Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 24
Found at i:3331112 original size:15 final size:14
Alignment explanation
Indices: 3331087--3331117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3331077 TTCAACACAA
3331087 AACTTTAATATAAT
1 AACTTTAATATAAT
3331101 AACTTATAATATAAT
1 AACTT-TAATATAAT
3331116 AA
1 AA
3331118 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:3331125 original size:16 final size:16
Alignment explanation
Indices: 3331092--3331138 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
3331082 CACAAAACTT
*
3331092 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
3331107 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
3331123 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
3331139 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:3331254 original size:32 final size:34
Alignment explanation
Indices: 3331179--3331260 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
3331169 CCAAACCCTT
* *
3331179 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
3331212 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
3331245 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
3331261 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:3331391 original size:45 final size:48
Alignment explanation
Indices: 3331301--3331391 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 48
3331291 CAACAAACAA
3331301 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
*
3331349 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
3331392 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 12 0.29
45 11 0.27
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
Found at i:3331460 original size:41 final size:40
Alignment explanation
Indices: 3331372--3331460 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
3331362 TTAACAAAAC
* *
3331372 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
3331413 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
3331454 AAACTAA
1 AAACTAA
3331461 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:3331525 original size:16 final size:18
Alignment explanation
Indices: 3331496--3331534 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
3331486 ACTAATTAAC
*
3331496 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
3331514 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
3331530 ATTTA
1 ATTTA
3331535 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:3331886 original size:29 final size:29
Alignment explanation
Indices: 3331844--3331909 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
3331834 GTGACGCCGG
**
3331844 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
*
3331873 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
3331902 GGCGACCT
1 GGCGACCT
3331910 TGTAATTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCCAGACTACAT
Found at i:3331977 original size:32 final size:32
Alignment explanation
Indices: 3331896--3331977 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
3331886 GTCGCCCAGA
**
3331896 CTGCATGGCGACCT-TGTAATTGGCTGGCTCGT
1 CTGCATGGCGACCTCT-CCATTGGCTGGCTCGT
3331928 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
*
3331960 TTGCATGGCGACCTCTCC
1 CTGCATGGCGACCTCTCC
3331978 TCGTATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.11, C:0.32, G:0.28, T:0.29
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:3332113 original size:29 final size:29
Alignment explanation
Indices: 3332071--3332130 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
3332061 GTATGGTATG
3332071 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
3332100 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
3332129 TC
1 TC
3332131 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:3332262 original size:2 final size:2
Alignment explanation
Indices: 3332255--3332284 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3332245 TCTTTTTACA
3332255 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
3332285 TATTAGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3337665 original size:63 final size:64
Alignment explanation
Indices: 3337582--3337717 Score: 159
Period size: 64 Copynumber: 2.1 Consensus size: 64
3337572 TTTTTCAACC
* * * * *
3337582 TGGAGTCTAGCTTCAA-TTTTTTTTATTTCTAGTCGA-TCATAAAAATTTTAAGCTCGCGAGCTT
1 TGGAGTCAAGCTTCAATTTTTTTTTATTTCTAATCGAGT-ATAAAAATTTTAAACTCACAAGCTT
* * * *
3337645 TGGAGTCAAGTTTTAATTTTTTTTTATTTCTAATCGAGTTTAACAATTTTAAACTCACAAGCTT
1 TGGAGTCAAGCTTCAATTTTTTTTTATTTCTAATCGAGTATAAAAATTTTAAACTCACAAGCTT
*
3337709 TCGAGTCAA
1 TGGAGTCAA
3337718 CTCGAGCTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
63 13 0.21
64 47 0.77
65 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (64 bp):
TGGAGTCAAGCTTCAATTTTTTTTTATTTCTAATCGAGTATAAAAATTTTAAACTCACAAGCTT
Found at i:3337693 original size:64 final size:64
Alignment explanation
Indices: 3337598--3337717 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
3337588 CTAGCTTCAA
* * * * *
3337598 TTTTTTTTATTTCTAGTCGATCATAAAAATTTTAAGCTCGCGAGCTTTGGAGTCAAGTTTTAAT
1 TTTTTTTTATTTCTAATCGATCATAAAAATTTTAAACTCACAAGCTTTCGAGTCAAGTTTTAAT
* *
3337662 TTTTTTTTATTTCTAATCGAGT-TTAACAATTTTAAACTCACAAGCTTTCGAGTCAA
1 TTTTTTTTATTTCTAATCGA-TCATAAAAATTTTAAACTCACAAGCTTTCGAGTCAA
3337718 CTCGAGCTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
64 47 0.98
65 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (64 bp):
TTTTTTTTATTTCTAATCGATCATAAAAATTTTAAACTCACAAGCTTTCGAGTCAAGTTTTAAT
Found at i:3342545 original size:28 final size:28
Alignment explanation
Indices: 3342481--3342569 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
3342471 TTTCTTTTTC
* * *
3342481 AATAAATACTTAAAGCATTTTTTTGTCAA
1 AATAAATACATAAAGTA-TTTTTAGTCAA
* *
3342510 AATAAATATATAAAGTTATTTTTAGTCAC
1 AATAAATACATAAAG-TATTTTTAGTCAA
3342539 AAT-AATACATAAAGTA-TTTTATGTCAA
1 AATAAATACATAAAGTATTTTTA-GTCAA
3342566 AATA
1 AATA
3342570 GATGTCTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.10
27 9 0.18
28 10 0.20
29 25 0.50
30 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (28 bp):
AATAAATACATAAAGTATTTTTAGTCAA
Found at i:3342765 original size:30 final size:30
Alignment explanation
Indices: 3342658--3342772 Score: 108
Period size: 30 Copynumber: 3.8 Consensus size: 30
3342648 ACTTAGATAA
* * *
3342658 AAAATAAAATACTTTAGGTACCTATTTTGATC
1 AAAA-AAAATAATTTAAGTACTTATTTTGA-C
** * *
3342690 -AAAAAAAT-ATTTTTGCTGCATATTTTGAC
1 AAAAAAAATAATTTAAG-TACTTATTTTGAC
*
3342719 AAAAAACATAACTTTAAGTACTTATTTTGAC
1 AAAAAAAATAA-TTTAAGTACTTATTTTGAC
3342750 AAAAAAAATAATTTAAGTACTTA
1 AAAAAAAATAATTTAAGTACTTA
3342773 AGTAAAAAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
29 5 0.07
30 34 0.50
31 25 0.37
32 4 0.06
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (30 bp):
AAAAAAAATAATTTAAGTACTTATTTTGAC
Found at i:3342842 original size:3 final size:3
Alignment explanation
Indices: 3342834--3342873 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3342824 ATAACCCTAT
3342834 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3342874 AACGGCTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3345095 original size:33 final size:33
Alignment explanation
Indices: 3345058--3345135 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
3345048 ATAAATCAAC
3345058 GTATTTGAGTCCTATTGAAACACTAAAACC-AA
1 GTATTTGAGTCCTATTGAAACACTAAAACCGAA
*
3345090 TGTATTTGAGTCCTATTGAAATACTAAAACCGAA
1 -GTATTTGAGTCCTATTGAAACACTAAAACCGAA
*
3345124 GCATTTGAGTCC
1 GTATTTGAGTCC
3345136 AAGTAGGACT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 40 0.95
34 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
GTATTTGAGTCCTATTGAAACACTAAAACCGAA
Found at i:3345681 original size:7 final size:7
Alignment explanation
Indices: 3345669--3345729 Score: 83
Period size: 7 Copynumber: 8.9 Consensus size: 7
3345659 ATGATAATAC
3345669 ATTATTT
1 ATTATTT
3345676 ATTATTT
1 ATTATTT
3345683 ATT-TATT
1 ATTAT-TT
3345690 ATTATTT
1 ATTATTT
3345697 ATTTATTT
1 A-TTATTT
3345705 ATTATTT
1 ATTATTT
3345712 A-T-TTT
1 ATTATTT
3345717 ATTATTT
1 ATTATTT
3345724 ATTATT
1 ATTATT
3345730 CATTTTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.08
6 3 0.06
7 34 0.69
8 8 0.16
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTATTT
Found at i:3345684 original size:4 final size:4
Alignment explanation
Indices: 3345670--3345726 Score: 70
Period size: 4 Copynumber: 15.2 Consensus size: 4
3345660 TGATAATACA
3345670 TTAT TTA- TTAT TTAT TTA- TTA- TTAT TTAT TTAT TTA- TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
3345714 TT-T ATTAT TTAT T
1 TTAT -TTAT TTAT T
3345727 ATTCATTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
3 13 0.27
4 34 0.71
5 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3345686 original size:11 final size:11
Alignment explanation
Indices: 3345670--3345726 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
3345660 TGATAATACA
3345670 TTATTTATTAT
1 TTATTTATTAT
3345681 TTATTTATTA-
1 TTATTTATTAT
3345691 TTA--T-TTAT
1 TTATTTATTAT
3345699 TTATTTATTAT
1 TTATTTATTAT
3345710 TTATTTTATTAT
1 TTA-TTTATTAT
3345722 TTATT
1 TTATT
3345727 ATTCATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
10 4 0.10
11 19 0.46
12 11 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:3345734 original size:11 final size:10
Alignment explanation
Indices: 3345669--3345734 Score: 77
Period size: 10 Copynumber: 6.7 Consensus size: 10
3345659 ATGATAATAC
3345669 ATTATTTATT
1 ATTATTTATT
3345679 ATTTATTTATT
1 A-TTATTTATT
3345690 ATTATTTA-T
1 ATTATTTATT
3345699 -TTATTTATT
1 ATTATTTATT
3345708 ATT-TATT-TT
1 ATTAT-TTATT
3345717 ATTATTTATT
1 ATTATTTATT
3345727 ATTCATTT
1 ATT-ATTT
3345735 TTTTTCTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.14
9 10 0.20
10 18 0.37
11 14 0.29
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTATTTATT
Found at i:3345735 original size:19 final size:19
Alignment explanation
Indices: 3345677--3345735 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
3345667 ACATTATTTA
3345677 TTATTTATTTATTATTA-T
1 TTATTTATTTATTATTATT
3345695 TTATTTATTTATTATTTATT
1 TTATTTATTTATTA-TTATT
3345715 TTA-TTATTTATTATTCATT
1 TTATTTATTTATTATT-ATT
3345734 TT
1 TT
3345736 TTTTCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 16 0.42
19 18 0.47
20 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTATTTATTATTATT
Found at i:3349465 original size:110 final size:106
Alignment explanation
Indices: 3349275--3349480 Score: 259
Period size: 110 Copynumber: 1.9 Consensus size: 106
3349265 GATGGTGGTT
* * *
