Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 12 of 199
Found at i:4882920 original size:15 final size:15
Alignment explanation
Indices: 4882876--4882931 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
4882866 TTTTTGTTAA
*
4882876 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
4882891 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
4882902 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
4882917 ATTATATATTATAAT
1 ATTATATTTTATAAT
4882932 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:4882920 original size:119 final size:120
Alignment explanation
Indices: 4882707--4882948 Score: 441
Period size: 119 Copynumber: 2.0 Consensus size: 120
4882697 TGATACAATC
* *
4882707 ATAAGAATATTTAATACTACGAATTTTATTAATTTATATATTTTTGTTAAATTATATTTAATAAT
1 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
* *
4882772 AATTATTTTAAATTATATTTTATAGTATTATATATTAT-GTTTTAGTAAATTCAT
66 AATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
4882826 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
1 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
4882891 AATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
66 AATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
4882946 ATA
1 ATA
4882949 TTTTATTAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 100 0.85
120 18 0.15
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (120 bp):
ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
AATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
Found at i:4882949 original size:41 final size:40
Alignment explanation
Indices: 4882785--4882967 Score: 109
Period size: 41 Copynumber: 4.6 Consensus size: 40
4882775 TATTTTAAAT
* *
4882785 TATATTTTATAGTATTATATATTAT-GTTTTAGTAAATTCA
1 TATATTTTATAATATTATATATTATAATTTTAGTAAATT-A
* * * *
4882825 TATA----AGAATATT-TAATACTAAGAATTTTATTAAATTA
1 TATATTTTATAATATTAT-ATA-TTATAATTTTAGTAAATTA
* **
4882862 TATATTTTTGTTAA-ATTATAT-TTAATAATAATTATTTTAAA-T-
1 TATA-TTTT-ATAATATTATATATT-ATAAT--TT-TAGTAAATTA
4882904 TATATTTTATAATATTATATATTATAATTTTAGTAAATTCA
1 TATATTTTATAATATTATATATTATAATTTTAGTAAATT-A
4882945 TATATTTTATTAA-ATTATATATT
1 TATATTTTA-TAATATTATATATT
4882968 TTTATTAAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 39
0.67 0.09 0.24
Matches are distributed among these distances:
35 1 0.01
36 9 0.08
37 7 0.06
38 16 0.15
39 3 0.03
40 8 0.07
41 39 0.36
42 14 0.13
43 6 0.06
44 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (40 bp):
TATATTTTATAATATTATATATTATAATTTTAGTAAATTA
Found at i:4883449 original size:15 final size:15
Alignment explanation
Indices: 4883429--4883460 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4883419 CAATTTTATC
4883429 CAGTTTTCTTGCAGA
1 CAGTTTTCTTGCAGA
4883444 CAGTTTTCTTGCAGA
1 CAGTTTTCTTGCAGA
4883459 CA
1 CA
4883461 AAAACACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (15 bp):
CAGTTTTCTTGCAGA
Found at i:4884423 original size:21 final size:21
Alignment explanation
Indices: 4884397--4884452 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
4884387 CGCTGTTTCT
* *
4884397 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACA
*
4884418 AATCTCACTGCTACAGTAACA
1 AATCTCACCGCTACAGTAACA
4884439 AATCTCACCGCTAC
1 AATCTCACCGCTAC
4884453 CGCTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACA
Found at i:4909160 original size:45 final size:44
Alignment explanation
Indices: 4909085--4909188 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 44
4909075 TTTTCTTTTC
*
4909085 TTTCTTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTTCTTT-CTCCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
* *
4909130 TTTCTTTCTTTCTCCCTTCTCTGT-TTTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTC-CT-TCTCTGTTTCGTTTTGCTCTCTG
4909175 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
4909189 TTCTTTGTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
44 7 0.13
45 36 0.68
46 10 0.19
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (44 bp):
TTTCTTTCTTTCTCCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:4910397 original size:14 final size:14
Alignment explanation
Indices: 4910378--4910405 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4910368 AATTATTAAA
4910378 TTATTTAAAAAATT
1 TTATTTAAAAAATT
4910392 TTATTTAAAAAATT
1 TTATTTAAAAAATT
4910406 AGACTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATTTAAAAAATT
Found at i:4919088 original size:17 final size:18
Alignment explanation
Indices: 4919052--4919089 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
4919042 TATCATTCTT
*
4919052 TTATTTTGATTTAGGGTA
1 TTATTTTGATTCAGGGTA
*
4919070 TTATTTTG-TTCATGGTA
1 TTATTTTGATTCAGGGTA
4919087 TTA
1 TTA
4919090 ACTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (18 bp):
TTATTTTGATTCAGGGTA
Found at i:4921647 original size:83 final size:83
Alignment explanation
Indices: 4921551--4921725 Score: 253
Period size: 83 Copynumber: 2.1 Consensus size: 83
4921541 AGCCACGTTA
* * * *
4921551 GGGAGTGGGGGAGGAGGAGGGGGAGCTGAAGATGAATTCTTTACGGTAA-AAGATGGAGATATAG
1 GGGAGGGGGGGAGGAGGAGGGGGAGCTGAAAACGAATTCTTTACAG-AAGAAGATGGAGATATAG
4921615 CTGAGAATGGAGGGAGTGG
65 CTGAGAATGGAGGGAGTGG
* *
4921634 GGGAGGGGGGGAGGGGGAGGGGGAGCTGAAAACGAATTCTTTACAGAAGAAGATGGAGATGTAGC
1 GGGAGGGGGGGAGGAGGAGGGGGAGCTGAAAACGAATTCTTTACAGAAGAAGATGGAGATATAGC
*
4921699 TGAGGATGGAGGGAGTGG
66 TGAGAATGGAGGGAGTGG
* *
4921717 TGGTGGGGG
1 GGGAGGGGG
4921726 AGGGGGAGAC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 2 0.02
83 80 0.98
ACGTcount: A:0.28, C:0.05, G:0.50, T:0.17
Consensus pattern (83 bp):
GGGAGGGGGGGAGGAGGAGGGGGAGCTGAAAACGAATTCTTTACAGAAGAAGATGGAGATATAGC
TGAGAATGGAGGGAGTGG
Found at i:4926567 original size:26 final size:26
Alignment explanation
Indices: 4926516--4926567 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4926506 AAAATGTGGC
* *
4926516 TCCATTTGTCATTACCCATTGGGATA
1 TCCATTTGTCATTACCCATAGCGATA
*
4926542 TCCATTTGTCATTACCGATAGCGATA
1 TCCATTTGTCATTACCCATAGCGATA
4926568 ATAAGGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (26 bp):
TCCATTTGTCATTACCCATAGCGATA
Found at i:4934036 original size:24 final size:24
Alignment explanation
Indices: 4934004--4934053 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
4933994 GAATCAGTTC
4934004 TCCATAAAAACATACGGAACAAGA
1 TCCATAAAAACATACGGAACAAGA
* *
4934028 TCCATAAAACCATACGGAATAAGA
1 TCCATAAAAACATACGGAACAAGA
4934052 TC
1 TC
4934054 TGGTCTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (24 bp):
TCCATAAAAACATACGGAACAAGA
Found at i:4944183 original size:20 final size:19
Alignment explanation
Indices: 4944160--4944199 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4944150 AGCATAAGTC
*
4944160 ATAGATTAATACAATAACAA
1 ATAGATTAATAAAAT-ACAA
*
4944180 ATAGTTTAATAAAATACAA
1 ATAGATTAATAAAATACAA
4944199 A
1 A
4944200 ACAAAGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (19 bp):
ATAGATTAATAAAATACAA
Found at i:4946244 original size:15 final size:14
Alignment explanation
Indices: 4946224--4946253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4946214 TTCAATAAAA
4946224 TATTTATTTTTATTT
1 TATTTA-TTTTATTT
4946239 TATTTATTTTATTT
1 TATTTATTTTATTT
4946253 T
1 T
4946254 CTACCACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTATTTTATTT
Found at i:4948797 original size:23 final size:24
Alignment explanation
Indices: 4948762--4948809 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
4948752 AAACATATAT
4948762 TTTTATACAATAAAAATTATTTAAA
1 TTTTATACAATAAAAATT-TTTAAA
*
4948787 TTTTAT-C-ATAAATATTTTTAAA
1 TTTTATACAATAAAAATTTTTAAA
4948809 T
1 T
4948810 GATTAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 1 0.05
25 6 0.27
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATACAATAAAAATTTTTAAA
Found at i:4951609 original size:25 final size:23
Alignment explanation
Indices: 4951581--4951645 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
4951571 TTAAGATATG
*
4951581 ATATGAAATAAATACAAATATGAGT
1 ATATGAAATAAATACAAATAT-A-A
* *
4951606 ATATAAAAAAAGATA-AAATATAA
1 ATATGAAATAA-ATACAAATATAA
*
4951629 ATACGAAATAAATACAA
1 ATATGAAATAAATACAA
4951646 GACTTTACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
22 3 0.09
23 10 0.31
24 1 0.03
25 15 0.47
26 3 0.09
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.23
Consensus pattern (23 bp):
ATATGAAATAAATACAAATATAA
Found at i:4956801 original size:18 final size:18
Alignment explanation
Indices: 4956768--4956802 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4956758 GCCTTCTCCG
