Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 132 of 171
Found at i:41208800 original size:61 final size:60
Alignment explanation
Indices: 41208643--41209155 Score: 494
Period size: 61 Copynumber: 8.6 Consensus size: 60
41208633 TTACATAGAT
* * *
41208643 AACACCAAAAAAATTT-AATTTTTTATC-AATAAAAAGGGGTGTCGGCCATGGCATGGCC
1 AACACCAAAAAAATTTAAATTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
* * * * * *
41208701 AACACAAAAAAAAATCAAATTTTTTATCTGACAAAAAGGGGTGTCGGCCATAGCATGGCC
1 AACACCAAAAAAATTTAAATTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
* * * *
41208761 AACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAAGGGGTATCGGCCATTGCATGGCT
1 AACACCAAAAAAATTT-AAA-TTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
* * * * *
41208822 AACACTAAAAAATTTTAAAATTTTTTTATCTGAAAAAAAGGGATGTCGACCA-TGACATGACC
1 AACACCAAAAAAATTT-AAA-TTTTTTATCTGATAAAAAGGGGTGTCGGCCATTG-CATGACC
* * * * *
41208884 AACA-CAAAAAAATTTGAATTTTTTATCTGATAAAAAGAGGTGTCAGTCATGGCATGACC
1 AACACCAAAAAAATTTAAATTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
* * * *
41208943 AACA-CAAAAAAATTT-TATTTTTTATTCGGATAAAAAGGGGGTGTCGACCATTGCATAACC
1 AACACCAAAAAAATTTAAATTTTTTA-TCTGATAAAAA-GGGGTGTCGGCCATTGCATGACC
* * * *
41209003 AATACAAAAAAAATTTGAAATTTTTTATCTG--GAAAAGGGGTGTCGGCCATTGCATGACT
1 AACACCAAAAAAATTT-AAATTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
* * * * *
41209062 AACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGAGGTGTCGACCATTTCATGGCC
1 AACACCAAAAAAATTT-AAA-TTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
* *
41209123 AACATCC--AAAAATTT-GATTTTTTATCAGATAAA
1 AACA-CCAAAAAAATTTAAATTTTTTATCTGATAAA
41209156 TGGTCGACAC
Statistics
Matches: 382, Mismatches: 57, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
57 11 0.03
58 25 0.07
59 105 0.27
60 85 0.22
61 107 0.28
62 41 0.11
63 8 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (60 bp):
AACACCAAAAAAATTTAAATTTTTTATCTGATAAAAAGGGGTGTCGGCCATTGCATGACC
Found at i:41209290 original size:59 final size:59
Alignment explanation
Indices: 41209162--41209343 Score: 179
Period size: 59 Copynumber: 3.1 Consensus size: 59
41209152 TAAATGGTCG
* * * ** * * *
41209162 ACACCCAAAAATTTAATTTTTTTATCAGATAAATAGGGGTGTCAACTATAG-TATGGTCA
1 ACACCCAAAAATTTAAATTTTTTATCAGAAAAAAAGGGGTGTCGCCCAT-GCAATGGCCA
* * * * * *
41209221 ACA-CAAAAAAATTAAATTTTTTATCTGACAAAAAAGGGGTGTTGGCCATGCAATGGCCG
1 ACACCCAAAAATTTAAATTTTTTATCAGA-AAAAAAGGGGTGTCGCCCATGCAATGGCCA
* **
41209280 ACACCCAAAAATTTAATTTTTTTATCAGATTAAAAGGGGTGTCGCCCATGCAATGGCCA
1 ACACCCAAAAATTTAAATTTTTTATCAGAAAAAAAGGGGTGTCGCCCATGCAATGGCCA
41209339 ACACC
1 ACACC
41209344 AATTTTTTTT
Statistics
Matches: 98, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
58 22 0.22
59 55 0.56
60 21 0.21
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (59 bp):
ACACCCAAAAATTTAAATTTTTTATCAGAAAAAAAGGGGTGTCGCCCATGCAATGGCCA
Found at i:41212622 original size:15 final size:16
Alignment explanation
Indices: 41212602--41212632 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41212592 AATATTATCC
41212602 AAAAAAT-GTAAAAAA
1 AAAAAATCGTAAAAAA
41212617 AAAAAATCGTAAAAAA
1 AAAAAATCGTAAAAAA
41212633 TTTATTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAAAATCGTAAAAAA
Found at i:41212775 original size:20 final size:22
Alignment explanation
Indices: 41212736--41212792 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
41212726 TAAAAAACTC
*
41212736 TTTTCATTTTTATAATATATAT-
1 TTTTAATTTTTATAATATAT-TG
41212758 TTTTAATTTTT-T-ATATATTG
1 TTTTAATTTTTATAATATATTG
*
41212778 TTTTGATTTTTATAA
1 TTTTAATTTTTATAA
41212793 AAAATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 2 0.07
22 11 0.37
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTAATTTTTATAATATATTG
Found at i:41231803 original size:76 final size:76
Alignment explanation
Indices: 41231663--41232591 Score: 1561
Period size: 76 Copynumber: 12.2 Consensus size: 76
41231653 GTAAGAGTGA
* * *
41231663 GAAGAAAGACCAACATCATTTCCTATCCTCTTGAAATTGAAGAAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41231728 TCTCTGAAATT
66 TCTCTGAAATT
* * * *
41231739 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41231804 TCTCTGAAATT
66 TCTCTGAAATT
* *
41231815 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41231880 TCTCTGAAATT
66 TCTCTGAAATT
* * *
41231891 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41231956 TCTCTGAAATT
66 TCTCTGAAATT
*
41231967 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41232032 TCTCTGAAATT
66 TCTCTGAAATT
*
41232043 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
*
41232108 TTTCTGAAATT
66 TCTCTGAAATT
* *
41232119 AAAGTAAGAGCAATATCATTTCCTATCCTCTTGAAAATTGAAGTAAAGCTGGATATCAAGTCTTT
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTG-AAATTGAAGTAAAGCTGGATATCAAGTCTTT
41232184 ATCTCTGAAATT
65 ATCTCTGAAATT
* * *
41232196 GAAGTAGGAGCGACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGATGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41232261 TCTCTGAAATT
66 TCTCTGAAATT
41232272 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAAATTGAAGTAAAGCTGGATATCAAGTCTTT
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTG-AAATTGAAGTAAAGCTGGATATCAAGTCTTT
41232337 ATCTCTGAAATT
65 ATCTCTGAAATT
* * * *
41232349 GAAGTAGGAGCGACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGATGAATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
*
41232414 TCGCTGAAATT
66 TCTCTGAAATT
* *
41232425 GAAGTAGGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGATGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41232490 TCTCTGAAATT
66 TCTCTGAAATT
*
41232501 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
*
41232566 TCTCTCTAAAATT
66 --TCTCTGAAATT
41232579 GAAGTAAGAGCAA
1 GAAGTAAGAGCAA
41232592 GATGAAGCCT
Statistics
Matches: 811, Mismatches: 38, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
76 644 0.79
77 144 0.18
78 23 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (76 bp):
GAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
TCTCTGAAATT
Found at i:41232912 original size:14 final size:15
Alignment explanation
Indices: 41232893--41232922 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41232883 ATCTTTTTAA
41232893 ATTTAAATTTA-TTT
1 ATTTAAATTTACTTT
41232907 ATTTAAATTTACTTT
1 ATTTAAATTTACTTT
41232922 A
1 A
41232923 AATTTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAAATTTACTTT
Found at i:41234771 original size:58 final size:58
Alignment explanation
Indices: 41234674--41235317 Score: 990
Period size: 59 Copynumber: 11.0 Consensus size: 58
41234664 GAACTGTCCG
*
41234674 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
41234733 AAAATTACCATTTTACCCCGAACTTTCCAAAATTCCA-TTTTAACCCCGGTTTCACCA
1 AAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
41234790 AAAAATACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* ** *
41234848 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCA-TA
1 AAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
41234905 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
41234964 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCTA-TTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
41235022 AAAAATACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* *
41235080 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* *
41235139 AAAATTATCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
41235198 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
41235257 AAAATTACCATTTTACCCTGAACTTTCCAAAATTCCTTTTTTTAGCCCCGATTTCACCA
1 AAAATTACCATTTTACCCCGAACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCACCA
41235316 AA
1 AA
41235318 GTTTCCAAAA
Statistics
Matches: 542, Mismatches: 34, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
57 107 0.20
58 171 0.32
59 263 0.49
60 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:41234957 original size:116 final size:116
Alignment explanation
Indices: 41234674--41235317 Score: 990
Period size: 116 Copynumber: 5.5 Consensus size: 116
41234664 GAACTGTCCG
41234674 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
*
41234739 ACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTAACCCCGGTTTCACCA
65 ACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCA
* *
41234790 AAAAATACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTA
1 AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* ** *
41234855 CCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCTAATTTCA-TA
66 CCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCA
* *
41234905 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
*
41234970 ACCATTTTA-CCCTCGAACTTTCCAAAATTCTATTTTAACCCCGATTTCACCA
65 ACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCA
* *
41235022 AAAAATACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTA
1 AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* *
41235087 CCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
66 CCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCA
* * *
41235139 AAAATTATCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
*
41235204 ACCATTTTA-CCCTCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCA
65 ACCATTTTACCCCT-GAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCA
** * *
41235257 AAAATTACCATTTTACCCTGAACTTTCCAAAATTCCTTTTTTTAGCCCCGATTTCACCAAA
1 AAAATTACCATTTTACCCCAAACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCACCAAA
41235318 GTTTCCAAAA
Statistics
Matches: 483, Mismatches: 36, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
115 79 0.16
116 200 0.41
117 78 0.16
118 126 0.26
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (116 bp):
AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
CCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCCGATTTCACCA
Found at i:41235300 original size:29 final size:28
Alignment explanation
Indices: 41234660--41235297 Score: 255
Period size: 29 Copynumber: 22.0 Consensus size: 28
41234650 ATTTTTAGGT
* *
41234660 CCCT-GAACTGTCCGAAAATTACCATTTTA
1 CCCTCGAACTTTCC-AAAATT-CCTTTTTA
*
41234689 CCC-CTAAACTTTCCAAAATTCCATTTTTAA
1 CCCTC-GAACTTTCCAAAATTCC-TTTTT-A
*
41234719 CCC-CG-A-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATT-CCTTTTTA
*
41234748 CCC-CGAACTTTCCAAAATTCCATTTTAA
1 CCCTCGAACTTTCCAAAATTCC-TTTTTA
* * *
41234776 CCC-CG--GTTTCACCAAAAAATACCATTTTA
1 CCCTCGAACTTT--CC--AAAATTCCTTTTTA
*
41234805 CCC-CAAACTTTCCAAAATTCCATTTTTAA
1 CCCTCGAACTTTCCAAAATTCC-TTTTT-A
* *
41234834 CCC-CG-ATTTTACCAAAAATTACCATTTTA
1 CCCTCGAACTTT-CC-AAAATT-CCTTTTTA
* *
41234863 CCC-CTAAACTTTCCAAAATTCCATTTTAA
1 CCCTC-GAACTTTCCAAAATTCC-TTTTTA
* *
41234892 CCCT--AA-TTTCATAAAAATTACCATTTTA
1 CCCTCGAACTTTC--CAAAATT-CCTTTTTA
41234920 CCCTCGAACTTTCCAAAATTCCATTTTTA
1 CCCTCGAACTTTCCAAAATTCC-TTTTTA
* *
41234949 ACCTCG-A-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATT-CCTTTTTA
41234979 CCCTCGAACTTTCCAAAATT-CTATTTTAA
1 CCCTCGAACTTTCCAAAATTCCT-TTTT-A
* *
41235008 CCC-CG-A-TTTCACCAAAAAATACCATTTTA
1 CCCTCGAACTTT--CC--AAAATTCCTTTTTA
*
41235037 CCC-CAAACTTTCCAAAATTCCATTTTTAA
1 CCCTCGAACTTTCCAAAATTCC-TTTTT-A
* *
41235066 CCC-CG-ATTTTACCAAAAATTACCATTTTA
1 CCCTCGAACTTT-CC-AAAATT-CCTTTTTA
*
41235095 CCC-CTAAACTTTCCAAAATTCCATTTTTA
1 CCCTC-GAACTTTCCAAAATTCC-TTTTTA
* * *
41235124 ACCTCG-A-TTTCACCAAAAATTATCATTTTA
1 CCCTCGAACTTT--CC-AAAATT-CCTTTTTA
41235154 CCCTCGAACTTTCCAAAATTCCATTTTTA
1 CCCTCGAACTTTCCAAAATTCC-TTTTTA
* *
41235183 ACCTCG-A-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATT-CCTTTTTA
*
41235213 CCCTCGAACTTTCCAAAATTCTATTTTTAA
1 CCCTCGAACTTTCCAAAATTC-CTTTTT-A
*
41235243 CCC-CG-A-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATT-CCTTTTTA
41235272 CCCT-GAACTTTCCAAAATTCCTTTTT
1 CCCTCGAACTTTCCAAAATTCCTTTTT
41235298 TTAGCCCCGA
Statistics
Matches: 473, Mismatches: 57, Indels: 160
0.69 0.08 0.23
Matches are distributed among these distances:
26 10 0.02
27 41 0.09
28 76 0.16
29 161 0.34
30 136 0.29
31 40 0.08
32 9 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTCGAACTTTCCAAAATTCCTTTTTA
Found at i:41235350 original size:38 final size:39
Alignment explanation
Indices: 41235280--41235353 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
41235270 TACCCTGAAC
* *
41235280 TTTCCAAAATTCCTTTTTTTAGCCCCGATTTCACCAAAG
1 TTTCCAAAATTCCTATTTTTAACCCCGATTTCACCAAAG
* *
41235319 TTTCCAAAATTCC-ATTTTTAACCTCGGTTTCACCA
