Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold813.1
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: 728368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2171 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1208 original size:18 final size:18
Alignment explanation
Indices: 1185--1222 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1175 GGGCTCCGCC
1185 CCGCACCCCTGGTCCATA
1 CCGCACCCCTGGTCCATA
1203 CCGCACCCCTGGTCCATA
1 CCGCACCCCTGGTCCATA
1221 CC
1 CC
1223 CCTGTCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.53, G:0.16, T:0.16
Consensus pattern (18 bp):
CCGCACCCCTGGTCCATA
Found at i:11004 original size:16 final size:16
Alignment explanation
Indices: 10983--11014 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10973 ATTTTGTTGC
*
10983 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
10999 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
11015 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:11300 original size:51 final size:50
Alignment explanation
Indices: 11242--11433 Score: 217
Period size: 51 Copynumber: 3.8 Consensus size: 50
11232 CCGGTTCACA
**
11242 TAGTAGCCTGCACATAGTACTACACATATGACCATCACTATCTAATACACG
1 TAGTAGCCTGCACATAGTACTACACATATGACCATCACT-TCTGGTACACG
* * * * ** *
11293 TAGTAGCCTGCACATAGTACTACACACATGATCA-AAGCTGTCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACATATGACCATCA-CT-TCTGGTACACG
* **
11344 TAGTAGCCTCCACATAGTACTACACATGCGACCTATCA-TTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATATGACC-ATCACTTCTGGTACACG
*
11394 TAGTAGCCTGCACATAGTACTACACATATGGCCATCACTT
1 TAGTAGCCTGCACATAGTACTACACATATGACCATCACTT
11434 TCACTTTCAC
Statistics
Matches: 113, Mismatches: 24, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
49 4 0.04
50 39 0.35
51 68 0.60
52 1 0.01
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATATGACCATCACTTCTGGTACACG
Found at i:11447 original size:101 final size:102
Alignment explanation
Indices: 11236--11459 Score: 251
Period size: 101 Copynumber: 2.2 Consensus size: 102
11226 ATGATACCGG
* *
11236 TTCACATAGTAGCCTGCACATAGTACTACACATATGACCATCACTATCTAATACACGTAGTAGCC
1 TTCACATAGTAGCCTACACATAGTACTACACATACGACCATCACTATCTAATACACGTAGTAGCC
*
11301 TGCACATAGTACTACACACATGATCAAAGCTGTCCGGT
66 TGCACATAGTACTACACACATGACCAAAGCTGTCC-GT
* * * * **
11339 AT-GCATAGTAGCCTCCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGC
1 TTCACATAGTAGCCTACACATAGTACTACACATACGACC-ATCACTATCTAATACACGTAGTAGC
* * * *
11401 CTGCACATAGTACTACACATATGGCCATCA-CTTTCAC-T
65 CTGCACATAGTACTACACACATGACCA-AAGCTGTC-CGT
*
11439 TTCACATAGTGGCCTACACAT
1 TTCACATAGTAGCCTACACAT
11460 TCACTTTCAC
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
100 2 0.02
101 59 0.58
102 35 0.35
103 5 0.05
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (102 bp):
TTCACATAGTAGCCTACACATAGTACTACACATACGACCATCACTATCTAATACACGTAGTAGCC
TGCACATAGTACTACACACATGACCAAAGCTGTCCGT
Found at i:11462 original size:26 final size:26
Alignment explanation
Indices: 11416--11484 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
11406 CATAGTACTA
*
11416 CACATA-TGGCC-ATCACTTTCACTTT
1 CACATAGTGGCCTA-CACATTCACTTT
11441 CACATAGTGGCCTACACATTCACTTT
1 CACATAGTGGCCTACACATTCACTTT
11467 CACATAGTGGCCTACACA
1 CACATAGTGGCCTACACA
11485 CAGTCCACGC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
25 6 0.15
26 34 0.83
27 1 0.02
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.29
Consensus pattern (26 bp):
CACATAGTGGCCTACACATTCACTTT
Found at i:19802 original size:14 final size:15
Alignment explanation
Indices: 19773--19805 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19763 TACAACAATT
*
19773 AATATTTTTAGTGAC
1 AATATTGTTAGTGAC
19788 AATATTGTT-GTGAC
1 AATATTGTTAGTGAC
19802 AATA
1 AATA
19806 AAAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (15 bp):
AATATTGTTAGTGAC
Found at i:21083 original size:16 final size:16
Alignment explanation
Indices: 21064--21095 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21054 ATTATTATAA
21064 AAATAAATTTAACATT
1 AAATAAATTTAACATT
21080 AAATAAATTTAACATT
1 AAATAAATTTAACATT
21096 TGTGAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAAATTTAACATT
Found at i:21747 original size:115 final size:116
Alignment explanation
Indices: 21564--21825 Score: 348
Period size: 115 Copynumber: 2.3 Consensus size: 116
21554 ATATATTTTT
* * * *
21564 ATTTTTATTTTTGGGATTTTAATAGAATTTTATGCCTCAATAATTTATTATCACATGGAAATGTT
1 ATTTTTATTTTTGGGAGTTTAATAGAATTTTAAGCCTCAATAATCTATTATCACATGAAAATGTT
*
21629 GCCTTATCTTTCTAAATAA-ATCA-ATTTAAAAAATTCTAGTAAATATTCCA
66 GCCTTATCTTTC-AAAAAAGATCATATTTAAAAAATTCTAGTAAATATTCCA
* * * * * *
21679 ATTTTTATTTTTGGAAGTTTATTAGAATTTTAAGCCTTAATGATCTATTATTACTTGAAAATGTT
1 ATTTTTATTTTTGGGAGTTTAATAGAATTTTAAGCCTCAATAATCTATTATCACATGAAAATGTT
* * *
21744 GCCTTATTTTTCAAAAAAGATTATATTTAAAAAATTCTAGTAAATTTTCCA
66 GCCTTATCTTTCAAAAAAGATCATATTTAAAAAATTCTAGTAAATATTCCA
* * *
21795 ATTTTTGTTGTTGGGAGTTTAATAGATTTTT
1 ATTTTTATTTTTGGGAGTTTAATAGAATTTT
21826 TTATTTTGCT
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
114 5 0.04
115 69 0.55
116 52 0.41
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (116 bp):
ATTTTTATTTTTGGGAGTTTAATAGAATTTTAAGCCTCAATAATCTATTATCACATGAAAATGTT
GCCTTATCTTTCAAAAAAGATCATATTTAAAAAATTCTAGTAAATATTCCA
Found at i:22184 original size:24 final size:25
Alignment explanation
Indices: 22150--22212 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
22140 TTTTTATAAG
* *
22150 ATTTAGTATTTATTAATATAATAT-
1 ATTTAGCATTTATTAACATAATATA
*
22174 ATTTAGCATTTATTAGCATAATATA
1 ATTTAGCATTTATTAACATAATATA
*
22199 ATTTA-CATTGATTA
1 ATTTAGCATTTATTA
22213 GAATTAGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTTAGCATTTATTAACATAATATA
Found at i:40261 original size:25 final size:24
Alignment explanation
Indices: 40221--40307 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 24
40211 CATGTTCATA
* *
40221 TATGCTCATACGAGCTGTGAATCGG
1 TATGCTCACACAAGCTGT-AATCGG
* *
40246 TATGCTCACTCAAGCTGTAGATCAG
1 TATGCTCACACAAGCTGTA-ATCGG
* * *
40271 TATGCTCTCACAAGTTATAAATCGG
1 TATGCTCACACAAGCTGT-AATCGG
*
40296 TATGCTCTCACA
1 TATGCTCACACA
40308 TGCTATGGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.02
25 49 0.96
26 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (24 bp):
TATGCTCACACAAGCTGTAATCGG
Found at i:42413 original size:45 final size:48
Alignment explanation
Indices: 42360--42461 Score: 138
Period size: 49 Copynumber: 2.2 Consensus size: 48
42350 TCCATATAGA
* * *
42360 ACTACACTTCTTTTATTT-TA-TT-TTAGAATAAGGTTTTTCAACCTT
1 ACTACACTTCATATATTTATATTTATTAGAATAAGGTATTTCAACCTT
*
42405 ATTACACTTCATATATTTGATATTTATTAGAATAAGGTATTTCAACCTT
1 ACTACACTTCATATATTT-ATATTTATTAGAATAAGGTATTTCAACCTT
42454 ACTACACT
1 ACTACACT
42462 CATTCTACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 15 0.31
47 2 0.04
48 2 0.04
49 29 0.60
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (48 bp):
ACTACACTTCATATATTTATATTTATTAGAATAAGGTATTTCAACCTT
Found at i:52633 original size:27 final size:27
Alignment explanation
Indices: 52602--52787 Score: 216
Period size: 27 Copynumber: 6.9 Consensus size: 27
52592 TAAACATGAT
*
52602 CGAAATCCCCTCGATGGGTAAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
* *
52629 CGAAATACCTTCGATGGGGAAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
* * *
52656 CAAAATACTCTCGATGGGGAAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
52683 CGAAATACCCTCGATAGGG-AAAATT-C
1 CGAAATACCCTCGAT-GGGTAAAATTAC
* *
52709 CTAAAATACCCTCGATGGATAAAATTAC
1 C-GAAATACCCTCGATGGGTAAAATTAC
* * *
52737 CGAAATACCCTCAATAGGTGAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
*
52764 CGAAATACCC-CTATAGGGTAAAAT
1 CGAAATACCCTCGAT-GGGTAAAAT
52788 GGCTGTTATA
Statistics
Matches: 136, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.05
27 124 0.91
28 5 0.04
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (27 bp):
CGAAATACCCTCGATGGGTAAAATTAC
Found at i:54555 original size:13 final size:13
Alignment explanation
Indices: 54537--54561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54527 TTTTATTTGT
54537 TTATTCCCACCGA
1 TTATTCCCACCGA
54550 TTATTCCCACCG
1 TTATTCCCACCG
54562 GCCGAATGTT
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:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:56592 original size:32 final size:32
Alignment explanation
Indices: 56549--56630 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
56539 ACGAGACTTG
*
56549 TACAACGCATTAATTAAATGTGTATATTCATA
1 TACAACTCATTAATTAAATGTGTATATTCATA
56581 TACAACTCATTAATTAAATGTGTATATTCATA
1 TACAACTCATTAATTAAATGTGTATATTCATA
*
56613 TACTACTCATTAATTAAA
1 TACAACTCATTAATTAAA
56631 AATTATTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.39
Consensus pattern (32 bp):
TACAACTCATTAATTAAATGTGTATATTCATA
Found at i:56816 original size:64 final size:64
Alignment explanation
Indices: 56747--57024 Score: 440
Period size: 64 Copynumber: 4.4 Consensus size: 64
56737 AAATAAAATA
* * * * *
56747 AAAATTAGATCATAACATATAATCAAGTAAACAAGTTGATTAAAAAACATATGGATAGTATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
*
56811 AAAATTGGATCATTACATATAATCAAGTAAACAAAC-TGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAAC-AACTTGATTAAAAAACATATGGATAATATATT
* *
56875 AAAATTGAATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATACGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
56939 --AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
57001 --AATTGGATCATTAGATATAATCAA
1 AAAATTGGATCATTAGATATAATCAA
57025 CTTGATTCTA
Statistics
Matches: 203, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
62 84 0.41
63 3 0.01
64 114 0.56
65 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
Found at i:56999 original size:126 final size:125
Alignment explanation
Indices: 56763--57024 Score: 429
Period size: 126 Copynumber: 2.1 Consensus size: 125
56753 AGATCATAAC
* * *
56763 ATATAATCAAGTAAACAAGTTGATTAAAAAACATATGGATAGTATATTAAAATTGGATCATTACA
1 ATATAATCAAGTAAACAACTTGATTAAAAAACATACGGATAATATATT-AAATTGGATCATTACA
56828 TATAATCAAGTAAACAAACTGATTAAAAAACATATGGATAATATATTAAAATTGAATCATTAG
65 TATAATCAAGTAAACAAACTGATTAAAAAACATATGGATAATATATT--AATTGAATCATTAG
*
56891 ATATAATCAAGTAAACAACTTGATTAAAAAACATACGGATAATATATT-AATTGGATCATTAGAT
1 ATATAATCAAGTAAACAACTTGATTAAAAAACATACGGATAATATATTAAATTGGATCATTACAT