* *
4956768 TTTCTCTTTTGTTTTCTC
1 TTTCTCTTTCGCTTTCTC
4956786 TTTCTCTTTCGCTTTCT
1 TTTCTCTTTCGCTTTCT
4956803 TGCTTAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTCTCTTTCGCTTTCTC
Found at i:4977226 original size:18 final size:20
Alignment explanation
Indices: 4977205--4977252 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
4977195 ACAAATTGAC
4977205 TTTATTTTTTAAATTT-AG-
1 TTTATTTTTTAAATTTGAGT
*
4977223 TTTA-ATTTTAAATTTGAGT
1 TTTATTTTTTAAATTTGAGT
4977242 TTTATTTTTTA
1 TTTATTTTTTA
4977253 TATAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 4 0.16
20 5 0.20
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTATTTTTTAAATTTGAGT
Found at i:4977568 original size:14 final size:15
Alignment explanation
Indices: 4977538--4977570 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4977528 AATCTGTATT
*
4977538 AAATTTTTTATATAA
1 AAATTTTTTATAAAA
4977553 AAATTTTTT-TAAAA
1 AAATTTTTTATAAAA
4977567 AAAT
1 AAAT
4977571 ATAATACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTTTATAAAA
Found at i:4978924 original size:15 final size:16
Alignment explanation
Indices: 4978906--4978938 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4978896 ATTTTTGTAT
*
4978906 TATTTT-AATATTAAA
1 TATTTTAAAGATTAAA
4978921 TATTTTAAAGATTAAA
1 TATTTTAAAGATTAAA
4978937 TA
1 TA
4978939 AATTATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTTTAAAGATTAAA
Found at i:5013309 original size:5 final size:5
Alignment explanation
Indices: 5013284--5013356 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
5013274 TTACTTTATT
* *
5013284 TAATA TATATAA TAATA TAATG TAATA TAAT- TAATA GAATA TAATA TATTATA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
*
5013337 TTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TA
5013357 CATAACATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 35 0.64
6 4 0.07
7 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:5013328 original size:19 final size:18
Alignment explanation
Indices: 5013285--5013354 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
5013275 TACTTTATTT
*
5013285 AATAT-ATATAATAATAT
1 AATATAATATAATAATAG
*
5013302 AATGTAATATAATTAATAG
1 AATATAATATAA-TAATAG
* *
5013321 AATATAATAT-ATTATAT
1 AATATAATATAATAATAG
* *
5013338 TATATAATAAAATAATA
1 AATATAATATAATAATA
5013355 TACATAACAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 16 0.38
18 12 0.29
19 14 0.33
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AATATAATATAATAATAG
Found at i:5033731 original size:50 final size:50
Alignment explanation
Indices: 5033607--5033855 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
5033597 GATAATAACA
* * ** * *
5033607 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
5033658 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5033708 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
5033758 TGCCCATGCCATGTCCCAAACATGGTCTTACAGGGGACCTTTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC--TC-TCATC-T-CGG
* *
5033813 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5033856 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 87 0.52
51 33 0.20
52 2 0.01
53 4 0.02
54 3 0.02
55 2 0.01
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:5033786 original size:100 final size:105
Alignment explanation
Indices: 5033606--5033855 Score: 341
Period size: 100 Copynumber: 2.4 Consensus size: 105
5033596 TGATAATAAC
**
5033606 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* * *
5033671 TCCCAGACATGGTCTTATAGGGGACC-TC-TCATC-T-CGG
65 TCCCAAACATGGTCTTACAGGGGACCTTCATCATCTTAAGG
* *
5033708 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
5033771 TCCCAAACATGGTCTTACAGGGGACCTTTCATGATCTTAAGG
65 TCCCAAACATGGTCTTACAGGGGACC-TTCATCATCTTAAGG
* *
5033813 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5033856 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 45 0.34
101 36 0.27
102 2 0.02
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAAACATGGTCTTACAGGGGACCTTCATCATCTTAAGG
Found at i:5033971 original size:13 final size:13
Alignment explanation
Indices: 5033950--5033981 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5033940 GCTTGGATCA
*
5033950 TCATCAAATAAAT
1 TCATAAAATAAAT
5033963 TCATAAAATAAAT
1 TCATAAAATAAAT
5033976 TCATAA
1 TCATAA
5033982 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5049530 original size:16 final size:17
Alignment explanation
Indices: 5049503--5049534 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5049493 AAATAAATCT
5049503 AAAAATATTAATTTTTG
1 AAAAATATTAATTTTTG
5049520 AAAAATA-TAATTTTT
1 AAAAATATTAATTTTT
5049535 CTTTGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAAAATATTAATTTTTG
Found at i:5053111 original size:21 final size:21
Alignment explanation
Indices: 5053085--5053125 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5053075 ATCTGCTCAA
* *
5053085 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5053106 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5053126 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5060844 original size:3 final size:3
Alignment explanation
Indices: 5060836--5060870 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5060826 ACCACTATAT
*
5060836 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5060871 GGTAATTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5060875 original size:15 final size:15
Alignment explanation
Indices: 5060836--5060876 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
5060826 ACCACTATAT
*
5060836 ATAATAATAATAATA
1 ATAATAGTAATAATA
5060851 ATAATAGTAATAATA
1 ATAATAGTAATAATA
*
5060866 ATAATGGTAAT
1 ATAATAGTAAT
5060877 TTCTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
ATAATAGTAATAATA
Found at i:5071110 original size:85 final size:85
Alignment explanation
Indices: 5070962--5071129 Score: 273
Period size: 85 Copynumber: 2.0 Consensus size: 85
5070952 CCTGGTTCTG
* * *
5070962 GGGTGATTTGAAGGTGCGGCCGTTCAGGAGGCTAAAAGGAATTCAAAATATTATTTCTCAGTTAT
1 GGGTCATTTGAAGGTGCGGCCATTCAGGAGGCTAAAAGGAATTCAAAATATTACTTCTCAGTTAT
5071027 TAAGCAGCCCAAATAAACTT
66 TAAGCAGCCCAAATAAACTT
* * *
5071047 GGGTCATTTGAATGTGCGGCCATTCAGGAGGCTGAAAGGAATTCAAAATGTTACTTCTCAGTTAT
1 GGGTCATTTGAAGGTGCGGCCATTCAGGAGGCTAAAAGGAATTCAAAATATTACTTCTCAGTTAT
*
5071112 TAAGCGGCCCAAATAAAC
66 TAAGCAGCCCAAATAAAC
5071130 ATTTCTTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (85 bp):
GGGTCATTTGAAGGTGCGGCCATTCAGGAGGCTAAAAGGAATTCAAAATATTACTTCTCAGTTAT
TAAGCAGCCCAAATAAACTT
Found at i:5071205 original size:30 final size:30
Alignment explanation
Indices: 5071171--5071239 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5071161 TCTTTTACCC
*
5071171 ACTTTTAATCGGTCCAAAAAGCTTTTATTA
1 ACTTTTAAGCGGTCCAAAAAGCTTTTATTA
* ****
5071201 ACTTTTAAGGGGTCCAAATTTTTTTTATTA
1 ACTTTTAAGCGGTCCAAAAAGCTTTTATTA
5071231 ACTTTTAAG
1 ACTTTTAAG
5071240 GGACCTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (30 bp):
ACTTTTAAGCGGTCCAAAAAGCTTTTATTA
Found at i:5075934 original size:33 final size:32
Alignment explanation
Indices: 5075888--5075949 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
5075878 TCCCCATAAT
*
5075888 ATTAAAAAATATAT-CAATTAAAAATAAAAAAA
1 ATTAAAAAATATATAAAATT-AAAATAAAAAAA
*
5075920 ATTAGAAAATTATATAAAATTAAAATAAAA
1 ATTA-AAAAATATATAAAATTAAAATAAAA
5075950 CAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.15
33 18 0.69
34 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (32 bp):
ATTAAAAAATATATAAAATTAAAATAAAAAAA
Found at i:5111324 original size:20 final size:19
Alignment explanation
Indices: 5111286--5111328 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
5111276 AATATTTTAT
*
5111286 TAATAAATTAAATTATAAAA
1 TAATAAATTAAAATAT-AAA
5111306 TAATAAATGTAAAAT-TAAA
1 TAATAAAT-TAAAATATAAA
5111325 TAAT
1 TAAT
5111329 TTATGAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TAATAAATTAAAATATAAA
Found at i:5117131 original size:29 final size:28
Alignment explanation
Indices: 5117099--5117181 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
5117089 CAAGTCCTTC
*
5117099 AAAAGTTTTGAAAATTTTATTTAGACCCT
1 AAAAGTTTTGAAAATTTTAATTA-ACCCT
* * *
5117128 AAAA-TCCTTGAAAATTTTAATTAAGCTT
1 AAAAGT-TTTGAAAATTTTAATTAACCCT
*
5117156 ACAAATGTTTTGAAAATATTAATTAA
1 A-AAA-GTTTTGAAAATTTTAATTAA
5117182 AACCCTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 5 0.11
29 22 0.50
30 16 0.36
31 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (28 bp):
AAAAGTTTTGAAAATTTTAATTAACCCT