1 TTTCCAAAATTCCTATTTTTAACCCCGATTTCACCA
41235354 GAAATTACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 18 0.58
39 13 0.42
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.39
Consensus pattern (39 bp):
TTTCCAAAATTCCTATTTTTAACCCCGATTTCACCAAAG
Found at i:41235403 original size:97 final size:96
Alignment explanation
Indices: 41235222--41235401 Score: 229
Period size: 97 Copynumber: 1.9 Consensus size: 96
41235212 ACCCTCGAAC
* ** *
41235222 TTTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTGAACTTTCCAA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAACTGTCCAA
* *
41235287 AATTCCTTTTTTTAGCCCCGATTTCACCAAAG
66 AATTCC-TATTTTACCCCCGATTTCACCAAAG
* * * *
41235319 TTTCCAAAATTCCATTTTTAACCTCGGTTTCACCAGAAATTACCATTTTGCCCCC-ACATGTCCA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAC-TGTCCA
41235383 AAATTACC-ATTTTACCCCC
65 AAATT-CCTATTTTACCCCC
41235402 CGGGCATCCA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
96 11 0.15
97 58 0.82
98 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.06, T:0.36
Consensus pattern (96 bp):
TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAACTGTCCAA
AATTCCTATTTTACCCCCGATTTCACCAAAG
Found at i:41237411 original size:57 final size:59
Alignment explanation
Indices: 41237316--41237479 Score: 179
Period size: 58 Copynumber: 2.8 Consensus size: 59
41237306 AATTTGGCAC
** * * **
41237316 TTTTTTTTAATTTGGTATTTAAACTTTTTTTGATCCAA-TTGATACTTGAACTTGACAT
1 TTTTTTTTAATTTGGTACCTAAACTTTTTTTAACCCAATTTGATACCGGAACTTGACAT
* *
41237374 TTTTTTTTAATTTGGTACCTAAA-TTTTTTTAACCCAATTTGGTACCGGAACTTGGCAT
1 TTTTTTTTAATTTGGTACCTAAACTTTTTTTAACCCAATTTGATACCGGAACTTGACAT
* * * * **
41237432 TTTTTTCTAATTAGGTACCTGAGCTTTTTTTAGATTCAATTTGATACC
1 TTTTTTTTAATTTGGTACCTAAACTTTTTTTA-ACCCAATTTGATACC
41237480 TAAATTTATT
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
57 12 0.14
58 56 0.64
59 8 0.09
60 12 0.14
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.50
Consensus pattern (59 bp):
TTTTTTTTAATTTGGTACCTAAACTTTTTTTAACCCAATTTGATACCGGAACTTGACAT
Found at i:41237796 original size:89 final size:89
Alignment explanation
Indices: 41237629--41237796 Score: 189
Period size: 89 Copynumber: 1.9 Consensus size: 89
41237619 TAAAAAAAGA
* * * * *
41237629 TTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAGGTACCAAATTGGACCTCAAAACATTTAAGT
1 TTAGGTACCAAATTAAAAAAAAATATCAAGTTCAGATACCAAATTGGACCTAAAAACATTTAAGT
*
41237694 ACCAACTTAAAAAAGGTGTCAAGT
66 ACCAAATTAAAAAAGGTGTCAAGT
* * * *
41237718 TTAGGTATCAAATTAAAAAAAAATATCAAGTT-TGAATACCAAATTTGACC-AAAAACGTTT-AG
1 TTAGGTACCAAATTAAAAAAAAATATCAAGTTCAG-ATACCAAATTGGACCTAAAAACATTTAAG
*
41237780 ATATCAAATTAGAAAAA
65 -TACCAAATTA-AAAAA
41237797 ATTTCAAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
87 2 0.03
88 17 0.26
89 46 0.71
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (89 bp):
TTAGGTACCAAATTAAAAAAAAATATCAAGTTCAGATACCAAATTGGACCTAAAAACATTTAAGT
ACCAAATTAAAAAAGGTGTCAAGT
Found at i:41243561 original size:29 final size:29
Alignment explanation
Indices: 41243528--41243584 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
41243518 AGACTAACTA
41243528 TCTATTAACAAACTAACAGCTAAAAGCTG
1 TCTATTAACAAACTAACAGCTAAAAGCTG
41243557 TCTATTAACAAACTAACAGCTAAAAGCT
1 TCTATTAACAAACTAACAGCTAAAAGCT
41243585 AACTCATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.25
Consensus pattern (29 bp):
TCTATTAACAAACTAACAGCTAAAAGCTG
Found at i:41245422 original size:15 final size:15
Alignment explanation
Indices: 41245399--41245438 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
41245389 TGAACTACTA
41245399 GAGACTCAACAATAG
1 GAGACTCAACAATAG
* * *
41245414 GAGATTCAATAATGG
1 GAGACTCAACAATAG
41245429 GAGACTCAAC
1 GAGACTCAAC
41245439 TAGGGGACTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (15 bp):
GAGACTCAACAATAG
Found at i:41247765 original size:22 final size:23
Alignment explanation
Indices: 41247740--41247782 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41247730 TCTCATTATA
*
41247740 TAAA-ATTATTTGCGTTTTTTTC
1 TAAAGATTATTTGCATTTTTTTC
*
41247762 TAAAGTTTATTTGCATTTTTT
1 TAAAGATTATTTGCATTTTTT
41247783 AAAATTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (23 bp):
TAAAGATTATTTGCATTTTTTTC
Found at i:41262049 original size:29 final size:29
Alignment explanation
Indices: 41261996--41262135 Score: 149
Period size: 29 Copynumber: 4.9 Consensus size: 29
41261986 ATCTGCCACT
* *
41261996 ATTTTAGAGTTTTGCCATTA-TTTTCCAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * *
41262024 ATTTTTCATTTTTGCCACTGGTTTTCCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
*
41262053 ATTTTACAGTTTTGCCACTAGTTTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* * * *
41262082 ATTTTACAGTTTTGCAAAT-GTTTTTCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCCAG
* *
41262110 ATTTTACAGTTTTACCACTATTTTTC
1 ATTTTACAGTTTTGCCACTAGTTTTC
41262136 AAAAAAAAAA
Statistics
Matches: 89, Mismatches: 21, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
28 37 0.42
29 52 0.58
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (29 bp):
ATTTTACAGTTTTGCCACTAGTTTTCCAG
Found at i:41262135 original size:57 final size:57
Alignment explanation
Indices: 41261996--41262133 Score: 179
Period size: 57 Copynumber: 2.4 Consensus size: 57
41261986 ATCTGCCACT
* * * * * *
41261996 ATTTTAGAGTTTTGCCATTATTTTCCAGATTTTTCATTTTTGCCACTGGTTTTCCAA
1 ATTTTACAGTTTTGCCACTATTTTCCAGATTTTACAGTTTTGCAAATGGTTTTCCAA
* *
41262053 ATTTTACAGTTTTGCCACTAGTTTTCTAGATTTTACAGTTTTGCAAAT-GTTTTTCAA
1 ATTTTACAGTTTTGCCACTA-TTTTCCAGATTTTACAGTTTTGCAAATGGTTTTCCAA
*
41262110 ATTTTACAGTTTTACCACTATTTT
1 ATTTTACAGTTTTGCCACTATTTT
41262134 TCAAAAAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
56 4 0.06
57 45 0.63
58 22 0.31
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (57 bp):
ATTTTACAGTTTTGCCACTATTTTCCAGATTTTACAGTTTTGCAAATGGTTTTCCAA
Found at i:41262682 original size:45 final size:45
Alignment explanation
Indices: 41262633--41263233 Score: 817
Period size: 45 Copynumber: 13.4 Consensus size: 45
41262623 AGTTAGTTAA
* * *
41262633 TATTTGATTAATTATGCTATACGATATGCATAATATGGTAAATGT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* *
41262678 TATTTGATTGATTATGCTATACGATTTGCATGACATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * *
41262723 TATTTGATTGATTATGTTATACGATTTGTATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * * *
41262768 TATTGGATTAATTATGCTAAATGATATGCATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * *
41262813 TATATGATCGATTATGCTATACGATATGTATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * * *
41262858 TATTTGATTGATTATACTATATGATATGCATGACT-TGATAAATAC
1 TATTTGATTGATTATGCTATACGATATGCATGA-TATGGTAAATAT
* * * *
41262903 TATTCGATTGATTATGTTATACGTTATGTATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * * *
41262948 TATTTGATTGATTATGCTATAAGATTTGTATGATATGGTAAATGT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * *
41262993 TATTGGATTGATTATGCTAAATGATATGCATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
41263038 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* *
41263083 AATTTGATTGATTATGCTATACGATATGTATGATATGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * * *
41263128 TATTTGATTGATTATGTTATATGATATGTATGATTTGGTAAATAT
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* * *
41263173 TATTTGATTGATTATGCTATACGATATACATGATGTGGTAAATAC
1 TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
* *
41263218 AATTTGATTAATTATG
1 TATTTGATTGATTATG
41263234 ATATGGCAAA
Statistics
Matches: 488, Mismatches: 66, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
44 1 0.00
45 486 1.00
46 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (45 bp):
TATTTGATTGATTATGCTATACGATATGCATGATATGGTAAATAT
Found at i:41262704 original size:22 final size:22
Alignment explanation
Indices: 41262679--41262750 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
41262669 GGTAAATGTT
41262679 ATTTGATTGATTATGCTATACG
1 ATTTGATTGATTATGCTATACG
* * **
41262701 ATTTGCA-TGA-CATGGTAAATATT
1 ATTTG-ATTGATTATGCT--ATACG
*
41262724 ATTTGATTGATTATGTTATACG
1 ATTTGATTGATTATGCTATACG
41262746 ATTTG
1 ATTTG
41262751 TATGATATGG
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
21 4 0.11
22 17 0.46
23 12 0.32
24 4 0.11
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (22 bp):
ATTTGATTGATTATGCTATACG
Found at i:41263149 original size:22 final size:22
Alignment explanation
Indices: 41263124--41263193 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
41263114 GATATGGTAA
41263124 ATATTATTTGATTGATTATGTT
1 ATATTATTTGATTGATTATGTT
* * *
41263146 ATATGATATG-TATGATT-TGGTAA
1 ATATTATTTGAT-TGATTAT-GT-T
*
41263169 ATATTATTTGATTGATTATGCT
1 ATATTATTTGATTGATTATGTT
41263191 ATA
1 ATA
41263194 CGATATACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
21 2 0.06
22 18 0.50
23 14 0.39
24 2 0.06
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (22 bp):
ATATTATTTGATTGATTATGTT
Found at i:41263245 original size:119 final size:119
Alignment explanation
Indices: 41263111--41263333 Score: 347
Period size: 119 Copynumber: 1.9 Consensus size: 119
41263101 ATACGATATG
* * * * * *
41263111 TATGATATGGTAAATATTATTTGATTGATTATGTTATATGATATGTATGATTTGGTAAATATTAT
1 TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTAT
* * *
41263176 TTGATTGATTATGCTATACGATATACATGATGTGGTAAATACAATTTGATTAAT
66 TTGATTGATTATGCTATAAGATATACATAATATGGTAAATACAATTTGATTAAT
41263230 TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTAT
1 TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTAT
* *
41263295 TTGATTGATTATGTTATAAGATATGCATAATATGGTAAA
66 TTGATTGATTATGCTATAAGATATACATAATATGGTAAA
41263334 ATATTATTTG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 93 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (119 bp):
TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTAT
TTGATTGATTATGCTATAAGATATACATAATATGGTAAATACAATTTGATTAAT
Found at i:41263279 original size:74 final size:74
Alignment explanation
Indices: 41263156--41263307 Score: 232
Period size: 74 Copynumber: 2.1 Consensus size: 74
41263146 ATATGATATG
* * * *
41263156 TATGATTTGGTAAATATTATTTGATTGATTATGCTATACGATATACATGATGTGGTAAATACAAT
1 TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATACATGATATGGTAAATACAAT
41263221 TTGATTAAT
66 TTGATTAAT
* **
41263230 TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATGCATGATATGGTAAATATTAT
1 TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATACATGATATGGTAAATACAAT
*
41263295 TTGATTGAT
66 TTGATTAAT
41263304 TATG
1 TATG
41263308 TTATAAGATA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (74 bp):
TATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATACATGATATGGTAAATACAAT
TTGATTAAT
Found at i:41263300 original size:45 final size:45
Alignment explanation
Indices: 41263231--41263350 Score: 186
Period size: 45 Copynumber: 2.6 Consensus size: 45
41263221 TTGATTAATT
* * *
41263231 ATGATATGGCAAATATTATCTGATTGATTATGCTATACGATATGC
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATAAGATATGC
*
41263276 ATGATATGGTAAATATTATTTGATTGATTATGTTATAAGATATGC
1 ATGATATGGTAAATATTATTTGATTGATTATGCTATAAGATATGC
*
41263321 ATAATATGGTAAAATATTATTTGATTGATT
1 ATGATATGGT-AAATATTATTTGATTGATT
41263351 TCGCTCAACA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 50 0.72
46 19 0.28
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (45 bp):
ATGATATGGTAAATATTATTTGATTGATTATGCTATAAGATATGC
Found at i:41264550 original size:21 final size:21
Alignment explanation
Indices: 41264502--41264550 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
41264492 ATCGATACCT
*
41264502 TACCTTACCCCTTGGTATCGA
1 TACCTTGCCCCTTGGTATCGA
41264523 TACCTTGCCCCTTGGTATCGA
1 TACCTTGCCCCTTGGTATCGA
41264544 TACCTTG
1 TACCTTG
41264551 GGTTATAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (21 bp):
TACCTTGCCCCTTGGTATCGA
Found at i:41276234 original size:50 final size:50
Alignment explanation
Indices: 41276175--41276271 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
41276165 ATTTTTTCAT
*
41276175 ATCTGATATTTTAAATAAATATAAATATTTATTTAAAGTGATTTGTTTAA
1 ATCTGATATTTTAAATAAAAATAAATATTTATTTAAAGTGATTTGTTTAA
* * * *
41276225 ATCTTATATTTTATATAAAAATAAATATTTATTTATAGTGTTTTGTT
1 ATCTGATATTTTAAATAAAAATAAATATTTATTTAAAGTGATTTGTT
41276272 CAATATTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (50 bp):
ATCTGATATTTTAAATAAAAATAAATATTTATTTAAAGTGATTTGTTTAA
Found at i:41279045 original size:28 final size:27
