Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 38
Found at i:2533495 original size:32 final size:33
Alignment explanation
Indices: 2533412--2533495 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 33
2533402 AATCGATCAC
* *
2533412 ATTCATTAAAAAATAAATAGAAAAAAACCAAAA
1 ATTCATTCAAATATAAATAGAAAAAAACCAAAA
** *
2533445 ATTCATTCAAAT-TGAAATA-AAAAAATTCAAAT
1 ATTCATTCAAATAT-AAATAGAAAAAAACCAAAA
*
2533477 ATTCGTTCAAATATAAATA
1 ATTCATTCAAATATAAATA
2533496 TGATTACCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 27 0.63
33 16 0.37
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.27
Consensus pattern (33 bp):
ATTCATTCAAATATAAATAGAAAAAAACCAAAA
Found at i:2545296 original size:17 final size:19
Alignment explanation
Indices: 2545266--2545301 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2545256 TTATTTTTAC
2545266 TTTATATCACTTTTTATTA
1 TTTATATCACTTTTTATTA
2545285 TTTA-ATCA-TTTTTATTA
1 TTTATATCACTTTTTATTA
2545302 AAACCCCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATCACTTTTTATTA
Found at i:2553313 original size:54 final size:54
Alignment explanation
Indices: 2553248--2553360 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
2553238 TGTATTTTTG
* **
2553248 GCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATAACCATTTCA
1 GCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCATTTCA
* * * ** *
2553302 GCACTATATGTGCAATCCATGGAATTCATAATAAGTTTGTGAATTTCCATTTCG
1 GCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCATTTCA
2553356 GCACT
1 GCACT
2553361 TCGGTGCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (54 bp):
GCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCATTTCA
Found at i:2555803 original size:50 final size:50
Alignment explanation
Indices: 2555745--2555841 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
2555735 AAGATACATT
2555745 TCCCTTGGCCGAATAGTGATATGGTT-GTTCATCTTGGAGCCAAAGTTATC
1 TCCCTTGGCCGAATAGTGATAT-GTTAGTTCATCTTGGAGCCAAAGTTATC
* * * * * *
2555795 TCCCTTGGCTGAATATTGATGTGTTATTTTATCTTGGCGCCAAAGTT
1 TCCCTTGGCCGAATAGTGATATGTTAGTTCATCTTGGAGCCAAAGTT
2555842 TTGATGTGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (50 bp):
TCCCTTGGCCGAATAGTGATATGTTAGTTCATCTTGGAGCCAAAGTTATC
Found at i:2556561 original size:2 final size:2
Alignment explanation
Indices: 2556554--2556617 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
2556544 ACTATTGATG
2556554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2556596 TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2556618 TATGTTATAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2560038 original size:17 final size:17
Alignment explanation
Indices: 2560008--2560056 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
2559998 ACCCACTAGA
*
2560008 TATGA-AATCTAGGAAT
1 TATGAGAATCAAGGAAT
2560024 TATGAGAATCAAGGAGGAAT
1 TATGAGAATC-A--AGGAAT
2560044 TATGAGAATCAAG
1 TATGAGAATCAAG
2560057 ATGAAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 5 0.18
17 6 0.21
19 1 0.04
20 16 0.57
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
TATGAGAATCAAGGAAT
Found at i:2560043 original size:20 final size:20
Alignment explanation
Indices: 2560018--2560056 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2560008 TATGAAATCT
2560018 AGGAATTATGAGAATCAAGG
1 AGGAATTATGAGAATCAAGG
2560038 AGGAATTATGAGAATCAAG
1 AGGAATTATGAGAATCAAG
2560057 ATGAAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (20 bp):
AGGAATTATGAGAATCAAGG
Found at i:2560605 original size:2 final size:2
Alignment explanation
Indices: 2560598--2560633 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2560588 TATAGAAGTA
2560598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2560634 GAATATAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2567885 original size:26 final size:26
Alignment explanation
Indices: 2567847--2567954 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
2567837 AGGACACTAA
*
2567847 GTGTA-TATGGTGGGCACGACCTTAT
1 GTGTATTATAGTGGGCACGACCTTAT
**
2567872 GCATATTATAGTGGGCACGACCTTAT
1 GTGTATTATAGTGGGCACGACCTTAT
*
2567898 GTGTATTATAGTGGGAACGACCTTAT
1 GTGTATTATAGTGGGCACGACCTTAT
* *
2567924 GTGTATTATGGTGGGTACGACCTTAT
1 GTGTATTATAGTGGGCACGACCTTAT
2567950 GTGTA
1 GTGTA
2567955 AGCACTACGG
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 3 0.04
26 71 0.96
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (26 bp):
GTGTATTATAGTGGGCACGACCTTAT
Found at i:2578865 original size:13 final size:13
Alignment explanation
Indices: 2578836--2578882 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
2578826 ATTTATTTCC
2578836 TTTTATTTTCAAG
1 TTTTATTTTCAAG
2578849 TTTTCATTTTCAA-
1 TTTT-ATTTTCAAG
*
2578862 TTTT-CTTTCAAG
1 TTTTATTTTCAAG
2578874 TTTTATTTT
1 TTTTATTTT
2578883 TAAACATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 11 0.38
14 8 0.28
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (13 bp):
TTTTATTTTCAAG
Found at i:2580420 original size:25 final size:25
Alignment explanation
Indices: 2580385--2580440 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2580375 GAAAAAAGGG
* *
2580385 GAAAAATAAAAA-AGGAAGAAAGAAA
1 GAAAAAGAAAAATA-GAAGAAAAAAA
2580410 GAAAAAGAAAAATAGAAGAAAAAAA
1 GAAAAAGAAAAATAGAAGAAAAAAA
*
2580435 TAAAAA
1 GAAAAA
2580441 TATGAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (25 bp):
GAAAAAGAAAAATAGAAGAAAAAAA
Found at i:2580453 original size:20 final size:19
Alignment explanation
Indices: 2580411--2580456 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2580401 AGAAAGAAAG
*
2580411 AAAAAGAAAAATAGAAGAA
1 AAAAATAAAAATAGAAGAA
2580430 AAAAATAAAAATATGAA-AA
1 AAAAATAAAAATA-GAAGAA
2580449 TAAAAATA
1 -AAAAATA
2580457 GGGGTTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAAATAAAAATAGAAGAA
Found at i:2580801 original size:21 final size:19
Alignment explanation
Indices: 2580775--2580813 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
2580765 TTGAATTTTT
2580775 AAATTTCAAGATTTCATCAAG
1 AAATTTCAAG-TTT-ATCAAG
*
2580796 AAATTTTAAGTTTATCAA
1 AAATTTCAAGTTTATCAA
2580814 TGTAAACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (19 bp):
AAATTTCAAGTTTATCAAG
Found at i:2582817 original size:24 final size:24
Alignment explanation
Indices: 2582790--2582861 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
2582780 GAATTTCATT
2582790 TTTTAGATCGTAATATTTTACATA
1 TTTTAGATCGTAATATTTTACATA
2582814 TTTTAGATCGTAATATTTTACATA
1 TTTTAGATCGTAATATTTTACATA
2582838 TTTTAGATCGTAATATTTTACATA
1 TTTTAGATCGTAATATTTTACATA
2582862 CTTGTTCCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (24 bp):
TTTTAGATCGTAATATTTTACATA
Found at i:2582831 original size:15 final size:15
Alignment explanation
Indices: 2582811--2582857 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2582801 AATATTTTAC
2582811 ATATTTTAGATCGTA
1 ATATTTTAGATCGTA
2582826 ATATTTT--A-C---
1 ATATTTTAGATCGTA
2582835 ATATTTTAGATCGTA
1 ATATTTTAGATCGTA
2582850 ATATTTTA
1 ATATTTTA
2582858 CATACTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 7 0.27
11 1 0.04
12 2 0.08
13 1 0.04
15 15 0.58
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (15 bp):
ATATTTTAGATCGTA
Found at i:2583561 original size:24 final size:24
Alignment explanation
Indices: 2583533--2583578 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2583523 ACATGTCCAG
*
2583533 AGGACCATTTCGATTAGTCGACAA
1 AGGACCATTTCAATTAGTCGACAA
*
2583557 AGGACCATTTCAATTATTCGAC
1 AGGACCATTTCAATTAGTCGAC
2583579 TGAATAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (24 bp):
AGGACCATTTCAATTAGTCGACAA
Found at i:2585022 original size:2 final size:2
Alignment explanation
Indices: 2585015--2585078 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
2585005 TTATTTCCTA
*
2585015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2585057 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2585079 TAAGAAGATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2590089 original size:22 final size:21
Alignment explanation
Indices: 2590044--2590089 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
2590034 AATTGGGATT
2590044 TTTGAAATTTGATTTAATTTAA
1 TTTGAAATTTGA-TTAATTTAA
2590066 TTTGAAATTTGGA-TAATTTGAA
1 TTTGAAATTT-GATTAATTT-AA
2590088 TT
1 TT
2590090 GGAGTCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 14 0.64
23 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (21 bp):
TTTGAAATTTGATTAATTTAA
Found at i:2590546 original size:12 final size:13
Alignment explanation
Indices: 2590518--2590551 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
2590508 ATACCATTGA
2590518 AATAAGTAAAAATG
1 AATAA-TAAAAATG
2590532 AATAATAAAAA-G
1 AATAATAAAAATG
2590544 AATAATAA
1 AATAATAA
2590552 TAAAATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 6 0.30
14 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AATAATAAAAATG
Found at i:2591916 original size:32 final size:33
Alignment explanation
Indices: 2591835--2591961 Score: 132
Period size: 32 Copynumber: 3.9 Consensus size: 33
2591825 TTTTCCAACT
* * *
2591835 TACTAACATTCTAA-ATTTTATTCTATCGTTCA
1 TACTAACATACTAACATTTTATTTTATTGTTCA
* *
2591867 AACTAACATTCTAAC-TTTTATTTTATTGTTCA
1 TACTAACATACTAACATTTTATTTTATTGTTCA
* * **
2591899 TACTAACATACTGACTTTTTATTTTTATTGTTTT
1 TACTAACATACTAACATTTTA-TTTTATTGTTCA
* *
2591933 TACTAACTTAATAACATTTTATTTTATTG
1 TACTAACATACTAACATTTTATTTTATTG
2591962 CACAAACTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
32 40 0.50
33 13 0.16
34 27 0.34
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (33 bp):
TACTAACATACTAACATTTTATTTTATTGTTCA
Found at i:2592176 original size:16 final size:16
Alignment explanation
Indices: 2592152--2592196 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2592142 ATTTCAGTAT
*
2592152 TTTATTTTCCTGCCCC
1 TTTAATTTCCTGCCCC
2592168 TTTAATTTCCTGCCCC
