Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 51
Found at i:2696579 original size:22 final size:21
Alignment explanation
Indices: 2696554--2696616 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
2696544 TTGAAAAAAA
*
2696554 TATTTGGGATTTATGTTTTTAT
1 TATTTGGGATTTAT-TTTTTAG
*
2696576 TATTTAGGG-TTTATCTTTCTAG
1 TATTT-GGGATTTAT-TTTTTAG
*
2696598 TATTTAGGATTTATTTTTT
1 TATTTGGGATTTATTTTTT
2696617 GGATATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.18
22 25 0.74
23 3 0.09
ACGTcount: A:0.19, C:0.03, G:0.16, T:0.62
Consensus pattern (21 bp):
TATTTGGGATTTATTTTTTAG
Found at i:2696623 original size:22 final size:22
Alignment explanation
Indices: 2696553--2696624 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
2696543 TTTGAAAAAA
* *
2696553 ATATTTGGGATTTATGTTTTT-
1 ATATTTAGGATTTATCTTTTTG
* *
2696574 ATTATTTAGGGTTTATCTTTCT-
1 A-TATTTAGGATTTATCTTTTTG
2696596 AGTATTTAGGATTTAT-TTTTTGG
1 A-TATTTAGGATTTATCTTTTT-G
2696619 ATATTT
1 ATATTT
2696625 TATTTCAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
21 5 0.12
22 35 0.85
23 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.17, T:0.60
Consensus pattern (22 bp):
ATATTTAGGATTTATCTTTTTG
Found at i:2698431 original size:2 final size:2
Alignment explanation
Indices: 2698374--2698413 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2698364 ATTAATCTTG
2698374 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
2698414 ATTAAAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2698702 original size:7 final size:7
Alignment explanation
Indices: 2698690--2698714 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2698680 ACCAAAATAT
2698690 TTTAGGG
1 TTTAGGG
2698697 TTTAGGG
1 TTTAGGG
2698704 TTTAGGG
1 TTTAGGG
2698711 TTTA
1 TTTA
2698715 CAAAATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:2698769 original size:27 final size:27
Alignment explanation
Indices: 2698696--2698775 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
2698686 ATATTTTAGG
* *
2698696 GTTTAGGGTTTAGGGTTTACAAAATCAATA
1 GTTTAGGGTTTAGGGTTT--AAGAT-TATA
* *
2698726 G-TTAAGGTTTAGGGTTTATGATTATA
1 GTTTAGGGTTTAGGGTTTAAGATTATA
*
2698752 GTTTAGGGTTTAGGGTTTAGGATT
1 GTTTAGGGTTTAGGGTTTAAGATT
2698776 TTCATCAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 23 0.53
29 15 0.35
30 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (27 bp):
GTTTAGGGTTTAGGGTTTAAGATTATA
Found at i:2699064 original size:7 final size:7
Alignment explanation
Indices: 2699052--2699111 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
2699042 TGATGAAAAT
2699052 CCTAAAC
1 CCTAAAC
2699059 CCTAAAC
1 CCTAAAC
*
2699066 ACTAAAC
1 CCTAAAC
*
2699073 TCTAAAC
1 CCTAAAC
2699080 CCTAAA-
1 CCTAAAC
* *
2699086 -TTATAAT
1 CCTA-AAC
2699093 CCTAAAC
1 CCTAAAC
2699100 CCTAAAC
1 CCTAAAC
*
2699107 TCTAA
1 CCTAA
2699112 TAATTGATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
5 2 0.05
6 2 0.05
7 37 0.86
8 2 0.05
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTAAAC
Found at i:2699318 original size:21 final size:20
Alignment explanation
Indices: 2699284--2699324 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2699274 TGGAGGGAGA
2699284 ATGATTAGGGTTTAGGGTTT
1 ATGATTAGGGTTTAGGGTTT
*
2699304 ATGATTTATGGTTTAGGGTTT
1 ATGA-TTAGGGTTTAGGGTTT
2699325 TCATTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.49
Consensus pattern (20 bp):
ATGATTAGGGTTTAGGGTTT
Found at i:2699363 original size:14 final size:14
Alignment explanation
Indices: 2699344--2699372 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2699334 ACTAAAATAT
2699344 TTTAGGATTTAGGG
1 TTTAGGATTTAGGG
2699358 TTTAGGATTTAGGG
1 TTTAGGATTTAGGG
2699372 T
1 T
2699373 CATAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:2701675 original size:14 final size:14
Alignment explanation
Indices: 2701658--2701684 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2701648 AGGATTTATC
2701658 TTTTAAATATTTTA
1 TTTTAAATATTTTA
2701672 TTTTAAATATTTT
1 TTTTAAATATTTT
2701685 TAGAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAAATATTTTA
Found at i:2703733 original size:12 final size:12
Alignment explanation
Indices: 2703716--2703740 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2703706 TATAGAGCTT
2703716 TCTTGTGAGTTG
1 TCTTGTGAGTTG
2703728 TCTTGTGAGTTG
1 TCTTGTGAGTTG
2703740 T
1 T
2703741 GAGTGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TCTTGTGAGTTG
Found at i:2707560 original size:12 final size:12
Alignment explanation
Indices: 2707543--2707567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2707533 TAGAGAGCTT
2707543 TCTTGTGAGTTG
1 TCTTGTGAGTTG
2707555 TCTTGTGAGTTG
1 TCTTGTGAGTTG
2707567 T
1 T
2707568 GAGTATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TCTTGTGAGTTG
Found at i:2708693 original size:21 final size:21
Alignment explanation
Indices: 2708655--2708719 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
2708645 TGTTTATTTT
*
2708655 AACTTAAAATATTAAATTTTAA
1 AACTTAAAAT-CTAAATTTTAA
*
2708677 AACTTAAAATCTAAATTCTAA
1 AACTTAAAATCTAAATTTTAA
*
2708698 AACTTTAAATCTAAATTTTAA
1 AACTTAAAATCTAAATTTTAA
2708719 A
1 A
2708720 CTCTAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 29 0.74
22 10 0.26
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.38
Consensus pattern (21 bp):
AACTTAAAATCTAAATTTTAA
Found at i:2708698 original size:14 final size:13
Alignment explanation
Indices: 2708667--2708733 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 13
2708657 CTTAAAATAT
* *
2708667 TAAATTTTAAAAC
1 TAAAATTTAAATC
*
2708680 TTAAAATCTAAATTC
1 -TAAAATTTAAA-TC
2708695 TAAAACTTTAAATC
1 TAAAA-TTTAAATC
*
2708709 TAAATTTTAAACTC
1 TAAAATTTAAA-TC
2708723 T-AAATTTAAAT
1 TAAAATTTAAAT
2708734 AAAGGCCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 1 0.02
13 14 0.32
14 23 0.52
15 6 0.14
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATTTAAATC
Found at i:2708934 original size:21 final size:21
Alignment explanation
Indices: 2708910--2708952 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2708900 TATTTTCGTC
*
2708910 TTAAATCCTAAAATTTAAAAT
1 TTAAAACCTAAAATTTAAAAT
*
2708931 TTAAAACCTAAAATTTTAAAT
1 TTAAAACCTAAAATTTAAAAT
2708952 T
1 T
2708953 CTAACATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAACCTAAAATTTAAAAT
Found at i:2709508 original size:19 final size:19
Alignment explanation
Indices: 2709481--2709522 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2709471 TGAGGGAAAA
* *
2709481 AAATCTGTGGAAAAAAATT
1 AAATATGTGGAAAAAAATC
*
2709500 AAATATGTGGGAAAAAATC
1 AAATATGTGGAAAAAAATC
2709519 AAAT
1 AAAT
2709523 GTGACTGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (19 bp):
AAATATGTGGAAAAAAATC
Found at i:2718986 original size:50 final size:50
Alignment explanation
Indices: 2718910--2719009 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
2718900 TCTTAGTTTG
2718910 CAGAAACAACAACAACTTGCTCCACAGCTTGCTCCTGAAACTCAGAAACT
1 CAGAAACAACAACAACTTGCTCCACAGCTTGCTCCTGAAACTCAGAAACT
* *
2718960 CAGAAACAACAACAACTTGCTTCACAGCTTGCTCCTGAAACTCAGCAACT
1 CAGAAACAACAACAACTTGCTCCACAGCTTGCTCCTGAAACTCAGAAACT
2719010 ATGTGCTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.19
Consensus pattern (50 bp):
CAGAAACAACAACAACTTGCTCCACAGCTTGCTCCTGAAACTCAGAAACT
Found at i:2726509 original size:3 final size:3
Alignment explanation
Indices: 2726501--2726571 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
2726491 CTATCTATCT
2726501 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2726549 ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
2726572 TAGTGTTTAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2730069 original size:51 final size:51
Alignment explanation
Indices: 2729845--2730468 Score: 655
Period size: 51 Copynumber: 11.8 Consensus size: 51
2729835 ACGAGTCTGT
* *
2729845 TCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAA-TGTGTCTGC
1 TCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACT-TGTCCGC
* * * * **
2729900 TCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACAGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAA-CAAACTTGTCCGC
* * * * * ** *
2729956 TCTCTACTCATTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACAGGCCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGC
* * * * *
2730011 TCTCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* **
2730062 TCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACGGGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGC
* * * *
2730117 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACTTGTCCGC
*
2730172 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* * *
2730223 TCCCTATTCATTCAGAGAGTATAGGACTAAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
*
2730274 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
* *
2730325 TCCCTATTCTTTCAGAGAGTATAGGACTTAATCTTCAACAAACTTGT-CGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
*
2730375 TCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
*
2730426 TCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
2730469 GAATTTGCTT
Statistics
Matches: 511, Mismatches: 42, Indels: 36
0.87 0.07 0.06
Matches are distributed among these distances:
50 49 0.10
51 251 0.49
52 1 0.00
54 2 0.00
55 164 0.32
56 44 0.09
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (51 bp):
TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGC
Found at i:2730289 original size:102 final size:102
Alignment explanation
Indices: 2729845--2730468 Score: 664
Period size: 106 Copynumber: 5.9 Consensus size: 102
2729835 ACGAGTCTGT
* * *
2729845 TCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAA-TGTGTCTGCTCTCTAT
1 TCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACT-TGTCCGCTCCCTAT
* * * **
2729907 TCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACAGGTCCGC
59 TCTTTCAGAGAGTATAGGAC-T--A-AATCTTCAA-CAAACTTGTCCGC
* * * * * ** * *
2729956 TCTCTACTCATTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACAGGCCCGCTCTCTATTCT
1 TCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGCTCCCTATTCT
* * * *
2730021 TTCAGAGAGTATAGGACTCAATCTTTAACAAACGTGTTCGC
62 TTCAGAGAGTATAGGACTAAATCTTCAACAAACTTGTCCGC
* ** *
2730062 TCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACGGGTCCGCTCTCTATTC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGCTCCCTATTC
* * * *
2730126 CTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCTGC
61 TTTCAGAGAGTATAGGACT---A-AATCTTCAACAAACTTGTCCGC
* *
2730172 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCA
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCA
*
2730237 GAGAGTATAGGACTAAATCTTCAACGAACTTGTCCGC
66 GAGAGTATAGGACTAAATCTTCAACAAACTTGTCCGC
*
2730274 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCTTTCA
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCA
*
2730339 GAGAGTATAGGACTTAATCTTCAACAAACTTGT-CGC
66 GAGAGTATAGGACTAAATCTTCAACAAACTTGTCCGC
*
2730375 TCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCA
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCA
*
2730440 GAGAGTATAGGACTCAATCTTCAACAAAC
66 GAGAGTATAGGACTAAATCTTCAACAAAC
2730469 GAATTTGCTT
Statistics
Matches: 452, Mismatches: 44, Indels: 44
0.84 0.08 0.08
Matches are distributed among these distances:
101 94 0.21
102 116 0.26
103 1 0.00
105 1 0.00
106 121 0.27
107 10 0.02
110 47 0.10
111 61 0.13
112 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCA
GAGAGTATAGGACTAAATCTTCAACAAACTTGTCCGC
Found at i:2731811 original size:16 final size:16
Alignment explanation
Indices: 2731792--2731889 Score: 78
Period size: 16 Copynumber: 5.9 Consensus size: 16
2731782 TTATTTCTTT
2731792 TTTTTTTCATTTTTCA
1 TTTTTTTCATTTTTCA
*
2731808 TTTTTTTCATTTTTTA
1 TTTTTTTCATTTTTCA
* *
2731824 TTTTTTCTTCCCTTTTCCA
1 -TTTTT-TT-CATTTTTCA
2731843 -TTTTTTC-TTTTT-A
1 TTTTTTTCATTTTTCA
2731856 TTTTTTCCATCATTTTTC-
1 TTTTTT---TCATTTTTCA
2731874 TTTTTTCTCATTTTTC
1 TTTTTT-TCATTTTTC
2731890 TCATTTTTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
15 1 0.01
16 26 0.39
17 11 0.16
18 13 0.19
19 6 0.09
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTCATTTTTCA
Found at i:2731847 original size:50 final size:50
Alignment explanation
Indices: 2731793--2731909 Score: 134
Period size: 50 Copynumber: 2.3 Consensus size: 50
2731783 TATTTCTTTT
* *
2731793 TTTTTTCATTTTTCATTTTTTTCAT-TTTTTATTTTTTCTTCCCTTTTC-CA
1 TTTTTTCATTTTT-ATTTTTTCCATATTTTTATTTTTTC-TCACTTTTCTCA
* *
2731843 TTTTTTC-TTTTTATTTTTTCCATCATTTTTCTTTTTTCTCATTTTTCTCA
1 TTTTTTCATTTTTATTTTTTCCAT-ATTTTTATTTTTTCTCACTTTTCTCA
2731893 TTTTTTC-TATTTTATTT
1 TTTTTTCAT-TTTTATTT
2731910 CTTCTTCAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
48 10 0.17
49 12 0.20
50 29 0.49
51 8 0.14
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (50 bp):
TTTTTTCATTTTTATTTTTTCCATATTTTTATTTTTTCTCACTTTTCTCA
Found at i:2731869 original size:25 final size:24
Alignment explanation
Indices: 2731841--2731909 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
2731831 TTCCCTTTTC
2731841 CATTTTTTCTTTTTATTTTTTCCAT
1 CATTTTTTCTTTTTATTTTTTCC-T
*
2731866 CA-TTTTTCTTTTT-TCTCATTTTTCT
1 CATTTTTTCTTTTTAT-T--TTTTCCT
2731891 CATTTTTTCTATTTTATTT
1 CATTTTTTCT-TTTTATTT
2731910 CTTCTTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
23 1 0.03
24 12 0.32
25 6 0.16
26 12 0.32
27 5 0.14
28 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (24 bp):
CATTTTTTCTTTTTATTTTTTCCT
Found at i:2731890 original size:16 final size:16
Alignment explanation
Indices: 2731791--2731890 Score: 71
Period size: 18 Copynumber: 6.1 Consensus size: 16
2731781 TTTATTTCTT
*
2731791 TTTTTTTTCATTTTTC
1 TTTTTTCTCATTTTTC
*
2731807 ATTTTTT-TCATTTTTTA
1 -TTTTTTCTCA-TTTTTC
* *
2731824 TTTTTTCTTCCCTTTTCC
1 TTTTTTC-T-CATTTTTC
* *
2731842 ATTTTT-TC-TTTTTA
1 TTTTTTCTCATTTTTC
2731856 TTTTTTCCATCATTTTTC
1 TTTTTT-C-TCATTTTTC
2731874 TTTTTTCTCATTTTTC
1 TTTTTTCTCATTTTTC
2731890 T
1 T
2731891 CATTTTTTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 20 0.30
17 14 0.21
18 21 0.32
19 1 0.02
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCTCATTTTTC
Found at i:2731904 original size:9 final size:10
Alignment explanation
Indices: 2731874--2731905 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
2731864 ATCATTTTTC
2731874 TTTTTTCTCA
1 TTTTTTCTCA
2731884 -TTTTTCTCA
1 TTTTTTCTCA
2731893 TTTTTTCT-A
1 TTTTTTCTCA
2731902 TTTT
1 TTTT
2731906 ATTTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:2745167 original size:13 final size:13
Alignment explanation
Indices: 2745149--2745173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2745139 GAATAGAATA
2745149 TTCGGTAAATCAT
1 TTCGGTAAATCAT
2745162 TTCGGTAAATCA
1 TTCGGTAAATCA
2745174 GATTGAATAG
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):
TTCGGTAAATCAT
Found at i:2747749 original size:20 final size:21
Alignment explanation
Indices: 2747709--2747760 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
2747699 TTATTTTGAG
2747709 TATATGTATTT-AATATACATA
1 TATATGT-TTTAAATATACATA
2747730 TATATGTTTTAAATAT-CATA
1 TATATGTTTTAAATATACATA
2747750 TGATA-GTTTTA
1 T-ATATGTTTTA
2747761 TTGAGATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (21 bp):
TATATGTTTTAAATATACATA
Found at i:2756302 original size:101 final size:101
Alignment explanation
Indices: 2756127--2756317 Score: 355
Period size: 101 Copynumber: 1.9 Consensus size: 101
2756117 ACTTCAACTC
*
2756127 TTTTTTAAGCATACTTTAAGGGGAGTCATCTGATCACACTACCATCCCACACTCTAAGTGAAAGG
1 TTTTTTAAGCATACTTTAAGGGGAGTCATCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
2756192 GAGCATACCTTCCACCCCCGAGCTAGTTAAGTAGAG
66 GAGCATACCTTCCACCCCCGAGCTAGTTAAGTAGAG
*
2756228 TTTTTTAAGCATACTTTAAGGGGAGTCATCTCATCACACTGCCATCCCACACTCTAAGTGAAAGG
1 TTTTTTAAGCATACTTTAAGGGGAGTCATCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
*
2756293 GAGTATACCTTCCACCCCCGAGCTA
66 GAGCATACCTTCCACCCCCGAGCTA
2756318 ATCAGGTAGA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (101 bp):
TTTTTTAAGCATACTTTAAGGGGAGTCATCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
GAGCATACCTTCCACCCCCGAGCTAGTTAAGTAGAG
Found at i:2759097 original size:32 final size:32
Alignment explanation
Indices: 2759056--2759148 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
2759046 AGTCGAGGGT
*
2759056 TTACCTATGTTCTACGAAACATATGGATAGAA
1 TTACCTATGTTCTACGAGACATATGGATAGAA
** * * *
2759088 TTACCTATG-TCTTTTGGGACATATGGACAGTA
1 TTACCTATGTTC-TACGAGACATATGGATAGAA
2759120 -TACCTATGTTCTAC-AGGACATATGGATAG
1 TTACCTATGTTCTACGA-GACATATGGATAG
2759149 TTTATCTAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
31 23 0.48
32 25 0.52
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTCTACGAGACATATGGATAGAA
Found at i:2759139 original size:31 final size:31
Alignment explanation
Indices: 2759104--2759180 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2759094 ATGTCTTTTG
*
2759104 GGACATATGGACAGTATACCTATGTTCTACA
1 GGACATATGGACAGTATACCTAGGTTCTACA
* * * * *
2759135 GGACATATGGATAGTTTATCTAGGTTCTTCG
1 GGACATATGGACAGTATACCTAGGTTCTACA
*
2759166 GGACCTATGGACAGT
1 GGACATATGGACAGT
2759181 TGCTGAGGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (31 bp):
GGACATATGGACAGTATACCTAGGTTCTACA
Found at i:2759939 original size:21 final size:21
Alignment explanation
Indices: 2759913--2759954 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2759903 TGTAGCAGTA
2759913 TTGTAGCAGGGTATCGATTCC
1 TTGTAGCAGGGTATCGATTCC
*
2759934 TTGTAGCAGGGTATCGGTTCC
1 TTGTAGCAGGGTATCGATTCC
2759955 CCTATGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGTAGCAGGGTATCGATTCC
Found at i:2770733 original size:3 final size:3
Alignment explanation
Indices: 2770725--2770759 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2770715 GAGCAGGGAA
2770725 ATT ATT ATT ATT ATT ATT ATT A-T ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2770760 ATAATAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2775265 original size:55 final size:55
Alignment explanation
Indices: 2775199--2775311 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 55
2775189 GCATTTATAT
*
2775199 GATTCATGAAGAAGAACATTCGACGAATGAAGAAATTTG-AACTTGAATGAAGAAC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAAC-TGAATGAAGAAC
* * * *
2775254 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGAATGAAGAAC
2775309 GAT
1 GAT
2775312 CCACAAAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
55 49 0.94
56 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGAATGAAGAAC
Found at i:2775321 original size:55 final size:55
Alignment explanation
Indices: 2775207--2775329 Score: 149
Period size: 55 Copynumber: 2.2 Consensus size: 55
2775197 ATGATTCATG
* * * **
2775207 AAGAAGAACATTCGACGAATGAAGAAATTTGAACTTGAATGAAGAACGATTCATG
1 AAGAAGGACATCCGACGAATGAAGAAATTTGAACTTGAATGAAGAACGATCCACA
* * *
2775262 AAGAAGGACATCCGATGAATGAAGAAATTTGAAAC-TGATTGAAGACCGATCCACA
1 AAGAAGGACATCCGACGAATGAAGAAATTTG-AACTTGAATGAAGAACGATCCACA
*
2775317 AAGAAAGACATCC
1 AAGAAGGACATCC
2775330 TGAAGATGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 55 0.95
56 3 0.05
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (55 bp):
AAGAAGGACATCCGACGAATGAAGAAATTTGAACTTGAATGAAGAACGATCCACA
Found at i:2776108 original size:72 final size:72
Alignment explanation
Indices: 2775991--2776141 Score: 230
Period size: 72 Copynumber: 2.1 Consensus size: 72
2775981 CCCTATTACA
* * * *
2775991 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTAATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATAATGATAGC
2776056 AAATGAT
66 AAATGAT
* *
2776063 CAAGAACAGATGAAGACTTCGAGTGAGAATCTTAATGTTAGTGGTGCAGCCAATATGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATAATGATAGC
*
2776128 AACTGAT
66 AAATGAT
*
2776135 TAAGAAC
1 CAAGAAC
2776142 CTGTTAGGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATAATGATAGC
AAATGAT
Found at i:2780744 original size:37 final size:37
Alignment explanation
Indices: 2780694--2780807 Score: 140
Period size: 37 Copynumber: 3.1 Consensus size: 37
2780684 AAAGCCAAGT
* *
2780694 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * *
2780731 CTTCACCAAAGAGTAGTGAATCCAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * * *
2780767 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAGGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
2780804 CTTC
1 CTTC
2780808 TCGGAAGAGT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 30 0.47
37 34 0.53
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
Found at i:2780779 original size:36 final size:37
Alignment explanation
Indices: 2780694--2780794 Score: 132
Period size: 36 Copynumber: 2.8 Consensus size: 37
2780684 AAAGCCAAGT
* * *
2780694 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATCTTAAGC
* *
2780731 CTTCACCAAAGAGTAGTGAATCCAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATCTTAAGC
* *
2780767 CTTCACCGAAGAGTAGTGAAGCATATCC
1 CTTCACCAAAGAGTAGTGAAGCAAATCC
2780795 TTTTTAGGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 30 0.56
37 24 0.44
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATCTTAAGC
Found at i:2781256 original size:54 final size:54
Alignment explanation
Indices: 2781194--2781762 Score: 534
Period size: 54 Copynumber: 10.6 Consensus size: 54
2781184 GTAGTAAAGC
*
2781194 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2781248 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCCTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
2781302 AGAAGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
2781356 AGAAGAATATGTTTGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAA-CCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2781409 AGAAGAAGATGCTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
2781463 AGAAGAATATGTTCGAGTTACATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * * * * *
2781517 AG-AGAATATGTTCGAG-TCTTATACTCTCT-GAAGGAATAGGGAG-TAGACACG-A
1 AGAAGAAGATGTTCGAGTTC-CATACTCCCTAG-AGAAAGAGGGAGCGA-ACCCGTA
* ** * * ** *
2781569 TTGTTGAAGATTGTTCGAG-TCTCATACTCTCT-GAAGAAATAGGGAGC-AGACACATTT
1 -AGAAGAAGA-TGTTCGAGTTC-CATACTCCCTAG-AGAAAGAGGGAGCGA-AC-CCGTA
** * * ** * *
2781626 TCAA-AAGATTTTCAAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * * * *
2781679 TGTAGAATATTTTCAAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTA
* *
2781733 GGCAA-AAGATTGTTCGAGTTTC-TACTCCCT
1 AG-AAGAAGA-TGTTCGAGTTCCATACTCCCT
2781763 GAAGGAATAG
Statistics
Matches: 434, Mismatches: 64, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
52 3 0.01
53 90 0.21
54 288 0.66
55 52 0.12
56 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:2781467 original size:161 final size:162
Alignment explanation
Indices: 2781194--2781533 Score: 542
Period size: 161 Copynumber: 2.1 Consensus size: 162
2781184 GTAGTAAAGC
* * *
2781194 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTAAGAAGAAGATG
1 AGAAGAATATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATG
*
2781259 TTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCCTAAGAAGAAGATATTCGAGTT-CT
66 CTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCCTAAGAAGAAGATATTCGAGTTAC-
* *
2781323 ATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
130 ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
*
2781356 AGAAGAATATGTTTGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAA-CCGTAAGAAGAAGATG
1 AGAAGAATATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATG
* * * * *
2781420 CTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAATATGTTCGAGTTACA
66 CTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCCTAAGAAGAAGATATTCGAGTTACA
2781485 TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
131 TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
2781517 AG-AGAATATGTTCGAGT
1 AGAAGAATATGTTCGAGT
2781534 CTTATACTCT
Statistics
Matches: 164, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
160 14 0.09
161 105 0.64
162 45 0.27
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (162 bp):
AGAAGAATATGTTCGAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATG
CTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCCTAAGAAGAAGATATTCGAGTTACA
TACTCCCTAAAGAAAGAGGGAGCGAACCCGTA
Found at i:2781972 original size:3 final size:3
Alignment explanation
Indices: 2781964--2782007 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
2781954 TGTCTGGGAA
2781964 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2782008 ATTAATAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2791546 original size:6 final size:6
Alignment explanation
Indices: 2791535--2791576 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
2791525 TATATTGCTC
2791535 CTCCAT CTCCAT CTCCAT CTCC-T CTCCAT CTCCAT C-CCAT CT
1 CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CT
2791577 GTGCTATCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.14, C:0.52, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCAT
Found at i:2791562 original size:11 final size:12
Alignment explanation
Indices: 2791535--2791576 Score: 70
Period size: 11 Copynumber: 3.7 Consensus size: 12
2791525 TATATTGCTC
2791535 CTCCATCTCCAT
1 CTCCATCTCCAT
2791547 CTCCATCTCC-T
1 CTCCATCTCCAT
2791558 CTCCATCTCCAT
1 CTCCATCTCCAT
2791570 C-CCATCT
1 CTCCATCT
2791577 GTGCTATCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.14, C:0.52, G:0.00, T:0.33
Consensus pattern (12 bp):
CTCCATCTCCAT
Found at i:2791562 original size:17 final size:18
Alignment explanation
Indices: 2791535--2791576 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
2791525 TATATTGCTC
2791535 CTCCATCTCCATCTCCAT
1 CTCCATCTCCATCTCCAT
2791553 CTCC-TCTCCATCTCCAT
1 CTCCATCTCCATCTCCAT
2791570 C-CCATCT
1 CTCCATCT
2791577 GTGCTATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.14, C:0.52, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCCATCTCCATCTCCAT
Found at i:2798441 original size:14 final size:15
Alignment explanation
Indices: 2798422--2798483 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 15
2798412 GAACTCAAAT
*
2798422 ATTAATATTTA-ATA
1 ATTAATAATTATATA
2798436 ATTAATAATTATATA
1 ATTAATAATTATATA
*
2798451 A-TAA-AATAATATA
1 ATTAATAATTATATA
2798464 A-TAATAA-TATA-A
1 ATTAATAATTATATA
*
2798476 ATAAATAA
1 ATTAATAA
2798484 ACGACTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 2 0.05
13 20 0.49
14 15 0.37
15 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAATAATTATATA
Found at i:2798454 original size:11 final size:11
Alignment explanation
Indices: 2798431--2798475 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
2798421 TATTAATATT
2798431 TAATAAT-TAA
1 TAATAATATAA
*
2798441 TAATTATATAA
1 TAATAATATAA
2798452 TAAAATAATATAA
1 T--AATAATATAA
2798465 TAATAATATAA
1 TAATAATATAA
2798476 ATAAATAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.20
11 14 0.47
13 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAATATAA
Found at i:2798483 original size:16 final size:16
Alignment explanation
Indices: 2798439--2798479 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2798429 TTTAATAATT
2798439 AATAAT-TATATAATAA
1 AATAATATA-ATAATAA
2798455 AATAATATAATAATAA
1 AATAATATAATAATAA
*
2798471 TATAA-ATAA
1 AATAATATAA
2798480 ATAAACGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 17 0.74
17 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATATAATAATAA
Found at i:2798483 original size:24 final size:23
Alignment explanation
Indices: 2798432--2798480 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
2798422 ATTAATATTT
*
2798432 AATAATTAATAATTATATAATAA
1 AATAATTAATAATAATATAATAA
2798455 AATAATATAATAATAATATAAATAA
1 AATAAT-TAATAATAATAT-AATAA
2798480 A
1 A
2798481 TAAACGACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAATTAATAATAATATAATAA
Found at i:2807023 original size:20 final size:21
Alignment explanation
Indices: 2806977--2807031 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2806967 AACTCTAACT
* *
2806977 TTAAAATCAAATAATTGAAAA
1 TTAAAAGCAAATAATCGAAAA
*
2806998 TTAAAAGCAAATAATCG-AAG
1 TTAAAAGCAAATAATCGAAAA
*
2807018 TTAAAAGTAAATAA
1 TTAAAAGCAAATAA
2807032 GTAAAAGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.25
Consensus pattern (21 bp):
TTAAAAGCAAATAATCGAAAA
Found at i:2807038 original size:14 final size:14
Alignment explanation
Indices: 2807016--2807058 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
2807006 AAATAATCGA
2807016 AGTTAAAAGTAAAT
1 AGTTAAAAGTAAAT
*
2807030 AAG-TAAAAGCAAAT
1 -AGTTAAAAGTAAAT
2807044 AGTTTAAAAGTAAAT
1 AG-TTAAAAGTAAAT
2807059 GATTGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 12 0.50
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.26
Consensus pattern (14 bp):
AGTTAAAAGTAAAT
Found at i:2807948 original size:16 final size:16
Alignment explanation
Indices: 2807920--2807964 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
2807910 TAAATTACAT
2807920 AATTAAA-AAATA-AA
1 AATTAAATAAATATAA
* *
2807934 AGTT-ATTAAATATAA
1 AATTAAATAAATATAA
2807949 AATTAAATAAATATAA
1 AATTAAATAAATATAA
2807965 TTATATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 1 0.04
14 8 0.33
15 5 0.21
16 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AATTAAATAAATATAA
Found at i:2808040 original size:39 final size:39
Alignment explanation
Indices: 2807995--2808112 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 39
2807985 AGTTAAAAGA
*
2807995 AATAATTTAGATTGTTAGGGTGAAATAGC-TTAAGAAATT
1 AATAATTTAGAATGTTAGGGTGAAATA-CTTTAAGAAATT
2808034 AATAATTTAGAATGTT-GTGGTGAAATACTTTAAGAAATT
1 AATAATTTAGAATGTTAG-GGTGAAATACTTTAAGAAATT
* * * * *
2808073 AAGAATTTAGAATGTTATGTTGAAATAATTTTAG-AATT
1 AATAATTTAGAATGTTAGGGTGAAATACTTTAAGAAATT
2808111 AA
1 AA
2808113 GAATAAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
38 8 0.11
39 62 0.89
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (39 bp):
AATAATTTAGAATGTTAGGGTGAAATACTTTAAGAAATT
Found at i:2814195 original size:10 final size:10
Alignment explanation
Indices: 2814171--2814205 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
2814161 TTTGTAAATA
2814171 ATAATATTA-
1 ATAATATTAT
2814180 ATAATATTAT
1 ATAATATTAT
2814190 ATAATATTAT
1 ATAATATTAT
2814200 ATAATA
1 ATAATA
2814206 ATAATACGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAATATTAT
Found at i:2815638 original size:56 final size:55
Alignment explanation
Indices: 2815576--2815736 Score: 241
Period size: 56 Copynumber: 2.9 Consensus size: 55
2815566 ACATCACAAG
*
2815576 AAAGGATTTATCATAATTCGTTTCATGTCTCCACATCTAATCATATCTCTTTTATA
1 AAAGGATTTATCATAATTC-TTTCATGTCTCCACATCTAATCATATCTCTTTCATA
2815632 AAAGGATTTATCATAATTCCTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
1 AAAGGATTTATCATAATT-CTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
* * * * *
2815688 AAAAGATTTATCCTAATTTCTTTAATGTCTCCATATCTAATCAAATCTC
1 AAAGGATTTATCATAA-TTCTTTCATGTCTCCACATCTAATCATATCTC
2815737 GAACAAGGTT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
56 94 0.97
57 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (55 bp):
AAAGGATTTATCATAATTCTTTCATGTCTCCACATCTAATCATATCTCTTTCATA
Found at i:2823355 original size:3 final size:3
Alignment explanation
Indices: 2823347--2823394 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
2823337 GGGCTTTGTA
* * *
