Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 160 of 190
Found at i:46625499 original size:15 final size:16
Alignment explanation
Indices: 46625479--46625512 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46625469 ACTAAAGTTC
*
46625479 AACTTTAGATTTAT-A
1 AACTTTAAATTTATCA
46625494 AACTTTAAATTTATCA
1 AACTTTAAATTTATCA
46625510 AAC
1 AAC
46625513 GCTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (16 bp):
AACTTTAAATTTATCA
Found at i:46633346 original size:9 final size:9
Alignment explanation
Indices: 46633332--46633362 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46633322 GTTAAACGAA
46633332 TCGAGTTAT
1 TCGAGTTAT
*
46633341 TCGAGTTAA
1 TCGAGTTAT
46633350 TCGAGTTAT
1 TCGAGTTAT
46633359 TCGA
1 TCGA
46633363 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:46633433 original size:9 final size:9
Alignment explanation
Indices: 46633416--46633452 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46633406 TGAGTTTTCA
46633416 AATTCGAAT
1 AATTCGAAT
*
46633425 AACTCGAAT
1 AATTCGAAT
46633434 AATTCGAAT
1 AATTCGAAT
46633443 AATTCGAAT
1 AATTCGAAT
46633452 A
1 A
46633453 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:46633713 original size:30 final size:30
Alignment explanation
Indices: 46633665--46633722 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
46633655 AAACCTTTTA
* *
46633665 TTTTCTCCCAAAATTTTTACTCCTTTCCGC
1 TTTTCTCCCAAAACTTTTACTCCCTTCCGC
*
46633695 TTTTC-CCCTAAAACTTTTATTCCCTTCC
1 TTTTCTCCC-AAAACTTTTACTCCCTTCC
46633723 CATCCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.17, C:0.34, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTTCTCCCAAAACTTTTACTCCCTTCCGC
Found at i:46642132 original size:21 final size:21
Alignment explanation
Indices: 46642108--46642147 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46642098 TCTTTTCATA
* *
46642108 TTAATTTCATGTATCATTTAC
1 TTAACTTCATATATCATTTAC
46642129 TTAACTTCATATATCATTT
1 TTAACTTCATATATCATTT
46642148 CATAAATATG
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:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAACTTCATATATCATTTAC
Found at i:46643539 original size:172 final size:172
Alignment explanation
Indices: 46643008--46643539 Score: 445
Period size: 172 Copynumber: 3.0 Consensus size: 172
46642998 CTCTTCACTA
* * *
46643008 AATTTTCTCCTATTTCATTGCTCAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACT
1 AATTTTCCCCTATTGCATTGCTTAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACT
46643073 GTACATAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAAC
66 GTACATAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAAC
*
46643138 ATATAAAGTTTAGCTCGTAATTATTTTTGTACAATTTTTAAC
131 ATATAAATTTTAGCTCGTAATTATTTTTGTACAATTTTTAAC
** * * * * **
46643180 AATTTT-CCAGAGTTAGAATACGGGATTCCAAATTCA-TTATGACC-CTGTCTCACTAAACTTGT
1 AATTTTCCCCTA-TT-GCAT---TGCTT---AA-T-AGTTATGACCTCTCT-TCACTAAAAAT-T
*** * * *** * * * * *
46643242 AA-TATCTCAAAATATATAACTCTTTTGCTTAC-TCTGTTTCTTTTA-TGTAAAAATAGACTCAT
54 AATTATCTCACTGTACATAATTCAGATG-GTACTTATGTTTATTTCAGT-TGAAAATAGACTCAT
* ** ** * * *** ** * ***
46643304 TAAACTTTC-ATTTCATAT--CTTATTCA-CTCTCTAATTCGATTTCCACCATTTTTGGT
117 TCAAGGTTCTA-AACATATAAATT-TT-AGCTC-GTAATTATTTTTGTACAATTTTTAAC
*
46643360 GATTTTCCCCTATTGCATTGCTTAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACT
1 AATTTTCCCCTATTGCATTGCTTAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACT
*
46643425 GTACAGAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAAC
66 GTACATAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAAC
46643490 ATATAAATTTTAGCTCGTAATTATTTTTGTACAATTTTTAAC
131 ATATAAATTTTAGCTCGTAATTATTTTTGTACAATTTTTAAC
46643532 AATTTTCC
1 AATTTTCC
46643540 AGAGTTAGAA
Statistics
Matches: 251, Mismatches: 81, Indels: 56
0.65 0.21 0.14
Matches are distributed among these distances:
171 9 0.04
172 101 0.40
173 14 0.06
174 2 0.01
176 5 0.02
178 1 0.00
179 15 0.06
180 94 0.37
181 10 0.04
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (172 bp):
AATTTTCCCCTATTGCATTGCTTAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACT
GTACATAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAAC
ATATAAATTTTAGCTCGTAATTATTTTTGTACAATTTTTAAC
Found at i:46643667 original size:352 final size:352
Alignment explanation
Indices: 46643009--46643717 Score: 1319
Period size: 352 Copynumber: 2.0 Consensus size: 352
46642999 TCTTCACTAA
* *
46643009 ATTTTCTCCTATTTCATTGCTCAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACTG
1 ATTTTCCCCTATTGCATTGCTCAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACTG
*
46643074 TACATAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAACA
66 TACAGAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAACA
46643139 TATAAAGTTTAGCTCGTAATTATTTTTGTACAATTTTTAACAATTTTCCAGAGTTAGAATACGGG
131 TATAAAGTTTAGCTCGTAATTATTTTTGTACAATTTTTAACAATTTTCCAGAGTTAGAATACGGG
*
46643204 ATTCCAAATTCATTATGACCCTGTCTCACTAAACTTGTAATATCTCAAAATATATAACTCTTTTG
196 ATTCCAAATTCATTATGACCCTGTCTCACTAAACTTATAATATCTCAAAATATATAACTCTTTTG
* * *
46643269 CTTACTCTGTTTCTTTTATGTAAAAATAGACTCATTAAACTTTCATTTCATATCTTATTCACTCT
261 CTTACTCTATTTCTTTTATGTAAAAATAGACACATTAAAATTTCATTTCATATCTTATTCACTCT
*
46643334 CTAATTCGATTTCCACCATTTTTGGTG
326 CTAATTCAATTTCCACCATTTTTGGTG
*
46643361 ATTTTCCCCTATTGCATTGCTTAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACTG
1 ATTTTCCCCTATTGCATTGCTCAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACTG
46643426 TACAGAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAACA
66 TACAGAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAACA
* *
46643491 TATAAATTTTAGCTCGTAATTATTTTTGTACAATTTTTAACAATTTTCCAGAGTTAGAATATGGG
131 TATAAAGTTTAGCTCGTAATTATTTTTGTACAATTTTTAACAATTTTCCAGAGTTAGAATACGGG
46643556 ATTCCAAATTCATTATGACCCTGTCTCACTAAACTTATAATATCTCAAAATATATAACTCTTTTG
196 ATTCCAAATTCATTATGACCCTGTCTCACTAAACTTATAATATCTCAAAATATATAACTCTTTTG
46643621 CTTACTCTATTTCTTTTATGTAAAAATAGACACATTAAAATTTCATTTCATATCTTATTCACTCT
261 CTTACTCTATTTCTTTTATGTAAAAATAGACACATTAAAATTTCATTTCATATCTTATTCACTCT
46643686 CTAATTCAATTTCCACCATTTTTGGTG
326 CTAATTCAATTTCCACCATTTTTGGTG
46643713 ATTTT
1 ATTTT
46643718 TCAAAGTCAT
Statistics
Matches: 346, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
352 346 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (352 bp):
ATTTTCCCCTATTGCATTGCTCAATAGTTATGACCTCTCTTCACTAAAAATTAATTATCTCACTG
TACAGAATTCAGATGGTACTTATGTTTATTTCAGTTGAAAATAGACTCATTCAAGGTTCTAAACA
TATAAAGTTTAGCTCGTAATTATTTTTGTACAATTTTTAACAATTTTCCAGAGTTAGAATACGGG
ATTCCAAATTCATTATGACCCTGTCTCACTAAACTTATAATATCTCAAAATATATAACTCTTTTG
CTTACTCTATTTCTTTTATGTAAAAATAGACACATTAAAATTTCATTTCATATCTTATTCACTCT
CTAATTCAATTTCCACCATTTTTGGTG
Found at i:46643970 original size:23 final size:23
Alignment explanation
Indices: 46643944--46644042 Score: 117
Period size: 23 Copynumber: 4.3 Consensus size: 23
46643934 ATAAGTGCCA
46643944 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
46643967 CACTGATACGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
46643990 CATTGAAATGTAGCTGAAACTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
46644013 CACTAATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
46644036 CACTGAT
1 CACTGAT
46644043 CAATAACACT
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:46645512 original size:17 final size:17
Alignment explanation
Indices: 46645474--46645513 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
46645464 TAACACAGAG
* *
46645474 TAAGCTTTTAAGCTTAG
1 TAAGTTTTTAAGCTTAA
46645491 TAAGTTTTTAAGCTTAA
1 TAAGTTTTTAAGCTTAA
46645508 TAAGTT
1 TAAGTT
46645514 CGTATAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (17 bp):
TAAGTTTTTAAGCTTAA
Found at i:46645933 original size:25 final size:25
Alignment explanation
Indices: 46645905--46646043 Score: 120
Period size: 25 Copynumber: 5.6 Consensus size: 25
46645895 TGTAAACAAT
* * *
46645905 AAGCTCTTCCGAGCTATATAACGGG
1 AAGCTCATGCGAGCTATATAACGAG
* *
46645930 AAGCTCATGTGAGCTAAATAACGAG
1 AAGCTCATGCGAGCTATATAACGAG
* *
46645955 AAGCTCATGCGAGCTGTATATCGAG
1 AAGCTCATGCGAGCTATATAACGAG
** **
46645980 AAGCTCATAAGAGCTGA-A-ATTGAG
1 AAGCTCATGCGAGCT-ATATAACGAG
* * *
46646004 AAGCTCATGCGAGCTAAATATCGGG
1 AAGCTCATGCGAGCTATATAACGAG
*
46646029 AAGCTCATGAGAGCT
1 AAGCTCATGCGAGCT
46646044 GTGGTGTGTC
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
23 1 0.01
24 19 0.20
25 73 0.78
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.22
Consensus pattern (25 bp):
AAGCTCATGCGAGCTATATAACGAG
Found at i:46646657 original size:27 final size:27
Alignment explanation
Indices: 46646623--46646676 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
46646613 TCTCTTTACA
46646623 AAAGTTGTTTATCTAACACCAACCTTT
1 AAAGTTGTTTATCTAACACCAACCTTT
*
46646650 AAAGTTGTTTATCTAACATCAACCTTT
1 AAAGTTGTTTATCTAACACCAACCTTT
46646677 CATTTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.39
Consensus pattern (27 bp):
AAAGTTGTTTATCTAACACCAACCTTT
Found at i:46648989 original size:28 final size:28
Alignment explanation
Indices: 46648957--46649029 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
46648947 TAATGAGATT
* *
46648957 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
46648985 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
46649013 AGCACTAAGTGTGCGAG
1 AGCACTAAGTGTGCGAG
46649030 CTTATTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:46649780 original size:23 final size:22
Alignment explanation
Indices: 46649754--46649937 Score: 134
Period size: 23 Copynumber: 7.8 Consensus size: 22
46649744 CAATTTGGTA
*
46649754 TATATATGCTGCCTAAATTATTG
1 TATATATGCTGCC-AAATTGTTG
* *
46649777 TATATATGCTGTCCAATTTTGATG
1 TATATATGCTG-CCAA-ATTGTTG
* * * * * *
46649801 TAAAAATGTTGCTCAATTTGGTA
1 TATATATGCTGC-CAAATTGTTG
*
46649824 TATATATGCTGCCCAATTTGTTG
1 TATATATGCTG-CCAAATTGTTG
*
46649847 TATATATGCTGTCCAATATTTGGTG
1 TATATATGCTG-CCAA-A-TTGTTG
* * *
46649872 TAAAAATGCTGCTCAATTTTGTTG
1 TATATATGCTGC-CAA-ATTGTTG
46649896 TATATATGCTGCCCAAATTGTTG
1 TATATATGCTG-CCAAATTGTTG
46649919 TATATATGCTGTCCAAATT
1 TATATATGCTG-CCAAATT
46649938 TTGGTGTGAA
Statistics
