Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 16 of 39
Found at i:2328939 original size:38 final size:38
Alignment explanation
Indices: 2328897--2328985 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
2328887 CAATGGCACA
* *
2328897 ATTCGAAACAAAAA-TCATTATTTTTAACAAGTAACACG
1 ATTCGAAACAAAAACT-ACTATTCTTAACAAGTAACACG
* ** *
2328935 ATTCGAAATAAAAACTACTATTCTTAATTAGTGACACG
1 ATTCGAAACAAAAACTACTATTCTTAACAAGTAACACG
2328973 ATTCGAAATCAAA
1 ATTCGAAA-CAAA
2328986 TTTTAATTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
38 38 0.90
39 4 0.10
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (38 bp):
ATTCGAAACAAAAACTACTATTCTTAACAAGTAACACG
Found at i:2333318 original size:51 final size:50
Alignment explanation
Indices: 2333162--2333669 Score: 157
Period size: 50 Copynumber: 10.1 Consensus size: 50
2333152 GAGCCGGCAT
* * * * *
2333162 CTAATAGAAGAGTAAAATCTTGTAGAGTCTAAAGTCCACACATGCTAGCAC
1 CTAATAGAAG-GTAAAGTCTTATAGAGTCCAAAGTCCACTCAAGCTAGCAC
* * * * * *
2333213 TTAATAAGAAGGTAAAGTCCTATAGAAT-CAAAGTTCACATGAA-TTAGCAC
1 CTAAT-AGAAGGTAAAGTCTTATAGAGTCCAAAGTCCAC-TCAAGCTAGCAC
* *
2333263 CTAATAGGAGGCTAAAGTCTTATAGAGTCCAAAGTCCACTCAAGCTGGCAC
1 CTAATAGAAGG-TAAAGTCTTATAGAGTCCAAAGTCCACTCAAGCTAGCAC
* * * * * * * *
2333314 CTAATAAAAGAGT-ATGATCTTATAAAGTCCAAAGTTCA-TAAAAACTGGCAT
1 CTAATAGAAG-GTAAAG-TCTTATAGAGTCCAAAGTCCACT-CAAGCTAGCAC
* * * * * * * *
2333365 TTAATATATGGGTAAAGTCTTATAGAGT-CAAAATCCACAT-GAGTTGGAAC
1 CTAATAGA-AGGTAAAGTCTTATAGAGTCCAAAGTCCAC-TCAAGCTAGCAC
* * * * * *
2333415 CTAATCA-AAGGGTAAAATCGTATCGAGT-CAAAATCCA-TACAAACTGGCAC
1 CTAAT-AGAA-GGTAAAGTCTTATAGAGTCCAAAGTCCACT-CAAGCTAGCAC
* * * * * ** * * *
2333465 TTAATAGAAAAGTAAAGTCCTATAGAGTCTAAGGTATAAAT-AAGTTGGCAC
1 CTAATAG-AAGGTAAAGTCTTATAGAGTCCAAAGT-CCACTCAAGCTAGCAC
* * * * ** *
2333516 TTAATAAAAGGGTAAAGT-TCTATAAAGT-CAAAGTCCA-TAAAAATTGGCAC
1 CTAATAGAA-GGTAAAGTCT-TATAGAGTCCAAAGTCCACT-CAAGCTAGCAC
* * * * * * *
2333566 AC-AATAGGAAAGTAAAGTCTTGT-GAAGTCCAAAGTTCACCCAATCTAACAT
1 -CTAATA-GAAGGTAAAGTCTTATAG-AGTCCAAAGTCCACTCAAGCTAGCAC
* * *
2333617 CTAATAGTAGGGTAAAGTCCTATAGAGT-CAAAGTCCACACAAGCTAGCAC
1 CTAATAG-AAGGTAAAGTCTTATAGAGTCCAAAGTCCACTCAAGCTAGCAC
2333667 CTA
1 CTA
2333670 GTAAAGAGGT
Statistics
Matches: 332, Mismatches: 91, Indels: 69
0.67 0.18 0.14
Matches are distributed among these distances:
48 2 0.01
49 7 0.02
50 156 0.47
51 154 0.46
52 12 0.04
53 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.25
Consensus pattern (50 bp):
CTAATAGAAGGTAAAGTCTTATAGAGTCCAAAGTCCACTCAAGCTAGCAC
Found at i:2333564 original size:101 final size:101
Alignment explanation
Indices: 2333308--2333584 Score: 263
Period size: 101 Copynumber: 2.8 Consensus size: 101
2333298 CCACTCAAGC
* * * * * *
2333308 TGGCACCTAATAAAAGAGT-ATGATCTTATAAAGTCCAAAGTTCATAAAAACTGGCATTTAATAT
1 TGGCACCTAATAAAAGGGTAAAGATCGTATAAAGT-CAAAGTCCATAAAAACTGGCACTTAATAG
*** * * * *
2333372 ATGGGTAAAGTCTTATAGAGTCAAAATCCACATGAGT
65 AAAAGTAAAGTCCTATAGAGTCAAAATACAAATAAGT
* * ** * *
2333409 TGGAACCTAATCAAAGGGTAAA-ATCGTATCGAGTCAAAATCCATACAAACTGGCACTTAATAGA
1 TGGCACCTAATAAAAGGGTAAAGATCGTATAAAGTCAAAGTCCATAAAAACTGGCACTTAATAGA
** *
2333473 AAAGTAAAGTCCTATAGAGTCTAAGGTATAAATAAGT
66 AAAGTAAAGTCCTATAGAGTC-AAAATACAAATAAGT
* * * ** *
2333510 TGGCACTTAATAAAAGGGTAAAGTTC-TATAAAGTCAAAGTCCATAAAAATTGGCACACAATAGG
1 TGGCACCTAATAAAAGGGTAAAGATCGTATAAAGTCAAAGTCCATAAAAACTGGCACTTAATAGA
2333574 AAAGTAAAGTC
66 AAAGTAAAGTC
2333585 TTGTGAAGTC
Statistics
Matches: 139, Mismatches: 34, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
100 42 0.30
101 94 0.68
102 3 0.02
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (101 bp):
TGGCACCTAATAAAAGGGTAAAGATCGTATAAAGTCAAAGTCCATAAAAACTGGCACTTAATAGA
AAAGTAAAGTCCTATAGAGTCAAAATACAAATAAGT
Found at i:2338199 original size:17 final size:18
Alignment explanation
Indices: 2338164--2338201 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2338154 GTGTGTGCAA
*
2338164 AAAAAAAAGTTAGAGAGT
1 AAAAAAAAGTGAGAGAGT
*
2338182 AAAAGAAAGTGAGA-AGT
1 AAAAAAAAGTGAGAGAGT
2338199 AAA
1 AAA
2338202 GGATTTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (18 bp):
AAAAAAAAGTGAGAGAGT
Found at i:2341127 original size:2 final size:2
Alignment explanation
Indices: 2341120--2341150 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2341110 AGTGGCAATT
2341120 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2341151 TTGTATGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2343503 original size:2 final size:2
Alignment explanation
Indices: 2343496--2343523 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2343486 TAGCATATTG
2343496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2343524 TGCTTCCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2343817 original size:19 final size:22
Alignment explanation
Indices: 2343779--2343820 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
2343769 ATTATAAATT
2343779 AAATAATATTAATTTAATTAAA
1 AAATAATATTAATTTAATTAAA
2343801 AAATAAT-TTAA-TT-ATTAAA
1 AAATAATATTAATTTAATTAAA
2343820 A
1 A
2343821 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 4 0.20
22 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAATATTAATTTAATTAAA
Found at i:2343990 original size:15 final size:15
Alignment explanation
Indices: 2343972--2344026 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
2343962 ACACTCATAA
2343972 AATTTTAATATATAT
1 AATTTTAATATATAT
*
2343987 AATTTTGATATATAAT
1 AATTTTAATATAT-AT
2344003 AA-TTT-ATATTATAT
1 AATTTTAATA-TATAT
*
2344017 AAATTTAATA
1 AATTTTAATA
2344027 ATTTAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 7 0.20
15 21 0.60
16 7 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTTTAATATATAT
Found at i:2343999 original size:17 final size:15
Alignment explanation
Indices: 2343975--2344044 Score: 51
Period size: 15 Copynumber: 4.8 Consensus size: 15
2343965 CTCATAAAAT
2343975 TTTA-ATATATATAA
1 TTTATATATATATAA
2343989 TTT-TGATATATAATAA
1 TTTAT-ATATAT-ATAA
2344005 TTTATAT-TATATAAA
1 TTTATATATATAT-AA
*
2344020 TTTA-ATA-ATTTAA
1 TTTATATATATATAA
* *
2344033 TATATTTATATA
1 TTTATATATATA
2344045 ATATTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
13 5 0.11
14 12 0.27
15 17 0.39
16 9 0.20
17 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
TTTATATATATATAA
Found at i:2348877 original size:38 final size:38
Alignment explanation
Indices: 2348835--2348911 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2348825 TCAGGATAAC
2348835 ATTAGATTATAGGTGAAGATAACATAGAACCTTAAAAA
1 ATTAGATTATAGGTGAAGATAACATAGAACCTTAAAAA
2348873 ATTAGATTATAGGTGAAGATAACATAGAACCTTAAAAA
1 ATTAGATTATAGGTGAAGATAACATAGAACCTTAAAAA
2348911 A
1 A
2348912 AATATTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (38 bp):
ATTAGATTATAGGTGAAGATAACATAGAACCTTAAAAA
Found at i:2350492 original size:10 final size:10
Alignment explanation
Indices: 2350474--2350507 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
2350464 TTATGATCAA
2350474 TTATAAATTAT
1 TTAT-AATTAT
2350485 TTATAATTAT
1 TTATAATTAT
2350495 TTAATAATTAT
1 TT-ATAATTAT
2350506 TT
1 TT
2350508 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATAATTAT
Found at i:2350574 original size:21 final size:21
Alignment explanation
Indices: 2350550--2350609 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
2350540 TGAAAAATAA
2350550 ATATA-AT-TTAAATAAAATG
1 ATATATATGTTAAATAAAATG
*
2350569 ATATATATGTTAGATAAAATG
1 ATATATATGTTAAATAAAATG
* *
2350590 ATGTA-ATAGTTAGATAAAAT
1 ATATATAT-GTTAAATAAAAT
2350610 TTTATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 27 0.75
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATATATGTTAAATAAAATG
Found at i:2352559 original size:51 final size:52
Alignment explanation
Indices: 2352502--2352615 Score: 142
Period size: 51 Copynumber: 2.2 Consensus size: 52
2352492 AAATAACGGA
* * * *
2352502 GTTGGAGTATCCT-TGATTGTGAAAATTTGATGTTCTGAAAATAAAATCAAG
1 GTTGGAGTATCCTCCGATGGTGAAAAATTGATGTTCTGAAAATAAAACCAAG
* * **
2352553 GTTGGAGTAT-CTCCGATGGTGAAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCTCCGATGGTGAAAAATTGATGTTCTGAAAATAAAACCAAG
2352604 GTTGGAGTATCC
1 GTTGGAGTATCC
2352616 CTTCAAAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 2 0.04
51 50 0.94
52 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCTCCGATGGTGAAAAATTGATGTTCTGAAAATAAAACCAAG
Found at i:2352640 original size:79 final size:78
Alignment explanation
Indices: 2352552--2353088 Score: 598
Period size: 79 Copynumber: 6.8 Consensus size: 78
2352542 ATAAAATCAA
* * *
2352552 GGTTGGAGTATCTCCGATGGTGAAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
*
2352617 TTCAAAAATAATGG
66 -TCAAAAATAACGG
* ** * *
2352631 GGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTTGAAAATAAAACTGGGGTTGGAGTATCTC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTATC-C
*
2352696 CTCAGAAATAACGG
65 CTCAAAAATAACGG
* * * * * * *
2352710 GGTTAGAGTATCCCTGATTGTGAAAAATCGGTATTTTGAAAATAAAACTGGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTAT-CC
***
2352775 CTCAAAAATAGTAG
65 CTCAAAAATAACGG
* * * ** *
2352789 GGTTGGAGTATCCCCGATTATAAAAAATT-AGTGTTTTG-AAATAAAATCGGAATTGGAATATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGA-TGTTTTGAAAATAAAACCGGGGTTGGAGTATCC
**
2352852 CTTTGAAAATAACGG
65 C-TCAAAAATAACGG
* * *
2352867 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAATCGGGGTTGGAGTATCTC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTATC-C
**
2352932 CTCCGAAATAACGG
65 CTCAAAAATAACGG
* * * *
2352946 GGTTGGAATATCCCTGATTATGAAAAATTGATGTTTT-AAAATAAAACTGGGGTTGGAG-ATCTC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTATC-C
*
2353009 CTCAGAAATAACGG
65 CTCAAAAATAACGG
* * *
2353023 GGTTGGAGTATCCCCGATTATGGAAAATCT-ATGTTTTGAAAATAAAACCGGGATTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAAT-TGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCC
2353087 CT
65 CT
2353089 TCGGAAGTAA
Statistics
Matches: 388, Mismatches: 60, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
77 53 0.14
78 99 0.26
79 231 0.60
80 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
TCAAAAATAACGG
Found at i:2352920 original size:157 final size:157
Alignment explanation
Indices: 2352552--2353087 Score: 666
Period size: 157 Copynumber: 3.4 Consensus size: 157
2352542 ATAAAATCAA
* * * *
2352552 GGTTGGAGTATCTCCGATGGTGAAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
* * * * * *
2352617 TTCAAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTTGAAAATAAAACTGG
66 CTCAAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTG-AAATAAAACTGG
*
2352682 GGTTGGAGTATCTCCTCAGAAATAACGG
130 GGTTGGAATATCTCCTCAGAAATAACGG
* * * * * *
2352710 GGTTAGAGTATCCCTGATTGTGAAAAATCGGTATTTTGAAAATAAAACTGGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
* * *
2352775 CTCAAAAATAGTAGGGTTGGAGTATCCCCGATTATAAAAAATTAGTGTTTTGAAATAAAA-TCGG
66 CTCAAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAATAAAACT-GG
** **
2352839 AATTGGAATATC-CCTTTGAAAATAACGG
130 GGTTGGAATATCTCCTCAG-AAATAACGG
* * *
