Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 153 of 250
Found at i:49347158 original size:32 final size:30
Alignment explanation
Indices: 49347097--49347160 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
49347087 ATAGTAAAAA
*
49347097 TATTATTTTTAAAAGATTAAATTAAAATTT
1 TATTATTTTTAAAAGATTAAAGTAAAATTT
*
49347127 TATTATTTTTAGAGGAAG-TTAAAGTACAATTT
1 TATTATTTTTA-A--AAGATTAAAGTAAAATTT
49347159 TA
1 TA
49347161 GTTTTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.38
31 1 0.03
32 14 0.48
33 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (30 bp):
TATTATTTTTAAAAGATTAAAGTAAAATTT
Found at i:49352897 original size:34 final size:35
Alignment explanation
Indices: 49352853--49352929 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
49352843 TTGAAATTTA
49352853 AAGACAGGAGAAACTGTATT-ACAAATTGAAAGATG
1 AAGA-AGGAGAAACTGTATTCACAAATTGAAAGATG
*
49352888 AAGAAGGAGAAACTGTATTCACAAATTGAAATATG
1 AAGAAGGAGAAACTGTATTCACAAATTGAAAGATG
49352923 AAGAAGG
1 AAGAAGG
49352930 GAGAGAAACG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 15 0.38
35 25 0.62
ACGTcount: A:0.49, C:0.08, G:0.23, T:0.19
Consensus pattern (35 bp):
AAGAAGGAGAAACTGTATTCACAAATTGAAAGATG
Found at i:49353086 original size:39 final size:39
Alignment explanation
Indices: 49353032--49353110 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
49353022 ATTTGCTATC
49353032 AGGAATTGATAGATGCATTTTCGAGGAGGATAATTAAAG
1 AGGAATTGATAGATGCATTTTCGAGGAGGATAATTAAAG
49353071 AGGAATTGATAGATGCATTTTCGAGGAGGATAATTAAAG
1 AGGAATTGATAGATGCATTTTCGAGGAGGATAATTAAAG
49353110 A
1 A
49353111 CTTATGTCGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.05, G:0.28, T:0.28
Consensus pattern (39 bp):
AGGAATTGATAGATGCATTTTCGAGGAGGATAATTAAAG
Found at i:49358739 original size:37 final size:37
Alignment explanation
Indices: 49358689--49358761 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
49358679 AATTTGTCAC
*
49358689 CTCATCATATTTATTTCCTATTAGTCATATACCATGT
1 CTCATCATATTTATTTCCTATCAGTCATATACCATGT
* *
49358726 CTCATCATGTTTATTTTCTATCAGTCATATACCATG
1 CTCATCATATTTATTTCCTATCAGTCATATACCATG
49358762 CCATATGACG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (37 bp):
CTCATCATATTTATTTCCTATCAGTCATATACCATGT
Found at i:49360882 original size:23 final size:22
Alignment explanation
Indices: 49360830--49360904 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
49360820 CCTGATCAGT
** *
49360830 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
49360851 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
49360872 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
49360895 ATACGACACA
1 ATACGACACA
49360905 GCCTGATCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:49361316 original size:15 final size:15
Alignment explanation
Indices: 49361298--49361338 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
49361288 TTTAATTAAT
49361298 ATAAATTCAATCAAA
1 ATAAATTCAATCAAA
* *
49361313 ATAATTTCAATCAAT
1 ATAAATTCAATCAAA
49361328 ATAAATTCAAT
1 ATAAATTCAAT
49361339 AAATTCATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAATTCAATCAAA
Found at i:49374849 original size:13 final size:13
Alignment explanation
Indices: 49374828--49374862 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
49374818 AACAAAATGA
*
49374828 GCCAAATGCTATG
1 GCCATATGCTATG
49374841 GCCATATGCTATG
1 GCCATATGCTATG
*
49374854 ACCATATGC
1 GCCATATGC
49374863 ATGTAGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (13 bp):
GCCATATGCTATG
Found at i:49380891 original size:11 final size:12
Alignment explanation
Indices: 49380877--49380940 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
49380867 AGATAAATAT
49380877 TATTTTATTA-A
1 TATTTTATTAGA
*
49380888 TATTTTAATAAGA
1 TATTTT-ATTAGA
*
49380901 TATTTTAATAAGA
1 TATTTT-ATTAGA
*
49380914 TATTTTATTA-T
1 TATTTTATTAGA
49380925 TATTTTATTAGTA
1 TATTTTATTAG-A
49380938 TAT
1 TAT
49380941 AAAGAAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
11 16 0.36
12 6 0.13
13 23 0.51
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (12 bp):
TATTTTATTAGA
Found at i:49380905 original size:13 final size:13
Alignment explanation
Indices: 49380887--49380920 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
49380877 TATTTTATTA
49380887 ATATTTTAATAAG
1 ATATTTTAATAAG
49380900 ATATTTTAATAAG
1 ATATTTTAATAAG
49380913 ATATTTTA
1 ATATTTTA
49380921 TTATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
ATATTTTAATAAG
Found at i:49382625 original size:33 final size:33
Alignment explanation
Indices: 49382522--49382677 Score: 93
Period size: 33 Copynumber: 4.7 Consensus size: 33
49382512 AATTGATAGA
* * * * * *
49382522 TAAGACCATGGTTGGGTCATGGCAATATATGTT
1 TAAGACCATAGCTGGGACATGGCAATACAAGTG
** ** *
49382555 TAAGACCATAGCTATGTTATGGC-ATCCTAA-TG
1 TAAGACCATAGCTGGGACATGGCAATAC-AAGTG
* * *
49382587 ATAAGACCATATCTGGGATATGGCACTACAAGTG
1 -TAAGACCATAGCTGGGACATGGCAATACAAGTG
* * * *
49382621 TAAGACCATGGCTGGGCCATGGGAATACATGTG
1 TAAGACCATAGCTGGGACATGGCAATACAAGTG
*
49382654 TAAGACCATAG-TTGGACTATGGCA
1 TAAGACCATAGCTGGGAC-ATGGCA
49382678 TCATGCCAGA
Statistics
Matches: 92, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
32 7 0.08
33 81 0.88
34 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (33 bp):
TAAGACCATAGCTGGGACATGGCAATACAAGTG
Found at i:49382837 original size:45 final size:46
Alignment explanation
Indices: 49382749--49382955 Score: 236
Period size: 46 Copynumber: 4.5 Consensus size: 46
49382739 TAAGACTATA
* * * ** * *
49382749 GTTGAAAGATACTATGACAATATGATGAGAAATGAATAAGACCATG
1 GTTGAAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATG
* * *
49382795 ATTGAAAGATACCATGGCAA-ATGACAAAAAACGAATAAGACCATG
1 GTTGAAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATG
*
49382840 GTTGGAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATG
1 GTTGAAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATG
* ** *
49382886 GTTGAAAGATACCATGGAAACATGACAGGAAATGAATAAAACCATA
1 GTTGAAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATG
* * * *
49382932 GTTGGAAGACACTATGGCATCATG
1 GTTGAAAGATACCATGGCAACATG
49382956 TCGAAGATAA
Statistics
Matches: 139, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 39 0.28
46 100 0.72
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (46 bp):
GTTGAAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATG
Found at i:49382849 original size:91 final size:92
Alignment explanation
Indices: 49382739--49382947 Score: 258
Period size: 91 Copynumber: 2.3 Consensus size: 92
49382729 TTCAGATATG
* * * ** * *
49382739 TAAGACTATAGTTGAAAGATACTATGACAATATGATGAGAAATGAATAAGACCATGATTGAAAGA
1 TAAGACCATAGTTGGAAGATACTATGACAACATGACAAAAAATGAATAAAACCATGATTGAAAGA
*
49382804 TACCATGGCAA-ATGACAAAAAACGAA
66 TACCATGGAAACATGACAAAAAACGAA
* * * *
49382830 TAAGACCATGGTTGGAAGATACCATGGCAACATGACAAAAAATGAATAAAACCATGGTTGAAAGA
1 TAAGACCATAGTTGGAAGATACTATGACAACATGACAAAAAATGAATAAAACCATGATTGAAAGA
** *
49382895 TACCATGGAAACATGACAGGAAATGAA
66 TACCATGGAAACATGACAAAAAACGAA
* *
49382922 TAAAACCATAGTTGGAAGACACTATG
1 TAAGACCATAGTTGGAAGATACTATG
49382948 GCATCATGTC
Statistics
Matches: 98, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
91 64 0.65
92 34 0.35
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (92 bp):
TAAGACCATAGTTGGAAGATACTATGACAACATGACAAAAAATGAATAAAACCATGATTGAAAGA
TACCATGGAAACATGACAAAAAACGAA
Found at i:49387895 original size:8 final size:8
Alignment explanation
Indices: 49387884--49387918 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
49387874 TTTTTAATTC
*
49387884 TTTATTAT
1 TTTATCAT
49387892 TTTATCAT
1 TTTATCAT
49387900 TTTATCAT
1 TTTATCAT
*
49387908 TTTATTAT
1 TTTATCAT
49387916 TTT
1 TTT
49387919 CTTTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTATCAT
Found at i:49388347 original size:18 final size:18
Alignment explanation
Indices: 49388319--49388353 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49388309 GACTTATTAT
49388319 TTATTCTTTTTA-TTTTG
1 TTATTCTTTTTACTTTTG
49388336 TTATTACTTTTTACTTTT
1 TTATT-CTTTTTACTTTT
49388354 CTTTTAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (18 bp):
TTATTCTTTTTACTTTTG
Found at i:49388444 original size:17 final size:18
Alignment explanation
Indices: 49388414--49388454 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
49388404 TTCATTTTAG
49388414 TTTGATTCAATTTT-TGA
1 TTTGATTCAATTTTATGA
49388431 TTTGATT-AAGTTTTATGA
1 TTTGATTCAA-TTTTATGA
49388449 TGTTGA
1 T-TTGA
49388455 GTTGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.10
17 11 0.52
18 4 0.19
19 4 0.19
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.56
Consensus pattern (18 bp):
TTTGATTCAATTTTATGA
Found at i:49389497 original size:6 final size:6
Alignment explanation
Indices: 49389481--49389534 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
49389471 GTTTTATTTG
* *
49389481 TTTTAT ATTTAT TTTTAT CTTTAT TTTTAT TTTTAGTT GTTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA--T -TTTTAT TTTTAT
49389532 TTT
1 TTT
49389535 CTTAGACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 34 0.83
7 1 0.02
8 1 0.02
9 5 0.12
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:49394417 original size:71 final size:71
Alignment explanation
Indices: 49394301--49394464 Score: 229
Period size: 71 Copynumber: 2.3 Consensus size: 71
49394291 AATGCTACTA
* * * * * *
49394301 ATACCGTGAGGACTTCTATCGAAACAAGTTAAGCCAGTAGCCAAAGTTCAGCATCTCTTGCATTT
1 ATACCTTGAGGACTTCTACCGAAACAAGTCAAGCCAGTAGCCAAAGTTCAGCATCCCCTGCACTT
49394366 CTATTG
66 CTATTG
**
49394372 ATACCTTGAGGACTTCTACCGAAACAAGTCAAGTTAGTAGCCAAAGTTCAGCATCCCCTGCACTT
1 ATACCTTGAGGACTTCTACCGAAACAAGTCAAGCCAGTAGCCAAAGTTCAGCATCCCCTGCACTT
49394437 CTATTG
66 CTATTG
* * *
49394443 ATACTTTGATGAGTTCTACCGA
1 ATACCTTGAGGACTTCTACCGA
