Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold383
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: 1247277
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.21
Warning! 434286 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:928749 original size:20 final size:20
Alignment explanation
Indices: 928724--928771 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
928714 AAATAAAAAT
*
928724 TAAGATAAAGAGATACTAAG
1 TAAGATAAAGAGATAATAAG
928744 TAAGATAAAGAGATAATAAG
1 TAAGATAAAGAGATAATAAG
*
928764 TATGATAA
1 TAAGATAA
928772 TGATATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (20 bp):
TAAGATAAAGAGATAATAAG
Found at i:930915 original size:15 final size:14
Alignment explanation
Indices: 930895--930955 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 14
930885 AATTTAAATT
930895 TTATAATACATAATA
1 TTATAATA-ATAATA
930910 TTATAAT-ATAATA
1 TTATAATAATAATA
930923 TTA-AATAAT-ATAA
1 TTATAATAATAAT-A
930936 TTAATAATAATAGATA
1 TT-ATAATAATA-ATA
930952 TTAT
1 TTAT
930956 CATTTAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
12 5 0.12
13 14 0.35
14 1 0.03
15 15 0.38
16 3 0.08
17 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
TTATAATAATAATA
Found at i:931126 original size:17 final size:18
Alignment explanation
Indices: 931104--931140 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
931094 AATAAAATGA
*
931104 TTCAGCTATCA-GTTCTT
1 TTCAGCTACCATGTTCTT
931121 TTCAGCTACCATGTTCTT
1 TTCAGCTACCATGTTCTT
931139 TT
1 TT
931141 GCCAACTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (18 bp):
TTCAGCTACCATGTTCTT
Found at i:932265 original size:2 final size:2
Alignment explanation
Indices: 932258--932287 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
932248 CAGCCCTTGA
932258 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
932288 GGATCCACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:933511 original size:22 final size:21
Alignment explanation
Indices: 933467--933515 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
933457 CAACTCAAAC
*
933467 AAAAAAAAAAGGAAAAAGGAG
1 AAAAAAAAAAGGAAAAAGAAG
*
933488 AAGAAAAAAGAGTGAAAAA-AAG
1 AA-AAAAAAAAG-GAAAAAGAAG
933510 AAAAAA
1 AAAAAA
933516 CCAAATAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 12 0.50
23 6 0.25
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAGGAAAAAGAAG
Found at i:934875 original size:27 final size:28
Alignment explanation
Indices: 934828--934897 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
934818 TGTCACAAAA
934828 CTTTAAATTAAATAATTACATAATTTAC
1 CTTTAAATTAAATAATTACATAATTTAC
* *
934856 CTTTAACTT-AATATTTACATAATTTAC
1 CTTTAAATTAAATAATTACATAATTTAC
934883 CTTTAAATTATAATA
1 CTTTAAATTA-AATA
934898 TTTTTTATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 25 0.68
28 8 0.22
29 4 0.11
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (28 bp):
CTTTAAATTAAATAATTACATAATTTAC
Found at i:935039 original size:211 final size:211
Alignment explanation
Indices: 934675--935083 Score: 818
Period size: 211 Copynumber: 1.9 Consensus size: 211
934665 TATTTTTCAA
934675 TAAATTATAATATTTTTTATAGTTTTAAATAATTGTATAAAATATGTACGTATAATTATATATTG
1 TAAATTATAATATTTTTTATAGTTTTAAATAATTGTATAAAATATGTACGTATAATTATATATTG
934740 TATTTTACTTAGGTTGTGAGAAATAAATAGTTTACCTTGTAACTTTAAATTGATACATAGTTATG
66 TATTTTACTTAGGTTGTGAGAAATAAATAGTTTACCTTGTAACTTTAAATTGATACATAGTTATG
934805 GGAAATGAATAATTGTCACAAAACTTTAAATTAAATAATTACATAATTTACCTTTAACTTAATAT
131 GGAAATGAATAATTGTCACAAAACTTTAAATTAAATAATTACATAATTTACCTTTAACTTAATAT
934870 TTACATAATTTACCTT
196 TTACATAATTTACCTT
934886 TAAATTATAATATTTTTTATAGTTTTAAATAATTGTATAAAATATGTACGTATAATTATATATTG
1 TAAATTATAATATTTTTTATAGTTTTAAATAATTGTATAAAATATGTACGTATAATTATATATTG
934951 TATTTTACTTAGGTTGTGAGAAATAAATAGTTTACCTTGTAACTTTAAATTGATACATAGTTATG
66 TATTTTACTTAGGTTGTGAGAAATAAATAGTTTACCTTGTAACTTTAAATTGATACATAGTTATG
935016 GGAAATGAATAATTGTCACAAAACTTTAAATTAAATAATTACATAATTTACCTTTAACTTAATAT
131 GGAAATGAATAATTGTCACAAAACTTTAAATTAAATAATTACATAATTTACCTTTAACTTAATAT
935081 TTA
196 TTA
935084 TATATAATTT
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 198 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (211 bp):
TAAATTATAATATTTTTTATAGTTTTAAATAATTGTATAAAATATGTACGTATAATTATATATTG
TATTTTACTTAGGTTGTGAGAAATAAATAGTTTACCTTGTAACTTTAAATTGATACATAGTTATG
GGAAATGAATAATTGTCACAAAACTTTAAATTAAATAATTACATAATTTACCTTTAACTTAATAT
TTACATAATTTACCTT
Found at i:935106 original size:38 final size:37
Alignment explanation
Indices: 935050--935122 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
935040 TTTAAATTAA
* * *
935050 ATAATTACATAATTTACCTT-TAACTTAATATTTATAT
1 ATAATTAAATAATATACCTTCTAA-TTAATAATTATAT
935087 ATAATTTAAATAATATACCTTCTAATTAATAATTAT
1 ATAA-TTAAATAATATACCTTCTAATTAATAATTAT
935123 TTACGTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 4 0.13
38 24 0.77
39 3 0.10
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.47
Consensus pattern (37 bp):
ATAATTAAATAATATACCTTCTAATTAATAATTATAT
Found at i:936912 original size:13 final size:13
Alignment explanation
Indices: 936894--936923 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
936884 ACTTTTTACC
936894 ATGTATCGATACA
1 ATGTATCGATACA
*
936907 ATGTATTGATACA
1 ATGTATCGATACA
936920 ATGT
1 ATGT
936924 CCCTTGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:937013 original size:19 final size:19
Alignment explanation
Indices: 936968--937023 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
936958 CTGCCAGTTT
*
936968 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
936988 TATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
937007 CATGTATCGATACAATG
1 CATGTATCGATACAATG
937024 CATAATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:937033 original size:20 final size:19
Alignment explanation
Indices: 936969--937040 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
936959 TGCCAGTTTC
936969 ATGTATCGATACAATTGAGT-
1 ATGTATCGATACAA-TGA-TA
*
936989 ATGTATCGATATAATGA-A
1 ATGTATCGATACAATGATA
937007 CATGTATCGATACAATGCATA
1 -ATGTATCGATACAATG-ATA
*
937028 ATGTATTGATACA
1 ATGTATCGATACA
937041 TCTGGATATG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
19 18 0.40
20 26 0.58
21 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGATA
Found at i:938467 original size:13 final size:13
Alignment explanation
Indices: 938449--938474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
938439 ATATTTTTTG
938449 TGTATCGATACAT
1 TGTATCGATACAT
938462 TGTATCGATACAT
1 TGTATCGATACAT
938475 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:938485 original size:32 final size:33
Alignment explanation
Indices: 938428--938492 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
938418 TACAAGCCAA
938428 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
938462 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
938493 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:938486 original size:19 final size:19
Alignment explanation
Indices: 938428--938492 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
938418 TACAAGCCAA
938428 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
938449 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
938462 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
938481 TGTATCGATACA
1 TGTATCGATACA
938493 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:939412 original size:23 final size:21
Alignment explanation
Indices: 939379--939422 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
939369 TATTATAGAT
*
939379 TAAAACTCAAAGTACAATGCAAA
1 TAAAACACAAAGT-CAA-GCAAA
939402 TAAAACACAAAGTCAAGCAAA
1 TAAAACACAAAGTCAAGCAAA
939423 AACATTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.14
Consensus pattern (21 bp):
TAAAACACAAAGTCAAGCAAA
Found at i:940607 original size:20 final size:21
Alignment explanation
Indices: 940559--940601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
940549 GACTAGTGTG
* *
940559 GGGACTGCCTGGTTGTGACCT
1 GGGAGTGCCTGGTTGCGACCT
940580 GGGAGTGCC-GGTTGCGACCT
1 GGGAGTGCCTGGTTGCGACCT
940600 GG
1 GG
940602 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.09, C:0.23, G:0.44, T:0.23
Consensus pattern (21 bp):
GGGAGTGCCTGGTTGCGACCT
Found at i:941050 original size:13 final size:13
Alignment explanation
Indices: 941032--941056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
941022 ATAATCCCCC
941032 TGTATCGATACAG
1 TGTATCGATACAG
941045 TGTATCGATACA
1 TGTATCGATACA
941057 TTATATCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:945002 original size:21 final size:21
Alignment explanation
Indices: 944973--945017 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
944963 AAGTTTTTAT
*
944973 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
944993 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
945015 TTT
1 TTT
945018 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:946920 original size:32 final size:30
Alignment explanation
Indices: 946884--946942 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
946874 GAAATCAAAT
946884 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
946916 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
946943 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:947241 original size:13 final size:13
Alignment explanation