1 TTTAATTTCCTGCCCC
2592184 TTTAATTTCCTGC
1 TTTAATTTCCTGC
2592197 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.11, C:0.33, G:0.07, T:0.49
Consensus pattern (16 bp):
TTTAATTTCCTGCCCC
Found at i:2599079 original size:102 final size:102
Alignment explanation
Indices: 2598883--2599079 Score: 218
Period size: 102 Copynumber: 1.9 Consensus size: 102
2598873 TTTCGTCTCA
* * *
2598883 CTTGAGACATTTTCCCTCAAAACACTAAAATTTGAATTGTTTCACTTGAAGCAAAATTGATAACA
1 CTTGAGACATTTTCCCTCAAAACACTAAAATTTGAAATGTTTCACTCGAAACAAAATTGATAACA
* ** *
2598948 TTTGAGATTGTTTTTCTTAAAAACCAATTTTGTGTCC
66 TTTGAGATAGTTCCTCTTAAAAACAAATTTTGTGTCC
* * * * * **
2598985 CTTGAGACAATTTTTCCTTAAAACAC-AAATTTTTAAATGTTTCACTCGAAACAAAATTTTATCT
1 CTTGAGAC-ATTTTCCCTCAAAACACTAAAATTTGAAATGTTTCACTCGAAACAAAA-TTGATAA
* *
2599049 CATTTGAGGTAGTTCCTCTT-GAAACAAATTT
64 CATTTGAGATAGTTCCTCTTAAAAACAAATTT
2599080 CCATCCACTC
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
102 42 0.55
103 35 0.45
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (102 bp):
CTTGAGACATTTTCCCTCAAAACACTAAAATTTGAAATGTTTCACTCGAAACAAAATTGATAACA
TTTGAGATAGTTCCTCTTAAAAACAAATTTTGTGTCC
Found at i:2599451 original size:83 final size:83
Alignment explanation
Indices: 2599266--2599454 Score: 234
Period size: 83 Copynumber: 2.3 Consensus size: 83
2599256 TAAAACGGCT
*
2599266 AGACTTCCTCAACACGAAGGAACAATATCATCCACCGACCAGATCTCCTCAATGCAAATGAACAG
1 AGACTTCCTCAACACGAAGGAACAATATCATCCACCGACCAGATCTCCTCAATGCAAACGAACAG
2599331 TGTCATCCTTAGACAACC
66 TGTCATCCTTAGACAACC
* * * * * * * * * * * *
2599349 ATACTTCCTTAATATGAAGGAACAATGTCGTCCACCGATCATATCTCTTTAATGCGAACGAGCAG
1 AGACTTCCTCAACACGAAGGAACAATATCATCCACCGACCAGATCTCCTCAATGCAAACGAACAG
*
2599414 TGTCATCCTTAGACAATC
66 TGTCATCCTTAGACAACC
* *
2599432 AGACTCCCTCAACGCGAAGGAAC
1 AGACTTCCTCAACACGAAGGAAC
2599455 CGTATTATCT
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (83 bp):
AGACTTCCTCAACACGAAGGAACAATATCATCCACCGACCAGATCTCCTCAATGCAAACGAACAG
TGTCATCCTTAGACAACC
Found at i:2599901 original size:122 final size:121
Alignment explanation
Indices: 2599492--2599880 Score: 427
Period size: 122 Copynumber: 3.2 Consensus size: 121
2599482 TTCTAGAATA
* * * * * * *
2599492 TCTTTAACACCAAATTATCTTCAGAATGATCCGAATTCCTTAACAAGAAGGAACAACGTCATCTT
1 TCTTCAACACCAAATTATCTCCAGATTGA-CCGACTTCCTCAACGAGAAGGAACAACGACATCTT
* * * *** *
2599557 CAGCAAACAATTTACCTAAAAGAGGCTAGAACTCTTCAACACATATGAGAAGAGTCG
65 CAGCAAACAATTTATCTGAAAGCGGCTAGAACTCTTCAACATGGATGAGAAGTGTCG
** * * * * *
2599614 TCTTCAACACCGTATTATCTCCGGATTGACCTAATTTCCTCAATGAGAAGGAACAACGTCATCTT
1 TCTTCAACACCAAATTATCTCCAGATTGACC-GACTTCCTCAACGAGAAGGAACAACGACATCTT
* * * * **
2599679 CAACAAACAATTTATCTGAAAGCGGCCAAAACTCTTCAACATGGATGACAAGTGTTA
65 CAGCAAACAATTTATCTGAAAGCGGCTAGAACTCTTCAACATGGATGAGAAGTGTCG
* * * * ***
2599736 TCTTTAACTCCAAGTTATCTCCAGATTGACCCGACTTCCTCAACGAGAAGGGACTGTGACATCTT
1 TCTTCAACACCAAATTATCTCCAGATTGA-CCGACTTCCTCAACGAGAAGGAACAACGACATCTT
* *
2599801 CAGCAAATAATTTATCTGAAAGCTGCTAGAACTCTTCAACATGGATGAGAAGTGTCG
65 CAGCAAACAATTTATCTGAAAGCGGCTAGAACTCTTCAACATGGATGAGAAGTGTCG
2599858 TCTTCAACACCAAATTATCTCCA
1 TCTTCAACACCAAATTATCTCCA
2599881 TATTAACTCG
Statistics
Matches: 216, Mismatches: 49, Indels: 4
0.80 0.18 0.01
Matches are distributed among these distances:
121 2 0.01
122 212 0.98
123 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (121 bp):
TCTTCAACACCAAATTATCTCCAGATTGACCGACTTCCTCAACGAGAAGGAACAACGACATCTTC
AGCAAACAATTTATCTGAAAGCGGCTAGAACTCTTCAACATGGATGAGAAGTGTCG
Found at i:2601316 original size:32 final size:32
Alignment explanation
Indices: 2601266--2601349 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
2601256 TTTCTAACTT
*
2601266 ACTATCATTCT-AATTTTATTCTATCATTCGA
1 ACTAACATTCTAAATTTTATTCTATCATTCGA
*
2601297 ACTAACATTCTAAATTTTATTCTATCGTTCGA
1 ACTAACATTCTAAATTTTATTCTATCATTCGA
2601329 ACTAACATTC-AAACTTTTATT
1 ACTAACATTCTAAA-TTTTATT
2601350 TTATTGTTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
31 13 0.27
32 36 0.73
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (32 bp):
ACTAACATTCTAAATTTTATTCTATCATTCGA
Found at i:2601398 original size:34 final size:34
Alignment explanation
Indices: 2601297--2601422 Score: 111
Period size: 32 Copynumber: 3.9 Consensus size: 34
2601287 TATCATTCGA
* * *
2601297 ACTAACATTCTAA-ATTTTA-TTCTATCGTTCGA-
1 ACTAACATACTAACATTTTATTTTTATTGTTC-AT
* *
2601329 ACTAACATTCAAAC-TTTTA-TTTTATTGTTCAT
1 ACTAACATACTAACATTTTATTTTTATTGTTCAT
* * * *
2601361 ACTAACATACTGACTTTTTATTTTTTTTGTTCTT
1 ACTAACATACTAACATTTTATTTTTATTGTTCAT
*
2601395 ACTAACTTACTAACATTTTA-TTTTATTG
1 ACTAACATACTAACATTTTATTTTTATTG
2601423 CACAAACTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
31 1 0.01
32 37 0.47
33 12 0.15
34 28 0.36
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.51
Consensus pattern (34 bp):
ACTAACATACTAACATTTTATTTTTATTGTTCAT
Found at i:2602920 original size:59 final size:59
Alignment explanation
Indices: 2602828--2602946 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2602818 AACGCAAACC
2602828 AATTTTTTTGTCTTTTAATGATTTTTCTGAACTCGTTAAAATGATATTTTAGGTATTCG
1 AATTTTTTTGTCTTTTAATGATTTTTCTGAACTCGTTAAAATGATATTTTAGGTATTCG
2602887 AATTTTTTTGTCTTTTAATGATTTTTCTGAACTCGTTAAAATGATATTTTAGGTATTCG
1 AATTTTTTTGTCTTTTAATGATTTTTCTGAACTCGTTAAAATGATATTTTAGGTATTCG
2602946 A
1 A
2602947 CCTTCCTAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.52
Consensus pattern (59 bp):
AATTTTTTTGTCTTTTAATGATTTTTCTGAACTCGTTAAAATGATATTTTAGGTATTCG
Found at i:2603933 original size:20 final size:20
Alignment explanation
Indices: 2603908--2603950 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2603898 CCATTATAGA
2603908 CTCTTATGAAACCCTAAAGC
1 CTCTTATGAAACCCTAAAGC
2603928 CTCTTATGAAACCCTAAAGC
1 CTCTTATGAAACCCTAAAGC
2603948 CTC
1 CTC
2603951 ATTCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.26
Consensus pattern (20 bp):
CTCTTATGAAACCCTAAAGC
Found at i:2604781 original size:3 final size:3
Alignment explanation
Indices: 2604768--2604812 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
2604758 AAATGTAAAC
*
2604768 AAT ATT AAT AAT AA- AA- AAT -AT AAT AAT AAT AAT AAT AAT GAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
2604811 AA
1 AA
2604813 AAAATAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 28 0.76
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2604811 original size:24 final size:23
Alignment explanation
Indices: 2604753--2604819 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
2604743 TACGCTTGTA
* * *
2604753 AATAAAAATGTAAACAATATTAAT
1 AATAAAAA-ATAAAAAATAATAAT
*
2604777 AATAAAAAATATAATAATAATAAT
1 AATAAAAAATA-AAAAATAATAAT
**
2604801 AATAATGAATAAAAAATAA
1 AATAAAAAATAAAAAATAA
2604820 AACCTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (23 bp):
AATAAAAAATAAAAAATAATAAT
Found at i:2613915 original size:111 final size:111
Alignment explanation
Indices: 2613721--2613943 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
2613711 TCTGAAGACA
2613721 ACATTATTCCTTCGCATTGAGAAAGTCTGGTTGCCTGAAGATAAATTGATTATGGAAACGACACG
1 ACATTATTCCTTCGCATTGAGAAAGTCTGGTTGCCTGAAGATAAATTGATTATGGAAACGACACG
2613786 CCTCCTACGTGATGAGGAGATCTATTCACTTTGGGTGATTTGCTCG
66 CCTCCTACGTGATGAGGAGATCTATTCACTTTGGGTGATTTGCTCG
2613832 ACATTATTCCTTCGCATTGAGAAAGTCTGGTTGCCTGAAGATAAATTGATTATGGAAACGACACG
1 ACATTATTCCTTCGCATTGAGAAAGTCTGGTTGCCTGAAGATAAATTGATTATGGAAACGACACG
2613897 CCTCCTACGTGATGAGGAGATCTATTCACTTTGGGTGATTTGCTCG
66 CCTCCTACGTGATGAGGAGATCTATTCACTTTGGGTGATTTGCTCG
2613943 A
1 A
2613944 TGCCAAATCT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (111 bp):
ACATTATTCCTTCGCATTGAGAAAGTCTGGTTGCCTGAAGATAAATTGATTATGGAAACGACACG
CCTCCTACGTGATGAGGAGATCTATTCACTTTGGGTGATTTGCTCG
Found at i:2622096 original size:445 final size:435
Alignment explanation
Indices: 2621253--2622131 Score: 1659
Period size: 445 Copynumber: 2.0 Consensus size: 435
2621243 ATCAAACCTC
2621253 AAGTTTGAGCATTTCAAAGATTTCATTCAATATTCATTTTGCTTTCAAGAACACTTTTTGTGCTC
1 AAGTTTGAGCATTTCAAAGATTTCATTCAATATTCATTTTGCTTTCAAGAACACTTTTTGTGCTC
2621318 AATTGTATTCATCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAG
66 AATTGTATTCATCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAG
2621383 GTTTTCTTGTAAGTTTGCAAATTTGTAATCTCTCTTTGAGAAAAGAGTGTTCTCAAGAGTTGGGG
131 GTTTTCTTGTAAGTTTGCAAATTTGTAATCTCTCTTTGAGAAAAGAGTGTTCTCAAGAGTTGGGG
*
2621448 ATACTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTGTT
196 ATACTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAAAAAATTAGTGAATTGTT
2621513 GGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTGAGAAAGTCGAACCAC
261 GGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTGAGAAAGTCGAACCAC
2621578 TGTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTTTATTGCCAAT
326 TGTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTTTATTGCCAAT
2621643 TCACCCCCCTCTTGGCCAATTTCGTCATTCGATTAACTCAACAAT
391 TCACCCCCCTCTTGGCCAATTTCGTCATTCGATTAACTCAACAAT
2621688 AAGTTTGAGCATTTCAAAGCCTATTTTCATTCAATATTCATTTTGCTTTCAAGAACACTTTTTGT
1 AAGTTTGAGCATTTCAAAG---A-TTTCATTCAATATTCATTTTGCTTTCAAGAACACTTTTTGT
2621753 GCTCAATTGTATTCATCTTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTT
62 GCTCAATTGTATTCATC-TTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTT
2621818 GTGAGGTTTTCTTGTAAGTTTGCAAATTTGTAATCTTCTCTTTGAGAAAAGAGTGTTCTCAAGAG
126 GTGAGGTTTTCTTGTAAGTTTGCAAATTTGTAATC-TCTCTTTGAGAAAAGAGTGTTCTCAAGAG
2621883 TTGGGGTATACTCTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAAAAAATTAG
190 TTGGGG-ATA--CTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAAAAAATTAG
2621948 TGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTGAGAAA
252 TGAA-TTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTGAGAAA
2622013 GTCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTT
316 GTCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTT
2622078 TATTGCCAATTCACCCCCCTCTTGGCCAATTTCGTCATTCGATTAACTCAACAA
381 TATTGCCAATTCACCCCCCTCTTGGCCAATTTCGTCATTCGATTAACTCAACAA
2622132 ATCGTTTTTG
Statistics
Matches: 433, Mismatches: 1, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
435 19 0.04
438 1 0.00
439 58 0.13
440 82 0.19
441 35 0.08
442 3 0.01
444 56 0.13
445 179 0.41
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (435 bp):
AAGTTTGAGCATTTCAAAGATTTCATTCAATATTCATTTTGCTTTCAAGAACACTTTTTGTGCTC
AATTGTATTCATCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTGTGAG
GTTTTCTTGTAAGTTTGCAAATTTGTAATCTCTCTTTGAGAAAAGAGTGTTCTCAAGAGTTGGGG
ATACTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAAAAAATTAGTGAATTGTT
GGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTGAGAAAGTCGAACCAC
TGTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTTTATTGCCAAT
TCACCCCCCTCTTGGCCAATTTCGTCATTCGATTAACTCAACAAT
Found at i:2623109 original size:25 final size:25
Alignment explanation
Indices: 2623070--2623186 Score: 84
Period size: 25 Copynumber: 4.8 Consensus size: 25
2623060 AAATTTGATG
*
2623070 AAGAATATTTG-AAAATGTTTTATTA
1 AAGAAT-TTTGAAAAATGTTTTATGA
* **
2623095 AAGAATTTTGAAAAAAGTTCGATGA
1 AAGAATTTTGAAAAATGTTTTATGA
* *
2623120 AATAATTTTGAGAAATGTTTGT-TGA
1 AAGAATTTTGAAAAATGTTT-TATGA
* *
2623145 AATAATTTTGAGAAAA-GTTTGATG-
1 AAGAATTTTGA-AAAATGTTTTATGA
*
2623169 AAG--TTTTGGAAAATGTTT
1 AAGAATTTTGAAAAATGTTT
2623187 CCCCTTACTT
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
21 4 0.05
22 9 0.12
24 6 0.08
25 52 0.70
26 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.19, T:0.39
Consensus pattern (25 bp):
AAGAATTTTGAAAAATGTTTTATGA
Found at i:2623152 original size:50 final size:49
Alignment explanation
Indices: 2623077--2623186 Score: 127
Period size: 50 Copynumber: 2.3 Consensus size: 49
2623067 ATGAAGAATA
*
2623077 TTTGAAAATGTTTTATTAAAGAATTTTGAAAAAAGTTCGATGAAATAAT
1 TTTGAAAATGTTTTATGAAAGAATTTTGAAAAAAGTTCGATGAAATAAT
* * * *
2623126 TTTGAGAAATGTTTGT-TGAAATAATTTTGAGAAAAGTTTGATGAAGT--T
1 TTTGA-AAATGTTT-TATGAAAGAATTTTGAAAAAAGTTCGATGAAATAAT
*
2623174 TTGGAAAATGTTT
1 TTTGAAAATGTTT
2623187 CCCCTTACTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
47 8 0.15
48 5 0.09
49 5 0.09
50 34 0.64
51 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.19, T:0.41
Consensus pattern (49 bp):
TTTGAAAATGTTTTATGAAAGAATTTTGAAAAAAGTTCGATGAAATAAT
Found at i:2639423 original size:16 final size:16
Alignment explanation
Indices: 2639402--2639432 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2639392 ACTATCCTTT
2639402 AAAACAATTTTAAGAA
1 AAAACAATTTTAAGAA
*
2639418 AAAACATTTTTAAGA
1 AAAACAATTTTAAGA
2639433 CATCGCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAACAATTTTAAGAA
Found at i:2639709 original size:14 final size:14
Alignment explanation
Indices: 2639678--2639716 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2639668 ATACCATGGA
* *
2639678 AATAAGTAAAATATT
1 AATAA-TAAAAGAAT
2639693 AATAATAAAAGAAT
1 AATAATAAAAGAAT
2639707 AATAATAAAA
1 AATAATAAAA
2639717 CATGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (14 bp):
AATAATAAAAGAAT
Found at i:2639825 original size:2 final size:2
Alignment explanation
Indices: 2639820--2639861 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2639810 CAACGTTTTA
2639820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2639862 GTAATATGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2640245 original size:2 final size:2
Alignment explanation
Indices: 2640238--2640263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2640228 TAGTTTATCC
2640238 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2640264 GCGTGTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2645086 original size:75 final size:74
Alignment explanation
Indices: 2644981--2645123 Score: 250
Period size: 75 Copynumber: 1.9 Consensus size: 74
2644971 CAAACATTGT
*
2644981 AAAATCAATCCAAGTTTGTATTCCAAAAGTGGTCTTGACAAAATCACCTAAAATTTCGATTTTCA
1 AAAATCAATCCAAGTTAGTATTCCAAAAGTGGTCTTGACAAAATCACCTAAAATTTCGATTTTCA
2645046 TCAAAAATA
66 TCAAAAATA
* *
2645055 AAAATCAATCCAAGTTAGTTTTTCCAAAAGTGGTCTTGACAAAATCACCTCAAATTTCGATTTTC
1 AAAATCAATCCAAGTTAG-TATTCCAAAAGTGGTCTTGACAAAATCACCTAAAATTTCGATTTTC
2645120 ATCA
65 ATCA
2645124 TCTTTCTACG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
74 17 0.26
75 48 0.74
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (74 bp):
AAAATCAATCCAAGTTAGTATTCCAAAAGTGGTCTTGACAAAATCACCTAAAATTTCGATTTTCA
TCAAAAATA
Found at i:2645481 original size:20 final size:20
Alignment explanation
Indices: 2645456--2645527 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
2645446 TTTTCCCAAT
*
2645456 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
2645476 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
2645497 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
2645517 TCGCAACGCGA
1 TCGCAACGCGA
2645528 TACTGACTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:2645539 original size:20 final size:20
Alignment explanation
Indices: 2645516--2645610 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
2645506 GAATAAGTAA
2645516 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2645536 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2645557 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2645577 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2645597 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2645611 ATACATAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2645558 original size:61 final size:63
Alignment explanation
Indices: 2645493--2645629 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 63
2645483 GCGAATTGGG
*
2645493 AAAATCGCAATGCGA-ATAAGTA-AATCGCAACGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGAGATAAGTACAATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
** ** * *
2645554 AAAATCGCAA--CGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGAGATAAGTACAATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
*
2645615 ATAATCGCAATGCGA
1 AAAATCGCAATGCGA
2645630 TTTTCAAAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 3 0.05
60 5 0.08
61 53 0.83
63 3 0.05
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (63 bp):
AAAATCGCAATGCGAGATAAGTACAATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
Found at i:2645559 original size:41 final size:42
Alignment explanation
Indices: 2645496--2645590 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
2645486 AATTGGGAAA
* *
2645496 ATCGCAATGCG--AATAAGTAAATCGCAACGCGATACTGACT
1 ATCGCAATGCGATAATAAGAAAATCGCAACGAGATACTGACT
*
2645536 ATCGCAATGCGATAATAA-AAAATCGCAACGAGATACTTACT
1 ATCGCAATGCGATAATAAGAAAATCGCAACGAGATACTGACT
* *
2645577 TTCGCAACGCGATA
1 ATCGCAATGCGATA
2645591 CTGACTTTCG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 11 0.23
41 32 0.67
42 5 0.10
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (42 bp):
ATCGCAATGCGATAATAAGAAAATCGCAACGAGATACTGACT
Found at i:2645826 original size:22 final size:22
Alignment explanation
Indices: 2645798--2645841 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2645788 CACTCTCTCA
2645798 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2645820 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2645842 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2646114 original size:20 final size:20
Alignment explanation
Indices: 2646085--2646128 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2646075 GCGATTTTAG
2646085 TTTCGAGTTGCGATAGTCAT
1 TTTCGAGTTGCGATAGTCAT
* **
2646105 TTTCGTGTTGCGATTTTCAT
1 TTTCGAGTTGCGATAGTCAT
2646125 TTTC
1 TTTC
2646129 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGAGTTGCGATAGTCAT
Found at i:2647440 original size:18 final size:18
Alignment explanation
Indices: 2647419--2647463 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2647409 TCCACTTCGG
*
2647419 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2647437 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2647455 GAGCCATCA
1 GAGCCATCA
2647464 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2647999 original size:19 final size:20
Alignment explanation
Indices: 2647945--2648011 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2647935 TAGTTTACTT
* *
2647945 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2647965 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2647985 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2648004 TCGCAACG
1 TCGCAACG
2648012 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2648057 original size:19 final size:19
Alignment explanation
Indices: 2648014--2648060 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2648004 TCGCAACGAC
* *
2648014 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCAAAATG
2648033 -AAATCGCAACGCAAAATG
1 AAAATCGCAACGCAAAATG
2648051 AAAATCGCAA
1 AAAATCGCAA
2648061 TGCGATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCAAAATG
Found at i:2648065 original size:37 final size:33
Alignment explanation
Indices: 2647984--2648049 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
2647974 GGAAATGGCT
2647984 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2648017 ATCGCAATGCGAAATG-AAATCGCAACG-CAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2648048 AT
1 AT
2648050 GAAAATCGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 6 0.18
32 11 0.33
33 16 0.48
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2648135 original size:19 final size:19
Alignment explanation
Indices: 2648109--2648175 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2648099 GCAATTTTGT
**
2648109 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
2648128 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