3349275 GCTCAACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTTATTTAGAGTAAATT
1 GCTCAACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTGCAGTTTCATTCAGAGTAAATT
*
3349340 TCAACTTCACAGCGAAAGATATTGGACTCGAGACAATACAA
66 TCAACTTCACAGCGAAAGAGATTGGACTCGAGACAATACAA
* * * * *
3349381 GCTCAACTTTACAGCGAATGGGCGACTGATTATCAATAAACAACTTTGCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAACGAAGGGGCGACTG----TCAACAAACAACTTTGCAGTTTCATTCAGAGTA
* * * *
3349446 AATTTTAACTTCGCGGCGAAGGAGATTGGACTCGA
62 AATTTCAACTTCACAGCGAAAGAGATTGGACTCGA
3349481 AACGACATAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 25 0.30
110 58 0.70
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (106 bp):
GCTCAACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTGCAGTTTCATTCAGAGTAAATT
TCAACTTCACAGCGAAAGAGATTGGACTCGAGACAATACAA
Found at i:3350062 original size:111 final size:110
Alignment explanation
Indices: 3349811--3350386 Score: 744
Period size: 111 Copynumber: 5.3 Consensus size: 110
3349801 GTTTCATAGC
* *
3349811 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAA
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
** * * *
3349876 GGGCGACTGGTTGTCAATAAACAACTTC-CCAG--T--TTCAGAGC
66 GGGCG-CTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
* *
3349917 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGATAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
3349982 GGGCAGCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
66 GGGC-GCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
* * * * *
3350028 CAATTTCAACTACACAGCGAAGAATATTGAACTCAAGACATCACAAGCTCAACTTCACAGTGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
3350093 GGGCGGCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAG-
66 GGGC-GCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
*
3350138 CTAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAA
1 C-AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAA
* * * * *
3350203 GGGTCGACTGACTATCAACAAACAACTTATTTAGTTCCATTCAGAGT
65 GGGGCG-CTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
* * *
3350250 CAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGAGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
* * * * *
3350315 GGGCGGCTGACTATCAACAAACAATTTCCT-AG---C-TCCAGATT
66 GGGC-GCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
*
3350356 CAATTTCAACTTCAC-GACGGAGGATATTGGA
1 CAATTTCAACTTCACAG-CGAAGGATATTGGA
3350387 TTCAGAGCAA
Statistics
Matches: 420, Mismatches: 39, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
105 1 0.00
106 117 0.28
107 5 0.01
109 1 0.00
110 4 0.01
111 290 0.69
112 2 0.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (110 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
GGGCGCTGACTGTCAACAAACAACTTCTTCAGTTTCATTCAGAGT
Found at i:3350961 original size:37 final size:36
Alignment explanation
Indices: 3350903--3350984 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 36
3350893 AGTCATCTCT
3350903 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
*
3350939 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCC
3350976 CTTGAAACA
1 CTTGAAACA
3350985 CCAATCTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 11 0.25
37 33 0.75
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
Found at i:3351041 original size:67 final size:68
Alignment explanation
Indices: 3350933--3351089 Score: 210
Period size: 67 Copynumber: 2.3 Consensus size: 68
3350923 TCTTGAGACA
* ** * * *
3350933 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAC-CAATCTTTGAA
1 GTTTCTCTTGAAACAAAAATTTGTCTCTCTGGAGACAGTTTCTCTTGAAACACAAAACCTTTGAA
3350997 -TAT
66 GT-T
3351000 GTTTCTCTTGAAACAAAAATTTGTCTCTCTGGAGACAGTTTCTCTTGAAACACAAAAAACCTTTG
1 GTTTCTCTTGAAACAAAAATTTGTCTCTCTGGAGACAGTTTCTCTTGAAACAC--AAAACCTTTG
3351065 AAGTT
64 AAGTT
3351070 GTTTCTCTTGAAACACAAAA
1 GTTTCTCTTGAAACA-AAAA
3351090 AACCTTTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
67 49 0.62
70 25 0.32
71 5 0.06
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (68 bp):
GTTTCTCTTGAAACAAAAATTTGTCTCTCTGGAGACAGTTTCTCTTGAAACACAAAACCTTTGAA
GTT
Found at i:3351079 original size:33 final size:32
Alignment explanation
Indices: 3351037--3351156 Score: 147
Period size: 33 Copynumber: 3.8 Consensus size: 32
3351027 TCTGGAGACA
* *
3351037 GTTTCTCTTGAAACACAAAAAACCTTTGAAGTT
1 GTTTCTCTTGAAACA-AAAAAACCTTTGAAATC
*
3351070 GTTTCTCTTGAAACACAAAAAACCTTTAAAATC
1 GTTTCTCTTGAAACA-AAAAAACCTTTGAAATC
*
3351103 GTTTCTCTTG--A-AAAAAAACCTTTGAAAAC
1 GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
* *
3351132 ATTTCTCTTGAAACAAAAAGACCTT
1 GTTTCTCTTGAAACAAAAAAACCTT
3351157 CGAGTTCGAC
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
29 24 0.31
30 1 0.01
31 2 0.03
32 10 0.13
33 40 0.52
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
Found at i:3351120 original size:29 final size:29
Alignment explanation
Indices: 3351053--3351150 Score: 99
Period size: 29 Copynumber: 3.2 Consensus size: 29
3351043 CTTGAAACAC
* * *
3351053 AAAAAACCTTTGAAGTTGTTTCTCTTGAAACA
1 AAAAAACCTTTAAAATCGTTTCTCTTG--A-A
3351085 CAAAAAACCTTTAAAATCGTTTCTCTTGAA
1 -AAAAAACCTTTAAAATCGTTTCTCTTGAA
*
3351115 AAAAAACCTTTGAAAA-CATTTCTCTTGAA
1 AAAAAACCTTT-AAAATCGTTTCTCTTGAA
3351144 ACAAAAA
1 A-AAAAA
3351151 GACCTTCGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
29 24 0.41
30 10 0.17
31 1 0.02
33 24 0.41
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAAACCTTTAAAATCGTTTCTCTTGAA
Found at i:3351301 original size:83 final size:83
Alignment explanation
Indices: 3351148--3351415 Score: 374
Period size: 83 Copynumber: 3.2 Consensus size: 83
3351138 CTTGAAACAA
* *
3351148 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTACAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACTA
*
3351213 GAAGGGTTATATGCCAAC
66 GAAGGGTTATCTGCCAAC
* * * * * ** * * *
3351231 AAAGACCTTCGAGTTCAACCATGCTCAGCTCAAAGGCACATCATTTGCAGCATGGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACTA
* *
3351296 TAAGGGTTATCTGCTAAC
66 GAAGGGTTATCTGCCAAC
*
3351314 AAAGAACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTACAGCATAACTCAAGACT
1 AAAG-ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACT
*
3351379 AGAAGGGTTATCTGTCAAC
65 AGAAGGGTTATCTGCCAAC
3351398 AAAGACCTTCGAGTTCGA
1 AAAGACCTTCGAGTTCGA
3351416 TTCCATTCAG
Statistics
Matches: 156, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
83 87 0.56
84 69 0.44
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGACTA
GAAGGGTTATCTGCCAAC
Found at i:3351783 original size:3 final size:3
Alignment explanation
Indices: 3351757--3351813 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
3351747 TCTACAAAAA
3351757 TAT T-T TAT TA- TAT TA- TAT TAAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
3351799 TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
3351814 TTTTTTATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 10 0.21
3 35 0.73
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3351822 original size:17 final size:17
Alignment explanation
Indices: 3351756--3351813 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
3351746 GTCTACAAAA
3351756 ATATT-TTATTA-TATT
1 ATATTATTATTATTATT
3351771 ATATTAATTATTATTATT
1 ATATT-ATTATTATTATT
3351789 ATATTATTATTATTATT
1 ATATTATTATTATTATT
*
3351806 ATTTTATT
1 ATATTATT
3351814 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
15 5 0.13
17 25 0.64
18 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATTATTATTATT
Found at i:3351826 original size:6 final size:6
Alignment explanation
Indices: 3351757--3351813 Score: 70
Period size: 5 Copynumber: 10.2 Consensus size: 6
3351747 TCTACAAAAA
3351757 TATT-T TATTA- TATTA- TATTAAT TATTAT TATTA- TATTAT TATTAT
1 TATTAT TATTAT TATTAT TATT-AT TATTAT TATTAT TATTAT TATTAT
3351802 TATTAT T-TTAT T
1 TATTAT TATTAT T
3351814 TTTTTTATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
5 23 0.48
6 21 0.44
7 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTAT
Found at i:3351913 original size:33 final size:33
Alignment explanation
Indices: 3351876--3351990 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
3351866 GAAAATAAAT
*
3351876 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
3351909 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
3351942 CAACGTATTTGAGTCCTATTAAAACACTAAAATC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAA-C
* *
3351976 GAA-GCATTTGAGTCC
1 CAACGTATTTGAGTCC
3351991 AAGTAGGACT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
33 75 0.96
34 3 0.04
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:3352540 original size:4 final size:4
Alignment explanation
Indices: 3352526--3352587 Score: 67
Period size: 4 Copynumber: 15.2 Consensus size: 4
3352516 TGATAATACA
3352526 TTAT TTA- TTAT TTAT TTAT TTAT TTA- TTAT TTATT TTATT TTATT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTA-T TTA-T TTAT
3352575 TTGA- TTAT TTAT T
1 TT-AT TTAT TTAT T
3352588 ATTCATTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
3 7 0.13
4 31 0.58
5 15 0.28
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3352546 original size:15 final size:15
Alignment explanation
Indices: 3352526--3352587 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
3352516 TGATAATACA
3352526 TTATTTATTATTTAT
1 TTATTTATTATTTAT
3352541 TTATTTATT-TATTAT
1 TTATTTATTAT-TTAT
3352556 TTA-TT-TTATTTTATT
1 TTATTTATTA-TTTA-T
3352571 TTATTTGATTATTTAT
1 TTATTT-ATTATTTAT
3352587 T
1 T
3352588 ATTCATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.05
14 6 0.15
15 21 0.52
16 4 0.10
17 4 0.10
18 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TTATTTATTATTTAT
Found at i:3352550 original size:19 final size:19
Alignment explanation
Indices: 3352526--3352595 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
3352516 TGATAATACA
3352526 TTATTTATTATTTATTTAT
1 TTATTTATTATTTATTTAT
3352545 TTATTTATTATTTATTT-T
1 TTATTTATTATTTATTTAT
*
3352563 AT-TTTA-T-TTTATTTGA-
1 TTATTTATTATTTATTT-AT
*
3352579 TTATTTATTATTCATTT
1 TTATTTATTATTTATTT
3352596 TTTCTTTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.16
16 2 0.05
17 8 0.19
18 3 0.07
19 23 0.53
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (19 bp):
TTATTTATTATTTATTTAT
Found at i:3352589 original size:15 final size:13
Alignment explanation
Indices: 3352525--3352597 Score: 56
Period size: 15 Copynumber: 5.0 Consensus size: 13
3352515 ATGATAATAC
3352525 ATTATTTATTATTT
1 ATTATTTATT-TTT
3352539 ATTTATTTATTTATT
1 A-TTATTTATTT-TT
3352554 ATTTATTTTATTTTAT
1 A-TTA-TTTATTTT-T
*
3352570 TTTATTTGATTATTT
