Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 62 of 182
Found at i:20112455 original size:20 final size:21
Alignment explanation
Indices: 20112423--20112461 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
20112413 TTTTACTTAT
20112423 GGTTTAGGATTTAA-GTTTAG
1 GGTTTAGGATTTAATGTTTAG
20112443 GGTTTAGTG-TTTAATGTTT
1 GGTTTAG-GATTTAATGTTT
20112462 TATATTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (21 bp):
GGTTTAGGATTTAATGTTTAG
Found at i:20123871 original size:15 final size:17
Alignment explanation
Indices: 20123842--20123877 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
20123832 TCTGTTGAAA
20123842 ATTATAAAATATAAAAT
1 ATTATAAAATATAAAAT
20123859 ATTA-AAAAT-TAAAAT
1 ATTATAAAATATAAAAT
20123874 -TTAT
1 ATTAT
20123878 TTTCGACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.17
15 6 0.33
16 5 0.28
17 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTATAAAATATAAAAT
Found at i:20136053 original size:4 final size:4
Alignment explanation
Indices: 20136032--20136065 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
20136022 TATTTTGGTT
*
20136032 TTTA TTTTA TTTA ATTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
20136066 AAAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:20136078 original size:4 final size:4
Alignment explanation
Indices: 20136067--20136113 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
20136057 TTTATTTATA
20136067 AAAT -AAT AAAT AAAT AAAT AAAT -AAT AAA- ATAAT -AAT AAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
20136111 AAA
1 AAA
20136114 ATTGAGTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
3 13 0.35
4 24 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:20161901 original size:19 final size:19
Alignment explanation
Indices: 20161877--20161914 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20161867 TACTAGCTGA
20161877 GATATAAAGGAACAGTGTG
1 GATATAAAGGAACAGTGTG
20161896 GATATAAAGGAACAGTGTG
1 GATATAAAGGAACAGTGTG
20161915 ACCAAGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.32, T:0.21
Consensus pattern (19 bp):
GATATAAAGGAACAGTGTG
Found at i:20171555 original size:13 final size:13
Alignment explanation
Indices: 20171537--20171574 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
20171527 TATTTCGAAC
20171537 ATAATAAATAATT
1 ATAATAAATAATT
*
20171550 ATAAT-ATTAAATT
1 ATAATAAAT-AATT
20171563 ATAATAAATAAT
1 ATAATAAATAAT
20171575 AAAAGGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAAATAATT
Found at i:20175688 original size:31 final size:31
Alignment explanation
Indices: 20175644--20175704 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
20175634 TTCAATATTT
*
20175644 TCACTAACGTTTTAGATCATTTCTATTTTGA
1 TCACTAACATTTTAGATCATTTCTATTTTGA
* **
20175675 TCACTCACATTTTAGATTGTTTCTATTTTG
1 TCACTAACATTTTAGATCATTTCTATTTTG
20175705 GTCAATTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (31 bp):
TCACTAACATTTTAGATCATTTCTATTTTGA
Found at i:20179458 original size:20 final size:20
Alignment explanation
Indices: 20179433--20179472 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20179423 GCATGGTTGT
20179433 TTGAGTAATTAATTATTTAA
1 TTGAGTAATTAATTATTTAA
** *
20179453 TTGAGTGCTTATTTATTTAA
1 TTGAGTAATTAATTATTTAA
20179473 AATTGGGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (20 bp):
TTGAGTAATTAATTATTTAA
Found at i:20181252 original size:58 final size:58
Alignment explanation
Indices: 20181185--20181312 Score: 166
Period size: 58 Copynumber: 2.2 Consensus size: 58
20181175 AAAACCCTTT
** * * *
20181185 AAACACAAACTTAATAACTCTAAGCACAATTTAATAAAAACTCAATTATTTAATTCAA
1 AAACACAAACCCAATAACTCTAAACACAATTTAATAAAAACCCAATTATTTAATCCAA
* * *
20181243 AAACCCAAACCCAATAACTTTAAACCCAATTTAATAAAAACCCAATTATTTAATCCAA
1 AAACACAAACCCAATAACTCTAAACACAATTTAATAAAAACCCAATTATTTAATCCAA
*
20181301 AAATCAAAAACC
1 AAA-CACAAACC
20181313 TTTTAAACCC
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
58 53 0.90
59 6 0.10
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.25
Consensus pattern (58 bp):
AAACACAAACCCAATAACTCTAAACACAATTTAATAAAAACCCAATTATTTAATCCAA
Found at i:20181289 original size:74 final size:74
Alignment explanation
Indices: 20181132--20181357 Score: 186
Period size: 74 Copynumber: 3.1 Consensus size: 74
20181122 CAATAACTCT
* * *
20181132 AAACCCAATTTAATAAAAACCCAATTATTTAATTCAAAAACCCAAAACC-----CTTTAAACACA
1 AAACCCAATTTAATAAAAACTCAATTATTTAATTCAAAAACCCAAACCCAATAACTTTAAAC-CC
*
20181192 AACTTAATAA
65 AATTTAATAA
* *
20181202 CTCTAAGCACAATTTAATAAAAACTCAATTATTTAATTCAAAAACCCAAACCCAATAACTTTAAA
1 ----AAACCCAATTTAATAAAAACTCAATTATTTAATTCAAAAACCCAAACCCAATAACTTTAAA
20181267 CCCAATTTAATAA
62 CCCAATTTAATAA
** *
20181280 AAACCCAATTATTTAATCCAAAAA-TCAAAAACCTT--TT---AAACCCAAACCCAATAACTTTA
1 AAACCC-A--ATTTAAT--AAAAACTCAATTA-TTTAATTCAAAAACCCAAACCCAATAACTTTA
*
20181339 AACCCAATTTAATCA
60 AACCCAATTTAATAA
20181354 AAAC
1 AAAC
20181358 TCAAATATGT
Statistics
Matches: 129, Mismatches: 12, Indels: 22
0.79 0.07 0.13
Matches are distributed among these distances:
74 89 0.69
75 1 0.01
77 9 0.07
78 15 0.12
79 15 0.12
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.26
Consensus pattern (74 bp):
AAACCCAATTTAATAAAAACTCAATTATTTAATTCAAAAACCCAAACCCAATAACTTTAAACCCA
ATTTAATAA
Found at i:20181347 original size:132 final size:132
Alignment explanation
Indices: 20181111--20181361 Score: 385
Period size: 132 Copynumber: 1.9 Consensus size: 132
20181101 TTTAAAAACC
* * *
20181111 AAACCTAAACCCAATAACTCTAAACCCAATTTAATAAAAACCCAATTATTTAATTCAAAAACCCA
1 AAACCCAAACCCAATAACTCTAAACCCAATTTAATAAAAACCCAATTATTTAATCCAAAAACCAA
** *
20181176 AAACCCTTTAAACACAAACTTAATAACTCTAAGCACAATTTAATAAAAACTCAATTATTTAATTC
66 AAACCCTTTAAACACAAACCCAATAACTCTAAACACAATTTAATAAAAACTCAATTATTTAATTC
20181241 AA
131 AA
* *
20181243 AAACCCAAACCCAATAACTTTAAACCCAATTTAATAAAAACCCAATTATTTAATCCAAAAATCAA
1 AAACCCAAACCCAATAACTCTAAACCCAATTTAATAAAAACCCAATTATTTAATCCAAAAACCAA
* * * * *
20181308 AAACCTTTTAAACCCAAACCCAATAACTTTAAACCCAATTTAATCAAAACTCAA
66 AAACCCTTTAAACACAAACCCAATAACTCTAAACACAATTTAATAAAAACTCAA
20181362 ATATGTTATT
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 106 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (132 bp):
AAACCCAAACCCAATAACTCTAAACCCAATTTAATAAAAACCCAATTATTTAATCCAAAAACCAA
AAACCCTTTAAACACAAACCCAATAACTCTAAACACAATTTAATAAAAACTCAATTATTTAATTC
AA
Found at i:20184521 original size:153 final size:153
Alignment explanation
Indices: 20184240--20184547 Score: 508
Period size: 153 Copynumber: 2.0 Consensus size: 153
20184230 TATGCAACCA
* * *
20184240 AGAGGCATGAGGATCATGATGAGCCTAATGTCATAGCGGGTACTTTTTCTATTAACTTTATCCTT
1 AGAGGCATGAGAATCATGATGAGCCTAATGTCATAGCGGGTACTTTTTCTATCAACTTTATCCAT
* *
20184305 TACTTTGCTTTACTTGATAATGGTTCGACGCATTTTTATGTGACGAGTATGGTATCTTCAGGTCT
66 TACTTTGCTTTACTTGATAATGGTTCGACGCATTTCTATGTGACGAGTACGGTATCTTCAGGTCT
* *
20184370 TAAAATTGTGGTCGAACATGTTG
131 TAAAATTGTGGTCGAAAAAGTTG
20184393 AGAGGCATGAGAATCATGATGAGCCTAATGTCATAGCGGGTACTTTTTCTATCAACTTTATCCAT
1 AGAGGCATGAGAATCATGATGAGCCTAATGTCATAGCGGGTACTTTTTCTATCAACTTTATCCAT
* ** * *
20184458 TACTTTGTTTTACTTGATAATGGTTCGACGCATTTCTATGTGGTGAGTGCGGTATCTTGAGGTCT
66 TACTTTGCTTTACTTGATAATGGTTCGACGCATTTCTATGTGACGAGTACGGTATCTTCAGGTCT
20184523 TAAAATTGTGGTCGAAAAAGTTG
131 TAAAATTGTGGTCGAAAAAGTTG
20184546 AG
1 AG
20184548 TCTGCAGTTA
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 143 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (153 bp):
AGAGGCATGAGAATCATGATGAGCCTAATGTCATAGCGGGTACTTTTTCTATCAACTTTATCCAT
TACTTTGCTTTACTTGATAATGGTTCGACGCATTTCTATGTGACGAGTACGGTATCTTCAGGTCT
TAAAATTGTGGTCGAAAAAGTTG
Found at i:20188539 original size:22 final size:21
Alignment explanation
Indices: 20188494--20188544 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
20188484 TATTCAATCC
* *
20188494 AAACCCAAACCCAAACCATTT
1 AAACCCAAACCCAAAACATCT
20188515 AAAACCCAAACCCAATAAC-TCT
1 -AAACCCAAACCCAA-AACATCT
20188537 AAACCCAA
1 AAACCCAA
20188545 TTTAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (21 bp):
AAACCCAAACCCAAAACATCT
Found at i:20188587 original size:27 final size:27
Alignment explanation
Indices: 20188552--20188610 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
20188542 CAATTTAATA
*
20188552 AAAACCCAATTA-TTAATCCAAAAACTT
1 AAAACCCAATTATTTAATCC-AAAACTC
20188579 AAAACCCAATTATTTAATCCAAAACTC
1 AAAACCCAATTATTTAATCCAAAACTC
20188606 AAAAC
1 AAAAC
20188611 TCTTTAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAACCCAATTATTTAATCCAAAACTC
Found at i:20188730 original size:94 final size:90
Alignment explanation
Indices: 20188522--20188713 Score: 228
Period size: 94 Copynumber: 2.1 Consensus size: 90
20188512 TTTAAAACCC
* * *
20188522 AAACCCAATAACTCTAAACCCAATTTAATAAAAACCCAATTATTAATCCAAAAACTTAAAACCCA
1 AAACCCAATAAATCAAAACCCAATTTAATAAAAACCCAATTATTAATCCAAAAACTCAAAA-CC-
* *
20188587 ATTATTTAATCCAAAACTCAAAACTCTTT
64 A-TATTTAAACCAAAACCCAAAACTC-TT
* * *
20188616 AAACCCAATAACTCTAAACCCAATTTAATAAAAACCCAATTATTTAATTCAAAAACTCAAAA-C-
1 AAACCCAATAAATCAAAACCCAATTTAATAAAAACCCAATTA-TTAATCCAAAAACTCAAAACCA
*
20188679 TATTTAAACCCAAACCCAATAACTC-T
65 TATTTAAACCAAAACCCAA-AACTCTT
20188705 AAACCCAAT
1 AAACCCAAT
20188714 TATTTAATCC
Statistics
Matches: 91, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
89 10 0.11
90 16 0.18
91 5 0.05
93 1 0.01
94 42 0.46
95 17 0.19
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (90 bp):
AAACCCAATAAATCAAAACCCAATTTAATAAAAACCCAATTATTAATCCAAAAACTCAAAACCAT
ATTTAAACCAAAACCCAAAACTCTT