2823347 AAT AAT AAT ACT AAT AAT ATT ATAT AAT ATT ATAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT
2823394 A
1 A
2823395 CGTCACTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 33 0.89
4 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:2823375 original size:10 final size:9
Alignment explanation
Indices: 2823349--2823394 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 9
2823339 GCTTTGTAAA
*
2823349 TAATAATAC
1 TAATAATAT
2823358 TAATAATAT
1 TAATAATAT
2823367 TATATAATAT
1 TA-ATAATAT
*
2823377 TATATAATAA
1 TA-ATAATAT
2823387 TAATAATA
1 TAATAATA
2823395 CGTCACTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 16 0.47
10 18 0.53
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATAATAT
Found at i:2824581 original size:2 final size:2
Alignment explanation
Indices: 2824527--2824566 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2824517 TAGTCACTGT
2824527 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
2824567 GGTTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2825919 original size:45 final size:46
Alignment explanation
Indices: 2825845--2825935 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 46
2825835 GTTTTTTATT
* * * *
2825845 TTATTTTTTAAATAAATGCATGCGAACTAGAAATCATGCGGTTAGG
1 TTATTTTTCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
2825891 TTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTATTTTT-CAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
2825936 ATATGATCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 21 0.52
46 13 0.32
47 6 0.15
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (46 bp):
TTATTTTTCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
Found at i:2829390 original size:24 final size:24
Alignment explanation
Indices: 2829363--2829410 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2829353 TTAAAAAGTA
2829363 AGAGTCATATATGCAATAAAGCTG
1 AGAGTCATATATGCAATAAAGCTG
2829387 AGAGTCATATATGCAATAAAGCTG
1 AGAGTCATATATGCAATAAAGCTG
2829411 CACCTCTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (24 bp):
AGAGTCATATATGCAATAAAGCTG
Found at i:2832623 original size:18 final size:18
Alignment explanation
Indices: 2832600--2832634 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2832590 TTCCAACCCG
*
2832600 ACCCGACCCGATCCGTTT
1 ACCCGACCCGACCCGTTT
2832618 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
2832635 GACCGACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.49, G:0.17, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:2833490 original size:17 final size:19
Alignment explanation
Indices: 2833468--2833508 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
2833458 TTTTACAAAC
2833468 ATATTGATCTG-ATAA-AA
1 ATATTGATCTGCATAAGAA
*
2833485 ATATTGATGTGCATAAGAA
1 ATATTGATCTGCATAAGAA
2833504 ATATT
1 ATATT
2833509 AGTTTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (19 bp):
ATATTGATCTGCATAAGAA
Found at i:2835015 original size:24 final size:24
Alignment explanation
Indices: 2834988--2835102 Score: 142
Period size: 24 Copynumber: 4.8 Consensus size: 24
2834978 TCGATTTGAT
*
2834988 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
2835012 TTCTGATATGATA-TCTAACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
2835036 TTCTGATATGATATTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* * *
2835060 TTCTGATCTAATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
2835084 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
2835103 GTGAATTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:2835329 original size:2 final size:2
Alignment explanation
Indices: 2835316--2835368 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2835306 CGGATGGGGG
*
2835316 TA TA TG 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
2835358 TA TA TA TA TA T
1 TA TA TA TA TA T
2835369 GATTTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2836101 original size:20 final size:20
Alignment explanation
Indices: 2836073--2836141 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
2836063 TTTCCCACAG
* * *
2836073 ATTTATAAAACCTCCGGGTT
1 ATTTGTAAAGCCTCCGGGTA
* *
2836093 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTCCGGGTA
**
2836113 ATTTGTAAAGCCTCCAAGTA
1 ATTTGTAAAGCCTCCGGGTA
2836133 ATTTGTAAA
1 ATTTGTAAA
2836142 TCCTTCAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
ATTTGTAAAGCCTCCGGGTA
Found at i:2836150 original size:20 final size:20
Alignment explanation
Indices: 2836093--2836151 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2836083 CCTCCGGGTT
** *
2836093 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCAAGTA
*
2836113 ATTTGTAAAGCCTCCAAGTA
1 ATTTGTAAAGCCTTCAAGTA
*
2836133 ATTTGTAAATCCTTCAAGT
1 ATTTGTAAAGCCTTCAAGT
2836152 CATCTGTCAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (20 bp):
ATTTGTAAAGCCTTCAAGTA
Found at i:2836285 original size:36 final size:36
Alignment explanation
Indices: 2836245--2836409 Score: 208
Period size: 36 Copynumber: 4.6 Consensus size: 36
2836235 CTTTGAATCT
2836245 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
1 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
*
2836281 AACCTTCACGGAATAGTAGTGGAGTAATGCAAATTC
1 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
* ** *
2836317 AGCCTTCATAGAAGAGTAGTGAAGTAGAT-CAAATTC
1 AACCTTCACGGAAGAGTAGTGGAGTA-ATGCAAATTC
* * * *
2836353 AACCTTAACGGAAGAGTAATAGAGTAATGC-AAGTC
1 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
*
2836388 AAGCCTTCACTGAAGAGTAGTG
1 AA-CCTTCACGGAAGAGTAGTG
2836410 AAGCTGGAGC
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
35 8 0.07
36 98 0.91
37 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (36 bp):
AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
Found at i:2837920 original size:24 final size:24
Alignment explanation
Indices: 2837893--2837971 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
2837883 TTGTTATATA
2837893 TATATATATATATTTAGGTTAAAT
1 TATATATATATATTTAGGTTAAAT
*
2837917 TATATATATATATATAGGTTAAAT
1 TATATATATATATTTAGGTTAAAT
2837941 TATATATATATATTTAGGTTAAAT
1 TATATATATATATTTAGGTTAAAT
2837965 TATATAT
1 TATATAT
2837972 TTAGTTCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (24 bp):
TATATATATATATTTAGGTTAAAT
Found at i:2839025 original size:25 final size:25
Alignment explanation
Indices: 2838989--2839051 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
2838979 AGGTTTTTTT
* *
2838989 TCTCAATTTTTTAACTTAGATTTGC
1 TCTCAATATTTTAACTTAAATTTGC
*
2839014 TCTCAATATTTTAACTTAAATTTTC
1 TCTCAATATTTTAACTTAAATTTGC
*
2839039 TATCAATAATTTT
1 TCTCAAT-ATTTT
2839052 TATTTTTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 28 0.85
26 5 0.15
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.52
Consensus pattern (25 bp):
TCTCAATATTTTAACTTAAATTTGC
Found at i:2840053 original size:65 final size:65
Alignment explanation
Indices: 2839923--2840078 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 65
2839913 CTAAGAGTGA
* * *
2839923 ATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTACATCGATGCATGATTGGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTACATCGATGCATGATTGGTGC
* * * * * *
2839987 ATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATCGGTGCATGGTAT-GTG
1 ATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTACATCGATGCATGAT-TGGTG
2840051 C
65 C
* *
2840052 ATCGATGCATGAAATGCATTCTATGTT
1 ATCGATGCATCAAATGCATTCGATGTT
2840079 CAATTTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 24 0.30
65 54 0.68
66 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
ATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTACATCGATGCATGATTGGTGC
Found at i:2840613 original size:2 final size:2
Alignment explanation
Indices: 2840601--2840645 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2840591 AATTGATTAA
*
2840601 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2840643 AT A
1 AT A
2840646 GCTTAAGCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2848600 original size:18 final size:17
Alignment explanation
Indices: 2848550--2848594 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
2848540 TTGGACCCTT
*
2848550 AGTGCATCG-TGCA-CG
1 AGTGCATCGATGCATCA
2848565 AGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
2848582 AGTGCATTCGATG
1 AGTGCA-TCGATG
2848595 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 4 0.15
17 7 0.27
18 6 0.23
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2849545 original size:178 final size:180
Alignment explanation
Indices: 2849202--2849669 Score: 604
Period size: 178 Copynumber: 2.6 Consensus size: 180
2849192 CGATCCAAAT
*
2849202 TAAAAATGTATCGATC-CATATCAATATAACAGGT--AAATATGATAAAACCGGTCA-CGAAA-A
1 TAAAAATGTATCGATCACA-A-CGATATAACAGGTAAAAATATGATAAAACCGGT-ATCGAAATA
* * * *
2849262 GTCAATACCGGTAAAGCCCTACCGGATATATTGAACGTG-TCGATACTTTAATATAAGGATGACA
63 AT-AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTTCGATACTTTAATATAAGGATGACA
*
2849326 CTTTGTGAATTTAAAAGAGAATCAGTTTTAACGCCTATAAAGTGTCAATACTTTA
127 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTG-CAATACTTTA
* *
2849381 T-AAAATGTATCGATACACAACGATATAACATGTAAAAATATGACAAAACCGGTATCGAAATAAT
1 TAAAAATGTATCGAT-CACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATAAT
* * *
2849445 -AAACCGGTAAAGCGCTACCGGATA-ATTTAAAGTGTTTG-TACTTTAATATAAGTATCGACACT
65 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTTCGATACTTTAATATAAGGAT-GACACT
* *
2849507 TTGTGAATTTAAAAGAGAAGCA-TTTTAGCGCCTATAAAGTGCGATACTTTA
129 TTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGCAATACTTTA
* * *
2849558 TAAAAATGTATCGATCACAACGATATAACAGGTAAAAATATGATAAAA-CGATATCAAAATGATA
1 TAAAAATGTATCGATCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATAATA
** *
2849622 AAACTTGTAAAACGCTACCGGATATATTGAAAGTG-TCGATAC-TTAATA
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTTCGATACTTTAATA
2849670 AGTACGTGTA
Statistics
Matches: 254, Mismatches: 23, Indels: 26
0.84 0.08 0.09
Matches are distributed among these distances:
176 12 0.05
177 70 0.28
178 91 0.36
179 55 0.22
180 24 0.09
181 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (180 bp):
TAAAAATGTATCGATCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATAATA
AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTTCGATACTTTAATATAAGGATGACACTTT
GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGCAATACTTTA
Found at i:2851412 original size:21 final size:20