1 ATTATTT-ATT-TTT
*
3352585 ATTATTCATTTTT
1 ATTATTTATTTTT
3352598 TCTTTTTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.06
14 8 0.16
15 29 0.58
16 10 0.20
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (13 bp):
ATTATTTATTTTT
Found at i:3355934 original size:21 final size:21
Alignment explanation
Indices: 3355882--3355934 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3355872 CAAGCAGGGT
* *
3355882 GTATCGATACTACCAAGGAGA
1 GTATCAATACTACCAAGGAAA
* *
3355903 GTACCAGTACTACCAAGGAAA
1 GTATCAATACTACCAAGGAAA
3355924 GTATCAATACT
1 GTATCAATACT
3355935 TCCCCTACAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
GTATCAATACTACCAAGGAAA
Found at i:3356116 original size:33 final size:33
Alignment explanation
Indices: 3356074--3356139 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
3356064 CTTTTGATGG
3356074 TTAATTTTGACCTATTTGAGGCCCATAAGAGCT
1 TTAATTTTGACCTATTTGAGGCCCATAAGAGCT
*
3356107 TTAATTTTGACCTATTTGATGCCCATAAGAGCT
1 TTAATTTTGACCTATTTGAGGCCCATAAGAGCT
3356140 AAGGAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (33 bp):
TTAATTTTGACCTATTTGAGGCCCATAAGAGCT
Found at i:3356835 original size:17 final size:16
Alignment explanation
Indices: 3356813--3356845 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3356803 AGAAGAGACT
3356813 TATAATAATAATGATTA
1 TATAATAATAAT-ATTA
3356830 TATAATAATAATATTA
1 TATAATAATAATATTA
3356846 ATTGTGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATAATAATAATATTA
Found at i:3359550 original size:14 final size:15
Alignment explanation
Indices: 3359526--3359558 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3359516 AAAAGTATTC
*
3359526 GTGTAGAGGATCTTA
1 GTGTAGAGGATCTAA
3359541 GTGT-GAGGATCTAA
1 GTGTAGAGGATCTAA
3359555 GTGT
1 GTGT
3359559 CGAGTAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.06, G:0.36, T:0.33
Consensus pattern (15 bp):
GTGTAGAGGATCTAA
Found at i:3361123 original size:17 final size:16
Alignment explanation
Indices: 3361101--3361134 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3361091 TAAAAACAGT
3361101 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3361118 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3361134 A
1 A
3361135 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3364718 original size:72 final size:72
Alignment explanation
Indices: 3364593--3364727 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
3364583 GCTAGGGATA
*
3364593 TAAGTTTCCAATGCACATAAAATTCTGGTTCTTACCCTGAGACTCTCAAGTATTCAAGATAGGAT
1 TAAGTTTCCAATGCACATAAAATTCTGGTTCTTACCCTGAGACTATCAAGTATTCAAGATAGGAT
3364658 AAGGGTG
66 AAGGGTG
* * * * * *
3364665 TAAGTTTTCTATGCA-AGTAAAATTTTGGTTCTTACCTTGAGACTATCACGTATTCAAGGTAGG
1 TAAGTTTCCAATGCACA-TAAAATTCTGGTTCTTACCCTGAGACTATCAAGTATTCAAGATAGG
3364728 CTAGTGTGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.02
72 54 0.98
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (72 bp):
TAAGTTTCCAATGCACATAAAATTCTGGTTCTTACCCTGAGACTATCAAGTATTCAAGATAGGAT
AAGGGTG
Found at i:3371789 original size:10 final size:10
Alignment explanation
Indices: 3371774--3371807 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3371764 ATATCCACTA
3371774 TATATTATAG
1 TATATTATAG
3371784 TATATTATAG
1 TATATTATAG
*
3371794 TTATAATATAG
1 -TATATTATAG
3371805 TAT
1 TAT
3371808 GTATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
TATATTATAG
Found at i:3371798 original size:21 final size:21
Alignment explanation
Indices: 3371774--3371820 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3371764 ATATCCACTA
3371774 TATATTATAGTATAT-TATAGT
1 TATATTATAGTATATATATA-T
* *
3371795 TATAATATAGTATGTATATAT
1 TATATTATAGTATATATATAT
3371816 TATAT
1 TATAT
3371821 AATATAAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (21 bp):
TATATTATAGTATATATATAT
Found at i:3371877 original size:25 final size:26
Alignment explanation
Indices: 3371809--3371877 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 26
3371799 ATATAGTATG
* *
3371809 TATATATTATATAATATAAACGTAACA
1 TATATATTATAAAATACAAAC-TAACA
**
3371836 TATATACTTATTCAATACAAA-TAA-A
1 TATATA-TTATAAAATACAAACTAACA
3371861 TATATAGTTATAAAATA
1 TATATA-TTATAAAATA
3371878 TTTATACTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 15 0.43
26 3 0.09
27 6 0.17
28 11 0.31
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (26 bp):
TATATATTATAAAATACAAACTAACA
Found at i:3371921 original size:251 final size:250
Alignment explanation
Indices: 3371487--3372234 Score: 1237
Period size: 251 Copynumber: 3.0 Consensus size: 250
3371477 ATACTATAAT
* *
3371487 ATAAATATGTTATGTAATGTATGGGCACAATATATATATCCACTATATATTATAG-------TA-
1 ATAAATATGTTATGTAATATATGGACACAATATATATATCCACTATATATTATAGTATATTATAT
*
3371544 TATAATATAGTATGTATATATTATATAATATAAACATAACATATATACTTATTCAATACAAATAA
66 TATAATATAGTATGTATATATTATATAATATAAACGTAACATATATACTTATTCAATACAAATAA
3371609 ATATATAGTCATATAATGTTTATACTATATAATATAAATAGACTAATATATTTAAATATAATAAT
131 ATATATAGTCATATAATGTTTATACTATATAATATAAATAGACTAATATATTTAAATATAATAAT
* * *
3371674 AATATATAAACAAGGGCAGACGAAAATGTGTGCCTACAACTGCCCCTCTTTACCC
196 AATATATAAACAAGGGCGGACGAAAATGTGTGTCTATAACTGCCCCTCTTTACCC
3371729 ATAAATATGTTATGTAATATATGGACACAATATATATATCCACTATATATTATAGTATATTATAG
1 ATAAATATGTTATGTAATATATGGACACAATATATATATCCACTATATATTATAGTATATTATA-
3371794 TTATAATATAGTATGTATATATTATATAATATAAACGTAACATATATACTTATTCAATACAAATA
65 TTATAATATAGTATGTATATATTATATAATATAAACGTAACATATATACTTATTCAATACAAATA
* * *
3371859 AATATATAGTTATAAAATATTTATACTATATAATATAAATAGACTAATATATTTAAATATAATAA
130 AATATATAGTCATATAATGTTTATACTATATAATATAAATAGACTAATATATTTAAATATAATAA
**
3371924 TAAT-TGATAAACAAGGGCGGATAAAAATGTGTGTCTATAACTGCCCCTCTTTACCC
195 TAATAT-ATAAACAAGGGCGGACGAAAATGTGTGTCTATAACTGCCCCTCTTTACCC
*
3371980 ATAAATATGTTATGTAATATATGGACACAATATATATATCCACTATATACTATAGTATATTATAA
1 ATAAATATGTTATGTAATATATGGACACAATATATATATCCACTATATATTATAGTATATTAT-A
3372045 TATATAATATAGTATGTATATATTATATAATATAAACGTAACATATATACTTATTCAATACAAAT
65 T-TATAATATAGTATGTATATATTATATAATATAAACGTAACATATATACTTATTCAATACAAA-
*
3372110 TAAA-ATATAGTCATATAATGTTTATACTATATAATATAAATAGACTAATATATATAAATATAAT
128 TAAATATATAGTCATATAATGTTTATACTATATAATATAAATAGACTAATATATTTAAATATAAT
* * *
3372174 AATAATAGATAAACAAGGGCGGACGAAAATATGTGTCTATATCTGCCCCTCTTTACCC
193 AATAATATATAAACAAGGGCGGACGAAAATGTGTGTCTATAACTGCCCCTCTTTACCC
3372232 ATA
1 ATA
3372235 GTCGTGCAAC
Statistics
Matches: 471, Mismatches: 21, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
242 53 0.11
249 2 0.00
250 1 0.00
251 237 0.50
252 174 0.37
253 4 0.01
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (250 bp):
ATAAATATGTTATGTAATATATGGACACAATATATATATCCACTATATATTATAGTATATTATAT
TATAATATAGTATGTATATATTATATAATATAAACGTAACATATATACTTATTCAATACAAATAA
ATATATAGTCATATAATGTTTATACTATATAATATAAATAGACTAATATATTTAAATATAATAAT
AATATATAAACAAGGGCGGACGAAAATGTGTGTCTATAACTGCCCCTCTTTACCC
Found at i:3372176 original size:18 final size:19
Alignment explanation
Indices: 3372138--3372177 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3372128 TGTTTATACT
*
3372138 ATATAATATAAATAGACTA
1 ATATAATATAAATAGAATA
*
3372157 ATAT-ATATAAATATAATA
1 ATATAATATAAATAGAATA
3372175 ATA
1 ATA
3372178 ATAGATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATAATATAAATAGAATA
Found at i:3373814 original size:15 final size:15
Alignment explanation
Indices: 3373785--3373831 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3373775 CACCCTAAAC
*
3373785 GTTTTTCTTTCTTTTT
1 GTTTTTGTTT-TTTTT
*
3373801 TTTTTTGTTTTTTTT
1 GTTTTTGTTTTTTTT
*
3373816 GTTTTAGTTTTTTTT
1 GTTTTTGTTTTTTTT
3373831 G
1 G
3373832 CTTCAACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (15 bp):
GTTTTTGTTTTTTTT
Found at i:3377417 original size:22 final size:22
Alignment explanation
Indices: 3377347--3377426 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
3377337 TCCCACACAG
3377347 AATGAAAGAAAATTAAATTCCAA
1 AATGAAAGAAAATTAAATT-CAA
* * * * *
3377370 AAGGAGATGAAACA--AAGTACAG
1 AATGA-AAGAAA-ATTAAATTCAA
3377392 AATGAAAGAAAATTAAATTCAA
1 AATGAAAGAAAATTAAATTCAA
*
3377414 AATGAAATAAAAT
1 AATGAAAGAAAAT
3377427 GAAGTAAGAA
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
20 1 0.02
21 5 0.12
22 23 0.55
23 7 0.17
24 5 0.12
25 1 0.02
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (22 bp):
AATGAAAGAAAATTAAATTCAA
Found at i:3383621 original size:3 final size:3
Alignment explanation
Indices: 3383602--3383636 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3383592 TAAATTTGAC
*
3383602 ATA ATA GTA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3383637 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3384303 original size:5 final size:5
Alignment explanation
Indices: 3384293--3384317 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3384283 GTGTCTTAAT
3384293 GGTTA GGTTA GGTTA GGTTA GGTTA
1 GGTTA GGTTA GGTTA GGTTA GGTTA
3384318 CGATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GGTTA
Found at i:3384456 original size:20 final size:20
Alignment explanation
Indices: 3384431--3384477 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3384421 ATAGATTGTC
3384431 ACATCAATACTGTAACTAAT
1 ACATCAATACTGTAACTAAT
*
3384451 ACATCAATATTGTAACTAAT
1 ACATCAATACTGTAACTAAT
3384471 ACATCAA
1 ACATCAA
3384478 CACCGTGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (20 bp):
ACATCAATACTGTAACTAAT
Found at i:3385195 original size:13 final size:13
Alignment explanation
Indices: 3385177--3385225 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3385167 TTTAAACTAT
3385177 AATAAAATATAAA
1 AATAAAATATAAA
3385190 AATAAAA-ATAAAA
1 AATAAAATAT-AAA
*
3385203 AATATAAT-T-AA
1 AATAAAATATAAA
3385214 AATAAAAATATA
1 AAT-AAAATATA
3385226 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
11 5 0.17
12 6 0.21
13 18 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAATATAAA
Found at i:3385196 original size:6 final size:6
Alignment explanation
Indices: 3385177--3385223 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
3385167 TTTAAACTAT
* *
3385177 AATAAA ATATAAA AATAAA AATAAA AA-ATAT AATTAA AATAAA AATA
1 AATAAA A-ATAAA AATAAA AATAAA AATA-AA AATAAA AATAAA AATA
3385224 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 1 0.03
6 27 0.79
7 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:3385201 original size:19 final size:19
Alignment explanation
Indices: 3385177--3385225 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3385167 TTTAAACTAT
3385177 AATAAAATATAAAAATAAA
1 AATAAAATATAAAAATAAA
* * *
3385196 AATAAAAAAT-ATAATTAA
1 AATAAAATATAAAAATAAA
3385214 AATAAAAATATA
1 AAT-AAAATATA
