Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005189.1 Hibiscus syriacus cultivar Beakdansim tig00011718_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: 1183632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:863371 original size:60 final size:60
Alignment explanation
Indices: 863297--863423 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
863287 TAGTCGGGTG
863297 ACCATTTTGTAACTTTTAATAGTTAAA-AGACTCAACAAAACAATATCTTATAATCGAGAA
1 ACCATTTTGTAACTTTTAATAGTTAAAGA-ACTCAACAAAACAATATCTTATAATCGAGAA
* * * * * * *
863357 ATCATTTTGTAACTTTTAATAGTTGAGGAACTCAATAAAACCATATCTTATAGTCGAGGA
1 ACCATTTTGTAACTTTTAATAGTTAAAGAACTCAACAAAACAATATCTTATAATCGAGAA
863417 ACCATTT
1 ACCATTT
863424 ATATACTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (60 bp):
ACCATTTTGTAACTTTTAATAGTTAAAGAACTCAACAAAACAATATCTTATAATCGAGAA
Found at i:865455 original size:41 final size:41
Alignment explanation
Indices: 865388--865584 Score: 191
Period size: 41 Copynumber: 4.8 Consensus size: 41
865378 GAGTTTACCC
*
865388 TTCGGGATAAATTTCACTTCGGAATATTC-GTGGATTCACCA
1 TTCGGGATAAATTTCACTTCGAAATA-TCAGTGGATTCACCA
* * *
865429 TTCGAGATAAATTTCACTTCGAAATATCAGTAGATTCACCC
1 TTCGGGATAAATTTCACTTCGAAATATCAGTGGATTCACCA
* * * * *
865470 TTCGGGATGAATTTCACTTTGGATTATCAGTGGATTCACCT
1 TTCGGGATAAATTTCACTTCGAAATATCAGTGGATTCACCA
* * * * *
865511 TTTGGGA-AGAATTTCACTTTGAAATATCAGCGAATTCACCC
1 TTCGGGATA-AATTTCACTTCGAAATATCAGTGGATTCACCA
* * * * *
865552 TTCGGGATGAATTTTACTTTGGATTATCAGTGG
1 TTCGGGATAAATTTCACTTCGAAATATCAGTGG
865585 CTCCCCCTCG
Statistics
Matches: 128, Mismatches: 25, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
40 2 0.02
41 126 0.98
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (41 bp):
TTCGGGATAAATTTCACTTCGAAATATCAGTGGATTCACCA
Found at i:865524 original size:82 final size:82
Alignment explanation
Indices: 865384--865584 Score: 273
Period size: 82 Copynumber: 2.5 Consensus size: 82
865374 GACTGAGTTT
* * *
865384 ACCCTTCGGGATAAATTTCACTTCGGAATATTC-GTGGATTCACCATTCGAGATAAATTTCACTT
1 ACCCTTCGGGATGAATTTCACTTTGGATTA-TCAGTGGATTCACCATTCGAGATAAATTTCACTT
865448 CGAAATATCAGTAG-ATTC
65 CGAAATATCAG-AGAATTC
* * *
865466 ACCCTTCGGGATGAATTTCACTTTGGATTATCAGTGGATTCACCTTTTGGGA-AGAATTTCACTT
1 ACCCTTCGGGATGAATTTCACTTTGGATTATCAGTGGATTCACCATTCGAGATA-AATTTCACTT
* *
865530 TGAAATATCAGCGAATTC
65 CGAAATATCAGAGAATTC
*
865548 ACCCTTCGGGATGAATTTTACTTTGGATTATCAGTGG
1 ACCCTTCGGGATGAATTTCACTTTGGATTATCAGTGG
865585 CTCCCCCTCG
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
81 4 0.04
82 103 0.96
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (82 bp):
ACCCTTCGGGATGAATTTCACTTTGGATTATCAGTGGATTCACCATTCGAGATAAATTTCACTTC
GAAATATCAGAGAATTC
Found at i:868448 original size:19 final size:17
Alignment explanation
Indices: 868406--868448 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
868396 ACCCGACTTG
868406 AAATAATATATTTATTT
1 AAATAATATATTTATTT
*
868423 AAA-AATATTATTTTTATT
1 AAATAATA-TATTTAT-TT
868441 AAATAATA
1 AAATAATA
868449 AAAATAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 5 0.23
19 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATAATATATTTATTT
Found at i:868804 original size:28 final size:29
Alignment explanation
Indices: 868763--868819 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
868753 CGGTTTAAAA
*
868763 TTGATTAAATAATATAATTGATTTAATTT
1 TTGAATAAATAATATAATTGATTTAATTT
* *
868792 TTGAATAAA-AATATATTTTATTTAATTT
1 TTGAATAAATAATATAATTGATTTAATTT
868820 CTTAGTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TTGAATAAATAATATAATTGATTTAATTT
Found at i:871080 original size:75 final size:74
Alignment explanation
Indices: 870895--871100 Score: 254
Period size: 74 Copynumber: 2.7 Consensus size: 74
870885 CAAAGCCAAA
* * **
870895 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAG
870960 TTTGGCTCCGAG
63 TTTGGCTCCGAG
* * *
870972 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAATCGATTCCCCCTAAACAGTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
* *
871036 TTGTTCCGAG
65 TGGCTCCGAG
* *
871046 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCC
871101 CTTGTACAAC
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
74 61 0.54
75 26 0.23
76 1 0.01
77 23 0.21
78 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:876880 original size:19 final size:19
Alignment explanation
Indices: 876856--876916 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
876846 TTTTGGTGCA
*
876856 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
876875 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
876896 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
876917 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:878902 original size:9 final size:8
Alignment explanation
Indices: 878879--878930 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
878869 TTGTTTCAAC
878879 TTTTTGGA
1 TTTTTGGA
878887 TATTTTGGA
1 T-TTTTGGA
878896 TTGTTT-GA
1 TT-TTTGGA
878904 TTTTGTGGA
1 TTTT-TGGA
*
878913 TTGTTGGA
1 TTTTTGGA
878921 -TTTTGGA
1 TTTTTGGA
878928 TTT
1 TTT
878931 ATGAATAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TTTTTGGA
Found at i:878914 original size:17 final size:17
Alignment explanation
Indices: 878882--878925 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
878872 TTTCAACTTT
878882 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
878899 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
878916 TTGGATTTTG
1 TTGGATTTTG
878926 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:879701 original size:74 final size:75
Alignment explanation
Indices: 879518--879726 Score: 262
Period size: 75 Copynumber: 2.8 Consensus size: 75
879508 CAAAGCCAAA
* * **
879518 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATG
1 AATTCCAGA-TGCTCGGAGGGAACCGATT--CCCCCCATAGGAGGAACCGATTCCCCCCTAAACA
879582 GTTTGGCTCCGAG
63 GTTTGGCTCCGAG
*
879595 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
879659 TTTGTTCCGAG
65 TTGGCTCCGAG
* * *
879670 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
879727 TGTACAACGG
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
74 21 0.18
75 64 0.55
76 6 0.05
77 25 0.21
78 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:881065 original size:3 final size:3
Alignment explanation
Indices: 881057--881084 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
881047 GAGTATGGTT
881057 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
881085 ACTAAGGCTA
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:881764 original size:6 final size:6
Alignment explanation
Indices: 881753--881782 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
881743 GCAATTTTTA
881753 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
881783 GTTAACGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAAAT
Found at i:889022 original size:25 final size:26
Alignment explanation
Indices: 888968--889023 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
888958 AAACTGGAAC
*
888968 AAAAAAACATTAGGCACCAAATTAGA
1 AAAAAAACATTAGACACCAAATTAGA
* * *
888994 AAAAAAACTTTAGACACTAAATTGGA
1 AAAAAAACATTAGACACCAAATTAGA
889020 AAAA
1 AAAA
889024 CGAGCATACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.18
Consensus pattern (26 bp):
AAAAAAACATTAGACACCAAATTAGA
Found at i:890764 original size:52 final size:48
Alignment explanation
Indices: 890701--890905 Score: 218
Period size: 49 Copynumber: 4.2 Consensus size: 48
890691 AAAAATGACC
* *
890701 TTTAGCGACGAAGGAAAAGATATAGCAGCGAAAAAAATAAAAGAAAATATGT
1 TTTAGCGACGAA-AAAAAGATATAGCGGCG--AAAAATAAAAGAAAATA-GT
* * *
890753 TTTAGCGACGAAGAAAAAGATATAGTGGCG-AAAAT-AAAGATAACAGT
1 TTTAGCGACGAA-AAAAAGATATAGCGGCGAAAAATAAAAGAAAATAGT
* * * * *
890800 TTTAGTGACGTAAGAAAGATATATCGGCTAAAAATAAAAGAAAATAGT
1 TTTAGCGACGAAAAAAAGATATAGCGGCGAAAAATAAAAGAAAATAGT
*
890848 TTTAGCGACGAAAACAAAGATATAGCGGCGAATAATAAAAGAAGAA-ATGT
1 TTTAGCGACGAAAA-AAAGATATAGCGGCGAAAAATAAAAGAA-AATA-GT
890898 TTTAGCGA
1 TTTAGCGA
890906 TGGAGAATAA
Statistics
Matches: 129, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
46 13 0.10
47 17 0.13
48 29 0.22
49 31 0.24
50 12 0.09
52 27 0.21
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.20
Consensus pattern (48 bp):
TTTAGCGACGAAAAAAAGATATAGCGGCGAAAAATAAAAGAAAATAGT
Found at i:894410 original size:12 final size:12
Alignment explanation
Indices: 894395--894436 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
894385 ACATATGTAC
894395 GTATGTATATAT
1 GTATGTATATAT
*
894407 GTATGTATGTAT
1 GTATGTATATAT
* *
894419 GTACGT-CATAT
1 GTATGTATATAT
894430 GTATGTA
1 GTATGTA
894437 CTTACGTACG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (12 bp):
GTATGTATATAT
Found at i:894436 original size:4 final size:4
Alignment explanation
