTAAAA
Found at i:48441 original size:22 final size:22
Alignment explanation
Indices: 48416--48732 Score: 181
Period size: 22 Copynumber: 14.5 Consensus size: 22
48406 AGTTTTGCAA
*
48416 TTAAACGCAACAACTATTGCGT
1 TTAAACGCAATAACTATTGCGT
* * *
48438 TTAAACCCAAT-ACATTTTGCGA
1 TTAAACGCAATAAC-TATTGCGT
****
48460 TTAAACGCAACGGTTATTGCGT
1 TTAAACGCAATAACTATTGCGT
*
48482 TTAATCGCAA-AA-TCATTGCGT
1 TTAAACGCAATAACT-ATTGCGT
* * *
48503 TTAATCGCAAAAACGT-TTGCGA
1 TTAAACGCAATAAC-TATTGCGT
** * * *
48525 TTATTCGGAAAAAAATATTGCGT
1 TTAAAC-GCAATAACTATTGCGT
48548 TTAAACGCAATATTACCT-TTGCGT
1 TTAAACGCAATA--A-CTATTGCGT
* *
48572 TTAAACGCAATAATGTTTTGCGT
1 TTAAACGCAATAA-CTATTGCGT
* * **
48595 TAAAACACAATGTTCT-TTGCGT
1 TTAAACGCAAT-AACTATTGCGT
*
48617 TTAAACGCAATAGCTATTGCGT
1 TTAAACGCAATAACTATTGCGT
* *
48639 TTAATCGCAAT--CTTTTGCGT
1 TTAAACGCAATAACTATTGCGT
*
48659 TTAAACGCAA-AACATATTGCAAT
1 TTAAACGCAATAAC-TATTGC-GT
* *
48682 TT-AACGC-ATAA-GATTGCGA
1 TTAAACGCAATAACTATTGCGT
*
48701 TTAAACGCAATAATTATTGCGT
1 TTAAACGCAATAACTATTGCGT
48723 TTAAACGCAA
1 TTAAACGCAA
48733 AAGAAATTAT
Statistics
Matches: 229, Mismatches: 44, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 28 0.12
21 27 0.12
22 117 0.51
23 34 0.15
24 20 0.09
25 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (22 bp):
TTAAACGCAATAACTATTGCGT
Found at i:48501 original size:21 final size:21
Alignment explanation
Indices: 48475--48514 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
48465 CGCAACGGTT
48475 ATTGCGTTTAATCGCAAAATC
1 ATTGCGTTTAATCGCAAAATC
48496 ATTGCGTTTAATCGCAAAA
1 ATTGCGTTTAATCGCAAAA
48515 ACGTTTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (21 bp):
ATTGCGTTTAATCGCAAAATC
Found at i:48707 original size:20 final size:20
Alignment explanation
Indices: 48674--48736 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
48664 CGCAAAACAT
* *
48674 ATTGCAATTTAACGCATAAG
1 ATTGCGATTAAACGCATAAG
*
48694 ATTGCGATTAAACGCAATAATT
1 ATTGCGATTAAACGC-ATAA-G
* *
48716 ATTGCGTTTAAACGCAAAAG
1 ATTGCGATTAAACGCATAAG
48736 A
1 A
48737 AATTATTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 14 0.40
21 7 0.20
22 14 0.40
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
ATTGCGATTAAACGCATAAG
Found at i:48730 original size:42 final size:41
Alignment explanation
Indices: 48431--48733 Score: 128
Period size: 42 Copynumber: 7.0 Consensus size: 41
48421 CGCAACAACT
* * * * *
48431 ATTGCGTTTAAACCCAATACATTTTGCGATTAAACGCAACGG
1 ATTGCGTTTAAACGCAATAAATATTGCGTTTAAACGCAA-AG
* *
48473 TTATTGCGTTTAATCGC-A-AAATCATTGCGTTTAATCGCAAAAACG
1 --ATTGCGTTTAAACGCAATAAAT-ATTGCGTTTAAACGC--AAA-G
* * ** * * *
48518 TTTGCGATTATTCGGAAAAAAATATTGCGTTTAAACGCAATATT
1 ATTGCGTTTAAAC-GCAATAAATATTGCGTTTAAACGCAA-A-G
* * * * *
48562 ACCTTTGCGTTTAAACGCAATAATGTTTTGCGTTAAAACACAATG
1 A---TTGCGTTTAAACGCAATAA-ATATTGCGTTTAAACGCAAAG
* ** * **
48607 TTCTTTGCGTTTAAACGCAATAGCTATTGCGTTTAATCGCAATCT
1 ---ATTGCGTTTAAACGCAATAAATATTGCGTTTAAACGCAA-AG
* *
48652 TTTGCGTTTAAACGCAA-AACATATTGCAATTT-AACGCATAAG
1 ATTGCGTTTAAACGCAATAA-ATATTGC-GTTTAAACGCA-AAG
* *
48694 ATTGCGATTAAACGCAATAATTATTGCGTTTAAACGCAAA
1 ATTGCGTTTAAACGCAATAAATATTGCGTTTAAACGCAAA
48734 AGAAATTATT
Statistics
Matches: 193, Mismatches: 45, Indels: 45
0.68 0.16 0.16
Matches are distributed among these distances:
41 6 0.03
42 58 0.30
43 31 0.16
44 29 0.15
45 36 0.19
46 9 0.05
47 24 0.12
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (41 bp):
ATTGCGTTTAAACGCAATAAATATTGCGTTTAAACGCAAAG
Found at i:53126 original size:34 final size:34
Alignment explanation
Indices: 53045--53126 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
53035 AACCACTGTC
* * * * *
53045 ACAGTTAAGCGTATAAGACCTCTTAACATGCAAT
1 ACAGTCAAGTGTATAAGACCCCTTAACATACAAA
* *
53079 ATAGTTAAGTGTATAAGACCCCTTAACATTACAAA
1 ACAGTCAAGTGTATAAGACCCCTTAACA-TACAAA
53114 ACAGTCAA-TGTAT
1 ACAGTCAAGTGTAT
53127 GACCAAAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 30 0.75
35 10 0.25
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (34 bp):
ACAGTCAAGTGTATAAGACCCCTTAACATACAAA
Found at i:65702 original size:20 final size:19
Alignment explanation
Indices: 65660--65761 Score: 81
Period size: 20 Copynumber: 5.4 Consensus size: 19
65650 TTGATTTATG
65660 AAACAAAACAAAAA-ATAACC
1 AAACAAAACAAAAACA-AA-C
65680 AAACAAAACAAAAACAGAAC
1 AAACAAAACAAAAACA-AAC
*
65700 AAA-GAAACAACAAACAAAC
1 AAACAAAACAA-AAACAAAC
*
65719 GAACAAAA-AAAAAC-AAC
1 AAACAAAACAAAAACAAAC
*
65736 AAAC-GAACAAACGAACAAA-
1 AAACAAAACAAA--AACAAAC
65755 AAACAAA
1 AAACAAA
65762 TAGAAGAGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
16 2 0.03
17 9 0.13
18 4 0.06
19 20 0.30
20 29 0.43
21 3 0.04
ACGTcount: A:0.75, C:0.20, G:0.05, T:0.01
Consensus pattern (19 bp):
AAACAAAACAAAAACAAAC
Found at i:65717 original size:4 final size:4
Alignment explanation
Indices: 65660--65761 Score: 67
Period size: 4 Copynumber: 26.8 Consensus size: 4
65650 TTGATTTATG
* * *
65660 AAAC AAAAC AAA- AAAT AACC AAAC AAA- ACAA- AAAC AGAAC AAAG AAAC
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC A-AAC AAAC A-AAC AAAC AAAC
* * *
65708 -AAC AAAC AAAC GAAC AAA- AAA- AAAC -AAC AAAC GAAC AAAC GAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
65752 AAA- AAAC AAA
1 AAAC AAAC AAA
65762 TAGAAGAGTG
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
3 21 0.27
4 49 0.63
5 8 0.10
ACGTcount: A:0.75, C:0.20, G:0.05, T:0.01
Consensus pattern (4 bp):
AAAC
Found at i:74682 original size:15 final size:15
Alignment explanation
Indices: 74662--74691 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
74652 ACCAATACGG
*
74662 GTCTATTTCGATGTC
1 GTCTATCTCGATGTC
74677 GTCTATCTCGATGTC
1 GTCTATCTCGATGTC
74692 CTGTATCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (15 bp):
GTCTATCTCGATGTC
Found at i:75168 original size:2 final size:2
Alignment explanation
Indices: 75161--75188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75151 AAGGAAGTCG
75161 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
75189 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75451 original size:2 final size:2
Alignment explanation
Indices: 75444--75525 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
75434 NNNNNNNNNN
75444 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
75486 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
75526 AGAAAAAGAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:75537 original size:2 final size:2
Alignment explanation
Indices: 75532--75570 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
75522 TGTGAGAAAA
75532 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
75571 CCCTAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:80380 original size:2 final size:2
Alignment explanation
Indices: 80373--80418 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
80363 AAAACTAAAT
80373 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
80415 TC TC
1 TC TC
80419 CCTCATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:104679 original size:11 final size:11
Alignment explanation
Indices: 104663--104691 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
104653 ATAAGTTGTC
104663 CTTAAAGGTGG
1 CTTAAAGGTGG
104674 CTTAAAGGTGG
1 CTTAAAGGTGG
104685 CTTAAAG
1 CTTAAAG
104692 ATAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:110351 original size:161 final size:160
Alignment explanation
Indices: 110057--110445 Score: 487
Period size: 161 Copynumber: 2.4 Consensus size: 160
110047 GACCTAGATG
* * *
110057 ATGATAAACCTGTATACCAAATTTCATTCCAA-AATTGTCTTCCTCTGCGAAGAAAATGAGCGGA
1 ATGATAAACCTGTATACCAAATTTCATTTCAATAAGT-TCATCCTCTGCGAAGAAAATGAGCGGA
* * * * * **
110121 AACTGCAATAACTCGAATTTTTCTAAGTCCAAGGACTATAACGCTGTCGAAAACGGATCGATTGT
65 AACTGCAATAACTAGAATTTTTCCAAGTCCAAGGACCACAACGCTGTCGAAAACGGATCCACCGT
*
110186 ACCCAATATCGAACTTGACCTT-GATATTACC
130 ACCCAATATCAAACTTGA-CTTAGATATTACC
* * * * * *
110217 TTGATAAACCTGTATACTAAATTTAATTTCAATACGTTCATCTTCTGCAAAGAAAATGAGCGGAA
1 ATGATAAACCTGTATACCAAATTTCATTTCAATAAGTTCATCCTCTGCGAAGAAAATGAGCGGAA
* * **
110282 ACTGCAAATAACTAGAATTTTTCCACGTCCAA-GAGCCACAACTCTGTCGAAAATTGATCCACCG
66 ACTGC-AATAACTAGAATTTTTCCAAGTCCAAGGA-CCACAACGCTGTCGAAAACGGATCCACCG
*
110346 TACCCAATATCAAACTTGACTTAGATATTATC
129 TACCCAATATCAAACTTGACTTAGATATTACC
* * **
110378 ATGATAATCCTGTATACCAAATTTCATTTCAATATGTTCATCCTCTGCGAAGAAAATGAAAGGAA
1 ATGATAAACCTGTATACCAAATTTCATTTCAATAAGTTCATCCTCTGCGAAGAAAATGAGCGGAA
110443 ACT
66 ACT
110446 ATTGATAGAC
Statistics
Matches: 194, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
160 63 0.32
161 131 0.68
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (160 bp):
ATGATAAACCTGTATACCAAATTTCATTTCAATAAGTTCATCCTCTGCGAAGAAAATGAGCGGAA
ACTGCAATAACTAGAATTTTTCCAAGTCCAAGGACCACAACGCTGTCGAAAACGGATCCACCGTA
CCCAATATCAAACTTGACTTAGATATTACC
Found at i:115822 original size:2 final size:2
Alignment explanation
Indices: 115815--115891 Score: 113
Period size: 2 Copynumber: 39.0 Consensus size: 2