Matches: 129, Mismatches: 24, Indels: 16
0.76 0.14 0.09
Matches are distributed among these distances:
23 74 0.57
24 36 0.28
25 19 0.15
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (22 bp):
TATATATGCTGCCAAATTGTTG
Found at i:46649802 original size:70 final size:70
Alignment explanation
Indices: 46649722--46649993 Score: 368
Period size: 70 Copynumber: 3.8 Consensus size: 70
46649712 TGTTCATGTT
* *
46649722 ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCTAAATTATTGTATATATGCT
1 ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCT
46649787 GTCCA
66 GTCCA
*
46649792 ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCT
1 ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCT
46649857 GTCCA
66 GTCCA
* * * *
46649862 ATATTTGGTGTAAAAATGCTGCTCAATTTTGTTGTATATATGCTGCCCAAATTGTTGTATATATG
1 AT-TTTGATGTAAAAATGTTGCTCAA-TTTGGTATATATATGCTGCCCAAATTGTTGTATATATG
46649927 CTGTCCAA
64 CTGTCC-A
* * * * * *
46649935 ATTTTGGTGTGAAAATGTTG-TCTAGTTTGGTATATA-AGGGCTGTCCAAATTGATGTATA
1 ATTTTGATGTAAAAATGTTGCTC-AATTTGGTATATATA-TGCTGCCCAAATTGTTGTATA
46649994 AGGGCTGTCC
Statistics
Matches: 181, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
70 70 0.39
71 50 0.28
72 58 0.32
73 3 0.02
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (70 bp):
ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCT
GTCCA
Found at i:46659421 original size:17 final size:17
Alignment explanation
Indices: 46659399--46659533 Score: 63
Period size: 17 Copynumber: 7.4 Consensus size: 17
46659389 ATTAAATCAC
46659399 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
46659416 TACATAAATATTTGAATCAC
1 TACAT-AAT-TAAAAAT-AT
46659436 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
* *** *
46659453 TAAATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
46659473 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
46659490 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
46659510 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
46659527 TACATAA
1 TACATAA
46659534 GTCTTGAATT
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
17 28 0.34
18 16 0.20
19 17 0.21
20 21 0.26
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:46659439 original size:37 final size:37
Alignment explanation
Indices: 46659393--46659558 Score: 264
Period size: 37 Copynumber: 4.5 Consensus size: 37
46659383 ACCCGAATTA
* *
46659393 AATCACTACATAATTAAAAATATTACATAAATATTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
46659430 AATCACTACATAATTAAAAATATTAAATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
46659467 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
46659504 AATCACTACATAATTAAAAACATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
46659540 AATTAAC-ACATAATTAAAA
1 AA-TCACTACATAATTAAAA
46659559 TATAAGTATT
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
36 17 0.14
37 105 0.86
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:46659515 original size:20 final size:20
Alignment explanation
Indices: 46659456--46659516 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
46659446 AAAATATTAA
46659456 ATAAGTCTTTGAATCACTAC
1 ATAAGTCTTTGAATCACTAC
*** *
46659476 ATAA-T-TAAAAAT-ATTAC
1 ATAAGTCTTTGAATCACTAC
46659493 ATAAGTCTTTGAATCACTAC
1 ATAAGTCTTTGAATCACTAC
46659513 ATAA
1 ATAA
46659517 TTAAAAACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 8 0.27
18 5 0.17
19 5 0.17
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (20 bp):
ATAAGTCTTTGAATCACTAC
Found at i:46661979 original size:20 final size:20
Alignment explanation
Indices: 46661954--46661995 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
46661944 CTGCAAGAAA
*
46661954 AAAAAAGTCTATAATAAATT
1 AAAAAAGTATATAATAAATT
46661974 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
46661994 AA
1 AA
46661996 TCAGCATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGTATATAATAAATT
Found at i:46664756 original size:50 final size:49
Alignment explanation
Indices: 46664702--46664916 Score: 191
Period size: 50 Copynumber: 4.3 Consensus size: 49
46664692 ATGTAATGGA
* ** * *
46664702 AAGCTCATGTGAGCTGTATAACGGGAAGCTCTTGCGAGCTAATTATCGGG
1 AAGCTCATGAGAGCCATATAACGGGAAGCTCATGAGAGC-AATTATCGGG
* * * * *
46664752 AAGCTTAT-ACGAGCCATA-AATGGGAAGCTCATGCGAGCAAAATATCAGG
1 AAGCTCATGA-GAGCCATATAACGGGAAGCTCATGAGAGC-AATTATCGGG
* * * *
46664801 AAGCTCGTGAGAGCCATATAACGGGAAGCTTAAGAGAGCCATTAATCGGG
1 AAGCTCATGAGAGCCATATAACGGGAAGCTCATGAGAGCAATT-ATCGGG
* * * * *
46664851 AAGCTCATGAGAGCTAAATAACAGAAAGCTCATGAGAGCCAAGTATCGGG
1 AAGCTCATGAGAGCCATATAACGGGAAGCTCATGAGAG-CAATTATCGGG
*
46664901 AAGCTCGTGAGAGCCA
1 AAGCTCATGAGAGCCA
46664917 AATATCAGGA
Statistics
Matches: 131, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
49 42 0.32
50 86 0.66
51 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (49 bp):
AAGCTCATGAGAGCCATATAACGGGAAGCTCATGAGAGCAATTATCGGG
Found at i:46664880 original size:75 final size:74
Alignment explanation
Indices: 46664687--46664905 Score: 235
Period size: 74 Copynumber: 2.9 Consensus size: 74
46664677 AAGCTCTTCC
* * ** * * * * *
46664687 GAGCCATGTAATGGAAAGCTCATGTGAGCTGTATAACGGGAAGCTCTTGCGAGCTAATTATCGGG
1 GAGCCAT-TAATGGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCAAGTATCGGG
*
46664752 AAGCTTATAC
65 AAGCTTATAA
* * * * * *
46664762 GAGCCATAAATGGGAAGCTCATGCGAGCAAAATATCAGGAAGCTCGTGAGAGCCATA-TAACGGG
1 GAGCCATTAATGGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCA-AGTATCGGG
46664826 AAGCTTA-AGA
65 AAGCTTATA-A
*
46664836 GAGCCATTAATCGGGAAGCTCATGAGAGCTAAATAACAGAAAGCTCATGAGAGCCAAGTATCGGG
1 GAGCCATTAAT-GGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCAAGTATCGGG
46664901 AAGCT
65 AAGCT
46664906 CGTGAGAGCC
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
73 1 0.01
74 61 0.51
75 58 0.48
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (74 bp):
GAGCCATTAATGGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCAAGTATCGGGA
AGCTTATAA
Found at i:46664911 original size:25 final size:25
Alignment explanation
Indices: 46664723--46664922 Score: 165
Period size: 25 Copynumber: 8.0 Consensus size: 25
46664713 AGCTGTATAA
* * * *
46664723 CGGGAAGCTCTTGCGAGCTAATTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
*
46664748 CGGGAAGCTTAT-ACGAGCCATAA-AT
1 CGGGAAGCTCATGA-GAGCCA-AATAT
* *
46664773 -GGGAAGCTCATGCGAGCAAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * *
46664797 CAGGAAGCTCGTGAGAGCCATATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* * *
46664822 CGGGAAGCTTAAGAGAGCC-ATTAAT
1 CGGGAAGCTCATGAGAGCCAAAT-AT
* *
46664847 CGGGAAGCTCATGAGAGCTAAATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* * *
46664872 CAGAAAGCTCATGAGAGCCAAGTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
*
46664897 CGGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
46664922 C
1 C
46664923 AGGACACTCA
Statistics
Matches: 133, Mismatches: 35, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
23 2 0.02
24 18 0.14
25 110 0.83
26 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAT
Found at i:46664913 original size:75 final size:73
Alignment explanation
Indices: 46664687--46664916 Score: 237
Period size: 75 Copynumber: 3.1 Consensus size: 73
46664677 AAGCTCTTCC
* * ** * * * *
46664687 GAGCCATGTAATGGAAAGCTCATGTGAGCTGTATAACGGGAAGCTCTTGCGAGCTAATTATCGGG
1 GAGCCAT-TAATGGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCAA-TATCGGG
46664752 AAGCTTAT-A
64 AAGCTTATGA
* * * * * *
46664761 CGAGCCATAAATGGGAAGCTCATGCGAGCAAAATATCAGGAAGCTCGTGAGAGCCATATAACGGG
1 -GAGCCATTAATGGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCA-ATATCGGG
*
46664826 AAGCTTAAGA
64 AAGCTTATGA
*
46664836 GAGCCATTAATCGGGAAGCTCATGAGAGCTAAATAACAGAAAGCTCATGAGAGCCAAGTATCGGG
1 GAGCCATTAAT-GGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCAA-TATCGGG
**
46664901 AAGCTCGTGA
64 AAGCTTATGA
46664911 GAGCCA
1 GAGCCA
46664917 AATATCAGGA
Statistics
Matches: 128, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
74 61 0.48
75 67 0.52
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (73 bp):
GAGCCATTAATGGGAAGCTCATGAGAGCTAAATAACAGGAAGCTCATGAGAGCCAATATCGGGAA
GCTTATGA
Found at i:46669714 original size:14 final size:14
Alignment explanation
Indices: 46669695--46669721 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46669685 AGTTTTGGAT
46669695 AAAAATTAAATATC
1 AAAAATTAAATATC
46669709 AAAAATTAAATAT
1 AAAAATTAAATAT
46669722 TTTATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAATTAAATATC
Found at i:46670156 original size:51 final size:50
Alignment explanation
Indices: 46670094--46670220 Score: 168
Period size: 51 Copynumber: 2.5 Consensus size: 50
46670084 AAAATTTTTT
**
46670094 AAAAATTAAAAAAGTATTTTAAAAATATTTTTAAAATATT-TTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATA-TTTTAAAAT-TTAAAAAAATTAAA
46670145 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAA
1 AAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAA
*
46670196 AAAGTATGTAAAAAA-TATTTTAAAA
1 AAA-AAT-TAAAAAAGTATTTTAAAA
46670221 TTAAAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
50 2 0.03
51 38 0.55
52 28 0.41
53 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (50 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAA
Found at i:46670158 original size:40 final size:40
Alignment explanation
Indices: 46670078--46670229 Score: 189
Period size: 41 Copynumber: 3.8 Consensus size: 40
46670068 GACCCATTTT
* * **
46670078 TATTTT-AAAATTTTTTAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATATTTT-AAAATTAAAAAA-AATTAAAAAAA
*
46670119 TATTTTTAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
* *
46670159 GTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAG
1 -TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
* *
46670200 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAA
46670230 TAAATATATT
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 35 0.35
41 55 0.56
42 9 0.09
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
Found at i:46670221 original size:10 final size:11
Alignment explanation
Indices: 46670078--46670180 Score: 69
