Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008658.1 Hibiscus syriacus cultivar Beakdansim tig00111653_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: 445414
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:281091 original size:19 final size:16
Alignment explanation
Indices: 281053--281096 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
281043 GGTTAGTGAC
281053 TAAAATATAAACAAAA
1 TAAAATATAAACAAAA
*
281069 TAAAATATGAAATCCAAAT
1 TAAAATAT-AAA--CAAAA
281088 TAAAATATA
1 TAAAATATA
281097 TGGAAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 1 0.04
19 12 0.50
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (16 bp):
TAAAATATAAACAAAA
Found at i:282533 original size:81 final size:82
Alignment explanation
Indices: 282377--282545 Score: 252
Period size: 81 Copynumber: 2.1 Consensus size: 82
282367 CACTCCACTC
282377 TTCTTTCAGGGGAGATAGGACTTGATATGTTCCTCTTTTTCAGGTAGTAAGATCAATTTTGGAAG
1 TTCTTTCAGGGGAGATAGGACTTGATATGTTCCTCTTTTTCAGGTAGTAAGATCAATTTTGGAAG
* *
282442 ACGGGTCTGCTCAACTA
66 ACGAGACTGCTCAACTA
* *
282459 TTCTTTCAGGGGAGATCA-GACTTGATATGTTCC-CTTTTTCGGGTAGTCAGATCAATTTTGGAA
1 TTCTTTCAGGGGAGAT-AGGACTTGATATGTTCCTCTTTTTCAGGTAGTAAGATCAATTTTGGAA
* * *
282522 GATGAGACTGCTCCACTT
65 GACGAGACTGCTCAACTA
282540 TTCTTT
1 TTCTTT
282546 TTGGGAGATA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
81 47 0.59
82 31 0.39
83 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (82 bp):
TTCTTTCAGGGGAGATAGGACTTGATATGTTCCTCTTTTTCAGGTAGTAAGATCAATTTTGGAAG
ACGAGACTGCTCAACTA
Found at i:282588 original size:55 final size:55
Alignment explanation
Indices: 282515--282657 Score: 189
Period size: 55 Copynumber: 2.6 Consensus size: 55
282505 TCAGATCAAT
* * * * *
282515 TTTGGAAGATGAGACTGCTCCACTTTTCTTTTTGGGAGATAAAACTCGATAAA-TC
1 TTTGGAAGATGGGTCTGCTCCACTCTTCTTTTAGCGAGATAAAACTCGA-AAATTC
* *
282570 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTTAGCGAGATAAGACTCGAAAATTC
1 TTTGGAAGATGGGTCTGCTCCACTCTTCTTTTAGCGAGATAAAACTCGAAAATTC
* *
282625 TTTGGAACATGGGTATGCTCCACTCTTCTTTTA
1 TTTGGAAGATGGGTCTGCTCCACTCTTCTTTTA
282658 AGGGATATCA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 3 0.04
55 74 0.96
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (55 bp):
TTTGGAAGATGGGTCTGCTCCACTCTTCTTTTAGCGAGATAAAACTCGAAAATTC
Found at i:282770 original size:82 final size:81
Alignment explanation
Indices: 282646--282799 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 81
282636 GGTATGCTCC
* * * *
282646 ACTCTTCTTTTAAGGGATATCATACTTGATTTGTTCAACTTTTTCGGGTAGTCAGAAT-AATTTT
1 ACTCTTCTTTCAAGGGATATCAGACATGATTTATTCAAC-TTTTCGGGTAGTCAG-ATCAATTTT
282710 GGAAAACGAATCTACTCT
64 GGAAAACGAATCTACTCT
* * **
282728 ACTCTTCTTTCAGGGGATATTAGACATGATTTATTCCTCTTTTCGGGTAGTCAGATCAATTTTGG
1 ACTCTTCTTTCAAGGGATATCAGACATGATTTATTCAACTTTTCGGGTAGTCAGATCAATTTTGG
282793 AAAACGA
66 AAAACGA
282800 GTTTGCTACA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.03
81 30 0.48
82 31 0.49
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (81 bp):
ACTCTTCTTTCAAGGGATATCAGACATGATTTATTCAACTTTTCGGGTAGTCAGATCAATTTTGG
AAAACGAATCTACTCT
Found at i:282796 original size:81 final size:81
Alignment explanation
Indices: 282646--282799 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 81
282636 GGTATGCTCC
* * * *
282646 ACTCTTCTTTTAAGGGATATCATACTTGATTTGTTCAACTTTTTCGGGTAGTCAGAATAATTTTG
1 ACTCTTCTTTCAAGGGATATCAGACATGATTTATTC-ACTTTTTCGGGTAGTCAGAATAATTTTG
282711 GAAAACGAATCTACTCT
65 GAAAACGAATCTACTCT
* *
282728 ACTCTTCTTTCAGGGGATATTAGACATGATTTATTC-CTCTTTTCGGGTAGTCAG-ATCAATTTT
1 ACTCTTCTTTCAAGGGATATCAGACATGATTTATTCACT-TTTTCGGGTAGTCAGAAT-AATTTT
282791 GGAAAACGA
64 GGAAAACGA
282800 GTTTGCTACA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
80 4 0.06
81 30 0.47
82 30 0.47
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (81 bp):
ACTCTTCTTTCAAGGGATATCAGACATGATTTATTCACTTTTTCGGGTAGTCAGAATAATTTTGG
AAAACGAATCTACTCT
Found at i:282863 original size:273 final size:273
Alignment explanation
Indices: 282369--282947 Score: 745
Period size: 273 Copynumber: 2.1 Consensus size: 273
282359 GGGAAATCCA
* **
282369 CTCCACTCTTCTTTCAGGGGAGAT-AGGACTTGATATGTTCCTCTTTTTCAGGTAGTAAGATCAA
1 CTCCACTCTTCTTTTAGGGGAGATCA-GACTTGATATGTTCAACTTTTTCAGGTAGTAAGATCAA
* ** * * *
282433 TTTTGGAAGACGGGTCTGCTCAACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCCTTTTT
65 TTTTGGAAAACGAATCTACTCAACTATTCTTTCAGGGGAGATCAGACATGATATATTCCCTTTTT
* * * *
282498 CGGGTAGTCAGATCAATTTTGGAAGATGAGACTGCTCCACTTTTCTTTTTGGGAGATAAAACTCG
130 CGGGTAGTCAGATCAATTTTGGAAAACGAGACTGCTACACTTTTCTTTTAGGGAGATAAAACTCG
* * * * *
282563 ATAAATCTTTGGAAGACGGGTCTGCTCCACTCTTCTTT-TAGCGAGATAAGACTCGAAAATTCTT
195 AGAAATCTTTGGAAGACGGGTCTGCTCCACACTTCTTTCAAG-GAGAGAAGACTCGAAAAATCTT
* *
282627 TGGAACATGGGTATG
259 TGGAAAATGAGTATG
* * * * * *
282642 CTCCACTCTTCTTTTAAGGGATATCATACTTGATTTGTTCAACTTTTTCGGGTAGTCAGAAT-AA
1 CTCCACTCTTCTTTTAGGGGAGATCAGACTTGATATGTTCAACTTTTTCAGGTAGTAAG-ATCAA
* * * * *
282706 TTTTGGAAAACGAATCTACTCTACTCTTCTTTCAGGGGATATTAGACATGATTTATT-CCTCTTT
65 TTTTGGAAAACGAATCTACTCAACTATTCTTTCAGGGGAGATCAGACATGATATATTCCCT-TTT
** *
282770 TCGGGTAGTCAGATCAATTTTGGAAAACGAGTTTGCTACACTTTTCTTTTAGGGAGATAAGACTC
129 TCGGGTAGTCAGATCAATTTTGGAAAACGAGACTGCTACACTTTTCTTTTAGGGAGATAAAACTC
282835 GAGAAATCTTTGGAAGAC-GGTCCTGCTCCACACTTCTTTCAAGGAGAGAAGACTCGAAAAATCT
194 GAGAAATCTTTGGAAGACGGGT-CTGCTCCACACTTCTTTCAAGGAGAGAAGACTCGAAAAATCT
*
282899 TTGGAAAATGAGTCTG
258 TTGGAAAATGAGTATG
* *
282915 TTCCACTCTTATTTTAGGGGAGATCAGACTTGA
1 CTCCACTCTTCTTTTAGGGGAGATCAGACTTGA
282948 GGATTGATTT
Statistics
Matches: 261, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
272 6 0.02
273 250 0.96
274 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (273 bp):
CTCCACTCTTCTTTTAGGGGAGATCAGACTTGATATGTTCAACTTTTTCAGGTAGTAAGATCAAT
TTTGGAAAACGAATCTACTCAACTATTCTTTCAGGGGAGATCAGACATGATATATTCCCTTTTTC
GGGTAGTCAGATCAATTTTGGAAAACGAGACTGCTACACTTTTCTTTTAGGGAGATAAAACTCGA
GAAATCTTTGGAAGACGGGTCTGCTCCACACTTCTTTCAAGGAGAGAAGACTCGAAAAATCTTTG
GAAAATGAGTATG
Found at i:282872 original size:55 final size:55
Alignment explanation
Indices: 282788--282944 Score: 163
Period size: 55 Copynumber: 2.8 Consensus size: 55
282778 TCAGATCAAT
* * ** *
282788 TTTGGAAAACGAGTTTGCTACACTTTTCTTTTAGGGAGATAAGACTCGAGAAATC
1 TTTGGAAAACGAGTCTGCTCCACACTTCTTTTAGGGAGATAAGACTCGAAAAATC
* * * *
282843 TTTGGAAGACG-GTCCTGCTCCACACTTCTTTCAAGGAGAGAAGACTCGAAAAATC
