Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
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 79 of 143
Found at i:25363432 original size:24 final size:24
Alignment explanation
Indices: 25363411--25363459 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25363401 ACCAAAAAGC
25363411 AGAAGCAA-TATTTGAGAGAAAACA
1 AGAA-CAAGTATTTGAGAGAAAACA
* *
25363435 AGAACAAGTTTTTGAGAGAGAACA
1 AGAACAAGTATTTGAGAGAAAACA
25363459 A
1 A
25363460 AAGTTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.18
Consensus pattern (24 bp):
AGAACAAGTATTTGAGAGAAAACA
Found at i:25365516 original size:26 final size:26
Alignment explanation
Indices: 25365461--25365543 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
25365451 TCATATGAGC
* * *
25365461 CCAGT-CAGTAAACCGCTCTTACGAGA
1 CCAGTACAGTATATCGCTCTTAC-AAA
*
25365487 -CAGTACAGTATGTCGCTCTTACAAA
1 CCAGTACAGTATATCGCTCTTACAAA
* * * *
25365512 CCAGTGCCGTATATTGCTCTTACAAG
1 CCAGTACAGTATATCGCTCTTACAAA
25365538 CCAGTA
1 CCAGTA
25365544 TCGCTCTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
25 6 0.13
26 39 0.87
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (26 bp):
CCAGTACAGTATATCGCTCTTACAAA
Found at i:25365551 original size:19 final size:19
Alignment explanation
Indices: 25365527--25365563 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25365517 GCCGTATATT
25365527 GCTCTTACAAGCCAGTATC
1 GCTCTTACAAGCCAGTATC
**
25365546 GCTCTTATGAGCCAGTAT
1 GCTCTTACAAGCCAGTAT
25365564 TGTTCCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (19 bp):
GCTCTTACAAGCCAGTATC
Found at i:25365596 original size:18 final size:18
Alignment explanation
Indices: 25365554--25365604 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
25365544 TCGCTCTTAT
* * *
25365554 GAGCCAGTATTGTTCCAAT
1 GAGCCAGTA-TGCTCAAAC
25365573 GAGCCAGTATGCTCAAAC
1 GAGCCAGTATGCTCAAAC
25365591 GAGCCAGTAATGCT
1 GAGCCAGT-ATGCT
25365605 ATTCCTTCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (18 bp):
GAGCCAGTATGCTCAAAC
Found at i:25366903 original size:16 final size:18
Alignment explanation
Indices: 25366874--25366907 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
25366864 TCATTTTCTT
25366874 TACTTCTAATTTTGTTTA
1 TACTTCTAATTTTGTTTA
25366892 TACTT-TAA-TTTGTTTA
1 TACTTCTAATTTTGTTTA
25366908 ATTACTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (18 bp):
TACTTCTAATTTTGTTTA
Found at i:25366913 original size:18 final size:19
Alignment explanation
Indices: 25366873--25366913 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
25366863 CTCATTTTCT
25366873 TTACTTCTAATTTTGTTTA
1 TTACTTCTAATTTTGTTTA
25366892 -TACTT-TAA-TTTGTTTAA
1 TTACTTCTAATTTTGTTT-A
25366909 TTACT
1 TTACT
25366914 CTTTTACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (19 bp):
TTACTTCTAATTTTGTTTA
Found at i:25369272 original size:7 final size:7
Alignment explanation
Indices: 25369260--25369284 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25369250 AATTGGACCC
25369260 AATTTTA
1 AATTTTA
25369267 AATTTTA
1 AATTTTA
25369274 AATTTTA
1 AATTTTA
25369281 AATT
1 AATT
25369285 ATTTTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:25369288 original size:17 final size:17
Alignment explanation
Indices: 25369268--25369323 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
25369258 CCAATTTTAA
25369268 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAACTT
* *
25369285 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAACTT
25369302 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAACTT
25369319 ATTTT
1 ATTTT
25369324 TTAGTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 6 0.17
17 29 0.83
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAACTT
Found at i:25369337 original size:35 final size:33
Alignment explanation
Indices: 25369268--25369352 Score: 116
Period size: 35 Copynumber: 2.5 Consensus size: 33
25369258 CCAATTTTAA
25369268 ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAATTATTTTAAGTTTAAATTT
* *
25369302 ATTTTAAATTTAAACTTATTTTTTAGTTTGAATTT
1 ATTTTAAATTTAAA-TTA-TTTTAAGTTTAAATTT
*
25369337 ATTTTGAATTTAAATT
1 ATTTTAAATTTAAATT
25369353 TAAAATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 6 0.13
34 13 0.28
35 27 0.59
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTAAGTTTAAATTT
Found at i:25369341 original size:17 final size:17
Alignment explanation
Indices: 25369277--25369354 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
25369267 AATTTTAAAT
25369277 TTTAAA-TTATTTTAAG
1 TTTAAATTTATTTTAAG
*
25369293 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAG
* *
25369310 TTTAAACTTATTTTTTAG
1 TTTAAATTTA-TTTTAAG
*
25369328 TTTGAATTTATTTTGAA-
1 TTTAAATTTATTTT-AAG
25369345 TTTAAATTTA
1 TTTAAATTTA
25369355 AAATTTAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.12
17 31 0.61
18 14 0.27
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:25371060 original size:29 final size:29
Alignment explanation
Indices: 25371026--25371344 Score: 235
Period size: 29 Copynumber: 11.0 Consensus size: 29
25371016 CGAAAACCAC
*
25371026 ATTTTTACCCTCAAACTTCTTAAAAATTAT
1 ATTTTTACCC-CAAACTTCTCAAAAATTAT
*
25371056 ATTTTTACCCTTAAACTT-TACAAAAATTAT
1 ATTTTTACCC-CAAACTTCT-CAAAAATTAT
* * * * *
25371086 ATTTTGACCCCAAACTTCT-GATAATCAC
1 ATTTTTACCCCAAACTTCTCAAAAATTAT
*
25371114 ATTTTTACCCCCAAACTTCTCAAAAATTAA
1 ATTTTTA-CCCCAAACTTCTCAAAAATTAT
* *
25371144 ACTTTTACCCCTAAACTT-TACAAAAATTAC
1 ATTTTTACCCC-AAACTTCT-CAAAAATTAT
* *
25371174 ATTTTGA-CCCGAACTTCT-AAAAATTAT
1 ATTTTTACCCCAAACTTCTCAAAAATTAT
* *
25371201 ATTTTTACCCTAAACTTCTCAAAAA-TAC
1 ATTTTTACCCCAAACTTCTCAAAAATTAT
** * *
25371229 ATTTTTACCTCTGAACTT-TCAAAAATCAC
1 ATTTTTACC-CCAAACTTCTCAAAAATTAT
* *
25371258 ATTTTTACCCCTAAACTTTTCCAAAAATTAC
1 ATTTTTACCCC-AAACTTCT-CAAAAATTAT
*** *
25371289 A-TTTTATCCTTGAACTT-TCAAAAATTAC
1 ATTTTTA-CCCCAAACTTCTCAAAAATTAT
* *
25371317 ATTTTTACCCCCGAACATC-CAAAAATTA
1 ATTTTTA-CCCCAAACTTCTCAAAAATTA
25371345 CCATTTTTGC
Statistics
Matches: 237, Mismatches: 35, Indels: 35
0.77 0.11 0.11
Matches are distributed among these distances:
27 14 0.06
28 55 0.23
29 78 0.33
30 78 0.33
31 12 0.05
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTTTTACCCCAAACTTCTCAAAAATTAT
Found at i:25371062 original size:30 final size:29
Alignment explanation
Indices: 25371024--25371380 Score: 270
Period size: 30 Copynumber: 12.2 Consensus size: 29
25371014 TTCGAAAACC
*
25371024 ACATTTTTACCCTCAAACTTCTTAAAAATT
1 ACATTTTTACCCTCAAACTT-TCAAAAATT
* *
25371054 ATATTTTTACCCTTAAACTTTACAAAAATT
1 ACATTTTTACCCTCAAACTTT-CAAAAATT
* * * * *
25371084 ATATTTTGACCC-CAAAC-TTCTGATAATC
1 ACATTTTTACCCTCAAACTTTC-AAAAATT
*
25371112 ACATTTTTACCCCCAAACTTCTCAAAAATT
1 ACATTTTTACCCTCAAACTT-TCAAAAATT
* *
25371142 AAACTTTTACCC-CTAAACTTTACAAAAATT
1 ACATTTTTACCCTC-AAACTTT-CAAAAATT
* *
25371172 ACATTTTGA-CC-CGAAC-TTCTAAAAATT
1 ACATTTTTACCCTCAAACTTTC-AAAAATT
*
25371199 ATATTTTTACCCT-AAACTTCTCAAAAA-T
1 ACATTTTTACCCTCAAACTT-TCAAAAATT
* *
25371227 ACATTTTTA-CCTCTGAACTTTCAAAAATC
1 ACATTTTTACCCTC-AAACTTTCAAAAATT
25371256 ACATTTTTACCC-CTAAACTTTTCCAAAAATT
1 ACATTTTTACCCTC-AAAC-TTT-CAAAAATT
* **
25371287 ACA-TTTTATCCTTGAACTTTCAAAAATT
1 ACATTTTTACCCTCAAACTTTCAAAAATT
* * * *
25371315 ACATTTTTACCCCCGAACATCCAAAAATT
1 ACATTTTTACCCTCAAACTTTCAAAAATT
* * *
25371344 ACCATTTTTGCCCTCGAAA-TTCCAAAAATC
1 A-CATTTTTACCCTC-AAACTTTCAAAAATT
25371374 ACATTTT
1 ACATTTT
25371381 CAACCTTAAA
Statistics
Matches: 265, Mismatches: 40, Indels: 45
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.00
27 20 0.08
28 51 0.19
29 70 0.26
30 109 0.41
31 14 0.05
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
ACATTTTTACCCTCAAACTTTCAAAAATT
Found at i:25371122 original size:58 final size:59
Alignment explanation
Indices: 25371024--25371380 Score: 324
Period size: 59 Copynumber: 6.1 Consensus size: 59
25371014 TTCGAAAACC
* * *
25371024 ACATTTTTA-CCCTCAAACTTCTTAAAAATTATATTTTTACCCTTAAACTTTACAAAAATT
1 ACATTTTTACCCCT-AAACTTCTCAAAAATTACATTTTTACCCTTGAACTTT-CAAAAATT
* * * * * ***
25371084 ATATTTTGACCCC-AAACTTCT-GATAATCACATTTTTACCCCCAAACTTCTCAAAAATT
1 ACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTACCCTTGAACTT-TCAAAAATT
* * *
25371142 AAACTTTTACCCCTAAACTT-TACAAAAATTACATTTTGACCC--GAAC-TTCTAAAAATT
1 ACATTTTTACCCCTAAACTTCT-CAAAAATTACATTTTTACCCTTGAACTTTC-AAAAATT
* *
25371199 ATATTTTTA-CCCTAAACTTCTCAAAAA-TACATTTTTA-CCTCTGAACTTTCAAAAATC
1 ACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTACCCT-TGAACTTTCAAAAATT
* *
25371256 ACATTTTTACCCCTAAACTTTTCCAAAAATTACA-TTTTATCCTTGAACTTTCAAAAATT
1 ACATTTTTACCCCTAAACTTCT-CAAAAATTACATTTTTACCCTTGAACTTTCAAAAATT
** * * * * * *
25371315 ACATTTTTACCCCCGAACATC-CAAAAATTACCATTTTTGCCCTCGAAATTCCAAAAATC
1 ACATTTTTACCCCTAAACTTCTCAAAAATTA-CATTTTTACCCTTGAACTTTCAAAAATT
25371374 ACATTTT
1 ACATTTT
25371381 CAACCTTAAA
Statistics
Matches: 247, Mismatches: 33, Indels: 35
0.78 0.10 0.11
Matches are distributed among these distances:
54 2 0.01
55 9 0.04
56 18 0.07
57 43 0.17
58 59 0.24
59 84 0.34
60 29 0.12
61 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (59 bp):
ACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTACCCTTGAACTTTCAAAAATT
Found at i:25371233 original size:115 final size:116
Alignment explanation
Indices: 25371069--25371327 Score: 321
Period size: 115 Copynumber: 2.2 Consensus size: 116
25371059 TTTACCCTTA
* * *
25371069 AACTTTACAAAAATTATATTTTGACCCCAAACTTCTGATAATCACATTTTTACCCCCAAACTTCT
1 AACTTT-CAAAAATTATATTTTTACCCCAAACTTCTAAAAATCACATTTTTACCCCCAAACTT-T
*
25371134 CAAAAATTAAACTTTTACCCCTAAAC-TTTACAAAAATTACATTTTGA-CC-CG
64 CAAAAATCAAACTTTTACCCCTAAACTTTTACAAAAATTACATTTT-ATCCTCG
* * **
25371185 AAC-TTCTAAAAATTATATTTTTACCCTAAACTTCTCAAAAAT-ACATTTTTACCTCTGAACTTT
1 AACTTTC-AAAAATTATATTTTTACCCCAAACTTCT-AAAAATCACATTTTTACCCCCAAACTTT
* * * *
25371248 CAAAAATCACATTTTTACCCCTAAACTTTTCCAAAAATTACATTTTATCCTTG
64 CAAAAATCAAACTTTTACCCCTAAACTTTTACAAAAATTACATTTTATCCTCG
*
25371301 AACTTTCAAAAATTACATTTTTACCCC
1 AACTTTCAAAAATTATATTTTTACCCC
25371328 CGAACATCCA
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
114 26 0.21
115 65 0.53
116 29 0.24
117 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (116 bp):
AACTTTCAAAAATTATATTTTTACCCCAAACTTCTAAAAATCACATTTTTACCCCCAAACTTTCA
AAAATCAAACTTTTACCCCTAAACTTTTACAAAAATTACATTTTATCCTCG
Found at i:25375963 original size:15 final size:14
Alignment explanation
Indices: 25375945--25375993 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
25375935 TAATAAATAA
25375945 AAAATATATAAAATT
1 AAAATATATAAAA-T
25375960 AAAATAT-TAAAAT
1 AAAATATATAAAAT
*
25375973 AAAATAAAATAAAAT
1 AAAAT-ATATAAAAT
25375988 AAAATA
1 AAAATA
25375994 AATATTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 6 0.19
14 7 0.23
15 18 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:25375977 original size:5 final size:5
Alignment explanation
Indices: 25375967--25375995 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
25375957 ATTAAAATAT
25375967 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
25375996 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:25378514 original size:20 final size:22
Alignment explanation
Indices: 25378475--25378519 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
25378465 GATAAGATGC
**
25378475 TATTTAATTTTTAATTTTAT-T
1 TATTTAATTTTTAACATTATAT
25378496 TATTT-ATTTTTAACATTATAT
1 TATTTAATTTTTAACATTATAT
25378517 TAT
1 TAT
25378520 CTTTTAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTAATTTTTAACATTATAT
Found at i:25379027 original size:20 final size:19
Alignment explanation
Indices: 25379002--25379044 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
25378992 TAGCTTTACT
25379002 TTTATTATCTA-TATAATAAA
1 TTTATT-TCTATTAT-ATAAA
*
25379022 TTTATTTTTATTATATAAA
1 TTTATTTCTATTATATAAA
25379041 TTTA