Period size: 11 Copynumber: 9.9 Consensus size: 11
46670068 GACCCATTTT
46670078 TATTTT-AAAA
1 TATTTTAAAAA
*
46670088 T-TTTTTAAAA
1 TATTTTAAAAA
*
46670098 -A-TTAAAAAA
1 TATTTTAAAAA
46670107 GTATTTTAAAAA
1 -TATTTTAAAAA
*
46670119 TATTTTTAAAA
1 TATTTTAAAAA
46670130 TATTTT--AAA
1 TATTTTAAAAA
*
46670139 -A-TTAAAAAA
1 TATTTTAAAAA
* **
46670148 AATTAAAAAAA
1 TATTTTAAAAA
46670159 GTATTTTAAAAA
1 -TATTTTAAAAA
46670171 TATTTTAAAA
1 TATTTTAAAA
46670181 TTTAAAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
7 2 0.03
8 1 0.01
9 16 0.22
10 6 0.08
11 34 0.46
12 15 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:46673892 original size:25 final size:25
Alignment explanation
Indices: 46673844--46673893 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
46673834 AACTCAAAAT
* * *
46673844 CCCAAGCCCGAGCCCGAACTCGAAC
1 CCCAAACCCAAGCCCGAACCCGAAC
*
46673869 CCCAAACCCAAGCCCGAGCCCGAAC
1 CCCAAACCCAAGCCCGAACCCGAAC
46673894 TCGAACCTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.30, C:0.50, G:0.18, T:0.02
Consensus pattern (25 bp):
CCCAAACCCAAGCCCGAACCCGAAC
Found at i:46674884 original size:21 final size:21
Alignment explanation
Indices: 46674841--46674886 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
46674831 GATGAAGGAT
* *
46674841 GAAAACATGAAGCAAAGCGAC
1 GAAAACACGAAGCAAAGCAAC
*
46674862 GAAAACACGAAGCAAAGTAAC
1 GAAAACACGAAGCAAAGCAAC
46674883 GAAA
1 GAAA
46674887 TCCCCCCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.17, G:0.22, T:0.04
Consensus pattern (21 bp):
GAAAACACGAAGCAAAGCAAC
Found at i:46677826 original size:6 final size:6
Alignment explanation
Indices: 46677815--46677849 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
46677805 TCATTATTGT
* *
46677815 AAATAA AAATAA AAATAA AAATCA AAATCA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA
46677850 TATTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:46681545 original size:21 final size:21
Alignment explanation
Indices: 46681519--46681561 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
46681509 TTTGGGTTGA
46681519 TCAGCTCTCAAGAGCTTCTGT
1 TCAGCTCTCAAGAGCTTCTGT
46681540 TCAGCTCTCAAGAGCTTCTGT
1 TCAGCTCTCAAGAGCTTCTGT
46681561 T
1 T
46681562 GGCGTGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (21 bp):
TCAGCTCTCAAGAGCTTCTGT
Found at i:46683145 original size:22 final size:22
Alignment explanation
Indices: 46683120--46683163 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
46683110 GATAATAAGT
46683120 AAAAA-AAAAACTAGAAAAACTA
1 AAAAATAAAAACTA-AAAAACTA
**
46683142 AAAAATTGAAACTAAAAAACTA
1 AAAAATAAAAACTAAAAAACTA
46683164 GTATTAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAACTAAAAAACTA
Found at i:46683370 original size:18 final size:18
Alignment explanation
Indices: 46683333--46683368 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46683323 TTAAAATCAT
*
46683333 ATAAAAGGATATAAATAA
1 ATAAAACGATATAAATAA
46683351 ATAAAACGATAT-AATAA
1 ATAAAACGATATAAATAA
46683368 A
1 A
46683369 ATGAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (18 bp):
ATAAAACGATATAAATAA
Found at i:46684547 original size:16 final size:17
Alignment explanation
Indices: 46684514--46684554 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
46684504 TTATTTATTA
46684514 TTTATTTTTATTGTGGT
1 TTTATTTTTATTGTGGT
*
46684531 TTTATTTTTTTTG-GGT
1 TTTATTTTTATTGTGGT
46684547 TTCTATTT
1 TT-TATTT
46684555 AGGCCCGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.10, C:0.02, G:0.15, T:0.73
Consensus pattern (17 bp):
TTTATTTTTATTGTGGT
Found at i:46685060 original size:45 final size:45
Alignment explanation
Indices: 46684993--46685438 Score: 271
Period size: 45 Copynumber: 9.9 Consensus size: 45
46684983 TAATTTATGG
* *
46684993 CTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGTTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGTTAT
* * * * *
46685038 CTTCAGTCTGCTCCCCTGCAACTTCAGGGAGATAAGAATTGTGACTTTAAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAG-A-T-T--CGTT-AT
* * * * **
46685089 CTTTAATCCGTTCCACTGCAACCTCAGGGAAATAAGATTCG-CGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGTTAT
* * * *
46685133 CTTCAATCTACTCCACTGCAACTTCA-GCAAGATAAGGTT--TATAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTCGT-TAT
* * * * * * *
46685177 CTTTAATCTGCTCTACTGCAATTTCAGAGAGATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGTTAT
* * * * * ** *
46685222 CTTCGATTTACTCCACTGCAACTTTAGGGAGATAAGA-TCCATAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGTTAT
* * *
46685266 CTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGTTAT
* * *
46685311 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTAC--TAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TT-CGTTAT
* ** * * * ** **
46685356 CTTCAGTCCACTCCACTGTAACTTTAGGTAGTTAAGACTT-G-TGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTCGTTAT
* * *
46685400 CTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT
46685439 TGCAGTCTGT
Statistics
Matches: 308, Mismatches: 77, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
43 5 0.02
44 121 0.39
45 139 0.45
46 4 0.01
47 2 0.01
48 2 0.01
49 1 0.00
50 4 0.01
51 30 0.10
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGTTAT
Found at i:46685168 original size:44 final size:44
Alignment explanation
Indices: 46685100--46685438 Score: 208
Period size: 44 Copynumber: 7.6 Consensus size: 44
46685090 TTTAATCCGT
* * *
46685100 TCCACTGCAACCTCAGGGAA-ATAAGATTCGCGTCTTCAATCTAC
1 TCCACTGCAACTTCA-GGAAGATAAGATTCGCATCTTCAATCTGC
* * *** * *
46685144 TCCACTGCAACTTCAGCAAGATAAGGTTTATAACTTTAATCTGC
1 TCCACTGCAACTTCAGGAAGATAAGATTCGCATCTTCAATCTGC
* * * * * *
46685188 TCTACTGCAATTTCA-GAGAGATAAGATTTGCTATCTTCGATTTAC
1 TCCACTGCAACTTCAGGA-AGATAAGATTCGC-ATCTTCAATCTGC
* * *
46685233 TCCACTGCAACTTTAGGGAGATAAGA-TC-CATAACTTCAATCTGT
1 TCCACTGCAACTTCAGGAAGATAAGATTCGCAT--CTTCAATCTGC
* *
46685277 TCCACTGCAACTTTAGGGAA-ATAAGATTCGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCA-GGAAGATAAGATTCGC-ATCTTCAATCTGC
* * * * **
46685322 TCCACTGCAACTTTAGGGAGATAAGACTTAC-TATCTTCAGTCCAC
1 TCCACTGCAACTTCAGGAAGATAAGA-TT-CGCATCTTCAATCTGC
* * * * *** *
46685367 TCCACTGTAACTTTAGGTAGTTAAGACTT-GTGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGAAGATAAGA-TTCGCATCTTCAATCTGC
46685411 TCCACTGCAACTTCAAGG-AGATAAGATT
1 TCCACTGCAACTTC-AGGAAGATAAGATT
46685439 TGCAGTCTGT
Statistics
Matches: 231, Mismatches: 49, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.01
43 7 0.03
44 112 0.48
45 103 0.45
46 4 0.02
47 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGAAGATAAGATTCGCATCTTCAATCTGC
Found at i:46685180 original size:95 final size:96
Alignment explanation
Indices: 46684956--46685182 Score: 246
Period size: 96 Copynumber: 2.4 Consensus size: 96
46684946 GATCTGTTCT
* * * *
46684956 ACTGCAACTTCAG-AGAGATAA-AATATCTAA-TTTATGGCTTCAATCTGTTCCACTACAACTTC
1 ACTGCAACTTCAGCA-AGATAAGAAT-TATAACTTTA-AGCTTCAATCCGTTCCACTACAACCTC
* * *
46685018 AGGGAAATAAGATTCGTTATCTTCAGTCTGCTCC
63 AGGGAAATAAGATTCGTCATCTTCAATCTACTCC
* ** * * * *
46685052 CCTGCAACTTCAGGGAGATAAGAATTGTGACTTTAAGCTTTAATCCGTTCCACTGCAACCTCAGG
1 ACTGCAACTTCAGCAAGATAAGAATTATAACTTTAAGCTTCAATCCGTTCCACTACAACCTCAGG
*
46685117 GAAATAAGATTCG-CGTCTTCAATCTACTCC
66 GAAATAAGATTCGTCATCTTCAATCTACTCC
**
46685147 ACTGCAACTTCAGCAAGATAAGGTTTATAACTTTAA
1 ACTGCAACTTCAGCAAGATAAGAATTATAACTTTAA
46685183 TCTGCTCTAC
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
95 42 0.39
96 59 0.55
97 7 0.06
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (96 bp):
ACTGCAACTTCAGCAAGATAAGAATTATAACTTTAAGCTTCAATCCGTTCCACTACAACCTCAGG
GAAATAAGATTCGTCATCTTCAATCTACTCC
Found at i:46685255 original size:89 final size:88
Alignment explanation
Indices: 46685100--46685347 Score: 284
Period size: 89 Copynumber: 2.8 Consensus size: 88
46685090 TTTAATCCGT
* * * * * **
46685100 TCCACTGCAACCTCAGGGAAATAAGATTCGC-GTCTTCAATCTACTCCACTGCAACTTCAGCAAG
1 TCCACTGCAACTTTAGAGAAATAAGATTCGCTATCTTC-ATCTACTCCACTGCAACTTTAGGGAG
* ** *
46685164 ATAAGGTTTATAACTTTAATCTGC
65 ATAAGATCCATAACTTCAATCTGC
* * * *
46685188 TCTACTGCAA-TTTCAGAGAGATAAGATTTGCTATCTTCGATTTACTCCACTGCAACTTTAGGGA
1 TCCACTGCAACTTT-AGAGAAATAAGATTCGCTATCTTC-ATCTACTCCACTGCAACTTTAGGGA
*
46685252 GATAAGATCCATAACTTCAATCTGT
64 GATAAGATCCATAACTTCAATCTGC
* *
46685277 TCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
1 TCCACTGCAACTTTAGAGAAATAAGATTCGCTATCTTCA-TCTACTCCACTGCAACTTTAGGGAG
46685342 ATAAGA
65 ATAAGA
46685348 CTTACTATCT
Statistics
Matches: 133, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
87 1 0.01
88 24 0.18
89 105 0.79
90 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (88 bp):
TCCACTGCAACTTTAGAGAAATAAGATTCGCTATCTTCATCTACTCCACTGCAACTTTAGGGAGA
TAAGATCCATAACTTCAATCTGC
Found at i:46687047 original size:100 final size:104
Alignment explanation
Indices: 46686904--46687089 Score: 245
Period size: 100 Copynumber: 1.8 Consensus size: 104
46686894 TTTCATGTAC
* * ** * *
46686904 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCAT-A-TC-GG-TGCCCATGTCA
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGACTCAGGATGCCAATGCCA
*
46686965 TGTCCCAGACATGGTCTTATAGGGTACCTCTCATCTCGG
66 TGACCCAGACATGGTCTTATAGGGTACCTCTCATCTCGG
* *
46687004 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGA-CTC-AGGATGCCAATGC
46687069 CATGACCCAGACATGGTCTTA
64 CATGACCCAGACATGGTCTTA
46687090 CATGGGATCT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 39 0.55
101 1 0.01
103 2 0.03
105 2 0.03
106 27 0.38
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (104 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGACTCAGGATGCCAATGCCA
TGACCCAGACATGGTCTTATAGGGTACCTCTCATCTCGG
Found at i:46687071 original size:56 final size:50
Alignment explanation
Indices: 46686855--46687101 Score: 221
Period size: 50 Copynumber: 4.8 Consensus size: 50
46686845 GATAATAACA
* * * * ** * *
46686855 TGCCAAAGCCATGTTCTAGACATGGTCTTACTTGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** *
46686904 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
46686954 TGCCCATGTCATGTCCCAGACATGGTCTTATA-GGGTACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATCTCGG
*
46687004 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
46687059 ATGCCAATGCCATGACCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46687102 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.24
50 73 0.45
51 3 0.02
53 5 0.03
55 2 0.01
56 39 0.24
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:46696418 original size:46 final size:46
Alignment explanation
Indices: 46696365--46696458 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
46696355 CCATGGTAAA
*
46696365 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
*
46696411 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
46696457 TT
1 TT
46696459 ATAGCATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAG
Found at i:46696780 original size:2 final size:2
Alignment explanation
Indices: 46696773--46696811 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
46696763 TAGATTGACG
46696773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46696812 GTTCAGAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46719403 original size:23 final size:23
Alignment explanation
Indices: 46719376--46719497 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
46719366 AGTGTTATTG
* *
46719376 ATCAGTGGTAGCTTTGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
46719399 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
46719422 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
46719445 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
46719468 AACAGCGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
46719491 ATCAGTG
1 ATCAGTG
46719498 TTGCACTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:46719431 original size:46 final size:46
Alignment explanation
Indices: 46719378--46719497 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
46719368 TGTTATTGAT
* *
46719378 CAGTGGTAGCTTTGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
46719424 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
* *
46719470 CAGCGGTAGCTTCGGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
46719498 TTGCACTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:46722110 original size:27 final size:26
Alignment explanation
Indices: 46722080--46722133 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
46722070 GAATGTTTTG
46722080 ATTTTGGTT-ATAATGGCATGTATATGT
1 ATTTTGGTTAATAATGGC-T-TATATGT
* *
46722107 ATTTTGTTTAATGATGGCTTATATGT
1 ATTTTGGTTAATAATGGCTTATATGT
46722133 A
1 A
46722134 GTATGTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 9 0.38
28 7 0.29
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (26 bp):
ATTTTGGTTAATAATGGCTTATATGT
Found at i:46724240 original size:2 final size:2
Alignment explanation
Indices: 46724233--46724258 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46724223 ATGGTCATTA
46724233 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
46724259 TGAATTCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46744902 original size:19 final size:18
Alignment explanation
Indices: 46744852--46744898 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
46744842 AAAAACAAAT
*
46744852 TTTTTTAGTTTAATGTAA
1 TTTTTTAATTTAATGTAA
*
46744870 TTTTTTAATTTAATGTGA
1 TTTTTTAATTTAATGTAA
46744888 TTTTTTAATTT
1 TTTTTTAATTT
46744899 TAATTACAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (18 bp):
TTTTTTAATTTAATGTAA
Found at i:46748846 original size:44 final size:43
Alignment explanation
Indices: 46748710--46748883 Score: 217
Period size: 43 Copynumber: 4.0 Consensus size: 43
46748700 CCACATAAAT
*
46748710 GCCGCTAAAGAACATGACGTTTAGC-AGCACTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGA-CACTTTTATCACAAAC
* * * *
46748753 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCACAATC
1 GCCGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
* * *
46748796 GTCGCTAAAGAACATGGCATTTAGCGACACTTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGACAC-TTTTATCACAAAC
* *
46748840 GCCGCTAAATAACATGACCTTTAGCGAC-GTTTTATTCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGACACTTTTA-TCACAAAC
46748883 G
1 G
46748884 ATGCTAAAAG
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 5 0.05
43 70 0.63
44 36 0.32
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
Found at i:46748857 original size:87 final size:86
Alignment explanation
Indices: 46748712--46748880 Score: 252
Period size: 87 Copynumber: 2.0 Consensus size: 86
46748702 ACATAAATGC
* *
46748712 CGCTAAAGAACATGACGTTTAGCAGCACTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAG
1 CGCTAAAGAACATGACATTTAGCAGCACTTTTATCACAAACGCCGCTAAAGAACATGACCTTTAG
*
46748777 CGGCGCTTTTA-TCACAATCGT
66 CGACG-TTTTATTCACAATCGT
* *
46748798 CGCTAAAGAACATGGCATTTAGC-GACACTTTTTATCACAAACGCCGCTAAATAACATGACCTTT
1 CGCTAAAGAACATGACATTTAGCAG-CAC-TTTTATCACAAACGCCGCTAAAGAACATGACCTTT
46748862 AGCGACGTTTTATTCACAA
64 AGCGACGTTTTATTCACAA
46748881 ACGATGCTAA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
85 1 0.01
86 29 0.39
87 45 0.60
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (86 bp):
CGCTAAAGAACATGACATTTAGCAGCACTTTTATCACAAACGCCGCTAAAGAACATGACCTTTAG
CGACGTTTTATTCACAATCGT
Found at i:46752121 original size:124 final size:124
Alignment explanation
Indices: 46751912--46752193 Score: 356
Period size: 124 Copynumber: 2.3 Consensus size: 124
46751902 CACCGTTCTG
* * *
46751912 AGAAATTTTAATACATAGTTGCGGCGTTTTTTGGTCCAAACGCTGATACTGATTACCATTTGCAG
1 AGAAATTTAAATACATAGTTGCGGCGTTTTTTGCTCCAAACGCCGATACTGATTACCATTTGCAG
* * *
46751977 CGTTTTCAGCAAAAACGCCACTAAAAATTTAAATTCCTATACCGAAACGGTGCTGC-TTTT
66 CGTTTTCAGCAAAAACGCCACTAAAAAATTAAATTCCTATACAGAAAC-G-GCTCCATTTT
* * * **
46752037 AGAAATTTAAATACATAGTTGCGGCGTTTTTT-CTCCAAATGCCGTTATTGCA-TACCATTTGTG
1 AGAAATTTAAATACATAGTTGCGGCGTTTTTTGCTCCAAACGCCGATACTG-ATTACCATTTGCA
* *
46752100 GCGTTTTCAAG-AAAAATGCCACTAAAAAATTAAATTTCTATACAGAAACGGCTCCATTTTT
65 GCGTTTTC-AGCAAAAACGCCACTAAAAAATTAAATTCCTATACAGAAACGGCTCCA-TTTT
* *
46752161 AGAAATTAAAATACATAGTTGCAGCGTTTTTTG
1 AGAAATTTAAATACATAGTTGCGGCGTTTTTTG
46752194 GACAAAACGC
Statistics
Matches: 137, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
122 4 0.03
123 1 0.01
124 98 0.72
125 34 0.25
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (124 bp):
AGAAATTTAAATACATAGTTGCGGCGTTTTTTGCTCCAAACGCCGATACTGATTACCATTTGCAG
CGTTTTCAGCAAAAACGCCACTAAAAAATTAAATTCCTATACAGAAACGGCTCCATTTT
Found at i:46752257 original size:82 final size:85
Alignment explanation
Indices: 46752112--46752286 Score: 205
Period size: 82 Copynumber: 2.1 Consensus size: 85
46752102 GTTTTCAAGA
* *
46752112 AAAATGCCACTAAAAAATTAAATTTCTATACAGAAACGGCTCCATTTTTAGAAATTAAAATACAT
1 AAAACGCCACTAAAAAATTAAATTTCTATACAGAAACGGCTCCATTTTAAGAAATTAAAATACAT
* *
46752177 AGTTGCAGCGTTTTTTGGAC
66 AATTGCAGCATTTTTTGGAC
** * **
46752197 AAAACGCCACTAAAAAATTAAA-TTCT-TGTA-AAACGG-TGCCGTTTTAAGAAATTTTAATACA
1 AAAACGCCACTAAAAAATTAAATTTCTATACAGAAACGGCT-CCATTTTAAGAAATTAAAATACA
* *
46752258 TAATTGCGGCATTTTTTGGTC
65 TAATTGCAGCATTTTTTGGAC
*
46752279 CAAACGCC
1 AAAACGCC
46752287 GTTATATCTT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 49 0.64
83 2 0.03
84 4 0.05
85 21 0.27
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (85 bp):
AAAACGCCACTAAAAAATTAAATTTCTATACAGAAACGGCTCCATTTTAAGAAATTAAAATACAT
AATTGCAGCATTTTTTGGAC
Found at i:46752406 original size:7 final size:7
Alignment explanation
Indices: 46752394--46752577 Score: 83
Period size: 7 Copynumber: 26.3 Consensus size: 7
46752384 CTAATTAATT
46752394 TAAACCC
1 TAAACCC
46752401 TAAACCC
1 TAAACCC
46752408 T-AACTCC
1 TAAAC-CC
* *
46752415 T-ATCCTT
1 TAAACC-C
46752422 TAAACCAC
1 TAAACC-C
46752430 -AAACCC
1 TAAACCC
*
46752436 TAAACCT
1 TAAACCC
* *
46752443 TGAACCT
1 TAAACCC
*
46752450 TAAATCC
1 TAAACCC
*
46752457 TAAACAC
1 TAAACCC
46752464 TAAACCC
1 TAAACCC
46752471 TAAACCC
1 TAAACCC
*
46752478 TAAACCA
1 TAAACCC
*
46752485 TAATCCC
1 TAAACCC
46752492 TAAACCCC
1 TAAA-CCC
*
46752500 T-AA-CT
1 TAAACCC
*
46752505 TATATCCC
1 TA-AACCC
*
46752513 TTAAACCT
1 -TAAACCC
* * *
46752521 TGAATCA
1 TAAACCC
46752528 TAAACCC
1 TAAACCC
*
46752535 TAACCCC
1 TAAACCC
*
46752542 TAACCCC
1 TAAACCC
*
46752549 T-AACCT
1 TAAACCC
*
46752555 TAAACCA
1 TAAACCC
*
46752562 TAAACCA
1 TAAACCC
*
46752569 TAATCCC
1 TAAACCC
46752576 TA
1 TA
46752578 TCCCCTATCC
Statistics
Matches: 133, Mismatches: 34, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
5 2 0.02
6 9 0.07
7 109 0.82
8 11 0.08
9 2 0.02
ACGTcount: A:0.40, C:0.36, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:46752583 original size:7 final size:7
Alignment explanation
Indices: 46752573--46752598 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
46752563 AAACCATAAT
46752573 CCCTATC
1 CCCTATC
46752580 CCCTATC
1 CCCTATC
46752587 CCCTATC
1 CCCTATC
46752594 CCCTA
1 CCCTA
46752599 AACCTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.58, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCTATC
Found at i:46752709 original size:57 final size:57
Alignment explanation
Indices: 46752601--46752709 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
46752591 ATCCCCTAAA
* * * * * *
46752601 CCTTGAATTATAAACCATAAACTATAAACCGTAAATCCCTAACCCTTAAACCCCAAC
1 CCTTAAATAATAAACAATAAACTATAAACCCTAAATCCATAACCCTAAAACCCCAAC
* *
46752658 CCTTAAATAATAAACAATAAATTATAATCCCTAAA-CCATAATCCCTAAAACC
1 CCTTAAATAATAAACAATAAACTATAAACCCTAAATCCATAA-CCCTAAAACC
46752710 ATAATCCCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 5 0.12
57 38 0.88
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (57 bp):
CCTTAAATAATAAACAATAAACTATAAACCCTAAATCCATAACCCTAAAACCCCAAC
Found at i:46752729 original size:15 final size:14
Alignment explanation
Indices: 46752681--46752722 Score: 75
Period size: 15 Copynumber: 2.9 Consensus size: 14
46752671 ACAATAAATT
46752681 ATAATCCCTAAACC
1 ATAATCCCTAAACC
46752695 ATAATCCCTAAAACC
1 ATAATCCCT-AAACC
46752710 ATAATCCCTAAAC
1 ATAATCCCTAAAC
46752723 TGCTAATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAATCCCTAAACC
Found at i:46752797 original size:22 final size:22
Alignment explanation