Indices: 947223--947248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
947213 ATATTTTTTG
947223 TGTATCGATACAT
1 TGTATCGATACAT
947236 TGTATCGATACAT
1 TGTATCGATACAT
947249 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:947259 original size:32 final size:33
Alignment explanation
Indices: 947202--947266 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
947192 TACAAGCCAA
947202 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
947236 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
947267 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:947260 original size:19 final size:19
Alignment explanation
Indices: 947202--947266 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
947192 TACAAGCCAA
947202 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
947223 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
947236 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
947255 TGTATCGATACA
1 TGTATCGATACA
947267 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:949524 original size:13 final size:13
Alignment explanation
Indices: 949506--949530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
949496 AATAGTAACC
949506 ATGTATCGATACA
1 ATGTATCGATACA
949519 ATGTATCGATAC
1 ATGTATCGATAC
949531 TTAGAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:950741 original size:13 final size:13
Alignment explanation
Indices: 950723--950752 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
950713 ACTTTTTACC
*
950723 ATGTATGGATACA
1 ATGTATCGATACA
950736 ATGTATCGATACA
1 ATGTATCGATACA
950749 ATGT
1 ATGT
950753 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:950823 original size:20 final size:20
Alignment explanation
Indices: 950797--950868 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
950787 TTGCCAATTT
* *
950797 CATGTATTGATACAATTGAG
1 CATGTATCGATACAATTGAA
* *
950817 TATGTATCAATACAA-TGAA
1 CATGTATCGATACAATTGAA
950836 CATGTATCGATACAA-TGCATA
1 CATGTATCGATACAATTG-A-A
950857 -ATGTATCGATAC
1 CATGTATCGATAC
950869 TTTCTAAGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 18 0.41
20 25 0.57
21 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:952193 original size:78 final size:78
Alignment explanation
Indices: 952096--952279 Score: 203
Period size: 78 Copynumber: 2.4 Consensus size: 78
952086 AAACTGAGTC
* * *
952096 TCTAGAGTCA-AGTGAGTATTTTCATGTCAATACATAT-TGATTAGGGTCATTTAGGTAATGGTA
1 TCTAGAGTCATA-TGGGTATTTTCATGTCAATACATATCT-ATTAGGGCCATTTAGGTAATAGTA
**
952159 CATTAAAATTAAGCTT
64 CATTAAAACCAAG-TT
* * * * *
952175 T-TAGGGTCATATGGGTATTTTCATGACAATTCATGTCTATTAGGGCCATTTAGGTAATAGTACT
1 TCTAGAGTCATATGGGTATTTTCATGTCAATACATATCTATTAGGGCCATTTAGGTAATAGTACA
*
952239 TTAAAACCGAGTT
66 TTAAAACCAAGTT
* *
952252 TCTAGAGTCATGTGGGTATTTTTATGTC
1 TCTAGAGTCATATGGGTATTTTCATGTC
952280 TACTAAGGTC
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
77 3 0.03
78 81 0.93
79 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (78 bp):
TCTAGAGTCATATGGGTATTTTCATGTCAATACATATCTATTAGGGCCATTTAGGTAATAGTACA
TTAAAACCAAGTT
Found at i:953394 original size:20 final size:20
Alignment explanation
Indices: 953347--953398 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
953337 ATAGCCAAAC
* **
953347 TTGTATCGATACACACAGTA
1 TTGTATCGATACACAAAAAA
953367 TT-TATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
953386 TTGTATCGATACA
1 TTGTATCGATACA
953399 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:953463 original size:20 final size:22
Alignment explanation
Indices: 953432--953475 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
953422 ACTATATTTT
953432 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
953453 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
953474 CA
1 CA
953476 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:958218 original size:13 final size:13
Alignment explanation
Indices: 958200--958225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
958190 TATACAAAGT
958200 ATGTATCGATACA
1 ATGTATCGATACA
958213 ATGTATCGATACA
1 ATGTATCGATACA
958226 CCATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:964428 original size:13 final size:13
Alignment explanation
Indices: 964410--964448 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
964400 ACATCATTCT
964410 TTGTATCGATACA
1 TTGTATCGATACA
*
964423 TTGTATGGATACA
1 TTGTATCGATACA
* *
964436 CTATATCGATACA
1 TTGTATCGATACA
964449 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:966253 original size:26 final size:26
Alignment explanation
Indices: 966222--966274 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
966212 CAAATAAATT
*
966222 TTTGATTAAGGGGAGAAAGAGATAAG
1 TTTGATTAAAGGGAGAAAGAGATAAG
966248 TTTGATTAAAGGGAGAAAGAGATAAG
1 TTTGATTAAAGGGAGAAAGAGATAAG
966274 T
1 T
966275 GCTTTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (26 bp):
TTTGATTAAAGGGAGAAAGAGATAAG
Found at i:966933 original size:13 final size:13
Alignment explanation
Indices: 966915--966939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
966905 ATGTTGCACA
966915 GTATCGATACATT
1 GTATCGATACATT
966928 GTATCGATACAT
1 GTATCGATACAT
966940 GTTGCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:966934 original size:33 final size:33
Alignment explanation
Indices: 966892--966957 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
966882 TACACATTTA
966892 ATTGTATCGATACATGTTGCACAGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
**
966925 ATTGTATCGATACATGTTGCATTGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
966958 TTGAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACATGTTGCACAGTATCGATAC
Found at i:974445 original size:18 final size:18
Alignment explanation
Indices: 974422--974460 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
974412 TCAATGAGAG
*
974422 AGAAAATAATTAAGATAA
1 AGAAAATAATGAAGATAA
**
974440 AGAAAATGGTGAAGATAA
1 AGAAAATAATGAAGATAA
974458 AGA
1 AGA
974461 GATGGTCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (18 bp):
AGAAAATAATGAAGATAA
Found at i:976506 original size:21 final size:20
Alignment explanation
Indices: 976477--976549 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
976467 TCTTTTTAAA
976477 ATTGATATCATTTTGAGCTT
1 ATTGATATCATTTTGAGCTT
*
976497 AATGACTATCATTTT-AGCTT
1 ATTGA-TATCATTTTGAGCTT
* *
976517 -TTGATATCCTTTTGAGTTT
1 ATTGATATCATTTTGAGCTT
976536 ATTGAATAT-ATTTT
1 ATTG-ATATCATTTT
976550 CTTATACATA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.18
19 7 0.16
20 16 0.36
21 13 0.30
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTGATATCATTTTGAGCTT
Found at i:978666 original size:13 final size:13
Alignment explanation
Indices: 978645--978675 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
978635 CGATACATGG
*
978645 TACAATGTATCGA
1 TACATTGTATCGA
978658 TACATTGTATCGA
1 TACATTGTATCGA
978671 TACAT
1 TACAT
978676 ACATTGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:984875 original size:33 final size:33
Alignment explanation
Indices: 984829--984937 Score: 200
Period size: 33 Copynumber: 3.3 Consensus size: 33
984819 AACCCAGATG
* *
984829 TATCGATATAATATTTCTTGTATCGATACACTA
1 TATCGATACAATATTTATTGTATCGATACACTA
984862 TATCGATACAATATTTATTGTATCGATACACTA
1 TATCGATACAATATTTATTGTATCGATACACTA
984895 TATCGATACAATATTTATTGTATCGATACACTA
1 TATCGATACAATATTTATTGTATCGATACACTA
984928 TATCGATACA
1 TATCGATACA
984938 TTGTATCGGT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (33 bp):
TATCGATACAATATTTATTGTATCGATACACTA
Found at i:984887 original size:20 final size:20
Alignment explanation
Indices: 984862--984924 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
984852 CGATACACTA
984862 TATCGATACAATATTTATTG
1 TATCGATACAATATTTATTG
*
984882 TATCGATAC---A-CTA---
1 TATCGATACAATATTTATTG
984895 TATCGATACAATATTTATTG
1 TATCGATACAATATTTATTG
984915 TATCGATACA
1 TATCGATACA
984925 CTATATCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
13 9 0.26
16 3 0.09
17 3 0.09
20 19 0.56
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACAATATTTATTG
Found at i:984944 original size:13 final size:13
Alignment explanation
Indices: 984911--984945 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
984901 TACAATATTT
984911 ATTGTATCGATAC
1 ATTGTATCGATAC
* *
984924 ACTATATCGATAC
1 ATTGTATCGATAC
984937 ATTGTATCG
1 ATTGTATCG
984946 GTACTATTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:985088 original size:22 final size:20
Alignment explanation
Indices: 985063--985110 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
985053 AAATTTTTTA
985063 AAAAT-TTCCACTTTTTCACTT
1 AAAATCTTCCA-TTTTTCA-TT
*
985084 CAAAATCTTTCATTTTTCATT
1 -AAAATCTTCCATTTTTCATT
985105 AAAATC
1 AAAATC
985111 ATCAACAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 2 0.08
22 12 0.50
23 4 0.17
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATCTTCCATTTTTCATT
Found at i:985418 original size:21 final size:21
Alignment explanation
Indices: 985377--985415 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
985367 CTAGGCAACC
* *
985377 CTCTCCAGGTCGCGATCGGCA
1 CTCTCCAGGTCGCAACCGGCA
985398 CTCT-CAGGTCGCAACCGG
1 CTCTCCAGGTCGCAACCGG
985416 GCAGCCCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.18
Consensus pattern (21 bp):
CTCTCCAGGTCGCAACCGGCA
Found at i:987489 original size:13 final size:13
Alignment explanation