2648148 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
2648167 CGTTGCGAT
1 CGTTGCGAT
2648176 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2648155 original size:20 final size:19
Alignment explanation
Indices: 2648121--2648175 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
2648111 TTGCGATTTT
*
2648121 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2648140 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
2648160 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
2648176 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2650065 original size:14 final size:14
Alignment explanation
Indices: 2650046--2650081 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2650036 ATTGTTTAAT
2650046 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2650060 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2650074 TGATTTGT
1 TGATTTGT
2650082 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2650192 original size:20 final size:20
Alignment explanation
Indices: 2650167--2650204 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2650157 GCAAAACAGA
*
2650167 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
2650187 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
2650205 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:2650263 original size:20 final size:20
Alignment explanation
Indices: 2650240--2650290 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
2650230 GCGATTTCCT
2650240 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
2650260 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
2650280 CGTTGCGATAG
1 CGTTGCGATAG
2650291 TCAAATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:2651373 original size:24 final size:24
Alignment explanation
Indices: 2651346--2651399 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2651336 GTATTCGAAA
* *
2651346 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2651370 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2651394 TTTGAT
1 TTTGAT
2651400 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2653912 original size:19 final size:19
Alignment explanation
Indices: 2653890--2653948 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
2653880 GGAAATTACT
2653890 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2653909 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2653923 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2653942 ATCGCAA
1 ATCGCAA
2653949 CGCTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2653932 original size:33 final size:33
Alignment explanation
Indices: 2653890--2654015 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
2653880 GGAAATTACT
2653890 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2653923 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
2653955 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2653989 ATTGCAATGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
2654016 TCGAATTTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2654023 original size:66 final size:66
Alignment explanation
Indices: 2653893--2654023 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
2653883 AATTACTATC
*
2653893 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
2653958 T
66 T
* * *
2653959 GCAATGCGAAATGAAAATCGCAACGAGGGAATTGCAATGCGAAATGAAAATCGCAACTCGAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
2654024 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (66 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
T
Found at i:2654214 original size:14 final size:14
Alignment explanation
Indices: 2654195--2654231 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2654185 CATCAATTAA
2654195 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2654209 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2654223 ACAAATCAA
1 ACAAATCAA
2654232 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2655648 original size:21 final size:21
Alignment explanation
Indices: 2655582--2655648 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2655572 GTGAATCGGG
*
2655582 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2655602 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2655624 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2655645 CTCT
1 CTCT
2655649 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2655667 original size:42 final size:41
Alignment explanation
Indices: 2655582--2655704 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2655572 GTGAATCGGG
* * * * *
2655582 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2655624 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2655666 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2655705 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:2657718 original size:20 final size:19
Alignment explanation
Indices: 2657687--2657747 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
2657677 TCTTTTGGTT
2657687 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
2657706 GATAATGAGAATCACAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2657727 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
2657746 GA
1 GA
2657748 GAATCGCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.12
20 27 0.82
21 2 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2657769 original size:33 final size:33
Alignment explanation
Indices: 2657712--2657808 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
2657702 ACGAGATAAT
* *
2657712 GAGAATCACAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2657746 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2657779 GACAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
2657809 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 43 0.77
34 13 0.23
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2657804 original size:19 final size:19
Alignment explanation
Indices: 2657687--2657813 Score: 76
Period size: 19 Copynumber: 7.1 Consensus size: 19
2657677 TCTTTTGGTT
* *
2657687 GAAATGAAAATCGCAACGA
1 GAAATGACAATCGCAACGC
* *
2657706 GATAATGAGAATCACAACGC
1 GA-AATGACAATCGCAACGC
*
2657726 GGAAATGACTATCGCAA--C
1 -GAAATGACAATCGCAACGC
*
2657744 G--A-GAGAATCGCAACGC
1 GAAATGACAATCGCAACGC
* *
2657760 GAAATGACTATCGCGAC-C
1 GAAATGACAATCGCAACGC
2657778 ---A-GACAATCGCAACGC
1 GAAATGACAATCGCAACGC
* *
2657793 GAAATGAAAATCGCAATGC
1 GAAATGACAATCGCAACGC
2657812 GA
1 GA
2657814 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
14 19 0.23
15 3 0.04
16 2 0.02
17 1 0.01
18 4 0.05
19 25 0.31
20 25 0.31
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGACAATCGCAACGC
Found at i:2658419 original size:20 final size:20
Alignment explanation
Indices: 2658390--2658442 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2658380 GCGCTATGTA
*
2658390 AATCGTGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2658410 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2658430 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2658443 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2658476 original size:20 final size:20
Alignment explanation
Indices: 2658451--2658504 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2658441 GATTTTGTAT
2658451 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2658471 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2658491 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2658505 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2658523 original size:61 final size:61
Alignment explanation
Indices: 2658391--2658525 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
2658381 CGCTATGTAA
* * * * * * ** *
2658391 ATCGTGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
2658452 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
2658514 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2658526 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:2658615 original size:21 final size:21
Alignment explanation
Indices: 2658575--2658615 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2658565 ATTGTATACC
**
2658575 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2658596 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2658616 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2661100 original size:65 final size:64
Alignment explanation
Indices: 2660911--2661111 Score: 199
Period size: 65 Copynumber: 3.1 Consensus size: 64
2660901 GCACTAAGAG
* * * * *
2660911 TGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCGA
1 TGCATCAAATGCATTCGATGTTTCATAAA-ATCCATAGTGCATCGATGCATGGTTGGTGCATCAA
* * **
2660975 TGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTAAGTGCATCAA
1 TGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGTTGGTGCATCAA
* ** * * * *
2661040 TGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGTATCGATGCATGGATTGGTGCATCG
1 TGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TTGGTGCATCA
*
2661104 G
64 A
2661105 TGCATCA
1 TGCATCA
2661112 CTTTGATAAA
Statistics
Matches: 111, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
63 3 0.03
64 40 0.36
65 65 0.59
66 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
TGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTTGGTGCATCAA
Found at i:2663281 original size:160 final size:160
Alignment explanation
Indices: 2663017--2663336 Score: 640
Period size: 160 Copynumber: 2.0 Consensus size: 160
2663007 TTAATCAATC
2663017 CCAAAACTCAATTGAGTCCTCAATAATTCAAGGTTATCTAAATCAAATCCTAATGGGAAATGTTT
1 CCAAAACTCAATTGAGTCCTCAATAATTCAAGGTTATCTAAATCAAATCCTAATGGGAAATGTTT
2663082 GGAAAATAATTTTTGAAAAGTCATAATATGTATATGAAAACAACATAATTAAATCAAAAACATCA
66 GGAAAATAATTTTTGAAAAGTCATAATATGTATATGAAAACAACATAATTAAATCAAAAACATCA
2663147 AATTTAAAAAATTAAATTCAGAATTTCGAA
131 AATTTAAAAAATTAAATTCAGAATTTCGAA