Indices: 46752767--46752809 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
46752757 ACAGCAGAAC
* *
46752767 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
46752789 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
46752810 AATGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:46752939 original size:42 final size:42
Alignment explanation
Indices: 46752884--46753176 Score: 405
Period size: 42 Copynumber: 7.0 Consensus size: 42
46752874 GCGCTTACAT
46752884 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * *
46752926 AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * *
46752968 AAAAAAATGCCGCTAAAGATCATGTTTTTTAGCGGCGCTTTG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
46753010 AAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTA-
1 -AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
46753052 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCCTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
46753094 AAACAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
** *
46753135 TTCAAAAACGCCGCTAAA-AGT-AGTGTTATTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
46753177 TTTCACAAAC
Statistics
Matches: 228, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
41 43 0.19
42 148 0.65
43 37 0.16
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:46753648 original size:21 final size:21
Alignment explanation
Indices: 46753622--46753690 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
46753612 GCTTCTCTCA
* *
46753622 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCACTCGCTGCAGCCT
* * *
46753643 CTGCTTGACTCGTTGTAGCCT
1 CTGCTTCACTCGCTGCAGCCT
* *
46753664 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCACTCGCTGCAGCCT
46753685 CTGCTT
1 CTGCTT
46753691 TAAGTTGCTG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.41, G:0.22, T:0.35
Consensus pattern (21 bp):
CTGCTTCACTCGCTGCAGCCT
Found at i:46759580 original size:9 final size:9
Alignment explanation
Indices: 46759566--46759603 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
46759556 NNNNNNNNNN
46759566 TAAGTTATG
1 TAAGTTATG
*
46759575 TAAGTTATT
1 TAAGTTATG
46759584 TAA-TTATG
1 TAAGTTATG
46759592 TAAGTTATG
1 TAAGTTATG
46759601 TAA
1 TAA
46759604 TTAACCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:46759592 original size:17 final size:17
Alignment explanation
Indices: 46759570--46759606 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
46759560 NNNNNNTAAG
*
46759570 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATGTAA
46759587 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
46759604 TTA
1 TTA
46759607 ACCAAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (17 bp):
TTATGTAAGTTATGTAA
Found at i:46760251 original size:13 final size:13
Alignment explanation
Indices: 46760229--46760265 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
46760219 CTCCATGGAA
46760229 ACAT-TTTTAATT
1 ACATATTTTAATT
*
46760241 AGATATTTTAATT
1 ACATATTTTAATT
46760254 ACATATTTTAAT
1 ACATATTTTAAT
46760266 AAACATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (13 bp):
ACATATTTTAATT
Found at i:46760430 original size:34 final size:34
Alignment explanation
Indices: 46760383--46760460 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
46760373 TGGAATTACA
* *
46760383 CAAATATATATATTTTATTTTACTTTTTAAAAAT
1 CAAATTTAAATATTTTATTTTACTTTTTAAAAAT
46760417 CAAATTTAAATATTTTATTTTACTTTTTAAAAAT
1 CAAATTTAAATATTTTATTTTACTTTTTAAAAAT
46760451 CAAATTTAAA
1 CAAATTTAAA
46760461 GCTGAAGGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (34 bp):
CAAATTTAAATATTTTATTTTACTTTTTAAAAAT
Found at i:46763073 original size:39 final size:38
Alignment explanation
Indices: 46763018--46763095 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
46763008 GCGTTTTTGT
* * *
46763018 TAATATCTTTTGCGGCGCTTAT-AAAAAAGCGCCGCTAA
1 TAATATCTTTAGCGGCG-ATATCAAAAAAGCGCCACTAA
*
46763056 TAATATACTTTAGCGGCGATATCCAAAAAGCGCCACTAA
1 TAATAT-CTTTAGCGGCGATATCAAAAAAGCGCCACTAA
46763095 T
1 T
46763096 TCTAATATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (38 bp):
TAATATCTTTAGCGGCGATATCAAAAAAGCGCCACTAA
Found at i:46764381 original size:40 final size:40
Alignment explanation
Indices: 46764285--46764396 Score: 95
Period size: 40 Copynumber: 2.8 Consensus size: 40
46764275 TTTTCAAAAT
* * *
46764285 GCGCCGCTAATGACT-GACCTTTAGTGGCGTTTGACATAAA
1 GCGCCGCTAATG-CTCGATCTTTAGCGGCGTTTCACATAAA
* * * * *
46764325 GCGTCACTATTTCTCGATCTTTAGCGGCGTTTCTC-TATAA
1 GCGCCGCTAATGCTCGATCTTTAGCGGCGTTTCACATA-AA
*
46764365 GCGCCGCTAATGCTCGATATATT-GCGGCGTTT
1 GCGCCGCTAATGCTCGATCT-TTAGCGGCGTTT
46764397 GTTAAAAAAC
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
39 4 0.07
40 50 0.89
41 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (40 bp):
GCGCCGCTAATGCTCGATCTTTAGCGGCGTTTCACATAAA
Found at i:46767309 original size:20 final size:20
Alignment explanation
Indices: 46767280--46767320 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46767270 AAAAACCTAT
* * *
46767280 AATTTGTAAAACATTATTAA
1 AATTTATAAAAAAATATTAA
46767300 AATTTATAAAAAAATATTAA
1 AATTTATAAAAAAATATTAA
46767320 A
1 A
46767321 TAAAATTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AATTTATAAAAAAATATTAA
Found at i:46783183 original size:51 final size:51
Alignment explanation
Indices: 46783107--46783209 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
46783097 ATGTACTTAA
46783107 AGAAAACTATTAACTATGGATTGTGTTATAATGGATATCCTCCAGTTTTAG
1 AGAAAACTATTAACTATGGATTGTGTTATAATGGATATCCTCCAGTTTTAG
46783158 AGAAAACTATTAACTATGGATTGTGTTATAATGGATATCCTCCAGTTTTAG
1 AGAAAACTATTAACTATGGATTGTGTTATAATGGATATCCTCCAGTTTTAG
46783209 A
1 A
46783210 AGGGTATTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (51 bp):
AGAAAACTATTAACTATGGATTGTGTTATAATGGATATCCTCCAGTTTTAG
Found at i:46789154 original size:10 final size:10
Alignment explanation
Indices: 46789126--46789155 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
46789116 TTTTTATTAT
*
46789126 AAATTATACA
1 AAATTATATA
46789136 AAATTATATA
1 AAATTATATA
46789146 AAATTATATA
1 AAATTATATA
46789156 GAGACAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATTATATA
Found at i:46804368 original size:27 final size:26
Alignment explanation
Indices: 46804327--46804379 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
46804317 AATGCGTTCA
*
46804327 TGCTTATATGTAGGTGCTGAAAGATTC
1 TGCTTATATGAAGGTGCTGAAA-ATTC
*
46804354 TGCTTATGTGAAGGTGCTGAAAATTC
1 TGCTTATATGAAGGTGCTGAAAATTC
46804380 CAAGAAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (26 bp):
TGCTTATATGAAGGTGCTGAAAATTC
Found at i:46810693 original size:22 final size:22
Alignment explanation
Indices: 46810665--46810733 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
46810655 TCTCAGATTA
* *
46810665 TTAGCACATTAGTGCTATCCGT
1 TTAGCACATTAGTGCTCTCTGT
*
46810687 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
46810709 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
46810731 TTA
1 TTA
46810734 ATAGTGCATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:46812487 original size:16 final size:16
Alignment explanation
Indices: 46812467--46812519 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
46812457 TTGGTTCGCT
*
46812467 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
* *
46812483 GTAATAGAATAGATGC
1 GTAATGGAATAGAGGC
46812499 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
46812515 GTAAT
1 GTAAT
46812520 AGGTAATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:46812588 original size:44 final size:46
Alignment explanation
Indices: 46812501--46812589 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
46812491 ATAGATGCGT
*
46812501 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTCGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTCGTTGAATGG
*
46812547 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTCGTTGAATG
46812590 TAATAGAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.46
45 3 0.07
46 19 0.46
ACGTcount: A:0.27, C:0.06, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTCGTTGAATGG
Found at i:46812589 original size:39 final size:44
Alignment explanation
Indices: 46812501--46812606 Score: 123
Period size: 39 Copynumber: 2.5 Consensus size: 44
46812491 ATAGATGCGT
*
46812501 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTCGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTCG-TG-ATGG
*
46812547 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTT-G-G-TTG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTCGTGATGG
* *
46812586 AATGTAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
46812607 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 19 0.35
40 1 0.02
41 1 0.02
43 1 0.02
44 11 0.20
45 3 0.05
46 19 0.35
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTCGTGATGG
Found at i:46812798 original size:15 final size:16
Alignment explanation
Indices: 46812778--46812807 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46812768 ATATATAATT
46812778 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
46812793 TAATAAATATTCTTA
1 TAATAAATATTCTTA
46812808 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:46812817 original size:56 final size:55
Alignment explanation
Indices: 46812752--46812942 Score: 190
Period size: 56 Copynumber: 3.3 Consensus size: 55
46812742 TTATTATTAA
46812752 ATATAATTTAATAAAAATATATAATTTAATAAAATT-CTTAATAATAAATATTCTT
1 ATATAATTTAAT-AAAATATATAATTTAATAAAATTACTTAATAATAAATATTCTT
* * * * * *
46812807 ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTA-AATAAGTATTATT
1 ATAT-AATTTAATAAAAT-AT-ATA-AT-TTA--ATAAAAT-TACTTAATAATAAATATTCTT
46812869 AAATATAATTTAATAAAATATATAA-TTAATAAAATTACTTAATAATAAATATTCTT
1 --ATATAATTTAATAAAATATATAATTTAATAAAATTACTTAATAATAAATATTCTT
*
46812925 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
46812943 CATAATATGT
Statistics
Matches: 110, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
54 4 0.04
55 26 0.24
56 27 0.25
57 3 0.03
58 4 0.04
59 2 0.02
60 1 0.01
61 10 0.09
62 14 0.13
63 15 0.14
64 4 0.04