Alignment explanation
Indices: 41279005--41279060 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
41278995 TAGAAAACCA
*
41279005 TCCTACAACCACTTGAAAATGTGGAGGG
1 TCCTACAACCACTTGAAAATAT-GAGGG
41279033 TCCTACAACCACTTGAAAATATGAGGG
1 TCCTACAACCACTTGAAAATATGAGGG
41279060 T
1 T
41279061 ATCTTGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (27 bp):
TCCTACAACCACTTGAAAATATGAGGG
Found at i:41282475 original size:30 final size:29
Alignment explanation
Indices: 41282410--41282781 Score: 402
Period size: 30 Copynumber: 12.6 Consensus size: 29
41282400 TTATGGGTCA
* * *
41282410 AAAATGCAATTTTGAAAAAGTTTGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
* *
41282439 AAAATGTAATTTTGGAAAGGTTTGGGAGTC
1 AAAATGTAATTTTGGAAAAGTTTGGG-GTT
* * *
41282469 AAAATGTAATTTTGGAAAATTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
* *
41282499 AAAATGTAATTTTAGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTG-GGGTT
** *
41282529 AAAATGGGATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
* ***
41282559 AAAATGTAATTTTGAAAAAGTTCAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
*
41282588 AAAATGTAATTTTGGAAAAGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
* * *
41282617 AAAATGTAATTTTAGAGAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
** *
41282647 AAAATGGGATTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
*
41282677 AAAATGTAACTTTGGAAAAGTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
*
41282706 AAAATGTAATTTTGGAATAGTTTGGGAGTT
1 AAAATGTAATTTTGGAAAAGTTTGGG-GTT
* * *
41282736 AAAATGTAATTTTGGAAGAGTTCGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTG-GGGTT
*
41282766 AAAATGCAATTTTGGA
1 AAAATGTAATTTTGGA
41282782 GAAACTTAGG
Statistics
Matches: 294, Mismatches: 42, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
29 102 0.35
30 187 0.64
31 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTGGGGTT
Found at i:41282520 original size:89 final size:89
Alignment explanation
Indices: 41282378--41282781 Score: 462
Period size: 89 Copynumber: 4.5 Consensus size: 89
41282368 GTTCGAGGGC
* * * *
41282378 AAAATGGTTATTTTAGG-AAAGTTTATGGGTCAAAAATGCAATTTTGAAAAAGTTTGA-GGTTAA
1 AAAAT-GTAATTTT-GGAAAAGTTTAAGGGTC-AAAATGTAATTTTGGAAAAGTTTGAGGGTTAA
* *
41282441 AATGTAATTTTGGAAAGGTTT-GGGAGTC
63 AATGTAATTTTAGAAA-GTTTAGGG-GTT
* * *
41282469 AAAATGTAATTTTGGAAAATTTTAAGGGTCAAAATGTAATTTTAGAGAAGTTTGAGGGTTAAAAT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTGAGGGTTAAAAT
**
41282534 GGGATTTTAGAAAAGTTTAGGGGTT
66 GTAATTTTAG-AAAGTTTAGGGGTT
* * *
41282559 AAAATGTAATTTTGAAAAAGTTCAA-GGTTAAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAAT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTGAGGGTTAAAAT
*
41282622 GTAATTTTAGAGAAGTTTAAGGGTT
66 GTAATTTTAGA-AAGTTTAGGGGTT
** * *
41282647 AAAATGGGATTTTGGAAAAGTTTAAGGGTTAAAATGTAACTTTGGAAAAGTTTG-GGGTTAAAAT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTGAGGGTTAAAAT
*
41282711 GTAATTTTGGAATAGTTT-GGGAGTT
66 GTAATTTTAGAA-AGTTTAGGG-GTT
* ** *
41282736 AAAATGTAATTTTGGAAGAGTTCGAGGGTCAAAATGCAATTTTGGA
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGA
41282782 GAAACTTAGG
Statistics
Matches: 269, Mismatches: 35, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
87 1 0.00
88 55 0.20
89 139 0.52
90 63 0.23
91 11 0.04
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (89 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTGAGGGTTAAAAT
GTAATTTTAGAAAGTTTAGGGGTT
Found at i:41282650 original size:118 final size:118
Alignment explanation
Indices: 41282425--41282748 Score: 479
Period size: 118 Copynumber: 2.7 Consensus size: 118
41282415 GCAATTTTGA
* * * *
41282425 AAAAGTTT-GAGGTTAAAATGTAATTTTGGAAAGGTTTGGGAGTCAAAATGTAATTTTGGAAAAT
1 AAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGG-GTTAAAATGTAATTTTGGAAAAG
* *
41282489 TTTAAGGGTCAAAATGTAATTTTAGAGAAGTTTGAGGGTTAAAATGGGATTTTAG
65 TTT-AGGGTTAAAATGTAATTTTAGAGAAGTTTAAGGGTTAAAATGGGATTTTAG
* ***
41282544 AAAAGTTTAGGGGTTAAAATGTAATTTTGAAAAAGTTCAAGGTTAAAATGTAATTTTGGAAAAGT
1 AAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTAATTTTGGAAAAGT
*
41282609 TTAGGGTTAAAATGTAATTTTAGAGAAGTTTAAGGGTTAAAATGGGATTTTGG
66 TTAGGGTTAAAATGTAATTTTAGAGAAGTTTAAGGGTTAAAATGGGATTTTAG
* * *
41282662 AAAAGTTTAAGGGTTAAAATGTAACTTTGGAAAAGTTTGGGGTTAAAATGTAATTTTGGAATAGT
1 AAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTAATTTTGGAAAAGT
*
41282727 TTGGGAGTTAAAATGTAATTTT
66 TTAGG-GTTAAAATGTAATTTT
41282749 GGAAGAGTTC
Statistics
Matches: 184, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
118 110 0.60
119 48 0.26
120 26 0.14
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (118 bp):
AAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTAATTTTGGAAAAGT
TTAGGGTTAAAATGTAATTTTAGAGAAGTTTAAGGGTTAAAATGGGATTTTAG
Found at i:41282807 original size:59 final size:59
Alignment explanation
Indices: 41282410--41282799 Score: 400
Period size: 59 Copynumber: 6.6 Consensus size: 59
41282400 TTATGGGTCA
* * *
41282410 AAAATGCAATTTTGAAAAAGTTT-GAGGTTAAAATGTAATTTTGGAA-AGGTTTG-GGAGTC
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTTGGAAGA-GTTTGAGG-GTT
* * *
41282469 AAAATGTAATTTTGGAAAATTTTAAGGGTCAAAATGTAATTTTAG-AGAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTGGAAG-AGTTTGAGGGTT
** * * * * *
41282529 AAAATGGGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGAAAAAG-TTCAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTTAAAATGTAATTTTGGAAGAGTTTGAGGGTT
* *
41282588 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAG-AGAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAG-AGTTTGAGGGTT
** * *
41282647 AAAATGGGATTTTGGAAAAGTTTAAGGGTTAAAATGTAACTTTGGAAAAGTTTG-GGGTT
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATGTAATTTTGGAAGAGTTTGAGGGTT
* * * *
41282706 AAAATGTAATTTTGGAATAGTTTGGGAGTTAAAATGTAATTTTGGAAGAGTTCGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTTAAAATGTAATTTTGGAAGAGTTTGAGGGTT
* * *
41282766 AAAATGCAATTTTGGAGAAA-CTTAGGGTCAAAAT
1 AAAATGTAATTTTGGA-AAAGTTTAGGGTTAAAAT
41282800 ATGATTTTTA
Statistics
Matches: 274, Mismatches: 43, Indels: 28
0.79 0.12 0.08
Matches are distributed among these distances:
57 1 0.00
58 22 0.08
59 134 0.49
60 109 0.40
61 8 0.03
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAGAGTTTGAGGGTT
Found at i:41284894 original size:39 final size:39
Alignment explanation
Indices: 41284773--41285411 Score: 268
Period size: 39 Copynumber: 16.4 Consensus size: 39
41284763 TCTGCCCCTG
* * *
41284773 GCTCGGGGTAAGAGATTGGCTAACGGTGATCTACCCTATA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTA-A
* * ** * **** * * *
41284813 -ATCGGGGTAAAAGATTGAATGGTTACAATCTACCCCAG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
*
41284851 GCTCGGGGTAAGAGGTTGGCTGATGGTGATCTGCCCTAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
* * *
41284890 GCTCGGGGTAAGAGA-T--CAGATGGCTACAATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGGCTGATGG-T--GATCTGCCCTAA
* * * *
41284929 GTTCTGGGTAAGAGATTGGCTGATGGTGATCTGTCCTAT
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
* * * * * * * ** *
41284968 GATCGGAGTAAAAGATCGAACAGCT-GCAATCTACCCTAA
1 GCTCGGGGTAAGAGATTG-GCTGATGGTGATCTGCCCTAA
** * *
41285007 GCTCAAGGTAAGAGATTGGCTGATAGTG-TCTGCCCTAG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
* * *
41285045 GCTCGAGGTAAGAGA-T--CGGATGGCTGCAATCTGCCTCATGA
1 GCTCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCC-C-TAA
* * ** *
41285086 GCT--GGGTAAGAGATAGGATGACT-GCAATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCTAA
* * * * *
41285123 GCTCGAGGCAAGGGATTGGTTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
* * * ** * * *
41285162 GCTCGAGGTAAGAGATCGGATGGCGGTAATCT-ACCTCAG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AA
* * *
41285201 GCTCGGGGTAAGAGATTAGCTGATGGTGATCTATCCC-AG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCTAA
* * * * * ** * *
41285240 GGTCGAGGTAAAAGATTGGATGCCT-GCAATCTACCCCAA
1 GCTCGGGGTAAGAGATTGGCTG-ATGGTGATCTGCCCTAA
*
41285279 GCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
* * ** * * *
41285318 GCTCGGGGTAAAAGATCGAAT-A-GTTGCAATCTGCCCCAG
1 GCTCGGGGTAAGAGATTGGCTGATGGTG--ATCTGCCCTAA
* * * *
41285357 GCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCAA
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
*
41285396 GCTCGGGGTAAAAGAT
1 GCTCGGGGTAAGAGAT
41285412 CAGATGGTTA
Statistics
Matches: 431, Mismatches: 136, Indels: 65
0.68 0.22 0.10
Matches are distributed among these distances:
35 5 0.01
36 8 0.02
37 9 0.02
38 35 0.08
39 348 0.81
40 7 0.02
41 9 0.02
42 9 0.02
43 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (39 bp):
GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAA
Found at i:41285026 original size:156 final size:155
Alignment explanation
Indices: 41284778--41285099 Score: 410
Period size: 156 Copynumber: 2.1 Consensus size: 155
41284768 CCCTGGCTCG
* * ** *
41284778 GGGTAAGAGATTGGCTAACGGTGATCTACCCTATAATCGGGGTAAAAGATTGAATGGTTACAATC
1 GGGTAAGAGATTGGCTAACGGTGATCTACCCTATAATCGGAGTAAAAGATCGAACAGCTACAATC
* ** * * *
41284843 TACCCCAGGCTCGGGGTAAGAGGTTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAGAGATCA
66 TACCCCAAGCTCAAGGTAAGAGATTGGCTGATAGTG-TCTGCCCTAAGCTCGAGGTAAGAGATCA
**
41284908 GATGGCTACAATCTGCCCCAAGTTCT
130 GATGGCTACAATCTGCCCCAAGAGCT
* * ** * *
41284934 GGGTAAGAGATTGGCTGATGGTGATCTGTCCTATGATCGGAGTAAAAGATCGAACAGCTGCAATC
1 GGGTAAGAGATTGGCTAACGGTGATCTACCCTATAATCGGAGTAAAAGATCGAACAGCTACAATC
* * *
41284999 TACCCTAAGCTCAAGGTAAGAGATTGGCTGATAGTGTCTGCCCTAGGCTCGAGGTAAGAGATCGG
66 TACCCCAAGCTCAAGGTAAGAGATTGGCTGATAGTGTCTGCCCTAAGCTCGAGGTAAGAGATCAG
* * *
41285064 ATGGCTGCAATCTGCCTCATGAGCT
131 ATGGCTACAATCTGCCCCAAGAGCT
41285089 GGGTAAGAGAT
1 GGGTAAGAGAT
41285100 AGGATGACTG
Statistics
Matches: 141, Mismatches: 25, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
155 57 0.40
156 84 0.60
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (155 bp):
GGGTAAGAGATTGGCTAACGGTGATCTACCCTATAATCGGAGTAAAAGATCGAACAGCTACAATC
TACCCCAAGCTCAAGGTAAGAGATTGGCTGATAGTGTCTGCCCTAAGCTCGAGGTAAGAGATCAG
ATGGCTACAATCTGCCCCAAGAGCT
Found at i:41285155 original size:78 final size:78
Alignment explanation
Indices: 41285073--41285450 Score: 304
Period size: 78 Copynumber: 4.8 Consensus size: 78
41285063 GATGGCTGCA
* * *
41285073 ATCTGCCTCATGAGCT-G-GGTAAGAGATAGGATGACTGCAATCTGCCCCAAGCTCGAGGCAAGG
1 ATCTGCC-CA-GAGCTCGAGGTAAGAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGA
*
41285136 GATTGGTTGATGGTG
64 GATTGGCTGATGGTG
* * * * * * *
41285151 ATCTGCCCCA-AGCTCGAGGTAAGAGATCGGATGGCGGTAATCTACCTCAGGCTCGGGGTAAGAG
1 ATCTG-CCCAGAGCTCGAGGTAAGAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAG
*
41285215 ATTAGCTGATGGTG
65 ATTGGCTGATGGTG
* * * * *
41285229 ATCTATCCCAG-GGTCGAGGTAAAAGATTGGATGCCTGCAATCTACCCCAAGCTCGAGGTAAGAG
1 ATCT-GCCCAGAGCTCGAGGTAAGAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAG
41285293 ATTGGCTGATGGTG
65 ATTGGCTGATGGTG
* * * * * * * *
41285307 ATCTGCCCTA-AGCTCGGGGTAAAAGATCGAAT-AGTTGCAATCTGCCCCAGGCTCGGGGTAAGA
1 ATCTGCCC-AGAGCTCGAGGTAAGAGATAGGATGA-CTGCAATCTACCCCAAGCTCGAGGTAAGA
* *
41285370 GATTGGCTAATGGTA
64 GATTGGCTGATGGTG
* * * ** * * * *
41285385 ATCTACCCCA-AGCTCGGGGTAAAAGATCA-GATGGTTACAATCTACCCCATGCTCGGGGTAAAA
1 ATCT-GCCCAGAGCTCGAGGTAAGAGAT-AGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGA
41285448 GAT
64 GAT
41285451 CGAATGGCTG
Statistics
Matches: 246, Mismatches: 43, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
76 4 0.02
77 4 0.02
78 233 0.95
79 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (78 bp):
ATCTGCCCAGAGCTCGAGGTAAGAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGA
TTGGCTGATGGTG
Found at i:41285195 original size:194 final size:195
Alignment explanation
Indices: 41284895--41285271 Score: 433
Period size: 194 Copynumber: 1.9 Consensus size: 195
41284885 CCTAAGCTCG
* * *
41284895 GGGTAAGAGATCAGATGGCTACAATCTGCCCCAAGTTCTGGGTAAGAGATTGGCTGATGGTGATC
1 GGGTAAGAGATCAGATGACTACAATCTGCCCCAAGCTCTGGGCAAGAGATTGGCTGATGGTGATC
* * * *
41284960 TGTCCTATGATCGGAGTAAAAGATCGAACAGCTGCAATCTACC-CTAAGCTCAAGGTAAGAGATT
66 TGCCCCAAGATCGGAGTAAAAGATCGAACAGCGGCAATCTACCTC-AAGCTCAAGGTAAGAGATT
* * *
41285024 GGCTGATAGTG-TCT-GCCCTAGGCTCGAGGTAAGAGATCGGATGGCTGCAATCTGCCTCATGAG
130 AGCTGATAGTGATCTAGCCC-AGGCTCGAGGTAAAAGATCGGATGCCTGCAATCTGCCTCATGAG
41285087 CT
194 CT
* * *