Indices: 894388--894421 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
894378 CATGCGTACA
* *
894388 TATG TACG TATG TATA TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
894422 CGTCATATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:894445 original size:23 final size:23
Alignment explanation
Indices: 894388--894469 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
894378 CATGCGTACA
* *
894388 TATGTACGTATGTATATATGTATG
1 TATGTACGTACGT-CATATGTATG
*
894412 TATGTATGTACGTCATATGTATG
1 TATGTACGTACGTCATATGTATG
* *
894435 TACT-TACGTACGTACGTACGTATG
1 TA-TGTACGTACGT-CATATGTATG
894459 --TGTACGTACGT
1 TATGTACGTACGT
894470 ATGTGTGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
21 1 0.02
22 9 0.18
23 19 0.39
24 20 0.41
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (23 bp):
TATGTACGTACGTCATATGTATG
Found at i:894465 original size:14 final size:14
Alignment explanation
Indices: 894446--894475 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
894436 ACTTACGTAC
894446 GTACGTACGTATGT
1 GTACGTACGTATGT
894460 GTACGTACGTATGT
1 GTACGTACGTATGT
894474 GT
1 GT
894476 GTATGCACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (14 bp):
GTACGTACGTATGT
Found at i:907655 original size:18 final size:17
Alignment explanation
Indices: 907615--907673 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
907605 ATACTAATAT
* *
907615 TATAATTAATCTTATAA
1 TATAATTAATATTAAAA
907632 TAATAATTAATGATTAAAA
1 T-ATAATTAAT-ATTAAAA
907651 TATAA--AATATTAAAA
1 TATAATTAATATTAAAA
907666 T-TAATTAA
1 TATAATTAA
907674 CCTAATTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
16 5 0.14
17 1 0.03
18 13 0.36
19 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TATAATTAATATTAAAA
Found at i:908955 original size:3 final size:3
Alignment explanation
Indices: 908947--908988 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
908937 GGTCTTTATA
*
908947 AAT AAT AAT AAT AAT AAT -AT AAT AAT -TT ATAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A
908989 TTATATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.85
4 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:909841 original size:29 final size:28
Alignment explanation
Indices: 909809--909899 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
909799 ATTGATCCTT
909809 AAACTTTTAAACATTCTAATTTCATCCCC
1 AAACTTTTAAACATTCTAATTT-ATCCCC
* * *
909838 AAACTATATT--TCATTCTAAATTAATCCTC
1 AAACT-T-TTAAACATTCT-AATTTATCCCC
*
909867 AAGCTTTTAAACATTCTAATTTATCCCC
1 AAACTTTTAAACATTCTAATTTATCCCC
909895 AAACT
1 AAACT
909900 ATGGATCTCG
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.04
28 14 0.29
29 26 0.53
30 5 0.10
31 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.38
Consensus pattern (28 bp):
AAACTTTTAAACATTCTAATTTATCCCC
Found at i:909947 original size:59 final size:58
Alignment explanation
Indices: 909809--909933 Score: 171
Period size: 59 Copynumber: 2.1 Consensus size: 58
909799 ATTGATCCTT
* *
909809 AAACTTTTAAACATTCTAATTTCATCCCCAAACTATATTTCATTCTAAATTAATCCTC
1 AAACTTTTAAACATTCTAATTTCATCCCCAAACTATATCTCATTCTAAATTAATCCCC
* * * *
909867 AAGCTTTTAAACATTCTAATTT-ATCCCCAAACTATGGATCTCGTTCTAGATTAGTCCCC
1 AAACTTTTAAACATTCTAATTTCATCCCCAAACTAT--ATCTCATTCTAAATTAATCCCC
909926 AAACTTTT
1 AAACTTTT
909934 GAATCTTTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
57 13 0.22
58 21 0.36
59 24 0.41
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (58 bp):
AAACTTTTAAACATTCTAATTTCATCCCCAAACTATATCTCATTCTAAATTAATCCCC
Found at i:915135 original size:4 final size:4
Alignment explanation
Indices: 915121--915169 Score: 89
Period size: 4 Copynumber: 12.2 Consensus size: 4
915111 TAACAATTAG
*
915121 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
915169 A
1 A
915170 GAGTTTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:921911 original size:12 final size:12
Alignment explanation
Indices: 921894--921926 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
921884 GGTTCTTGAA
921894 TTCATCAGCTAG
1 TTCATCAGCTAG
921906 TTCATCAGCTAG
1 TTCATCAGCTAG
921918 TTCATCAGC
1 TTCATCAGC
921927 AAGGCACTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (12 bp):
TTCATCAGCTAG
Found at i:926123 original size:17 final size:17
Alignment explanation
Indices: 926101--926134 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
926091 TACTTGTACC
926101 GAATACATAGTCGTATT
1 GAATACATAGTCGTATT
* *
926118 GAATACGTAGTTGTATT
1 GAATACATAGTCGTATT
926135 CGATATAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (17 bp):
GAATACATAGTCGTATT
Found at i:928809 original size:24 final size:24
Alignment explanation
Indices: 928771--928817 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
928761 GTTATTTAGA
*
928771 AATTTCTTTATTTTTAATATAATTG
1 AATTTCTTTAATTTTAA-ATAATTG
928796 AATTT-TTTAATTTTAAATAATT
1 AATTTCTTTAATTTTAAATAATT
928818 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTTCTTTAATTTTAAATAATTG
Found at i:931329 original size:22 final size:23
Alignment explanation
Indices: 931301--931350 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
931291 ATATTATGTT
931301 TAAAAAT-AAA-CTTAAAATAAAA
1 TAAAAATGAAAGCTTAAAA-AAAA
931323 TAAAAATGAAAGCTTAAAAAAAA
1 TAAAAATGAAAGCTTAAAAAAAA
*
931346 GAAAA
1 TAAAA
931351 GAAGAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 11 0.44
24 7 0.28
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (23 bp):
TAAAAATGAAAGCTTAAAAAAAA
Found at i:931360 original size:22 final size:23
Alignment explanation
Indices: 931301--931350 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
931291 ATATTATGTT
931301 TAAAAAT--AAACTTAAAATAAAA
1 TAAAAATGAAAACTTAAAA-AAAA
*
931323 TAAAAATGAAAGCTTAAAAAAAA
1 TAAAAATGAAAACTTAAAAAAAA
*
931346 GAAAA
1 TAAAA
931351 GAAGAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 9 0.38
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (23 bp):
TAAAAATGAAAACTTAAAAAAAA
Found at i:932267 original size:99 final size:99
Alignment explanation
Indices: 932075--932272 Score: 380
Period size: 99 Copynumber: 2.0 Consensus size: 99
932065 TTTTAGAGAT
932075 TACGAATCGAGAAAAATCGGACACCTCCGATTTCAGCTGTACTACCATCTGTTCTCGTAACCCAT
1 TACGAATCGAGAAAAATCGGACACCTCCGATTTCAGCTGTACTACCATCTGTTCTCGTAACCCAT
932140 GACATTAAATTTTCAAAAATCGATTGCGAGAGCC
66 GACATTAAATTTTCAAAAATCGATTGCGAGAGCC
932174 TACGAATCGAGAAAAATCGGACACCTCCGATTTCAGCTGTACTACCATCTGTTCTCGTAACCCAT
1 TACGAATCGAGAAAAATCGGACACCTCCGATTTCAGCTGTACTACCATCTGTTCTCGTAACCCA-
932239 TGACATTAAATTTTCAAAAATCGA-TGCGAGAGCC
65 TGACATTAAATTTTCAAAAATCGATTGCGAGAGCC
932273 GACCATTTCA
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
99 74 0.76
100 24 0.24
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (99 bp):
TACGAATCGAGAAAAATCGGACACCTCCGATTTCAGCTGTACTACCATCTGTTCTCGTAACCCAT
GACATTAAATTTTCAAAAATCGATTGCGAGAGCC
Found at i:942309 original size:44 final size:44
Alignment explanation
Indices: 942241--942361 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 44
942231 ATCTCAACTT
*
942241 TTAAGTATTACAAGTTCCAAGAGCAGTAGGTAAAGTTTTGGCTA
1 TTAAATATTACAAGTTCCAAGAGCAGTAGGTAAAGTTTTGGCTA
* * * ** *
942285 TTAAATATTACAAGTTGCAAGAGCAATAGCTGGAGTTTTTGCTA
1 TTAAATATTACAAGTTCCAAGAGCAGTAGGTAAAGTTTTGGCTA
* *
942329 TTAAATATTACAAGATCCAAGAACAGTAAGGTA
1 TTAAATATTACAAGTTCCAAGAGCAGT-AGGTA
942362 GACGTTGATC
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
44 60 0.95
45 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (44 bp):
TTAAATATTACAAGTTCCAAGAGCAGTAGGTAAAGTTTTGGCTA
Found at i:950638 original size:18 final size:19
Alignment explanation
Indices: 950603--950638 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
950593 AAATGAATAT
*
950603 TTTCAAAGTTTTGGGTTTA
1 TTTCAAAGTTTTGCGTTTA
950622 TTTCAAA-TTTTGCGTTT
1 TTTCAAAGTTTTGCGTTT
950639 TCTATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (19 bp):
TTTCAAAGTTTTGCGTTTA
Found at i:955577 original size:50 final size:50
Alignment explanation
Indices: 955497--955595 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
955487 GCACTTACTC
* *
955497 TTGAAGAAGTGTATGATAACATGCATTCGTATGACAAAATAGAACATCTA
1 TTGAAGAAGTGTATGATAACATGCACTCGTATGACAAAATAAAACATCTA
*
955547 TTGAAGAAGTGTATGATAACATGCACTCGTATGATAAAATAAAACATCT
1 TTGAAGAAGTGTATGATAACATGCACTCGTATGACAAAATAAAACATCT
955596 CGTATTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (50 bp):
TTGAAGAAGTGTATGATAACATGCACTCGTATGACAAAATAAAACATCTA
Found at i:959353 original size:42 final size:42
Alignment explanation
Indices: 959307--959387 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
959297 AAAACAAAAT
*
959307 TATTATAAATTATACTAATTATTTATTAAAATAAAAATAATA
1 TATTATAAATTATACTAATTACTTATTAAAATAAAAATAATA
* * * *
959349 TATTATTAATTATATTATTTACTTATTAAAATAATAATA
1 TATTATAAATTATACTAATTACTTATTAAAATAAAAATA