1 TTTA
25379045 AGTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTTCTATTATATAAA
Found at i:25379051 original size:22 final size:20
Alignment explanation
Indices: 25379013--25379065 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
25379003 TTATTATCTA
*
25379013 TATAATAAATTT-ATTTTTAT
1 TATAATAAATTTAAGTTTT-T
25379033 TAT-ATAAATTTAAGTTTTT
1 TATAATAAATTTAAGTTTTT
25379052 TATAATAAATTTAA
1 TATAATAAATTTAA
25379066 ATATCAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATAATAAATTTAAGTTTTT
Found at i:25380508 original size:30 final size:30
Alignment explanation
Indices: 25380449--25380682 Score: 158
Period size: 30 Copynumber: 7.9 Consensus size: 30
25380439 TAAGGAAAAA
* * *
25380449 TAGGGGT-AAAATCAAAATTTTGGAAAGTT
1 TAGGGGTCAAAATGAAATTTTTAGAAAGTT
* *
25380478 TAGGGGTTAAAATGAAATTTTTAGATAGTT
1 TAGGGGTCAAAATGAAATTTTTAGAAAGTT
* * *
25380508 TGAGGGTTAAAAATGAAA-TTTTAGAATGTT
1 T-AGGGGTCAAAATGAAATTTTTAGAAAGTT
* * * *
25380538 CAAGGGTCAAAAT-ATATTTTTCA-AAAATT
1 TAGGGGTCAAAATGAAATTTTT-AGAAAGTT
* * *
25380567 TAAAGGGTCAAAATGACATTTCTAGAAAGTT
1 T-AGGGGTCAAAATGAAATTTTTAGAAAGTT
* * *
25380598 TAGGTGTCAAAATGATATTTTTAAAAAGTT
1 TAGGGGTCAAAATGAAATTTTTAGAAAGTT
* * * * *
25380628 CAGGGATCGAAATGACATTTTCAGAAAGTT
1 TAGGGGTCAAAATGAAATTTTTAGAAAGTT
*
25380658 T-GGAGATCAAAAT-ATAA-TTTTAGAA
1 TAGG-GGTCAAAATGA-AATTTTTAGAA
25380683 CAAAACAAGG
Statistics
Matches: 161, Mismatches: 35, Indels: 18
0.75 0.16 0.08
Matches are distributed among these distances:
28 2 0.01
29 34 0.21
30 99 0.61
31 26 0.16
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.34
Consensus pattern (30 bp):
TAGGGGTCAAAATGAAATTTTTAGAAAGTT
Found at i:25380818 original size:32 final size:32
Alignment explanation
Indices: 25380782--25380845 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
25380772 GAAATGAAAT
* *
25380782 CAAAAGGGA-AAATTGAAATAAATTAAAAATAG
1 CAAAA-GGACAAATTGAAACAAATAAAAAATAG
25380814 CAAAAGGACCAAATTGAAACAAATAAAAAATA
1 CAAAAGGA-CAAATTGAAACAAATAAAAAATA
25380846 CGGAATGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 3 0.11
32 5 0.18
33 20 0.71
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (32 bp):
CAAAAGGACAAATTGAAACAAATAAAAAATAG
Found at i:25381133 original size:22 final size:22
Alignment explanation
Indices: 25381107--25381164 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
25381097 GGCCATCGGA
*
25381107 GCCACCATCGACTCCACCTCCG
1 GCCACCGTCGACTCCACCTCCG
* * *
25381129 GCCACCGTCAACTCCGCCTCTG
1 GCCACCGTCGACTCCACCTCCG
*
25381151 GCCACTGTCGACTC
1 GCCACCGTCGACTC
25381165 TGTCGCTGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.50, G:0.17, T:0.17
Consensus pattern (22 bp):
GCCACCGTCGACTCCACCTCCG
Found at i:25381435 original size:2 final size:2
Alignment explanation
Indices: 25381428--25381487 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
25381418 GGTCAAAGTA
25381428 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
*
25381470 AT AT -T AT AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT
25381488 TAGTGTTAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25381488 original size:14 final size:14
Alignment explanation
Indices: 25381432--25381534 Score: 57
Period size: 14 Copynumber: 7.0 Consensus size: 14
25381422 AAAGTAATAT
*
25381432 ATATATATATATATAT
1 ATAT-TATAT-TATAA
*
25381448 ATATATATATATATAT
1 ATAT-TATAT-TATAA
25381464 ATATATATATTATAA
1 ATAT-TATATTATAA
*
25381479 ATATTATATTAGT-G
1 ATATTATATTA-TAA
* * *
25381493 TTAATATATGATAA
1 ATATTATATTATAA
*
25381507 ATAATAGTATTAT-A
1 ATATTA-TATTATAA
*
25381521 ATAATATATTATAA
1 ATATTATATTATAA
25381535 TAAAAAAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
13 7 0.09
14 28 0.37
15 14 0.19
16 26 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.47
Consensus pattern (14 bp):
ATATTATATTATAA
Found at i:25381499 original size:28 final size:28
Alignment explanation
Indices: 25381436--25381534 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
25381426 TAATATATAT
*
25381436 ATATATATATATATATATA-TATATATATATA
1 ATATAT-TATAAATA-ATAGTAT-TATA-ATA
* **
25381467 TATATATTATAAATATTA-TATTAGTGTTA
1 -ATATATTATAAATAATAGTATTA-TAATA
*
25381496 ATATATGATAAATAATAGTATTATAATA
1 ATATATTATAAATAATAGTATTATAATA
25381524 ATATATTATAA
1 ATATATTATAA
25381535 TAAAAAAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
28 28 0.50
29 9 0.16
30 6 0.11
31 7 0.12
32 6 0.11
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATATTATAAATAATAGTATTATAATA
Found at i:25388128 original size:29 final size:29
Alignment explanation
Indices: 25388089--25388484 Score: 276
Period size: 30 Copynumber: 13.4 Consensus size: 29
25388079 AAAATCAAAC
* *
25388089 TTTTGGAAAATTTGAGGTTGAAAATGTGAT
1 TTTTGGAAAGTTTGAGGTT-AAAATGTAAT
*
25388119 TTTTGGAAA-TTT-AGGGTAAAATGGTAAT
1 TTTTGGAAAGTTTGAGGTTAAAAT-GTAAT
* *
25388147 TTTTGGATA-TTT-AGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTTGA-GGTTAAAAT-GTAAT
** * * *
25388176 TTTTGG-TTGTTCGAAGG-CAAAATCATAA-
1 TTTTGGAAAGTTTG-AGGTTAAAAT-GTAAT
* **
25388204 TTTTGGAGAAGTTT-AGGGTCAAAATGGGA-
1 TTTTGGA-AAGTTTGA-GGTTAAAATGTAAT
25388233 TTTTGGAGAAGTTTGAGGGTTAAAATGTAA-
1 TTTTGGA-AAGTTTGA-GGTTAAAATGTAAT
* * *
25388263 TTTTGGAAAAAGTTTAGGGGTGAAAATGTGAT
1 TTTTGG--AAAGTTT-GAGGTTAAAATGTAAT
*
25388295 TTTTAGAAAGTTT-AGGGTTAAAATGTAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTAAT
* *
25388324 TTTTAGAAAGTTTAGGGGTTAAAATGTAAT
1 TTTTGGAAAGTTT-GAGGTTAAAATGTAAT
* * *
25388354 TTTTGAAAAGTTTGGGGGTTAGAATGTAAT
1 TTTTGGAAAGTTT-GAGGTTAAAATGTAAT
* * *
25388384 TTTTGGAAA-TTTTAGGGGTCAAATGTAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTAAT
* **
25388413 TTTTGGAAAGTTTAAGGGTCGAAATGTAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTAAT
*
25388443 TTTTGGAAAGTTTGAGGGTTAAAATATAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTAAT
25388473 TTTTGGAAAGTT
1 TTTTGGAAAGTT
25388485 CGGGGTCGAA
Statistics
Matches: 304, Mismatches: 43, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
27 5 0.02
28 28 0.09
29 99 0.33
30 147 0.48
31 18 0.06
32 7 0.02
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.39
Consensus pattern (29 bp):
TTTTGGAAAGTTTGAGGTTAAAATGTAAT
Found at i:25388312 original size:60 final size:59
Alignment explanation
Indices: 25388089--25388484 Score: 350
Period size: 59 Copynumber: 6.7 Consensus size: 59
25388079 AAAATCAAAC
* * *
25388089 TTTTGGAAAATTT-GAGGTTGAAAATGTGATTTTTGGAAA-TTT-AGGG-TAAAATGGTAA
1 TTTTGGAAAGTTTAGGGGTT-AAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAAT-GTAA
* ** * * * *
25388146 TTTTTGGATA-TTTAGGGG-TAAAATGGTAATTTTTGG-TTGTTCGAAGG-CAAAATCATAA
1 -TTTTGGAAAGTTTAGGGGTTAAAAT-GTAATTTTTGGAAAGTTTGAGGGTTAAAAT-GTAA
* **
25388204 TTTTGGAGAAGTTTA-GGGTCAAAATGGGA-TTTTGGAGAAGTTTGAGGGTTAAAATGTAA
1 TTTTGGA-AAGTTTAGGGGTTAAAATGTAATTTTTGGA-AAGTTTGAGGGTTAAAATGTAA
* * *
25388263 TTTTGGAAAAAGTTTAGGGGTGAAAATGTGATTTTTAGAAAGTTT-AGGGTTAAAATGTAA
1 TTTTGG--AAAGTTTAGGGGTTAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAA
* * * *
25388323 TTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTTGAAAAGTTTGGGGGTTAGAATGTAA
1 -TTTTGGAAAGTTTAGGGGTTAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAA
* * * **
25388383 TTTTTGGAAATTTTAGGGG-TCAAATGTAATTTTTGGAAAGTTTAAGGGTCGAAATGTAA
1 -TTTTGGAAAGTTTAGGGGTTAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAA
*
25388442 TTTTTGGAAAGTTT-GAGGGTTAAAATATAATTTTTGGAAAGTT
1 -TTTTGGAAAGTTTAG-GGGTTAAAATGTAATTTTTGGAAAGTT
25388485 CGGGGTCGAA
Statistics
Matches: 278, Mismatches: 42, Indels: 34
0.79 0.12 0.10
Matches are distributed among these distances:
56 5 0.02
57 29 0.10
58 29 0.10
59 107 0.38
60 78 0.28
61 24 0.09
62 6 0.02
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.39
Consensus pattern (59 bp):
TTTTGGAAAGTTTAGGGGTTAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAA
Found at i:25388409 original size:89 final size:88
Alignment explanation
Indices: 25388104--25388506 Score: 329
Period size: 89 Copynumber: 4.5 Consensus size: 88
25388094 GAAAATTTGA
* * * *
25388104 GGTTGAAAATGTGATTTTTGGAAATTTA-GGGTAAAATGGTAATTTTTGGATA-TTTAGGGG-TA
1 GGTT-AAAATGTAATTTTTGGAAATTTAGGGGTCAAAT-GTAATTTTTAGAAAGTTTAGGGGTTA
*** * **
25388166 AAATGGTAATTTTTG-GTTGTTCGAA
64 AAAT-GTAATTTTTGAAAAGTTTGGG
* * ** *
25388191 GG-CAAAATCATAA-TTTTGGAGAAGTTTA-GGGTCAAAATGGGA-TTTTGGAGAAGTTT-GAGG
1 GGTTAAAAT-GTAATTTTTGGA-AA-TTTAGGGGTC-AAATGTAATTTTTAGA-AAGTTTAG-GG
* *
25388251 GTTAAAATGTAATTTTGGAAAAAGTTTAGG
60 GTTAAAATGTAATTTTTG-AAAAGTTTGGG
* * * * *
25388281 GGTGAAAATGTGATTTTTAGAAAGTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTAGGGGTTAA
1 GGTTAAAATGTAATTTTTGGAAA-TTTAGGGGTCAAATGTAATTTTTAGAAAGTTTAGGGGTTAA
25388346 AATGTAATTTTTGAAAAGTTTGGG
65 AATGTAATTTTTGAAAAGTTTGGG
* * * **
25388370 GGTTAGAATGTAATTTTTGGAAATTTTAGGGGTCAAATGTAATTTTTGGAAAGTTTAAGGGTCGA
1 GGTTAAAATGTAATTTTTGGAAA-TTTAGGGGTCAAATGTAATTTTTAGAAAGTTTAGGGGTTAA
* *
25388435 AATGTAATTTTTGGAAAGTTTGAG
65 AATGTAATTTTTGAAAAGTTTGGG
* * * *
25388459 GGTTAAAATATAATTTTTGGAAAGTTCGGGGTCGAAATGTAGTTTTTA
1 GGTTAAAATGTAATTTTTGGAAATTTAGGGGTC-AAATGTAATTTTTA
25388507 AACAAAACAG
Statistics
Matches: 255, Mismatches: 45, Indels: 30
0.77 0.14 0.09
Matches are distributed among these distances:
85 12 0.05
86 11 0.04
87 14 0.05
88 27 0.11
89 125 0.49
90 45 0.18
91 21 0.08
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (88 bp):
GGTTAAAATGTAATTTTTGGAAATTTAGGGGTCAAATGTAATTTTTAGAAAGTTTAGGGGTTAAA
ATGTAATTTTTGAAAAGTTTGGG
Found at i:25388491 original size:59 final size:58
Alignment explanation
Indices: 25388040--25388505 Score: 340
Period size: 59 Copynumber: 7.9 Consensus size: 58
25388030 TTTCGAGGAA
* * ** * ** * *
25388040 TTTAGGGTCAAAAT-TGAATTTTTTGGAAAATTTGGAATAAAAATCAAACTTTTGGAAAA
1 TTTAGGGTTAAAATGT-AA-TTTTTGGAAAGTTTGGGGTCAAAATGTAATTTTTGGAAAG
* * *
25388099 TTT-GAGGTTGAAAATGTGATTTTTGGAAA-TTTAGGGT-AAAATGGTAATTTTTGGATA-
1 TTTAG-GGTT-AAAATGTAATTTTTGGAAAGTTTGGGGTCAAAAT-GTAATTTTTGGAAAG
* ** * * *
25388156 TTTAGGGGTAAAATGGTAATTTTTGG-TTGTTCGAAGG-CAAAATCATAA-TTTTGGAGAAG
1 TTTAGGGTTAAAAT-GTAATTTTTGGAAAGTTTG-GGGTCAAAAT-GTAATTTTTGGA-AAG
* ** *
25388215 TTTAGGGTCAAAATGGGA-TTTTGGAGAAGTTTGAGGGTTAAAATGTAA-TTTTGGAAAAAG
1 TTTAGGGTTAAAATGTAATTTTTGGA-AAGTTTG-GGGTCAAAATGTAATTTTTGG--AAAG
* * * * * *
25388275 TTTAGGGGTGAAAATGTGATTTTTAGAAAGTTTAGGGTTAAAATGTAATTTTTAGAAAG
1 TTTA-GGGTTAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGTAATTTTTGGAAAG
* * * *
25388334 TTTAGGGGTTAAAATGTAATTTTTGAAAAGTTTGGGGGTTAGAATGTAATTTTTGGAAAT
1 TTTA-GGGTTAAAATGTAATTTTTGGAAAGTTT-GGGGTCAAAATGTAATTTTTGGAAAG
* * * *
25388394 TTTAGGGGTCAAATGTAATTTTTGGAAAGTTTAAGGGTCGAAATGTAATTTTTGGAAAG
1 TTTAGGGTTAAAATGTAATTTTTGGAAAGTTT-GGGGTCAAAATGTAATTTTTGGAAAG
* * * *
25388453 TTTGAGGGTTAAAATATAATTTTTGGAAAGTTCGGGGTCGAAATGTAGTTTTT
1 TTT-AGGGTTAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGTAATTTTT
25388506 AAACAAAACA
Statistics
Matches: 329, Mismatches: 57, Indels: 42
0.77 0.13 0.10
Matches are distributed among these distances:
56 5 0.02
57 36 0.11
58 30 0.09
59 144 0.44
60 83 0.25
61 25 0.08
62 6 0.02
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (58 bp):
TTTAGGGTTAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGTAATTTTTGGAAAG
Found at i:25390779 original size:49 final size:46
Alignment explanation
Indices: 25390706--25390865 Score: 142
Period size: 49 Copynumber: 3.5 Consensus size: 46
25390696 GATTTGGTTT
*
25390706 ACTTCTCTATATCTCATCAGGAAGATTACCGCATCACTTGTTTTAATCC
1 ACTTCTCTGTATCTCATCAGGAAGA--ACCGCATCA-TTGTTTTAATCC
* * *
25390755 GCTTCTCTGTATCTCATCAGGAAG-A-CGGAT--TTG-----GTCC
1 ACTTCTCTGTATCTCATCAGGAAGAACCGCATCATTGTTTTAATCC
*
25390792 ACTTCTCTGTATCTCAACAGGAAGACAACCGTC-TCATTTGTTTTAATCC
1 ACTTCTCTGTATCTCATCAGGAAG--AACCG-CATCA-TTGTTTTAATCC
25390841 ACTTCTCTGTATCTCATCAGGAAGA