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (55 bp):
ATATAATTTAATAAAATATATAATTTAATAAAATTACTTAATAATAAATATTCTT
Found at i:46812899 original size:16 final size:17
Alignment explanation
Indices: 46812871--46812903 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
46812861 GTATTATTAA
46812871 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
46812888 ATATAA-TTAATAAAAT
1 ATATAATTTAATAAAAT
46812904 TACTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:46812917 original size:118 final size:120
Alignment explanation
Indices: 46812732--46812965 Score: 420
Period size: 118 Copynumber: 2.0 Consensus size: 120
46812722 TTAATCATAT
*
46812732 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAAGTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
46812797 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
46812852 TTTAA-ATAAGTATTATTAAATATAATTTAAT-AAAATATATAA-TTAATAAAATTACTTAATAA
1 TTTAACATAAGTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATT-CTTAATAA
*
46812914 TAAATATTCTTATATGAATTTACTAAAATCATAATATGTAATACTATAAAAT
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAT
46812966 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
117 11 0.10
118 70 0.63
119 25 0.23
120 5 0.05
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (120 bp):
TTTAACATAAGTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:46813396 original size:15 final size:16
Alignment explanation
Indices: 46813376--46813405 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46813366 ATATATAATT
46813376 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
46813391 TAATAAATATTCTTA
1 TAATAAATATTCTTA
46813406 TATGGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:46813588 original size:102 final size:102
Alignment explanation
Indices: 46813368--46813938 Score: 373
Period size: 102 Copynumber: 5.6 Consensus size: 102
46813358 TAATAAAAAT
* *
46813368 ATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGGATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATAT
46813433 AATACTATAAAATATAATTTAAAATAATTATTATTAA
66 AATACTATAAAATATAATTTAAAATAATTATTATTAA
*
46813470 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATGT
1 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATAT
* * * *
46813535 AATACTATAAAATATAGTTT-AATTAGTTTTTATTAA
66 AATACTATAAAATATAATTTAAAATAATTATTATTAA
* * * *
46813571 ATATAATTTAATAAAAATATATAATTTAATAAA-ATTATTAATAATAAATATTAGT--AAT-A-A
1 ATATAATTTAATAAAATTCT-TAA--TAATAAATATTATT-AT-ATGAAT-TTACTAAAATCATA
** **
46813631 ATAT-TCTTA-TATGAATTTGTATAATTTAAAATAATTATTATTAA
60 ATATATAATACTAT-AA--AATATAATTTAAAATAATTATTATTAA
* * * * * * *
46813675 ATATAATTTAATAATAATAT-ATAATTTAATAAA-ATTCTTACTAATAAATTTTCTTATA-C-GA
1 ATATAATTTAATAA-AAT-TCTTAA--TAATAAATATTATTA-T-ATGAATTTACTAAAATCATA
* * * * * * *
46813736 ATTTGT-ATAATTTAAAATATTTATTATTAAATATAATTTAATAATAA
60 ATATATAATACTATAAAATA--TAAT-TTAAA-ATAA-TTATTATTAA
* * * * * * * *
46813783 TATATAATTTCATAAAATTCTTACTAATAAATTTTCTTATACGAATTT-GTATAAT-TTAA-A-A
1 -ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATA
* *
46813844 TAATTATTATTAAATATAATTT--AATAA-TA--A-T--
65 TAA-TACTATAAAATATAATTTAAAATAATTATTATTAA
* * * * *
46813875 ATATAATTTTACAAAATTCTTACTAATAAATTTTCTTATATGAATTTACTAAAATCATAATATA
1 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATA
46813939 ACTTGATAAT
Statistics
Matches: 378, Mismatches: 56, Indels: 77
0.74 0.11 0.15
Matches are distributed among these distances:
91 44 0.12
92 5 0.01
93 3 0.01
94 2 0.01
95 2 0.01
97 2 0.01
99 4 0.01
100 4 0.01
101 36 0.10
102 91 0.24
103 24 0.06
104 67 0.18
105 36 0.10
106 21 0.06
107 11 0.03
108 13 0.03
109 13 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (102 bp):
ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATAT
AATACTATAAAATATAATTTAAAATAATTATTATTAA
Found at i:46813628 original size:13 final size:13
Alignment explanation
Indices: 46813596--46813635 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
46813586 AATATATAAT
*
46813596 TTAATAA-AATTA
1 TTAATAATAAATA
46813608 TTAATAATAAATA
1 TTAATAATAAATA
*
46813621 TTAGTAATAAATA
1 TTAATAATAAATA
46813634 TT
1 TT
46813636 CTTATATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
TTAATAATAAATA
Found at i:46813628 original size:16 final size:15
Alignment explanation
Indices: 46813597--46813630 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
46813587 ATATATAATT
*
46813597 TAATAAAATTATTAA
1 TAATAAAATTAGTAA
46813612 TAATAAATATTAGTAA
1 TAATAAA-ATTAGTAA
46813628 TAA
1 TAA
46813631 ATATTCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAATAAAATTAGTAA
Found at i:46813676 original size:44 final size:44
Alignment explanation
Indices: 46813628--46813860 Score: 176
Period size: 44 Copynumber: 5.2 Consensus size: 44
46813618 ATATTAGTAA
46813628 TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
1 TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
* * *
46813672 TAAATATAAT-TTA-AT-AATAATATATAATTTAATAA-AATTCTTACT
1 TAAATAT--TCTTATATGAAT-TTGTATAATTTAA-AATAATTATTA-T
* * *
46813717 AATAAATTTTCTTATACGAATTTGTATAATTTAAAATATTTATTAT
1 --TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
* * * *
46813763 TAAATATAAT-TTA-AT-AATAATATATAATTTCATAA-AATTCTTACT
1 TAAATAT--TCTTATATGAAT-TTGTATAATTT-AAAATAATTATTA-T
* *
46813808 AATAAATTTTCTTATACGAATTTGTATAATTTAAAATAATTATTAT
1 --TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
46813854 TAAATAT
1 TAAATAT
46813861 AATTTAATAA
Statistics
Matches: 144, Mismatches: 23, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
43 6 0.04
44 55 0.38
45 15 0.10
46 15 0.10
47 47 0.33
48 6 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (44 bp):
TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
Found at i:46813738 original size:91 final size:91
Alignment explanation
Indices: 46813589--46813921 Score: 534
Period size: 91 Copynumber: 3.7 Consensus size: 91
46813579 TAATAAAAAT
* * * *
46813589 ATATAATTTAATAA-AAT-TATTAA--TAAT-AAA-TATTAGTAATAAATATTCTTATATGAATT
1 ATATAATTTAATAATAATATA-TAATTTAATAAAATTCTTACTAATAAATTTTCTTATACGAATT
46813648 TGTATAATTTAAAATAATTATTATTAA
65 TGTATAATTTAAAATAATTATTATTAA
46813675 ATATAATTTAATAATAATATATAATTTAATAAAATTCTTACTAATAAATTTTCTTATACGAATTT
1 ATATAATTTAATAATAATATATAATTTAATAAAATTCTTACTAATAAATTTTCTTATACGAATTT
*
46813740 GTATAATTTAAAATATTTATTATTAA
66 GTATAATTTAAAATAATTATTATTAA
*
46813766 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTACTAATAAATTTTCTTATACGAATTT
1 ATATAATTTAATAATAATATATAATTTAATAAAATTCTTACTAATAAATTTTCTTATACGAATTT
46813831 GTATAATTTAAAATAATTATTATTAA
66 GTATAATTTAAAATAATTATTATTAA
* * *
46813857 ATATAATTTAATAATAATATATAATTTTACAAAATTCTTACTAATAAATTTTCTTATATGAATTT
1 ATATAATTTAATAATAATATATAATTTAATAAAATTCTTACTAATAAATTTTCTTATACGAATTT
46813922 ACTAAAATCA
Statistics
Matches: 231, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
86 14 0.06
87 6 0.03
88 2 0.01
89 4 0.02
90 3 0.01
91 202 0.87
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (91 bp):
ATATAATTTAATAATAATATATAATTTAATAAAATTCTTACTAATAAATTTTCTTATACGAATTT
GTATAATTTAAAATAATTATTATTAA
Found at i:46815831 original size:45 final size:45
Alignment explanation
Indices: 46815764--46816053 Score: 411
Period size: 45 Copynumber: 6.4 Consensus size: 45
46815754 AGTATACAGT
* * * * *
46815764 AATCAGTAACGGTAGCAATAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* * *
46815809 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGTCG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
46815854 AATC-GATAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
1 AATCAG-TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* *
46815899 AGTCAGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
46815944 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTCG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* * * * *
46815989 AGTCGGTAATAGTAACAGTAACATTATTCGACACACCAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
46816034 AATCAGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTA
46816054 GTCGGCACAT
Statistics
Matches: 217, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
44 1 0.00
45 215 0.99
46 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (45 bp):
AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:46816077 original size:38 final size:39
Alignment explanation
Indices: 46815995--46816080 Score: 113
Period size: 39 Copynumber: 2.3 Consensus size: 39
46815985 GTCGAGTCGG
* *
46815995 TAAT-AGTAACAGTAACATTATTCGACACACCAAGTGCC
1 TAATCAGTAACAGTAACAGTAGTCGACACACCAAGTGCC
* * *
46816033 GAATCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCC
1 TAATCAGTAACAGTAACAGTAGTCGACACACCAAGTGCC
46816071 TAATCAGTAA
1 TAATCAGTAA
46816081 GCCGGCAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 19 0.46
39 22 0.54
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (39 bp):
TAATCAGTAACAGTAACAGTAGTCGACACACCAAGTGCC
Found at i:46816511 original size:22 final size:22
Alignment explanation
Indices: 46816485--46816530 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
46816475 TTTAACGTGA
46816485 CATAATTCAGCCACTACTTGGC
1 CATAATTCAGCCACTACTTGGC
46816507 CATAATTCAGCCACTACTTGGC
1 CATAATTCAGCCACTACTTGGC
46816529 CA
1 CA
46816531 AAGCCTAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.26
Consensus pattern (22 bp):
CATAATTCAGCCACTACTTGGC
Found at i:46820502 original size:23 final size:22
Alignment explanation
Indices: 46820470--46820514 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
46820460 TTGAAAGTAA
46820470 GAAATGAAACAGGAATAGAAAT
1 GAAATGAAACAGGAATAGAAAT
46820492 GAAAGTGAAACAGGAATAGAAAT
1 GAAA-TGAAACAGGAATAGAAAT
46820515 CGGGAGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.58, C:0.04, G:0.24, T:0.13
Consensus pattern (22 bp):
GAAATGAAACAGGAATAGAAAT
Found at i:46824849 original size:16 final size:16
Alignment explanation
Indices: 46824830--46824868 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
46824820 AACTGATGTG
46824830 AAGAAAATATAGAGGA
1 AAGAAAATATAGAGGA
46824846 AAGAAAATATAGAGGA
1 AAGAAAATATAGAGGA
46824862 AAGAAAA
1 AAGAAAA