Indices: 987468--987531 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
987458 CGATACATGG
*
987468 TACAATGTATCGA
1 TACATTGTATCGA
*
987481 TACATTGTATTGA
1 TACATTGTATCGA
987494 TACA-TG-AT-G-
1 TACATTGTATCGA
987503 -A-ATTGTATCGA
1 TACATTGTATCGA
*
987514 TACAATGTATCGA
1 TACATTGTATCGA
987527 TACAT
1 TACAT
987532 GATGCTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
7 1 0.02
8 3 0.07
9 2 0.05
10 2 0.05
11 2 0.05
12 3 0.07
13 28 0.68
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:987496 original size:33 final size:33
Alignment explanation
Indices: 987452--987535 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
987442 CTACCACTGT
*
987452 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
* *
987485 TTGTATTGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
*
987518 ATGTATCGATACATGATG
1 TTGTATCGATACATGATG
987536 CTTGTAACGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
33 44 0.98
34 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:993178 original size:41 final size:41
Alignment explanation
Indices: 993130--993213 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
993120 GAAAGATGAA
993130 TATTGTGAGGACGAATAAGAAGCATTTCTCAAATGAAAATT
1 TATTGTGAGGACGAATAAGAAGCATTTCTCAAATGAAAATT
*
993171 TATTGTGAGGACGAATGAGAAGCATTTCTCAAATGAAAATT
1 TATTGTGAGGACGAATAAGAAGCATTTCTCAAATGAAAATT
993212 TA
1 TA
993214 GAAGAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (41 bp):
TATTGTGAGGACGAATAAGAAGCATTTCTCAAATGAAAATT
Found at i:993959 original size:23 final size:23
Alignment explanation
Indices: 993903--993985 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
993893 AAATTATTAA
*
993903 TTTATATTATATAAAT-TTAATAT
1 TTTATATTATATTAATATTAAT-T
*
993926 TTT-TATAATATTAATATTAATT
1 TTTATATTATATTAATATTAATT
* *
993948 TTTATATTATATT-TTATTATTT
1 TTTATATTATATTAATATTAATT
993970 TATTATAATTA-ATTAA
1 T-TTAT-ATTATATTAA
993986 ACACTTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 22 0.45
23 23 0.47
24 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATATTATATTAATATTAATT
Found at i:993984 original size:18 final size:19
Alignment explanation
Indices: 993941--993984 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
993931 TAATATTAAT
993941 ATTAATT-TTTATATTATA
1 ATTAATTATTTATATTATA
* *
993959 TTTTATTATTT-TATTATA
1 ATTAATTATTTATATTATA
993977 ATTAATTA
1 ATTAATTA
993985 AACACTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTAATTATTTATATTATA
Found at i:994905 original size:26 final size:25
Alignment explanation
Indices: 994876--994933 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
994866 CATTATTTTC
*
994876 TAATTTGATAAAAATAATATATTAAA
1 TAATTTGATAAAAATAATA-ATAAAA
** *
994902 TAATTTTTTTAAATATAATAATAAAA
1 TAA-TTTGATAAAAATAATAATAAAA
994928 TAATTT
1 TAATTT
994934 TTAATTGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 3 0.11
26 11 0.41
27 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATTTGATAAAAATAATAATAAAA
Found at i:994935 original size:26 final size:27
Alignment explanation
Indices: 994884--994935 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
994874 TCTAATTTGA
*
994884 TAAAAATAATATATTAAATAATTTTTT
1 TAAAAATAATATATAAAATAATTTTTT
*
994911 TAAATATAATA-ATAAAATAATTTTT
1 TAAAAATAATATATAAAATAATTTTT
994936 AATTGATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAAATAATATATAAAATAATTTTTT
Found at i:996644 original size:48 final size:49
Alignment explanation
Indices: 996583--996675 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 49
996573 AATTTCATGG
*
996583 TTATTGTAAAGAATATTACGCAATAATTATACAATGTCAAACCTTTAGA
1 TTATTGTAAAGAATATTACACAATAATTATACAATGTCAAACCTTTAGA
* * *
996632 TTATT-TACAGAATATTACACAATATTTATATAATGTCAAACCTT
1 TTATTGTAAAGAATATTACACAATAATTATACAATGTCAAACCTT
996676 CTAATATTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 35 0.88
49 5 0.12
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.38
Consensus pattern (49 bp):
TTATTGTAAAGAATATTACACAATAATTATACAATGTCAAACCTTTAGA
Found at i:1003757 original size:70 final size:71
Alignment explanation
Indices: 1003631--1003768 Score: 233
Period size: 70 Copynumber: 2.0 Consensus size: 71
1003621 AAAGTCACAT
*
1003631 TTTTTACCCAGATGTATCGATATATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
1003696 TCTGTC
66 TCTGTC
* * *
1003702 TTTTTACTCAGATTTATCGATACATTTTT-AATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
1003766 TCT
66 TCT
1003769 TCAATGTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 37 0.59
71 26 0.41
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
TCTGTC
Found at i:1003774 original size:20 final size:19
Alignment explanation
Indices: 1003642--1003869 Score: 94
Period size: 20 Copynumber: 11.4 Consensus size: 19
1003632 TTTTACCCAG
*
1003642 ATGTATCGATATATTTTTCA
1 ATGTATCGATACA-TTTTCA
*
1003662 ATGTATCGATACATGTATCA
1 ATGTATCGATACAT-TTTCA
1003682 ATGTATCGATACA--TTC-
1 ATGTATCGATACATTTTCA
* ***
1003698 -TGTCTTTTTAC----TCA
1 ATGTATCGATACATTTTCA
* *
1003712 GATTTATCGATACATTTTTA
1 -ATGTATCGATACATTTTCA
* *
1003732 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTCA
1003752 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATT-TTCA
* *
1003772 ATGTATTGGTATATTCTGTCTTTTTACCCA
1 ATGTA-TCG-ATA------CATTTT---CA
1003802 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACA-TTTTCA
* *
1003823 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTCA
1003843 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATT-TTCA
1003863 ATGTATC
1 ATGTATC
1003870 TACATTCATA
Statistics
Matches: 157, Mismatches: 26, Indels: 50
0.67 0.11 0.21
Matches are distributed among these distances:
13 2 0.01
15 7 0.04
16 6 0.04
17 2 0.01
19 17 0.11
20 94 0.60
21 4 0.03
22 3 0.02
23 1 0.01
24 4 0.03
27 2 0.01
28 3 0.02
29 3 0.02
30 4 0.03
31 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:1003795 original size:90 final size:91
Alignment explanation
Indices: 1003642--1003876 Score: 343
Period size: 90 Copynumber: 2.6 Consensus size: 91
1003632 TTTTACCCAG
* * * * *
1003642 ATGTATCGATATATTTTTCAATGTATCGATACATGT-ATCAATGTATCGATACATTCTGTCTTTT
1 ATGTATCGATACATGTATGAATGTATCGATACAT-TCTTCAATGTATCGATACATTCTGTCTTTT
* *
1003706 TACTCAGATTTATCGATACATTTTT-A
65 TACCCAGATGTATCGATACATTTTTCA
* * *
1003732 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATTGGTATATTCTGTCTTTTT
1 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTT
1003797 ACCCAGATGTATCGATACATTTTTCA
66 ACCCAGATGTATCGATACATTTTTCA
1003823 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATC--TACATTC
1 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTC
1003877 ATACATGTAT
Statistics
Matches: 131, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
89 7 0.05
90 77 0.59
91 47 0.36
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (91 bp):
ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTT
ACCCAGATGTATCGATACATTTTTCA
Found at i:1003819 original size:24 final size:20
Alignment explanation
Indices: 1003803--1003869 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1003793 TTTTACCCAG
1003803 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1003823 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1003843 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1003863 ATGTATC
1 ATGTATC
1003870 TACATTCATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1003885 original size:38 final size:39
Alignment explanation
Indices: 1003803--1003897 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
1003793 TTTTACCCAG
*
1003803 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATC-ATACATGTATGA
1003843 ATGTATCGATACATTCTTCAATGTATC-TACAT-TCAT-A
1 ATGTATCGATACATTCTTCAATGTATCATACATGT-ATGA
*
1003880 CATGTATCGATACGTTCT
1 -ATGTATCGATACATTCT
1003898 GTCTTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
37 2 0.04
38 23 0.45
40 26 0.51
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATGTATCATACATGTATGA
Found at i:1003912 original size:109 final size:109
Alignment explanation
Indices: 1003716--1003945 Score: 295
Period size: 109 Copynumber: 2.1 Consensus size: 109
1003706 TACTCAGATT
* * * * * *
1003716 TATCGATACATTTTTAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATTGG
1 TATCGATACATTATGAATGTATCGATACATGTATCAATGTATC-ATACATTCTACAATGTATCGA
*
1003781 TATATTCTGTCTTTTTACCCAGATGTATCGATACATTTTTCAATG
65 TACATTCTGTCTTTTTACCCAGATGTATCGATACATTTTTCAATG
*
1003826 TATCGATACATGTATGAATGTATCGATACAT-TCTTCAATGTATC-TACATTCATAC-ATGTATC
1 TATCGATACAT-TATGAATGTATCGATACATGT-ATCAATGTATCATACATTC-TACAATGTATC
* ** *
1003888 GATACGTTCTGTCTTTTTTTCCAGATGTATCGATATATTTTTCAATG
63 GATACATTCTGTCTTTTTACCCAGATGTATCGATACATTTTTCAATG
1003935 TATCGATACAT
1 TATCGATACAT
1003946 ATAGTTAAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
109 65 0.62
110 14 0.13
111 26 0.25
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (109 bp):
TATCGATACATTATGAATGTATCGATACATGTATCAATGTATCATACATTCTACAATGTATCGAT
ACATTCTGTCTTTTTACCCAGATGTATCGATACATTTTTCAATG
Found at i:1003947 original size:22 final size:22
Alignment explanation
Indices: 1003903--1003942 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1003893 GTTCTGTCTT
1003903 TTTTTCCAGATGTATCGATATA
1 TTTTTCCAGATGTATCGATATA
1003925 TTTTT-CA-ATGTATCGATA
1 TTTTTCCAGATGTATCGATA
1003943 CATATAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 2 0.11
