Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold274
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: 1642345
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 31972 characters in sequence are not A, C, G, or T
File 3 of 10
Found at i:322688 original size:130 final size:130
Alignment explanation
Indices: 322346--322742 Score: 430
Period size: 129 Copynumber: 3.1 Consensus size: 130
322336 ATTTTTTAGG
* * * *
322346 GGATACT-TCAACCCCGGTTTTATTTCTAAAACATCGATTTTGCACCATTG-GGGATACTCCAAC
1 GGATACTCT-AACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCGAGGGATACTTCAAC
* * * *
322409 CCTGTTATTTTCGAGGGGATACT-TCAACCCCAGTTTTATTTCTAAAACACCAATTTTTCATC-T
65 CCCGTTATTTTCGAAGGGATACTCT-AACCCCAGTTTTATTTCTAAAACATCAA-TTTTCACCAT
322472 CGA
128 CGA
* * * * **
322475 GGATACTCAAACCCCGATTTTATTTCCAAAATATCGATTTTCTACCATC-AAAGATAC-TCTAAC
1 GGATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCGAGGGATACTTC-AAC
*
322538 CCCGTTATTTTCGAAGGGATACTCTAACCCCAGTTTTATTTCTAAAACATCGATTTTCCACCATC
65 CCCGTTATTTTCGAAGGGATACTCTAACCCCAGTTTTATTTCTAAAACATCAATTTT-CACCATC
322603 GA
129 GA
* ** *
322605 GGATACTCTAACACCGATTTTATTTCTAAAACATATATTTTCCACCATCGAGGGATACTTCAGCC
1 GGATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCGAGGGATACTTCAACC
* * * * * * * * *
322670 CCGTTA-TTTCTAAAGGATACTCCAACCTCGGTTTTATTCCCAAAGCATCAACTTTTCACCATTG
66 CCGTTATTTTCGAAGGGATACTCTAACCCCAGTTTTATTTCTAAAACATCAA-TTTTCACCATCG
*
322734 G
130 A
322735 GGATACTC
1 GGATACTC
322743 CAACTCCGTT
Statistics
Matches: 223, Mismatches: 36, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
128 5 0.02
129 99 0.44
130 98 0.44
131 19 0.09
132 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (130 bp):
GGATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCGAGGGATACTTCAACC
CCGTTATTTTCGAAGGGATACTCTAACCCCAGTTTTATTTCTAAAACATCAATTTTCACCATCGA
Found at i:322846 original size:158 final size:158
Alignment explanation
Indices: 322605--322904 Score: 392
Period size: 158 Copynumber: 1.9 Consensus size: 158
322595 CCACCATCGA
* * *
322605 GGATACTCTAACACCGATTTTATTTCTAAAACATATATTTTCCACCATCGAGGGATACTTCAGCC
1 GGATACTCTAACACCGATTTTATTTCCAAAACATATATTTTCCACAATCGAGGGATACTTCAACC
* * * *
322670 CCGTTATTTCTAAAGGATACTCCAACCTCGGTTTTATTCCCAAAGCATCAACTTTTCACCATTGG
66 CCGTTATTTCTAAAGGATACTCCAACCTCAGTTTTATTCCCAAAACATCAACTTTTCACCATCGA
322735 GGATACTCCAACTCCGTTATTTTCGAGG
131 GGATACTCCAACTCCGTTATTTTCGAGG
* * *
322763 GGATACTCTAAC-CCTGGTTTTATTTCCAAACCACTGAT-TTTT-CACAATCGA-TGATACTTCA
1 GGATACTCTAACACC-GATTTTATTTCCAAAACA-T-ATATTTTCCACAATCGAGGGATACTTCA
* * * * * *
322824 ACCCCGTTATTTTTGAAGGGATACTCTAATCTCAGTTTTATTTCCAAAACATCAATTTTTCACCA
63 ACCCCGTTATTTCT-AAAGGATACTCCAACCTCAGTTTTATTCCCAAAACATCAACTTTTCACCA
322889 TCGAGGATACTCCAAC
127 TCGAGGATACTCCAAC
322905 CCTGGTTTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
157 23 0.19
158 92 0.75
159 5 0.04
160 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (158 bp):
GGATACTCTAACACCGATTTTATTTCCAAAACATATATTTTCCACAATCGAGGGATACTTCAACC
CCGTTATTTCTAAAGGATACTCCAACCTCAGTTTTATTCCCAAAACATCAACTTTTCACCATCGA
GGATACTCCAACTCCGTTATTTTCGAGG
Found at i:322913 original size:51 final size:51