115805 CTAATAGTGA
115815 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AT- TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC
* *
115857 TC CC TC TC -C TC TC TC TC TC TC AC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
115892 AAAATAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
1 2 0.03
2 65 0.96
3 1 0.01
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:122475 original size:15 final size:16
Alignment explanation
Indices: 122449--122487 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
122439 CACCCCTCCT
*
122449 TTTCTATTTTTTTCAA
1 TTTCTTTTTTTTTCAA
122465 TTT-TTTTTTTTTCAA
1 TTTCTTTTTTTTTCAA
122480 TTTCTTTT
1 TTTCTTTT
122488 ATTAGTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTTTTCAA
Found at i:126067 original size:17 final size:17
Alignment explanation
Indices: 126047--126079 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
126037 AACTCTCAGT
126047 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
126064 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
126080 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:129093 original size:2 final size:2
Alignment explanation
Indices: 129086--129116 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
129076 CGCTTGACTC
129086 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
129117 TTTAAGGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:129671 original size:62 final size:60
Alignment explanation
Indices: 129552--129678 Score: 148
Period size: 62 Copynumber: 2.1 Consensus size: 60
129542 TTATTCTTTA
* * *
129552 AAATTGAAATAAAATCAAATTACATTGTTAGATATTTAAAGGAATGGAAAAACCTAAACTG
1 AAATTGAAACAAAAACAAATTACATTGTTAGATATTTAAA-GAACGGAAAAACCTAAACTG
* * * *
129613 AAATTGAAACAATAAACAAATTACATTGTTGGATTTTTAGAA-AAGCGGACAAATCTAAACTG
1 AAATTGAAACAA-AAACAAATTACATTGTTAGATATTTA-AAGAA-CGGAAAAACCTAAACTG
129675 AAAT
1 AAAT
129679 GGATAGTGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
61 13 0.23
62 41 0.73
63 2 0.04
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (60 bp):
AAATTGAAACAAAAACAAATTACATTGTTAGATATTTAAAGAACGGAAAAACCTAAACTG
Found at i:132736 original size:23 final size:23
Alignment explanation
Indices: 132703--132746 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
132693 GGATGTAATC
132703 AACATTATGATTCTAATGCATGA
1 AACATTATGATTCTAATGCATGA
*
132726 AACATTGTGATTCTAATGCAT
1 AACATTATGATTCTAATGCAT
132747 ATGAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (23 bp):
AACATTATGATTCTAATGCATGA
Found at i:140203 original size:4 final size:4
Alignment explanation
Indices: 140194--140219 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
140184 GTTACCCTGT
140194 TCCG TCCG TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TC
140220 TGTCACGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.23, T:0.27
Consensus pattern (4 bp):
TCCG
Found at i:144164 original size:12 final size:12
Alignment explanation
Indices: 144133--144167 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
144123 TTGCTAAAAC
*
144133 GCGGAACAGAAA
1 GCGGAACGGAAA
*
144145 ACGGAACGGAAA
1 GCGGAACGGAAA
144157 GCGGAACGGAA
1 GCGGAACGGAA
144168 TGGAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.37, T:0.00
Consensus pattern (12 bp):
GCGGAACGGAAA
Found at i:145351 original size:12 final size:12
Alignment explanation
Indices: 145336--145370 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
145326 CCGTTTTCCC
145336 TTCCGTTCCGCT
1 TTCCGTTCCGCT
*
145348 TTCCGTTCCGTT
1 TTCCGTTCCGCT
145360 TTCCGTTCCGC
1 TTCCGTTCCGC
145371 GTTTTAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.43
Consensus pattern (12 bp):
TTCCGTTCCGCT
Found at i:145369 original size:17 final size:17
Alignment explanation
Indices: 145324--145359 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
145314 AGATAAGATT
*
145324 TTCCGTTTTCCCTTCCG
1 TTCCGCTTTCCCTTCCG
*
145341 TTCCGCTTTCCGTTCCG
1 TTCCGCTTTCCCTTCCG
145358 TT
1 TT
145360 TTCCGTTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.39, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCCGCTTTCCCTTCCG
Found at i:148000 original size:184 final size:184
Alignment explanation
Indices: 147653--148096 Score: 490
Period size: 184 Copynumber: 2.4 Consensus size: 184
147643 GTTCAATGTT
* * * * * * * *
147653 GGTAAAGATAGATAACTCTTACGTAGAATTCAGACGCCTGCCGAGGAAATCTAGACGCCTGCCGT
1 GGTAAA-ATAGATAACTCTTACGAAAAATGCATACGCCTCCCAAGAAAATCTATACGCCTGCCGT
* * * * * * *
147718 TTATTTGATGGATTATTTTACTTTTTTCTTTTATATTTTATTTCTTGTAACTAAATAGATGTTAA
65 TTATTTGATGAATTATTTTAATTATTTCTTTGATATTTTATTTCTTGTAACTAAATAAACGTAAA
* *
147783 TAGAAATCAAAAGTTGATTTTATATTAGTTAATTAACACAAAATAAGTAAAAATC
130 TAGAAATCAAAAGTTGACTTTAAATTAGTTAATTAACACAAAATAAGTAAAAATC
** *
147838 GGGTAAGCT-GATAGCTCTTACGAATAAAT-CATACGCCTCCCAAGAAAATGC-ATACGCCTGCC
1 -GGTAAAATAGATAACTCTTACGAA-AAATGCATACGCCTCCCAAGAAAAT-CTATACGCCTGCC
*
147900 GTTTATTTGATGAATTATTTTAATTATTTCTTTGATATTTTAGTTTAC-T-TAGCTTAAA-AAAC
63 GTTTATTTGATGAATTATTTTAATTATTTCTTTGATATTTTA-TTT-CTTGTAAC-TAAATAAAC
* **
147962 G-AAGATAGAAAT-AAAAGCTTGACTTTAAATTCGTTAATTAACACAAAATTGGTAAAAATC
125 GTAA-ATAGAAATCAAAAG-TTGACTTTAAATTAGTTAATTAACACAAAATAAGTAAAAATC
* * * *
148022 GGTAAAATAGATAACTCTTACGCAGAATGCATACGCCTGCCGAGAAAATCTATACGCCTGCCGTT
1 GGTAAAATAGATAACTCTTACGAAAAATGCATACGCCTCCCAAGAAAATCTATACGCCTGCCGTT
*
148087 TATCTGATGA
66 TATTTGATGA
148097 TGGATATTTT
Statistics
Matches: 217, Mismatches: 31, Indels: 22
0.80 0.11 0.08
Matches are distributed among these distances:
183 16 0.07
184 182 0.84
185 13 0.06
186 6 0.03
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (184 bp):
GGTAAAATAGATAACTCTTACGAAAAATGCATACGCCTCCCAAGAAAATCTATACGCCTGCCGTT
TATTTGATGAATTATTTTAATTATTTCTTTGATATTTTATTTCTTGTAACTAAATAAACGTAAAT
AGAAATCAAAAGTTGACTTTAAATTAGTTAATTAACACAAAATAAGTAAAAATC
Found at i:149281 original size:2 final size:2
Alignment explanation
Indices: 149274--149310 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
149264 TAAAACACAT
149274 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
149311 GGGGGGGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:149923 original size:15 final size:17
Alignment explanation
Indices: 149898--149929 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
149888 TATCGGGTTC
149898 ATTTTTGACTCA-GAAA
1 ATTTTTGACTCATGAAA
149914 ATTTTT-ACTCATGAAA
1 ATTTTTGACTCATGAAA
149930 TAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (17 bp):
ATTTTTGACTCATGAAA
Found at i:154002 original size:5 final size:5
Alignment explanation
Indices: 153992--154018 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
153982 ACGTTAAGTT
153992 CTATC CTATC CTATC CTATC CTATC CT
1 CTATC CTATC CTATC CTATC CTATC CT
154019 GCATCCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATC
Found at i:168362 original size:4 final size:4
Alignment explanation
Indices: 168355--168439 Score: 116
Period size: 4 Copynumber: 21.2 Consensus size: 4
168345 AGATAGATAA
* * * ** *
168355 ACAG ACAG ACAG ACGG ACGG ACGG ATGG ACGG ACAG ACAG ACAG ACAG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
168403 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG A
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG A
168440 TAGATGATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.45, C:0.24, G:0.31, T:0.01
Consensus pattern (4 bp):
ACAG
Found at i:172594 original size:17 final size:18
Alignment explanation
Indices: 172568--172611 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
172558 TATTTACGCA
*
172568 AAAATATGAAAGAAC-TG
1 AAAATTTGAAAGAACTTG
**
172585 AAAATTTGAATTAACTTG
1 AAAATTTGAAAGAACTTG
172603 AAAATTTGA
1 AAAATTTGA
172612 GCAAACCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (18 bp):
AAAATTTGAAAGAACTTG
Found at i:186308 original size:48 final size:48
Alignment explanation
Indices: 186244--186408 Score: 158
Period size: 48 Copynumber: 3.4 Consensus size: 48
186234 ATATGTTTTA
**
186244 CAATATCATACAATACAATTTCATGTGATAATATATCATATTATAAAC
1 CAATATCATATTATACAATTTCATGTGATAATATATCATATTATAAAC
* * * * * *
186292 CAATATTATATTATACAATATCATATGATACA-ATATTATATAATATTA-
1 CAATATCATATTATACAATTTCATGTGATA-ATATATCATATTATA-AAC
*
186340 CAGTATCATATTATACAATTTCATGTGAT-ATA-ATTCTATATTATAGAAAC
1 CAATATCATATTATACAATTTCATGTGATAATATA-TC-ATATTAT--AAAC
*
186390 TAATATCATATTATACAAT
1 CAATATCATATTATACAAT
186409 ATCGTATGAT
Statistics
Matches: 92, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
46 2 0.02
47 2 0.02
48 67 0.73
49 3 0.03
50 18 0.20
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (48 bp):
CAATATCATATTATACAATTTCATGTGATAATATATCATATTATAAAC
Found at i:186317 original size:33 final size:33
Alignment explanation
Indices: 186276--186358 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
186266 ATGTGATAAT
186276 ATATCATATTATAAACCAATATTATAT-TA-TACA
1 ATATCATATTAT-AA-CAATATTATATATATTACA
*
186309 ATATCATATGAT-ACAATATTATATAATATTACA