2352867 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAATCGGGGTTGGAGTATCTC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
** * * * *
2352932 CTCCGAAATAACGGGGTTGGAATATCCCTGATTATGAAAAATT-GATGTTTTAAAATAAAACTGG
66 CTCAAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAG-TGTTTTGAAATAAAACTGG
*
2352996 GGTTGG-AGATCTCCTCAGAAATAACGG
130 GGTTGGAATATCTCCTCAGAAATAACGG
* * * *
2353023 GGTTGGAGTATCCCCGATTATGGAAAATCTATGTTTTGAAAATAAAACCGGGATTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
2353088 TTCGGAAGTA
Statistics
Matches: 321, Mismatches: 52, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
156 77 0.24
157 143 0.45
158 101 0.31
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (157 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
CTCAAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAATAAAACTGGG
GTTGGAATATCTCCTCAGAAATAACGG
Found at i:2352972 original size:236 final size:235
Alignment explanation
Indices: 2352552--2353090 Score: 751
Period size: 236 Copynumber: 2.3 Consensus size: 235
2352542 ATAAAATCAA
* ** * *
2352552 GGTTGGAGTATCTCCGATGGTGAAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGGATTGGAGTATCCC
* * *
2352617 TTCAAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTTGAAAATAAAACTGG
66 TTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAAAAATAAAACTGG
* * *
2352682 GGTTGGAGTATCTCCTCAGAAATAACGGGGTTAGAGTATCCCTGATTGTGAAAAATCGGTATTTT
131 GGTTGGAGTATCTCCTCAGAAATAACGGGGTTAGAATATCCCTGATTATGAAAAATCGATATTTT
**
2352747 GAAAATAAAACTGGGGTTAGAGTATCCCCTCAAAAATAGTAG
196 -AAAATAAAACTGGGGTTAGAG-ATCCCCTCAAAAATAACAG
* * * *
2352789 GGTTGGAGTATCCCCGATTATAAAAAATTAGTGTTTTG-AAATAAAATCGGAATTGGAATATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGGATTGGAGTATCCC
** * *
2352853 TTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAA-TCG
66 TTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAAAAATAAAACT-G
* * * *
2352917 GGGTTGGAGTATCTCCTCCGAAATAACGGGGTTGGAATATCCCTGATTATGAAAAATTGATGTTT
130 GGGTTGGAGTATCTCCTCAGAAATAACGGGGTTAGAATATCCCTGATTATGAAAAATCGATATTT
* * * *
2352982 TAAAATAAAACTGGGGTTGGAGATCTCCTCAGAAATAACGG
195 TAAAATAAAACTGGGGTTAGAGATCCCCTCAAAAATAACAG
*
2353023 GGTTGGAGTATCCCCGATTATGGAAAATCTA-TGTTTTGAAAATAAAACCGGGATTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAAT-TAGTGTTTTGAAAATAAAACCGGGATTGGAGTATCC
2353087 CTTC
65 CTTC
2353091 GGAAGTAAAA
Statistics
Matches: 264, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
234 47 0.18
235 48 0.18
236 136 0.52
237 33 0.12
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (235 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGGATTGGAGTATCCC
TTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAAAAATAAAACTGG
GGTTGGAGTATCTCCTCAGAAATAACGGGGTTAGAATATCCCTGATTATGAAAAATCGATATTTT
AAAATAAAACTGGGGTTAGAGATCCCCTCAAAAATAACAG
Found at i:2355506 original size:19 final size:20
Alignment explanation
Indices: 2355482--2355534 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2355472 TAAAACCTAG
2355482 AATGTATCGATACAAT-AAC
1 AATGTATCGATACAATGAAC
2355501 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
2355521 AATGTATCGATACA
1 AATGTATCGATACA
2355535 TCTAGGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:2355543 original size:69 final size:70
Alignment explanation
Indices: 2355432--2355585 Score: 229
Period size: 69 Copynumber: 2.2 Consensus size: 70
2355422 AAAATACTTG
* * * * *
2355432 AATGTATCAATACATTAAAAAATGTATCGATACATCTGGGTAAAACCTAGAATGTATCGATACAA
1 AATGTATCGATACAATAAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAA
2355497 T-AAC
66 TGAAC
* *
2355501 AATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAA
1 AATGTATCGATACAATAAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAA
2355566 TGAAC
66 TGAAC
*
2355571 AATGTATCGAGACAA
1 AATGTATCGATACAA
2355586 ATTGTGGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
69 59 0.78
70 17 0.22
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (70 bp):
AATGTATCGATACAATAAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATACAA
TGAAC
Found at i:2356516 original size:105 final size:105
Alignment explanation
Indices: 2356334--2356543 Score: 341
Period size: 105 Copynumber: 2.0 Consensus size: 105
2356324 ATGTCTTAAG
* *
2356334 CCTATAGCAAGATTCATAATGGAAAGTCTCAACATATTAGCTTGAGACATAAATATGTAAAGCAG
1 CCTATAGCAAGATTCATAATGAAAAGTCTCAACATATTAGCTTGAGACATAAATATGCAAAGCAG
2356399 TTAATAAGAGATGGTATAATCACCATCACCTATGTTAGGT
66 TTAATAAGAGATGGTATAATCACCATCACCTATGTTAGGT
* * * *
2356439 CCTATAGCAAGGTTCATAATGAAAAGTCT-AGATATATTAGCTTGAGACATGAGTATGCAAAGCA
1 CCTATAGCAAGATTCATAATGAAAAGTCTCA-ACATATTAGCTTGAGACATAAATATGCAAAGCA
*
2356503 GTTAATAAGAGATGGTATAATCACTATCACCTATGTTAGGT
65 GTTAATAAGAGATGGTATAATCACCATCACCTATGTTAGGT
2356544 AAATAACAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
104 1 0.01
105 96 0.99
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (105 bp):
CCTATAGCAAGATTCATAATGAAAAGTCTCAACATATTAGCTTGAGACATAAATATGCAAAGCAG
TTAATAAGAGATGGTATAATCACCATCACCTATGTTAGGT
Found at i:2359291 original size:1 final size:1
Alignment explanation
Indices: 2359285--2359316 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
2359275 TGACATCAAG
2359285 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2359317 CTGGCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2363483 original size:27 final size:27
Alignment explanation
Indices: 2363408--2363511 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
2363398 TAAAAAATAG
*
2363408 CCACCAATTTTGACAAACAAC-AAGG--
1 CCACCATTTTTGACAAA-AACAAAGGAA
* * *
2363433 -CACAATTTTTGACAAACAAAAAAGGAT
1 CCACCATTTTTGACAAA-AACAAAGGAA
* * * *
2363460 TCATCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAAAACAAAGGAA
*
2363487 CCACCATTTTTGACAAACACAAAGG
1 CCACCATTTTTGACAAAAACAAAGG
2363512 GTGGTTTTTG
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 17 0.27
25 4 0.06
27 27 0.44
28 14 0.23
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAAAACAAAGGAA
Found at i:2365403 original size:21 final size:22
Alignment explanation
Indices: 2365377--2365422 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2365367 TTTAGTTGAA
* *
2365377 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
*
2365398 ACTCCACTTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
2365420 ACT
1 ACT
2365423 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:2374143 original size:23 final size:23
Alignment explanation
Indices: 2374117--2374167 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2374107 ATTTCCTTGA
*
2374117 AATTCTCATATTTC-ATTGAAAAT
1 AATTCT-ATATTTCTATGGAAAAT
* *
2374140 AATTATTTATTTCTATGGAAAAT
1 AATTCTATATTTCTATGGAAAAT
2374163 AATTC
1 AATTC
2374168 CTTCACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (23 bp):
AATTCTATATTTCTATGGAAAAT
Found at i:2376284 original size:19 final size:20
Alignment explanation
Indices: 2376260--2376297 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2376250 GTGTCGAGTT
2376260 AGGTTTTGAAAT-TTAAAAA
1 AGGTTTTGAAATCTTAAAAA
2376279 AGGTTTTGAAATCTTAAAA
1 AGGTTTTGAAATCTTAAAA
2376298 CCTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.37
Consensus pattern (20 bp):
AGGTTTTGAAATCTTAAAAA
Found at i:2379614 original size:20 final size:20
Alignment explanation
Indices: 2379586--2379625 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2379576 TCGATACAAC
*
2379586 AAGTTAATGTATCAATACAT
1 AAGTAAATGTATCAATACAT
2379606 AAGTAAATGTATCAATACAT
1 AAGTAAATGTATCAATACAT
2379626 GTTTGCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
AAGTAAATGTATCAATACAT
Found at i:2384115 original size:23 final size:23
Alignment explanation
Indices: 2384083--2384129 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2384073 GACTAAATGG
* * *
2384083 ATTTTGGATGGTATTGGGATTGT
1 ATTTTAGATGGCATTAGGATTGT
2384106 ATTTTAGATGGCATTAGGATTGT
1 ATTTTAGATGGCATTAGGATTGT
2384129 A
1 A
2384130 ATTTGGGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (23 bp):
ATTTTAGATGGCATTAGGATTGT
Found at i:2386760 original size:13 final size:13
Alignment explanation
Indices: 2386742--2386767 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2386732 CATTTTTCTG
2386742 TGTATCGATACAT
1 TGTATCGATACAT
2386755 TGTATCGATACAT
1 TGTATCGATACAT
2386768 GGATCTTTGT
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:2386764 original size:33 final size:33
Alignment explanation
Indices: 2386722--2386788 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2386712 GCCAAGGAAA
***
2386722 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2386755 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2386788 T
1 T
2386789 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2389260 original size:27 final size:28
Alignment explanation
Indices: 2389230--2389305 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
2389220 AATTTTCACA
2389230 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
2389257 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
2389285 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2389306 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:2389508 original size:52 final size:51
Alignment explanation
Indices: 2389121--2389509 Score: 299
Period size: 51 Copynumber: 7.4 Consensus size: 51
2389111 CTCAATTCTC
* * * * *
2389121 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * *
2389171 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTTCC---AAAACACCAATTTTT
* * ** * *
2389226 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA-----TT-TTT
* * * **
2389284 C-CGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * * * *
2389332 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* *
2389383 CCACAATC-GGGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTT
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* *
2389434 C-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CAC---AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTT
*
2389488 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
2389510 TCGTTATCTC
Statistics
Matches: 268, Mismatches: 45, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 2 0.01
51 107 0.40
52 38 0.14
53 27 0.10
54 49 0.18
55 24 0.09
56 2 0.01
57 7 0.03
58 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
Found at i:2389528 original size:28 final size:28
Alignment explanation
Indices: 2389492--2389568 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
2389482 ATTTTTCACA
* *
2389492 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
*
2389520 ATCGGGGATATTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2389548 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2389569 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2389586 original size:263 final size:262
Alignment explanation
Indices: 2389119--2389619 Score: 790
Period size: 263 Copynumber: 1.9 Consensus size: 262
2389109 TTCTCAATTC
* * * *
2389119 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
2389184 TACTCCAACTCCGATTTTATTTCCAAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCC
*
2389249 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