*
56955 ATAATCAAGTAAAC-AACTTGATTAAAAAACATATGGATAATATATTAATTGGATCATTAG
66 ATAATCAAGTAAACAAAC-TGATTAAAAAACATATGGATAATATATTAATTGAATCATTAG
57015 ATATAATCAA
1 ATATAATCAA
57025 CTTGATTCTA
Statistics
Matches: 128, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
124 23 0.18
125 3 0.02
126 57 0.45
128 45 0.35
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (125 bp):
ATATAATCAAGTAAACAACTTGATTAAAAAACATACGGATAATATATTAAATTGGATCATTACAT
ATAATCAAGTAAACAAACTGATTAAAAAACATATGGATAATATATTAATTGAATCATTAG
Found at i:58689 original size:15 final size:17
Alignment explanation
Indices: 58651--58684 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
58641 TTTATTAACA
58651 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
58668 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
58685 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:58698 original size:16 final size:15
Alignment explanation
Indices: 58651--58698 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
58641 TTTATTAACA
*
58651 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
58668 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
58683 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
58699 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:58869 original size:39 final size:39
Alignment explanation
Indices: 58821--58929 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 39
58811 TTTTTTTCTT
* * *
58821 ATACTATTACACCTCTATTCCATTCAACCAAACACAAGA
1 ATACCATTACGCCTCTATTCCATTCAACCAAACAAAAGA
58860 ATACCATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGA
1 ATACCATTACGCCTCTATT-C----CATTCAACCAAACAAAAGA
58904 ATTACCTATTACGCCTCTATTCCATT
1 A-TACC-ATTACGCCTCTATTCCATT
58930 ACGCCTCTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
39 17 0.28
40 1 0.02
41 4 0.07
44 19 0.32
45 5 0.08
46 14 0.23
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (39 bp):
ATACCATTACGCCTCTATTCCATTCAACCAAACAAAAGA
Found at i:58904 original size:44 final size:46
Alignment explanation
Indices: 58841--58931 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
58831 ACCTCTATTC
*
58841 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
58885 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
58931 C
1 C
58932 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:58932 original size:16 final size:16
Alignment explanation
Indices: 58911--58947 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
58901 AGAATTACCT
58911 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
58927 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
58943 ATTAC
1 ATTAC
58948 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:60836 original size:32 final size:31
Alignment explanation
Indices: 60800--60932 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 31
60790 TGGCACAAAG
60800 CCATCAGTACTAGTGATATGATCAGTACACAA
1 CCATCAGTAC-AGTGATATGATCAGTACACAA
* * * *
60832 CCATCAGTAACGGTAACATGATCGGTACA-AA
1 CCATCAGT-ACAGTGATATGATCAGTACACAA
* * *
60863 GCCATTAGTAGCAGTGATATGAT-TGCCACACAA
1 -CCATCAGTA-CAGTGATATGATCAG-TACACAA
* *
60896 CCATCAGTAACAGTGAAATGATCGGTACACAA
1 CCATCAGT-ACAGTGATATGATCAGTACACAA
60928 CCATC
1 CCATC
60933 GGTAATGGTA
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
31 4 0.05
32 70 0.88
33 6 0.08
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (31 bp):
CCATCAGTACAGTGATATGATCAGTACACAA
Found at i:60879 original size:64 final size:62
Alignment explanation
Indices: 60794--60998 Score: 206
Period size: 64 Copynumber: 3.2 Consensus size: 62
60784 TGTGATTGGC
60794 ACAAAGCCATCAGTACTAGTGATATGATCAGTACACAACCATCAGTAACGGTAACATGATCGGT
1 ACAAAGCCATCAGTAC-AGTGATATGATCAG-ACACAACCATCAGTAACGGTAACATGATCGGT
* * *
60858 ACAAAGCCATTAGTAGCAGTGATATGATTGC-CACACAACCATCAGTAACAGTGAA-ATGATCGG
1 ACAAAGCCATCAGTA-CAGTGATATGA-T-CAGACACAACCATCAGTAACGGT-AACATGATCGG
60921 T
62 T
* *
60922 ACACAA-CCATCGGTA-ATGGTAATATGATCA-ACACAAAGCCATCAGTAACGGT-ACTATGATC
1 ACA-AAGCCATCAGTACA--GTGATATGATCAGACAC-AA-CCATCAGTAACGGTAAC-ATGATC
*
60983 GGC
60 GGT
60986 ACAAAGCCATCAG
1 ACAAAGCCATCAG
60999 CAGCATCGCA
Statistics
Matches: 119, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
62 7 0.06
63 5 0.04
64 100 0.84
65 6 0.05
66 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (62 bp):
ACAAAGCCATCAGTACAGTGATATGATCAGACACAACCATCAGTAACGGTAACATGATCGGT
Found at i:60943 original size:96 final size:96
Alignment explanation
Indices: 60769--60998 Score: 259
Period size: 96 Copynumber: 2.4 Consensus size: 96
60759 ATGTCTATAA
* * *
60769 CCATAAGT-GCAGTAATGTGATTGGCACAAAGCCATCAGTACTAGTGATATGATCAGTACACAAC
1 CCATAAGTAGCAGTAATATGATTGCCACAAAGCCATCAGTACTAGTGAAATGATCAGTACACAAC
***
60833 CATCAGTAACGGTAACATGATCGGTACAAAG
66 CATCAGTAACGGTAACATGATCAACACAAAG
* * *
60864 CCATTAGTAGCAGTGATATGATTGCCACACAA-CCATCAGTAAC-AGTGAAATGATCGGTACACA
1 CCATAAGTAGCAGTAATATGATTGCCACA-AAGCCATCAGT-ACTAGTGAAATGATCAGTACACA
* * *
60927 ACCATCGGTAATGGTAATATGATCAACACAAAG
64 ACCATCAGTAACGGTAACATGATCAACACAAAG
* * * * * *
60960 CCATCAGTAACGGTACTATGATCGGCACAAAGCCATCAG
1 CCATAAGTAGCAGTAATATGATTGCCACAAAGCCATCAG
60999 CAGCATCGCA
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
95 9 0.08
96 99 0.88
97 4 0.04
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (96 bp):
CCATAAGTAGCAGTAATATGATTGCCACAAAGCCATCAGTACTAGTGAAATGATCAGTACACAAC
CATCAGTAACGGTAACATGATCAACACAAAG
Found at i:60949 original size:32 final size:32
Alignment explanation
Indices: 60815--60998 Score: 153
Period size: 32 Copynumber: 5.8 Consensus size: 32
60805 AGTACTAGTG
*
60815 ATATGATCAGTACACAACCATCAGTAACGGTA
1 ATATGATCGGTACACAACCATCAGTAACGGTA
* * * * *
60847 ACATGATCGGTACA-AAGCCATTAGTAGCAGTG
1 ATATGATCGGTACACAA-CCATCAGTAACGGTA
* ** *
60879 ATATGATTGCCACACAACCATCAGTAACAGTGA
1 ATATGATCGGTACACAACCATCAGTAACGGT-A
* *
60912 A-ATGATCGGTACACAACCATCGGTAATGGTA
1 ATATGATCGGTACACAACCATCAGTAACGGTA
*
60943 ATATGATC--AACACAAAGCCATCAGTAACGGTA
1 ATATGATCGGTACAC-AA-CCATCAGTAACGGTA
* *
60975 CTATGATCGGCACA-AAGCCATCAG
1 ATATGATCGGTACACAA-CCATCAG
60999 CAGCATCGCA
Statistics
Matches: 120, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
30 4 0.03
31 6 0.05
32 104 0.87
33 3 0.03
34 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (32 bp):
ATATGATCGGTACACAACCATCAGTAACGGTA
Found at i:61081 original size:26 final size:26
Alignment explanation
Indices: 61003--61082 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 26
60993 CATCAGCAGC
*
61003 ATCGCAGCAAAGTTGCCAGAAACAAT
1 ATCGCAGCAAAGTTGCCAGAAACAGT
* * * *
61029 ATCGTAGTAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGTTGCCAGAAACAGT
* *
61055 ATCGCAGCAAAGTTGCCAGTAATAGT
1 ATCGCAGCAAAGTTGCCAGAAACAGT
61081 AT
1 AT
61083 ATGTGGCCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (26 bp):
ATCGCAGCAAAGTTGCCAGAAACAGT
Found at i:61241 original size:24 final size:25
Alignment explanation
Indices: 61209--61255 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
61199 ATCAGTCGTT
61209 CAAATCACAGAAAAATCAGTCATAC
1 CAAATCACAGAAAAATCAGTCATAC
**
61234 CAAA-CACAGACGAATCAGTCAT
1 CAAATCACAGAAAAATCAGTCAT
61256 TTAACCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.15
Consensus pattern (25 bp):
CAAATCACAGAAAAATCAGTCATAC
Found at i:61363 original size:27 final size:27
Alignment explanation
Indices: 61327--61539 Score: 236
Period size: 27 Copynumber: 8.0 Consensus size: 27
61317 GGCATTATGG
*
61327 TCATTTTACCCTACAGGGGTGTTACGA
1 TCATTTTACCCTACAGGGGTATTACGA
61354 TCATTTTACCCTACAGGGGTATTACGA
1 TCATTTTACCCTACAGGGGTATTACGA
* *
61381 TCTTTTTACCCTATAGGGGTATTAC-A
1 TCATTTTACCCTACAGGGGTATTACGA
*
61407 GTCATTCTACCCTACAGGGGTATTAC-A
1 -TCATTTTACCCTACAGGGGTATTACGA
* * *
61434 GTCATTTTACCTTAAAGGGGTATTACGG
1 -TCATTTTACCCTACAGGGGTATTACGA
* *
61462 T-ATTTTACCCTATAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTACGA
* * * *
61488 TTATTTTACCCTATA-GGGTATTATGG
1 TCATTTTACCCTACAGGGGTATTACGA
* * *
61514 TCAGTTTATCCTACAGGGGCATTACG
1 TCATTTTACCCTACAGGGGTATTACG
61540 GTCAAGATAT
Statistics
Matches: 163, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 46 0.28
27 117 0.72
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACGA
Found at i:61494 original size:53 final size:54
Alignment explanation
Indices: 61320--61543 Score: 281
Period size: 54 Copynumber: 4.2 Consensus size: 54
61310 CCACCAGGGC
* * * *
61320 ATTATGGTCATTTTACCCTACAGGGGTGTTACGATCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGT
* * * *
61374 ATTACGATCTTTTTACCCTATAGGGGTATTACAGTCATTCTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGT
* * * *
61428 ATTACAGTCATTTTACCTTAAAGGGGTATTACGGT-ATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGT
* * * * *
61481 ATTACGGTTATTTTACCCTATA-GGGTATTATGGTCAGTTTATCCTACAGGGGC
1 ATTACGGTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGT
61534 ATTACGGTCA
1 ATTACGGTCA
61544 AGATATCGAC
Statistics
Matches: 143, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
52 11 0.08
53 57 0.40
54 75 0.52
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (54 bp):
ATTACGGTCATTTTACCCTATAGGGGTATTACGGTCATTTTACCCTACAGGGGT
Found at i:62964 original size:21 final size:21
Alignment explanation
Indices: 62922--62966 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
62912 AAGTTTTTGG
*
62922 TAGGGGTGGTGTACAGCTACC
1 TAGGGGTGGTGTACAGCCACC
*
62943 TAGGGGTGGT-TAGTAGCCACC
1 TAGGGGTGGTGTA-CAGCCACC
62964 TAG
1 TAG
62967 AGGTCGTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.24
Consensus pattern (21 bp):
TAGGGGTGGTGTACAGCCACC
Found at i:65743 original size:10 final size:10
Alignment explanation
Indices: 65721--65767 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
65711 CTGCCTATCG
*
65721 AAAA-TAATC
1 AAAATTAATT
65730 AAAATTAATT
1 AAAATTAATT
65740 AAAATTAATTAT
1 AAAATTAA-T-T
65752 AAAATTAATT
1 AAAATTAATT
65762 AAAATT
1 AAAATT
65768 CAACATGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.12
10 19 0.56
11 2 0.06
12 9 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTAATT
Found at i:65756 original size:12 final size:12
Alignment explanation
Indices: 65730--65762 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
65720 GAAAATAATC
65730 AAAATTAA-T-T
1 AAAATTAATTAT
65740 AAAATTAATTAT
1 AAAATTAATTAT
65752 AAAATTAATTA
1 AAAATTAATTA