Found at i:5125239 original size:24 final size:24
Alignment explanation
Indices: 5125201--5125452 Score: 143
Period size: 24 Copynumber: 10.8 Consensus size: 24
5125191 TGAATTGGAT
* *
5125201 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
5125226 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
5125250 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
5125270 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
5125295 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
* *
5125319 AATTT-AAA-AATATTA-ATGACA
1 AATTTAAAATAATAATATATGATA
* *
5125340 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** **
5125364 AATTTAAAATAATGTTA-ACAATA
1 AATTTAAAATAATAATATATGATA
5125387 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
5125410 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
5125434 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
5125453 CAATATACAC
Statistics
Matches: 172, Mismatches: 37, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.03
21 12 0.07
22 19 0.11
23 50 0.29
24 72 0.42
25 14 0.08
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:5125297 original size:69 final size:69
Alignment explanation
Indices: 5125223--5125450 Score: 180
Period size: 69 Copynumber: 3.3 Consensus size: 69
5125213 ATAATATATA
* * * *
5125223 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGA-TAATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGACAAATT-TGA-AATAGAT
*
5125284 CATACGTG
63 -ATACATG
** * *
5125292 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGACAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGACAAATTTGAAATAGATATA
5125357 CATG
66 CATG
** * * * * **
5125361 ATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAATTACAAATA-ATA
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGACAAATTTGAAATAGAT-
*
5125424 AAACATG
63 ATACATG
*
5125431 ATAAATCTAAAATAATAATA
1 ATAAATTTAAAATAATAATA
5125451 TACAATATAC
Statistics
Matches: 129, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
68 10 0.08
69 68 0.53
70 51 0.40
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.33
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGACAAATTTGAAATAGATATA
CATG
Found at i:5126313 original size:22 final size:21
Alignment explanation
Indices: 5126288--5126335 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
5126278 TACAAATTAA
*
5126288 ATCTCTAATATTACAAAATCTT
1 ATCTCTAAGATTAC-AAATCTT
* *
5126310 ATCTTCTAAGATTGCATATCTT
1 ATC-TCTAAGATTACAAATCTT
5126332 ATCT
1 ATCT
5126336 AAGATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (21 bp):
ATCTCTAAGATTACAAATCTT
Found at i:5127933 original size:79 final size:78
Alignment explanation
Indices: 5127798--5127959 Score: 227
Period size: 79 Copynumber: 2.1 Consensus size: 78
5127788 CCAAAATACT
* * *
5127798 ACTGT-ATATATACATCATGTTATACATCACATGATAAGCATGGATTTACTCCTAACACTATACA
1 ACTGTAATATATACATCATATTAAACATCACATGATAAGCATGGAATTACTCCTAACACTATACA
* *
5127862 CACTTATATAAAG
66 CACATATACAAAG
* * *
5127875 ACTGTAATATATATATCATATTAAAGATCACATGAATAAGCATGGAATTACTCCTAACACTATAT
1 ACTGTAATATATACATCATATTAAACATCACATG-ATAAGCATGGAATTACTCCTAACACTATAC
*
5127940 ACACATATACACAG
65 ACACATATACAAAG
5127954 ACTGTA
1 ACTGTA
5127960 TCCAGATCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 5 0.07
78 24 0.32
79 45 0.61
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (78 bp):
ACTGTAATATATACATCATATTAAACATCACATGATAAGCATGGAATTACTCCTAACACTATACA
CACATATACAAAG
Found at i:5138823 original size:14 final size:14
Alignment explanation
Indices: 5138801--5138831 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5138791 GATATTTTAC
5138801 CTTTCGAAGAACAA
1 CTTTCGAAGAACAA
*
5138815 CTTTTGAAGAACAA
1 CTTTCGAAGAACAA
5138829 CTT
1 CTT
5138832 ACGGATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (14 bp):
CTTTCGAAGAACAA
Found at i:5158563 original size:24 final size:22
Alignment explanation
Indices: 5158536--5158583 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
5158526 TGGTTACAAC
*
5158536 TTTATAAAATGTACATAAATTATT
1 TTTATAAAATATA-ATAAA-TATT
*
5158560 TTTATAATATATAATAAATATT
1 TTTATAAAATATAATAAATATT
5158582 TT
1 TT
5158584 ATCATAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTATAAAATATAATAAATATT
Found at i:5163826 original size:18 final size:19
Alignment explanation
Indices: 5163798--5163837 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
5163788 TGAATATAAT
5163798 AAATATATTTTTATTTTTA
1 AAATATATTTTTATTTTTA
5163817 AAATAT-TTTTTATTTTTA
1 AAATATATTTTTATTTTTA
5163835 AAA
1 AAA
5163838 CAATTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATATATTTTTATTTTTA
Found at i:5163843 original size:19 final size:18
Alignment explanation
Indices: 5163805--5163846 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5163795 AATAAATATA
*
5163805 TTTTTATTTTTAAAATAT
1 TTTTTATTTTTAAAAAAT
5163823 TTTTTATTTTTAAAACAAT
1 TTTTTATTTTTAAAA-AAT
5163842 TTTTT
1 TTTTT
5163847 GGTGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATTTTTAAAAAAT
Found at i:5166408 original size:14 final size:14
Alignment explanation
Indices: 5166389--5166445 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
5166379 GTTTGACAGT
5166389 AAAATATTTTCTGG
1 AAAATATTTTCTGG
*
5166403 AAAATAATTTCTGG
1 AAAATATTTTCTGG
* *
5166417 AAAATGATTTACTAG
1 AAAAT-ATTTTCTGG
5166432 AAAATATTTTCTGG
1 AAAATATTTTCTGG
5166446 TGTTTGGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (14 bp):
AAAATATTTTCTGG
Found at i:5166434 original size:29 final size:28
Alignment explanation
Indices: 5166389--5166445 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
5166379 GTTTGACAGT
* *
5166389 AAAATATTTTCTGGAAAATAATTTCTGG
1 AAAATATTTACTAGAAAATAATTTCTGG
*
5166417 AAAATGATTTACTAGAAAATATTTTCTGG
1 AAAAT-ATTTACTAGAAAATAATTTCTGG
5166446 TGTTTGGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
AAAATATTTACTAGAAAATAATTTCTGG
Found at i:5171347 original size:18 final size:18
Alignment explanation
Indices: 5171324--5171360 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5171314 GATTATCTGC
5171324 TGTCGGAATCTTCTGAAG
1 TGTCGGAATCTTCTGAAG
5171342 TGTCGGAATCTTCTGAAG
1 TGTCGGAATCTTCTGAAG
5171360 T
1 T
5171361 AGAATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (18 bp):
TGTCGGAATCTTCTGAAG
Found at i:5173038 original size:21 final size:21
Alignment explanation
Indices: 5173012--5173052 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5173002 ATCTGCTCAA
* *
5173012 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5173033 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5173053 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5177661 original size:25 final size:25
Alignment explanation
Indices: 5177612--5177662 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5177602 ATACTTTTAC
* *
5177612 AAATATTAAATTATTTTTCTTTTCA
1 AAATATTAAATTATTTTTATGTTCA
5177637 AAATAATTAAA-TATTTTTATGTTCA
1 AAAT-ATTAAATTATTTTTATGTTCA
5177662 A
1 A
5177663 TTAAAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATATTAAATTATTTTTATGTTCA
Found at i:5187481 original size:5 final size:5
Alignment explanation
Indices: 5187471--5187504 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5187461 ATCTACGGCC
5187471 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCT
5187505 GTCCTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (5 bp):
CCCTT
Found at i:5194193 original size:16 final size:17
Alignment explanation
Indices: 5194171--5194211 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
5194161 TATGTATGTA
*
5194171 TGTATGTACGTACGTAC
1 TGTATGTACGTACATAC
5194188 -GTATGTACGTACATAC
1 TGTATGTACGTACATAC
5194204 TGTATGTA
1 TGTATGTA
5194212 TGAAGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (17 bp):
TGTATGTACGTACATAC
Found at i:5201877 original size:411 final size:411
Alignment explanation
Indices: 5201110--5201939 Score: 1414
Period size: 411 Copynumber: 2.0 Consensus size: 411
5201100 TGACTCTAAT
* *
5201110 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCTGAAACGTTATGATGATTAGAAG
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAACGTTATGATGATTAGAAG
* * ** *
5201175 TCATAGTCTCCAATTTTTCAGAAAGTTTATCCCTCTTAAGTGTAACTGATTGAAGGTCTGCCCCA
66 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAACGTAACTGATTGAAGATCTGCCCCA
*
5201240 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
131 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCAAG
* *
5201305 ATTATCAATCTTCTTCTGCAAAGAGTTTCTTTCATGATTAGCCTCTGTAATCGCCCTCCCGAACC