130 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* *
2389314 TCCAAAATATTAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
195 CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
2389379 TTT
260 TTT
* *
2389382 TCCACAATC-GGGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATCGGG
* *
2389446 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAACC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACC
* * * *
2389510 TCGTTATCTCATCGGGGATATTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
129 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTA
* *
2389575 TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 TTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCG
2389620 TTATTTTCGA
Statistics
Matches: 217, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
262 73 0.34
263 108 0.50
264 36 0.17
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TT
Found at i:2402133 original size:1 final size:1
Alignment explanation
Indices: 2402122--2402173 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
2402112 CCTTCTCTTC
* * * * * *
2402122 AAAAAAGAAAAAAAAACAAAAAAACAAAAAAAACAAAACAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2402174 TCTGCTTAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2402136 original size:9 final size:9
Alignment explanation
Indices: 2402121--2402172 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 9
2402111 ACCTTCTCTT
*
2402121 CAAAAAAGA
1 CAAAAAAAA
2402130 -AAAAAAAA
1 CAAAAAAAA
2402138 C-AAAAAAA
1 CAAAAAAAA
2402146 CAAAAAAAA
1 CAAAAAAAA
*
2402155 CAAAACAAA
1 CAAAAAAAA
*
2402164 GAAAAAAAA
1 CAAAAAAAA
2402173 ATCTGCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 15 0.41
9 22 0.59
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:2402145 original size:18 final size:18
Alignment explanation
Indices: 2402122--2402173 Score: 79
Period size: 17 Copynumber: 2.9 Consensus size: 18
2402112 CCTTCTCTTC
2402122 AAAAAAGAAAAAAAAACA
1 AAAAAAGAAAAAAAAACA
*
2402140 AAAAAA-CAAAAAAAACA
1 AAAAAAGAAAAAAAAACA
2402157 AAACAAAGAAAAAAAAA
1 AAA-AAAGAAAAAAAAA
2402174 TCTGCTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 13 0.43
18 9 0.30
19 8 0.27
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAACA
Found at i:2403292 original size:59 final size:59
Alignment explanation
Indices: 2403141--2403976 Score: 1117
Period size: 59 Copynumber: 14.3 Consensus size: 59
2403131 TCCGCTTTTT
* **
2403141 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTT-CTTTT-AAAGCCCACACAAGTTGGTGGCACCTT-C
* * *
2403203 AGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTCGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
2403262 AATCCTCAAAGAGCAGGACGTCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * **
2403321 AATCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCATTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
2403380 TAGTCCTCAAAGAGCGGGACGTCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 -AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
2403440 AGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
2403499 AGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
2403558 AATCCTCAAAAAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
2403617 AATCCTCAAAAAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
2403676 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
2403735 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* * * * **
2403796 AGTCCCCGAAGAGCATGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
*
2403851 AGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * *
2403906 AGTCCTCAAAGAGCAGGATGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
2403961 AGTCCTCAAAGAGCAG
1 AGTCCTCAAAGAGCAG
2403977 AATACACTTT
Statistics
Matches: 711, Mismatches: 53, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
53 2 0.00
54 2 0.00
55 128 0.18
56 2 0.00
57 2 0.00
59 423 0.59
60 103 0.14
61 24 0.03
62 25 0.04
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:2403448 original size:178 final size:176
Alignment explanation
Indices: 2403141--2403976 Score: 1115
Period size: 178 Copynumber: 4.8 Consensus size: 176
2403131 TCCGCTTTTT
* *
2403141 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 AGTCCTCAAAGAGCAGGACGCCTTTT-CTTTT-AAAGCCCACACAAGTTGGTGGCACTTT-CAGT
* * *
2403206 CCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTCGGTGGCACCTTCAATCCTCAA
63 CCTCAAAGAGCGGGATG-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAA
*
2403271 AGAGCAGGACGTCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
127 AGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
2403321 AATCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCATTTTCTAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCC
*
2403386 TCAAAGAGCGGGACGTCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
65 TCAAAGAGCGGGATG-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* *
2403451 AGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
129 AGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
2403499 AGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAATCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCT
* * * * *
2403564 CAAAAAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAAA
66 CAAAGAGCGGGATG-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGA
*
2403629 GCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
130 GCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
2403676 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCT
* * *
2403741 CAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCGAA
66 CAAAGAGCGGGATGC-TTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT-AGTCCTCAAA
* * **
2403806 GAGCATGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
128 GAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
*
2403851 AGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCC
* * * *
2403911 TCAAAGAGCAGGATGC----CTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAG
65 TCAAAGAGCGGGATGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTTAGTCCTCAAAG
2403972 AGCAG
129 AGCAG
2403977 AATACACTTT
Statistics
Matches: 597, Mismatches: 52, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
165 36 0.06
166 7 0.01
170 23 0.04
171 25 0.04
172 2 0.00
174 25 0.04
175 21 0.04
176 1 0.00
177 193 0.32
178 220 0.37
179 20 0.03
180 24 0.04
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (176 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCT
CAAAGAGCGGGATGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAG
CAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:2404126 original size:42 final size:43
Alignment explanation
Indices: 2404068--2404159 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
2404058 TGGGACGTAC
* *
2404068 TCTTCT-TTCACTTTGTCCTCAAGAAGCAGGA-CACTTTCCTTT
1 TCTTCTCTTCACTTTGTCCTCAAGAAGCAAGACCA-TTTCATTT
* *
2404110 TCTTCTCTTC-CTTTGTCTTCAAGGAGCAAGACCTATTTCATTT
1 TCTTCTCTTCACTTTGTCCTCAAGAAGCAAGACC-ATTTCATTT
2404153 TCTTCTC
1 TCTTCTC
2404160 CTTTGTCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
42 24 0.56
43 18 0.42
44 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.43
Consensus pattern (43 bp):
TCTTCTCTTCACTTTGTCCTCAAGAAGCAAGACCATTTCATTT
Found at i:2404781 original size:19 final size:19
Alignment explanation
Indices: 2404757--2404824 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2404747 AATTCAACAG
2404757 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2404776 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2404791 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2404808 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2404825 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2404795 original size:32 final size:32
Alignment explanation
Indices: 2404759--2404821 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2404749 TTCAACAGTT
*
2404759 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2404791 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2404822 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2404796 original size:13 final size:13
Alignment explanation
Indices: 2404778--2404802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2404768 ACATAAGTTT
2404778 TGTATCGATACAA
1 TGTATCGATACAA
2404791 TGTATCGATACA
1 TGTATCGATACA
2404803 TAAGTATTGT
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:2407424 original size:28 final size:27
Alignment explanation
Indices: 2407354--2407429 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
2407344 AATTTTCACA
2407354 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2407381 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2407407 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
2407430 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 23 0.51
28 18 0.40
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:2407480 original size:51 final size:52
Alignment explanation
Indices: 2407412--2407633 Score: 243
Period size: 51 Copynumber: 4.3 Consensus size: 52
2407402 TTATTTTCGA
* * ** *
2407412 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTAATTTTT-CATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCCACAATC
* * * *
2407463 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCCACAATC
* * * * **
2407515 -GAGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCC-ACAATC
* *
2407567 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCCACAATC
*
2407619 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2407634 TCGTTATCTC
Statistics
Matches: 142, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
51 77 0.54
52 27 0.19
53 24 0.17
54 14 0.10
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCCACAATC
Found at i:2407619 original size:104 final size:103
Alignment explanation
Indices: 2407414--2407633 Score: 273
Period size: 104 Copynumber: 2.1 Consensus size: 103
2407404 ATTTTCGAGG
* **
2407414 GGATACTCCAACCCCGACTTTATTTCCAAAATATTAATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
* * * *
2407479 CGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGA
66 CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
* ** * *
2407517 -GATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATCGGGGATACTCCAAC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTT-C-ATAATCGGGGATACTCCAAC
* *
2407581 TCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
64 CCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATCGA
2407621 GGATACTCCAACC
1 GGATACTCCAACC
2407634 TCGTTATCTC
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
102 34 0.35
103 1 0.01
104 36 0.37
105 27 0.28
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (103 bp):
GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:2407629 original size:52 final size:51
Alignment explanation
Indices: 2407245--2407633 Score: 241
Period size: 51 Copynumber: 7.4 Consensus size: 51
2407235 CTCAATTCTC
* * * * * *
2407245 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAA-TTTT