65763 AAATTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 1 0.05
12 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATTAATTAT
Found at i:68378 original size:15 final size:16
Alignment explanation
Indices: 68349--68380 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
68339 ATTTCCTATT
68349 AATTTATTAAAATAAA
1 AATTTATTAAAATAAA
68365 AATTTATT-AAATAAA
1 AATTTATTAAAATAAA
68380 A
1 A
68381 TATGATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTATTAAAATAAA
Found at i:75357 original size:25 final size:25
Alignment explanation
Indices: 75311--75360 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
75301 AAGGGAATGA
* * *
75311 AGAATAATGGAAGGGAAATGAAGAG
1 AGAAAAATGAAAGAGAAATGAAGAG
*
75336 AGAAAAATGAAAGAGAAGTGAAGAG
1 AGAAAAATGAAAGAGAAATGAAGAG
75361 TTGAGATGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.34, T:0.10
Consensus pattern (25 bp):
AGAAAAATGAAAGAGAAATGAAGAG
Found at i:85679 original size:24 final size:24
Alignment explanation
Indices: 85652--85704 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
85642 TAATCAATGT
* *
85652 TAAATATATTATGTTAATAAATTC
1 TAAATATATTATATTAATAAATAC
85676 TAAATATATTATATTAATAAATAC
1 TAAATATATTATATTAATAAATAC
85700 TAAAT
1 TAAAT
85705 TTTCTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAATATATTATATTAATAAATAC
Found at i:87013 original size:17 final size:17
Alignment explanation
Indices: 86991--87037 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
86981 AGAGAAAAAC
86991 AAAATAAAAAAGGGAA-G
1 AAAATAAAAAA-GGAAGG
87008 AAAATAATAAAAGGAAGGG
1 AAAATAA-AAAAGGAA-GG
87027 AAAATAAAAAA
1 AAAATAAAAAA
87038 ACTTTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 11 0.41
18 8 0.30
19 8 0.30
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (17 bp):
AAAATAAAAAAGGAAGG
Found at i:87288 original size:6 final size:6
Alignment explanation
Indices: 87277--87307 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
87267 TTACACTCCC
87277 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
87308 TTTATTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:88487 original size:16 final size:17
Alignment explanation
Indices: 88468--88508 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
88458 CATTATAAAA
*
88468 ACAAAAATT-TATAGTG
1 ACAAAAATTGTATAGTC
*
88484 ACAAAAATTGTATCGTC
1 ACAAAAATTGTATAGTC
88501 ACAAAAAT
1 ACAAAAAT
88509 GGTTAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (17 bp):
ACAAAAATTGTATAGTC
Found at i:91745 original size:27 final size:26
Alignment explanation
Indices: 91708--92035 Score: 352
Period size: 27 Copynumber: 12.2 Consensus size: 26
91698 TTACACTGTT
*
91708 ATGATCGAAATAACCCCATAGGGTAAA
1 ATGACCGAAAT-ACCCCATAGGGTAAA
* * **
91735 ATGAACAAAATACCCCCATAGAATAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
91762 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
*
91789 ATGATCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
* *
91816 ATGATCGAAATACCCCTATAAGGTAAA
1 ATGACCGAAATACCCC-ATAGGGTAAA
* *
91843 ATAACCAAAATACCCCATAGGGTAAA
1 ATGACCGAAATACCCCATAGGGTAAA
* *
91869 ATGACCGAAATACCCTTATAAGGTAAA
1 ATGACCGAAATACCC-CATAGGGTAAA
*
91896 ATAACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
* * *
91923 TTGACCAAAATACCCTGATAGGGTAAA
1 ATGACCGAAATACCC-CATAGGGTAAA
*
91950 ATGACCGAAATACCCCTATGGGGTAAA
1 ATGACCGAAATACCCC-ATAGGGTAAA
* *
91977 ATGATCGAAATACCCCCGA-AAGGTAAA
1 ATGACCGAAATA-CCCC-ATAGGGTAAA
*
92004 ATGACCAAAATACCTCCATAGGGTAAA
1 ATGACCGAAATACC-CCATAGGGTAAA
*
92031 TTGAC
1 ATGAC
92036 TGTTATACCC
Statistics
Matches: 255, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
26 33 0.13
27 214 0.84
28 8 0.03
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (26 bp):
ATGACCGAAATACCCCATAGGGTAAA
Found at i:92048 original size:81 final size:80
Alignment explanation
Indices: 91708--92035 Score: 419
Period size: 81 Copynumber: 4.1 Consensus size: 80
91698 TTACACTGTT
* * * * *
91708 ATGATCGAAATAACCCC-ATAGGGTAAAATGAACAAAATACCCCCAT-AGAATAAAATGACCGAA
1 ATGACCGAAAT-ACCCCTATAGGGTAAAATGATCGAAATACCCCCATAAG-GTAAAATGACCAAA
91771 ATACCCCCATAGGGTAAA
64 ATA-CCCCATAGGGTAAA
* * * *
91789 ATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAAGGTAAAATAACCAAAAT
1 ATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGACCAAAAT
91854 ACCCCATAGGGTAAA
66 ACCCCATAGGGTAAA
* * * * * *
91869 ATGACCGAAATACCCTTATAAGGTAAAATAACCGAAATACCCCCATAGGGTAAATTGACCAAAAT
1 ATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGACCAAAAT
*
91934 ACCCTGATAGGGTAAA
66 ACCC-CATAGGGTAAA
*
91950 ATGACCGAAATACCCCTATGGGGTAAAATGATCGAAATACCCCCGA-AAGGTAAAATGACCAAAA
1 ATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCC-ATAAGGTAAAATGACCAAAA
92014 TACCTCCATAGGGTAAA
65 TACC-CCATAGGGTAAA
*
92031 TTGAC
1 ATGAC
92036 TGTTATACCC
Statistics
Matches: 216, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
80 78 0.36
81 134 0.62
82 4 0.02
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (80 bp):
ATGACCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGACCAAAAT
ACCCCATAGGGTAAA
Found at i:92234 original size:26 final size:26
Alignment explanation
Indices: 92198--92278 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
92188 TGGAGGAAGT
* *
92198 ATACTGTTACTGGCAACTTTCCTGCG
1 ATACTGTTACTAGCAACTTTGCTGCG
* *
92224 ATACTGTTACTATCAGCTTTGCTGCG
1 ATACTGTTACTAGCAACTTTGCTGCG
* *
92250 ATACTATTACTAGCAACTTTGCTGTG
1 ATACTGTTACTAGCAACTTTGCTGCG
92276 ATA
1 ATA
92279 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (26 bp):
ATACTGTTACTAGCAACTTTGCTGCG
Found at i:92433 original size:28 final size:28
Alignment explanation
Indices: 92392--92553 Score: 245
Period size: 28 Copynumber: 5.8 Consensus size: 28
92382 CTAGTAACTA
92392 TATTGGGCTAAGGCCCACACTGTTATTG
1 TATTGGGCTAAGGCCCACACTGTTATTG
* *
92420 TATTGGGCTGAGGCCCACACTATTATTG
1 TATTGGGCTAAGGCCCACACTGTTATTG
*
92448 TATTGGGCTAAGGCCCTCACTGTTATTG
1 TATTGGGCTAAGGCCCACACTGTTATTG
*
92476 TATTGGGCTAAGGCCCACACTGTTACTG
1 TATTGGGCTAAGGCCCACACTGTTATTG
* * *
92504 TATTGGGCTAATGCCCACACTATTACTG
1 TATTGGGCTAAGGCCCACACTGTTATTG
*
92532 TATCGGGCTAAGG-CCACACTGT
1 TATTGGGCTAAGGCCCACACTGT
92554 ACCGTTACTG
Statistics
Matches: 122, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
27 8 0.07
28 114 0.93
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACACTGTTATTG
Found at i:92590 original size:60 final size:56
Alignment explanation
Indices: 92396--92591 Score: 185
Period size: 56 Copynumber: 3.4 Consensus size: 56
92386 TAACTATATT
* * * ** * * *
92396 GGGCTAAGGCCCACACTGTTATTGTATTGGGCTGAGGCCCACACTATTATTGTATT
1 GGGCTAAGGCCCACACTGTTACTGTATCGGGCTAAGGCCCACACCGTTACTGAATA
* * * * * *
92452 GGGCTAAGGCCCTCACTGTTATTGTATTGGGCTAAGGCCCACACTGTTACTGTATT
1 GGGCTAAGGCCCACACTGTTACTGTATCGGGCTAAGGCCCACACCGTTACTGAATA
* *
92508 GGGCTAATGCCCACACTATTACTGTATCGGGCTAAGGCCACACTGTACCGTTACTGAATA
1 GGGCTAAGGCCCACACTGTTACTGTATCGGGCTAAGGCC-CAC---ACCGTTACTGAATA
* * *
92568 GGGCTTAGGCCTAGACTGTTACTG
1 GGGCTAAGGCCCACACTGTTACTG
92592 CATGTTGTAT
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
56 86 0.72
57 3 0.03
60 30 0.25
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (56 bp):
GGGCTAAGGCCCACACTGTTACTGTATCGGGCTAAGGCCCACACCGTTACTGAATA
Found at i:94935 original size:15 final size:14
Alignment explanation
Indices: 94924--94957 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
94914 CCAATTTATT
94924 AATAAAATATTTAA
1 AATAAAATATTTAA
94938 AATAAAATA-TTAA
1 AATAAAATATTTAA
94951 ATATAAA
1 A-ATAAA
94958 TTTATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAAAATATTTAA
Found at i:100306 original size:40 final size:40
Alignment explanation
Indices: 100215--100517 Score: 362
Period size: 40 Copynumber: 7.6 Consensus size: 40
100205 TCCTCGTTCA
* * * * *
100215 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
100254 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
100294 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
100334 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
100374 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
100414 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCACG
** * * * *
100454 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
100494 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
100518 CAGCATTCAA
Statistics
Matches: 237, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
39 39 0.16
40 186 0.78
41 12 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:100526 original size:41 final size:41
Alignment explanation
Indices: 100449--100526 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
100439 TTTGTATCTC
* * *
100449 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
100490 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
100527 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:108322 original size:40 final size:40
Alignment explanation
Indices: 108224--108486 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
108214 TCCTCGTTCA
* * * * *
108224 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
108263 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
108303 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
108343 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
108383 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
108423 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
108463 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
108487 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:115792 original size:19 final size:20
Alignment explanation
Indices: 115748--115792 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
115738 ATCATGTTCA
*
115748 TATTTTTAACATAATTTATT
1 TATTTTTAACATAATTTAAT
115768 TA-TTTTATA-AT-ATTTAAT
1 TATTTTTA-ACATAATTTAAT
115786 TATTTTT
1 TATTTTT
115793 CTACAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 8 0.36
19 11 0.50
20 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTTAACATAATTTAAT
Found at i:130741 original size:27 final size:27
Alignment explanation
Indices: 130657--130730 Score: 116
Period size: 26 Copynumber: 2.8 Consensus size: 27
130647 TAACAGTCAG
*
130657 TTTACCCTAT-AGGGGTATTTCTATAAT
1 TTTACCC-ATCAGGGGTATTTCAATAAT
130684 TTTACCCATC-GGGGTATTTCAATAAT
1 TTTACCCATCAGGGGTATTTCAATAAT
130710 TTTACCCATCAGGGGTATTTC