1 ATATCATATTATAACAATATTATAT-ATATTACA
*
186342 GTATCATATTAT-ACAAT
1 ATATCATATTATAACAAT
186359 TTCATGTGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.25
31 1 0.02
32 2 0.05
33 30 0.68
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (33 bp):
ATATCATATTATAACAATATTATATATATTACA
Found at i:186363 original size:15 final size:15
Alignment explanation
Indices: 186181--186425 Score: 118
Period size: 15 Copynumber: 15.3 Consensus size: 15
186171 GATAAAGTAA
* *
186181 AATATTATATAATAC
1 AATATCATATTATAC
*
186196 AATATTATATTATAC
1 AATATCATATTATAC
*
186211 ATATTGTATCATATGATAC
1 A-A---TATCATATTATAC
* *
186230 AATAAT-ATGTTTTAC
1 AAT-ATCATATTATAC
**
186245 AATATCATACAATAC
1 AATATCATATTATAC
* * *
186260 AATTTCATGTGATA-
1 AATATCATATTATAC
186274 ATATATCATATTATAAACC
1 A-ATATCATATTAT--A-C
*
186293 AATATTATATTATAC
1 AATATCATATTATAC
*
186308 AATATCATATGATAC
1 AATATCATATTATAC
*
186323 AATATTATATAATATTAC
1 AATATCATAT--TA-TAC
*
186341 AGTATCATATTATAC
1 AATATCATATTATAC
* * * *
186356 AATTTCATGTGATAT
1 AATATCATATTATAC
186371 AAT-TCTATATTATAGAAAC
1 AATATC-ATATTAT----AC
186390 TAATATCATATTATAC
1 -AATATCATATTATAC
* *
186406 AATATCGTATGATAC
1 AATATCATATTATAC
186421 AATAT
1 AATAT
186426 TATAGAATAT
Statistics
Matches: 175, Mismatches: 34, Indels: 42
0.70 0.14 0.17
Matches are distributed among these distances:
14 5 0.03
15 111 0.63
16 8 0.05
17 2 0.01
18 23 0.13
19 14 0.08
20 10 0.06
21 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.40
Consensus pattern (15 bp):
AATATCATATTATAC
Found at i:186692 original size:20 final size:20
Alignment explanation
Indices: 186669--186711 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
186659 ATATGATATT
**
186669 ATATTGTGTCATATTAAACA
1 ATATTGTGTCATACCAAACA
*
186689 ATATTGTTTCATACCAAACA
1 ATATTGTGTCATACCAAACA
186709 ATA
1 ATA
186712 CTTTATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATTGTGTCATACCAAACA
Found at i:186720 original size:20 final size:20
Alignment explanation
Indices: 186669--186721 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
186659 ATATGATATT
* **
186669 ATATTGTGTCATATTAAACA
1 ATATTGTATCATACCAAACA
*
186689 ATATTGTTTCATACCAAACA
1 ATATTGTATCATACCAAACA
186709 ATACTT-TATCATA
1 ATA-TTGTATCATA
186722 GGAATCATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (20 bp):
ATATTGTATCATACCAAACA
Found at i:187667 original size:177 final size:176
Alignment explanation
Indices: 187357--187899 Score: 777
Period size: 177 Copynumber: 3.1 Consensus size: 176
187347 TAACTTTATC
* * * ** *
187357 CAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGA
1 CAGCATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGTCTGGTGCATCAGTATCATAAGA
* * * * ** * *
187422 CGCACCATCCATGGAAGTCTGGTGAAGTTA-GGAAAAGTAGTAACTAAGATATAAT-C-ATCAGA
66 CACACCATCCATGCAAGTTTGGTGAAG-TACAGACCAGCAGTAACTTAGATAT--TGCTATCA-A
187484 GGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTT
127 GGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTT
* * *
187534 CAACATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGCCTGGTGCATCAGTATCATAAAA
1 CAGCATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGTCTGGTGCATCAGTATCATAAGA
* *
187599 CACACCATCAATGCAAGTTTCGTGAAGTACAGACCAGCAGTAACTTAGATATTGCTATCAACGGG
66 CACACCATCCATGCAAGTTTGGTGAAGTACAGACCAGCAGTAACTTAGATATTGCTATCAA-GGG
187664 CACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTT
130 CACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTT
187711 CAGCATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGTCTGGTGCATCAGTATCATAAGA
1 CAGCATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGTCTGGTGCATCAGTATCATAAGA
*
187776 CACACCATCCATGCAAGTTTGGTGAAGTACAGACCTGCAGTAACTTAGATATTGCTATCAAAGGG
66 CACACCATCCATGCAAGTTTGGTGAAGTACAGACCAGCAGTAACTTAGATATTGCTATC-AAGGG
* * * * * *
187841 CACCTGCAACAAAAATTTTAACCTGGTCCAACAACCTTAACCTCCTC
130 CACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTT
187888 CAGCATCTGAAA
1 CAGCATCTGAAA
187900 TTTAGGACTC
Statistics
Matches: 330, Mismatches: 31, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
175 1 0.00
176 4 0.01
177 323 0.98
178 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (176 bp):
CAGCATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGTCTGGTGCATCAGTATCATAAGA
CACACCATCCATGCAAGTTTGGTGAAGTACAGACCAGCAGTAACTTAGATATTGCTATCAAGGGC
ACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTT
Found at i:188002 original size:177 final size:175
Alignment explanation
Indices: 187355--188003 Score: 626
Period size: 177 Copynumber: 3.7 Consensus size: 175
187345 CTTAACTTTA
* * * ** * * *
187355 TCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAA
1 TCCAGCATCTGAAA-CTATAGCACAGATTCAGCACCCAAGCCTGTCAAGTCCATAAGTATCA-AA
* * * * * * * *
187420 GACGCACCATCCATGGAAGTCTGGTGAAGTTA-GGAAAAGTAGTAACTAAGATATAAT-C-ATCA
64 GACACACCATCCATGCAAGTTTGGTGAAG-TACAGACAAGCAATAACTTAGATAT--TGCTATCA
* *
187482 GAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
126 AAGGGCACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCC
* * * ** * *
187532 TTCAACATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGCCTGGTGCATCAGTATCATAA
1 TCCAGCATCTGAAA-CTATAGCACAGATTCAGCACCCAAGCCTGTCAAGTCCATAAGTATCA-AA
* * * * * *
187597 AACACACCATCAATGCAAGTTTCGTGAAGTACAGACCAGCAGTAACTTAGATATTGCTATCAACG
64 GACACACCATCCATGCAAGTTTGGTGAAGTACAGACAAGCAATAACTTAGATATTGCTATCAAAG
*
187662 GGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
129 GGCACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCC
* ** * *
187709 TTCAGCATCTGAAACCTATAGCACAGATTCAGCACCCAAGCCTGTCTGGTGCATCAGTATCATAA
1 TCCAGCATCTGAAA-CTATAGCACAGATTCAGCACCCAAGCCTGTCAAGTCCATAAGTATCA-AA
** *
187774 GACACACCATCCATGCAAGTTTGGTGAAGTACAGACCTGCAGTAACTTAGATATTGCTATCAAAG
64 GACACACCATCCATGCAAGTTTGGTGAAGTACAGACAAGCAATAACTTAGATATTGCTATCAAAG
* * * *
187839 GGCACCTGCAACAAAAATTTTAACCTGGTCCAACAACCTTAACCTCC
129 GGCACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCC
* * * * *
187886 TCCAGCATCTGAAA-TTTAGGACTCAGATTCAGCATCCAAGTCTTTCAAGTCCATAAGTAGGTC-
1 TCCAGCATCTGAAACTATA-G-CACAGATTCAGCACCCAAGCCTGTCAAGTCCATAAGTA--TCA
* ** * * * *
187949 CAGATGCATCATCCATGCAAGTTTGGTGAAGATA-GGACAAGTAATAGCTTAGATA
62 AAGACACACCATCCATGCAAGTTTGGTGAAG-TACAGACAAGCAATAACTTAGATA
188004 CAGGACCTGC
Statistics
Matches: 410, Mismatches: 54, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
175 4 0.01
176 4 0.01
177 398 0.97
178 2 0.00
179 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (175 bp):
TCCAGCATCTGAAACTATAGCACAGATTCAGCACCCAAGCCTGTCAAGTCCATAAGTATCAAAGA
CACACCATCCATGCAAGTTTGGTGAAGTACAGACAAGCAATAACTTAGATATTGCTATCAAAGGG
CACCTGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCC
Found at i:188179 original size:14 final size:14
Alignment explanation
Indices: 188160--188194 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
188150 CAGCATTTTG
*
188160 ACTGTTGGACTGGA
1 ACTGTTAGACTGGA
*
188174 ACTGTTAGATTGGA
1 ACTGTTAGACTGGA
188188 ACTGTTA
1 ACTGTTA
188195 AAATCGACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (14 bp):
ACTGTTAGACTGGA
Found at i:189286 original size:5 final size:5
Alignment explanation
Indices: 189276--189301 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
189266 CAAACAAGCT
189276 CTATC CTATC CTATC CTATC CTATC C
1 CTATC CTATC CTATC CTATC CTATC C
189302 CATATTTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.38
Consensus pattern (5 bp):
CTATC
Found at i:191412 original size:100 final size:101
Alignment explanation
Indices: 191216--191424 Score: 239
Period size: 100 Copynumber: 2.1 Consensus size: 101
191206 GGAAGCTACC
*
191216 CAAAATGGCCCCTTAAATCATCCCAACAAAGATACACAAAATCTTAAGTACACAAACAAAAGATA
1 CAAAATGGCCCCTTAAATCATCCCAAC-AAGATACACAAAATCTAAAGTACACAAACAAAAGATA
* * * *
191281 TGAAATTGGTCCCCGTAATCATCCCAGCAAAGATATA
65 TGAAATTGGTCCCCATAATCATACAAACAAAGATATA
* * * *
191318 CAAAAGTGGTCCCCTT-AATCATTCCAAC-AGATACATAAAATGTAAAGTATA-AAACAAAAGAT
1 CAAAA-TGG-CCCCTTAAATCATCCCAACAAGATACACAAAATCTAAAGTACACAAACAAAAGAT
* *
191380 ACT-AAATTGGTCTCCATAATCCTACAAACAAAGATACT-
64 A-TGAAATTGGTCCCCATAATCATACAAACAAAGATA-TA
191418 CAAAATG
1 CAAAATG
191425 TAGAGTATAT
Statistics
Matches: 92, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
99 2 0.02
100 44 0.48
101 21 0.23
102 5 0.05
103 14 0.15
104 6 0.07
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (101 bp):
CAAAATGGCCCCTTAAATCATCCCAACAAGATACACAAAATCTAAAGTACACAAACAAAAGATAT
GAAATTGGTCCCCATAATCATACAAACAAAGATATA
Found at i:195616 original size:21 final size:21
Alignment explanation
Indices: 195592--195669 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
195582 TACAAGATAA
195592 ACGATAGGATAGGATACACGC
1 ACGATAGGATAGGATACACGC
195613 ACGATAGGATAGGATTA-ACGC
1 ACGATAGGATAGGA-TACACGC
* * *
195634 ACAATA-AAGCAGGATACACGC
1 ACGATAGGA-TAGGATACACGC
* *
195655 ATGATATGATAGGAT
1 ACGATAGGATAGGAT
195670 TGATACACGA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATACACGC
Found at i:195690 original size:42 final size:42