Alignment explanation
Indices: 2851388--2851434 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
2851378 TGTGTTTTTA
*
2851388 TATAAAATGATATATAGTTAT
1 TATAAAATGATAAAT-GTTAT
* *
2851409 TATAAAATTATAAATTTTAT
1 TATAAAATGATAAATGTTAT
2851429 TATAAA
1 TATAAA
2851435 TGCAGGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAATGATAAATGTTAT
Found at i:2851430 original size:20 final size:20
Alignment explanation
Indices: 2851383--2851434 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2851373 TTTTTTGTGT
*
2851383 TTTTA-TATAAAATGATATA
1 TTTTATTATAAAATGATAAA
* *
2851402 TAGTTATTATAAAATTATAAA
1 T-TTTATTATAAAATGATAAA
2851423 TTTTATTATAAA
1 TTTTATTATAAA
2851435 TGCAGGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 13 0.48
21 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTATTATAAAATGATAAA
Found at i:2851848 original size:19 final size:20
Alignment explanation
Indices: 2851816--2851853 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2851806 TCAAGAGTCG
2851816 AAGAGAAACTTGAGAGAGTA
1 AAGAGAAACTTGAGAGAGTA
2851836 AAGAGAAAC-TGAGAGAGT
1 AAGAGAAACTTGAGAGAGT
2851854 CGAAGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.32, T:0.13
Consensus pattern (20 bp):
AAGAGAAACTTGAGAGAGTA
Found at i:2851859 original size:20 final size:21
Alignment explanation
Indices: 2851809--2851871 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
2851799 AAGACAATCA
2851809 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
2851830 AGAGT-AAAGAGAAAC-TGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2851849 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2851870 AG
1 AG
2851872 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.25
20 16 0.44
21 11 0.31
ACGTcount: A:0.44, C:0.10, G:0.32, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2852178 original size:21 final size:20
Alignment explanation
Indices: 2852147--2852199 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
2852137 GAAAAAATAT
*
2852147 GAAGATAAAAGAGGGAGGAG
1 GAAGAAAAAAGAGGGAGGAG
2852167 GAAGAAGAAAAGAGGGAGGAG
1 GAAGAA-AAAAGAGGGAGGAG
2852188 GAAGAAAAAAGA
1 GAAGAAAAAAGA
2852200 TGGAAGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.02
Consensus pattern (20 bp):
GAAGAAAAAAGAGGGAGGAG
Found at i:2853760 original size:19 final size:18
Alignment explanation
Indices: 2853738--2853780 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
2853728 TAGGGTTATG
2853738 TTGTATAAGATTTATAATT
1 TTGTATAAGATTTATAA-T
*
2853757 TTGTATACGATTTATAAT
1 TTGTATAAGATTTATAAT
2853775 TTGTAT
1 TTGTAT
2853781 GTGAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (18 bp):
TTGTATAAGATTTATAAT
Found at i:2854371 original size:198 final size:199
Alignment explanation
Indices: 2853989--2855156 Score: 1565
Period size: 196 Copynumber: 5.8 Consensus size: 199
2853979 GTAAGCATAT
* * * *
2853989 GTGTCGATCCATATATAAAAATTATCGATCACAGAAACATCGAAACCAATAAGTATAAAGTAATA
1 GTGTCGAT-CATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* ** * *
2854054 GGTAA-TTTTCAATGTAACCAGTATAAATATAGTGG-TTTATGAGAGAATAGGTCTACAACATTT
65 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
2854117 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCA-AATGAATGCCAAAAAAGGGTGCAAC
130 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCC-AAAAAGGGTGCAAC
*
2854181 AAT-AA
194 CATAAA
2854186 GTGTCGAT-ATATATATAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCATATATA-AAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * *
2854250 GGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCTAAAACATAT
65 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* *
2854315 ATCGACACTTTTTAATTTTGTGTCGATACTTTAGGTCCCAGAATG-ATGCCAAAAAGGGTGCAAC
130 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGT-CCAGAATGAATGCCAAAAAGGGTGCAAC
2854379 CATAAA
194 CATAAA
* * *
2854385 GTGTTGATCCATTTAT-AAAAGTATCGATCTCAG-AA-ATCG-AACCCATAAGTATAATGTAATA
1 GTGTCGAT-CATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * *
2854446 GGTAATTTTTCAATCTAATCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGT
65 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* *
2854511 ATCGACACATTTTAATTTTGTCTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGGTGCAACC
130 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
2854576 ATAAA
195 ATAAA
* *
2854581 GTGTCGAT-ATATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTGTAATGTAAT
1 GTGTCGATCATA--TATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAAT
* *
2854645 AGGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAACATG
64 AGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATG
* *
2854710 TATCGACAC-TTTTAATTTT-TGTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGGTGCAAC
129 TATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAAC
2854773 CATAAA
194 CATAAA
*
2854779 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGAT-CATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAG--T-A--TAAT-
* *
2854844 GATAATTTTTCAATGTAATAGATAATTTTTCAATGTAATCGGTATAAATATACCGGTTTTACAAG
59 G-TAA----T--A-G-----G-TAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAG
*
2854909 ATAATAGGTCTACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGA
110 AGAATAGGTCTACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGA
* *
2854974 ATCCCAAAAAGGGTGTAACCATAAA
175 ATGCCAAAAAGGGTGCAACCATAAA
* * *
2854999 GTGTCAATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
1 GTGTCGAT-CATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * ** *
2855064 GGTAAATTTTCAATGTAACCGGTATAAATATACTGGTTTTATAAGAGAATATGTCTACAACATGT
65 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
*
2855129 ATCGACAC--TTTAATTTTGTGTCGATACT
130 ATCGACACTTTTTAATTTTGTCTCGATACT
2855157 AATTTAAATA
Statistics
Matches: 871, Mismatches: 61, Indels: 77
0.86 0.06 0.08
Matches are distributed among these distances:
194 2 0.00
195 14 0.02
196 197 0.23
197 53 0.06
198 194 0.22
199 47 0.05
200 160 0.18
201 6 0.01
203 4 0.00
204 1 0.00
205 3 0.00
206 1 0.00
207 1 0.00
209 2 0.00
211 1 0.00
212 1 0.00
213 3 0.00
214 1 0.00
215 4 0.00
217 2 0.00
218 67 0.08
219 10 0.01
220 97 0.11
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
GTGTCGATCATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAG
GTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTA
TCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCA
TAAA
Found at i:2854860 original size:20 final size:20
Alignment explanation
Indices: 2854835--2854882 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2854825 CCATAAGTAT
2854835 AATGTAATAGATAATTTTTC
1 AATGTAATAGATAATTTTTC
2854855 AATGTAATAGATAATTTTTC
1 AATGTAATAGATAATTTTTC
2854875 AATGTAAT
1 AATGTAAT
2854883 CGGTATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (20 bp):
AATGTAATAGATAATTTTTC
Found at i:2855036 original size:220 final size:218
Alignment explanation
Indices: 2854637--2855081 Score: 746
Period size: 220 Copynumber: 2.0 Consensus size: 218
2854627 CCATAAGTGT
* * *
2854637 AATGTAATAGGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTACGAGAGAATAGGTCT
1 AATGTAATAGATAATTTTTCAATGTAACCGATATAAATATACCGGTTTTACAAGAGAATAGGTCT
* * *
2854702 ACAACATGTATCGACACTTTTAATTTTTGTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGG
66 ACAACATGTATCGACACTTTTAATTTTTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGG
*
2854767 TGCAACCATAAAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAG
131 TGCAACCATAAAGTGTCAATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAG
*
2854832 TATAATGTAATAGATAATTTTTC
196 TATAATGTAATAGATAAATTTTC
* * *
2854855 AATGTAATAGATAATTTTTCAATGTAATCGGTATAAATATACCGGTTTTACAAGATAATAGGTCT
1 AATGTAATAGATAATTTTTCAATGTAACCGATATAAATATACCGGTTTTACAAGAGAATAGGTCT
2854920 ACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAG
66 ACAACATGTATCGACAC-TTTTAATTTT-TCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAG
* *
2854985 GGTGTAACCATAAAGTGTCAATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATA
129 GGTGCAACCATAAAGTGTCAATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATA
*
2855050 AGTATAATGTAATAGGTAAATTTTC
194 AGTATAATGTAATAGATAAATTTTC
2855075 AATGTAA
1 AATGTAA
2855082 CCGGTATAAA
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 76 0.36
219 10 0.05
220 125 0.59
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (218 bp):
AATGTAATAGATAATTTTTCAATGTAACCGATATAAATATACCGGTTTTACAAGAGAATAGGTCT
ACAACATGTATCGACACTTTTAATTTTTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGG
TGCAACCATAAAGTGTCAATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAG
TATAATGTAATAGATAAATTTTC
Found at i:2856642 original size:12 final size:12
Alignment explanation
Indices: 2856622--2856673 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
2856612 CAAGCGGTCA
*
2856622 ATGAAGATGAAG
1 ATGACGATGAAG
2856634 ATGACGATGAAG
1 ATGACGATGAAG
* *
2856646 ATGACGACGACG
1 ATGACGATGAAG
* *
2856658 ACGACGATGATG
1 ATGACGATGAAG
2856670 ATGA
1 ATGA
2856674 TGGTGATGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.33, T:0.15
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2856675 original size:6 final size:6
Alignment explanation
Indices: 2856622--2856673 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
2856612 CAAGCGGTCA
* * * * * *
2856622 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ACGACG ACGACG ATGATG
1 ATGACG ATGACG ATGACG ATGACG ATGACG ATGACG ATGACG ATGACG
2856670 ATGA
1 ATGA
2856674 TGGTGATGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.33, T:0.15
Consensus pattern (6 bp):
ATGACG
Found at i:2858665 original size:200 final size:199
Alignment explanation
Indices: 2858088--2858850 Score: 963
Period size: 200 Copynumber: 3.8 Consensus size: 199
2858078 TTGTATGCAT
* * *
2858088 AAAGTTTCGATACATTTAT-TAAAAGTGTCGATCCAAAAAACATCGAAACCCCATAATTATAATG
1 AAAGTGTCGATACATTT-TCAAAAAGTGTCGATCCCAAAAACATCGAAA-CCCATAATTATAATG
* * * * *
2858152 TAATA-G------GTAATATAACTGGTATACATATACCAATTTTATGAGAAAATAGGTCTATAAC
64 TAATAGGAAATTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAAC
* * *
2858210 ATGTATCGACACTTCTTAATATTGTGTCGATAATTTTTGTCCAAAATGGATGCCAAAAAGGGTGA
129 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGA
*
2858275 ACGCAT
194 ACGCAC
** *
2858281 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCGATCCCGACGACATTGAAACCCATAATTAT
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCC-A-----AAAACATCGAAACCCATAATTAT