1 TTTGGAAAACGAGT-CTGCTCCACACTTCTTTTAGGGAGATAAGACTCGAAAAATC
* * * * *
282898 TTTGGAAAATGAGTCTGTTCCACTCTTATTTTAGGGGAGATCAGACT
1 TTTGGAAAACGAGTCTGCTCCACACTTCTTTTA-GGGAGATAAGACT
282945 TGAGGATTGA
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
54 2 0.02
55 67 0.83
56 12 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (55 bp):
TTTGGAAAACGAGTCTGCTCCACACTTCTTTTAGGGAGATAAGACTCGAAAAATC
Found at i:283180 original size:89 final size:89
Alignment explanation
Indices: 282931--283180 Score: 338
Period size: 89 Copynumber: 2.8 Consensus size: 89
282921 TCTTATTTTA
* * *
282931 GGGGAGATCAGACTTGAGGATTGATTTGCTTCGCTGTTTCTTTAGGAAGACCAAATCTGAAATAA
1 GGGGAGATCAGAC-TCAAGATTGATTTGCTTCGCTGATTCTTTAGGAAGACCAAATCTGAAATAA
* * *
282996 GAAGAACATATTCCACTACTCTTCC
65 GAAGAATATACTACACTACTCTTCC
* * * * *
283021 GGGGAGATCAGATTCAAGATTGATTTTCTTCGCTTATTCTTTAGGAAGACTAAATCTGAAATAAA
1 GGGGAGATCAGACTCAAGATTGATTTGCTTCGCTGATTCTTTAGGAAGACCAAATCTGAAATAAG
* * *
283086 AAGAATATGCTATACTACTTTTCC
66 AAGAATATACTACACTACTCTTCC
* * *
283110 GGGGAGATCAGACTCAATATTGATTTGCTTCACTGCTTCTTTAGGAAGACCAAATCTGAAATAAG
1 GGGGAGATCAGACTCAAGATTGATTTGCTTCGCTGATTCTTTAGGAAGACCAAATCTGAAATAAG
283175 AAGAAT
66 AAGAAT
283181 TTGTACTCTT
Statistics
Matches: 138, Mismatches: 22, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
89 126 0.91
90 12 0.09
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (89 bp):
GGGGAGATCAGACTCAAGATTGATTTGCTTCGCTGATTCTTTAGGAAGACCAAATCTGAAATAAG
AAGAATATACTACACTACTCTTCC
Found at i:283443 original size:34 final size:30
Alignment explanation
Indices: 283405--283473 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
283395 TTGATATAAC
283405 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
283439 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
283468 AATTTA
1 AATTTA
283474 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:283484 original size:29 final size:30
Alignment explanation
Indices: 283414--283473 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
283404 CAATTTAAGG
283414 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
283445 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
283474 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:283739 original size:20 final size:21
Alignment explanation
Indices: 283651--283727 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
283641 AATGCAATTA
***
283651 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAAGGCT
283671 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
*
283692 GTGCATCGATACATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
283713 GTGCATCGATGCATC
1 GTGCATCGATGCATC
283728 CTGTTGTGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 15 0.29
21 36 0.71
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:284150 original size:34 final size:32
Alignment explanation
Indices: 284111--284180 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
284101 TTTTGTAAAG
* *
284111 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
284145 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
284177 GGGA
1 GGGA
284181 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:285073 original size:20 final size:19
Alignment explanation
Indices: 285040--285087 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
285030 AATGATTTTC
* *
285040 TTTTGAAAACAAAAATAGA
1 TTTTGAAAACAAAAAGAAA
285059 TTTTGAAAGACAAAAAGAAA
1 TTTTGAAA-ACAAAAAGAAA
285079 TTTTGAAAA
1 TTTTGAAAA
285088 AGGATTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.27
Consensus pattern (19 bp):
TTTTGAAAACAAAAAGAAA
Found at i:286400 original size:30 final size:31
Alignment explanation
Indices: 286326--286416 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
286316 TAATTTAAGG
286326 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
286357 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
286388 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
286417 TTCAAAGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:286529 original size:21 final size:21
Alignment explanation
Indices: 286496--286615 Score: 125
Period size: 21 Copynumber: 5.7 Consensus size: 21
286486 AGTGTGTCAA
286496 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGT
* * *
286517 AGTTCATCTATGCATCCCTGT
1 AGTGCATCCATGCACCCCTGT
* *
286538 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGT
* **
286559 AGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACC-CCTGT
* *
286581 AGTGCATCGATGCA-CCATGT
1 AGTGCATCCATGCACCCCTGT
*
286601 AGTGGATCCATGCAC
1 AGTGCATCCATGCAC
286616 TCAAACACCG
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 13 0.16
21 52 0.66
22 14 0.18
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGT
Found at i:286602 original size:63 final size:63
Alignment explanation
Indices: 286496--286614 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
286486 AGTGTGTCAA
** * * *
286496 AGTGCATCCATGCACCCCTGTAGTTCATCTATGCATCCCTGTAGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCACTAGTGCATCGATGCATCCATGTAGTGCATCCATGCATCCCTGC
* *
286559 AGTGCATCCATGCACCTGCACTAGTGCATCGATGCA-CCATGTAGTGGATCCATGCA
1 AGTGCATCCATGCACC-CCACTAGTGCATCGATGCATCCATGTAGTGCATCCATGCA
286615 CTCAAACACC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
63 34 0.71
64 14 0.29
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (63 bp):
AGTGCATCCATGCACCCCACTAGTGCATCGATGCATCCATGTAGTGCATCCATGCATCCCTGC
Found at i:286661 original size:20 final size:20
Alignment explanation
Indices: 286636--286702 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
286626 AATTCAATTA
* * *
286636 GTGCATTGATACATCTTTCT
1 GTGCATTGATGCATCATGCT
* *
286656 GTGCATCGATGCATCAAGGCT
1 GTGCATTGATGCATC-ATGCT
*
286677 GTGCATTGATGCATCCTGCT
1 GTGCATTGATGCATCATGCT
286697 GTGCAT
1 GTGCAT
286703 CCATGCACGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (20 bp):
GTGCATTGATGCATCATGCT
Found at i:286680 original size:21 final size:21
Alignment explanation
Indices: 286654--286718 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
286644 ATACATCTTT
286654 CTGTGCATCGATGCATCAAGG
1 CTGTGCATCGATGCATCAAGG
* **
286675 CTGTGCATTGATGCATC-CTG
1 CTGTGCATCGATGCATCAAGG
*
286695 CTGTGCATCCATGCA-CGAAGG
1 CTGTGCATCGATGCATC-AAGG
286716 CTG
1 CTG
286719 CAACGACTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.03
20 14 0.40
21 20 0.57