Alignment explanation
Indices: 195587--195691 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
195577 TTTTTTACAA
* *
195587 GATAAACGATAGGATAGGATACACGCACGATAGGATAGGATT
1 GATACACGATAGGAAAGGATACACGCACGATAGGATAGGATT
* ** * * *
195629 AACGCACAATA--AAGCAGGATACACGCATGATATGATAGGATT
1 GATACACGATAGGAA--AGGATACACGCACGATAGGATAGGATT
195671 GATACACGATAGGAAAGGATA
1 GATACACGATAGGAAAGGATA
195692 AATGATGTTC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
40 1 0.02
42 44 0.94
44 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.18
Consensus pattern (42 bp):
GATACACGATAGGAAAGGATACACGCACGATAGGATAGGATT
Found at i:196462 original size:16 final size:16
Alignment explanation
Indices: 196441--196476 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
196431 AACACGATAG
196441 GATAAACGAAAATACT
1 GATAAACGAAAATACT
* *
196457 GATAAACGATAATTCT
1 GATAAACGAAAATACT
196473 GATA
1 GATA
196477 GGATTAACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (16 bp):
GATAAACGAAAATACT
Found at i:196497 original size:21 final size:21
Alignment explanation
Indices: 196473--196561 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
196463 CGATAATTCT
196473 GATAGGATTAACGCACAATAG
1 GATAGGATTAACGCACAATAG
*
196494 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACAATAG
* * * * *
196515 AACAGTA-TACACGCACGATAC
1 GATAGGATTA-ACGCACAATAG
196536 GATAGGATTAACGCACAATAG
1 GATAGGATTAACGCACAATAG
196557 GATAG
1 GATAG
196562 AATAGGATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
GATAGGATTAACGCACAATAG
Found at i:197474 original size:2 final size:2
Alignment explanation
Indices: 197467--197527 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
197457 CCAACAAACC
197467 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
197509 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
197528 ATGCTTTAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:202724 original size:47 final size:47
Alignment explanation
Indices: 202655--202750 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
202645 CCCTCACTAC
202655 GGCATCTTTATCATCTGACAAACAACAAACCAATCAATTTTGACCAA
1 GGCATCTTTATCATCTGACAAACAACAAACCAATCAATTTTGACCAA
202702 GGCATCTTTATCATCTGACAAACAACAAACCAATCAATTTTGACCAA
1 GGCATCTTTATCATCTGACAAACAACAAACCAATCAATTTTGACCAA
202749 GG
1 GG
202751 TGGTCAACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (47 bp):
GGCATCTTTATCATCTGACAAACAACAAACCAATCAATTTTGACCAA
Found at i:202903 original size:20 final size:20
Alignment explanation
Indices: 202865--202903 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
202855 TCCTCACTTT
*
202865 TTGGCATACTGGCAAACAGG
1 TTGGCATACTGCCAAACAGG
* *
202885 TTGGCATCCTGCCAGACAG
1 TTGGCATACTGCCAAACAG
202904 TCCCAGTAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (20 bp):
TTGGCATACTGCCAAACAGG
Found at i:203010 original size:36 final size:36
Alignment explanation
Indices: 202963--203095 Score: 124
Period size: 37 Copynumber: 3.7 Consensus size: 36
202953 TATACATAGG
*
202963 ATCTATCATATTAGATCCATTCATGCAAACATTACA
1 ATCTATCATATTAGATCCATTCATGCAAACATTAAA
* * * ** * *
202999 ATCTAGCATATTTGATCAATTCATTTATAAGATTATA
1 ATCTATCATATTAGATCCATTCATGCA-AACATTAAA
* ** *
203036 ATCTATCATATTAGATTCATTTGTGCAAAACAATAAA
1 ATCTATCATATTAGATCCATTCATGC-AAACATTAAA
*
203073 ATCTATCATA-TAAATCCATTCAT
1 ATCTATCATATTAGATCCATTCAT
203096 TATATCATAT
Statistics
Matches: 73, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
36 31 0.42
37 41 0.56
38 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (36 bp):
ATCTATCATATTAGATCCATTCATGCAAACATTAAA
Found at i:203124 original size:22 final size:23
Alignment explanation
Indices: 203077--203129 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
203067 AATAAAATCT
*
203077 ATCATA-TAAATCCATTCATTAT
1 ATCATATTAAATCCATTCATTAC
203099 ATCATATTAAATCC-TT-ATATAC
1 ATCATATTAAATCCATTCAT-TAC
*
203121 ATCAGATTA
1 ATCATATTA
203130 TAATATATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 18 0.67
23 7 0.26
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.40
Consensus pattern (23 bp):
ATCATATTAAATCCATTCATTAC
Found at i:203137 original size:37 final size:38
Alignment explanation
Indices: 203098--203292 Score: 173
Period size: 37 Copynumber: 5.1 Consensus size: 38
203088 CCATTCATTA
* * *
203098 TATCATATTAAATCCTTAT-ATACATCAGATTATAATA
1 TATCTTATTAAATCCTTATCATACATAAGATTATAATC
* *
203135 TATCTTATTAAATCCATTAATCATTCACAAGATTATAATC
1 TATCTTATTAAATCC-TT-ATCATACATAAGATTATAATC
* * **
203175 TAACTTATTTAATCCACCAATCATACATAAGATTATAATC
1 TATCTTATTAAAT-C-CTTATCATACATAAGATTATAATC
* *
203215 TATCATT-TTAAATCCAT-TCATACATAAGATAATAATC
1 TATC-TTATTAAATCCTTATCATACATAAGATTATAATC
* * * * *
203252 TATCTTATTAAGTCCTT-TCATATATAATATCATAACC
1 TATCTTATTAAATCCTTATCATACATAAGATTATAATC
203289 TATC
1 TATC
203293 ACATTGGATC
Statistics
Matches: 129, Mismatches: 22, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
36 2 0.02
37 65 0.50
38 3 0.02
39 3 0.02
40 52 0.40
41 3 0.02
42 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (38 bp):
TATCTTATTAAATCCTTATCATACATAAGATTATAATC
Found at i:203182 original size:40 final size:39
Alignment explanation
Indices: 203098--203262 Score: 178
Period size: 40 Copynumber: 4.3 Consensus size: 39
203088 CCATTCATTA
* * * *
203098 TATCATATTAAATCC-TTAT-ATACATCAGATTATAATA
1 TATCTTATTAAATCCATAATCATACATAAGATTATAATC
* *
203135 TATCTTATTAAATCCATTAATCATTCACAAGATTATAATC
1 TATCTTATTAAATCCA-TAATCATACATAAGATTATAATC
* * *
203175 TAACTTATTTAATCCACCAATCATACATAAGATTATAATC
1 TATCTTATTAAATCCA-TAATCATACATAAGATTATAATC
*
203215 TATCATT-TTAAATCCAT--TCATACATAAGATAATAATC
1 TATC-TTATTAAATCCATAATCATACATAAGATTATAATC
203252 TATCTTATTAA
1 TATCTTATTAA
203263 GTCCTTTCAT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
36 2 0.02
37 41 0.38
39 3 0.03
40 59 0.55
41 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.39
Consensus pattern (39 bp):
TATCTTATTAAATCCATAATCATACATAAGATTATAATC
Found at i:206229 original size:4 final size:4
Alignment explanation
Indices: 206220--206274 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
206210 ATCTTAAAGT
206220 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
206268 GATA GAT
1 GATA GAT
206275 GGATGGATGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:206279 original size:4 final size:4
Alignment explanation
Indices: 206272--206314 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
206262 TAGATAGATA
206272 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GAT
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GAT
206315 NACGATCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.49, T:0.26
Consensus pattern (4 bp):
GATG
Found at i:209122 original size:3 final size:3
Alignment explanation
Indices: 209101--209136 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
209091 GTTTATCTTA
* *
209101 GAT GAC GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
209137 TTGAAGAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:213744 original size:167 final size:166
Alignment explanation
Indices: 213411--214121 Score: 955
Period size: 167 Copynumber: 4.2 Consensus size: 166
213401 AAAGAATCAT
* *
213411 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTCCTATGTAAAA-A
** * *
213476 TTAACCCCCCCCCCCCAATGTGGCCCCACCCTACCCCCGGGGTTCGTGAATTTCACAACTTTGAA
65 TT-----CGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGTTCATGAATTTCACAACTTTGAA
*
213541 TTTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
125 TCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
*
213583 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTCCTATGTAAAAAT
* * *
213648 TCGACCCCCCATTTTGGCCCCCATCCTACCCCCGGGGTTCGTGAATTTCACAACTTTGAATCTAC
66 TCGACCCCCCATTGTGG-CCCCACCCTACCCCCGGGGTTCATGAATTTCACAACTTTGAATCTAC
213713 ACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
130 ACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
* *
213750 CTGGCTGATTAGTTTCTGAGAAGAATATTTTAAAAGATTTACTCTATATATATTCCTATGTAAAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTA-A-ATATTCCTATGTAAAA
* * *
213815 ATTCGA-CCCCCATTGTGGCCCCACCCTACCCCCGGGGGGTCAAGATTTTCACAACTTTGAATCT
64 ATTCGACCCCCCATTGTGGCCCCACCCTACCCCC-GGGGTTCATGAATTTCACAACTTTGAATCT
* *
213879 ACACTACCTG-GGAATGCTTCCACACAAGTTTCAGCTTTT
128 ACACTACCTGAGG-ATACTTCCACACAAGTTTCAGCTTTC
* **
213918 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTGACTCTTTATATTCCTATGTAAAAAT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTCCTATGTAAAAAT
* *
213983 TCGACCCCCCCCCCCCATTGGGGCCCCACCCTACCCCCGGGATTCATGAATTTCACAACTGTT-A
66 TCGA------CCCCCCATTGTGGCCCCACCCTACCCCCGGGGTTCATGAATTTCACAACT-TTGA
* * *
214047 ATCTACACTACCTGAGGATGCTTCCATAGAAGTTTCAGCTTTC
124 ATCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
* *
214090 CTGGCT--TTATGGTTCTTGGGAAGAAGATTTTT
1 CTGGCTGATTA-GTTTC-TGAGAAGAAGATTTTT
214122 GAAAATGTCT
Statistics
Matches: 489, Mismatches: 34, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