1 CACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * * *
2407295 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAAATTTT
1 C-ACAATCGAGGATACTCCAACCCCGATTTTATTTCC---AAAACACCAATTTTT
* * * ** * * ***
2407350 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTT
1 CACAATCGAGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA--TTTTT
*** * * **
2407404 -ATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTAATTTTT
1 CACAATCGA--GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * * * * *
2407456 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * *
2407507 CCACAATCGA-GATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTT
1 -CACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
* * *
2407558 C-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CAC---AATCGAGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTT
2407612 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
2407634 TCGTTATCTC
Statistics
Matches: 261, Mismatches: 56, Indels: 42
0.73 0.16 0.12
Matches are distributed among these distances:
49 1 0.00
50 2 0.01
51 104 0.40
52 42 0.16
53 33 0.13
54 51 0.20
55 22 0.08
56 2 0.01
57 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT
Found at i:2407652 original size:28 final size:28
Alignment explanation
Indices: 2407616--2407692 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
2407606 ATTTTTCACA
* *
2407616 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
2407644 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2407672 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2407693 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2407710 original size:263 final size:262
Alignment explanation
Indices: 2407243--2407743 Score: 772
Period size: 263 Copynumber: 1.9 Consensus size: 262
2407233 TTCTCAATTC
* * * * *
2407243 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
2407308 TACTCCAACTCCGATTTTATTTCCAAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCC
* *
2407373 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATT
130 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* *
2407438 TCCAAAATATTAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
195 CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
2407503 TTT
260 TTT
* * *
2407506 TCCACAATC-GAGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATCGGG
1 TCCACAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATCGGG
* *
2407570 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAACC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACC
* * *
2407634 TCGTTATCTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
129 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTA
* *
2407699 TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 TTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCG
2407744 TTATTTTCGA
Statistics
Matches: 215, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
262 71 0.33
263 108 0.50
264 36 0.17
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
TCCACAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TT
Found at i:2407795 original size:79 final size:79
Alignment explanation
Indices: 2407646--2407850 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 79
2407636 GTTATCTCAT
* * * *
2407646 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
2407711 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** **
2407725 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TGATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
2407789 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * *
2407804 CGGGGATACTCCAGCCCCGTTATTTTC-AATGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAA-GGGATACTCCAACCCCG
2407851 TTATTATCTC
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 4 0.04
79 100 0.96
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:2409251 original size:212 final size:211
Alignment explanation
Indices: 2408878--2409314 Score: 712
Period size: 212 Copynumber: 2.1 Consensus size: 211
2408868 ATCTATTTAC
* *
2408878 ATTTTATGTTATACATTAAAGTATTTAATTCAATTATGTTTATGTTTTATATTATATTAATTAAA
1 ATTTTATATTATACATTAAAGTATTTAATTCAATTATATTTATGTTTTATATTATATTAATTAAA
*
2408943 AATTATACATTTGACAATGCTAAAAAATAAAAATCATATGAAGTGCGAAATTAAACATATCTTAT
66 AATTATACATTTGACAATGCTAAAAAATAAAAATCATATGAAGTGCAAAATTAAACATATCTTAT
* * * * *
2409008 AAAATAAGATGAAAGTTATCTTTAATACTTGACACGTATGGCATGTAATTATAATTTTTCTTATA
131 AAAATAAGATGAAAGCTATCTCTAATACTTGACACGTATGGCATGCAATTATAATATAT-TTATA
2409073 ATTACAACATTTGTATT
195 ATTACAACATTTGTATT
2409090 ATTTTATATTATACATTAAAGTATTTAATTCAATTATATTTATGTTTTATATTATATTAATTAAA
1 ATTTTATATTATACATTAAAGTATTTAATTCAATTATATTTATGTTTTATATTATATTAATTAAA
* * * *
2409155 AATTATACATTTGATAATGCTGAAAAATAAAAATCATATGAAGTGCAAAATTAGACATATTTTAT
66 AATTATACATTTGACAATGCTAAAAAATAAAAATCATATGAAGTGCAAAATTAAACATATCTTAT
*
2409220 AAAATAAGATGAAAGCTATCTCTATTACTTGACACGTATGGCATGCAATTATAATATATTTATAA
131 AAAATAAGATGAAAGCTATCTCTAATACTTGACACGTATGGCATGCAATTATAATATATTTATAA
* *
2409285 TTATAATATTTGTATT
196 TTACAACATTTGTATT
*
2409301 ATTTTTTTATTATA
1 A-TTTTATATTATA
2409315 ATCGTATTAT
Statistics
Matches: 208, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
211 21 0.10
212 187 0.90
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (211 bp):
ATTTTATATTATACATTAAAGTATTTAATTCAATTATATTTATGTTTTATATTATATTAATTAAA
AATTATACATTTGACAATGCTAAAAAATAAAAATCATATGAAGTGCAAAATTAAACATATCTTAT
AAAATAAGATGAAAGCTATCTCTAATACTTGACACGTATGGCATGCAATTATAATATATTTATAA
TTACAACATTTGTATT
Found at i:2409385 original size:25 final size:27
Alignment explanation
Indices: 2409357--2409406 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
2409347 GACATGTCAT
2409357 AAATAAAATATGA-A-AAAAATAATTA
1 AAATAAAATATGATATAAAAATAATTA
**
2409382 AAATAGGATATGATATAAAAATAAT
1 AAATAAAATATGATATAAAAATAAT
2409407 ATGAACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 1 0.05
27 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (27 bp):
AAATAAAATATGATATAAAAATAATTA
Found at i:2410058 original size:17 final size:17
Alignment explanation
Indices: 2410038--2410072 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2410028 TTCAATTTAT
2410038 ATGAATCATAATAGAAG
1 ATGAATCATAATAGAAG
*
2410055 ATGAATTATAATAGAAG
1 ATGAATCATAATAGAAG
2410072 A
1 A
2410073 ATTAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.17, T:0.26
Consensus pattern (17 bp):
ATGAATCATAATAGAAG
Found at i:2415750 original size:19 final size:20
Alignment explanation
Indices: 2415704--2415756 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
2415694 TTATTTTTGT
* *
2415704 TTTATTTTAAATAATATTTTA
1 TTTA-TTTAAATAGTATTTAA
2415725 TTT-TTTAAATAGTA-TTAA
1 TTTATTTAAATAGTATTTAA
*
2415743 TTTATTTAATTAGT
1 TTTATTTAAATAGT
2415757 CAATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 6 0.21
19 19 0.68
21 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATTTAAATAGTATTTAA
Found at i:2416000 original size:20 final size:20
Alignment explanation
Indices: 2415975--2416046 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
2415965 TGCTAGTTTG
*
2415975 ATATAATTTTGTAACTTCTA
1 ATATAATTTTGTAACTTTTA
* *
2415995 ATATAATTTTAATAATTTTTA
1 ATATAATTTT-GTAACTTTTA
*
2416016 ATATAATTTTGATAACTTTTT
1 ATATAATTTTG-TAACTTTTA
2416037 ATAT-ATTTTG
1 ATATAATTTTG
2416047 ATAGCCCTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
ATATAATTTTGTAACTTTTA
Found at i:2416047 original size:20 final size:21
Alignment explanation
Indices: 2415975--2416049 Score: 93
Period size: 20 Copynumber: 3.7 Consensus size: 21
2415965 TGCTAGTTTG
* *
2415975 ATATAATTTTG-TAACTTCTA
1 ATATAATTTTGATAACTTTTT
*
2415995 ATATAATTTTAATAA-TTTTT
1 ATATAATTTTGATAACTTTTT
2416015 AATATAATTTTGATAACTTTTT
1 -ATATAATTTTGATAACTTTTT
2416037 ATAT-ATTTTGATA
1 ATATAATTTTGATA
2416050 GCCCTTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
20 22 0.46
21 21 0.44
22 5 0.10
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
ATATAATTTTGATAACTTTTT
Found at i:2416057 original size:21 final size:21
Alignment explanation
Indices: 2415975--2416058 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
2415965 TGCTAGTTTG
*
2415975 ATATAATTTTG-TAA-CTTCTA
1 ATATAATTTTGATAACCTT-TT
* *
2415995 ATATAATTTTAATAA-TTTTT
1 ATATAATTTTGATAACCTTTT
*
2416015 AATATAATTTTGATAACTTTTT
1 -ATATAATTTTGATAACCTTTT
*
2416037 ATAT-ATTTTGATAGCCCTTTT
1 ATATAATTTTGATA-ACCTTTT
2416058 A
1 A
2416059 ATTTGATCGG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 20 0.37
21 29 0.54
22 5 0.09
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (21 bp):
ATATAATTTTGATAACCTTTT
Found at i:2416269 original size:41 final size:42
Alignment explanation
Indices: 2416224--2416352 Score: 154
Period size: 41 Copynumber: 3.1 Consensus size: 42
2416214 GTGATGTTTC
* *
2416224 TTTT-ATAACTTTTAATGCAATTTTGGTAGCCTTTGATATGA
1 TTTTAATAACTTTTAATGCAATTTTGATAGCCTTTGATATAA
* * *
2416265 TTTTAATAA-TTTTTATGCGATTTTGATAGCGTTTGATATAA
1 TTTTAATAACTTTTAATGCAATTTTGATAGCCTTTGATATAA
** ** *
2416306 TTTTAATAACTTTTAATATAATTTTGATATTCTTTAATATAA
1 TTTTAATAACTTTTAATGCAATTTTGATAGCCTTTGATATAA
2416348 TTTTA
1 TTTTA
2416353 GTAATATGCA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 40 0.55
42 33 0.45
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (42 bp):
TTTTAATAACTTTTAATGCAATTTTGATAGCCTTTGATATAA
Found at i:2416319 original size:10 final size:9
Alignment explanation
Indices: 2416302--2416472 Score: 56
Period size: 9 Copynumber: 16.9 Consensus size: 9
2416292 AGCGTTTGAT
2416302 ATAATTTTA
1 ATAATTTTA
2416311 ATAACTTTTAA
1 ATAA-TTTT-A
*
2416322 TATAATTTTG
1 -ATAATTTTA
*
2416332 ATATTCTTTAA
1 ATAAT-TTT-A
2416343 TATAATTTTA
1 -ATAATTTTA
* **
2416353 GTAATATGCA
1 ATAAT-TTTA
2416363 ATATAATTTTA
1 A--TAATTTTA
*
2416374 ATAACCTTTA
1 ATAA-TTTTA
*
2416384 ATATGATTTTG
1 ATA--ATTTTA
2416395 ATAATTTTA
1 ATAATTTTA
*
2416404 GTAATTTTCA
1 ATAATTTT-A
2416414 ATATCATTTTA
1 ATA--ATTTTA
2416425 ATAACTTTTGA
1 ATAA-TTTT-A
2416436 TATAATTTTGA
1 -ATAATTTT-A
* *
2416447 TTACCTTTT-
1 ATA-ATTTTA
2416456 ATAATTTTA
1 ATAATTTTA
*
2416465 ATAGTTTT
1 ATAATTTT
2416473 TAAGTGATTT
Statistics
Matches: 121, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
8 4 0.03
9 37 0.31
10 26 0.21
11 32 0.26
12 22 0.18
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (9 bp):
ATAATTTTA
Found at i:2416324 original size:21 final size:20
Alignment explanation
Indices: 2416300--2416575 Score: 106
Period size: 21 Copynumber: 13.6 Consensus size: 20
2416290 ATAGCGTTTG
2416300 ATATAATTTTAATAACTTTTA
1 ATATAATTTTAATAA-TTTTA
* *
2416321 ATATAATTTTGATATTCTTTA
1 ATATAATTTTAATAAT-TTTA
* **
2416342 ATATAATTTTAGTAATATGCA
1 ATATAATTTTAATAAT-TTTA
*
2416363 ATATAATTTTAATAACCTTTA
1 ATATAATTTTAATAA-TTTTA
* *
2416384 ATATGATTTTGATAATTTT-
1 ATATAATTTTAATAATTTTA
*
2416403 A-GTAATTTTCAATATCATTTTA
1 ATATAATTTT-AATA--ATTTTA
* *
2416425 ATA-ACTTTTGATATAATTTTG
1 ATATAATTTT-A-ATAATTTTA
*
2416446 AT-TACCTTTT-ATAATTTTA
1 ATATA-ATTTTAATAATTTTA
*
2416465 ATAGT--TTTTAAGTGA-TTT-
1 ATA-TAATTTTAA-TAATTTTA