Found at i:20195651 original size:19 final size:19
Alignment explanation
Indices: 20195627--20195666 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
20195617 ATTAATTTTG
20195627 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
20195646 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
20195665 AT
1 AT
20195667 ATTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:20196152 original size:27 final size:26
Alignment explanation
Indices: 20196091--20196162 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 26
20196081 ATTTTAATAG
*
20196091 ATTTAATATTTA-ATT-TA-AT-TTA
1 ATTTAATATTTATCTTGTAGATATTA
*
20196113 ATTTAATACTTATCTTGTAGATATTA
1 ATTTAATATTTATCTTGTAGATATTA
20196139 TATTTAATATTTATCTTGTAGATA
1 -ATTTAATATTTATCTTGTAGATA
20196163 AATATTCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 11 0.26
23 2 0.05
24 2 0.05
25 2 0.05
26 3 0.07
27 22 0.52
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (26 bp):
ATTTAATATTTATCTTGTAGATATTA
Found at i:20204745 original size:101 final size:101
Alignment explanation
Indices: 20204569--20204894 Score: 483
Period size: 101 Copynumber: 3.2 Consensus size: 101
20204559 GACCTGTTCC
*
20204569 GTCTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTTCT
1 GTCTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACATGGTCCACCGTTGCGACTTAGACCTTTCT
*
20204634 CTTTTATCTTTTTGCGGTATTGAATCCGTCGTTACG
66 CTTTTATCTTTTTACGGTATTGAATCCGTCGTTACG
* * *
20204670 GTCTTAGATCTTTTCCGTCTTGTCTTTTGAGGTACATGGTCCACCGTTGCGACTTAGACCTTTCT
1 GTCTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACATGGTCCACCGTTGCGACTTAGACCTTTCT
* * * * *
20204735 TTTTTGTCTTTTTATGGTATTGAATTCGTCGTTGCG
66 CTTTTATCTTTTTACGGTATTGAATCCGTCGTTACG
* * *
20204771 GTCTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACACGGTCTACCGTTACGACTTAGACCTTT-T
1 GTCTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACATGGTCCACCGTTGCGACTTAGACCTTTCT
* * *
20204835 CCTTTTATCTTTTTACGGTACTGGATCCGCCGTTACG
66 -CTTTTATCTTTTTACGGTATTGAATCCGTCGTTACG
*
20204872 GTCTTAGATCTTTCCTGTCGTGT
1 GTCTTAGATCTTTCCCGTCGTGT
20204895 TTTCATGATA
Statistics
Matches: 199, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
100 1 0.01
101 198 0.99
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (101 bp):
GTCTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACATGGTCCACCGTTGCGACTTAGACCTTTCT
CTTTTATCTTTTTACGGTATTGAATCCGTCGTTACG
Found at i:20204768 original size:50 final size:50
Alignment explanation
Indices: 20204608--20204784 Score: 137
Period size: 51 Copynumber: 3.5 Consensus size: 50
20204598 AGGTACATGG
* * *
20204608 TCCGCCGTTGC-GACTTAGACCTTTCTCTTTTATCTTTTTGCGGTATTGAA
1 TCCGTCGTTGCGGACTTAGACCTTTCTCTTTTGTCTTTTT-AGGTATTGAA
* * * * * * *
20204658 TCCGTCGTTACGGTCTTAGATCTTT-TCCGTCTTGTCTTTTGAGGTACATG-G
1 TCCGTCGTTGCGGACTTAGACCTTTCT-C-TTTTGTCTTTTTAGGTA-TTGAA
** *
20204709 TCCACCGTTGC-GACTTAGACCTTTCTTTTTTGTCTTTTTATGGTATTGAA
1 TCCGTCGTTGCGGACTTAGACCTTTCTCTTTTGTCTTTTTA-GGTATTGAA
* * *
20204759 TTCGTCGTTGCGGTCTTAGATCTTTC
1 TCCGTCGTTGCGGACTTAGACCTTTC
20204785 CCGTCGTGTC
Statistics
Matches: 94, Mismatches: 25, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
49 13 0.14
50 33 0.35
51 37 0.39
52 11 0.12
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (50 bp):
TCCGTCGTTGCGGACTTAGACCTTTCTCTTTTGTCTTTTTAGGTATTGAA
Found at i:20204868 original size:50 final size:49
Alignment explanation
Indices: 20204571--20204946 Score: 170
Period size: 50 Copynumber: 7.5 Consensus size: 49
20204561 CCTGTTCCGT
* ** * * *
20204571 CTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACATGG-TCCGCCGTTGCGA
1 CTTAGATCTTTTCC-TTTTGTCTTTTTAGGTAC-TGGATCCGCCGTTACGA
* * * * * * *
20204621 CTTAGA-CCTTTCTCTTTTATCTTTTTGCGGTATTGAATCCGTCGTTACGGT
1 CTTAGATCTTTTC-CTTTTGTCTTTTT-AGGTACTGGATCCGCCGTTAC-GA
* * * *
20204672 CTTAGATCTTTTCCGTCTTGTCTTTTGAGGTACATGG-TCCACCGTTGCGA
1 CTTAGATCTTTTCC-TTTTGTCTTTTTAGGTAC-TGGATCCGCCGTTACGA
* * * * * * * *
20204722 CTTAGA-CCTTTCTTTTTTGTCTTTTTATGGTATTGAATTCGTCGTTGCGGT
1 CTTAGATCTTTTC-CTTTTGTCTTTTTA-GGTACTGGATCCGCCGTTAC-GA
* ** * * * **
20204773 CTTAGATCTTTCCCGTCGTGTCTTCTGAGGTACACGG-TCTACCGTTACGA
1 CTTAGATCTTTTCC-TTTTGTCTTTTTAGGTAC-TGGATCCGCCGTTACGA
* * *
20204823 CTTAGACCTTTTCCTTTTATCTTTTTACGGTACTGGATCCGCCGTTACGGT
1 CTTAGATCTTTTCCTTTTGTCTTTTTA-GGTACTGGATCCGCCGTTAC-GA
* * * * * * *
20204874 CTTAGATC-TTTCCTGTCGTGTTTTCATGATACTGGATCCGCCGTCACGG
1 CTTAGATCTTTTCCTTTTGTCTTTTTA-GGTACTGGATCCGCCGTTACGA
* *
20204923 CTTAGATCTTTCCCTTGTGTCTTT
1 CTTAGATCTTTTCCTTTTGTCTTT
20204947 GCGTGGTATT
Statistics
Matches: 232, Mismatches: 76, Indels: 36
0.67 0.22 0.10
Matches are distributed among these distances:
49 50 0.22
50 107 0.46
51 45 0.19
52 30 0.13
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (49 bp):
CTTAGATCTTTTCCTTTTGTCTTTTTAGGTACTGGATCCGCCGTTACGA
Found at i:20206198 original size:21 final size:22
Alignment explanation
Indices: 20206174--20206222 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
20206164 CTTCATTTCT
20206174 TTTTTCTCTTTTTGTT-TTTTG-
1 TTTTTCTCTTTTT-TTCTTTTGC
20206195 TTTTTCTCTTTTTTTCTTTTGC
1 TTTTTCTCTTTTTTTCTTTTGC
20206217 TTTTTC
1 TTTTTC
20206223 CATTGAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.08
21 18 0.69
22 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (22 bp):
TTTTTCTCTTTTTTTCTTTTGC
Found at i:20211814 original size:28 final size:28
Alignment explanation
Indices: 20211783--20211841 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
20211773 AAAATGAGAC
*
20211783 TTTGGACACCTGAGGGCAAAATGGTAAT
1 TTTGGACACCTGAAGGCAAAATGGTAAT
* *
20211811 TTTGGACTCTTGAAGGCAAAATGGTAAT
1 TTTGGACACCTGAAGGCAAAATGGTAAT
20211839 TTT
1 TTT
20211842 AGGAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (28 bp):
TTTGGACACCTGAAGGCAAAATGGTAAT
Found at i:20211977 original size:59 final size:58
Alignment explanation
Indices: 20211914--20212224 Score: 212
Period size: 59 Copynumber: 5.3 Consensus size: 58
20211904 AAAATCAAGA
20211914 TCAAAAAT-AGAGTTTTTGGACATCTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGG
1 TCAAAAATGA-AGTTTTTGGACAT-TAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGG
* * * * ** * * *
20211973 TC-AAAGTGAAG-TTTTAGATATTCGAGGGTGGAATGGTAATTTTTAAAAGTTTCAGAG
1 TCAAAAATGAAGTTTTTGGACATTAG-GGGTAAAATGGTAATTTTTGAAAGTTTTAGGG
* * * * *
20212030 TTAAAAATGGAGTTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGTAAGTTTTAAGG
1 TCAAAAATGAAGTTTTTGGACATT-AGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGG
* * ** * *
20212089 TTAAAAATGAAATTTTTGGATGTTTAGGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGG
1 TCAAAAATGAAGTTTTTGGA-CATTAGGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGG
** * * *
20212148 T--AAAATGTAA--TTTTCAAAAGTTTTAGGGTGAAAAAT-GTAATTTTTGAAAGTTTAAGGG
1 TCAAAAATG-AAGTTTTTGGACA---TTAGGG-GTAAAATGGTAATTTTTGAAAGTTTTAGGG
20212206 T-AAAAATGTAA-TTTTTGGA
1 TCAAAAATG-AAGTTTTTGGA
20212225 AGTTTTGAGG
Statistics
Matches: 198, Mismatches: 40, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
56 7 0.04
57 42 0.21
58 46 0.23
59 90 0.45
60 13 0.07
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (58 bp):
TCAAAAATGAAGTTTTTGGACATTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGG
Found at i:20212190 original size:87 final size:87
Alignment explanation
Indices: 20212056--20212312 Score: 327
Period size: 87 Copynumber: 2.9 Consensus size: 87
20212046 TGGACATTCG
** * * *
20212056 GGGGTAAAATGGTAATTTTTGTAAGTTTTAAGGTTAAAAATGAAATTTTTGGATGTTTAGGGGTA
1 GGGGTAAAAT-GTAATTTTTAAAAGTTTTAGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTA
20212121 AAAATGTAATTTTTGGAAGTTTT
65 AAAATGTAATTTTTGGAAGTTTT
* * * *
20212144 GGGGTAAAATGTAATTTTCAAAAGTTTTAGGGTGAAAAATGTAATTTTTGAAAGTTTAAGGGTAA
1 GGGGTAAAATGTAATTTTTAAAAGTTTTAGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTAA
20212209 AAATGTAATTTTTGGAAGTTTT
66 AAATGTAATTTTTGGAAGTTTT
* ** * * *
20212231 GAGGTCAAAAAATAATTTTTAGAAGTTTT-GGGTTAAAAATGTAATTTTGGAGAAGTTTGGGGGT
1 GGGGT-AAAATGTAATTTTTAAAAGTTTTAGGGTTAAAAATGTAATTTTTG-GAAGTTTAGGGGT
* *
20212295 CAAAATATAATTTTTGGA
64 AAAAATGTAATTTTTGGA
20212313 CAATTTAGGG
Statistics
Matches: 146, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
87 91 0.62
88 55 0.38
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.39
Consensus pattern (87 bp):
GGGGTAAAATGTAATTTTTAAAAGTTTTAGGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTAA
AAATGTAATTTTTGGAAGTTTT
Found at i:20212287 original size:30 final size:29
Alignment explanation
Indices: 20212061--20212312 Score: 240
Period size: 29 Copynumber: 8.6 Consensus size: 29
20212051 ATTCGGGGGT
* *
20212061 AAAATGGTAATTTTTGTAAGTTTTAAGGTTA
1 AAAAT-GTAATTTTTGGAAGTTTT-GGGTTA
* * * *
20212092 AAAATGAAATTTTTGGATGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTTTGGGTTA
*
20212121 AAAATGTAATTTTTGGAAGTTTTGGGGT-
1 AAAATGTAATTTTTGGAAGTTTTGGGTTA
*** *
20212149 AAAATGTAATTTTCAAAAGTTTTAGGGTGA
1 AAAATGTAATTTTTGGAAGTTTT-GGGTTA
* *
20212179 AAAATGTAATTTTTGAAAGTTTAAGGG-TA
1 AAAATGTAATTTTTGGAAGTTT-TGGGTTA
*
20212208 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGTAATTTTTGGAAGTTTTG-GGTTA
* *
20212238 AAAA-ATAATTTTTAGAAGTTTTGGGTTA
1 AAAATGTAATTTTTGGAAGTTTTGGGTTA
* * * *
20212266 AAAATGTAATTTTGGAGAAGTTTGGGGGTC
1 AAAATGTAATTTTTG-GAAGTTTTGGGTTA
*
20212296 AAAATATAATTTTTGGA
1 AAAATGTAATTTTTGGA
20212313 CAATTTAGGG
Statistics
Matches: 182, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
28 29 0.16
29 82 0.45
30 66 0.36
31 5 0.03