2663177 CCAAAACTCAATTGAGTCCTCAATAATTCAAGGTTATCTAAATCAAATCCTAATGGGAAATGTTT
1 CCAAAACTCAATTGAGTCCTCAATAATTCAAGGTTATCTAAATCAAATCCTAATGGGAAATGTTT
2663242 GGAAAATAATTTTTGAAAAGTCATAATATGTATATGAAAACAACATAATTAAATCAAAAACATCA
66 GGAAAATAATTTTTGAAAAGTCATAATATGTATATGAAAACAACATAATTAAATCAAAAACATCA
2663307 AATTTAAAAAATTAAATTCAGAATTTCGAA
131 AATTTAAAAAATTAAATTCAGAATTTCGAA
2663337 ATACACATTT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 160 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (160 bp):
CCAAAACTCAATTGAGTCCTCAATAATTCAAGGTTATCTAAATCAAATCCTAATGGGAAATGTTT
GGAAAATAATTTTTGAAAAGTCATAATATGTATATGAAAACAACATAATTAAATCAAAAACATCA
AATTTAAAAAATTAAATTCAGAATTTCGAA
Found at i:2663792 original size:23 final size:22
Alignment explanation
Indices: 2663762--2663841 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
2663752 GCATGACCCT
2663762 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2663784 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
2663806 GTGTATCAATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
2663828 ATGCATCGATGCAC
1 GTGCATCGATGCAC
2663842 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 15 0.33
23 16 0.36
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2665982 original size:30 final size:30
Alignment explanation
Indices: 2665946--2666008 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
2665936 ATTATCATCG
2665946 AAAACAACATGTATAGACTCTTCTACAACT
1 AAAACAACATGTATAGACTCTTCTACAACT
2665976 AAAACAACATGTATAGACTCTTCTACAACT
1 AAAACAACATGTATAGACTCTTCTACAACT
2666006 AAA
1 AAA
2666009 GTTCTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.25
Consensus pattern (30 bp):
AAAACAACATGTATAGACTCTTCTACAACT
Found at i:2669743 original size:19 final size:19
Alignment explanation
Indices: 2669719--2669770 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2669709 AATAGCCAAA
2669719 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
2669738 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
2669757 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2669771 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:2669831 original size:84 final size:83
Alignment explanation
Indices: 2669674--2669836 Score: 231
Period size: 84 Copynumber: 2.0 Consensus size: 83
2669664 TGCACTAAGA
* *
2669674 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTAG
2669739 TGCATCGATGCATGGCTG
66 TGCATCGATGCATGGCTG
* ** *
2669757 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAAAGTGCATCGATGCATGGCT
2669820 AAGTGCATCGATGCATG
64 -AGTGCATCGATGCATG
2669837 AAATGCATTC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
83 29 0.41
84 39 0.55
85 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (83 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTAG
TGCATCGATGCATGGCTG
Found at i:2669894 original size:65 final size:64
Alignment explanation
Indices: 2669738--2669902 Score: 181
Period size: 65 Copynumber: 2.5 Consensus size: 64
2669728 TGCATGGCTG
* *
2669738 GTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTA
1 GTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATA
* ** * ** *
2669803 GTGCATCGGTGCATGGTAAGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCAT-
1 GTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATA
* *
2669866 GTTGCATCGATGCATGGATTGGTACATCGGTGCATCA
1 G-TGCATCGATGCATGG-TTGGTGCATCGATGCATCA
2669903 CTTTGATAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
63 4 0.05
64 21 0.26
65 57 0.70
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATA
Found at i:2670717 original size:32 final size:32
Alignment explanation
Indices: 2670675--2670740 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
2670665 AAGGATTATT
2670675 TCCTTCTGATTACTT-GGTTGCGAAAATTAAAA
1 TCCTTCTGATTA-TTGGGTTGCGAAAATTAAAA
* *
2670707 TCCTTTTGATTATTGGGTTGTGAAAATTAAAA
1 TCCTTCTGATTATTGGGTTGCGAAAATTAAAA
2670739 TC
1 TC
2670741 AAATGATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (32 bp):
TCCTTCTGATTATTGGGTTGCGAAAATTAAAA
Found at i:2670760 original size:45 final size:44
Alignment explanation
Indices: 2670709--2670827 Score: 184
Period size: 45 Copynumber: 2.7 Consensus size: 44
2670699 AATTAAAATC
*
2670709 CTTTTGATTATTGGGTTGTGAAAATTAAAATCAAATGATTAGTTT
1 CTTTTGATTATTGGGTTGTAAAAATTAAAATCAAATGATTAG-TT
* *
2670754 CTTTTGATTATTGGATTATAAAAATTAAAATCAAATGATTAGTT
1 CTTTTGATTATTGGGTTGTAAAAATTAAAATCAAATGATTAGTT
*
2670798 CATTTTAATTATTGGGTTGTAAAAATTAAA
1 C-TTTTGATTATTGGGTTGTAAAAATTAAA
2670828 GGATGAATTG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 3 0.04
45 64 0.96
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (44 bp):
CTTTTGATTATTGGGTTGTAAAAATTAAAATCAAATGATTAGTT
Found at i:2671213 original size:39 final size:39
Alignment explanation
Indices: 2671170--2671261 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
2671160 TTATGTCTTT
*
2671170 TAAAAGGAAATAAACCGTCAGATTAATTTTCCTAG-TTTG
1 TAAAAGAAAATAAACCGTCAGATTAATTTTCCT-GTTTTG
* ** ** *
2671209 TAAAAGTAAATAAATTGTTTGATTTATTTTCCTGTTTTG
1 TAAAAGAAAATAAACCGTCAGATTAATTTTCCTGTTTTG
2671248 TAAAAGAAAATAAA
1 TAAAAGAAAATAAA
2671262 TCGTTGAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (39 bp):
TAAAAGAAAATAAACCGTCAGATTAATTTTCCTGTTTTG
Found at i:2671262 original size:39 final size:39
Alignment explanation
Indices: 2671190--2671318 Score: 136
Period size: 39 Copynumber: 3.3 Consensus size: 39
2671180 TAAACCGTCA
* *
2671190 GATTAATTTTCCTAG-TTTGTAAAAGTAAATAAATTGTTT
1 GATTTATTTTCCT-GTTTTGTAAAAGAAAATAAATTGTTT
*
2671229 GATTTATTTTCCTGTTTTGTAAAAGAAAATAAATCG-TT
1 GATTTATTTTCCTGTTTTGTAAAAGAAAATAAATTGTTT
** * * * *
2671267 GAATTTATTTTTTTGTTCTATAAAAGGAAATAAATTGTTA
1 G-ATTTATTTTCCTGTTTTGTAAAAGAAAATAAATTGTTT
*
2671307 AATTTATTTTCC
1 GATTTATTTTCC
2671319 ATTGAATCTT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 4 0.05
39 69 0.93
40 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (39 bp):
GATTTATTTTCCTGTTTTGTAAAAGAAAATAAATTGTTT
Found at i:2671349 original size:136 final size:133
Alignment explanation
Indices: 2671209--2671543 Score: 317
Period size: 136 Copynumber: 2.5 Consensus size: 133
2671199 TCCTAGTTTG
* *
2671209 TAAAAGTAAATAAATTGTTTGATTTATTTTCCTGTTTTGTAAAAGAAAATAAATCGTTGAATTTA
1 TAAAAGAAAATAAATTG-TTGATTTATTTTCTTGTTTTGTAAAAGAAAATAAATCGTTGAATTTA
** * * *
2671274 TTTTTTTGTTCTAT-AAAAGGAAATAAATTGTTAAATTTATTTTCCATTG-AATCTTAGATGATT
65 TTTTCCTATT-T-TGAAAAGAAAATAAATTGGTAAATTTA-TTT-CATTGAAATCTTAGATGATT
2671337 CTG-GTTCA
126 CTGAGTT-A
* ** * * * *
2671345 TAAAAGGAAATAAATCATTAGATTTATTTTTTTATTTTGTAAAAGGAAATAAATCG-TCAGATTT
1 TAAAAGAAAATAAATTGTT-GATTTATTTTCTTGTTTTGTAAAAGAAAATAAATCGTTGA-ATTT
* * * *
2671409 ATTTTCCTATTTTGAAAAGAAAATAACTTGGTGAATTTATTTCTTTGATAATCTTATATGATTCT
64 ATTTTCCTATTTTGAAAAGAAAATAAATTGGTAAATTTATTTCATTGA-AATCTTAGATGATTCT
*
2671474 GAGTTG
128 GAGTTA
* * * * *
2671480 TAAAAGAAAAT-CATTG--AATTTATTTTCTTG-GTTGTAAAATAAAATAAATCATTGAATTTAT
1 TAAAAGAAAATAAATTGTTGATTTATTTTCTTGTTTTGTAAAAGAAAATAAATCGTTGAATTTAT
2671541 TTT
66 TTT
2671544 ATTGGTAATT
Statistics
Matches: 162, Mismatches: 30, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
130 26 0.16
131 13 0.08
133 4 0.02
134 6 0.04
135 52 0.32
136 61 0.38
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.44
Consensus pattern (133 bp):
TAAAAGAAAATAAATTGTTGATTTATTTTCTTGTTTTGTAAAAGAAAATAAATCGTTGAATTTAT
TTTCCTATTTTGAAAAGAAAATAAATTGGTAAATTTATTTCATTGAAATCTTAGATGATTCTGAG
TTA
Found at i:2671351 original size:175 final size:174
Alignment explanation
Indices: 2671118--2671455 Score: 421
Period size: 175 Copynumber: 1.9 Consensus size: 174
2671108 CTTGAATAAA
* * * **
2671118 GAAATAAATTGTTGAATTTATTTTCTTATGACTCTTTAATGATTATGTCTTTTAAAAGGAAATAA
1 GAAATAAATTGTTAAATTTATTTTCATATGAATCTTTAATGATTATGTCTCATAAAAGGAAATAA
* * * ** *
2671183 ACCGTCAGATTAATTTTCCTAGTTTGTAAAAGTAAATAAATTGTTTGATTTATTTTCCTGTTTTG
66 ACCATCAGATTAATTTTCCTAGTTTGTAAAAGGAAATAAATCGTCAGATTTATTTTCCTATTTTG
* *
2671248 TAAAAGAAAATAAATCGTTGAATTTATTTTTTTGTTCTATAAAAG
131 -AAAAGAAAATAAATCGGTGAATTTATTTCTTTGTTCTATAAAAG
*
2671293 GAAATAAATTGTTAAATTTATTTTCCAT-TGAATC-TTAGATGATTCTGGT-TCATAAAAGGAAA
1 GAAATAAATTGTTAAATTTATTTT-CATATGAATCTTTA-ATGATTAT-GTCTCATAAAAGGAAA
* * * ** *
2671355 TAAATCATTAGATTTATTTTTTTATTTTGTAAAAGGAAATAAATCGTCAGATTTATTTTCCTATT
63 TAAACCATCAGATTAATTTTCCTAGTTTGTAAAAGGAAATAAATCGTCAGATTTATTTTCCTATT
* *
2671420 TTGAAAAGAAAATAACTTGGTGAATTTATTTCTTTG
128 TTGAAAAGAAAATAAATCGGTGAATTTATTTCTTTG
2671456 ATAATCTTAT
Statistics
Matches: 138, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
174 32 0.23
175 102 0.74
176 4 0.03
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (174 bp):
GAAATAAATTGTTAAATTTATTTTCATATGAATCTTTAATGATTATGTCTCATAAAAGGAAATAA
ACCATCAGATTAATTTTCCTAGTTTGTAAAAGGAAATAAATCGTCAGATTTATTTTCCTATTTTG
AAAAGAAAATAAATCGGTGAATTTATTTCTTTGTTCTATAAAAG
Found at i:2671389 original size:39 final size:39
Alignment explanation
Indices: 2671345--2671434 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
2671335 TTCTGGTTCA
* **
2671345 TAAAAGGAAATAAATCATTAGATTTATTTTTTTATTTTG
1 TAAAAGGAAATAAATCATCAGATTTATTTTCCTATTTTG
*
2671384 TAAAAGGAAATAAATCGTCAGATTTATTTTCCTATTTTG
1 TAAAAGGAAATAAATCATCAGATTTATTTTCCTATTTTG
*
2671423 -AAAAGAAAATAA
1 TAAAAGGAAATAA
2671435 CTTGGTGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 11 0.24
39 35 0.76
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (39 bp):
TAAAAGGAAATAAATCATCAGATTTATTTTCCTATTTTG
Found at i:2671524 original size:34 final size:36
Alignment explanation
Indices: 2671476--2671549 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 36
2671466 ATGATTCTGA
*
2671476 GTTGTAAAAG-A-AAATCATTGAATTTATTTTCTTG
1 GTTGTAAAAGAATAAATCATTGAATTTATTTTATTG
*
2671510 GTTGTAAAATAAAATAAATCATTGAATTTATTTTATTG
1 GTTGT-AAA-AGAATAAATCATTGAATTTATTTTATTG
2671548 GT
1 GT