959388 TTATTAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (42 bp):
TATTATAAATTATACTAATTACTTATTAAAATAAAAATAATA
Found at i:959393 original size:17 final size:17
Alignment explanation
Indices: 959340--959395 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
959330 TATTAAAATA
959340 AAAATAAT-ATATTATT
1 AAAATAATAATATTATT
* * *
959356 AATTATATTATTTACTTATT
1 AA-AATAATA-ATA-TTATT
959376 AAAATAATAATATTATT
1 AAAATAATAATATTATT
959393 AAA
1 AAA
959396 CTATTAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
16 2 0.07
17 12 0.40
18 2 0.07
19 7 0.23
20 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAATAATAATATTATT
Found at i:959400 original size:25 final size:26
Alignment explanation
Indices: 959355--959416 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
959345 AATATATTAT
* *
959355 TAATTATATTATTTACTTATT-AAAA
1 TAATAATATTATTAACTTATTAAAAA
959380 TAATAATATTATTAAAC-TATTAAAAA
1 TAATAATATTATT-AACTTATTAAAAA
*
959406 TTATAATATTA
1 TAATAATATTA
959417 AATAAGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (26 bp):
TAATAATATTATTAACTTATTAAAAA
Found at i:964502 original size:12 final size:12
Alignment explanation
Indices: 964485--964509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
964475 AGAGCACCGG
964485 CATCATCAGCTT
1 CATCATCAGCTT
964497 CATCATCAGCTT
1 CATCATCAGCTT
964509 C
1 C
964510 TGCAGTGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCATCAGCTT
Found at i:971295 original size:23 final size:23
Alignment explanation
Indices: 971269--971332 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
971259 CAACTCATAT
971269 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
971292 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
971315 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
971333 TATAATAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:971521 original size:103 final size:103
Alignment explanation
Indices: 971348--971668 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
971338 TAATGTCCAT
* *
971348 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
* *
971413 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAATACATATATATCCCG
* *
971451 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
*
971516 TACTTCACACATATTCCAAAGAATACATATATATCCCG
66 GACTTCACACATATTCCAAAGAATACATATATATCCCG
971554 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
971619 GACTTCACACATATTCCAAAGAATACATATATATCCCG
66 GACTTCACACATATTCCAAAGAATACATATATATCCCG
971657 AAGGACCACATA
1 AAGGACCACATA
971669 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATACATATATATCCCG
Found at i:974273 original size:75 final size:75
Alignment explanation
Indices: 974150--974300 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
974140 AAAGTAAAAT
*
974150 AGTTGAATAGTTTAATGATTTATTTAAAAATATTTCCTGAAAGTTGTTAGTAATTATCAAAGGAA
1 AGTTGAATAGTTCAATGATTTATTTAAAAATATTTCCTGAAAGTTGTTAGTAATTATCAAAGGAA
974215 TTAAAGGGCA
66 TTAAAGGGCA
** * *
974225 AGTTGAATAGTTCAATGATTTATTTGGAAATGTTTCCTGAAAGTTGTTAGTAATTATCAAATGAA
1 AGTTGAATAGTTCAATGATTTATTTAAAAATATTTCCTGAAAGTTGTTAGTAATTATCAAAGGAA
974290 TTAAAGGGCA
66 TTAAAGGGCA
974300 A
1 A
974301 AATGGTCATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (75 bp):
AGTTGAATAGTTCAATGATTTATTTAAAAATATTTCCTGAAAGTTGTTAGTAATTATCAAAGGAA
TTAAAGGGCA
Found at i:976481 original size:20 final size:21
Alignment explanation
Indices: 976456--976497 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
976446 TCAAAAGTTA
*
976456 CTGTAGCA-AGGTATCGGTAC
1 CTGTAGCAGAGGTATCGATAC
*
976476 CTGTAGCAGGGGTATCGATAC
1 CTGTAGCAGAGGTATCGATAC
976497 C
1 C
976498 CCTGAAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (21 bp):
CTGTAGCAGAGGTATCGATAC
Found at i:977405 original size:21 final size:21
Alignment explanation
Indices: 977381--977423 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
977371 TTTAGATGTA
977381 ACCACAGTAGGTTCAA-ATGCC
1 ACCACAGTAGGTT-AAGATGCC
* *
977402 ACCATAGTCGGTTAAGATGCC
1 ACCACAGTAGGTTAAGATGCC
977423 A
1 A
977424 TCATCGCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (21 bp):
ACCACAGTAGGTTAAGATGCC
Found at i:977960 original size:29 final size:29
Alignment explanation
Indices: 977921--977988 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
977911 GTTTTTATTA
*
977921 TTTAATTGTTTGAATT-GTAACATTTGTAT
1 TTTAATAGTTTGAATTAGTAA-ATTTGTAT
* * * *
977950 TTTAATAGTTTGTATTATTTAGTTTGTAT
1 TTTAATAGTTTGAATTAGTAAATTTGTAT
977979 TTTAATAGTT
1 TTTAATAGTT
977989 ATATAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.59
Consensus pattern (29 bp):
TTTAATAGTTTGAATTAGTAAATTTGTAT
Found at i:977963 original size:15 final size:15
Alignment explanation
Indices: 977921--977988 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 15
977911 GTTTTTATTA
* *
977921 TTTAATTGTTTGAAT
1 TTTAATAGTTTGTAT
* *
977936 TGTAACA-TTTGTAT
1 TTTAATAGTTTGTAT
977950 TTTAATAGTTTGTAT
1 TTTAATAGTTTGTAT
977965 TATT--TAGTTTGTAT
1 T-TTAATAGTTTGTAT
977979 TTTAATAGTT
1 TTTAATAGTT
977989 ATATAACATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.05
14 22 0.51
15 17 0.40
16 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTAATAGTTTGTAT
Found at i:982487 original size:37 final size:38
Alignment explanation
Indices: 982436--982511 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
982426 TGTTTCACTC
982436 TAATTGGATTTTCGAAACATATTTTCCTCATTTTTCGG
1 TAATTGGATTTTCGAAACATATTTTCCTCATTTTTCGG
*
982474 TAATTGG-TTTTCGAAACATATTTTCCTCCTTTTTCGG
1 TAATTGGATTTTCGAAACATATTTTCCTCATTTTTCGG
982511 T
1 T
982512 GTTTAGTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (38 bp):
TAATTGGATTTTCGAAACATATTTTCCTCATTTTTCGG
Found at i:982526 original size:37 final size:37
Alignment explanation
Indices: 982448--982526 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
982438 ATTGGATTTT
* **
982448 CGAAACATATTTTCCTCATTTTTCGGTAATTGGTTTT
1 CGAAACATATTTTCCTCATTTTTCGGTAATTAGTTGA
* **
982485 CGAAACATATTTTCCTCCTTTTTCGGTGTTTAGTTGA
1 CGAAACATATTTTCCTCATTTTTCGGTAATTAGTTGA
982522 CGAAA
1 CGAAA
982527 AACAAATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (37 bp):
CGAAACATATTTTCCTCATTTTTCGGTAATTAGTTGA
Found at i:985828 original size:34 final size:33
Alignment explanation
Indices: 985752--985828 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 33
985742 GTGGTAAGAA
*
985752 ATTTATTTTTATATTAGTATTTTTTAAAATAGTT
1 ATTT-TTTTTATATTAATATTTTTTAAAATAGTT
985786 ATTATTTTTTATATTAATATATTTATGT-AAATA-TT
1 ATT-TTTTTTATATTAATAT-TTT-T-TAAAATAGTT
985821 ATTTTTTT
1 ATTTTTTT
985829 ATTAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
34 22 0.58
35 9 0.24
36 6 0.16
37 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (33 bp):
ATTTTTTTTATATTAATATTTTTTAAAATAGTT
Found at i:985853 original size:32 final size:31
Alignment explanation
Indices: 985784--985860 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 31
985774 TTTAAAATAG
985784 TTATTATTTTTTATATTAATATATTTATGTAA
1 TTATTATTTTTTATATTAATATATTTA-GTAA
*
985816 ATATTATTTTTT-TATTAAAATAATATTTA-TAA
1 TTATTATTTTTTATATT--AAT-ATATTTAGTAA
*
985848 TTATTATTATTTA
1 TTATTATTTTTTA
985861 GAATTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 4 0.11
32 24 0.63
33 3 0.08
34 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
TTATTATTTTTTATATTAATATATTTAGTAA
Found at i:985860 original size:16 final size:16
Alignment explanation
Indices: 985839--985869 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
985829 ATTAAAATAA
*
985839 TATTTATAATTATTAT
1 TATTTAGAATTATTAT
985855 TATTTAGAATTATTA
1 TATTTAGAATTATTA
985870 ATTTTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTTAGAATTATTAT
Found at i:987610 original size:21 final size:21
Alignment explanation
Indices: 987580--987627 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
987570 GCAGGGGTAC
* *
987580 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
987601 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
987622 ATGCCA
1 ATGCCA
987628 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:987657 original size:21 final size:21
Alignment explanation
Indices: 987631--987721 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
987621 TATGCCATCT
*
987631 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
987652 CCGCAGGGTTACATTCCTAG-
1 CCGCAGGGTTACATTCCTAGC
*
987672 CC-CA-GGTTACATACCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
987691 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
987712 CCGCAGGGTT
1 CCGCAGGGTT
987722 TTATACCATA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.21
19 4 0.06
20 4 0.06
21 42 0.67
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:987680 original size:39 final size:39
Alignment explanation