49394465 TACCAAATGA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (71 bp):
ATACCTTGAGGACTTCTACCGAAACAAGTCAAGCCAGTAGCCAAAGTTCAGCATCCCCTGCACTT
CTATTG
Found at i:49398656 original size:16 final size:16
Alignment explanation
Indices: 49398635--49398698 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
49398625 CCCCAAATAC
*
49398635 TAAAATCCCTAATTCG
1 TAAAATCCCTAAATCG
*
49398651 TCAAATTCCCTAAATCG
1 T-AAAATCCCTAAATCG
*
49398668 TGAAA-CCTCTAAATCG
1 TAAAATCC-CTAAATCG
*
49398684 TAAAATCCTTAAATC
1 TAAAATCCCTAAATC
49398699 TATAACATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.05
16 21 0.54
17 16 0.41
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (16 bp):
TAAAATCCCTAAATCG
Found at i:49404960 original size:23 final size:23
Alignment explanation
Indices: 49404934--49404980 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
49404924 CTACATATCC
49404934 TTTGACTTAGGTCCATTGTATAT
1 TTTGACTTAGGTCCATTGTATAT
49404957 TTTGACTTAGGTCCATTGTATAT
1 TTTGACTTAGGTCCATTGTATAT
49404980 T
1 T
49404981 GATAACTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (23 bp):
TTTGACTTAGGTCCATTGTATAT
Found at i:49406645 original size:51 final size:51
Alignment explanation
Indices: 49406569--49406713 Score: 229
Period size: 51 Copynumber: 2.8 Consensus size: 51
49406559 TTGCAATAGT
* * *
49406569 AACATTATCCACTCCATATGATGTTGCAAAATCACTAACATATCCAGTAGC
1 AACATTATCCACTCCATCTGATGTTGCAAAATCACCAACATATCCACTAGC
*
49406620 AACATTATCTC-CTCCATCTGATGTTGCAAAATCACCAACATATCTACTAGC
1 AACATTATC-CACTCCATCTGATGTTGCAAAATCACCAACATATCCACTAGC
*
49406671 AACATTATCCATTCCATCTGATGTTGCAAAATCACCAACATAT
1 AACATTATCCACTCCATCTGATGTTGCAAAATCACCAACATAT
49406714 TCATCAGCAG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
50 1 0.01
51 85 0.98
52 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (51 bp):
AACATTATCCACTCCATCTGATGTTGCAAAATCACCAACATATCCACTAGC
Found at i:49406937 original size:33 final size:32
Alignment explanation
Indices: 49406862--49406964 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 32
49406852 CTTACATCCT
*
49406862 CCTCCTCA-CAGATTCTACCCTTTCCAGATCAC
1 CCTCCTCATCAGATTCTACCCTTT-CACATCAC
* *
49406894 CTTCAC-CATCAGATTCTACCCCTTCATCATCAC
1 CCTC-CTCATCAGATTCTACCCTTTCA-CATCAC
*
49406927 CCTCCTCATCA-ACTTCTACCCTTTTAACATCAC
1 CCTCCTCATCAGA-TTCTACCC-TTTCACATCAC
49406960 CCTCC
1 CCTCC
49406965 CCAACAGTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 9 0.15
33 47 0.80
34 3 0.05
ACGTcount: A:0.22, C:0.45, G:0.03, T:0.30
Consensus pattern (32 bp):
CCTCCTCATCAGATTCTACCCTTTCACATCAC
Found at i:49414462 original size:56 final size:55
Alignment explanation
Indices: 49414397--49414504 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 55
49414387 TTATAGATTG
* * *
49414397 CAAATTAATTATTCATAAGCACTTTTCAAATTAAAAGTGATGATTTATCATCTTA
1 CAAATTAATTATTCATAAGAACTATTCAAATTAAAAGGGATGATTTATCATCTTA
49414452 CAAATTTAATTATTCATAAGAACTATTCAAATTAAAAGGGATGATTTATCATC
1 CAAA-TTAATTATTCATAAGAACTATTCAAATTAAAAGGGATGATTTATCATC
49414505 CAATGGATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 4 0.08
56 45 0.92
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGAACTATTCAAATTAAAAGGGATGATTTATCATCTTA
Found at i:49415395 original size:76 final size:76
Alignment explanation
Indices: 49415271--49415572 Score: 457
Period size: 76 Copynumber: 4.0 Consensus size: 76
49415261 CCATTTTGGT
* *
49415271 ATTTAATT--TTTTTTTGGATTATTATTGTAAAAGAACTACATTTTACAAATGTTGAATATTTGT
1 ATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTGAATATCTGT
49415334 TACATAATAAA
66 TACATAATAAA
* * *
49415345 ATTTAATTAATTTTTTTGGATTATTGTGGTAAAAGAACTACATTTTACAAATGTTGAATACCGGT
1 ATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTGAATATCTGT
*
49415410 TACTTAATAAA
66 TACATAATAAA
* * * *
49415421 ATTTAATTAA-TTTTTTGGATTATTGTGGAAAAAAAACTATATTTTACAAATGTTGAATATCTGT
1 ATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTGAATATCTGT
49415485 TACATAATAAA
66 TACATAATAAA
* * *
49415496 ATTTAATTACTTTTTTTGGATTATTATGGTAAAAGAATTACATTTTACAAATGTTGAATATATGT
1 ATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTGAATATCTGT
*
49415561 TACGTAATAAA
66 TACATAATAAA
49415572 A
1 A
49415573 AATTTTTATT
Statistics
Matches: 205, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
74 8 0.04
75 68 0.33
76 129 0.63
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (76 bp):
ATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTGAATATCTGT
TACATAATAAA
Found at i:49415465 original size:151 final size:150
Alignment explanation
Indices: 49415271--49415555 Score: 471
Period size: 151 Copynumber: 1.9 Consensus size: 150
49415261 CCATTTTGGT
* * * * *
49415271 ATTTAATTTTTTTTTGGATTATTATTGTAAAAGAACTACATTTTACAAATGTTGAATATTTGTTA
1 ATTTAATTATTTTTTGGATTATTATGGAAAAAAAACTACATTTTACAAATGTTGAATATCTGTTA
*
49415336 CATAATAAAATTTAATTAATTTTTTTGGATTATTGTGGTAAAAGAACTACATTTTACAAATGTTG
66 CATAATAAAATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTG
49415401 AATACCGGTTACTTAATAAA
131 AATACCGGTTACTTAATAAA
* *
49415421 ATTTAATTAATTTTTTGGATTATTGTGGAAAAAAAACTATATTTTACAAATGTTGAATATCTGTT
1 ATTTAATT-ATTTTTTGGATTATTATGGAAAAAAAACTACATTTTACAAATGTTGAATATCTGTT
* *
49415486 ACATAATAAAATTTAATTACTTTTTTTGGATTATTATGGTAAAAGAATTACATTTTACAAATGTT
65 ACATAATAAAATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTT
49415551 GAATA
130 GAATA
49415556 TATGTTACGT
Statistics
Matches: 124, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
150 8 0.06
151 116 0.94
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (150 bp):
ATTTAATTATTTTTTGGATTATTATGGAAAAAAAACTACATTTTACAAATGTTGAATATCTGTTA
CATAATAAAATTTAATTAATTTTTTTGGATTATTATGGTAAAAGAACTACATTTTACAAATGTTG
AATACCGGTTACTTAATAAA
Found at i:49417622 original size:18 final size:18
Alignment explanation
Indices: 49417581--49417628 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
49417571 AAATTTGGGG
*
49417581 ATGTGGG-CCACACGAGC
1 ATGTGGGCCCATACGAGC
* *
49417598 GTGTGGGCCCATACGGGC
1 ATGTGGGCCCATACGAGC
49417616 ATGTGGGCCCATA
1 ATGTGGGCCCATA
49417629 TTTCTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.19, C:0.27, G:0.38, T:0.17
Consensus pattern (18 bp):
ATGTGGGCCCATACGAGC
Found at i:49419041 original size:28 final size:28
Alignment explanation
Indices: 49418994--49419056 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
49418984 ATATTCAATA
* * *
49418994 CATGTTA--TTAATTGTGTTACTACCTT
1 CATGTTATTTTAATCGTGTTACTACATC
*
49419020 CATGTTATTTTAATCGTTTTACTACATC
1 CATGTTATTTTAATCGTGTTACTACATC
49419048 CATGTTATT
1 CATGTTATT
49419057 AATTGTACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 7 0.23
28 24 0.77
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.51
Consensus pattern (28 bp):
CATGTTATTTTAATCGTGTTACTACATC
Found at i:49423137 original size:32 final size:32
Alignment explanation
Indices: 49423061--49423147 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
49423051 AGCCTCCACA
*
49423061 AATGCCGCCTCTCTCTCACCCTCTACTTCCATT
1 AATGCCGCCTCTCTCTCACCCTCCACTTCCA-T
**
49423094 AATGTTGCCTCTCTCTCACCCTCCACTTACC-T
1 AATGCCGCCTCTCTCTCACCCTCCACTT-CCAT
* * *
49423126 AATGCCCCCTCTTTTTCACCCT
1 AATGCCGCCTCTCTCTCACCCT
49423148 TCACCATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
32 18 0.40
33 25 0.56
34 2 0.04
ACGTcount: A:0.15, C:0.45, G:0.06, T:0.34
Consensus pattern (32 bp):
AATGCCGCCTCTCTCTCACCCTCCACTTCCAT
Found at i:49423256 original size:50 final size:52
Alignment explanation
Indices: 49423192--49423330 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 52
49423182 ACTAATATCA
* * *
49423192 CCCATCTCTTTCCCTCTACCTTTAAAAAAT-ATTTTT-TTATACTGGTGCTG
1 CCCATCTCTCTCCCTCTACCCTTAAAAAATAATTTTTGTTATACTAGTGCTG
**
49423242 CCCATCTCTCTCCCTCTACCCTTAAAAAATAATTTTTGTTATACTAGTGCCA
1 CCCATCTCTCTCCCTCTACCCTTAAAAAATAATTTTTGTTATACTAGTGCTG
*
49423294 CTCCATCTC-C-CCCTTTCCACCCTT-AAAAATAATTTTT
1 C-CCATCTCTCTCCC--TCTACCCTTAAAAAATAATTTTT
49423331 TTTAAAAACA
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
50 28 0.36
51 9 0.12
52 26 0.33
53 15 0.19
ACGTcount: A:0.24, C:0.31, G:0.05, T:0.40
Consensus pattern (52 bp):
CCCATCTCTCTCCCTCTACCCTTAAAAAATAATTTTTGTTATACTAGTGCTG
Found at i:49441752 original size:10 final size:9
Alignment explanation
Indices: 49441736--49441766 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
49441726 AACTGTGAAA
49441736 AAATAAAAT
1 AAATAAAAT
49441745 ATAATAAAAT
1 A-AATAAAAT
49441755 AAATAAAAT
1 AAATAAAAT
49441764 AAA
1 AAA
49441767 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:49446194 original size:10 final size:9
Alignment explanation
Indices: 49446178--49446208 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
49446168 ATTTGTGAAA
49446178 AAATAAAAT
1 AAATAAAAT
49446187 ATAATAAAAT
1 A-AATAAAAT
49446197 AAATAAAAT
1 AAATAAAAT
49446206 AAA
1 AAA
49446209 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:49453478 original size:10 final size:10
Alignment explanation
Indices: 49453463--49453487 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49453453 ACCAAGCATT
49453463 TATAAATATA
1 TATAAATATA
49453473 TATAAATATA
1 TATAAATATA
49453483 TATAA
1 TATAA
49453488 GCTTACAACC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TATAAATATA
Found at i:49461711 original size:13 final size:13
Alignment explanation
Indices: 49461693--49461719 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49461683 TTCGGCAGGC
49461693 ACACGCTCGTATG
1 ACACGCTCGTATG
49461706 ACACGCTCGTATG
1 ACACGCTCGTATG
49461719 A
1 A
49461720 GATTACTTTA
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:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (13 bp):
ACACGCTCGTATG
Found at i:49472299 original size:332 final size:332
Alignment explanation
Indices: 49471693--49472697 Score: 2001
Period size: 332 Copynumber: 3.0 Consensus size: 332