41285089 GGGTAAGAGAT-AGGATGACTGCAATCTGCCCCAAGCTC-GAGGCAAGGGATTGGTTGATGGTGA
1 GGGTAAGAGATCA-GATGACTACAATCTGCCCCAAGCTCTG-GGCAAGAGATTGGCTGATGGTGA
* * * ** * * **
41285152 TCTGCCCCAAGCTC-GAGGTAAGAGATCGGATGGCGGTAATCTACCTCAGGCTCGGGGTAAGAGA
64 TCTGCCCCAAGATCGGA-GTAAAAGATCGAACAGCGGCAATCTACCTCAAGCTCAAGGTAAGAGA
* * * *
41285216 TTAGCTGATGGTGATCTATCCCAGGGTCGAGGTAAAAGATTGGATGCCTGCAATCT
128 TTAGCTGATAGTGATCTAGCCCAGGCTCGAGGTAAAAGATCGGATGCCTGCAATCT
41285272 ACCCCAAGCT
Statistics
Matches: 151, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
193 4 0.03
194 110 0.73
195 34 0.23
196 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (195 bp):
GGGTAAGAGATCAGATGACTACAATCTGCCCCAAGCTCTGGGCAAGAGATTGGCTGATGGTGATC
TGCCCCAAGATCGGAGTAAAAGATCGAACAGCGGCAATCTACCTCAAGCTCAAGGTAAGAGATTA
GCTGATAGTGATCTAGCCCAGGCTCGAGGTAAAAGATCGGATGCCTGCAATCTGCCTCATGAGCT
Found at i:41285328 original size:156 final size:156
Alignment explanation
Indices: 41285090--41285450 Score: 436
Period size: 156 Copynumber: 2.3 Consensus size: 156
41285080 TCATGAGCTG
* * * * *
41285090 GGTAAGAGATAGGATGACTGCAATCTGCCCCAAGCTCGAGGCAAGGGATTGGTTGATGGTGATCT
1 GGTAAAAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTGATCT
* * * * *
41285155 GCCCCAAGCTCGAGGTAAGAGATCGGATGGCGGTAATCTACCTCAGGCTCGGGGTAAGAGATTAG
66 GCCCCAAGCTCGAGGTAAAAGATCGAATAGCGGCAATCTACCCCAGGCTCGGGGTAAGAGATTAG
* * * * *
41285220 CTGATGGTGATCTATCCCAGGGTCGA
131 CTAATGGTAATCTACCCCAAGCTCGA
* *
41285246 GGTAAAAGATTGGATGCCTGCAATCTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTGATCT
1 GGTAAAAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTGATCT
* * ** * *
41285311 GCCCTAAGCTCGGGGTAAAAGATCGAATAGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGG
66 GCCCCAAGCTCGAGGTAAAAGATCGAATAGCGGCAATCTACCCCAGGCTCGGGGTAAGAGATTAG
*
41285376 CTAATGGTAATCTACCCCAAGCTCGG
131 CTAATGGTAATCTACCCCAAGCTCGA
** * * * *
41285402 GGTAAAAGATCA-GATGGTTACAATCTACCCCATGCTCGGGGTAAAAGAT
1 GGTAAAAGAT-AGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGAT
41285451 CGAATGGCTG
Statistics
Matches: 173, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
156 173 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (156 bp):
GGTAAAAGATAGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTGATCT
GCCCCAAGCTCGAGGTAAAAGATCGAATAGCGGCAATCTACCCCAGGCTCGGGGTAAGAGATTAG
CTAATGGTAATCTACCCCAAGCTCGA
Found at i:41285427 original size:39 final size:39
Alignment explanation
Indices: 41285307--41285493 Score: 195
Period size: 39 Copynumber: 4.8 Consensus size: 39
41285297 GCTGATGGTG
* *
41285307 ATCTGCCCTAAGCTCGGGGTAAAAGATCGAATAGTTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCA
* * *
41285346 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGG-T--A
1 ATCTGCCCCAAGCTCGGGGTAAAAGA-T--CGAATGGTTGCA
* *
41285385 ATCTACCCCAAGCTCGGGGTAAAAGATC-AGATGGTTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGA-ATGGTTGCA
* * *
41285424 ATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCA
*
41285463 ATCTGCCCCAGGCTCGGGGTAAGAA-ATCGAA
1 ATCTGCCCCAAGCTCGGGGTAA-AAGATCGAA
41285494 ATTTTCAATT
Statistics
Matches: 126, Mismatches: 13, Indels: 18
0.80 0.08 0.11
Matches are distributed among these distances:
35 1 0.01
36 5 0.04
37 1 0.01
38 1 0.01
39 108 0.86
40 4 0.03
41 1 0.01
42 5 0.04
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCA
Found at i:41285466 original size:78 final size:77
Alignment explanation
Indices: 41285145--41285493 Score: 244
Period size: 78 Copynumber: 4.5 Consensus size: 77
41285135 GGATTGGTTG
* * * * * **** *
41285145 ATGGTGATCTGCCCCAAGCTCGAGGTAAGAGATCGGATGGCGGTAATCTACCTCAGGCTCGGGGT
1 ATGGTAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATAGTTACAATCTACCCCAGGCTCGGGGT
*
41285210 AAGAGATTAGCTG-
66 AAAAGATT-GC-GA
* ** * * * * * * * * *
41285223 ATGGTGATCTATCCCAGGGTCGAGGTAAAAGATTGGAT-GCCTGCAATCTACCCCAAGCTCGAGG
1 ATGGTAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATAG-TTACAATCTACCCCAGGCTCGGGG
*
41285287 TAAGAGATTGGCTG-
65 TAAAAGATT-GC-GA
* * * *
41285301 ATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGAATAGTTGCAATCTGCCCCAGGCTCGGGGT
1 ATGGTAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATAGTTACAATCTACCCCAGGCTCGGGGT
* *
41285366 AAGAGATTGGCTA
66 AAAAGATT-GCGA
* * *
41285379 ATGGTAATCTACCCCAAGCTCGGGGTAAAAGATC-AGATGGTTACAATCTACCCCATGCTCGGGG
1 ATGGTAATCTGCCCCAAGCTCGGGGTAAAAGATCGA-ATAGTTACAATCTACCCCAGGCTCGGGG
41285443 TAAAAGA-T-CGA
65 TAAAAGATTGCGA
*
41285454 ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAA-ATCGAA
1 ATGG-T--AATCTGCCCCAAGCTCGGGGTAA-AAGATCGAA
41285494 ATTTTCAATT
Statistics
Matches: 226, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
75 6 0.03
76 1 0.00
77 3 0.01
78 212 0.94
79 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (77 bp):
ATGGTAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATAGTTACAATCTACCCCAGGCTCGGGGT
AAAAGATTGCGA
Found at i:41285485 original size:117 final size:115
Alignment explanation
Indices: 41284761--41285486 Score: 376
Period size: 117 Copynumber: 6.2 Consensus size: 115
41284751 GGATTATTGT
* * * * * * *
41284761 AATCTGCCCCTGGCTCGGGGTAAGAGATTGGCTAACGGTGATCTACCCTATA-ATCGGGGTAAAA
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCA-AGCTCGAGGTAAGA
* * *
41284825 GAT-TGAATGGTTACAATCTACCCCAGGCTCGGGGTAAGAGGTTGGCTG-ATGG-TG-
65 GATCTG-ATGG-T-CAATCTACCCCATGCTCGGGGTAA-AAGAT--C-GAATGGCTGC
* * * *
41284879 -ATCTGCCCTAAGCTCGGGGTAAGAGA-T--C-AGATGGCTACAATCTGCCCCAAGTTCTG-GGT
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTA-ATGG-T--AATCTACCCCAAGCTC-GAGGT
* ** * * * **
41284938 AAGAGATTGGCTGATGGT-GATCTGTCCTATGATCGGAGTAAAAGATCGAACAGCTGC
61 AAGAGA-T--CTGATGGTCAATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGC
* * * ** * * * * * *
41284995 AATCTACCCTAAGCTCAAGGTAAGAGATTGGCTGATAGT-GTCTGCCCTAGGCTCGAGGTAAGAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCAAGCTCGAGGTAAGAG
* * * ** * * * * *
41285059 ATCGGATGGCTGCAATCTGCCTCATGAGCTGGGTAAGAGATAGGATGACTGC
66 ATCTGATGG-T-CAATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGC
* * * * * * * *
41285111 AATCTGCCCCAAGCTCGAGGCAAGGGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGGTAAGAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCAAGCTCGAGGTAAGAG
* * * *
41285176 ATCGGATGG-CGGTAATCTACCTCAGGCTCGGGGTAAGAGATTAGCTG-ATGG-TG-
66 ATCTGATGGTC---AATCTACCCCATGCTCGGGGTAAAAGA-T--C-GAATGGCTGC
** * * * * ** *
41285229 -ATCTATCCCAGGGTCGAGGTAAAAGATTGGATGCCT-GCAATCTACCCCAAGCTCGAGGTAAGA
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-AATGGTAATCTACCCCAAGCTCGAGGTAAGA
* * * * * *
41285292 GATTGGCTGATGGT-GATCTGCCCTAAGCTCGGGGTAAAAGATCGAATAGTTGC
65 GA-T--CTGATGGTCAATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGC
* *
41285345 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCAAGCTCGGGGTAAAAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCAAGCTCGAGGTAAGAG
*
41285410 ATCAGATGGTTACAATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGC
66 ATCTGATGG-T-CAATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGC
41285462 AATCTGCCCCAGGCTCGGGGTAAGA
1 AATCTGCCCCAGGCTCGGGGTAAGA
41285487 AATCGAAATT
Statistics
Matches: 466, Mismatches: 99, Indels: 87
0.71 0.15 0.13
Matches are distributed among these distances:
113 9 0.02
114 19 0.04
115 8 0.02
116 86 0.18
117 314 0.67
118 6 0.01
119 4 0.01
120 17 0.04
121 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (115 bp):
AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTAATCTACCCCAAGCTCGAGGTAAGAG
ATCTGATGGTCAATCTACCCCATGCTCGGGGTAAAAGATCGAATGGCTGC
Found at i:41293002 original size:58 final size:58
Alignment explanation
Indices: 41292940--41293131 Score: 221
Period size: 58 Copynumber: 3.3 Consensus size: 58
41292930 ATTGAGATCA
* *
41292940 AAAATGGAATTTTTGGACATCCAG-GGTTAAAATGGTAATTTTTGAAAGTTTCGGGGTC
1 AAAATGGAATTTTTGGACATTCAGAGG-TAAAATGGTAATTTTTGAAAGTTTTGGGGTC
* * * * *
41292998 AAAATAGAGTTTTTGGACTTTCAGAGGTAAAATGGTAATTTTTTAAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGACATTCAGAGGTAAAATGGTAATTTTTGAAAGTTTTGGGG-TC
* * *
41293057 AAAATGGAATTTTTGGA-AGTTC-GTGGGTAAAAT-GTAATTTTTGGAAGTTTTGGCGTC
1 AAAATGGAATTTTTGGACA-TTCAG-AGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTC
41293114 AAAAATGGAATTTTTGGA
1 -AAAATGGAATTTTTGGA
41293132 GAAGTTTAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 84 0.74
59 29 0.25
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (58 bp):
AAAATGGAATTTTTGGACATTCAGAGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTC
Found at i:41293039 original size:29 final size:27
Alignment explanation
Indices: 41292940--41293101 Score: 90
Period size: 28 Copynumber: 5.6 Consensus size: 27
41292930 ATTGAGATCA
* *
41292940 AAAATGGAATTTTTGGACATCCAGGGTT
1 AAAATGGAATTTTTGGACTTTCAGGG-T
* * *
41292968 AAAATGGTAATTTTTGAAAGTTTCGGGGT
1 AAAATGG-AATTTTTG-GACTTTCAGGGT
* *
41292997 CAAAATAGAGTTTTTGGACTTTCAGAGGT
1 -AAAATGGAATTTTTGGACTTTCAG-GGT
** * **
41293026 AAAATGGTAATTTTTTAAAGTTTTGGGGTT
1 AAAATGG-AA-TTTTTGGACTTTCAGGG-T
** *
41293056 AAAAATGGAATTTTTGGAAGTTCGTGGGT
1 -AAAATGGAATTTTTGGACTTTC-AGGGT
*
41293085 AAAATGTAATTTTTGGA
1 AAAATGGAATTTTTGGA
41293102 AGTTTTGGCG
Statistics
Matches: 101, Mismatches: 24, Indels: 18
0.71 0.17 0.13
Matches are distributed among these distances:
28 35 0.35
29 31 0.31
30 28 0.28
31 7 0.07
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (27 bp):
AAAATGGAATTTTTGGACTTTCAGGGT
Found at i:41293059 original size:30 final size:29
Alignment explanation
Indices: 41292940--41293131 Score: 144
Period size: 30 Copynumber: 6.6 Consensus size: 29
41292930 ATTGAGATCA
* *
41292940 AAAATGGAATTTTTGGACA--TCCAGGGTT
1 AAAATGGAATTTTTGGA-AGTTTCGGGGTT
* *
41292968 AAAATGGTAATTTTTGAAAGTTTCGGGGTC
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTT
* * * *
41292998 AAAATAGAGTTTTTGG-ACTTTCAGAGG-T
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTT
** *
41293026 AAAATGGTAATTTTTTAAAGTTTTGGGGTT
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTT
41293056 AAAAATGGAATTTTTGGAAG-TTCGTGGG-T
1 -AAAATGGAATTTTTGGAAGTTTCG-GGGTT
* * * *
41293085 AAAATGTAATTTTTGGAAGTTTTGGCGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-T
41293115 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
41293132 GAAGTTTAAA
Statistics
Matches: 127, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
28 39 0.31
29 35 0.28
30 46 0.36
31 7 0.06
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTT
Found at i:41295796 original size:206 final size:206
Alignment explanation
Indices: 41295356--41296065 Score: 940
Period size: 205 Copynumber: 3.5 Consensus size: 206
41295346 TTTCATTGAG
* *
41295356 TTGGTCTACTTCTCTA-TATC-CTATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
1 TTGGTCCACTTCTC-AGTATCTC-ATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* * * * *
41295419 GTATCTCATCAGAAAGCTGGGGTTCGAAGAGTTGCTCGCATCGAGT-GTCGAG-TTGGTAT--AC
64 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGA-TCGTCG-GTTTGATTTGGTC
* * *
41295480 TTCT-C-T-GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCTGCTTCTCTGTATCTC
127 TTCTCCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTC
* *
41295542 GTTAGGAAGACGAAT
192 ATCAGGAAGACGAAT
* *
41295557 TTGGTCCACTTATCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* *
41295622 TTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGATCGTCGGTTTGATTTGGTCTTCT
66 ATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGATCGTCGGTTTGATTTGGTCTTCT
* * *
41295687 CCTTAGTATCTTATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATATCTCATCG
131 CCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCA
41295752 GGAAGACGAAT
196 GGAAGACGAAT
* *
41295763 TTGGTCCACTTCTCAGCATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACTTGCTTCTCAGT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* * * * * *
41295828 TTCTCATCAGGAAG-TTGGGTTCGAAGATTTTCTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
66 ATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGATCGTCGGTTTGATTTGGTCTTCT
* * * * *
41295892 CCTCAGTATCTCATTAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTTTTTGTATCTCATCA
131 CCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCA
*
41295957 AGAAGACGAAT
196 GGAAGACGAAT
* * * *
41295968 TTGGTCCACTTCTCAGTAT-TCATCAGGAAGCTAACAATTTTATTGTTTCAACCTGCTTCTCAAT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* *