166 34 0.07
167 142 0.29
168 114 0.23
169 21 0.04
170 3 0.01
171 6 0.01
172 139 0.28
173 30 0.06
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (166 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTCCTATGTAAAAAT
TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGTTCATGAATTTCACAACTTTGAATCTACA
CTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
Found at i:218451 original size:20 final size:20
Alignment explanation
Indices: 218413--218451 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
218403 TCCTCACTTT
*
218413 TTGGCATACTGGCAAACAGG
1 TTGGCATACTGCCAAACAGG
* *
218433 TTGGCATCCTGCCAGACAG
1 TTGGCATACTGCCAAACAG
218452 TCCCAGTAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (20 bp):
TTGGCATACTGCCAAACAGG
Found at i:218551 original size:36 final size:37
Alignment explanation
Indices: 218511--219021 Score: 336
Period size: 36 Copynumber: 13.6 Consensus size: 37
218501 TATACATAGG
218511 ATTATAATCTATCATATTAGATCCATTCGTGCA-AAC
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* * ** **
218547 ATTATAATCTAGCATATTTGATCCATTC-TATATAGG
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
*
218583 ATTATAATCTATCATATTAGATTCATTCGTGC-TAAC
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* * * * **
218619 ATTATAATCTAGCATATTTGATCCATTCATTCATAGG
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
*
218656 ATTATAATCTATCATATTAGATTCATTCGTGC-TAAC
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* * ** **
218692 ATTATAATCTAGCATATTTGATCCATTC-TTTATAGG
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* *
218728 ATTATTATCTATCATATTAGATTCATTCGTGC-TAAC
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* * * * *
218764 ATTATAATCTATCATATAAGATACATTCATTCATAAG
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* * ** * * * *
218801 ATTGTAATCTATCTTATTTCATCCACCAATCATACATAAG
1 ATTATAATCTATCATATTAGAT---CCATTCGTGCATAAC
* * * * *
218841 ATTATAATCTATCTTATTTA-ATCCACAAATCATACATAAG
1 ATTATAATCTATCATA-TTAGAT-C-C-ATTCGTGCATAAC
* * * * *
218881 ATTATAATCTATCATTTTAAATCCATTCATACATAAA
1 ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
* * * * *
218918 ATAATAATCTATATCTTATTAAATCCATTCGATCATACATAAG
1 ATTATAATC--TATCATATTAGATCCATTCG----TGCATAAC
** * ** *
218961 ATTATAATCTATCATATTA-AGTCTTTTCATATATAAG
1 ATTATAATCTATCATATTAGA-TCCATTCGTGCATAAC
218998 ATTATAATCTATCATATTAGATCC
1 ATTATAATCTATCATATTAGATCC
219022 TTTCATTCTT
Statistics
Matches: 379, Mismatches: 75, Indels: 41
0.77 0.15 0.08
Matches are distributed among these distances:
35 3 0.01
36 163 0.43
37 98 0.26
38 3 0.01
39 22 0.06
40 59 0.16
41 16 0.04
43 15 0.04
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.41
Consensus pattern (37 bp):
ATTATAATCTATCATATTAGATCCATTCGTGCATAAC
Found at i:218759 original size:145 final size:145
Alignment explanation
Indices: 218505--218818 Score: 529
Period size: 145 Copynumber: 2.2 Consensus size: 145
218495 GCCATTTATA
218505 CATAGGATTATAATCTATCATATTAGATCCATTCGTGCAAACATTATAATCTAGCATATTTGATC
1 CATAGGATTATAATCTATCATATTAGATCCATTCGTGCAAACATTATAATCTAGCATATTTGATC
218570 CATTCTATATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATA
66 CATTCTATATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATA
** *
218635 TTTGATCCATTCATT
131 TAAGATACATTCATT
* *
218650 CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
1 CATAGGATTATAATCTATCATATTAGATCCATTCGTGCAAACATTATAATCTAGCATATTTGATC
* * *
218715 CATTCTTTATAGGATTATTATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTATCATA
66 CATTCTATATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATA
218780 TAAGATACATTCATT
131 TAAGATACATTCATT
* * *
218795 CATAAGATTGTAATCTATCTTATT
1 CATAGGATTATAATCTATCATATT
218819 TCATCCACCA
Statistics
Matches: 158, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
145 158 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (145 bp):
CATAGGATTATAATCTATCATATTAGATCCATTCGTGCAAACATTATAATCTAGCATATTTGATC
CATTCTATATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATA
TAAGATACATTCATT
Found at i:218791 original size:72 final size:73
Alignment explanation
Indices: 218505--218818 Score: 499
Period size: 72 Copynumber: 4.3 Consensus size: 73
218495 GCCATTTATA
* *
218505 CATAGGATTATAATCTATCATATTAGATCCATTCGTGCAAACATTATAATCTAGCATATTTGATC
1 CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
218570 CATTC-TAT
66 CATTCAT-T
218578 -ATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
1 CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
218642 CATTCATT
66 CATTCATT
218650 CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
1 CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
218715 CATTC-TT
66 CATTCATT
* * * ** *
218722 TATAGGATTATTATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTATCATATAAGATA
1 CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
218787 CATTCATT
66 CATTCATT
* * *
218795 CATAAGATTGTAATCTATCTTATT
1 CATAGGATTATAATCTATCATATT
218819 TCATCCACCA
Statistics
Matches: 225, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
72 134 0.60
73 91 0.40
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (73 bp):
CATAGGATTATAATCTATCATATTAGATTCATTCGTGCTAACATTATAATCTAGCATATTTGATC
CATTCATT
Found at i:218840 original size:40 final size:40
Alignment explanation
Indices: 218790--218978 Score: 199
Period size: 40 Copynumber: 4.7 Consensus size: 40
218780 TAAGATACAT
* * * *
218790 TCATTCATAAGATTGTAATCTATCTTATTTCATCCACCAA
1 TCATACATAAGATTATAATCTATCTTATTTAATCCACAAA
218830 TCATACATAAGATTATAATCTATCTTATTTAATCCACAAA
1 TCATACATAAGATTATAATCTATCTTATTTAATCCACAAA
* *
218870 TCATACATAAGATTATAATCTATCATT-TTAAAT-C-C-AT
1 TCATACATAAGATTATAATCTATC-TTATTTAATCCACAAA
* * * *
218907 TCATACATAAAATAATAATCTATATCTTATTAAATCCATTC-GA
1 TCATACATAAGATTATAATC--TATCTTATTTAATCCA--CAAA
*
218950 TCATACATAAGATTATAATCTATCATATT
1 TCATACATAAGATTATAATCTATCTTATT
218979 AAGTCTTTTC
Statistics
Matches: 128, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
37 19 0.15
38 3 0.02
39 11 0.09
40 66 0.52
41 10 0.08
43 19 0.15
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.39
Consensus pattern (40 bp):
TCATACATAAGATTATAATCTATCTTATTTAATCCACAAA
Found at i:218990 original size:80 final size:79
Alignment explanation
Indices: 218830--219009 Score: 240
Period size: 80 Copynumber: 2.3 Consensus size: 79
218820 CATCCACCAA
*
218830 TCATACATAAGATTATAATC--TATCTTATTTAATCCACAAATCATACATAAGATTATAATCTAT
1 TCATACATAAGATTATAATCTATATCTTATTAAATCCACAAATCATACATAAGATTATAATCTAT
*
218893 CATTTTAAATCCAT
66 CATATTAAATCCAT
* * *
218907 TCATACATAAAATAATAATCTATATCTTATTAAATCCATTC-GATCATACATAAGATTATAATCT
1 TCATACATAAGATTATAATCTATATCTTATTAAATCCA--CAAATCATACATAAGATTATAATCT
* **
218971 ATCATATTAAGTCTTT
64 ATCATATTAAATCCAT
*
218987 TCATATATAAGATTATAATCTAT
1 TCATACATAAGATTATAATCTAT
219010 CATATTAGAT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
77 18 0.20
79 15 0.17
80 54 0.61
81 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (79 bp):
TCATACATAAGATTATAATCTATATCTTATTAAATCCACAAATCATACATAAGATTATAATCTAT
CATATTAAATCCAT
Found at i:223909 original size:16 final size:16
Alignment explanation
Indices: 223890--223939 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
223880 CCAACGGTAT
223890 CAGGAGAAAACGTACC
1 CAGGAGAAAACGTACC
*
223906 CAGGAGAAAACGTACT
1 CAGGAGAAAACGTACC
*
223922 CAGGAGAAAATGTACC
1 CAGGAGAAAACGTACC
223938 CA
1 CA
223940 ATTTACCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (16 bp):
CAGGAGAAAACGTACC
Found at i:230269 original size:17 final size:17
Alignment explanation
Indices: 230243--230276 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
230233 CTAAGGACAT
230243 CATTTAAAAT-GTTTAA
1 CATTTAAAATGGTTTAA
230259 CATTATAAAATGGTTTAA
1 CATT-TAAAATGGTTTAA
230277 GTAATATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (17 bp):
CATTTAAAATGGTTTAA
Found at i:233751 original size:18 final size:18
Alignment explanation
Indices: 233728--233766 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
233718 GCTATTTTGA
233728 ATAGCTTTATAAAGCTAT
1 ATAGCTTTATAAAGCTAT
* *
233746 ATAGCTTTTTCAAGCTAT
1 ATAGCTTTATAAAGCTAT
233764 ATA
1 ATA
233767 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (18 bp):
ATAGCTTTATAAAGCTAT
Found at i:239411 original size:21 final size:21
Alignment explanation
Indices: 239385--239466 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
239375 TTTTTCTATC
*
239385 AAATATGTCGACATGCAAGAT
1 AAATATGTTGACATGCAAGAT
239406 AAATATGTTGACATGCAAGATT
1 AAATATGTTGACATGCAAGA-T
** **
239428 ACTTATGTTGACATGTGAGAT
1 AAATATGTTGACATGCAAGAT
*
239449 GAATATGTTGACATGCAA
1 AAATATGTTGACATGCAA
239467 CTTATAAGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 33 0.66
22 17 0.34
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (21 bp):
AAATATGTTGACATGCAAGAT
Found at i:239509 original size:21 final size:21
Alignment explanation
Indices: 239470--239535 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