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (21 bp):
CTGTGCATCGATGCATCAAGG
Found at i:286699 original size:41 final size:41
Alignment explanation
Indices: 286636--286718 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
286626 AATTCAATTA
* * *
286636 GTGCATTGATACATCTTTCTGTGCATCGATGCATC-AAGGCT
1 GTGCATTGATACATCCTGCTGTGCATCCATGCA-CGAAGGCT
*
286677 GTGCATTGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
1 GTGCATTGATACATCCTGCTGTGCATCCATGCACGAAGGCT
286718 G
1 G
286719 CAACGACTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.30
Consensus pattern (41 bp):
GTGCATTGATACATCCTGCTGTGCATCCATGCACGAAGGCT
Found at i:287825 original size:20 final size:20
Alignment explanation
Indices: 287797--287834 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
287787 AAATTTATTC
287797 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
287817 ATTGGTGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
287835 TCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:290454 original size:23 final size:22
Alignment explanation
Indices: 290422--290500 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
290412 TGTCCTTGTG
290422 CATCGATGCACATTCAAGGAGT
1 CATCGATGCACATTCAAGGAGT
* * * *
290444 ACATCGGTGCACCTTCATGGTGT
1 -CATCGATGCACATTCAAGGAGT
290467 -ATCGATGCACATTCAAAGG-GAT
1 CATCGATGCACATTC-AAGGAG-T
290489 GCATCGATGCAC
1 -CATCGATGCAC
290501 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.29
22 4 0.09
23 18 0.40
24 10 0.22
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGAGT
Found at i:296346 original size:66 final size:66
Alignment explanation
Indices: 296223--296382 Score: 220
Period size: 66 Copynumber: 2.5 Consensus size: 66
296213 GCACTAAGAG
* * *
296223 TGCATCGATGCATGAAGTGCATTCGATG--TTTCAAAATAGCCTGAGTGCATCGATGCATGA-AT
1 TGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCTGAGTGCATCGATGCATGATA-
296285 TA
65 TA
* * *
296287 TGCATCGATGTATCAAATGCATTCGATGTTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGTA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTTCA-AAATACCCTGAGTGCATCGATGCATGATA
296351 TA
65 TA
296353 TGCATCGATGCATAAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
296383 CAATTTATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
64 25 0.29
66 56 0.66
67 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (66 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTTCAAAATACCCTGAGTGCATCGATGCATGATAT
A
Found at i:296856 original size:90 final size:89
Alignment explanation
Indices: 296678--297032 Score: 457
Period size: 89 Copynumber: 4.0 Consensus size: 89
296668 GTTTTCAACA
* * * * * * *
296678 GGATTGATTTGCTTTGCTACTCTATC-AGGAATACCAAATTTGAAATAAGAAGAATCTAG-TCCT
1 GGATTGATTTGCTTCGCTACTCTTTCGA-GAAGACCAAATCTAAAATAAGAAGAATAT-GCTCCA
*
296741 CTACTCTTCTGAGGAGATCAGACTTG
64 CTACTCTTCTGGGGAGATCAGACTTG
* * * *
296767 GGATTGATTTGCTTCGCTACTCTTTCGAGAATACCAAATTTAAAAATAAGAAGAATCTGGTCCAC
1 GGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAATCT-AAAATAAGAAGAATATGCTCCAC
*
296832 TACTCTTCTGGGGAGATCAAACTTG
65 TACTCTTCTGGGGAGATCAGACTTG
* *
296857 GGATTGATTTGCTTCGCTACTCTTTAGGGAAGACCAAATCTAAAATAAGAAGAATATGCTCCACT
1 GGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAATCTAAAATAAGAAGAATATGCTCCACT
**
296922 ACTCTT-TCGGGGAGATCAGACTCA
66 ACTCTTCT-GGGGAGATCAGACTTG
* * *
296946 AGATTGATTTGCTTCGCTACTCTTTCGGGAAGACCAAATCTGAAATAAGAAGAATATGCT-CATC
1 GGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAATCTAAAATAAGAAGAATATGCTCCA-C
297010 TACTCTTCTGGGGAGATCAGACT
65 TACTCTTCTGGGGAGATCAGACT
297033 CAATATCTTT
Statistics
Matches: 242, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
88 3 0.01
89 158 0.65
90 81 0.33
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (89 bp):
GGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAATCTAAAATAAGAAGAATATGCTCCACT
ACTCTTCTGGGGAGATCAGACTTG
Found at i:296984 original size:179 final size:178
Alignment explanation
Indices: 296678--297028 Score: 476
Period size: 179 Copynumber: 2.0 Consensus size: 178
296668 GTTTTCAACA
* * * * * *
296678 GGATTGATTTGCTTTGCTACTCTATCAGGAATACCAAATTTGAAATAAGAAGAATCTAGTCCTCT
1 GGATTGATTTGCTTCGCTACTCTATCAGGAAGACCAAATCTAAAATAAGAAGAATATAGTCCACT
*** * *
296743 ACTCTTCTGAGGAGATCAGACTTGGGATTGATTTGCTTCGCTACTCTTTCGAGAATACCAAATTT
66 ACTCTTCTGAGGAGATCAGACTCAAGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAATCT
* *
296808 AAAAATAAGAAGAATCTGGTCCA-CTACTCTTCTGGGGAGATCAAACTTG
131 -AAAATAAGAAGAATATGCT-CATCTACTCTTCTGGGGAGATCAAACTTG
*
296857 GGATTGATTTGCTTCGCTACTCT-TTAGGGAAGACCAAATCTAAAATAAGAAGAATAT-GCTCCA
1 GGATTGATTTGCTTCGCTACTCTATCA-GGAAGACCAAATCTAAAATAAGAAGAATATAG-TCCA
* *
296920 CTACTCTT-TCGGGGAGATCAGACTCAAGATTGATTTGCTTCGCTACTCTTTCGGGAAGACCAAA
64 CTACTCTTCT-GAGGAGATCAGACTCAAGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAA
*
296984 TCTGAAATAAGAAGAATATGCTCATCTACTCTTCTGGGGAGATCA
128 TCTAAAATAAGAAGAATATGCTCATCTACTCTTCTGGGGAGATCA
297029 GACTCAATAT
Statistics
Matches: 151, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
177 2 0.01
178 40 0.26
179 109 0.72
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (178 bp):
GGATTGATTTGCTTCGCTACTCTATCAGGAAGACCAAATCTAAAATAAGAAGAATATAGTCCACT
ACTCTTCTGAGGAGATCAGACTCAAGATTGATTTGCTTCGCTACTCTTTCGAGAAGACCAAATCT
AAAATAAGAAGAATATGCTCATCTACTCTTCTGGGGAGATCAAACTTG
Found at i:301763 original size:62 final size:62
Alignment explanation
Indices: 301666--302181 Score: 480
Period size: 62 Copynumber: 8.5 Consensus size: 62
301656 CTCAAATCCT
* * * *
301666 AAAGGTTGACTTCTCTTCACGAGGAAGGCAAGGATTAACTCTACTGGGGAGTCACGAATAAC
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* * * * *
301728 AAAGGTTAACTTCTCTTCATGAAAAATTCAAGGATTGACTCTACT-GGGAGTTAGGAATAAC
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* * * * * *
301789 AAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTGCCGAGGATTCAGGAATAAT
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* * * * * *
301851 AAAGGTTGAATTCTCTTCATGAGAAAGTCAAGGATTGTCTCTATTAGGGAGTCAGGAATAAA
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* *
301913 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTATGCTGGGGAGTCAGG------
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* * ** * * * *
301969 --A--TTGACTCCTCTTCGCGAGGGAGTCAAAGATTGGCTCTACTAGAGAGTCAGGAATAAC
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* * ** * * * * *