Indices: 987637--987713 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
987627 ATCTCCGCAG
* *
987637 GGTTACATTCCGAGCCCG-CAGGGTTACATTCCTAGCCCA
1 GGTTACATACCGAGCCCGCCA-GGTTACATGCCTAGCCCA
*
987676 GGTTACATACCTAGCCCGCCAGGTTACATGCCTAGCCC
1 GGTTACATACCGAGCCCGCCAGGTTACATGCCTAGCCC
987714 GCAGGGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.22
Consensus pattern (39 bp):
GGTTACATACCGAGCCCGCCAGGTTACATGCCTAGCCCA
Found at i:988300 original size:33 final size:34
Alignment explanation
Indices: 988241--988337 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
988231 AAATGTTTTT
*
988241 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
988275 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
988308 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
988338 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:988344 original size:34 final size:33
Alignment explanation
Indices: 988239--988344 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
988229 ATAAATGTTT
*
988239 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
988273 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
988305 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
988340 TTAAA
1 TTAAA
988345 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:988952 original size:128 final size:126
Alignment explanation
Indices: 988725--988953 Score: 404
Period size: 128 Copynumber: 1.8 Consensus size: 126
988715 TTTAAGTTAT
* *
988725 TCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACGTATTCTCTGAAAATAATGGAAGGC
1 TCCCCAAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGAAAATAATGGAAGGC
*
988790 GCGCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
988851 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCAAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGA--AAATAATGGAAG
988916 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
64 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
988954 CCGATTATAG
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
126 48 0.49
128 49 0.51
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCAAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGAAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:989034 original size:8 final size:8
Alignment explanation
Indices: 989021--989061 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
989011 TCACAATCTT
989021 TCAAATTC
1 TCAAATTC
989029 TCAAATTC
1 TCAAATTC
* *
989037 CCAAACTC
1 TCAAATTC
989045 T-AAATTC
1 TCAAATTC
989052 TCAAATTC
1 TCAAATTC
989060 TC
1 TC
989062 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:992077 original size:12 final size:13
Alignment explanation
Indices: 992044--992081 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
992034 AAATACATAA
992044 ATATATTTAATAT
1 ATATATTTAATAT
*
992057 ATTTATTTAATAT
1 ATATATTTAATAT
992070 A-ATATTTAATAT
1 ATATATTTAATAT
992082 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:993583 original size:10 final size:11
Alignment explanation
Indices: 993560--993584 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
993550 TCTTTTTATA
993560 TTTGTTTAATT
1 TTTGTTTAATT
993571 TTTGTTTAATT
1 TTTGTTTAATT
993582 TTT
1 TTT
993585 ACATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTGTTTAATT
Found at i:994291 original size:20 final size:20
Alignment explanation
Indices: 994266--994404 Score: 97
Period size: 20 Copynumber: 6.8 Consensus size: 20
994256 ATGCGAAACA
*
994266 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
994286 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
994306 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
994326 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
994347 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
994368 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
994388 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
994405 CCAAGAATCG
Statistics
Matches: 93, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 70 0.75
21 7 0.08
22 14 0.15
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:994413 original size:20 final size:20
Alignment explanation
Indices: 994328--994417 Score: 110
Period size: 20 Copynumber: 4.4 Consensus size: 20
994318 GTCAAAAGAA
994328 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
994350 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
994370 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
994390 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
994410 AATCGCAA
1 AATCGCAA
994418 AACGTCAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 45 0.76
21 1 0.02
22 12 0.20
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:995305 original size:6 final size:6
Alignment explanation
Indices: 995294--995326 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
995284 TCTCGTCTCG
995294 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
995327 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:995464 original size:20 final size:20
Alignment explanation
Indices: 995439--995633 Score: 155
Period size: 20 Copynumber: 9.4 Consensus size: 20
995429 TTTTGCCGTT
995439 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
995459 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
995479 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
995499 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
995519 TTGCGATTATTTTCTCG-ATCGCG
1 TTGCG---ATTCT-TGGAATCGCG
* *
995542 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
* *
995562 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTT-GGA-ATCGCG
* *
995584 TTGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCG
995604 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
995626 TTGCGATT
1 TTGCGATT
995634 TTCTTTTGAC
Statistics
Matches: 143, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.07
20 84 0.59
21 3 0.02
22 28 0.20
23 16 0.11
24 1 0.01
25 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:995486 original size:40 final size:40
Alignment explanation
Indices: 995439--995714 Score: 208
Period size: 40 Copynumber: 6.8 Consensus size: 40
995429 TTTTGCCGTT
995439 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
995479 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
* * * *
995519 TTGCGATTATTTTCTCG-ATCGCGTTGCGATTCTT-TGAATCGCA
1 TTGCG---ATTCT-TGGAATCGCGTTGCGATT-TTCTCAATCGCG
* * *** *
995562 TTGCGATTCTTCGAAGATCGCATTGCGATTCTT-TGGCTCGCA
1 TTGCGATTCTT-GGA-ATCGCGTTGCGATT-TTCTCAATCGCG
* *
995604 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT--TTTGACCG
1 TTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTCAATCG--CG
**** * *
995646 TTGCGATT-TTCTTTTCAACGTTGCGATTTTCTAAATCGCG
1 TTGCGATTCTTGGAATC-GCGTTGCGATTTTCTCAATCGCG
995686 TTGCGATT-TT-GATATCGCGTTGCGATTTT
1 TTGCGATTCTTGGA-ATCGCGTTGCGATTTT
995715 GTTGGTCATT
Statistics
Matches: 194, Mismatches: 26, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
39 15 0.08
40 79 0.41
41 5 0.03
42 61 0.31
43 30 0.15
44 4 0.02
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.41
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
Found at i:995550 original size:63 final size:62
Alignment explanation
Indices: 995452--995637 Score: 209
Period size: 63 Copynumber: 3.0 Consensus size: 62
995442 CGATTCTTGG
* *
995452 AATCGCGTTGCG--ATTTTCTCAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATATTTTCTCGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTA
* * *
995512 AATCGCGTTGCGATTATTTTCTCGATCGCGTTGCGATTCTTTGAATCGCATTGCGATTCTTCGA
1 AATCGCGTTGCGA-TATTTTCTCGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT-TTCTA
* * * * *
995576 AGATCGCATTGCGAT-TCTT-TGGCTCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATATTTTCTCGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCT
995638 TTTGACCGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
60 12 0.11
62 18 0.17
63 47 0.44
64 18 0.17
65 11 0.10
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (62 bp):
AATCGCGTTGCGATATTTTCTCGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTA
Found at i:995592 original size:42 final size:41
Alignment explanation
Indices: 995439--995637 Score: 199
Period size: 42 Copynumber: 4.8 Consensus size: 41
995429 TTTTGCCGTT
* *
995439 TTGCGATTCTTGGA-ATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGAAGATCGCGTTGCGATTTTCTCAATCGCA
* *
995479 TTGCGATTCTTGGA-ATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGAAGATCGCGTTGCGATTTTCTCAATCGCA
* *** *
995519 TTGCGATTATTTTCTCGATCGCGTTGCGATTCTT-TGAATCGCA
1 TTGCGA-T-TCTTGAAGATCGCGTTGCGATT-TTCTCAATCGCA
* ***
995562 TTGCGATTCTTCGAAGATCGCATTGCGATTCTT-TGGCTCGCA
1 TTGCGATTCTT-GAAGATCGCGTTGCGATT-TTCTCAATCGCA
995604 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 TTGCGATTCTT-GAAGATCGCGTTGCGATTTTCT