1 ACTTCTCTGTATCTCATCAGGAAGA
25390866 CGGATTTAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
37 25 0.28
40 1 0.01
41 3 0.03
42 3 0.03
44 3 0.03
45 4 0.04
46 1 0.01
47 1 0.01
49 48 0.54
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (46 bp):
ACTTCTCTGTATCTCATCAGGAAGAACCGCATCATTGTTTTAATCC
Found at i:25390806 original size:37 final size:37
Alignment explanation
Indices: 25390756--25390901 Score: 148
Period size: 37 Copynumber: 3.6 Consensus size: 37
25390746 TTTTAATCCG
25390756 CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCA
1 CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCA
* * *
25390793 CTTCTCTGTATCTCAACAGGAAGACAACCGTCTCATTTGTTTTAATCCA
1 CTTCTCTGTATCTCATCAGGAAG---A-CG---GATTTG-----GTCCA
*
25390842 CTTCTCTGTATCTCATCAGGAAGACGGATTTAGTCCA
1 CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCA
25390879 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
25390902 GTGACCATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
37 49 0.54
40 1 0.01
41 2 0.02
42 4 0.04
44 5 0.06
45 2 0.02
46 1 0.01
49 26 0.29
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (37 bp):
CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCA
Found at i:25390846 original size:86 final size:86
Alignment explanation
Indices: 25390696--25390901 Score: 315
Period size: 86 Copynumber: 2.4 Consensus size: 86
25390686 TTCTTCATTT
** * ** *
25390696 GATTTGGTTTACTTCTCTATATCTCATCAGGAAGATTACCGCATCACTTGTTTTAATCCGCTTCT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCGCATCACTTGTTTTAATCCACTTCT
25390761 CTGTATCTCATCAGGAAGACG
66 CTGTATCTCATCAGGAAGACG
* *
25390782 GATTTGGTCCACTTCTCTGTATCTCAACAGGAAGACAACCGTC-TCATTTGTTTTAATCCACTTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCG-CATCACTTGTTTTAATCCACTTC
25390846 TCTGTATCTCATCAGGAAGACG
65 TCTGTATCTCATCAGGAAGACG
*
25390868 GATTTAGTCCACTTCTCTGTATCTCATCAGGAAG
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAG
25390902 GTGACCATTT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 108 0.99
87 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (86 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCGCATCACTTGTTTTAATCCACTTCT
CTGTATCTCATCAGGAAGACG
Found at i:25391039 original size:209 final size:209
Alignment explanation
Indices: 25390782--25391235 Score: 667
Period size: 209 Copynumber: 2.2 Consensus size: 209
25390772 CAGGAAGACG
** * *
25390782 GATTTGGTCCACTTCTCTGTATCTCAACAGGAAGACAACCGTCTCATTTGTTTTAATCCACTTCT
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGACAACCGCCTCATTTGTTTTAATCCACTTCT
* * ** *
25390847 CTGTATCTCATCAGGAAGACGGATTTAGTCCACTTCTCTGTATCTCATCAGGAAGGTGACCATTT
66 CTGTATCTCATCAAGAAGACGGATTTAGTCCACTTCTCTGTATCTCATCAAGAAGACGACCACTT
* * * *
25390912 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGAGTTTGAAGTTTTGCTCACATT
131 TATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGA-TTCGAAGTTTCGCTCACATT
25390976 GAGCTTTGTTTCATT
195 GAGCTTTGTTTCATT
**
25390991 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATCCACTTCT
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGACAACCGCCTCATTTGTTTTAATCCACTTCT
* * * * *
25391056 TTGTATCTCATCAAGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACGATCGCTT
66 CTGTATCTCATCAAGAAGACGGATTTAGTCCACTTCTCTGTATCTCATCAAGAAGACGACCACTT
* * *
25391121 TATTGCTTTGACCTGCTTCTCAATATCTTATCAAGAAGTTGGGATTCGAAGTTTCGCTCACATTG
131 TATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGATTCGAAGTTTCGCTCACATTG
25391186 AGCTTTGTTTCATT
196 AGCTTTGTTTCATT
* *
25391200 GATTTGGTATACTTCTTTGTATCTCATCAAGAAGAC
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGAC
25391236 GATCGCTTTA
Statistics
Matches: 218, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
209 215 0.99
210 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (209 bp):
GATTTGGTATACTTCTCTGTATCTCATCAGGAAGACAACCGCCTCATTTGTTTTAATCCACTTCT
CTGTATCTCATCAAGAAGACGGATTTAGTCCACTTCTCTGTATCTCATCAAGAAGACGACCACTT
TATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGATTCGAAGTTTCGCTCACATTG
AGCTTTGTTTCATT
Found at i:25391296 original size:123 final size:123
Alignment explanation
Indices: 25391077--25391357 Score: 483
Period size: 123 Copynumber: 2.3 Consensus size: 123
25391067 CAAGAAGATG
**
25391077 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACGATCGCTTTATTGCTTTGACCTGCTTCTC
1 GATTTGGTATACTTCTCTGTATCTCATCAAGAAGACGATCGCTTTATTGCTTTGACCTGCTTCTC
* *
25391142 AATATCTTATCAAGAAGTTGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATT
66 AATATCTCATCAAGAAGATGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATT
*
25391200 GATTTGGTATACTTCTTTGTATCTCATCAAGAAGACGATCGCTTTATTG-TTTCGACCTGCTTCT
1 GATTTGGTATACTTCTCTGTATCTCATCAAGAAGACGATCGCTTTATTGCTTT-GACCTGCTTCT
*
25391264 CAGTATCTCATCAAGAAGATGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATT
65 CAATATCTCATCAAGAAGATGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATT
*
25391323 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGA
1 GATTTGGTATACTTCTCTGTATCTCATCAAGAAGA
25391358 TAAGGTTTGG
Statistics
Matches: 149, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
122 3 0.02
123 146 0.98
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (123 bp):
GATTTGGTATACTTCTCTGTATCTCATCAAGAAGACGATCGCTTTATTGCTTTGACCTGCTTCTC
AATATCTCATCAAGAAGATGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATT
Found at i:25403612 original size:28 final size:29
Alignment explanation
Indices: 25403572--25403643 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
25403562 TTTGAGGTTG
* *
25403572 AAAATGGTGATTTTTGGAA-ATTTGA-AGC
1 AAAATGGTAATTTTT-GAATATTCGAGAGC
* *
25403600 AAAATGGTAATTTTTGAATATTCGAGGGT
1 AAAATGGTAATTTTTGAATATTCGAGAGC
25403629 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
25403644 AGATGTTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.08
28 19 0.50
29 16 0.42
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAATATTCGAGAGC
Found at i:25403754 original size:30 final size:30
Alignment explanation
Indices: 25403648--25403967 Score: 241
Period size: 30 Copynumber: 10.8 Consensus size: 30
25403638 ATTTTTAGAT
* * *
25403648 GTTTAGGAG-CAAAATCATAATTTTGGAGAA
1 GTTTAGGGGTCAAAAT-GTAATTTTGGAAAA
* *
25403678 GTTT-GGGGTCAAAATAG-GATTTTGGAGAA
1 GTTTAGGGGTCAAAAT-GTAATTTTGGAAAA
* * * *
25403707 G-TTCGAGAGT-TAAATGTAATTATGGAAAA
1 GTTTAG-GGGTCAAAATGTAATTTTGGAAAA
* *
25403736 GTTTAGGGGTGAAAATGTAATTTTAGAAAA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
* * *
25403766 GTTTAGGGGTGAAAATGTAATTTTAGAATA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
* * *
25403796 GTTTAGAGGTAAAAATATAATTTT-GAAAA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
* *
25403825 GTTTAAGGGTTAAAATG-AGATTTTTGG-AAA
1 GTTTAGGGGTCAAAATGTA-A-TTTTGGAAAA
* * **
25403855 GTTTGGGGGTCAAAATATTGTTTTTGG-AAA
1 GTTTAGGGGTCAAAAT-GTAATTTTGGAAAA
**
25403885 GTTTAGGGGTCAAAATGTAATTTTTAAAAA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
25403915 GTTT-GAGGGTCAAAATGTAATTTTTGG-AAA
1 GTTTAG-GGGTCAAAATGTAA-TTTTGGAAAA
* *
25403945 GTTT-GGGGTCGAAATGTAGTTTT
1 GTTTAGGGGTCAAAATGTAATTTT
25403968 AAAACAAAAC
Statistics
Matches: 237, Mismatches: 39, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.03
29 69 0.29
30 155 0.65
31 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
GTTTAGGGGTCAAAATGTAATTTTGGAAAA
Found at i:25403824 original size:89 final size:88
Alignment explanation
Indices: 25403731--25403968 Score: 250
Period size: 89 Copynumber: 2.7 Consensus size: 88
25403721 TGTAATTATG
* * *
25403731 GAAAAGTTTAGGGGTGAAAATGTAATTTTAGAAAAGTTTAGGGGTGAAAATGTAATTTTAGAATA
1 GAAAAGTTTAGGGGTCAAAATGTAATTTTTGGAAAGTTT-GGGGTGAAAATGTAATTTTAGAA-A
25403796 GTTTAGAGGTAAAAATATAA-TTTT
64 GTTTAGAGGTAAAAATATAATTTTT
* * * * ** *
25403820 GAAAAGTTTAAGGGTTAAAATG-AGATTTTTGGAAAGTTTGGGGGTCAAAATATTGTTTTTGGAA
1 GAAAAGTTTAGGGGTCAAAATGTA-ATTTTTGGAAAGTTT-GGGGTGAAAAT-GTAATTTTAGAA
* * *
25403884 AGTTTAGGGGTCAAAATGTAATTTTT
63 AGTTTAGAGGTAAAAATATAATTTTT
* *
25403910 AAAAAGTTT-GAGGGTCAAAATGTAATTTTTGGAAAGTTTGGGGTCG-AAATGTAGTTTTA
1 GAAAAGTTTAG-GGGTCAAAATGTAATTTTTGGAAAGTTTGGGGT-GAAAATGTAATTTTA
25403969 AAACAAAACA
Statistics
Matches: 122, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
88 6 0.05
89 70 0.57
90 45 0.37
91 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (88 bp):
GAAAAGTTTAGGGGTCAAAATGTAATTTTTGGAAAGTTTGGGGTGAAAATGTAATTTTAGAAAGT
TTAGAGGTAAAAATATAATTTTT
Found at i:25409519 original size:31 final size:31
Alignment explanation
Indices: 25409441--25409519 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
25409431 TTATTTCATG
25409441 GAAA-AAATTAGGCAAAAAAGCATTAATTCCAA
1 GAAAGAAATTAGGC--AAAAGCATTAATTCCAA
* *
25409473 GGAAGAAATTAGGCAAAAGTATTAATAT-CAA
1 GAAAGAAATTAGGCAAAAGCATTAAT-TCCAA
* *
25409504 GAAAGATATTTGGCAA
1 GAAAGAAATTAGGCAA
25409520 CAAGGATAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 27 0.68
32 4 0.10
33 9 0.22
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.22
Consensus pattern (31 bp):
GAAAGAAATTAGGCAAAAGCATTAATTCCAA
Found at i:25409989 original size:21 final size:22
Alignment explanation
Indices: 25409963--25410005 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25409953 GCCTAATTTC
25409963 CTTC-TTGGAATTAATGCTTTT
1 CTTCTTTGGAATTAATGCTTTT
25409984 CTTCTTTGGAATTAATGCTTTT
1 CTTCTTTGGAATTAATGCTTTT
25410006 TTGCCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (22 bp):
CTTCTTTGGAATTAATGCTTTT
Found at i:25411541 original size:58 final size:59
Alignment explanation
Indices: 25411464--25411808 Score: 258
Period size: 59 Copynumber: 5.9 Consensus size: 59
25411454 TTTGGATACC
* * * *
25411464 CGAGGGTAAAATGGTAATTTTTGG-ACGTACGAGGGCAAAATGGTGATTTTTGGTGAAA-
1 CGAGGTTAAAATGG-AATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTTGGTAAAAT
* * ** *
25411522 CTGGGGTTAAAATAGAA-TTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTAAAAT
1 C-GAGGTTAAAATGGAATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTTGGTAAAAT
* ** * * *
25411581 CGAGGTTAAAAATGGAA-TTTTGGAAGGTTTGGGGGTAAAATGGTAA-TTTTGTGTGAAAT
1 CGAGGTT-AAAATGGAATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTTG-GTAAAAT
* * * ** * * *
25411640 CGGGGGTAAGAATGGAA-TTTTGGAAGGTTTGGGGGTAAATTGGT-ATTTTTGGGTAAAAT
1 CGAGGTTAA-AATGGAATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTT-GGTAAAAT
*** * * *
25411699 CGAGGTTAAAAATGGAA-TTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTGGGTGAAAT
1 CGAGGTT-AAAATGGAATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTTGGTAAAAT
* ** *
25411758 CGGGGTTAAAAATGGAA-TTTTGGAAAGTTTGGGGGCAAAATGGTAATTTTT
1 CGAGGTT-AAAATGGAATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTT
25411809 AAACAGTTCA
Statistics
Matches: 246, Mismatches: 31, Indels: 19
0.83 0.10 0.06
Matches are distributed among these distances:
57 6 0.02
58 44 0.18
59 188 0.76
60 8 0.03
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (59 bp):
CGAGGTTAAAATGGAATTTTTGGAAAGTACGAGGGCAAAATGGTAATTTTTGGTAAAAT
Found at i:25411557 original size:29 final size:30
Alignment explanation
Indices: 25411525--25411807 Score: 147
Period size: 29 Copynumber: 9.6 Consensus size: 30
25411515 GGTGAAACTG
*
25411525 GGGTTAAAATAG-AATTTTGGAAAGTTTGA
1 GGGTTAAAATGGTAATTTTGGAAAGTTTGA
* *
25411554 GGG-TAAAATGGTAATTTTTGGTAAA-ATCGA
1 GGGTTAAAATGGTAA-TTTTGG-AAAGTTTGA
*
25411584 -GGTTAAAAATGG-AATTTTGGAAGGTTTG-
1 GGGTT-AAAATGGTAATTTTGGAAAGTTTGA
* *
25411612 GGGGTAAAATGGTAATTTTGTGTGAAA--TCG-
1 GGGTTAAAATGGTAA-TTT-TG-GAAAGTTTGA
* *
25411642 GGGGTAAGAATGG-AATTTTGGAAGGTTTG-
1 GGGTTAA-AATGGTAATTTTGGAAAGTTTGA
* * * * *
25411671 GGGGTAAATTGGTATTTTTGGGTAAA-ATCGA
1 GGGTTAAAATGGTAATTTT-GG-AAAGTTTGA
*
25411702 -GGTTAAAAATGG-AATTTTGGAAAGTTTAA
1 GGGTT-AAAATGGTAATTTTGGAAAGTTTGA
*
25411731 GGG-TAAAATGGTAATTTTGGGTGAAA--TCG-
1 GGGTTAAAATGGTAATTTT--G-GAAAGTTTGA