1 TTTACCCATCAGGGGTATTTC
130731 GGTAACTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 27 0.61
27 17 0.39
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (27 bp):
TTTACCCATCAGGGGTATTTCAATAAT
Found at i:137173 original size:27 final size:27
Alignment explanation
Indices: 137129--137329 Score: 195
Period size: 27 Copynumber: 7.4 Consensus size: 27
137119 TTGGGATTTG
* * * *
137129 GGGTAAAATAACCCAAATAACCCTATA
1 GGGTAAAATGACCGAAATACCCCCATA
* *
137156 GGGTAAAATGACCGAAATACCCTCACA
1 GGGTAAAATGACCGAAATACCCCCATA
*** * * *
137183 TCATAAAATAACTGAAATACTCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
* *
137210 GGGTAAAATAATCGAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
***
137237 GGGTAAAATGATTTAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
**
137264 GGGTAAAATGACTAAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
* *
137291 GGGTAAAATGATCAAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
* *
137318 AGGTAAAGTGAC
1 GGGTAAAATGAC
137330 TGTTATACCC
Statistics
Matches: 144, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.20
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCCCATA
Found at i:137271 original size:81 final size:81
Alignment explanation
Indices: 137129--137329 Score: 231
Period size: 81 Copynumber: 2.5 Consensus size: 81
137119 TTGGGATTTG
* * * * * *
137129 GGGTAAAATAACCCAAATAACCCTATAGGGTAAAATGACCGAAATACCCTCACATCATAAAATAA
1 GGGTAAAATAATCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCACAGCATAAAATAA
* *
137194 CTGAAATACTCCCATA
66 CTAAAATACCCCCATA
* *** * ** *
137210 GGGTAAAATAATCGAAATACCCCCATAGGGTAAAATGATTTAAATACCCCCATAGGGTAAAATGA
1 GGGTAAAATAATCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCACAGCATAAAATAA
137275 CTAAAATACCCCCATA
66 CTAAAATACCCCCATA
* * *
137291 GGGTAAAATGATCAAAATACCCCCATAAGGTAAAGTGAC
1 GGGTAAAATAATCAAAATACCCCCATAGGGTAAAATGAC
137330 TGTTATACCC
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 100 1.00
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.20
Consensus pattern (81 bp):
GGGTAAAATAATCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCACAGCATAAAATAA
CTAAAATACCCCCATA
Found at i:139972 original size:40 final size:39
Alignment explanation
Indices: 139911--140058 Score: 154
Period size: 40 Copynumber: 3.7 Consensus size: 39
139901 AGCGGCGCTT
* * *
139911 TTAGCGGCGTTTGGACAAAAAACGCCACTAACAGTCGAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCGCTAA-AATCGAGCA
* *
139952 TTAGCGGCATTTTACAAAAAACGCCGCAAAATATCGAGCA
1 TTAGCGGCGTTTTACAAAAAACGCCGCTAAA-ATCGAGCA
* * * *
139992 TTAGCGACGTTACATA-AAAAAACGCCGCTAAAACCAAGCA
1 TTAGCGGCGTT--TTACAAAAAACGCCGCTAAAATCGAGCA
*
140032 TTAGCGGCGTTTTACAAAAAGCGCCGC
1 TTAGCGGCGTTTTACAAAAAACGCCGC
140059 AATAGAGTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.02
39 12 0.13
40 47 0.53
41 26 0.29
42 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAAACGCCGCTAAAATCGAGCA
Found at i:140376 original size:41 final size:42
Alignment explanation
Indices: 140331--140423 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
140321 TATGGAGAAT
* * *
140331 CGCCGCG-AATGT-TCCGGTCTATAGCGGCGTTTGTGTAACAG
1 CGCCGCGTAAT-TCTCCGGTCTATAGCAGCGTTTGTGTAAAAA
*
140372 CGCCG-GTAATTCTTCGGTCTATAGCAGCGTTTGTGTAAAAA
1 CGCCGCGTAATTCTCCGGTCTATAGCAGCGTTTGTGTAAAAA
140413 CGCCGC-TAATT
1 CGCCGCGTAATT
140424 AGAAAGTCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
40 2 0.04
41 43 0.96
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (42 bp):
CGCCGCGTAATTCTCCGGTCTATAGCAGCGTTTGTGTAAAAA
Found at i:140433 original size:41 final size:41
Alignment explanation
Indices: 140347--140433 Score: 93
Period size: 41 Copynumber: 2.1 Consensus size: 41
140337 GAATGTTCCG
* * * * *****
140347 GTCTATAGCGGCGTTTGTGTAACAGCGCCGGTAATTCTTCG
1 GTCTATAGCAGCGTTTGTGTAAAAACGCCGCTAATTAGAAA
140388 GTCTATAGCAGCGTTTGTGTAAAAACGCCGCTAATTAGAAA
1 GTCTATAGCAGCGTTTGTGTAAAAACGCCGCTAATTAGAAA
140429 GTCTA
1 GTCTA
140434 AAATATTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (41 bp):
GTCTATAGCAGCGTTTGTGTAAAAACGCCGCTAATTAGAAA
Found at i:142399 original size:785 final size:787
Alignment explanation
Indices: 140888--142474 Score: 3016
Period size: 785 Copynumber: 2.0 Consensus size: 787
140878 CCGCAAAATG
140888 TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTTTTGTAAAAAAGT
1 TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTTTTGTAAAAAAGT
* * * *
140953 CGCAAATGAAAGTTATGTATTTTAGGGTTTTGGGATTAATATTTAAGTTTTGTTGTATACGGTTT
66 CACAAATGAAAGTTATGTATTTTAGGGTATTAGGATTAATATTTAAGTTTTGTTGCATACGGTTT
141018 AGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
131 AGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
* * *
141083 GGGTTTAGGTTTATGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGTG
196 GGGTTTAGGTTTATGGCTTGAGGAATGGGGGTTAGGGGTTGAGTTTACATGTTAGTTTTAATGCG
* *
141148 AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGT
261 AGGTTTACGGCTTATAAGA-ATAGTAATGATCAAATTTACTGTTTTACGGCTTGATGTTTATGGT
141213 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
325 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
141278 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCT
390 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCT
141343 TCAGGTTTTAGGGTACAAAAGCAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATG
455 TCAGGTTTTAGGGTACAAAAGCAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATG
141408 TCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATAATATGCCACGATATATATCTATG
520 TCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATAATATGCCACGATATATATCTATG
141473 CATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAATGT
585 CATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAATGT
141538 ATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACTTA
650 ATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACTTA
141603 TAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCTATAGA
715 TAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCTATAGA
*
141668 ATAAGATT
780 ACAAGATT
* *
141676 TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGTGTTTTTTGTAAAAACGT
1 TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTTTTGTAAAAAAGT
141741 CACAAATGAAAGTTATGTATTTTAGGGTATTAGGATTAATATTTAAGTTTTGTTGCATACGGTTT
66 CACAAATGAAAGTTATGTATTTTAGGGTATTAGGATTAATATTTAAGTTTTGTTGCATACGGTTT
* *
141806 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
131 AGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
141871 GGGTTTAGGTTTATGGCTTGAGGAATGGGGGTTAGGGGTTGAGTTTACATGTTAGTTTTAATGCG
196 GGGTTTAGGTTTATGGCTTGAGGAATGGGGGTTAGGGGTTGAGTTTACATGTTAGTTTTAATGCG
141936 AGGTTTACGGCTTATAAG-AT-GTAATGATCAAATTTACTGTTTTACGGCTTGATGTTTATGGTT
261 AGGTTTACGGCTTATAAGAATAGTAATGATCAAATTTACTGTTTTACGGCTTGATGTTTATGGTT
141999 TATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAAG
326 TATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAAG
142064 AATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCTT
391 AATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCTT
142129 CAGGTTTTAGGGTACAAAAGCAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATGT
456 CAGGTTTTAGGGTACAAAAGCAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATGT
142194 CACTAGTATATAGGATTATAAGAGACAGGGTTATATATATAATATGCCACGATATATATCTATGC
521 CACTAGTATATAGGATTATAAGAGACAGGGTTATATATATAATATGCCACGATATATATCTATGC
*
142259 ATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAATGTA
586 ATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAATGTA
142324 TCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACTTAT
651 TCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACTTAT
142389 AAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCTATAGAA
716 AAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCTATAGAA
142454 CAAGATT
781 CAAGATT
142461 TGTAACCGAAACGA
1 TGTAACCGAAACGA
142475 NCAAATATAT
Statistics
Matches: 784, Mismatches: 15, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
785 515 0.66
786 2 0.00
788 267 0.34
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (787 bp):
TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTTTTGTAAAAAAGT
CACAAATGAAAGTTATGTATTTTAGGGTATTAGGATTAATATTTAAGTTTTGTTGCATACGGTTT
AGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
GGGTTTAGGTTTATGGCTTGAGGAATGGGGGTTAGGGGTTGAGTTTACATGTTAGTTTTAATGCG
AGGTTTACGGCTTATAAGAATAGTAATGATCAAATTTACTGTTTTACGGCTTGATGTTTATGGTT
TATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAAG
AATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCTT
CAGGTTTTAGGGTACAAAAGCAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATGT
CACTAGTATATAGGATTATAAGAGACAGGGTTATATATATAATATGCCACGATATATATCTATGC
ATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAATGTA
TCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACTTAT
AAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCTATAGAA
CAAGATT
Found at i:142589 original size:16 final size:16
Alignment explanation
Indices: 142565--142595 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
142555 ATTTTTTCTC
142565 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
142581 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
142596 CTCCATTTAC
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:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:146285 original size:21 final size:21
Alignment explanation
Indices: 146261--146300 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
146251 AGCATATGCG
146261 GCAGCAAGAGAAGCAGAGGCA
1 GCAGCAAGAGAAGCAGAGGCA
* *
146282 GCAGCGAGAGAAGCTGAGG
1 GCAGCAAGAGAAGCAGAGG
146301 TTCAACGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.42, T:0.03
Consensus pattern (21 bp):
GCAGCAAGAGAAGCAGAGGCA
Found at i:146295 original size:87 final size:86
Alignment explanation
Indices: 146184--146381 Score: 247
Period size: 87 Copynumber: 2.3 Consensus size: 86
146174 ACACAACTTA
* * * *
146184 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG-GTACAAC
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAACAACTCCAGAGT--AAC
*
146247 TTAAAGCATATGCGGCAGCAAGAG
63 TTAAAGCAGATGCGGCAGCAAGAG
* *
146271 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAACAACTCCAGCAGTAGCTT
1 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAG-AGTAACTT