22 5 0.28
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (22 bp):
TTTTTCCAGATGTATCGATATA
Found at i:1017869 original size:16 final size:15
Alignment explanation
Indices: 1017844--1017879 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1017834 TTCGTACCCC
*
1017844 AAAAAAACAAAGAAA
1 AAAAAAACAAACAAA
1017859 AAAACAAACAAACAAA
1 AAAA-AAACAAACAAA
1017875 AAAAA
1 AAAAA
1017880 GGGGTCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAACAAA
Found at i:1019058 original size:13 final size:13
Alignment explanation
Indices: 1019040--1019064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1019030 ATAATGCACA
1019040 GTATCGATACATT
1 GTATCGATACATT
1019053 GTATCGATACAT
1 GTATCGATACAT
1019065 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1019171 original size:13 final size:13
Alignment explanation
Indices: 1019153--1019201 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
1019143 ACATACAAGA
1019153 TGTATCGATACAT
1 TGTATCGATACAT
1019166 TGTATCGATACA-
1 TGTATCGATACAT
*
1019178 TG-A-CCA-A-AT
1 TGTATCGATACAT
1019187 TGTATCGATACAT
1 TGTATCGATACAT
1019200 TG
1 TG
1019202 GCTTGTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 3 0.10
11 3 0.10
12 3 0.10
13 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1019196 original size:34 final size:32
Alignment explanation
Indices: 1019133--1019201 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1019123 CCTTAACTGT
1019133 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1019165 TTGTATCGATACATGACCAA-ATTGTATCGATACA
1 TTGTATCGATACAT-A-CAAGA-TGTATCGATACA
1019199 TTG
1 TTG
1019202 GCTTGTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 2 0.06
34 18 0.53
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1021678 original size:50 final size:50
Alignment explanation
Indices: 1021603--1021702 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1021593 TTTGTTAAGC
1021603 ATAATCCACATTTTAATGCCTCATATGTGTGTTCATTGTGTCATAAACAT
1 ATAATCCACATTTTAATGCCTCATATGTGTGTTCATTGTGTCATAAACAT
1021653 ATAATCCACATTTTAATGCCTCATATGTGTGTTCATTGTGTCATAAACAT
1 ATAATCCACATTTTAATGCCTCATATGTGTGTTCATTGTGTCATAAACAT
1021703 GGTCACACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (50 bp):
ATAATCCACATTTTAATGCCTCATATGTGTGTTCATTGTGTCATAAACAT
Found at i:1027298 original size:22 final size:23
Alignment explanation
Indices: 1027266--1027313 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
1027256 ATGATTAAAG
1027266 GAAATTGTTTT-ATTAAGGGGGA
1 GAAATTGTTTTGATTAAGGGGGA
*
1027288 GAAATTTTTTTGGATTAAGGGGGA
1 GAAATTGTTTT-GATTAAGGGGGA
1027312 GA
1 GA
1027314 GAAAAGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.35
Consensus pattern (23 bp):
GAAATTGTTTTGATTAAGGGGGA
Found at i:1028526 original size:28 final size:28
Alignment explanation
Indices: 1028494--1029004 Score: 329
Period size: 28 Copynumber: 17.7 Consensus size: 28
1028484 CTAAAATGTT
* *
1028494 CATCTCTTCAAAGCCCACAGGTTAGTGG
1 CATCTCTTCAAAGCCCACAAGTCAGTGG
* *
1028522 CATCTTTTCAAAGCCCACAAGTCGGTGG
1 CATCTCTTCAAAGCCCACAAGTCAGTGG
* *
1028550 CAACTCTTTTTAAAGCCCACAAGTCAGTGG
1 C-A-TCTCTTCAAAGCCCACAAGTCAGTGG
* *
1028580 CATCTCTTCAAAAGACCACAAGTTAGTGG
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
*
1028609 CATC-CTTTCAAAGCCCACAAGTCGGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
* *
1028637 CA-CCCTTTCAAAGCCCACACAAGTCGGTGG
1 CATCTC-TTCAAAG-CC-CACAAGTCAGTGG
* * * * **
1028667 CAACTTTTTTCAAAGTCCAC-AGTTTAGTAA
1 C-A-TCTCTTCAAAGCCCACAAG-TCAGTGG
*
1028697 CATCTCTTCAAAAGCCCACAAGTTAGTGG
1 CATCTCTTC-AAAGCCCACAAGTCAGTGG
* * *
1028726 CA-CATTTTCAAAGCCCACACAAATCGGTGG
1 CATC-TCTTCAAAG-CC-CACAAGTCAGTGG
* *
1028756 TAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 -CA-TCTCTTCAAAGCCCACAAGTCAGTGG
* * *
1028786 CATCTCTTCAAAGCCTACATAAATCAGTGA
1 CATCTCTTCAAAGCC--CACAAGTCAGTGG
* * * * *
1028816 CA-CCCTTCCAAAGTCCACAAATTAGTGA
1 CATCTCTT-CAAAGCCCACAAGTCAGTGG
* * *
1028844 CACCTTTTCAAAGCCCACAAGTCAATGG
1 CATCTCTTCAAAGCCCACAAGTCAGTGG
* * *
1028872 CA-CCCTTTCAAAGCTCACAAGTTAGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
*
1028900 CA-CCCTTCCAAAGCCCACAAGTCAGTGG
1 CATCTCTT-CAAAGCCCACAAGTCAGTGG
* * * *
1028928 TA-CCCTTTCACAGCTCACAAGTCAGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
* *
1028956 TA-CCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTC-TTCAAAGCCCACAAGTCAGTGG
*
1028984 CATCCCCTTTCAAAGCCCACA
1 CAT-CTC-TTCAAAGCCCACA
1029005 CAAGTCGGTG
Statistics
Matches: 393, Mismatches: 62, Indels: 54
0.77 0.12 0.11
Matches are distributed among these distances:
27 4 0.01
28 201 0.51
29 62 0.16
30 104 0.26
31 5 0.01
32 16 0.04
33 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
CATCTCTTCAAAGCCCACAAGTCAGTGG
Found at i:1028891 original size:56 final size:56
Alignment explanation
Indices: 1028500--1029004 Score: 415
Period size: 56 Copynumber: 8.7 Consensus size: 56
1028490 TGTTCATCTC
* * * * *
1028500 TTCAAAGCCCACAGGTTAGTGGCATCTTTTCAAAGCCCACAAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-AC-CTT
* * * *
1028558 TTTAAAGCCCACAAGTCAGTGGCA-TCTCTTCAAAAGACCACAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCA-CCTT
* * *
1028615 TTCAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-AC-CTT
* * ** * * *
1028675 TTCAAAGTCCAC-AGTTTAGTAACA-TCTCTTCAAAAGCCCACAAGTTAGTGGCACATT
1 TTCAAAGCCCACAAG-TCAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCACCTT
* * * * * *
1028732 TTCAAAGCCCACACAAATCGGTGGTAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTC
1 TTCAAAG-CC-CACAAGTCAGTGG-CAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * * * * * * *
1028792 TTCAAAGCCTACATAAATCAGTGACACCCTTCCAAAGTCCACAAATTAGTGACACCTT
1 TTCAAAGCC--CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * * *
1028850 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCTCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
* * * * * *
1028906 TCCAAAGCCCACAAGTCAGTGGTACCCTTTCACAGCTCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
1028962 TTCAAAGCCCACAAGTCAGTGGCATCCCCTTTCAAAGCCCACA
1 TTCAAAGCCCACAAGTCAGTGGCA--CCCTTTCAAAGCCCACA
1029005 CAAGTCGGTG
Statistics
Matches: 357, Mismatches: 69, Indels: 42
0.76 0.15 0.09
Matches are distributed among these distances:
56 113 0.32
57 37 0.10
58 91 0.25
59 45 0.13
60 63 0.18
61 7 0.02
62 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:1028961 original size:84 final size:84
Alignment explanation
Indices: 1028500--1029004 Score: 395
Period size: 84 Copynumber: 5.8 Consensus size: 84
1028490 TGTTCATCTC
* * * * * * **
1028500 TTCAAAGCCCACAGGTTAGTGGCATCTTTTCAAAGCCCACAAGTCGGTGGCAACTCTTTTTAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-AC-CCTTCCAAAG
* * * *
1028565 CCCACAAGTCAGTGGCATCTC
64 CCCACAAATCAGTGGTACCTT
* * * * *
1028586 TTCAAAAGACCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGC
1 TTC-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGC
* * *
1028651 CCACACAAGTCGGTGGCAACTTTT
65 CCACA-AA-TCAGTGG-TAC-CTT
* * ** * * ** *
1028675 TTCAAAGTCCAC-AGTTTAGTAACA-TCTCTTCAAAAGCCCACAAGTTAGTGGCACATTTTCAAA
1 TTCAAAGCCCACAAG-TCAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCACCCTTCCAAA
*
1028738 GCCCACACAAATCGGTGGTAACTCTT
63 G-CC-CACAAATCAGTGGT-AC-CTT
* * * *
1028764 TTCAAAGCCCACAAGTCAGTGGCA-TCTCTTCAAAGCCTACATAAATCAGTGACACCCTTCCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACCCT-TTCAAAGCC--CACAAGTCAGTGGCACCCTTCCAAA
* * **
1028828 GTCCACAAATTAGTGACACCTT
63 GCCCACAAATCAGTGGTACCTT
* * *
1028850 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCTCACAAGTTAGTGGCACCCTTCCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGCC
* *
1028915 CACAAGTCAGTGGTACCCT
66 CACAAATCAGTGGTACCTT
* * * *
1028934 TTCACAGCTCACAAGTCAGTGGTACCCTTTCAAAGCCCACAAGTCAGTGGCATCCCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA--CCCTTCCAAAG
1028999 CCCACA
64 CCCACA
1029005 CAAGTCGGTG
Statistics
Matches: 345, Mismatches: 57, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
84 83 0.24
85 14 0.04
86 56 0.16
87 59 0.17
88 35 0.10
89 69 0.20
90 25 0.07
91 4 0.01
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGCC
CACAAATCAGTGGTACCTT
Found at i:1029168 original size:45 final size:46
Alignment explanation
Indices: 1029119--1029279 Score: 144
Period size: 48 Copynumber: 3.4 Consensus size: 46
1029109 AAGTCCGATA
* * *
1029119 TCGCTGGCATTGAATCAGCATATTGGCACCTTT-ATTAGGTCAATG
1 TCGCTGGCCTTGAATCAGCATATTGCCACCTTTCATTAGCTCAATG
* * * * *
1029164 TCGCTAGCCTTGAATCAGCACATTATCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCATATT-GCCACCTTT-CATTAGCTCAATG
* * * *
1029212 TTGCTGGCCTTGAATCAGCATATTGTCCACTTTTCCCTTAGCTCGATG
1 TCGCTGGCCTTGAATCAGCATATTG-CCACCTTT-CATTAGCTCAATG
* * *
1029260 TTGTTGGCCTTGAATTAGCA
1 TCGCTGGCCTTGAATCAGCA
1029280 CAATGACACT
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
45 21 0.22
46 6 0.06
48 70 0.72
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCATATTGCCACCTTTCATTAGCTCAATG
Found at i:1029222 original size:48 final size:48
Alignment explanation
Indices: 1029153--1029281 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
1029143 GGCACCTTTA
* * *
1029153 TTAGGTCAATGTCGCTAGCCTTGAATCAGCACATTATCCACTTTTCCC
1 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
* *
1029201 TTAGCTCAATGTTGCTGGCCTTGAATCAGCATATTGTCCACTTTTCCC