25411760 GGGTTAAAAATGG-AATTTTGGAAAGTTTG-
1 GGGTT-AAAATGGTAATTTTGGAAAGTTTGA
**
25411789 GGGGCAAAATGGTAATTTT
1 GGGTTAAAATGGTAATTTT
25411808 TAAACAGTTC
Statistics
Matches: 197, Mismatches: 27, Indels: 60
0.69 0.10 0.21
Matches are distributed among these distances:
27 7 0.04
28 40 0.20
29 62 0.31
30 48 0.24
31 33 0.17
32 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (30 bp):
GGGTTAAAATGGTAATTTTGGAAAGTTTGA
Found at i:25411617 original size:59 final size:59
Alignment explanation
Indices: 25411500--25411808 Score: 419
Period size: 59 Copynumber: 5.3 Consensus size: 59
25411490 GTACGAGGGC
* * *
25411500 AAAATGGTGATTTTTGGTGAAA-CTGGGGTT-AAAATAGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
25411558 AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
25411617 AAAATGGTAA-TTTTGTGTGAAATCGGGGGTAAGAATGGAATTTTGGAAGGTTTGGGGGT
1 AAAATGGTAATTTTTG-GTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * * **
25411676 AAATTGGT-ATTTTTGGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGT
1 AAAATGGTAATTTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
25411735 AAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGC
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
25411794 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
25411809 AAACAGTTCA
Statistics
Matches: 219, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
58 31 0.14
59 182 0.83
60 6 0.03
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:25413618 original size:17 final size:17
Alignment explanation
Indices: 25413565--25413629 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
25413555 ATATTTAAAC
25413565 ATTTAAATTCAAAATAA
1 ATTTAAATTCAAAATAA
* * *
25413582 ATTCAAATTTAACATAA
1 ATTTAAATTCAAAATAA
* *
25413599 ATTTAAATTCCAAATGA
1 ATTTAAATTCAAAATAA
*
25413616 ATTTAAATTTAAAA
1 ATTTAAATTCAAAA
25413630 AAAAACTAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTTAAATTCAAAATAA
Found at i:25416362 original size:31 final size:32
Alignment explanation
Indices: 25416301--25416371 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
25416291 GACATTTATT
* *
25416301 TCAAGGAGAAAATTAGGCAAAAAAGCATTAAT-
1 TCAAGAAGGAAATTAGGC-AAAAAGCATTAATA
*
25416333 TCCAAGAAGGAAATTAGGC-AAAAGTATTAATA
1 T-CAAGAAGGAAATTAGGCAAAAAGCATTAATA
25416365 TCAAGAA
1 TCAAGAA
25416372 AGATATTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 17 0.50
32 2 0.06
33 15 0.44
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.20
Consensus pattern (32 bp):
TCAAGAAGGAAATTAGGCAAAAAGCATTAATA
Found at i:25416384 original size:31 final size:31
Alignment explanation
Indices: 25416310--25416384 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
25416300 TTCAAGGAGA
*
25416310 AAATTAGGCAAAAAAGCATTAATTCCAAGAAGG
1 AAATTAGGC--AAAAGCATTAATTCCAAGAAAG
*
25416343 AAATTAGGCAAAAGTATTAATAT-CAAGAAAG
1 AAATTAGGCAAAAGCATTAAT-TCCAAGAAAG
* *
25416374 ATATTTGGCAA
1 AAATTAGGCAA
25416385 CAAGGATAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 27 0.73
32 1 0.03
33 9 0.24
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (31 bp):
AAATTAGGCAAAAGCATTAATTCCAAGAAAG
Found at i:25416545 original size:16 final size:16
Alignment explanation
Indices: 25416524--25416555 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25416514 TTAGTTTATG
25416524 TTATCCTTCAGCTTCT
1 TTATCCTTCAGCTTCT
25416540 TTATCCTTCAGCTTCT
1 TTATCCTTCAGCTTCT
25416556 CTATAAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.50
Consensus pattern (16 bp):
TTATCCTTCAGCTTCT
Found at i:25418442 original size:22 final size:22
Alignment explanation
Indices: 25418417--25418464 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
25418407 AATTTAAGAG
25418417 CACTTCTTTCTAGCCAACCAAA
1 CACTTCTTTCTAGCCAACCAAA
* *
25418439 CACTTCTTTCTAGCTAACCAAG
1 CACTTCTTTCTAGCCAACCAAA
25418461 CACT
1 CACT
25418465 AAATTCGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.29
Consensus pattern (22 bp):
CACTTCTTTCTAGCCAACCAAA
Found at i:25419452 original size:17 final size:17
Alignment explanation
Indices: 25419432--25419503 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
25419422 ATTTAAATTT
**
25419432 AAAAAATTTGAGTTCGA
1 AAAAAATTTGAACTCGA
* **
25419449 AAAAAATTT-AAATTTA
1 AAAAAATTTGAACTCGA
* *
25419465 AGAAAATTTTGAGCTC-A
1 A-AAAAATTTGAACTCGA
25419482 AAAAAATTTGAACTCGA
1 AAAAAATTTGAACTCGA
25419499 AAAAA
1 AAAAA
25419504 TTAAAACTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
16 16 0.38
17 24 0.57
18 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (17 bp):
AAAAAATTTGAACTCGA
Found at i:25419459 original size:32 final size:32
Alignment explanation
Indices: 25419406--25419490 Score: 127
Period size: 32 Copynumber: 2.6 Consensus size: 32
25419396 TTTCGTGTTG
*
25419406 ATTTGAGCTCAAAACAATTTAAATTTAA-AAA
1 ATTTGAGCTCAAAAAAATTTAAATTTAAGAAA
*
25419437 ATTTGAGTTCGAAAAAAATTTAAATTTAAGAAA
1 ATTTGAGCTC-AAAAAAATTTAAATTTAAGAAA
25419470 ATTTTGAGCTCAAAAAAATTT
1 A-TTTGAGCTCAAAAAAATTT
25419491 GAACTCGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
31 9 0.19
32 17 0.35
33 14 0.29
34 8 0.17
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.34
Consensus pattern (32 bp):
ATTTGAGCTCAAAAAAATTTAAATTTAAGAAA
Found at i:25419486 original size:16 final size:17
Alignment explanation
Indices: 25419467--25419505 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
25419457 TAAATTTAAG
*
25419467 AAAATTTTGAGCTC-AA
1 AAAATTTTGAACTCGAA
*
25419483 AAAAATTTGAACTCGAA
1 AAAATTTTGAACTCGAA
25419500 AAAATT
1 AAAATT
25419506 AAAACTCGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (17 bp):
AAAATTTTGAACTCGAA
Found at i:25420580 original size:20 final size:20
Alignment explanation
Indices: 25420555--25420595 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25420545 AAGATGGCTT
*
25420555 AGTGCATTCTTAAGGATTTA
1 AGTGCATTATTAAGGATTTA
25420575 AGTGCATTATTAAGGATTTA
1 AGTGCATTATTAAGGATTTA
25420595 A
1 A
25420596 TTGATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (20 bp):
AGTGCATTATTAAGGATTTA
Found at i:25420852 original size:24 final size:24
Alignment explanation
Indices: 25420825--25420874 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
25420815 TGTACATATC
* *
25420825 ATAAACCATAAATGTTCCATACAA
1 ATAAACCAAAAATATTCCATACAA
*
25420849 ATAAACCAAAAATATTGCATACAA
1 ATAAACCAAAAATATTCCATACAA
25420873 AT
1 AT
25420875 TCATATACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.24
Consensus pattern (24 bp):
ATAAACCAAAAATATTCCATACAA
Found at i:25421275 original size:17 final size:17
Alignment explanation
Indices: 25421234--25421266 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25421224 AAAATTCATG
25421234 CCCAA-AAAAATCCAAA
1 CCCAAGAAAAATCCAAA
25421250 CCCAAGAAAAATCCAAA
1 CCCAAGAAAAATCCAAA
25421267 TTCAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.30, G:0.03, T:0.06
Consensus pattern (17 bp):
CCCAAGAAAAATCCAAA
Found at i:25432126 original size:8 final size:8
Alignment explanation
Indices: 25432113--25432137 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25432103 CCCTAAATAA
25432113 AAATTGAT
1 AAATTGAT
25432121 AAATTGAT
1 AAATTGAT
25432129 AAATTGAT
1 AAATTGAT
25432137 A
1 A
25432138 TAGTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (8 bp):
AAATTGAT
Found at i:25432502 original size:23 final size:23
Alignment explanation
Indices: 25432462--25432526 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
25432452 TTCTATGCAC
*
25432462 GCAAGT-TATAGTGACACTAC-GAT
1 GCAAGTGT-TAGTGGCACTACAG-T
* *
25432485 GCATGTTTTAGTGGCACTACAGT
1 GCAAGTGTTAGTGGCACTACAGT
*
25432508 GTAAGTGTTAGTGGCACTA
1 GCAAGTGTTAGTGGCACTA
25432527 TGGTGAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (23 bp):
GCAAGTGTTAGTGGCACTACAGT
Found at i:25432536 original size:23 final size:23
Alignment explanation
Indices: 25432492--25432536 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25432482 GATGCATGTT
*
25432492 TTAGTGGCACTACAGTGTAAGTG
1 TTAGTGGCACTACAGTGAAAGTG
**
25432515 TTAGTGGCACTATGGTGAAAGT
1 TTAGTGGCACTACAGTGAAAGT
25432537 CACAGTAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (23 bp):
TTAGTGGCACTACAGTGAAAGTG
Found at i:25434403 original size:25 final size:23
Alignment explanation
Indices: 25434375--25434420 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
25434365 GTTGAATCCA
25434375 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
25434400 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
25434421 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:25435495 original size:13 final size:13
Alignment explanation
Indices: 25435475--25435509 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
25435465 ATTTTCTCTC
25435475 TTTTTTTTCAA-T
1 TTTTTTTTCAACT
25435487 TTTTCTTTTCAACT
1 TTTT-TTTTCAACT
25435501 TTTTTTTTC
1 TTTTTTTTC
25435510 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 12 0.57
14 5 0.24
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCAACT
Found at i:25436398 original size:11 final size:11
Alignment explanation
Indices: 25436382--25436431 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
25436372 AATAGTACAT
25436382 AATAAAATAAA
1 AATAAAATAAA
25436393 AATAAAATAAA
1 AATAAAATAAA
*
25436404 ACTAAAA-ACTAA
1 AATAAAATA--AA
*
25436416 AA-AAAATGAA
1 AATAAAATAAA
25436426 AATAAA
1 AATAAA
25436432 TGTACTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 24 0.75
12 3 0.09
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:25443069 original size:25 final size:23
Alignment explanation
Indices: 25443041--25443086 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
25443031 GTTGGATCCA
25443041 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
25443066 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
25443087 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:25447772 original size:17 final size:17
Alignment explanation
Indices: 25447752--25447797 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
25447742 TTATTGAATG
25447752 TGCGAGCTCACCACAAC
1 TGCGAGCTCACCACAAC
* * * *
25447769 TGCGAGCTTATCATAGC
1 TGCGAGCTCACCACAAC
25447786 TGCGAGCTCACC
1 TGCGAGCTCACC
25447798 TAAGTTAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.20
Consensus pattern (17 bp):
TGCGAGCTCACCACAAC
Found at i:25450086 original size:28 final size:28
Alignment explanation
Indices: 25450046--25450101 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
25450036 TTAAAAGGGC
25450046 TTTAAAGTATTTTGAATTGATCTCATAT
1 TTTAAAGTATTTTGAATTGATCTCATAT
25450074 TTTAAAGTATTTTGAATTGATCTCATAT
1 TTTAAAGTATTTTGAATTGATCTCATAT
25450102 CTCCTTATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (28 bp):
TTTAAAGTATTTTGAATTGATCTCATAT
Found at i:25452853 original size:12 final size:12
Alignment explanation
Indices: 25452838--25452865 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25452828 TATAATATTT
25452838 TTTTGAAAATAA
1 TTTTGAAAATAA
25452850 TTTTGAAAATAA
1 TTTTGAAAATAA
25452862 TTTT
1 TTTT
25452866 TTATATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TTTTGAAAATAA
Found at i:25459666 original size:26 final size:26
Alignment explanation
Indices: 25459631--25459742 Score: 170
Period size: 26 Copynumber: 4.3 Consensus size: 26
25459621 CCCTGTTAGG
* *
25459631 ATATCACTCTTACGAGCCAGTTCAGT
1 ATATCGCTCTTACGAGCCAATTCAGT
* * * *
25459657 AGATCGCTCTTACGAGTCAGTTTAGT
1 ATATCGCTCTTACGAGCCAATTCAGT
25459683 ATATCGCTCTTACGAGCCAATTCAGT
1 ATATCGCTCTTACGAGCCAATTCAGT
25459709 ATATCGCTCTTACGAGCCAATTCAGT
1 ATATCGCTCTTACGAGCCAATTCAGT
25459735 ATATCGCT
1 ATATCGCT
25459743 TCAGAGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (26 bp):
ATATCGCTCTTACGAGCCAATTCAGT
Found at i:25464482 original size:9 final size:9
Alignment explanation
Indices: 25464470--25464494 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25464460 TTAATTGATT