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTTGGGTTA
Found at i:20212993 original size:17 final size:17
Alignment explanation
Indices: 20212968--20213062 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
20212958 AATCATTTTT
*
20212968 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
20212985 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * * *
20213002 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTCA
*
20213019 AATTTAAAATAAATTCG
1 AATTTAAAATAAATTCA
* *
20213036 AATTTAAAATAATTTAA
1 AATTTAAAATAAATTCA
20213053 AATTTAAAAT
1 AATTTAAAAT
20213063 TAAAAGTTGG
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 65 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:20213020 original size:23 final size:23
Alignment explanation
Indices: 20212994--20213043 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20212984 AAATTTAAAA
*
20212994 TAAATTTAAACTCAAAAT-GAATT
1 TAAATTTAAAAT-AAAATCGAATT
*
20213017 TAAATTTAAAATAAATTCGAATT
1 TAAATTTAAAATAAAATCGAATT
20213040 TAAA
1 TAAA
20213044 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (23 bp):
TAAATTTAAAATAAAATCGAATT
Found at i:20213448 original size:22 final size:22
Alignment explanation
Indices: 20213416--20213465 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
20213406 ATTTTTAGGA
*
20213416 GAATAAGGAAGAGCAGTTTCAT
1 GAATAAAGAAGAGCAGTTTCAT
*
20213438 GAATAAAGAAGAGTAGTTTCAT
1 GAATAAAGAAGAGCAGTTTCAT
20213460 GAATAA
1 GAATAA
20213466 TACTTGGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (22 bp):
GAATAAAGAAGAGCAGTTTCAT
Found at i:20215268 original size:21 final size:21
Alignment explanation
Indices: 20215244--20215285 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20215234 GCTATTTTCG
* *
20215244 TGTTTTTTTTATTGTTATTTT
1 TGTTGTTTTTAATGTTATTTT
*
20215265 TGTTGTTTTTAATGTTGTTTT
1 TGTTGTTTTTAATGTTATTTT
20215286 GTCGTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (21 bp):
TGTTGTTTTTAATGTTATTTT
Found at i:20215316 original size:24 final size:21
Alignment explanation
Indices: 20215255--20215341 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 21
20215245 GTTTTTTTTA
* *
20215255 TTGTTATTTTTGTTGTT-TTT
1 TTGTTGTTTTGGTTGTTATTT
* *
20215275 AATGTTGTTTT-GTCGTTATTT
1 -TTGTTGTTTTGGTTGTTATTT
20215296 TTGCTGCTGTTTTGGTTGTTATTT
1 TTG-T--TGTTTTGGTTGTTATTT
*
20215320 TTGTTG-TTTGGATGTTATTT
1 TTGTTGTTTTGGTTGTTATTT
20215340 TT
1 TT
20215342 TATGCGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
20 22 0.40
21 14 0.25
23 7 0.13
24 12 0.22
ACGTcount: A:0.08, C:0.03, G:0.21, T:0.68
Consensus pattern (21 bp):
TTGTTGTTTTGGTTGTTATTT
Found at i:20218329 original size:17 final size:18
Alignment explanation
Indices: 20218309--20218343 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20218299 TGAATTTTTC
*
20218309 CTAAATT-TTATTTTTAT
1 CTAAATTATAATTTTTAT
20218326 CTAAATTATAATTTTTAT
1 CTAAATTATAATTTTTAT
20218344 TATTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
CTAAATTATAATTTTTAT
Found at i:20225741 original size:16 final size:18
Alignment explanation
Indices: 20225710--20225742 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
20225700 GCAAATTATT
20225710 TTAACAGAATCTTTAACA
1 TTAACAGAATCTTTAACA
20225728 TTAACA-AA-CTTTAAC
1 TTAACAGAATCTTTAAC
20225743 GTTATCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.33
Consensus pattern (18 bp):
TTAACAGAATCTTTAACA
Found at i:20229508 original size:2 final size:2
Alignment explanation
Indices: 20229494--20229534 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
20229484 ACTGAACGAA
*
20229494 AG AG AG -G ATG AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG A
1 AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20229535 AGGTTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.05
Consensus pattern (2 bp):
AG
Found at i:20229989 original size:22 final size:19
Alignment explanation
Indices: 20229954--20230023 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 19
20229944 ATTTTAAAAA
**
20229954 AAAATTAAGTATATATACAT
1 AAAATTAAAAATATATA-AT
20229974 AAATATGTAAAAATATATAAT
1 AAA-AT-TAAAAATATATAAT
20229995 AAAATTAAAAA-ATA-ATAT
1 AAAATTAAAAATATATA-AT
*
20230013 AAAAATAAAAA
1 AAAATTAAAAA
20230024 AATTCCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 1 0.02
18 15 0.34
19 6 0.14
20 5 0.11
21 7 0.16
22 10 0.23
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAATTAAAAATATATAAT
Found at i:20230005 original size:20 final size:20
Alignment explanation
Indices: 20229964--20230024 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 20
20229954 AAAATTAAGT
20229964 ATATATACATAAATATGT-AAAA
1 ATATATA-ATAAA-AT-TAAAAA
20229986 ATATATAATAAAATTAAAAA
1 ATATATAATAAAATTAAAAA
*
20230006 ATA-AT-ATAAAAATAAAAA
1 ATATATAATAAAATTAAAAA
20230024 A
1 A
20230025 ATTCCCTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 13 0.35
19 3 0.08
20 9 0.24
21 5 0.14
22 7 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
ATATATAATAAAATTAAAAA
Found at i:20230024 original size:19 final size:20
Alignment explanation
Indices: 20229982--20230026 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
20229972 ATAAATATGT
*
20229982 AAAAATATATAATAAAATTA
1 AAAAATATATAATAAAATAA
20230002 AAAAATA-AT-ATAAAAATAA
1 AAAAATATATAAT-AAAATAA
20230021 AAAAAT
1 AAAAAT
20230027 TCCCTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATATAATAAAATAA
Found at i:20235020 original size:57 final size:57
Alignment explanation
Indices: 20234906--20235020 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 57
20234896 ACCCATAAGA
* * *
20234906 ACAAAGTTTTATTTGAAGCTGCCATGCAAAAATACCAAAATAGTGTTGAGATCAACAT
1 ACAAAGTTTTATTTGAAGCTGCCA-GCAAAAATACCAAAACAATGTTAAGATCAACAT
* * * *
20234964 ACAAAGTTTTATTTGAAGGTGTCA-CACCAAATACCACAACAATGTTAAGATCAACAT
1 ACAAAGTTTTATTTGAAGCTGCCAGCA-AAAATACCAAAACAATGTTAAGATCAACAT
20235021 TGGCATTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 2 0.04
57 25 0.51
58 22 0.45
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (57 bp):
ACAAAGTTTTATTTGAAGCTGCCAGCAAAAATACCAAAACAATGTTAAGATCAACAT
Found at i:20236289 original size:21 final size:21
Alignment explanation
Indices: 20236263--20236308 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
20236253 ACTCATATTG
20236263 ATAACCCTTGATGCTGTTCAA
1 ATAACCCTTGATGCTGTTCAA
20236284 ATAACCCTTGATGCTGTTCAA
1 ATAACCCTTGATGCTGTTCAA
20236305 ATAA
1 ATAA
20236309 TCAACTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (21 bp):
ATAACCCTTGATGCTGTTCAA
Found at i:20251613 original size:10 final size:10
Alignment explanation
Indices: 20251590--20251644 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
20251580 AAAATTAAGT
20251590 ATATATACATAA
1 ATATATA-A-AA
*
20251602 ATATTTAAAA
1 ATATATAAAA
20251612 ATATATAATAA
1 ATATATAA-AA
20251623 A-AT-TAAAAA
1 ATATAT-AAAA
20251632 ATATATAAAA
1 ATATATAAAA
20251642 ATA
1 ATA
20251645 AAAAAAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 4 0.11
10 22 0.59
11 5 0.14
12 6 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATATAAAA
Found at i:20251630 original size:18 final size:18
Alignment explanation
Indices: 20251580--20251647 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 18
20251570 AATTCTAAAA
*
20251580 AAAATTAAGTATATATACAT
1 AAAATTAA-AATATATA-AT
20251600 AAATATTTAAAAATATATAAT
1 AAA-A-TT-AAAATATATAAT
*
20251621 AAAATTAAAAAATAT-AT
1 AAAATTAAAATATATAAT
*
20251638 AAAAATAAAA
1 AAAATTAAAA
20251648 AAAATTCCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 11 0.26
18 8 0.19
19 2 0.05
20 4 0.10
21 6 0.14
22 9 0.21
23 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAATTAAAATATATAAT
Found at i:20251631 original size:20 final size:21
Alignment explanation
Indices: 20251590--20251652 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
20251580 AAAATTAAGT
*
20251590 ATATATACATAAATATTTAAAA
1 ATATATA-ATAAATATTAAAAA
20251612 ATATATAATAAA-ATTAAAAA
1 ATATATAATAAATATTAAAAA
*
20251632 ATATATAA-AAATA-AAAAAA
1 ATATATAATAAATATTAAAAA
20251651 AT
1 AT
20251653 TCCCTTATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 10 0.26
20 16 0.42
21 5 0.13
22 7 0.18
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATATAATAAATATTAAAAA
Found at i:20251648 original size:18 final size:20
Alignment explanation
Indices: 20251608--20251650 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
20251598 ATAAATATTT
*
20251608 AAAAATATATAATAAAATTA
1 AAAAATATATAATAAAATAA
20251628 AAAAATATAT-A-AAAATAA
1 AAAAATATATAATAAAATAA
20251646 AAAAA
1 AAAAA
20251651 ATTCCCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATATATAATAAAATAA
Found at i:20251835 original size:19 final size:19
Alignment explanation
Indices: 20251810--20251855 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
20251800 GGCTGATGTT
* *
20251810 TATTTTTTAAAT-TTATTA
1 TATTTTTAAAATATTAATA
20251828 TAATTTTTAAAATATTAATA
1 T-ATTTTTAAAATATTAATA
20251848 TATTTTTA
1 TATTTTTA
20251856 TCTATTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.71
20 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTAAAATATTAATA
Found at i:20255201 original size:20 final size:20
Alignment explanation
Indices: 20255152--20255469 Score: 368
Period size: 20 Copynumber: 15.8 Consensus size: 20
20255142 CATCTACGTA
* **
20255152 TTCAGGCTTCGTGATGGTGT
1 TTCAGGCTTTGTGCCGGTGT
* *
20255172 ATCAGGCTTTGTGCTGGTGT
1 TTCAGGCTTTGTGCCGGTGT
*
20255192 TTCAGGCTTTATGTCC-GTGT
1 TTCAGGCTTTGTG-CCGGTGT
20255212 TTCAGGCTTTGTGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