Alignment explanation
Indices: 322858--322956 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
322848 TCTAATCTCA
* * * *
322858 GTTTTATTTCCAAAACATCA-ATTTTTCACCATCGAGGATACTCCAACCCTG
1 GTTTTATTTCCAAAACAT-AGATTTTCCACAACCAAGGATACTCCAACCCTG
* *
322909 GTTTTATTTTCAGAACATAGATTTTCCACAACCAAGGATACTCCAACC
1 GTTTTATTTCCAAAACATAGATTTTCCACAACCAAGGATACTCCAACC
322957 TCGTTATTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 40 0.98
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (51 bp):
GTTTTATTTCCAAAACATAGATTTTCCACAACCAAGGATACTCCAACCCTG
Found at i:322932 original size:130 final size:130
Alignment explanation
Indices: 322763--323036 Score: 340
Period size: 130 Copynumber: 2.1 Consensus size: 130
322753 ATTTTCGAGG
* * * * * *
322763 GGATACTCTAACCCTGGTTTTATTTCCAAACCACTGATTTTTCACAATCGATGATACTTCAACCC
1 GGATACTCCAACCCTGGTTTTATTTCCAAACCACTGATTTTCCACAACCAAGGATACTCCAACCC
** * * *
322828 CGTTATTTTTGAAGGGATACTCTAATCTC-AGTTTTATTTCCAAAACA-TCAATTTTTCACCATC
66 CGTTATTCCTGAAGGGATACTCCAACCTCGA-TTTTATTTCCAAAACACT-AATTTTTCACAATC
322891 GA
129 GA
*
322893 GGATACTCCAACCCTGGTTTTATTTTCAGAA-CA-TAGATTTTCCACAACCAAGGATACTCCAAC
1 GGATACTCCAACCCTGGTTTTATTTCCA-AACCACT-GATTTTCCACAACCAAGGATACTCCAAC
* * *
322956 CTCGTTATTCCTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACTAATTTTTCACAATC
64 CCCGTTATTCCTGAAGGGATACTCCAACCTCGATTTTATTTCCAAAACACTAATTTTTCACAATC
323021 GA
129 GA
*
323023 CGATACTCCAACCC
1 GGATACTCCAACCC
323037 CGTTTATTTT
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
129 1 0.01
130 119 0.96
131 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (130 bp):
GGATACTCCAACCCTGGTTTTATTTCCAAACCACTGATTTTCCACAACCAAGGATACTCCAACCC
CGTTATTCCTGAAGGGATACTCCAACCTCGATTTTATTTCCAAAACACTAATTTTTCACAATCGA
Found at i:323073 original size:80 final size:79
Alignment explanation
Indices: 322893--323079 Score: 209
Period size: 79 Copynumber: 2.4 Consensus size: 79
322883 TCACCATCGA
* * * *
322893 GGATACTCCAACCCTGGTTTTATTT-TCAGAACATAGATTTTCCACAACCAAGGATACTCCAACC
1 GGATACTCCAACCCCGATTTTATTTCT-AAAACATAGATTTTCCACAACCAACGATACTCCAACC
*
322957 TCGTTATTCCTGAGG
65 CCGTTATTCCTGAGG
* * * *
322972 GGATACTCCAACCTCGATTTTATTTCTAAAACACTA-ATTTTTCACAATCGACGATACTCCAACC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACA-TAGATTTTCCACAACCAACGATACTCCAACC
*
323036 CCGTTTATT-TTCGAGG
65 CCG-TTATTCCT-GAGG
* *
323052 GGATACTCCAACCCCGTTTTTATCTCTA
1 GGATACTCCAACCCCGATTTTATTTCTA
323080 GAATATTAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 54 0.59
80 37 0.41
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTATTTCTAAAACATAGATTTTCCACAACCAACGATACTCCAACCC
CGTTATTCCTGAGG
Found at i:324162 original size:58 final size:59
Alignment explanation
Indices: 324081--324191 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 59
324071 TATATAGGTT
* *
324081 ATTTTCATAATCTAAAGACCA-TTTAG-CATTTTCCATGCATTTTAAGATCATTTAGGATA
1 ATTTTCATAATATAAAGACCATTTTAGACATTTT-CAT-CACTTTAAGATCATTTAGGATA
** *
324140 ATTTTCATAATAT-AAGGTCATTTTAGAGATTTTCATCACTTTAAGATCATTT
1 ATTTTCATAATATAAAGACCATTTTAGACATTTTCATCACTTTAAGATCATTT
324192 GAGAACCTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 20 0.44