3385226 TTTTTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAAAATATAAAAATAAA
Found at i:3385226 original size:19 final size:19
Alignment explanation
Indices: 3385180--3385226 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3385170 AAACTATAAT
*
3385180 AAAATATAAAAATAAAAATA
1 AAAATAT-ATAATAAAAATA
*
3385200 AAAA-ATATAATTAAAATA
1 AAAATATATAATAAAAATA
3385218 AAAATATAT
1 AAAATATAT
3385227 TTTTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.58
19 6 0.25
20 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATATATAATAAAAATA
Found at i:3386772 original size:21 final size:21
Alignment explanation
Indices: 3386746--3386785 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3386736 CCAAAGCATG
*
3386746 AATACTCGCTCTCATATCATC
1 AATACTAGCTCTCATATCATC
3386767 AATACTAGCTCTCATATCA
1 AATACTAGCTCTCATATCA
3386786 ACAACATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (21 bp):
AATACTAGCTCTCATATCATC
Found at i:3386796 original size:21 final size:21
Alignment explanation
Indices: 3386753--3386802 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3386743 ATGAATACTC
* *
3386753 GCTCTCATATCATCAATACTA
1 GCTCTCATATCAACAACACTA
*
3386774 GCTCTCATATCAACAACATTA
1 GCTCTCATATCAACAACACTA
*
3386795 GCTTTCAT
1 GCTCTCAT
3386803 GGCATCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (21 bp):
GCTCTCATATCAACAACACTA
Found at i:3390494 original size:2 final size:2
Alignment explanation
Indices: 3390487--3390511 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3390477 TTTATCATGA
3390487 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3390512 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3398819 original size:29 final size:29
Alignment explanation
Indices: 3398771--3398843 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
3398761 TGGACGAACT
3398771 TAATTGATTTTTTAGTTATGTTCAAGGACC
1 TAATTGA-TTTTTAGTTATGTTCAAGGACC
3398801 TAATTGATTTTTAGTTATGTTCAAGGACC
1 TAATTGATTTTTAGTTATGTTCAAGGACC
3398830 TAATTGATTTTTAG
1 TAATTGATTTTTAG
3398844 AATATCGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 36 0.84
30 7 0.16
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.48
Consensus pattern (29 bp):
TAATTGATTTTTAGTTATGTTCAAGGACC
Found at i:3399213 original size:8 final size:8
Alignment explanation
Indices: 3399185--3399239 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
3399175 ACAAAAAAAT
3399185 AATAAT-A
1 AATAATAA
3399192 AATGAATAA
1 AAT-AATAA
3399201 GAATAATAA
1 -AATAATAA
*
3399210 AATAAAAA
1 AATAATAA
3399218 AATAATATA
1 AATAATA-A
3399227 AAT-ATAA
1 AATAATAA
3399234 AATAAT
1 AATAAT
3399240 TAAACAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.17
8 21 0.51
9 10 0.24
10 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:3399237 original size:29 final size:29
Alignment explanation
Indices: 3399205--3399277 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
3399195 GAATAAGAAT
3399205 AATAAAATAAAAAAATA-ATATAAATATAA
1 AATAAAATAAAAAAATATATATAAA-ATAA
* *
3399234 AAT-AATTAAACAAAATATATGTAAAATAA
1 AATAAAATAAA-AAAATATATATAAAATAA
**
3399263 TTTAAAAATAAAAAA
1 AAT-AAAATAAAAAA
3399278 GAATAAGTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.17
29 14 0.40
30 9 0.26
31 6 0.17
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (29 bp):
AATAAAATAAAAAAATATATATAAAATAA
Found at i:3400809 original size:31 final size:30
Alignment explanation
Indices: 3400702--3400810 Score: 77
Period size: 31 Copynumber: 3.6 Consensus size: 30
3400692 AAACTATACA
*
3400702 ATATATTTTCCAAAAAAAATTTTTTAAAA-ATT
1 ATATATTTT-C-AAAAAAATTTTTCAAAATA-T
* **
3400734 ATATAATTTCAAAAGCA--TTTCAAACTATAT
1 ATATATTTTCAAAAAAATTTTTCAAA--ATAT
3400764 ATATATGTTT---AAAAATGTTTTCAAAATAT
1 ATATAT-TTTCAAAAAAAT-TTTTCAAAATAT
3400793 ATATATTTTCAAAAAAAT
1 ATATATTTTCAAAAAAAT
3400811 AATTTTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 21
0.68 0.08 0.24
Matches are distributed among these distances:
28 12 0.20
29 10 0.17
30 12 0.20
31 18 0.30
32 8 0.13
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (30 bp):
ATATATTTTCAAAAAAATTTTTCAAAATAT
Found at i:3400886 original size:36 final size:34
Alignment explanation
Indices: 3400836--3400957 Score: 126
Period size: 36 Copynumber: 3.6 Consensus size: 34
3400826 AACTATATAG
*
3400836 TATATATATGTTTTCAAAAAAAGGTTTTTTCAAAAC
1 TATATATATATTTTCAAAAAAA--TTTTTTCAAAAC
*
3400872 TATATATATATTTTC---AAAA-TATTTCAAAAC
1 TATATATATATTTTCAAAAAAATTTTTTCAAAAC
* **
3400902 TATATATATATGTTTTCAAAAATATTTTTAAAAAAC
1 TATATATATA--TTTTCAAAAAAATTTTTTCAAAAC
3400938 TATATATTATATTTTCAAAA
1 TATATA-TATATTTTCAAAA
3400958 TGATTTCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
30 20 0.27
32 5 0.07
33 4 0.05
35 12 0.16
36 28 0.38
37 4 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (34 bp):
TATATATATATTTTCAAAAAAATTTTTTCAAAAC
Found at i:3400910 original size:34 final size:34
Alignment explanation
Indices: 3400872--3401052 Score: 178
Period size: 35 Copynumber: 5.3 Consensus size: 34
3400862 TTTTCAAAAC
*
3400872 TATATATATATTTTC-AAAATATTTCAAAA-CTA
1 TATATATATATTTTCAAAAATATTTCAAAATATA
* * *
3400904 TATATATATGTTTTCAAAAATATTTTTAAAAAACTA
1 TATATATATATTTTCAAAAATA-TTTCAAAATA-TA
3400940 TATAT-TATATTTTC-AAAATGATTTCAAAA-ATTA
1 TATATATATATTTTCAAAAAT-ATTTCAAAATA-TA
* * *
3400973 TATATATTATATTTTCTAAAATGTTTTAAAATATA
1 TATATA-TATATTTTCAAAAATATTTCAAAATATA
*
3401008 T-TATATA-ATTTTCAAAAATCATTTGCAAACTATA
1 TATATATATATTTTCAAAAAT-ATTT-CAAAATATA
3401042 TATATATATAT
1 TATATATATAT
3401053 ATATGTAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
32 25 0.20
33 19 0.15
34 31 0.25
35 34 0.27
36 15 0.12
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (34 bp):
TATATATATATTTTCAAAAATATTTCAAAATATA
Found at i:3400919 original size:68 final size:66
Alignment explanation
Indices: 3400836--3401048 Score: 229
Period size: 68 Copynumber: 3.1 Consensus size: 66
3400826 AACTATATAG
3400836 TATATATATGTTTTCAAAAAAAGGTTTTTTCAAAACTATATATATATTTTCAAAAT-ATTTCAAA
1 TATATATATGTTTTCAAAAAAA--TTTTTT-AAAACTATATATATATTTTCAAAATCATTTCAAA
3400900 ACTA
63 ACTA
* * *
3400904 TATATATATGTTTTCAAAAATATTTTTAAAAAACTATATATTATATTTTCAAAATGATTTCAAAA
1 TATATATATGTTTTCAAAAAAATTTTT-TAAAACTATATA-TATATTTTCAAAATCATTTC-AAA
*
3400969 ATTA
63 ACTA
* * *
3400973 TATATATTATATTTTC--TAAAATGTTTTAAAA-TATATTATATAATTTTCAAAAATCATTTGC-
1 TATATA-TATGTTTTCAAAAAAATTTTTTAAAACTATA-TATAT-ATTTTC-AAAATCATTT-CA
3401034 AAACTA
61 AAACTA
3401040 TATATATAT
1 TATATATAT
3401049 ATATATATGT
Statistics
Matches: 126, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
66 26 0.21
67 37 0.29
68 42 0.33
69 13 0.10
70 8 0.06
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (66 bp):
TATATATATGTTTTCAAAAAAATTTTTTAAAACTATATATATATTTTCAAAATCATTTCAAAACT
A
Found at i:3402466 original size:80 final size:80
Alignment explanation
Indices: 3402354--3402598 Score: 388
Period size: 80 Copynumber: 3.1 Consensus size: 80
3402344 ACCTTTTTTG
* *
3402354 TGATGTATATAGATTGAAT-AGATCTGGACCGATTAGTATCATGCGGGTGAATGTCTATGTCTGC
1 TGATGTATACAGATTGAATAAGATCTGGACCGATTAGTATCATGCGGGTGAATATCTATGTCTGC
*
3402418 TGGTTTAATTCTTGT
66 TGGTTTGATTCTTGT
* *
3402433 TGATGTATACAGATTGAATAAGATCTGGACCGATTAGTATCATGCGGGTGAATATCTATATCTTC
1 TGATGTATACAGATTGAATAAGATCTGGACCGATTAGTATCATGCGGGTGAATATCTATGTCTGC
*
3402498 TGGTTTGATTCTTCT
66 TGGTTTGATTCTTGT
3402513 TGATGTATACAGATTG-ATAAGATCTGGACCGATTAGTATCATGCGGGTGAATATCTATGT-TGC
1 TGATGTATACAGATTGAATAAGATCTGGACCGATTAGTATCATGCGGGTGAATATCTATGTCTGC
* *
3402576 TGTTTTGATTCTTGG
66 TGGTTTGATTCTTGT
*
3402591 TGGTGTAT
1 TGATGTAT
3402599 TTTGGGGTGG
Statistics
Matches: 153, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
78 21 0.14
79 61 0.40
80 71 0.46
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (80 bp):
TGATGTATACAGATTGAATAAGATCTGGACCGATTAGTATCATGCGGGTGAATATCTATGTCTGC
TGGTTTGATTCTTGT
Found at i:3403746 original size:92 final size:96
Alignment explanation
Indices: 3403636--3403823 Score: 348
Period size: 96 Copynumber: 2.0 Consensus size: 96
3403626 ATGAATTCTA
3403636 TATAGTCCAAAATTCGATTGTATTTC-TCCTTGC-TATTTATATGC-A-ATTTCTTTCAGGGAAT
1 TATAGTCCAAAATTCGATTGTATTTCGTCCTTGCTTATTTATATGCAATATTTCTTTCAGGGAAT
3403697 TTGCAAAAAACTCGGGAAGGTTTTACGTTCG
66 TTGCAAAAAACTCGGGAAGGTTTTACGTTCG
3403728 TATAGTCCAAAATTCGATTGTATTTCGTCCTTGCTTATTTATATGCAATATTTCTTTCAGGGAAT
1 TATAGTCCAAAATTCGATTGTATTTCGTCCTTGCTTATTTATATGCAATATTTCTTTCAGGGAAT
3403793 TTGCAAAAAACTCGGGAAGGTTTTACGTTCG
66 TTGCAAAAAACTCGGGAAGGTTTTACGTTCG
3403824 AGTTCGTGGC
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
92 26 0.28
93 7 0.08
94 11 0.12
95 1 0.01
96 47 0.51
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (96 bp):
TATAGTCCAAAATTCGATTGTATTTCGTCCTTGCTTATTTATATGCAATATTTCTTTCAGGGAAT
TTGCAAAAAACTCGGGAAGGTTTTACGTTCG
Found at i:3404314 original size:92 final size:93
Alignment explanation
Indices: 3404207--3404558 Score: 373
Period size: 92 Copynumber: 3.8 Consensus size: 93
3404197 GGAAACGGAC
*
3404207 GGTAGAACAAGATGAAGA-GAAAGAA-AGAGAGAAAAAAGACAAGGATGAGAAGGAGAAGAAAAA
1 GGTAGAAGAAGATGAAGATGAAAGAAGAGA-AGAAAAAAGACAAGGATGAGAAGGAGAAGAAAAA
3404270 -GAAAAGAAGCACAAGAAAAAGGAGGTCGA
65 GGAAAAGAAGCACAAGAAAAA-GAGGTCGA
* * * * * * *
3404299 GGGAGAAGGAGATGAAG-TGAAAGATGAGAAGAAAAAAGAAAAAGAACATGGGAAGGATAAGAAA
1 GGTAGAAGAAGATGAAGATGAAAGAAGAGAAGAAAAAAG-ACAAG--GATGAGAAGGAGAAGAAA
* *
3404363 AAGGAAAATACGCACAAGGAAAAAGAGGTCGA
63 AAGGAAAAGAAGCACAA-GAAAAAGAGGTCGA
3404395 GGTAGAAGAAGATGAAGATG-AAGAAGAGAAGAAGAAAA-ACAAGGATGAGAAGGAGAAGAAAAA
1 GGTAGAAGAAGATGAAGATGAAAGAAGAGAAGAA-AAAAGACAAGGATGAGAAGGAGAAGAAAAA
** * *
3404458 GGATGAGAAGCATAAGGAAAAGAGGTCGA
65 GGAAAAGAAGCACAAGAAAAAGAGGTCGA
* * * * * *
3404487 GGTAAAAGAAGAAGAA-ATGAGAAGAA-AAAAGAAGATAGACAAGGATGATAAGGAGAA-AAGAA
1 GGTAGAAGAAGATGAAGATGA-AAGAAGAGAAGAAAAAAGACAAGGATGAGAAGGAGAAGAA-AA
3404549 AGG-AAAGAAG
64 AGGAAAAGAAG
3404559 TTTGAAAGAT
Statistics
Matches: 216, Mismatches: 31, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
91 12 0.06
92 85 0.39
93 39 0.18
95 21 0.10
96 47 0.22
97 12 0.06
ACGTcount: A:0.57, C:0.04, G:0.32, T:0.07
Consensus pattern (93 bp):
GGTAGAAGAAGATGAAGATGAAAGAAGAGAAGAAAAAAGACAAGGATGAGAAGGAGAAGAAAAAG
GAAAAGAAGCACAAGAAAAAGAGGTCGA
Found at i:3404402 original size:96 final size:92
Alignment explanation
Indices: 3404236--3404519 Score: 300
Period size: 96 Copynumber: 3.1 Consensus size: 92
3404226 AAAGAAAGAG
* *
3404236 AGAAAAAAG-ACAAGGATGAGAAGGAGAAGAAAAA-GAAAAGAAGCACAA-GAAAAAGGAGGTCG
1 AGAAAAAAGAAAAAGCATGAGAAGGAGAAGAAAAAGGAAAAGAAGCACAAGGAAAAA-GAGGTCG
*
3404298 AGGGAGAAGGAGATGAAGTGAAAGATGAGA