1 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
* * *
1029249 TTAGCTCGATGTTGTTGGCCTTGAATTAGCACA
1 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACA
1029282 ATGACACTCC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (48 bp):
TTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
Found at i:1030016 original size:20 final size:20
Alignment explanation
Indices: 1029991--1030061 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1029981 TTTTACCCAG
1029991 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
1030011 ATGTATCAATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
1030031 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
**
1030051 ACATATCGATA
1 ATGTATCGATA
1030062 TGTTCTATCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1035181 original size:13 final size:13
Alignment explanation
Indices: 1035163--1035188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1035153 ACATTTCTTC
1035163 ATGTATCGATACA
1 ATGTATCGATACA
1035176 ATGTATCGATACA
1 ATGTATCGATACA
1035189 TAGCTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1035293 original size:13 final size:13
Alignment explanation
Indices: 1035275--1035301 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1035265 CAATTTGTCC
1035275 ATGTATCGATACA
1 ATGTATCGATACA
1035288 ATGTATCGATACA
1 ATGTATCGATACA
1035301 A
1 A
1035302 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1035886 original size:18 final size:18
Alignment explanation
Indices: 1035863--1035916 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1035853 TATTCTCCCC
1035863 CTTAAATGATTATCTTCT
1 CTTAAATGATTATCTTCT
** * * *
1035881 CTTAAAAAATTCTC-CCC
1 CTTAAATGATTATCTTCT
1035898 CTTAAATGATTATCTTCT
1 CTTAAATGATTATCTTCT
1035916 C
1 C
1035917 CTCTTTTTAT
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.43
Consensus pattern (18 bp):
CTTAAATGATTATCTTCT
Found at i:1035900 original size:35 final size:37
Alignment explanation
Indices: 1035838--1035916 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 37
1035828 TTTTCGTTTT
*
1035838 TCTTCCCTTAAAAAATATTCTCCCCCTTAAATGATTA
1 TCTTCTCTTAAAAAATATTCTCCCCCTTAAATGATTA
1035875 TCTTCTCTT-AAAAA-ATTCTCCCCCTTAAATGATTA
1 TCTTCTCTTAAAAAATATTCTCCCCCTTAAATGATTA
1035910 TCTTCTC
1 TCTTCTC
1035917 CTCTTTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 28 0.68
36 5 0.12
37 8 0.20
ACGTcount: A:0.29, C:0.28, G:0.03, T:0.41
Consensus pattern (37 bp):
TCTTCTCTTAAAAAATATTCTCCCCCTTAAATGATTA
Found at i:1046247 original size:52 final size:52
Alignment explanation
Indices: 1046099--1046227 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1046089 CGAAATATGA
*
1046099 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1046151 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
*
1046203 AAATTTGCCTGCATGTATTGATACA
1 AAATTTGCCTGCATGTATCGATACA
1046228 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
Found at i:1046254 original size:13 final size:13
Alignment explanation
Indices: 1046236--1046261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1046226 CAAAGATCAG
1046236 TGTATCGATACAA
1 TGTATCGATACAA
1046249 TGTATCGATACAA
1 TGTATCGATACAA
1046262 CACTTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1047037 original size:52 final size:51
Alignment explanation
Indices: 1046963--1047109 Score: 184
Period size: 43 Copynumber: 3.0 Consensus size: 51
1046953 AAGATGAGAA
* * *
1046963 AAAAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
1047015 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T-
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1047059 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1047109 A
1 A
1047110 TGAGGATGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
43 39 0.49
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 37 0.46
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (51 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:1047210 original size:55 final size:53
Alignment explanation
Indices: 1047144--1047372 Score: 186
Period size: 49 Copynumber: 4.6 Consensus size: 53
1047134 CCAATACGTC
* * * * *
1047144 GATTCACGGCCAACGATATTGGGT-TTAAAGATGAGAAAAAGGATGTCAATGTGCT
1 GATTCAAGGCCAACTATATTGGATCTTAAAGATG-G-AAAAGG-TGCCAATATGCT
* * *
1047199 GATTCAAGGCCAGCTACATT-GATCTTAAAGATGGAAAATGTGCCAATATGCT
1 GATTCAAGGCCAACTATATTGGATCTTAAAGATGGAAAAGGTGCCAATATGCT
*
1047251 GATTCAAGGCCAACTATATTGGA-C-T-----T---AAAGGTGCCAATGTGCT
1 GATTCAAGGCCAACTATATTGGATCTTAAAGATGGAAAAGGTGCCAATATGCT
* * *
1047294 GATTCAAGGCCAGCTACATTAGA-CTTAAAGAT-G--AAGGTGCCAATATGCT
1 GATTCAAGGCCAACTATATTGGATCTTAAAGATGGAAAAGGTGCCAATATGCT
* *
1047343 GACTCAAGGCCAGCTATATTGGA-CTTAAAG
1 GATTCAAGGCCAACTATATTGGATCTTAAAG
1047373 GTGCCAATGT
Statistics
Matches: 146, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
43 36 0.25
44 1 0.01
46 1 0.01
49 43 0.29
51 1 0.01
52 29 0.20
53 7 0.05
54 3 0.02
55 25 0.17
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (53 bp):
GATTCAAGGCCAACTATATTGGATCTTAAAGATGGAAAAGGTGCCAATATGCT
Found at i:1047236 original size:218 final size:218
Alignment explanation
Indices: 1046845--1047327 Score: 849
Period size: 218 Copynumber: 2.2 Consensus size: 218
1046835 GTTTTGCAAT
* * * * *
1046845 GTGCCACTGTGCAGATTCAAGGCCTGCAACACTGGACTTAAAGATGATGAGGATGAAGAGTGATA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGAGGATGAAGAGTGATA
* *
1046910 AAAGGACCAATACGTTGATTCACGGCTAACGATATTGGGTTCAAAGATGAGAAAAAAGATGTCAA
66 AAAGGACCAATACGTCGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAAGATGTCAA
1046975 TGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
131 TGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
*
1047040 GGCCAGCTATATTGGACTTAAAG
196 GGCCAACTATATTGGACTTAAAG
1047063 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGAGGATGAAGAGTGATA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGAGGATGAAGAGTGATA
* *
1047128 AAAGGACCAATACGTCGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAA
66 AAAGGACCAATACGTCGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAAGATGTCAA
* *
1047193 TGTGCTGATTCAAGGCCAGCTACATTGATCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAA
131 TGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
1047258 GGCCAACTATATTGGACTTAAAG
196 GGCCAACTATATTGGACTTAAAG
*
1047281 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
1047328 AGGTGCCAAT
Statistics
Matches: 252, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 252 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (218 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGAGGATGAAGAGTGATA
AAAGGACCAATACGTCGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAAGATGTCAA
TGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
GGCCAACTATATTGGACTTAAAG
Found at i:1047333 original size:49 final size:47
Alignment explanation
Indices: 1047181--1047418 Score: 233
Period size: 43 Copynumber: 5.0 Consensus size: 47
1047171 AAGATGAGAA
* *
1047181 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GATCTTAAAGATGG
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGA-CTT-AA-A--G
* * *
1047233 AAAATGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT----
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
1047277 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
1047324 ATGAAGGTGCCAATATGCTGACTCAAGGCCAGCTATATTGGACTT----
1 A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
*
1047369 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA-AAG
1047417 AA
1 AA
1047419 GATGCCACCA
Statistics
Matches: 156, Mismatches: 17, Indels: 29
0.77 0.08 0.14
Matches are distributed among these distances:
43 77 0.49
45 1 0.01
47 1 0.01
48 2 0.01
49 38 0.24
52 31 0.20
53 6 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (47 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
Found at i:1047370 original size:92 final size:93
Alignment explanation
Indices: 1047181--1047417 Score: 352
Period size: 92 Copynumber: 2.5 Consensus size: 93
1047171 AAGATGAGAA
* *
1047181 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGATCTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGA-CTTAAAGATGG-AAAGGTGCCAAT
*
1047246 ATGCTGATTCAAGGCCAACTATATTGGACTT
63 ATGCTGACTCAAGGCCAACTATATTGGACTT
1047277 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGAT-G-AAGGTGCCAATAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT-GACTTAAAGATGGAAAGGTGCCAATAT
*
1047340 GCTGACTCAAGGCCAGCTATATTGGACTT
65 GCTGACTCAAGGCCAACTATATTGGACTT
* *
1047369 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT-GACTTA-AAGA
1047418 AGATGCCACC
Statistics
Matches: 132, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
92 80 0.61
93 4 0.03
94 1 0.01
95 40 0.30
96 7 0.05
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (93 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGACTTAAAGATGGAAAGGTGCCAATATG
CTGACTCAAGGCCAACTATATTGGACTT
Found at i:1047550 original size:59 final size:59
Alignment explanation
Indices: 1047480--1047767 Score: 398
Period size: 59 Copynumber: 4.8 Consensus size: 59
1047470 TTTTGAAAGT
* * * *
1047480 TGCCACTGACTTGTGGGCTTTTGAAGAGATACCATTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGG
* * *
1047539 TGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTCTGGGCTTTGGAAAA-GA
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACTGACTTGTGGGCTTTGGAAAAGGG
