Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 13 of 30
Found at i:2140856 original size:58 final size:56
Alignment explanation
Indices: 2140754--2140866 Score: 145
Period size: 58 Copynumber: 2.0 Consensus size: 56
2140744 CCTTAAGGAC
* ** *
2140754 TTGTTAATAATTCTAAATCATGGAAAATGACTAATGCGACCCTAAGATGCATGAAT
1 TTGTTAATAATTCTAAATCATAGAAAATGACTAAAACGACCCTAAAATGCATGAAT
* * *
2140810 TTGTATAATAGTTCCTAAATCATAGAAAATGACTAAAATGACCCTAAAATGCTTGAA
1 TTGT-TAATAATT-CTAAATCATAGAAAATGACTAAAACGACCCTAAAATGCATGAA
2140867 AGTGCATGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
56 4 0.08
57 7 0.15
58 37 0.77
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (56 bp):
TTGTTAATAATTCTAAATCATAGAAAATGACTAAAACGACCCTAAAATGCATGAAT
Found at i:2140879 original size:58 final size:57
Alignment explanation
Indices: 2140766--2140937 Score: 159
Period size: 58 Copynumber: 3.0 Consensus size: 57
2140756 GTTAATAATT
*** * ** *
2140766 CTAAATCATGGAAAATGACTAATGCGACCCTAAGATGCATGAATTTGTATAATAGTTC-
1 CTAAATCAT-GAAAATGACTAAAATGACCCTAAAATGCATGAAAGTGCATAATAG-TCA
* *
2140824 CTAAATCATAGAAAATGACTAAAATGACCCTAAAATGCTTGAAAGTGCATGATAGTCA
1 CTAAATCAT-GAAAATGACTAAAATGACCCTAAAATGCATGAAAGTGCATAATAGTCA
* * * * *
2140882 CTAAAACATGAAAAATGATTAAAATAACTCTCAAATGCATGAAA-TGACATAATAGT
1 CTAAATCATG-AAAATGACTAAAATGACCCTAAAATGCATGAAAGTG-CATAATAGT
2140938 GCTTCATATG
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
57 5 0.05
58 89 0.95
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (57 bp):
CTAAATCATGAAAATGACTAAAATGACCCTAAAATGCATGAAAGTGCATAATAGTCA
Found at i:2142447 original size:19 final size:19
Alignment explanation
Indices: 2142403--2142458 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2142393 TAGCCAGTTT
* **
2142403 CATGTATTGATACAATTGTC
1 CATGTATCGATACAA-TGAA
2142423 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
2142442 CATGTATCGATATAATG
1 CATGTATCGATACAATG
2142459 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2142465 original size:32 final size:33
Alignment explanation
Indices: 2142424--2142486 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
2142414 ACAATTGTCC
*
2142424 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
2142456 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
2142487 CTTCTGAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:2143125 original size:32 final size:33
Alignment explanation
Indices: 2143084--2143147 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2143074 TAGCCAAACT
* *
2143084 TGTATCGATACACCAAATA-TGTATCAATACAA
1 TGTATCGATACACAAAAAATTGTATCAATACAA
*
2143116 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCAATACA
2143148 TTGGCTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCAATACAA
Found at i:2147215 original size:15 final size:15
Alignment explanation
Indices: 2147195--2147226 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2147185 ATAAAAATGT
*
2147195 TCAAAATGAGGAAGC
1 TCAAAATGAAGAAGC
2147210 TCAAAATGAAGAAGC
1 TCAAAATGAAGAAGC
2147225 TC
1 TC
2147227 CAAACGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (15 bp):
TCAAAATGAAGAAGC
Found at i:2149319 original size:13 final size:13
Alignment explanation
Indices: 2149301--2149338 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2149291 CATTTTTCTT
2149301 TGTATCGATACAA
1 TGTATCGATACAA
*
2149314 TGTATCGATACAC
1 TGTATCGATACAA
2149327 TGTATCGATACA
1 TGTATCGATACA
2149339 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2149493 original size:20 final size:20
Alignment explanation
Indices: 2149450--2149495 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2149440 AAATCTTTTG
2149450 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2149471 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2149491 CAAAA
1 CAAAA
2149496 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2151889 original size:19 final size:18
Alignment explanation
Indices: 2151867--2151921 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 18
2151857 TTGGCAGTAG
2151867 CCAAACTTGTATCGATACA
1 CCAAA-TTGTATCGATACA
2151886 CCAAATATGTATCGATACA
1 CCAAAT-TGTATCGATACA
*
2151905 CAAAAAATTGTATCGAT
1 C--CAAATTGTATCGAT
2151922 GCATTGGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 9 0.28
21 4 0.12
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (18 bp):
CCAAATTGTATCGATACA
Found at i:2151918 original size:20 final size:20
Alignment explanation
Indices: 2151873--2151921 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
2151863 GTAGCCAAAC
* *
2151873 TTGTATCGATACACCAAATA
1 TTGTATCGATACACAAAAAA
2151893 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
2151912 TTGTATCGAT
1 TTGTATCGAT
2151922 GCATTGGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:2161106 original size:20 final size:20
Alignment explanation
Indices: 2161081--2161134 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2161071 GTTACAAGCA
2161081 ATGTATCGATACAAT-TCAT
1 ATGTATCGATACAATGTCAT
*
2161100 CATGTATCGATACAATGTCCT
1 -ATGTATCGATACAATGTCAT
2161121 ATGTATCGATACAA
1 ATGTATCGATACAA
2161135 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTCAT
Found at i:2161201 original size:13 final size:13
Alignment explanation
Indices: 2161183--2161209 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2161173 TATAATGAAC
2161183 ATGTATCGATACA
1 ATGTATCGATACA
2161196 ATGTATCGATACA
1 ATGTATCGATACA
2161209 A
1 A
2161210 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2162045 original size:52 final size:52
Alignment explanation
Indices: 2161962--2162069 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
2161952 ATGCATTTGA
* *
2161962 AATTCTAGCCGTTGGGCTCAATGTATCGATACAATTCAAAATGTATCGATAC
1 AATTATAGCCATTGGGCTCAATGTATCGATACAATTCAAAATGTATCGATAC
* **
2162014 AATTATAGCCATTGGGCTTAATGTATCGATACAATTCACCATGTATCGATAC
1 AATTATAGCCATTGGGCTCAATGTATCGATACAATTCAAAATGTATCGATAC
2162066 AATT
1 AATT
2162070 CAATTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (52 bp):
AATTATAGCCATTGGGCTCAATGTATCGATACAATTCAAAATGTATCGATAC
Found at i:2162059 original size:20 final size:20
Alignment explanation
Indices: 2162034--2162071 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2162024 ATTGGGCTTA
2162034 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
2162054 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
2162072 ATTATGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:2162157 original size:19 final size:20
Alignment explanation
Indices: 2162129--2162179 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2162119 CATTTTAGAG
*
2162129 TGTATTGATACAAAG-AACA
1 TGTATCGATACAAAGCAACA
* *
2162148 TGTATCGATACTAAGCAATA
1 TGTATCGATACAAAGCAACA
2162168 TGTATCGATACA
1 TGTATCGATACA
2162180 TTAGGGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAGCAACA
Found at i:2165124 original size:15 final size:15
Alignment explanation
Indices: 2165104--2165151 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
2165094 TTTTATATTA
2165104 ATTTTAAAATTTTTT
1 ATTTTAAAATTTTTT
*
2165119 ATTTTAAAATTTTAT
1 ATTTTAAAATTTTTT
* *
2165134 ATTATATAATTTTTT
1 ATTTTAAAATTTTTT
2165149 ATT
1 ATT
2165152 AATAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTAAAATTTTTT
Found at i:2165152 original size:15 final size:15
Alignment explanation
Indices: 2165111--2165156 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2165101 TTAATTTTAA
* *
2165111 AATTTTTTATTTTAA
1 AATTTTTTATTATAT
*
2165126 AATTTTATATTATAT
1 AATTTTTTATTATAT
2165141 AATTTTTTATTA-AT
1 AATTTTTTATTATAT
2165155 AA
1 AA
2165157 AATTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTTTTTATTATAT
Found at i:2165738 original size:13 final size:14
Alignment explanation
Indices: 2165704--2165736 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2165694 TAATTAAACT
2165704 ATATTTTA-AAAAA
1 ATATTTTATAAAAA
2165717 ATATTTTATAAAAA
1 ATATTTTATAAAAA
2165731 ATATTT
1 ATATTT
2165737 ATTTATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTTTATAAAAA
Found at i:2167381 original size:10 final size:10
Alignment explanation
Indices: 2167361--2167394 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2167351 TTCATCACCC
2167361 AAAGAAAAAA
1 AAAGAAAAAA
2167371 AAA-ACAAAAA
1 AAAGA-AAAAA
2167381 AAAGAAAAAA
1 AAAGAAAAAA
2167391 AAAG
1 AAAG
2167395 TGTTCTCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:2173329 original size:105 final size:106
Alignment explanation
Indices: 2173132--2173344 Score: 320
Period size: 105 Copynumber: 2.0 Consensus size: 106
2173122 GACTAAATGC
* * * *
2173132 GAACGTTAGGCTGAAATCATAACCTAAAACCTAATTGGATGGAATTAGACCCCTAGAATCGTCTT
1 GAACGTTAGGCTAAAATCACAACCTAAAACCCAATTGGATGGAATTAGACCCCTAGAATCATCTT
*
2173197 CAAAGTCAAGCAAAGAAAACTTGACCCCAATCAAACCTGCT
66 CAAAGTCAAGCAAAGAAAACTTCACCCCAATCAAACCTGCT
* * * *
2173238 GAACTTTAGGCTAAAATCACAACTTAAAACCCGATTGGATGGAATT-GACCCCTAGGATCATCTT
1 GAACGTTAGGCTAAAATCACAACCTAAAACCCAATTGGATGGAATTAGACCCCTAGAATCATCTT
* *
2173302 CAAAGTCAAGCAAAGAGAGCTTCACCCCAATCAAACCTGCT
66 CAAAGTCAAGCAAAGAAAACTTCACCCCAATCAAACCTGCT
2173343 GA
1 GA
2173345 TTAGAATCAA
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 56 0.58
106 40 0.42
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (106 bp):
GAACGTTAGGCTAAAATCACAACCTAAAACCCAATTGGATGGAATTAGACCCCTAGAATCATCTT
CAAAGTCAAGCAAAGAAAACTTCACCCCAATCAAACCTGCT
Found at i:2173620 original size:66 final size:66
Alignment explanation
Indices: 2173514--2173646 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 66
2173504 GTCCTAACTA
*
2173514 AGCAAGAACAATCCTATCCAACAAGAAAAAGTCTATTCCTTCTCCTAATAT-ATTTAGGACTTAT
1 AGCAAGAACAATCCTATCCAACAAGAAAAAGTCTATTCCTTATCCTAATATGA-TTAGGACTTAT
2173578 CT
65 CT
* * *
2173580 AGCAAGAACAATCCTATCCAATAAGAAAAAGTCTATTCCTTATCTTAATCTGATTAGGACTTATC
1 AGCAAGAACAATCCTATCCAACAAGAAAAAGTCTATTCCTTATCCTAATATGATTAGGACTTATC
2173645 T
66 T
2173646 A
1 A
2173647 AACAAATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 61 0.98
67 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (66 bp):
AGCAAGAACAATCCTATCCAACAAGAAAAAGTCTATTCCTTATCCTAATATGATTAGGACTTATC
T
Found at i:2177850 original size:65 final size:65
Alignment explanation
Indices: 2177746--2177888 Score: 277
Period size: 65 Copynumber: 2.2 Consensus size: 65
2177736 CTTGACCATT