*
20255232 TTCAGGCTTTATGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
* *
20255252 TTCAAGCTTTATGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
*
20255272 TTCAGGCTTTATGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
* * *
20255292 TTCAAGCTTTGTGTCGATGT
1 TTCAGGCTTTGTGCCGGTGT
* **
20255312 TTCAGGCTTTATGCTAGTGT
1 TTCAGGCTTTGTGCCGGTGT
*
20255332 ATCAGGCTTTTGTGCCGGTGT
1 TTCAGGC-TTTGTGCCGGTGT
*
20255353 ATCAGGCTTTGTGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
*
20255373 ATTCAGGCTTTATGCCGGTGT
1 -TTCAGGCTTTGTGCCGGTGT
*
20255394 TTCAGGCTTTGTGCCAGTGT
1 TTCAGGCTTTGTGCCGGTGT
* *
20255414 ATCAGGCTTTGTACCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
* *
20255434 ATCAAGCTTTGTGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGT
*
20255454 ATTCAGGCTATGTGCC
1 -TTCAGGCTTTGTGCC
20255470 TATCAGGATT
Statistics
Matches: 257, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
19 2 0.01
20 207 0.81
21 48 0.19
ACGTcount: A:0.12, C:0.19, G:0.30, T:0.39
Consensus pattern (20 bp):
TTCAGGCTTTGTGCCGGTGT
Found at i:20255231 original size:60 final size:60
Alignment explanation
Indices: 20255152--20255489 Score: 407
Period size: 60 Copynumber: 5.7 Consensus size: 60
20255142 CATCTACGTA
* ** *
20255152 TTCAGGCTTCGTGATGGTGTATCAGGCTTTGTGCTGGTGTTTCAGGCTTTATGTCC-GTGT
1 TTCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTTTCAGGCTTTATG-CCGGTGT
* * *
20255212 TTCAGGCTTTGTGCCGGTGTTTCAGGCTTTATGCCGGTGTTTCAAGCTTTATGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTTTCAGGCTTTATGCCGGTGT
* * * * * **
20255272 TTCAGGCTTTATGCCGGTGTTTCAAGCTTTGTGTCGATGTTTCAGGCTTTATGCTAGTGT
1 TTCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTTTCAGGCTTTATGCCGGTGT
*
20255332 ATCAGGCTTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATTCAGGCTTTATGCCGGTGT
1 TTCAGGC-TTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGT-TTCAGGCTTTATGCCGGTGT
* * * * *
20255394 TTCAGGCTTTGTGCCAGTGTATCAGGCTTTGTACCGGTGTATCAAGCTTTGTGCCGGTGT
1 TTCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTTTCAGGCTTTATGCCGGTGT
* *
20255454 ATTCAGGCTATGTGCC----TATCAGGATTTGTGCCGGTG
1 -TTCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTG
20255490 ATCCATGAAC
Statistics
Matches: 242, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
57 18 0.07
59 2 0.01
60 125 0.52
61 73 0.30
62 24 0.10
ACGTcount: A:0.12, C:0.19, G:0.30, T:0.39
Consensus pattern (60 bp):
TTCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTTTCAGGCTTTATGCCGGTGT
Found at i:20257723 original size:22 final size:22
Alignment explanation
Indices: 20257695--20257744 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
20257685 ATTTTTTGGA
20257695 GAATAAGGAAGAGTAGTTTCAT
1 GAATAAGGAAGAGTAGTTTCAT
20257717 GAATAAGGAAGAGTAGTTTCAT
1 GAATAAGGAAGAGTAGTTTCAT
20257739 GAATAA
1 GAATAA
20257745 TACTTGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (22 bp):
GAATAAGGAAGAGTAGTTTCAT
Found at i:20261397 original size:17 final size:18
Alignment explanation
Indices: 20261375--20261409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20261365 AAATATTTTC
*
20261375 CTAAATT-TTATTTTTAT
1 CTAAATTATAATTTTTAT
20261392 CTAAATTATAATTTTTAT
1 CTAAATTATAATTTTTAT
20261410 TAGTATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
CTAAATTATAATTTTTAT
Found at i:20264770 original size:24 final size:23
Alignment explanation
Indices: 20264743--20264829 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
20264733 TCATTAACAT
20264743 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
20264767 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
* *
20264790 TGTTCGTGAAAATGTTTAATTAA
1 TGTTCGTGAACATGTTCAATTAA
**
20264813 -GTTAAATGAACATGTTC
1 TGTT-CGTGAACATGTTC
20264830 GTGAACACAA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.06
23 28 0.56
24 19 0.38
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:20265845 original size:5 final size:5
Alignment explanation
Indices: 20265835--20265868 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
20265825 TAAATTTCAA
20265835 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
20265869 ATCCTCACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20270171 original size:20 final size:21
Alignment explanation
Indices: 20270124--20270171 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20270114 CTTTTGATTG
20270124 ATGTTTGCCATTTTTTGACCA
1 ATGTTTGCCATTTTTTGACCA
** * *
20270145 ACATTTGCTA-TTTTTGATCA
1 ATGTTTGCCATTTTTTGACCA
20270165 ATGTTTG
1 ATGTTTG
20270172 TAATCTTTTG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.50
Consensus pattern (21 bp):
ATGTTTGCCATTTTTTGACCA
Found at i:20271243 original size:49 final size:50
Alignment explanation
Indices: 20270868--20271244 Score: 235
Period size: 49 Copynumber: 7.7 Consensus size: 50
20270858 ATAGAGTTTG
* * * * *
20270868 AAGAGGGATAGGTTGAAGCCACAACGACAGACCTAGCATCC-TAAAA-CCA
1 AAGAGGGATAGATTGAAGCCGCAACGACAGATCTAACA-CCTTAAAATCGA
* * * *
20270917 AAGAGGGATAGATTGAAGCCACAATGACAAATCTAACACCCTAAAATCGA
1 AAGAGGGATAGATTGAAGCCGCAACGACAGATCTAACACCTTAAAATCGA
* * * * *
20270967 AA-AGGGAAAAATTGAAGCCGTAACGATC-GACCTTACACCTTAAAA-CTG-
1 AAGAGGGATAGATTGAAGCCGCAACGA-CAGATCTAACACCTTAAAATC-GA
* * * * *
20271015 AAGAGGGATAGGTTGAAGTCGCAACGA-TGAACCTAACACCCTAAAA-CTG-
1 AAGAGGGATAGATTGAAGCCGCAACGACAG-ATCTAACACCTTAAAATC-GA
* * * *
20271064 AAGAGGGATAGATTAAAGCCGTAA-TAGCGGATCTAACACCTTAAAATCGA
1 AAGAGGGATAGATTGAAGCCGCAACGA-CAGATCTAACACCTTAAAATCGA
* * **** * * * *
20271114 GA-AGGGAAAGATTGAAGTTATAA-TAGCGGATCTTACACCTTAAAATTG-
1 AAGAGGGATAGATTGAAGCCGCAACGA-CAGATCTAACACCTTAAAATCGA
* *
20271162 AAGAGGGATAGATTGAAGCTGCAATGGA-AGATCTAACACCTTAAAATC-A
1 AAGAGGGATAGATTGAAGCCGCAA-CGACAGATCTAACACCTTAAAATCGA
* * *
20271211 AATAGGGAAAGATTGAAGCTGCAACGACAGATCT
1 AAGAGGGATAGATTGAAGCCGCAACGACAGATCT
20271245 TATAACATCC
Statistics
Matches: 262, Mismatches: 50, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
48 10 0.04
49 243 0.93
50 8 0.03
51 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (50 bp):
AAGAGGGATAGATTGAAGCCGCAACGACAGATCTAACACCTTAAAATCGA
Found at i:20271244 original size:147 final size:143
Alignment explanation
Indices: 20270865--20271244 Score: 377
Period size: 147 Copynumber: 2.6 Consensus size: 143
20270855 ATCATAGAGT
** *
20270865 TTGAAGAGGGATAGGTTGAAGCCACAACGACAGACCTAGCATCCTAAAACCAAAGAGGGATAGAT
1 TTGAAGAGGGATAGGTTGAAGCTGCAACGA-AGACCTAACA-CCTAAAA-CAAAGAGGGATAGAT
* * * *
20270930 TGAAGCCACAATGACAAATCTAACACCCTAAAATCGAAAAGGGAAAAATTGAAGCCGTAACGATC
63 TGAAGCCGCAA-GACAGATCTAACACCCTAAAATCGAAAAGGGAAAAATTGAAGCCATAACGAGC
20270995 GACCTTACACCTTAAAA
127 GACCTTACACCTTAAAA
* * *
20271012 CTGAAGAGGGATAGGTTGAAG-TCGCAACGATGAACCTAACACCCTAAAACTGAAGAGGGATAGA
1 TTGAAGAGGGATAGGTTGAAGCT-GCAACGAAG-ACCTAACA-CCTAAAAC-AAAGAGGGATAGA
* * * * * * * ** *
20271076 TTAAAGCCGTAATAGCGGATCTAACACCTTAAAATCGAGAAGGGAAAGATTGAAGTTATAA-TAG
62 TTGAAGCCGCAAGA-CAGATCTAACACCCTAAAATCGAAAAGGGAAAAATTGAAGCCATAACGAG
*
20271140 CGGATCTTACACCTTAAAA
126 C-GACCTTACACCTTAAAA
* * * * *
20271159 TTGAAGAGGGATAGATTGAAGCTGCAATGGAAGATCTAACACCTTAAAATCAAATAGGGAAAGAT
1 TTGAAGAGGGATAGGTTGAAGCTGCAA-CGAAGACCTAACACC-TAAAA-CAAAGAGGGATAGAT
*
20271224 TGAAGCTGCAACGACAGATCT
63 TGAAGCCGCAA-GACAGATCT
20271245 TATAACATCC
Statistics
Matches: 188, Mismatches: 35, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
146 7 0.04
147 175 0.93
148 6 0.03
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (143 bp):
TTGAAGAGGGATAGGTTGAAGCTGCAACGAAGACCTAACACCTAAAACAAAGAGGGATAGATTGA
AGCCGCAAGACAGATCTAACACCCTAAAATCGAAAAGGGAAAAATTGAAGCCATAACGAGCGACC
TTACACCTTAAAA
Found at i:20272372 original size:22 final size:21
Alignment explanation
Indices: 20272347--20272400 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
20272337 GTTCTCTGTT
*
20272347 TATTAGCACGTGTAGTGCTCTC
1 TATTAGCACAT-TAGTGCTCTC
* *
20272369 TATTTTGCACATTTGTGCTCTC
1 TA-TTAGCACATTAGTGCTCTC
20272391 TGATTAGCAC
1 T-ATTAGCAC
20272401 CTCAATGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (21 bp):
TATTAGCACATTAGTGCTCTC
Found at i:20273576 original size:49 final size:49
Alignment explanation
Indices: 20273497--20273731 Score: 195
Period size: 49 Copynumber: 4.8 Consensus size: 49
20273487 TACAGATCTT
* * *
20273497 ACACCTTAAAACTGACGAGGGATAGCTTGAAGCCGTAATGGAGAACCTA
1 ACACCTTAAAACCGAAGAGGGATAGATTGAAGCCGTAATGGAGAACCTA
* * * * * * *
20273546 ACACCCTAAAACCGAAGAGGGAAAGATTGAAGTCGCAAT-GATAGATCTT
1 ACACCTTAAAACCGAAGAGGGATAGATTGAAGCCGTAATGGAGA-ACCTA
* * * * *
20273595 ACACCTTAAAACCGAAAAGGGATAGGTTGAAGCCGTTAA-GGCGGACCCA
1 ACACCTTAAAACCGAAGAGGGATAGATTGAAGCCG-TAATGGAGAACCTA
* * * * * * * *
20273644 ATACCCTAAAACTGAAGAGGGATAGATTGAAGCCATGACGGCGAATCTA
1 ACACCTTAAAACCGAAGAGGGATAGATTGAAGCCGTAATGGAGAACCTA
* * *
20273693 ACACCTTGAAACCAAAGAGGGAACAGATTGAAGCCGTAA
1 ACACCTTAAAACCGAAGAGGG-ATAGATTGAAGCCGTAA
20273732 CAGCGAATCT
Statistics
Matches: 141, Mismatches: 40, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
48 5 0.04
49 119 0.84
50 17 0.12
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (49 bp):
ACACCTTAAAACCGAAGAGGGATAGATTGAAGCCGTAATGGAGAACCTA
Found at i:20273661 original size:98 final size:98
Alignment explanation
Indices: 20273490--20273675 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 98
20273480 AGGGTGTTAC
* ** *
20273490 AGATCTTACACCTTAAAACTGACGAGGGATAGCTTGAAGCCGTAATGGAGAACCTAACACCCTAA
1 AGATCTTACACCTTAAAACCGAAAAGGGATAGCTTGAAGCCGTAATGGAGAACCCAACACCCTAA