59 20 0.44
60 5 0.11
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (59 bp):
ATTTTCATAATATAAAGACCATTTTAGACATTTTCATCACTTTAAGATCATTTAGGATA
Found at i:326843 original size:30 final size:31
Alignment explanation
Indices: 326796--326857 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
326786 GTATTCAAGG
*
326796 GAGGTTATTTCCTTAGCCATCTAAAAG-TAAA
1 GAGGTTATATCCTTAGCCATC-AAAAGATAAA
*
326827 GAGGTTATAT-CTTAGCCTTCAAAAGATAAA
1 GAGGTTATATCCTTAGCCATCAAAAGATAAA
326857 G
1 G
326858 GAAAAAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.18
30 14 0.50
31 9 0.32
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (31 bp):
GAGGTTATATCCTTAGCCATCAAAAGATAAA
Found at i:326883 original size:36 final size:35
Alignment explanation
Indices: 326819--326886 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
326809 TAGCCATCTA
* * *
326819 AAAGTAAAGAGGTTATATCTTAGCCTTCAAAAGAT
1 AAAGGAAAAAGGTTATATCTAAGCCTTCAAAAGAT
*
326854 AAAGGAAAAAGGTTACTATCTAAGTCTTCAAAA
1 AAAGGAAAAAGGTTA-TATCTAAGCCTTCAAAA
326887 AATAGGGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 13 0.46
36 15 0.54
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (35 bp):
AAAGGAAAAAGGTTATATCTAAGCCTTCAAAAGAT
Found at i:328755 original size:7 final size:7
Alignment explanation
Indices: 328743--328776 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
328733 TGCTAAGTTT
328743 TTTTTTC
1 TTTTTTC
328750 TTTTTTC
1 TTTTTTC
328757 TTTTTTC
1 TTTTTTC
328764 TTTTTTCC
1 TTTTTT-C
328772 TTTTT
1 TTTTT
328777 AACTTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:331184 original size:80 final size:80
Alignment explanation
Indices: 330968--331187 Score: 234
Period size: 79 Copynumber: 2.8 Consensus size: 80
330958 AACGAGGCTG
* * * * * * *
330968 GAGTATTCCCGATTATGAAAA-ATCGGTGTTCTGGAAATAAAATCGGGGTTGGAGTATCCTCTCA
1 GAGTATCCCCGATTATGAAAAGATCAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCTAA
*
331032 AAAATAACAGGGTTG
66 AAAATAACAGGGTTA
* * * *
331047 GAGTATCCCTGATTATAGAAAATCGA-CA-T-TTTGA-AAATAAAATTAGGGTTCGAGTATCCCC
1 GAGTATCCCCGATTAT-GAAAA--GATCAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCC
* *
331108 TAAAAAATGACGGGGTTA
63 TAAAAAATAACAGGGTTA
* *
331126 GAGTATCCCCGATTGTGAAAAGATTAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCC
1 GAGTATCCCCGATTATGAAAAGATCAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCC
331188 GACTATGAGA
Statistics
Matches: 113, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
76 2 0.02
77 1 0.01
78 6 0.05
79 69 0.61
80 32 0.28
81 1 0.01
82 1 0.01
83 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (80 bp):
GAGTATCCCCGATTATGAAAAGATCAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCTAA
AAAATAACAGGGTTA
Found at i:331353 original size:77 final size:77
Alignment explanation
Indices: 331171--331395 Score: 254
Period size: 79 Copynumber: 2.9 Consensus size: 77
331161 AAATAAAATT
* * ** * * *
331171 GGGGTTGGAGTATCCCCGACTATGAGAAATCAATATTTTAGAAATAAAACCAGGATTGGAGGATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGATTGGAGTAT-
* *
331236 CTCTCGAAAATAGC
65 C-CTCAAAAATAAC