196 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCGAACC
*
5201370 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
261 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
*
5201435 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGATTGTTCCAAC-TGTTCATTTCGTT
326 TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAT-TTCATTTCGTT
* *
5201499 CTGCCAACCTATAAATCTTGCC
390 CTGCCAACCTATAAAACTTACC
*
5201521 CTGAAGGTTTTCATTCTCAACTTCAAATTGAGCTGCCTTCGCCGAAA-GATTATGATGATTAGAA
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAACG-TTATGATGATTAGAA
*
5201585 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAACGTAACTGATTGAAGATCTGCCTC
65 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAACGTAACTGATTGAAGATCTGCCCC
5201650 AAGATCAGCTACTCTCTTTTCTGGAC-CCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCA
130 AAGATCAGCTACTCTCTTTTCT-GACTCCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCA
* *
5201714 AGATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTTCCTAA
194 AGATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCGAA
* *
5201779 CCATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAGGGCATGTTGATTCCATCCAAAA
259 CCATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAA
* *
5201844 GCTCCTCCCATTTTTGCAACAAGTGGTTCCTTTCCATTAAGGATTGTTCCAGCATTTCATTTCGT
324 GCTCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACATTTCATTTCGT
5201909 TCTGCCAACCTATAAAACTTACC
389 TCTGCCAACCTATAAAACTTACC
5201932 CTGAAGGT
1 CTGAAGGT
5201940 CCTCATATTT
Statistics
Matches: 394, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
410 1 0.00
411 389 0.99
412 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (411 bp):
CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAACGTTATGATGATTAGAAG
TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAACGTAACTGATTGAAGATCTGCCCCA
AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCAAG
ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCGAACC
ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACATTTCATTTCGTTC
TGCCAACCTATAAAACTTACC
Found at i:5216566 original size:13 final size:14
Alignment explanation
Indices: 5216548--5216579 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5216538 CTAGTTCATC
5216548 TATATTATT-TTTT
1 TATATTATTATTTT
5216561 TATATTATTATTTT
1 TATATTATTATTTT
5216575 TATAT
1 TATAT
5216580 AAAAATAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATATTATTATTTT
Found at i:5216571 original size:16 final size:16
Alignment explanation
Indices: 5216550--5216580 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5216540 AGTTCATCTA
*
5216550 TATTATTTTTTTATAT
1 TATTATTTTTATATAT
5216566 TATTATTTTTATATA
1 TATTATTTTTATATA
5216581 AAAATAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTATATAT
Found at i:5219876 original size:25 final size:25
Alignment explanation
Indices: 5219815--5219870 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
5219805 ACCTTAGCGC
5219815 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
5219840 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACATCAGT
5219865 GCTCTC
1 GCTCTC
5219871 CTATTAGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:5219900 original size:22 final size:22
Alignment explanation
Indices: 5219825--5219892 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
5219815 GCTCTCTGAT
* *
5219825 TATTAGCACATCAGTGCTCTCTGAT
1 TATTAGCACATTAGTGCTCTC---C
*
5219850 TATTAGCACGTTAGTGCTCTCC
1 TATTAGCACATTAGTGCTCTCC
*
5219872 TATTAGCACATTTGTGCTCTC
1 TATTAGCACATTAGTGCTCTC
5219893 AGTATAGCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 19 0.50
25 19 0.50
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (22 bp):
TATTAGCACATTAGTGCTCTCC
Found at i:5228703 original size:3 final size:3
Alignment explanation
Indices: 5228697--5228725 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5228687 ATCATCATCA
5228697 TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
5228726 ATTTTCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:5232389 original size:4 final size:4
Alignment explanation
Indices: 5232380--5232410 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5232370 ATCCGGTGGT
5232380 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
5232411 ACTACACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:5251240 original size:18 final size:18
Alignment explanation
Indices: 5251217--5251252 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5251207 GCGCTGGACT
5251217 ACCAGAATAAATTCGTCA
1 ACCAGAATAAATTCGTCA
5251235 ACCAGAATAAATTCGTCA
1 ACCAGAATAAATTCGTCA
5251253 TTGGGTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
ACCAGAATAAATTCGTCA
Found at i:5255753 original size:6 final size:6
Alignment explanation
Indices: 5255731--5255810 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
5255721 CTGCCTTTGG
* * * * *
5255731 CTCTGT CTTTTT CTCTGT CTCTGT CTCTGT CTTTTT CTCTGC CTCTGT
1 CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT
* * **
5255779 ATCTGT CTTTTGT -TCTAC CTCTGT CTCTGT CT
1 CTCTGT C-TCTGT CTCTGT CTCTGT CTCTGT CT
5255811 TTTGCTGTGC
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
5 2 0.04
6 48 0.89
7 4 0.07
ACGTcount: A:0.03, C:0.30, G:0.12, T:0.55
Consensus pattern (6 bp):
CTCTGT
Found at i:5255758 original size:24 final size:24
Alignment explanation
Indices: 5255719--5255870 Score: 153
Period size: 24 Copynumber: 6.3 Consensus size: 24
5255709 TTTGCTCTGC
* *
5255719 CTCTGCCTTTGGCTCTGTCTTTTT
1 CTCTGCCTCTGTCTCTGTCTTTTT
*
5255743 CTCTGTCTCTGTCTCTGTCTTTTT
1 CTCTGCCTCTGTCTCTGTCTTTTT
*
5255767 CTCTGCCTCTGTATCTGTCTTTTGT
1 CTCTGCCTCTGTCTCTGTCTTTT-T
* *
5255792 -TCTACCTCTGTCTCTGTCTTTTG
1 CTCTGCCTCTGTCTCTGTCTTTTT
* * * *
5255815 CTGTGCCTCCGTCTCTGCCTTTTG
1 CTCTGCCTCTGTCTCTGTCTTTTT
* * * * *
5255839 GTCTGCCTCTGGCTCTGCCTCTAT
1 CTCTGCCTCTGTCTCTGTCTTTTT
5255863 CTCTGCCT
1 CTCTGCCT
5255871 TTTGCTCTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
24 105 0.99
25 1 0.01
ACGTcount: A:0.02, C:0.33, G:0.16, T:0.49
Consensus pattern (24 bp):
CTCTGCCTCTGTCTCTGTCTTTTT
Found at i:5255855 original size:12 final size:12
Alignment explanation
Indices: 5255827--5255892 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
5255817 GTGCCTCCGT
*
5255827 CTCTGCCTTTTGG
1 CTCTGCC-TCTGG
5255840 -TCTGCCTCTGG
1 CTCTGCCTCTGG
**
5255851 CTCTGCCTCTAT
1 CTCTGCCTCTGG
* *
5255863 CTCTGCCTTTTG
1 CTCTGCCTCTGG
**
5255875 CTCTTTCTCTGG
1 CTCTGCCTCTGG
5255887 CTCTGC
1 CTCTGC
5255893 GTCTAATTCT
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
11 4 0.10
12 36 0.90
ACGTcount: A:0.02, C:0.36, G:0.18, T:0.44
Consensus pattern (12 bp):
CTCTGCCTCTGG
Found at i:5255866 original size:36 final size:36
Alignment explanation
Indices: 5255826--5255897 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
5255816 TGTGCCTCCG
*
5255826 TCTCTGCCTTTTGGTCTGCCTCTGGCTCTGCCTCTA
1 TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
** *
5255862 TCTCTGCCTTTTGCTCTTTCTCTGGCTCTGCGTCTA
1 TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
5255898 ATTCTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.03, C:0.35, G:0.18, T:0.44
Consensus pattern (36 bp):
TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
Found at i:5256285 original size:6 final size:6
Alignment explanation
Indices: 5256245--5256273 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5256235 CGGACTATGA
5256245 GGCTCG GGCTCG GGCTCG GGCTCG GGCTC
1 GGCTCG GGCTCG GGCTCG GGCTCG GGCTC
5256274 TGTCTCGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.48, T:0.17
Consensus pattern (6 bp):
GGCTCG
Found at i:5262459 original size:42 final size:42
Alignment explanation
Indices: 5262412--5262498 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
5262402 CTCTATAGGG
5262412 AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
1 AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
*
5262454 AGAGGCATATTGAAATCTTAGTAGTCTGTTTGTAGTATCATT
1 AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
5262496 AGA
1 AGA
5262499 TTATTGAAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (42 bp):
AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
Found at i:5267306 original size:5 final size:5
Alignment explanation
Indices: 5267296--5267321 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5267286 TCGCTGCTAC
5267296 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
5267322 TTTACCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:5280112 original size:22 final size:21