**
146336 AAAGCAGATGCGGCAGTGAGAG
65 AAAGCAGATGCGGCAGCAAGAG
* *
146358 AAGCAGAGGCTGCAGCGAGGGAAG
1 AAGCAGAGGCAGCAGCGAGAGAAG
146382 TAGAGGCTAC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 91 0.94
88 4 0.04
89 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (86 bp):
AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGAGTAACTTA
AAGCAGATGCGGCAGCAAGAG
Found at i:146372 original size:21 final size:21
Alignment explanation
Indices: 146337--146406 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
146327 CAGTAGCTTA
* * *
146337 AAGCAGATGCGGCAGTGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
146358 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
* *
146379 AAGTAGAGGCTACAGCGA-AGG
1 AAGCAGAGGCTGCAGCGAGA-G
146400 AAGCAGA
1 AAGCAGA
146407 ACAGCTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.41, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:146757 original size:43 final size:43
Alignment explanation
Indices: 146710--147003 Score: 364
Period size: 43 Copynumber: 6.8 Consensus size: 43
146700 GTTTTTCTAA
*
146710 AAGCGCCGCTAAAAACCATGAG-CTATAGCGGCGTTTGT-TGGTT
1 AAGCGCCGCTAAAGACCATG-GTCTATAGCGGCGTTT-TATGGTT
* *
146753 AAGCGCCTCTAAAGACCATGGTCTATAGTGGCGTTTGTATGG-T
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTT-TATGGTT
* * * *
146796 AAGCGCCACTAAAGACCAAGATCTATAGCGGCGTTTTATGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGGTT
* *
146839 AAGCGCCACTAAA-AGCCATGGGCTATAGCGGCGTTTTATGGGTT
1 AAGCGCCGCTAAAGA-CCATGGTCTATAGCGGCGTTTTAT-GGTT
* * *
146883 -AGTGCCGCTAAAGACCATGGTCTATAGCCGCGTTTTATGGAT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGGTT
* * *
146925 AAGCGCTGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGCT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGGTT
*
146968 AAGCGCCGCTAAAGACCCTGGTCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTT
147004 ATTATAAAAA
Statistics
Matches: 221, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
42 10 0.05
43 204 0.92
44 7 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (43 bp):
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTTATGGTT
Found at i:156690 original size:19 final size:19
Alignment explanation
Indices: 156666--156703 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
156656 TCTGGAAATG
156666 TGAAAA-ATGAAATATTTTT
1 TGAAAATATGAAAT-TTTTT
156685 TGAAAATATGAAATTTTTT
1 TGAAAATATGAAATTTTTT
156704 ATCTGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
TGAAAATATGAAATTTTTT
Found at i:161397 original size:23 final size:23
Alignment explanation
Indices: 161354--161397 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
161344 AAAAATATTT
*
161354 TTTCAAAAAATTAATTTTAAAGA
1 TTTCAAAAAATTAATTCTAAAGA
*
161377 TTTCAAATAATT-ATTACTAAA
1 TTTCAAAAAATTAATT-CTAAA
161398 AATAATCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTCAAAAAATTAATTCTAAAGA
Found at i:165189 original size:44 final size:43
Alignment explanation
Indices: 165086--165191 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
165076 GTGGTGCTTA
* * * *
165086 TCCTACAAATGCCACTATAGATCATGATTTTTAGCGGCACTTT
1 TCCTACAAATGCCGCTATAGATCATCAGTTTTAGCGACACTTT
* *
165129 TCCCACAAATGCCGCTATAGATCATCAGTTTTAGCGACGCTTTT
1 TCCTACAAATGCCGCTATAGATCATCAGTTTTAGCGACAC-TTT
*
165173 TCGTACAAATGCCGCTATA
1 TCCTACAAATGCCGCTATA
165192 AAACATACCT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
43 34 0.63
44 20 0.37
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (43 bp):
TCCTACAAATGCCGCTATAGATCATCAGTTTTAGCGACACTTT
Found at i:165567 original size:43 final size:43
Alignment explanation
Indices: 165492--165582 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
165482 ACATATGCAA
* * * * *
165492 GGTAATAAAACATACAATGCGTTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTAAATCAAGGAAATCTT
* *
165535 GGTAATAAAAGATATAATACATTTACTAAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTACTAAATCAAGGAAATCTT
165578 -GTAAT
1 GGTAAT
165583 GAACTCAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTAAATCAAGGAAATCTT
Found at i:169709 original size:7 final size:7
Alignment explanation
Indices: 169699--169729 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
169689 CTCTAACTCT
169699 TAACCCC
1 TAACCCC
169706 TAACCCC
1 TAACCCC
*
169713 TAACTCC
1 TAACCCC
169720 TAACCCC
1 TAACCCC
169727 TAA
1 TAA
169730 ACATTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (7 bp):
TAACCCC
Found at i:171714 original size:123 final size:123
Alignment explanation
Indices: 171513--171736 Score: 299
Period size: 123 Copynumber: 1.8 Consensus size: 123
171503 CAAAAAATGT
* ** * *
171513 CGCTAAAAACCCAAGCATTAGCGGTGCTTTTTCAAAAATGCCGCTAAAACCCCGAGCATTAGCGA
1 CGCTAAAAACCCAAGCATTAGCGGCGCTTCATAAAAAACGCCGCTAAAACCCCGAGCATTAGCGA
** *
171578 CGCTTTTCTAAAAATGCTGCTAAAACCC-CGAGCATTAGTGGCGCTTTTCTAAAAACGC
66 CGCTTTTCTAAAAACACAGCTAAAACCCAC-AGCATTAGTGGCGCTTTTCTAAAAACGC
* * * * *
171636 CGCTAAAACCCCGAGCATTAGTGGCGCTTCATAAAAAACGCCGCTAAAACCTCGAGCATTAGCGG
1 CGCTAAAAACCCAAGCATTAGCGGCGCTTCATAAAAAACGCCGCTAAAACCCCGAGCATTAGCGA
171701 CGCTTTT-TAAAAAACACAGCTAAAACCCACAGCATT
66 CGCTTTTCT-AAAAACACAGCTAAAACCCACAGCATT
171737 GGCAGCGCTA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
122 1 0.01
123 84 0.98
124 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.21
Consensus pattern (123 bp):
CGCTAAAAACCCAAGCATTAGCGGCGCTTCATAAAAAACGCCGCTAAAACCCCGAGCATTAGCGA
CGCTTTTCTAAAAACACAGCTAAAACCCACAGCATTAGTGGCGCTTTTCTAAAAACGC
Found at i:171726 original size:41 final size:40
Alignment explanation
Indices: 171513--171745 Score: 261
Period size: 41 Copynumber: 5.7 Consensus size: 40
171503 CAAAAAATGT
* * * *
171513 CGCTAAAAACCCAAGCATTAGCGGTGCTTTTTCAAAAATGC
1 CGCTAAAACCCCGAGCATTAGCGGCGCTTTTT-AAAAACGC
* *
171554 CGCTAAAACCCCGAGCATTAGCGACGCTTTTCTAAAAATGC
1 CGCTAAAACCCCGAGCATTAGCGGCGCTTTT-TAAAAACGC
* *
171595 TGCTAAAACCCCGAGCATTAGTGGCGCTTTTCTAAAAACGC
1 CGCTAAAACCCCGAGCATTAGCGGCGCTTTT-TAAAAACGC
* * *
171636 CGCTAAAACCCCGAGCATTAGTGGCGCTTCATAAAAAACGC
1 CGCTAAAACCCCGAGCATTAGCGGCGCTT-TTTAAAAACGC
* *
171677 CGCTAAAACCTCGAGCATTAGCGGCGCTTTTTAAAAAACAC
1 CGCTAAAACCCCGAGCATTAGCGGCGCTTTTT-AAAAACGC
* * *
171718 AGCTAAAACCCAC-AGCATTGGCAGCGCT
1 CGCTAAAACCC-CGAGCATTAGCGGCGCT
171746 ACTCCAAAAA
Statistics
Matches: 168, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
40 1 0.01
41 164 0.98
42 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (40 bp):
CGCTAAAACCCCGAGCATTAGCGGCGCTTTTTAAAAACGC
Found at i:171765 original size:82 final size:79
Alignment explanation
Indices: 171502--171765 Score: 262
Period size: 82 Copynumber: 3.2 Consensus size: 79
171492 TGCGGCGCAT
* * * *
171502 TCAAAAAATGTCGCTAAAAACCCAAGCATTAGCGGTGCTTTTTCAAAAATGCCGCTAAAACCCCG
1 TCAAAAAATGCCGCT-AAAACCCGAGCATTAGCGGCGCTTTTT-AAAAACGCCGCTAAAACCCCG
*
171567 AGCATTAGCGACGCTTT
64 AGCATTAGCG-CGCTTC
* * *
171584 TCTAAAAATGCTGCTAAAACCCCGAGCATTAGTGGCGCTTTTCTAAAAACGCCGCTAAAACCCCG
1 TCAAAAAATGCCGCTAAAA-CCCGAGCATTAGCGGCGCTTTT-TAAAAACGCCGCTAAAACCCCG
*
171649 AGCATTAGTGGCGCTTC
64 AGCATTAG-CGCGCTTC
* * *
171666 AT-AAAAAACGCCGCTAAAACCTCGAGCATTAGCGGCGCTTTTTAAAAAACACAGCTAAAACCCA
1 -TCAAAAAATGCCGCTAAAACC-CGAGCATTAGCGGCGCTTTTT-AAAAACGCCGCTAAAACCC-
* *
171730 C-AGCATTGGCAGCGCTAC
62 CGAGCATTAGC-GCGCTTC
* * *
171748 TCCAAAAATACCACTAAA
1 TCAAAAAATGCCGCTAAA
171766 GCCCCCGATA
Statistics
Matches: 151, Mismatches: 22, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
81 8 0.05
82 139 0.92
83 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (79 bp):
TCAAAAAATGCCGCTAAAACCCGAGCATTAGCGGCGCTTTTTAAAAACGCCGCTAAAACCCCGAG
CATTAGCGCGCTTC
Found at i:171765 original size:123 final size:123
Alignment explanation
Indices: 171546--171770 Score: 274
Period size: 123 Copynumber: 1.8 Consensus size: 123
171536 GTGCTTTTTC
* ** *
171546 AAAAATGCCGCTAAAACCCCGAGCATTAGCGACGCTTTTCTAAAAATGCTGCTAAAACCCCGAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCTTTTCTAAAAACACAGCTAAAACCCCGAGC
** ** * * *
171611 ATTAGTGGCGCTTTTCTAAAAACGCCGCTAAAACCCCGAGCATTAGTGGCGCTTCATA
66 ATTAGCAGCGCTACTCCAAAAACACCACTAAAACCCCGAGCATTAGTGGCGCTTCATA
* *
171669 AAAAACGCCGCTAAAACCTCGAGCATTAGCGGCGCTTTT-TAAAAAACACAGCTAAAACCCAC-A
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCTTTTCT-AAAAACACAGCTAAAACCC-CGA
* * *
171732 GCATTGGCAGCGCTACTCCAAAAATACCACTAAAGCCCC
64 GCATTAGCAGCGCTACTCCAAAAACACCACTAAAACCCC
171771 CGATAGGTCA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
122 1 0.01
123 82 0.98
124 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (123 bp):
AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCTTTTCTAAAAACACAGCTAAAACCCCGAGC
ATTAGCAGCGCTACTCCAAAAACACCACTAAAACCCCGAGCATTAGTGGCGCTTCATA
Found at i:175138 original size:45 final size:45
Alignment explanation
Indices: 175058--175280 Score: 227
Period size: 45 Copynumber: 5.0 Consensus size: 45
175048 ACCGTTACAT
* * * * *
175058 GGTGG-ATCAGCATATAG-CACCACCCTTATAATCAATTATATTC
1 GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGATACTC
* ** *
175101 GGTGGAATCAACACATAGAAACCACCTTTATTTTCAATGAT-TTC
1 GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGATACTC
* * * *
175145 TGGTGGAGTCAGTACATAGAAACCACCTTTATAATCAATGGTACAC
1 -GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGATACTC
* * * * *
175191 GGTGGAATCAGCATATAGCAACCACCGTTATAATCAATGGTACCC
1 GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGATACTC
* * *
175236 AGTGGAATCAGCACATAGCAACCATCTTTATAATCAATGATACTC
1 GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGATACTC
175281 AGTACACGTA
Statistics
Matches: 149, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
43 5 0.03
44 13 0.09
45 130 0.87
46 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGAAACCACCTTTATAATCAATGATACTC
Found at i:183648 original size:33 final size:33
Alignment explanation
Indices: 183606--183706 Score: 175
Period size: 33 Copynumber: 3.1 Consensus size: 33
183596 GTTAACTTGG
* *
183606 TATGCCATTATTTCATAATAGAGTTACTGTGTA
1 TATGCCATTATTTCATAACAGAGTTACTGTGCA
183639 TATGCCATTATTTCATAACAGAGTTACTGTGCA
1 TATGCCATTATTTCATAACAGAGTTACTGTGCA
*
183672 TGTGCCATTATTTCATAACAGAGTTACTGTGCA
1 TATGCCATTATTTCATAACAGAGTTACTGTGCA
183705 TA
1 TA
183707 CTTTTGACTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TATGCCATTATTTCATAACAGAGTTACTGTGCA