25464470 TATTTAATA
1 TATTTAATA
25464479 TATTTAATA
1 TATTTAATA
25464488 TATTTAA
1 TATTTAA
25464495 CTAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTTAATA
Found at i:25464499 original size:22 final size:22
Alignment explanation
Indices: 25464457--25464499 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
25464447 AAATAAAATG
**
25464457 TATTTAATTGATTTATTTAATA
1 TATTTAATTGATTTAACTAATA
25464479 TATTTAATAT-ATTTAACTAAT
1 TATTTAAT-TGATTTAACTAAT
25464500 TAATATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTAATTGATTTAACTAATA
Found at i:25474153 original size:46 final size:46
Alignment explanation
Indices: 25474036--25474164 Score: 152
Period size: 46 Copynumber: 2.8 Consensus size: 46
25474026 GATTCTTGCC
* * * * *
25474036 TAGGTTCCCAGCTCCTGTATATGTTACAGATTGGAGAATACGGATG
1 TAGGTTCCCAGCTCCTGCATATGTTGCGGAATGGAGAATACAGATG
* * *
25474082 TAGGTTCCCTA-CTCTTGCATATGTTGCGGACTGGAGAATACAGATT
1 TAGGTTCCC-AGCTCCTGCATATGTTGCGGAATGGAGAATACAGATG
* *
25474128 TAGGTTCCCAGTTCCTGCATATGTTGTGGAATGGAGA
1 TAGGTTCCCAGCTCCTGCATATGTTGCGGAATGGAGA
25474165 GTAAAAAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
45 1 0.01
46 68 0.97
47 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (46 bp):
TAGGTTCCCAGCTCCTGCATATGTTGCGGAATGGAGAATACAGATG
Found at i:25475956 original size:52 final size:52
Alignment explanation
Indices: 25475679--25475967 Score: 275
Period size: 52 Copynumber: 5.6 Consensus size: 52
25475669 ACCTTTGATA
* * * * * *
25475679 ACTCACGATGATACAGAGTCATCGGA-CTTTTAATCCGTAATAGGATCCATGT
1 ACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATA-GATTCATAT
* * * *
25475731 ACTCACGATGACACATAAT-A-CTAGGA-CTAG-TAATCCATAGTAGGATTCGTAT
1 ACTCACGATGACACATAGTCATC-A-GACCT-GTTAATCCGTAATA-GATTCATAT
* *
25475783 ACTCACGATGACATATAGTCATCAGACCTGTTAATTCGTAATAGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGATTCATAT
* * * *
25475835 ACTCACGATGACACATAGTTATCAGACCTGTTAATCTGTAATGGATTCACAT
1 ACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGATTCATAT
** ** *
25475887 ACTCACGATGACACATAGTCATTGGACCTCATAATCCATAA-ATGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATA-GATTCATAT
* *
25475939 ATTCACGATGACACATAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCAGACCT
25475968 TTTACATTTA
Statistics
Matches: 196, Mismatches: 33, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 180 0.92
53 13 0.07
54 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCAGACCTGTTAATCCGTAATAGATTCATAT
Found at i:25475967 original size:156 final size:156
Alignment explanation
Indices: 25475679--25475967 Score: 361
Period size: 156 Copynumber: 1.9 Consensus size: 156
25475669 ACCTTTGATA
* * * **
25475679 ACTCACGATGATACAGAGTCATCGGACTTTTAATCCGTAATAGGATCCATGTACTCACGATGACA
1 ACTCACGATGACACAGAGTCATCAGACTGTTAATCCGTAATAGGATCCACATACTCACGATGACA
* * *
25475744 CATAATACTAGGACTAGTAATCCATAGTAGGATTCGTATACTCACGATGACATATAGTCATCAGA
66 CATAATACTAGGACTAGTAATCCATAGAAGGATTCATATACTCACGATGACACATAGTCATCAGA
25475809 CCTGTTAATTCGTAATAGATTCATAT
131 CCTGTTAATTCGTAATAGATTCATAT
* * * *
25475835 ACTCACGATGACACATAGTTATCAGACCTGTTAATCTGTAAT-GGATTCACATACTCACGATGAC
1 ACTCACGATGACACAGAGTCATCAGA-CTGTTAATCCGTAATAGGATCCACATACTCACGATGAC
* * * *
25475899 ACATAGT-CATTGGACCTCA-TAATCCATA-AATGATTCATATATTCACGATGACACATAGTCAT
65 ACATAATAC-TAGGA-CT-AGTAATCCATAGAAGGATTCATATACTCACGATGACACATAGTCAT
*
25475961 CGGACCT
127 CAGACCT
25475968 TTTACATTTA
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
155 1 0.01
156 86 0.77
157 24 0.21
158 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (156 bp):
ACTCACGATGACACAGAGTCATCAGACTGTTAATCCGTAATAGGATCCACATACTCACGATGACA
CATAATACTAGGACTAGTAATCCATAGAAGGATTCATATACTCACGATGACACATAGTCATCAGA
CCTGTTAATTCGTAATAGATTCATAT
Found at i:25476655 original size:212 final size:211
Alignment explanation
Indices: 25476279--25476710 Score: 729
Period size: 212 Copynumber: 2.0 Consensus size: 211
25476269 TTTTGAGAAA
* * *
25476279 TTTATGAAATTACCCCTAGCATTTCACTTTTATTCTATTTAGTCACTAAACACAAAACATGTGAA
1 TTTATAAAATTACCCCTAGCATTTCACTTTTACTCCATTTAGTCACTAAACACAAAACATGTGAA
* * *
25476344 ATAACCCCTTTCTCACTAAACCTATACCAACCGATTGCTCCAAGCTTCCATACAAGTTCTTACAA
66 ATAACCCCTTTCTCACTAAACCCATACCAACCGATTGCTCCAAGCTTCCATACAAGTCCCTACAA
* *
25476409 TTTAGCCATTTCACACCAAATACCCATATTTTCATCATTTTAGCATTTTAGTCCACAAACTCTAA
131 TTTAGCCATTTCACACCAAATACCCACATTTTCATCATTTTAACATTTTAGTCCACAAACTCTAA
25476474 TTTCATCAAAAATCAC
196 TTTCATCAAAAATCAC
* *
25476490 TTTATAAAATTTACCCCTAGCATTTCACTTTTACTCCATTTAGTCCCTAAACACAAAATATGTGA
1 TTTATAAAA-TTACCCCTAGCATTTCACTTTTACTCCATTTAGTCACTAAACACAAAACATGTGA
* * *
25476555 AATAACCCCTTTCTCACTAAACCCATACTAGCCGATTGCTCCAAGCTTCCATAGAAGTCCCTACA
65 AATAACCCCTTTCTCACTAAACCCATACCAACCGATTGCTCCAAGCTTCCATACAAGTCCCTACA
25476620 ATTTAGCCATTTCACACCAAATACCCACATTTTCATCATTTTAACATTTTAGTCCACAAACTCTA
130 ATTTAGCCATTTCACACCAAATACCCACATTTTCATCATTTTAACATTTTAGTCCACAAACTCTA
25476685 ATTTCATCAAAAATCAC
195 ATTTCATCAAAAATCAC
*
25476702 TTTACAAAA
1 TTTATAAAA
25476711 ATCTCAAACC
Statistics
Matches: 206, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
211 8 0.04
212 198 0.96
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (211 bp):
TTTATAAAATTACCCCTAGCATTTCACTTTTACTCCATTTAGTCACTAAACACAAAACATGTGAA
ATAACCCCTTTCTCACTAAACCCATACCAACCGATTGCTCCAAGCTTCCATACAAGTCCCTACAA
TTTAGCCATTTCACACCAAATACCCACATTTTCATCATTTTAACATTTTAGTCCACAAACTCTAA
TTTCATCAAAAATCAC
Found at i:25478809 original size:33 final size:34
Alignment explanation
Indices: 25478747--25478824 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 34
25478737 TTATAATGCT
* *
25478747 AAAATAAATAAAAAAATACATGAATTTAAATGTC
1 AAAATAAACAAAAAAATACATGAAATTAAATGTC
*
25478781 AAAATAAACAAAAAAAT-CAAT-AAATTAAATGTG
1 AAAATAAACAAAAAAATAC-ATGAAATTAAATGTC
25478814 AAAATAAACAA
1 AAAATAAACAA
25478825 CTAAATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 22 0.55
34 18 0.45
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.22
Consensus pattern (34 bp):
AAAATAAACAAAAAAATACATGAAATTAAATGTC
Found at i:25479699 original size:43 final size:43
Alignment explanation
Indices: 25479533--25480222 Score: 675
Period size: 43 Copynumber: 15.8 Consensus size: 43
25479523 CAATCCGTCT
* * *
25479533 CTCTAGATTAGGGGTAAGAGATTGGATGATGGCTTCAATCTGCCC
1 CTCTGGATTA-GGGTAAAAGATTGGATGGTGGCTTCAATCTG-CC
* * * **
25479578 CTTTGGATTGGGGGTAAGAGATTGGATTATGGCTTCAATCTGCC
1 CTCTGGATT-AGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * * ** * * *
25479622 CTTTTAGATTGGGGGTAAGAGATTAAATGATGGCTTTAATTTGCC
1 C-TCTGGATT-AGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * *
25479667 CTCTAGATTAGGGTAAAAGATTGGTTGGTGGCTTTAATCTACC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * *
25479710 CTTTTGGATTAGGGGCAAAAGATTAGATGGTTGCTTCAATCTGCC
1 C-TCTGGATTA-GGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
** *
25479755 CTCTGGATTAGGGT-AAAGATTAGTTTGGTGGCTTTAATCTGCCC
1 CTCTGGATTAGGGTAAAAGATT-GGATGGTGGCTTCAATCTG-CC
* *
25479799 CTTTGGATTAGGGGTAAAAGATTGGATGGTTGCTTCAATCTGCC
1 CTCTGGATTA-GGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * *
25479843 CTCTGGATTAAGGTAAAAGATTGGATGGTGACATCAATTTGCC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * * *
25479886 CTCTGGATTAGGGTAAAAGATTAGTTAGTAGCTTCAATATGCC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * * * * *
25479929 TTTTGGATTAGAGTAAACGATTGGATGGTAGCTTCAATTTGCT
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * *
25479972 CTCTGGATTAAGGTAAAAGATTGGTTGGTGGCTTCAATTTGCCC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTG-CC
* * * *
25480016 CTCTGAATAAAGGGTAAAAGATTGGATGGTTGCTTCAATCTG-T
1 CTCTGGAT-TAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * *
25480059 CTCTAGATTAGGGTAAAAGATTGGATGATGGCTTCTATCTGCC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * * * *
25480102 CTCTAGATTAGGGTAAAAGATTGGTTGGTGG-TTTAATATACC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* *
25480144 CTTTAGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
*
25480187 CTCTAGATTAGGGTAAAAGATTGGATGGTGGCTTCA
1 CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCA
25480223 CTCCATTCCA
Statistics
Matches: 537, Mismatches: 96, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
42 72 0.13
43 253 0.47
44 55 0.10
45 150 0.28
46 7 0.01
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (43 bp):
CTCTGGATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
Found at i:25479733 original size:88 final size:86
Alignment explanation
Indices: 25479538--25480222 Score: 667
Period size: 88 Copynumber: 7.9 Consensus size: 86
25479528 CGTCTCTCTA
* * * *
25479538 GATTAGGGGTAAGAGATTGGATGATGGCTTCAATCTGCCCCTTTGGATTGGGGGTAAGAGATTGG
1 GATTA-GGGTAAAAGATTGGATGATGGCTTCAATCTG-CCCTCTGGATT-AGGGTAAAAGATTGG
** *
25479603 ATTATGGCTTCAATCTGCCCTTTTA
63 ATGGTGGCTTCAATCTGCCC-TTTG
* * ** * * * *
25479628 GATTGGGGGTAAGAGATTAAATGATGGCTTTAATTTGCCCTCTAGATTAGGGTAAAAGATTGGTT
1 GATT-AGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGAT
* *
25479693 GGTGGCTTTAATCTACCCTTTTG
65 GGTGGCTTCAATCTGCCC-TTTG
* * * * **
25479716 GATTAGGGGCAAAAGATTAGATGGTTGCTTCAATCTGCCCTCTGGATTAGGGT-AAAGATTAGTT
1 GATTA-GGGTAAAAGATTGGATGATGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATT-GGA
*
25479780 TGGTGGCTTTAATCTGCCCCTTTG
64 TGGTGGCTTCAATCTG-CCCTTTG
* * *
25479804 GATTAGGGGTAAAAGATTGGATGGTTGCTTCAATCTGCCCTCTGGATTAAGGTAAAAGATTGGAT
1 GATTA-GGGTAAAAGATTGGATGATGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGAT
* * * *
25479869 GGTGACATCAATTTGCCCTCTG
65 GGTGGCTTCAATCTGCCCTTTG
* * * * * * * *
25479891 GATTAGGGTAAAAGATTAG-TTAGTAGCTTCAATATGCCTTTTGGATTAGAGTAAACGATTGGAT
1 GATTAGGGTAAAAGATTGGATGA-TGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGAT
* * * *
25479955 GGTAGCTTCAATTTGCTCTCTG
65 GGTGGCTTCAATCTGCCCTTTG
* * * * * *
25479977 GATTAAGGTAAAAGATTGGTTGGTGGCTTCAATTTGCCCCTCTGAATAAAGGGTAAAAGATTGGA
1 GATTAGGGTAAAAGATTGGATGATGGCTTCAATCTG-CCCTCTGGAT-TAGGGTAAAAGATTGGA
* * * *
25480042 TGGTTGCTTCAATCTG-TCTCTA
64 TGGTGGCTTCAATCTGCCCTTTG
* * *
25480064 GATTAGGGTAAAAGATTGGATGATGGCTTCTATCTGCCCTCTAGATTAGGGTAAAAGATTGGTTG
1 GATTAGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
* * * *
25480129 GTGG-TTTAATATACCCTTTA
66 GTGGCTTCAATCTGCCCTTTG
* *
25480149 GATTAGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCTCTAGATTAGGGTAAAAGATTGGATG
1 GATTAGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
25480214 GTGGCTTCA
66 GTGGCTTCA
25480223 CTCCATTCCA
Statistics
Matches: 500, Mismatches: 84, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
84 6 0.01
85 91 0.18
86 104 0.21
87 62 0.12
88 187 0.37
89 19 0.04
90 31 0.06
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (86 bp):
GATTAGGGTAAAAGATTGGATGATGGCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
GTGGCTTCAATCTGCCCTTTG
Found at i:25481253 original size:22 final size:23
Alignment explanation
Indices: 25481226--25481287 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
25481216 TCTTGACCCC
25481226 TCCTTTTTTTCTTCTTTCTT-TTT
1 TCCTTTTTTTCTTCTTT-TTCTTT
25481249 T-C-TTTTTTCTCTCTTTTTCTTT
1 TCCTTTTTTTCT-TCTTTTTCTTT
*
25481271 TCCTTTTCTT-TTCTTTT
1 TCCTTTTTTTCTTCTTTT
25481288 GCTAGTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
21 10 0.29
22 16 0.47
23 3 0.09
24 5 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (23 bp):
TCCTTTTTTTCTTCTTTTTCTTT
Found at i:25481263 original size:18 final size:18
Alignment explanation
Indices: 25481232--25481272 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
25481222 CCCCTCCTTT
*
25481232 TTTTCTTCTTTCTTTTTTC
1 TTTTCTTCTCTC-TTTTTC
25481251 TTTT-TTCTCTCTTTTTC
1 TTTTCTTCTCTCTTTTTC
25481268 TTTTC
1 TTTTC
25481273 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 10 0.50
18 6 0.30
19 4 0.20