302027 AAAGGTTGACTTCTCTTTAC-AAAGAAGTCAAATATTGACTCTGCTAGGGAGTTAGGGATAAA
1 AAAGGTTGACTTCTCTTCACGAGA-AAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
* * * * * * * *
302089 AAAGATTGACTTTTCTTTATGAGGAAGTCAAAGATTGACTCTGCTGGAGAGTCAGGAATAAC
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
** *
302151 AAAAATTGACTTCTCTTCACGAGGAAGTCAA
1 AAAGGTTGACTTCTCTTCACGAGAAAGTCAA
302182 ATTGAAATTT
Statistics
Matches: 365, Mismatches: 76, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
52 41 0.11
54 1 0.00
60 1 0.00
61 53 0.15
62 268 0.73
63 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (62 bp):
AAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACTGGGGAGTCAGGAATAAC
Found at i:302077 original size:176 final size:176
Alignment explanation
Indices: 301666--302145 Score: 473
Period size: 176 Copynumber: 2.7 Consensus size: 176
301656 CTCAAATCCT
* * * * * * * *
301666 AAAGGTTGACTTCTCTTCACGAGGAAGGCAAGGATTAACTCTACTGGGGAGTCACGAATAACAAA
1 AAAGGTTGACTTCTCTTTACAAAGAAGTCAAGGATTGACTCTACTAGGGAGTCAGGAATAAAAAA
* * * *
301731 GGTTAACTTCTCTTCATGAAAAATTCAAGGATTGACTCTACTGGGAGTTAGGAATAACAAAGG-T
66 GGTTGACTTCTCTTCATGAGAAAGTCAAGGATTGACTCTGCTGGG-G--A-G--T--C--AGGAT
* * * * * *
301795 TGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTGCCGAGGATTCAGGAATAAT
121 TGACTCCTCTTCACGAGGAAGTCAAAGATTGACTCTACAGAGGAGTCAGGAATAAC
* * * *
301851 AAAGGTTGAATTCTC-TT-CATGAGAAAGTCAAGGATTGTCTCTATTAGGGAGTCAGGAATAAAA
1 AAAGGTTGACTTCTCTTTACA-AAG-AAGTCAAGGATTGACTCTACTAGGGAGTCAGGAATAAAA
* *
301914 AAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTATGCTGGGGAGTCAGGATTGACTCCT
64 AAGGTTGACTTCTCTTCATGAGAAAGTCAAGGATTGACTCTGCTGGGGAGTCAGGATTGACTCCT
* * *
301979 CTTCGCGAGGGAGTCAAAGATTGGCTCTACTAGA-GAGTCAGGAATAAC
129 CTTCACGAGGAAGTCAAAGATTGACTCTAC-AGAGGAGTCAGGAATAAC
** * * *
302027 AAAGGTTGACTTCTCTTTACAAAGAAGTCAAATATTGACTCTGCTAGGGAGTTAGGGATAAAAAA
1 AAAGGTTGACTTCTCTTTACAAAGAAGTCAAGGATTGACTCTACTAGGGAGTCAGGAATAAAAAA
* * * * * *
302092 GATTGACTTTTCTTTATGAGGAAGTCAAAGATTGACTCTGCTGGAGAGTCAGGA
66 GGTTGACTTCTCTTCATGAGAAAGTCAAGGATTGACTCTGCTGGGGAGTCAGGA
302146 ATAACAAAAA
Statistics
Matches: 245, Mismatches: 44, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
175 3 0.01
176 139 0.57
177 7 0.03
178 2 0.01
179 1 0.00
181 1 0.00
182 1 0.00
183 1 0.00
184 3 0.01
185 87 0.36
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (176 bp):
AAAGGTTGACTTCTCTTTACAAAGAAGTCAAGGATTGACTCTACTAGGGAGTCAGGAATAAAAAA
GGTTGACTTCTCTTCATGAGAAAGTCAAGGATTGACTCTGCTGGGGAGTCAGGATTGACTCCTCT
TCACGAGGAAGTCAAAGATTGACTCTACAGAGGAGTCAGGAATAAC
Found at i:303309 original size:40 final size:39
Alignment explanation
Indices: 303220--303326 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 39
303210 GGGTGATATG
*
303220 GGCCTTCAAAAATGCCCCAACATTTATTATTTCTTGTTGTTATA
1 GGCCTTC-AAAATGCCCCAACA--T-TTATTTCTTGATG-TATA
*
303264 GGCCTTCAAAATTCCCCAACATTTATTTCTTGATG-ATA
1 GGCCTTCAAAATGCCCCAACATTTATTTCTTGATGTATA
*
303302 CGAGCCTTCAAAAGGCCCCAACATT
1 -G-GCCTTCAAAATGCCCCAACATT
303327 CATCATTTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
38 3 0.05
39 1 0.02
40 32 0.56
41 1 0.02
43 13 0.23
44 7 0.12
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (39 bp):
GGCCTTCAAAATGCCCCAACATTTATTTCTTGATGTATA
Found at i:311519 original size:3 final size:3
Alignment explanation
Indices: 311513--311540 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
311503 ATTATTAAAT
311513 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
311541 AATGTAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:313393 original size:18 final size:18
Alignment explanation
Indices: 313372--313410 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
313362 CTTTAACCTT
313372 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* *
313390 ACAACATTTGCCACGACA
1 ACAACACTTACCACGACA
313408 ACA
1 ACA
313411 CCATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:319803 original size:18 final size:18
Alignment explanation
Indices: 319782--319820 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
319772 CTTTAACCTT
319782 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* *
319800 ACAACATTTGCCACGACA
1 ACAACACTTACCACGACA
319818 ACA
1 ACA
319821 CCATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:323099 original size:26 final size:26
Alignment explanation
Indices: 323066--323122 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
323056 AAAACTTCTA
323066 AAATGCCTCTATAGGCTAAAATGATT
1 AAATGCCTCTATAGGCTAAAATGATT
*
323092 AAATGCCTTTATAGGCTAAAATGATT
1 AAATGCCTCTATAGGCTAAAATGATT
323118 AAATG
1 AAATG
323123 ACCCTTACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (26 bp):
AAATGCCTCTATAGGCTAAAATGATT
Found at i:323143 original size:26 final size:26
Alignment explanation
Indices: 323081--323137 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
323071 CCTCTATAGG
* * *
323081 CTAAAATGATTAAATGCCTTTATAGG
1 CTAAAATGATTAAATGCCCTTACAGC
323107 CTAAAATGATTAAATGACCCTTACAGC
1 CTAAAATGATTAAATG-CCCTTACAGC
323134 CTAA
1 CTAA
323138 GTGATTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (26 bp):
CTAAAATGATTAAATGCCCTTACAGC
Found at i:328383 original size:3 final size:3
Alignment explanation
Indices: 328375--328404 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
328365 AATATAAGGC
328375 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
328405 CCTCTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:330681 original size:21 final size:21
Alignment explanation
Indices: 330652--330693 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
330642 GAATTTAAAA
*
330652 TGTGTATCGATGCACTACTAC
1 TGTGCATCGATGCACTACTAC
* *
330673 TGTGCATCGATGTACTGCTAC
1 TGTGCATCGATGCACTACTAC
330694 AGTAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (21 bp):
TGTGCATCGATGCACTACTAC
Found at i:335960 original size:23 final size:23
Alignment explanation
Indices: 335934--336007 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
335924 AAGTGTCACA
*
335934 TAGATTTGTCCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCGCG
* ** ** *
335957 TAGAATTATCCATAAGGACTACA
1 TAGAATTGTCCCGAAGGACCGCG
335980 TAGAATTGTCCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCGCG
336003 TAGAA
1 TAGAA
336008 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCGCG
Found at i:336149 original size:15 final size:15
Alignment explanation
Indices: 336109--336178 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