49471683 AATCTTTTAA
49471693 AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
1 AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
49471758 TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
66 TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
49471823 TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
131 TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
49471888 GATGATCAAAGTAACAAGTGAATAATGACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
196 GATGATCAAAGTAACAAGTGAATAATGACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
49471953 TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
261 TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
49472018 AACCTCT
326 AACCTCT
49472025 AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
1 AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
49472090 TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
66 TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
49472155 TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
131 TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
49472220 GATGATCAAAGTAACAAGTGAATAATGACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
196 GATGATCAAAGTAACAAGTGAATAATGACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
49472285 TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
261 TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
49472350 AACCTCT
326 AACCTCT
49472357 AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
1 AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
49472422 TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
66 TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
49472487 TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
131 TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
*
49472552 GATGATCAAAGTAACAAGTGAATAATAACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
196 GATGATCAAAGTAACAAGTGAATAATGACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
49472617 TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
261 TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
49472682 AACCTCT
326 AACCTCT
49472689 AAATTATAA
1 AAATTATAA
49472698 TCACACCTAT
Statistics
Matches: 672, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
332 672 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (332 bp):
AAATTATAAAGATATAAGCTATTAAAATGATGAAATTACATTTTTACTATCGTAAAAATATACAA
TTTAATTCCGATCATTTCAAAAAAAAATTGACTTCATCCCAAAAGCCATTAACATAGAACAATTT
TCATTTTCTAGAAACGTGGACTTTAAATATTATATACAAAAATATAAGATGTAGTTAATCATCAT
GATGATCAAAGTAACAAGTGAATAATGACTTAAAAATCTTAAACTTGCCAAACAATTAAATTTAG
TGTTGAGCTTAACTTTATAGCATAATTTATTGTTTAGTTTTGTAAGGAGCAAATAAACAAAAGAC
AACCTCT
Found at i:49478773 original size:33 final size:32
Alignment explanation
Indices: 49478735--49478799 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
49478725 TAGTAAATGT
*
49478735 AAAATTACACTTTTGCCCTTTAAAAATAATAAA
1 AAAATTACA-TTTAGCCCTTTAAAAATAATAAA
** * *
49478768 AAAATTTTATTTAGTCCTTTAAAAATTATAAA
1 AAAATTACATTTAGCCCTTTAAAAATAATAAA
49478800 GATATAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAATTACATTTAGCCCTTTAAAAATAATAAA
Found at i:49485563 original size:17 final size:17
Alignment explanation
Indices: 49485529--49485570 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
49485519 AACATAACAT
*
49485529 ATAATTATATTTTAAAA
1 ATAATTATATCTTAAAA
49485546 ATAATATATATCTTAAAA
1 ATAAT-TATATCTTAAAA
*
49485564 TTAATTA
1 ATAATTA
49485571 ATATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATTATATCTTAAAA
Found at i:49487424 original size:2 final size:2
Alignment explanation
Indices: 49487411--49487474 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
49487401 TATGTTTTAT
* * * * *
49487411 TA TA TA TG TA TA TA TC TT TA -A TA TA TA TA T- TT TA -A TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
49487450 TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49487475 CGTTATTATT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:49487430 original size:21 final size:20
Alignment explanation
Indices: 49487384--49487438 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
49487374 TTGATATTAT
49487384 TATTATTAATAT-TA-GTATA
1 TATT-TTAATATATATGTATA
* *
49487403 TGTTTTATTATATATGTATA
1 TATTTTAATATATATGTATA
49487423 TATCTTTAATATATAT
1 TAT-TTTAATATATAT
49487439 ATTTTAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 7 0.24
21 11 0.38
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TATTTTAATATATATGTATA
Found at i:49487471 original size:14 final size:14
Alignment explanation
Indices: 49487419--49487474 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
49487409 ATTATATATG
*
49487419 TATATATCTTTA-A
1 TATATATATTTATA
49487432 TATATATATTT-TA
1 TATATATATTTATA
* *
49487445 -ATACATATATATA
1 TATATATATTTATA
49487458 TATATATATTTATA
1 TATATATATTTATA
49487472 TAT
1 TAT
49487475 CGTTATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 8 0.23
13 13 0.37
14 14 0.40
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATATATTTATA
Found at i:49499779 original size:77 final size:77
Alignment explanation
Indices: 49499595--49500073 Score: 662
Period size: 77 Copynumber: 6.1 Consensus size: 77
49499585 ATGTTTTAAT
* * * *
49499595 TTCTGTTTTTC--AAAAATCAACTCATATTGTGAGAGATGAGTTGAGCCTCGGGTTACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
49499658 GGTA-TTTCAAA
66 GGTATTTTCAAA
*
49499669 TTCTGTTTTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
49499734 GGTATTTTCAAA
66 GGTATTTTCAAA
*
49499746 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
49499811 GGTATTTTCAAA
66 GGTATTTTCAAA
* *
49499823 TTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
49499888 GGTATTTTCAAA
66 GGTATTTTCAAA
* * * **
49499900 TTCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTACATGTTGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
*
49499965 GGTATTTTCAAT
66 GGTATTTTCAAA
49499977 TTCTGTTTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTCTG----------T-T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
* * *
49500042 G--ACACGCTGAGGTATTTTCAAT
54 GTCACATGCCGAGGTATTTTCAAA
49500064 TTCTGTTTTT
1 TTCTGTTTTT
49500074 TCAATTTATG
Statistics
Matches: 370, Mismatches: 20, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
74 11 0.03
75 3 0.01
76 52 0.14
77 233 0.63
87 25 0.07
88 1 0.00
89 45 0.12
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (77 bp):
TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
GGTATTTTCAAA
Found at i:49499885 original size:154 final size:155
Alignment explanation
Indices: 49499595--49500239 Score: 722
Period size: 154 Copynumber: 4.1 Consensus size: 155
49499585 ATGTTTTAAT
* * *
49499595 TTCTGTTTTTC--AAAAATCAACTCATATTGTGAGAGATGAGTTGAGCCTCGGGTTACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
*
49499658 GGTA-TTTCAAA-TTCTGTTTTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCA
66 GGTATTTTCAAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
49499721 GGTCACATGCCGAGGTATTTTCAAA
131 GGTCACATGCCGAGGTATTTTCAAA
* *
49499746 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
*
49499811 GGTATTTTCAAATTT-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
66 GGTATTTTCAAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
49499875 GGTCACATGCCGAGGTATTTTCAAA
131 GGTCACATGCCGAGGTATTTTCAAA
* * **
49499900 TTCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTACATGTTGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
49499965 GGTATTTTC-AATTTCTGTTTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTG
66 GGTATTTTCAAATTTCTG----------T-T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTG
* * *
49500029 AGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAAT
119 AGTTGAGCCTCAGGTCACATGCCGAGGTATTTTCAAA
49500064 TTCTGTTTTTTCAATTTATGTCTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTCTG---------TTT-T-TC------AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * * * *
49500129 CTCAGG--ACACGCTGAGGTATTTT-TAATTTCTGTTTTTC--AAAAATCAACTCATACTGCTAG
49 CTCAGGTTACATGCCGAGGTATTTTCAAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAG
* * * * *
49500189 AGGTGAGTTGAGTCTCGGGCCACATGCCAAGGTCTTTTCAAA
114 AGGTGAGTTGAGCCTCAGGTCACATGCCGAGGTATTTTCAAA
49500231 TTCTGTTTT
1 TTCTGTTTT
49500240 AAATTTCTAT
Statistics
Matches: 427, Mismatches: 30, Indels: 68
0.81 0.06 0.13
Matches are distributed among these distances:
151 11 0.03
153 56 0.13
154 149 0.35
155 2 0.00
157 1 0.00
158 3 0.01
164 24 0.06
165 38 0.09
166 46 0.11
167 25 0.06
168 1 0.00
169 1 0.00
173 3 0.01
174 1 0.00
175 1 0.00
179 23 0.05
181 42 0.10
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (155 bp):
TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
GGTATTTTCAAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
GGTCACATGCCGAGGTATTTTCAAA
Found at i:49499988 original size:14 final size:14
Alignment explanation
Indices: 49499969--49499998 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49499959 TGTTGAGGTA
*
49499969 TTTTCAATTTCTGT
1 TTTTCAATTTATGT
49499983 TTTTCAATTTATGT
1 TTTTCAATTTATGT
49499997 TT
1 TT
49499999 CAAAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:49500076 original size:15 final size:16
Alignment explanation
Indices: 49500056--49500090 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
49500046 CGCTGAGGTA
*
49500056 TTTTCAATTTCTGT-T
1 TTTTCAATTTATGTCT
49500071 TTTTCAATTTATGTCT
1 TTTTCAATTTATGTCT
49500087 TTTT
1 TTTT
49500091 AAAAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTCAATTTATGTCT
Found at i:49500128 original size:92 final size:90
Alignment explanation
Indices: 49499892--49500523 Score: 490
Period size: 88 Copynumber: 7.0 Consensus size: 90
49499882 TGCCGAGGTA
* * *