Alignment explanation
Indices: 5280087--5280145 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
5280077 AAATACATTG
*
5280087 TATTCAAATAAAATTTTACTCA
1 TATTCAAATAAAATTTCA-TCA
* *
5280109 TATTGAAATATAATTTCATCA
1 TATTCAAATAAAATTTCATCA
*
5280130 -AATCAAAATAAAATTT
1 TATTC-AAATAAAATTT
5280146 GGATTGAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.07
21 13 0.43
22 15 0.50
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (21 bp):
TATTCAAATAAAATTTCATCA
Found at i:5299732 original size:12 final size:12
Alignment explanation
Indices: 5299715--5299750 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5299705 ATAGTCGTAG
*
5299715 TCATCAAAATCA
1 TCATCATAATCA
*
5299727 TCATCATAACCA
1 TCATCATAATCA
5299739 TCATCATAATCA
1 TCATCATAATCA
5299751 ATTCCACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (12 bp):
TCATCATAATCA
Found at i:5301293 original size:21 final size:23
Alignment explanation
Indices: 5301251--5301293 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
5301241 GTTATTTGTT
* *
5301251 TATTATAATTATTTTTTTAATGA
1 TATTATAATTATTATTTGAATGA
5301274 TATTAT-A-TATTATTTGAATG
1 TATTATAATTATTATTTGAATG
5301294 TTAATACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
TATTATAATTATTATTTGAATGA
Found at i:5303062 original size:20 final size:20
Alignment explanation
Indices: 5303029--5303077 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
5303019 ATACAACGTT
5303029 TTAAAAATAAATAAATACAG-
1 TTAAAAATAAATAAA-ACAGA
**
5303049 TTAAAAATTTATAAAACAGAA
1 TTAAAAATAAATAAAACAG-A
5303070 TTAAAAAT
1 TTAAAAAT
5303078 GTAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (20 bp):
TTAAAAATAAATAAAACAGA
Found at i:5306405 original size:21 final size:21
Alignment explanation
Indices: 5306372--5306416 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5306362 TACGAGACTA
* * * *
5306372 CAAAAGGATATGGGAGTTATG
1 CAAAAAGACATGGGACTGATG
5306393 CAAAAAGACATGGGACTGATG
1 CAAAAAGACATGGGACTGATG
5306414 CAA
1 CAA
5306417 CAGGAACTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
CAAAAAGACATGGGACTGATG
Found at i:5312166 original size:63 final size:63
Alignment explanation
Indices: 5312067--5312188 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
5312057 GTTTCGATGA
* *
5312067 GTATGGGTTGGGTGAGATATCTCTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTGCTGG
1 GTATGGGTTGGGCGAGATATCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTGCTGG
*
5312130 GTATGGGTTGGGCGAGATGTCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTG
1 GTATGGGTTGGGCGAGATATCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTG
5312189 GGCCGTGCTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.29
Consensus pattern (63 bp):
GTATGGGTTGGGCGAGATATCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTGCTGG
Found at i:5319956 original size:21 final size:21
Alignment explanation
Indices: 5319931--5319986 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5319921 TGTTTCAAGC
5319931 TTTTTTTAATTAATTAATAT-A
1 TTTTTTTAATTAATTAAT-TCA
* **
5319952 TTTTTTCAATTTTTTAATTCA
1 TTTTTTTAATTAATTAATTCA
*
5319973 TCTTTTTAATTAAT
1 TTTTTTTAATTAAT
5319987 AACTCTTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTTAATTAATTAATTCA
Found at i:5320231 original size:18 final size:18
Alignment explanation
Indices: 5320210--5320244 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5320200 TAATATTATA
5320210 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
5320228 AAATATAATTATTATTT
1 AAATAAAATAATTATTT
5320245 TTATATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:5320303 original size:45 final size:47
Alignment explanation
Indices: 5320218--5320309 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 47
5320208 TAAAATAAAA
*
5320218 TAATTATTTCAAATATAATTATTATTTTTATATGTAAAATATTTCAAT
1 TAATTATTTCAAATATAATTATTATTTATATATG-AAAATATTTCAAT
* *
5320266 TAATTATTTCAAATATCATTA-TGTTTATATATG-AAATATTTCAA
1 TAATTATTTCAAATATAATTATTATTTATATATGAAAATATTTCAA
5320310 ATAAACATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 11 0.27
47 10 0.24
48 20 0.49
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (47 bp):
TAATTATTTCAAATATAATTATTATTTATATATGAAAATATTTCAAT
Found at i:5320426 original size:19 final size:20
Alignment explanation
Indices: 5320384--5320426 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5320374 TATTGCACAT
*
5320384 ATAAA-AATTATATTTACTA
1 ATAAATAATAATATTTACTA
5320403 A-AAATAATAATATTTA-TA
1 ATAAATAATAATATTTACTA
5320421 ATAAAT
1 ATAAAT
5320427 TATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAATAATAATATTTACTA
Found at i:5320811 original size:123 final size:124
Alignment explanation
Indices: 5320513--5320860 Score: 581
Period size: 124 Copynumber: 2.8 Consensus size: 124
5320503 TTATTTCGAG
* * * *
5320513 TTGACGTTTCCGAGCAAATAGTATAAAATCGCTTCTACCAGGTTGCTAGTTGAGAAGAAACTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
5320578 AAATCACGCCCTCATGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
*
5320637 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAATAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * * *
5320702 AAATCGTGCCCTCGTAGACGCGATTTTGCTACAGTTGGTCATGTAAGAAAT-ATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
*
5320760 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
5320825 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTA
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTA
5320861 ACAAGTTTGG
Statistics
Matches: 208, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
123 102 0.49
124 106 0.51
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
Found at i:5323980 original size:10 final size:10
Alignment explanation
Indices: 5323965--5323989 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5323955 CAAATCTAAC
5323965 ATTATGTAAA
1 ATTATGTAAA
5323975 ATTATGTAAA
1 ATTATGTAAA
5323985 ATTAT
1 ATTAT
5323990 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:5324303 original size:18 final size:21
Alignment explanation
Indices: 5324259--5324310 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 21
5324249 AGGTTAGGGT
5324259 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAA-TA-G
5324282 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAA-TA-G
5324305 TTAGGG
1 TTAGGG
5324311 CAGTGGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTTAATTAAATAG
Found at i:5324345 original size:142 final size:141
Alignment explanation
Indices: 5324038--5324431 Score: 578
Period size: 142 Copynumber: 2.7 Consensus size: 141
5324028 AAATTATGTA
*
5324038 AAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGCAGT-GAGTTTTTAATTAAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGGA-TTTTTAATTAAATT
*
5324102 ATGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
65 AGGTTAGGGTTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTTA
*
5324167 GGGTTAGGGTTTTTAATT
124 GGGGTAGGGTTTTTAATT
*
5324185 AAATTATGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGGATTTTTAATTAAATTA
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGGATTTTTAATTAAATTA
5324250 GGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGT
66 GGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG--GT
5324315 -GGGTTTTTAATT
129 AGGGTTTTTAATT
* **
5324327 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGGGTTTTTAATTAGTTTA
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGGATTTTTAATTAAATTA
*** *
5324392 GGTTATGGCAGT-GGGTTTTTAATTAAATTGGGTTAGGGTT
66 GGTTA-GGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
5324432 AGGGTTTTTA
Statistics
Matches: 231, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
141 31 0.13
142 108 0.47
143 4 0.02
144 1 0.00
146 2 0.01
147 83 0.36
148 2 0.01
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.44
Consensus pattern (141 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTGGATTTTTAATTAAATTA
GGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGGTAG
GGTTTTTAATT
Found at i:5324451 original size:89 final size:89
Alignment explanation
Indices: 5324056--5324452 Score: 566
Period size: 89 Copynumber: 4.5 Consensus size: 89
5324046 TTAGGGTTAA
* * *
5324056 GGTTTTTAATTAAATTAGGTTAGGG-CAGTGAGTTTTTAATTAAATTATGTTAGGGTTTAGGGTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTAG-G-GTTTTTAATTAAATTAGGTTAGGGATTAGGGTT
*
5324120 TTTAATTAAATTAGGTTAGGG--TTAG
64 TTTAATTAAATTAGGTTAGGGCAGT-G
*
5324145 GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTATGTTAGGG-TTAGGGTTTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGATTAGGGTTTT
5324209 TAATTAAATTAGGTTAGGGCAGTG
66 TAATTAAATTAGGTTAGGGCAGTG
*
5324233 GATTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT-AA--A--TTA-GG-TTAGGGTTT
1 GGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGATTAGGGTTT
5324291 TTAATTAAATTAGGTTAGGGCAGTG
65 TTAATTAAATTAGGTTAGGGCAGTG
*
5324316 GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGT-GGGTTT
1 GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-ATTAGGGTTT
** *
5324380 TTAATTAGTTTAGGTTATGGCAGTG
65 TTAATTAAATTAGGTTAGGGCAGTG
*
5324405 GGTTTTTAATTAAATTGGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
1 GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
5324453 GTTTTTATTA
Statistics
Matches: 287, Mismatches: 9, Indels: 24
0.90 0.03 0.08
Matches are distributed among these distances:
82 15 0.05
83 62 0.22
84 3 0.01
85 1 0.00
86 1 0.00
87 32 0.11
88 53 0.18
89 117 0.41
90 3 0.01
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (89 bp):
GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGATTAGGGTTTT
TAATTAAATTAGGTTAGGGCAGTG
Found at i:5324455 original size:30 final size:29
Alignment explanation
Indices: 5324038--5324452 Score: 539
Period size: 29 Copynumber: 14.3 Consensus size: 29
5324028 AAATTATGTA
*
5324038 AAATTAGGTTAGGGTTAAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5324067 AAATTAGGTTAGGG-CAGTGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAG-G-GTTTTTAATT
*
5324097 AAATTATGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
5324127 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
5324156 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5324185 AAATTATGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5324214 AAATTAGGTTAGGG-CAGTGGATTTTTAATT
1 AAATTAGGTTAGGGTTAG-GG-TTTTTAATT
5324244 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
5324274 -AA--A--TTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5324297 AAATTAGGTTAGGG-CAGTGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATT
5324327 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5324356 AAATTAGGTTAGGG-CAGTGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATT
**
5324386 AGTTTAGGTTATGGCAG-T-GGGTTTTTAATT
1 AAATTAGGTTA-GG--GTTAGGGTTTTTAATT
*
5324416 AAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
5324445 AAATTAGG
1 AAATTAGG
5324453 GTTTTTATTA
Statistics
Matches: 343, Mismatches: 19, Indels: 48
0.84 0.05 0.12
Matches are distributed among these distances:
23 15 0.04
24 4 0.01
25 3 0.01
26 1 0.00
27 2 0.01
28 9 0.03
29 153 0.45
30 145 0.42
31 6 0.02
32 4 0.01
33 1 0.00
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:5324941 original size:9 final size:9
Alignment explanation
Indices: 5324927--5324957 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5324917 GTTAAATGAA
5324927 TCGAGTTAT
1 TCGAGTTAT
*
5324936 TCGAGTTAA
1 TCGAGTTAT
5324945 TCGAGTTAT
1 TCGAGTTAT
5324954 TCGA
1 TCGA
5324958 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5325295 original size:30 final size:31
Alignment explanation
Indices: 5325261--5325321 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
5325251 AAACATTTTA
*
5325261 TTTTCCCCCAAAATTTTTACTCCC-TCCCAT
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAT
* *
5325291 TTTTCCCCTAAAACTTTTATTCCCTTCCCAT
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAT
5325322 CCCGCCTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAT
Found at i:5326725 original size:7 final size:7
Alignment explanation
Indices: 5326715--5326739 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5326705 TTATATACAT
5326715 AATACTA
1 AATACTA
5326722 AATACTA
1 AATACTA
5326729 AATACTA
1 AATACTA
5326736 AATA
1 AATA
5326740 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:5327153 original size:195 final size:195
Alignment explanation
Indices: 5326821--5327212 Score: 705
Period size: 195 Copynumber: 2.0 Consensus size: 195
5326811 AATAGAAGCT
5326821 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCGGATGGTTCCACCTAATTAAATAA
1 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCGGATGGTTCCACCTAATTAAATAA
* *
5326886 ATTTTTAGCATACTTTTATTTTTTAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
66 AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
5326951 CCTCGTTACGAGT-AGGAATGTATATAGGCGGTTCACTCAAGGACGTAGAAATGGAAAGCGAAAC
131 CCTCGTTACGAGTGA-GAATGTATATAGGCGGTTCACTCAAGGACGTAGAAATGGAAAGCGAAAC
5327015 C
195 C
5327016 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCGGATGGTTCCACCTAATTAAATAA
1 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCGGATGGTTCCACCTAATTAAATAA
*
5327081 AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAATTTTA
66 AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
* * * *
5327146 CCTCGTTACGAGTGAGAATGTATATGGGTGGTTCACTCGATGACGTAGAAATGGAAAGCGAAACC
131 CCTCGTTACGAGTGAGAATGTATATAGGCGGTTCACTCAAGGACGTAGAAATGGAAAGCGAAACC
5327211 GT
1 GT
5327213 GCCCATGATT
Statistics
Matches: 189, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
195 188 0.99
196 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (195 bp):
GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCGGATGGTTCCACCTAATTAAATAA
AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
CCTCGTTACGAGTGAGAATGTATATAGGCGGTTCACTCAAGGACGTAGAAATGGAAAGCGAAACC
Found at i:5329090 original size:50 final size:50
Alignment explanation
Indices: 5328966--5329214 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
5328956 GATAATAACA
* * ** * *
5328966 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
5329017 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5329067 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
5329117 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
5329172 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5329215 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:5329144 original size:100 final size:104
Alignment explanation
Indices: 5328965--5329214 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
5328955 TGATAATAAC
**
5328965 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
5329030 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
5329067 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
5329130 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
5329172 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5329215 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:5329330 original size:13 final size:13
Alignment explanation
Indices: 5329309--5329340 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5329299 GCTTGGATCA
*
5329309 TCATCAAATAAAT
1 TCATAAAATAAAT
5329322 TCATAAAATAAAT
1 TCATAAAATAAAT
5329335 TCATAA
1 TCATAA
5329341 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5329587 original size:30 final size:30
Alignment explanation
Indices: 5329552--5329609 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5329542 CCTCGACTCT
*
5329552 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
5329582 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
5329610 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:5337131 original size:50 final size:49
Alignment explanation
Indices: 5337013--5337155 Score: 214
Period size: 50 Copynumber: 2.9 Consensus size: 49
5337003 TTGGTGGGCC
* *
5337013 CCCATGCCATGTCCGAGACATGGTCTTATAGGGACCTCTCATCTCGGTG
1 CCCATGCCATGTCCCAGACATGGTCTTACAGGGACCTCTCATCTCGGTG
* * *
5337062 CCAACGCCATGTCCGCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTG
1 CCCATGCCATGTCC-CAGACATGGTCTTACA-GGGACCTCTCATCTCGGTG
5337113 CCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT
1 CCCATGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCAT
5337156 GATCTTAAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
49 12 0.14
50 41 0.49
51 30 0.36
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (49 bp):
CCCATGCCATGTCCCAGACATGGTCTTACAGGGACCTCTCATCTCGGTG
Found at i:5337329 original size:13 final size:13
Alignment explanation
Indices: 5337311--5337337 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5337301 ATCATCAATC
5337311 AAATAAATTCATA
1 AAATAAATTCATA
5337324 AAATAAATTCATA
1 AAATAAATTCATA
5337337 A
1 A
5337338 TTTCTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTCATA
Found at i:5337586 original size:30 final size:28
Alignment explanation
Indices: 5337552--5337610 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
5337542 CCCCTCGACT
*
5337552 CTAACTTTTTCAAATATTACAATTTTGCCC