336099 AAGTTTCATT
336109 TATTCACATAG-ACTA
1 TATTCACATAGAAC-A
* *
336124 TAATCACATAGAGCA
1 TATTCACATAGAACA
*
336139 TATTCATATAGAACA
1 TATTCACATAGAACA
* *
336154 TTTTCACGTAGAACA
1 TATTCACATAGAACA
336169 TATTCACATA
1 TATTCACATA
336179 ATAGTAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
15 43 0.98
16 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:337527 original size:13 final size:13
Alignment explanation
Indices: 337500--337534 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
337490 GGGAAATAAA
*
337500 TTTAATAA-TTAT
1 TTTAATAAGGTAT
337512 TTTAATAAGGTAT
1 TTTAATAAGGTAT
337525 TTTAATAAGG
1 TTTAATAAGG
337535 AAAAGGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (13 bp):
TTTAATAAGGTAT
Found at i:338974 original size:54 final size:54
Alignment explanation
Indices: 338568--338962 Score: 569
Period size: 54 Copynumber: 7.3 Consensus size: 54
338558 GTTAAAAATG
* *
338568 TATGTGGATGAATAACCGTTTCGACACTAATTGTGCATTTCACGAAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATCC
*
338622 TATGTGGATGAATAACCGTTTCAACACTAAGTGTGCATTTCATGAAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATCC
*
338676 TATGTGGATGAATAACCGTTTCAACACTAAGTGTGCATTTCATGAAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATCC
** * * *
338730 TATGTGGATGAATAATTGTTTCGGCACTAAGTGTGCATTTCATGAAATTTATCA
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATCC
* * * *
338784 TATGTGGATGAATAATCGTTTCGGCACTAAGTGTGTATTTCA-CAGAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGA-AATTCATCC
* ** *
338838 TATGTCGATGAATAATAGTTTCGACACTAAGTGTGCATTTCA-CAGAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGA-AATTCATCC
* * *
338892 TATATGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCATGGAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATCC
*
338946 CATGTGGATGAATAACC
1 TATGTGGATGAATAACC
338963 ATTTTGGCAC
Statistics
Matches: 312, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 311 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATCC
Found at i:338994 original size:54 final size:54
Alignment explanation
Indices: 338881--338997 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 54
338871 TGCATTTCAC
* * * * ***
338881 AGAATTCATCCTATATGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCAT
1 AGAATTCATCCCATATGGATGAATAACCATTTCGGCACTAAGGGTACAAAACAT
* * * *
338935 GGAATTCATCCCATGTGGATGAATAACCATTTTGGCACTATGGGTACAAAACAT
1 AGAATTCATCCCATATGGATGAATAACCATTTCGGCACTAAGGGTACAAAACAT
338989 AGAATTCAT
1 AGAATTCAT
338998 AATATGTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (54 bp):
AGAATTCATCCCATATGGATGAATAACCATTTCGGCACTAAGGGTACAAAACAT
Found at i:344917 original size:11 final size:11
Alignment explanation
Indices: 344901--344935 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
344891 AAGCAATTAG
344901 AATCAAGAGAA
1 AATCAAGAGAA
*
344912 AATCAAGAGAG
1 AATCAAGAGAA
344923 AATCAAAGAGAA
1 AATC-AAGAGAA
344935 A
1 A
344936 GCATCAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.63, C:0.09, G:0.20, T:0.09
Consensus pattern (11 bp):
AATCAAGAGAA
Found at i:350449 original size:21 final size:22
Alignment explanation
Indices: 350419--350467 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
350409 AGGGAATAGA
350419 TCCCCCTTG-A-GGGAACCGAT
1 TCCCCCTTGAAGGGGAACCGAT
350439 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCC-TTGAAGGGGAACCGAT
350462 TCCCCC
1 TCCCCC
350468 CACAGGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.23
21 3 0.12
22 1 0.04
23 16 0.62
ACGTcount: A:0.18, C:0.39, G:0.22, T:0.20
Consensus pattern (22 bp):
TCCCCCTTGAAGGGGAACCGAT
Found at i:350488 original size:21 final size:21
Alignment explanation
Indices: 350450--350489 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
350440 CCCCCTTTGA
*
350450 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
* *
350471 AGGGGAATCGATAGCCCCC
1 AGGGGAACCGATACCCCCC
350490 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:358100 original size:12 final size:11
Alignment explanation
Indices: 358068--358101 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
358058 AAGCAATTAC
*
358068 AATCAATAGAG
1 AATCAAGAGAG
358079 AATCAAGAGAG
1 AATCAAGAGAG
358090 AATCAA-AGAG
1 AATCAAGAGAG
358100 AA
1 AA
358102 AGCATCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.59, C:0.09, G:0.21, T:0.12
Consensus pattern (11 bp):
AATCAAGAGAG
Found at i:360472 original size:215 final size:216
Alignment explanation
Indices: 360087--360516 Score: 630
Period size: 215 Copynumber: 2.0 Consensus size: 216
360077 TTACCAAATA
* *
360087 GGCACTAAGTGTGTATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTG
*
360152 TGCATTTCACAGAATTCATCCTAAATGGATGAATAACCGTTTCGGCACTAAGTGTACATTTCACG
66 TGCATTTCACAGAATTCATCCTAAATGGATGAATAACCGTTTCAGCACTAAGTGTACATTTCACG
* * * *
360217 GAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGTGTGCATTTCATGAAATTCATCCT
131 GAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGAAATTCATCCC
*
360282 ATGTGGATG-ATAATCGTTTC
196 ATGTGGATGAATAACCGTTTC
* * **
360302 GGCACTAAGTGTGCATTTCAC-ATAATTCTTCCTATTTGGATGAATAATTGTTTCGACACTAAGT
1 GGCACTAAGTGTGCATTTCACGA-AATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGT
* ** ** ** * **
360366 GTGCATTTCACGGAATTCATCCTATGTGGATGTCTAATTGTTTTAGCACTAAGTGTGTATTTCAC
65 GTGCATTTCACAGAATTCATCCTAAATGGATGAATAACCGTTTCAGCACTAAGTGTACATTTCAC
*
360431 GGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
130 GGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGAAATTCATCC
360496 CATGTGGATGAATAACCGTTT
195 CATGTGGATGAATAACCGTTT
360517 TAGCACTATA
Statistics
Matches: 190, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
214 1 0.01
215 180 0.95
216 9 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (216 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTG
TGCATTTCACAGAATTCATCCTAAATGGATGAATAACCGTTTCAGCACTAAGTGTACATTTCACG
GAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGAAATTCATCCC
ATGTGGATGAATAACCGTTTC
Found at i:360547 original size:54 final size:54
Alignment explanation
Indices: 360087--360516 Score: 619
Period size: 54 Copynumber: 8.0 Consensus size: 54
360077 TTACCAAATA
* *
360087 GGCACTAAGTGTGTATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* **
360141 GGCACTAAGTGTGCATTTCACAGAATTCATCCTAAATGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
360195 GGCACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