239460 CATGCAACTT
* **
239470 ATAAGTTGTATGTCAACATAA
1 ATAAGTTGCATGTTGACATAA
*
239491 TTAAGTTGCATGTTGACATAA
1 ATAAGTTGCATGTTGACATAA
* *
239512 ATATGTTGCATGTTGACATCA
1 ATAAGTTGCATGTTGACATAA
239533 ATA
1 ATA
239536 GGTAGCGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (21 bp):
ATAAGTTGCATGTTGACATAA
Found at i:239633 original size:21 final size:21
Alignment explanation
Indices: 239609--239686 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
239599 ATTTGATTGC
* *
239609 AGTTTTCTTTCATGTCAACAT
1 AGTTATCTTGCATGTCAACAT
* **
239630 AGTTATGTTGCATGTTGACAT
1 AGTTATCTTGCATGTCAACAT
**
239651 AACTATCTTGCATGTCAACAT
1 AGTTATCTTGCATGTCAACAT
*
239672 ATTTATCTTGCATGT
1 AGTTATCTTGCATGT
239687 TGACATAATT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (21 bp):
AGTTATCTTGCATGTCAACAT
Found at i:239683 original size:42 final size:42
Alignment explanation
Indices: 239614--239694 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
239604 ATTGCAGTTT
* *
239614 TCTTTCATGTCAACATAGTTATGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTTGACATAACTA
*
239656 TCTTGCATGTCAACATATTTATCTTGCATGTTGACATAA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTTGACATAA
239695 TTAATAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTATCTTGCATGTTGACATAACTA
Found at i:239692 original size:21 final size:21
Alignment explanation
Indices: 239626--239697 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
239616 TTTCATGTCA
* *
239626 ACATAGTTATGTTGCATGTTG
1 ACATAATTATCTTGCATGTTG
* **
239647 ACATAACTATCTTGCATGTCA
1 ACATAATTATCTTGCATGTTG
*
239668 ACATATTTATCTTGCATGTTG
1 ACATAATTATCTTGCATGTTG
239689 ACATAATTA
1 ACATAATTA
239698 ATAGAAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (21 bp):
ACATAATTATCTTGCATGTTG
Found at i:241738 original size:40 final size:40
Alignment explanation
Indices: 241693--241825 Score: 169
Period size: 40 Copynumber: 3.2 Consensus size: 40
241683 ATAATACATG
*
241693 TACATGTTTAATAAACTTGTAATTTAATGTATACGTATAAAACA
1 TACATGTTTAATAAACTGGTAATTTAATGTATACGTAT---A-A
*
241737 TGTACATGTTTAAGAAACTGGTAATTTAATGTATACGTATAA
1 --TACATGTTTAATAAACTGGTAATTTAATGTATACGTATAA
*
241779 TACAT-TTACAATAAACTGGTAATTTAATGTATACGTATAA
1 TACATGTT-TAATAAACTGGTAATTTAATGTATACGTATAA
241819 TACATGT
1 TACATGT
241826 ACATTTAAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
39 2 0.02
40 40 0.49
41 1 0.01
42 1 0.01
43 1 0.01
46 36 0.44
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (40 bp):
TACATGTTTAATAAACTGGTAATTTAATGTATACGTATAA
Found at i:241742 original size:46 final size:46
Alignment explanation
Indices: 241675--241829 Score: 232
Period size: 46 Copynumber: 3.5 Consensus size: 46
241665 ATAAACTGGC
*
241675 GTATACGTATAATACATGTACATGTTTAATAAACTTGTAATTTAAT
1 GTATACGTATAATACATGTACATGTTTAATAAACTGGTAATTTAAT
* *
241721 GTATACGTATAAAACATGTACATGTTTAAGAAACTGGTAATTTAAT
1 GTATACGTATAATACATGTACATGTTTAATAAACTGGTAATTTAAT
*
241767 GTATACGTATAATACATTTAC------AATAAACTGGTAATTTAAT
1 GTATACGTATAATACATGTACATGTTTAATAAACTGGTAATTTAAT
241807 GTATACGTATAATACATGTACAT
1 GTATACGTATAATACATGTACAT
241830 TTAAGTCAAT
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
40 38 0.38
46 62 0.62
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (46 bp):
GTATACGTATAATACATGTACATGTTTAATAAACTGGTAATTTAAT
Found at i:243056 original size:6 final size:6
Alignment explanation
Indices: 243045--243069 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
243035 GCTATACCCC
243045 CGGCGT CGGCGT CGGCGT CGGCGT C
1 CGGCGT CGGCGT CGGCGT CGGCGT C
243070 AGGACCTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.48, T:0.16
Consensus pattern (6 bp):
CGGCGT
Found at i:243419 original size:177 final size:174
Alignment explanation
Indices: 243207--244120 Score: 943
Period size: 177 Copynumber: 5.2 Consensus size: 174
243197 CAGTCTTAAA
* * * *
243207 TTTCAGATGCTGGAGGACGTTCAGGTTGTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
* *
243272 GATAGCAAAATCTAAGTTATTGCTGGTCCATACTTCACCAAACTTGCATGGATGGTGTGTCTTAT
66 GAT-G-AAAATCTAAGTTACTGCTAGTCC-TACTTCACCAAACTTGCATGGATGGTGTGTCTTAT
* * * * *
243337 AATACTGATGCACCAGACATGCTTGAGTGCTGAATCTGAGCTATAGG
128 GATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
*
243384 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGTCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
* *
243449 GATAGCAAAATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATTGATGGTGTGTCTTAT
66 GAT-G-AAAATCTAAGTTACTGCTAGTCC-TACTTCACCAAACTTGCATGGATGGTGTGTCTTAT
* * *
243514 AATACTGATGCA-CTAGACAGGCTT-AAGTGCTGAATCTGAGCTATAAG
128 GATACTGATGCACCT-GACAGGCTTGAA-TGCTGAATCTGAGCCATAGG
*
243561 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTG-CC-CT
* * * * * * *
243626 ATTGAT-TATATCTTAGTTACTACTAGTCCTAACTTCACCAAACTTGTATGGATTGTGCGTCTTA
64 -TTGATGAAAATCTAAGTTACTGCTAGTCCT-ACTTCACCAAACTTGCATGGATGGTGTGTCTTA
* *
243690 TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCAAAGG
127 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* * * * * * *
243738 TTTTGGATGCTGGAAGAGGTCAAGGTTTTTAGAGCTGTTTAAAGTTTTCTG-AGCAGGTGCCCTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTT-TGTTGCAGGTGCCCTT
* * * ** * * * * * * *
243802 TAATG--ATTATATCTTA--GCTACTCCTA-GT--GCTAACTTGCGTGAATGGTTTGTCTTATGA
65 TGATGAAAATCTAAGTTACTGCTAGTCCTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGA
243860 TACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
130 TACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* ** * * *** *
243905 TTTTGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGCTTAAAGTTTTTGAAACAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
* * * * * * * * **
243970 GATGATTATATCTTAGTTATTACTTGTCTTTACTTTACCAGACTT-CAATGGATGGTGCATCTTA
66 GATGA--AAATCTAAGTTACTGCTAGTC-CTACTTCACCAAACTTGC-ATGGATGGTGTGTCTTA
* * *
244034 TGATACTGATGCACCTGACCGGCTTGAATGCCGAGTCTGAGCCATAGG
127 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
** * *
244082 TTTCGGATGCTGGATAAGGTTAAGTTTTTTGGAACAGGT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
244121 CACATTTTTA
Statistics
Matches: 623, Mismatches: 92, Indels: 44
0.82 0.12 0.06
Matches are distributed among these distances:
166 2 0.00
167 124 0.20
169 1 0.00
170 1 0.00
171 12 0.02
173 9 0.01
174 6 0.01
175 3 0.00
176 6 0.01
177 445 0.71
178 7 0.01
179 2 0.00
180 5 0.01
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (174 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
GATGAAAATCTAAGTTACTGCTAGTCCTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGAT
ACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
Found at i:243441 original size:19 final size:19
Alignment explanation
Indices: 243394--243433 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
243384 TTTCGGATGC
* *
243394 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
243413 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
243432 TG
1 TG
243434 TTGCAGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:243765 original size:354 final size:344
Alignment explanation
Indices: 243207--244120 Score: 1022
Period size: 344 Copynumber: 2.6 Consensus size: 344
243197 CAGTCTTAAA
* * * * * *
243207 TTTCAGATGCTGGAGGACGTTCAGGTTGTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * * * *
243272 GATAGCA--AAATCTAAGTTATTGCTGGTCC-ATACTTCACCAAACTTGCATGGATGGTGTGTCT
66 GATTG-ATTATATCTTAGTTATTACTAGTCCTA-ACTTCACCAAACTTGAATGGATGGTGCGTCT
* * * * * *
243334 TATAATACTGATGCACCAGACATGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAG
129 TATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAA
* * *
243399 GAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTT-TGTTGCAGGTGTCCTTTGATAGCA-AAATCT
194 GAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTCTG-AGCAGGTGCCCTTTAAT-G-ATAAATCT
* * * *
243462 AAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATTG-ATGGTGTGTCTTATAATACTGATGCA
256 AAGCTACTCCTAGT--G--C-T-----AACTTGC-GTGAATGGTGTGTCTTATAATACTGATGCA
*
243526 -CTAGACAGGCTT-AAGTGCTGAATCTGAGCTATAAG
310 CCT-GACAGGCTTGAA-TGCTGAATCTGAGCCATAAG
243561 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * *
243626 -ATTGATTATATCTTAGTTACTACTAGTCCTAACTTCACCAAACTTGTATGGATTGTGCGTCTTA
66 GATTGATTATATCTTAGTTATTACTAGTCCTAACTTCACCAAACTTGAATGGATGGTGCGTCTTA
* *
243690 TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCAAAGGTTTTGGATGCTGGAAGA
131 TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAAGA
* * * * * *
243755 GGTCAAGGTTTTTAGAGCTGTTTAAAGTTTTCTGAGCAGGTGCCCTTTAATGATTATATCTTAGC
196 GGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTCTGAGCAGGTGCCCTTTAATGA-TAAATCTAAGC
* *
243820 TACTCCTAGTGCTAACTTGCGTGAATGGTTTGTCTTATGATACTGATGCACCTGACAGGCTTGAA
260 TACTCCTAGTGCTAACTTGCGTGAATGGTGTGTCTTATAATACTGATGCACCTGACAGGCTTGAA
*
243885 TGCTGAATCTGAGCCATAGG
325 TGCTGAATCTGAGCCATAAG
* ** * ***
243905 TTTTGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGCTTAAAGTTTTTGAAACAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * * * *
243970 GA-TGATTATATCTTAGTTATTACTTGTCTTTACTTTACCAGACTTCAATGGATGGTGCATCTTA
66 GATTGATTATATCTTAGTTATTACTAGTCCTAACTTCACCAAACTTGAATGGATGGTGCGTCTTA
** * *
244034 TGATACTGATGCACCTGACCGGCTTGAATGCCGAGTCTGAGCCATAGGTTTCGGATGCTGGATA-
131 TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGA-AG
* *
244098 AGGTTAAGTTTTTTGGAACAGGT
195 AGGTTAAGGTTTTTGGAGCAGGT
244121 CACATTTTTA
Statistics
Matches: 480, Mismatches: 69, Indels: 32
0.83 0.12 0.06
Matches are distributed among these distances:
343 2 0.00
344 241 0.50
345 6 0.01
349 1 0.00
350 1 0.00
352 3 0.01
353 4 0.01
354 219 0.46
355 3 0.01
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (344 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
GATTGATTATATCTTAGTTATTACTAGTCCTAACTTCACCAAACTTGAATGGATGGTGCGTCTTA
TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAAGA
GGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTCTGAGCAGGTGCCCTTTAATGATAAATCTAAGCT
ACTCCTAGTGCTAACTTGCGTGAATGGTGTGTCTTATAATACTGATGCACCTGACAGGCTTGAAT
GCTGAATCTGAGCCATAAG
Found at i:243885 original size:167 final size:167
Alignment explanation
Indices: 243684--243985 Score: 507
Period size: 167 Copynumber: 1.8 Consensus size: 167
243674 TGGATTGTGC
243684 GTCTTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCAAAGGTTTTGGATGCT
1 GTCTTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCAAAGGTTTTGGATGCT
* * * *
243749 GGAAGAGGTCAAGGTTTTTAGAGCTGTTTAAAGTTTTCTG-AGCAGGTGCCCTTTAATGATTATA
66 GGAAGAGGTCAAGGTTTTAAGAGCTGCTTAAAGTTTT-TGAAACAGGTGCCCTCTAATGATTATA
243813 TCTTAGCTACTCCTAGTGCTAACTTGCGTGAATGGTTT
130 TCTTAGCTACTCCTAGTGCTAACTTGCGTGAATGGTTT
* *
243851 GTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTTGGATGCT
1 GTCTTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCAAAGGTTTTGGATGCT
* * *
243916 GGAGGAGGTTAAGGTTTTAAGAGCTGCTTAAAGTTTTTGAAACAGGTGCCCTCTGATGATTATAT
66 GGAAGAGGTCAAGGTTTTAAGAGCTGCTTAAAGTTTTTGAAACAGGTGCCCTCTAATGATTATAT
243981 CTTAG
131 CTTAG
243986 TTATTACTTG
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
166 2 0.02
167 123 0.98
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (167 bp):
GTCTTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCCAAAGGTTTTGGATGCT
GGAAGAGGTCAAGGTTTTAAGAGCTGCTTAAAGTTTTTGAAACAGGTGCCCTCTAATGATTATAT
CTTAGCTACTCCTAGTGCTAACTTGCGTGAATGGTTT
Found at i:244861 original size:15 final size:15
Alignment explanation
Indices: 244841--244877 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
244831 TCAATTTTTT
*
244841 TGATATTTTATCATA
1 TGATATTGTATCATA
244856 TGATATTGTATC--A
1 TGATATTGTATCATA
244869 TGATATTGT
1 TGATATTGT
244878 TATGTATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
15 11 0.52
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (15 bp):
TGATATTGTATCATA
Found at i:245043 original size:15 final size:15
Alignment explanation
Indices: 245023--245058 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
245013 TATTCTTTAT
*
245023 TATTGTATCATACGA
1 TATTGTATAATACGA
*
245038 TATTGTATAATATGA
1 TATTGTATAATACGA
245053 TATTGT
1 TATTGT
245059 TTTATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (15 bp):
TATTGTATAATACGA
Found at i:245382 original size:20 final size:20
Alignment explanation
Indices: 245357--245395 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
245347 ATAAAGTATC
*
245357 ATACAATATCATACTATATT
1 ATACAATATAATACTATATT
*
245377 ATACAATATAATATTATAT
1 ATACAATATAATACTATAT
245396 GTTTCAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
ATACAATATAATACTATATT
Found at i:245765 original size:16 final size:16
Alignment explanation
Indices: 245744--245777 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
245734 AAAGATGGTG
245744 TCATAAAGGTGATGTC
1 TCATAAAGGTGATGTC
*
245760 TCATAAGGGTGATGTC
1 TCATAAAGGTGATGTC
245776 TC
1 TC
245778 GTCTCGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (16 bp):
TCATAAAGGTGATGTC
Found at i:253287 original size:13 final size:14
Alignment explanation
Indices: 253249--253291 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
253239 TTCAGAAATA
253249 TATTTGAATTTATT
1 TATTTGAATTTATT
* *
253263 AATTTAAATTTATT
1 TATTTGAATTTATT
253277 TA-TTGAATTTATT
1 TATTTGAATTTATT
253290 TA
1 TA
253292 GAATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (14 bp):
TATTTGAATTTATT
Found at i:253619 original size:15 final size:16
Alignment explanation
Indices: 253592--253627 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
253582 TAAAATACAA
*
253592 GATATTGTGAATAGAT
1 GATATTGTGAATAGAC
253608 GATATT-TGAATAGAC
1 GATATTGTGAATAGAC
253623 GATAT
1 GATAT
253628 AATAATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (16 bp):
GATATTGTGAATAGAC
Found at i:261989 original size:88 final size:88
Alignment explanation
Indices: 261879--262089 Score: 341
Period size: 88 Copynumber: 2.4 Consensus size: 88
261869 TCCATGAATC
*
261879 CAAATGGTTTCCGCAACAGAAACTTACTGAAACTTGAAGTTTCTGCATAGTTTCAATCTCCATAT
1 CAAATGGTTTCCGCAACAGAAACTTACTGAAACTTGAAGTTTCTGCATAGTTTCAACCTCCATAT
**
261944 ACGTTTGGGATACATATTGTTTA
66 ACAATTGGGATACATATTGTTTA
** *
261967 CAAATGGTTTCCGTGACGGAAACTTACTGAAACTTGAAGTTTCTGCATAGTTTCAACCTCCATAT
1 CAAATGGTTTCCGCAACAGAAACTTACTGAAACTTGAAGTTTCTGCATAGTTTCAACCTCCATAT
262032 ACAATTGGGATACATATTGTTTA
66 ACAATTGGGATACATATTGTTTA
* * *
262055 CAAAGGGTTTCTGCAACTGAAACTTACTGAAACTT
1 CAAATGGTTTCCGCAACAGAAACTTACTGAAACTT
262090 TTTATATTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 112 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (88 bp):
CAAATGGTTTCCGCAACAGAAACTTACTGAAACTTGAAGTTTCTGCATAGTTTCAACCTCCATAT
ACAATTGGGATACATATTGTTTA
Found at i:271309 original size:22 final size:22
Alignment explanation
Indices: 271284--271328 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
271274 AAGCAATTCT
271284 CGAGTAAACCCAAAGTAAACCC
1 CGAGTAAACCCAAAGTAAACCC
*
271306 CGAGTAAACCCAACGTAAACCC
1 CGAGTAAACCCAAAGTAAACCC
271328 C
1 C
271329 AAGTGGACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.36, G:0.13, T:0.09
Consensus pattern (22 bp):
CGAGTAAACCCAAAGTAAACCC
Found at i:271338 original size:22 final size:22
Alignment explanation
Indices: 271286--271341 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
271276 GCAATTCTCG
*
271286 AGTAAACCCAAAGTAAACCCCG
1 AGTAAACCCAAAGTAAACCCCA
*
271308 AGTAAACCCAACGTAAACCCCA
1 AGTAAACCCAAAGTAAACCCCA
**
271330 AGTGGACCCAAA
1 AGTAAACCCAAA
271342 TTTTCAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.32, G:0.14, T:0.09
Consensus pattern (22 bp):
AGTAAACCCAAAGTAAACCCCA
Found at i:271376 original size:13 final size:11
Alignment explanation
Indices: 271286--271383 Score: 65
Period size: 11 Copynumber: 8.8 Consensus size: 11
271276 GCAATTCTCG
271286 AGTAAACCCAA
1 AGTAAACCCAA
**
271297 AGTAAACCCCG
1 AGTAAACCCAA
271308 AGTAAACCCAA
1 AGTAAACCCAA
* *
271319 CGTAAACCCCA
1 AGTAAACCCAA
**
271330 AGTGGACCCAA
1 AGTAAACCCAA
*** *
271341 A-T-TTTCAAA
1 AGTAAACCCAA
271350 TAGTAAACCCAA
1 -AGTAAACCCAA
271362 AGTAAACCCAGAA
1 AGTAAACCC--AA
271375 AGTAAACCC
1 AGTAAACCC
271384 GGGGTTTAGT
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
9 3 0.05
10 2 0.03
11 45 0.70
12 3 0.05
13 11 0.17
ACGTcount: A:0.46, C:0.29, G:0.12, T:0.13
Consensus pattern (11 bp):
AGTAAACCCAA
Found at i:271723 original size:140 final size:139
Alignment explanation
Indices: 271447--271759 Score: 332
Period size: 140 Copynumber: 2.2 Consensus size: 139
271437 ATAAAGTGTA
* * * * **
271447 ATGACCTTGACCCAAGGTTATTTGGGCAAGGTC-CTTGGCAGGAAAAATGCAAATTTTTTACCGG
1 ATGACATTGACCAAAGGTCA-TTGGGCAAGGTCACTTGGCAGGAAAAATGAAAATTTGCTACCGG
* * *
271511 TACATATCTTTCTAATGAGACAACATTGAAAGTTCCTACTTCACACAAAGATTGCTTATGACTTA
65 TACATATCTTTCAAATGAGACAACATAGAAAGTTCCTACTTCACACAAAGATTGCTTATGACCTA
*
271576 AGAGTGTGTC
130 AGAGTGTGCC
**
271586 ATGATC-TTGACTTAAGGTCACTTGGGCAAGGTCACTT-GCAGGAAAAATGAAAAAATTTGCT-C
1 ATGA-CATTGACCAAAGGTCA-TTGGGCAAGGTCACTTGGCAGGAAAAATG--AAAATTTGCTAC
* * * * *
271648 CGGTCCATATCTATT-AAATGGAGA-AACATAGGAAGTTTCTACTTTATACAAAGATTGCTTATG
62 CGGTACATATCT-TTCAAAT-GAGACAACATAGAAAGTTCCTACTTCACACAAAGATTGCTTATG
* *
271711 ACCTGAGTGTGTGCC
125 ACCTAAGAGTGTGCC
*
271726 ATGACATTGACCAAAGGTCATTCGGGGAAGGTCA
1 ATGACATTGACCAAAGGTCATT-GGGCAAGGTCA
271760 AGATTACTGA
Statistics
Matches: 145, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
139 42 0.29
140 90 0.62
141 13 0.09
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (139 bp):
ATGACATTGACCAAAGGTCATTGGGCAAGGTCACTTGGCAGGAAAAATGAAAATTTGCTACCGGT
ACATATCTTTCAAATGAGACAACATAGAAAGTTCCTACTTCACACAAAGATTGCTTATGACCTAA
GAGTGTGCC
Found at i:274081 original size:41 final size:40
Alignment explanation
Indices: 274024--274104 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
274014 CAAGCCTTAC
* *
274024 CCCAGACCACCCATATACCGCA-CTAAATGCAATACAAAATA
1 CCCAGACCACCAATATACC-AAGCTAAATGCAATA-AAAATA
*
274065 CCCAGACCACCAATATACCAAGCTGAATGCAATAAAAATA
1 CCCAGACCACCAATATACCAAGCTAAATGCAATAAAAATA