2177746 AAGATATTTCAATGATTCATGGTCACTATGGATTACAAATTCTCTAGATAAAAGGTAATGTTGCC
1 AAGATATTTCAATGATTCATGGTCACTATGGATTACAAATTCTCTAGATAAAAGGTAATGTTGCC
*
2177811 AAGATATTTCAATGATTCATGGTCACTATGGATTACAAATTCTCTAGGTAAAAGGTAATGTTGCC
1 AAGATATTTCAATGATTCATGGTCACTATGGATTACAAATTCTCTAGATAAAAGGTAATGTTGCC
2177876 AAGATATTTCAAT
1 AAGATATTTCAAT
2177889 CAAAGCATAC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 77 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (65 bp):
AAGATATTTCAATGATTCATGGTCACTATGGATTACAAATTCTCTAGATAAAAGGTAATGTTGCC
Found at i:2180736 original size:42 final size:42
Alignment explanation
Indices: 2180680--2180781 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
2180670 TTCTTCTCTC
* * * * *
2180680 CTCCTCCTACCATCCCTCCCCTTTTTATTAACTCTCCTATCT
1 CTCCTCCTATCATCCCTCCCATCTCTACTAACTCTCCTATCT
* ** * *
2180722 CTCTTCCTATCATCCCTCTTATCTCTACTATCTCTCCTTTCT
1 CTCCTCCTATCATCCCTCCCATCTCTACTAACTCTCCTATCT
2180764 CTCCTCCTATCATCCCTC
1 CTCCTCCTATCATCCCTC
2180782 ATATCTCTTC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCCATCTCTACTAACTCTCCTATCT
Found at i:2180787 original size:42 final size:42
Alignment explanation
Indices: 2180711--2180798 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
2180701 TTTTTATTAA
* *
2180711 CTCTCCTATCTCTCTTCCTATCATCCCTCTTATCTCTACTAT
1 CTCTCCTATCTCTCCTCCTATCATCCCTCATATCTCTACTAT
* * *
2180753 CTCTCCTTTCTCTCCTCCTATCATCCCTCATATCTCTTCTTT
1 CTCTCCTATCTCTCCTCCTATCATCCCTCATATCTCTACTAT
2180795 CTCT
1 CTCT
2180799 TTGAGGGCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (42 bp):
CTCTCCTATCTCTCCTCCTATCATCCCTCATATCTCTACTAT
Found at i:2183593 original size:13 final size:13
Alignment explanation
Indices: 2183575--2183600 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2183565 CAATTTTTTG
2183575 TGTATCGATACAT
1 TGTATCGATACAT
2183588 TGTATCGATACAT
1 TGTATCGATACAT
2183601 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2183685 original size:20 final size:20
Alignment explanation
Indices: 2183660--2183732 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2183650 CATCCTTTTT
2183660 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2183680 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2183701 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2183721 ATGTATCGATAC
1 ATGTATCGATAC
2183733 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2183705 original size:21 final size:21
Alignment explanation
Indices: 2183639--2183715 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2183629 CTGCCAAGAA
*
2183639 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
2183660 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
2183680 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
2183701 ATGTATCGATACATT
1 ATGTATCGATACATT
2183716 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:2183705 original size:41 final size:41
Alignment explanation
Indices: 2183639--2183732 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
2183629 CTGCCAAGAA
2183639 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
2183680 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
2183721 ATGTATCGATAC
1 ATGTATCGATAC
2183733 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:2184339 original size:48 final size:48
Alignment explanation
Indices: 2184284--2184379 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2184274 AAATTTTACG
2184284 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2184332 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2184380 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:2186238 original size:13 final size:13
Alignment explanation
Indices: 2186220--2186258 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2186210 ATAATCACCC
*
2186220 TGTATCGATACAG
1 TGTATCGATACAA
2186233 TGTATCGATACAA
1 TGTATCGATACAA
2186246 TGTATCGATACAA
1 TGTATCGATACAA
2186259 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2188357 original size:15 final size:15
Alignment explanation
Indices: 2188337--2188367 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2188327 ATTTCGTTTG
*
2188337 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2188352 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2188367 G
1 G
2188368 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2192447 original size:13 final size:13
Alignment explanation
Indices: 2192429--2192454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2192419 CAATTTTTTG
2192429 TGTATCGATACAT
1 TGTATCGATACAT
2192442 TGTATCGATACAT
1 TGTATCGATACAT
2192455 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2192539 original size:20 final size:20
Alignment explanation
Indices: 2192514--2192586 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2192504 CATCCTTTTT
2192514 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2192534 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2192555 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2192575 ATGTATCGATAC
1 ATGTATCGATAC
2192587 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2192559 original size:21 final size:21
Alignment explanation
Indices: 2192493--2192569 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
2192483 CTGCCAAGAA
*
2192493 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
2192514 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
2192534 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
2192555 ATGTATCGATACATT
1 ATGTATCGATACATT
2192570 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:2192559 original size:41 final size:41
Alignment explanation
Indices: 2192493--2192586 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
2192483 CTGCCAAGAA
2192493 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
2192534 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
2192575 ATGTATCGATAC
1 ATGTATCGATAC
2192587 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:2195622 original size:27 final size:28
Alignment explanation
Indices: 2195570--2195622 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2195560 TCAGGAAAGT
* * *
2195570 GAAATCAACAAGAAATTTGAAGGGAAAC
1 GAAATCAACAAGAAATATCAAAGGAAAC
2195598 GAAAT-AACAAGAAATATCAAAGGAA
1 GAAATCAACAAGAAATATCAAAGGAA
2195623 GAGAACTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.58, C:0.09, G:0.19, T:0.13
Consensus pattern (28 bp):
GAAATCAACAAGAAATATCAAAGGAAAC
Found at i:2199773 original size:33 final size:33
Alignment explanation
Indices: 2199736--2199802 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2199726 TTCAACGATT
2199736 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2199769 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2199802 T
1 T
2199803 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2199774 original size:13 final size:13
Alignment explanation
Indices: 2199756--2199780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2199746 CATAAAATGT
2199756 TGTATCGATACAA
1 TGTATCGATACAA
2199769 TGTATCGATACA
1 TGTATCGATACA
2199781 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2199863 original size:13 final size:13
Alignment explanation
Indices: 2199845--2199869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2199835 ATTACTCACA
2199845 TGTATCGATACAT
1 TGTATCGATACAT
2199858 TGTATCGATACA
1 TGTATCGATACA
2199870 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2199920 original size:52 final size:50
Alignment explanation
Indices: 2199858--2199998 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
2199848 ATCGATACAT
*
2199858 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2199910 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
2199962 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATT--ATGTATCGATACATGCAG
2199999 ATAAATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2200006 original size:52 final size:52
Alignment explanation
Indices: 2199878--2199998 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2199868 CACTGATCTT
*
2199878 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2199930 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2199982 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2199999 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2206889 original size:1 final size:1
Alignment explanation
Indices: 2206878--2206977 Score: 56
Period size: 1 Copynumber: 100.0 Consensus size: 1
2206868 AGAAGTGATG
* * * * * * * * * * *
2206878 AAAAGAAAAAAACAAACAAACAAAAAAAAACACACACAAAAAAAAAAACAAAAAAACACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
2206943 CAAAAAACAAAAAAAAAAAACAACACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2206978 GGTGCAAAGG
Statistics
Matches: 67, Mismatches: 32, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:2206904 original size:16 final size:16
Alignment explanation
Indices: 2206883--2206975 Score: 89
Period size: 17 Copynumber: 5.4 Consensus size: 16
2206873 TGATGAAAAG
2206883 AAAAAAACAAACAAAC
1 AAAAAAACAAACAAAC
*
2206899 AAAAAAAAACACACACAAAA
1 --AAAAAAACA-A-ACAAAC
*
2206919 AAAAAAACAAAAAAAC
1 AAAAAAACAAACAAAC
2206935 ACAAAAAACAAA-AAAC
1 A-AAAAAACAAACAAAC
*
2206951 AAAAAAAAAAAACAACAC
1 -AAAAAAACAAACAA-AC
2206969 AAAAAAA
1 AAAAAAA
2206976 AAGGTGCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
16 18 0.28
17 21 0.32
18 20 0.31
19 1 0.02
20 5 0.08
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAACAAAC
Found at i:2206916 original size:24 final size:22
Alignment explanation
Indices: 2206878--2206977 Score: 100
Period size: 22 Copynumber: 4.5 Consensus size: 22
2206868 AGAAGTGATG
* *
2206878 AAAAGAAAAAAACA-AACAAAC
1 AAAAAAAAAAAACACAAAAAAC
*
2206899 AAAAAAAAACACACACAAAAAA-
1 AAAAAAAAA-AAACACAAAAAAC
2206921 AAAAACAAAAAAACACAAAAAAC
1 AAAAA-AAAAAAACACAAAAAAC
*
2206944 AAAAAACAAAAA-A-AAAAAAC
1 AAAAAAAAAAAACACAAAAAAC
2206964 AACACAAAAAAAAA
1 AA-A-AAAAAAAAA
2206978 GGTGCAAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.13
21 10 0.15
22 34 0.51
23 14 0.21
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAACACAAAAAAC
Found at i:2206976 original size:16 final size:15
Alignment explanation
Indices: 2206883--2206977 Score: 83
Period size: 16 Copynumber: 6.5 Consensus size: 15
2206873 TGATGAAAAG
*
2206883 AAAAAAACAAACA-A
1 AAAAAAAAAAACACA
*
2206897 ACAAAAAAAAACAC-