2671550 AATTAAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 5 0.15
35 3 0.09
36 1 0.03
37 1 0.03
38 24 0.71
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.45
Consensus pattern (36 bp):
GTTGTAAAAGAATAAATCATTGAATTTATTTTATTG
Found at i:2676227 original size:192 final size:192
Alignment explanation
Indices: 2675900--2676284 Score: 770
Period size: 192 Copynumber: 2.0 Consensus size: 192
2675890 AAATAAGAAG
2675900 AATAAGGAGGTAGCCATTGCATTCATGTCCATCAATGAGAGCTATCAAGATTCAAGTGAAGAGGT
1 AATAAGGAGGTAGCCATTGCATTCATGTCCATCAATGAGAGCTATCAAGATTCAAGTGAAGAGGT
2675965 GGATGAAGACAATGAAGAATAAGAGATGGCCAAGCTCTTCAAAAAGTTCAAGAGATTTATGTCTT
66 GGATGAAGACAATGAAGAATAAGAGATGGCCAAGCTCTTCAAAAAGTTCAAGAGATTTATGTCTT
2676030 CCAAGGAAGTGAAGCATAAATCAACCAAGAAGAAGGGTCCACCGGTGTGCTTCAATTGTCAA
131 CCAAGGAAGTGAAGCATAAATCAACCAAGAAGAAGGGTCCACCGGTGTGCTTCAATTGTCAA
2676092 AATAAGGAGGTAGCCATTGCATTCATGTCCATCAATGAGAGCTATCAAGATTCAAGTGAAGAGGT
1 AATAAGGAGGTAGCCATTGCATTCATGTCCATCAATGAGAGCTATCAAGATTCAAGTGAAGAGGT
2676157 GGATGAAGACAATGAAGAATAAGAGATGGCCAAGCTCTTCAAAAAGTTCAAGAGATTTATGTCTT
66 GGATGAAGACAATGAAGAATAAGAGATGGCCAAGCTCTTCAAAAAGTTCAAGAGATTTATGTCTT
2676222 CCAAGGAAGTGAAGCATAAATCAACCAAGAAGAAGGGTCCACCGGTGTGCTTCAATTGTCAA
131 CCAAGGAAGTGAAGCATAAATCAACCAAGAAGAAGGGTCCACCGGTGTGCTTCAATTGTCAA
2676284 A
1 A
2676285 GAACGGGGCA
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
192 193 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (192 bp):
AATAAGGAGGTAGCCATTGCATTCATGTCCATCAATGAGAGCTATCAAGATTCAAGTGAAGAGGT
GGATGAAGACAATGAAGAATAAGAGATGGCCAAGCTCTTCAAAAAGTTCAAGAGATTTATGTCTT
CCAAGGAAGTGAAGCATAAATCAACCAAGAAGAAGGGTCCACCGGTGTGCTTCAATTGTCAA
Found at i:2683794 original size:22 final size:21
Alignment explanation
Indices: 2683752--2683791 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2683742 AAGACTATTT
2683752 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
2683773 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
2683792 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:2694092 original size:7 final size:7
Alignment explanation
Indices: 2694082--2694112 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2694072 AAAAATGAAG
2694082 AAATTTT
1 AAATTTT
2694089 AAATTTT
1 AAATTTT
2694096 AAATTTT
1 AAATTTT
2694103 AAATTTT
1 AAATTTT
2694110 AAA
1 AAA
2694113 AGAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:2694157 original size:46 final size:44
Alignment explanation
Indices: 2694096--2694213 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 44
2694086 TTTAAATTTT
*
2694096 AAATTTTAAATTTTAAAAGAAATTTAAAAATAAATAAAAA-AGAAAA
1 AAATATTAAATTTTAAAAGAAA--TAAAAATAAATAAAAAGAG-AAA
* *
2694142 AAATATTAATTTTTAAAAGAAAT-AATA-AAATAAAAAGAGAAA
1 AAATATTAAATTTTAAAAGAAATAAAAATAAATAAAAAGAGAAA
* *
2694184 AAATGTTAAATTTTAGAAGAAATAAAAATA
1 AAATATTAAATTTTAAAAGAAATAAAAATA
2694214 GTAAAAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 32 0.52
43 8 0.13
44 2 0.03
46 20 0.32
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (44 bp):
AAATATTAAATTTTAAAAGAAATAAAAATAAATAAAAAGAGAAA
Found at i:2695384 original size:46 final size:45
Alignment explanation
Indices: 2695321--2695486 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 45
2695311 ACAAAAAAAT
2695321 TAATATA-AT-AAT-AAATAAATATATAATATAAATAATAATATA
1 TAATATATATAAATAAAATAAATATATAATATAAATAATAATATA
*
2695363 TAATATATATAAATACAAAT-AATA-ATAA-AT-AATATTAATAT-
1 TAATATATATAAATA-AAATAAATATATAATATAAATAATAATATA
*
2695404 TAATATACTATATAATATAATAAATAATAATACATATAAAATAAATAATAT-
1 TAATATA-TATA-AATAAAATAAAT-AT-ATA-ATAT-AAAT-AATAATATA
*
2695455 TAATATAATATATAAT-AAA-AACTATATAATAT
1 TAATAT-ATATA-AATAAAATAAATATATAATAT
2695487 TATATTTTCA
Statistics
Matches: 103, Mismatches: 5, Indels: 28
0.76 0.04 0.21
Matches are distributed among these distances:
41 7 0.07
42 24 0.23
43 11 0.11
44 8 0.08
45 4 0.04
46 11 0.11
47 4 0.04
48 4 0.04
49 3 0.03
50 5 0.05
51 21 0.20
52 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (45 bp):
TAATATATATAAATAAAATAAATATATAATATAAATAATAATATA
Found at i:2695394 original size:36 final size:36
Alignment explanation
Indices: 2695323--2695468 Score: 119
Period size: 36 Copynumber: 4.1 Consensus size: 36
2695313 AAAAAAATTA
* *
2695323 ATATAATAATAAATAAATATATAATATAA-ATAATAAT
1 ATATAAT-ATATATAAATACA-AATATAATATAATAAT
2695360 ATATAATATATATAAATACAAATAATAATA-AATAAT
1 ATATAATATATATAAATACAAAT-ATAATATAATAAT
* *
2695396 AT-TAATAT-TA-ATATAC-TATATAATATAATAA-
1 ATATAATATATATAAATACAAATATAATATAATAAT
* *
2695427 ATAATAATACATATAAAATAAATAATATTAATATAAT-AT
1 AT-ATAATATATAT-AAATACA-AATA-TAATATAATAAT
2695466 ATA
1 ATA
2695469 ATAAAAACTA
Statistics
Matches: 89, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
31 8 0.09
32 7 0.08
33 10 0.11
34 4 0.04
35 9 0.10
36 27 0.30
37 8 0.09
38 5 0.06
39 11 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (36 bp):
ATATAATATATATAAATACAAATATAATATAATAAT
Found at i:2695422 original size:72 final size:65
Alignment explanation
Indices: 2695321--2695486 Score: 183
Period size: 68 Copynumber: 2.4 Consensus size: 65
2695311 ACAAAAAAAT
* *
2695321 TAATATAATAATAAATAAATATATAATATAAATAATAATATATAATATATATAAATACAAATAAT
1 TAATAT-ATAATAAA-AACTATATAATAT-AAT-A-AATA-ATAATACATATAAA-ACAAATAAT
2695386 AATAA-A
59 AATAATA
* *
2695392 TAATAT-TAATATTAATATACTATATAATATAATAAATAATAATACATATAAAATAAATAATATT
1 TAATATATAATA--AA-A-ACTATATAATATAATAAATAATAATACATATAAAACAAATAATAAT
2695456 AATA
62 AATA
2695460 TAATATATAATAAAAACTATATAATAT
1 TAATATATAATAAAAACTATATAATAT
2695487 TATATTTTCA
Statistics
Matches: 86, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
65 12 0.14
66 1 0.01
67 14 0.16
68 20 0.23
69 14 0.16
70 1 0.01
71 13 0.15
72 11 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (65 bp):
TAATATATAATAAAAACTATATAATATAATAAATAATAATACATATAAAACAAATAATAATAATA
Found at i:2695459 original size:39 final size:41
Alignment explanation
Indices: 2695325--2695485 Score: 115
Period size: 41 Copynumber: 3.9 Consensus size: 41
2695315 AAAAATTAAT
*
2695325 ATAATAATAA-ATAAATAT-ATAAT-ATAA-ATAATAATAT
1 ATAATAATAATATAAATATAATAATAATAATATAATAATAA
* *
2695362 ATAATATATATAAATACAA-ATAATAATAAATAATATTAATATTAA
1 ATAATA-ATA-ATATA-AATATAATAAT-AATAATA-TAATAATAA
*
2695407 TATACTATATAATAT-AATA-AATAATAATACATATAA-AATAA
1 -ATAATA-ATAATATAAATATAATAATAATA-ATATAATAATAA
* *
2695448 ATAATATTAATATAATATATAATAAAAACT-ATATAATA
1 ATAATAATAATATAA-ATATAATAATAA-TAATATAATA
2695486 TTATATTTTC
Statistics
Matches: 99, Mismatches: 8, Indels: 29
0.73 0.06 0.21
Matches are distributed among these distances:
37 6 0.06
38 3 0.03
39 7 0.07
40 11 0.11
41 20 0.20
42 15 0.15
43 16 0.16
44 2 0.02
45 10 0.10
46 9 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (41 bp):
ATAATAATAATATAAATATAATAATAATAATATAATAATAA
Found at i:2695504 original size:19 final size:19
Alignment explanation
Indices: 2695482--2695519 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2695472 AAAACTATAT
*
2695482 AATATTATATTTTCAAAAA
1 AATAATATATTTTCAAAAA
*
2695501 AATAATATGTTTTCAAAAA
1 AATAATATATTTTCAAAAA
2695520 TTATATACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (19 bp):
AATAATATATTTTCAAAAA
Found at i:2695752 original size:37 final size:36
Alignment explanation
Indices: 2695510--2695753 Score: 160
Period size: 37 Copynumber: 6.6 Consensus size: 36
2695500 AAATAATATG
* **
2695510 TTTTCAAAAATTATATACTATATATGTTTCCAAAAGAACG
1 TTTTCAAAAACTATATA-T-TATATGTTT-CAAAA-AATA
* *
2695550 TTTTTAAAAA-TATATATATATAT-TTTCAAAAACATG
1 TTTTCAAAAACTATATAT-TATATGTTTCAAAAA-ATA
* * **
2695586 TTTTC-AAAACTATATAATATATGTTTTTTAAAACGTA
1 TTTTCAAAAACTATATATTATATG--TTTCAAAAAATA
*
2695623 TTTTCAAAATC-ATAT-TATATAT-TTTC-AAAAATCAA
1 TTTTCAAAAACTATATAT-TATATGTTTCAAAAAAT--A
* *
2695658 TTTTTCAAAAACTATATATTATATACTTTCAAAAAATG
1 -TTTTCAAAAACTATATATTATAT-GTTTCAAAAAATA
* ** *
2695696 TCTTCTGAAACTATATATTATATGTTTTAAAAAATA
1 TTTTCAAAAACTATATATTATATGTTTCAAAAAATA
*
2695732 TTTTCAAAAATTATATTATTAT
1 TTTTCAAAAACTATA-TATTAT
2695754 TATTATATAT
Statistics
Matches: 163, Mismatches: 25, Indels: 35
0.73 0.11 0.16
Matches are distributed among these distances:
33 4 0.02
34 3 0.02
35 11 0.07
36 48 0.29
37 53 0.33
38 19 0.12
39 10 0.06
40 15 0.09
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTCAAAAACTATATATTATATGTTTCAAAAAATA
Found at i:2707927 original size:47 final size:45
Alignment explanation
Indices: 2707859--2708007 Score: 205
Period size: 46 Copynumber: 3.3 Consensus size: 45
2707849 ATTAAAAGAG
*
2707859 AAATAAATAAAAAATGAAGAAAATGTTAAATTTTAAAAGAAATTTA
1 AAATAAATAAAAAATGAAGAAAATGTTAAATTTTAAAAGAAA-TAA
*
2707905 AAATAAATAAATAAATGAAGAAAATATTAAATTTTAAAAGAAATAA
1 AAATAAATAAA-AAATGAAGAAAATGTTAAATTTTAAAAGAAATAA
*
2707951 AAATAAAATAAAAAGA-GAA-ATAAATGTTAAATTTTAGAAGAAATAA
1 AAAT-AAATAAAAA-ATGAAGA-AAATGTTAAATTTTAAAAGAAATAA
2707997 AAAT-AATAAAA
1 AAATAAATAAAA
2708008 TTTCTTTAAG
Statistics
Matches: 95, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
44 7 0.07
45 1 0.01
46 49 0.52
47 38 0.40
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (45 bp):
AAATAAATAAAAAATGAAGAAAATGTTAAATTTTAAAAGAAATAA
Found at i:2707959 original size:23 final size:23
Alignment explanation
Indices: 2707933--2708002 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2707923 AGAAAATATT
2707933 AAATTTTAAAAGAAATAAAAATA
1 AAATTTTAAAAGAAATAAAAATA
** ** *
2707956 AAA-TAAAAAGAGAAATAAATGTT
1 AAATTTTAAA-AGAAATAAAAATA
*
2707979 AAATTTTAGAAGAAATAAAAATA
1 AAATTTTAAAAGAAATAAAAATA
2708002 A
1 A
2708003 TAAAATTTCT
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
22 4 0.12
23 27 0.79
24 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (23 bp):
AAATTTTAAAAGAAATAAAAATA
Found at i:2709137 original size:3 final size:3
Alignment explanation
Indices: 2709129--2709213 Score: 56