41296032 ATCTCATCTA-GAAGCTGAGGTTTGAAGATTTGCT
66 ATCTCATC-AGGAAGCTGGGGTTCGAAGATTTGCT
41296066 TTTATCGAGC
Statistics
Matches: 449, Mismatches: 49, Indels: 18
0.87 0.09 0.03
Matches are distributed among these distances:
200 3 0.01
201 104 0.23
202 1 0.00
203 5 0.01
204 52 0.12
205 146 0.33
206 138 0.31
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
ATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGATCGTCGGTTTGATTTGGTCTTCT
CCTTAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCA
GGAAGACGAAT
Found at i:41296075 original size:205 final size:205
Alignment explanation
Indices: 41295356--41296065 Score: 943
Period size: 206 Copynumber: 3.5 Consensus size: 205
41295346 TTTCATTGAG
* *
41295356 TTGGTCTACTTCTCTA-TATC-CTATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCA
1 TTGGTCCACTTCTC-AGTATCTC-ATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* * * * * *
41295419 GTATCTCATCAGAAAGCTGGGGTTCGAAGAGTTGCTCGCATCGA--GT-G-TCGAGTTGGTATAC
64 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGAGCGTGGTTTGATTTGGTCTTC
* * * * * * *
41295480 TTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCTGCTTCTCTGTATCTCGTT
129 TCCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATC
41295545 AGGAAGACGAAT
194 AGGAAGACGAAT
* *
41295557 TTGGTCCACTTATCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* * *
41295622 TTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGATCGTCGGTTTGATTTGGTCTTCT
66 ATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGAGCGT-GGTTTGATTTGGTCTTCT
* * * *
41295687 CCTTAGTATCTTATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATATCTCATCG
130 CCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCA
41295752 GGAAGACGAAT
195 GGAAGACGAAT
* *
41295763 TTGGTCCACTTCTCAGCATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACTTGCTTCTCAGT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* * * *
41295828 TTCTCATCAGGAAG-TTGGGTTCGAAGATTTTCTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
66 ATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGAGCGT-GGTTTGATTTGGTCTTCT
* * * *
41295892 CCTCAGTATCTCATTAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTTTTTGTATCTCATCA
130 CCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCA
*
41295957 AGAAGACGAAT
195 GGAAGACGAAT
* * * *
41295968 TTGGTCCACTTCTCAGTAT-TCATCAGGAAGCTAACAATTTTATTGTTTCAACCTGCTTCTCAAT
1 TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
* *
41296032 ATCTCATCTA-GAAGCTGAGGTTTGAAGATTTGCT
66 ATCTCATC-AGGAAGCTGGGGTTCGAAGATTTGCT
41296066 TTTATCGAGC
Statistics
Matches: 447, Mismatches: 53, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
200 1 0.00
201 95 0.21
202 1 0.00
203 2 0.00
204 51 0.11
205 146 0.33
206 151 0.34
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (205 bp):
TTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGT
ATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCGAGCGTGGTTTGATTTGGTCTTCTC
CTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAG
GAAGACGAAT
Found at i:41296263 original size:39 final size:39
Alignment explanation
Indices: 41296220--41296364 Score: 150
Period size: 39 Copynumber: 3.7 Consensus size: 39
41296210 AGATGGTTGC
* * *
41296220 AATCTGCCCTAGGCTCGGGGTGAGAGATTGGTTGACGAT
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGACGAT
* * * * *
41296259 AATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTG-C
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGAC-GAT
*
41296298 AATCTGCCCCTA-GCTCGGGGTAAGAGATTGATTGATGAT
1 AATCTGCCCC-AGGCTCGGGGTAAGAGATTGATTGACGAT
* **
41296337 GATCTGCCCCAGGCTCAAGGTAAGAGAT
1 AATCTGCCCCAGGCTCGGGGTAAGAGAT
41296365 CAAATAGCTT
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
38 2 0.02
39 81 0.95
40 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (39 bp):
AATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGACGAT
Found at i:41296282 original size:78 final size:78
Alignment explanation
Indices: 41296159--41296393 Score: 278
Period size: 78 Copynumber: 3.0 Consensus size: 78
41296149 CCCGTGATCA
* * * * * *
41296159 GGGTAGGAGATTGGTTGATGATGATCTGCTCCAAGCTTGGAGTAAAAGGTC-AGATGGTTGCAAT
1 GGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGAGTAAAAGATCGA-ATGGCTGCAAT
41296223 CTG-CCCTAGGCTCG
65 CTGCCCCTA-GCTCG
* * * *
41296237 GGGTGAGAGATTGGTTGACGATAATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGAGTAAAAGATCGAATGGCTGCAATC
41296302 TGCCCCTAGCTCG
66 TGCCCCTAGCTCG
* * * * * *
41296315 GGGTAAGAGATTGATTGATGATGATCTGCCCCAGGCTC-AAGGTAAGAGATCAAATAGCTTCAAT
1 GGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGA-GTAAAAGATCGAATGGCTGCAAT
41296379 CTGCCCCTAGCTCG
65 CTGCCCCTAGCTCG
41296393 G
1 G
41296394 AGAGATCAGA
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
78 128 0.96
79 6 0.04
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (78 bp):
GGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGAGTAAAAGATCGAATGGCTGCAATC
TGCCCCTAGCTCG
Found at i:41296736 original size:50 final size:50
Alignment explanation
Indices: 41296682--41297017 Score: 170
Period size: 50 Copynumber: 6.7 Consensus size: 50
41296672 AAATATTCGT
* *
41296682 GGTACTGGATCTGCCATTGCGGCCTTAGATCTTTCCCATCGTGTCTCTGA
1 GGTACTGGATCTGCCATTGCGGACTTAGATCTTTCCCATCGTGTCTTTGA
** * * * * * * * * *
41296732 GGTACAAGTTTTGCCGTTGC-GACTTAAACCTTTCCCTTTTGTATCTTTGGC
1 GGTACTGGATCTGCCATTGCGGACTTAGATCTTTCCC-ATCGTGTCTTT-GA
*
41296783 GGTACTGGATCCGCCATTGC-GATCTTAGATCTTTCCCATCGTGTCTTTTGA
1 GGTACTGGATCTGCCATTGCGGA-CTTAGATCTTTCCCATCGTGTC-TTTGA
* * * * ** *
41296834 GGTACACGG-TCTACCGTTGC-GACTTAGACCTTTCCC-TTTTGTCTTTTTA
1 GGTAC-TGGATCTGCCATTGCGGACTTAGATCTTTCCCATCGTGTC-TTTGA
* * * * * * *
41296883 CGGTACTGTATCCGCCGTTAC-GATCTTAGAACTTTCCCGTCGTGT-TTTCA
1 -GGTACTGGATCTGCCATTGCGGA-CTTAGATCTTTCCCATCGTGTCTTTGA
* * * * ** * *
41296933 TAGTACTGGATCCGCTATTGCGG-CTTAGATCTTTTCC-TTATGTCTTCGC
1 -GGTACTGGATCTGCCATTGCGGACTTAGATCTTTCCCATCGTGTCTTTGA
* * *
41296982 GGTATTGGATCCGCCGTTGC-GACTTAGATCTTTCCC
1 GGTACTGGATCTGCCATTGCGGACTTAGATCTTTCCC
41297018 TTGTGTTTTT
Statistics
Matches: 214, Mismatches: 60, Indels: 26
0.71 0.20 0.09
Matches are distributed among these distances:
47 1 0.00
48 33 0.15
49 38 0.18
50 69 0.32
51 52 0.24
52 21 0.10
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (50 bp):
GGTACTGGATCTGCCATTGCGGACTTAGATCTTTCCCATCGTGTCTTTGA
Found at i:41296803 original size:51 final size:51
Alignment explanation
Indices: 41296744--41297019 Score: 199
Period size: 50 Copynumber: 5.5 Consensus size: 51
41296734 TACAAGTTTT
* * * *
41296744 GCCGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGGCGGTACTGGATCC
1 GCCGTTGCGACTTAGATCTTTCCCTTTTGTGTCTTTCGCGGTACTGGATCC
* * * * * * *
41296795 GCCATTGCGATCTTAGATCTTTCCC-ATCGTGTCTTTTGAGGTACACGG-TCT
1 GCCGTTGCGA-CTTAGATCTTTCCCTTTTGTGTCTTTCGCGGTAC-TGGATCC
* * * ** *
41296846 ACCGTTGCGACTTAGACCTTTCCCTTTTGTCT-TTTTACGGTACTGTATCC
1 GCCGTTGCGACTTAGATCTTTCCCTTTTGTGTCTTTCGCGGTACTGGATCC
* * * * ***
41296896 GCCGTTACGATCTTAGAACTTTCCC-GTCGTGT-TTTCATAGTACTGGATCC
1 GCCGTTGCGA-CTTAGATCTTTCCCTTTTGTGTCTTTCGCGGTACTGGATCC
** * * * *
41296946 GCTATTGCGGCTTAGATCTTTTCC--TTATGTC-TTCGCGGTATTGGATCC
1 GCCGTTGCGACTTAGATCTTTCCCTTTTGTGTCTTTCGCGGTACTGGATCC
41296994 GCCGTTGCGACTTAGATCTTTCCCTT
1 GCCGTTGCGACTTAGATCTTTCCCTT
41297020 GTGTTTTTGT
Statistics
Matches: 170, Mismatches: 47, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
48 37 0.22
49 13 0.08
50 56 0.33
51 50 0.29
52 14 0.08
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.39
Consensus pattern (51 bp):
GCCGTTGCGACTTAGATCTTTCCCTTTTGTGTCTTTCGCGGTACTGGATCC
Found at i:41296813 original size:101 final size:101
Alignment explanation
Indices: 41296682--41296927 Score: 323
Period size: 101 Copynumber: 2.4 Consensus size: 101
41296672 AAATATTCGT
* ** * * *
41296682 GGTACTGGATCTGCCATTGCGGCCTTAGATCTTTCCCATCGTGTC-TCTGAGGTACAAGTTTTGC
1 GGTACTGGATCCGCCATTGCGATCTTAGATCTTTCCCATCGTGTCTTCTGAGGTACAAGGTCTAC
*
41296746 CGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGGC
66 CGTTGCGACTTAAACCTTTCCCTTTTGTAT-TTTGAC
* *
41296783 GGTACTGGATCCGCCATTGCGATCTTAGATCTTTCCCATCGTGTCTTTTGAGGTACACGGTCTAC
1 GGTACTGGATCCGCCATTGCGATCTTAGATCTTTCCCATCGTGTCTTCTGAGGTACAAGGTCTAC
* * *
41296848 CGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTAC
66 CGTTGCGACTTAAACCTTTCCCTTTTGTATTTTGAC
* * * * *
41296884 GGTACTGTATCCGCCGTTACGATCTTAGAACTTTCCCGTCGTGT
1 GGTACTGGATCCGCCATTGCGATCTTAGATCTTTCCCATCGTGT
41296928 TTTCATAGTA
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
101 85 0.67
102 42 0.33
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.37
Consensus pattern (101 bp):
GGTACTGGATCCGCCATTGCGATCTTAGATCTTTCCCATCGTGTCTTCTGAGGTACAAGGTCTAC
CGTTGCGACTTAAACCTTTCCCTTTTGTATTTTGAC
Found at i:41298223 original size:14 final size:14
Alignment explanation
Indices: 41298204--41298235 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
41298194 TCTTTGTTTT
41298204 TTTTGTTTTTTTGC
1 TTTTGTTTTTTTGC
*
41298218 TTTTGTTTTTTTTC
1 TTTTGTTTTTTTGC
41298232 TTTT
1 TTTT
41298236 ATTCATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (14 bp):
TTTTGTTTTTTTGC
Found at i:41303569 original size:28 final size:28
Alignment explanation
Indices: 41303536--41303596 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
41303526 AAAATGAGAC
*
41303536 TTTGGA-TACCCAGGAGCAAAATGGTAAT
1 TTTGGACT-CCCAGGAGAAAAATGGTAAT
* * *
41303564 TTTGGACTCTCGGGTGAAAAATGGTAAT
1 TTTGGACTCCCAGGAGAAAAATGGTAAT
41303592 TTTGG
1 TTTGG
41303597 GAAAATTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (28 bp):
TTTGGACTCCCAGGAGAAAAATGGTAAT
Found at i:41303708 original size:29 final size:28
Alignment explanation
Indices: 41303676--41303834 Score: 103
Period size: 29 Copynumber: 5.5 Consensus size: 28
41303666 TCAAAAATAG
*
41303676 AATTTTTAGACATTCAGGGGTAAAATGGT
1 AATTTTT-GAAATTCAGGGGTAAAATGGT
41303705 AATTTTTGAAAGTTTCA-GGGTAAGAAATGG-
1 AATTTTTGAAA--TTCAGGGGT-A-AAATGGT
* * *
41303735 AGTTTTTGGATATTCGGGGGTAAAATGGT
1 AATTTTT-GAAATTCAGGGGTAAAATGGT
*
41303764 AATTTTTGAAAGTTTTA-GGGTCAAAAATGG-
1 AATTTTTGAAA--TTCAGGGGT--AAAATGGT
* *
41303794 AATTTTTGGAAGTTTA-GGGTAAAATGGT
1 AATTTTT-GAAATTCAGGGGTAAAATGGT
* *
41303822 AACTTTTAAAATT
1 AATTTTTGAAATT
41303835 TTTTGGGTTA
Statistics
Matches: 105, Mismatches: 12, Indels: 28
0.72 0.08 0.19
Matches are distributed among these distances:
27 11 0.10
28 18 0.17
29 33 0.31
30 24 0.23
31 19 0.18
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (28 bp):
AATTTTTGAAATTCAGGGGTAAAATGGT
Found at i:41303741 original size:59 final size:58
Alignment explanation
Indices: 41303668--41303934 Score: 281
Period size: 59 Copynumber: 4.6 Consensus size: 58
41303658 AATCGGGATC
* *
41303668 AAAAATAGAATTTTTAGACA-TTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCAGGGT
1 AAAAATGGAATTTTTGGA-AGTTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCAGGGT
* * *
41303726 AAGAAATGGAGTTTTTGGATA-TTCGGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGT
1 AA-AAATGGAATTTTTGGA-AGTTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCAGGGT
* * * * **
41303785 CAAAAATGGAATTTTTGGAAGTTTA-GGGTAAAATGGTAACTTTTAAAATTTTTTGGGT
1 -AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCAGGGT
* * * * * *
41303843 TAAAATGGAATGTTTGGAAGTTTAGGGTTAAAAAT-GTAATTTTTGGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGAAGTTCAGGGGT-AAAATGGTAATTTTTGAAAGTTTC-AGGGT
* *
41303902 AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAA
1 AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAA
41303935 ATATAATTTT
Statistics
Matches: 176, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
57 22 0.12
58 52 0.30
59 100 0.57
60 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGAAAGTTTCAGGGT
Found at i:41303887 original size:29 final size:29
Alignment explanation
Indices: 41303697--41303958 Score: 196
Period size: 30 Copynumber: 8.9 Consensus size: 29
41303687 ATTCAGGGGT
*
41303697 AAAATGGTAATTTTTGAAAGTTTCAGGG-TA
1 AAAAT-GTAATTTTTGGAAGTTT-AGGGTTA
* * ** *
41303727 AGAAATGGAGTTTTTGGATA-TTCGGGGGT-
1 A-AAATGTAATTTTTGGA-AGTTTAGGGTTA
* *
41303756 AAAATGGTAATTTTTGAAAGTTTTAGGGTCA
1 AAAAT-GTAATTTTTGGAAG-TTTAGGGTTA
*
41303787 AAAATGGAATTTTTGGAAGTTTAGGG-T-
1 AAAATGTAATTTTTGGAAGTTTAGGGTTA
* ** * *
41303814 AAAATGGTAACTTTTAAAATTTTTTGGGTT-
1 AAAAT-GTAATTTTTGGAA-GTTTAGGGTTA
* *
41303844 AAAATGGAATGTTTGGAAGTTTAGGGTTA
1 AAAATGTAATTTTTGGAAGTTTAGGGTTA
*