** * *
331250 AAGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGATTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGATTGGAGTATC
331315 CTCAAAAATAAC
66 CTCAAAAATAAC
* * **
331327 GGGGTTGGAGTATCCCCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTGAGG-TTGGAGTA
1 GGGGTTGGAGTATCCCCGATTATGAAAA-ATTGATGTTTTAGAAATAAAACCG-GGATTGGAGTA
331391 TCCTC
64 TCCTC
331396 GATTGTGAGA
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
77 34 0.28
78 34 0.28
79 55 0.45
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (77 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGATTGGAGTATC
CTCAAAAATAAC
Found at i:331379 original size:208 final size:208
Alignment explanation
Indices: 331001--331523 Score: 692
Period size: 208 Copynumber: 2.5 Consensus size: 208
330991 CGGTGTTCTG
* * * *
331001 GAAATAAAATCGGGGTTGGAGTATCCTCTCAAAAATAACAGGGTTGGAGTATCCCTGATTAT-AG
1 GAAATAAAACCGGGGTTGGAGTATCCTCTCGAAAATAACAGGATTGGAGTATCCCCGATTATGA-
* ** * *** * *
331065 AAAATCGACATTTTGAAAATAAAATTAGGGTTCGAGTATCCCCTAAAAAATGACGGGGTTAGAGT
65 AAAATTGATGTTTTGGAAATAAAACCCGGGTTGGAGTAT--CCTAAAAAATAACGGGGTTAGAGT
*
331130 ATCCCCGATTGTGAAAAGATTAGTGTTTTAGAAATAAAATTGGGGTTGGAGTATCCCCGACTATG
128 ATCCCCGATTGTGAAAAGATTAGTGTTTTAGAAATAAAATTGAGGTTGGAGTATCCCCGACTATG
331195 AGAAATCAATATTTTA
193 AGAAATCAATATTTTA
* * * * *
331211 GAAATAAAACCAGGATTGGAGGATCCTCTCGAAAATAGCAAGATTGGAGTATCCCCGATTATGAA
1 GAAATAAAACCGGGGTTGGAGTATCCTCTCGAAAATAACAGGATTGGAGTATCCCCGATTATGAA
* *
331276 AAATTGATGTTTTGGAAATAAAA-CCGGGATTGGAGTATCCTCAAAAATAACGGGGTTGGAGTAT
66 AAATTGATGTTTTGGAAATAAAACCCGGG-TTGGAGTATCCTAAAAAATAACGGGGTTAGAGTAT
* * * *
331340 CCCCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTGAGGTTGGAGTATCCTCGATTGTGAG
130 CCCCGATTGTGAAAAGATTAGTGTTTTAGAAATAAAATTGAGGTTGGAGTATCCCCGACTATGAG
*
331405 AAATCAATGTTTTA
195 AAATCAATATTTTA
* * * * *
331419 GAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAAC-GGAATTAGAGTATTCCCGGTTATGA
1 GAAATAAAACCGGGGTTGGAGTATCCTCTCGAAAATAACAGG-ATTGGAGTATCCCCGATTATGA
*
331483 AAAATTTATGTTTTGGAAATAAAACCCGGGTTGGAGTATCC
65 AAAATTGATGTTTTGGAAATAAAACCCGGGTTGGAGTATCC
331524 CCGAGATGAA
Statistics
Matches: 273, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
207 1 0.00
208 182 0.67
209 8 0.03
210 81 0.30
211 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (208 bp):
GAAATAAAACCGGGGTTGGAGTATCCTCTCGAAAATAACAGGATTGGAGTATCCCCGATTATGAA
AAATTGATGTTTTGGAAATAAAACCCGGGTTGGAGTATCCTAAAAAATAACGGGGTTAGAGTATC
CCCGATTGTGAAAAGATTAGTGTTTTAGAAATAAAATTGAGGTTGGAGTATCCCCGACTATGAGA
AATCAATATTTTA
Found at i:331423 original size:129 final size:129
Alignment explanation
Indices: 331254--331527 Score: 327
Period size: 129 Copynumber: 2.1 Consensus size: 129
331244 AATAGCAAGA
** *
331254 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGATTGGAGTAT-CCTC
1 TTGGAGTATCCCCGATTATGAAAAATCAATGTTTTAGAAATAAAACCGGGATTGGAGTATCCCTC
** * * * **
331318 AAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAA-TTGAG
66 AAAAATAACGGAATTAGAGTATCCCCGATTATGAAAA-ATTGATGTTTTAGAAATAAAACCCG-G
331382 G
129 G
* * * * *
331383 TTGGAGTATCCTCGATTGTGAGAAATCAATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCT
1 TTGGAGTATCCCCGATTATGAAAAATCAATGTTTTAGAAATAAAACCGGGATTGGAGTAT-CCCT
* * * * *
331448 CGAAAATAACGGAATTAGAGTATTCCCGGTTATGAAAAATTTATGTTTTGGAAATAAAACCCGGG
65 CAAAAATAACGGAATTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCCGGG
331513 TTGGAGTATCCCCGA
1 TTGGAGTATCCCCGA
331528 GATGAATAAT
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
129 52 0.43
130 34 0.28
131 35 0.29
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (129 bp):
TTGGAGTATCCCCGATTATGAAAAATCAATGTTTTAGAAATAAAACCGGGATTGGAGTATCCCTC
AAAAATAACGGAATTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCCGGG
Found at i:331437 original size:51 final size:52
Alignment explanation
Indices: 331326--331446 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 52
331316 TCAAAAATAA
*** *
331326 CGGGGTTGGAGTATCCCCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAGATCAATGTTTTAGAAATAAAAC
* * * * *
331378 TGAGGTTGGAGTATCCTCGATTGTGAGAA-ATCAATGTTTTAGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAGATCAATGTTTTAGAAATAAAAC
331429 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
331447 TCGAAAATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
51 32 0.56
52 25 0.44
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (52 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAGATCAATGTTTTAGAAATAAAAC
Found at i:334367 original size:39 final size:40
Alignment explanation
Indices: 334271--334370 Score: 139
Period size: 39 Copynumber: 2.5 Consensus size: 40
334261 GTTAAGAATA
*
334271 ACCCTAAAGGCTCAGTTTTGACATAAAATATACTAAAATG
1 ACCCTAAAGGCTCAGTTTTGACACAAAATATACTAAAATG
* * * *
334311 TCCCTAAAAGCTTAGTTTTGACACAAAA-GTACTAAAATG
1 ACCCTAAAGGCTCAGTTTTGACACAAAATATACTAAAATG
*
334350 ACCTTAAAGGCTCAGTTTTGA
1 ACCCTAAAGGCTCAGTTTTGA
334371 AATGGAAGTA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
39 27 0.53
40 24 0.47
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (40 bp):
ACCCTAAAGGCTCAGTTTTGACACAAAATATACTAAAATG
Found at i:334380 original size:39 final size:39
Alignment explanation
Indices: 334249--334445 Score: 161
Period size: 38 Copynumber: 5.1 Consensus size: 39
334239 CGGGCTTGGA
*
334249 TTTGACATGGAAGT--TAAGAATAACCCTAAAGGCTCAGT
1 TTTGACATGAAAGTACTAA-AATAACCCTAAAGGCTCAGT
* * ** * *
334287 TTTGACATAAAATATACTAAAATGTCCCTAAAAGCTTAGT
1 TTTGACATGAAA-GTACTAAAATAACCCTAAAGGCTCAGT
** * *
334327 TTTGACACAAAAGTACTAAAATGACCTTAAAGGCTCAGT
1 TTTGACATGAAAGTACTAAAATAACCCTAAAGGCTCAGT
* * * * *
334366 TTTGAAATGGAAGTA-TAAAAAAATCCTAAAGGCTCAAT
1 TTTGACATGAAAGTACTAAAATAACCCTAAAGGCTCAGT
* * **
334404 TTTGATATGAAAGTACT-AAA-AACCCTAATGGCTTGGT
1 TTTGACATGAAAGTACTAAAATAACCCTAAAGGCTCAGT
334441 TTTGA
1 TTTGA
334446 TTGTAGCGTA
Statistics
Matches: 126, Mismatches: 29, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
37 17 0.13
38 44 0.35
39 35 0.28
40 27 0.21
41 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (39 bp):
TTTGACATGAAAGTACTAAAATAACCCTAAAGGCTCAGT
Found at i:335353 original size:39 final size:39
Alignment explanation
Indices: 335310--335387 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
335300 CTAAATAACT
* *