49499892 TTTTCAAATTCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTATGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--A
* *
49499957 CATGTTGAGGTATTTTCAATTTCTG-T
64 CACGCTGAGGTATTTTCAATTTCTGTT
*
49499983 TTTTCAATTTATG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTATGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
49500046 CGCTGAGGTATTTTCAATTTCTGTT
66 CGCTGAGGTATTTTCAATTTCTGTT
49500071 TTTTCAATTTATGTCTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
1 TTTTCAATTTATGT-TTTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
*
49500136 CACGCTGAGGTATTTTTAATTTCTG-T
64 CACGCTGAGGTATTTTCAATTTCTGTT
** * ** * * *
49500162 TTTTCAA---A--------AATCAACTCATACTGC-TAGAG-GTGAGTTGAGTCTCG-GGC-C--
1 TTTTCAATTTATGTTTTTTAAAAAAATCA-ACT-CATATTGCGAGAGGTGAGT-T-GAGCCTCAG
* ** * *
49500210 -ACATGCCAAGGTCTTTTCAAATTCTGTTT
62 GACACGCTGAGGTATTTTCAATTTCTG-TT
* * **
49500239 TAAATTTCTATTTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 T---TTTC-A-ATTT--ATGT-T-TTTTAAAAAA-----ATCAACTCATATTGCGAGAGGTGAGT
* *
49500304 TGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTG-C
52 TGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
* * * * *
49500342 TTTTCAATTTCTG-CTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTAAGCCTCAGGACA
1 TTTTCAATTTATGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* * *
49500406 CACTGAGGTATTTTCAATTTTTG-C
66 CGCTGAGGTATTTTCAATTTCTGTT
* * *
49500430 TTTTCAATTTATG-TGTTT-CAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTATGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--A
* * *
49500493 CACGCCGAGGTATTTCCAATTTCAGTT
64 CACGCTGAGGTATTTTCAATTTCTGTT
49500520 TTTT
1 TTTT
49500524 AAAAAAATCA
Statistics
Matches: 432, Mismatches: 63, Indels: 93
0.73 0.11 0.16
Matches are distributed among these distances:
75 20 0.05
77 2 0.00
78 17 0.04
79 9 0.02
80 6 0.01
81 1 0.00
87 63 0.15
88 89 0.21
89 66 0.15
90 4 0.01
91 22 0.05
92 68 0.16
93 8 0.02
96 1 0.00
97 2 0.00
98 3 0.01
99 1 0.00
100 6 0.01
101 9 0.02
102 13 0.03
103 1 0.00
105 21 0.05
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (90 bp):
TTTTCAATTTATGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTATTTTCAATTTCTGTT
Found at i:49500258 original size:14 final size:13
Alignment explanation
Indices: 49500223--49500270 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
49500213 TGCCAAGGTC
* *
49500223 TTTTCAAATTCTG
1 TTTTCAATTTCTT
*
49500236 TTTTAAATTTCTAT
1 TTTTCAATTTCT-T
49500250 TTTTCAATTTCTGT
1 TTTTCAATTTCT-T
49500264 TTTTCAA
1 TTTTCAA
49500271 AAAAAAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.23, C:0.12, G:0.04, T:0.60
Consensus pattern (13 bp):
TTTTCAATTTCTT
Found at i:49500347 original size:14 final size:14
Alignment explanation
Indices: 49500328--49500362 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
49500318 CGCTGAGGTA
49500328 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
49500342 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
49500356 TTTTCAA
1 TTTTCAA
49500363 AAAATCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:49500436 original size:180 final size:176
Alignment explanation
Indices: 49499892--49500521 Score: 632
Period size: 180 Copynumber: 3.5 Consensus size: 176
49499882 TGCCGAGGTA
* * *
49499892 TTTTCAAATTCTGTTTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTT
1 TTTTCAATTTATGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--
* * * *
49499956 ACATGTTGAGGTATTTTCAATTTCTGTTTTTCAATTTATG-TTTCAAAAAAATCAACTCATATTG
64 ACACGCTGAGGTATTTTCAATTTCTG-TTTTCAATTTCTGTTTTC-AAAAAATCAACTCATACTG
* * *
49500020 CGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
127 CGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTTTG-C
* *
49500071 TTTTCAATTTATGTCTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
1 TTTTCAATTTATGT-TTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
* *
49500136 CACGCTGAGGTATTTTTAATTTCTG-----------T-TTTTC-AAAAATCAACTCATACTGCTA
65 CACGCTGAGGTATTTTCAATTTCTGTTTTCAATTTCTGTTTTCAAAAAATCAACTCATACTGCGA
* * * * *
49500188 GAGGTGAGTTGAGTCTCGGGCCACA-TGCCAAGGTCTTTTCAAATTCTGTTTTAAATTTC
130 GAGGTGAGTTGAGCCTCAGGACACACTG---AGGTATTTTC-AA------TTT---TTGC
*
49500247 TATTTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ---TTTTCAATTTATGTTTTTC--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
49500312 GGGACACGCTGAGGTATTTTCAATTTCTGCTTTTCAATTTCTGCTTTTCAAAAAATCAACTCATA
61 GGGACACGCTGAGGTATTTTCAATTTCTG-TTTTCAATTTCTG-TTTTCAAAAAATCAACTCATA
*
49500377 CTGCGAGAGGTGAGTTAAGCCTCAGGACACACTGAGGTATTTTCAATTTTTGC
124 CTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTTTGC
* * *
49500430 TTTTCAATTTATGTGTTTC---AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTC
1 TTTTCAATTTATGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-G
* * *
49500492 ACACGCCGAGGTATTTCCAATTTCAGTTTT
64 ACACGCTGAGGTATTTTCAATTTCTGTTTT
49500522 TTAAAAAAAT
Statistics
Matches: 377, Mismatches: 35, Indels: 81
0.76 0.07 0.16
Matches are distributed among these distances:
164 2 0.01
165 40 0.11
167 14 0.04
168 2 0.01
174 3 0.01
175 37 0.10
176 6 0.02
177 24 0.06
178 4 0.01
179 48 0.13
180 89 0.24
181 42 0.11
183 3 0.01
186 3 0.01
192 3 0.01
193 9 0.02
194 5 0.01
195 41 0.11
196 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (176 bp):
TTTTCAATTTATGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
ACGCTGAGGTATTTTCAATTTCTGTTTTCAATTTCTGTTTTCAAAAAATCAACTCATACTGCGAG
AGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTTTGC
Found at i:49500495 original size:87 final size:88
Alignment explanation
Indices: 49499907--49500168 Score: 339
Period size: 92 Copynumber: 2.9 Consensus size: 88
49499897 AAATTCTGTT
* * ***
49499907 TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTACATGTTGAGGTATTT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACACTGAGGTATTT
*
49499972 TCAATTTCTGTTTTTCAATTTATG-
64 TCAATTTCTGCTTTTCAATTTATGC
*
49499996 -TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
1 TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTT
*
49500060 CAATTTCTGTTTTTTCAATTTATGTC
65 CAATTTCTG-CTTTTCAATTTATG-C
* *
49500086 TTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
1 -TTTT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTT
* *
49500151 TTAATTTCTGTTTTTCAA
64 TCAATTTCTGCTTTTCAA
49500169 AAATCAACTC
Statistics
Matches: 160, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
87 24 0.15
88 17 0.11
89 41 0.26
91 8 0.05
92 70 0.44
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (88 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
AATTTCTGCTTTTCAATTTATGC
Found at i:49501862 original size:29 final size:29
Alignment explanation
Indices: 49501829--49501885 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
49501819 GGAACCTGGA
49501829 CCTGCAGAGAAAACAAGGAAGAAATTTAG
1 CCTGCAGAGAAAACAAGGAAGAAATTTAG
49501858 CCTGCAGAGAAAACAAGGAAGAAATTTA
1 CCTGCAGAGAAAACAAGGAAGAAATTTA
49501886 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (29 bp):
CCTGCAGAGAAAACAAGGAAGAAATTTAG
Found at i:49502428 original size:18 final size:19
Alignment explanation
Indices: 49502391--49502437 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
49502381 ATGTTTTATT
*
49502391 ATATATGTATATATCTTTA
1 ATATATATATATATCTTTA
49502410 ATATATATATATA-CTTTA
1 ATATATATATATATCTTTA
*
49502428 ATACATATAT
1 ATATATATAT
49502438 GTATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATATATATATCTTTA
Found at i:49502495 original size:18 final size:18
Alignment explanation
Indices: 49502457--49502491 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
49502447 TATATATCGT
*
49502457 TATTATTAGTTATTTTTA
1 TATTATTAGCTATTTTTA
49502475 TATTATTA-CTATTTTTA
1 TATTATTAGCTATTTTTA
49502492 ATATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TATTATTAGCTATTTTTA
Found at i:49513056 original size:48 final size:48
Alignment explanation
Indices: 49512981--49513368 Score: 629
Period size: 48 Copynumber: 8.0 Consensus size: 48
49512971 CAAGACAAAT
* *
49512981 ATATGTATATGTGGTAAATCCGTATGGCTAAG-GTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCT-AGTGTGAAATATGTATGAG
*
49513029 ATATGTATATGTGGTAAAGCCGAATGGCTAGAGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
49513077 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
49513125 ATATATATATGTGTGGTAAAGCC-ATATGGCTAAG-GTGAAATATATATGAG
1 ATATGTATA--TGTGGTAAAGCCGA-ATGGCT-AGTGTGAAATATGTATGAG
49513175 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
49513223 ATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
49513271 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
49513319 ATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
49513367 AT
1 AT
49513369 GTGTGTATAT
Statistics
Matches: 321, Mismatches: 12, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
47 4 0.01
48 272 0.85
49 2 0.01
50 41 0.13
51 2 0.01
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:49513378 original size:146 final size:144
Alignment explanation
Indices: 49512981--49513368 Score: 638
Period size: 146 Copynumber: 2.7 Consensus size: 144
49512971 CAAGACAAAT
* *
49512981 ATATGTATATGTGGTAAATCCGTATGGCTAAGGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAAGGTGAAATATGTATGAGATATGTATATGTGGTAA
*
49513046 AGCCGAATGGCTAGA-GTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTG
66 AGCCGAATGGCTA-ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTG
49513110 TGAAATATGTATGAG
130 TGAAATATGTATGAG
* *
49513125 ATATATATATGTGTGGTAAAGCC-ATATGGCTAAGGTGAAATATATATGAGATATGTATATGTGG
1 ATATGTATA--TGTGGTAAAGCCGA-ATGGCTAAGGTGAAATATGTATGAGATATGTATATGTGG
*
49513189 TAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAG
63 TAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAG
49513254 TGTGAAATATGTATGAG
128 TGTGAAATATGTATGAG