41303873 AAAATGTAATTTTTGGAAGTTTCAAGGTTA
1 AAAATGTAATTTTTGGAAGTTT-AGGGTTA
*
41303903 AAAATGGAATTTTTGGAAGTTTAAGGG-TA
1 AAAATGTAATTTTTGGAAGTTT-AGGGTTA
* *
41303932 AAAATATAATTTTTGGGCAGTTTAGGG
1 AAAATGTAATTTTT-GGAAGTTTAGGG
41303959 ACCCTTAGGG
Statistics
Matches: 182, Mismatches: 37, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
27 5 0.03
28 22 0.12
29 72 0.40
30 73 0.40
31 10 0.05
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTAGGGTTA
Found at i:41305038 original size:15 final size:15
Alignment explanation
Indices: 41305018--41305050 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41305008 TTCAGTTTTT
41305018 TTATTAAT-AATATTA
1 TTATTAATGAA-ATTA
41305033 TTATTAATGAAATTA
1 TTATTAATGAAATTA
41305048 TTA
1 TTA
41305051 AATATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TTATTAATGAAATTA
Found at i:41305756 original size:17 final size:17
Alignment explanation
Indices: 41305751--41305807 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
41305741 AAAATAAATT
*
41305751 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
* *
41305768 TAAA-TTCAATCTCAAAA
1 TAAATTTAAAT-TTAAAA
* *
41305785 TGAATTTGAATTTAAAA
1 TAAATTTAAATTTAAAA
41305802 TAAATT
1 TAAATT
41305808 CAAACTTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
16 5 0.16
17 21 0.68
18 5 0.16
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:41306405 original size:24 final size:24
Alignment explanation
Indices: 41306378--41306425 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41306368 CAAGAATATG
*
41306378 AAAGTTTAAAGAAGATAGAAGGTT
1 AAAGTTCAAAGAAGATAGAAGGTT
* *
41306402 AAAGTTCAAGGAAGATGGAAGGTT
1 AAAGTTCAAAGAAGATAGAAGGTT
41306426 GAACATCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.23
Consensus pattern (24 bp):
AAAGTTCAAAGAAGATAGAAGGTT
Found at i:41309515 original size:22 final size:21
Alignment explanation
Indices: 41309483--41309529 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
41309473 ATTTTTTTAA
*
41309483 TTTTTAATAAAATTTAAATACT
1 TTTTTAATAAAATTT-AATAAT
*
41309505 TTTTTATTAAAATTTAATAAT
1 TTTTTAATAAAATTTAATAAT
41309526 TTTT
1 TTTT
41309530 ATAACTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAATAAAATTTAATAAT
Found at i:41311412 original size:10 final size:10
Alignment explanation
Indices: 41311397--41311426 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41311387 AAAAAACTAC
41311397 AAATATATAA
1 AAATATATAA
*
41311407 AAATATAAAA
1 AAATATATAA
41311417 AAATATATAA
1 AAATATATAA
41311427 TATTATCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATATATAA
Found at i:41312894 original size:27 final size:27
Alignment explanation
Indices: 41312864--41312922 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
41312854 AACTTTAATT
*
41312864 TTATTATTA-TAATATTTCATT-TTATCG
1 TTATTATTATTAATA--TCATTGTTACCG
*
41312891 TTATAATTATTAATATCATTGTTACCG
1 TTATTATTATTAATATCATTGTTACCG
41312918 TTATT
1 TTATT
41312923 TTTAATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.19
27 17 0.63
28 5 0.19
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (27 bp):
TTATTATTATTAATATCATTGTTACCG
Found at i:41313222 original size:26 final size:28
Alignment explanation
Indices: 41313186--41313241 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
41313176 TATTTTTTTT
*
41313186 TTCAGTTTTTAAAGGG-TTCAAA-AAAA
1 TTCAGTTTTTAAAGGGCTTAAAAGAAAA
*
41313212 TTCAGTTTTTAAGGGGCTTAAAAGAAAA
1 TTCAGTTTTTAAAGGGCTTAAAAGAAAA
41313240 TT
1 TT
41313242 TTACCAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 15 0.58
27 5 0.19
28 6 0.23
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (28 bp):
TTCAGTTTTTAAAGGGCTTAAAAGAAAA
Found at i:41314735 original size:21 final size:23
Alignment explanation
Indices: 41314704--41314748 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
41314694 GCATCGACCC
41314704 ATTTTCAATTTAATA-TTTTAAT
1 ATTTTCAATTTAATATTTTTAAT
41314726 ATTTT-AATTTAATATTTTTAAT
1 ATTTTCAATTTAATATTTTTAAT
41314748 A
1 A
41314749 ATTATTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTCAATTTAATATTTTTAAT
Found at i:41314849 original size:21 final size:20
Alignment explanation
Indices: 41314816--41314878 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 20
41314806 ATTTTACTAT
41314816 TAATTTTAATTTTATTGTTA
1 TAATTTTAATTTTATTGTTA
* *
41314836 TAATATTTCATTTTATCGTTA
1 TAAT-TTTAATTTTATTGTTA
41314857 TAATTATTAATTTTATTGTTA
1 TAATT-TTAATTTTATTGTTA
41314878 T
1 T
41314879 CGGTATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 5 0.14
21 32 0.86
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TAATTTTAATTTTATTGTTA
Found at i:41318472 original size:61 final size:61
Alignment explanation
Indices: 41318368--41318519 Score: 175
Period size: 61 Copynumber: 2.5 Consensus size: 61
41318358 AACTTGATAC
* * * *
41318368 TTTTTCTTAATTTGGTACTTAAACTTTTTTTGACCCAACTTGGTACTTGAACTTGACACTTT
1 TTTTTCTTAATTTGATACCTAAACTTTTTTTAACCCAACTTGGTACCTGAACTTGACA-TTT
* * *
41318430 TTTTTTTTAATTTGATACCT-AATTTTTTTTAACCCAATTTGGTACCTGAACTTGACA-TT
1 TTTTTCTTAATTTGATACCTAAACTTTTTTTAACCCAACTTGGTACCTGAACTTGACATTT
* * * *
41318489 TTTTTC-TAATTAGGTACCTGAGCTTTTTTTA
1 TTTTTCTTAATTTGATACCTAAACTTTTTTTA
41318520 GATTCAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 11 0.14
59 16 0.21
61 33 0.43
62 17 0.22
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.51
Consensus pattern (61 bp):
TTTTTCTTAATTTGATACCTAAACTTTTTTTAACCCAACTTGGTACCTGAACTTGACATTT
Found at i:41318493 original size:62 final size:62
Alignment explanation
Indices: 41318348--41318519 Score: 178
Period size: 59 Copynumber: 2.9 Consensus size: 62
41318338 AATATAATAT
* * * * *
41318348 TTGGTATCTGAACTTGATAC---TTTTTCTTAATTTGGTACTTAAACTTTTTTTGACCCAAC
1 TTGGTACCTGAACTTGACACTTTTTTTTCTTAATTTGATACCTAAACTTTTTTTAACCCAAC
* * * *
41318407 TTGGTACTTGAACTTGACACTTTTTTTTTTTAATTTGATACCT-AATTTTTTTTAACCCAAT
1 TTGGTACCTGAACTTGACACTTTTTTTTCTTAATTTGATACCTAAACTTTTTTTAACCCAAC
* * * *
41318468 TTGGTACCTGAACTTGACA--TTTTTTTC-TAATTAGGTACCTGAGCTTTTTTTA
1 TTGGTACCTGAACTTGACACTTTTTTTTCTTAATTTGATACCTAAACTTTTTTTA
41318520 GATTCAATTT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 11 0.12
59 33 0.35
61 33 0.35
62 17 0.18
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (62 bp):
TTGGTACCTGAACTTGACACTTTTTTTTCTTAATTTGATACCTAAACTTTTTTTAACCCAAC
Found at i:41319083 original size:28 final size:28
Alignment explanation
Indices: 41319052--41319112 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
41319042 AAAATGAGAC
41319052 TTTGGA-TGCCCGAGGGCAAAATGATAAT
1 TTTGGACT-CCCGAGGGCAAAATGATAAT
* * *
41319080 TTTGGACTCTCGAGGGTAAAATGGTAAT
1 TTTGGACTCCCGAGGGCAAAATGATAAT
41319108 TTTGG
1 TTTGG
41319113 GAAAATTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (28 bp):
TTTGGACTCCCGAGGGCAAAATGATAAT
Found at i:41319123 original size:28 final size:28
Alignment explanation
Indices: 41319062--41319174 Score: 79
Period size: 28 Copynumber: 4.0 Consensus size: 28
41319052 TTTGGATGCC
* * ***
41319062 CGAGGGCAAAATGATAATTTTGGACTCT
1 CGAGGGTAAAATGGTAATTTTGGAAAAT
41319090 CGAGGGTAAAATGGTAATTTTGGGAAAAT
1 CGAGGGTAAAATGGTAATTTT-GGAAAAT
* * *
41319119 -TAGGGGTTAAAAAT-GAAATTTT-AAAAAT
1 CGA-GGG-T-AAAATGGTAATTTTGGAAAAT
*
41319147 CGAGGGTAAAACGGTAATTTTTGGAAAA
1 CGAGGGTAAAATGGTAA-TTTTGGAAAA
41319175 ATCAAGATCA
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
26 4 0.06
27 4 0.06
28 32 0.49
29 12 0.18
30 8 0.12
31 5 0.08
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (28 bp):
CGAGGGTAAAATGGTAATTTTGGAAAAT
Found at i:41319188 original size:57 final size:58
Alignment explanation
Indices: 41319089--41319198 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 58
41319079 TTTTGGACTC
* * * * * *
41319089 TCGAGGGTAAAATGGTAATTTTGGGAAAATTAGGGGTTAAAAAT-GAAATTTTAAAAA
1 TCGAGGGTAAAACGGTAATTTTGGAAAAATCAGAGATCAAAAATAGAAATTTTAAAAA
*
41319146 TCGAGGGTAAAACGGTAATTTTTGGAAAAATCA-AGATCAAAAATAGAATTTTT
1 TCGAGGGTAAAACGGTAA-TTTTGGAAAAATCAGAGATCAAAAATAGAAATTTT
41319199 TGGACATCCG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
57 25 0.57
58 19 0.43
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.30
Consensus pattern (58 bp):
TCGAGGGTAAAACGGTAATTTTGGAAAAATCAGAGATCAAAAATAGAAATTTTAAAAA
Found at i:41319255 original size:29 final size:30
Alignment explanation
Indices: 41319216--41319382 Score: 191
Period size: 29 Copynumber: 5.7 Consensus size: 30
41319206 CCGAGGGTAG
* *
41319216 AATGGTAA-TTTTGAAAGTTTCGGGGTCAAA
1 AATGG-AATTTTTGGAAGTTTAGGGGTCAAA
41319246 AATGGAATTTTTGGAAGTTTAGGGG-CAAA
1 AATGGAATTTTTGGAAGTTTAGGGGTCAAA
** *
41319275 AATATAATTTTTGGAAGTTTAGGGAT-AAA
1 AATGGAATTTTTGGAAGTTTAGGGGTCAAA
* *
41319304 AATGTAATTTTTGGAAGTTTTGGGGTCAAA
1 AATGGAATTTTTGGAAGTTTAGGGGTCAAA
*
41319334 AATGGAATTTTTGGAAATTT-GAGGGTC-AA
1 AATGGAATTTTTGGAAGTTTAG-GGGTCAAA
* *
41319363 AATGTAATTTTAGGAAGTTT
1 AATGGAATTTTTGGAAGTTT
41319383 CAAGGTTAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
29 74 0.62
30 46 0.38
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
AATGGAATTTTTGGAAGTTTAGGGGTCAAA
Found at i:41319287 original size:59 final size:58
Alignment explanation
Indices: 41319224--41319413 Score: 197
Period size: 59 Copynumber: 3.2 Consensus size: 58
41319214 AGAATGGTAA
* *
41319224 TTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGCAAAAATATAAT
1 TTTTGAAAGTTT-GGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGCAAAAATACAAT
* * * **
41319283 TTTTGGAAGTTTAGGGAT-AAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAAT
1 TTTTGAAAGTTT-GGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGG-CAAAAATACAAT
* * **
41319342 TTTTGGAAA-TTTGAGGGTC-AAAATGTAATTTTAGGAAGTTTCAAGGTTAAAAATACAAT
1 TTTT-GAAAGTTTG-GGGTCAAAAATGTAATTTTTGGAAGTTT-AGGGGCAAAAATACAAT
41319401 TTTTGAACAGTTT
1 TTTTGAA-AGTTT
41319414 AGGAACCTCC
Statistics
Matches: 108, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
58 30 0.28
59 70 0.65
60 8 0.07
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (58 bp):
TTTTGAAAGTTTGGGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGCAAAAATACAAT
Found at i:41319393 original size:29 final size:28
Alignment explanation
Indices: 41319220--41319416 Score: 171
Period size: 29 Copynumber: 6.7 Consensus size: 28
41319210 GGGTAGAATG
* *
41319220 GTAA-TTTTGAAAGTTTCGGGGTCAAAAAT
1 GTAATTTTTGGAAGTTT-AGGGT-AAAAAT
* *
41319249 GGAATTTTTGGAAGTTTAGGGGCAAAAAT
1 GTAATTTTTGGAAGTTTA-GGGTAAAAAT
*
41319278 ATAATTTTTGGAAGTTTAGGGATAAAAAT
1 GTAATTTTTGGAAGTTTAGGG-TAAAAAT
*
41319307 GTAATTTTTGGAAGTTTTGGGGTCAAAAAT
1 GTAATTTTTGGAAG-TTTAGGGT-AAAAAT
* * *
41319337 GGAATTTTTGGAAATTTGAGGGTCAAAAT
1 GTAATTTTTGGAAGTTT-AGGGTAAAAAT
* *
41319366 GTAATTTTAGGAAGTTTCAAGGTTAAAAAT
1 GTAATTTTTGGAAGTTT--AGGGTAAAAAT
** *
41319396 ACAATTTTTGAACAGTTTAGG
1 GTAATTTTTGGA-AGTTTAGG
41319417 AACCTCCAAA
Statistics
Matches: 137, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.02
29 70 0.51
30 59 0.43
31 5 0.04
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (28 bp):
GTAATTTTTGGAAGTTTAGGGTAAAAAT
Found at i:41320534 original size:14 final size:14
Alignment explanation
Indices: 41320495--41320538 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
41320485 TACTAATAAA
*
41320495 TATTAATTAATAAGT
1 TATTAATTAATTA-T
41320510 TATT-ATTAATTAT
1 TATTAATTAATTAT
*
41320523 TATTAATGAATTAT
1 TATTAATTAATTAT
41320537 TA
1 TA
41320539 AAAATAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 17 0.65
15 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
TATTAATTAATTAT
Found at i:41321416 original size:28 final size:28
Alignment explanation
Indices: 41321385--41321441 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
41321375 ACAATAATAG
*
41321385 TAAATTTAAATTAAAATTAAATTTAAAA
1 TAAATTTAAATTAAAAGTAAATTTAAAA
* *
41321413 TAAATTTAATTTCAAAGTAAATTTAAAA
1 TAAATTTAAATTAAAAGTAAATTTAAAA
41321441 T
1 T
41321442 GGTTTGGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TAAATTTAAATTAAAAGTAAATTTAAAA
Found at i:41321419 original size:11 final size:12
Alignment explanation
Indices: 41321385--41321421 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
41321375 ACAATAATAG
*
41321385 TAAATTTAAA-T
1 TAAAATTAAATT
41321396 TAAAATTAAATT
1 TAAAATTAAATT
41321408 TAAAA-TAAATT
1 TAAAATTAAATT
41321419 TAA
1 TAA
41321422 TTTCAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATTAAATT
Found at i:41321421 original size:17 final size:17
Alignment explanation