Period size: 3 Copynumber: 28.7 Consensus size: 3
2709119 TATAAATACA
* *
2709129 AAT AAT AAT AAAT AAT ATT AAT -GT AAT -AT AAT -AT AAT AAAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
*
2709173 AAT ACAT -AT AA- AAT AAAT AAT ATT AAT -AT AAT ATAT AAT AA
1 AAT A-AT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT AAT AA
2709214 AAACTATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
2 11 0.17
3 40 0.62
4 14 0.22
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2709184 original size:44 final size:45
Alignment explanation
Indices: 2709084--2709214 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 45
2709074 AAAAATATAT
*
2709084 ATAATAAATTATAATATATAATAAATATAAATATATATAAATACAAATA
1 ATAATAAA--ATAATAT-TAATTAATAT-AATATATATAAATACAAATA
2709133 ATAAT-AAATAATATTAATGTAATATAATATA-ATAAATA-ATAATA
1 ATAATAAAATAATATTAAT-TAATATAATATATATAAATACA-AATA
*
2709177 CAT-ATAAAATAA-ATAATATTAATATAATATATAATAAA
1 -ATAATAAAATAATATTA-ATTAATATAATATAT-ATAAA
2709215 AACTATATAC
Statistics
Matches: 73, Mismatches: 2, Indels: 17
0.79 0.02 0.18
Matches are distributed among these distances:
43 1 0.01
44 28 0.38
45 20 0.27
46 17 0.23
48 2 0.03
49 5 0.07
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.35
Consensus pattern (45 bp):
ATAATAAAATAATATTAATTAATATAATATATATAAATACAAATA
Found at i:2709188 original size:49 final size:50
Alignment explanation
Indices: 2709080--2709223 Score: 163
Period size: 49 Copynumber: 2.9 Consensus size: 50
2709070 ACCAAAAAAT
* * * *
2709080 ATATATAATAAATTATAAT-ATATAATA-AATATAAATATATATAAATAC
1 ATATAAAATAAATAATATTAATATAATATAATATAAAAATATATAAATAC
* *
2709128 AAATAATAATAAATAATATTAATGTAATATAATATAATAAATA-AT-AATAC
1 ATATAA-AATAAATAATATTAATATAATATAATATAA-AAATATATAAATAC
2709178 ATATAAAATAAATAATATTAATATAATAT-ATAATAAAAACTATATA
1 ATATAAAATAAATAATATTAATATAATATAAT-ATAAAAA-TATATA
2709224 CTGTTATATT
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
48 9 0.11
49 39 0.49
50 19 0.24
51 9 0.11
52 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (50 bp):
ATATAAAATAAATAATATTAATATAATATAATATAAAAATATATAAATAC
Found at i:2709223 original size:60 final size:59
Alignment explanation
Indices: 2709096--2709223 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 59
2709086 AATAAATTAT
* *
2709096 AATATATAATAAATATAAATATATATAAATACAAATAATAATAAATAATAT-TAATGTAA
1 AATATATAATAAATATAAATACATATAAATACAAATAATAATAAATAATATATAAT-AAA
* * *
2709155 TATAATATAATAAATA-ATAATACATATAAA-ATAAATAATATTAATATAATATATAATAAA
1 AAT-ATATAATAAATATA-AATACATATAAATACAAATAATAATAA-ATAATATATAATAAA
2709215 AACTATATA
1 AA-TATATA
2709224 CTGTTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
59 15 0.26
60 38 0.66
61 5 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (59 bp):
AATATATAATAAATATAAATACATATAAATACAAATAATAATAAATAATATATAATAAA
Found at i:2709270 original size:39 final size:38
Alignment explanation
Indices: 2709227--2709495 Score: 113
Period size: 37 Copynumber: 7.2 Consensus size: 38
2709217 CTATATACTG
*
2709227 TTATATTTTCAAAAACAATATGTTTTCAAAAATTATTTA
1 TTATATTTTCAAAAAC-ATATGTTTTCAAAAACTATTTA
* * *
2709266 TTATATATGTTTCCAAAAGAT-TGCTTTT-AAAAACTATATA
1 -T-TATAT-TTTCAAAAACATATG-TTTTCAAAAACTATTTA
* * * *
2709306 -TATGTTTTCAAAAAC--GTGTTTTC-AAAATTATATAA
1 TTATATTTTCAAAAACATATGTTTTCAAAAACTAT-TTA
* **
2709341 TATATGTTTTTTAAAACATA--TTTTC-AAAA-TATATTA
1 T-TATATTTTCAAAAACATATGTTTTCAAAAACTAT-TTA
* *
2709377 -TATATTTTCAAAAAC-TGAT-TTTTTAAAAACTATATA
1 TTATATTTTCAAAAACAT-ATGTTTTCAAAAACTATTTA
* ** *
2709413 TTATATACTTTCAAAAA-A-ATCGTCTTCTGAAACTATATA
1 TTATAT--TTTCAAAAACATAT-GTTTTCAAAAACTATTTA
* * *
2709452 TTATATGTTTTAAAAA-A-ATATTTTCAAAAATTATATTA
1 TTATAT-TTTCAAAAACATATGTTTTCAAAAACTAT-TTA
2709490 TTATAT
1 TTATAT
2709496 ATACACTAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 44
0.70 0.12 0.17
Matches are distributed among these distances:
33 1 0.01
34 24 0.14
35 7 0.04
36 20 0.11
37 46 0.26
38 19 0.11
39 28 0.16
40 13 0.07
41 11 0.06
42 8 0.05
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
TTATATTTTCAAAAACATATGTTTTCAAAAACTATTTA
Found at i:2709344 original size:37 final size:37
Alignment explanation
Indices: 2709303--2709480 Score: 139
Period size: 37 Copynumber: 4.8 Consensus size: 37
2709293 TAAAAACTAT
* * *
2709303 ATATATGTTTTCAAAAACGTGTTTTCAAAATTATATA
1 ATATATGTTTTCAAAAACATATTTTCAAAACTATATA
**
2709340 ATATATGTTTTTTAAAACATATTTTCAAAA-TATAT-
1 ATATATGTTTTCAAAAACATATTTTCAAAACTATATA
* * *
2709375 -TATATATTTTCAAAAACTGATTTTTTAAAAACTATATA
1 ATATATGTTTTCAAAAAC--ATATTTTCAAAACTATATA
* ** * * * *
2709413 TTATATACTTTCAAAAAAATCGTCTTCTGAAACTATATA
1 ATATATGTTTTCAAAAACAT-ATTTTC-AAAACTATATA
* *
2709452 TTATATGTTTT-AAAAAAATATTTTCAAAA
1 ATATATGTTTTCAAAAACATATTTTCAAAA
2709481 ATTATATTAT
Statistics
Matches: 114, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
34 14 0.12
36 18 0.16
37 37 0.32
38 11 0.10
39 34 0.30
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATGTTTTCAAAAACATATTTTCAAAACTATATA
Found at i:2710658 original size:17 final size:17
Alignment explanation
Indices: 2710623--2710678 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
2710613 ATAGGATGTA
*
2710623 TTAATTT-TGTTATTCTT
1 TTAATTTAT-TTATTTTT
*
2710640 TTATTTTTATTTATTTTT
1 TTA-ATTTATTTATTTTT
2710658 TTAATTTATTTCATTTTT
1 TTAATTTATTT-ATTTTT
2710676 TTA
1 TTA
2710679 TTCGAATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 10 0.30
18 22 0.67
19 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (17 bp):
TTAATTTATTTATTTTT
Found at i:2710659 original size:18 final size:18
Alignment explanation
Indices: 2710632--2710680 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
2710622 ATTAATTTTG
*
2710632 TTATTCTTTTATTTTTAT
1 TTATTTTTTTATTTTTAT
*
2710650 TTATTTTTTTA-ATTTAT
1 TTATTTTTTTATTTTTAT
2710667 TTCATTTTTTTATT
1 TT-ATTTTTTTATT
2710681 CGAATTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTTTTTTATTTTTAT
Found at i:2723276 original size:21 final size:21
Alignment explanation
Indices: 2723224--2723320 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
2723214 CCTCTCTTGC
*
2723224 TAGGTATCGGTACTACTATC-A
1 TAGGTATCGATACTACT-TCAA
*
2723245 TA-GTATTGATACTACTTCAA
1 TAGGTATCGATACTACTTCAA
**
2723265 TAGGTATCGATA-TTGTTCTTAA
1 TAGGTATCGATACTACTTC--AA
* *
2723287 T-GGTATCGATACTCCTTGAA
1 TAGGTATCGATACTACTTCAA
2723307 T-GTGTATCGATACT
1 TAG-GTATCGATACT
2723321 CCTTTAGGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
19 2 0.03
20 23 0.37
21 31 0.50
22 6 0.10
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (21 bp):
TAGGTATCGATACTACTTCAA
Found at i:2723321 original size:21 final size:20
Alignment explanation
Indices: 2723285--2723324 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
2723275 TATTGTTCTT
2723285 AATGGTATCGATACTCCTTG
1 AATGGTATCGATACTCCTTG
2723305 AATGTGTATCGATACTCCTT
1 AATG-GTATCGATACTCCTT
2723325 TAGGGGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (20 bp):
AATGGTATCGATACTCCTTG
Found at i:2723647 original size:16 final size:16
Alignment explanation
Indices: 2723605--2723639 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2723595 TTTTTGAACA
*
2723605 TAGGATTAGTTTTAGT
1 TAGGACTAGTTTTAGT
2723621 TAGGACTAGTTTTAGT
1 TAGGACTAGTTTTAGT
2723637 TAG
1 TAG
2723640 TTCTAGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (16 bp):
TAGGACTAGTTTTAGT
Found at i:2727484 original size:14 final size:14
Alignment explanation
Indices: 2727461--2727499 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
2727451 CTTCATTAAG
2727461 GTGCGTCTCCTGCC
1 GTGCGTCTCCTGCC
*
2727475 GTGTGTCTCCTGCC
1 GTGCGTCTCCTGCC
2727489 GTGCGTCTCCT
1 GTGCGTCTCCT
2727500 TTTCTCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.38, G:0.28, T:0.33
Consensus pattern (14 bp):
GTGCGTCTCCTGCC
Found at i:2728278 original size:19 final size:19
Alignment explanation
Indices: 2728234--2728280 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2728224 TTGAAAACCC
*
2728234 AGAATTTTTTTTTCTATTT
1 AGAATTTATTTTTCTATTT
*
2728253 AGCATTTATTTTTCT-TTT
1 AGAATTTATTTTTCTATTT
2728271 AGTAATTTAT
1 AG-AATTTAT
2728281 GCCCCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.64
Consensus pattern (19 bp):
AGAATTTATTTTTCTATTT
Found at i:2730634 original size:42 final size:42
Alignment explanation
Indices: 2730587--2730672 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
2730577 TACAAATATC
2730587 ATCACATTTGAAACATGACCCCACAGCAAGATGCTTTGGACA
1 ATCACATTTGAAACATGACCCCACAGCAAGATGCTTTGGACA
2730629 ATCACATTTGAAACATGACCCCACAGCAAGATGCTTTGGACA
1 ATCACATTTGAAACATGACCCCACAGCAAGATGCTTTGGACA
2730671 AT
1 AT
2730673 ATCCATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (42 bp):
ATCACATTTGAAACATGACCCCACAGCAAGATGCTTTGGACA
Found at i:2739680 original size:3 final size:3
Alignment explanation
Indices: 2739672--2739723 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
2739662 AGCATACCAA
*
2739672 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2739720 AAT A
1 AAT A
2739724 TGAATATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2740168 original size:134 final size:133
Alignment explanation
Indices: 2739904--2740618 Score: 630
Period size: 134 Copynumber: 5.3 Consensus size: 133
2739894 TCGAGAAACG
* ** * * *
2739904 TTGATATATTCCACTGTTCTTCAAGGAAGATTGAATTGA-G-TCAGACTTGTTCCACAGTTACTC
1 TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGTTC-GACTTGTTCCACTGTTACTC
* * * * * * * *
2739967 ATGTAATATCAAATCTTGAAAGAGAAGGATTTTTTTCGCTTCTTCTTGAGGGAAAATCGGATCTG
65 AGGGAATATCAAATCTTGAAAGAGAGGGA-TTATTTCTCTTTTTCTT-AGGGAAAATCAGATATG
2740032 GGGATA
128 GGGATA
* * ** * *
2740038 CTGATTCATTTTATTGTTAATCAGGGAAGATTGAATC-AGGTTCGACTTGTTTCACTGTTACTCA
1 TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGTTCGACTTGTTCCACTGTTACTCA
* * * * *
2740102 GGGAATATCAAATCGTGAAAGATAGGGATCTATTTCTCTTTTTTTTAAGGAAAAATAAGATATGG