Found at i:185795 original size:13 final size:14
Alignment explanation
Indices: 185773--185806 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
185763 TTGTATTGGT
185773 AACT-TTTAAAA-A
1 AACTATTTAAAATA
185785 AACTATTTAAAATA
1 AACTATTTAAAATA
185799 AACTATTT
1 AACTATTT
185807 CGTGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 9 0.45
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTATTTAAAATA
Found at i:186589 original size:30 final size:30
Alignment explanation
Indices: 186555--186614 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
186545 TATTTTATTA
186555 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
* *
186585 TTAATTTTGTTATTATTTTAGAGATATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
186615 CTTGATAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:186733 original size:18 final size:19
Alignment explanation
Indices: 186696--186738 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
186686 GAAAAATATT
*
186696 TATTTTGATGTTTTTAATA
1 TATTTTGATGTTATTAATA
186715 T-TTTTGATG-TATTACATA
1 TATTTTGATGTTATTA-ATA
186733 TATTTT
1 TATTTT
186739 AAAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (19 bp):
TATTTTGATGTTATTAATA
Found at i:189857 original size:14 final size:13
Alignment explanation
Indices: 189832--189886 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
189822 TGTAGGTGTC
189832 TGAAAAAA-AAAA
1 TGAAAAAATAAAA
189844 TGAAAAAATCAAAA
1 TGAAAAAAT-AAAA
189858 T-AAATCAAATAAAA
1 TGAAA--AAATAAAA
*
189872 TTAAAAAATTAAAA
1 TGAAAAAA-TAAAA
189886 T
1 T
189887 TTTACCGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.22
13 6 0.16
14 16 0.43
15 7 0.19
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (13 bp):
TGAAAAAATAAAA
Found at i:193712 original size:22 final size:23
Alignment explanation
Indices: 193685--193730 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
193675 TTAGATTAGT
*
193685 GAAATTAAAA-TAAAATTAAAAA
1 GAAATTAAAAGAAAAATTAAAAA
193707 GAAATTAAAAGGAAAAATTAAAAA
1 GAAATTAAAA-GAAAAATTAAAAA
193731 TTTTGTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
24 11 0.52
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (23 bp):
GAAATTAAAAGAAAAATTAAAAA
Found at i:200026 original size:27 final size:27
Alignment explanation
Indices: 199995--200060 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
199985 CTCAATAAAA
199995 TTTCATCTTATCCATTGTGATAATCTT
1 TTTCATCTTATCCATTGTGATAATCTT
200022 TTTCATCTTATCCATTGTGATAATCTT
1 TTTCATCTTATCCATTGTGATAATCTT
*
200049 TTTCATATTATC
1 TTTCATCTTATC
200061 TTAGCAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (27 bp):
TTTCATCTTATCCATTGTGATAATCTT
Found at i:200652 original size:24 final size:24
Alignment explanation
Indices: 200620--200677 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
200610 ATATCCCAAA
*
200620 ATTATAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
*
200644 ATTACAGTGGATTGAACTTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
200668 ATTACAGTGG
1 ATTACAGTGG
200678 GGGCAATCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCTTGAAG
Found at i:201425 original size:50 final size:50
Alignment explanation
Indices: 200969--201436 Score: 355
Period size: 50 Copynumber: 9.4 Consensus size: 50
200959 GTTGCAGTTA
* * *
200969 AAAAGATTGAAGCCACAACGGCAAATCTTACTT-CCTGGCGATGCATTGG
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* ** * * * **
201018 AACAGATTGAAGCTACAACGGTGAATCTTATTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* * * *
201068 AAAAGATTGAAACTACAACGGCAAATCTTACTTCCCTAGCGATGCAGTGG
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* * * * * * **
201118 AACAGATTGAAGCTACAATGGCAAATCTTGCTTCCCCGACATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* * * * * *
201168 AAAAGGA-TGAAGCCACAACAGCGAATCTTACTTTCCTGGCGGTGCAGTGG
1 AAAA-GATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* ** * * * * **
201218 AACAGATTGAAAATACAACGGCAAATCTTGCTTCCCCGACATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* ** ** * * *
201268 AAAATATTGAAGCCCCAACGGTGAATCTTACTTCCCTGGTGGTGCAGTGG
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
** * * * * * **
201318 AGCAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTA
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
* * * * * *
201368 AAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTGGTGGTGTAGTGG
1 AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
*
201418 AATAGATTGAAGCTACAAC
1 AAAAGATTGAAGCTACAAC
201437 AGCGAATTTT
Statistics
Matches: 303, Mismatches: 113, Indels: 5
0.72 0.27 0.01
Matches are distributed among these distances:
49 30 0.10
50 271 0.89
51 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACGGCAAATCTTACTTCCCTGGCGTTGCAATGG
Found at i:201497 original size:100 final size:100
Alignment explanation
Indices: 200960--201479 Score: 711
Period size: 100 Copynumber: 5.2 Consensus size: 100
200950 ACCCCTGAGG
* * *
200960 TTGCAGTTAAAAAGATTGAAGCCACAACGGCAAATCTTACTT-CCTGGCGATGCATTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* ** *
201024 TTGAAGCTACAACGGTGAATCTTATTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
201059 TTGCAATTAAAAAGATTGAAACTACAACGGCAAATCTTACTTCCCTAGCGATGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *
201124 TTGAAGCTACAATGGCAAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * *
201159 TTGCAATTAAAAAGGA-TGAAGCCACAACAGCGAATCTTACTTTCCTGGCGGTGCAGTGGAACAG
1 TTGCAATTAAAAA-GATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAG
** *
201223 ATTGAAAATACAACGGCAAATCTTGCTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * ** * *
201259 TTGCAATTAAAAATATTGAAGCCCCAACGGTGAATCTTACTTCCCTGGTGGTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
201324 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
201359 TTGCAATTAAAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTGGTGGTGTAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *
201424 TTGAAGCTACAACAGCGAATTTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* **
201459 TTGCAGTTAAATGGATTGAAG
1 TTGCAATTAAAAAGATTGAAG
201480 TCATCATGGC
Statistics
Matches: 376, Mismatches: 42, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
99 40 0.11
100 334 0.89
101 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
Found at i:201740 original size:44 final size:44
Alignment explanation
Indices: 201491--201876 Score: 160
Period size: 44 Copynumber: 8.8 Consensus size: 44
201481 CATCATGGCG
* * * * *** *
201491 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAATTGAAGCCACT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
* * * * * *
201535 AATCTTATC-CCTCTAAAGTTGCAGTGGGGCAGATTGAAGATAACA
1 AATCCTATCTCC-CTGAAGTTGCAGTGGAGCAGATAGAA-AAAACC
* * * * * * *
201580 AATCTTATTTCCTTGAAGTTGTAGTGGAACAGATTGAAGCTAAATAAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAA---AAA-ACC
* * * * * * *
201628 AGATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATTG---CATCC
1 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
* * *
201670 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
* * * *
201714 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGAT--TAAAACCAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAAC-C
* *** * * * * *
201757 AGATCTTATCTTTTTGAAGTTGCAATAGAGCAGATCG---CATCC
1 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
* ** * * *
201799 AGTTTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAACC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
* *
201843 AATCCTATCTCCCTGAAGTTGCACTGGAACAGAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT
201877 TGAAGCTAAA
Statistics
Matches: 255, Mismatches: 70, Indels: 34
0.71 0.19 0.09
Matches are distributed among these distances:
41 54 0.21
42 9 0.04
43 7 0.03
44 118 0.46
45 31 0.12
46 2 0.01
47 2 0.01
48 2 0.01
49 30 0.12
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACC
Found at i:201921 original size:129 final size:131
Alignment explanation
Indices: 201537--201900 Score: 425
Period size: 129 Copynumber: 2.8 Consensus size: 131
201527 AAGCCACTAA
* * * * * * *
201537 TCTTATC-CCTCTAAAGTTGCAGTGGGGCAGATTGAAGATAACAAATCTTATTTCCTTGAAGTTG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATAGAAGA-AACCAATCCTATCTCCCTGAAGTTG
* *
201601 TAGTGGAACAGATTGAAGCTAAATAACAGATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATTGC
64 TAGTGGAACAGATTGAAGCTAAATAACAGATCTTATTT-T-TGAAGTTGCAATAGA-CAGATCGC
201666 ATCCAG
126 ATCCAG
* *
201672 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATAGAAAAAACCAATCCTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGTA
* * **
201737 GTGGAGCGGATT--A---AAACCACAGATCTTATCTTTTTGAAGTTGCAATAGAGCAGATCGCAT
66 GTGGAACAGATTGAAGCTAAATAACAGATCTTA--TTTTTGAAGTTGCAATAGA-CAGATCGCAT
201797 CCAG
128 CCAG
* * * *
201801 TTTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGTA
* *
201866 CTGGAACAGATTGAAGCTAAATAATAGATCTTATT
66 GTGGAACAGATTGAAGCTAAATAACAGATCTTATT
201901 GTTAGAGTAT
Statistics
Matches: 194, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
129 109 0.56
130 1 0.01
131 4 0.02
132 3 0.02
134 45 0.23
135 31 0.16
136 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (131 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGTA
GTGGAACAGATTGAAGCTAAATAACAGATCTTATTTTTGAAGTTGCAATAGACAGATCGCATCCA
G
Found at i:203634 original size:129 final size:128
Alignment explanation
Indices: 203389--203637 Score: 347
Period size: 129 Copynumber: 1.9 Consensus size: 128
203379 GATCCAACAC
* * * * *
203389 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAACAGTAGTGGAG
1 TTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCAAGCCTTATCTCCCGAAACAGCAGTGGAG
*
203454 CAGACAGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAAATG
66 CAGACAGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAACCACAAATG
* ***
203517 TTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAGCCTTATCTCCCGGAAGTTGCAGTGGA
1 TTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCAAGCCTTATCTCCC-GAAACAGCAGTGGA
* ** *
203582 GCAGACTGAAGCTA-CTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAAC
65 GCAGACAGAAGAAATC-AATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAAC
203638 GATGAATCCT
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
128 47 0.45
129 58 0.55