995638 TTTGACCGTT
Statistics
Matches: 138, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
40 46 0.33
41 6 0.04
42 57 0.41
43 27 0.20
44 2 0.01
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (41 bp):
TTGCGATTCTTGAAGATCGCGTTGCGATTTTCTCAATCGCA
Found at i:995687 original size:20 final size:20
Alignment explanation
Indices: 995452--995714 Score: 153
Period size: 20 Copynumber: 12.8 Consensus size: 20
995442 CGATTCTTGG
*
995452 AATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTA
**
995472 AATCGCGTTGCGATTCTT-GG
1 AATCGCGTTGCGATT-TTCTA
*
995492 AATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTA
*
995512 AATCGCGTTGCGATTATTTTCTC
1 AATCGCGTTGCG---ATTTTCTA
* *
995535 GATCGCGTTGCGATTCTT-TG
1 AATCGCGTTGCGATT-TTCTA
* *
995555 AATCGCATTGCGATTCTTCGA
1 AATCGCGTTGCGATT-TTCTA
* *
995576 AGATCGCATTGCGATTCTT-TG
1 A-ATCGCGTTGCGATT-TTCTA
** * **
995597 GCTCGCATTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
995618 AGATCGCGTTGCGATTTTCT-
1 A-ATCGCGTTGCGATTTTCTA
* *
995638 -TTTGACCGTTGCGATTTTCT-
1 AATCG--CGTTGCGATTTTCTA
** *
995658 TTTCAACGTTGCGATTTTCTA
1 AATC-GCGTTGCGATTTTCTA
*
995679 AATCGCGTTGCGATTTT-GA
1 AATCGCGTTGCGATTTTCTA
*
995698 TATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
995715 GTTGGTCATT
Statistics
Matches: 198, Mismatches: 30, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.01
19 19 0.10
20 118 0.60
21 11 0.06
22 29 0.15
23 19 0.10
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCTA
Found at i:1003546 original size:14 final size:14
Alignment explanation
Indices: 1003527--1003554 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1003517 TGAGGATCAA
1003527 ATTAATTATTATTT
1 ATTAATTATTATTT
1003541 ATTAATTATTATTT
1 ATTAATTATTATTT
1003555 TTATCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTAATTATTATTT
Found at i:1003877 original size:11 final size:11
Alignment explanation
Indices: 1003857--1003902 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1003847 TCATATATTT
*
1003857 AAAATTCAATA
1 AAAATACAATA
1003868 AAAATACAATA
1 AAAATACAATA
*
1003879 AAAA-A-AATT
1 AAAATACAATA
*
1003888 AAAATTCAATA
1 AAAATACAATA
1003899 AAAA
1 AAAA
1003903 GAATGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.24
10 1 0.03
11 21 0.72
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATACAATA
Found at i:1003912 original size:20 final size:20
Alignment explanation
Indices: 1003868--1003916 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1003858 AAATTCAATA
1003868 AAAATACAATAAAAAAAATT
1 AAAATACAATAAAAAAAATT
* *
1003888 AAAATTCAATAAAAAGAATGT
1 AAAATACAATAAAAAAAAT-T
1003909 -AAATACAA
1 AAAATACAA
1003917 AATATCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATACAATAAAAAAAATT
Found at i:1003971 original size:7 final size:7
Alignment explanation
Indices: 1003959--1003986 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1003949 AATAATAATT
1003959 TAAAATA
1 TAAAATA
1003966 TAAAATA
1 TAAAATA
1003973 TAAAATA
1 TAAAATA
1003980 TAAAATA
1 TAAAATA
1003987 AATATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAAATA
Found at i:1004906 original size:17 final size:17
Alignment explanation
Indices: 1004884--1004916 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1004874 TAATTATACG
1004884 TTAAATATTT-TAAATTT
1 TTAAAT-TTTATAAATTT
1004901 TTAAATTTTATAAATT
1 TTAAATTTTATAAATT
1004917 AAATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATTTTATAAATTT
Found at i:1015089 original size:20 final size:21
Alignment explanation
Indices: 1015050--1015090 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1015040 CAGTCTGAAT
1015050 GCTGAACGGTTCAACATTCAGC
1 GCTGAACGGTTC-ACATTCAGC
*
1015072 GCTGAATGGTTC-CATTCAG
1 GCTGAACGGTTCACATTCAG
1015091 AGCCAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
GCTGAACGGTTCACATTCAGC
Found at i:1018241 original size:31 final size:31
Alignment explanation
Indices: 1018203--1018424 Score: 381
Period size: 31 Copynumber: 7.2 Consensus size: 31
1018193 GGTCACAATA
1018203 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
1018234 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1018265 CAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
1018296 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1018327 CAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1018358 TAGACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1018389 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1018420 TAAAC
1 TAAAC
1018425 CCTCGACTCT
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 177 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:1019009 original size:64 final size:64
Alignment explanation
Indices: 1018930--1019109 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 64
1018920 TTTTAATGAA
* * * * * **
1018930 GGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCT
1 GGTATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGT-GTCACTATTAAT
* * ** *
1018994 GGTATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAT
1 GGTATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTGTCACTATTAAT
* * **
1019058 GGGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 GGTATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGT
1019110 CTTTATTTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 99 0.99
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (64 bp):
GGTATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTGTCACTATTAAT
Found at i:1019906 original size:16 final size:16
Alignment explanation
Indices: 1019885--1019915 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1019875 ATAGTTTGGG
1019885 ATGTTACATGATATGT
1 ATGTTACATGATATGT
1019901 ATGTTACATGATATG
1 ATGTTACATGATATG
1019916 AACTTATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (16 bp):
ATGTTACATGATATGT
Found at i:1020252 original size:31 final size:31
Alignment explanation
Indices: 1020168--1020273 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
1020158 GTCGAGGGTT
* * *
1020168 TACCTATGTTTTACGGAACATATGGACAGAA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
* *
1020199 TTACCTATGACTT-T-TGGGACATATGGACAGTA
1 -TACCTATG--TTCTAAGGAACATATGGACAGTA
*
1020231 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTA
*
1020262 TACCTAGGTTCT
1 TACCTATGTTCT
1020274 TCGGGACCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
29 2 0.03
30 1 0.02
31 34 0.54
32 23 0.37
33 1 0.02
34 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:1020286 original size:31 final size:31
Alignment explanation
Indices: 1020214--1020293 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
1020204 TATGACTTTT
* *
1020214 GGGACATATGGACAGTATACCTATGTTCTAA
1 GGGACATATGGACAGTTTACCTAGGTTCTAA
* **
1020245 GGAACATATGGACAGTTTACCTAGGTTCTTC
1 GGGACATATGGACAGTTTACCTAGGTTCTAA
* *
1020276 GGGACCTATGGATAGTTT
1 GGGACATATGGACAGTTT
1020294 TCGAGGTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (31 bp):
GGGACATATGGACAGTTTACCTAGGTTCTAA
Found at i:1025360 original size:16 final size:17
Alignment explanation
Indices: 1025337--1025385 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1025327 ATTAGTTTAT
1025337 GTTCGGGTTGCTTTCAG
1 GTTCGGGTTGCTTTCAG
***
1025354 G-TCGGGTTAAATTC-G
1 GTTCGGGTTGCTTTCAG
1025369 GTTCGGGTTGCTTTCAG
1 GTTCGGGTTGCTTTCAG
1025386 ATCGAGTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.10, C:0.16, G:0.35, T:0.39
Consensus pattern (17 bp):
GTTCGGGTTGCTTTCAG
Found at i:1025378 original size:32 final size:33
Alignment explanation
Indices: 1025337--1025416 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 33
1025327 ATTAGTTTAT
* *
1025337 GTTCGGGTTGCTTTCAGGTCGGGTT-AAATTCG
1 GTTCGGGTTGCTTTCAGATCGAGTTAAAATTCG
1025369 GTTCGGGTTGCTTTCAGATCGAGTTAAAATTCG
1 GTTCGGGTTGCTTTCAGATCGAGTTAAAATTCG
* *
1025402 GTTCAGGTTTCTTTC
1 GTTCGGGTTGCTTTC
1025417 GGTTTGGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 23 0.53
33 20 0.47
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (33 bp):
GTTCGGGTTGCTTTCAGATCGAGTTAAAATTCG
Found at i:1027950 original size:60 final size:58
Alignment explanation
Indices: 1027884--1028068 Score: 180
Period size: 60 Copynumber: 3.1 Consensus size: 58
1027874 TTTGGATGAA
* * *
1027884 TTTGGGGATGAAATTAGAATATCTAAAAGTTTAGGGACCAATTTATAATGAGATTCATAG
1 TTTGGGGATGAAATTAGAATAT-TAAAAGTTTAAGGACTAATTTA-AATGAGAGTCATAG
* *
1027944 TTTGGGGAT-AATATTAAAATATTCAAAA-TTTAAGGTCTAATTTAGAA--AGAGTCATAG
1 TTTGGGGATGAA-ATTAGAATATT-AAAAGTTTAAGGACTAATTTA-AATGAGAGTCATAG
* * * * * *
1028001 TTTGAGGATGAAACTGGAATGATTGAGAGTTTAAAGACTAATTTGAAATGAGAGTCATAG
1 TTTGGGGATGAAATTAGAAT-ATTAAAAGTTTAAGGACTAATTT-AAATGAGAGTCATAG
1028061 TTTGGGGA
1 TTTGGGGA
1028069 CATATGATGA
Statistics