*
49513271 ATATGTATATGTGGTAAAGCCGAATGGCT-AGTGTGAAATATGTATGAGATATGTATATTTGGTA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAAG-GTGAAATATGTATGAGATATGTATATGTGGTA
*
49513335 AAGCCGAATGGCTAATGTGAAATATGTAGGAGAT
65 AAGCCGAATGGCTAATGTGAAATATGTATGAGAT
49513369 GTGTGTATAT
Statistics
Matches: 227, Mismatches: 11, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
143 2 0.01
144 88 0.39
145 1 0.00
146 136 0.60
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (144 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAAGGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGT
GAAATATGTATGAG
Found at i:49519506 original size:28 final size:28
Alignment explanation
Indices: 49519472--49519526 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
49519462 GTGAGCAACC
* *
49519472 CAAATATCACAACTTGTGTTAGAAAATT
1 CAAATATCACAACTCGTGTGAGAAAATT
* *
49519500 CAAATATCATAGCTCGTGTGAGAAAAT
1 CAAATATCACAACTCGTGTGAGAAAAT
49519527 AAAATAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (28 bp):
CAAATATCACAACTCGTGTGAGAAAATT
Found at i:49520942 original size:38 final size:37
Alignment explanation
Indices: 49520898--49521008 Score: 97
Period size: 38 Copynumber: 3.0 Consensus size: 37
49520888 TAATTATGTA
49520898 AATATATATAATTTAATTATTAATTACTT-TTTTATTT
1 AATATATATAATTTAATTATTAATTA-TTATTTTATTT
* * *
49520935 AAGTATATAGATATTT-ATTATTTATTATTATTCTA-TT
1 AA-TATATATA-ATTTAATTATTAATTATTATTTTATTT
*
49520972 AA-AT-TATAATTTATATTATTAAATTATGATTATTATT
1 AATATATATAATTTA-ATTATT-AATTATTATT-TTATT
49521009 ATTGTTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
33 4 0.07
34 3 0.05
35 8 0.14
36 8 0.14
37 10 0.17
38 22 0.37
39 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.57
Consensus pattern (37 bp):
AATATATATAATTTAATTATTAATTATTATTTTATTT
Found at i:49520991 original size:20 final size:20
Alignment explanation
Indices: 49520958--49521011 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
49520948 TTTATTATTT
49520958 ATTATTATTCTATTAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
49520980 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
49521000 ATTATTATTATT
1 ATTATTATTATT
49521012 GTTAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 21 0.72
21 3 0.10
22 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:49520997 original size:25 final size:26
Alignment explanation
Indices: 49520949--49520997 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
49520939 ATATAGATAT
* **
49520949 TTATTATTTATTATTATTCTATTAAA
1 TTATAATTTATTATTATTAAATTAAA
49520975 TTATAATTTA-TATTATTAAATTA
1 TTATAATTTATTATTATTAAATTA
49520998 TGATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATAATTTATTATTATTAAATTAAA
Found at i:49521326 original size:13 final size:14
Alignment explanation
Indices: 49521308--49521345 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
49521298 TTATAAAGTT
49521308 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
49521321 AATAAAAGAAATGA
1 AATAAAATAAAAGA
49521335 AATAAAATAAA
1 AATAAAATAAA
49521346 GTAAAGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:49522457 original size:45 final size:45
Alignment explanation
Indices: 49522407--49522519 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
49522397 CGACTATTGT
49522407 TACTGTTACTGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCAG-CACTTTGTGTGTCGAA
* ** *
49522452 TACTGTTACCGTTACTGTTATAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
49522497 TACTGTTACTGTTACTGTTACCG
1 TACTGTTACTGTTACTGTTACCG
49522520 TTACTATTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 59 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:49522508 original size:6 final size:6
Alignment explanation
Indices: 49522497--49522549 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
49522487 GTGTGTTGAA
* * * *
49522497 TACTGT TACTGT TACTGT TACCGT TACTAT TACTGC TACCGT TACTGAT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T
49522546 TACT
1 TACT
49522550 TATTAGATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:49522524 original size:18 final size:18
Alignment explanation
Indices: 49522501--49522549 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
49522491 GTTGAATACT
*
49522501 GTTACTGTTACTGTTACC
1 GTTACTGTTACTGCTACC
*
49522519 GTTACTATTACTGCTACC
1 GTTACTGTTACTGCTACC
49522537 GTTACTGATTACT
1 GTTACTG-TTACT
49522550 TATTAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.43
Consensus pattern (18 bp):
GTTACTGTTACTGCTACC
Found at i:49523291 original size:9 final size:9
Alignment explanation
Indices: 49523272--49523308 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
49523262 GTCGAAATTT
49523272 ATAAAAA-A
1 ATAAAAATA
49523280 ATAAAAATA
1 ATAAAAATA
49523289 ATAAAAAATA
1 AT-AAAAATA
49523299 ATAAAAATA
1 ATAAAAATA
49523308 A
1 A
49523309 AAATTTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 7 0.26
9 11 0.41
10 9 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
ATAAAAATA
Found at i:49523296 original size:16 final size:16
Alignment explanation
Indices: 49523275--49523311 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
49523265 GAAATTTATA
49523275 AAAAAATAA-AAATAAT
1 AAAAAATAATAAA-AAT
49523291 AAAAAATAATAAAAAT
1 AAAAAATAATAAAAAT
49523307 AAAAA
1 AAAAA
49523312 TTTGGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATAATAAAAAT
Found at i:49523297 original size:10 final size:10
Alignment explanation
Indices: 49523274--49523305 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
49523264 CGAAATTTAT
49523274 AAAAA-AAT-
1 AAAAATAATA
49523282 AAAAATAATA
1 AAAAATAATA
49523292 AAAAATAATA
1 AAAAATAATA
49523302 AAAA
1 AAAA
49523306 TAAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.23
9 3 0.14
10 14 0.64
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATAATA
Found at i:49534064 original size:33 final size:34
Alignment explanation
Indices: 49533999--49534071 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 34
49533989 GCACAGTCAA
* * *
49533999 ACAGTCTTGGGCCTAAGCCCCTTTCAGTATCAGT
1 ACAGTCTTGGGCCTAAGCCCATCTCAGCATCAGT
49534033 ACAG-CTTGGGCCTTAA-CCCATCTCAGCATCAGT
1 ACAGTCTTGGGCC-TAAGCCCATCTCAGCATCAGT
49534066 ATCAGT
1 A-CAGT
49534072 ATCAGTCATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGCATCAGT
Found at i:49536712 original size:32 final size:33
Alignment explanation
Indices: 49536672--49536746 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
49536662 TGAATGTGGC
*
49536672 CGTGTGGGCCATACGGGC-TAGGCCAAGT-TGGG
1 CGTGTGGGCCATACGGGCAAAGGCCAA-TCTGGG
* *
49536704 TGTGTGGGCCATATGGGCAAAGGCCAATCTGGG
1 CGTGTGGGCCATACGGGCAAAGGCCAATCTGGG
49536737 CGTGTGGGCC
1 CGTGTGGGCC
49536747 CACAAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 17 0.46
33 20 0.54
ACGTcount: A:0.16, C:0.21, G:0.43, T:0.20
Consensus pattern (33 bp):
CGTGTGGGCCATACGGGCAAAGGCCAATCTGGG
Found at i:49540894 original size:79 final size:82
Alignment explanation
Indices: 49540781--49540965 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
49540771 GCTACTCGTT
* * *
49540781 CAAATGCCTTGGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
49540844 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
**
49540861 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
49540924 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
49540941 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49540966 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.61
80 33 0.36
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:49540965 original size:40 final size:40
Alignment explanation
Indices: 49540762--49540965 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
49540752 TGGAATTTAA
** * *
49540762 CCGGATATAGCT-ACTCGTTCAAATGCCTTGGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49540802 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
49540842 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
49540881 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
49540921 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
49540961 CCGGA
1 CCGGA
49540966 CATCATTCAA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 94 0.66
41 12 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:49547190 original size:79 final size:82
Alignment explanation
Indices: 49547079--49547263 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
49547069 GCTACTCGTT
* *
49547079 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
49547142 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
49547159 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
49547222 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
49547239 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49547264 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:49547263 original size:40 final size:40
Alignment explanation
Indices: 49547060--49547263 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
49547050 CGGAATTTAA
** *
49547060 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49547100 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
49547140 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49547179 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
49547219 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
49547259 CCGGA
1 CCGGA
49547264 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:49558768 original size:10 final size:10
Alignment explanation
Indices: 49558741--49558790 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
49558731 TTAAATTCTA
*
49558741 AAAGATAATT
1 AAAGATAAAT
49558751 ACAA-ATAAAT
1 A-AAGATAAAT
*
49558761 AAAGATAATT
1 AAAGATAAAT
49558771 AAAGATAAAT
1 AAAGATAAAT
49558781 GAAA-ATAAAT
1 -AAAGATAAAT
49558791 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:49558788 original size:20 final size:20