Indices: 41321367--41321439 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 17
41321357 GGATATTTTA
*
41321367 TTAAATTTACAAT-AAT
1 TTAAATTTAAAATAAAT
* * *
41321383 AGTAAATTTAAATTAAAA
1 -TTAAATTTAAAATAAAT
41321401 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
41321418 TT-AATTTCAAAGTAAAT
1 TTAAATTT-AAAATAAAT
41321435 TTAAA
1 TTAAA
41321440 ATGGTTTGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
16 5 0.11
17 36 0.80
18 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:41322272 original size:19 final size:19
Alignment explanation
Indices: 41322250--41322294 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41322240 TTATATTAGG
41322250 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATAT
* *
41322269 ATTTATTATTTAAATTTAT
1 ATTTAATATTTAAATATAT
41322288 ATTTAAT
1 ATTTAAT
41322295 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATAT
Found at i:41324717 original size:21 final size:21
Alignment explanation
Indices: 41324692--41324741 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
41324682 GAATTTCAGC
*
41324692 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* * *
41324713 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
41324734 AGAAAACT
1 AGCAAACT
41324742 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:41324742 original size:21 final size:21
Alignment explanation
Indices: 41324703--41324742 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41324693 GCAATCTATA
*
41324703 GATTTCCAAAAGCAAACTGTG
1 GATTTCCAAAAGAAAACTGTG
*
41324724 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
41324743 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:41325922 original size:6 final size:6
Alignment explanation
Indices: 41325911--41325960 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
41325901 GGCAACCCAA
*
41325911 TTATTT TTATTT TTATTT TTATTT TT-TTA TTA-TT TTATTTAT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTA-TT-T TTATTT
41325959 TT
1 TT
41325961 GTCCAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 8 0.21
6 23 0.61
7 3 0.08
8 4 0.11
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:41325939 original size:8 final size:8
Alignment explanation
Indices: 41325911--41325960 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
41325901 GGCAACCCAA
41325911 TTATTTTT
1 TTATTTTT
*
41325919 ATTTTTATTT
1 -TTATT-TTT
41325929 TTATTTTT
1 TTATTTTT
*
41325937 TTATTATT
1 TTATTTTT
*
41325945 TTATTTAT
1 TTATTTTT
41325953 TTATTTTT
1 TTATTTTT
41325961 GTCCAGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 23 0.68
9 8 0.24
10 3 0.09
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTATTTTT
Found at i:41325939 original size:20 final size:20
Alignment explanation
Indices: 41325914--41325959 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
41325904 AACCCAATTA
*
41325914 TTTTTATT-TTTATTTTTATT
1 TTTTTATTATTT-TATTTATT
41325934 TTTTTATTATTTTATTTATT
1 TTTTTATTATTTTATTTATT
41325954 TATTTT
1 T-TTTT
41325960 TGTCCAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTATTATTTTATTTATT
Found at i:41327408 original size:19 final size:19
Alignment explanation
Indices: 41327386--41327430 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41327376 TTATATTAGG
41327386 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATAT
* *
41327405 ATTTATTATTTAAATTTAT
1 ATTTAATATTTAAATATAT
41327424 ATTTAAT
1 ATTTAAT
41327431 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATAT
Found at i:41327453 original size:14 final size:14
Alignment explanation
Indices: 41327430--41327459 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41327420 TTATATTTAA
*
41327430 TTTATGTTTATCTT
1 TTTATATTTATCTT
41327444 TTTATATTTATCTT
1 TTTATATTTATCTT
41327458 TT
1 TT
41327460 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:41334610 original size:17 final size:16
Alignment explanation
Indices: 41334588--41334626 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41334578 ATATTTTTTT
41334588 TTATTTAATCAACTAAA
1 TTATTT-ATCAACTAAA
* *
41334605 TTATTTCTCAATTAAA
1 TTATTTATCAACTAAA
41334621 TTATTT
1 TTATTT
41334627 TCTTGACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATTTATCAACTAAA
Found at i:41334629 original size:17 final size:16
Alignment explanation
Indices: 41334596--41334626 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41334586 TTTTATTTAA
41334596 TCAACTAAATTATTTC
1 TCAACTAAATTATTTC
*
41334612 TCAATTAAATTATTT
1 TCAACTAAATTATTT
41334627 TCTTGACTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (16 bp):
TCAACTAAATTATTTC
Found at i:41347047 original size:16 final size:16
Alignment explanation
Indices: 41347026--41347063 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41347016 AAAAGTTCTA
41347026 AGAGAGGGAGAGAGAG
1 AGAGAGGGAGAGAGAG
*
41347042 AGAGAGGGAGGGAGAG
1 AGAGAGGGAGAGAGAG
*
41347058 AAAGAG
1 AGAGAG
41347064 ATTATCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (16 bp):
AGAGAGGGAGAGAGAG
Found at i:41356628 original size:17 final size:17
Alignment explanation
Indices: 41356606--41356644 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41356596 AAATAATCCT
* *
41356606 AATAATAATTCATAATG
1 AATAATAAATCAAAATG
*
41356623 AATAATAAATGAAAATG
1 AATAATAAATCAAAATG
41356640 AATAA
1 AATAA
41356645 ATAGAAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (17 bp):
AATAATAAATCAAAATG
Found at i:41357655 original size:20 final size:20
Alignment explanation
Indices: 41357630--41357684 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
41357620 AAAAGTCAAT
* *
41357630 GGTCAAAGTTAATGACCAAA
1 GGTCAAAGTCAACGACCAAA
* *
41357650 GGTCAAGGTCAACGACCAAC
1 GGTCAAAGTCAACGACCAAA
*
41357670 GGTCAAGGTCAACGA
1 GGTCAAAGTCAACGA
41357685 TCAACTCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (20 bp):
GGTCAAAGTCAACGACCAAA
Found at i:41357689 original size:20 final size:20
Alignment explanation
Indices: 41357643--41357689 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
41357633 CAAAGTTAAT
*
41357643 GACCAAAGGTCAAGGTCAAC
1 GACCAACGGTCAAGGTCAAC
41357663 GACCAACGGTCAAGGTCAAC
1 GACCAACGGTCAAGGTCAAC
*
41357683 GATCAAC
1 GACCAAC
41357690 TCGATCAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.28, G:0.23, T:0.11
Consensus pattern (20 bp):
GACCAACGGTCAAGGTCAAC
Found at i:41360046 original size:25 final size:25
Alignment explanation
Indices: 41359991--41360046 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
41359981 AAATATCCCT
41359991 AGAATAATCAAAGTTTAACTGGAAA
1 AGAATAATCAAAGTTTAACTGGAAA
* * *
41360016 AAAATAA-CATAGTTTAACTGGCAGA
1 AGAATAATCAAAGTTTAACTGG-AAA
41360041 AGAATA
1 AGAATA
41360047 TGAGGCACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (25 bp):
AGAATAATCAAAGTTTAACTGGAAA
Found at i:41368246 original size:17 final size:18
Alignment explanation
Indices: 41368221--41368262 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
41368211 CAACAATACC
41368221 TTTTT-TAATTTATAT-A
1 TTTTTATAATTTATATGA
41368237 TTTTTATAATTTATATGA
1 TTTTTATAATTTATATGA
*
41368255 TTTATATA
1 TTTTTATA
41368263 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTATATGA
Found at i:41368308 original size:20 final size:19
Alignment explanation
Indices: 41368285--41368357 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
41368275 TTGTTGCACT
41368285 TTTCTATATTTTTTATAATA
1 TTTCTATATTTTTTAT-ATA
*
41368305 TTTCTA-ATAATTTTATATA
1 TTTCTATAT-TTTTTATATA
* * *
41368324 TTTTTAGTATTTTTCATAGA
1 TTTCTA-TATTTTTTATATA
*
41368344 TTTCAAATATTTTT
1 TTTC-TATATTTTT
41368358 AAATTTTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 10 0.24
20 29 0.69
21 3 0.07
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTCTATATTTTTTATATA
Found at i:41368337 original size:10 final size:10
Alignment explanation
Indices: 41368229--41368329 Score: 54
Period size: 10 Copynumber: 10.4 Consensus size: 10
41368219 CCTTTTTTAA
41368229 TTTATATATT
1 TTTATATATT
41368239 TTTATA-A--
1 TTTATATATT
41368246 TTTATATGATT
1 TTTATAT-ATT
* *
41368257 TATATATTTT
1 TTTATATATT
41368267 TTTATA-ATT
1 TTTATATATT
**
41368276 TGTTGCACT-TT
1 T-TTATA-TATT
*
41368287 TCTATAT-TT
1 TTTATATATT
41368296 TTTATAATATT
1 TTTAT-ATATT
* *
41368307 TCTA-ATAAT
1 TTTATATATT
41368316 TTTATATATT
1 TTTATATATT
41368326 TTTA
1 TTTA
41368330 GTATTTTTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
7 6 0.09
9 19 0.28
10 28 0.42
11 14 0.21
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTATATATT
Found at i:41368483 original size:18 final size:18
Alignment explanation
Indices: 41368460--41368504 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
41368450 ATAATACTTG
41368460 TTTTATA-ATTTTTTGCAT
1 TTTTATATATTTTTT-CAT
41368478 TTTTATATATTTTTTCAT
1 TTTTATATATTTTTTCAT
*
41368496 TTTAATATA
1 TTTTATATA
41368505 GATTATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATATATTTTTTCAT
Found at i:41369938 original size:87 final size:88
Alignment explanation
Indices: 41369842--41370002 Score: 209
Period size: 87 Copynumber: 1.8 Consensus size: 88
41369832 AAATTCTTAA
* * * * *
41369842 ATTTTTTCAAAAAAAGTAATTAAATCTCTCTTTTTTT-TCACTCAATT-GAGCACTTGAAATTTT
1 ATTTCTTCAAAAAAAGCAATTAAACCTCTCTTTTTTTCCCACTCAATTGGA-CACTTGAAATTTC
41369905 AAAATGCATAGAAAAGGCCCTCAC
65 AAAATGCATAGAAAAGGCCCTCAC
* * * *
41369929 ATTTCTTCAAAAAAAGCAATTAAACCTTTGTTTTTTTCCCCACTCAATTGGATACTTGAACTTTC
1 ATTTCTTCAAAAAAAGCAATTAAACCTCTCTTTTTTT-CCCACTCAATTGGACACTTGAAATTTC
41369994 AAAATGCAT
65 AAAATGCAT
41370003 CAAAAAGACA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 32 0.52
89 28 0.45
90 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (88 bp):
ATTTCTTCAAAAAAAGCAATTAAACCTCTCTTTTTTTCCCACTCAATTGGACACTTGAAATTTCA
AAATGCATAGAAAAGGCCCTCAC
Found at i:41370100 original size:20 final size:20
Alignment explanation
Indices: 41370075--41370119 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41370065 TATAAAAAAT
*
41370075 AAATTTTAGAAAAAT-TAATA
1 AAATTTAAGAAAAATATAA-A
*
41370095 AAATTTAATAAAAATATAAA
1 AAATTTAAGAAAAATATAAA
41370115 AAATT
1 AAATT
41370120 CAAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATTTAAGAAAAATATAAA
Found at i:41370116 original size:29 final size:29
Alignment explanation
Indices: 41370084--41370164 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
41370074 TAAATTTTAG
41370084 AAAAATTAATAAAATTTAATAAAAAT-ATA
1 AAAAATTAA-AAAATTTAATAAAAATCATA
* ** *
41370113 AAAAATTCAAATTTTTTATAAAAATCATA
1 AAAAATTAAAAAATTTAATAAAAATCATA
* *
41370142 AAAACATAAAAAAAATT-ATAAAA
1 AAAA-ATTAAAAAATTTAATAAAA
41370165 TTTTATAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
28 13 0.32
29 21 0.51
30 7 0.17
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAAATTAAAAAATTTAATAAAAATCATA
Found at i:41370155 original size:39 final size:38
Alignment explanation
Indices: 41370104--41370186 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 38
41370094 AAAATTTAAT
* **
41370104 AAAAATATAAAAAATTCA-AATTTTTTATAAAAATCATA
1 AAAAATAAAAAAAATT-ATAAAATTTTATAAAAATCATA
*
41370142 AAAACATAAAAAAAATTATAAAATTTTATAGAAATCATA
1 AAAA-ATAAAAAAAATTATAAAATTTTATAAAAATCATA
41370181 AAAAAT
1 AAAAAT
41370187 TATAAAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 7 0.18
39 32 0.82
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (38 bp):
AAAAATAAAAAAAATTATAAAATTTTATAAAAATCATA
Found at i:41370430 original size:10 final size:9
Alignment explanation
Indices: 41370376--41370503 Score: 52
Period size: 10 Copynumber: 13.4 Consensus size: 9
41370366 TTTTGATACG
41370376 ATAATTTTT
1 ATAATTTTT
*
41370385 GTAATTCTTT
1 ATAATT-TTT
41370395 AACTAA-TTTT
1 -A-TAATTTTT
41370405 ATAATTCTTT
1 ATAATT-TTT
41370415 AT-ATTTTGT
1 ATAATTTT-T
41370424 ATAATTTTCT
1 ATAATTTT-T
**
41370434 -TACAACTTT
1 ATA-ATTTTT
*
41370443 ATAAAATTTT
1 AT-AATTTTT
41370453 ATAATTTTT
1 ATAATTTTT
*
41370462 TTACATTTCTT
1 ATA-ATTT-TT
41370473 -T-ATATTTT
1 ATAAT-TTTT
41370481 ATAATTTTT
1 ATAATTTTT
41370490 -TAAGATTTTT
1 AT-A-ATTTTT
41370500 ATAA
1 ATAA
41370504 AATGTTACGC
Statistics
Matches: 93, Mismatches: 8, Indels: 36
0.68 0.06 0.26
Matches are distributed among these distances:
8 10 0.11
9 33 0.35
10 42 0.45
11 5 0.05
12 3 0.03
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.59
Consensus pattern (9 bp):
ATAATTTTT
Found at i:41370489 original size:28 final size:27
Alignment explanation
Indices: 41370408--41370490 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 27
41370398 TAATTTTATA