360249 GGCACTAAGTGTGCATTTCATGAAATTCATCCTATGTGGATG-ATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * * **
360302 GGCACTAAGTGTGCATTTCACATAATTCTTCCTATTTGGATGAATAATTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* ** ** *
360356 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGTCTAATTGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
360410 AGCACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
360464 GACACTAAGTGTGCATTTCACGGAATTCATCCCATGTGGATGAATAACCGTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTT
360517 TAGCACTATA
Statistics
Matches: 334, Mismatches: 41, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
53 46 0.14
54 288 0.86
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:362450 original size:24 final size:24
Alignment explanation
Indices: 362418--362476 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
362408 CAGTCGAAAC
* *
362418 TGCCGCGTAGAATTTGCACCAAAG
1 TGCCACGTAGAATATGCACCAAAG
*
362442 TGCCACGTAGAATATGCACCTAAG
1 TGCCACGTAGAATATGCACCAAAG
*
362466 TGCCACATAGA
1 TGCCACGTAGA
362477 GTTTTCCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.20
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCAAAG
Found at i:362499 original size:23 final size:23
Alignment explanation
Indices: 362481--362546 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
362471 CATAGAGTTT
362481 TCCCGAATGACCGCGTAGAATTG
1 TCCCGAATGACCGCGTAGAATTG
* * *
362504 TACCGAATGACCACATAGAATTG
1 TCCCGAATGACCGCGTAGAATTG
* *
362527 TCCCAAAGGACCGCGTAGAA
1 TCCCGAATGACCGCGTAGAA
362547 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (23 bp):
TCCCGAATGACCGCGTAGAATTG
Found at i:362679 original size:15 final size:15
Alignment explanation
Indices: 362648--362717 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
362638 AAGCATCATT
362648 TATTCACATA-AACCA
1 TATTCACATAGAA-CA
*
362663 TAATCACATAGAACA
1 TATTCACATAGAACA
* *
362678 TATTCATATAGATCA
1 TATTCACATAGAACA
* * *
362693 TTTTCACGTAGAATA
1 TATTCACATAGAACA
362708 TATTCACATA
1 TATTCACATA
362718 ATAGTAAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
15 41 0.95
16 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:362682 original size:30 final size:30
Alignment explanation
Indices: 362648--362718 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
362638 AAGCATCATT
362648 TATTCACATAAACCATAATCACATAGAACA
1 TATTCACATAAACCATAATCACATAGAACA
* * * ** * *
362678 TATTCATATAGATCATTTTCACGTAGAATA
1 TATTCACATAAACCATAATCACATAGAACA
362708 TATTCACATAA
1 TATTCACATAA
362719 TAGTAAAATC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (30 bp):
TATTCACATAAACCATAATCACATAGAACA
Found at i:365092 original size:53 final size:52
Alignment explanation
Indices: 364986--365104 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 52
364976 TTAGAATTAG
* ** * *
364986 ATTTATTATTTTATTATGAATTAAGATTGAGTTAAAACATTATTCTTAATTT
1 ATTTATTATTTTATTAGGAATTAAGATAAAATCAAAACATTATTCTTAATTT
* **
365038 ATTTATTATTATTATTAGGAATTATGATAAAATCAAAACATTA-TCTTTGGTTT
1 ATTTATTATT-TTATTAGGAATTAAGATAAAATCAAAACATTATTC-TTAATTT
365091 A-TTATTATTTTATT
1 ATTTATTATTTTATT
365105 CATTAGTTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
51 5 0.09
52 20 0.35
53 32 0.56
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (52 bp):
ATTTATTATTTTATTAGGAATTAAGATAAAATCAAAACATTATTCTTAATTT
Found at i:365497 original size:27 final size:27
Alignment explanation
Indices: 365467--365518 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
365457 GGATAAGTTA
*
365467 TTCTTATC-CTATTATTATTCTTATTTT
1 TTCTTATCTCTATT-TTATCCTTATTTT
*
365494 TTCTTATCTTTATTTTATCCTTATT
1 TTCTTATCTCTATTTTATCCTTATT
365519 GTCTTAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (27 bp):
TTCTTATCTCTATTTTATCCTTATTTT
Found at i:366436 original size:16 final size:16
Alignment explanation
Indices: 366407--366445 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
366397 GGTTTTCCAA
366407 ATTGTTTT-TGTTCTT
1 ATTGTTTTATGTTCTT
366422 ATTGTTTTATGTTCTT
1 ATTGTTTTATGTTCTT
366438 -TTGTTTTA
1 ATTGTTTTA
366446 CTCTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.10, C:0.05, G:0.13, T:0.72
Consensus pattern (16 bp):
ATTGTTTTATGTTCTT
Found at i:366454 original size:15 final size:15
Alignment explanation
Indices: 366408--366457 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
366398 GTTTTCCAAA
*
366408 TTGTTTT-TGTTCTT
1 TTGTTTTATCTTCTT
*
366422 ATTGTTTTATGTTCTT
1 -TTGTTTTATCTTCTT
366438 TTGTTTTACTCTT-TT
1 TTGTTTTA-TCTTCTT
366453 TTGTT
1 TTGTT
366458 ACTTTACATC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.06, C:0.08, G:0.12, T:0.74
Consensus pattern (15 bp):
TTGTTTTATCTTCTT
Found at i:366457 original size:23 final size:25
Alignment explanation
Indices: 366412--366462 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
366402 TCCAAATTGT
* *
366412 TTTTGTTCTTATTGTTTTATGTT-C
1 TTTTGTTCTTACTCTTTTATGTTAC
*
366436 TTTTGTT-TTACTCTTTTTTGTTAC
1 TTTTGTTCTTACTCTTTTATGTTAC
366460 TTT
1 TTT
366463 ACATCATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.73
Consensus pattern (25 bp):
TTTTGTTCTTACTCTTTTATGTTAC
Found at i:375049 original size:51 final size:51
Alignment explanation
Indices: 374986--375100 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
374976 AGAATTAGAT
* * * *
374986 TTATTATTTTATTATAAATTAAAATTGAGTTAAAACATTAT-TCTTAGTTTA
1 TTATTATTTTATTAGAAATTAAAATAGAATCAAAACATTATCT-TTAGTTTA
** *
375037 TTATTATTTTATTAGAAATTAGGATAGAATCAAAACGTTATCTTTAGTTTA
1 TTATTATTTTATTAGAAATTAAAATAGAATCAAAACATTATCTTTAGTTTA
375088 TTATTATTTTATT
1 TTATTATTTTATT
375101 CCTTAGTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (51 bp):
TTATTATTTTATTAGAAATTAAAATAGAATCAAAACATTATCTTTAGTTTA
Found at i:375412 original size:9 final size:9
Alignment explanation
Indices: 375393--375438 Score: 65
Period size: 9 Copynumber: 4.8 Consensus size: 9
375383 GGTATCTATC
375393 CATCAATCGT
1 CATC-ATCGT
375403 CATCATCGT
1 CATCATCGT
375412 CATCATCGT
1 CATCATCGT
375421 CATCATCGAAT
1 CATCATCG--T
375432 CATCATC
1 CATCATC
375439 ATTGAATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
9 22 0.65
10 4 0.12
11 8 0.24
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (9 bp):
CATCATCGT
Found at i:376087 original size:22 final size:22
Alignment explanation
Indices: 376046--376087 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