* * *
1047598 TGCCACTGACTTTTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACTGACTTGTGGGC-TTTGGAAAAGGG
* * * *
1047659 TGCCCCTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGG
* *
1047718 TGCCACTGACTTGTGGGCTTTGGAAAAGATGTCATTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT
1047768 TGAAGGGTGA
Statistics
Matches: 202, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
59 127 0.63
60 51 0.25
61 24 0.12
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (59 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGG
Found at i:1047551 original size:30 final size:30
Alignment explanation
Indices: 1047480--1047767 Score: 386
Period size: 30 Copynumber: 9.7 Consensus size: 30
1047470 TTTTGAAAGT
* * *
1047480 TGCCACTGACTTGTGGGCTTTTGAAGA-GA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
* *
1047509 TACCATTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
1047539 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
* *
1047569 TGCCACTGACTTCTGGGCTTTGGAAAA-GA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
*
1047598 TGCCACTGACTTTTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
*
1047628 TGCCACTGACTTGTGGGCTTTTGAAAAAGGG
1 TGCCACTGACTTGTGGGC-TTTGGAAAAGGG
* * * *
1047659 TGCCCCTAACTTGTGGGCTTTTGAAAA-GA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
*
1047688 TACCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
*
1047718 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
* *
1047747 TGTCATTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
1047768 TGAAGGGTGA
Statistics
Matches: 228, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
29 94 0.41
30 107 0.47
31 27 0.12
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (30 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGGG
Found at i:1047706 original size:90 final size:90
Alignment explanation
Indices: 1047460--1047771 Score: 429
Period size: 90 Copynumber: 3.5 Consensus size: 90
1047450 GGTTGTACCA
* * * * *
1047460 ACTTGTGTGCTTTTG--AAA-GTTGCCACTGACTTGTGGGCTTTTGAAGAGATACCATTGACTTG
1 ACTTGTGGGCTTTTGAAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
1047522 TGGGCTTTGGAAAAGGGTGCCACTG
66 TGGGCTTTGGAAAAGGGTGCCACTG
* * * * * *
1047547 ACTTGTGGGC-TTTGGAAAAGGGTGCCACTGACTTCTGGGCTTTGGAAAAGATGCCACTGACTTT
1 ACTTGTGGGCTTTTGAAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
1047611 TGGGCTTTGGAAAAGGGTGCCACTG
66 TGGGCTTTGGAAAAGGGTGCCACTG
*
1047636 ACTTGTGGGCTTTTGAAAAAGGGTGCCCCTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
1 ACTTGTGGGCTTTTGAAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
1047701 TGGGCTTTGGAAAAGGGTGCCACTG
66 TGGGCTTTGGAAAAGGGTGCCACTG
* * * * *
1047726 ACTTGTGGGC-TTTGGAAAA-GATGTCATTGACTTGTGGGCTTTTGAA
1 ACTTGTGGGCTTTTGAAAAAGGGTGCCACTAACTTGTGGGCTTTTGAA
1047772 GGGTGAGGAA
Statistics
Matches: 200, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
86 4 0.02
87 9 0.05
88 25 0.12
89 80 0.40
90 82 0.41
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (90 bp):
ACTTGTGGGCTTTTGAAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
TGGGCTTTGGAAAAGGGTGCCACTG
Found at i:1049242 original size:8 final size:7
Alignment explanation
Indices: 1049198--1049263 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
1049188 ATCTGGACCC
1049198 TTTTTG-
1 TTTTTGT
*
1049204 TTGTTGT
1 TTTTTGT
1049211 TTTTT-T
1 TTTTTGT
**
1049217 TTTCTTCC
1 TTT-TTGT
1049225 TTTTT-T
1 TTTTTGT
*
1049231 TTTTGGT
1 TTTTTGT
1049238 TTTTTG-
1 TTTTTGT
1049244 TTTTTGTT
1 TTTTTG-T
1049252 TTTTTGT
1 TTTTTGT
1049259 TTTTT
1 TTTTT
1049264 TTTCTTCCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
6 19 0.40
7 20 0.42
8 9 0.19
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (7 bp):
TTTTTGT
Found at i:1049242 original size:14 final size:13
Alignment explanation
Indices: 1049207--1049266 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
1049197 CTTTTTGTTG
1049207 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
**
1049220 CTTCCTTTTTTTTT
1 -TTGTTTTTTTTTT
* *
1049234 TGGTTTTTTGTTT
1 TTGTTTTTTTTTT
1049247 TTGTTTTTTTGTTT
1 TTGTTTTTTT-TTT
1049261 TT-TTTT
1 TTGTTTT
1049267 CTTCCTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
13 21 0.57
14 16 0.43
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (13 bp):
TTGTTTTTTTTTT
Found at i:1049265 original size:9 final size:8
Alignment explanation
Indices: 1049198--1049264 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
1049188 ATCTGGACCC
1049198 TTTTTGTT
1 TTTTTGTT
1049206 GTTGTTT-TT
1 -TT-TTTGTT
*
1049215 TTTTTCTT
1 TTTTTGTT
**
1049223 CCTTT-TT
1 TTTTTGTT
*
1049230 TTTTTGGT
1 TTTTTGTT
1049238 TTTTTG--
1 TTTTTGTT
1049244 TTTTTGTT
1 TTTTTGTT
1049252 TTTTTGTT
1 TTTTTGTT
1049260 TTTTT
1 TTTTT
1049265 TTCTTCCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
6 6 0.12
7 8 0.17
8 27 0.56
9 4 0.08
10 3 0.06
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1049289 original size:47 final size:45
Alignment explanation
Indices: 1049198--1049299 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 45
1049188 ATCTGGACCC
* * *
1049198 TTTTTGTTGTTGTTTTTTTTTTCTTCCTTTTTTTTTTGGTTTTTTG
1 TTTTTGTTGTTGTTTTTTTTTTCTTCCTTTTTTGTTT-GATTTTTA
* *
1049244 TTTTTGTTTTTTTGTTTTTTTTTCTTCCTTTTTTCCGTTT-ATTTTTA
1 TTTTTGTTGTTGT-TTTTTTTTTCTTCCTTTTTT--GTTTGATTTTTA
1049291 TTTTT-TTGT
1 TTTTTGTTGT
1049300 GGAGGACGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
46 14 0.30
47 30 0.64
49 3 0.06
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.80
Consensus pattern (45 bp):
TTTTTGTTGTTGTTTTTTTTTTCTTCCTTTTTTGTTTGATTTTTA
Found at i:1063228 original size:13 final size:13
Alignment explanation
Indices: 1063210--1063234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1063200 CAAAGATCAG
1063210 TGTATCGATACAA
1 TGTATCGATACAA
1063223 TGTATCGATACA
1 TGTATCGATACA
1063235 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1063313 original size:13 final size:13
Alignment explanation
Indices: 1063295--1063321 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1063285 TACAAAACTT
1063295 ATGTATCGATACA
1 ATGTATCGATACA
1063308 ATGTATCGATACA
1 ATGTATCGATACA
1063321 A
1 A
1063322 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1063318 original size:32 final size:33
Alignment explanation
Indices: 1063277--1063341 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1063267 TAGCTTAAAT
1063277 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
*
1063309 TGTATCGATACAACACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
1063342 ATCGTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:1064521 original size:33 final size:33
Alignment explanation
Indices: 1064484--1064550 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
1064474 GTTACAAGCT
*
1064484 ATGTATCGATACATT-TCTTCATGTATCGATACA
1 ATGTATCGATACATTAT-ATCATGTATCGATACA
1064517 ATGTATCGATACATTATATCATGTATCGATACA
1 ATGTATCGATACATTATATCATGTATCGATACA
1064550 A
1 A
1064551 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTATATCATGTATCGATACA
Found at i:1064522 original size:13 final size:13
Alignment explanation
Indices: 1064504--1064529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1064494 ACATTTCTTC
1064504 ATGTATCGATACA
1 ATGTATCGATACA
1064517 ATGTATCGATACA
1 ATGTATCGATACA
1064530 TTATATCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1064605 original size:21 final size:21
Alignment explanation
Indices: 1064579--1064639 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1064569 CAGCCAATTT
1064579 CATGTATCGATACAATTTATC
1 CATGTATCGATACAATTTATC
*
1064600 CATGTATCGATAC-ATTGAAT-
1 CATGTATCGATACAATT-TATC
*
1064620 -ATGTATCGATACAATGTATC
1 CATGTATCGATACAATTTATC
1064640 GATACAAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 14 0.41
20 5 0.15
21 15 0.44
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (21 bp):
CATGTATCGATACAATTTATC
Found at i:1064638 original size:13 final size:13
Alignment explanation
Indices: 1064620--1064646 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1064610 TACATTGAAT
1064620 ATGTATCGATACA
1 ATGTATCGATACA
1064633 ATGTATCGATACA
1 ATGTATCGATACA
1064646 A
1 A
1064647 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1065897 original size:162 final size:160
Alignment explanation
Indices: 1065631--1065920 Score: 411
Period size: 162 Copynumber: 1.8 Consensus size: 160
1065621 TCAATTTTTG
* * *
1065631 TTTTACTTATTTTTGAAAATACCATTTCGTACCTAATAGAAGCTTGAAAGAATATGAAAAGTTTT
1 TTTTACTTATTTTTGAAAATAACATTTCGTACCTAATAGAAGCTCGAAAGAATACGAAAAGTTTT
* * * *
1065696 TTAAATCTTTTATACATCTATAGATGCCTATAAGAATATAAAAAATTAGAAAAAATAAATATTAG
66 TGAAATCTTTTATACACCTATAGAAGCCCATAAGAATATAAAAAATTAGAAAAAA-AAATATTAG
1065761 AATTTATCCCAATAATACCAATTTAAGTTAA
130 AATTTATCCCAATAATACCAATTTAAGTTAA
* * * *
1065792 TTTTATTTATTTTTGAAAATAACATTTCGTATCCTAATGGAAGCTCGAAAGAATGCGAAAGGTTT
1 TTTTACTTATTTTTGAAAATAACATTTCGTA-CCTAATAGAAGCTCGAAAGAATACGAAAAGTTT
* * * *
1065857 TTGAAATCTTTTATACCCCTAT-GAAAGCCCATAGGAATATAAAAGATTAGAAAATAAAATATTA
65 TTGAAATCTTTTATACACCTATAG-AAGCCCATAAGAATATAAAAAATTAGAAAAAAAAATATTA
1065921 TTTAATTTTA
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
161 38 0.34
162 74 0.66
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (160 bp):
TTTTACTTATTTTTGAAAATAACATTTCGTACCTAATAGAAGCTCGAAAGAATACGAAAAGTTTT