66 GGGAATATCAAATCTTGAAAGAGAGGGAT-TATTTCTCTTTTTCTT-AGGGAAAATCAGATATGG
**
2740167 GGACG
129 GGATA
* ** ***
2740172 TTGATTTATTCCACTATTGTTCAATAAAGATTGAATCGAGGTAT--ACTTGTTCCACTGTTACTC
1 TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGT-TCGACTTGTTCCACTGTTACTC
* * * *
2740235 AGGGAATATCAAATCTTGAAAGAGATGGA-TATGTTACGCTTCTTTTTTAGGGAAAATAAGATCA
65 AGGGAATATCAAATCTTGAAAGAGAGGGATTAT-TT-CTCTT-TTTCTTAGGGAAAATCAGAT-A
*
2740299 -GGGGATG
126 TGGGGATA
* ** ** *
2740306 TTGATTTATTCCAATGTTGCTCAGGGAAGATTGAATCGAGG-AAGACTTGTTCCACTGATACTCA
1 TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGTTCGACTTGTTCCACTGTTACTCA
* * * * *
2740370 GAGCATATCAAATCTTGAAAGAAATGGA-TATGTTCTGCTTCTTCTTGAGGGAAAATCAGATCA-
66 GGGAATATCAAATCTTGAAAGAGAGGGATTAT-TTCT-CTTTTTCTT-AGGGAAAATCAGAT-AT
* *
2740433 AGGGACA
127 GGGGATA
* * *
2740440 TTGATTTATTCCACTGTCACTCATGGAAGATTGAATCGAGG--CAGACTTGTTCCACTGTTACTC
1 TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGTTC-GACTTGTTCCACTGTTACTC
*
2740503 AGGGAATATCAAATCTTGAAAGAGAGGGATT-TGTTCTGCTTTTTCCTTAGGGAAAATCAGATCT
65 AGGGAATATCAAATCTTGAAAGAGAGGGATTAT-TTCT-CTTTTT-CTTAGGGAAAATCAGATAT
*
2740567 GGGGATT
127 GGGGATA
* * **
2740574 TTGACTCATTCCACTGTCCATCAGGGAAGATTGAATCGA-GTTCGA
1 TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGTTCGA
2740619 TTCACTTCTC
Statistics
Matches: 478, Mismatches: 84, Indels: 38
0.80 0.14 0.06
Matches are distributed among these distances:
132 3 0.01
133 10 0.02
134 446 0.93
135 18 0.04
136 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (133 bp):
TTGATTTATTCCACTGTTAATCAGGGAAGATTGAATCGAGGTTCGACTTGTTCCACTGTTACTCA
GGGAATATCAAATCTTGAAAGAGAGGGATTATTTCTCTTTTTCTTAGGGAAAATCAGATATGGGG
ATA
Found at i:2740334 original size:268 final size:267
Alignment explanation
Indices: 2739901--2740618 Score: 797
Period size: 268 Copynumber: 2.7 Consensus size: 267
2739891 AGATCGAGAA
* * * * *
2739901 ACGTTGATATATTCCACTGTTCTTCAAGGAAGATTGAATTGA-GTCAGACTTGTTCCACAGTTAC
1 ACGTTGATTTATTCCACTGTTATTCAATGAAGATTGAATCGAGGT-AGACTTGTTCCACTGTTAC
* * * * * *
2739965 TCATGTAATATCAAATCTTGAAAGAGAAGGATTTTTTTCGCTTCTTCTTGAGGGAAAATCGGATC
65 TCAGGGAATATCAAATCTTGAAAGAGAAGGA-TTTGTTCGCTTCTTTTTTAGGGAAAATCAGATC
* ** * * *
2740030 TGGGGATACTGATTCATTTTATTGTTAATCAGGGAAGATTGAATCAGGTTCGACTTGTTTCACTG
129 TGGGGATATTGATTCATTCCAATGTTACTCAGGGAAGATTGAATCAGGTTCGACTTGTTCCACTG
* * * * *
2740095 TTACTCAGGGAATATCAAATCGTGAAAGATAGGGATCTAT-TTCT-CTTTTTTTTAAGGAAAAAT
194 ATACTCAGAGAATATCAAATCGTGAAAGAAAGGGA--TATGTTCTGCTTCTTCTTAAGGAAAAAT
*
2740158 AAGAT-ATGGGG
257 AAGATCA-AGGG
* * * *
2740169 ACGTTGATTTATTCCACTATTGTTCAATAAAGATTGAATCGAGGTATACTTGTTCCACTGTTACT
1 ACGTTGATTTATTCCACTGTTATTCAATGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACT
* * * *
2740234 CAGGGAATATCAAATCTTGAAAGAGATGGATATGTTACGCTTCTTTTTTAGGGAAAATAAGATCA
66 CAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTT-CGCTTCTTTTTTAGGGAAAATCAGATCT
* * * **
2740299 GGGGATGTTGATTTATTCCAATGTTGCTCAGGGAAGATTGAATCGAGG-AAGACTTGTTCCACTG
130 GGGGATATTGATTCATTCCAATGTTACTCAGGGAAGATTGAATC-AGGTTCGACTTGTTCCACTG
* * * * * *
2740363 ATACTCAGAGCATATCAAATCTTGAAAGAAATGGATATGTTCTGCTTCTTCTTGAGGGAAAATCA
194 ATACTCAGAGAATATCAAATCGTGAAAGAAAGGGATATGTTCTGCTTCTTCTTAAGGAAAAATAA
2740428 GATCAAGGG
259 GATCAAGGG
* * * *
2740437 ACATTGATTTATTCCACTGTCACTC-ATGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
1 ACGTTGATTTATTCCACTGTTATTCAAT-GAAGATTGAATCGAGGTAGACTTGTTCCACTGTTAC
* *
2740501 TCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTT-TTTCCTTAGGGAAAATCAGAT
65 TCAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTTC-GCTTCTTT-TTTAGGGAAAATCAGAT
* * * *
2740565 CTGGGGATTTTGACTCATTCCACTG-TCCATCAGGGAAGATTGAATC-GAGTTCGA
128 CTGGGGATATTGATTCATTCCAATGTTAC-TCAGGGAAGATTGAATCAG-GTTCGA
2740619 TTCACTTCTC
Statistics
Matches: 377, Mismatches: 61, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
266 4 0.01
267 17 0.05
268 350 0.93
269 6 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (267 bp):
ACGTTGATTTATTCCACTGTTATTCAATGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACT
CAGGGAATATCAAATCTTGAAAGAGAAGGATTTGTTCGCTTCTTTTTTAGGGAAAATCAGATCTG
GGGATATTGATTCATTCCAATGTTACTCAGGGAAGATTGAATCAGGTTCGACTTGTTCCACTGAT
ACTCAGAGAATATCAAATCGTGAAAGAAAGGGATATGTTCTGCTTCTTCTTAAGGAAAAATAAGA
TCAAGGG
Found at i:2752612 original size:7 final size:7
Alignment explanation
Indices: 2752600--2752635 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
2752590 TCAATCAAAA
2752600 CCTAAAC
1 CCTAAAC
*
2752607 CCTAAAT
1 CCTAAAC
2752614 CCTAAAC
1 CCTAAAC
2752621 CCTAAAC
1 CCTAAAC
2752628 CCTAAAC
1 CCTAAAC
2752635 C
1 C
2752636 ATGAAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:2767570 original size:23 final size:23
Alignment explanation
Indices: 2767544--2767605 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
2767534 AAAAATATAA
2767544 TTATGTCTTTATGACATATTTAT
1 TTATGTCTTTATGACATATTTAT
* *
2767567 TTATGTTTTTACGACATATTTAT
1 TTATGTCTTTATGACATATTTAT
* * *
2767590 CTCTGTCTTTGTGACA
1 TTATGTCTTTATGACA
2767606 CGATATTCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (23 bp):
TTATGTCTTTATGACATATTTAT
Found at i:2770685 original size:29 final size:30
Alignment explanation
Indices: 2770649--2770825 Score: 183
Period size: 29 Copynumber: 6.1 Consensus size: 30
2770639 CATTTTACAG
* * *
2770649 AAATAGCACCATTTTTAAAAT-AATTACCA
1 AAATAGCACCATTTTTGAATTAAATTCCCA
*
2770678 AAATAGCACC-TTTTCGAATTAAATTCCCA
1 AAATAGCACCATTTTTGAATTAAATTCCCA
2770707 AAATAGCA-CATTTTTGAATTAAATTCCCA
1 AAATAGCACCATTTTTGAATTAAATTCCCA
*
2770736 AAATAGCA--ATTTCCTGAA-TAAATTCCCA
1 AAATAGCACCATTT-TTGAATTAAATTCCCA
* *
2770764 AAATAACACCCTTTTTGAATT-AATTCCCA
1 AAATAGCACCATTTTTGAATTAAATTCCCA
* * *
2770793 AAATAACAAC-TATTTCGAATT-AATTCCCA
1 AAATAGCACCAT-TTTTGAATTAAATTCCCA
2770822 AAAT
1 AAAT
2770826 GTCACCTGGT
Statistics
Matches: 130, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
28 30 0.23
29 96 0.74
30 4 0.03
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATAGCACCATTTTTGAATTAAATTCCCA
Found at i:2770737 original size:58 final size:57
Alignment explanation
Indices: 2770649--2770825 Score: 216
Period size: 58 Copynumber: 3.1 Consensus size: 57
2770639 CATTTTACAG
* * *
2770649 AAATAGCACCATTTTTAAAATAATTACCAAAATAGCACCTTTTCGAATTAAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCAAAATAGCA-CTTTTCGAATTAAATTCCCA
* *
2770707 AAATAGCA-CATTTTTGAATTAAATTCCCAAAATAGCAATTTCCTGAA-TAAATTCCCA
1 AAATAGCACCATTTTTGAATT-AATTCCCAAAATAGCACTTTTC-GAATTAAATTCCCA
* * *
2770764 AAATAACACCCTTTTTGAATTAATTCCCAAAATAACAACTATTTCGAATT-AATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCAAAATAGC-ACT-TTTCGAATTAAATTCCCA
2770822 AAAT
1 AAAT
2770826 GTCACCTGGT
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
57 45 0.44
58 54 0.52
59 4 0.04
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (57 bp):
AAATAGCACCATTTTTGAATTAATTCCCAAAATAGCACTTTTCGAATTAAATTCCCA
Found at i:2778034 original size:27 final size:28
Alignment explanation
Indices: 2777956--2778102 Score: 156
Period size: 29 Copynumber: 5.1 Consensus size: 28
2777946 CATTTTATAG
* **
2777956 AAATAGCACCATTTTT-AAAATAATTATCA
1 AAATAGCA-CATTTTTGAATA-AATTCCCA
* *
2777985 AAATAGCACCTTTTTTGAATAAATTCTCA
1 AAATAGCA-CATTTTTGAATAAATTCCCA
2778014 AAATAGCAC-TTTTTGAATAAATTCCCA
1 AAATAGCACATTTTTGAATAAATTCCCA
2778041 AAATAGCACATTTTCTGAATAAATTCCCA
1 AAATAGCACATTTT-TGAATAAATTCCCA
* *
2778070 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA--CATTTTTGAATAAATTCCCA
2778099 AAAT
1 AAAT
2778103 GTCACCTGGT
Statistics
Matches: 107, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
27 26 0.24
28 5 0.05
29 68 0.64
30 6 0.06
31 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (28 bp):
AAATAGCACATTTTTGAATAAATTCCCA
Found at i:2778044 original size:56 final size:57
Alignment explanation
Indices: 2777956--2778102 Score: 170
Period size: 56 Copynumber: 2.6 Consensus size: 57
2777946 CATTTTATAG
** * ** * * *
2777956 AAATAGCACCATTTTTAAAATAATTATCAAAATAGCACCTTTTTTGAATAAATTCTCA
1 AAATAGCACCATTTCGAATA-AATTCCCAAAATAGCACATTTTCTGAATAAATTCCCA
* *
2778014 AAATAGCA-CTTTTTGAATAAATTCCCAAAATAGCACATTTTCTGAATAAATTCCCA
1 AAATAGCACCATTTCGAATAAATTCCCAAAATAGCACATTTTCTGAATAAATTCCCA
*
2778070 AAATAGCACCCATTTCGAATTAATTCCCAAAAT
1 AAATAGCA-CCATTTCGAATAAATTCCCAAAAT
2778103 GTCACCTGGT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
56 40 0.53
57 8 0.11
58 28 0.37
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (57 bp):
AAATAGCACCATTTCGAATAAATTCCCAAAATAGCACATTTTCTGAATAAATTCCCA
Found at i:2778135 original size:22 final size:19
Alignment explanation
Indices: 2778109--2778186 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 19
2778099 AAATGTCACC
2778109 TGGTCAACGGTCAATGGTCGG
1 TGGTCAACGGTC-A-GGTCGG
*
2778130 TCGGTCAACGGTCGGGTC-G
1 T-GGTCAACGGTCAGGTCGG
2778149 -GGTCAACGGTCAGGTCGGG
1 TGGTCAACGGTCAGGTC-GG
*
2778168 TGGTCAACGGTCGGGTCGG
1 TGGTCAACGGTCAGGTCGG
2778187 GTCGGACCGG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
17 15 0.30
19 4 0.08
20 19 0.38
21 1 0.02
22 11 0.22
ACGTcount: A:0.14, C:0.22, G:0.44, T:0.21
Consensus pattern (19 bp):
TGGTCAACGGTCAGGTCGG
Found at i:2778154 original size:17 final size:17
Alignment explanation
Indices: 2778117--2778189 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
2778107 CCTGGTCAAC
*
2778117 GGTCAATGGTC-GGTC-
1 GGTCAACGGTCGGGTCG
2778132 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
2778149 GGTCAACGGTCAGGTCGGG
1 GGTCAACGGTCGGGTC--G
2778168 TGGTCAACGGTCGGGTCG
1 -GGTCAACGGTCGGGTCG
2778186 GGTC
1 GGTC
2778190 GGACCGGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
15 10 0.20
16 4 0.08
17 19 0.38
18 1 0.02
19 1 0.02
20 15 0.30
ACGTcount: A:0.12, C:0.22, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Done.