1 AAAAAAAAAAACACA
* *
2206911 -ACACAAAAAA-A-A
1 AAAAAAAAAAACACA
*
2206923 AAACAAAAAAACACA
1 AAAAAAAAAAACACA
*
2206938 AAAAACAAAAAACAAA
1 AAAAA-AAAAAACACA
2206954 AAAAAAAAACAACACA
1 AAAAAAAAA-AACACA
2206970 AAAAAAAA
1 AAAAAAAA
2206978 GGTGCAAAGG
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
12 1 0.02
13 14 0.22
14 12 0.19
15 9 0.14
16 27 0.43
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACACA
Found at i:2207268 original size:15 final size:14
Alignment explanation
Indices: 2207224--2207270 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2207214 CCAAACACCA
2207224 AAAAAAAGCAAAAA-
1 AAAAAAA-CAAAAAG
* *
2207238 AAAAAAAGAAGAAG
1 AAAAAAACAAAAAG
2207252 AAAAAAACAAAACAG
1 AAAAAAACAAAA-AG
2207267 AAAA
1 AAAA
2207271 TCTTGATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 4 0.15
14 17 0.63
15 6 0.22
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAG
Found at i:2208372 original size:35 final size:34
Alignment explanation
Indices: 2208292--2208555 Score: 256
Period size: 33 Copynumber: 7.6 Consensus size: 34
2208282 ATTTTGTCTC
* * *
2208292 AAAGTCCACGACTCAGTGGCA-T-TTTTTC-TTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
2208323 AAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
* * *
2208359 -AAGTCCACAACTCCGTGGCA-TCTTTCTCCCTTCCT
1 AAAGCCCACAACTCCGTGGCACTCTTT-T-TCTT-TT
*
2208394 AAAGCCCACACAACTCCGTGGCAAC-CTTCTTCTTTT
1 AAAG-CC-CACAACTCCGTGGC-ACTCTTTTTCTTTT
*
2208430 CAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
**
2208464 AAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTT-CTTTT
2208500 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
2208534 AAAGCCCACAACTCTGTGGCAC
1 AAAGCCCACAACTCCGTGGCAC
2208556 CGACGACTTT
Statistics
Matches: 197, Mismatches: 18, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
31 17 0.09
32 1 0.01
33 46 0.23
34 27 0.14
35 44 0.22
36 15 0.08
37 28 0.14
38 15 0.08
39 4 0.02
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
Found at i:2208499 original size:70 final size:70
Alignment explanation
Indices: 2208290--2208754 Score: 437
Period size: 70 Copynumber: 6.4 Consensus size: 70
2208280 GCATTTTGTC
* * * * * *
2208290 TCAAAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCATAACTCCGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
2208353 CCTTT
66 CCTTT
* * * *
2208358 T--AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTCCGTGGCAAC-C
1 TCAAAGCCCACAACTCCGTGGCACCTTT-T-TCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTC
*
2208420 -TTCTT-CTTT
60 TTTTTTCCTTT
* **
2208429 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
2208494 CCTTT
66 CCTTT
*
2208499 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCGACGACT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGT-G----G-C-AC-
*
2208564 TTGTGGCACTCTCTTTCTCTTT
58 ---T----CT-TTTTTC-CTTT
* *
2208586 TTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
2208651 CCCTTT
65 TCCTTT
*
2208657 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC-TTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
2208721 CACTTT
66 C-CTTT
* *
2208727 T--AAGTCCACAACTCCGTGGCATCTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTT
2208755 TCCTTCCCAA
Statistics
Matches: 334, Mismatches: 31, Indels: 64
0.78 0.07 0.15
Matches are distributed among these distances:
66 18 0.05
67 5 0.01
68 39 0.12
69 12 0.04
70 93 0.28
71 46 0.14
72 10 0.03
73 38 0.11
74 2 0.01
75 1 0.00
76 1 0.00
77 3 0.01
81 3 0.01
82 1 0.00
83 1 0.00
85 2 0.01
86 5 0.01
87 34 0.10
88 20 0.06
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (70 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
CCTTT
Found at i:2208701 original size:104 final size:108
Alignment explanation
Indices: 2208566--2208772 Score: 309
Period size: 104 Copynumber: 2.0 Consensus size: 108
2208556 CGACGACTTT
2208566 GTGGCACTCTCTTTCTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC-CGTTTAAAGCCC
1 GTGGCACTCTCTTTCTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCAC-TTTAAAGCCC
**
2208629 ACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
65 ACAACTCCGTGGCA-TCTTTTTCCCTTCCCAAAGCCCACAACTCC
* *
2208674 GTGGCACT-T-TTT-TC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCACTTTTAAGTCCA
1 GTGGCACTCTCTTTCTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCACTTTAAAGCCCA
*
2208735 CAACTCCGTGGCATCTTTTTTCCTTCCCAAAGCCCACA
66 CAACTCCGTGGCATCTTTTTCCCTTCCCAAAGCCCACA
2208773 CAAGTCGGTG
Statistics
Matches: 92, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
104 48 0.52
105 31 0.34
106 4 0.04
107 1 0.01
108 8 0.09
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (108 bp):
GTGGCACTCTCTTTCTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCACTTTAAAGCCCA
CAACTCCGTGGCATCTTTTTCCCTTCCCAAAGCCCACAACTCC
Found at i:2208711 original size:158 final size:157
Alignment explanation
Indices: 2208424--2208713 Score: 499
Period size: 158 Copynumber: 1.8 Consensus size: 157
2208414 GCAACCTTCT
* **
2208424 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCGTTTAAAGCCCACAACTCCGTGGCACTCT
* *
2208489 TTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
66 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
2208554 ACCGACGACTTTGTGGCACTCTCTTTC
131 ACCGACGACTTTGTGGCACTCTCTTTC
* *
2208581 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTC
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT-CGTTTAAAGCCCACAACTCCGTGGCACTC
*
2208646 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGG
65 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG
2208711 CAC
130 CAC
2208714 TCTTTTTCAC
Statistics
Matches: 124, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
157 33 0.27
158 91 0.73
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (157 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCGTTTAAAGCCCACAACTCCGTGGCACTCT
TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
ACCGACGACTTTGTGGCACTCTCTTTC
Found at i:2208800 original size:104 final size:102
Alignment explanation
Indices: 2208588--2208805 Score: 262
Period size: 104 Copynumber: 2.1 Consensus size: 102
2208578 TTCTCTTTTT
2208588 AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
** * **
2208653 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
66 CTTCCCAAAGCCCACAACTCCGTGGCAC--TCTTCTTCC
* *
2208692 AAAGCCCACAACTCCGTGGCACTCTTTTTCAC-TTTTAAGTCCACAACTCCGTGGCA-TCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTC-CGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
* * *
2208755 TCCTTCCCAAAGCCCACACAAGTCGGTGGCAAC-CTTCTTCC
64 CCCTTCCCAAAG-CC-CACAACTCCGTGGC-ACTCTTCTTCC
2208796 AAAGCCCACA
1 AAAGCCCACA
2208806 CAAGTCGGTG
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
104 53 0.54
105 31 0.31
106 13 0.13
107 2 0.02
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.29
Consensus pattern (102 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
CTTCCCAAAGCCCACAACTCCGTGGCACTCTTCTTCC
Found at i:2208944 original size:49 final size:49
Alignment explanation
Indices: 2208823--2209292 Score: 595
Period size: 49 Copynumber: 9.7 Consensus size: 49
2208813 GTGGCAACCC
* *
2208823 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CAT
* *
2208875 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2208924 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2208973 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2209022 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2209071 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGTACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2209114 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
2209163 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2209206 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CAT
* *
2209258 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAC
2209293 GTTGACATCC
Statistics
Matches: 366, Mismatches: 37, Indels: 30
0.85 0.09 0.07
Matches are distributed among these distances:
43 77 0.21
45 2 0.01
47 1 0.00
49 211 0.58
50 3 0.01
52 72 0.20
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:2209002 original size:98 final size:98
Alignment explanation
Indices: 2208823--2209358 Score: 745
Period size: 98 Copynumber: 5.5 Consensus size: 98
2208813 GTGGCAACCC
* * *
2208823 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCCAAT
2208888 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
63 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2208924 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
2208989 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2209022 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2209087 GCTGGCCTTGACTCAGTACATTGGCA----C--
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2209114 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2209179 GCTGGCCTTGAATCAGCACATTGGCA----C--
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* * *
2209206 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
* * *
2209271 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
63 GTAGCTGGCCTTGACTCAGCACATTGGCA-CC----T-TCAT
* * * *
2209313 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
2209359 TATCACTTTT
Statistics
Matches: 403, Mismatches: 17, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
92 129 0.32
94 6 0.01
95 42 0.10
98 142 0.35
99 3 0.01
101 40 0.10
105 6 0.01
107 35 0.09
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (98 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
Found at i:2209142 original size:92 final size:93
Alignment explanation
Indices: 2209022--2209292 Score: 447
Period size: 92 Copynumber: 2.9 Consensus size: 93
2209012 GCACCTTCAT
2209022 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2209087 GCTGGCCTTGACTCAGTACATTGGCA-C
66 GCTGGCCTTGACTCAGCACATTGGCACC
2209114 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2209179 GCTGGCCTTGAATCAGCACATTGGCA-C
66 GCTGGCCTTGACTCAGCACATTGGCACC
* * *
2209206 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
*
2209271 GTAGCTGGCCTTGAATCAGCAC
63 GTAGCTGGCCTTGACTCAGCAC
2209293 GTTGACATCC
Statistics
Matches: 171, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
92 129 0.75
94 5 0.03
95 37 0.22