376036 CTTTACATAG
* *
376046 TGGTATCGATATTGTGAAACTC
1 TGGTATCGATATTATAAAACTC
376068 TGGTATCGATATTATAAAAC
1 TGGTATCGATATTATAAAAC
376088 CCTATTGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (22 bp):
TGGTATCGATATTATAAAACTC
Found at i:377934 original size:25 final size:27
Alignment explanation
Indices: 377887--377937 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
377877 TTAGATCATG
*
377887 AATTCCAAATATAAGAAATTGATTTTTA
1 AATTCCAAATAT-AGAAAATGATTTTTA
377915 AATT-CAAATAT-GAAAATGATTTT
1 AATTCCAAATATAGAAAATGATTTT
377938 ATTATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
27 7 0.32
28 4 0.18
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (27 bp):
AATTCCAAATATAGAAAATGATTTTTA
Found at i:380444 original size:3 final size:3
Alignment explanation
Indices: 380429--380472 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
380419 GGGTTATTTA
* *
380429 TAT TAT AAT TAT TAT TATT TAA TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT
380473 AACTACTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 30 0.86
4 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:384568 original size:21 final size:21
Alignment explanation
Indices: 384543--384582 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
384533 AAGACTTTAT
384543 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
384564 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
384583 AAATTGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:388435 original size:23 final size:22
Alignment explanation
Indices: 388401--388446 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
388391 GGAATTGATA
388401 CCCCCTTAAAGGGGAACCGATT
1 CCCCCTTAAAGGGGAACCGATT
*
388423 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-TTAAAGGGGAACCGATT
388446 C
1 C
388447 TGTAACATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
CCCCCTTAAAGGGGAACCGATT
Found at i:390150 original size:88 final size:90
Alignment explanation
Indices: 389979--390150 Score: 303
Period size: 90 Copynumber: 1.9 Consensus size: 90
389969 TAATCCCGAA
* *
389979 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
390044 TAGGGTAACTTGGATATAAGAGGAT
66 TAGGGTAACTTGGATATAAGAGGAT
390069 TATTAAATTCCAATTAATTAAATATAGATTTAATTAA-TTGAAATAATAAAA-CCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
*
390132 TAGGGTAACTTGGCTATAA
66 TAGGGTAACTTGGATATAA
390151 AAGGGTGTGT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 30 0.38
89 14 0.18
90 35 0.44
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
TAGGGTAACTTGGATATAAGAGGAT
Found at i:391440 original size:31 final size:31
Alignment explanation
Indices: 391402--391526 Score: 171
Period size: 31 Copynumber: 4.0 Consensus size: 31
391392 AGGGTCGAGG
* *
391402 GTTTACCTATGTTCTTTGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
391433 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
391464 ATTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
391495 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
391526 G
1 G
391527 GTCCTTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:392313 original size:23 final size:21
Alignment explanation
Indices: 392266--392313 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
392256 GAAGTGCTGT
**
392266 AGCAGGGAATCGGTACCCTGT
1 AGCAGGGAATCGGTACCCTCA
*
392287 AGCAGGGGAATCGGTTCCCCTCA
1 AGCA-GGGAATCGG-TACCCTCA
392310 AGCA
1 AGCA
392314 ATCTGGGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (21 bp):
AGCAGGGAATCGGTACCCTCA
Found at i:399376 original size:55 final size:55
Alignment explanation
Indices: 399324--399700 Score: 529
Period size: 55 Copynumber: 6.9 Consensus size: 55
399314 CGGATACGGT
* * * * *
399324 AATTCACAAACTCATTATGAATTACGTGGGGTTGTACACATAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
* * *
399379 AATTCATAAACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACAAA
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
*
399434 AATTCATAAACTCATTATGAATTTCGTGAGCTTGCACACATAGTGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
** * * ** *
399489 AATTCATAAACTCATTATGAATTTATTGAGGTTGTACACACAGTGTTAATACGGA
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
* *
399544 AATTCATAAACTCATTATGAATTTCTTGAGGTTGCACACATAGTGCCAATACAAA
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
* * *
399599 AATTCATAAACTCATTATGAATTTCGTGAGGCTGTACACATAGTGCCAATACAAA
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
* * * *
399654 AATTCATAAACTCATTATGAATTTCTTAAGGTTACACACACAGTGCC
1 AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCC
399701 CTTTCGGTAA
Statistics
Matches: 288, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 288 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (55 bp):
AATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACAGA
Found at i:399603 original size:165 final size:165
Alignment explanation
Indices: 399324--399700 Score: 605
Period size: 165 Copynumber: 2.3 Consensus size: 165
399314 CGGATACGGT
* * * *
399324 AATTCACAAACTCATTATGAA-TTACGTGGGGTTGTACACATAGTGCCAATACGGAAATTCATAA
1 AATTCATAAACTCATTATGAATTTA-TTGAGGTTGTACACACAGTGCCAATACGGAAATTCATAA
*
399388 ACTCATTATGAATTTCTTGGGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATG
65 ACTCATTATGAATTTCTTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATG
*
399453 AATTTCGTGA-GCTTGCACACATAGTGCCAATACAGA
130 AATTTCGTGAGGC-TGCACACATAGTGCCAATACAAA
**
399489 AATTCATAAACTCATTATGAATTTATTGAGGTTGTACACACAGTGTTAATACGGAAATTCATAAA
1 AATTCATAAACTCATTATGAATTTATTGAGGTTGTACACACAGTGCCAATACGGAAATTCATAAA
399554 CTCATTATGAATTTCTTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGA
66 CTCATTATGAATTTCTTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGA
*
399619 ATTTCGTGAGGCTGTACACATAGTGCCAATACAAA
131 ATTTCGTGAGGCTGCACACATAGTGCCAATACAAA
* * **
399654 AATTCATAAACTCATTATGAATTTCTTAAGGTTACACACACAGTGCC
1 AATTCATAAACTCATTATGAATTTATTGAGGTTGTACACACAGTGCC
399701 CTTTCGGTAA
Statistics
Matches: 195, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
165 190 0.97
166 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (165 bp):
AATTCATAAACTCATTATGAATTTATTGAGGTTGTACACACAGTGCCAATACGGAAATTCATAAA
CTCATTATGAATTTCTTGAGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGA
ATTTCGTGAGGCTGCACACATAGTGCCAATACAAA
Found at i:401191 original size:22 final size:22
Alignment explanation
Indices: 401165--401228 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