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (128 bp):
TTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCAAGCCTTATCTCCCGAAACAGCAGTGGAG
CAGACAGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAACCACAAATG
Found at i:203646 original size:44 final size:44
Alignment explanation
Indices: 203559--203649 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
203549 CATCCAGCCT
* * *
203559 TATCTCCCGGAAGTTGCAGTGGAGCAGACTGAAGCTACTAATCC
1 TATCTCCCGGAAGTTGCAGTGGAGCAGACTAAAACGACTAATCC
* *
203603 TATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACGA-TGAATCC
1 TATCTCCCGGAAGTTGCAGTGGAGCAG-ACTAAAACGACT-AATCC
203647 TAT
1 TAT
203650 ACCTTTGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (44 bp):
TATCTCCCGGAAGTTGCAGTGGAGCAGACTAAAACGACTAATCC
Found at i:212249 original size:47 final size:47
Alignment explanation
Indices: 212153--212249 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
212143 TTGAAACATT
* * *
212153 TTGATATATTTTGGTAGTATTTGATGATGGTTTATAGTGTTTTTGAA
1 TTGATACATTTTGGTAGTATTTGATGATGGTTTATAGTGTTATTAAA
212200 TTGATACATTTTGGTAGTATTTGATGATGGTTTAT-GTGCTTATTAAA
1 TTGATACATTTTGGTAGTATTTGATGATGGTTTATAGTG-TTATTAAA
212247 TTG
1 TTG
212250 CTAACTTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 3 0.07
47 43 0.93
ACGTcount: A:0.24, C:0.02, G:0.23, T:0.52
Consensus pattern (47 bp):
TTGATACATTTTGGTAGTATTTGATGATGGTTTATAGTGTTATTAAA
Found at i:213664 original size:13 final size:13
Alignment explanation
Indices: 213646--213670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213636 AAAATTCATC
213646 AAAATTAATTATA
1 AAAATTAATTATA
213659 AAAATTAATTAT
1 AAAATTAATTAT
213671 GTACACTTTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTAATTATA
Found at i:214948 original size:20 final size:18
Alignment explanation
Indices: 214901--215007 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
214891 CAAGATAAAC
214901 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
*
214918 ATTAAGA-TAATCACTTTAGT
1 ATTAA-ATTAAT-A-TTTAAT
**
214938 ATTAAATTAATAAAATAAT
1 ATTAAATTAAT-ATTTAAT
214957 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
214974 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
214994 ATTAAAATAATATT
1 ATTAAATTAATATT
215008 ATTTTTCAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 15 0.21
18 10 0.14
19 21 0.30
20 23 0.33
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:218154 original size:38 final size:38
Alignment explanation
Indices: 218091--218166 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
218081 TGTGTAGCCT
* * *
218091 TTCCCTACCAGTCTAGCTTTGTGTGTTTCCACTTTCCC
1 TTCCCTACAAGTCTAACTTTATGTGTTTCCACTTTCCC
*
218129 TTCCCTACAATTCTAACTTTATGTGTTTCCACTTTCCC
1 TTCCCTACAAGTCTAACTTTATGTGTTTCCACTTTCCC
218167 GTCCGCATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.14, C:0.33, G:0.09, T:0.43
Consensus pattern (38 bp):
TTCCCTACAAGTCTAACTTTATGTGTTTCCACTTTCCC
Found at i:225361 original size:27 final size:27
Alignment explanation
Indices: 225330--225382 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
225320 TTTCGAGTCG
**
225330 TCTAGGATGAGTGCTTCGACCGAGTAT
1 TCTAGGATGAGCACTTCGACCGAGTAT
*
225357 TCTAGGATGAGCACTTCGACTGAGTA
1 TCTAGGATGAGCACTTCGACCGAGTA
225383 GTCTTCTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (27 bp):
TCTAGGATGAGCACTTCGACCGAGTAT
Found at i:225681 original size:12 final size:12
Alignment explanation
Indices: 225664--225714 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
225654 ACTTAATCAC
225664 TTTAATATTAAA
1 TTTAATATTAAA
*
225676 TTTAAT-CTAATA
1 TTTAATATTAA-A
*
225688 TATATTATATTAAA
1 T-T-TAATATTAAA
225702 TTTAATATTAAA
1 TTTAATATTAAA
225714 T
1 T
225715 CTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.10
12 18 0.58
13 2 0.06
14 5 0.16
15 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:225692 original size:21 final size:21
Alignment explanation
Indices: 225668--225709 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
225658 AATCACTTTA
*
225668 ATATTAAATTTAATCTAATAT
1 ATATTAAATTAAATCTAATAT
* *
225689 ATATTATATTAAATTTAATAT
1 ATATTAAATTAAATCTAATAT
225710 TAAATCTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTAAATTAAATCTAATAT
Found at i:230000 original size:13 final size:13
Alignment explanation
Indices: 229982--230007 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
229972 CTAGATTAAA
229982 TAATTAATTCAAT
1 TAATTAATTCAAT
229995 TAATTAATTCAAT
1 TAATTAATTCAAT
230008 AACTTACAAA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTAATTCAAT
Found at i:235700 original size:28 final size:29
Alignment explanation
Indices: 235573--235768 Score: 195
Period size: 29 Copynumber: 6.9 Consensus size: 29
235563 CCACAAGGCA
* * *
235573 TTTAACTGAGATAGCCATAAAGGCATCCT
1 TTTAACAGAGATAGCCACAAAGGCTTCCT
*
235602 TTTAACCGAGATAGCCACAAAGG-TATCCT
1 TTTAACAGAGATAGCCACAAAGGCT-TCCT
* *
235631 TTTAACTAG-TATAGCCACAAAGGCATCCT
1 TTTAAC-AGAGATAGCCACAAAGGCTTCCT
* * *
235660 TTTAACTGAGATTGCCACAAAGGCTTAC-
1 TTTAACAGAGATAGCCACAAAGGCTTCCT
** * *
235688 TTTAACAGAGATTTCCATAAAGGCTT-CG
1 TTTAACAGAGATAGCCACAAAGGCTTCCT
* * *
235716 TTTAATAGAGATCGCCACAAAGGTTTCC-
1 TTTAACAGAGATAGCCACAAAGGCTTCCT
235744 TTTAACAGAGATAGCCACAAAGGCT
1 TTTAACAGAGATAGCCACAAAGGCT
235769 CACTTATACA
Statistics
Matches: 139, Mismatches: 22, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.01
28 67 0.48
29 70 0.50
30 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (29 bp):
TTTAACAGAGATAGCCACAAAGGCTTCCT
Found at i:239590 original size:19 final size:19
Alignment explanation
Indices: 239548--239584 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
239538 AGTGAGAGAT
*
239548 ATTTGTAACTGTAAGGAGC
1 ATTTCTAACTGTAAGGAGC
*
239567 ATTTCTAACTGTGAGGAG
1 ATTTCTAACTGTAAGGAG
239585 TTTTTCAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (19 bp):
ATTTCTAACTGTAAGGAGC
Found at i:248765 original size:25 final size:25
Alignment explanation
Indices: 248727--248779 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
248717 TTTGTGAAGC
*
248727 CTTTGTGGAGAACT-CTCTGTAAATT
1 CTTTGTGGAGAACTCCT-TGTAAAAT
248752 CTTTGTGGCA-AACTCCTTGTAAAAT
1 CTTTGTGG-AGAACTCCTTGTAAAAT
248777 CTT
1 CTT
248780 CTTGGCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (25 bp):
CTTTGTGGAGAACTCCTTGTAAAAT
Found at i:257894 original size:6 final size:6
Alignment explanation
Indices: 257841--257891 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
257831 TCATCCCCAA
* * *
257841 AAATCA AAATCA AAATCC AAATCC AAATCC AAATCC AAATCC AAACCC
1 AAATCC AAATCC AAATCC AAATCC AAATCC AAATCC AAATCC AAATCC
257889 AAA
1 AAA
257892 CCCTAATCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (6 bp):
AAATCC
Found at i:257899 original size:18 final size:18
Alignment explanation
Indices: 257857--257900 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
257847 AAATCAAAAT
* *
257857 CCAAATCCAAATCCAAAT
1 CCAAATCCAAACCCAAAC
257875 CCAAATCCAAACCCAAAC
1 CCAAATCCAAACCCAAAC
*
257893 CCTAATCC
1 CCAAATCC
257901 CACCTCCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (18 bp):
CCAAATCCAAACCCAAAC
Found at i:261970 original size:36 final size:30
Alignment explanation
Indices: 261896--261982 Score: 165
Period size: 30 Copynumber: 2.9 Consensus size: 30
261886 ATTTAAGGAA
261896 TGATAAAGGGAAAGGGAAAATGGTTGATGC
1 TGATAAAGGGAAAGGGAAAATGGTTGATGC
261926 TGATAAAGGGAAAGGGAAAATGGTTGATGC
1 TGATAAAGGGAAAGGGAAAATGGTTGATGC
*
261956 TGATAAAGGGAAAGGGAAACTGGTTGA
1 TGATAAAGGGAAAGGGAAAATGGTTGA
261983 CATCATACCG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.40, C:0.03, G:0.37, T:0.20
Consensus pattern (30 bp):
TGATAAAGGGAAAGGGAAAATGGTTGATGC
Found at i:266730 original size:30 final size:30
Alignment explanation
Indices: 266694--266752 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
266684 GATACATAGC
266694 TTGTCACTTAAGCTCGAGTGAGGAGCTTTA
1 TTGTCACTTAAGCTCGAGTGAGGAGCTTTA
266724 TTGTCACTTAAGCTCGAGTGAGGAGCTTT
1 TTGTCACTTAAGCTCGAGTGAGGAGCTTT
266753 GCTGATACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (30 bp):
TTGTCACTTAAGCTCGAGTGAGGAGCTTTA
Found at i:266800 original size:42 final size:42
Alignment explanation
Indices: 266727--266884 Score: 203
Period size: 42 Copynumber: 3.8 Consensus size: 42
266717 AGCTTTATTG
*
266727 TCACTTAAGCTCGA-GT-GAGGAGCTTTGCTGATACACAACTTA
1 TCACTTAAGCTC-ATGTAG-GGAGCTTCGCTGATACACAACTTA
* * * **
266769 TCGCTTAAGCTCACGTAGGGAGTTTTTCTGATACACAACTTA
1 TCACTTAAGCTCATGTAGGGAGCTTCGCTGATACACAACTTA
* *
266811 TCACTTAAGCTCATGTGGGGAGCTTCGCTAATACACAACTTA
1 TCACTTAAGCTCATGTAGGGAGCTTCGCTGATACACAACTTA
*
266853 TCACTTAAGCTCATGTAGGGAGCTTCTCTGAT
1 TCACTTAAGCTCATGTAGGGAGCTTCGCTGAT
266885 CCATAGCTTG
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 99 0.98
43 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
TCACTTAAGCTCATGTAGGGAGCTTCGCTGATACACAACTTA
Found at i:266871 original size:84 final size:84
Alignment explanation
Indices: 266727--266884 Score: 237
Period size: 84 Copynumber: 1.9 Consensus size: 84
266717 AGCTTTATTG
* * * *
266727 TCACTTAAGCTCGAGTGAGGAGCTTTGCTGATACACAACTTATCGCTTAAGCTCACGTAGGGAGT
1 TCACTTAAGCTCGAGTGAGGAGCTTCGCTAATACACAACTTATCACTTAAGCTCACGTAGGGAGC
*
266792 TTTTCTGATACACAACTTA
66 TTCTCTGATACACAACTTA
* *
266811 TCACTTAAGCTC-ATGTGGGGAGCTTCGCTAATACACAACTTATCACTTAAGCTCATGTAGGGAG
1 TCACTTAAGCTCGA-GTGAGGAGCTTCGCTAATACACAACTTATCACTTAAGCTCACGTAGGGAG
266875 CTTCTCTGAT
65 CTTCTCTGAT
266885 CCATAGCTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
83 1 0.02
84 65 0.98
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (84 bp):
TCACTTAAGCTCGAGTGAGGAGCTTCGCTAATACACAACTTATCACTTAAGCTCACGTAGGGAGC
TTCTCTGATACACAACTTA
Found at i:277556 original size:21 final size:20
Alignment explanation
Indices: 277523--277561 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
277513 GTTTTCTCAT
*
277523 TCAATTGTATTTACAAGTTAG
1 TCAATTATATTTA-AAGTTAG
*
277544 TCAATTATGTTTAAAGTT
1 TCAATTATATTTAAAGTT
277562 GAGAACATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
TCAATTATATTTAAAGTTAG
Found at i:277789 original size:8 final size:8
Alignment explanation
Indices: 277776--277809 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
277766 TGAAACTAAA
277776 AGAGGGAG
1 AGAGGGAG
277784 AGAGGGAG
1 AGAGGGAG
277792 AGAGGGAG
1 AGAGGGAG
277800 AGAGAGGAG