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTCTCTCTTTTTC
Found at i:25483686 original size:21 final size:21
Alignment explanation
Indices: 25483656--25483702 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25483646 TTTGTTTGGG
* *
25483656 TTCAACTTCAACTAGAACTTT
1 TTCAACTTCAACAACAACTTT
* *
25483677 TTCAATTTCAAGAACAACTTT
1 TTCAACTTCAACAACAACTTT
25483698 TTCAA
1 TTCAA
25483703 AATCTTCACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.38
Consensus pattern (21 bp):
TTCAACTTCAACAACAACTTT
Found at i:25490207 original size:24 final size:22
Alignment explanation
Indices: 25490157--25490231 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
25490147 TTATAATGAC
25490157 AAAATAAA-TAAATAATACATGAAT
1 AAAATAAATTAAATAATAC---AAT
25490181 AAAATAAATTAAATGAATACAAT
1 AAAATAAATTAAAT-AATACAAT
* *
25490204 TAAATACAATT-AATAACACAAT
1 AAAATA-AATTAAATAATACAAT
25490226 AAAATA
1 AAAATA
25490232 GTAAATACGA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
22 12 0.27
23 11 0.24
24 12 0.27
25 5 0.11
26 5 0.11
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAATAAATTAAATAATACAAT
Found at i:25490573 original size:26 final size:25
Alignment explanation
Indices: 25490494--25490581 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 25
25490484 AATTGTAATT
* *
25490494 AAATAAAA-AAATAAAATTTAATTA
1 AAATAAAATAAATAAAAATTAAATA
**
25490518 TAAAT-AAATAAATAAACAAGCAAA-A
1 -AAATAAAATAAATAAA-AATTAAATA
*
25490543 TAATAACAATAAATAAAAATTAAATA
1 AAATAA-AATAAATAAAAATTAAATA
25490569 AAATAATAATAAA
1 AAATAA-AATAAA
25490582 AGAGAGAACA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
24 6 0.12
25 18 0.37
26 25 0.51
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (25 bp):
AAATAAAATAAATAAAAATTAAATA
Found at i:25492081 original size:20 final size:18
Alignment explanation
Indices: 25491997--25492105 Score: 71
Period size: 20 Copynumber: 5.9 Consensus size: 18
25491987 ATTCCAAAAA
*
25491997 TAAATATTATTTTAATAAT
1 TAAATATTAATTTAAT-AT
*
25492016 TTAATATTTAATTTAAT-T
1 TAAATA-TTAATTTAATAT
* * *
25492034 T-AATAATTATTTTGATAC
1 TAAAT-ATTAATTTAATAT
**
25492052 TATTTTATTAATTTAATAT
1 TA-AATATTAATTTAATAT
*
25492071 TAAAATGATTATTTTAATAT
1 T-AAAT-ATTAATTTAATAT
25492091 TAAAT-TTAATTTAAT
1 TAAATATTAATTTAAT
25492106 GTTTATCTTA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
17 20 0.29
18 4 0.06
19 21 0.30
20 24 0.35
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
TAAATATTAATTTAATAT
Found at i:25496081 original size:23 final size:23
Alignment explanation
Indices: 25496050--25496094 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25496040 TGATCACATA
25496050 AACAATCCTA-AGTATCCATAACT
1 AACAATCCTAGA-TATCCATAACT
*
25496073 AACAGTCCTAGATATCCATAAC
1 AACAATCCTAGATATCCATAAC
25496095 AATCACACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (23 bp):
AACAATCCTAGATATCCATAACT
Found at i:25497795 original size:23 final size:23
Alignment explanation
Indices: 25497739--25497806 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
25497729 GTTCGATTAA
* * *
25497739 AGTTAACGGTTCGGGTTGGGCTC
1 AGTTAACGGGTCGAGTTGGGTTC
* * *
25497762 AATCAATGGGTCGAGTTGGGTTC
1 AGTTAACGGGTCGAGTTGGGTTC
*
25497785 AGTTAACGGGTTGA-TTGGGTTC
1 AGTTAACGGGTCGAGTTGGGTTC
25497807 GGTCAATGGG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 8 0.23
23 27 0.77
ACGTcount: A:0.18, C:0.13, G:0.37, T:0.32
Consensus pattern (23 bp):
AGTTAACGGGTCGAGTTGGGTTC
Found at i:25497817 original size:22 final size:23
Alignment explanation
Indices: 25497753--25497819 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
25497743 AACGGTTCGG
* * *
25497753 GTTGGGCTCAATCAATGGGTCGA
1 GTTGGGTTCAGTCAATGGGTTGA
* *
25497776 GTTGGGTTCAGTTAACGGGTTGA
1 GTTGGGTTCAGTCAATGGGTTGA
*
25497799 -TTGGGTTCGGTCAATGGGTTG
1 GTTGGGTTCAGTCAATGGGTTG
25497820 CATCAAATGG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.16, C:0.12, G:0.39, T:0.33
Consensus pattern (23 bp):
GTTGGGTTCAGTCAATGGGTTGA
Found at i:25502724 original size:239 final size:237
Alignment explanation
Indices: 25502300--25502777 Score: 798
Period size: 239 Copynumber: 2.0 Consensus size: 237
25502290 TAAAAAATGT
* * *
25502300 CTCCAATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
1 CTCCAATTTACTTGCAACTTAACTAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
* *
25502365 AAAGATTTTTACTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATGCTTTCAA
66 AAAGATTTTTACTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAA
*
25502430 TTCTTAAAATTAATTCTATTTTTAGATCCTAAAAAACCTAAAAAAAATTACTAATGAATTAAGAG
131 TTCTTAAAATTAATTCTATTTTTAGATCCTAAAAAACCT--AAAAAATTACTAATGAATTAAAAG
25502495 AAATATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
194 AAATATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
*
25502539 CTCCGATTTACTTGCAACTTAACTAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
1 CTCCAATTTACTTGCAACTTAACTAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
* *
25502604 AAAGATTTTTATTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCGA
66 AAAGATTTTTACTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAA
*
25502669 TTCTTAAAATTAATTCTA-TTTTAGAATCCTAAAAAAAAGCCT-AAAAGTTACTAATGAATTAAA
131 TTCTTAAAATTAATTCTATTTTTAG-ATCCT--AAAAAA-CCTAAAAAATTACTAATGAATTAAA
25502732 AGAAATATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
192 AGAAATATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
25502778 TTATGATTTT
Statistics
Matches: 225, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
238 6 0.03
239 210 0.93
241 6 0.03
242 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (237 bp):
CTCCAATTTACTTGCAACTTAACTAAAACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATT
AAAGATTTTTACTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAA
TTCTTAAAATTAATTCTATTTTTAGATCCTAAAAAACCTAAAAAATTACTAATGAATTAAAAGAA
ATATTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
Found at i:25504116 original size:171 final size:168
Alignment explanation
Indices: 25503820--25504125 Score: 465
Period size: 171 Copynumber: 1.8 Consensus size: 168
25503810 AAATCACAAC
* * * *
25503820 TTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTAAAAGTTT
1 TTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAATAAAAACTTCGTTAAAAATTT
* ** *
25503885 ACTTTTTCTTTAAAATAACTAAAAATCAGATTTTTGTTTTTTTTTTAAATCTAAACTTTCTCTTT
66 ACTTTTTCTTTAAAATAACTAAAAATCAGATTTTTGTATTTTTTAAAAATCTAAACTTTCTATTT
25503950 TTTTTTCATTTGATTTTTTAAAATAGTAAAAATCAGAT
131 TTTTTTCATTTGATTTTTTAAAATAGTAAAAATCAGAT
25503988 TTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAGAAAAAAAATAAAAACTTCGTTAAAAA
1 TTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTT---AAAAAAATAAAAACTTCGTTAAAAA
25504053 TTTAAACTTTTTCTTTAAAATAACTAAAAAAT-AGA-TTTT-TATTTTTTAAAAATCTAAACTTT
63 TTT--ACTTTTTCTTTAAAATAACT-AAAAATCAGATTTTTGTATTTTTTAAAAATCTAAACTTT
25504115 CTATTTTTTTT
125 CTATTTTTTTT
25504126 AAAGAAAATC
Statistics
Matches: 124, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
168 36 0.29
171 55 0.44
172 4 0.03
173 23 0.19
174 6 0.05
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (168 bp):
TTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAATAAAAACTTCGTTAAAAATTT
ACTTTTTCTTTAAAATAACTAAAAATCAGATTTTTGTATTTTTTAAAAATCTAAACTTTCTATTT
TTTTTTCATTTGATTTTTTAAAATAGTAAAAATCAGAT
Found at i:25504154 original size:21 final size:22
Alignment explanation
Indices: 25504115--25504157 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25504105 TCTAAACTTT
**
25504115 CTATTTTTTTTAAAGAAAATCA
1 CTATTTTGCTTAAAGAAAATCA
25504137 CTATTTTGCTTAAA-AAAATCA
1 CTATTTTGCTTAAAGAAAATCA
25504158 AAGCTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (22 bp):
CTATTTTGCTTAAAGAAAATCA
Found at i:25505079 original size:42 final size:42
Alignment explanation
Indices: 25505015--25505639 Score: 788
Period size: 42 Copynumber: 14.9 Consensus size: 42
25505005 GAAATAAATG
* * * * *
25505015 AATGGACCTCTACACTTAGGCCTCTATATGCAATAAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* *
25505057 AATGGGCCTTCACACCTGGGCCTCTAAATGCAATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * *
25505099 AATGGACCTCCACACCTGGGCCTTTGAATGCAGTGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * *
25505141 AATGGACCACCACACCTAGGCCTCTAAATGTAATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * * *
25505183 AATGGGCCTCCACACCTGGAG-CTCTGAATGCTATGAAAAGCA
1 AATGGACCTCCACACCTGG-GCCTCTAAATGCAATGAAAAGTA
* *
25505225 AATGGACCTCCACACCTGGGCCTCTGAACGCAATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * * * * * *
25505267 AATGGGCC-CTCACACTTTGGCCTTTGAATACGATGAAAAGTA
1 AATGGACCTC-CACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * * ** *
25505309 AATGGATCTCCACACTTGAGCCTCTAAATGTGATGCAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
*
25505351 AATAGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * * *
25505393 AATGGGCATCCACACCTAGGCCTCTAAATGCATTGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
*
25505435 AATAGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * *
25505477 AATGGACCTCCACACCTAGACC-CTTAAATGCAATAAAAAGTA
1 AATGGACCTCCACACCTGGGCCTC-TAAATGCAATGAAAAGTA
* *
25505519 AATGGACCTCCACACCTGAGCCTCTAAATGTAATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
* * *
25505561 AATGGGCCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
25505603 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
1 AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
25505640 TGCTTTCCTT
Statistics
Matches: 498, Mismatches: 79, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
41 3 0.01
42 492 0.99
43 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
AATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTA
Found at i:25506077 original size:8 final size:8
Alignment explanation
Indices: 25506041--25506067 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
25506031 TTGCTCTCTC
25506041 TTTCTATT
1 TTTCTATT
25506049 TTTCTATT
1 TTTCTATT
25506057 TTTCTATT
1 TTTCTATT
25506065 TTT
1 TTT
25506068 TTGTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTATT
Found at i:25514284 original size:4 final size:4
Alignment explanation
Indices: 25514271--25514324 Score: 81
Period size: 4 Copynumber: 13.5 Consensus size: 4
25514261 TAAATAAAAA
* * *
25514271 AATG AGTG AATG AATG AATG AATG AACG AATG AATG AATG AGTG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
25514319 AATG AA
1 AATG AA
25514325 ATTGAGGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (4 bp):
AATG
Found at i:25518045 original size:236 final size:236
Alignment explanation
Indices: 25517616--25518082 Score: 740
Period size: 236 Copynumber: 2.0 Consensus size: 236
25517606 TACCTCAAAT
* * *
25517616 TTACTTGTAACTTGACTAAGACGTGTTAATCAAACTTATCTAATTGAAAATTTAAATTAAAGATT
1 TTACTTGT-ACTTGACTAAAACGTGTTAACCAAACTTATCTAATTGAAAACTTAAATTAAAGATT
* *
25517681 TTTACTCCTAATAAGAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACTTTCAATTCTTAA
65 TTTACTCCTAATAAAAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAATTCTTAA
*
25517746 AATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAAATTACTAATGAATTAAGAAAAATATTA
130 AATTAATTATATTTTAGAATCCTAAAAAAACCT-AAAAATTACTAATGAATTAAGAAAAATATTA
*
25517811 AAATTCTCCTACAACTTATTCGATCTTTTATCATTACTTCGAA
194 AAATTCACCTACAACTTATTCGATCTTTTATCATTACTTCGAA
* * *
25517854 TTACTTGT-CTTGACTAAAACGTGTTCACCAAACTTATTTAATTTAAAACTTAAATTAAAGATTT
1 TTACTTGTACTTGACTAAAACGTGTTAACCAAACTTATCTAATTGAAAACTTAAATTAAAGATTT
* * * *
25517918 TTATTCCTGATAAAAACCTTAAAGGATGCCTAAATAATTCTAGTAAAATACCTTCAATTCTTAAA
66 TTACTCCTAATAAAAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAATTCTTAAA
*
25517983 ATTAATTATATTTTAGAATCCTAAAAAAAAGCCT-AAAATTACTAATGAATTAAGAGAAATATTA
131 ATTAATTATATTTTAGAATCCT-AAAAAAA-CCTAAAAATTACTAATGAATTAAGAAAAATATTA
*
25518047 AAATTCACCTACAACTTATTTGATCTTTTATCATTA