65 AGGTAGAA-GAGATGAAGTG-AAGATGAGA
* * * *
3404328 AGAAAAAAGAAAAAGAACATGGGAAGGATAAGAAAAAGGAAAATACGCACAAGGAAAAAGAGGTC
1 AGAAAAAAGAAAAAG--CATGAGAAGGAGAAGAAAAAGGAAAAGAAGCACAAGGAAAAAGAGGTC
*
3404393 GAGGTAGAAGAAGATGAAGATGAAGAAGAGA
64 GAGGTAGAAG-AGATGAAG-TGAAGATGAGA
* * * ** *
3404424 AGAAGAAA-AACAAGGATGAGAAGGAGAAGAAAAAGGATGAGAAGCATAAGG-AAAAGAGGTCGA
1 AGAAAAAAGAAAAAGCATGAGAAGGAGAAGAAAAAGGAAAAGAAGCACAAGGAAAAAGAGGTCGA
*
3404487 GGTA-AA-AGAAGAA--GAA-ATGAGA
66 GGTAGAAGAGATGAAGTGAAGATGAGA
3404509 AGAAAAAAGAA
1 AGAAAAAAGAA
3404520 GATAGACAAG
Statistics
Matches: 163, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
85 12 0.07
86 5 0.03
89 6 0.04
91 2 0.01
92 25 0.15
93 33 0.20
95 23 0.14
96 49 0.30
97 8 0.05
ACGTcount: A:0.57, C:0.04, G:0.32, T:0.06
Consensus pattern (92 bp):
AGAAAAAAGAAAAAGCATGAGAAGGAGAAGAAAAAGGAAAAGAAGCACAAGGAAAAAGAGGTCGA
GGTAGAAGAGATGAAGTGAAGATGAGA
Found at i:3404446 original size:21 final size:21
Alignment explanation
Indices: 3404420--3404467 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3404410 AGATGAAGAA
3404420 GAGAAGAAGAA-AAACAAGGAT
1 GAGAAGAAGAAGAAA-AAGGAT
*
3404441 GAGAAGGAGAAGAAAAAGGAT
1 GAGAAGAAGAAGAAAAAGGAT
3404462 GAGAAG
1 GAGAAG
3404468 CATAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.04
Consensus pattern (21 bp):
GAGAAGAAGAAGAAAAAGGAT
Found at i:3404478 original size:21 final size:21
Alignment explanation
Indices: 3404420--3404479 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
3404410 AGATGAAGAA
*
3404420 GAGAAGAAGAA-AAACAAGGAT
1 GAGAAGCAGAAGAAA-AAGGAT
*
3404441 GAGAAGGAGAAGAAAAAGGAT
1 GAGAAGCAGAAGAAAAAGGAT
* *
3404462 GAGAAGCATAAGGAAAAG
1 GAGAAGCAGAAGAAAAAG
3404480 AGGTCGAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.33, T:0.05
Consensus pattern (21 bp):
GAGAAGCAGAAGAAAAAGGAT
Found at i:3404681 original size:39 final size:39
Alignment explanation
Indices: 3404635--3404729 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 39
3404625 TGAAAGGAGG
**
3404635 AGAGAAGAAAGAAAAG-AAAAAGAGGATGA-GGTGAAAGA
1 AGAGAAGAAAGAAAAGAAAAAAGAGGA-GACGAAGAAAGA
*
3404673 AGATGAAGAAATAGAAGAGAAAAAAGAGGAGACGAAGAAAGA
1 AGA-GAAG-AA-AGAAAAGAAAAAAGAGGAGACGAAGAAAGA
*
3404715 TGAGAAGAAAGAAAA
1 AGAGAAGAAAGAAAA
3404730 ACATGAGAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
38 3 0.06
39 9 0.19
40 4 0.09
41 12 0.26
42 19 0.40
ACGTcount: A:0.62, C:0.01, G:0.32, T:0.05
Consensus pattern (39 bp):
AGAGAAGAAAGAAAAGAAAAAAGAGGAGACGAAGAAAGA
Found at i:3404821 original size:111 final size:108
Alignment explanation
Indices: 3404734--3404985 Score: 256
Period size: 111 Copynumber: 2.4 Consensus size: 108
3404724 AGAAAAACAT
* * * *
3404734 GAGAAGGAGAAGAAGAAAG-ATAAGAAGGATAAAGAGGTAGA-AGAAGATGACGATGATGAAATA
1 GAGAAGGAGAAGAAGAAAGAATAAGAAGGATAAAGAGGAAGAGAGAAAAAGACGACGATGAAATA
** * *
3404797 AAAGAGAGGAAGAAAGATAAGAAGAAAGA-CAAAGAGGAGAAG
66 AAAGAGAAAAAGAAAGATAAGAAGAAAGATCAAAGAGAAAAAG
* * *
3404839 GAGAAGGAGAAGAAGAAAGAAAATATGAAGGATAAAGAGGAAGAGGTAGAAAAAGATGACGGTGA
1 GAGAAGGAGAAGAAGAAAG--AATAAGAAGGATAAAGAGGAAGA-G-AGAAAAAGACGACGATGA
* *
3404904 AATGAAAGAGAAAAAGAAAGATAAGAAGAAAGAT-----A-AACAA-
62 AATAAAAGAGAAAAAGAAAGATAAGAAGAAAGATCAAAGAGAAAAAG
* *
3404944 GAGAAGGAGAAGAAGAAAGAA-AAGGAGGATAATGAGGAAGAG
1 GAGAAGGAGAAGAAGAAAGAATAAGAAGGATAAAGAGGAAGAG
3404986 GTAGATGAAG
Statistics
Matches: 125, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
101 1 0.01
102 17 0.14
103 2 0.02
105 38 0.30
106 3 0.02
107 1 0.01
108 20 0.16
111 43 0.34
ACGTcount: A:0.58, C:0.02, G:0.33, T:0.08
Consensus pattern (108 bp):
GAGAAGGAGAAGAAGAAAGAATAAGAAGGATAAAGAGGAAGAGAGAAAAAGACGACGATGAAATA
AAAGAGAAAAAGAAAGATAAGAAGAAAGATCAAAGAGAAAAAG
Found at i:3404924 original size:12 final size:12
Alignment explanation
Indices: 3404907--3404963 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
3404897 ACGGTGAAAT
3404907 GAAAGAGAAAAA
1 GAAAGAGAAAAA
* *
3404919 GAAAGATAAGAA
1 GAAAGAGAAAAA
*
3404931 GAAAGATAAACAA
1 GAAAGAGAAA-AA
*
3404944 GAGAAGGAGAAGAA
1 GA-AA-GAGAAAAA
3404958 GAAAGA
1 GAAAGA
3404964 AAAGGAGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
12 21 0.57
13 6 0.16
14 6 0.16
15 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.04
Consensus pattern (12 bp):
GAAAGAGAAAAA
Found at i:3405025 original size:105 final size:105
Alignment explanation
Indices: 3404717--3405088 Score: 286
Period size: 105 Copynumber: 3.5 Consensus size: 105
3404707 AAGAAAGATG
* * * *
3404717 AGAAGAAAGAAAAAC-ATGAGAAGGAGAAGAAGAAAGATAAGAAGGATAAAGAGGTAGA---AGA
1 AGAAG-AAGAAAGACAAAGAGAAGGAGAAGAAGAAAGAAAAGAAGGATAAAGAGGAAGAGGTAGA
* * * * * * ** *
3404778 AGATGACGATGATGAAATAAAAGAGAGGAAGAAAGATAAGA
65 AAAAGATGACGGTGAAATGAAAGAGAAAAAGAAAGAGAAGA
* *
3404819 AGAAAGACA-AAGAGGAGAAGGAGAAGGAGAAGAAGAAAGAAAATATGAAGGATAAAGAGGAAGA
1 AG-AAGA-AGAA-A-GACAAAGAGAAGGAGAAGAAGAAAG-AAA-A-GAAGGATAAAGAGGAAGA
*
3404883 GGTAGAAAAAGATGACGGTGAAATGAAAGAGAAAAAGAAAGATAAGA
59 GGTAGAAAAAGATGACGGTGAAATGAAAGAGAAAAAGAAAGAGAAGA
* *
3404930 AG-A-AAGATAA-AC-AAGAGAAGGAGAAGAAGAAAGAAAAGGAGGATAATGAGGAAGAGGTAGA
1 AGAAGAAGA-AAGACAAAGAGAAGGAGAAGAAGAAAGAAAAGAAGGATAAAGAGGAAGAGGTAGA
** *
3404991 TGAAGATGA-GGCTGACGAAATTG-AAGATG-GAAAGAAAGAGAAGA
65 AAAAGATGACGG-T---GAAA-TGAAAGA-GAAAAAGAAAGAGAAGA
3405035 AGAAGAAGAAAGACAAAGAGGTGAAGGA-AAGAAGAAAGAAAAGAA-GATCAAAGA
1 AGAAGAAGAAAGACAAAGA---GAAGGAGAAGAAGAAAGAAAAGAAGGAT-AAAGA
3405089 TGGAGAAGGT
Statistics
Matches: 220, Mismatches: 23, Indels: 46
0.76 0.08 0.16
Matches are distributed among these distances:
101 2 0.01
102 35 0.16
103 6 0.03
104 4 0.02
105 63 0.29
106 9 0.04
107 8 0.04
108 24 0.11
109 5 0.02
110 20 0.09
111 44 0.20
ACGTcount: A:0.58, C:0.02, G:0.32, T:0.08
Consensus pattern (105 bp):
AGAAGAAGAAAGACAAAGAGAAGGAGAAGAAGAAAGAAAAGAAGGATAAAGAGGAAGAGGTAGAA
AAAGATGACGGTGAAATGAAAGAGAAAAAGAAAGAGAAGA
Found at i:3405079 original size:12 final size:12
Alignment explanation
Indices: 3405021--3405081 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
3405011 TTGAAGATGG
3405021 AAAGAAAGAGAAGA
1 AAAG-AAGA-AAGA
3405035 AGAAGAAGAAAGA
1 A-AAGAAGAAAGA
* * *
3405048 CAAAGAGGTGAAGG
1 -AAAGAAG-AAAGA
3405062 AAAGAAGAAAGA
1 AAAGAAGAAAGA
3405074 AAAGAAGA
1 AAAGAAGA
3405082 TCAAAGATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
12 11 0.29
13 15 0.39
14 9 0.24
15 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.31, T:0.02
Consensus pattern (12 bp):
AAAGAAGAAAGA
Found at i:3405097 original size:36 final size:37
Alignment explanation
Indices: 3405014--3405112 Score: 102
Period size: 36 Copynumber: 2.8 Consensus size: 37
3405004 GACGAAATTG
*
3405014 AAGATGGA-AAGAAAGAGAAG-AAGAAGAAGAAAGACA
1 AAGATGGAGAAGGAA-AGAAGAAAGAAGAAGAAAGACA
*
3405050 AAGA-GGTGAAGGAAAGAAGAAAGAA-AAG-AAGATCA
1 AAGATGGAGAAGGAAAGAAGAAAGAAGAAGAAAGA-CA
*
3405085 AAGATGGAGAAGGTGAAG-AGAAAGAAGA
1 AAGATGGAGAAGG-AAAGAAGAAAGAAGA
3405113 GACAAAGAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
34 4 0.08
35 16 0.30
36 29 0.55
37 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.05
Consensus pattern (37 bp):
AAGATGGAGAAGGAAAGAAGAAAGAAGAAGAAAGACA
Found at i:3405150 original size:14 final size:14
Alignment explanation
Indices: 3405106--3405143 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
3405096 GGTGAAGAGA
3405106 AAGAAGAGACAAAG
1 AAGAAGAGACAAAG
3405120 AAGAAGAGACAAAG
1 AAGAAGAGACAAAG
3405134 AAGATAGAGA
1 AAGA-AGAGA
3405144 TAAGAAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.63, C:0.05, G:0.29, T:0.03
Consensus pattern (14 bp):
AAGAAGAGACAAAG
Found at i:3405848 original size:36 final size:36
Alignment explanation
Indices: 3405801--3405872 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3405791 ATTAAAGGAA
3405801 CTGTAGATGTGAAGACAATCGTTTTGATGTATCCTT
1 CTGTAGATGTGAAGACAATCGTTTTGATGTATCCTT
3405837 CTGTAGATGTGAAGACAATCGTTTTGATGTATCCTT
1 CTGTAGATGTGAAGACAATCGTTTTGATGTATCCTT
3405873 GGAAGAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (36 bp):
CTGTAGATGTGAAGACAATCGTTTTGATGTATCCTT
Found at i:3413035 original size:158 final size:153
Alignment explanation
Indices: 3412736--3413039 Score: 563
Period size: 158 Copynumber: 2.0 Consensus size: 153
3412726 GCAGGTAGCT
3412736 TTTAACGTAATAGGTGTCTTTTTAAAGTTGATGGGACCTTAGAAATCCGACGATAACAAAATGGT
1 TTTAACGTAATAGGTGTCTTTTTAAAGTTGATGGGACCTTAGAAATCCGACGATAACAAAATGGT
3412801 TAATTACATAATTTGTTATCATATTATAAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTT
66 TAATTACATAATTTGTTATCATATTATAAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTT
3412866 AAGCTGATGGAGCCTTGCATTTA
131 AAGCTGATGGAGCCTTGCATTTA
3412889 TTTAACGTAATATGTAGTGTCTTTTTAAAGTTGATGGGACCTTAGAAATCCGACGATAACAAAAT
1 TTTAACGTAATA-G--GTGTCTTTTTAAAGTTGATGGGACCTTAGAAATCCGACGATAACAAAAT
3412954 AGGTTAATTACATAATTTGTTATCAATATTATAAACATATTAGGTAATGCCTAAAATGTTACCAA
63 -GGTTAATTACATAATTTGTTATC-ATATTATAAACATATTAGGTAATGCCTAAAATGTTACCAA
3413019 AGTTTAAGCTGATGGAGCCTT
126 AGTTTAAGCTGATGGAGCCTT
3413040 AGAAATCTGA
Statistics
Matches: 146, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
153 12 0.08
154 1 0.01
156 49 0.34
157 23 0.16
158 61 0.42
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (153 bp):
TTTAACGTAATAGGTGTCTTTTTAAAGTTGATGGGACCTTAGAAATCCGACGATAACAAAATGGT
TAATTACATAATTTGTTATCATATTATAAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTT
AAGCTGATGGAGCCTTGCATTTA
Found at i:3413689 original size:131 final size:131
Alignment explanation
Indices: 3413219--3413700 Score: 707
Period size: 131 Copynumber: 3.7 Consensus size: 131
3413209 TATCAACATA
* *
3413219 TTACTGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCGAAATTATAAGTATCG
1 TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* * * *
3413284 ATAC-TTATATGA-CAGTATCAATACTTATACATTTACGCCTATTTTCATTATACCGATAGAAAT
66 ATACTTTATAT-ATGAGTATCGATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAAC
*
3413347 AT
130 GT
* * * *
3413349 TTAACGTGTACATTTATTAATTTACCTATTACTTTAAAGTAATAGGTTTCGATATTATAAGTATC
1 TTACCGTGTACA-TTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATC
* * * *
3413414 GATACTTTATATATGAGTATCGATACTTAGACATTTATGGCTATTTTCATTATACCGGTAAAAAC
65 GATACTTTATATATGAGTATCGATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAAC
3413479 GT
130 GT
* * *
3413481 TTATCGTATACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
1 TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* * * *
3413546 ATACATTGTATATGAGCATCGATACTTGGACATTTACGCCTATTTTCATTATACCGATAGAAACG
66 ATACTTTATATATGAGTATCGATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAACG
3413611 T
131 T
* *