Alignment explanation
Indices: 49558741--49558780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
49558731 TTAAATTCTA
49558741 AAAGATAATTACAAATAAAT
1 AAAGATAATTACAAATAAAT
49558761 AAAGATAATTA-AAGATAAAT
1 AAAGATAATTACAA-ATAAAT
49558781 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAGATAATTACAAATAAAT
Found at i:49559457 original size:20 final size:20
Alignment explanation
Indices: 49559434--49559472 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49559424 CTTTTTCTTT
49559434 CTTT-TTTACTTTAATTTCAA
1 CTTTATTTA-TTTAATTTCAA
*
49559454 CTTTATTTATTTACTTTCA
1 CTTTATTTATTTAATTTCA
49559473 CTTAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTTATTTATTTAATTTCAA
Found at i:49559633 original size:96 final size:96
Alignment explanation
Indices: 49559473--49559653 Score: 299
Period size: 96 Copynumber: 1.9 Consensus size: 96
49559463 TTTACTTTCA
* *
49559473 CTTAGGAAAATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
1 CTTAAGAAAATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCCCAGTTAC
49559538 TCAGCCCAACACATTCTTAATTTTTATTTTT
66 TCAGCCCAACACATTCTTAATTTTTATTTTT
* * * **
49559569 CTTAAGAACATATTGAACCTTTTGACGTGAAGAGAGATGACAGCCAAACACCTCACCCTGGTTAC
1 CTTAAGAAAATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCCCAGTTAC
49559634 TCAGCCCAACACATTCTTAA
66 TCAGCCCAACACATTCTTAA
49559654 AAATTAATAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (96 bp):
CTTAAGAAAATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCCCAGTTAC
TCAGCCCAACACATTCTTAATTTTTATTTTT
Found at i:49560787 original size:5 final size:5
Alignment explanation
Indices: 49560759--49560870 Score: 83
Period size: 5 Copynumber: 22.6 Consensus size: 5
49560749 ATTAATATCC
*
49560759 AAAATT AAAAT AATAA- ATAAT AAAAT AAAAT AAAAT AAAAT AAAAT --AAT
1 AAAA-T AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * *
49560808 ACTAAT AAAAT AAAAT GAAAT AAAAT AATAA- ATAAT AAAATT AAGA-
1 A-AAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAA-T AAAAT
*
49560854 AAAGT AAAA- AAAAT AAA
1 AAAAT AAAAT AAAAT AAA
49560871 GGTTGGGTTG
Statistics
Matches: 85, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
3 3 0.04
4 10 0.12
5 56 0.66
6 16 0.19
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:49560865 original size:9 final size:9
Alignment explanation
Indices: 49560780--49560870 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 9
49560770 AATAAATAAT
49560780 AAAATAAAA
1 AAAATAAAA
49560789 TAAAATAAAA
1 -AAAATAAAA
*
49560799 TAAAATAATA
1 -AAAATAAAA
**
49560809 CTAATAAAA
1 AAAATAAAA
*
49560818 TAAAATGAAAT
1 -AAAAT-AAAA
49560829 AAAAT--AA
1 AAAATAAAA
* *
49560836 TAAATAATA
1 AAAATAAAA
* *
49560845 AAATTAAGA
1 AAAATAAAA
*
49560854 AAAGTAAAA
1 AAAATAAAA
49560863 AAAATAAA
1 AAAATAAA
49560871 GGTTGGGTTG
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
7 5 0.08
9 27 0.44
10 26 0.43
11 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAATAAAA
Found at i:49560867 original size:34 final size:32
Alignment explanation
Indices: 49560765--49560869 Score: 108
Period size: 34 Copynumber: 3.2 Consensus size: 32
49560755 ATCCAAAATT
*
49560765 AAAATAATAAATAATAAAATAAAATAAAATAAAA
1 AAAATAATAAATAATAAAAT-AAA-AAAGTAAAA
* * *
49560799 TAAAATAAT-ACTAATAAAAT-AAAATG-AAAT
1 -AAAATAATAAATAATAAAATAAAAAAGTAAAA
49560829 AAAATAATAAATAATAAAATTAAGAAAAGTAAAA
1 AAAATAATAAATAATAAAA-TAA-AAAAGTAAAA
49560863 AAAATAA
1 AAAATAA
49560870 AGGTTGGGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
29 8 0.14
30 12 0.21
31 3 0.05
32 3 0.05
33 4 0.07
34 20 0.34
35 8 0.14
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (32 bp):
AAAATAATAAATAATAAAATAAAAAAGTAAAA
Found at i:49560868 original size:39 final size:39
Alignment explanation
Indices: 49560777--49560870 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
49560767 AATAATAAAT
* *
49560777 AATAAAATAAAATAAAATAAAATAAAATAATACTAATAA
1 AATAAAATAAAATAAAATAAAATAAAATAAAACTAAGAA
* * *
49560816 AATAAAATGAAATAAAATAATAA-ATAATAAAATTAAGAA
1 AATAAAATAAAATAAAATAA-AATAAAATAAAACTAAGAA
49560855 AAGTAAAA-AAAATAAA
1 AA-TAAAATAAAATAAA
49560871 GGTTGGGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 40 0.85
40 7 0.15
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.21
Consensus pattern (39 bp):
AATAAAATAAAATAAAATAAAATAAAATAAAACTAAGAA
Found at i:49564609 original size:10 final size:10
Alignment explanation
Indices: 49564582--49564631 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
49564572 TTAAATTCTA
*
49564582 AAAGATAATT
1 AAAGATAAAT
49564592 ACAA-ATAAAT
1 A-AAGATAAAT
*
49564602 AAAGATAATT
1 AAAGATAAAT
49564612 AAAGATAAAT
1 AAAGATAAAT
49564622 GAAA-ATAAAT
1 -AAAGATAAAT
49564632 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:49564629 original size:20 final size:20
Alignment explanation
Indices: 49564582--49564621 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
49564572 TTAAATTCTA
49564582 AAAGATAATTACAAATAAAT
1 AAAGATAATTACAAATAAAT
49564602 AAAGATAATTA-AAGATAAAT
1 AAAGATAATTACAA-ATAAAT
49564622 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAGATAATTACAAATAAAT
Found at i:49572366 original size:24 final size:24
Alignment explanation
Indices: 49572336--49572427 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
49572326 ATTGACATTT
**
49572336 AAATCCGCACACATAGTGTTATAC
1 AAATCCGCACACATAGTGCCATAC
*
49572360 AAGTCCGCACACATAGTGCCATAC
1 AAATCCGCACACATAGTGCCATAC
* ** *
49572384 AATTTTGCACACATAGTGCCATTC
1 AAATCCGCACACATAGTGCCATAC
*
49572408 AAATTCGCACACATAGTGCC
1 AAATCCGCACACATAGTGCC
49572428 GAAGTCAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCCATAC
Found at i:49577519 original size:23 final size:23
Alignment explanation
Indices: 49577489--49577535 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
49577479 GCTAAAGTCT
49577489 CACATACATATGAATGAGTAGAA
1 CACATACATATGAATGAGTAGAA
49577512 CACATACATATGAATGAGTAGAA
1 CACATACATATGAATGAGTAGAA
49577535 C
1 C
49577536 CAGGGTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (23 bp):
CACATACATATGAATGAGTAGAA
Found at i:49580434 original size:24 final size:24
Alignment explanation
Indices: 49580399--49580490 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
49580389 ATTGACATTT
*
49580399 AAATCCGCACACATAGTGCTATAC
1 AAATCCGCACACATAGTGCCATAC
* *
49580423 AAGTCCGTACACATAGTGCCATAC
1 AAATCCGCACACATAGTGCCATAC
* * *
49580447 AATTTCGCACACATAGTGCCATTC
1 AAATCCGCACACATAGTGCCATAC
*
49580471 AAATTCGCACACATAGTGCC
1 AAATCCGCACACATAGTGCC
49580491 GAAGTCAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCCATAC
Found at i:49580498 original size:26 final size:23
Alignment explanation
Indices: 49580404--49580502 Score: 85
Period size: 24 Copynumber: 4.1 Consensus size: 23
49580394 CATTTAAATC
* *
49580404 CGCACACATAGTGCTA-TACAAGTC
1 CGCACACATAGTGCCAGT-CAA-TT
*
49580428 CGTACACATAGTGCCA-TACAATTT
1 CGCACACATAGTGCCAGT-CAA-TT
*
49580452 CGCACACATAGTGCCATTCAAATT
1 CGCACACATAGTGCCAGTC-AATT
49580476 CGCACACATAGTGCCGAAGTCAATT
1 CGCACACATAGTGCC--AGTCAATT
49580501 CG
1 CG
49580503 TTTTTAACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
24 53 0.82
25 9 0.14
26 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (23 bp):
CGCACACATAGTGCCAGTCAATT
Found at i:49585695 original size:43 final size:42
Alignment explanation
Indices: 49585630--49585751 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
49585620 AGTACCATGC
* * * *
49585630 CAATGCTATATCCTAGATATGGTCTTACATGAAATCTCGTAT
1 CAATGCCATAGCCCAGATATGGTCTTACACGAAATCTCGTAT
* *
49585672 CAATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCGTAT
1 CAATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCGTAT
* * * *
49585715 CGATGCCATATCCTAGATATGGTCTTACACGTAATCT
1 CAATGCCATAGCCCAGATATGGTCTTACACGAAATCT
49585752 TAGTAACCCT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 31 0.46
43 36 0.54
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
CAATGCCATAGCCCAGATATGGTCTTACACGAAATCTCGTAT
Found at i:49587745 original size:6 final size:6
Alignment explanation
Indices: 49587734--49587758 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49587724 TCTTGAAAGT
49587734 TTGAGA TTGAGA TTGAGA TTGAGA T
1 TTGAGA TTGAGA TTGAGA TTGAGA T
49587759 CGAGCTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TTGAGA
Found at i:49591774 original size:35 final size:34
Alignment explanation
Indices: 49591731--49591806 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
49591721 CCATCTCAGT
**
49591731 ACAGTATCAAATATGCAGTAGGGCCTTAGCCCATC
1 ACAGTATC-AATACACAGTAGGGCCTTAGCCCATC
* * * *
49591766 ACAGTATCAGTACACATTAGGGCTTTAGCCCATT
1 ACAGTATCAATACACAGTAGGGCCTTAGCCCATC
49591800 ACAGTAT
1 ACAGTAT
49591807 TAGTAACAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 27 0.77
35 8 0.23
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (34 bp):
ACAGTATCAATACACAGTAGGGCCTTAGCCCATC
Found at i:49594441 original size:18 final size:18
Alignment explanation
Indices: 49594418--49594481 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
49594408 AGAAAATGAA
49594418 AATGAACCATTCGATCAT
1 AATGAACCATTCGATCAT
* * * *
49594436 AATGAACAATTAGAAAATGAA
1 AATGAACCATTCG---ATCAT
49594457 AATGAACCATTCGATCAT
1 AATGAACCATTCGATCAT
49594475 AATGAAC
1 AATGAAC
49594482 AAGTTGAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
18 21 0.60
21 14 0.40
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (18 bp):
AATGAACCATTCGATCAT
Found at i:49594449 original size:39 final size:39
Alignment explanation
Indices: 49594406--49594483 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
49594396 TATTTTAAAG
49594406 TTAGAAAATGAAAATGAACCATTCGATCATAATGAACAA
1 TTAGAAAATGAAAATGAACCATTCGATCATAATGAACAA
49594445 TTAGAAAATGAAAATGAACCATTCGATCATAATGAACAA