274105 AACCAATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 7 0.19
41 29 0.81
ACGTcount: A:0.46, C:0.31, G:0.09, T:0.15
Consensus pattern (40 bp):
CCCAGACCACCAATATACCAAGCTAAATGCAATAAAAATA
Found at i:294748 original size:34 final size:36
Alignment explanation
Indices: 294705--294788 Score: 109
Period size: 34 Copynumber: 2.4 Consensus size: 36
294695 CGCTCTAATT
294705 TTCCAATGACCTTGTAAAGAACGC-A-ATGCAGCTG
1 TTCCAATGACCTTGTAAAGAACGCAATATGCAGCTG
* * * *
294739 TTCCAATGACCTTGTCAAGAGCTCAATATGCGGCTG
1 TTCCAATGACCTTGTAAAGAACGCAATATGCAGCTG
*
294775 TTCCAATGATCTTG
1 TTCCAATGACCTTG
294789 CCAAGGGCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 21 0.49
35 1 0.02
36 21 0.49
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (36 bp):
TTCCAATGACCTTGTAAAGAACGCAATATGCAGCTG
Found at i:294782 original size:36 final size:34
Alignment explanation
Indices: 294705--294793 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 34
294695 CGCTCTAATT
*
294705 TTCCAATGACCTTGTAAAGAACGCAATGCAGCTG
1 TTCCAATGACCTTGTCAAGAACGCAATGCAGCTG
* * *
294739 TTCCAATGACCTTGTCAAGAGCTCAATATGCGGCTG
1 TTCCAATGACCTTGTCAAGAACGC-A-ATGCAGCTG
* *
294775 TTCCAATGATCTTGCCAAG
1 TTCCAATGACCTTGTCAAG
294794 GGCCCAAGGC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 21 0.45
35 1 0.02
36 25 0.53
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (34 bp):
TTCCAATGACCTTGTCAAGAACGCAATGCAGCTG
Found at i:296714 original size:16 final size:15
Alignment explanation
Indices: 296689--296721 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
296679 AAGGTTTGAG
296689 AAAATGAATTGAATT
1 AAAATGAATTGAATT
296704 AAAATTGAATTGAATT
1 AAAA-TGAATTGAATT
296720 AA
1 AA
296722 CATGCTACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
AAAATGAATTGAATT
Found at i:301596 original size:2 final size:2
Alignment explanation
Indices: 301589--301636 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
301579 TATACAAATA
301589 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
301631 TC TC TC
1 TC TC TC
301637 GTTAAGACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:303874 original size:2 final size:2
Alignment explanation
Indices: 303869--303900 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
303859 TAATACATTC
303869 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
303901 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:305162 original size:15 final size:15
Alignment explanation
Indices: 305138--305171 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
305128 AAACAAGTAT
*
305138 TTATACGAATATTTA
1 TTATACGAATATATA
*
305153 TTATATGAATATATA
1 TTATACGAATATATA
305168 TTAT
1 TTAT
305172 CTGCATTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATACGAATATATA
Found at i:305371 original size:2 final size:2
Alignment explanation
Indices: 305364--305390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
305354 CATGGAAGTC
305364 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
305391 CAGACAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:305395 original size:4 final size:4
Alignment explanation
Indices: 305388--305418 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
305378 AGAGAGAGAG
305388 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
305419 GTTATTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:305809 original size:2 final size:2
Alignment explanation
Indices: 305797--305848 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
305787 CCATGCGCAT
*
305797 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
305839 GA GA GA GA GA
1 GA GA GA GA GA
305849 TTATTACAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:310399 original size:2 final size:2
Alignment explanation
Indices: 310392--310452 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
310382 TATTACTCAT
310392 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
310434 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
310453 GCTTTACCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:313302 original size:21 final size:21
Alignment explanation
Indices: 313276--313323 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
313266 TTGTTTCTGT
313276 TGTTGTCGTCATTCGTT-TTTC
1 TGTTGTCGTCATT-GTTATTTC
* *
313297 TGTTGTCTTGATTGTTATTTC
1 TGTTGTCGTCATTGTTATTTC
313318 TGTTGT
1 TGTTGT
313324 TGATGTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.60
Consensus pattern (21 bp):
TGTTGTCGTCATTGTTATTTC
Found at i:313345 original size:15 final size:15
Alignment explanation
Indices: 313327--313385 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
313317 CTGTTGTTGA
313327 TGTTGTCGTTGGTTT
1 TGTTGTCGTTGGTTT
*
313342 TGTTGTTATC-TTTGTTGT
1 TGTTG---TCGTTGGTT-T
313360 TGTTGTCGTTGGTTT
1 TGTTGTCGTTGGTTT
*
313375 TGTTGTAGTTG
1 TGTTGTCGTTG
313386 TATCAGGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 18 0.50
16 5 0.14
17 5 0.14
18 8 0.22
ACGTcount: A:0.03, C:0.05, G:0.31, T:0.61
Consensus pattern (15 bp):
TGTTGTCGTTGGTTT
Found at i:316587 original size:2 final size:2
Alignment explanation
Indices: 316580--316633 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
316570 ATTCTAGATT
316580 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
316622 TC TC TC TC TC TC
1 TC TC TC TC TC TC
316634 ATGTAATTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:323788 original size:2 final size:2
Alignment explanation
Indices: 323769--323826 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
323759 ACTCTTCAAA
* *
323769 CT CT CA CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
323811 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
323827 GTCGTCTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:345442 original size:18 final size:18
Alignment explanation
Indices: 345419--345453 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
345409 GGCTACTGTT
345419 TCTTAA-ATAATAATTATA
1 TCTTAATATAAT-ATTATA
345437 TCTTAATATAATATTAT
1 TCTTAATATAATATTAT
345454 GAGTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTTAATATAATATTATA
Found at i:348520 original size:21 final size:20
Alignment explanation
Indices: 348494--348562 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
348484 TTATCTCTGA
*
348494 TGTTGTCGTCGTTGGTTTTGT
1 TGTTGTTGTCGTT-GTTTTGT
** * *
348515 TGTTGTTGTTATCTCTGTTGT
1 TGTTGTTGTCGT-TGTTTTGT
348536 TGTTGTTGTCGTTCGTTTTGT
1 TGTTGTTGTCGTT-GTTTTGT
348557 TGTTGT
1 TGTTGT
348563 ATCAGGGATG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.01, C:0.09, G:0.29, T:0.61
Consensus pattern (20 bp):
TGTTGTTGTCGTTGTTTTGT
Found at i:348524 original size:39 final size:40
Alignment explanation
Indices: 348481--348562 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 40
348471 GTTTTCTTGA
*
348481 TTGTTATCTC-TGATGTTGTCGTCGTTGGTTTTGTTGTTG
1 TTGTTATCTCTTGATGTTGTCGTCGTTCGTTTTGTTGTTG
* *
348520 TTGTTATCTCTGTTGTTGTTGTTGTCGTTCGTTTTGTTGTTG
1 TTGTTATCTC--TTGATGTTGTCGTCGTTCGTTTTGTTGTTG
348562 T
1 T
348563 ATCAGGGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 10 0.27
42 27 0.73
ACGTcount: A:0.04, C:0.10, G:0.27, T:0.60
Consensus pattern (40 bp):
TTGTTATCTCTTGATGTTGTCGTCGTTCGTTTTGTTGTTG
Found at i:348556 original size:18 final size:18
Alignment explanation
Indices: 348494--348562 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
348484 TTATCTCTGA
* *
348494 TGTTGTCGTCGTTGGTTT
1 TGTTGTTGTCGTTCGTTT
*
348512 TGTTGTTGTTGTTATCTCTGTTGT
1 TGTTGTTGTCG---T-TC-GTT-T
348536 TGTTGTTGTCGTTCGTTT
1 TGTTGTTGTCGTTCGTTT
348554 TGTTGTTGT
1 TGTTGTTGT
348563 ATCAGGGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 19 0.46
19 3 0.07
20 2 0.05
21 2 0.05
22 1 0.02
23 3 0.07
24 11 0.27
ACGTcount: A:0.01, C:0.09, G:0.29, T:0.61
Consensus pattern (18 bp):
TGTTGTTGTCGTTCGTTT
Found at i:352974 original size:55 final size:56
Alignment explanation
Indices: 352859--353016 Score: 167
Period size: 55 Copynumber: 2.7 Consensus size: 56
352849 TATCATCTAG
* * *
352859 TATAAAATAAATCTATAGTTATTCAGATATATCATATAGGAGGTATTTATTTGGTTCTGTA
1 TATAAAATAAAT-TATAGTTATTCAGATATATC-T-T-GTAGGTATGTA-TTGGTGCTGTA
352920 TATAAAATTAAATTATAGTTATTCAGATATATCTTGTAGGT-TGTA-TGGTGCTGTA
1 TATAAAA-TAAATTATAGTTATTCAGATATATCTTGTAGGTATGTATTGGTGCTGTA
* * * * *
352975 TATAACACTATATTATTGTAATTCAAATATATCTTGTAGGTA
1 TATAA-AATAAATTATAGTTATTCAGATATATCTTGTAGGTA
353017 GTTACATGTA
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
55 43 0.50
56 1 0.01
57 3 0.03
58 5 0.06
59 1 0.01
60 1 0.01
61 27 0.31
62 5 0.06
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (56 bp):
TATAAAATAAATTATAGTTATTCAGATATATCTTGTAGGTATGTATTGGTGCTGTA
Found at i:355301 original size:2 final size:2
Alignment explanation
Indices: 355296--355345 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
355286 ATAACCCCCC
355296 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
355338 CT CT CT CT
1 CT CT CT CT
355346 GTTTTTCTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.