** *
2416483 -TATCGTTTTCATAATTTTTA
1 ATATAATTTTAATAA-TTTTA
* * * *
2416503 CTATAATTTTGATTATTTTT
1 ATATAATTTTAATAATTTTA
* ** *
2416523 ATAAAATTTTGGTAACTATTA
1 ATATAATTTTAATAA-TTTTA
* *
2416544 AAATAATTTTACTAACTTTT-
1 ATATAATTTTAATAA-TTTTA
2416564 ATATAATTTTAA
1 ATATAATTTTAA
2416576 AAAGATTTAA
Statistics
Matches: 190, Mismatches: 44, Indels: 43
0.69 0.16 0.16
Matches are distributed among these distances:
16 1 0.01
17 4 0.02
18 15 0.08
19 21 0.11
20 31 0.16
21 103 0.54
22 12 0.06
23 3 0.02
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (20 bp):
ATATAATTTTAATAATTTTA
Found at i:2416346 original size:42 final size:40
Alignment explanation
Indices: 2416224--2416403 Score: 128
Period size: 42 Copynumber: 4.3 Consensus size: 40
2416214 GTGATGTTTC
* * * *
2416224 TTTT-ATAACTTTTAATGCAATTTTGGTAGCCTTTGATATGA
1 TTTTAATAA-TTTTAATACAATTTTGATA-CCTTTAATATAA
* * * * *
2416265 TTTTAATAATTTTTATGCGATTTTGATAGCGTTTGATATAA
1 TTTTAATAATTTTAATACAATTTTGATA-CCTTTAATATAA
* *
2416306 TTTTAATAACTTTTAATATAATTTTGATATTCTTTAATATAA
1 TTTTAATAA-TTTTAATACAATTTTGATA-CCTTTAATATAA
* ** * * *
2416348 TTTTAGTAATATGCAATATAATTTTAATAACCTTTAATATGA
1 TTTTAATAAT-TTTAATACAATTTTGAT-ACCTTTAATATAA
*
2416390 TTTTGATAATTTTA
1 TTTTAATAATTTTA
2416404 GTAATTTTCA
Statistics
Matches: 112, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 43 0.38
42 68 0.61
43 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.51
Consensus pattern (40 bp):
TTTTAATAATTTTAATACAATTTTGATACCTTTAATATAA
Found at i:2416402 original size:51 final size:51
Alignment explanation
Indices: 2416344--2416447 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
2416334 ATTCTTTAAT
*
2416344 ATAATTTTAGTAATATGCAATATAATTTTAATAACCTTTAATATGATTTTG
1 ATAATTTTAGTAATATGCAATATAATTTTAATAACCTTTAATATAATTTTG
* * * * *
2416395 ATAATTTTAGTAATTTTCAATATCATTTTAATAACTTTTGATATAATTTTG
1 ATAATTTTAGTAATATGCAATATAATTTTAATAACCTTTAATATAATTTTG
2416446 AT
1 AT
2416448 TACCTTTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.50
Consensus pattern (51 bp):
ATAATTTTAGTAATATGCAATATAATTTTAATAACCTTTAATATAATTTTG
Found at i:2416417 original size:30 final size:30
Alignment explanation
Indices: 2416365--2416433 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
2416355 AATATGCAAT
* *
2416365 ATAATTTTAATAACCTTTAATATGATTTTG
1 ATAATTTTAATAACCTTTAATATCATTTTA
* *
2416395 ATAATTTTAGTAA-TTTTCAATATCATTTTA
1 ATAATTTTAATAACCTTT-AATATCATTTTA
2416425 ATAACTTTT
1 ATAA-TTTT
2416434 GATATAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 26 0.79
31 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.52
Consensus pattern (30 bp):
ATAATTTTAATAACCTTTAATATCATTTTA
Found at i:2416888 original size:21 final size:22
Alignment explanation
Indices: 2416864--2416919 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
2416854 TGAATATAAT
*
2416864 AAATATATTA-AAATTTATTTA
1 AAATATATTATAAATTTATTAA
* *
2416885 AAATAAATTATTAATTTATTAA
1 AAATATATTATAAATTTATTAA
2416907 AAAT-TA-TATAAAT
1 AAATATATTATAAAT
2416920 ATATAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 10 0.34
22 13 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATATATTATAAATTTATTAA
Found at i:2418208 original size:5 final size:5
Alignment explanation
Indices: 2418198--2418233 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
2418188 ATATAATTTT
* *
2418198 TTTAA TTTAA TTTAA GTTAA TTTAA TTTAA ATTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
2418234 ATTTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:2418219 original size:15 final size:15
Alignment explanation
Indices: 2418199--2418233 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2418189 TATAATTTTT
*
2418199 TTAATTTAATTTAAG
1 TTAATTTAATTTAAA
2418214 TTAATTTAATTTAAA
1 TTAATTTAATTTAAA
2418229 TTAAT
1 TTAAT
2418234 ATTTAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TTAATTTAATTTAAA
Found at i:2418255 original size:30 final size:30
Alignment explanation
Indices: 2418221--2418295 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
2418211 AAGTTAATTT
2418221 AATTTAAATTAATATTTAATAATAAAA-ATA
1 AATTTAAATTAA-ATTTAATAATAAAATATA
* *
2418251 AATTTTTAATTAAATTTAATTATAAAATATA
1 AA-TTTAAATTAAATTTAATAATAAAATATA
*
2418282 AATATTAATTTAAA
1 AAT-TTAAATTAAA
2418296 AATATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AATTTAAATTAAATTTAATAATAAAATATA
Found at i:2418267 original size:47 final size:47
Alignment explanation
Indices: 2418208--2418309 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 47
2418198 TTTAATTTAA
2418208 TTTAAGTTAATTTAATT-T-AAAT-T-AATATTTAATAATAAAAATAAATT
1 TTTAA-TTAATTTAATTATAAAATATAAATA-TTAAT-ATAAAAAT-AATT
* *
2418255 TTTAATTAAATTTAATTATAAAATATAAATATTAATTTAAAAATATTT
1 TTTAATT-AATTTAATTATAAAATATAAATATTAATATAAAAATAATT
2418303 TTTAATT
1 TTTAATT
2418310 TTTATTAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
46 2 0.04
47 14 0.29
48 11 0.23
49 11 0.23
50 6 0.12
51 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (47 bp):
TTTAATTAATTTAATTATAAAATATAAATATTAATATAAAAATAATT
Found at i:2418295 original size:31 final size:30
Alignment explanation
Indices: 2418227--2418291 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
2418217 ATTTAATTTA
*
2418227 AATTAATATTTAATAATAAAAATAAATTTTT
1 AATTAA-ATTTAATAATAAAAATAAATTATT
*
2418258 AATTAAATTTAATTATAAAATATAAA-TATT
1 AATTAAATTTAATAATAAAA-ATAAATTATT
2418288 AATT
1 AATT
2418292 TAAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATTAAATTTAATAATAAAAATAAATTATT
Found at i:2418344 original size:30 final size:28
Alignment explanation
Indices: 2418284--2418344 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
2418274 AAAATATAAA
*
2418284 TATTAATTTAAAAATATTTTTTAATTTT
1 TATTAATTTAAAAATATTTTTGAATTTT
*
2418312 TATTAATATT-AAAATATTAATTTGAGTTTT
1 TATTAAT-TTAAAAATATT--TTTGAATTTT
2418342 TAT
1 TAT
2418345 ACTAAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 15 0.54
29 2 0.07
30 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TATTAATTTAAAAATATTTTTGAATTTT
Found at i:2418875 original size:23 final size:22
Alignment explanation
Indices: 2418838--2418880 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2418828 TTTCCTTACT
*
2418838 TATTTTTATATAATAAAATATA
1 TATTTTTATAAAATAAAATATA
*
2418860 TATTTTTATTAAAATATAATA
1 TATTTTTA-TAAAATAAAATA
2418881 AGATTGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTTTATAAAATAAAATATA
Found at i:2419573 original size:17 final size:16
Alignment explanation
Indices: 2419553--2419589 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
2419543 TTATTAACAT
2419553 ATAAAAAATATATAAAA
1 ATAAAAAATAT-TAAAA
*
2419570 ATAAAATATATTAAAA
1 ATAAAAAATATTAAAA
2419586 ATAA
1 ATAA
2419590 TTATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAAATATTAAAA
Found at i:2419575 original size:15 final size:15
Alignment explanation
Indices: 2419557--2419607 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
2419547 TAACATATAA
2419557 AAAATATATAAAAAT
1 AAAATATATAAAAAT
2419572 AAAATATATTAAAAAT
1 AAAATATA-TAAAAAT
*
2419588 -AATTATA-ATAAAAT
1 AAAATATATA-AAAAT
2419602 AAAATA
1 AAAATA
2419608 AAATAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 18 0.58
16 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATATAAAAAT
Found at i:2419577 original size:5 final size:5
Alignment explanation
Indices: 2419567--2419631 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
2419557 AAAATATATA
* * * * *
2419567 AAAAT AAAAT ATATT AAAA- ATAATT ATAAT AAAAT AAAAT AAAAT -AATT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
2419616 ATAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT A
2419632 CATAAAAATT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
4 4 0.09
5 40 0.89
6 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
AAAAT
Found at i:2419602 original size:14 final size:14
Alignment explanation
Indices: 2419583--2419627 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
2419573 AAATATATTA
2419583 AAAATAATTATAAT
1 AAAATAATTATAAT
2419597 AAAAT-A--A-AAT
1 AAAATAATTATAAT
2419607 AAAATAATTATAAT
1 AAAATAATTATAAT
2419621 AAAATAA
1 AAAATAA
2419628 AATACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 8 0.30
11 2 0.07
13 2 0.07
14 15 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAATTATAAT
Found at i:2419615 original size:24 final size:24
Alignment explanation
Indices: 2419569--2419631 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
2419559 AATATATAAA
* *
2419569 AATAAAATATATTAAAAATAATTAT
1 AATAAAATAAAAT-AAAATAATTAT
2419594 AATAAAATAAAATAAAATAATTAT
1 AATAAAATAAAATAAAATAATTAT
2419618 AATAAAATAAAATA
1 AATAAAATAAAATA
2419632 CATAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 25 0.69
25 11 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAAAATAAAATAAAATAATTAT
Found at i:2419636 original size:14 final size:13
Alignment explanation
Indices: 2419557--2419638 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 13
2419547 TAACATATAA
2419557 AAAATATATAAAAAT
1 AAAATA-AT-AAAAT
2419572 AAAATATATTAAAAAT
1 AAAATA-A-T-AAAAT
*
2419588 AATTATAATAAAAT
1 AA-AATAATAAAAT
2419602 --AA-AATAAAAT
1 AAAATAATAAAAT
*
2419612 AATTATAATAAAAT
1 AA-AATAATAAAAT
2419626 AAAATACATAAAA
1 AAAATA-ATAAAA
2419639 ATTACACATA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
10 8 0.14
11 1 0.02
13 4 0.07
14 21 0.38
15 9 0.16
16 10 0.18
17 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:2419899 original size:23 final size:22
Alignment explanation
Indices: 2419873--2419916 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2419863 TCATAAATAA
2419873 AAAAATATTGATTAAAAT-TTTGG
1 AAAAATA-T-ATTAAAATATTTGG
*
2419896 AAAAGTATATTAAAATATTTG
1 AAAAATATATTAAAATATTTG
2419917 ATTCATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (22 bp):
AAAAATATATTAAAATATTTGG
Found at i:2420329 original size:25 final size:26
Alignment explanation
Indices: 2420281--2420329 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2420271 TTTTAGTGCT
2420281 TAAATTAAAATATAAAAAAATTATGA
1 TAAATTAAAATATAAAAAAATTATGA
2420307 TAAATTAAAATAT-AAAAAATTAT
1 TAAATTAAAATATAAAAAAATTAT
2420330 AAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAATTAAAATATAAAAAAATTATGA
Found at i:2420332 original size:17 final size:17
Alignment explanation
Indices: 2420312--2420358 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2420302 TATGATAAAT
2420312 TAAAATATAAAAAATTA
1 TAAAATATAAAAAATTA
*
2420329 TAAAATAATAAAAATTTA
1 TAAAAT-ATAAAAAATTA
2420347 -AAAATATAAAAA
1 TAAAATATAAAAA
2420359 TGATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.25
17 11 0.39
18 10 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAATATAAAAAATTA
Found at i:2420342 original size:26 final size:25
Alignment explanation
Indices: 2420282--2420358 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
2420272 TTTAGTGCTT
* * *
2420282 AAATTAAAATATAAAAAAATTATGAT
1 AAATAAAAATAT-AAAAAATTATAAA
*
2420308 AAATTAAAATATAAAAAATTATAAA
1 AAATAAAAATATAAAAAATTATAAA
*
2420333 ATAATAAAAAT-TTAAAAA-TATAAA
1 A-AATAAAAATATAAAAAATTATAAA
2420357 AA
1 AA