** * * *
2858346 AATGTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTTATGAGAGAATAGGTC
60 AATGTAATAGG-AAATTTGTAATATAACCGGTATAAATATACC-GATTTTATGAGAGAATAGGTC
* * * * * * *
2858411 TATAACATGTATTGACACTATATAA-ATTTGTATCGATACTTTTTGTTCAGAATGGATGTCAAAA
123 TACAACATGTATCGACACTTTTTAATA-TTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAA
* *
2858475 ATGATGAACGCAC
187 AGGGTGAACGCAC
*
2858488 AAAGTGTCGATACATTTAT-TAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTT-TCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
*
2858552 AATAGGAAATTTTGTAATATAACCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAAC
65 AATAGGAAA-TTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAAC
*
2858617 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGA
129 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGA
2858682 ACGCAC
194 ACGCAC
*
2858688 AAAGTGTCAATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
* * * *
2858753 ATAGGTAATTTTTTAATATAACCGGTATAAATATACC-ATTTTATAAGAGAATAGGTCTACAATA
66 ATAGG-AAATTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACA
* * *
2858817 TGTAACGACACTTTTTTATTTTGTGTCGATACTT
130 TGTATCGACACTTTTTAATATTGTGTCGATACTT
2858851 ATAATATATG
Statistics
Matches: 491, Mismatches: 57, Indels: 38
0.84 0.10 0.06
Matches are distributed among these distances:
192 1 0.00
193 30 0.06
194 1 0.00
198 20 0.04
199 67 0.14
200 180 0.37
201 57 0.12
206 21 0.04
207 113 0.23
208 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
ATAGGAAATTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACAT
GTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGAAC
GCAC
Found at i:2858694 original size:407 final size:392
Alignment explanation
Indices: 2858088--2858820 Score: 1081
Period size: 407 Copynumber: 1.8 Consensus size: 392
2858078 TTGTATGCAT
*
2858088 AAAGTTTCGATACATTTATTAAAAGTGTCGATCCAAAAAACATCGAAACCCCATAATTATAATGT
1 AAAGTGTCGATACATTTATTAAAAGTGTCGATCCAAAAAACATCGAAACCCCATAATTATAATGT
** * *
2858153 AATAGGTAATATAACTGGTATACATATACCAATTTTATGAGAAAATAGGTCTATAACATGTATCG
66 AATAGGTAATATAACCAGTATAAATATACCAATTTTATGAGAAAATAGGTCTACAACATGTATCG
* *
2858218 ACACTTCTTAATATTGTGTCGATAATTTTTGTCCAAAATGGATGCCAAAAAGGGTGAACGCATAA
131 ACACTTCTTAATATTGTGTCGATAATTTATGTCCAAAATGGATGCCAAAAAGGGTGAACGCACAA
* ** *
2858283 AGTGTCGATACATTTTCAAAAAGTGTCGATCCCGATCCCGACGACATTGAAACCCATAATTATAA
196 AGTGTCAATACATTTTCAAAAAGTGTCGATCCC-A-----AAAACATCGAAACCCATAATTATAA
* * *
2858348 TGTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTTATGAGAGAATAGGTCTA
255 TGTAATAGGTAAATTTACAATATAACCGATATAAATATACC--ATTTTATAAGAGAATAGGTCTA
*
2858413 TAACATGTATTGACACTATATAAATTTGTATCGATACTTTTTGTTCAGAATGGATGTCAAAAATG
318 CAACATGTATTGACACTATATAAATTTGTATCGATACTTTTTGTTCAGAATGGATGTCAAAAATG
2858478 ATGAACGCAC
383 ATGAACGCAC
*
2858488 AAAGTGTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAA-CCCATAATTATAATGT
1 AAAGTGTCGATACATTTATTAAAAGTGTCGATCCAAAAAACATCGAAACCCCATAATTATAATGT
* *
2858552 AATAGGAAATTTTGTAATATAACCAGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAAC
66 AATA-G-------GTAATATAACCAGTATAAATATACCAATTTTATGAGAAAATAGGTCTACAAC
* * *
2858617 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGA
123 ATGTATCGACACTTCTTAATATTGTGTCGATAATTTATGTCCAAAATGGATGCCAAAAAGGGTGA
2858682 ACGCACAAAGTGTCAATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAT
188 ACGCACAAAGTGTCAATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAT
* ** *
2858747 AATGTAATAGGTAATTTTTTAATATAACCGGTATAAATATACCATTTTATAAGAGAATAGGTCTA
253 AATGTAATAGGTAAATTTACAATATAACCGATATAAATATACCATTTTATAAGAGAATAGGTCTA
*
2858812 CAATATGTA
318 CAACATGTA
2858821 ACGACACTTT
Statistics
Matches: 299, Mismatches: 26, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
399 47 0.16
400 47 0.16
401 58 0.19
406 1 0.00
407 146 0.49
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (392 bp):
AAAGTGTCGATACATTTATTAAAAGTGTCGATCCAAAAAACATCGAAACCCCATAATTATAATGT
AATAGGTAATATAACCAGTATAAATATACCAATTTTATGAGAAAATAGGTCTACAACATGTATCG
ACACTTCTTAATATTGTGTCGATAATTTATGTCCAAAATGGATGCCAAAAAGGGTGAACGCACAA
AGTGTCAATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
AGGTAAATTTACAATATAACCGATATAAATATACCATTTTATAAGAGAATAGGTCTACAACATGT
ATTGACACTATATAAATTTGTATCGATACTTTTTGTTCAGAATGGATGTCAAAAATGATGAACGC
AC
Found at i:2861622 original size:200 final size:197
Alignment explanation
Indices: 2861221--2861929 Score: 765
Period size: 200 Copynumber: 3.5 Consensus size: 197
2861211 ACCTAAATAT
* * *
2861221 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAAACATCAAAACCAATCATTATAATGTA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC--AAAAACATCGAAACCAATAATTATAATGTA
* * * * *
2861284 ATAGGT-AATTTAACAATGTAACTGGTATAAATATATCGG-CTAATTAGAAAACAGGTCAACATA
63 ATAGGTAAATTT-ACAATGTAACTGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATA
* * * *
2861347 ATGTATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGGATGAATG-CACAAATGAGGT
126 ATGTATCGACACTTGT-AAATTTGTGTCGATACTT-TTGTCCAGAATAAATGACA-AAAAG-GGT
2861411 GC-ACGCATAAA
187 GCAAC-CATAAA
* * *
2861422 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATTGAAACCAATAATTATAATGTATTA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
2861487 GGTAAATTTACAATGTAACTGATATAAATATACCGGTTTTATGATAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACTGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-CATAATGT
2861552 ATCGACACTTGCTAAATTTGTGTCGATACTTTTGGTCCAGAATAAATGACAAAAAGGGTGCAACC
130 ATCGACACTTG-TAAATTTGTGTCGATACTTTT-GTCCAGAATAAATGACAAAAAGGGTGCAACC
2861617 ATAAA
193 ATAAA
* * * *
2861622 GTGTCGATACATTTATAAAAAGTATCGATCCCGAAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
2861687 GGTAAATTTTCAATGTAA-TCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAATAATG
66 GGTAAATTTACAATGTAACT-GGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAATG
* * * **
2861751 TATCGACACTTTGTTATTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCCTAACCA-G
129 TATCGACAC-TTGTAAATTTGTGTCGATACTTTTGTCCAGAAT--AA-ATG-A---C-AAAAAGG
*
2861815 GTGCAAGCATAAA
185 GTGCAACCATAAA
* * * * *
2861828 GTGTTGATACATTTA--AAATTGTATCGAT-CTAAAAACATCGAAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAAT
* * *
2861890 AGGTAAATTTGCAATGTTACCGGTATAAATATACCGGTTT
65 AGGTAAATTTACAATGTAACTGGTATAAATATACCGGTTT
2861930 ACTTCGAAAA
Statistics
Matches: 439, Mismatches: 47, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
199 9 0.02
200 210 0.48
201 102 0.23
202 10 0.02
203 1 0.00
204 68 0.15
205 8 0.02
206 28 0.06
207 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACTGGTATAAATATACCGGTTTTATGAGAAAATAGGTCACATAATGTA
TCGACACTTGTAAATTTGTGTCGATACTTTTGTCCAGAATAAATGACAAAAAGGGTGCAACCATA
AA
Found at i:2862081 original size:23 final size:23
Alignment explanation
Indices: 2862031--2862075 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2862021 TGCCTATTTT
* *
2862031 ATTATATAAACGCTATCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
2862054 ATTATATAAGCGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
2862076 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:2862493 original size:27 final size:27
Alignment explanation
Indices: 2862434--2862491 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2862424 ATTTTAAATA
* * * *
2862434 AAAATAAAAATATTATTATATTTTATT
1 AAAATAAAAAAAATATTAAATTATATT
2862461 AAAATAAAAAAAATATTACAATTATATT
1 AAAATAAAAAAAATATTA-AATTATATT
2862489 AAA
1 AAA
2862492 TATATATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATAAAAAAAATATTAAATTATATT
Found at i:2862507 original size:39 final size:37
Alignment explanation
Indices: 2862457--2862592 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 37
2862447 TATTATATTT
2862457 TATTAAAATAAAAAAAATATTACAATTATATTAAATATA
1 TATTAAAATAAAAAAAATATTA-AA-TATATTAAATATA
2862496 TATTAAAATAAAAAATAATATATTATTAAGTATATTAAATACT-
1 TATTAAAAT-AAAAA-AA-ATATTA--AA-TATATTAAATA-TA
* * *
2862539 TATTAAAATAATAATATTATTAAA-ATATTAAAACTTATAA
1 TATTAAAATAAAAAAAATATTAAATATATT-AAA--TAT-A
2862579 TATTAAAATAAAAA
1 TATTAAAATAAAAA
2862593 TATTATATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
36 5 0.06
37 3 0.04
38 3 0.04
39 11 0.14
40 23 0.28
41 3 0.04
42 10 0.12
43 22 0.27
44 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (37 bp):
TATTAAAATAAAAAAAATATTAAATATATTAAATATA
Found at i:2862543 original size:43 final size:39
Alignment explanation
Indices: 2862447--2862549 Score: 118
Period size: 43 Copynumber: 2.5 Consensus size: 39
2862437 ATAAAAATAT
* * *
2862447 TATTATATTTTATTAAAAT-AAAAAAAATATTACAATTA
1 TATTAAATATTATTAAAATAAAAAAAAATATTACAAGTA
*
2862485 TATTAAATATATATTAAAATAAAAAATAATATATTATTAAGTA
1 TATTAAATAT-TATTAAAATAAAAAA-AA-ATATTA-CAAGTA
2862528 TATTAAATACTTATTAAAATAA
1 TATTAAATA-TTATTAAAATAA
2862550 TAATATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 8 0.15
39 9 0.16
40 5 0.09
41 2 0.04
42 6 0.11
43 24 0.44
44 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (39 bp):
TATTAAATATTATTAAAATAAAAAAAAATATTACAAGTA
Found at i:2862547 original size:36 final size:35
Alignment explanation
Indices: 2862507--2862576 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
2862497 ATTAAAATAA
*
2862507 AAAATAAT-ATATTATTAAGTATATTAAATACTTATT
1 AAAATAATAATATTATTAA-AATATTAAA-ACTTATT
2862543 AAAATAATAATATTATTAAAATATTAAAACTTAT
1 AAAATAATAATATTATTAAAATATTAAAACTTAT
2862577 AATATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 6 0.19
36 16 0.50
37 10 0.31
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAATAATAATATTATTAAAATATTAAAACTTATT
Found at i:2862560 original size:17 final size:17
Alignment explanation
Indices: 2862507--2862565 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
2862497 ATTAAAATAA
2862507 AAAATAAT-ATATTATT
1 AAAATAATAATATTATT
* *
2862523 AAGTATATTAAATACTTATT
1 AA-AATAAT-AATA-TTATT
2862543 AAAATAATAATATTATT
1 AAAATAATAATATTATT
2862560 AAAATA
1 AAAATA
2862566 TTAAAACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 4 0.11
19 7 0.20
20 7 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATAATAATATTATT
Found at i:2862569 original size:8 final size:8
Alignment explanation
Indices: 2862539--2862597 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 8
2862529 ATTAAATACT
2862539 TATTAAAA
1 TATTAAAA
* *
2862547 TAATAATAT
1 TATTAA-AA
2862556 TATTAAAA
1 TATTAAAA
2862564 TATTAAAA
1 TATTAAAA
* *
2862572 -CTTATAA
1 TATTAAAA
2862579 TATTAAAA
1 TATTAAAA
2862587 TA--AAAA
1 TATTAAAA