3413612 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATTG
1 TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
*
3413677 ATACTTTATATATGTGTATCGATA
66 ATACTTTATATATGAGTATCGATA
3413701 TATTTTGTGT
Statistics
Matches: 311, Mismatches: 38, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
130 10 0.03
131 241 0.77
132 60 0.19
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (131 bp):
TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
ATACTTTATATATGAGTATCGATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAACG
T
Found at i:3413698 original size:262 final size:261
Alignment explanation
Indices: 3413227--3413700 Score: 781
Period size: 262 Copynumber: 1.8 Consensus size: 261
3413217 TATTACTGTG
* *
3413227 TACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCGAAATTATAAGTATCGATACTTAT
1 TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATACTTAT
* * *
3413292 ATGACAGTATCAATACTTATACATTTACGCCTATTTTCATTATACCGATAGAAATATTTAACGTG
66 ATGA-AGCATCAATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAACATTTAACGTG
*
3413357 TACATTTATTAATTTACCTATTACTTTAAAGTAATAGGTTTCGATATTATAAGTATCGATACTTT
130 TACATTTATTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTT
3413422 ATATATGAGTATCGATACTTAGACATTTATGGCTATTTTCATTATACCGGTAAAAACGTTTATCG
195 ATATATGAGTATCGATACTTAGACATTTATGGCTATTTTCATTATACCGGTAAAAACGTTTATCG
3413487 TA
260 TA
3413489 TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATACATTG
1 TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATAC--T-
* * * *
3413554 TATATG-AGCATCGATACTTGGACATTTACGCCTATTTTCATTATACCGATAGAAACGTTTACCG
63 TATATGAAGCATCAATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAACATTTAACG
* *
3413618 TGTACA-TTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATTGATACT
128 TGTACATTTATTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACT
*
3413682 TTATATATGTGTATCGATA
193 TTATATATGAGTATCGATA
3413701 TATTTTGTGT
Statistics
Matches: 196, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
262 132 0.67
263 57 0.29
264 1 0.01
265 6 0.03
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (261 bp):
TACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATACTTAT
ATGAAGCATCAATACTTAGACATTTACGCCTATTTTCATTATACCGATAGAAACATTTAACGTGT
ACATTTATTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTTA
TATATGAGTATCGATACTTAGACATTTATGGCTATTTTCATTATACCGGTAAAAACGTTTATCGT
A
Found at i:3414319 original size:380 final size:379
Alignment explanation
Indices: 3413563--3414448 Score: 1210
Period size: 380 Copynumber: 2.3 Consensus size: 379
3413553 GTATATGAGC
* * * * *
3413563 ATCGATACTTGGACATTTACGCCTATTTTCATTATACCGATAGAAACGTTTACCGTGTACATTGT
1 ATCGATACTTGG-TATTTACGCCTATTATCATTATACCGGTAG--ACTTTTACCGTTTACATTGT
* * *
3413628 TAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTAT-AAGTATTGATACTTTATATATGT
63 TAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTTTCAAGTATCGATACTTTATATATAT
* * * * *
3413692 GTATCGATATATTTTGTGTGCAAATTGTTTGAGAATCATACCAGAATAAAAGTATTGATACTTGG
128 GTATCGATACATTTTGAGTGCAAATTGTCTGAGAATCATACCAGAATAAAAGCATTGATACTTGA
** * * *
3413757 TATTTACACCTATTATCAATATAACGGTAGACTTTTATCGTTTAAATTGTTAATTTATCAATTAC
193 TAAGTACACCTATTATCAATATAACGGTAGACTTTTACCATTTAAATTGTTAATTTACCAATTAC
* * *
3413822 TTTAAAGTAATATGTTTCGAAATTCCAAGTATCAATGCTTTATATATGTGTATCAATACATTTTG
258 TTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATACA-GTGTATCAATACATTTTG
* *
3413887 CGTGCAAATTGTTTGAGAAGCATTCTGGAATAAAAGTATCCATACATATATAAA-AGT
322 CGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATACATATATAAAGAGT
* *
3413944 ATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCATTTACATTATTAA
1 ATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGTTAA
* * *
3414009 TCTACCTATTACATTAAAGTAATAGGTTTCAAAATTTTCAAGTATCGATACTTTATATATATGTA
66 TTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTTTCAAGTATCGATACTTTATATATATGTA
* *
3414074 TCGATACATTTTGAGTGCAAATTGTCTGAGAATGATA-CTGAAATAAAAGCATTGATACCTAT-A
131 TCGATACATTTTGAGTGCAAATTGTCTGAGAATCATACCAG-AATAAAAGCATTGATA-CT-TGA
*** * * *
3414137 TAAAAGTATGTCTATTATCATTAT-ACTGGTAGACTTTTACCATTTATATTGTTAATTTACCTAT
193 T--AAGTACACCTATTATCAATATAAC-GGTAGACTTTTACCATTTAAATTGTTAATTTACCAAT
* * *
3414201 TACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATACA-TGTATCAGTACGTTT
255 TACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATACAGTGTATCAATACATTT
*
3414265 TGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATACCTATATAAAGAGT
320 TGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATACATATATAAAGAGT
* * * *
3414325 ATCGGTACTTGGTATTTACACCTATTATCATTATACCGGTAGATTTTTATCGTTTACATTGTTAA
1 ATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGTTAA
* * *
3414390 TTTACCTATTATTTTAAACTAATAGGTTTCGGAA-TTTCAAGTATCGATACTTTATATAT
66 TTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTTTCAAGTATCGATACTTTATATAT
3414449 GTATATGTGC
Statistics
Matches: 445, Mismatches: 52, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
378 55 0.12
379 72 0.16
380 121 0.27
381 105 0.24
382 92 0.21
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (379 bp):
ATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGTTAA
TTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTTTCAAGTATCGATACTTTATATATATGTA
TCGATACATTTTGAGTGCAAATTGTCTGAGAATCATACCAGAATAAAAGCATTGATACTTGATAA
GTACACCTATTATCAATATAACGGTAGACTTTTACCATTTAAATTGTTAATTTACCAATTACTTT
AAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATACAGTGTATCAATACATTTTGCGTG
CAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATACATATATAAAGAGT
Found at i:3427023 original size:101 final size:102
Alignment explanation
Indices: 3426843--3427046 Score: 385
Period size: 101 Copynumber: 2.0 Consensus size: 102
3426833 ACACTAAGTG
3426843 AAGATAGGTTGGTCAAACCTAATTCTCTCCTAAGTGTCCCAAAATCTTTCCTTGTCTAAAGGTTT
1 AAGATAGGTTGGTCAAACCTAATTCTCTCCTAAGTGTCCCAAAATCTTTCCTTGTCTAAAGGTTT
3426908 TGTAAGATATCCGCTAATTGGTGCAAAGTATCAACAA
66 TGTAAGATATCCGCTAATTGGTGCAAAGTATCAACAA
3426945 AAGATAGGTTGGTCAAACCTAATTCTCTCCTAAGTGT-CCAAAATCTTTCCTTGTCTAAAGG-TT
1 AAGATAGGTTGGTCAAACCTAATTCTCTCCTAAGTGTCCCAAAATCTTTCCTTGTCTAAAGGTTT
3427008 TGTAAAGATATCCGCTAATTGGTGCAAAGTATCAACAA
66 TGT-AAGATATCCGCTAATTGGTGCAAAGTATCAACAA
3427046 A
1 A
3427047 TTCTAGAACT
Statistics
Matches: 101, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
100 5 0.05
101 59 0.58
102 37 0.37
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (102 bp):
AAGATAGGTTGGTCAAACCTAATTCTCTCCTAAGTGTCCCAAAATCTTTCCTTGTCTAAAGGTTT
TGTAAGATATCCGCTAATTGGTGCAAAGTATCAACAA
Found at i:3429564 original size:69 final size:70
Alignment explanation
Indices: 3429426--3429566 Score: 266
Period size: 69 Copynumber: 2.0 Consensus size: 70
3429416 TGCAAAACAC
3429426 TCATACTAGCATGTCCTAGTCTCCTATGCCATAACCAACTATCATGTTCATCCTTAGCAACTAGG
1 TCATACTAGCATGTCCTAGTCTCCTATGCCATAA-CAACTATCATGTTCATCCTTAGCAACTAGG
3429491 CACAAA
65 CACAAA
3429497 TCATACTAGCATGTCCTAGTCTCCTATGCCATAA-AACTATCATGTTCATCCTTAGCAACTAGGC
1 TCATACTAGCATGTCCTAGTCTCCTATGCCATAACAACTATCATGTTCATCCTTAGCAACTAGGC
3429561 ACAAA
66 ACAAA
3429566 T
1 T
3429567 TAGTATATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 36 0.51
71 34 0.49
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.29
Consensus pattern (70 bp):
TCATACTAGCATGTCCTAGTCTCCTATGCCATAACAACTATCATGTTCATCCTTAGCAACTAGGC
ACAAA
Found at i:3430417 original size:22 final size:21
Alignment explanation
Indices: 3430375--3430414 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3430365 GAGTTTATTT
*
3430375 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3430396 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3430415 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3438688 original size:60 final size:60
Alignment explanation
Indices: 3438565--3438797 Score: 238
Period size: 60 Copynumber: 3.9 Consensus size: 60
3438555 CCATAACAAA
* * ** * * * * *
3438565 CATCAATAAGAACTTACTTTAGACCC-TAGAATCTAGGAGTCTATTATAGAAGATACGTA
1 CATCCATAAGGACTTACCCTAGACCCTTAGGATCTAGGAGTCCATTATGGAAGATACATG
* *
3438624 CATCCATAAGGACTTACCCTAGACCCTTAGGATATAGGAGTCCATTATGGATGATACATG
1 CATCCATAAGGACTTACCCTAGACCCTTAGGATCTAGGAGTCCATTATGGAAGATACATG
* * * * * * *
3438684 CATCCATATGTACTTACTCTAGACCCTTAGGATCTATGAGTCTA-CATGAAAGATACATG
1 CATCCATAAGGACTTACCCTAGACCCTTAGGATCTAGGAGTCCATTATGGAAGATACATG
* * * *
3438743 CATTCATTTA-GACTTACCCTAGACCCTTAGGATCTAGGGGTCCAATATGGAAGAT
1 CATCCA-TAAGGACTTACCCTAGACCCTTAGGATCTAGGAGTCCATTATGGAAGAT
3438798 CAGAACATGC
Statistics
Matches: 141, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
59 68 0.48
60 73 0.52
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (60 bp):
CATCCATAAGGACTTACCCTAGACCCTTAGGATCTAGGAGTCCATTATGGAAGATACATG
Found at i:3441306 original size:23 final size:23
Alignment explanation
Indices: 3441280--3441357 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
3441270 CACCACAACT
3441280 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
3441303 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
3441326 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
3441349 TATAATAAT
1 CAT-ATAAT
3441358 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:3441546 original size:103 final size:103
Alignment explanation
Indices: 3441364--3441581 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
3441354 TAATGTCCAT
* *
3441364 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3441429 GACTTCACACATGTTCCAAAGAATACATATATACCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATACCCCG
*
3441467 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* **
3441532 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATACCCCG
3441570 AAGGACCACATA
1 AAGGACCACATA
3441582 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATACCCCG
Found at i:3445759 original size:28 final size:28
Alignment explanation
Indices: 3445719--3445816 Score: 124
Period size: 28 Copynumber: 3.4 Consensus size: 28
3445709 TATTTTTCAC
* *
3445719 CCGACCCGAATATCACACTTTAAAAAAT
1 CCGACCCGAATATCACACTTAAAAAAAA
3445747 CCGACCCGAATATCACACTTAAAAAAACCCGA
1 CCGACCCGAATATCACACTTAAAAAAA----A
* *
3445779 CCGACCCGAATATCAAACTTAAAAAAAC
1 CCGACCCGAATATCACACTTAAAAAAAA
3445807 CCGACCCGAA
1 CCGACCCGAA
3445817 CCCGATTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
28 36 0.58
32 26 0.42
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.14
Consensus pattern (28 bp):
CCGACCCGAATATCACACTTAAAAAAAA
Found at i:3445788 original size:32 final size:32
Alignment explanation
Indices: 3445719--3445821 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