401155 CAGATTGCTC
* *
401165 AGAGGGAACTGATTCCCCCTTA
1 AGAGGGAACCGATTCCCCCTCA
*
401187 AGAGGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCTCA
* *
401209 AGGGGGTACCGATTCCCCCT
1 AGAGGGAACCGATTCCCCCT
401229 GAATGGTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.17
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCTCA
Found at i:407036 original size:22 final size:22
Alignment explanation
Indices: 407010--407090 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 22
407000 TTGGTGCAGA
407010 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
407032 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
*
407055 GGGAA-CTGATTCCCCCTT--AG
1 GGGAATC-GATACCCCCTTGAAG
407075 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
407091 CACAGGTTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
20 15 0.28
21 1 0.02
22 17 0.32
23 20 0.38
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:417772 original size:21 final size:20
Alignment explanation
Indices: 417744--417806 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
417734 CATTTTGGTG
417744 CAGAGGGAATCGATCCCCCC
1 CAGAGGGAATCGATCCCCCC
*
417764 CATGAGGGAACCGATTCCCCCC
1 CA-GAGGGAATCGA-TCCCCCC
417786 ACAG-GGGAATCGATACCCCCC
1 -CAGAGGGAATCGAT-CCCCCC
417807 TGGGGTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 3 0.08
21 24 0.65
22 8 0.22
23 2 0.05
ACGTcount: A:0.25, C:0.40, G:0.24, T:0.11
Consensus pattern (20 bp):
CAGAGGGAATCGATCCCCCC
Found at i:425669 original size:53 final size:53
Alignment explanation
Indices: 425585--425690 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
425575 TGAGTTGAAA
425585 ACCAAACCATACAGTCATGCTGTGGTCGAGATGAAATCGAGAAGACAAGTATT
1 ACCAAACCATACAGTCATGCTGTGGTCGAGATGAAATCGAGAAGACAAGTATT
* *
425638 ACCAAACCGTACAGTCATGCTGTGGTTGAGATGAAATCGAGAAGACAAGTATT
1 ACCAAACCATACAGTCATGCTGTGGTCGAGATGAAATCGAGAAGACAAGTATT
425691 TATTTTTGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (53 bp):
ACCAAACCATACAGTCATGCTGTGGTCGAGATGAAATCGAGAAGACAAGTATT
Found at i:431095 original size:20 final size:20
Alignment explanation
Indices: 431066--431103 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
431056 TTTCAAAGGG
431066 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
431086 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
431104 GAATATATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:431186 original size:65 final size:63
Alignment explanation
Indices: 431066--431272 Score: 213
Period size: 65 Copynumber: 3.2 Consensus size: 63
431056 TTTCAAAGGG
* * *
431066 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CAATGAATATATTGAAA-ATCGAATGCAGT
1 ATGCATCGATGCA-CAATCCATGCATCGATGCACTCAA-GATTTTA-TGAAACATCGAATGCA-T
431129 TT
62 TT
* * *
431131 ATGCATCGATGCACTATCCATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACAATCCATGCATCGATGCACTCAAGATTTTATG-AAACATCGAATGCATTT
* * * * *
431195 GATGCATCGATGCACAAGCCATGCATCGATGCGCTCAAGCTATTT-TGAAACATCGTATGTACTT
1 -ATGCATCGATGCACAATCCATGCATCGATGCACTCAAGAT-TTTATGAAACATCGAATGCA-TT
*
431259 C
63 T
431260 ATGCATCGATGCA
1 ATGCATCGATGCA
431273 ATCTTAGTGC
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 2 0.02
64 54 0.44
65 63 0.52
66 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAATCCATGCATCGATGCACTCAAGATTTTATGAAACATCGAATGCATTT
Found at i:431289 original size:129 final size:129
Alignment explanation
Indices: 431065--431299 Score: 289
Period size: 129 Copynumber: 1.8 Consensus size: 129
431055 TTTTCAAAGG
* *
431065 GATGCACCGATGCACCAATCCATGCATCGATGCACCAATGAATATATTGAAAATCGAATGCAGTT
1 GATGCACCGATGCACCAAGCCATGCATCGATGCACCAATGAATATATTGAAAATCGAATGCACTT
* * *
431130 TATGCATCGATGCACTATCCATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTT
66 CATGCATCGATGCAC-ATCCATGCACCGATGCACTAAGGGTTTTATGAAAACATCGAATGCATTT
* * * * * *
431195 GATGCATCGATGCA-CAAGCCATGCATCGATGCGCTCAA-G-CTATTTTGAAACATCGTATGTAC
1 GATGCACCGATGCACCAAGCCATGCATCGATGCAC-CAATGAATATATTGAAA-ATCGAATGCAC
*
431257 TTCATGCATCGATGCA-ATCTTAGTGCACCGATGCACTAAGGGT
64 TTCATGCATCGATGCACATC-CA-TGCACCGATGCACTAAGGGT
431300 CCAACTGTCG
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
127 3 0.03
128 10 0.11
129 60 0.67
130 16 0.18
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (129 bp):
GATGCACCGATGCACCAAGCCATGCATCGATGCACCAATGAATATATTGAAAATCGAATGCACTT
CATGCATCGATGCACATCCATGCACCGATGCACTAAGGGTTTTATGAAAACATCGAATGCATTT
Found at i:438721 original size:21 final size:21
Alignment explanation
Indices: 438679--438722 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
438669 ACTCCGGGAG
* *
438679 CTAGTTCTTCACGGGCTGCTC
1 CTAGCTCTTCACGGGCTCCTC
* *
438700 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGGGCTCCTC
438721 CT
1 CT
438723 TCGACACCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.39, G:0.18, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGGGCTCCTC
Found at i:439474 original size:18 final size:18
Alignment explanation
Indices: 439441--439475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
439431 AAGGGAAGTA
*
439441 ATTTCAAACTTGATTTTG
1 ATTTCAAAATTGATTTTG
*
439459 ATTTCAAAATTTATTTT
1 ATTTCAAAATTGATTTT
439476 CAAAGAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTCAAAATTGATTTTG
Found at i:439946 original size:64 final size:65
Alignment explanation
Indices: 439830--439952 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 65
439820 AATGCAGTTT
** * * *
439830 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGTATTTGATGCATCGATGCACAAGCC
1 ATGCATCGATGCACTCAGACTTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGCC
*
439895 ATGCATCGATGCACTCAGACTATTT-TG-AAACATCGTATGCACTTCATGCATCGATGCA
1 ATGCATCGATGCACTCAGACT-TTTATGAAAACATCGAATGCACTTCATGCATCGATGCA
439953 TTCTTAGTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 27 0.53
65 21 0.41
66 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGACTTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGCC
Found at i:443455 original size:25 final size:25
Alignment explanation
Indices: 443402--443457 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
443392 CCCATATGGC
* *
443402 GCAAATCTACAAGGCACATTTGAGT
1 GCAAATCTACAAGGAACATTTGAGG
*
443427 GCAATTCTACAAGGAAC-TTTCGAGG
1 GCAAATCTACAAGGAACATTT-GAGG
443452 GCAAAT
1 GCAAAT
443458 ATATTACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (25 bp):
GCAAATCTACAAGGAACATTTGAGG
Done.