Matches: 102, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
57 24 0.24
58 20 0.20
59 19 0.19
60 39 0.38
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (58 bp):
TTTGGGGATGAAATTAGAATATTAAAAGTTTAAGGACTAATTTAAATGAGAGTCATAG
Found at i:1028733 original size:77 final size:77
Alignment explanation
Indices: 1028600--1028742 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 77
1028590 ATGAATGTTT
* * *
1028600 TACCTCTTTTACAAGGGTTCTAAGTTCAATCTTCCCTAATAATAACATTTTATCTTCATTTTCAT
1 TACCTCTTTTACAAAGGTTCTAAGTTCAATCCTCCCTAATAATAACATTTTATCTTCATCTTCAT
1028665 TCACAAACAAAG
66 TCACAAACAAAG
** * * *
1028677 TACCTCTTTTACAAAGGTTCTAAGTTTGATCCTCTCTAATAGTTACA-TTTAGTCTTCATCTTCA
1 TACCTCTTTTACAAAGGTTCTAAGTTCAATCCTCCCTAATAATAACATTTTA-TCTTCATCTTCA
1028741 TT
65 TT
1028743 AATCAATAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 4 0.07
77 53 0.93
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.42
Consensus pattern (77 bp):
TACCTCTTTTACAAAGGTTCTAAGTTCAATCCTCCCTAATAATAACATTTTATCTTCATCTTCAT
TCACAAACAAAG
Found at i:1036203 original size:21 final size:21
Alignment explanation
Indices: 1036178--1036241 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
1036168 TTGTCAACCG
1036178 CTGTGGACTACCACATCAACA
1 CTGTGGACTACCACATCAACA
*
1036199 CTGTGGACAACCACATCAACA
1 CTGTGGACTACCACATCAACA
* *
1036220 CTTTGAACTACCACATCAACA
1 CTGTGGACTACCACATCAACA
1036241 C
1 C
1036242 GTAATGGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.19
Consensus pattern (21 bp):
CTGTGGACTACCACATCAACA
Found at i:1036422 original size:31 final size:32
Alignment explanation
Indices: 1036384--1036470 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 32
1036374 CATTTTTACC
*
1036384 TAAATTTAATGATCATTTTGTAACAGTT-CAA
1 TAAATTTAATGATCATTTTGTAACAGTTAAAA
* **
1036415 TAAATTTAATGTTCATTTTGTAACTTTTAAAA
1 TAAATTTAATGATCATTTTGTAACAGTTAAAA
* * *
1036447 AAAAATTAATGATCATTTTATAAC
1 TAAATTTAATGATCATTTTGTAAC
1036471 TTTTAAAAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (32 bp):
TAAATTTAATGATCATTTTGTAACAGTTAAAA
Found at i:1036463 original size:32 final size:32
Alignment explanation
Indices: 1036389--1036478 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
1036379 TTACCTAAAT
** * * *
1036389 TTAATGATCATTTTGTAACAGTT-CAATAAAT
1 TTAATGATCATTTTGTAACTTTTAAAAAAAAA
*
1036420 TTAATGTTCATTTTGTAACTTTTAAAAAAAAA
1 TTAATGATCATTTTGTAACTTTTAAAAAAAAA
*
1036452 TTAATGATCATTTTATAACTTTTAAAA
1 TTAATGATCATTTTGTAACTTTTAAAA
1036479 GTTTAGTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 20 0.40
32 30 0.60
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (32 bp):
TTAATGATCATTTTGTAACTTTTAAAAAAAAA
Found at i:1038612 original size:31 final size:31
Alignment explanation
Indices: 1038574--1038634 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
1038564 AATTGGTAAC
1038574 CATATCTTAATTAAATAAAAACGAAAGTGAT
1 CATATCTTAATTAAATAAAAACGAAAGTGAT
*
1038605 CATATCTTAATTAAATAAAAATGAAAGTGA
1 CATATCTTAATTAAATAAAAACGAAAGTGA
1038635 CCCTATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (31 bp):
CATATCTTAATTAAATAAAAACGAAAGTGAT
Found at i:1040728 original size:109 final size:110
Alignment explanation
Indices: 1040536--1040749 Score: 295
Period size: 109 Copynumber: 2.0 Consensus size: 110
1040526 CACTGTGCAT
* * * *
1040536 TACATGAGAAAAAGAAAGGTTATGAACAGGATTGGTTCAAATGATATACAGTTTAATAAGAATTA
1 TACATGAGAAAAAGAAAGGTTACGAACAGGATTGGTTCAAATGATAAACAATTTAATAAGAACTA
* * *
1040601 AGTAAGTTTCGAGTTCGAGTCTTTGTGTAAATAAAAAATCCCTGC
66 AGCAAGTTTCGAATTCGAGCCTTTGTGTAAATAAAAAATCCCTGC
* * * * *
1040646 TACATGAGAAAAAGAAATGTTACGAAC-GGGTTGGTTCAAGTGATAAACAATTTAATATGACCTA
1 TACATGAGAAAAAGAAAGGTTACGAACAGGATTGGTTCAAATGATAAACAATTTAATAAGAACTA
* *
1040710 AGCAAGTTTCGAATTCGAGCCTTTGTGTATATATAAAATC
66 AGCAAGTTTCGAATTCGAGCCTTTGTGTAAATAAAAAATC
1040750 ATTGCTTGGA
Statistics
Matches: 90, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
109 65 0.72
110 25 0.28
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (110 bp):
TACATGAGAAAAAGAAAGGTTACGAACAGGATTGGTTCAAATGATAAACAATTTAATAAGAACTA
AGCAAGTTTCGAATTCGAGCCTTTGTGTAAATAAAAAATCCCTGC
Found at i:1042311 original size:21 final size:23
Alignment explanation
Indices: 1042287--1042334 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1042277 ACTTAACGTT
1042287 AAATTTTGAAC-A-GAGATACTA
1 AAATTTTGAACGAGGAGATACTA
*
1042308 AAATTTTGAACGAGGATATACTA
1 AAATTTTGAACGAGGAGATACTA
1042331 AAAT
1 AAAT
1042335 GAAACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 1 0.04
23 12 0.50
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (23 bp):
AAATTTTGAACGAGGAGATACTA
Found at i:1043974 original size:26 final size:28
Alignment explanation
Indices: 1043928--1043981 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
1043918 ATTGACCCGA
1043928 AAATCTAAAAGTTGACACGAACCGAAAC
1 AAATCTAAAAGTTGACACGAACCGAAAC
*
1043956 AAATCT-AAA-TTGACCCGAACCGAAAC
1 AAATCTAAAAGTTGACACGAACCGAAAC
1043982 CAACCGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.64
27 3 0.12
28 6 0.24
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.15
Consensus pattern (28 bp):
AAATCTAAAAGTTGACACGAACCGAAAC
Found at i:1044002 original size:31 final size:30
Alignment explanation
Indices: 1043939--1044074 Score: 100
Period size: 31 Copynumber: 4.5 Consensus size: 30
1043929 AATCTAAAAG
* *
1043939 TTGACACGAACCGAAA-CAA--ATCT-AAA
1 TTGACCCGAACCGAAACCAACCATCTGATA
1043965 TTGACCCGAACCGAAACCAACCGATCTGATA
1 TTGACCCGAACCGAAACCAACC-ATCTGATA
* * *
1043996 TTGACCCGACCCAAAACCAACCAATCTGACA
1 TTGACCCGAACCGAAACCAACC-ATCTGATA
* * * * *
1044027 ATAACCCAAACCGGAAGCCAACCATTCTGATT
1 TTGACCCGAACC-GAAACCAACCA-TCTGATA
* *
1044059 TTGATCCGACCCGAAA
1 TTGACCCGAACCGAAA
1044075 ATCAATTGAT
Statistics
Matches: 83, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
26 15 0.18
27 3 0.04
30 4 0.05
31 41 0.49
32 20 0.24
ACGTcount: A:0.39, C:0.32, G:0.13, T:0.16
Consensus pattern (30 bp):
TTGACCCGAACCGAAACCAACCATCTGATA
Found at i:1044183 original size:15 final size:14
Alignment explanation
Indices: 1044163--1044201 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1044153 AGTATGACTT
1044163 GAAATGATCCGATTC
1 GAAATGATCCGA-TC
*
1044178 GAAATGACCCGATC
1 GAAATGATCCGATC
*
1044192 CAAATGATCC
1 GAAATGATCC
1044202 AATTGCCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (14 bp):
GAAATGATCCGATC
Found at i:1046254 original size:11 final size:11
Alignment explanation
Indices: 1046238--1046266 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1046228 AGGATGCAAT
1046238 GGGTCGGGTTA
1 GGGTCGGGTTA
1046249 GGGTCGGGTTA
1 GGGTCGGGTTA
1046260 GGGTCGG
1 GGGTCGG
1046267 TTTTTGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.59, T:0.24
Consensus pattern (11 bp):
GGGTCGGGTTA
Found at i:1046345 original size:32 final size:34
Alignment explanation
Indices: 1046287--1046352 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
1046277 ACCCGACCCG
*
1046287 AAAATATACATCCTCCACCTGAACTCG-ATCCGA
1 AAAATATACATCCTCCACCCGAACTCGAATCCGA
*
1046320 AAAATATATA-CCTTCCACCCG-ACTCGAATCCGA
1 AAAATATACATCC-TCCACCCGAACTCGAATCCGA
1046353 CCCGACCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.36, C:0.33, G:0.09, T:0.21
Consensus pattern (34 bp):
AAAATATACATCCTCCACCCGAACTCGAATCCGA
Found at i:1048143 original size:36 final size:36
Alignment explanation
Indices: 1048098--1048227 Score: 161
Period size: 36 Copynumber: 3.6 Consensus size: 36
1048088 CCTTCACCAG
* * *
1048098 CTTACGTCTATAAGTCACCACCCCCACCAACTCCCA
1 CTTATGTCTACAAGTCACCACCACCACCAACTCCCA
* * * * *
1048134 CTTATGTCTACAAGTCACCTCCTCCATCATCTCCTA
1 CTTATGTCTACAAGTCACCACCACCACCAACTCCCA
*
1048170 CTTATGTCTATAAGTCACCACCACCACCAACTCCCA
1 CTTATGTCTACAAGTCACCACCACCACCAACTCCCA
* *
1048206 CATATGTCTACAAATCACCACC
1 CTTATGTCTACAAGTCACCACC
1048228 TCCTCTGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 78 1.00
ACGTcount: A:0.28, C:0.42, G:0.05, T:0.25
Consensus pattern (36 bp):
CTTATGTCTACAAGTCACCACCACCACCAACTCCCA
Found at i:1048371 original size:36 final size:35
Alignment explanation
Indices: 1048291--1048479 Score: 98
Period size: 36 Copynumber: 5.6 Consensus size: 35
1048281 CTCCATAATA
* * * *
1048291 CTACAAGTCACCTCCTCCACC-GTCACCTACCTTTGT
1 CTACAAGTCACCACCACCACCACTC-CC-ACCTATGT
* *
1048327 TTATAAGTCACCACCACCACCAACTCCCACCTATGT
1 CTACAAGTCACCACCACCACC-ACTCCCACCTATGT
* *
1048363 CTACAAGT---CACCACC-TC-CTCCC-CATAT-T
1 CTACAAGTCACCACCACCACCACTCCCACCTATGT
* *
1048391 ACTACAAGTCTCCACCACCACCATCCCCCACCTATGT
1 -CTACAAGTCACCACCACCACCA-CTCCCACCTATGT
* * * * *
1048428 TTACAAGTCACCTCCTCCTCCAC-CACA-CTA---
1 CTACAAGTCACCACCACCACCACTCCCACCTATGT
*
1048458 CTACAAGTCTCCACCACCACCA
1 CTACAAGTCACCACCACCACCA
1048480 GTCTACTCTC
Statistics
Matches: 118, Mismatches: 24, Indels: 28
0.69 0.14 0.16