3445709 TATTTTTCAC
* *
3445719 CCGACCCGAATATCACACTTTAAAAAA----T
1 CCGACCCGAATATCACACTTAAAAAAACCCGA
3445747 CCGACCCGAATATCACACTTAAAAAAACCCGA
1 CCGACCCGAATATCACACTTAAAAAAACCCGA
*
3445779 CCGACCCGAATATCAAACTTAAAAAAACCCGA
1 CCGACCCGAATATCACACTTAAAAAAACCCGA
3445811 CCCGAACCCGA
1 -CCG-ACCCGA
3445822 TTTTTTTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
28 26 0.39
32 31 0.47
33 3 0.05
34 6 0.09
ACGTcount: A:0.43, C:0.34, G:0.10, T:0.14
Consensus pattern (32 bp):
CCGACCCGAATATCACACTTAAAAAAACCCGA
Found at i:3445835 original size:32 final size:32
Alignment explanation
Indices: 3445799--3445946 Score: 152
Period size: 32 Copynumber: 4.4 Consensus size: 32
3445789 TATCAAACTT
* *
3445799 AAAAAAACCCGACCCGAACCCGATTTTTTTTA
1 AAAAAAATCCGACCCGAACCCGAATTTTTTTA
* *
3445831 AAAAAAATCCGACCCGATCCTGAATTTTTTTTTGA
1 AAAAAAATCCGACCCGAACCCGAA--TTTTTTT-A
*
3445866 AAAAATATGACCCGACCCGAACCCGAATTTTTTTA
1 AAAAA-A--ATCCGACCCGAACCCGAATTTTTTTA
* * * **
3445901 AAAAAAATCCGTCCCGATCCTGAATTTTTAAA
1 AAAAAAATCCGACCCGAACCCGAATTTTTTTA
3445933 AAAAAAATCCGACC
1 AAAAAAATCCGACC
3445947 TGAATACCAA
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
32 53 0.55
34 8 0.08
35 12 0.12
36 8 0.08
38 15 0.16
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.26
Consensus pattern (32 bp):
AAAAAAATCCGACCCGAACCCGAATTTTTTTA
Found at i:3445939 original size:70 final size:70
Alignment explanation
Indices: 3445805--3445939 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 70
3445795 ACTTAAAAAA
* *****
3445805 ACCCGACCCGAACCCGATTTTTTTTAAAAAAAATCCGACCCGATCCTGAATTTTTTTTTGAAAAA
1 ACCCGACCCGAACCCGAATTTTTTTAAAAAAAATCCGACCCGATCCTGAATTTTTAAAAAAAAAA
3445870 ATATG
66 ATATG
*
3445875 ACCCGACCCGAACCCGAATTTTTTTAAAAAAAATCCGTCCCGATCCTGAATTTTTAAAAAAAAAA
1 ACCCGACCCGAACCCGAATTTTTTTAAAAAAAATCCGACCCGATCCTGAATTTTTAAAAAAAAAA
3445940 TCCGACCTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (70 bp):
ACCCGACCCGAACCCGAATTTTTTTAAAAAAAATCCGACCCGATCCTGAATTTTTAAAAAAAAAA
ATATG
Found at i:3451842 original size:2 final size:2
Alignment explanation
Indices: 3451835--3451861 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3451825 TTATTTTTAT
3451835 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3451862 TAGTATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3452002 original size:37 final size:37
Alignment explanation
Indices: 3451913--3452160 Score: 231
Period size: 37 Copynumber: 6.6 Consensus size: 37
3451903 TTTGGAAATA
* * *
3451913 TATATAATATATGGTTTTTGAATACATTTTAAATATA-T
1 TATATAATATATAGTTTTTAAAAACATTTTAAA-A-ACT
* *
3451951 ATATATAATATATAGTTTTTAAAAACGTTTTAAAAATT
1 -TATATAATATATAGTTTTTAAAAACATTTTAAAAACT
*
3451989 TATATAATATATAG-TTTTAAAATCATTTTGAAAAACT
1 TATATAATATATAGTTTTTAAAAACATTTT-AAAAACT
* *
3452026 TATATAATATATAG-TTTTAAAATCATTTTGAAAACT
1 TATATAATATATAGTTTTTAAAAACATTTTAAAAACT
* * *
3452062 TATATAATATATAG-TTTTGAAAACATTTTTTGAAAACCC
1 TATATAATATATAGTTTTTAAAAACA--TTTT-AAAAACT
* *
3452101 TATATAATATATAGTTTTAAAAAAACATTTTTTTAAAA--
1 TATATAATATATAGTTTT-TAAAAACA--TTTTAAAAACT
*
3452139 TATATAATATAT-GGTTTTAAAA
1 TATATAATATATAGTTTTTAAAA
3452161 TATTTTTATA
Statistics
Matches: 183, Mismatches: 19, Indels: 17
0.84 0.09 0.08
Matches are distributed among these distances:
36 46 0.25
37 54 0.30
38 18 0.10
39 47 0.26
40 6 0.03
41 12 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAAACATTTTAAAAACT
Found at i:3452067 original size:36 final size:36
Alignment explanation
Indices: 3451952--3452166 Score: 240
Period size: 37 Copynumber: 5.8 Consensus size: 36
3451942 TAAATATATA
* * * *
3451952 TATATAATATATAGTTTTTAAAAACGTTTTAAAAATT
1 TATATAATATATAG-TTTTAAAATCATTTTGAAAACT
3451989 TATATAATATATAGTTTTAAAATCATTTTGAAAAACT
1 TATATAATATATAGTTTTAAAATCATTTTG-AAAACT
3452026 TATATAATATATAGTTTTAAAATCATTTTGAAAACT
1 TATATAATATATAGTTTTAAAATCATTTTGAAAACT
*
3452062 TATATAATATATAGTTTTGAAAA-CATTTTTTGAAAACCC
1 TATATAATATATAGTTTT-AAAATCA--TTTTGAAAA-CT
* *
3452101 TATATAATATATAGTTTTAAAAAAACATTTTTTTAAAA--
1 TATATAATATATAGTTTT--AAAATCA--TTTTGAAAACT
*
3452139 TATATAATATATGGTTTTAAAAT-ATTTT
1 TATATAATATATAGTTTTAAAATCATTTT
3452167 TATATAGTGT
Statistics
Matches: 162, Mismatches: 9, Indels: 18
0.86 0.05 0.10
Matches are distributed among these distances:
33 4 0.02
35 1 0.01
36 43 0.27
37 53 0.33
38 26 0.16
39 19 0.12
40 4 0.02
41 12 0.07
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAATCATTTTGAAAACT
Found at i:3452142 original size:75 final size:73
Alignment explanation
Indices: 3451952--3452167 Score: 249
Period size: 73 Copynumber: 2.9 Consensus size: 73
3451942 TAAATATATA
*
3451952 TATATAATATATAGTTTTTAAAAACGTTTT-AAAAATTTATATAATATATAGTTTTAAAATCA--
1 TATATAATATATAG-TTTTAAAAACATTTTGAAAAA--TATATAATATATAGTTTTAAAA-CATT
*
3452014 TTTTGAAAAACT
62 TTTTGAAAAACC
* *
3452026 TATATAATATATAGTTTTAAAATCATTTTGAAAACTTATATAATATATAGTTTTGAAAACATTTT
1 TATATAATATATAGTTTTAAAAACATTTTGAAAA-ATATATAATATATAGTTTT-AAAACATTTT
*
3452091 TTGAAAACCC
64 TTGAAAAACC
** * *
3452101 TATATAATATATAGTTTTAAAAAAACATTTTTTTAAAATATATAATATATGGTTTTAAAATATTT
1 TATATAATATATAGTTTT--AAAAACA-TTTTGAAAAATATATAATATATAGTTTTAAAACATTT
3452166 TT
63 TT
3452168 ATATAGTGTA
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
73 33 0.27
74 22 0.18
75 28 0.23
76 10 0.08
77 23 0.19
78 7 0.06
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (73 bp):
TATATAATATATAGTTTTAAAAACATTTTGAAAAATATATAATATATAGTTTTAAAACATTTTTT
GAAAAACC
Found at i:3453041 original size:28 final size:28
Alignment explanation
Indices: 3453001--3453062 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
3452991 GGGTTAATTA
3453001 TTGTTTAGTCCTCCTAACCTTTTATTCT
1 TTGTTTAGTCCTCCTAACCTTTTATTCT
*
3453029 TTGTTTAGTCCTCCTAACTTTTTATTCT
1 TTGTTTAGTCCTCCTAACCTTTTATTCT
3453057 TTGTTT
1 TTGTTT
3453063 TTGCATCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.13, C:0.21, G:0.08, T:0.58
Consensus pattern (28 bp):
TTGTTTAGTCCTCCTAACCTTTTATTCT
Found at i:3453270 original size:29 final size:29
Alignment explanation
Indices: 3453228--3453360 Score: 83
Period size: 29 Copynumber: 4.8 Consensus size: 29
3453218 TTAAAATTTC
3453228 TTATTT-A-TTATTTTATT-TC-ATGTGTTT
1 TTATTTGATTTATTTTATTATCTAT-T-TTT
* *
3453255 TTCTTTGATTTATTTTTTTATCTATTTTT
1 TTATTTGATTTATTTTATTATCTATTTTT
3453284 TTATTTGATTTA--TT-TT-TCT-TTTTT
1 TTATTTGATTTATTTTATTATCTATTTTT
* * *
3453308 CT-TTTGATTTGTTATTATTAT-TATTATGT
1 TTATTTGATTTATT-TTATTATCTATT-TTT
*
3453337 TTATTT-ATTTATTGTTTTTATCTA
1 TTATTTGATTTATT-TTATTATCTA
3453361 ACATTTTTGA
Statistics
Matches: 83, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
23 8 0.10
24 6 0.07
25 3 0.04
26 4 0.05
27 10 0.12
28 4 0.05
29 38 0.46
30 8 0.10
31 2 0.02
ACGTcount: A:0.17, C:0.05, G:0.06, T:0.72
Consensus pattern (29 bp):
TTATTTGATTTATTTTATTATCTATTTTT
Found at i:3453317 original size:52 final size:51
Alignment explanation
Indices: 3453252--3453349 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
3453242 ATTTCATGTG
* *
3453252 TTTTTCTTTGATTTATT-TTTTTATCTATT-TTTTTATTTGATTTATTTTTCT
1 TTTTTCTTTGATTTATTATTATTAT-TATTATGTTTATTT-ATTTATTTTTCT
*
3453303 TTTTTCTTTTGATTTGTTATTATTATTATTATGTTTATTTATTTATT
1 TTTTTC-TTTGATTTATTATTATTATTATTATGTTTATTTATTTATT
3453350 GTTTTTATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
51 6 0.15
52 21 0.51
53 14 0.34
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.74
Consensus pattern (51 bp):
TTTTTCTTTGATTTATTATTATTATTATTATGTTTATTTATTTATTTTTCT
Found at i:3454868 original size:2 final size:2
Alignment explanation
Indices: 3454861--3454898 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3454851 AATGTGTAGA
3454861 AT AT AT AT AT AT AT AT AT A- 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 AT A
3454899 AAGTAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3454884 original size:19 final size:19
Alignment explanation
Indices: 3454860--3454899 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3454850 AAATGTGTAG
3454860 AATATATATATATATATAT
1 AATATATATATATATATAT
3454879 AATATATATATATATATAT
1 AATATATATATATATATAT
3454898 AA
1 AA
3454900 AGTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATATATATATATATAT
Found at i:3454885 original size:17 final size:17
Alignment explanation
Indices: 3454863--3454896 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3454853 TGTGTAGAAT
3454863 ATATATATATATATATA
1 ATATATATATATATATA
3454880 ATATATATATATATATA
1 ATATATATATATATATA
3454897 TAAAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:3454942 original size:28 final size:28
Alignment explanation
Indices: 3454886--3454944 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3454876 TATAATATAT
* *
3454886 ATATATATATATAAAGTAAAATAATAAA
1 ATATATACATATAAAGTAAAATAAAAAA
* * *
3454914 ATATATACATATAAATTTAGATAAAAAA
1 ATATATACATATAAAGTAAAATAAAAAA
3454942 ATA
1 ATA
3454945 ATAATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (28 bp):
ATATATACATATAAAGTAAAATAAAAAA
Found at i:3456840 original size:104 final size:103
Alignment explanation
Indices: 3456645--3457307 Score: 980
Period size: 104 Copynumber: 6.4 Consensus size: 103
3456635 GTATTGTTCC
* *** * * * *
3456645 GAGTCCAATATCCTCCACCGTGGAGTTGAAATTGGTTCTGGAA-CTGGGAAATTGTTTCTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTTGAG-AATTGTTT-TTGAC-
*
3456709 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
62 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3456751 GAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGCTTATGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-TTGTTTTTGAC-AC
*
3456816 CAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3456855 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATAT-TTTTTGACAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAG-AAT-TGTTTTTGACAC
3456919 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3456959 GAGTCCAATATCCTTCGTTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-TATTGTTGACAAC
1 GAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAATTGTTTTTGAC-AC
3457023 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3457063 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACACC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAATTGTTT-TTGACACC
*
3457128 AGCGGTCCCTTCGT-GTGAAGTTGAACTTGCGTCGTCT-
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3457165 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACACC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAATTGTTT-TTGACACC
3457230 AGCGG-CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3457268 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