194 AAATTCACCTACAACTTATTCGATCTTTTATCATTA
25518083 TTATGATTTT
Statistics
Matches: 211, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
236 193 0.91
237 7 0.03
238 11 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (236 bp):
TTACTTGTACTTGACTAAAACGTGTTAACCAAACTTATCTAATTGAAAACTTAAATTAAAGATTT
TTACTCCTAATAAAAACCCTAAAGGATACCTAAATAATTCTAGTAAAATACCTTCAATTCTTAAA
ATTAATTATATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAAAAATATTAAA
ATTCACCTACAACTTATTCGATCTTTTATCATTACTTCGAA
Found at i:25519477 original size:153 final size:153
Alignment explanation
Indices: 25519117--25519486 Score: 481
Period size: 152 Copynumber: 2.4 Consensus size: 153
25519107 TGATTAAACA
* *
25519117 AAAATCACTACTTT-ACTTAAAAATCCAAACTTTTATTTCGAAATAG-TT-AAAAAAATCAAAAT
1 AAAATCACTATTTTGA-TTAAAAATCCAAACTTTTATTTCGAAATAGTTTAAAAAAAATCAAAAC
* * **
25519179 TTTGTAAAAATTTACTTTTTCTTTAAAATAACTAAAAACCAGATTTTTGTTTTTTTTTAAATCTA
65 TTTGTAAAAATTTACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTGATTTTTTAAAAATCTA
*
25519244 AACTTTCTCTTCTTTTTTTTTAAAG
130 AAC-TTCTCTTCTATTTTTTTAAAG
* *
25519269 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGGAAAAAAAATCAAAA
1 AAAATCACTATTTTGATTAAAAATCCAAACTTTTATTTCGAAATAGTT--TAAAAAAAATCAAAA
*
25519334 CTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAGAGATTTTT-ATTTTTTAAAAA
64 CTTTG-TAAAAATTT--ACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTGATTTTTTAAAAA
25519398 TCTAAAC-T-TC-T-TATTTTTTTAAAG
126 TCTAAACTTCTCTTCTATTTTTTTAAAG
*
25519422 AAAATCACTATTTTGATTAAAAAAAT-CAAAGCTTTTATTTCGAAATTGTTTAAAAAAAA-CAAA
1 AAAATCACTATTTTGATT--AAAAATCCAAA-CTTTTATTTCGAAATAGTTTAAAAAAAATCAAA
25519485 AC
63 AC
25519487 ATTTCCCAAA
Statistics
Matches: 194, Mismatches: 13, Indels: 22
0.85 0.06 0.10
Matches are distributed among these distances:
152 49 0.25
153 38 0.20
154 5 0.03
155 26 0.13
156 18 0.09
157 9 0.05
158 16 0.08
159 33 0.17
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (153 bp):
AAAATCACTATTTTGATTAAAAATCCAAACTTTTATTTCGAAATAGTTTAAAAAAAATCAAAACT
TTGTAAAAATTTACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTGATTTTTTAAAAATCTAA
ACTTCTCTTCTATTTTTTTAAAG
Found at i:25519510 original size:153 final size:152
Alignment explanation
Indices: 25519117--25519518 Score: 460
Period size: 153 Copynumber: 2.6 Consensus size: 152
25519107 TGATTAAACA
* * *
25519117 AAAATCACTACTTT-ACTTAAAAATCCAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAATT
1 AAAATCACTATTTTGA-TTAAAAATCCAAACTTTTATTTCGAAATAGTTTAAAAAAAACAAAACT
* * * * **
25519180 TTGTAAAAATTTACTTTTTCTTTAAAATAACTAAAAACCAGATTTTTGTTTTTTTTTAAATCTAA
65 TTCTAAAAATTAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTGATTTTTTAAAAATCTAA
*
25519245 ACTTTCTCTTCTTTTTTTTTAAAG
130 AC-TTCTCTTCTATTTTTTTAAAG
* *
25519269 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGGAAAAAAAATCAAAA
1 AAAATCACTATTTTGATTAAAAATCCAAACTTTTATTTCGAAATAGTT--TAAAAAAAA-CAAAA
* *
25519334 CTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAGAGATTTTT-ATTTTTTAAAAA
63 CTTT-CTAAAAA-TT-AACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTGATTTTTTAAAAA
25519398 TCTAAAC-T-TC-T-TATTTTTTTAAAG
125 TCTAAACTTCTCTTCTATTTTTTTAAAG
*
25519422 AAAATCACTATTTTGATTAAAAAAAT-CAAAGCTTTTATTTCGAAATTGTTTAAAAAAAACAAAA
1 AAAATCACTATTTTGATT--AAAAATCCAAA-CTTTTATTTCGAAATAGTTTAAAAAAAACAAAA
**
25519486 CATTTCCCAAAATTAAGCTATTTTTCTTTAAAA
63 C-TTTCTAAAAATTAA-C--TTTTTCTTTAAAA
25519519 AAAATTATTT
Statistics
Matches: 216, Mismatches: 19, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
150 2 0.01
151 3 0.01
152 53 0.25
153 54 0.25
154 5 0.02
155 33 0.15
156 9 0.04
157 6 0.03
158 18 0.08
159 33 0.15
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (152 bp):
AAAATCACTATTTTGATTAAAAATCCAAACTTTTATTTCGAAATAGTTTAAAAAAAACAAAACTT
TCTAAAAATTAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTGATTTTTTAAAAATCTAAA
CTTCTCTTCTATTTTTTTAAAG
Found at i:25519969 original size:11 final size:11
Alignment explanation
Indices: 25519955--25519979 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25519945 CCCAAAAAGG
25519955 AAAGAAAAATA
1 AAAGAAAAATA
25519966 AAAGAAAAATA
1 AAAGAAAAATA
25519977 AAA
1 AAA
25519980 ACCCCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:25523069 original size:23 final size:23
Alignment explanation
Indices: 25523043--25523087 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
25523033 GTTTGGGTTA
25523043 GGTTCGATCAATGGGTCGGGTCG
1 GGTTCGATCAATGGGTCGGGTCG
* *
25523066 GGTTCGGTCAATGGGTTGGGTC
1 GGTTCGATCAATGGGTCGGGTC
25523088 AAATGTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.44, T:0.29
Consensus pattern (23 bp):
GGTTCGATCAATGGGTCGGGTCG
Found at i:25523102 original size:18 final size:20
Alignment explanation
Indices: 25523081--25523126 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
25523071 GGTCAATGGG
*
25523081 TTGGGTCAAATGTTT-GG-T
1 TTGGGTCAAACGTTTGGGTT
25523099 TTGGTGT-AAACGTTTGGGTT
1 TTGG-GTCAAACGTTTGGGTT
25523119 TTGGGTCA
1 TTGGGTCA
25523127 CCACTTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 11 0.48
19 6 0.26
20 6 0.26
ACGTcount: A:0.15, C:0.07, G:0.35, T:0.43
Consensus pattern (20 bp):
TTGGGTCAAACGTTTGGGTT
Found at i:25524612 original size:56 final size:56
Alignment explanation
Indices: 25524494--25524611 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 56
25524484 AATCAAAATT
* ** * * * * *
25524494 CTTTTTGTATTATTCAATTGATCACTTTTGATAAAGAACGATTTGCAATCAGATTT
1 CTTTTTATATTATTCAATTGATCACTTTTGATAAAGAACGAACTACAATAACACTA
*
25524550 CTTTTTATATTATTTAATTGATCACTTTTGATAAAGAACGAACTACAATGAACACTA
1 CTTTTTATATTATTCAATTGATCACTTTTGATAAAGAACGAACTACAAT-AACACTA
25524607 CTTTT
1 CTTTT
25524612 AATAATAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
56 44 0.85
57 8 0.15
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (56 bp):
CTTTTTATATTATTCAATTGATCACTTTTGATAAAGAACGAACTACAATAACACTA
Found at i:25525898 original size:29 final size:29
Alignment explanation
Indices: 25525850--25525965 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
25525840 ACTAGTACAT
* * *
25525850 AGTACCTGATAAATATAACA-TCGGCACAA
1 AGTACTTGATAACTGTAACACT-GGCACAA
* *
25525879 AGTGCTTGATAACTGTAACACTGGTACAA
1 AGTACTTGATAACTGTAACACTGGCACAA
* *
25525908 AGTACTTGATAACTGTAATACTGGTACAA
1 AGTACTTGATAACTGTAACACTGGCACAA
* *
25525937 AGTACTTGATAATTGTAATCACCGGCACA
1 AGTACTTGATAACTGTAA-CACTGGCACA
25525966 TAATGTCTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
29 66 0.89
30 8 0.11
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (29 bp):
AGTACTTGATAACTGTAACACTGGCACAA
Found at i:25528200 original size:2 final size:2
Alignment explanation
Indices: 25528193--25528230 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25528183 AAGATCGAAC
25528193 AT AT AT AT AT 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 AT AT AT AT AT
25528231 CTGAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25528857 original size:16 final size:15
Alignment explanation
Indices: 25528838--25528880 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
25528828 CTTAAGACCA
25528838 AAAAAATTTAAACTC
1 AAAAAATTTAAACTC
* *
25528853 GAAAAAACTTAAATTC
1 -AAAAAATTTAAACTC
*
25528869 AAAAAATCTAAA
1 AAAAAATTTAAA
25528881 TCTTAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAAAATTTAAACTC
Found at i:25531254 original size:58 final size:59
Alignment explanation
Indices: 25531181--25531429 Score: 251
Period size: 58 Copynumber: 4.3 Consensus size: 59
25531171 TTTCAGGGTC
* * *
25531181 AAAATGGAATTTTTGGAAG-TTCGGGATCAAAAACGGAATTTTTTGAAGTTTGGGTGCA
1 AAAATGTAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTTAGAAGTTTGGGTGCA
* * * *
25531239 AAAATGTAATTTTTGGAAGTTTCGAGG-TCAAAAATGGAAATTTTGGAAGTTTGGGGGTA
1 AAAATGTAATTTTTGGAAGTTTCG-GGATCAAAAATGGAATTTTTAGAAGTTTGGGTGCA
* * * * **
25531298 AAAATGTAATTTTTGAAAGTTTTGGGGT-TAAAATGGAATTTTTAGAAGTTTGGG-GGT
1 AAAATGTAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTTAGAAGTTTGGGTGCA
* ** * *
25531355 AAAATGTAATTTTTGAAAGTTT-TAGAGTCAAAAATGTAATTTTCAGAAGTTTTGGGT-C-
1 AAAATGTAATTTTTGGAAGTTTCGGGA-TCAAAAATGGAATTTTTAGAAG-TTTGGGTGCA
*
25531413 GAAATGTAATTTTTGGA
1 AAAATGTAATTTTTGGA
25531430 CAATTTAAGG
Statistics
Matches: 162, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.01
57 24 0.15
58 75 0.46
59 60 0.37
60 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTTAGAAGTTTGGGTGCA
Found at i:25531273 original size:30 final size:29
Alignment explanation
Indices: 25531169--25531429 Score: 214
Period size: 29 Copynumber: 9.0 Consensus size: 29
25531159 TAATTTCGAG
*
25531169 AGTTTCAGGGTC-AAAATGGAATTTTTGGA
1 AGTTTC-GGGTCAAAAATGTAATTTTTGGA
* * *
25531198 AG-TTCGGGATCAAAAACGGAATTTTTTGA
1 AGTTTCGGG-TCAAAAATGTAATTTTTGGA
25531227 AGTTT-GGGTGCAAAAATGTAATTTTTGGA
1 AGTTTCGGGT-CAAAAATGTAATTTTTGGA
* *
25531256 AGTTTCGAGGTCAAAAATGGAAATTTTGGA
1 AGTTTCG-GGTCAAAAATGTAATTTTTGGA
* *
25531286 AGTTTGGGGGT-AAAAATGTAATTTTTGAA
1 AGTTT-CGGGTCAAAAATGTAATTTTTGGA
* * * *
25531315 AGTTTTGGGGT-TAAAATGGAATTTTTAGA
1 AG-TTTCGGGTCAAAAATGTAATTTTTGGA
* *
25531344 AGTTTGGGGGT--AAAATGTAATTTTTGAA
1 AGTTT-CGGGTCAAAAATGTAATTTTTGGA
* * **
25531372 AGTTTTAGAGTCAAAAATGTAATTTTCAGA
1 AG-TTTCGGGTCAAAAATGTAATTTTTGGA
* *
25531402 AGTTTTGGGTC-GAAATGTAATTTTTGGA
1 AGTTTCGGGTCAAAAATGTAATTTTTGGA
25531430 CAATTTAAGG
Statistics
Matches: 192, Mismatches: 28, Indels: 25
0.78 0.11 0.10
Matches are distributed among these distances:
27 3 0.02
28 42 0.22
29 96 0.50
30 47 0.24
31 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
AGTTTCGGGTCAAAAATGTAATTTTTGGA
Found at i:25533066 original size:25 final size:25
Alignment explanation
Indices: 25533038--25533094 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
25533028 GGCAGCGGCG
* *
25533038 GTGGCAGGACAGGTTGGAGCTGGTA
1 GTGGCAGGACAAGTTGAAGCTGGTA
** *
25533063 GTGGCAGGGTAAGTTGAAGCTGGTG
1 GTGGCAGGACAAGTTGAAGCTGGTA
25533088 GTGGCAG
1 GTGGCAG
25533095 AAAACAAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.49, T:0.21
Consensus pattern (25 bp):
GTGGCAGGACAAGTTGAAGCTGGTA
Found at i:25533316 original size:5 final size:5
Alignment explanation
Indices: 25533306--25533371 Score: 53
Period size: 5 Copynumber: 12.4 Consensus size: 5
25533296 AATTTTAGAT
*
25533306 TTAAA TTAAA TTCAAAA TTAAA TTAAA TTTAAA TTTAA -TAAA TCTAAA
1 TTAAA TTAAA TT--AAA TTAAA TTAAA -TTAAA TTAAA TTAAA T-TAAA
* *
25533354 TTTAAA ATAAA TTTAA TT
1 -TTAAA TTAAA TTAAA TT
25533372 TTAAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
4 3 0.06
5 28 0.56
6 13 0.26
7 6 0.12
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:25533325 original size:12 final size:11
Alignment explanation
Indices: 25533308--25533389 Score: 53
Period size: 11 Copynumber: 7.4 Consensus size: 11
25533298 TTTTAGATTT
25533308 AAATTAAATTCA
1 AAATTAAATT-A
25533320 AAATTAAATTA
1 AAATTAAATTA
*
25533331 AATTTAAATT-
1 AAATTAAATTA
*
25533341 TAA-TAAATCTA
1 AAATTAAAT-TA
* *
25533352 AATTTAAAATA
1 AAATTAAATTA
* *
25533363 AATTTAATTTTA
1 AAATTAA-ATTA
25533375 AAA-TAAATTTA
1 AAATTAAA-TTA
25533386 AAAT
1 AAAT
25533390 GGTTTGGTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
9 5 0.09
10 2 0.04
11 29 0.54
12 18 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:25533339 original size:6 final size:6
Alignment explanation
Indices: 25533299--25533387 Score: 66
Period size: 6 Copynumber: 16.0 Consensus size: 6
25533289 TTATAATAAT
* * *
25533299 TTTAGA TTTAAA -TTAAA TTCAAA ATTAAA -TTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
25533344 --TAAA TCTAAA TTTAAA -ATAAA TTTAAT TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
25533388 ATGGTTTGGT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 20 0.31
6 42 0.65
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:25533339 original size:11 final size:11