*
41370408 ATTCTTTATATTTTGTATAATTTTCTTAC
1 ATTCTTTATA-TTT-TATAATTTTTTTAC
*
41370437 A-ACTTTATAAAATTTTATAATTTTTTTAC
1 ATTCTTTAT---ATTTTATAATTTTTTTAC
41370466 ATTTCTTTATATTTTATAATTTTTT
1 A-TTCTTTATATTTTATAATTTTTT
41370491 AAGATTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
28 21 0.46
29 15 0.33
30 3 0.07
31 7 0.15
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (27 bp):
ATTCTTTATATTTTATAATTTTTTTAC
Found at i:41370719 original size:89 final size:88
Alignment explanation
Indices: 41370636--41370829 Score: 243
Period size: 88 Copynumber: 2.2 Consensus size: 88
41370626 TAAAAGCATG
* * * *
41370636 GGCTTAATTACTTTTTTTTTTTGAAAAAGTTTGAAGGCCTTTTTGATGCA-TTTTAAAAGTTCAA
1 GGCTTAATTAC-TTTTTTTTTTGAAAAAGTTTAAAAGCCTTTTTGATACACTTTGAAAA-TTCAA
41370700 GTACCTAATTGAATGTAAAAAAAAA
64 GTACCTAATTGAATGTAAAAAAAAA
* * *
41370725 GGCTTAATTGCTTTTTTTTTTGAAAAGGTTTAAAAGTCTTTTTGATACACTTTGAAAATTCAAGT
1 GGCTTAATTACTTTTTTTTTTGAAAAAGTTTAAAAGCCTTTTTGATACACTTTGAAAATTCAAGT
*
41370790 A-CTCAAATG-A-GTAAAAAAAAAA
66 ACCT-AATTGAATGT-AAAAAAAAA
*
41370812 GACTTAATTACTTTTTTT
1 GGCTTAATTACTTTTTTT
41370830 GAGAAAATTT
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
86 2 0.02
87 28 0.30
88 45 0.49
89 17 0.18
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (88 bp):
GGCTTAATTACTTTTTTTTTTGAAAAAGTTTAAAAGCCTTTTTGATACACTTTGAAAATTCAAGT
ACCTAATTGAATGTAAAAAAAAA
Found at i:41372438 original size:21 final size:21
Alignment explanation
Indices: 41372412--41372453 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41372402 ATAAACAATA
*
41372412 TAATAGTTTTGCCTTTTAACT
1 TAATAGTTTTGACTTTTAACT
41372433 TAATAGTTTTGACTTTTAACT
1 TAATAGTTTTGACTTTTAACT
41372454 ATAAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (21 bp):
TAATAGTTTTGACTTTTAACT
Found at i:41373622 original size:29 final size:31
Alignment explanation
Indices: 41373552--41373627 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 31
41373542 AAAAAAAAAA
*
41373552 TTTATCAACTTTTAAGGGGCTCCAAAATTTT
1 TTTATCAACTTTTAAGAGGCTCCAAAATTTT
*
41373583 TTT-T-AGCTTTTAA-AGGC-CCAAAATTTT
1 TTTATCAACTTTTAAGAGGCTCCAAAATTTT
*
41373610 TTTATCAATTTTTAAGAG
1 TTTATCAACTTTTAAGAG
41373628 ACCTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 13 0.34
28 4 0.11
29 15 0.39
30 3 0.08
31 3 0.08
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (31 bp):
TTTATCAACTTTTAAGAGGCTCCAAAATTTT
Found at i:41380426 original size:6 final size:6
Alignment explanation
Indices: 41380415--41380471 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
41380405 AAGAAATGAA
* * *
41380415 TTTATG TTTATG TTTATG TTTATG TTTGTTTG TTTATT TTTAAG -TT-TG
1 TTTATG TTTATG TTTATG TTTATG -TT-TATG TTTATG TTTATG TTTATG
41380463 TTTATG TTT
1 TTTATG TTT
41380472 CTTAAGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 1 0.02
5 4 0.10
6 29 0.71
7 4 0.10
8 3 0.07
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (6 bp):
TTTATG
Found at i:41380450 original size:20 final size:20
Alignment explanation
Indices: 41380425--41380465 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41380415 TTTATGTTTA
*
41380425 TGTTTATGTTTATGTTTGTT
1 TGTTTATGTTTAAGTTTGTT
*
41380445 TGTTTATTTTTAAGTTTGTT
1 TGTTTATGTTTAAGTTTGTT
41380465 T
1 T
41380466 ATGTTTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71
Consensus pattern (20 bp):
TGTTTATGTTTAAGTTTGTT
Found at i:41381294 original size:18 final size:18
Alignment explanation
Indices: 41381271--41381307 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41381261 AAATTGAATT
*
41381271 AATTCGGTTAACCGATCG
1 AATTCGATTAACCGATCG
*
41381289 AATTCGATTAACCGGTCG
1 AATTCGATTAACCGATCG
41381307 A
1 A
41381308 TTAACCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
AATTCGATTAACCGATCG
Found at i:41382281 original size:17 final size:17
Alignment explanation
Indices: 41382233--41382281 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 17
41382223 AAAAAAAACC
41382233 TTTA-AAAAATA-TTTT
1 TTTATAAAAATACTTTT
41382248 TTT-TAAAAAGTTCACTTTT
1 TTTATAAAAA--T-ACTTTT
41382267 TTTATAAAAATACTT
1 TTTATAAAAATACTT
41382282 AAGATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 8 0.29
17 5 0.18
18 2 0.07
19 7 0.25
20 6 0.21
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTATAAAAATACTTTT
Found at i:41382387 original size:22 final size:22
Alignment explanation
Indices: 41382362--41382403 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41382352 TGTAAAAGAT
* *
41382362 ATATAAAATTTTATAAAAATAC
1 ATATAAAATTATAAAAAAATAC
41382384 ATATAAAATTATAAAAAAAT
1 ATATAAAATTATAAAAAAAT
41382404 TGTTGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAAAATTATAAAAAAATAC
Found at i:41382807 original size:21 final size:21
Alignment explanation
Indices: 41382783--41382845 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
41382773 AAACCCTTTT
41382783 AAAAACTTAAAAATTATTAAA
1 AAAAACTTAAAAATTATTAAA
*
41382804 AAAATCTTAAAAATTA-TAAA
1 AAAAACTTAAAAATTATTAAA
* * *
41382824 CACAATTTATAAAATT-TTAAA
1 AAAAACTTA-AAAATTATTAAA
41382845 A
1 A
41382846 TTATAAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAACTTAAAAATTATTAAA
Found at i:41386714 original size:73 final size:75
Alignment explanation
Indices: 41386623--41386767 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
41386613 AAAACAGAGG
* *
41386623 TTAAAGTGTAAATTTATTATATA-TTAGTTTATAAGTTATT-TATTTACT-AGAAGATTAAATT-
1 TTAAAGTGTAAATTTATTATATAGTTAATTTATAA-TTATTCTATTTA-TAAGAAAATTAAATTG
41386684 AAAATTTTAGGT
64 AAAATTTTAGGT
* *
41386696 TTAAAGTGTAATTTTATTATATATGTTAATTTATAATTTTTCTATTTATAAGAAAATTAAATTGA
1 TTAAAGTGTAAATTTATTATATA-GTTAATTTATAATTATTCTATTTATAAGAAAATTAAATTGA
41386761 AAATTTT
65 AAATTTT
41386768 TAATTTTAGG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
73 22 0.35
74 5 0.08
75 28 0.44
76 8 0.13
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (75 bp):
TTAAAGTGTAAATTTATTATATAGTTAATTTATAATTATTCTATTTATAAGAAAATTAAATTGAA
AATTTTAGGT
Found at i:41389079 original size:15 final size:16
Alignment explanation
Indices: 41389052--41389083 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41389042 AAATAAGGTT
41389052 AAAATAAACACAAAAA
1 AAAATAAACACAAAAA
41389068 AAAATAAA-ACAAAAA
1 AAAATAAACACAAAAA
41389083 A
1 A
41389084 GGGTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAATAAACACAAAAA
Found at i:41389748 original size:30 final size:29
Alignment explanation
Indices: 41389709--41389961 Score: 248
Period size: 30 Copynumber: 8.5 Consensus size: 29
41389699 TTTTATTTAG
41389709 AAATTATATTTTGACCCTAAACTTTCCAA
1 AAATTATATTTTGACCCTAAACTTTCCAA
*
41389738 ATATTCATA-TTTGACCCCTAAACTTTCCAA
1 AAATT-ATATTTTGA-CCCTAAACTTTCCAA
* *
41389768 ATATTCATA-TTTAACCCTCAAACTTTCCAA
1 AAATT-ATATTTTGACCCT-AAACTTTCCAA
* * *
41389798 AAATTATGTTTTGACCCCTAAAATTTTCAA
1 AAATTATATTTTGA-CCCTAAACTTTCCAA
* *
41389828 AAATTATGTTTTGACCCCTAAAATTTCCAA
1 AAATTATATTTTGA-CCCTAAACTTTCCAA
*
41389858 AAATTA-AGTTTTGACCCCCAAACTTTCCAA
1 AAATTATA-TTTTGA-CCCTAAACTTTCCAA
**
41389888 AAATTA-AGACTTGACCTCTAAACTTTCCAA
1 AAATTATA-TTTTGACC-CTAAACTTTCCAA
41389918 AAATTATATTTTGACACC-AAACTTTCCAA
1 AAATTATATTTTGAC-CCTAAACTTTCCAA
*
41389947 AATTTCAT-TTTTGAC
1 AAATT-ATATTTTGAC
41389962 TCCATTTTTC
Statistics
Matches: 197, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
29 39 0.20
30 152 0.77
31 6 0.03
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (29 bp):
AAATTATATTTTGACCCTAAACTTTCCAA
Found at i:41389880 original size:90 final size:89
Alignment explanation
Indices: 41389709--41389948 Score: 288
Period size: 90 Copynumber: 2.7 Consensus size: 89
41389699 TTTTATTTAG
* * * *
41389709 AAATTATATTTTGA-CCCTAAACTTTCCAAATATTCATATTTGACCCCTAAACTTTCCAAATATT
1 AAATTATGTTTTGACCCCTAAACTTTCCAAAAATT-ATTTTTGACCCCTAAACTTTCCAAAAATT
* *
41389773 CATATTTAACCCTCAAACTTTCCAA
65 AATATTTAACCCCCAAACTTTCCAA
* * *
41389798 AAATTATGTTTTGACCCCTAAAATTTTCAAAAATTATGTTTTGACCCCTAAAATTTCCAAAAATT
1 AAATTATGTTTTGACCCCTAAACTTTCCAAAAATTAT-TTTTGACCCCTAAACTTTCCAAAAATT
*
41389863 AAGT-TTTGACCCCCAAACTTTCCAA
65 AA-TATTTAACCCCCAAACTTTCCAA
* ** * *
41389888 AAATTAAGACTTGACCTCTAAACTTTCCAAAAATTATATTTTGACACC-AAACTTTCCAAAA
1 AAATTATGTTTTGACCCCTAAACTTTCCAAAAATTAT-TTTTGACCCCTAAACTTTCCAAAA
41389949 TTTCATTTTT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
89 27 0.21
90 101 0.78
91 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (89 bp):
AAATTATGTTTTGACCCCTAAACTTTCCAAAAATTATTTTTGACCCCTAAACTTTCCAAAAATTA
ATATTTAACCCCCAAACTTTCCAA
Found at i:41391273 original size:18 final size:17
Alignment explanation
Indices: 41391250--41391302 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
41391240 TATAAATTGA
41391250 TTATTTGAATTTAATAAT
1 TTATTT-AATTTAATAAT
*
41391268 TTATTTTAAATTAATTAAT
1 TTA-TTTAATTTAA-TAAT
* *
41391287 TAATTTAATTTGATAA
1 TTATTTAATTTAATAA
41391303 CTCATATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 17 0.59
19 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
TTATTTAATTTAATAAT
Found at i:41391883 original size:43 final size:43
Alignment explanation
Indices: 41391767--41391945 Score: 192
Period size: 43 Copynumber: 4.3 Consensus size: 43
41391757 TTATGCGGAA
*
41391767 AAGCG-CAGCTAAAGGCCTTGTTCTTTAGCGGCGCTTT-TCCCAC
1 AAGCGCCA-CTAAAGGCCATGTTCTTTAGCGGCGCTTTCT-CCAC
*
41391810 AAGCGCCGCT-AA----ATGTTCTTTAGCGGCGCTTTCTCCAC
1 AAGCGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
* *
41391848 AAGCGTCACTAAAGGCCATGTTCTTTAGTGGCGCTTTCTCCAC
1 AAGCGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
* * * * * *
41391891 AAACGCCGCTAAAGACCATGTTCTTTATCGACGCTTTCTCCAA
1 AAGCGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
*
41391934 AAGCGCCGCTAA
1 AAGCGCCACTAA
41391946 TATAACAGAT
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
38 31 0.27
39 3 0.03
42 2 0.02
43 78 0.68
44 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (43 bp):
AAGCGCCACTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAC
Found at i:41392034 original size:15 final size:15
Alignment explanation
Indices: 41392014--41392042 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41392004 CCTATAAATT
41392014 CAAATCCAACCAATG
1 CAAATCCAACCAATG
41392029 CAAATCCAACCAAT
1 CAAATCCAACCAAT
41392043 AACTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:41392375 original size:66 final size:66
Alignment explanation
Indices: 41392264--41392417 Score: 227
Period size: 66 Copynumber: 2.3 Consensus size: 66
41392254 GCTTGCCTCG
* * * * *
41392264 CTGCTGCCTCCACTTTAAGTTGTGGGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTC
41392329 A
66 A
* *
41392330 CTGCAGCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTC
*
41392395 G
66 A
*
41392396 TTGCAGCCTCCTCTTTAAGTTG
1 CTGCAGCCTCCTCTTTAAGTTG
41392418 AGCAATTTGC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (66 bp):
CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTC
A
Found at i:41394881 original size:20 final size:20
Alignment explanation
Indices: 41394853--41394897 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
41394843 GTAATCTTTG
*
41394853 AGAGCGTAAACGAGATCTCA
1 AGAGTGTAAACGAGATCTCA
41394873 AGAGTGTAAACGAGATCTCA
1 AGAGTGTAAACGAGATCTCA
41394893 AGAGT
1 AGAGT
41394898 TGTTTATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.18
Consensus pattern (20 bp):
AGAGTGTAAACGAGATCTCA
Found at i:41397816 original size:31 final size:33
Alignment explanation
Indices: 41397774--41397840 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
41397764 TTGATTTAAA
41397774 TTTAAAA-ATATATATTAGTGACAACATTTTAC
1 TTTAAAATATATATATTAGTGACAACATTTTAC
41397806 TTTAAAATATATATATTAGTGACAACATTTTAC
1 TTTAAAATATATATATTAGTGACAACATTTTAC
41397839 TT
1 TT
41397841 AAATATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
TTTAAAATATATATATTAGTGACAACATTTTAC
Found at i:41397875 original size:8 final size:8
Alignment explanation
Indices: 41397862--41397927 Score: 61
Period size: 8 Copynumber: 8.8 Consensus size: 8
41397852 TTGTTTTTAT
41397862 TAATTAAA
1 TAATTAAA
41397870 TAATTAAA
1 TAATTAAA
41397878 TAATT-AA
1 TAATTAAA
*
41397885 T--TTAGTA
1 TAATTA-AA
*
41397892 TAATGAAA
1 TAATTAAA
*
41397900 TAATTAAT
1 TAATTAAA
41397908 TAATT-AA
1 TAATTAAA
41397915 -AATTAAA
1 TAATTAAA
41397922 TAATTA
1 TAATTA
41397928 TATATATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
5 2 0.04
6 4 0.09
7 8 0.17
8 30 0.65
9 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (8 bp):
TAATTAAA
Done.