Matches are distributed among these distances:
28 1 0.01
29 12 0.10
30 22 0.19
32 8 0.07
33 11 0.09
34 3 0.03
35 5 0.04
36 51 0.43
37 3 0.03
38 2 0.02
ACGTcount: A:0.26, C:0.46, G:0.05, T:0.22
Consensus pattern (35 bp):
CTACAAGTCACCACCACCACCACTCCCACCTATGT
Found at i:1048380 original size:72 final size:71
Alignment explanation
Indices: 1048070--1048445 Score: 229
Period size: 72 Copynumber: 5.2 Consensus size: 71
1048060 ACCGTATTAT
* * * *
1048070 TACAAGTCTCCACCGCCACCTTCACC-AGCTTACGTCTATAAGTCACCACCCCCACCAACTCCCA
1 TACAAGTCACCACCTCCACC-TCACCTA-CTTATGTCTATAAGTCACCACCACCACCAACTCCCA
*
1048134 CTTATGTC
64 CCTATGTC
* * *
1048142 TACAAGTCACCTCCTCCATCATCTCCTACTTATGTCTATAAGTCACCACCACCACCAACTCCCAC
1 TACAAGTCACCACCTCCA-CCTCACCTACTTATGTCTATAAGTCACCACCACCACCAACTCCCAC
*
1048207 ATATGTC
65 CTATGTC
* * * ** * * *
1048214 TACAAATCACCACCTCC-TCTGAAATAC-TA--T-TAAAAGTCTCCAACACCACCGAAACACGTT
1 TACAAGTCACCACCTCCACCTCACCTACTTATGTCTATAAGTCACCACCACCACC---A-AC--T
*** *
1048274 GAGAATCCTCCATAATAC
60 -CCCA-CCT--AT-GT-C
* *
1048292 TACAAGTCACCTCCTCCACCGTCACCTACCTT-TGTTTATAAGTCACCACCACCACCAACTCCCA
1 TACAAGTCACCACCTCCACC-TCACCTA-CTTATGTCTATAAGTCACCACCACCACCAACTCCCA
1048356 CCTATGTC
64 CCTATGTC
* * * * * *
1048364 TACAAGTCACCACCTCCTCC-C-CATA-TTA---CTACAAGTCTCCACCACCACCATCCCCCACC
1 TACAAGTCACCACCTCCACCTCACCTACTTATGTCTATAAGTCACCACCACCACCAACTCCCACC
*
1048423 TATGTT
66 TATGTC
*
1048429 TACAAGTCACCTCCTCC
1 TACAAGTCACCACCTCC
1048446 TCCACCACAC
Statistics
Matches: 235, Mismatches: 47, Indels: 51
0.71 0.14 0.15
Matches are distributed among these distances:
65 47 0.20
66 17 0.07
67 3 0.01
69 6 0.03
70 7 0.03
72 95 0.40
73 4 0.02
74 4 0.02
76 5 0.02
77 2 0.01
78 17 0.07
79 1 0.00
80 6 0.03
81 2 0.01
82 1 0.00
83 1 0.00
84 17 0.07
ACGTcount: A:0.28, C:0.41, G:0.07, T:0.24
Consensus pattern (71 bp):
TACAAGTCACCACCTCCACCTCACCTACTTATGTCTATAAGTCACCACCACCACCAACTCCCACC
TATGTC
Found at i:1048412 original size:65 final size:66
Alignment explanation
Indices: 1048331--1048479 Score: 228
Period size: 65 Copynumber: 2.3 Consensus size: 66
1048321 CTTTGTTTAT
* * * *
1048331 AAGTCACCACCACCACCAACTCCCACCTATGTCTACAAGTCACCACCTCCTCC-CCATATTACTA
1 AAGTCTCCACCACCACCAACCCCCACCTATGTCTACAAGTCACCACCTCCTCCACCACACTACTA
1048395 C
66 C
* * *
1048396 AAGTCTCCACCACCACCATCCCCCACCTATGTTTACAAGTCACCTCCTCCTCCACCACACTACTA
1 AAGTCTCCACCACCACCAACCCCCACCTATGTCTACAAGTCACCACCTCCTCCACCACACTACTA
1048461 C
66 C
1048462 AAGTCTCCACCACCACCA
1 AAGTCTCCACCACCACCA
1048480 GTCTACTCTC
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
65 48 0.63
66 28 0.37
ACGTcount: A:0.28, C:0.48, G:0.05, T:0.19
Consensus pattern (66 bp):
AAGTCTCCACCACCACCAACCCCCACCTATGTCTACAAGTCACCACCTCCTCCACCACACTACTA
C
Found at i:1048508 original size:48 final size:49
Alignment explanation
Indices: 1048447--1048575 Score: 163
Period size: 48 Copynumber: 2.7 Consensus size: 49
1048437 ACCTCCTCCT
* * *
1048447 CCACCACACTACTACAAGTCTCCACCACCACCAGTCTAC-TCTCTACCA
1 CCACCATACTACTACAAGTCTCCACCACCACCAGTCTACATCACCACCA
* * * *
1048495 CCACCATATTACTACAAGTCTCCACCACCACC-TTCTTCATCACCACCT
1 CCACCATACTACTACAAGTCTCCACCACCACCAGTCTACATCACCACCA
* *
1048543 TCACCGTACTACTACAAGTCTCCACCACCACCA
1 CCACCATACTACTACAAGTCTCCACCACCACCA
1048576 AAGCATGTAG
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 4 0.06
48 65 0.94
ACGTcount: A:0.29, C:0.47, G:0.04, T:0.21
Consensus pattern (49 bp):
CCACCATACTACTACAAGTCTCCACCACCACCAGTCTACATCACCACCA
Found at i:1048642 original size:24 final size:24
Alignment explanation
Indices: 1048594--1048643 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1048584 AGAGCAACCC
* * *
1048594 CCATACTACTACAAGTCTCCTCCA
1 CCATACTACTACAAATCACCCCCA
*
1048618 CCATACTATTACAAATCACCCCCA
1 CCATACTACTACAAATCACCCCCA
1048642 CC
1 CC
1048644 CCCACCGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.44, G:0.02, T:0.22
Consensus pattern (24 bp):
CCATACTACTACAAATCACCCCCA
Found at i:1048840 original size:48 final size:47
Alignment explanation
Indices: 1048785--1048960 Score: 162
Period size: 48 Copynumber: 3.7 Consensus size: 47
1048775 TCCTCCACTG
*
1048785 GTTCACTCTCCACCACCACCCTACTACTACAAGTCTCCACCACCACCA
1 GTTCACTCTCCACCACCACCATACTACTACAAGTCTCC-CCACCACCA
* *
1048833 GTTCACTCTCCACCACTC-CCATACTACTACAAGTC-CCCTTCTCCA-CT
1 GTTCACTCTCCACCAC-CACCATACTACTACAAGTCTCCC--CACCACCA
* * *
1048880 GTCTC-CATCTCCTCCTCCACCATACTACTACAAATCTCTCCCACCACCA
1 GT-TCAC-TCTCCACCACCACCATACTACTACAAGTCTC-CCCACCACCA
* * * * *
1048929 GTCCACTCTTCACCACTACCATATTATTACAA
1 GTTCACTCTCCACCACCACCATACTACTACAA
1048961 ATCGACACCC
Statistics
Matches: 103, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
46 1 0.01
47 7 0.07
48 87 0.84
49 6 0.06
50 2 0.02
ACGTcount: A:0.26, C:0.46, G:0.03, T:0.25
Consensus pattern (47 bp):
GTTCACTCTCCACCACCACCATACTACTACAAGTCTCCCCACCACCA
Found at i:1052735 original size:17 final size:17
Alignment explanation
Indices: 1052692--1052743 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1052682 CGTACATTAG
*
1052692 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
1052709 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
1052724 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
1052741 AAA
1 AAA
1052744 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:1053611 original size:2 final size:2
Alignment explanation
Indices: 1053604--1053644 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1053594 CTCATTGAAC
1053604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1053645 GCAAACTCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1056435 original size:24 final size:23
Alignment explanation
Indices: 1056392--1056436 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1056382 ATTAAATATA
* *
1056392 AATAAATTAAAAGAACACAAACG
1 AATAAAATAAAAGAAAACAAACG
1056415 AATAAAATAAAATGAAAACAAA
1 AATAAAATAAAA-GAAAACAAA
1056437 AGGATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.71, C:0.09, G:0.07, T:0.13
Consensus pattern (23 bp):
AATAAAATAAAAGAAAACAAACG
Found at i:1057189 original size:63 final size:59
Alignment explanation
Indices: 1057064--1057293 Score: 298
Period size: 59 Copynumber: 3.8 Consensus size: 59
1057054 GGCACGTTAT
* * * * *
1057064 GAAGACTTAATGCTTTGGGGTTTGAGCTAAAAGAACTAACATCACATGGAGAACGTTGC
1 GAAGGCTTAATGCTCTGGGGTTTGAGCTAAAAAAACTAACATCACGTGGAGAGCGTTGC
* *
1057123 GAAGGCTTAATGCTTTGGGGTTTGAGCTGAAAAAAAAAACTAACATCACGTGGAGAGCGTTTC
1 GAAGGCTTAATGCTCTGGGGTTTGAGCT----AAAAAAACTAACATCACGTGGAGAGCGTTGC
* *
1057186 GAAGGCTTAATGCTCTGGGGTTTGAGCTAAAAAAACTAACATCACGTGGGGGGCGTTGC
1 GAAGGCTTAATGCTCTGGGGTTTGAGCTAAAAAAACTAACATCACGTGGAGAGCGTTGC
* *** *
1057245 GAAGGCTTAATGCTCTAGGGTTTGAGGGGAAAAAACTAACATCATGTGG
1 GAAGGCTTAATGCTCTGGGGTTTGAGCTAAAAAAACTAACATCACGTGG
1057294 TGGGGAGGTA
Statistics
Matches: 153, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
59 99 0.65
63 54 0.35
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (59 bp):
GAAGGCTTAATGCTCTGGGGTTTGAGCTAAAAAAACTAACATCACGTGGAGAGCGTTGC
Found at i:1058498 original size:2 final size:2
Alignment explanation
Indices: 1058491--1058521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1058481 TCTAGCGAAA
1058491 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1058522 AGAACTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1074331 original size:21 final size:21
Alignment explanation
Indices: 1074282--1074343 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1074272 CGCAAATCAG
1074282 TTTCCAAAATCGCAATGCGAT
1 TTTCCAAAATCGCAATGCGAT
** * * *
1074303 AGTACAAATTCGCATTGCGAT
1 TTTCCAAAATCGCAATGCGAT
*
1074324 TTTCCAAAATCGCAACGCGA
1 TTTCCAAAATCGCAATGCGA
1074344 ATATGAAAAT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (21 bp):
TTTCCAAAATCGCAATGCGAT
Found at i:1074392 original size:20 final size:20
Alignment explanation
Indices: 1074330--1074523 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1074320 CGATTTTCCA
* ** *
1074330 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1074350 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1074370 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1074390 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1074410 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1074430 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1074450 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1074470 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1074490 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1074511 AAATCGCAACGCG
1 AAATCGCAACGCG
1074524 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1074400 original size:60 final size:60
Alignment explanation
Indices: 1074330--1074524 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
1074320 CGATTTTCCA