46824869 AAACGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (16 bp):
AAGAAAATATAGAGGA
Found at i:46824941 original size:17 final size:16
Alignment explanation
Indices: 46824915--46824946 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
46824905 TTTTACTTCC
46824915 AAAAATAAAATAAATT
1 AAAAATAAAATAAATT
46824931 AAAAATCAAAATAAAT
1 AAAAAT-AAAATAAAT
46824947 AACTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:46831279 original size:42 final size:42
Alignment explanation
Indices: 46831216--46831361 Score: 141
Period size: 42 Copynumber: 3.5 Consensus size: 42
46831206 ATATTTGCTT
* * *
46831216 GTTTAGCTCTTTTGAGTTTCAGTTTAACCCTAATGGGTTTTA
1 GTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTTA
* * * * *
46831258 GTTTAGCTCTTCTGAGCTTCAGATTAACCTTTATGGATTTTC
1 GTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTTA
* * * *
46831300 GTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATAGGTTTCT-
1 GTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTT-TA
* * *
46831342 TTTTAGCACTTATGTGCTTC
1 GTTTAGCTCTTATGAGCTTC
46831362 TGTGCAGCCT
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 83 0.99
43 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (42 bp):
GTTTAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTTA
Found at i:46840200 original size:6 final size:6
Alignment explanation
Indices: 46840191--46840230 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
46840181 AAAACGACCA
* *
46840191 CCACGT CCACGT CCAGGT CCACGC CCACGT CCACGT CCAC
1 CCACGT CCACGT CCACGT CCACGT CCACGT CCACGT CCAC
46840231 CTCGATGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.12
Consensus pattern (6 bp):
CCACGT
Found at i:46843910 original size:18 final size:15
Alignment explanation
Indices: 46843873--46843909 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
46843863 TCTTTCTTTC
46843873 TCATCATAATAAATA
1 TCATCATAATAAATA
46843888 TCATCATAATAAATA
1 TCATCATAATAAATA
46843903 TCATCAT
1 TCATCAT
46843910 CTTATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (15 bp):
TCATCATAATAAATA
Found at i:46843924 original size:8 final size:8
Alignment explanation
Indices: 46843911--46843958 Score: 87
Period size: 8 Copynumber: 6.0 Consensus size: 8
46843901 TATCATCATC
46843911 TTATTATT
1 TTATTATT
46843919 TTATTATT
1 TTATTATT
46843927 TTATTATT
1 TTATTATT
46843935 TTATTATT
1 TTATTATT
46843943 TTATTATT
1 TTATTATT
*
46843951 TTTTTATT
1 TTATTATT
46843959 ACTATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTATT
Found at i:46843966 original size:24 final size:24
Alignment explanation
Indices: 46843912--46843969 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
46843902 ATCATCATCT
*
46843912 TATTATTTTATTATTTTATTATTT
1 TATTATTTTATTATTTTATTATTC
*
46843936 TATTATTTTATTATTTTTTTATTAC
1 TATTATTTTATTATTTTATTATT-C
46843961 TA-TATTTTA
1 TATTATTTTA
46843970 CAATACTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTATTTTATTATTTTATTATTC
Found at i:46845704 original size:44 final size:44
Alignment explanation
Indices: 46845599--46845810 Score: 219
Period size: 44 Copynumber: 4.5 Consensus size: 44
46845589 TATGTATGAT
* *
46845599 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGTTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTAC
*
46845642 CACTTATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CAC-T-T-A--T--CACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTAC
* *
46845693 CACTTATCACTTTTCACTGATCAGATAAGTGCAGCTGAAGCTATCAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGC--T-AC
* *
46845740 TTATCACTTGTCACTTGTCACTGATCAGATAACTGTAGCTGAAGCTAC
1 ----CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTAC
*
46845788 TACTTATCACTTGTCACTGATCA
1 CACTTATCACTTGTCACTGATCA
46845811 AAAATACTCA
Statistics
Matches: 143, Mismatches: 11, Indels: 29
0.78 0.06 0.16
Matches are distributed among these distances:
43 3 0.02
44 53 0.37
45 1 0.01
46 3 0.02
47 2 0.01
48 4 0.03
49 2 0.01
50 29 0.20
51 46 0.32
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTAC
Found at i:46845748 original size:51 final size:51
Alignment explanation
Indices: 46845597--46845805 Score: 265
Period size: 51 Copynumber: 4.3 Consensus size: 51
46845587 CTTATGTATG
* * * *
46845597 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGTTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
* * *
46845647 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
*
46845698 ATCAC---T---TT-TCACTGATCAGATAAGTGCAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
*
46845742 ATCACTTGTCACTTGTCACTGATCAGATAACTGTAGCTGAAGCTA-CTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATC-ACTT
46845793 ATCACTTGTCACT
1 ATCACTTGTCACT
46845806 GATCAAAAAT
Statistics
Matches: 140, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
44 38 0.27
45 2 0.01
47 1 0.01
50 38 0.27
51 61 0.44
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
Found at i:46845764 original size:95 final size:94
Alignment explanation
Indices: 46845599--46845810 Score: 334
Period size: 95 Copynumber: 2.2 Consensus size: 94
46845589 TATGTATGAT
* * *
46845599 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAGTTACCACTTATCACTTGCCACTTGTC
1 CACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAGCTACCACTTATCACTTGCCACTTGTC
*
46845664 ACTGATCAGATAAGTGTAGCTAAAGCTAC
66 ACTGATCAGATAACTGTAGCTAAAGCTAC
* * *
46845693 CACTTATCACTTTTCACTGATCAGATAAGTGCAGCTGAAGCTATCACTTATCACTTGTCACTTGT
1 CACTTATCACTTGTCACTGATCAGATAAGTGCAGCT-AAGCTACCACTTATCACTTGCCACTTGT
*
46845758 CACTGATCAGATAACTGTAGCTGAAGCTAC
65 CACTGATCAGATAACTGTAGCTAAAGCTAC
*
46845788 TACTTATCACTTGTCACTGATCA
1 CACTTATCACTTGTCACTGATCA
46845811 AAAATACTCA
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 33 0.31
95 74 0.69
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (94 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAGCTACCACTTATCACTTGCCACTTGTC
ACTGATCAGATAACTGTAGCTAAAGCTAC
Found at i:46849224 original size:30 final size:31
Alignment explanation
Indices: 46849179--46849238 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
46849169 GGAGGTGGGA
*
46849179 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
46849210 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
46849239 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:46849464 original size:9 final size:9
Alignment explanation
Indices: 46849450--46849486 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46849440 TATAGTTTGA
46849450 TATTCGAAT
1 TATTCGAAT
46849459 TATTCGAAT
1 TATTCGAAT
*
46849468 TATTCGAGT
1 TATTCGAAT
46849477 TATTCGAAT
1 TATTCGAAT
46849486 T
1 T
46849487 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:46850153 original size:31 final size:31
Alignment explanation
Indices: 46850112--46850173 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
46850102 AGATAATTTT
*
46850112 AAAGATTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
46850143 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
46850174 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:46850734 original size:10 final size:11
Alignment explanation
Indices: 46850719--46850743 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46850709 ATTATTCTTT
46850719 AAAAAAAACAA
1 AAAAAAAACAA
46850730 AAAAAAAACAA
1 AAAAAAAACAA
46850741 AAA
1 AAA
46850744 GCGCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:46850823 original size:15 final size:15
Alignment explanation
Indices: 46850803--46850836 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46850793 CTTCTTTTCC
46850803 TATTATTGTTATTGT
1 TATTATTGTTATTGT
* *
46850818 TATTATTTTTATTTT
1 TATTATTGTTATTGT
46850833 TATT
1 TATT
46850837 TTTCCCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TATTATTGTTATTGT
Found at i:46864945 original size:45 final size:45
Alignment explanation
Indices: 46864881--46865040 Score: 302
Period size: 45 Copynumber: 3.6 Consensus size: 45
46864871 TGTCCTGAAG
46864881 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
1 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
46864926 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
1 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
*
46864971 ACAAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
1 ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
*
46865016 ACTAGGAAGGAACCTGAGGATGGTG
1 ACTAGGAAGGAGCCTGAGGATGGTG
46865041 AGAACAGAAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.26, C:0.09, G:0.47, T:0.17
Consensus pattern (45 bp):
ACTAGGAAGGAGCCTGAGGATGGTGGGTTGGAGGGAGGAGTGCAT
Found at i:46871148 original size:17 final size:17
Alignment explanation
Indices: 46871123--46871172 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
46871113 TTTCATAAAA
46871123 ATATAATAAAATTAAATT
1 ATAT-ATAAAATTAAATT
*
46871141 ATATATAATATTAATATT
1 ATATATAAAATTAA-ATT
*
46871159 A-ATATTAAA-TAAAT
1 ATATATAAAATTAAAT
46871173 ATAATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 15 0.54
18 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATAAAATTAAATT
Found at i:46872000 original size:30 final size:30
Alignment explanation
Indices: 46871964--46872023 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
46871954 TTTTGATTTT
46871964 AACGGGAATGACTAAAATGATCAAATTATG
1 AACGGGAATGACTAAAATGATCAAATTATG
46871994 AACGGGAATGACTAAAATGATCAAATTATG
1 AACGGGAATGACTAAAATGATCAAATTATG
46872024 TAGCATGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (30 bp):
AACGGGAATGACTAAAATGATCAAATTATG
Found at i:46872155 original size:3 final size:3
Alignment explanation
Indices: 46872147--46872193 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
46872137 ATCATAAAAT
46872147 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
46872194 GACAAATAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:46881730 original size:24 final size:25
Alignment explanation
Indices: 46881677--46881730 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
46881667 TTACTCTAAT
46881677 TTTTTAGTATGCTTAAAATTTAATAA
1 TTTTTAGTATGC-TAAAATTTAATAA
46881703 --TTTAGTAT-C-AAAATTTCAATAA
1 TTTTTAGTATGCTAAAATTT-AATAA
46881725 TTTTTA