3457308 GGTAAATCCT
Statistics
Matches: 518, Mismatches: 27, Indels: 27
0.91 0.05 0.05
Matches are distributed among these distances:
101 8 0.02
102 92 0.18
103 107 0.21
104 217 0.42
105 55 0.11
106 39 0.08
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (103 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAATTGTTTTTGACACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3458152 original size:57 final size:58
Alignment explanation
Indices: 3458055--3458164 Score: 168
Period size: 59 Copynumber: 1.9 Consensus size: 58
3458045 TTTTCTCTTC
*
3458055 TTTTTTCTTTTTCTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAACGTTT
1 TTTTTTCTTTTTCTTTTTTCAACTTAGGACGCCC-TTCGGGTTTTCACCCTAAACGTTT
* * *
3458114 TTTTTTTTTTTTTTTTTTTCAACTTAGGACGCCC-TCGGGTTTTCATCCTAA
1 TTTTTTCTTTTTCTTTTTTCAACTTAGGACGCCCTTCGGGTTTTCACCCTAA
3458165 GCGAATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
57 16 0.34
59 31 0.66
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.54
Consensus pattern (58 bp):
TTTTTTCTTTTTCTTTTTTCAACTTAGGACGCCCTTCGGGTTTTCACCCTAAACGTTT
Found at i:3468570 original size:40 final size:41
Alignment explanation
Indices: 3468512--3468595 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
3468502 TAGAATATAT
* * **
3468512 ATATATATATATATAATATGTA-ATAAAGTAA-AATAATAAA
1 ATATATACATATAAAATAT-TAGATAAAAAAATAATAATAAA
3468552 ATATATACATATAAAATATTAGATAAAAAAATAATAATAAA
1 ATATATACATATAAAATATTAGATAAAAAAATAATAATAAA
3468593 ATA
1 ATA
3468596 AATATATACA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.05
40 24 0.63
41 12 0.32
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (41 bp):
ATATATACATATAAAATATTAGATAAAAAAATAATAATAAA
Found at i:3468713 original size:24 final size:24
Alignment explanation
Indices: 3468686--3468737 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
3468676 TAATAGTGAT
3468686 GTATACATATACATTTAAACTAAA
1 GTATACATATACATTTAAACTAAA
3468710 GTATACATATACATTTAAACTAAA
1 GTATACATATACATTTAAACTAAA
3468734 GTAT
1 GTAT
3468738 TGAAAGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (24 bp):
GTATACATATACATTTAAACTAAA
Found at i:3471817 original size:34 final size:34
Alignment explanation
Indices: 3471779--3471869 Score: 148
Period size: 34 Copynumber: 2.7 Consensus size: 34
3471769 TTAACCACTA
3471779 TCATACTAACATTCTAACATTTTTATTTTATTAT
1 TCATACTAACATTCTAACATTTTTATTTTATTAT
* *
3471813 TCATACTAACATTCTAACACTTTTATTTTATTGT
1 TCATACTAACATTCTAACATTTTTATTTTATTAT
3471847 TCATACTAAC-TTGCTAACATTTT
1 TCATACTAACATT-CTAACATTTT
3471870 ATCTTATAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
33 2 0.04
34 51 0.96
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (34 bp):
TCATACTAACATTCTAACATTTTTATTTTATTAT
Found at i:3474540 original size:12 final size:12
Alignment explanation
Indices: 3474523--3474568 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3474513 CACCTTGTGC
3474523 ATTTGCATTTGT
1 ATTTGCATTTGT
3474535 ATTTGCATTCTTGCT
1 ATTTGCA-T-TTG-T
3474550 -TTT-CATTTGT
1 ATTTGCATTTGT
3474560 ATTTGCATT
1 ATTTGCATT
3474569 CTTGCTTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
10 1 0.03
11 6 0.21
12 12 0.41
13 3 0.10
14 6 0.21
15 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.59
Consensus pattern (12 bp):
ATTTGCATTTGT
Found at i:3474560 original size:25 final size:25
Alignment explanation
Indices: 3474524--3474581 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
3474514 ACCTTGTGCA
3474524 TTTGCATTTGTATTTGCATTCTTGC
1 TTTGCATTTGTATTTGCATTCTTGC
*
3474549 TTTTCATTTGTATTTGCATTCTTGC
1 TTTGCATTTGTATTTGCATTCTTGC
3474574 TTTGCATT
1 TTTGCATT
3474582 AGGTTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.59
Consensus pattern (25 bp):
TTTGCATTTGTATTTGCATTCTTGC
Found at i:3474579 original size:13 final size:13
Alignment explanation
Indices: 3474536--3474581 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3474526 TGCATTTGTA
3474536 TTTGCATTCTTGC
1 TTTGCATTCTTGC
* *
3474549 TTTTCA-T-TTGTA
1 TTTGCATTCTTG-C
3474561 TTTGCATTCTTGC
1 TTTGCATTCTTGC
3474574 TTTGCATT
1 TTTGCATT
3474582 AGGTTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
11 3 0.12
12 6 0.23
13 14 0.54
14 3 0.12
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (13 bp):
TTTGCATTCTTGC
Found at i:3481078 original size:259 final size:260
Alignment explanation
Indices: 3480424--3481229 Score: 1065
Period size: 260 Copynumber: 3.1 Consensus size: 260
3480414 GAAAAAAACA
* *
3480424 ATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAATAAAGTGATTT
1 ATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAATGATTT
* **
3480489 TCAAAGTTTCTTACCTCAA-AAACTATTTCCAAAATTGGTAAGTCCTTTTGGCCATCAGTAAGTC
66 CCAAAGTTTCTTACC-CAATAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
* * *
3480553 TTTCGAGCATGAT-ATTTAAATCCTTCGGGTCATATGTAAGCCTTTCGAGCAAGATGATAAGTCC
130 TTTCGAGCATGATGA-TTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCC
* * *
3480617 TTTGGACCATCTATAAGACCTTCAAGCAGGATGTTTTCACTTGATTTTCAAAAAAAATGAGAAAG
194 TTTGGGCCATCTATAAGACCTTCAAGCAGGATGTTTTCACATGATTATCAAAAAAAATGAGAAAG
3480682 CG
259 CG
* *
3480684 A-TTTCAAAAGTTTCTCATTTAATATTTTTAGAAAATAAAATTTTTGAAAAGTAAGAAAATGATT
1 ATTTTC-AAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAATGATT
* * * * * *
3480748 TCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGAGCCATCAGGAAGTA
65 TCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
* *
3480813 TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAACTCAT
130 TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCT
**
3480878 TTGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTAT-AAAATAATAA-GA-AAA
195 TTGGGCCATCTATAAGACCTTCAAGCAGGATGTTTTCACATGATTATCAAAA-AA-AATGAGAAA
3480940 GC-
258 GCG
* * *
3480942 ATTTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAATAAAT
1 A-TTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAATGATT
* *
3481007 TCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGTTAAGTCCTTCGGGCCATCTGTAAGTC
65 TCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC
* * * *
3481072 TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGCCAATCTTTCGATCAAGAAGATAAGTCCT
130 TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCT
* ** * * ** ** * *
3481137 TCGGGCCATCTATAAGACCCTTGGA-CAAGATGCTTTCATTTGGTATT-TGTAAGAGAATGAGAA
195 TTGGGCCATCTATAAGA-CCTTCAAGCAGGATGTTTTCACAT-G-ATTATCAAAAAAAATGAGAA
3481200 AGCG
257 AGCG
*
3481204 ACTTTCAAAGTTTCTCATTTAA-ATTT
1 ATTTTCAAAGTTTCTCATTTAATATTT
3481230 AAAAAAAAGA
Statistics
Matches: 479, Mismatches: 53, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
258 1 0.00
259 213 0.44
260 231 0.48
261 33 0.07
262 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (260 bp):
ATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAATGATTT
CCAAAGTTTCTTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT
TTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTT
TGGGCCATCTATAAGACCTTCAAGCAGGATGTTTTCACATGATTATCAAAAAAAATGAGAAAGCG
Found at i:3481116 original size:42 final size:42
Alignment explanation
Indices: 3481045--3481147 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
3481035 TCCAAAATTG
* * *
3481045 TTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGA
1 TTAAGTCCTTCGGGCCATCTGCAAGTCTTTCGAGCAAGAAGA
* * *
3481087 TTAAATCCTTCGGGTCATCTGCCAA-TCTTTCGATCAAGAAGA
1 TTAAGTCCTTCGGGCCATCTG-CAAGTCTTTCGAGCAAGAAGA
3481129 -TAAGTCCTTCGGGCCATCT
1 TTAAGTCCTTCGGGCCATCT
3481148 ATAAGACCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
41 17 0.33
42 33 0.63
43 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (42 bp):
TTAAGTCCTTCGGGCCATCTGCAAGTCTTTCGAGCAAGAAGA
Found at i:3483197 original size:34 final size:34
Alignment explanation
Indices: 3483158--3483337 Score: 238
Period size: 34 Copynumber: 5.3 Consensus size: 34
3483148 TTTAACCACT
3483158 TTCATACTAACATTCTAACACTTTTATTTTATTG
1 TTCATACTAACATTCTAACACTTTTATTTTATTG
* * * *
3483192 TTCATATTAACATTCTAACATTTTTATTCTATCG
1 TTCATACTAACATTCTAACACTTTTATTTTATTG
* * *
3483226 TTCATATTAACATTCTAACATTTTTATTTTATTA
1 TTCATACTAACATTCTAACACTTTTATTTTATTG
*
3483260 TTCATACTAACATTCTAACACTTTTATTTTTTTG
1 TTCATACTAACATTCTAACACTTTTATTTTATTG
* *
3483294 TTAATACTAAC-TTACCAACA-TTTTATTTTATTG
1 TTCATACTAACATT-CTAACACTTTTATTTTATTG
*
3483327 TTCAAACTAAC
1 TTCATACTAAC
3483338 CCTCTAACTT
Statistics
Matches: 129, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 23 0.18
34 106 0.82
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (34 bp):
TTCATACTAACATTCTAACACTTTTATTTTATTG
Found at i:3485656 original size:43 final size:43
Alignment explanation
Indices: 3485587--3485668 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
3485577 TAAGTTGTTG
* * *
3485587 CTGCCAATGCGGTCCAGCTTTTGTGGACGTTCGGGCACTATTA
1 CTGCCAATACGATCCAGCTTTTGTGGACGTCCGGGCACTATTA
*
3485630 CTGCCAATACGATCCAG-TTTTGGTGGATGTCCGGGCACT
1 CTGCCAATACGATCCAGCTTTT-GTGGACGTCCGGGCACT
3485669 TTCAGATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 4 0.12
43 30 0.88
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (43 bp):
CTGCCAATACGATCCAGCTTTTGTGGACGTCCGGGCACTATTA
Found at i:3487843 original size:22 final size:22
Alignment explanation
Indices: 3487808--3487858 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
3487798 CACCGACGTG
3487808 CCACATA-TTTGTCC-GAAGGA
1 CCACATAGTTTGTCCTGAAGGA
3487828 CCACATAGTTTTGTCCTGAAGGA
1 CCACATAG-TTTGTCCTGAAGGA
3487851 CCACATAG
1 CCACATAG
3487859 AACCTTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.25
22 7 0.25
23 14 0.50
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (22 bp):
CCACATAGTTTGTCCTGAAGGA
Found at i:3488429 original size:15 final size:15
Alignment explanation
Indices: 3488409--3488439 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3488399 GTACTCCCAC
*
3488409 TACAGTATCGATACT
1 TACAGTACCGATACT
3488424 TACAGTACCGATACT
1 TACAGTACCGATACT
3488439 T
1 T
3488440 CCCTTCTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (15 bp):
TACAGTACCGATACT
Found at i:3494691 original size:22 final size:21
Alignment explanation
Indices: 3494666--3494735 Score: 52
Period size: 23 Copynumber: 3.2 Consensus size: 21
3494656 CCATAGCTTG
3494666 CATAATTTGCACCGAAGTG-CCA
1 CATAATTTGC-CCGAAG-GACCA
* *
3494688 CATATTTTTCCCGAAGGACCA
1 CATAATTTGCCCGAAGGACCA
* * *
3494709 CATAGTTTTTTCCCGAAAGACCA
1 CATA--ATTTGCCCGAAGGACCA
3494732 CATA
1 CATA
3494736 GAACCTCGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.02
21 13 0.31
22 8 0.19
23 20 0.48
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (21 bp):
CATAATTTGCCCGAAGGACCA
Done.