TGAAATCTTTTATACACCTATAGAAGCCCATAAGAATATAAAAAATTAGAAAAAAAAATATTAGA
ATTTATCCCAATAATACCAATTTAAGTTAA
Found at i:1068842 original size:19 final size:19
Alignment explanation
Indices: 1068820--1068857 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1068810 GAAAAAAAAA
1068820 TCGGGATTGGAGTATCCCC
1 TCGGGATTGGAGTATCCCC
*
1068839 TCGGGGTTGGAGTATCCCC
1 TCGGGATTGGAGTATCCCC
1068858 AATTATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (19 bp):
TCGGGATTGGAGTATCCCC
Found at i:1069025 original size:51 final size:53
Alignment explanation
Indices: 1068923--1069043 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 53
1068913 AAGTAACGGG
* * * *
1068923 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGAATATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGA
1068977 GTTGGAGTATCCCCGAATAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGAATATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGA
*
1069028 GTTGGAATATCCCCGA
1 GTTGGAGTATCCCCGA
1069044 TTGTGGAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 33 0.54
52 2 0.03
53 8 0.13
54 18 0.30
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (53 bp):
GTTGGAGTATCCCCGAATATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:1071426 original size:13 final size:13
Alignment explanation
Indices: 1071408--1071433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1071398 ACAAAGATCC
1071408 ATGTATCGATACA
1 ATGTATCGATACA
1071421 ATGTATCGATACA
1 ATGTATCGATACA
1071434 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1071429 original size:33 final size:33
Alignment explanation
Indices: 1071387--1071453 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1071377 AAAATTTCCA
***
1071387 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1071420 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1071453 A
1 A
1071454 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1071497 original size:19 final size:18
Alignment explanation
Indices: 1071473--1071572 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
1071463 CAGTAGCTAA
1071473 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1071492 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1071507 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1071524 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1071539 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1071556 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1071573 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1071513 original size:13 final size:13
Alignment explanation
Indices: 1071495--1071551 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1071485 ACAATACTTA
1071495 TGTATCGATACAT
1 TGTATCGATACAT
1071508 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
1071526 ATGTATCGATACAT
1 -TGTATCGATACAT
1071540 TGTATCGATACA
1 TGTATCGATACA
1071552 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1071517 original size:32 final size:32
Alignment explanation
Indices: 1071476--1071570 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
1071466 TAGCTAATTA
*
1071476 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1071508 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1071540 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1071571 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1071652 original size:21 final size:21
Alignment explanation
Indices: 1071628--1071684 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1071618 CATTTGTAGG
1071628 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1071649 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1071670 ATGTATCGATACATT
1 ATGTATCGATACATT
1071685 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1072907 original size:33 final size:33
Alignment explanation
Indices: 1072864--1072961 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
1072854 TTTGGGACAA
1072864 TGTATCGATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGATACAATATGC--CATGTATCGATACAT
* *
1072897 TGTATAGATACAATGTGCCATGTATCGATACAT
1 TGTATCGATACAATATGCCATGTATCGATACAT
1072930 TGTATCGATACAATATGCCATGTATCGATACA
1 TGTATCGATACAATATGCCATGTATCGATACA
1072962 AATAGTGGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
33 58 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATATGCCATGTATCGATACAT
Found at i:1072926 original size:20 final size:19
Alignment explanation
Indices: 1072863--1072962 Score: 64
Period size: 20 Copynumber: 5.7 Consensus size: 19
1072853 GTTTGGGACA
1072863 ATGTATCGATACAATT-CTTC
1 ATGTATCGATACAATTGC--C
1072883 ATGTATCGATAC-A-T---
1 ATGTATCGATACAATTGCC
*
1072897 -TGTATAGATACAATGTGCC
1 ATGTATCGATACAAT-TGCC
1072916 ATGTATCGATAC-A-T---
1 ATGTATCGATACAATTGCC
1072930 -TGTATCGATACAATATGCC
1 ATGTATCGATACAAT-TGCC
1072949 ATGTATCGATACAA
1 ATGTATCGATACAA
1072963 ATAGTGGTAA
Statistics
Matches: 64, Mismatches: 2, Indels: 28
0.68 0.02 0.30
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 2 0.03
17 1 0.02
18 1 0.02
19 2 0.03
20 35 0.55
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACAATTGCC
Found at i:1072935 original size:13 final size:13
Alignment explanation
Indices: 1072917--1072941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1072907 CAATGTGCCA
1072917 TGTATCGATACAT
1 TGTATCGATACAT
1072930 TGTATCGATACA
1 TGTATCGATACA
1072942 ATATGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1075518 original size:13 final size:13
Alignment explanation
Indices: 1075486--1075524 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1075476 ATAGTAACCC
1075486 ATGTATCGATACA
1 ATGTATCGATACA
* *
1075499 TTATATCGATACA
1 ATGTATCGATACA
1075512 ATGTATCG-TACA
1 ATGTATCGATACA
1075524 A
1 A
1075525 AGAACATTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1078556 original size:48 final size:48
Alignment explanation
Indices: 1078484--1078633 Score: 273
Period size: 48 Copynumber: 3.1 Consensus size: 48
1078474 GTGTGTCTCA
1078484 TGATTGTTTTCGATTAATGATGTATAATCGCGATAACAATATTGAGACT
1 TGATT-TTTTCGATTAATGATGTATAATCGCGATAACAATATTGAGACT
*
1078533 TGATTTTTTCGATTAATGATGTATAATCGCGTTAACAATATTGAGACT
1 TGATTTTTTCGATTAATGATGTATAATCGCGATAACAATATTGAGACT
*
1078581 TGATTTTTTCGAGTAATGATGTATAATCGCGATAACAATATTGAGACT
1 TGATTTTTTCGATTAATGATGTATAATCGCGATAACAATATTGAGACT
1078629 TGATT
1 TGATT
1078634 GGATTCTGTG
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
48 93 0.95
49 5 0.05
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (48 bp):
TGATTTTTTCGATTAATGATGTATAATCGCGATAACAATATTGAGACT
Found at i:1079870 original size:28 final size:28
Alignment explanation
Indices: 1079816--1079890 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
1079806 AATAAAGTCT
*** **
1079816 GGGTTGGAGTATCCCCTCGGAGGTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
1079844 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
* *
1079872 AGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCCCGAT
1079891 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:1082367 original size:21 final size:21
Alignment explanation
Indices: 1082341--1082397 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1082331 GTAAACTTCC
1082341 TAGATGTATCGATACAAAGAA
1 TAGATGTATCGATACAAAGAA
*
1082362 TAGATGTATCGATACACAGAA
1 TAGATGTATCGATACAAAGAA
*
1082383 -AAATGTATCGATACA
1 TAGATGTATCGATACA
1082398 TTTCCTTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TAGATGTATCGATACAAAGAA
Found at i:1082453 original size:19 final size:19
Alignment explanation
Indices: 1082429--1082489 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1082419 AGCGATACAT
1082429 TCGATACAAAACTTATGTA
1 TCGATACAAAACTTATGTA
1082448 TCGATAC---A--T-TGTA
1 TCGATACAAAACTTATGTA
*
1082461 TCGATACAACACTTATGTA
1 TCGATACAAAACTTATGTA
*
1082480 TTGATACAAA
1 TCGATACAAA
1082490 TCGCTGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 11 0.32
14 1 0.03
16 2 0.06
18 1 0.03
19 19 0.56
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (19 bp):
TCGATACAAAACTTATGTA
Found at i:1082457 original size:28 final size:30
Alignment explanation
Indices: 1082421--1082487 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
1082411 AGCTTCCTAG
1082421 CGATACA-T-TCGATACAAAACTTATGTAT
1 CGATACATTATCGATACAAAACTTATGTAT
*
1082449 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACA-T-TATCGATACAAAACTTATGTAT
*
1082481 TGATACA
1 CGATACA
1082488 AATCGCTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 7 0.21
31 1 0.03
32 25 0.76
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (30 bp):
CGATACATTATCGATACAAAACTTATGTAT
Found at i:1082462 original size:13 final size:13
Alignment explanation
Indices: 1082444--1082468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1082434 ACAAAACTTA
1082444 TGTATCGATACAT
1 TGTATCGATACAT
1082457 TGTATCGATACA
1 TGTATCGATACA
1082469 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1083477 original size:61 final size:61
Alignment explanation
Indices: 1083382--1084168 Score: 1045
Period size: 61 Copynumber: 13.3 Consensus size: 61
1083372 TTGAAAGGTG
* * *
1083382 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* * **
1083443 TCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
*
1083498 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
*