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (93 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACC
Found at i:2209335 original size:55 final size:55
Alignment explanation
Indices: 2209206--2209589 Score: 282
Period size: 67 Copynumber: 6.7 Consensus size: 55
2209196 ACATTGGCAC
* *
2209206 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2209258 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2209313 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
2209377 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2209429 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2209484 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
2209549 AT
54 AT
*
2209551 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2209590 GCTTATCATC
Statistics
Matches: 259, Mismatches: 40, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
49 36 0.14
50 1 0.00
52 42 0.16
54 8 0.03
55 65 0.25
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
61 8 0.03
62 6 0.02
63 5 0.02
64 7 0.03
66 4 0.02
67 70 0.27
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:2209495 original size:171 final size:172
Alignment explanation
Indices: 2209206--2209591 Score: 711
Period size: 171 Copynumber: 2.2 Consensus size: 172
2209196 ACATTGGCAC
*
2209206 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTTCCATCTTTAAGTTCAAT
2209271 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
64 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
2209336 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
129 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2209380 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT-CATCTTTAAGTTCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCCATCTTTAAGTTCAATGT
2209444 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
66 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
2209509 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
*
2209551 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
2209592 TTATCATCTC
Statistics
Matches: 207, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
171 164 0.79
172 5 0.02
174 38 0.18
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (172 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCCATCTTTAAGTTCAATGT
AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:2210432 original size:33 final size:33
Alignment explanation
Indices: 2210395--2210461 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2210385 TTCAACGATT
2210395 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2210428 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2210461 T
1 T
2210462 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2210433 original size:13 final size:13
Alignment explanation
Indices: 2210415--2210439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2210405 CATAAAATGT
2210415 TGTATCGATACAA
1 TGTATCGATACAA
2210428 TGTATCGATACA
1 TGTATCGATACA
2210440 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2210522 original size:13 final size:13
Alignment explanation
Indices: 2210504--2210528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2210494 ATTACTCACA
2210504 TGTATCGATACAT
1 TGTATCGATACAT
2210517 TGTATCGATACA
1 TGTATCGATACA
2210529 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2210579 original size:52 final size:50
Alignment explanation
Indices: 2210517--2210657 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
2210507 ATCGATACAT
*
2210517 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2210569 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
2210621 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATT--ATGTATCGATACATGCAG
2210658 ATAAATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2210665 original size:52 final size:52
Alignment explanation
Indices: 2210537--2210657 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2210527 CACTGATCTT
*
2210537 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2210589 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2210641 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2210658 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2217564 original size:17 final size:17
Alignment explanation
Indices: 2217542--2217634 Score: 118
Period size: 17 Copynumber: 5.4 Consensus size: 17
2217532 TGATGAAAAG
2217542 AAAAAAACAAACAAACA
1 AAAAAAACAAACAAACA
2217559 AAAAAAACACACACAAA-A
1 AAAAAAACA-A-ACAAACA
*
2217577 AAAAAAACAAAAAAACA
1 AAAAAAACAAACAAACA
*
2217594 CAAAAAACAAA-AAACA
1 AAAAAAACAAACAAACA
*
2217610 AAAAAAAAAAACAACACA
1 AAAAAAACAAACAA-ACA
2217628 AAAAAAA
1 AAAAAAA
2217635 AGGTGCAAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.27
17 23 0.34
18 21 0.31
19 5 0.07
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAACAAACA
Found at i:2217577 original size:1 final size:1
Alignment explanation
Indices: 2217573--2217635 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
2217563 AAACACACAC
* * * * * * * *
2217573 AAAAAAAAAAACAAAAAAACACAAAAAACAAAAAACAAAAAAAAAAAACAACACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2217636 GGTGCAAAGG
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2217584 original size:35 final size:32
Alignment explanation
Indices: 2217537--2217634 Score: 115
Period size: 35 Copynumber: 2.9 Consensus size: 32
2217527 AGAAGTGATG
*
2217537 AAAAGAAAAAAACAAACAAACAAAAAAAACACA
1 AAAAAAAAAAAACAAACAAACAAAAAAAACA-A
* *
2217570 CACAAAAAAAAAAACAAAAAAACACAAAAAACAA
1 -A-AAAAAAAAAAACAAACAAACAAAAAAAACAA
*
2217604 AAAACAAAAAAAAAAAACAACACAAAAAAAA
1 AAAA-AAAAAAAACAAACAA-ACAAAAAAAA
2217635 AGGTGCAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.05
33 14 0.25
34 11 0.20
35 27 0.49
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (32 bp):
AAAAAAAAAAAACAAACAAACAAAAAAAACAA
Found at i:2217594 original size:24 final size:24
Alignment explanation
Indices: 2217543--2217635 Score: 102
Period size: 24 Copynumber: 3.8 Consensus size: 24
2217533 GATGAAAAGA
2217543 AAAAAACAAACAAACAAAAAAAACAC
1 AAAAAACAAA-AAAC-AAAAAAACAC
*
2217569 ACACAAAAAAAAAAACAAAAAAACAC
1 A-A-AAAACAAAAAACAAAAAAACAC
2217595 AAAAAACAAAAAACAAAAAAA-A-
1 AAAAAACAAAAAACAAAAAAACAC
*
2217617 AAAACAACACAAAA-AAAAA
1 AAAA-AACAAAAAACAAAAA
2217636 GGTGCAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.15
23 9 0.15
24 18 0.30
25 1 0.02
26 12 0.20
27 5 0.08
28 7 0.11
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAACAAAAAACAAAAAAACAC
Found at i:2217630 original size:13 final size:13
Alignment explanation
Indices: 2217537--2217633 Score: 74
Period size: 13 Copynumber: 7.3 Consensus size: 13
2217527 AGAAGTGATG
*
2217537 AAAAGAAAA-AAA
1 AAAACAAAACAAA
*
2217549 CAAAC-AAACAAAA
1 AAAACAAAAC-AAA
*
2217562 AAAACACACACAAA
1 AAAACA-AAACAAA
2217576 AAAA-AAAACAAAA
1 AAAACAAAAC-AAA
*
2217589 AAACACAAAAAACAA
1 AAA-ACAAAACA-AA
*
2217604 AAAACAAAAAAAA
1 AAAACAAAACAAA
*
2217617 AAAACAACACAAA
1 AAAACAAAACAAA
2217630 AAAA
1 AAAA
2217634 AAGGTGCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
11 3 0.04
12 6 0.09
13 31 0.45
14 17 0.25
15 12 0.17
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (13 bp):
AAAACAAAACAAA
Found at i:2217634 original size:16 final size:15
Alignment explanation
Indices: 2217542--2217635 Score: 81
Period size: 16 Copynumber: 6.5 Consensus size: 15
2217532 TGATGAAAAG
*
2217542 AAAAAAACAA-ACAA
1 AAAAAAAAAACACAA
*
2217556 ACAAAAAAAACAC--
1 AAAAAAAAAACACAA
* *
2217569 ACACAAAAAA-A-AA
1 AAAAAAAAAACACAA
*
2217582 AACAAAAAAACACAA
1 AAAAAAAAAACACAA
*
2217597 AAAACAAAAAACAAAA
1 AAAA-AAAAAACACAA
2217613 AAAAAAAACAACACAA
1 AAAAAAAA-AACACAA
2217629 AAAAAAA
1 AAAAAAA
2217636 GGTGCAAAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
12 1 0.02
13 16 0.25
14 9 0.14
15 11 0.17
16 27 0.42
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACACAA
Found at i:2217635 original size:35 final size:34
Alignment explanation
Indices: 2217537--2217635 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 34
2217527 AGAAGTGATG
* * *
2217537 AAAAGAAAAAAACAAACAAACAAAAAAAACACAC
1 AAAAAAAAAAAACAAACAAACAAAAAAAAAAAAC
*
2217571 ACAAAAAAAAAAACAAAAAAACACAAAAAACAAAAAAC
1 A-AAAAAAAAAAAC-AAACAA-ACAAAAAA-AAAAAAC
2217609 AAAAAAAAAAAACAACACAAA-AAAAAA
1 AAAAAAAAAAAACAA-ACAAACAAAAAA
2217636 GGTGCAAAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
34 1 0.02
35 17 0.31
36 8 0.15
37 23 0.42
38 6 0.11
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAAACAAACAAACAAAAAAAAAAAAC
Found at i:2217926 original size:15 final size:14
Alignment explanation
Indices: 2217882--2217928 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2217872 CCAAACACCA
2217882 AAAAAAAGCAAAAA-
1 AAAAAAA-CAAAAAG
* *
2217896 AAAAAAAGAAGAAG
1 AAAAAAACAAAAAG
2217910 AAAAAAACAAAACAG
1 AAAAAAACAAAA-AG
2217925 AAAA
1 AAAA
2217929 TCTTGATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 4 0.15
14 17 0.63
15 6 0.22
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAG
Found at i:2219031 original size:35 final size:34
Alignment explanation
Indices: 2218951--2219214 Score: 256
Period size: 33 Copynumber: 7.6 Consensus size: 34
2218941 ATTTTGTCTC
* * *
2218951 AAAGTCCACGACTCAGTGGCA-T-TTTTTC-TTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
2218982 AAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
* * *
2219018 -AAGTCCACAACTCCGTGGCA-TCTTTCTCCCTTCCT
1 AAAGCCCACAACTCCGTGGCACTCTTT-T-TCTT-TT
*
2219053 AAAGCCCACACAACTCCGTGGCAAC-CTTCTTCTTTT
1 AAAG-CC-CACAACTCCGTGGC-ACTCTTTTTCTTTT
*
2219089 CAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
**
2219123 AAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTT-CTTTT
2219159 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
2219193 AAAGCCCACAACTCTGTGGCAC
1 AAAGCCCACAACTCCGTGGCAC
2219215 CGACGACTTT
Statistics
Matches: 197, Mismatches: 18, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
31 17 0.09
32 1 0.01
33 46 0.23
34 27 0.14
35 44 0.22
36 15 0.08
37 28 0.14
38 15 0.08
39 4 0.02
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
Found at i:2219158 original size:70 final size:70
Alignment explanation
Indices: 2218949--2219413 Score: 428
Period size: 70 Copynumber: 6.4 Consensus size: 70
2218939 GCATTTTGTC
* * * * * *