2420359 TGATATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.02
24 7 0.15
25 18 0.39
26 20 0.43
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (25 bp):
AAATAAAAATATAAAAAATTATAAA
Found at i:2424107 original size:24 final size:23
Alignment explanation
Indices: 2424061--2424115 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
2424051 AATTTTTTAA
2424061 TTTTTTTCTTTTTTTTCAATTTT
1 TTTTTTTCTTTTTTTTCAATTTT
*
2424084 CTTTTTTTCTTTTTTTT-TATTTT
1 -TTTTTTTCTTTTTTTTCAATTTT
2424107 TTATTTTTC
1 TT-TTTTTC
2424116 ACCTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 2 0.07
23 11 0.38
24 16 0.55
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTCTTTTTTTTCAATTTT
Found at i:2426902 original size:22 final size:23
Alignment explanation
Indices: 2426868--2426912 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2426858 GAAAAAAAAA
2426868 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
2426890 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
2426913 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:2427307 original size:11 final size:11
Alignment explanation
Indices: 2427269--2427309 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2427259 AAATTTAGGT
2427269 AAAAAAGAAAG
1 AAAAAAGAAAG
*
2427280 AAAGAAGATGAAG
1 AAAAAAGA--AAG
2427293 AAAAAAGAAAG
1 AAAAAAGAAAG
2427304 AAAAAA
1 AAAAAA
2427310 AAATATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:2427709 original size:2 final size:2
Alignment explanation
Indices: 2427696--2427728 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2427686 TTATTTTATT
*
2427696 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2427729 TTTGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2435169 original size:27 final size:27
Alignment explanation
Indices: 2435127--2436294 Score: 1997
Period size: 27 Copynumber: 43.0 Consensus size: 27
2435117 TGGCATTTCT
**
2435127 TTTTCAAGTCCACAACTCCGTGGCATTC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
2435155 TTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
2435182 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435209 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435236 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2435264 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435291 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
2435319 TTTTAAGTCCACAACTCCGTGGCATCTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2435347 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435374 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
* *
2435402 TTTTAAGTGCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435429 ---T-AGT-CACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435451 -TTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435477 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
2435504 TTTTAAGTCCACAACTCCATGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435531 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435558 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2435586 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
2435613 TTTTAAGTCCACAACTCCATGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435640 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435667 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2435695 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435722 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
2435750 TTTTAAGTCCACAACTCCGTGGCATCTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2435778 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435805 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
* *
2435833 TTTTAAGTGCACAACTCCGTGGCATCTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2435861 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
**
2435888 TTTTAAGTCCACAACTCCGTGGCATTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435915 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435942 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435969 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2435996 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2436023 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
2436051 TTTTAAGTCCACAACTCCGTGGCATCTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
2436079 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2436106 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2436133 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
2436160 TTTTAAGACCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2436187 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2436214 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
2436241 TTTTAAGTCCATAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
2436268 TTTTAAATCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
2436295 ATTTCAAAGC
Statistics
Matches: 1092, Mismatches: 35, Indels: 27
0.95 0.03 0.02
Matches are distributed among these distances:
22 17 0.02
23 3 0.00
24 2 0.00
25 3 0.00
26 18 0.02
27 724 0.66
28 325 0.30
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:2436335 original size:32 final size:32
Alignment explanation
Indices: 2436277--2436654 Score: 632
Period size: 32 Copynumber: 11.8 Consensus size: 32
2436267 CTTTTAAATC
* *
2436277 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2436308 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2436340 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2436372 CACAAGTCGGTGGCAACACATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2436404 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2436436 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2436468 CACAAGTCGATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2436500 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2436532 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2436564 CACAAGTCGGTGGTAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2436596 CACAAATCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
2436628 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
2436655 TCACCATTTT
Statistics
Matches: 326, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
31 12 0.04
32 314 0.96
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:2437515 original size:22 final size:23
Alignment explanation
Indices: 2437481--2437525 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2437471 CGAAAAAAAA
2437481 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
2437503 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
2437526 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:2437920 original size:11 final size:11
Alignment explanation
Indices: 2437882--2437922 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2437872 AAATTTAGGT
2437882 AAAAAAGAAAG
1 AAAAAAGAAAG
*
2437893 AAAGAAGATGAAG
1 AAAAAAGA--AAG
2437906 AAAAAAGAAAG
1 AAAAAAGAAAG
2437917 AAAAAA
1 AAAAAA
2437923 AATATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:2445798 original size:2 final size:2
Alignment explanation
Indices: 2445780--2445855 Score: 62
Period size: 2 Copynumber: 38.0 Consensus size: 2
2445770 AAAACAATGT
* * * * * * * *
2445780 TA TA CA TA TA CA TA TA TA TA TA TA CA TA CA CA CA CA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2445822 TA TA TA TA TA TA TA TA TA TA TA CA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2445856 AACAAAGACA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (2 bp):
TA
Found at i:2448696 original size:14 final size:15
Alignment explanation
Indices: 2448677--2448709 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2448667 TTAATACTTT
*
2448677 TAAATATGAT-TATA
1 TAAATATAATATATA
2448691 TAAATATAATATATA
1 TAAATATAATATATA
2448706 TAAA
1 TAAA
2448710 GTAATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TAAATATAATATATA
Found at i:2453470 original size:19 final size:19
Alignment explanation
Indices: 2453446--2453513 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2453436 AATTCAACAA
2453446 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2453465 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2453480 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2453497 CTTGTATCGATACATAA
1 TTTGTATCGATACATAA
2453514 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2453485 original size:13 final size:13
Alignment explanation
Indices: 2453467--2453491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2453457 ACATAAGTTT
2453467 TGTATCGATACAA
1 TGTATCGATACAA
2453480 TGTATCGATACA
1 TGTATCGATACA
2453492 TAAGTCTTGT
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:2453489 original size:32 final size:32
Alignment explanation
Indices: 2453448--2453510 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2453438 TTCAACAATT
*
2453448 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTCTTGTATCGATACAA
2453480 TGTATCGATACATAAGTCTTGTATCGATACA
1 TGTATCGATACATAAGTCTTGTATCGATACA
2453511 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTCTTGTATCGATACAA
Found at i:2453571 original size:13 final size:13
Alignment explanation
Indices: 2453553--2453578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2453543 CATTTTTCTG
2453553 TGTATCGATACAT
1 TGTATCGATACAT
2453566 TGTATCGATACAT
1 TGTATCGATACAT
2453579 GGATCTTTGT
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:2453575 original size:33 final size:33
Alignment explanation
Indices: 2453533--2453599 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2453523 GCCAAGGAAA
***
2453533 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2453566 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2453599 T
1 T
2453600 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2455983 original size:51 final size:53
Alignment explanation
Indices: 2455914--2456255 Score: 174
Period size: 52 Copynumber: 6.5 Consensus size: 53
2455904 AGTTTATCAA
* * * * * *
2455914 TTCTCCACAATCGAGGATATTCCAACTCTGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
2455965 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * * *
2456019 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAAT
** *** * * *
2456072 CCCGTT-ATTTTCGAGGGGATACTCCAAC-CTCGGTTTTA--TCGCTAAAACACTAAT
1 TTC-TTCACAATC--GGGGATACTCCAACTC-CGATTTTATTTC-CAAAAACACCAAT
* * *
2456126 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAAT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAAT
* *
2456178 TCTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 T-T-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
2456231 TT-TTCACGATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
2456256 CTCGTTATTT
Statistics
Matches: 217, Mismatches: 48, Indels: 51
0.69 0.15 0.16
Matches are distributed among these distances:
50 4 0.02
51 32 0.15
52 81 0.37
53 37 0.17
54 39 0.18
55 21 0.10
57 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:2456098 original size:28 final size:27
Alignment explanation
Indices: 2456028--2456100 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