1 AGAG-GGAG
277809 A
1 A
277810 TAACTATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.80
9 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (8 bp):
AGAGGGAG
Found at i:280085 original size:24 final size:25
Alignment explanation
Indices: 280052--280105 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
280042 TTACTTGATG
280052 TATTCTTTTATATAATATTTAAAAT
1 TATTCTTTTATATAATATTTAAAAT
280077 TATT-TTTTATATAATATTTAAAAT
1 TATTCTTTTATATAATATTTAAAAT
280101 TATTC
1 TATTC
280106 ATAATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTCTTTTATATAATATTTAAAAT
Found at i:280112 original size:24 final size:24
Alignment explanation
Indices: 280061--280112 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
280051 GTATTCTTTT
** *
280061 ATATAATATTTAAAATTATTTTTT
1 ATATAATATTTAAAATTATTCATA
280085 ATATAATATTTAAAATTATTCATA
1 ATATAATATTTAAAATTATTCATA
280109 ATAT
1 ATAT
280113 TAAGATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATAATATTTAAAATTATTCATA
Found at i:282749 original size:41 final size:41
Alignment explanation
Indices: 282664--282749 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
282654 GGAGCAGTGT
* * *
282664 TAGCGGGGTTTTTCCCATAAACGCCGCAAAAGGTAAAGTAA
1 TAGCGGAGTTTTTCCCATAAACACCGCAAAAGGTAAAATAA
* * *
282705 TAGCGGAGTTTTT-GCATAAACATCGCAAAAGGTTAAAATTA
1 TAGCGGAGTTTTTCCCATAAACACCGCAAAAGG-TAAAATAA
282746 TAGC
1 TAGC
282750 ACCATTTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 16 0.42
41 22 0.58
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (41 bp):
TAGCGGAGTTTTTCCCATAAACACCGCAAAAGGTAAAATAA
Found at i:284157 original size:29 final size:29
Alignment explanation
Indices: 284113--284170 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
284103 AGACTTGGCT
* *
284113 TCCCTGCACTCCTAGTCAGGATGAGTTTC
1 TCCCTACACTCCTAGTAAGGATGAGTTTC
*
284142 TCCCTACACTCTTAGTAAGGATGAGTTTC
1 TCCCTACACTCCTAGTAAGGATGAGTTTC
284171 AATTGGAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (29 bp):
TCCCTACACTCCTAGTAAGGATGAGTTTC
Found at i:291973 original size:43 final size:43
Alignment explanation
Indices: 291883--291974 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
291873 TTTTGCGGCG
* * ***
291883 TTTGTAAAAAAAACGTCGCTAAAAATCATGTTCTTTAGTGGTG
1 TTTGTAAAAAAAACGTCGCTAAAAATCATGTTCTATAGCGACA
* ** *
291926 TTTGTAATAAAAGTGTCGCTAAAGATCATGTTCTATAGCGACA
1 TTTGTAAAAAAAACGTCGCTAAAAATCATGTTCTATAGCGACA
291969 TTTGTA
1 TTTGTA
291975 GGGAAAGTGC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (43 bp):
TTTGTAAAAAAAACGTCGCTAAAAATCATGTTCTATAGCGACA
Found at i:292414 original size:21 final size:21
Alignment explanation
Indices: 292374--292415 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
292364 AAAAGTTAGA
292374 AAAATGAATTATATTCTTTCC
1 AAAATGAATTATATTCTTTCC
292395 AAAA-GAATATATGATT-TTTCC
1 AAAATGAAT-TAT-ATTCTTTCC
292416 CATATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAATGAATTATATTCTTTCC
Found at i:292460 original size:75 final size:75
Alignment explanation
Indices: 292337--292504 Score: 264
Period size: 75 Copynumber: 2.2 Consensus size: 75
292327 ACTATAATTA
* * * *
292337 TTCCCTTATTAATAGAGAAGACAAGTGAAAAGTTAGAAAAATGAATTATATTCTTTCCAAAAGAA
1 TTCCCTTATTAATAGAAAAGAAAAATGAAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAGAA
*
292402 TATATGATTT
66 TATAAGATTT
* *
292412 TTCCCATATTAATAGAAAAGAAAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAGAA
1 TTCCCTTATTAATAGAAAAGAAAAATGAAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAGAA
292477 TATAAGATTT
66 TATAAGATTT
*
292487 TTCCCTTATTAATGGAAA
1 TTCCCTTATTAATAGAAA
292505 GTTAGAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (75 bp):
TTCCCTTATTAATAGAAAAGAAAAATGAAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAGAA
TATAAGATTT
Found at i:298253 original size:25 final size:25
Alignment explanation
Indices: 298193--298282 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
298183 GTACATGTAT
* *
298193 GCTCATAAGAGCTGTA-AACGGTAA
1 GCTCATAAGAGCTGAATAATGGTAA
* **
298217 GCTCCTCCGAGCTGAATAATGGTAA
1 GCTCATAAGAGCTGAATAATGGTAA
* *
298242 GCTCATATGAGCTGAGT-ATCGGTAA
1 GCTCATAAGAGCTGAATAAT-GGTAA
298267 GCTCATAAGAGCTGAA
1 GCTCATAAGAGCTGAA
298283 ATCGATAACC
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
24 14 0.26
25 39 0.74
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
GCTCATAAGAGCTGAATAATGGTAA
Found at i:306695 original size:48 final size:48
Alignment explanation
Indices: 306599--306832 Score: 229
Period size: 48 Copynumber: 4.9 Consensus size: 48
306589 GATTTCTCGA
* * * * * * * *
306599 TGGCCGACACACAGTCTGTACCACCTTTGTGTAAGAACA-AATTTTTGG
1 TGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAA-TATTGG
* * * * *
306647 TGGCCTGCACATATTCCGTGCCACCCTTGTATCTTAACAGATTATTGG
1 TGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAATATTGG
* * * *
306695 TGGCCTACACATAGTCTGTGCCACCCTTGTATCATAATAGAATATCGG
1 TGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAATATTGG
* *
306743 TGGCCTACACACAGCCCATGCCACCCTTGTATCATAACAGAATATCT-G
1 TGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAATAT-TGG
* * * *
306791 TGGCCTGCACACAGTCTGTGCCACTCTTGTGTCATAACAGAA
1 TGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAA
306833 CATCGGTACG
Statistics
Matches: 152, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
48 151 0.99
49 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (48 bp):
TGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAATATTGG
Found at i:340501 original size:69 final size:68
Alignment explanation
Indices: 340366--340501 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
340356 TAGATTAGAT
* * * * *
340366 TTAATATTAAATTCAATTTGATACTTATATTGATAGTATTTTATTAATTTAATATTACAGTCATT
1 TTAATATTAAATTCAATTTAATACTTATATAGATAGTATTATATTAATTTAATACTAAAGTCATT
340431 ATC
66 ATC
* * * * *
340434 TTAATATTAAATTGAATTTAATATTTATCTAGATAAGTATTATATTAATTTAATGCTAAAGTGAT
1 TTAATATTAAATTCAATTTAATACTTATATAGAT-AGTATTATATTAATTTAATACTAAAGTCAT
340499 TAT
65 TAT
340502 GTTTAATCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
68 29 0.51
69 28 0.49
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (68 bp):
TTAATATTAAATTCAATTTAATACTTATATAGATAGTATTATATTAATTTAATACTAAAGTCATT
ATC
Found at i:346808 original size:10 final size:10
Alignment explanation
Indices: 346793--346841 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
346783 AGTAACATTT
346793 TTAATTTTAA
1 TTAATTTTAA
346803 TTAATTTTATAA
1 TTAA-TTT-TAA
*
346815 TTAATTTTGA
1 TTAATTTTAA
*
346825 TTAATTTTGA
1 TTAATTTTAA
346835 TT-ATTTT
1 TTAATTTT
346842 CGACATTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 5 0.14
10 18 0.50
11 6 0.17
12 7 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:354411 original size:113 final size:114
Alignment explanation
Indices: 354212--354511 Score: 444
Period size: 113 Copynumber: 2.6 Consensus size: 114
354202 ATTAGAAAAT
* *
354212 GCCGCAAAAAACCTAAGCCCAGCGACATCGTTTTTCTTAGTTTTCGAGGCTTTGGTGGCGTTTTT
1 GCCGCAAAAAACCTAAGCCCAACGACGTCGTTTTTCTTAGTTTTCGAGGCTTTGGTGGCGTTTTT
* *
354277 GGAGAAGCACCGCTAATTCTCAGGGTTTTAGC-GACGTTTTTGAAAAAGC
66 GGAGAAGCACCGCTAATTCTCAAGGTTTTAGCAG-CATTTTTGAAAAAGC
* * *
354326 GCCGCAAAAGACCTAAGCCCAACGATGTCG-TTTTCTTAGTTTTCGAGGCTTTGGTGGCATTTTT
1 GCCGCAAAAAACCTAAGCCCAACGACGTCGTTTTTCTTAGTTTTCGAGGCTTTGGTGGC-GTTTT
* *
354390 TGGA-AAGCGCCGCTAATTCTCAAGGTTTTAGCAGCATTTTTTAAAAAGC
65 TGGAGAAGCACCGCTAATTCTCAAGGTTTTAGCAGCATTTTTGAAAAAGC
* ** *
354439 ACCATAAAAAAACTAAGCCCAACGACGTCGTTTTTCTTAGTTTTCGAGGCTTTGGTGGCGTTTTT
1 GCCGCAAAAAACCTAAGCCCAACGACGTCGTTTTTCTTAGTTTTCGAGGCTTTGGTGGCGTTTTT
354504 GGAGAAGC
66 GGAGAAGC
354512 CCATTATAAT
Statistics
Matches: 166, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
113 99 0.60
114 67 0.40
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (114 bp):
GCCGCAAAAAACCTAAGCCCAACGACGTCGTTTTTCTTAGTTTTCGAGGCTTTGGTGGCGTTTTT
GGAGAAGCACCGCTAATTCTCAAGGTTTTAGCAGCATTTTTGAAAAAGC
Found at i:358166 original size:12 final size:13
Alignment explanation
Indices: 358148--358178 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
358138 ATGTTGAATT
358148 TTAATTAATTTTA
1 TTAATTAATTTTA
358161 -TAATTAATTTTA
1 TTAATTAATTTTA
358173 TTAATT
1 TTAATT
358179 TTGATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAATTAATTTTA
Found at i:358177 original size:9 final size:10
Alignment explanation
Indices: 358144--358189 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
358134 TAACATGTTG
358144 AATTTTAATT
1 AATTTTAATT
358154 AATTTTATAATT
1 AA-TTT-TAATT
358166 AATTTT-ATT
1 AATTTTAATT
*
358175 AATTTTGATT
1 AATTTTAATT
358185 -ATTTT
1 AATTTT
358190 CGACAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 14 0.42
10 6 0.18
11 6 0.18
12 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
AATTTTAATT
Found at i:359953 original size:50 final size:50
Alignment explanation
Indices: 359829--360077 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
359819 GATAATAACA
* * ** * *
359829 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
359880 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
359930 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
359980 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGCCCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
360035 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
360078 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:360007 original size:100 final size:104
Alignment explanation
Indices: 359828--360077 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
359818 TGATAATAAC
**
359828 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
359893 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
359930 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
359993 TCCCAGACATGGTCTTACAGGGGCCCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
360035 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
360078 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:360193 original size:13 final size:13
Alignment explanation
Indices: 360172--360203 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
360162 GCTTGGATCA
*
360172 TCATCAAATAAAT
1 TCATAAAATAAAT
360185 TCATAAAATAAAT
1 TCATAAAATAAAT
360198 TCATAA
1 TCATAA
360204 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Done.