20273555 AACCGAAGAGGGAAAGATTGAAGTCGCAATGAT
66 AACCGAAGAGGGAAAGATTGAAGTCGCAATGAT
* * * *
20273588 AGATCTTACACCTTAAAACCGAAAAGGGATAGGTTGAAGCCGTTAA-GGCGGACCCAATACCCTA
1 AGATCTTACACCTTAAAACCGAAAAGGGATAGCTTGAAGCCG-TAATGGAGAACCCAACACCCTA
* *
20273652 AAACTGAAGAGGGATAGATTGAAG
65 AAACCGAAGAGGGAAAGATTGAAG
20273676 CCATGACGGC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
98 74 0.96
99 3 0.04
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
AGATCTTACACCTTAAAACCGAAAAGGGATAGCTTGAAGCCGTAATGGAGAACCCAACACCCTAA
AACCGAAGAGGGAAAGATTGAAGTCGCAATGAT
Found at i:20273705 original size:98 final size:99
Alignment explanation
Indices: 20273490--20273729 Score: 240
Period size: 98 Copynumber: 2.4 Consensus size: 99
20273480 AGGGTGTTAC
* ** * * *
20273490 AGATCTTACACCTTAAAACTGACGAGGGATAGCTTGAAGCCG-TAATGGAGAACCTAACACCCTA
1 AGATCTAACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTTAATGGAGAACCCAACACCCTA
*
20273554 AAACCGAAGAGGGAAAGATTGAAGTCGCAATGAT
66 AAACCGAAGAGGGAAAGATTGAAGTCGCAATGAG
* * * * *
20273588 AGATCTTACACCTTAAAACCGAAA-AGGGATAGGTTGAAGCCGTTAA-GGCGGACCCAATACCCT
1 AGATCTAACACCTTAAAACC-AAAGAGGGATAGATTGAAGCCGTTAATGGAGAACCCAACACCCT
* *
20273651 AAAACTGAAGAGGGATAGATTGAAG-C-C-ATGACGG
65 AAAACCGAAGAGGGAAAGATTGAAGTCGCAATGA--G
* * *
20273685 CGAATCTAACACCTTGAAACCAAAGAGGGAACAGATTGAAGCCGT
1 AG-ATCTAACACCTTAAAACCAAAGAGGG-ATAGATTGAAGCCGT
20273730 AACAGCGAAT
Statistics
Matches: 119, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
95 4 0.03
96 1 0.01
97 5 0.04
98 92 0.77
99 17 0.14
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.17
Consensus pattern (99 bp):
AGATCTAACACCTTAAAACCAAAGAGGGATAGATTGAAGCCGTTAATGGAGAACCCAACACCCTA
AAACCGAAGAGGGAAAGATTGAAGTCGCAATGAG
Found at i:20274358 original size:24 final size:23
Alignment explanation
Indices: 20274324--20274378 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
20274314 TGAGGAGATT
*
20274324 TTTTTTATTTTGTTCAGAGAGGAGG
1 TTTTTT-TTTTGTTCAGAGAGGA-A
20274349 TTTTTTTTTTGTTCAGAGAGGAA
1 TTTTTTTTTTGTTCAGAGAGGAA
20274372 TTTTTTT
1 TTTTTTT
20274379 AATAAGATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 16 0.55
25 6 0.21
ACGTcount: A:0.18, C:0.04, G:0.22, T:0.56
Consensus pattern (23 bp):
TTTTTTTTTTGTTCAGAGAGGAA
Found at i:20275880 original size:28 final size:28
Alignment explanation
Indices: 20275835--20275900 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
20275825 CATCATCCAA
* *
20275835 AATTTGGTTGTAAGTATTTCAAGTAGTT
1 AATTTTGTTTTAAGTATTTCAAGTAGTT
* * *
20275863 AATTTTGTTTTAATTATTTTAATTAGTT
1 AATTTTGTTTTAAGTATTTCAAGTAGTT
*
20275891 AATTATGTTT
1 AATTTTGTTT
20275901 ATTAAGTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.56
Consensus pattern (28 bp):
AATTTTGTTTTAAGTATTTCAAGTAGTT
Found at i:20279592 original size:63 final size:63
Alignment explanation
Indices: 20279525--20279666 Score: 182
Period size: 62 Copynumber: 2.3 Consensus size: 63
20279515 GTCTCGCCAT
** * * *
20279525 AGATAAAAAAAATAATTTTTTTTGGGTTTTGGTCATCTAAT-G-GATGATACCAAGTCCTATCAC
1 AGATAAAAAAAATAATTTTTTTTGGGTTTTGACCATCTAATAGCCA-G-CACCAAGTCCCATCAC
*
20279588 AGATAAAAAAAAT-ATTTTTTTTTGGTTTTGACCATCTAATAGCCAGCACCAAGTCCCATCAC
1 AGATAAAAAAAATAATTTTTTTTGGGTTTTGACCATCTAATAGCCAGCACCAAGTCCCATCAC
*
20279650 AGATAAAAATAATAATT
1 AGATAAAAAAAATAATT
20279667 ATTTGATTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
62 50 0.72
63 18 0.26
64 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (63 bp):
AGATAAAAAAAATAATTTTTTTTGGGTTTTGACCATCTAATAGCCAGCACCAAGTCCCATCAC
Found at i:20280103 original size:25 final size:25
Alignment explanation
Indices: 20280066--20280135 Score: 104
Period size: 25 Copynumber: 2.7 Consensus size: 25
20280056 TAGTTGGGAG
20280066 TTTTAAGTCTATTTAAAACTAAATT
1 TTTTAAGTCTATTTAAAACTAAATT
* *
20280091 TTTAAAGTTTATTTAAAACTAAATTT
1 TTTTAAGTCTATTTAAAACTAAA-TT
20280117 ATTTTAAGTCTATTTAAAA
1 -TTTTAAGTCTATTTAAAA
20280136 TTTTTCATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 21 0.54
26 2 0.05
27 16 0.41
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTTAAGTCTATTTAAAACTAAATT
Found at i:20282760 original size:33 final size:34
Alignment explanation
Indices: 20282722--20282799 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
20282712 AAATGAAATT
*
20282722 ATATTTGGGTTAGGTAAAAGAT-AAAAATTAAAA
1 ATATTTGGGTTAAGTAAAAGATAAAAAATTAAAA
* *
20282755 ATATTTGGGTCAAGTAAAAGGTAAAAAATTAAAA
1 ATATTTGGGTTAAGTAAAAGATAAAAAATTAAAA
20282789 ATATTTGGGTT
1 ATATTTGGGTT
20282800 TAGTTTATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 19 0.47
34 21 0.52
ACGTcount: A:0.47, C:0.01, G:0.19, T:0.32
Consensus pattern (34 bp):
ATATTTGGGTTAAGTAAAAGATAAAAAATTAAAA
Found at i:20296926 original size:74 final size:74
Alignment explanation
Indices: 20296823--20296974 Score: 297
Period size: 74 Copynumber: 2.1 Consensus size: 74
20296813 CAAAGTAGGA
20296823 GCTT-CTTTAATAGATGGCTTGAAAATTGGAGCCGTTCTATTGGCTAAGTCTAAAGATTCAATTT
1 GCTTGCTTTAATAGATGGCTTGAAAATTGGAGCCGTTCTATTGGCTAAGTCTAAAGATTCAATTT
20296887 GCCATCCAT
66 GCCATCCAT
20296896 GCTTGCTTTAATAGATGGCTTGAAAATTGGAGCCGTTCTATTGGCTAAGTCTAAAGATTCAATTT
1 GCTTGCTTTAATAGATGGCTTGAAAATTGGAGCCGTTCTATTGGCTAAGTCTAAAGATTCAATTT
20296961 GCCATCCAT
66 GCCATCCAT
20296970 GCTTG
1 GCTTG
20296975 AGTTCAATGT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 4 0.05
74 74 0.95
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (74 bp):
GCTTGCTTTAATAGATGGCTTGAAAATTGGAGCCGTTCTATTGGCTAAGTCTAAAGATTCAATTT
GCCATCCAT
Found at i:20303832 original size:14 final size:14
Alignment explanation
Indices: 20303810--20303839 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20303800 TTTATCAAAA
20303810 TTTAAAATTTAATT
1 TTTAAAATTTAATT
*
20303824 TTTATAATTTAATT
1 TTTAAAATTTAATT
20303838 TT
1 TT
20303840 GAGGCTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAAAATTTAATT
Found at i:20305315 original size:23 final size:23
Alignment explanation
Indices: 20305269--20305437 Score: 191
Period size: 23 Copynumber: 7.4 Consensus size: 23
20305259 ATCTTAATTC
20305269 TTTAAGCATAAATCA-ATT-ATA
1 TTTAAGCATAAATCATATTAATA
* * *
20305290 TTTAACCATAAACCAGATTAATA
1 TTTAAGCATAAATCATATTAATA
*
20305313 TTTAAGCACT-AATCACATTAATA
1 TTTAAGCA-TAAATCATATTAATA
* *
20305336 TTTGAGCACAAATCATATTAATA
1 TTTAAGCATAAATCATATTAATA
**
20305359 TTTAAGCATAAATCACGTTAATA
1 TTTAAGCATAAATCATATTAATA
* *
20305382 CTTAAGCACAAATCATATTAATA
1 TTTAAGCATAAATCATATTAATA
** *
20305405 TTTAATAATAAACCATATTAATA
1 TTTAAGCATAAATCATATTAATA
20305428 TTTAAGCATA
1 TTTAAGCATA
20305438 GATATAAGAA
Statistics
Matches: 121, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
21 13 0.11
22 3 0.02
23 104 0.86
24 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTAAGCATAAATCATATTAATA
Found at i:20305369 original size:69 final size:69
Alignment explanation
Indices: 20305269--20305437 Score: 218
Period size: 69 Copynumber: 2.5 Consensus size: 69
20305259 ATCTTAATTC
* * *
20305269 TTTAAGCATAAATCA-ATT-ATATTTAACCATAAACCA-GATTAATATTTAAGCACTAATCACAT
1 TTTAAGCATAAATCATATTAATATTTAAGCATAAACCACG-TTAATACTTAAGCACAAATCACAT
20305331 TAATA
65 TAATA
* * * *
20305336 TTTGAGCACAAATCATATTAATATTTAAGCATAAATCACGTTAATACTTAAGCACAAATCATATT
1 TTTAAGCATAAATCATATTAATATTTAAGCATAAACCACGTTAATACTTAAGCACAAATCACATT
20305401 AATA
66 AATA
** *
20305405 TTTAATAATAAACCATATTAATATTTAAGCATA
1 TTTAAGCATAAATCATATTAATATTTAAGCATA
20305438 GATATAAGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
67 13 0.15
68 3 0.03
69 70 0.80
70 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (69 bp):
TTTAAGCATAAATCATATTAATATTTAAGCATAAACCACGTTAATACTTAAGCACAAATCACATT
AATA
Found at i:20309249 original size:36 final size:36
Alignment explanation
Indices: 20309199--20309299 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
20309189 TTGTTATTTG
** * * *
20309199 TTTTACTCGTTGTTGACCTGGAGGTCATGTTGCTCA
1 TTTTACTCCCTGTTGACCCGAAGGTCATGTTACTCA
20309235 TTTTACTCCCTGTTGACCCGAAGGTCATGTTACTCA
1 TTTTACTCCCTGTTGACCCGAAGGTCATGTTACTCA
* * * *
20309271 TTTTACTACCTATTGAACCGAAGGACATG
1 TTTTACTCCCTGTTGACCCGAAGGTCATG
20309300 CCTGTTACCA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (36 bp):
TTTTACTCCCTGTTGACCCGAAGGTCATGTTACTCA
Found at i:20320981 original size:36 final size:36
Alignment explanation
Indices: 20320931--20321067 Score: 229
Period size: 36 Copynumber: 3.8 Consensus size: 36
20320921 TCTTTATTTG
20320931 TTTTACTCCTTGTTGACCCGAAGGTCATGTTGCTCA
1 TTTTACTCCTTGTTGACCCGAAGGTCATGTTGCTCA
* *
20320967 TTTTACTCCCTGTTGACCCGAAGGTCATGTTGATCA
1 TTTTACTCCTTGTTGACCCGAAGGTCATGTTGCTCA
* *
20321003 TTTTACTCCTTATTGACCAGAAGGTCATGTTGCTCA
1 TTTTACTCCTTGTTGACCCGAAGGTCATGTTGCTCA
*
20321039 TTTTACTCCTTGTTAACCCGAAGGTCATG
1 TTTTACTCCTTGTTGACCCGAAGGTCATG
20321068 CCTGTTACCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 92 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (36 bp):
TTTTACTCCTTGTTGACCCGAAGGTCATGTTGCTCA
Found at i:20325448 original size:7 final size:7
Alignment explanation
Indices: 20325436--20325466 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
20325426 GGTCTTCTTC
20325436 TTCCCTT
1 TTCCCTT
20325443 TTCCCTT
1 TTCCCTT
20325450 TTCCCTT
1 TTCCCTT
20325457 TTCCCTT
1 TTCCCTT
20325464 TTC
1 TTC
20325467 TTTCTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TTCCCTT
Found at i:20331227 original size:28 final size:28
Alignment explanation
Indices: 20331194--20331297 Score: 147
Period size: 28 Copynumber: 3.7 Consensus size: 28
20331184 ATAAGTTAAA