1 TTTTTA
46881731 AAAACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 7 0.28
22 5 0.20
23 1 0.04
24 12 0.48
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (25 bp):
TTTTTAGTATGCTAAAATTTAATAA
Found at i:46887910 original size:73 final size:73
Alignment explanation
Indices: 46887814--46887967 Score: 236
Period size: 73 Copynumber: 2.1 Consensus size: 73
46887804 CGTGTGGTCA
** *
46887814 GGCCGTGTGTCTCACATGGTCAAGAGACACGCCTGTGTCTCAAGCCATGTGGACATTCGAAATAG
1 GGCCGTGTGTCTCACACAGTCAAGAGACACGCCTGTGTCTCAAGCCATGTGGACATTCAAAATAG
46887879 GGGCACAC
66 GGGCACAC
* * * *
46887887 GGCTGTGTGTCTCACACAGTCAAGAGACACGTCTGTGTCTCAGGCCGTGTGGACATTCAAAATAG
1 GGCCGTGTGTCTCACACAGTCAAGAGACACGCCTGTGTCTCAAGCCATGTGGACATTCAAAATAG
*
46887952 GGGCACAT
66 GGGCACAC
46887960 GGCCGTGT
1 GGCCGTGT
46887968 CCCAGCCCGT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.22
Consensus pattern (73 bp):
GGCCGTGTGTCTCACACAGTCAAGAGACACGCCTGTGTCTCAAGCCATGTGGACATTCAAAATAG
GGGCACAC
Found at i:46888261 original size:54 final size:54
Alignment explanation
Indices: 46888178--46888293 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
46888168 ACGGCTTAGC
* * *
46888178 ACATGAGCGTGTGACTTGGCCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
1 ACATGGGCATGTGACTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
*
46888232 ACATGGGCATGTGGCTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
1 ACATGGGCATGTGACTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
*
46888286 ACACGGGC
1 ACATGGGC
46888294 TGGGACACAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.22
Consensus pattern (54 bp):
ACATGGGCATGTGACTTGACCGTGTGACCCAAGTCAGTAAGCACCCTAATTTGG
Found at i:46889396 original size:24 final size:24
Alignment explanation
Indices: 46889369--46889464 Score: 68
Period size: 24 Copynumber: 4.0 Consensus size: 24
46889359 GTGAGTCGTG
*
46889369 TAACGGAAAGCTCTGGAGAGCCAT
1 TAACGGAAAGCTCAGGAGAGCCAT
* * * * *
46889393 TAACGGGAAGTTCAAGCGAGCCAA
1 TAACGGAAAGCTCAGGAGAGCCAT
* *
46889417 TATC-GAGAAGCTCCGGAGAGCCAT
1 TAACGGA-AAGCTCAGGAGAGCCAT
* * *
46889441 TAATCGGGAAGTTCATGAGAGCCA
1 TAA-CGGAAAGCTCAGGAGAGCCA
46889465 GTTATCGGGA
Statistics
Matches: 51, Mismatches: 18, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
23 1 0.02
24 35 0.69
25 14 0.27
26 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (24 bp):
TAACGGAAAGCTCAGGAGAGCCAT
Found at i:46889401 original size:25 final size:24
Alignment explanation
Indices: 46889336--46889474 Score: 89
Period size: 25 Copynumber: 5.6 Consensus size: 24
46889326 AAGCTCTTTC
* * *
46889336 GAGCCATATAATGGGAAGCTCAAGT
1 GAGCCAT-TAACGGGAAGCTCAGGA
* * * *
46889361 GAGTCGTGTAACGGAAAGCTCTGGA
1 GAGCCAT-TAACGGGAAGCTCAGGA
* * *
46889386 GAGCCATTAACGGGAAGTTCAAGC
1 GAGCCATTAACGGGAAGCTCAGGA
* * * *
46889410 GAGCCAATATCGAGAAGCTCCGGA
1 GAGCCATTAACGGGAAGCTCAGGA
* *
46889434 GAGCCATTAATCGGGAAGTTCATGA
1 GAGCCATTAA-CGGGAAGCTCAGGA
*
46889459 GAGCCAGTTATCGGGA
1 GAGCCA-TTAACGGGA
46889475 TGCTTTGAAG
Statistics
Matches: 83, Mismatches: 29, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
24 37 0.45
25 43 0.52
26 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.31, T:0.19
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCAGGA
Found at i:46891944 original size:27 final size:25
Alignment explanation
Indices: 46891921--46891995 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 25
46891911 ACTAGGGTAG
46891921 GAAAAGAAAAAGAAAAAAAAAGGGAA
1 GAAAAGAAAAAGAAAAAAAAAGGG-A
46891947 GAAAA-AAACAA-AAGAAGAAAAAGGGA
1 GAAAAGAAA-AAGAA-AA-AAAAAGGGA
*
46891973 -AAATGAAAAAGAATAAAAAAAGG
1 GAAAAGAAAAAGAA-AAAAAAAGG
46891996 TGCAAATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 17 0.40
26 17 0.40
27 8 0.19
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (25 bp):
GAAAAGAAAAAGAAAAAAAAAGGGA
Found at i:46891952 original size:16 final size:16
Alignment explanation
Indices: 46891930--46891968 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
46891920 GGAAAAGAAA
**
46891930 AAGAAAAAAA-AAGGG
1 AAGAAAAAAACAAAAG
46891945 AAGAAAAAAACAAAAG
1 AAGAAAAAAACAAAAG
46891961 AAGAAAAA
1 AAGAAAAA
46891969 GGGAAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAACAAAAG
Found at i:46894989 original size:30 final size:30
Alignment explanation
Indices: 46894955--46895012 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
46894945 ATGATTTTGC
46894955 ATGCAATATTATTGTTGAGACAATGAGGAG
1 ATGCAATATTATTGTTGAGACAATGAGGAG
46894985 ATGCAATATTATTGTTGAGACAATGAGG
1 ATGCAATATTATTGTTGAGACAATGAGG
46895013 GGGATCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (30 bp):
ATGCAATATTATTGTTGAGACAATGAGGAG
Found at i:46897566 original size:2 final size:2
Alignment explanation
Indices: 46897561--46897599 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
46897551 AAAAAAAAAA
46897561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46897600 AAAGAAGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46900005 original size:20 final size:20
Alignment explanation
Indices: 46899982--46900029 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
46899972 ATTTATTTAT
*
46899982 TAAAATAACAATTTTATAAA
1 TAAAATAACAATCTTATAAA
* *
46900002 TAAAATCATAATCTTATAAA
1 TAAAATAACAATCTTATAAA
46900022 TAAAATAA
1 TAAAATAA
46900030 TTTAAGGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAACAATCTTATAAA
Found at i:46904048 original size:43 final size:43
Alignment explanation
Indices: 46903990--46904153 Score: 217
Period size: 42 Copynumber: 3.9 Consensus size: 43
46903980 GTGCTTACAA
* * * *
46903990 AAAAAAACGCCGCTAAAGGTCATGTTTTTTAGCGGCGCTTAGG
1 AAAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGG
*
46904033 AAAAAAACGCTGCTAAAAGTAATGTTCTATAGCGGCGCTTA--
1 AAAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGG
*
46904074 ATAAAAAACGTCGCTAAAAGTAATGTTCTATAGCGGCGCTT-GG
1 A-AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGG
* * *
46904117 TAGAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCG
1 AAAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCG
46904154 TTTCATCTAC
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.65
43 36 0.34
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (43 bp):
AAAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGG
Found at i:46904093 original size:42 final size:42
Alignment explanation
Indices: 46903991--46904187 Score: 216
Period size: 42 Copynumber: 4.6 Consensus size: 42
46903981 TGCTTACAAA
* * * *
46903991 AAAAAACGCCGCTAAAGGTCATGTTTTTTAGCGGCGCTTAGGA-
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTA--AT
*
46904034 AAAAAACGCTGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
* **
46904076 AAAAAACGTCGCTAAAAGTAATGTTCTATAGCGGCGCTTGGT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
* * * *
46904118 AGAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGTTTCAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
* * * *
46904160 CTACAAACGCAGCTAAAAGTAGTGTTCT
1 -AAAAAACGCCGCTAAAAGTAATGTTCT
46904188 TTCGCGACGC
Statistics
Matches: 132, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 74 0.56
43 57 0.43
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT
Found at i:46904150 original size:84 final size:85
Alignment explanation
Indices: 46903991--46904187 Score: 243
Period size: 85 Copynumber: 2.3 Consensus size: 85
46903981 TGCTTACAAA
* * * * *
46903991 AAAAAACGCCGCTAAAGGTCATGTTTTTTAGCGGCGCTTAGGAAAAAAACGCTGCTAAAAGTAAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
46904056 GTTCTATAGCGGCGCTTAAT
66 GTTCTATAGCGGCGCTTAAT
* * *
46904076 AAAAAACGTCGCTAAAAGTAATGTTCTATAGCGGCGCTT-GGTAGAAAACGCCGCTAAAAGTAAT
1 AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
* * *
46904140 GTTCTTTAGCGGCGTTTCAT
66 GTTCTATAGCGGCGCTTAAT
* * * *
46904160 CTACAAACGCAGCTAAAAGTAGTGTTCT
1 -AAAAAACGCCGCTAAAAGTAATGTTCT
46904188 TTCGCGACGC
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 39 0.41
85 56 0.59
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (85 bp):
AAAAAACGCCGCTAAAAGTAATGTTCTATAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
GTTCTATAGCGGCGCTTAAT
Found at i:46904209 original size:43 final size:43
Alignment explanation
Indices: 46904037--46904212 Score: 144
Period size: 42 Copynumber: 4.1 Consensus size: 43
46904027 CTTAGGAAAA
* * * * * *
46904037 AAACGCTGCTAAAAGTAATGTTCTATAGCGGCGCTTAAT-AAA
1 AAACGCAGCTAAAAGTAATGTTCTTTAGCGACGCTTCATCTAC
* * ** **
46904079 AAACGTC-GCTAAAAGTAATGTTCTATAGCGGCGCTTGGTAGA-
1 AAACG-CAGCTAAAAGTAATGTTCTTTAGCGACGCTTCATCTAC
* * *
46904121 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGTTTCATCTAC
1 AAACGCAGCTAAAAGTAATGTTCTTTAGCGACGCTTCATCTAC
* * *
46904164 AAACGCAGCTAAAAGTAGTGTTCTTTCGCGACGCTT-ATTTCAC
1 AAACGCAGCTAAAAGTAATGTTCTTTAGCGACGCTTCATCT-AC
46904207 AAACGC
1 AAACGC
46904213 CACTATATGA
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 72 0.63
43 41 0.36
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (43 bp):
AAACGCAGCTAAAAGTAATGTTCTTTAGCGACGCTTCATCTAC
Found at i:46904653 original size:12 final size:12
Alignment explanation
Indices: 46904636--46904683 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
46904626 TTTTGAACCT
46904636 CTGCTTCTCTCG
1 CTGCTTCTCTCG
46904648 CTGCTTCTCTCG
1 CTGCTTCTCTCG
**
46904660 CTGCGGC-CT--
1 CTGCTTCTCTCG
46904669 CTGCTTCTCTCG
1 CTGCTTCTCTCG
46904681 CTG
1 CTG
46904684 TAGCCTCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 5 0.17
10 2 0.07
11 2 0.07
12 20 0.69
ACGTcount: A:0.00, C:0.42, G:0.21, T:0.38
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:46904672 original size:21 final size:21
Alignment explanation
Indices: 46904648--46904713 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
46904638 GCTTCTCTCG
*
46904648 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
46904669 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
46904690 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
46904711 CTG
1 CTG
46904714 TTTTAAGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.02, C:0.44, G:0.21, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Done.