1 TTAGAAAATGAAAATGAACCATTCGATCATAATGAACAA
49594484 GTTGAATGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (39 bp):
TTAGAAAATGAAAATGAACCATTCGATCATAATGAACAA
Found at i:49625491 original size:19 final size:19
Alignment explanation
Indices: 49625463--49625500 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
49625453 TAGTCAATCT
49625463 CGGTACGACCTACAAACTA
1 CGGTACGACCTACAAACTA
*
49625482 CGGTATGACCTACAAACTA
1 CGGTACGACCTACAAACTA
49625501 ACTCTTGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (19 bp):
CGGTACGACCTACAAACTA
Found at i:49626211 original size:13 final size:13
Alignment explanation
Indices: 49626179--49626257 Score: 89
Period size: 13 Copynumber: 6.5 Consensus size: 13
49626169 TAGATTTTTC
49626179 CTAAATATTATCA
1 CTAAATATTATCA
*
49626192 CT-AAT-TAATC-
1 CTAAATATTATCA
49626202 CTAAATATTATCA
1 CTAAATATTATCA
49626215 CTAAATATTATCA
1 CTAAATATTATCA
* *
49626228 C-AAA-ATAAT-T
1 CTAAATATTATCA
49626238 CTAAATATTATCA
1 CTAAATATTATCA
49626251 CTAAATA
1 CTAAATA
49626258 AATCAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 3 0.06
11 14 0.26
12 14 0.26
13 23 0.43
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:49626226 original size:36 final size:36
Alignment explanation
Indices: 49626179--49626257 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
49626169 TAGATTTTTC
* *
49626179 CTAAATATTATCACTAATTAATCCTAAATATTATCA
1 CTAAATATTATCACAAAATAATCCTAAATATTATCA
*
49626215 CTAAATATTATCACAAAATAATTCTAAATATTATCA
1 CTAAATATTATCACAAAATAATCCTAAATATTATCA
49626251 CTAAATA
1 CTAAATA
49626258 AATCAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (36 bp):
CTAAATATTATCACAAAATAATCCTAAATATTATCA
Found at i:49626245 original size:23 final size:23
Alignment explanation
Indices: 49626215--49626258 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
49626205 AATATTATCA
49626215 CTAAATATTATCACAAAATAATT
1 CTAAATATTATCACAAAATAATT
*
49626238 CTAAATATTATCACTAAATAA
1 CTAAATATTATCACAAAATAA
49626259 ATCAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (23 bp):
CTAAATATTATCACAAAATAATT
Found at i:49626896 original size:41 final size:40
Alignment explanation
Indices: 49626795--49626953 Score: 169
Period size: 40 Copynumber: 4.0 Consensus size: 40
49626785 TGTAAAATAT
***
49626795 AGAGCAATAGCGGCG-TTTTACCAAAAACGCCGCTAAAAAC
1 AGAGCAATAGCGGCGCTTTT-GGTAAAACGCCGCTAAAAAC
* *
49626835 AGAGCAATAACGGCGTTTTTGGTAAAACGCCGCTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAA-C
* *
49626876 AGAGCAATAGCGGTGCTTTTGGT-AAACGCCGCTAAAAAT
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* * * * *
49626915 TGAAGCATTAGCGGCGCTTTCGATAAAACGCCTCTAAAA
1 AG-AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
49626954 GTCATATAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 62 0.61
41 38 0.38
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (40 bp):
AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
Found at i:49627279 original size:15 final size:15
Alignment explanation
Indices: 49627256--49627309 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
49627246 TATTTTAAGT
*
49627256 TTTATGGATTATGGG
1 TTTAGGGATTATGGG
49627271 TTTAGGGATTAT-GG
1 TTTAGGGATTATGGG
*
49627285 TTTAAGGG-TTAGGGG
1 TTT-AGGGATTATGGG
*
49627300 TCTA-GGATTA
1 TTTAGGGATTA
49627310 AGAGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 19 0.58
ACGTcount: A:0.22, C:0.02, G:0.35, T:0.41
Consensus pattern (15 bp):
TTTAGGGATTATGGG
Found at i:49627282 original size:22 final size:21
Alignment explanation
Indices: 49627257--49627311 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
49627247 ATTTTAAGTT
*
49627257 TTATGGATTATGGGTTTAGGGA
1 TTATGGATTAAGGG-TTAGGGA
* *
49627279 TTATGGTTTAAGGGTTAGGGG
1 TTATGGATTAAGGGTTAGGGA
49627300 TCTA-GGATTAAG
1 T-TATGGATTAAG
49627312 AGTTTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTATGGATTAAGGGTTAGGGA
Found at i:49627870 original size:15 final size:15
Alignment explanation
Indices: 49627850--49627883 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
49627840 TTTATGATTT
*
49627850 AGGGTTTTGGGTTTA
1 AGGGTTTGGGGTTTA
49627865 AGGG-TTGGGGTTTA
1 AGGGTTTGGGGTTTA
49627879 AGGGT
1 AGGGT
49627884 AAATATAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (15 bp):
AGGGTTTGGGGTTTA
Found at i:49629629 original size:46 final size:45
Alignment explanation
Indices: 49629576--49629750 Score: 167
Period size: 45 Copynumber: 3.8 Consensus size: 45
49629566 TATTTGGGCA
49629576 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
49629622 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * * * *
49629669 TCCGAGCTCATTTAGTTGAGTCTGAGTTCACTTGTGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
49629715 -CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
49629751 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 32 0.31
46 32 0.31
47 29 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:49635165 original size:43 final size:42
Alignment explanation
Indices: 49635099--49635295 Score: 166
Period size: 43 Copynumber: 4.6 Consensus size: 42
49635089 TAATTTTTTT
*
49635099 AAAGTTCATGATT-TTTAGCGGCGTTTGTGAGAAAAGCGTCGCTA
1 AAAG-TCATG-TTCTTTAGCGGCGTTTGT-AAAAAAGCGTCGCTA
** * ** * *
49635143 AAAGTCATGTTCTTTAATGGCGTTTTTTTGAAAAGTGCCGCTA
1 AAAGTCATGTTCTTTAGCGGCG-TTTGTAAAAAAGCGTCGCTA
* * *
49635186 AAGGTCATGGTCTTTAGCAGCGTTTGTAAAAAAGCG-CTGCT-
1 AAAGTCATGTTCTTTAGCGGCGTTTGTAAAAAAGCGTC-GCTA
* * ***
49635227 AAAGATCATGATCTTTAGGGGCGTTTGTAAAAAAAATATCGCTA
1 AAAG-TCATGTTCTTTAGCGGCGTTTGT-AAAAAAGCGTCGCTA
49635271 AAAGTCATGTTCTTTAGCGGCGTTT
1 AAAGTCATGTTCTTTAGCGGCGTTT
49635296 TTTAAAATAA
Statistics
Matches: 122, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
41 4 0.03
42 35 0.29
43 70 0.57
44 13 0.11
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (42 bp):
AAAGTCATGTTCTTTAGCGGCGTTTGTAAAAAAGCGTCGCTA
Found at i:49643057 original size:40 final size:41
Alignment explanation
Indices: 49642895--49643067 Score: 235
Period size: 41 Copynumber: 4.3 Consensus size: 41
49642885 GGGCACTAAA
* * * *
49642895 GTGC-ATTCAGGGGTACCGAAGTACAAATAGGGGCACGTAT
1 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCATGTAT
49642935 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCATGTAT
1 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCATGTAT
*
49642976 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCACGTAT
1 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCATGTAT
* **
49643017 GTGCAATTCA-GGGTA-CTGAAGTACAAGCATAAGCATGTAT
1 GTGCAATTCAGGGGTATC-GAAGTACAAACATGGGCATGTAT
*
49643057 GTACAATTCAG
1 GTGCAATTCAG
49643068 TAATCATCAA
Statistics
Matches: 120, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 37 0.31
41 82 0.68
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.23
Consensus pattern (41 bp):
GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCATGTAT
Found at i:49644606 original size:17 final size:17
Alignment explanation
Indices: 49644586--49644625 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
49644576 TCGAAAAATA
49644586 ATTTTACAAAAAAATTT
1 ATTTTACAAAAAAATTT
* *
49644603 ATTTGAACAAAAAATTTT
1 ATTT-TACAAAAAAATTT
49644621 ATTTT
1 ATTTT
49644626 TTGAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTTTACAAAAAAATTT
Found at i:49649649 original size:119 final size:120
Alignment explanation
Indices: 49649411--49649877 Score: 884
Period size: 120 Copynumber: 3.9 Consensus size: 120
49649401 ACTAGCATCA
*
49649411 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
49649476 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
49649531 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAA-TTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
49649595 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
49649650 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
49649715 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
49649770 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
49649835 AATTATATA-TTGTAATTAAAATATATTTAATAATAATTATGTT
66 AATTATATAGTT-TAATTAAAATATATTTAATAATAATTATGTT
49649878 TAAATATGAT
Statistics
Matches: 342, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
119 121 0.35
120 221 0.65
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (120 bp):
ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
Found at i:49649830 original size:239 final size:240
Alignment explanation
Indices: 49649411--49649877 Score: 893
Period size: 239 Copynumber: 1.9 Consensus size: 240
49649401 ACTAGCATCA
49649411 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAATTTTTTTA
49649476 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
*
49649541 ATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTT-TTAAATTATATAG
131 ATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA-
49649605 TT-TAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
195 TTGTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
49649650 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAATTTTTTTA
49649715 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
49649780 ATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAT
131 ATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAT
49649845 TGTAATTAAAATATATTTAATAATAATTATGTT
196 TGTAATTAAAATATATTTAATAATAATTATGTT
49649878 TAAATATGAT
Statistics
Matches: 224, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
239 181 0.81
240 43 0.19
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (240 bp):
ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAATTTTTTTA
AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
ATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAT
TGTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
Found at i:49650074 original size:44 final size:45
Alignment explanation