* *
20331194 ACCGCACTT-TGGTACTGGATGAGTTATT
1 ACCGCACTTAT-GTGCTGGACGAGTTATT
20331222 ACCGCACTTATGTGCTGGACGAGTTATT
1 ACCGCACTTATGTGCTGGACGAGTTATT
** *
20331250 ACAACACTTATGTGCTGGACGAGTTAAT
1 ACCGCACTTATGTGCTGGACGAGTTATT
20331278 ACCGCACTTATGTGCTGGAC
1 ACCGCACTTATGTGCTGGAC
20331298 AAGTATTGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 67 0.99
29 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (28 bp):
ACCGCACTTATGTGCTGGACGAGTTATT
Found at i:20332095 original size:20 final size:20
Alignment explanation
Indices: 20332064--20332110 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20332054 TGGGTTTTTG
20332064 GTATCG-TTTTTAAAGAAAA
1 GTATCGATTTTTAAAGAAAA
**
20332083 GTATCGATTTTTATTGAAAA
1 GTATCGATTTTTAAAGAAAA
*
20332103 TTATCGAT
1 GTATCGAT
20332111 ACCTCTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (20 bp):
GTATCGATTTTTAAAGAAAA
Found at i:20336906 original size:28 final size:28
Alignment explanation
Indices: 20336882--20336951 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
20336872 TCACACTTCG
20336882 GTGCTGGACGAGTTATTA-CTGCACTTAT
1 GTGCTGGACGAGTTATTACCT-CACTTAT
20336910 GTGCTGGACGAGTTATTACCTCACTTAT
1 GTGCTGGACGAGTTATTACCTCACTTAT
*
20336938 GTGTTGGACGAGTT
1 GTGCTGGACGAGTT
20336952 TGTTTTGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (28 bp):
GTGCTGGACGAGTTATTACCTCACTTAT
Found at i:20344767 original size:20 final size:20
Alignment explanation
Indices: 20344742--20344874 Score: 99
Period size: 20 Copynumber: 6.6 Consensus size: 20
20344732 TTTCTTGGAA
20344742 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGGTC
* **
20344762 AAAGTCAACGGTCAACTATC
1 AAAGTCAACGATCAACGGTC
* *
20344782 AAAGTCAATGATAAACGGTC
1 AAAGTCAACGATCAACGGTC
* * *
20344802 AAAGTCAACGGTAAACAGTC
1 AAAGTCAACGATCAACGGTC
* * *
20344822 AATGGTCAAAG-TCAACCGTC
1 AA-AGTCAACGATCAACGGTC
* *
20344842 AATAGTTAAAG-TCAACGGTC
1 AA-AGTCAACGATCAACGGTC
*
20344862 AATGATCAACGAT
1 AAAG-TCAACGAT
20344875 TAAAGTCACC
Statistics
Matches: 89, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
19 1 0.01
20 81 0.91
21 7 0.08
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAGTCAACGATCAACGGTC
Found at i:20344771 original size:13 final size:13
Alignment explanation
Indices: 20344753--20344843 Score: 78
Period size: 13 Copynumber: 6.8 Consensus size: 13
20344743 AAGTCAACGA
20344753 TCAACGGTCAAAG
1 TCAACGGTCAAAG
20344766 TCAACGGTCAACTA-
1 TCAACGGTCAA--AG
* *
20344780 TCAA-AGTCAATG
1 TCAACGGTCAAAG
*
20344792 ATAAACGGTCAAAG
1 -TCAACGGTCAAAG
*
20344806 TCAACGGTAAACAG
1 TCAACGGTCAA-AG
*
20344820 TCAATGGTCAAAG
1 TCAACGGTCAAAG
*
20344833 TCAACCGTCAA
1 TCAACGGTCAA
20344844 TAGTTAAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
13 39 0.64
14 21 0.34
15 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (13 bp):
TCAACGGTCAAAG
Found at i:20344843 original size:40 final size:40
Alignment explanation
Indices: 20344742--20344843 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 40
20344732 TTTCTTGGAA
* *
20344742 AAAGTCAACGATCAACGGTCAAAGTCAACGGTCAACTATC
1 AAAGTCAAAGATCAACGGTCAAAGTCAACGGTAAACTATC
* *
20344782 AAAGTCAATGATAAACGGTCAAAGTCAACGGTAAAC-AGTC
1 AAAGTCAAAGATCAACGGTCAAAGTCAACGGTAAACTA-TC
* *
20344822 AATGGTCAAAG-TCAACCGTCAA
1 AA-AGTCAAAGATCAACGGTCAA
20344844 TAGTTAAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.02
40 46 0.87
41 6 0.11
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (40 bp):
AAAGTCAAAGATCAACGGTCAAAGTCAACGGTAAACTATC
Found at i:20344898 original size:27 final size:27
Alignment explanation
Indices: 20344847--20344898 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
20344837 CCGTCAATAG
*
20344847 TTAAAGTCAACGGTCAATGATCAACGA
1 TTAAAGTCAACGGTCAACGATCAACGA
*
20344874 TTAAAGTCACCGGTCAACGATCAAC
1 TTAAAGTCAACGGTCAACGATCAAC
20344899 TCTCGATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (27 bp):
TTAAAGTCAACGGTCAACGATCAACGA
Found at i:20345913 original size:23 final size:23
Alignment explanation
Indices: 20345877--20345999 Score: 138
Period size: 23 Copynumber: 5.3 Consensus size: 23
20345867 CATATTTGTT
20345877 CACAATATCATATTAATATTTAAG
1 CACAA-ATCATATTAATATTTAAG
20345901 CACAAATCATATTAATATTTAAG
1 CACAAATCATATTAATATTTAAG
* ** * * *
20345924 CATAAATCACGTCAATACTTAAA
1 CACAAATCATATTAATATTTAAG
* *
20345947 CACAAATCACATTAATATTTAAT
1 CACAAATCATATTAATATTTAAG
* * *
20345970 AATAAATCATATTAATATTTTAG
1 CACAAATCATATTAATATTTAAG
20345993 CACAAAT
1 CACAAAT
20346000 ATAAGAACAC
Statistics
Matches: 81, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
23 76 0.94
24 5 0.06
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (23 bp):
CACAAATCATATTAATATTTAAG
Found at i:20345997 original size:46 final size:46
Alignment explanation
Indices: 20345883--20345999 Score: 153
Period size: 46 Copynumber: 2.5 Consensus size: 46
20345873 TGTTCACAAT
* *
20345883 ATCATATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAA
1 ATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGAATAA
** * * * *
20345929 ATCACGTCAATACTTAAACACAAATCACATTAATATTTAATAATAA
1 ATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGAATAA
*
20345975 ATCATATTAATATTTTAGCACAAAT
1 ATCATATTAATATTTAAGCACAAAT
20346000 ATAAGAACAC
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (46 bp):
ATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGAATAA
Found at i:20354914 original size:21 final size:21
Alignment explanation
Indices: 20354881--20354935 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
20354871 GGAAGTATGG
**
20354881 CTTGTATAAGTAGAA-GAGTCA
1 CTTGTATCGGTAGAACGA-TCA
*
20354902 CTTGTATCGGTAGAACTATCA
1 CTTGTATCGGTAGAACGATCA
20354923 CTTGTATCGGTAG
1 CTTGTATCGGTAG
20354936 GAGTCTGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (21 bp):
CTTGTATCGGTAGAACGATCA
Found at i:20357425 original size:9 final size:9
Alignment explanation
Indices: 20357384--20357423 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
20357374 CACATTTGAA
20357384 GAAGATGAT
1 GAAGATGAT
20357393 GAAGATGAT
1 GAAGATGAT
*
20357402 GAAGAAGAT
1 GAAGATGAT
*
20357411 GAAGGTGAT
1 GAAGATGAT
20357420 GAAG
1 GAAG
20357424 GTTTTAGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.38, T:0.17
Consensus pattern (9 bp):
GAAGATGAT
Found at i:20357941 original size:22 final size:21
Alignment explanation
Indices: 20357901--20357957 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
20357891 TATTTCTTAG
*
20357901 AAATAAAAATCGTACTTTTTAAA
1 AAATAAAAAT-ATA-TTTTTAAA
*
20357924 AAATAAAATATATATTTTTCAA
1 AAATAAAA-ATATATTTTTAAA
20357946 AAATAAAAATAT
1 AAATAAAAATAT
20357958 GAAGAAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.13
22 15 0.48
23 10 0.32
24 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATAAAAATATATTTTTAAA
Found at i:20358479 original size:13 final size:13
Alignment explanation
Indices: 20358461--20358485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20358451 ATATTTTTTA
20358461 TTTTTAAAATATT
1 TTTTTAAAATATT
20358474 TTTTTAAAATAT
1 TTTTTAAAATAT
20358486 CCTTTATGTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTAAAATATT
Found at i:20358992 original size:19 final size:18
Alignment explanation
Indices: 20358968--20359003 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20358958 AAAAATATTA
*
20358968 AAACAAATATAAGAACAAC
1 AAACAAAT-TAAAAACAAC
20358987 AAACAAATTAAAAACAA
1 AAACAAATTAAAAACAA
20359004 TATTAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.14, G:0.03, T:0.11
Consensus pattern (18 bp):
AAACAAATTAAAAACAAC
Found at i:20359014 original size:41 final size:43
Alignment explanation
Indices: 20358961--20359048 Score: 128
Period size: 41 Copynumber: 2.1 Consensus size: 43
20358951 TACACTTAAA
20358961 AATATTAAAACAAAT-ATAAGAACAACAAACAAATT-AAAA-AC
1 AATATTAAAACAAATCATAA-AACAACAAACAAATTGAAAATAC
* *
20359002 AATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAATAC
1 AATATTAAAACAAATCATAAAACAACAAACAAATTGAAAATAC
20359045 AATA
1 AATA
20359049 AGAACCCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 29 0.69
42 7 0.17
43 6 0.14
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.19
Consensus pattern (43 bp):
AATATTAAAACAAATCATAAAACAACAAACAAATTGAAAATAC
Found at i:20359245 original size:23 final size:23
Alignment explanation
Indices: 20359201--20359292 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
20359191 AAACAACAAT
*
20359201 AAAACAGCACC-AAAACA-T-CC
1 AAAACAACACCAAAAACAGTACC
* *
20359221 AAAACAACATCGAAAACAGTACC
1 AAAACAACACCAAAAACAGTACC
* * *
20359244 AAAATAGCACCAAAAATAGTACC
1 AAAACAACACCAAAAACAGTACC
* *
20359267 AAAGCTACACCAAAAACAGTACC
1 AAAACAACACCAAAAACAGTACC
20359290 AAA
1 AAA
20359293 GCTGCACAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 9 0.16
21 6 0.11
22 1 0.02
23 41 0.72
ACGTcount: A:0.57, C:0.27, G:0.08, T:0.09
Consensus pattern (23 bp):
AAAACAACACCAAAAACAGTACC
Found at i:20359293 original size:23 final size:23
Alignment explanation
Indices: 20359233--20359307 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
20359223 AACAACATCG
*
20359233 AAAACAGTACCAAA-ATAGCACCA
1 AAAACAGTACCAAAGCTA-CACCA
*
20359256 AAAATAGTACCAAAGCTACACCA
1 AAAACAGTACCAAAGCTACACCA
* *
20359279 AAAACAGTACCAAAGCTGCACAA
1 AAAACAGTACCAAAGCTACACCA
20359302 AAAACA
1 AAAACA
20359308 ACTTGCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 44 0.96
24 2 0.04
ACGTcount: A:0.56, C:0.25, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAACAGTACCAAAGCTACACCA
Found at i:20360870 original size:54 final size:53
Alignment explanation
Indices: 20360801--20360902 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
20360791 TTAATATAAT
* * * *
20360801 ATTTGGTATTTAAATTTAATATTTTTTTAA-TTTAGTATTTAATTTTTTTATTTA
1 ATTTGGTACTCAAATTTAATA-TTTTTTAAGTTGA-TATTTAAATTTTTTATTTA
*
20360855 ATTTGGTACTCAAATTTGATATTTTTTAAGTTGATATTTAAATTTTTT
1 ATTTGGTACTCAAATTTAATATTTTTTAAGTTGATATTTAAATTTTTT
20360903 GGGATCTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 21 0.50
54 21 0.50
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (53 bp):
ATTTGGTACTCAAATTTAATATTTTTTAAGTTGATATTTAAATTTTTTATTTA
Found at i:20361289 original size:58 final size:58
Alignment explanation
Indices: 20361139--20361291 Score: 168
Period size: 57 Copynumber: 2.6 Consensus size: 58
20361129 AAGCTTAGAG
* ** *
20361139 ACCAAATTAGGAAAAAATACCAAGTTCAAGTACTAAATTGGATCCAAAAAAAGTTTAAAT
1 ACCAAATTAAG-AAAAATGTCAAGTTCAA-TACCAAATTGGATCCAAAAAAAGTTTAAAT
* *
20361199 ACCAAATT-AGTAAAAATGTCAAGTTCAAATACCAAATTGGGT-C-AAAAAAGTTTAAGT
1 ACCAAATTAAG-AAAAATGTCAAGTTC-AATACCAAATTGGATCCAAAAAAAGTTTAAAT
*
20361256 ATCAAATTAAGAAAAAGTGTCAAGTTCAGATACCAA
1 ACCAAATTAAGAAAAA-TGTCAAGTTCA-ATACCAA
20361292 TATTATATTA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
57 26 0.32
58 20 0.25
59 25 0.31
60 10 0.12
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (58 bp):
ACCAAATTAAGAAAAATGTCAAGTTCAATACCAAATTGGATCCAAAAAAAGTTTAAAT
Found at i:20362623 original size:30 final size:30
Alignment explanation
Indices: 20362565--20362625 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
20362555 TACATATCAA
20362565 ATCTCTAAATATTTTAAATTATAACATTTG
1 ATCTCTAAATATTTTAAATTATAACATTTG
20362595 ATCTCTAAATATTTTAAATTATAACATTTG
1 ATCTCTAAATATTTTAAATTATAACATTTG
20362625 A
1 A
20362626 GTCTAATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (30 bp):
ATCTCTAAATATTTTAAATTATAACATTTG
Found at i:20370873 original size:23 final size:21
Alignment explanation
Indices: 20370847--20370891 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
20370837 TTAAAACCCT
20370847 AGAAAAAATGCAGAGAAAACTAA
1 AGAAAAAAT--AGAGAAAACTAA
*
20370870 AGAAAACATAGAGAAAACTAA
1 AGAAAAAATAGAGAAAACTAA
20370891 A
1 A
20370892 CCAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.67, C:0.09, G:0.16, T:0.09
Consensus pattern (21 bp):
AGAAAAAATAGAGAAAACTAA
Found at i:20371165 original size:21 final size:21
Alignment explanation
Indices: 20371139--20371193 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
20371129 TTGGAGGTGA
20371139 ATATCGTGATACCCAATAGGC
1 ATATCGTGATACCCAATAGGC
* *
20371160 ATATCGTGATACCCAATGGGG
1 ATATCGTGATACCCAATAGGC
*
20371181 ATATCGCGATACC
1 ATATCGTGATACC
20371194 ACTAAAGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
ATATCGTGATACCCAATAGGC
Found at i:20379353 original size:21 final size:19
Alignment explanation
Indices: 20379329--20379376 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
20379319 ATTTTGTAAT
*
20379329 TATAAATATTTTTTTATTATC
1 TATAAATA-TTTATTA-TATC
* *
20379350 TATAAAGATTTATTATATT
1 TATAAATATTTATTATATC
20379369 TATAAATA
1 TATAAATA
20379377 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.43
20 6 0.26
21 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TATAAATATTTATTATATC
Found at i:20385928 original size:13 final size:13
Alignment explanation
Indices: 20385910--20385984 Score: 63
Period size: 13 Copynumber: 6.2 Consensus size: 13
20385900 TTTTCGAAAA
20385910 AAAGTCAACGATC
1 AAAGTCAACGATC
20385923 AAAGTCAACGATC
1 AAAGTCAACGATC
20385936 -AA--C-A-G-TC
1 AAAGTCAACGATC
*
20385943 AAAGTCAACGGTC
1 AAAGTCAACGATC
** *
20385956 AGTGGTCAACGGTC
1 A-AAGTCAACGATC
20385970 AAAGTCAACGATC
1 AAAGTCAACGATC
20385983 AA
1 AA
20385985 CGGTCGGTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 1 0.02
10 2 0.04
11 1 0.02
12 3 0.06
13 27 0.54
14 11 0.22
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:20385984 original size:20 final size:20
Alignment explanation
Indices: 20385914--20385989 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
20385904 CGAAAAAAAG
*
20385914 TCAACGATCAAAGTCAACGA
1 TCAACGGTCAAAGTCAACGA
*
20385934 TCAACAGTCAAAGTCAACGGTCA
1 TCAACGGTCAAAGTCAAC-G--A
20385957 GTGGTCAACGGTCAAAGTCAACGA
1 ----TCAACGGTCAAAGTCAACGA
20385981 TCAACGGTC
1 TCAACGGTC
20385990 GGTCAACACC
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
20 25 0.54
21 1 0.02
23 1 0.02
24 1 0.02
26 1 0.02
27 17 0.37
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCAACGGTCAAAGTCAACGA
Found at i:20385989 original size:27 final size:27
Alignment explanation
Indices: 20385927--20385989 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
20385917 ACGATCAAAG
* *
20385927 TCAACGATCAACAGTCAAAGTCAACGG
1 TCAACGGTCAACAGTCAAAGTCAACGA
** *
20385954 TCAGTGGTCAACGGTCAAAGTCAACGA
1 TCAACGGTCAACAGTCAAAGTCAACGA
20385981 TCAACGGTC
1 TCAACGGTC
20385990 GGTCAACACC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.17
Consensus pattern (27 bp):
TCAACGGTCAACAGTCAAAGTCAACGA
Found at i:20386110 original size:15 final size:15
Alignment explanation
Indices: 20386092--20386157 Score: 78
Period size: 15 Copynumber: 4.0 Consensus size: 15
20386082 AAATGGGTTT
20386092 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
20386107 GGTTTGGTTTAAATGAATGTG
1 GGTTTGGTTT--A--AA--TG
20386128 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
20386143 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
20386158 AATGTGGGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
15 27 0.60
17 3 0.07
19 3 0.07
21 12 0.27
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (15 bp):
GGTTTGGTTTAAATG
Found at i:20386116 original size:20 final size:20
Alignment explanation
Indices: 20386053--20386152 Score: 111
Period size: 20 Copynumber: 5.2 Consensus size: 20
20386043 GGTTCAATTA
*
20386053 GTTTGGTTCAAATGGGTTTG
1 GTTTGGTTTAAATGGGTTTG
*
20386073 GTTAGGTTTAAATGGGTTTG
1 GTTTGGTTTAAATGGGTTTG
20386093 GTTTGGTTTAAAT--G---G
1 GTTTGGTTTAAATGGGTTTG
** *
20386108 GTTTGGTTTAAATGAATGTGG
1 GTTTGGTTTAAATGGGT-TTG
20386129 GTTTGGTTTAAATGGGTTTG
1 GTTTGGTTTAAATGGGTTTG
20386149 GTTT
1 GTTT
20386153 AAATGAATGT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
15 14 0.21
18 1 0.01
20 36 0.54
21 16 0.24
ACGTcount: A:0.18, C:0.01, G:0.34, T:0.47
Consensus pattern (20 bp):
GTTTGGTTTAAATGGGTTTG
Found at i:20386131 original size:21 final size:21
Alignment explanation
Indices: 20386105--20386178 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
20386095 TTGGTTTAAA
20386105 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATG
20386126 TGGGTTTGGTTT--A--AA--
1 TGGGTTTGGTTTAAATGAATG
20386141 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATG
20386162 TGGGTTTGGTTTAAATG
1 TGGGTTTGGTTTAAATG
20386179 GGATTTGAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
15 12 0.26
17 3 0.06
19 3 0.06
21 29 0.62
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.45
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATG
Found at i:20386139 original size:36 final size:36
Alignment explanation
Indices: 20386092--20386185 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
20386082 AAATGGGTTT
20386092 GGTTTGGTTTAAATGGGTTTGGTTTAAATGAATGTG
1 GGTTTGGTTTAAATGGGTTTGGTTTAAATGAATGTG
20386128 GGTTTGGTTTAAATGGGTTTGGTTTAAATGAATGTG
1 GGTTTGGTTTAAATGGGTTTGGTTTAAATGAATGTG
20386164 GGTTTGGTTTAAATGGGATTTG
1 GGTTTGGTTTAAATGGG-TTTG
20386186 AGCTTGATGG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 53 0.93
37 4 0.07
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (36 bp):
GGTTTGGTTTAAATGGGTTTGGTTTAAATGAATGTG
Found at i:20388246 original size:62 final size:62
Alignment explanation
Indices: 20388149--20388272 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
20388139 GACACAAAAT
20388149 CCACCACATCCCTTTTCAAACCCTTCCACCAATACCTGTCACGAAGGTTTTTATACATCTTA
1 CCACCACATCCCTTTTCAAACCCTTCCACCAATACCTGTCACGAAGGTTTTTATACATCTTA
20388211 CCACCACATCCCTTTTCAAACCCTTCCACCAATACCTGTCACGAAGGTTTTTATACATCTTA
1 CCACCACATCCCTTTTCAAACCCTTCCACCAATACCTGTCACGAAGGTTTTTATACATCTTA
20388273 TCTCCGCCAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.27, C:0.35, G:0.06, T:0.31
Consensus pattern (62 bp):
CCACCACATCCCTTTTCAAACCCTTCCACCAATACCTGTCACGAAGGTTTTTATACATCTTA
Found at i:20392487 original size:13 final size:13
Alignment explanation
Indices: 20392469--20392531 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
20392459 TTTTTTGAAA
20392469 AAAGTCAACGATC
1 AAAGTCAACGATC
20392482 AAAGTCAACGATC
1 AAAGTCAACGATC
* *
20392495 AACAATCAAAG-TC
1 AA-AGTCAACGATC
*
20392508 AACGGTCAAC-AGTC
1 AA-AGTCAACGA-TC
20392522 AAAGTCAACG
1 AAAGTCAACG
20392532 GTCGGTCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 30 0.75
14 10 0.25
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:20392532 original size:20 final size:20
Alignment explanation
Indices: 20392472--20392534 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
20392462 TTTGAAAAAA
*
20392472 GTCAACGATCAAAGTCAACG
1 GTCAACAATCAAAGTCAACG
*
20392492 ATCAACAATCAAAGTCAACG
1 GTCAACAATCAAAGTCAACG
*
20392512 GTCAACAGTCAAAGTCAACG
1 GTCAACAATCAAAGTCAACG
20392532 GTC
1 GTC
20392535 GGTCAACGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.16
Consensus pattern (20 bp):
GTCAACAATCAAAGTCAACG
Found at i:20392541 original size:11 final size:11
Alignment explanation
Indices: 20392525--20392575 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
20392515 AACAGTCAAA
20392525 GTCAACGGTCG