1083559 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1083620 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* *
1083681 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTCAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* *
1083742 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* **
1083803 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* ** * **
1083858 TCATGCTCTTTGAGGACTGAAAAATGTCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* * **
1083913 TCCTGCTCTTTGAGGACTGGAAA-ATACCACCAACTTGTGTGGGCTTTG-AAAG-----GGG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
*
1083968 TTCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* *
1084029 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGTAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* * * *
1084090 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT-AAGAGGAACAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AAGAAAAAGCA
1084151 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1084169 AAAAAGCGGA
Statistics
Matches: 657, Mismatches: 48, Indels: 42
0.88 0.06 0.06
Matches are distributed among these distances:
54 5 0.01
55 179 0.27
56 8 0.01
57 3 0.00
58 9 0.01
60 5 0.01
61 443 0.67
62 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
Found at i:1083665 original size:122 final size:118
Alignment explanation
Indices: 1083272--1084168 Score: 1099
Period size: 122 Copynumber: 7.7 Consensus size: 118
1083262 AATAAAGTGT
* * * *
1083272 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCCACTCGTGTGGGCTTTG-AAAG-----GCGTCC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* *
1083331 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTG-GTGGGCTTTGAAAG--GT
66 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAGC
* * *
1083381 GTCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* * *
1083446 TGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAGAGGT
66 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAGC
*
1083497 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
*
1083562 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGC
66 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG---AAGC
*
1083619 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* *
1083684 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTCAAAAGAAAAAGC
66 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAG---AAGC
* * *
1083741 ATCTTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* *
1083806 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAGAGGT
66 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAGC
* * * * **
1083857 GTCATGCTCTTTGAGGACTGAAAAATGTCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* * *
1083916 TGCTCTTTGAGGACTGGAAA-ATACCACCAACTTGTGTGGGCTTTGAAAG--GG
66 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAGC
* * *
1083967 GTTCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATC
1 ATCCTGCTCTTTGA-GGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATC
*
1084031 CTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGTAAAGAAAAAGC
65 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG---AAGC
* * * * *
1084089 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT-AAGAGGAACAGGCATC
1 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AAGAAAAAGCATC
1084153 CTGCTCTTTGAGGACT
65 CTGCTCTTTGAGGACT
1084169 AAAAAGCGGA
Statistics
Matches: 705, Mismatches: 48, Indels: 57
0.87 0.06 0.07
Matches are distributed among these distances:
109 46 0.07
110 88 0.12
111 8 0.01
112 3 0.00
114 7 0.01
115 36 0.05
116 208 0.30
117 4 0.01
119 6 0.01
121 2 0.00
122 296 0.42
123 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (118 bp):
ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAGC
Found at i:1084019 original size:470 final size:465
Alignment explanation
Indices: 1083276--1084168 Score: 1318
Period size: 470 Copynumber: 1.9 Consensus size: 465
1083266 AAGTGTATCC
* *
1083276 TGCTCTTTGAGGACTAAAAAGTGCCACCCACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
1 TGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGA
* * *
1083341 GGACTGGAAAATGCCACCAACTTGGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAAG
66 GGACTGGAAAATGCCACCAACTTGGTGGGCTTTGAAAGGTGTCATGCTCTTTGAGGACTGAAAAA
* *
1083406 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAAGACTGAAAGGTGCC
131 TGCCACCAACTCGTGTGGGCTTTGAAAAG----AGCATCCTGCTCTTTGAAGACTGAAAGATACC
*
1083471 ACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGT
192 ACCAACTTGTGTGGGCTTTAAGAGGGGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGT
*
1083536 GTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTATGTG
257 GTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTATGTG
*
1083600 GGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCT
321 GGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCT
1083665 TTGAA-AAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTC
386 TT-AAGAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTC
1083729 AAAAGAAAAAGCATCT
450 AAAAGAAAAAGCATCT
* * * *
1083745 TGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCT
1 TGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAG-----GCATCCTGCT
*
1083810 CTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCATGCTCTTTGAGG
60 CTTTGAGGACTGGAAA-ATGCCACCAACTTG-GTGGGCTTTGAA-AGGTGTCATGCTCTTTGAGG
* * ** *
1083873 ACTGAAAAATGTCACCAACTTGTGTGGGCTTTG-AAAG-GTGTCCTGCTCTTTGAGGACTGGAAA
122 ACTGAAAAATGCCACCAACTCGTGTGGGCTTTGAAAAGAGCATCCTGCTCTTTGAAGACT-GAAA
* *
1083936 -ATACCACCAACTTGTGTGGGCTTTGAA-AGGGGTTCTGCTCTTT-AGGGACTGAAAGGTGCCAC
186 GATACCACCAACTTGTGTGGGCTTT-AAGAGGGGTCCTGCTCTTTGA-GGACTGAAAAGTGCCAC
1083998 CAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAAC
249 CAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAAC
* *
1084063 TTGTGTGGGCTTTGTAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTAT
314 TTATGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTAT
* * *
1084128 GTGGGCTTTAAGAGGAACAGGCATCCTGCTCTTTGAGGACT
379 GTGGGCTTTAAGAAGAAAAAGCATCCTGCTCTTTGAGGACT
1084169 AAAAAGCGGA
Statistics
Matches: 383, Mismatches: 27, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
469 43 0.11
470 230 0.60
471 10 0.03
474 4 0.01
475 39 0.10
476 57 0.15
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (465 bp):
TGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGA
GGACTGGAAAATGCCACCAACTTGGTGGGCTTTGAAAGGTGTCATGCTCTTTGAGGACTGAAAAA
TGCCACCAACTCGTGTGGGCTTTGAAAAGAGCATCCTGCTCTTTGAAGACTGAAAGATACCACCA
ACTTGTGTGGGCTTTAAGAGGGGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGG
GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTATGTGGGCTT
TGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAG
AAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTCAAAAGA
AAAAGCATCT
Found at i:1097513 original size:52 final size:51
Alignment explanation
Indices: 1097457--1097555 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
1097447 ATATTTCCTG
*
1097457 ATGAGAAATTTAATATTTT-GGAGA-AAATAACGGGGTTGGAGTATCCCCAATT
1 ATGAGAAA-TCAATATTTTAGGA-ATAAA-AACGGGGTTGGAGTATCCCCAATT
**
1097509 ATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTATCCCC
1 ATGAGAAATCAATATTTTAGGAATAAAAACGGGGTTGGAGTATCCCC
1097556 TCGGAGGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
51 28 0.67
52 14 0.33
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (51 bp):
ATGAGAAATCAATATTTTAGGAATAAAAACGGGGTTGGAGTATCCCCAATT
Found at i:1097594 original size:28 final size:28
Alignment explanation
Indices: 1097538--1097614 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1097528 GGAATAAAGC
*** **
1097538 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1097566 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1097594 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1097615 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1097667 original size:52 final size:52
Alignment explanation
Indices: 1097598--1097719 Score: 137
Period size: 51 Copynumber: 2.4 Consensus size: 52
1097588 AAATAACGAG
* * * *
1097598 GTTGGAGTATCCTCGATTGTGAAA-A-ATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-AAAGAGATTAGTG-TCTTGAAAATAAAATCGGA
1097650 GTTGGAGTATCCCCGA-T-TAAAGGAGATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAA-GAGATTAGTGTCTTGAAAATAAAATCGGA
1097701 GTTGG-GATATCCCCGATTG
1 GTTGGAG-TATCCCCGATTG
1097720 CGGAGAATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
49 3 0.05
50 2 0.03
51 33 0.55
52 22 0.37
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.31
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTAAAGAGATTAGTGTCTTGAAAATAAAATCGGA
Found at i:1100103 original size:13 final size:13
Alignment explanation
Indices: 1100085--1100110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1100075 CAAAGAATAG
1100085 ATGTATCGATACA
1 ATGTATCGATACA
1100098 ATGTATCGATACA
1 ATGTATCGATACA
1100111 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1100107 original size:34 final size:33
Alignment explanation
Indices: 1100064--1100130 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1100054 AACTTCCTAG
*
1100064 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
1100098 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
1100131 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Done.