1 CTAAC-TTTACAAA-ATTACAATTTTGCCC
* *
5337582 CTAACTTTACATAATTACATTTTTGCCC
1 CTAACTTTACAAAATTACAATTTTGCCC
5337610 C
1 C
5337611 AAGGCTCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.58
29 6 0.23
30 5 0.19
ACGTcount: A:0.29, C:0.25, G:0.03, T:0.42
Consensus pattern (28 bp):
CTAACTTTACAAAATTACAATTTTGCCC
Found at i:5338960 original size:24 final size:26
Alignment explanation
Indices: 5338914--5338963 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
5338904 GAAAATATAA
5338914 AAAAATTTAAAATTATTTAAAAAAAT
1 AAAAATTTAAAATTATTTAAAAAAAT
*
5338940 AAAAA-TTAAAA-TATTTTAAAAAAT
1 AAAAATTTAAAATTATTTAAAAAAAT
5338964 GAATTGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 6 0.26
26 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATTTAAAATTATTTAAAAAAAT
Found at i:5339025 original size:48 final size:51
Alignment explanation
Indices: 5338965--5339083 Score: 147
Period size: 51 Copynumber: 2.3 Consensus size: 51
5338955 TTAAAAAATG
*
5338965 AATTGAGGGGAAATTGAA-TT-AATATGGATTGAGAGAA-TTTGG-AAGGA
1 AATTGAGAGGAAATTGAATTTAAATATGGATTGAGAGAATTTTGGAAAGGA
*
5339012 TAATTGAGAGGAAATTGAAATTTAAATATGGTTTGAGAGAATTTTTGGAAAGGA
1 -AATTGAGAGGAAATTG-AATTTAAATATGGATTGAGAGAA-TTTTGGAAAGGA
*
5339066 AATTTAGAAGGAAATTGA
1 AATTGAG-AGGAAATTGA
5339084 GAGGATAGAG
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
48 15 0.25
49 2 0.03
50 2 0.03
51 16 0.26
53 12 0.20
54 14 0.23
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (51 bp):
AATTGAGAGGAAATTGAATTTAAATATGGATTGAGAGAATTTTGGAAAGGA
Found at i:5342259 original size:14 final size:14
Alignment explanation
Indices: 5342242--5342272 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5342232 ATAATATAGT
5342242 ATAATGAATAAAGA
1 ATAATGAATAAAGA
*
5342256 ATAATGAGTAAAGA
1 ATAATGAATAAAGA
5342270 ATA
1 ATA
5342273 GAAAGTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (14 bp):
ATAATGAATAAAGA
Found at i:5342305 original size:4 final size:4
Alignment explanation
Indices: 5342296--5342327 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
5342286 AGCAAACGTG
*
5342296 AGAA AGAA AGAA AGAA AGAA AGAT AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
5342328 CTAACAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (4 bp):
AGAA
Found at i:5347186 original size:7 final size:7
Alignment explanation
Indices: 5347176--5347205 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5347166 AAATATAAAT
5347176 AAAATTA
1 AAAATTA
5347183 AAAATTA
1 AAAATTA
5347190 AAAATT-
1 AAAATTA
5347196 AAAATTA
1 AAAATTA
5347203 AAA
1 AAA
5347206 TATAGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:5347191 original size:13 final size:14
Alignment explanation
Indices: 5347176--5347205 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5347166 AAATATAAAT
5347176 AAAATTAAAAATTA
1 AAAATTAAAAATTA
5347190 AAAATT-AAAATTA
1 AAAATTAAAAATTA
5347203 AAA
1 AAA
5347206 TATAGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:5351945 original size:5 final size:5
Alignment explanation
Indices: 5351937--5351968 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5351927 AGATTGGATT
5351937 GATCA GATCA GATCA GATCA GATCA GATCA GA
1 GATCA GATCA GATCA GATCA GATCA GATCA GA
5351969 GTAAGTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (5 bp):
GATCA
Found at i:5390343 original size:16 final size:16
Alignment explanation
Indices: 5390324--5390355 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5390314 TCAAGTCATG
*
5390324 CAAATATATTGTCAGA
1 CAAATATATTGACAGA
5390340 CAAATATATTGACAGA
1 CAAATATATTGACAGA
5390356 TTTTGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
CAAATATATTGACAGA
Found at i:5394958 original size:64 final size:64
Alignment explanation
Indices: 5394886--5395009 Score: 203
Period size: 64 Copynumber: 1.9 Consensus size: 64
5394876 TATCTGTTTC
* ** *
5394886 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTTGGGATGAGTGGAGCTATGTTGCTCCTGG
1 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTCCTGG
*
5394950 GAATGATGAAAAGGTTTAAATGTTTCAATATTGTTGGGGATGAGAAGAACTATGTTGCTC
1 GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTC
5395010 TGACTCTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (64 bp):
GAATGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGTTGCTCCTGG
Found at i:5400996 original size:30 final size:30
Alignment explanation
Indices: 5400962--5401022 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5400952 TAGGTTGTCA
5400962 ACAGTAAAAACTAGGTGATGTACAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
*
5400992 ACAGTAAAAACTAGGTGATGTAGAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
5401022 A
1 A
5401023 GAAACTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (30 bp):
ACAGTAAAAACTAGGTGATGTACAACTTTG
Found at i:5403408 original size:12 final size:12
Alignment explanation
Indices: 5403382--5403418 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5403372 CGTATCTAAA
*
5403382 ATATACA-AAAT
1 ATATACATATAT
5403393 ATATACATATAT
1 ATATACATATAT
5403405 ATATACATATAT
1 ATATACATATAT
5403417 AT
1 AT
5403419 TTTGCGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATACATATAT
Found at i:5405058 original size:14 final size:14
Alignment explanation
Indices: 5405039--5405068 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5405029 TAAAATTGAA
5405039 AAAAATCGAAAATC
1 AAAAATCGAAAATC
5405053 AAAAATCGAAAATC
1 AAAAATCGAAAATC
5405067 AA
1 AA
5405069 GACAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAATCGAAAATC
Found at i:5405496 original size:19 final size:20
Alignment explanation
Indices: 5405464--5405504 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5405454 GCCAAGGTGG
5405464 AAAAAGCCTGATATTAGACT
1 AAAAAGCCTGATATTAGACT
*
5405484 AAAAA-CCTTATATTAGACT
1 AAAAAGCCTGATATTAGACT
5405503 AA
1 AA
5405505 GTCTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (20 bp):
AAAAAGCCTGATATTAGACT
Found at i:5424467 original size:24 final size:25
Alignment explanation
Indices: 5424408--5424467 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5424398 AATAATCACC
5424408 AAAATTTTATTTTAAAAATAAAAAAT
1 AAAA-TTTATTTTAAAAATAAAAAAT
** *
5424434 AAAAAGTATTTTAAAATTAAAAAAT
1 AAAATTTATTTTAAAAATAAAAAAT
*
5424459 -ATATTTATT
1 AAAATTTATT
5424468 ATATTCGGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 6 0.21
25 18 0.64
26 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAATTTATTTTAAAAATAAAAAAT
Found at i:5431395 original size:12 final size:12
Alignment explanation
Indices: 5431380--5431405 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5431370 TTAAGTAATA
5431380 ATCTTTTTTCTC
1 ATCTTTTTTCTC
5431392 ATCTTTTTTCTC
1 ATCTTTTTTCTC
5431404 AT
1 AT
5431406 TTATGTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (12 bp):
ATCTTTTTTCTC
Found at i:5435558 original size:35 final size:35
Alignment explanation
Indices: 5435509--5435612 Score: 172
Period size: 35 Copynumber: 3.0 Consensus size: 35
5435499 ATATGTTATC
*
5435509 TCACTATTACCATTACATTTGAATCCAAATACATA
1 TCACTATTATCATTACATTTGAATCCAAATACATA
* *
5435544 TCATTATTGTCATTACATTTGAATCCAAATACATA
1 TCACTATTATCATTACATTTGAATCCAAATACATA
*
5435579 TCACTATTATCATTACATTTGAATCCAAACACAT
1 TCACTATTATCATTACATTTGAATCCAAATACAT
5435613 TAATTAATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (35 bp):
TCACTATTATCATTACATTTGAATCCAAATACATA
Found at i:5435889 original size:170 final size:166
Alignment explanation
Indices: 5435623--5435960 Score: 640
Period size: 170 Copynumber: 2.0 Consensus size: 166
5435613 TAATTAATCT
5435623 ATCAGTCCAAATTAAGCATAAATGAATTACACGCGTCAATCTAAGCTTAAAAAAAAGAAAAAAAA
1 ATCAGTCCAAATTAAGCATAAATGAATTACACGCGTCAATCTAAGCTTAAAAAAAAGAAAAAAAA
5435688 AAGAATTTACGGCAACCAATATACTAAGATCAAGAGTTGAGGTCCCACGGGTTTATTTCGTCAAA
66 AAGAATTTACGGCAACCAATATACTAAGATCAAGAGTTGAGGTCCCACGGGTTTATTTCGTCAAA
5435753 GTCAACACATTAATTTGAAGTCACATAAATAAAACC
131 GTCAACACATTAATTTGAAGTCACATAAATAAAACC
5435789 ATCAGTCCAAATTAAGCATAAATGAATTACACGCGTCAATCTAAGCTTAAAAAAAAGAAAAAAAA
1 ATCAGTCCAAATTAAGCATAAATGAATTACACGCGTCAATCTAAGCTTAAAAAAAAG---AAAAA
5435854 AAAGAAGAATTTACGGCAACCAATATACTAAGATCAAGAGTTGAGGTCCCACGGGTTTATTTCGT
63 AAA-AAGAATTTACGGCAACCAATATACTAAGATCAAGAGTTGAGGTCCCACGGGTTTATTTCGT
5435919 CAAAGTCAACACATTAATTTGAAGTCACATAAATAAAACC
127 CAAAGTCAACACATTAATTTGAAGTCACATAAATAAAACC
5435959 AT
1 AT
5435961 TAAGATTTTA
Statistics
Matches: 168, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
166 57 0.34
169 8 0.05
170 103 0.61