1 GTCAACGGTCG
*
20392536 GTCAACGGTCA
1 GTCAACGGTCG
*
20392547 ATCAACGGTCG
1 GTCAACGGTCG
20392558 GTCAACGGTCG
1 GTCAACGGTCG
*
20392569 GTTAACG
1 GTCAACG
20392576 CCGATCAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:20392554 original size:22 final size:24
Alignment explanation
Indices: 20392510--20392567 Score: 93
Period size: 22 Copynumber: 2.5 Consensus size: 24
20392500 TCAAAGTCAA
*
20392510 CGGTCAACAGTCAAAGTCAACGGT
1 CGGTCAACGGTCAAAGTCAACGGT
20392534 CGGTCAACGGTC-AA-TCAACGGT
1 CGGTCAACGGTCAAAGTCAACGGT
20392556 CGGTCAACGGTC
1 CGGTCAACGGTC
20392568 GGTTAACGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 20 0.61
23 2 0.06
24 11 0.33
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (24 bp):
CGGTCAACGGTCAAAGTCAACGGT
Found at i:20392628 original size:14 final size:15
Alignment explanation
Indices: 20392609--20392643 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20392599 TGGGTTGGAC
*
20392609 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
20392623 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
20392638 TTGGTT
1 TTGGTT
20392644 TGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:20392641 original size:20 final size:20
Alignment explanation
Indices: 20392618--20392664 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20392608 CTTGGTTCAA
20392618 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
*
20392638 TTGGTTTGGTTTAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
20392658 TTGGTTT
1 TTGGTTT
20392665 AAATGAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.02, G:0.34, T:0.51
Consensus pattern (20 bp):
TTGGTTTGGTTCAAATGGGT
Found at i:20392658 original size:15 final size:15
Alignment explanation
Indices: 20392640--20392669 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20392630 AAATGGGTTT
20392640 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
20392655 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
20392670 AATGTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTGGTTTAAATG
Found at i:20393923 original size:18 final size:18
Alignment explanation
Indices: 20393900--20393947 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
20393890 TAATTCTCTT
*
20393900 ACGAGCCAGTATGCTCCA
1 ACGAGCCAGTATGCTCAA
*
20393918 ACGAGCCAATATGCTCAA
1 ACGAGCCAGTATGCTCAA
*
20393936 ACAAGCCAGTAT
1 ACGAGCCAGTAT
20393948 TCTATTCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (18 bp):
ACGAGCCAGTATGCTCAA
Found at i:20397684 original size:21 final size:21
Alignment explanation
Indices: 20397658--20397700 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
20397648 AACGGTCAAA
20397658 GTCAACAGTCAACGATCAATG
1 GTCAACAGTCAACGATCAATG
*
20397679 GTCAACGGTCAACGATCAATG
1 GTCAACAGTCAACGATCAATG
20397700 G
1 G
20397701 GTCGGGTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (21 bp):
GTCAACAGTCAACGATCAATG
Found at i:20397697 original size:14 final size:14
Alignment explanation
Indices: 20397645--20397697 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
20397635 TCTCAAAAAA
*
20397645 ATCAACGGTCAAAG
1 ATCAACGGTCAACG
*
20397659 -TCAACAGTCAACG
1 ATCAACGGTCAACG
*
20397672 ATCAATGGTCAACG
1 ATCAACGGTCAACG
* *
20397686 GTCAACGATCAA
1 ATCAACGGTCAA
20397698 TGGGTCGGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (14 bp):
ATCAACGGTCAACG
Found at i:20397774 original size:24 final size:24
Alignment explanation
Indices: 20397746--20397802 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
20397736 GTTAGGTTCA
*
20397746 ATTAGGTTTGGGCTATAAGGGTTT
1 ATTAGGTTCGGGCTATAAGGGTTT
20397770 ATTAGGTTCGGGCTATAAGGGTTT
1 ATTAGGTTCGGGCTATAAGGGTTT
20397794 ATTAGGTTC
1 ATTAGGTTC
20397803 AGGCAAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.07, G:0.32, T:0.40
Consensus pattern (24 bp):
ATTAGGTTCGGGCTATAAGGGTTT
Found at i:20404474 original size:20 final size:21
Alignment explanation
Indices: 20404445--20404485 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
20404435 CTCAAAAAAA
*
20404445 ATCAATGGTCAA-AGTCAACG
1 ATCAACGGTCAACAGTCAACG
20404465 ATCAACGGTCAACAGTCAACG
1 ATCAACGGTCAACAGTCAACG
20404486 GGTCGGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (21 bp):
ATCAACGGTCAACAGTCAACG
Found at i:20404569 original size:21 final size:21
Alignment explanation
Indices: 20404543--20404592 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
20404533 GGTTTGAGTG
20404543 TTGGGTTTGGTTCAATTGGGT
1 TTGGGTTTGGTTCAATTGGGT
20404564 TTGGGTTTGGTTCAATTGGGT
1 TTGGGTTTGGTTCAATTGGGT
*
20404585 TTAGGTTT
1 TTGGGTTT
20404593 AGTTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.10, C:0.04, G:0.36, T:0.50
Consensus pattern (21 bp):
TTGGGTTTGGTTCAATTGGGT
Found at i:20405880 original size:30 final size:30
Alignment explanation
Indices: 20405841--20405917 Score: 145
Period size: 30 Copynumber: 2.5 Consensus size: 30
20405831 TCCCCAAAAA
20405841 CCCTCAAAACTTTTACTCTCTCTCACTTTCC
1 CCCT-AAAACTTTTACTCTCTCTCACTTTCC
20405872 CCCTAAAACTTTTACTCTCTCTCACTTTCC
1 CCCTAAAACTTTTACTCTCTCTCACTTTCC
20405902 CCCTAAAACTTTTACT
1 CCCTAAAACTTTTACT
20405918 TCCCTCCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 42 0.91
31 4 0.09
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (30 bp):
CCCTAAAACTTTTACTCTCTCTCACTTTCC
Found at i:20409083 original size:36 final size:36
Alignment explanation
Indices: 20409007--20409083 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
20408997 ATATAATCAG
* * **
20409007 TCACATGACATGAAGAATATACCCACATATTTTCTA
1 TCACATGACATGAAGAACATACCAACATATTAACTA
* * *
20409043 TCACATGGCATGAAGAACATACTAACATATTAACTT
1 TCACATGACATGAAGAACATACCAACATATTAACTA
20409079 TCACA
1 TCACA
20409084 ACAATCATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (36 bp):
TCACATGACATGAAGAACATACCAACATATTAACTA
Found at i:20409863 original size:21 final size:22
Alignment explanation
Indices: 20409830--20409872 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
20409820 GCTATTATTC
* * *
20409830 AAAACTTGCGTTTTAATGGCTA
1 AAAACTTGAGTTTAAAGGGCTA
20409852 AAAACTT-AGTTTAAAGGGCTA
1 AAAACTTGAGTTTAAAGGGCTA
20409873 GATATCATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (22 bp):
AAAACTTGAGTTTAAAGGGCTA
Found at i:20413900 original size:25 final size:24
Alignment explanation
Indices: 20413830--20413900 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 24
20413820 ACATAAATTT
*
20413830 GAGAAAAAAAAGTTTTGGGGGTTTG
1 GAGAAAAAAAA-TTTTAGGGGTTTG
*
20413855 G-GAAGAGAAAATTTTTAGGGGTTTG
1 GAGAA-A-AAAAATTTTAGGGGTTTG
20413880 AGAGAAATAAAAATTTT-GGGG
1 -GAGAAA-AAAAATTTTAGGGG
20413901 AAAAGCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 3 0.08
25 18 0.47
26 14 0.37
27 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (24 bp):
GAGAAAAAAAATTTTAGGGGTTTG
Found at i:20414013 original size:18 final size:18
Alignment explanation
Indices: 20413968--20414014 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
20413958 AGGGAAGTAA
20413968 AATGATTTG-A-TATTTG
1 AATGATTTGAATTATTTG
* * *
20413984 ATTTATTCGAATTATTTG
1 AATGATTTGAATTATTTG
20414002 AATGATTTGAATT
1 AATGATTTGAATT
20414015 CGAAAATTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 6 0.26
17 1 0.04
18 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (18 bp):
AATGATTTGAATTATTTG
Found at i:20415071 original size:29 final size:30
Alignment explanation
Indices: 20415029--20415085 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
20415019 TAGTTTAATG
* *
20415029 TGTAGTTTTATACATG-TATTTTGATTTTT
1 TGTAATTTTATACATGAAATTTTGATTTTT
20415058 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTTTATACATGAAATTTTGATTT
20415086 GATCAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (30 bp):
TGTAATTTTATACATGAAATTTTGATTTTT
Found at i:20417066 original size:30 final size:30
Alignment explanation
Indices: 20417032--20417195 Score: 146
Period size: 30 Copynumber: 5.6 Consensus size: 30
20417022 CCCTGAACTG
*
20417032 TCCAAAAATCATATTTTAACCCCAAACTTT
1 TCCAAAAATCACATTTTAACCCCAAACTTT
*
20417062 TCC-AAAATCACATTTTAACCCCTAAAATTT
1 TCCAAAAATCACATTTTAACCCC-AAACTTT
*
20417092 TCC-AAAATCACATTTTAACCCTTAAAC-TT
1 TCCAAAAATCACATTTTAACCC-CAAACTTT
* * *
20417121 T-CAAAAATTACA-TTTATGCCCTCGAAC--T
1 TCCAAAAATCACATTTTA-ACCC-CAAACTTT
* *
20417149 TCCAAAAATTACATTTTAACCCCCAAACTTC
1 TCCAAAAATCACATTTTAA-CCCCAAACTTT
*
20417180 T-CAAAAATTACATTTT
1 TCCAAAAATCACATTTT
20417196 TCCCTTGAAC
Statistics
Matches: 114, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
28 7 0.06
29 51 0.45
30 55 0.48
31 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.01, T:0.34
Consensus pattern (30 bp):
TCCAAAAATCACATTTTAACCCCAAACTTT
Found at i:20417069 original size:29 final size:29
Alignment explanation
Indices: 20417036--20417195 Score: 139
Period size: 29 Copynumber: 5.4 Consensus size: 29
20417026 GAACTGTCCA
*
20417036 AAAATCATATTTTAACCCCAAACTTTTCC
1 AAAATCACATTTTAACCCCAAACTTTTCC
*
20417065 AAAATCACATTTTAACCCCTAAAATTTTCC
1 AAAATCACATTTTAACCCC-AAACTTTTCC
* *
20417095 AAAATCACATTTTAACCCTTAAAC-TTTCA
1 AAAATCACATTTTAACCC-CAAACTTTTCC
* * *
20417124 AAAATTACA-TTTATGCCCTCGAAC--TTCC
1 AAAATCACATTTTA-ACCC-CAAACTTTTCC
* * *
20417152 AAAAATTACATTTTAACCCCCAAACTTCTCA
1 -AAAATCACATTTTAA-CCCCAAACTTTTCC
*
20417183 AAAATTACATTTT
1 AAAATCACATTTT
20417196 TCCCTTGAAC
Statistics
Matches: 109, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
28 7 0.06
29 50 0.46
30 50 0.46
31 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAATCACATTTTAACCCCAAACTTTTCC
Done.