2456018 TTTCTTCACA
2456028 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2456055 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2456081 TTCGAGGGGATACTCCAACC
1 ATC--GGGGATACTCCAACC
2456101 TCGGTTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
26 4 0.10
27 23 0.55
28 15 0.36
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:2456275 original size:28 final size:28
Alignment explanation
Indices: 2456239--2456315 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2456229 ATTTTTCACG
* * *
2456239 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2456267 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2456295 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2456316 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2456284 original size:212 final size:212
Alignment explanation
Indices: 2455917--2456322 Score: 611
Period size: 212 Copynumber: 1.9 Consensus size: 212
2455907 TTATCAATTC
* * *
2455917 TCCACAATCGAGGATATTCCAACTCTGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCTGATTTTATTTTCAAAACACCAATTTCCTATAATCGGGGA
* *
2455982 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
2456047 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
2456112 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
2456129 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTCTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACT-CTGATTTTATTTTCAAAACACCAATT-TCCTATAATCGGG
* *
2456193 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACGATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
2456256 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
2456321 AT
193 AT
2456323 TCCCAAAATA
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 28 0.16
212 110 0.63
213 36 0.21
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCTGATTTTATTTTCAAAACACCAATTTCCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:2468862 original size:14 final size:14
Alignment explanation
Indices: 2468843--2468880 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2468833 ACATTCTTTT
2468843 AAAAAAAAAGCAAA
1 AAAAAAAAAGCAAA
*
2468857 AAAAAAAAAGGAAA
1 AAAAAAAAAGCAAA
2468871 AAAACAAAAA
1 AAAA-AAAAA
2468881 AACAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGCAAA
Found at i:2468871 original size:22 final size:22
Alignment explanation
Indices: 2468845--2468887 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2468835 ATTCTTTTAA
2468845 AAAAAAAGCAAAAAAAAAAAAGG
1 AAAAAAA-CAAAAAAAAAAAAGG
*
2468868 AAAAAAACAAAAAAACAAAA
1 AAAAAAACAAAAAAAAAAAA
2468888 CAAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAAAAAGG
Found at i:2468896 original size:22 final size:23
Alignment explanation
Indices: 2468845--2468896 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2468835 ATTCTTTTAA
*
2468845 AAAAAAAGCAAAAAAAAAAAAGG
1 AAAAAAAGCAAAAAAAAAAAAGC
*
2468868 AAAAAAA-CAAAAAAACAAAA-C
1 AAAAAAAGCAAAAAAAAAAAAGC
2468889 AAAGAAAA
1 AAA-AAAA
2468897 AGAGAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAAAAAGCAAAAAAAAAAAAGC
Found at i:2469972 original size:55 final size:55
Alignment explanation
Indices: 2469885--2470119 Score: 341
Period size: 55 Copynumber: 4.3 Consensus size: 55
2469875 GCTTTTAAGC
2469885 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
* *
2469940 CCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGT
1 CCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
*
2469995 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACGCAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
* * * * *
2470050 CCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTTACT
1 CCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGT
*
2470105 CCTCAATGAGCAGGA
1 CCTCAAAGAGCAGGA
2470120 TACACTTTAT
Statistics
Matches: 163, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
54 7 0.04
55 151 0.93
56 5 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (55 bp):
CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
Found at i:2470078 original size:110 final size:110
Alignment explanation
Indices: 2469885--2470119 Score: 391
Period size: 110 Copynumber: 2.1 Consensus size: 110
2469875 GCTTTTAAGC
2469885 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
1 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
*
2469950 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGT
66 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CACT
* *
2469995 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACGCAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
1 CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
* * *
2470060 CAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACT
66 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCACT
*
2470105 CCTCAATGAGCAGGA
1 CCTCAAAGAGCAGGA
2470120 TACACTTTAT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
110 113 0.97
111 4 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (110 bp):
CCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCACT
Found at i:2470980 original size:19 final size:19
Alignment explanation
Indices: 2470956--2471023 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2470946 AATTCAACAA
2470956 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2470975 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2470990 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2471007 CTTGTATCGATACATAA
1 TTTGTATCGATACATAA
2471024 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2470995 original size:13 final size:13
Alignment explanation
Indices: 2470977--2471001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2470967 ACATAAGTTT
2470977 TGTATCGATACAA
1 TGTATCGATACAA
2470990 TGTATCGATACA
1 TGTATCGATACA
2471002 TAAGTCTTGT
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:2470999 original size:32 final size:32
Alignment explanation
Indices: 2470958--2471020 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2470948 TTCAACAATT
*
2470958 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTCTTGTATCGATACAA
2470990 TGTATCGATACATAAGTCTTGTATCGATACA
1 TGTATCGATACATAAGTCTTGTATCGATACA
2471021 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTCTTGTATCGATACAA
Found at i:2471081 original size:13 final size:13
Alignment explanation
Indices: 2471063--2471088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2471053 CATTTTTCTG
2471063 TGTATCGATACAT
1 TGTATCGATACAT
2471076 TGTATCGATACAT
1 TGTATCGATACAT
2471089 GGATCTTTGT
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:2471085 original size:33 final size:33
Alignment explanation
Indices: 2471043--2471109 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2471033 GCCAAGGAAA
***
2471043 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2471076 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2471109 T
1 T
2471110 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2473584 original size:27 final size:28
Alignment explanation
Indices: 2473554--2473637 Score: 107
Period size: 27 Copynumber: 3.0 Consensus size: 28
2473544 TTTCTTCACA
2473554 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
2473581 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*** *
2473609 CGAGGGGATACTCCAACCCCAGTTTTATC
1 ATCGGGGATACTCCAACCCC-GTTATATC
2473638 GCTAAAACAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 24 0.49
28 19 0.39
29 6 0.12
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:2473767 original size:52 final size:51
Alignment explanation
Indices: 2473445--2473780 Score: 202
Period size: 51 Copynumber: 6.4 Consensus size: 51
2473435 ATCAATTCTC
* * * * *
2473445 CACAATCGAGGATATTCCAACTCTGATTTTATTTTCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
* *
2473495 CTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTT-TT
* * * ** * *
2473550 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACACCAA-----TT-TTT
* * ** * *
2473608 C-CGA--GGGGATACTCCAAC-CCCAGTTTTATCGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAACACCAATTTTT
* * * * *
2473656 CACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTCTC
1 CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTTT
** *
2473707 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTTT
*
2473760 CACAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
2473781 CTCGTTATTT
Statistics
Matches: 213, Mismatches: 48, Indels: 48
0.69 0.16 0.16
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 1 0.00
51 62 0.29
52 48 0.23
53 33 0.15
54 31 0.15
55 17 0.08
56 1 0.00
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
Found at i:2473882 original size:79 final size:79
Alignment explanation
Indices: 2473719--2473968 Score: 204
Period size: 79 Copynumber: 3.2 Consensus size: 79
2473709 TTAATCGGGG
* * * * * * * * *
2473719 ATACTCCAACTCCGATTTTATTTCCAAAAAT-ACCAATTTTTCACAATCGAGGATACTCCAACCT
1 ATACTCCAACCCCGACTTTA-TTCC-CAAATCATCGATTTCTCACAACCGGGGATACTCCAACCC
*
2473783 CGTTATTTCATCG--GGG
64 CGTTATTT--TCGAAGGA
* * * **
2473799 ATACTCCAACCCCGGCTTTATTCCCAAAAT-ATTGATTTCTCATAATTGGGGATACTCCAACCCC
1 ATACTCCAACCCCGACTTTATTCCC-AAATCATCGATTTCTCACAACCGGGGATACTCCAACCCC
2473863 GTTATTTTCGAAGGA
65 GTTATTTTCGAAGGA
* * * ** * *
2473878 ATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTCTCACAACCGGGGATACTCCAGCCCCG
1 ATACTCCAACCCCGACTTTATTCCCAAATCATCGATTTCTCACAACCGGGGATACTCCAACCCCG
2473943 TTATTTTC-AAGGGA
66 TTATTTTCGAA-GGA
*
2473957 ACACTCCAACCC
1 ATACTCCAACCC
2473969 TATTATTATC
Statistics
Matches: 138, Mismatches: 27, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
77 3 0.02
78 5 0.04
79 113 0.82
80 17 0.12
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (79 bp):
ATACTCCAACCCCGACTTTATTCCCAAATCATCGATTTCTCACAACCGGGGATACTCCAACCCCG
TTATTTTCGAAGGA
Found at i:2478394 original size:22 final size:20
Alignment explanation
Indices: 2478347--2478394 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
2478337 TTTACTTTGC
2478347 TGTTG-CTTTTTCATGTGTT
1 TGTTGTCTTTTTCATGTGTT
*
2478366 TGCTTGTCTTTTCTCATTTGCTT
1 TG-TTGTCTTTT-TCATGTG-TT
2478389 TGTTGT
1 TGTTGT
2478395 TGGACACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 5 0.21
22 10 0.42
23 4 0.17
ACGTcount: A:0.04, C:0.15, G:0.19, T:0.62
Consensus pattern (20 bp):
TGTTGTCTTTTTCATGTGTT
Found at i:2478497 original size:20 final size:18
Alignment explanation
Indices: 2478474--2478592 Score: 115
Period size: 17 Copynumber: 6.4 Consensus size: 18
2478464 ATCTACGTTA
2478474 CATGCTTTACATCATTATTT
1 CATGCTTT-CATCA-TATTT
2478494 CATGCTTTCA-CA-ACTTT
1 CATGCTTTCATCATA-TTT
2478511 CATGCTTTGCATCATCATTT
1 CATGCTTT-CATCAT-ATTT
2478531 CATGCTTTCA-CA-ACTTT
1 CATGCTTTCATCATA-TTT
2478548 CATGCTTTGCATCATCATTT
1 CATGCTTT-CATCAT-ATTT
2478568 CATGCTTTCA-CA-ACTTT
1 CATGCTTTCATCATA-TTT
2478585 CATGCTTT
1 CATGCTTT
2478593 GCATTTTCAT
Statistics
Matches: 88, Mismatches: 0, Indels: 25
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.03
17 33 0.38
18 10 0.11
19 10 0.11
20 30 0.34
21 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.45