2218949 TCAAAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCATAACTCCGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
2219012 CCTTT
66 CCTTT
* * * *
2219017 T--AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAACTCCGTGGCAAC-C
1 TCAAAGCCCACAACTCCGTGGCACCTTT-T-TCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTC
*
2219079 -TTCTT-CTTT
60 TTTTTTCCTTT
* **
2219088 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
2219153 CCTTT
66 CCTTT
*
2219158 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCGACGACT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGT-G----G-C-AC-
*
2219223 TTGTGGCACTCTCTTTCTCTTT
58 ---T----CT-TTTTTC-CTTT
* * *
2219245 TTAAAGCCCACAACTCTGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
2219310 CCCTTT
65 TCCTTT
*
2219316 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC-TTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
2219380 CACTTT
66 C-CTTT
* *
2219386 T--AAGTCCACAACTCCGTGGCATCTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTT
2219414 TCCTTCCCAA
Statistics
Matches: 332, Mismatches: 33, Indels: 64
0.77 0.08 0.15
Matches are distributed among these distances:
66 18 0.05
67 5 0.02
68 39 0.12
69 12 0.04
70 93 0.28
71 45 0.14
72 10 0.03
73 38 0.11
74 2 0.01
75 1 0.00
76 1 0.00
77 3 0.01
81 3 0.01
82 1 0.00
83 1 0.00
85 2 0.01
86 5 0.02
87 33 0.10
88 20 0.06
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (70 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
CCTTT
Found at i:2219343 original size:35 final size:35
Alignment explanation
Indices: 2219225--2219418 Score: 234
Period size: 34 Copynumber: 5.5 Consensus size: 35
2219215 CGACGACTTT
* * *
2219225 GTGGCACTCTCTTTCTCTTTTTAAAGCCCACAACTCT
1 GTGGCAC-CTTTTTC-CCTTTTAAAGCCCACAACTCC
*
2219262 GTGGCACCTTTTT-CCGTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCCCTTTTAAAGCCCACAACTCC
2219296 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCAC-CTTTTTCCCTTTT-AAAGCCCACAACTCC
*
2219333 GTGGCA-CTTTTT-TCTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCCCTTTTAAAGCCCACAACTCC
* *
2219366 GTGGCACTCTTTTTCACTTTT-AAGTCCACAACTCC
1 GTGGCAC-CTTTTTCCCTTTTAAAGCCCACAACTCC
* *
2219401 GTGGCATCTTTTTTCCTT
1 GTGGCACCTTTTTCCCTT
2219419 CCCAAAGCCC
Statistics
Matches: 140, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
33 21 0.15
34 39 0.28
35 37 0.26
36 15 0.11
37 28 0.20
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (35 bp):
GTGGCACCTTTTTCCCTTTTAAAGCCCACAACTCC
Found at i:2219370 original size:158 final size:157
Alignment explanation
Indices: 2219083--2219372 Score: 490
Period size: 158 Copynumber: 1.8 Consensus size: 157
2219073 GCAACCTTCT
* **
2219083 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCGTTTAAAGCCCACAACTCCGTGGCACTCT
* *
2219148 TTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
66 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
2219213 ACCGACGACTTTGTGGCACTCTCTTTC
131 ACCGACGACTTTGTGGCACTCTCTTTC
* * *
2219240 TCTTTTTAAAGCCCACAACTCTGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTC
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT-CGTTTAAAGCCCACAACTCCGTGGCACTC
*
2219305 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGG
65 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG
2219370 CAC
130 CAC
2219373 TCTTTTTCAC
Statistics
Matches: 123, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
157 32 0.26
158 91 0.74
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (157 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCGTTTAAAGCCCACAACTCCGTGGCACTCT
TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
ACCGACGACTTTGTGGCACTCTCTTTC
Found at i:2219452 original size:104 final size:102
Alignment explanation
Indices: 2219243--2219431 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 102
2219233 CTCTTTCTCT
*
2219243 TTTTAAAGCCCACAACTCTGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTT
** *
2219308 TTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
66 TTCCCTTCCCAAAGCCCACAACTCCGTGGCAC--TCTTC
* *
2219347 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCAC-TTTTAAGTCCACAACTCCGTGGCA-TCT
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC-CGTTTAAAGCCCACAACTCCGTGGCACTCT
*
2219410 TTTTTCCTTCCCAAAGCCCACA
64 TTTTCCCTTCCCAAAGCCCACA
2219432 CAAGTCGGTG
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
104 47 0.61
105 29 0.38
106 1 0.01
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (102 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTT
TTCCCTTCCCAAAGCCCACAACTCCGTGGCACTCTTC
Found at i:2219459 original size:104 final size:102
Alignment explanation
Indices: 2219247--2219464 Score: 253
Period size: 104 Copynumber: 2.1 Consensus size: 102
2219237 TTCTCTTTTT
*
2219247 AAAGCCCACAACTCTGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
** * **
2219312 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
66 CTTCCCAAAGCCCACAACTCCGTGGCAC--TCTTCTTCC
* *
2219351 AAAGCCCACAACTCCGTGGCACTCTTTTTCAC-TTTTAAGTCCACAACTCCGTGGCA-TCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTC-CGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
* * *
2219414 TCCTTCCCAAAGCCCACACAAGTCGGTGGCAAC-CTTCTTCC
64 CCCTTCCCAAAG-CC-CACAACTCCGTGGC-ACTCTTCTTCC
2219455 AAAGCCCACA
1 AAAGCCCACA
2219465 CAAGTCGGTG
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
104 52 0.53
105 31 0.32
106 13 0.13
107 2 0.02
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (102 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
CTTCCCAAAGCCCACAACTCCGTGGCACTCTTCTTCC
Found at i:2219603 original size:49 final size:49
Alignment explanation
Indices: 2219482--2219951 Score: 595
Period size: 49 Copynumber: 9.7 Consensus size: 49
2219472 GTGGCAACCC
* *
2219482 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CAT
* *
2219534 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2219583 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2219632 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2219681 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2219730 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGTACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
2219773 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
2219822 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
2219865 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CAT
* *
2219917 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAC
2219952 GTTGACATCC
Statistics
Matches: 366, Mismatches: 37, Indels: 30
0.85 0.09 0.07
Matches are distributed among these distances:
43 77 0.21
45 2 0.01
47 1 0.00
49 211 0.58
50 3 0.01
52 72 0.20
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:2219661 original size:98 final size:98
Alignment explanation
Indices: 2219482--2220017 Score: 745
Period size: 98 Copynumber: 5.5 Consensus size: 98
2219472 GTGGCAACCC
* * *
2219482 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCCAAT
2219547 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
63 GTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2219583 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
2219648 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2219681 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2219746 GCTGGCCTTGACTCAGTACATTGGCA----C--
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
2219773 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2219838 GCTGGCCTTGAATCAGCACATTGGCA----C--
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
* * *
2219865 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
* * *
2219930 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
63 GTAGCTGGCCTTGACTCAGCACATTGGCA-CC----T-TCAT
* * * *
2219972 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
2220018 TATCACTTTT
Statistics
Matches: 403, Mismatches: 17, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
92 129 0.32
94 6 0.01
95 42 0.10
98 142 0.35
99 3 0.01
101 40 0.10
105 6 0.01
107 35 0.09
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (98 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
Found at i:2219801 original size:92 final size:93
Alignment explanation
Indices: 2219681--2219951 Score: 447
Period size: 92 Copynumber: 2.9 Consensus size: 93
2219671 GCACCTTCAT
2219681 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2219746 GCTGGCCTTGACTCAGTACATTGGCA-C
66 GCTGGCCTTGACTCAGCACATTGGCACC
2219773 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
2219838 GCTGGCCTTGAATCAGCACATTGGCA-C
66 GCTGGCCTTGACTCAGCACATTGGCACC
* * *
2219865 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
*
2219930 GTAGCTGGCCTTGAATCAGCAC
63 GTAGCTGGCCTTGACTCAGCAC
2219952 GTTGACATCC
Statistics
Matches: 171, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
92 129 0.75
94 5 0.03
95 37 0.22
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (93 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACC
Found at i:2219994 original size:55 final size:55
Alignment explanation
Indices: 2219865--2220248 Score: 282
Period size: 67 Copynumber: 6.7 Consensus size: 55
2219855 ACATTGGCAC
* *
2219865 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2219917 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2219972 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
2220036 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2220088 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2220143 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
2220208 AT
54 AT
*
2220210 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2220249 GCTTATCATC
Statistics
Matches: 259, Mismatches: 40, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
49 36 0.14
50 1 0.00
52 42 0.16
54 8 0.03
55 65 0.25
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
61 8 0.03
62 6 0.02
63 5 0.02
64 7 0.03
66 4 0.02
67 70 0.27
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:2220154 original size:171 final size:172
Alignment explanation
Indices: 2219865--2220250 Score: 711
Period size: 171 Copynumber: 2.2 Consensus size: 172
2219855 ACATTGGCAC
*
2219865 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTTCCATCTTTAAGTTCAAT
2219930 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
64 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