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (166 bp):
ATCAGTCCAAATTAAGCATAAATGAATTACACGCGTCAATCTAAGCTTAAAAAAAAGAAAAAAAA
AAGAATTTACGGCAACCAATATACTAAGATCAAGAGTTGAGGTCCCACGGGTTTATTTCGTCAAA
GTCAACACATTAATTTGAAGTCACATAAATAAAACC
Found at i:5449178 original size:19 final size:19
Alignment explanation
Indices: 5449154--5449190 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5449144 CGTACTTCGA
*
5449154 TGAAAAAATTTAAAATATT
1 TGAAAAAAGTTAAAATATT
*
5449173 TGAAAAACGTTAAAATAT
1 TGAAAAAAGTTAAAATAT
5449191 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
TGAAAAAAGTTAAAATATT
Found at i:5456067 original size:2 final size:2
Alignment explanation
Indices: 5456060--5456114 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5456050 TTATAATTAT
5456060 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5456102 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
5456115 TTTCTTTTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5456622 original size:29 final size:29
Alignment explanation
Indices: 5456580--5456635 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
5456570 TGATTTGGTC
5456580 TATGCAAAAGATTATGAAAATTGTTTAGT
1 TATGCAAAAGATTATGAAAATTGTTTAGT
5456609 TATGCAAAAGATTATGAAAATTGTTTA
1 TATGCAAAAGATTATGAAAATTGTTTA
5456636 TTTTCATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.38
Consensus pattern (29 bp):
TATGCAAAAGATTATGAAAATTGTTTAGT
Found at i:5464271 original size:30 final size:29
Alignment explanation
Indices: 5464228--5464294 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
5464218 ATTACATTTT
5464228 ATTTTTTAATTAAA-AAATAGA-TAAATTA
1 ATTTTTTAATTAAATAAA-AGAGTAAATTA
*
5464256 ATTTTTATATATTAAATTAAAGAGTAAATTA
1 ATTTTT-TA-ATTAAATAAAAGAGTAAATTA
5464287 ATTTTTTA
1 ATTTTTTA
5464295 TTGAGTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.18
29 2 0.06
30 11 0.32
31 15 0.44
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTTTTTAATTAAATAAAAGAGTAAATTA
Found at i:5465088 original size:126 final size:126
Alignment explanation
Indices: 5464902--5465446 Score: 801
Period size: 126 Copynumber: 4.3 Consensus size: 126
5464892 AGTGTTAATT
* * * * *
5464902 TAAAA-AAGCTCCCACGTAGACG-ATCTTCTGCTACAATAGCTACTGAAAAAATAATTTCGAGAA
1 TAAAAGAAGCTCCCACGTGGACGCA-CTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTA
*
5464965 GACGTTTCTGAGCAAATAGTGTCAAAAATGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
65 GACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
* *
5465027 TGAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
* * *
5465092 ACGTTTTTGAGCAAATAGTGTCAAAAACGCTTTAAGTAAGATGTTTTGTCAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
* ** * ** *
5465153 TAAAATAATATCCTACGTGGACGCGTTTTTGCTACAGTAGCTCCT-AAAAAATAATTTCAAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
*
5465217 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAGGCATA-ATGCTTTGTCAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCA-AGATGCTTTGTCAGCAAAAGTAC
* *
5465278 TAAAAGAAGCTCCCACGTGGATGCACTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
* * * *
5465343 ACGTTTTTGAGAAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTCAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
* *
5465404 TGAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTC
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTC
5465447 TTGTTTGGCC
Statistics
Matches: 374, Mismatches: 41, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
125 114 0.30
126 259 0.69
127 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
Found at i:5465393 original size:251 final size:252
Alignment explanation
Indices: 5464902--5465446 Score: 826
Period size: 251 Copynumber: 2.2 Consensus size: 252
5464892 AGTGTTAATT
* * ** * * * *
5464902 TAAAA-AAGCTCCCACGTAGACGATCTTCTGCTACAATAGCTACTGAAAAAATAATTTCGAGAAG
1 TAAAAGAAGATCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGAAG
* *
5464966 ACGTTTCTGAGCAAATAGTGTCAAAAATGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTGAA
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTAAA
*
5465031 AGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGACGT
131 AGAAGCTCCCACGTGGACGCACTTTTGCTACAATAGCTCCTAAAAAAATAATTTCGAGTAGACGT
* ** *
5465096 TTTTGAGCAAATAGTGTCAAAAACGCTTTAAGTAAGATGTTTTGTCAGCAAAAGTAC
196 TTTTGAGAAAATAGTGTCAAAAACGCTTTAAACAAGATGCTTTGTCAGCAAAAGTAC
* * * * *
5465153 TAAAATAATATCCTACGTGGACGCGTTTTTGCTACAGTAGCTCCT-AAAAAATAATTTCAAGTAG
1 TAAAAGAAGATCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGAAG
*
5465217 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAGGCATA-ATGCTTTGTCAGCAAAAGTACTAA
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCA-AGATGCTTTGTCAGCAAAAGTACTAA
* *
5465281 AAGAAGCTCCCACGTGGATGCACTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTAGACG
130 AAGAAGCTCCCACGTGGACGCACTTTTGCTACAATAGCTCCTAAAAAAATAATTTCGAGTAGACG
*
5465346 TTTTTGAGAAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTCAGCAAAAGTAC
195 TTTTTGAGAAAATAGTGTCAAAAACGCTTTAAACAAGATGCTTTGTCAGCAAAAGTAC
* *
5465404 TGAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTC
1 TAAAAGAAGATCCCACGTGGACGCGCTTTTGCTACAGTAGCTC
5465447 TTGTTTGGCC
Statistics
Matches: 263, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
251 233 0.89
252 30 0.11
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (252 bp):
TAAAAGAAGATCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGAAG
ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTAAA
AGAAGCTCCCACGTGGACGCACTTTTGCTACAATAGCTCCTAAAAAAATAATTTCGAGTAGACGT
TTTTGAGAAAATAGTGTCAAAAACGCTTTAAACAAGATGCTTTGTCAGCAAAAGTAC
Found at i:5472616 original size:7 final size:7
Alignment explanation
Indices: 5472604--5472628 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5472594 TATTAGTTAT
5472604 ATACATA
1 ATACATA
5472611 ATACATA
1 ATACATA
5472618 ATACATA
1 ATACATA
5472625 ATAC
1 ATAC
5472629 TAAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:5472634 original size:7 final size:7
Alignment explanation
Indices: 5472624--5472649 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5472614 CATAATACAT
5472624 AATACTA
1 AATACTA
5472631 AATACTA
1 AATACTA
5472638 AATACTA
1 AATACTA
5472645 AATAC
1 AATAC
5472650 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:5472634 original size:14 final size:14
Alignment explanation
Indices: 5472604--5472649 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
5472594 TATTAGTTAT
5472604 ATACATAATAC-ATA
1 ATACATAATACTA-A
5472618 ATACATAATACTAA
1 ATACATAATACTAA
5472632 ATAC-TAAATACTAA
1 ATACAT-AATACTAA
5472646 ATAC
1 ATAC
5472650 CAATCGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (14 bp):
ATACATAATACTAA
Found at i:5473866 original size:11 final size:11
Alignment explanation
Indices: 5473852--5473899 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
5473842 AGTTTTTTTA
*
5473852 AGAGGAATTTG
1 AGAGGAAATTG
5473863 AGAGGAAATTG
1 AGAGGAAATTG
5473874 AGA-GAATATTG
1 AGAGGAA-ATTG
5473885 -GAGAGAAATTG
1 AGAG-GAAATTG
5473896 AGAG
1 AGAG
5473900 AAAGGATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.16
11 21 0.66
12 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:5473877 original size:22 final size:23
Alignment explanation
Indices: 5473852--5473899 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5473842 AGTTTTTTTA
5473852 AGAGGAAT-TT-GAGAGGAAATTG
1 AGAGGAATATTGGAGA-GAAATTG
5473874 AGA-GAATATTGGAGAGAAATTG
1 AGAGGAATATTGGAGAGAAATTG
5473896 AGAG
1 AGAG
5473900 AAAGGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (23 bp):
AGAGGAATATTGGAGAGAAATTG
Found at i:5473898 original size:10 final size:10
Alignment explanation
Indices: 5473860--5473902 Score: 59
Period size: 11 Copynumber: 4.0 Consensus size: 10
5473850 TAAGAGGAAT
5473860 TTGAGAGGAAA
1 TTGAGA-GAAA
5473871 TTGAGAGAATA
1 TTGAGAGAA-A
5473882 TTGGAGAGAAA
1 TT-GAGAGAAA
5473893 TTGAGAGAAA
1 TTGAGAGAAA
5473903 GGATTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.37
11 12 0.40
12 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:5484064 original size:29 final size:29
Alignment explanation
Indices: 5484000--5484066 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
5483990 TAGCGCGCTC
* *
5484000 TTTGTTTTGTTATTGCACTTTGGTGCTAA
1 TTTGTTTTGTTATAGCACTTTAGTGCTAA
** *
5484029 TACGTTTTGATTA-AGCACTTTAGTGCTAT
1 TTTGTTTTG-TTATAGCACTTTAGTGCTAA
5484058 TTTGTTTTG
1 TTTGTTTTG
5484067 GCATTACACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.54
Consensus pattern (29 bp):
TTTGTTTTGTTATAGCACTTTAGTGCTAA
Done.