Consensus pattern (18 bp):
CATGCTTTCATCATATTT
Found at i:2478513 original size:17 final size:17
Alignment explanation
Indices: 2478491--2478624 Score: 133
Period size: 17 Copynumber: 7.4 Consensus size: 17
2478481 TACATCATTA
2478491 TTTCATGCTTTCACAAC
1 TTTCATGCTTTCACAAC
*
2478508 TTTCATGCTTTGCATCATC
1 TTTCATGCTTT-CA-CAAC
2478527 ATTTCATGCTTTCACAAC
1 -TTTCATGCTTTCACAAC
*
2478545 TTTCATGCTTTGCATCATC
1 TTTCATGCTTT-CA-CAAC
2478564 ATTTCATGCTTTCACAAC
1 -TTTCATGCTTTCACAAC
***
2478582 TTTCATGCTTTGCATTTTC
1 TTTCATGCTTT-CA-CAAC
*
2478601 ATTTCATGTTTTCACAAC
1 -TTTCATGCTTTCACAAC
2478619 TTTCAT
1 TTTCAT
2478625 TCATTCGTCA
Statistics
Matches: 97, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
17 39 0.40
18 13 0.13
19 13 0.13
20 32 0.33
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.46
Consensus pattern (17 bp):
TTTCATGCTTTCACAAC
Found at i:2478517 original size:37 final size:37
Alignment explanation
Indices: 2478447--2478624 Score: 257
Period size: 37 Copynumber: 4.8 Consensus size: 37
2478437 TTGTTTGCTG
* * * * *
2478447 CATCATTTCATACTTGCATCTACGTTACATGCTTTACAT
1 CATCATTTCATGCTTTCA-CAAC-TTTCATGCTTTGCAT
*
2478486 CATTATTTCATGCTTTCACAACTTTCATGCTTTGCAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
2478523 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
2478560 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
** *
2478597 TTTCATTTCATGTTTTCACAACTTTCAT
1 CATCATTTCATGCTTTCACAACTTTCAT
2478625 TCATTCGTCA
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
37 111 0.86
38 3 0.02
39 15 0.12
ACGTcount: A:0.22, C:0.25, G:0.07, T:0.45
Consensus pattern (37 bp):
CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
Found at i:2478607 original size:20 final size:20
Alignment explanation
Indices: 2478447--2478608 Score: 148
Period size: 20 Copynumber: 8.6 Consensus size: 20
2478437 TTGTTTGCTG
*
2478447 CATCATTTCATAC-TTGCAT
1 CATCATTTCATGCTTTGCAT
* * *
2478466 C-TACGTTACATGCTTTACAT
1 CAT-CATTTCATGCTTTGCAT
*
2478486 CATTATTTCATGCTTT-CA-
1 CATCATTTCATGCTTTGCAT
*
2478504 CAAC-TTTCATGCTTTGCAT
1 CATCATTTCATGCTTTGCAT
2478523 CATCATTTCATGCTTT-CA-
1 CATCATTTCATGCTTTGCAT
*
2478541 CAAC-TTTCATGCTTTGCAT
1 CATCATTTCATGCTTTGCAT
2478560 CATCATTTCATGCTTT-CA-
1 CATCATTTCATGCTTTGCAT
*
2478578 CAAC-TTTCATGCTTTGCAT
1 CATCATTTCATGCTTTGCAT
**
2478597 TTTCATTTCATG
1 CATCATTTCATG
2478609 TTTTCACAAC
Statistics
Matches: 115, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
17 33 0.29
18 15 0.13
19 21 0.18
20 45 0.39
21 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.44
Consensus pattern (20 bp):
CATCATTTCATGCTTTGCAT
Found at i:2479355 original size:43 final size:43
Alignment explanation
Indices: 2479301--2479483 Score: 146
Period size: 43 Copynumber: 4.3 Consensus size: 43
2479291 AAACAAAAGA
*
2479301 TAAGAATGGTTGACCGAGGACAAAGTCGACAGGTCACTAAGGG
1 TAAGAAAGGTTGACCGAGGACAAAGTCGACAGGTCACTAAGGG
* *
2479344 TAAGAAAGGTTGACCGGGGACAAAGCCGAC--G-CA-TCAAGGGG
1 TAAGAAAGGTTGACCGAGGACAAAGTCGACAGGTCACT-AA-GGG
* * * * * *
2479385 TAAG-AA-GTTTACTGAGGACATAGTCGATAGGTAAACAAAGGG
1 TAAGAAAGGTTGACCGAGGACAAAGTCGACAGGT-CACTAAGGG
* * * * * *
2479427 TTATAATGGTTGACCGAGGACAAAG-CTGACAAGTTACCAAGGG
1 TAAGAAAGGTTGACCGAGGACAAAGTC-GACAGGTCACTAAGGG
2479470 TAAGAAAGGTTGAC
1 TAAGAAAGGTTGAC
2479484 TGAGATTAAA
Statistics
Matches: 106, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
39 17 0.16
40 6 0.06
41 9 0.08
42 5 0.05
43 50 0.47
44 19 0.18
ACGTcount: A:0.37, C:0.15, G:0.31, T:0.17
Consensus pattern (43 bp):
TAAGAAAGGTTGACCGAGGACAAAGTCGACAGGTCACTAAGGG
Found at i:2479819 original size:84 final size:83
Alignment explanation
Indices: 2479729--2480777 Score: 717
Period size: 84 Copynumber: 12.5 Consensus size: 83
2479719 GAGACGAGGT
* * * *
2479729 AGTCTCCAAGGTCAAAGCCGATAAGCAGACTTTAGATGAGGTAGTCTCCAAGGTCAAAGTCGATA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAG-CGACA
2479794 GGCAGACTGAAGGTAGGAA
65 GGCAGACTGAAGGTAGGAA
* * * * * *
2479813 AATCTCCAGGGTTAAAGCCGACAGGTAGACTTTAGAT-GGGACAGTCTCCAAGGTCAAAGTCGAC
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGG-CAGTCTCCAAGGTCAAAG-CGAC
*
2479877 AAGCAGACTGAAGGTAGGAA
64 AGGCAGACTGAAGGTAGGAA
* * * * *
2479897 AATCTCCAAAGTCAAAGCTGATAGGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAG-CGACA
* *
2479962 GGTAGACT-AAGGGTAAGAA
65 GGCAGACTGAA-GGTAGGAA
* * * * **
2479981 AGTCTCCAGGGTCAAAGCCGACAGGCAAACTTTTGATAAGGCAGTCT-TTAGGTTCAAAGCTGAC
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGG-TCAAAGC-GAC
* *
2480045 AGGCAAACTGAGGGTAGGAA
64 AGGCAGACTGAAGGTAGGAA
* * * * * ** * * * *
2480065 AGTCTCTAGGGTCAAAGCTGATAAGCAGAC-TTAGGGT-AGAAAAGTCTCTAGGGTTAAAACCGA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTA-GATAAG-GCAGTCTCCAAGG-TCAAAGCGA
* * * ** * *
2480128 CAAGTAAACTTTAGATAAGG-C
63 CAGGCAGACTGAAGGT-AGGAA
* * ** *
2480149 AGTCTCCAGGGTCAAAGCCGACAAGCAGAC-TGAGAGT-AGAAAAATCTCCAAGGTCAAAGCTGA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGA-TAAG-GCAGTCTCCAAGGTCAAAGC-GA
* ** * * *
2480212 CACGCAGA-TTTAGATAATG-T
63 CAGGCAGACTGAAGGT-AGGAA
* * ** * * * *
2480232 AGTCTCTATGGTCAAAGTTGACAGGCAGACTTTAGATAAGACAGTTTCCAGGGTCAAAGCTGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGC-GACA
* * ** * *
2480297 AGCATACTTTAGATAAGG-T
65 GGCAGACTGAAGGT-AGGAA
* * * *
2480316 AGTCTCCAAGGTCAAAGCTGACAGGCATACTTTAGATAAGGTAGTCTCCAAGGTCAAAGCTGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGC-GACA
* *
2480381 AGCAGACTGAGGGTAGGAA
65 GGCAGACTGAAGGTAGGAA
* * * * * *
2480400 AGTCTCCAAGATCAAAGCCGACAAGCAGACTTTAAATAAGGCAGTCTCTAGGGTCAAAGTTGGCA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAG-CGACA
2480465 GGCAGACTGAAGGTAGGAA
65 GGCAGACTGAAGGTAGGAA
* * * *
2480484 AGTCTCCAAGATCAAAGCCGAC-AGACAGACTTTAGATAAGGCAGTTTCCAAGGTTAAAGCCA-A
1 AGTCTCCAAGGTCAAAGCCGACAAG-CAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCGACA
* **
2480547 TGGACAGACTGAGGGTAAAAA
65 -GG-CAGACTGAAGGTAGGAA
* * * * * * *
2480568 AGTCTCTAAGGTCAAAGCCAACACGGAGATTTTAGATAAGGTAGTCTCCAAGGTCAAAGTTGACA
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAG-CGACA
** *
2480633 GGCAGACTCTAGATA--AA
65 GGCAGACTGAAGGTAGGAA
* * * ** * *
2480650 GTAGTCTCCAAAGTCAAAGTCGAC-AGATAGACTTTAGATAAGGCAGTCTTTAATGTCCAAACCG
1 --AGTCTCCAAGGTCAAAGCCGACAAG-CAGACTTTAGATAAGGCAGTCTCCAAGGT-CAAAGCG
* * * *
2480714 ACAAGCAAACTGAGGGTAGAAA
62 ACAGGCAGACTGAAGGTAGGAA
* * * * *
2480736 ACTCTCTAGGGTCAAAACCGACAAGCAAACTTTAGATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGC
2480778 CAAATATGGT
Statistics
Matches: 774, Mismatches: 161, Indels: 60
0.78 0.16 0.06
Matches are distributed among these distances:
82 3 0.00
83 87 0.11
84 656 0.85
85 25 0.03
86 3 0.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (83 bp):
AGTCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATAAGGCAGTCTCCAAGGTCAAAGCGACAG
GCAGACTGAAGGTAGGAA
Found at i:2480646 original size:42 final size:42
Alignment explanation
Indices: 2479729--2480698 Score: 603
Period size: 42 Copynumber: 23.1 Consensus size: 42
2479719 GAGACGAGGT
* * * *
2479729 AGTCTCCAAGGTCAAAGCCGATAAGCAGACTTTAGATGAGGT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * ** *
2479771 AGTCTCCAAGGTCAAAGTCGATAGGCAGACTGAAGGT-AGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGG-A
* * * * *
2479813 AATCTCCAGGGTTAAAGCCGACAGGTAGACTTTAGAT-GGGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * ** *
2479854 CAGTCTCCAAGGTCAAAGTCGACAAGCAGACTGAAGGT-AGGAA
1 -AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGG-A
* * * * *
2479897 AATCTCCAAAGTCAAAGCTGATAGGCAGACTTTAGATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * * *
2479939 AGTCTCCAAGGTCAAAGCCGACAGGTAGAC-TAAGGGTAAGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTA-GATAAGGA
* * * *
2479981 AGTCTCCAGGGTCAAAGCCGACAGGCAAACTTTTGATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
** * * * *
2480023 AGTCT-TTAGGTTCAAAGCTGACAGGCAAAC-TGAGGGT-AGGAA
1 AGTCTCCAAGG-TCAAAGCCGACAGGCAGACTTTA-GATAAGG-A
* * * * * * *
2480065 AGTCTCTAGGGTCAAAGCTGATAAGCAGAC-TTAGGGT-AGAAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTA-GATAAG-GA
* * * * * * * *
2480107 AGTCTCTAGGGTTAAAACCGACAAGTAAACTTTAGATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * * *
2480149 AGTCTCCAGGGTCAAAGCCGACAAGCAGAC-TGAGAGT-AGAAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGA-TAAG-GA
* * * * *
2480191 AATCTCCAAGGTCAAAGCTGACACGCAGA-TTTAGATAATGT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * **
2480232 AGTCTCTATGGTCAAAGTTGACAGGCAGACTTTAGATAA-GA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * * * * *
2480273 CAGTTTCCAGGGTCAAAGCTGACAAGCATACTTTAGATAAGGT
1 -AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * *
2480316 AGTCTCCAAGGTCAAAGCTGACAGGCATACTTTAGATAAGGT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * * *
2480358 AGTCTCCAAGGTCAAAGCTGACAAGCAGAC-TGAGGGT-AGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTA-GATAAGG-A
* * * *
2480400 AGTCTCCAAGATCAAAGCCGACAAGCAGACTTTAAATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * ** * ** *
2480442 AGTCTCTAGGGTCAAAGTTGGCAGGCAGACTGAAGGT-AGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGG-A
* * *
2480484 AGTCTCCAAGATCAAAGCCGACAGACAGACTTTAGATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * * * **
2480526 AGTTTCCAAGGTTAAAGCC-A-ATGGACAGAC-TGAGGGTAAAAA
1 AGTCTCCAAGGTCAAAGCCGACA-GG-CAGACTTTA-GATAAGGA
* * * *
2480568 AGTCTCTAAGGTCAAAGCCAACACGG-AGATTTTAGATAAGGT
1 AGTCTCCAAGGTCAAAGCCGACA-GGCAGACTTTAGATAAGGA
** * * *
2480610 AGTCTCCAAGGTCAAAGTTGACAGGCAGACTCTAGATAAAGT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
* * ** *
2480652 AGTCTCCAAAGTCAAAGTCGACAGATAGACTTTAGATAAGGC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
2480694 AGTCT
1 AGTCT
2480699 TTAATGTCCA
Statistics
Matches: 719, Mismatches: 176, Indels: 66
0.75 0.18 0.07
Matches are distributed among these distances:
40 1 0.00
41 58 0.08
42 632 0.88
43 25 0.03
44 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (42 bp):
AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTTAGATAAGGA
Found at i:2480883 original size:44 final size:43
Alignment explanation
Indices: 2480835--2481033 Score: 123
Period size: 44 Copynumber: 4.5 Consensus size: 43
2480825 ACGCAAATCG
**
2480835 TTTGACTAGGGTGGTAACCATACATCAAACAAGAAGGAGGCAG-A
1 TTTGACTAGGGTGGTAACCATACATCAAACAA-AAGGA-AAAGAA
* ** * *
2480879 TTTGACTAGGGTAGTAACTTTACATCTAATCAAAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACATC-AAACAAAAGGAAAAGAA
* * ** ** * * * **
2480923 TCTGACCAGGGTGGTAATGATATGTCAGATAAGGAGGATGCAG-A
1 TTTGACTAGGGTGGTAACCATACATCAAACAA-AAGGA-AAAGAA
* * ** *
2480967 CTTGACTAGGGTGGTGACCATATGTCAAATCAAAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACATCAAA-CAAAAGGAAAAGAA
2481011 TTTGACTAGGGTGGTAACCATAC
1 TTTGACTAGGGTGGTAACCATAC
2481034 GTCAGACAGG
Statistics
Matches: 112, Mismatches: 37, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
43 7 0.06
44 96 0.86
45 9 0.08
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (43 bp):
TTTGACTAGGGTGGTAACCATACATCAAACAAAAGGAAAAGAA
Done.