2219995 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
129 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2220039 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT-CATCTTTAAGTTCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCCATCTTTAAGTTCAATGT
2220103 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
66 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
2220168 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
131 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
*
2220210 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
2220251 TTATCATCTC
Statistics
Matches: 207, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
171 164 0.79
172 5 0.02
174 38 0.18
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (172 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCCATCTTTAAGTTCAATGT
AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCAT
GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:2221091 original size:33 final size:33
Alignment explanation
Indices: 2221054--2221120 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2221044 TTCAACGATT
2221054 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2221087 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2221120 T
1 T
2221121 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2221092 original size:13 final size:13
Alignment explanation
Indices: 2221074--2221098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2221064 CATAAAATGT
2221074 TGTATCGATACAA
1 TGTATCGATACAA
2221087 TGTATCGATACA
1 TGTATCGATACA
2221099 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2221181 original size:13 final size:13
Alignment explanation
Indices: 2221163--2221187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2221153 ATTACTCACA
2221163 TGTATCGATACAT
1 TGTATCGATACAT
2221176 TGTATCGATACA
1 TGTATCGATACA
2221188 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2221238 original size:52 final size:50
Alignment explanation
Indices: 2221176--2221316 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
2221166 ATCGATACAT
*
2221176 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2221228 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
2221280 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATT--ATGTATCGATACATGCAG
2221317 ATAAATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2221324 original size:52 final size:52
Alignment explanation
Indices: 2221196--2221316 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2221186 CACTGATCTT
*
2221196 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2221248 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2221300 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2221317 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2226110 original size:19 final size:20
Alignment explanation
Indices: 2226086--2226125 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2226076 TTTTTTCAAG
2226086 AATACAAAAA-AAAAGAAAA
1 AATACAAAAAGAAAAGAAAA
*
2226105 AATACAAAAAGAAAGGAAAA
1 AATACAAAAAGAAAAGAAAA
2226125 A
1 A
2226126 CCAGCATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (20 bp):
AATACAAAAAGAAAAGAAAA
Found at i:2226939 original size:19 final size:19
Alignment explanation
Indices: 2226912--2226976 Score: 114
Period size: 19 Copynumber: 3.5 Consensus size: 19
2226902 AGAGACAGTA
*
2226912 GAGATAGGAGGGATGATAG
1 GAGAGAGGAGGGATGATAG
2226931 GAGAGAGGAGGGATGATAG
1 GAGAGAGGAGGGATGATAG
2226950 GAGAGAGGAGGGATGATAG
1 GAGAGAGGAGGGATGATAG
2226969 GAG-GAGGA
1 GAGAGAGGA
2226977 AAGAAGAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.11
19 40 0.89
ACGTcount: A:0.37, C:0.00, G:0.52, T:0.11
Consensus pattern (19 bp):
GAGAGAGGAGGGATGATAG
Found at i:2233023 original size:21 final size:20
Alignment explanation
Indices: 2232995--2233039 Score: 81
Period size: 21 Copynumber: 2.2 Consensus size: 20
2232985 AATCCACAAT
2232995 GTGATTGGGAGACAAATTGG
1 GTGATTGGGAGACAAATTGG
2233015 GTGACTTGGGAGACAAATTGG
1 GTGA-TTGGGAGACAAATTGG
2233036 GTGA
1 GTGA
2233040 AACTATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.29, C:0.07, G:0.40, T:0.24
Consensus pattern (20 bp):
GTGATTGGGAGACAAATTGG
Found at i:2233425 original size:94 final size:94
Alignment explanation
Indices: 2233318--2233505 Score: 331
Period size: 94 Copynumber: 2.0 Consensus size: 94
2233308 AACTGAATCA
* *
2233318 TTTCAGGTTTGAGTTAAATTTTTTGTTTGTATCATTTTCAAATTCAAGTTAAAAGTTTAAATTGT
1 TTTCAGGTTTGAGTTAAATTTTTTATTTGTATCATTTTCAAATTCAAGTTAAAAGTTCAAATTGT
*
2233383 TAACTTTTTATGATCAAATTAGATTAAGG
66 TAACTTTTTATGATCAAATTAAATTAAGG
* *
2233412 TTTCAGGTTTGAGTTAAATTTTTTATTTGTATCGTTTTCAAATTCAGGTTAAAAGTTCAAATTGT
1 TTTCAGGTTTGAGTTAAATTTTTTATTTGTATCATTTTCAAATTCAAGTTAAAAGTTCAAATTGT
2233477 TAACTTTTTATGATCAAATTAAATTAAGG
66 TAACTTTTTATGATCAAATTAAATTAAGG
2233506 CGTTGTTTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 89 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (94 bp):
TTTCAGGTTTGAGTTAAATTTTTTATTTGTATCATTTTCAAATTCAAGTTAAAAGTTCAAATTGT
TAACTTTTTATGATCAAATTAAATTAAGG
Found at i:2233556 original size:15 final size:15
Alignment explanation
Indices: 2233524--2233557 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2233514 AATAAATAAA
**
2233524 TAAAAAATTAAGTGC
1 TAAAAAATTAAGCAC
2233539 TAAAAAATTAAGCAC
1 TAAAAAATTAAGCAC
2233554 TAAA
1 TAAA
2233558 TTTATAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (15 bp):
TAAAAAATTAAGCAC
Found at i:2237093 original size:25 final size:25
Alignment explanation
Indices: 2237065--2237115 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2237055 ATATTTCAAA
*
2237065 ATTAGTTTCACCAAAATGAAAATTG
1 ATTAGTTGCACCAAAATGAAAATTG
2237090 ATTAGTTGCACCAAAATGAAAATTG
1 ATTAGTTGCACCAAAATGAAAATTG
2237115 A
1 A
2237116 ATATGGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (25 bp):
ATTAGTTGCACCAAAATGAAAATTG
Found at i:2237570 original size:38 final size:38
Alignment explanation
Indices: 2237528--2237657 Score: 251
Period size: 38 Copynumber: 3.4 Consensus size: 38
2237518 ATACATGCTT
2237528 GAAATGTATCGATACAAACCACCCTGCATTTTGGAAAG
1 GAAATGTATCGATACAAACCACCCTGCATTTTGGAAAG
2237566 GAAATGTATCGATACAAACCACCCTGCATTTTGGAAAG
1 GAAATGTATCGATACAAACCACCCTGCATTTTGGAAAG
*
2237604 GAAATGTATCGATACAAACCACCTTGCATTTTGGAAAG
1 GAAATGTATCGATACAAACCACCCTGCATTTTGGAAAG
2237642 GAAATGTATCGATACA
1 GAAATGTATCGATACA
2237658 TGCTCAACAT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 91 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (38 bp):
GAAATGTATCGATACAAACCACCCTGCATTTTGGAAAG
Found at i:2244559 original size:16 final size:16
Alignment explanation
Indices: 2244540--2244570 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2244530 TAAAATATAA
*
2244540 ATTTAAACTTAAACTC
1 ATTTAAACATAAACTC
2244556 ATTTAAACATAAACT
1 ATTTAAACATAAACT
2244571 AAAATTCCAT
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:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTTAAACATAAACTC
Found at i:2244643 original size:22 final size:22
Alignment explanation
Indices: 2244605--2244664 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2244595 CAACCTAATT
2244605 AAAACCT-AAT-AAAAAATAAC
1 AAAACCTAAATAAAAAAATAAC
2244625 AAAACCTAAATAAAAAAATAAC
1 AAAACCTAAATAAAAAAATAAC
* * *
2244647 AAAGCCCAATTAAAAAAA
1 AAAACCTAAATAAAAAAA
2244665 AGAAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 7 0.20
21 3 0.09
22 25 0.71
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (22 bp):
AAAACCTAAATAAAAAAATAAC
Found at i:2245626 original size:44 final size:44
Alignment explanation
Indices: 2245572--2245669 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
2245562 AAAACTTGTT
* *
2245572 ATTATGGTTTAATTAAGAATTGGGCTTGTTAGCACAATAAGTCC
1 ATTAGGGTTTAATTAAGAATTGGGCTTGTTAGCAAAATAAGTCC
2245616 ATTAGGGTTTAATTAAGAATTGGGCTTGTTAGCAAAATAAGTCC
1 ATTAGGGTTTAATTAAGAATTGGGCTTGTTAGCAAAATAAGTCC
2245660 ATTAGGGTTT
1 ATTAGGGTTT
2245670 GTGTTAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (44 bp):
ATTAGGGTTTAATTAAGAATTGGGCTTGTTAGCAAAATAAGTCC
Found at i:2262808 original size:28 final size:28
Alignment explanation
Indices: 2262737--2263411 Score: 738
Period size: 28 Copynumber: 23.6 Consensus size: 28
2262727 AATGTTCATC
*
2262737 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
* *
2262766 CTTTTCAAAGCCCACAAGTTAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
2262794 CATTTCAAAGCCCACGAGTCGGTGGCAACT
1 CCTTTCAAAGCCCACAAGTCAGTGGC-A-T
* * *
2262824 CTTTTTAAAGCCCACAAGTTAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2262852 CCTTTCAAAGCCCACGAGTCGGTGGCAACT
1 CCTTTCAAAGCCCACAAGTCAGTGGC-A-T
* * *
2262882 CTTTTCAAAGCCCACAAGGCAGTGGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
2262910 CCTTTCAAAGCCCATAAGTCAATGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
2262938 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
* * *
2262967 CTTTTCAAAACCCATAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
2262995 CCTTTAAAAGCCCATAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2263023 CCTTTAAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2263051 CCTTTAAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2263079 CCTTTCAAAGCCCATAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
*
2263108 CTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
2263136 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
2263164 CCTTTAAAAGCCCACAAGTCAATGGAAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
2263192 CCTTTCAAAGCCCACAAGTCAATGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2263220 CCTTTTAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2263248 CCTTTCAAAGCCCACAAGTAAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
*
2263276 CCTTTCAAAGCCTACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
2263304 CCATTCAAAGCGCACAAGTCAGTGGCGCT
1 CCTTTCAAAGCCCACAAGTCAGTGGC-AT
* * * * * *
2263333 CTTTTCAAGGCCCATAAGCCAGTGGTAAC
1 CCTTTCAAAGCCCACAAGTCAGTGG-CAT
*
2263362 CCTTTTCAAAAGCCCACACGAGTCGGTGGCAACT
1 CC-TTTC-AAAGCCCACA--AGTCAGTGGC-A-T
*
2263396 CTTTTCAAAGCCCACA
1 CCTTTCAAAGCCCACA
2263412 CGATTAGTGG
Statistics
Matches: 549, Mismatches: 83, Indels: 25
0.84 0.13 0.04
Matches are distributed among these distances:
28 372 0.68
29 98 0.18
30 48 0.09
31 8 0.01
32 10 0.02
33 12 0.02
34 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:2263070 original size:141 final size:141
Alignment explanation
Indices: 2262736--2263411 Score: 823
Period size: 141 Copynumber: 4.7 Consensus size: 141
2262726 GAATGTTCAT
* * * * * *
2262736 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCATTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCA
* * * *
2262801 AAGCCCACGAGTCGGTGGCAACTCTTTTTAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCA
65 AAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCA
* *
2262866 CGAGTCGGTGGCAA
129 CAAGTCAGTGGC-A
* * * * *
2262880 CTCTTTTCAAAGCCCACAAGGCAGTGGTATCCTTTCAAAGCCCATAAGTCAATGGCACCCTTTCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCA
* * * * *
2262945 AAGCCCACAAGTTAGTGGCACTCTTTTCAAAACCCATAAGTCAGTGGCATCCTTTAAAAGCCCAT
65 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC
2263010 AAGTCAGTGGCA
130 AAGTCAGTGGCA
* * *
2263022 CCCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAA
* *
2263087 AGCCCATAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
66 AGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
2263152 AGTCAGTGGCA
131 AGTCAGTGGCA
* * * * *
2263163 CCCTTTAAAAGCCCACAAGTCAATGGAACCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTTAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAA
* * * *
2263228 AGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTAAGTGGCACCCTTTCAAAGCCTACA
66 AGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
2263292 AGTCAGTGGCA
131 AGTCAGTGGCA
* * * * * * * * * *
2263303 TCCATTCAAAGCGCACAAGTCAGTGGCGCTCTTTTCAAGGCCCATAAGCCAGTGGTAACCCTTTT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAATGG-CACCC-TTT
*
2263368 CAAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACA
63 C-AAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAGCCCACA
2263412 CGATTAGTGG
Statistics
Matches: 459, Mismatches: 64, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
140 73 0.16
141 224 0.49
142 5 0.01
143 52 0.11
144 56 0.12
145 23 0.05
146 9 0.02
147 2 0.00
148 15 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (141 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAA
AGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
AGTCAGTGGCA
Found at i:2264346 original size:20 final size:20
Alignment explanation
Indices: 2264321--2264394 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
2264311 TACCCAGATA
2264321 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * * *
2264341 TATCGATACATGTATGAATT
1 TATCGATACATTTTTCAATG
*
2264361 TATCGATACATTCTTCAATG
1 TATCGATACATTTTTCAATG
2264381 TATCGATACATTTT
1 TATCGATACATTTT
2264395 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:2267796 original size:3 final size:3
Alignment explanation
Indices: 2267735--2267775 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2267725 TTTTTCACCA
*
2267735 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2267776 AGAATACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2267797 original size:21 final size:21
Alignment explanation
Indices: 2267768--2267809 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2267758 GAAAAAGAAG
2267768 AAGAAGAAAGAATACAAAAAA
1 AAGAAGAAAGAATACAAAAAA
*
2267789 AAGAAGAAATAATACAAAAAA
1 AAGAAGAAAGAATACAAAAAA
2267810 TAATACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
AAGAAGAAAGAATACAAAAAA
Found at i:2267812 original size:12 final size:12
Alignment explanation
Indices: 2267795--2267833 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
2267785 AAAAAAGAAG
2267795 AAATAATACAAA
1 AAATAATACAAA
2267807 AAATAATACAAAA
1 AAATAATAC-AAA
2267820 AAATAATA-AAA
1 AAATAATACAAA
2267831 AAA
1 AAA
2267834 AACCCAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.23
12 9 0.35
13 11 0.42
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAATACAAA
Found at i:2267822 original size:13 final size:13
Alignment explanation
Indices: 2267795--2267834 Score: 66
Period size: 12 Copynumber: 3.2 Consensus size: 13
2267785 AAAAAAGAAG
2267795 AAATAATAC-AAA
1 AAATAATACAAAA
2267807 AAATAATACAAAA
1 AAATAATACAAAA
2267820 AAATAATA-AAAA
1 AAATAATACAAAA
2267832 AAA
1 AAA
2267835 ACCCAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAATACAAAA
Found at i:2273177 original size:43 final size:44
Alignment explanation
Indices: 2273099--2273190 Score: 141
Period size: 43 Copynumber: 2.1 Consensus size: 44
2273089 TTATTATTTT
* * *
2273099 GGTTTAATTAAGAATTGGGCTTGTTACCACTATAAGTCCGTTAG
1 GGTTTAATTAAGAATTGGGCTTGTTACCACAATAAGTCCATTAA
*
2273143 GGTTTAATTAAGAATT-GGCTTGTTAGCACAATAAGTCCATTAA
1 GGTTTAATTAAGAATTGGGCTTGTTACCACAATAAGTCCATTAA
2273186 GGTTT
1 GGTTT
2273191 GTGTTAATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 28 0.64
44 16 0.36
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (44 bp):
GGTTTAATTAAGAATTGGGCTTGTTACCACAATAAGTCCATTAA
Found at i:2273875 original size:16 final size:16
Alignment explanation
Indices: 2273842--2273879 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
2273832 GCAAAAGCAT
2273842 AAAAAAAGGCCAAAAAC
1 AAAAAAAGG-CAAAAAC
2273859 AAAAAAAGG-AAACAAC
1 AAAAAAAGGCAAA-AAC
2273875 AAAAA
1 AAAAA
2273880 TTAAAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 8 0.40
17 9 0.45
ACGTcount: A:0.76, C:0.13, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAGGCAAAAAC
Found at i:2274150 original size:14 final size:16
Alignment explanation
Indices: 2274131--2274166 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
2274121 ATCTTGGTAA
2274131 AAAAAACAAA-AA-AG
1 AAAAAACAAAGAAGAG
2274145 AAAAAACAAAGAAGAG
1 AAAAAACAAAGAAGAG
2274161 AAAAAA
1 AAAAAA
2274167 TTCCACCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 2 0.10
16 8 0.40
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAGAAGAG
Found at i:2275131 original size:31 final size:31
Alignment explanation
Indices: 2275063--2275332 Score: 257
Period size: 31 Copynumber: 8.6 Consensus size: 31
2275053 AACCTTCTAA
* **
2275063 AAGTCCACAACT-TAGTGGCATC-TTTCTTCA
1 AAGTCCACAACTCT-GTGGCACCTTTTCTTTT
** **
2275093 AAGTCCACAACTCCATGGCACCTTACCTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTT
* *
2275124 AAGTCCACAACTCCGTGGCACCTTTTTCTTTA
1 AAGTCCACAACTCTGTGGCACC-TTTTCTTTT
*
2275156 AAGTCCAAAACTCTGTGGCACCTTTTTTCTTTT
1 AAGTCCACAACTCTGTGGCACC--TTTTCTTTT
** *
2275189 AAAGTCCACAACTCCATGGCACCTTTTTCTTTG
1 -AAGTCCACAACTCTGTGGCACC-TTTTCTTTT
* *
2275222 AAGTCCAAAACTCTGTGGCA-CTTTTTTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTT
*
2275252 AAAGTCCACGACTCTGTGGCACC----CTTTT
1 -AAGTCCACAACTCTGTGGCACCTTTTCTTTT
*
2275280 AAGTCCACAACTCTGTGGCACTTTTTTTCTTTT
1 AAGTCCACAACTCTGTGGCAC--CTTTTCTTTT
2275313 AAGTCCACAACTCTGTGGCA
1 AAGTCCACAACTCTGTGGCA
2275333 TCTGTGCCAC
Statistics
Matches: 199, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
27 20 0.10
28 4 0.02
30 25 0.13
31 44 0.22
32 44 0.22
33 43 0.22
34 19 0.10
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (31 bp):
AAGTCCACAACTCTGTGGCACCTTTTCTTTT
Found at i:2275216 original size:66 final size:64
Alignment explanation
Indices: 2275063--2275332 Score: 281
Period size: 63 Copynumber: 4.3 Consensus size: 64
2275053 AACCTTCTAA
** * * * ** **
2275063 AAGTCCACAACTTAGTGGCA--TCTTTCTTCAAAGTCCACAACTCCATGGCACC-TTACCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTAAAGTCCAAAACTCTGTGGCACCTTTTTCTTTT
2275124 AAGTCCACAACTCCGTGGCACCTTTTTCTTTAAAGTCCAAAACTCTGTGGCACCTTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTAAAGTCCAAAACTCTGTGGCACC-TTTTTCTTTT
* *
2275189 AAAGTCCACAACTCCATGGCACCTTTTTCTTTGAAGTCCAAAACTCTGTGGCA-CTTTTT-TTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTAAAGTCCAAAACTCTGTGGCACCTTTTTCTTTT
* * * * *
2275252 AAAGTCCACGACTCTGTGGCACC-----CTTTTAAGTCCACAACTCTGTGGCACTTTTTTTCTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTAAAGTCCAAAACTCTGTGGCAC-CTTTTTCTTT
2275312 T
64 T
*
2275313 AAGTCCACAACTCTGTGGCA
1 AAGTCCACAACTCCGTGGCA
2275333 TCTGTGCCAC
Statistics
Matches: 183, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
58 23 0.13
60 24 0.13
61 22 0.12
63 51 0.28
64 5 0.03
65 8 0.04
66 50 0.27
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (64 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTAAAGTCCAAAACTCTGTGGCACCTTTTTCTTTT
Found at i:2275246 original size:97 final size:92
Alignment explanation
Indices: 2275092--2275577 Score: 305
Period size: 97 Copynumber: 5.1 Consensus size: 92
2275082 ATCTTTCTTC
** *
2275092 AAAGTCCACAACTCCATGGCACC-TTACCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTA
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTA
2275156 AAGTCCAAAACTCTGTGGCACCTTTTTTCTTTT
66 AAGTCCAAAACTCTGTGGCACC------CTTTT
* * *
2275189 AAAGTCCACAACTCCATGGCACCTTTTTCTTTGAAGTCCAAAACTCTGTGGCA-CTTTTTTTTTA
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTA
**
2275253 AAGTCCACGACTCTGTGGCACCCTTTT
66 AAGTCCAAAACTCTGTGGCACCCTTTT
** * * ***
2275280 -AAGTCCACAACTCTGTGGCACTTTTTTTCTTTTAAGTCCACAACTCTGTGGCATCTGTGCCACC
1 AAAGTCCACAACTCCATGGCAC-CTTTTTCTTTTAAGTCCACAACTCTGTGGCACCT-T---TTT
* *
2275344 CTTTCAAAGTCCACAACTCTGTGGCATCTGTGCCACCCTTTC
61 CTTT-AAAGTCCAAAACTC--T-G----TG-G-CACCCTTTT
* * * * *
2275386 AAAGTCCACAACTCCGTGGCACC-----CTTCTAAGTCTACAACTCCGTGGCACCCTTCTTCTTT
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTTAAGTCCACAACTCTGTGGCA-CCTTTTTC-TT
* * * * *
2275446 TTAAGTCTATAACTC--CGGTACCCTTTT
64 TAAAGTCCAAAACTCTGTGGCACCCTTTT
* * * * *
2275473 -AAGTCCATAACTGCATGGCA-CATTTTCTTTTCAAGTTCACAACTCCGTGGCACCTTTTTCCTT
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTT-AAGTCCACAACTCTGTGGCACCTTTTT-CTT
* * *
2275536 TTAAGTCCACACAAGTC-GCTGGCAACCCTTCT
64 TAAAGTCCA-A-AACTCTG-TGGC-ACCCTTTT
2275568 AAAGTCCACA
1 AAAGTCCACA
2275578 CAAGTTAGTG
Statistics
Matches: 308, Mismatches: 48, Indels: 67
0.73 0.11 0.16
Matches are distributed among these distances:
85 1 0.00
86 17 0.06
87 7 0.02
88 1 0.00
89 1 0.00
90 39 0.13
91 52 0.17
92 6 0.02
93 1 0.00
94 2 0.01
95 7 0.02
96 11 0.04
97 66 0.21
98 36 0.12
99 4 0.01
100 1 0.00
101 23 0.07
102 2 0.01
104 2 0.01
105 1 0.00
106 8 0.03
107 20 0.06
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (92 bp):
AAAGTCCACAACTCCATGGCACCTTTTTCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTA
AAGTCCAAAACTCTGTGGCACCCTTTT
Found at i:2275326 original size:33 final size:32
Alignment explanation
Indices: 2275063--2275332 Score: 254
Period size: 32 Copynumber: 8.6 Consensus size: 32
2275053 AACCTTCTAA
* **
2275063 AAGTCCACAACT-TAGTGGCA--TCTTTCTTCA
1 AAGTCCACAACTCT-GTGGCACTTTTTTCTTTT
** * **
2275093 AAGTCCACAACTCCATGGCAC-CTTACCTTTT
1 AAGTCCACAACTCTGTGGCACTTTTTTCTTTT
* * *
2275124 AAGTCCACAACTCCGTGGCACCTTTTTCTTTA
1 AAGTCCACAACTCTGTGGCACTTTTTTCTTTT
*
2275156 AAGTCCAAAACTCTGTGGCACCTTTTTTCTTTT
1 AAGTCCACAACTCTGTGGCA-CTTTTTTCTTTT
** * *
2275189 AAAGTCCACAACTCCATGGCACCTTTTTCTTTG
1 -AAGTCCACAACTCTGTGGCACTTTTTTCTTTT
* *
2275222 AAGTCCAAAACTCTGTGGCACTTTTTT-TTTA
1 AAGTCCACAACTCTGTGGCACTTTTTTCTTTT
* *
2275253 AAGTCCACGACTCTGTGGCAC-----CCTTTT
1 AAGTCCACAACTCTGTGGCACTTTTTTCTTTT
2275280 AAGTCCACAACTCTGTGGCACTTTTTTTCTTTT
1 AAGTCCACAACTCTGTGGCAC-TTTTTTCTTTT
2275313 AAGTCCACAACTCTGTGGCA
1 AAGTCCACAACTCTGTGGCA
2275333 TCTGTGCCAC
Statistics
Matches: 195, Mismatches: 33, Indels: 21
0.78 0.13 0.08
Matches are distributed among these distances:
27 23 0.12
30 17 0.09
31 46 0.24
32 47 0.24
33 45 0.23
34 17 0.09
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (32 bp):
AAGTCCACAACTCTGTGGCACTTTTTTCTTTT
Found at i:2275363 original size:37 final size:37
Alignment explanation
Indices: 2275313--2275406 Score: 179
Period size: 37 Copynumber: 2.5 Consensus size: 37
2275303 TTTTTCTTTT
2275313 AAGTCCACAACTCTGTGGCATCTGTGCCACCCTTTCA
1 AAGTCCACAACTCTGTGGCATCTGTGCCACCCTTTCA
2275350 AAGTCCACAACTCTGTGGCATCTGTGCCACCCTTTCA
1 AAGTCCACAACTCTGTGGCATCTGTGCCACCCTTTCA
*
2275387 AAGTCCACAACTCCGTGGCA
1 AAGTCCACAACTCTGTGGCA
2275407 CCCTTCTAAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.24
Consensus pattern (37 bp):
AAGTCCACAACTCTGTGGCATCTGTGCCACCCTTTCA
Found at i:2275423 original size:27 final size:27
Alignment explanation
Indices: 2275377--2275440 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
2275367 GCATCTGTGC
*
2275377 CACCCTTTCAAAGTCCACAACTCCGTGG
1 CACCC-TTCTAAGTCCACAACTCCGTGG
*
2275405 CACCCTTCTAAGTCTACAACTCCGTGG
1 CACCCTTCTAAGTCCACAACTCCGTGG
2275432 CACCCTTCT
1 CACCCTTCT
2275441 TCTTTTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.22, C:0.41, G:0.12, T:0.25
Consensus pattern (27 bp):
CACCCTTCTAAGTCCACAACTCCGTGG
Found at i:2275632 original size:66 final size:64
Alignment explanation
Indices: 2275542--2275697 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 64
2275532 CCTTTTAAGT
* * *
2275542 CCACACAAGTCGCTGGCAA--CCCTTCTAAAG-TCCACACAAGTTAGTGGCAACCCCTTTCGAAA
1 CCACACAAGTCG-TGGCAATCCCCTTCTAAAGCT-CACACAAGTCAGTGGC-ACCCCCTTCAAAA
2275604 GC
63 GC
* *
2275606 CCACACAAGTCAGTGGCAATCCCCTTCAAAAGCTCACACAAGTCGGTGGCACCCCCTTCAAAAGC
1 CCACACAAGTC-GTGGCAATCCCCTTCTAAAGCTCACACAAGTCAGTGGCACCCCCTTCAAAAGC
*
2275671 CCACACAAGTCGGTGGC-ATCTCCTTCT
1 CCACACAAGTC-GTGGCAATCCCCTTCT
2275698 TAGCCTAATG
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
64 25 0.31
65 30 0.38
66 24 0.30
67 1 0.01
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (64 bp):
CCACACAAGTCGTGGCAATCCCCTTCTAAAGCTCACACAAGTCAGTGGCACCCCCTTCAAAAGC
Found at i:2275696 original size:32 final size:32
Alignment explanation
Indices: 2275542--2275688 Score: 188
Period size: 33 Copynumber: 4.6 Consensus size: 32
2275532 CCTTTTAAGT
* * *
2275542 CCACACAAGTCGCTGGCAA-CCCTTCTAAAGT
1 CCACACAAGTCGGTGGCAACCCCTTCAAAAGC
** *
2275573 CCACACAAGTTAGTGGCAACCCCTTTCGAAAGC
1 CCACACAAGTCGGTGGCAACCCC-TTCAAAAGC
*
2275606 CCACACAAGTCAGTGGCAATCCCCTTCAAAAGC
1 CCACACAAGTCGGTGGCAA-CCCCTTCAAAAGC
* *
2275639 TCACACAAGTCGGTGGCACCCCCTTCAAAAGC
1 CCACACAAGTCGGTGGCAACCCCTTCAAAAGC
2275671 CCACACAAGTCGGTGGCA
1 CCACACAAGTCGGTGGCA
2275689 TCTCCTTCTT
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
31 16 0.16
32 33 0.32
33 49 0.48
34 4 0.04
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.16
Consensus pattern (32 bp):
CCACACAAGTCGGTGGCAACCCCTTCAAAAGC
Found at i:2275826 original size:52 final size:52
Alignment explanation
Indices: 2275750--2276274 Score: 260
Period size: 52 Copynumber: 9.9 Consensus size: 52
2275740 TCAAACCATC
* * *
2275750 TCTTTC-TAAGTCCAATTTCACTGGCCTTGAATCAACACATTGGCACCTTTT
1 TCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
* * * *
2275801 TCTTTCTTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG
1 TCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
* * * *
2275853 TC-ATCTTAAAGTCCGATATCACTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TCTTTCTT-AAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
* ** * * *
2275905 TCATTCCCAAG-CCTAATGTCACTGGCCTTGAATCAGCACATTGGCATACGTATA
1 TCTTTCTTAAGTCC-AATATCACTGGCCTTGAATCAGCACATTGGC--ACCTTTA
* * * *
2275959 TCATTT-TTAAGCCCAATATCGCTGGCGTTGAATCAGCATATTGGCA--TTCT-
1 TC-TTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTT-TA
* * * * * *
2276009 TCTCATCTTCAAGTCTAATGTCGCTGGCCATGAATCAACACATTGGCACTCTTCTCA
1 TCT-TTCTT-AAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCAC-CTT-T-A
* * ** * * **** *
2276066 CCCTTCTCATCTCTAAGTCCAACATTGCTGGCCTTGATTCAGCATATCAATACCTTTT
1 ----TCT-TTCT-TAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
* *** * ** * *
2276124 TCTCTC-TAAGTTTGACATCTTTGGCCTTGAATCAGCACATAGGCACCTTTG
1 TCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
* * * * * * * *
2276175 TCACTT-TTAAGCCCAATGTTATTGGCCTTGAATCAGCATATTGGCACCCTTG
1 TC-TTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
* * ** * *
2276227 TCATTT-TTAAGTCTAATGTCGTTGGCCTTAAATCAACACATTGGCACC
1 TC-TTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACC
2276275 CTTCTCATCT
Statistics
Matches: 365, Mismatches: 85, Indels: 47
0.73 0.17 0.09
Matches are distributed among these distances:
49 1 0.00
50 4 0.01
51 49 0.13
52 220 0.60
53 4 0.01
54 39 0.11
55 8 0.02
59 1 0.00
60 3 0.01
61 35 0.10
62 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.34
Consensus pattern (52 bp):
TCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTTTA
Found at i:2276005 original size:106 final size:105
Alignment explanation
Indices: 2275761--2276056 Score: 282
Period size: 106 Copynumber: 2.8 Consensus size: 105
2275751 CTTTCTAAGT
* * * * * * * *
2275761 CCAATTTCACTGGCCTTGAATCAACACATTGGCACCTTTTTCT-TTCTT-AAGTCC-AGTATCGC
1 CCAATATCACTGGCCTTGAATCAGCATATTGGCA--TTCTTCTCATCTTCAAG-CCTAATGTCAC
* * * *
2275823 TGGCCTTGAATCAGCATATTGGC-ACCTTTGTCATCTTAAAGT
63 TGGCCTTGAATCAGCACATTGGCAACCTATATCATCTTAAAGC
*
2275865 CCGATATCACTGGCCTTGAATCAGCATATTGGCA-TCTT-T-ATCATTCCCAAGCCTAATGTCAC
1 CCAATATCACTGGCCTTGAATCAGCATATTGGCATTCTTCTCATC-TT--CAAGCCTAATGTCAC
* * *
2275927 TGGCCTTGAATCAGCACATTGGCATACGTATATCATTTTTAAGC
63 TGGCCTTGAATCAGCACATTGGCA-ACCTATATCATCTTAAAGC
* * * *
2275971 CCAATATCGCTGGCGTTGAATCAGCATATTGGCATTCTTCTCATCTTCAAGTCTAATGTCGCTGG
1 CCAATATCACTGGCCTTGAATCAGCATATTGGCATTCTTCTCATCTTCAAGCCTAATGTCACTGG
* *
2276036 CCATGAATCAACACATTGGCA
66 CCTTGAATCAGCACATTGGCA
2276057 CTCTTCTCAC
Statistics
Matches: 159, Mismatches: 23, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
100 3 0.02
101 5 0.03
103 2 0.01
104 60 0.38
106 79 0.50
107 4 0.03
108 3 0.02
109 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (105 bp):
CCAATATCACTGGCCTTGAATCAGCATATTGGCATTCTTCTCATCTTCAAGCCTAATGTCACTGG
CCTTGAATCAGCACATTGGCAACCTATATCATCTTAAAGC
Found at i:2276015 original size:158 final size:157
Alignment explanation
Indices: 2275767--2276061 Score: 380
Period size: 158 Copynumber: 1.9 Consensus size: 157
2275757 AAGTCCAATT
* * * *
2275767 TCACTGGCCTTGAATCAACACATTGGCACCTTTTTCTTTCTTAAGTCCAGTATCGCTGGCCTTGA
1 TCACTGGCCTTGAATCAACACATTGGCACCTATATCTTTCTTAAGCCCAATATCGCTGGCCTTGA
* * * * *
2275832 ATCAGCATATTGGCACCTTTGTCATCTTAAAGTCCGATATCACTGGCCTTGAATCAGCATATTGG
66 ATCAGCATATTGGCACCTTTCTCATCTTAAAGTCCAATATCACTGGCCATGAATCAACACATTGG
2275897 CA-TCTTTATCATTCCCAAGCCTAATG
131 CACTCTTTATCATTCCCAAGCCTAATG
* * *
2275923 TCACTGGCCTTGAATCAGCACATTGGCATACGTATATCATTT-TTAAGCCCAATATCGCTGGCGT
1 TCACTGGCCTTGAATCAACACATTGGC--ACCTATATC-TTTCTTAAGCCCAATATCGCTGGCCT
* * * * *
2275987 TGAATCAGCATATTGGCA-TTCTTCTCATCTTCAAGTCTAATGTCGCTGGCCATGAATCAACACA
63 TGAATCAGCATATTGGCACCT-TTCTCATCTTAAAGTCCAATATCACTGGCCATGAATCAACACA
2276051 TTGGCACTCTT
127 TTGGCACTCTT
2276062 CTCACCCTTC
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
156 26 0.22
157 1 0.01
158 83 0.71
159 7 0.06
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (157 bp):
TCACTGGCCTTGAATCAACACATTGGCACCTATATCTTTCTTAAGCCCAATATCGCTGGCCTTGA
ATCAGCATATTGGCACCTTTCTCATCTTAAAGTCCAATATCACTGGCCATGAATCAACACATTGG
CACTCTTTATCATTCCCAAGCCTAATG
Found at i:2277102 original size:22 final size:20
Alignment explanation
Indices: 2277051--2277126 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
2277041 GAAAAAGAAA
* * *
2277051 TGTATCGATACATAAGTAAA
1 TGTATCGATACATTATTAAT
*
2277071 TGTATTGATACATGCTCA-TAAT
1 TGTATCGATACAT--T-ATTAAT
*
2277093 TGTATCGATACATTATTCAT
1 TGTATCGATACATTATTAAT
2277113 TGTATCGATACATT
1 TGTATCGATACATT
2277127 TTGGATTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 30 0.64
22 15 0.32
23 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTATTAAT
Found at i:2279018 original size:23 final size:22
Alignment explanation
Indices: 2278975--2279018 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2278965 CCACTAGCTA
**
2278975 ATTTTTTCCAAATTTTCTGAAC
1 ATTTTTTCCAAAAGTTCTGAAC
*
2278997 ATTTTTTCTAAAAGTTCATGAA
1 ATTTTTTCCAAAAGTTC-TGAA
2279019 GTTCCTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTTTTTCCAAAAGTTCTGAAC
Found at i:2284527 original size:7 final size:7
Alignment explanation
Indices: 2284515--2284548 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2284505 AGATTGAGAT
2284515 AAAAATA
1 AAAAATA
2284522 AAAAATA
1 AAAAATA
2284529 AAAAAT-
1 AAAAATA
*
2284535 AAAATTA
1 AAAAATA
2284542 AAAAATA
1 AAAAATA
2284549 GTTTTAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:2284531 original size:13 final size:13
Alignment explanation
Indices: 2284515--2284548 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2284505 AGATTGAGAT
2284515 AAAAATAAAAAATA
1 AAAAAT-AAAAATA
*
2284529 AAAAATAAAATTA
1 AAAAATAAAAATA
2284542 AAAAATA
1 AAAAATA
2284549 GTTTTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAATAAAAATA
Done.