2862593 TATTA
1 TATTA
2862598 TATTATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
6 6 0.15
7 5 0.13
8 22 0.56
9 6 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
TATTAAAA
Found at i:2862589 original size:37 final size:37
Alignment explanation
Indices: 2862505--2862576 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
2862495 ATATTAAAAT
*
2862505 AAAAAATAATATATTATTAAGTATATTAAATACTTATTA
1 AAAAAAT-A-ATATTATTAAGAATATTAAATACTTATTA
*
2862544 AAATAATAATATTATTAA-AATATTAAA-ACTTAT
1 AAAAAATAATATTATTAAGAATATTAAATACTTAT
2862577 AATATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 6 0.19
36 8 0.26
37 10 0.32
38 1 0.03
39 6 0.19
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (37 bp):
AAAAAATAATATTATTAAGAATATTAAATACTTATTA
Found at i:2862801 original size:28 final size:31
Alignment explanation
Indices: 2862741--2862812 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
2862731 AATATAATTT
* *
2862741 AATAACTAATATTTTTATTAACATGATATTAA
1 AATAA-TAATATTATTATTAAAATGATATTAA
2862773 AATAAT-ATATTATTATTAAAAT-ATA-TAA
1 AATAATAATATTATTATTAAAATGATATTAA
2862801 AATAATAATATT
1 AATAATAATATT
2862813 TTGAGTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.24
29 8 0.22
30 14 0.38
31 1 0.03
32 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
AATAATAATATTATTATTAAAATGATATTAA
Found at i:2868418 original size:21 final size:21
Alignment explanation
Indices: 2868370--2868418 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2868360 ATCTAATATT
*
2868370 ACAATGCCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
2868391 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
*
2868412 ATAATGT
1 ACAATGT
2868419 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (21 bp):
ACAATGTCAAAATTAGGTGCA
Found at i:2873054 original size:21 final size:21
Alignment explanation
Indices: 2873029--2873076 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2873019 CCTAATATTG
2873029 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
2873050 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
2873071 TAATGT
1 CAATGT
2873077 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:2873568 original size:18 final size:18
Alignment explanation
Indices: 2873547--2873590 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2873537 ACACCAACAT
*
2873547 CAACTCTAACACCATCTC
1 CAACTCCAACACCATCTC
* * *
2873565 CAACCCCGACCCCATCTC
1 CAACTCCAACACCATCTC
2873583 CAACTCCA
1 CAACTCCA
2873591 TCTCCAGTAC
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.52, G:0.02, T:0.16
Consensus pattern (18 bp):
CAACTCCAACACCATCTC
Found at i:2874042 original size:2 final size:2
Alignment explanation
Indices: 2874035--2874071 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2874025 ATATGAGATG
2874035 AT AT AT AT 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 AT AT AT AT A
2874072 AGAATGGTTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2874181 original size:31 final size:30
Alignment explanation
Indices: 2874146--2874238 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
2874136 GTTGATGGAA
2874146 TAAAATCAAATTGATCGATAACATTAGAGAC
1 TAAAATCAAA-TGATCGATAACATTAGAGAC
*
2874177 TAAAATCAAAATAATCGATAACATTATG-GAC
1 TAAAATC-AAATGATCGATAACATTA-GAGAC
* * * *
2874208 TATAATCGAAATGATTGATAAAATTAAAGAC
1 TAAAATC-AAATGATCGATAACATTAGAGAC
2874239 AATGTACTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 48 0.92
32 4 0.08
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.27
Consensus pattern (30 bp):
TAAAATCAAATGATCGATAACATTAGAGAC
Found at i:2875378 original size:2 final size:2
Alignment explanation
Indices: 2875371--2875398 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2875361 CTTGATTCAA
2875371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2875399 TTACTTTTAT
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):
AT
Found at i:2875594 original size:23 final size:23
Alignment explanation
Indices: 2875568--2875624 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
2875558 TTTTAATAAT
*
2875568 TTTATCTTTATGTTACGTTTTTC
1 TTTATCTTTATGATACGTTTTTC
* *
2875591 TTTATATTTATGATATGTTTTTC
1 TTTATCTTTATGATACGTTTTTC
*
2875614 TCTATCTTTAT
1 TTTATCTTTAT
2875625 AACATAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTATCTTTATGATACGTTTTTC
Found at i:2878851 original size:29 final size:29
Alignment explanation
Indices: 2878809--2878995 Score: 155
Period size: 29 Copynumber: 6.6 Consensus size: 29
2878799 CCGTTGATCG
*
2878809 GGTGGTATTTTGGTAATTATTTAGAAAAT
1 GGTGATATTTTGGTAATTATTTAGAAAAT
* * * *
2878838 GGTGGTATTATGGTAATTATTTTGAAAAG
1 GGTGATATTTTGGTAATTATTTAGAAAAT
* * * *
2878867 GGTGCTATTTTTGTAATTTTTTA-AAAAA
1 GGTGATATTTTGGTAATTATTTAGAAAAT
* * * * *
2878895 AGTGATAATATCGTAATTTTTTA-AAAA-
1 GGTGATATTTTGGTAATTATTTAGAAAAT
* * *
2878922 AGTGATATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTAGAAAAT
* *
2878951 TGTGATATTTTGGTAATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTAGAAAAT
* * *
2878980 GATGCTATTTTCGTAA
1 GGTGATATTTTGGTAA
2878996 AATGGTTGAT
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
27 18 0.14
28 30 0.23
29 83 0.63
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (29 bp):
GGTGATATTTTGGTAATTATTTAGAAAAT
Found at i:2885520 original size:35 final size:35
Alignment explanation
Indices: 2885453--2885522 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
2885443 TTAAAAACTC
* ** *
2885453 TATTAATATACTAAATTAAAAGTAGGGTTCATAAA
1 TATTAATAAACTAAATTAAAAACAGGGCTCATAAA
*
2885488 TATTAATAAACTAAATTAAAAACATGGCTCATAAA
1 TATTAATAAACTAAATTAAAAACAGGGCTCATAAA
2885523 CTTATTTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (35 bp):
TATTAATAAACTAAATTAAAAACAGGGCTCATAAA
Found at i:2885785 original size:6 final size:6
Alignment explanation
Indices: 2885774--2885800 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2885764 GTGTTTCCAA
2885774 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
2885801 ATATATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:2908396 original size:4 final size:4
Alignment explanation
Indices: 2908382--2908418 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
2908372 GAGCTTAATA
2908382 ATAG TATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
2908419 TTGCCTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:2928967 original size:255 final size:255
Alignment explanation
Indices: 2928516--2929287 Score: 1436
Period size: 255 Copynumber: 3.0 Consensus size: 255
2928506 CAAAATTATC
* *
2928516 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAACGACATGATAAA
1 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
* *
2928581 AATATCAGGCCAATCCAAAACTCTAAGCCTAGTACTCTACTACAAGTACATTCATATTGATAAAT
66 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
*
2928646 CTAACAATTAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
131 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
**
2928711 TTTTTAAACTACTGTAAATGGATCTAGACCTGGGTTACTGGACAGGATACAAAAATAAAA
196 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAA
2928771 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
1 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
2928836 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
66 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
2928901 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
131 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
*
2928966 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAGTAAAAA
196 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAAT-AAAA
* *
2929027 AAACTATTTGTTCAATACAAAATGCTTTCAACATTTTAAAACAAAGTCTTAAATGACAAGATAAA
1 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
2929092 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
66 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
*
2929157 CTAACAATCAGATTGTTATAATATTACTCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
131 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
2929222 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAA
196 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAA
2929282 AAACTA
1 AAACTA
2929288 AAGCACTATA
Statistics
Matches: 504, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
255 253 0.50
256 251 0.50
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (255 bp):
AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAA
Found at i:2929153 original size:256 final size:256
Alignment explanation
Indices: 2928516--2929284 Score: 1432
Period size: 256 Copynumber: 3.0 Consensus size: 256
2928506 CAAAATTATC
* *
2928516 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAACGACATGATAAA
1 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
* *
2928581 AATATCAGGCCAATCCAAAACTCTAAGCCTAGTACTCTACTACAAGTACATTCATATTGATAAAT
66 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
*
2928646 CTAACAATTAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
131 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
**
2928711 TTTTTAAACTACTGTAAATGGATCTAGACCTGGGTTACTGGACAGGATACAAAAAT-AAAA
196 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAAA
2928771 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
1 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
2928836 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
66 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
2928901 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
131 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
*
2928966 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAGTAAAAA
196 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAAA
* *
2929027 AAACTATTTGTTCAATACAAAATGCTTTCAACATTTTAAAACAAAGTCTTAAATGACAAGATAAA
1 AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
2929092 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
66 AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
*
2929157 CTAACAATCAGATTGTTATAATATTACTCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
131 CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
2929222 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAAA
196 TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAAA
2929283 AA
1 AA
2929285 CTAAAGCACT
Statistics
Matches: 501, Mismatches: 12, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
255 243 0.49
256 258 0.51
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (256 bp):