Alignment explanation
Indices: 25533282--25533369 Score: 67
Period size: 11 Copynumber: 8.0 Consensus size: 11
25533272 TGGACAATTT
25533282 ATTAAATTTATA
1 ATTAAATTTA-A
*
25533294 A-TAATTTTAGA
1 ATTAAATTTA-A
*
25533305 TTTAAA-TTAA
1 ATTAAATTTAA
*
25533315 ATTCAAAATTAA
1 ATT-AAATTTAA
25533327 ATTAAATTTAA
1 ATTAAATTTAA
*
25533338 ATTTAA--TAA
1 ATTAAATTTAA
25533347 ATCTAAATTTAA
1 AT-TAAATTTAA
*
25533359 AATAAATTTAA
1 ATTAAATTTAA
25533370 TTTTAAAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.08
10 6 0.10
11 35 0.57
12 15 0.25
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:25533343 original size:17 final size:16
Alignment explanation
Indices: 25533283--25533387 Score: 104
Period size: 17 Copynumber: 6.3 Consensus size: 16
25533273 GGACAATTTA
*
25533283 TTAAATTTATAATAATT
1 TTAAATTTA-AATAAAT
*
25533300 TTAGATTTAAATTAAAT
1 TTAAATTTAAA-TAAAT
* *
25533317 TCAAAATTAAATTAAAT
1 TTAAATTTAAA-TAAAT
25533334 TTAAATTT-AATAAAT
1 TTAAATTTAAATAAAT
*
25533349 CTAAATTTAAAATAAAT
1 TTAAATTT-AAATAAAT
*
25533366 TTAATTTTAAAATAAAT
1 TTAAATTT-AAATAAAT
25533383 TTAAA
1 TTAAA
25533388 ATGGTTTGGT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
15 12 0.16
16 4 0.05
17 58 0.78
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:25534071 original size:206 final size:201
Alignment explanation
Indices: 25533780--25534228 Score: 632
Period size: 206 Copynumber: 2.2 Consensus size: 201
25533770 GTAACAGGCG
* * *
25533780 TTGAGTTGGTCTACTTCTCTA-TATCTCATCAGGTAGATGACCGCCTCACTTGTTTCAATTCGCT
1 TTGAGTTGGTCTACTTCTC-AGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATTCGCT
* * *
25533844 TCTCTGTATCTCATCAGGAAGACGAATTTGGTGCACTTCTCAGTATCTCATCAGGAAGCTAACCG
65 TCTCTGGATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
25533909 TTTTATTGCTTCGACCTGCTTCTCTGTGTCTCATCAGGAAGCT-AGGGTTCGAAGATTTGCTCGC
130 TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCACGAAGCTGA-GGTTCGAAGATTTGCTCGC
25533973 ATTGAGCC
194 ATTGAGCC
* * * ** *
25533981 TGGGTTGGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCACATTGCTTGTTTTAATT
1 ----TT-GAGTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATT
* *
25534046 CGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTA
61 CGCTTCTCTGGATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
* *
25534111 ACCATTTTATTGCTTTGACCTTCTTCTCAGTGTCTCATCACGAAGCTGAGGTTCGAAGATTTGCT
126 ACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCACGAAGCTGAGGTTCGAAGATTTGCT
*
25534176 CGTATTGAGCC
191 CGCATTGAGCC
* *
25534187 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACC
1 TTGAGTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACC
25534229 GCCTCACTGT
Statistics
Matches: 217, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
201 35 0.16
202 2 0.01
205 3 0.01
206 176 0.81
207 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (201 bp):
TTGAGTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATTCGCTT
CTCTGGATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCACGAAGCTGAGGTTCGAAGATTTGCTCGCAT
TGAGCC
Found at i:25545866 original size:95 final size:94
Alignment explanation
Indices: 25545683--25545872 Score: 228
Period size: 95 Copynumber: 2.0 Consensus size: 94
25545673 AATTTTAAAG
* * * *
25545683 AAGGATATTTGATTATCTTGATTTGAAAAAGGATGCACCTAGTGAGTTAAGGCGCAAATTTTCAT
1 AAGGATATTCGATTATCTTGATTTGAAAAAGAATGCACCTAGTAAGTTAAGGCGCAAATTTT-AG
*
25545748 AACCGAAGATAAGGAAATATTGCCTCGATT
65 AACCGAAGATAAAGAAATATTGCCTCGATT
*
25545778 AAGGGTATTCGATTAT-TTCGATTTGAAGAAA-AATCGCACCTAGTAAGTTAAGGCGCAAAATTT
1 AAGGATATTCGATTATCTT-GATTTGAA-AAAGAAT-GCACCTAGTAAGTTAAGGCGC-AAATTT
25545841 T-GAACTCGAA-ATAAA-AGAATATTGCCTCGATT
62 TAGAAC-CGAAGATAAAGA-AATATTGCCTCGATT
25545873 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
94 3 0.04
95 46 0.55
96 27 0.33
97 7 0.08
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (94 bp):
AAGGATATTCGATTATCTTGATTTGAAAAAGAATGCACCTAGTAAGTTAAGGCGCAAATTTTAGA
ACCGAAGATAAAGAAATATTGCCTCGATT
Found at i:25546204 original size:28 final size:28
Alignment explanation
Indices: 25546099--25546205 Score: 67
Period size: 28 Copynumber: 3.8 Consensus size: 28
25546089 TTTGGATACC
* **
25546099 TAGGGGCAAAATGGTAATTTTGGAC-TT
1 TAGGGGTAAAATGGTAATTTTAAACATT
* **
25546126 TCGAGGAAAAAATGGTAATTTTGGGAAA-ATT
1 TAG-GGGTAAAATGGTAATTTT---AAACATT
* * *
25546157 TTGGGTTAAAAATGAT-ATTTTAAACATT
1 TAGGGGT-AAAATGGTAATTTTAAACATT
25546185 TAGGGGTAAAATGGTAATTTT
1 TAGGGGTAAAATGGTAATTTT
25546206 CATAAAAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
27 12 0.20
28 29 0.48
30 7 0.12
31 12 0.20
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (28 bp):
TAGGGGTAAAATGGTAATTTTAAACATT
Found at i:25546301 original size:30 final size:29
Alignment explanation
Indices: 25546267--25546469 Score: 169
Period size: 30 Copynumber: 6.9 Consensus size: 29
25546257 TAATTTCGGG
** *
25546267 AGTTTCAGGGTCAAAAATGGAATTTTTGAA
1 AGTTTC-GGGTCAAAAATATAATTTTTGGA
25546297 AGTTT-GGGTGCAAAAATATAATTTTTGGA
1 AGTTTCGGGT-CAAAAATATAATTTTTGGA
* * *
25546326 AGTTTCGAGGTCAAAAATAGAAATTTTGTA
1 AGTTTCG-GGTCAAAAATATAATTTTTGGA
* * * *
25546356 AGTTTGGGGGT-AAAATTGTAATTTTTGAA
1 AGTTT-CGGGTCAAAAATATAATTTTTGGA
* *
25546385 ATTTTTGGGGTCAAAAATATAATTTTTGGA
1 A-GTTTCGGGTCAAAAATATAATTTTTGGA
* *
25546415 AGTTTTAGGGT-AAAAATGTAATTTTTGGA
1 AG-TTTCGGGTCAAAAATATAATTTTTGGA
* * *
25546444 AGTTTTCGAGTCAAAAGTGTAATTTT
1 AG-TTTCGGGTCAAAAATATAATTTT
25546470 CAAAAGTTCT
Statistics
Matches: 143, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.03
29 66 0.46
30 69 0.48
31 4 0.03
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (29 bp):
AGTTTCGGGTCAAAAATATAATTTTTGGA
Found at i:25546342 original size:59 final size:58
Alignment explanation
Indices: 25546250--25546459 Score: 203
Period size: 59 Copynumber: 3.6 Consensus size: 58
25546240 ATTCGAGGGT
* * *
25546250 AAAATGGTAA-TTTCGGGAGTTTC-AGGGTCAAAAATGGAATTTTTGAAAGTTTGGGTGCA
1 AAAAT-GTAATTTTTGGAAGTTTCGA-GGTCAAAAATAGAATTTTTGAAAGTTTGGGTG-A
* * * *
25546309 AAAATATAATTTTTGGAAGTTTCGAGGTCAAAAATAGAAATTTTGTAAGTTTGGGGGTA
1 AAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGAAAGTTTGGGTG-A
* * * * * * *
25546368 AAATTGTAATTTTTGAAATTTTTGGGGTCAAAAATATAATTTTTGGAAGTTTTAGGGT-A
1 AAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGAAAG-TTT-GGGTGA
25546427 AAAATGTAATTTTTGGAAGTTTTCGA-GTCAAAA
1 AAAATGTAATTTTTGGAAG-TTTCGAGGTCAAAA
25546460 GTGTAATTTT
Statistics
Matches: 123, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
58 3 0.02
59 109 0.89
60 8 0.07
61 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATAGAATTTTTGAAAGTTTGGGTGA
Found at i:25546449 original size:29 final size:30
Alignment explanation
Indices: 25546250--25546469 Score: 184
Period size: 29 Copynumber: 7.4 Consensus size: 30
25546240 ATTCGAGGGT
* * *
25546250 AAAATGGTAA-TTTCGGGAGTTTCAGGGTCA
1 AAAAT-GTAATTTTTGGAAGTTTTAGGGTCA
* *
25546280 AAAATGGAATTTTTGAAAG-TTT-GGGTGCA
1 AAAATGTAATTTTTGGAAGTTTTAGGGT-CA
* *
25546309 AAAATATAATTTTTGGAAG-TTTCGAGGTCA
1 AAAATGTAATTTTTGGAAGTTTTAG-GGTCA
* * **
25546339 AAAATAG-AAATTTTGTAAGTTTGGGGGT-A
1 AAAAT-GTAATTTTTGGAAGTTTTAGGGTCA
* * * *
25546368 AAATTGTAATTTTTGAAATTTTTGGGGTCA
1 AAAATGTAATTTTTGGAAGTTTTAGGGTCA
*
25546398 AAAATATAATTTTTGGAAGTTTTAGGGT-A
1 AAAATGTAATTTTTGGAAGTTTTAGGGTCA
* *
25546427 AAAATGTAATTTTTGGAAGTTTTCGAGTCA
1 AAAATGTAATTTTTGGAAGTTTTAGGGTCA
*
25546457 AAAGTGTAATTTT
1 AAAATGTAATTTT
25546470 CAAAAGTTCT
Statistics
Matches: 154, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
28 5 0.03
29 74 0.48
30 69 0.45
31 6 0.04
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTTAGGGTCA
Found at i:25547683 original size:26 final size:26
Alignment explanation
Indices: 25547639--25547688 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
25547629 TTATTAAAAC
* **
25547639 AATATTTAATATATTTATTAATTAAT
1 AATATTTAATACACCTATTAATTAAT
25547665 AATATTTAATACACCTATTAATTA
1 AATATTTAATACACCTATTAATTA
25547689 TATATAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATTTAATACACCTATTAATTAAT
Found at i:25548382 original size:17 final size:17
Alignment explanation
Indices: 25548360--25548479 Score: 135
Period size: 17 Copynumber: 7.3 Consensus size: 17
25548350 GGACACTTTA
25548360 TTAAATTTATAATAAAT
1 TTAAATTTATAATAAAT
25548377 TTAAATTTA-AATTAAAT
1 TTAAATTTATAA-TAAAT
*
25548394 TCAAATTTA-AATTAAAT
1 TTAAATTTATAA-TAAAT
25548411 TTAAA-TT-TAATAAAT
1 TTAAATTTATAATAAAT
* *
25548426 CTAAATTTAAAATAAAT
1 TTAAATTTATAATAAAT
25548443 TTAAA-TT-TAATAAAT
1 TTAAATTTATAATAAAT
* *
25548458 CTAAATTTAAAATAAAT
1 TTAAATTTATAATAAAT
25548475 TTAAA
1 TTAAA
25548480 ATGGTTTGGT
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
15 20 0.23
16 12 0.14
17 56 0.64
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTATAATAAAT
Found at i:25548383 original size:6 final size:6
Alignment explanation
Indices: 25548360--25548479 Score: 102
Period size: 6 Copynumber: 21.8 Consensus size: 6
25548350 GGACACTTTA
*
25548360 TTAAAT TTATAA- -TAAAT TTAAAT TTAAA- TTAAAT TCAAAT TTAAA-
1 TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
25548405 TTAAAT TTAAAT TT-AA- -TAAAT CTAAAT TTAAA- ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
25548449 TT-AA- -TAAAT CTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
25548480 ATGGTTTGGT
Statistics
Matches: 93, Mismatches: 8, Indels: 26
0.73 0.06 0.20
Matches are distributed among these distances:
3 2 0.02
4 6 0.06
5 24 0.26
6 59 0.63
7 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:25548432 original size:32 final size:32
Alignment explanation
Indices: 25548361--25548479 Score: 186
Period size: 32 Copynumber: 3.7 Consensus size: 32
25548351 GACACTTTAT
*
25548361 TAAATTTATAATAAATTTAAATTTAAATTAAAT-
1 TAAATTTAAAATAAATTTAAATTT-AA-TAAATC
*
25548394 TCAAATTTAAATTAAATTTAAATTTAATAAATC
1 T-AAATTTAAAATAAATTTAAATTTAATAAATC
25548427 TAAATTTAAAATAAATTTAAATTTAATAAATC
1 TAAATTTAAAATAAATTTAAATTTAATAAATC
25548459 TAAATTTAAAATAAATTTAAA
1 TAAATTTAAAATAAATTTAAA
25548480 ATGGTTTGGT
Statistics
Matches: 81, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
32 56 0.69
33 4 0.05
34 21 0.26
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAATTTAAAATAAATTTAAATTTAATAAATC
Found at i:25549129 original size:2 final size:2
Alignment explanation
Indices: 25549122--25549147 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25549112 GTGAGTTCTC
25549122 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
25549148 CTCACACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25550565 original size:20 final size:21
Alignment explanation
Indices: 25550540--25550585 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
25550530 AAAAGTTATG
*
25550540 AAATA-TTAAATTTTAATAAA
1 AAATATTTAAAATTTAATAAA
*
25550560 AAATATTTAAAATTTATTAAA
1 AAATATTTAAAATTTAATAAA
25550581 AAATA
1 AAATA
25550586 GAAAATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATATTTAAAATTTAATAAA
Found at i:25550590 original size:9 final size:9
Alignment explanation
Indices: 25550578--25550611 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
25550568 AAAATTTATT
25550578 AAAAAATAG
1 AAAAAATAG
*
25550587 AAAATATAG
1 AAAAAATAG
25550596 AAAAATATAG
1 AAAAA-ATAG
25550606 AAAAAA
1 AAAAAA
25550612 ATATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (9 bp):
AAAAAATAG
Found at i:25550616 original size:12 final size:10
Alignment explanation
Indices: 25550578--25550610 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
25550568 AAAATTTATT
25550578 AAAAA-ATAG
1 AAAAATATAG
25550587 -AAAATATAG
1 AAAAATATAG
25550596 AAAAATATAG
1 AAAAATATAG
25550606 AAAAA
1 AAAAA
25550611 AATATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 4 0.18
10 14 0.64
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (10 bp):
AAAAATATAG
Done.