Indices: 49650025--49650115 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
49650015 ACCTCTATTC
* * *
49650025 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
49650069 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
49650114 CA
1 CA
49650116 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:49650117 original size:16 final size:16
Alignment explanation
Indices: 49650096--49650164 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
49650086 GATTAGCTAT
49650096 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49650112 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
49650129 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
49650145 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
49650161 TACA
1 TACA
49650165 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:49650138 original size:33 final size:32
Alignment explanation
Indices: 49650096--49650164 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
49650086 GATTAGCTAT
49650096 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
49650129 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
49650161 TACA
1 TACA
49650165 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:49651541 original size:25 final size:26
Alignment explanation
Indices: 49651513--49651566 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
49651503 CTCTTTTATT
49651513 TATAAA-ATAAAATAATTATTGCAAA
1 TATAAAGATAAAATAATTATTGCAAA
* * * *
49651538 TATAAAGTTTAATTAATTATTTCAAA
1 TATAAAGATAAAATAATTATTGCAAA
49651564 TAT
1 TAT
49651567 CATTATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
TATAAAGATAAAATAATTATTGCAAA
Found at i:49654978 original size:3 final size:3
Alignment explanation
Indices: 49654970--49654996 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49654960 CAATAGAATG
49654970 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
49654997 GGGACTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49655968 original size:20 final size:17
Alignment explanation
Indices: 49655928--49655995 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
49655918 ATTATTTCAT
** *
49655928 ATTTTTTTCGAATTATA
1 ATTTTTTTATAATTTTA
49655945 ATTTTTATATATAATTTTTA
1 ATTTTT-T-TATAA-TTTTA
49655965 ATTTTTTTATAATTTTA
1 ATTTTTTTATAATTTTA
*
49655982 ATTTATTTACTAAT
1 ATTTTTTTA-TAAT
49655996 GCCAGCAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 19 0.44
18 10 0.23
19 4 0.09
20 10 0.23
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (17 bp):
ATTTTTTTATAATTTTA
Found at i:49657424 original size:9 final size:9
Alignment explanation
Indices: 49657384--49657480 Score: 54
Period size: 9 Copynumber: 10.2 Consensus size: 9
49657374 AATTTTAAAA
49657384 TTTTAACTTT
1 TTTTAA-TTT
49657394 TTTTATATATT
1 TTTTA-AT-TT
*
49657405 CTTTAGA-TT
1 TTTTA-ATTT
49657414 TTTTAATTT
1 TTTTAATTT
49657423 TTTTGGAATTT
1 TTTT--AATTT
* * *
49657434 TATAAATAT
1 TTTTAATTT
49657443 TTTTAATTT
1 TTTTAATTT
***
49657452 TAAAAATTAT
1 TTTTAATT-T
49657462 TTTTAATTT
1 TTTTAATTT
49657471 TTTT-ATTT
1 TTTTAATTT
49657479 TT
1 TT
49657481 ATTTTTATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
8 7 0.11
9 32 0.48
10 12 0.18
11 15 0.23
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTAATTT
Found at i:49657445 original size:19 final size:19
Alignment explanation
Indices: 49657418--49657471 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
49657408 TAGATTTTTT
* *
49657418 AATTTTTTTGGAATTTTATA
1 AATTATTTT-GAATTTTAAA
*
49657438 AA-TATTTTTAATTTTAAA
1 AATTATTTTGAATTTTAAA
*
49657456 AATTATTTTTAATTTT
1 AATTATTTTGAATTTT
49657472 TTTATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.33
19 18 0.60
20 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
AATTATTTTGAATTTTAAA
Found at i:49657450 original size:18 final size:19
Alignment explanation
Indices: 49657429--49657471 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
49657419 ATTTTTTTGG
*
49657429 AATTTTATAAA-TATTTTT
1 AATTTTAAAAATTATTTTT
49657447 AATTTTAAAAATTATTTTT
1 AATTTTAAAAATTATTTTT
49657466 AATTTT
1 AATTTT
49657472 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTT
Found at i:49658300 original size:55 final size:55
Alignment explanation
Indices: 49658232--49658481 Score: 290
Period size: 55 Copynumber: 4.5 Consensus size: 55
49658222 GATAGCCTGT
** * * * *
49658232 GAATACTGTTTCTTTTGAATCGATTGTTTGTATGTTTAAATCAATTGTCATGTT-
1 GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
*
49658286 GTAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATAG-TG
1 G-AATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTAT-GTTA
* *
49658342 GAATACTGTTTCTTCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTA
1 GAATA------CTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
* * *
49658403 GAATATTACTTCTTTTAAATCAATTATTTATATGTTTAAATCGATTGTTATGTTA
1 GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
*
49658458 GAATACTGCTTC-TTTGAATCAATT
1 GAATACTACTTCTTTTGAATCAATT
49658482 ATTATGTTAG
Statistics
Matches: 169, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
54 12 0.07
55 104 0.62
56 2 0.01
60 1 0.01
61 50 0.30
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.50
Consensus pattern (55 bp):
GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
Found at i:49658370 original size:116 final size:116
Alignment explanation
Indices: 49658241--49658471 Score: 358
Period size: 116 Copynumber: 2.0 Consensus size: 116
49658231 TGAATACTGT
* *
49658241 TTCTTTTGAATCGATTGTTTGTATGTTTAAATCAATTGTCATGTT-GTAATACTACTTCTTTTGA
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTAG-AATACTACTTCTTTTAA
* * *
49658305 ATCAATTGTTTATATGTTTAAATCGATTGTTATAG-TGGAATACTGTTTCTTC
65 ATCAATTATTTATATGTTTAAATCGATTGTTAT-GTTAGAATACTGCTTCTTC
* * *
49658357 TTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTAGAATATTACTTCTTTTAAA
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTAGAATACTACTTCTTTTAAA
49658422 TCAATTATTTATATGTTTAAATCGATTGTTATGTTAGAATACTGCTTCTT
66 TCAATTATTTATATGTTTAAATCGATTGTTATGTTAGAATACTGCTTCTT
49658472 TGAATCAATT
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
115 1 0.01
116 103 0.98
117 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (116 bp):
TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTAGAATACTACTTCTTTTAAA
TCAATTATTTATATGTTTAAATCGATTGTTATGTTAGAATACTGCTTCTTC
Found at i:49658492 original size:33 final size:33
Alignment explanation
Indices: 49658441--49658505 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
49658431 TATATGTTTA
* * *
49658441 AATCGATTGTTATGTTAGAATACTGCTTCTTTG
1 AATCAATTATTATGTTAGAATACTACTTCTTTG
49658474 AATCAATTATTATGTTAGAATACTACTTCTTT
1 AATCAATTATTATGTTAGAATACTACTTCTTT
49658506 TTAATCGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (33 bp):
AATCAATTATTATGTTAGAATACTACTTCTTTG
Found at i:49666364 original size:20 final size:21
Alignment explanation
Indices: 49666339--49666381 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
49666329 CAACCTACAC
49666339 ATTAAATAATAAATTC-AATT
1 ATTAAATAATAAATTCGAATT
* *
49666359 ATTAAATATTAAGTTCGAATT
1 ATTAAATAATAAATTCGAATT
49666380 AT
1 AT
49666382 AGAAACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTAAATAATAAATTCGAATT
Found at i:49666968 original size:21 final size:22
Alignment explanation
Indices: 49666944--49666993 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
49666934 AAACCTTGAA
49666944 TTTTCCCCTTTTTC-TTCTTTC
1 TTTTCCCCTTTTTCTTTCTTTC
*
49666965 TTTT-CTCTTTTTCTTTCTTTC
1 TTTTCCCCTTTTTCTTTCTTTC
*
49666986 -CTTCCCCT
1 TTTTCCCCT
49666994 GCTCTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCCCCTTTTTCTTTCTTTC
Found at i:49667224 original size:3 final size:3
Alignment explanation
Indices: 49667198--49667284 Score: 60
Period size: 3 Copynumber: 30.3 Consensus size: 3
49667188 TTATTTAATT
* * *
49667198 TAA TAA T-A TAA T-A TCAA TTA -AA TAA TAA TAA CAA TAA CAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
49667241 TAA TTA -AA T-A TAA AAA T-A TAA TAA TAAA TAA TAA GAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
49667284 T
1 T
49667285 TTAATATATT
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
2 10 0.16
3 49 0.77
4 5 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:49667244 original size:21 final size:20
Alignment explanation
Indices: 49667218--49667284 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
49667208 ATATCAATTA
*
49667218 AATAATAATAACAATAACAAT
1 AATAATAATAA-AATAAAAAT
49667239 AATAAT--TAAATATAAAAAT
1 AATAATAATAAA-ATAAAAAT
* *
49667258 -ATAATAAT-AAATAATAAG
1 AATAATAATAAAATAAAAAT
49667276 AATAATAAT
1 AATAATAAT
49667285 TTAATATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 12 0.31
19 20 0.51
20 1 0.03
21 6 0.15
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (20 bp):
AATAATAATAAAATAAAAAT
Found at i:49669423 original size:21 final size:21
Alignment explanation
Indices: 49669399--49669440 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
49669389 AAACCTTGAA
49669399 TTTTCCCTTTTTTCTTCTTTC
1 TTTTCCCTTTTTTCTTCTTTC
* *
49669420 TTTTCTCTTTTTTTTTCTTTC
1 TTTTCCCTTTTTTCTTCTTTC
49669441 CTTCCCCTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCCCTTTTTTCTTCTTTC
Found at i:49669677 original size:3 final size:3
Alignment explanation
Indices: 49669651--49669737 Score: 60
Period size: 3 Copynumber: 30.3 Consensus size: 3
49669641 TTATTTAATT
* * * *
49669651 TAA TAA T-A TAA TAT TAA TTA -AA TAA TAA TAA CAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
49669697 TTA -AA T-A TAA -AA CT-A TAA TAA TAAA TAA TAA GAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA T
49669738 TTAATATATT
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
2 9 0.14
3 52 0.81
4 3 0.05
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Done.