AAACTATTTGTTCAATACAAAAAGCTTTCAACATTTTAAAACAAAGTCTCAAATGACAAGATAAA
AATATCAGGCCAATCCAAAACTCTAAGTCTAGTACTCTACTACAAGTACATTCATATTGTTAAAT
CTAACAATCAGATTGTTATAATATTAATCATATTAAAAGTTATAAAAGTGTGTAAAACTAATTTA
TTTTTAAACTACTGTAAATGGATCTAGACCTGGAATACTGGACAGGATACAAAAATAAAAA
Found at i:2930867 original size:25 final size:25
Alignment explanation
Indices: 2930803--2930867 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
2930793 TCAATTTAAA
*
2930803 TTATAATAAAAATATAAAAAATATTT
1 TTAT-ATAAAAATATTAAAAATATTT
* * ** *
2930829 TAACAT-AACTTATTAATAATATTT
1 TTATATAAAAATATTAAAAATATTT
2930853 TTATATAAAAATATT
1 TTATATAAAAATATT
2930868 TTATTAAAAA
Statistics
Matches: 28, Mismatches: 10, Indels: 3
0.68 0.24 0.07
Matches are distributed among these distances:
24 18 0.64
25 8 0.29
26 2 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
TTATATAAAAATATTAAAAATATTT
Found at i:2930877 original size:14 final size:15
Alignment explanation
Indices: 2930838--2930877 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2930828 TTAACATAAC
*
2930838 TTATTAATAATATTT
1 TTATTAAAAATATTT
2930853 TTATATAAAAATA-TT
1 TTAT-TAAAAATATTT
2930868 TTATTAAAAA
1 TTATTAAAAA
2930878 AATATGTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 10 0.43
16 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTAAAAATATTT
Found at i:2930878 original size:15 final size:16
Alignment explanation
Indices: 2930846--2930877 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2930836 ACTTATTAAT
2930846 AATATTTTTATATAAA
1 AATATTTTTATATAAA
2930862 AATA-TTTTAT-TAAA
1 AATATTTTTATATAAA
2930876 AA
1 AA
2930878 AATATGTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTTTTATATAAA
Found at i:2934960 original size:23 final size:23
Alignment explanation
Indices: 2934928--2935032 Score: 133
Period size: 23 Copynumber: 4.7 Consensus size: 23
2934918 TCGAGGGTTC
2934928 TATGTGGTCCTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGACAAAAT
* **
2934951 TATATGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAAAT
* * *
2934974 TATGTGGTCATTCGTGACAAACT
1 TATGTGGTCCTTCGGGACAAAAT
2934997 TATGTGGTCCTTCGGGAC--AAT
1 TATGTGGTCCTTCGGGACAAAAT
*
2935018 TATGTGGTACTTCGG
1 TATGTGGTCCTTCGG
2935033 TGCAAATTAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 16 0.23
23 55 0.77
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAT
Found at i:2939109 original size:44 final size:44
Alignment explanation
Indices: 2939046--2939386 Score: 513
Period size: 44 Copynumber: 7.8 Consensus size: 44
2939036 GCATATGCAA
* *
2939046 TATTTTACCAATATACTTACCATTTATCCATAAGCTTGAAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
* *
2939090 TATTTTATCAATACACTTACCATTTATCCATAAGCTCGTAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
* *
2939134 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
* *
2939178 TATTTTACCAATACACTTGCCATTTATCCATAAGCTCGTAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
* * *
2939222 TATTTTACCCATATACTTACCATTTATCCATAAGCTCAAAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
* * *
2939266 TATTTTACCAATACACTTGCCATTTATCCATAAGCTTGTAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
* *
2939310 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCT
1 TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
*
2939354 TATTTTACCAATACACTTGCCA-TTATTCCATAA
1 TATTTTACCAATACACTTACCATTTA-TCCATAA
2939387 CCATATACCA
Statistics
Matches: 265, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
43 3 0.01
44 262 0.99
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (44 bp):
TATTTTACCAATACACTTACCATTTATCCATAAGCTCGAAAGCT
Found at i:2939145 original size:25 final size:25
Alignment explanation
Indices: 2939112--2939234 Score: 67
Period size: 25 Copynumber: 5.4 Consensus size: 25
2939102 ACACTTACCA
*
2939112 TTTATCCATAAGCTCGTAAGCTTAT
1 TTTACCCATAAGCTCGTAAGCTTAT
*
2939137 TTTACCCATATA-CT--T-A-C-CA-
1 TTTACCCATA-AGCTCGTAAGCTTAT
* *
2939156 TTTATCCATAAGCTCGAAAGCTTAT
1 TTTACCCATAAGCTCGTAAGCTTAT
* *
2939181 TTTACCAATACA-CT--T--GC-CA-
1 TTTACCCATA-AGCTCGTAAGCTTAT
*
2939200 TTTATCCATAAGCTCGTAAGCTTAT
1 TTTACCCATAAGCTCGTAAGCTTAT
2939225 TTTACCCATA
1 TTTACCCATA
2939235 TACTTACCAT
Statistics
Matches: 69, Mismatches: 13, Indels: 32
0.61 0.11 0.28
Matches are distributed among these distances:
18 2 0.03
19 21 0.30
20 2 0.03
21 4 0.06
22 2 0.03
23 4 0.06
24 2 0.03
25 30 0.43
26 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.37
Consensus pattern (25 bp):
TTTACCCATAAGCTCGTAAGCTTAT
Found at i:2939195 original size:88 final size:88
Alignment explanation
Indices: 2939046--2939386 Score: 612
Period size: 88 Copynumber: 3.9 Consensus size: 88
2939036 GCATATGCAA
* * * *
2939046 TATTTTACCAATATACTTACCATTTATCCATAAGCTTGAAAGCTTATTTTATCAATACACTTACC
1 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
2939111 ATTTATCCATAAGCTCGTAAGCT
66 ATTTATCCATAAGCTCGTAAGCT
2939134 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
1 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
2939199 ATTTATCCATAAGCTCGTAAGCT
66 ATTTATCCATAAGCTCGTAAGCT
*
2939222 TATTTTACCCATATACTTACCATTTATCCATAAGCTCAAAAGCTTATTTTACCAATACACTTGCC
1 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
*
2939287 ATTTATCCATAAGCTTGTAAGCT
66 ATTTATCCATAAGCTCGTAAGCT
2939310 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
1 TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
2939375 A-TTATTCCATAA
66 ATTTA-TCCATAA
2939387 CCATATACCA
Statistics
Matches: 245, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
87 3 0.01
88 242 0.99
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (88 bp):
TATTTTACCCATATACTTACCATTTATCCATAAGCTCGAAAGCTTATTTTACCAATACACTTGCC
ATTTATCCATAAGCTCGTAAGCT
Found at i:2939508 original size:40 final size:40
Alignment explanation
Indices: 2939464--2939584 Score: 199
Period size: 40 Copynumber: 3.0 Consensus size: 40
2939454 CCGTAGCTCC
*
2939464 ACACATAAGGTCGTCCCCACCATATACACCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
2939504 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
* *
2939544 ACACATAAAGTCGTGCCCACCATATACATC-AAGGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAA-GTGTATT
2939584 A
1 A
2939585 TAAACCTACA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
39 2 0.03
40 75 0.97
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
Found at i:2939773 original size:45 final size:43
Alignment explanation
Indices: 2939715--2939850 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 43
2939705 GCTGCTAAAA
* * *
2939715 TTAGCGGCGTTTTTTAAAAACAAACGTCGCAATAGGTGTTGTTAT
1 TTAGCGGC-ATTTTTAAAAA-AAACGCCGCAATAGGTGTTGATAT
* * *
2939760 TTAGCGGCATTTTTCAGAAAAACGCCGCAATAGGTGTTGATGT
1 TTAGCGGCATTTTTAAAAAAAACGCCGCAATAGGTGTTGATAT
* ** *** * * *
2939803 TTAGCAGTGTTTTTGCTAAAACCGCCGCAGTAGGTGTTGAGAT
1 TTAGCGGCATTTTTAAAAAAAACGCCGCAATAGGTGTTGATAT
2939846 TTAGC
1 TTAGC
2939851 AGCGTTTTAC
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 59 0.79
44 8 0.11
45 8 0.11
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
TTAGCGGCATTTTTAAAAAAAACGCCGCAATAGGTGTTGATAT
Found at i:2939816 original size:43 final size:43
Alignment explanation
Indices: 2939736--2939858 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
2939726 TTTTAAAAAC
* * * * *
2939736 AAACGTCGCAATAGGTGTTGTTATTTAGCGGCATTTTT-CAGAA
1 AAACGCCGCAATAGGTGTTGATGTTTAGCAGCGTTTTTGC-GAA
* *
2939779 AAACGCCGCAATAGGTGTTGATGTTTAGCAGTGTTTTTGCTAA
1 AAACGCCGCAATAGGTGTTGATGTTTAGCAGCGTTTTTGCGAA
* *
2939822 AACCGCCGCAGTAGGTGTTGA-GATTTAGCAGCGTTTT
1 AAACGCCGCAATAGGTGTTGATG-TTTAGCAGCGTTTT
2939859 ACTTAAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.01
43 66 0.97
44 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATGTTTAGCAGCGTTTTTGCGAA
Found at i:2939866 original size:43 final size:42
Alignment explanation
Indices: 2939736--2939901 Score: 127
Period size: 43 Copynumber: 3.9 Consensus size: 42
2939726 TTTTAAAAAC
* * ** * * * *
2939736 AAACGTCGCAATAGGTGTTGTTATTTAGCGGCATTTTTCAGAA
1 AAACGCCGCAGTAGGTGTTGAGATTTAGCAGCGTTTTAC-TAA
* * *
2939779 AAACGCCGCAATAGGTGTTGATG-TTTAGCAGTGTTTTTGCTAA
1 AAACGCCGCAGTAGGTGTTGA-GATTTAGCAGCG-TTTTACTAA
*
2939822 AACCGCCGCAGTAGGTGTTGAGATTTAGCAGCGTTTTACTTAA
1 AAACGCCGCAGTAGGTGTTGAGATTTAGCAGCGTTTTAC-TAA
* * * * * *
2939865 AAATGTCGCAGTAGGTTTTGATATTTTGCGGCGTTTT
1 AAACGCCGCAGTAGGTGTTGAGATTTAGCAGCGTTTT
2939902 TCCCACAAAC
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
42 6 0.06
43 89 0.89
44 5 0.05
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (42 bp):
AAACGCCGCAGTAGGTGTTGAGATTTAGCAGCGTTTTACTAA
Found at i:2939978 original size:43 final size:43
Alignment explanation
Indices: 2939828--2939985 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 43
2939818 CTAAAACCGC
* **
2939828 CGCAGTAGGTGTTGAGATTTAGCAGCGTTTTACTTAAAAATGT
1 CGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACCCAAAAATGT
* * * * * *
2939871 CGCAGTAGGTTTTGATATTTTGCGGCGTTTTTCCCACAAACGT
1 CGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACCCAAAAATGT
* * * ** * * *
2939914 CGTAGTAGATGATGATTTTTAGCGGCATTTTCCCCATAAATGT
1 CGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACCCAAAAATGT
* * *
2939957 CGCAGTAGGTTTTTAGATTTAGCGACGTT
1 CGCAGTAGGTGTTGAGATTTAGCGGCGTT
2939986 GTATCGAAAA
Statistics
Matches: 87, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
43 87 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (43 bp):
CGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACCCAAAAATGT
Found at i:2940438 original size:21 final size:21
Alignment explanation
Indices: 2940413--2940469 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2940403 GATATGTTGT
* *
2940413 TTCTCTTTGTGCTGCCGCTGC
1 TTCTCTCTATGCTGCCGCTGC
* *
2940434 TTCTCTCTATGCTGGCGTTGC
1 TTCTCTCTATGCTGCCGCTGC
* *
2940455 TTCTTTCTCTGCTGC
1 TTCTCTCTATGCTGC
2940470 TCTGCCTGCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.32, G:0.21, T:0.46
Consensus pattern (21 bp):
TTCTCTCTATGCTGCCGCTGC
Found at i:2940509 original size:21 final size:21
Alignment explanation
Indices: 2940463--2940503 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2940453 GCTTCTTTCT
2940463 CTGCTGCTCTGCCTGCTTCCG
1 CTGCTGCTCTGCCTGCTTCCG
2940484 CTGCTGCTCT-CTCTGCTTCC
1 CTGCTGCTCTGC-CTGCTTCC
2940504 CTTGCTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.00, C:0.44, G:0.20, T:0.37
Consensus pattern (21 bp):
CTGCTGCTCTGCCTGCTTCCG
Done.