** * *
1074330 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * * *** *
1074390 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
1074450 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1074511 AAATCGCAACGCGA
1 AAATCGCAACGCGA
1074525 TATTTAAAGC
Statistics
Matches: 112, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1074945 original size:33 final size:33
Alignment explanation
Indices: 1074906--1074976 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1074896 TTCACTTAGA
*
1074906 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1074939 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1074972 TTTCA
1 TTTCA
1074977 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1075100 original size:20 final size:20
Alignment explanation
Indices: 1075056--1075165 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1075046 TGCAGAAGAG
*
1075056 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1075077 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1075097 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1075118 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1075132 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1075151 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1075166 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1075113 original size:41 final size:38
Alignment explanation
Indices: 1075049--1075165 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
1075039 TTCAATTTGC
* *
1075049 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1075087 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1075128 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1075161 AGAAT
1 AGAAT
1075166 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1075135 original size:14 final size:14
Alignment explanation
Indices: 1075116--1075172 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1075106 GAGAAATGAA
1075116 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1075130 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1075149 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1075163 AATCGCAACG
1 AATCGCAACG
1075173 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1075148 original size:33 final size:33
Alignment explanation
Indices: 1075108--1075187 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1075098 CGCAACGAGA
1075108 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1075141 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1075174 GAAACCAAAATCGC
1 GAAATGAAAATCGC
1075188 TTTGCGATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1075206 original size:19 final size:19
Alignment explanation
Indices: 1075184--1075297 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
1075174 GAAACCAAAA
*
1075184 TCGCTTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1075203 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1075217 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1075236 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1075256 CTCTCGTTGCGACAATCATT
1 -TCGCGTTGCGATTTTCATT
*
1075276 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1075296 TC
1 TC
1075298 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 28 0.36
20 21 0.27
21 13 0.17
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1075275 original size:40 final size:41
Alignment explanation
Indices: 1075214--1075297 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
1075204 CGCGTTGCGA
***
1075214 TTCTCTCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAATCATTCTCGCGTTGCGATTTTCAT
*
1075254 TTCTCTCGTTGCGACAATCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAATCATTCTCGCGTTGCGATTTTCAT
1075295 TTC
1 TTC
1075298 AACCAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 19 0.49
41 20 0.51
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.48
Consensus pattern (41 bp):
TTCTCTCGTTGCGACAATCATTCTCGCGTTGCGATTTTCAT
Found at i:1075279 original size:20 final size:20
Alignment explanation
Indices: 1075213--1075295 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
1075203 TCGCGTTGCG
1075213 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1075233 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1075252 ATTTCTCTCGTTGCGACAATC
1 A-TTCTCTCGTTGCGATTTTC
1075273 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1075293 ATT
1 ATT
1075296 TCAACCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.30
20 24 0.45
21 13 0.25
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1077154 original size:93 final size:93
Alignment explanation
Indices: 1076995--1077556 Score: 1081
Period size: 93 Copynumber: 6.1 Consensus size: 93
1076985 TAGATTGCTT
*
1076995 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1077060 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1077088 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1077153 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1077181 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1077246 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1077274 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1077339 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1077367 AGTAAATTTGTTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1077432 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1077460 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1077525 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1077552 AGTAA
1 AGTAA
1077557 TGCAATCCAT
Statistics
Matches: 462, Mismatches: 7, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 6 0.01
93 456 0.99
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1077644 original size:19 final size:19
Alignment explanation
Indices: 1077604--1077713 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
1077594 TAGTTTACTT
*
1077604 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAC-CAAAA
*
1077624 TCGCAATACGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
1077643 TCGC-A-ACG--A-CAGAA
1 TCGCAACACGAAACCAAAA
*
1077657 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
1077676 TCGC-A-ACG--A-CAAGA
1 TCGCAACACGAAACCAAAA
*
1077690 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
1077709 TCGCA
1 TCGCA
1077714 TTGCGATTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
14 16 0.23
15 4 0.06
16 4 0.06
17 5 0.07
18 4 0.06
19 25 0.35
20 13 0.18
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.09
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:1077669 original size:33 final size:32
Alignment explanation
Indices: 1077621--1077713 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1077611 ACGAAACTTA
**
1077621 AAATCGCAATACGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1077653 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1077686 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1077714 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1077731 original size:19 final size:19
Alignment explanation
Indices: 1077709--1077881 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
1077699 GAAACCAAAA
*
1077709 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1077728 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1077744 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1077761 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1077777 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1077794 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1077813 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1077832 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
* *
1077851 TCGTGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1077871 TCGTGTTGCGA
1 TCGCGTTGCGA
1077882 AAGTAAACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 78 0.61
20 13 0.10
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1077750 original size:14 final size:14
Alignment explanation
Indices: 1077731--1077787 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1077721 TTTCATTTCG
1077731 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1077745 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1077762 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1077778 CGTTGCGATT
1 CGTTGCGATT
1077788 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1077756 original size:33 final size:33
Alignment explanation
Indices: 1077714--1077806 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1077704 CAAAATCGCA
*
1077714 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1077747 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1077780 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1077807 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Done.