335310 TTAATAGACATATTTTGACACAAAGGTTC-CTACATGACC
1 TTAATAGACATATATTGACACAAAAGTTCTC-ACATGACC
*
335349 TTAATAGACATGTATTGACACAAAAGTTCTCACATGACC
1 TTAATAGACATATATTGACACAAAAGTTCTCACATGACC
335388 CTAAACTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (39 bp):
TTAATAGACATATATTGACACAAAAGTTCTCACATGACC
Found at i:335840 original size:17 final size:16
Alignment explanation
Indices: 335818--335880 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
335808 AAATTTTCAT
335818 GTCATTTTTGGGTTCGA
1 GTCA-TTTTGGGTTCGA
*
335835 GTCATTTTGGGTTCGG
1 GTCATTTTGGGTTCGA
* *
335851 GTTATTTCGGGTTC-A
1 GTCATTTTGGGTTCGA
*
335866 GATCATTTCGGGTTC
1 G-TCATTTTGGGTTC
335881 AGATTGTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
15 1 0.03
16 35 0.88
17 4 0.10
ACGTcount: A:0.11, C:0.14, G:0.30, T:0.44
Consensus pattern (16 bp):
GTCATTTTGGGTTCGA
Found at i:335844 original size:16 final size:16
Alignment explanation
Indices: 335827--335906 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
335817 TGTCATTTTT
*
335827 GGGTTCGAGTCATTTT
1 GGGTTCGAGTCATTTC
* *
335843 GGGTTCGGGTTATTTC
1 GGGTTCGAGTCATTTC
335859 GGGTTC-AGATCATTTC
1 GGGTTCGAG-TCATTTC
**
335875 GGGTTC-AGATTGTTTC
1 GGGTTCGAG-TCATTTC
*
335891 GGGTTCGAGTTATTTC
1 GGGTTCGAGTCATTTC
335907 AGATTTGGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
15 1 0.02
16 51 0.94
17 2 0.04
ACGTcount: A:0.12, C:0.14, G:0.31, T:0.42
Consensus pattern (16 bp):
GGGTTCGAGTCATTTC
Found at i:335872 original size:32 final size:32
Alignment explanation
Indices: 335827--335906 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
335817 TGTCATTTTT
* * *
335827 GGGTTCGAGTCATTTTGGGTTCGGGTTATTTC
1 GGGTTCGAGTCATTTCGGGTTCAGATTATTTC
*
335859 GGGTTC-AGATCATTTCGGGTTCAGATTGTTTC
1 GGGTTCGAG-TCATTTCGGGTTCAGATTATTTC
*
335891 GGGTTCGAGTTATTTC
1 GGGTTCGAGTCATTTC
335907 AGATTTGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.05
32 37 0.90
33 2 0.05
ACGTcount: A:0.12, C:0.14, G:0.31, T:0.42
Consensus pattern (32 bp):
GGGTTCGAGTCATTTCGGGTTCAGATTATTTC
Found at i:335955 original size:15 final size:15
Alignment explanation
Indices: 335935--335979 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
335925 TTTAACGCTT
335935 GGGTCAATTGAGTTC
1 GGGTCAATTGAGTTC
*
335950 GGGTCATTTTG-GATTC
1 GGGTCA-ATTGAG-TTC
335966 GGGTCAATTGAGTT
1 GGGTCAATTGAGTT
335980 TAACATTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.18, C:0.11, G:0.33, T:0.38
Consensus pattern (15 bp):
GGGTCAATTGAGTTC
Found at i:344604 original size:176 final size:175
Alignment explanation
Indices: 344267--344771 Score: 419
Period size: 176 Copynumber: 2.9 Consensus size: 175
344257 CATGATTATG
* * * * * *
344267 TCAAATTTAATTTTATATAATATAAATTATTAATATATTAAATTAATATAAATATATAATACTTT
1 TCAAAATTAATTTTATATAATATAAATGATTAATATATCAAATTAATATAAACACATAATACCTT
* * * * * * * * *
344332 AATTATAATTATGATATATGAAAGTATATGTATAAGATATATATACACTAACTATCATATTTACT
66 AATTATAATTATAACACATGAAAGCATACGAACAAGATATACATACACTAACTATCATATCTACT
* * *
344397 TAGAGCTAATCATCACCCTTTGTAGGGTTTTTTCTTCACTAGTCA
131 TAGAGCTAATCATCACCCTTTGTAAGGTTTTTTATTCACTAATCA
* * * * *
344442 TTAAAATTGATTTTATATAATATGAATGATTAATGTATCAAATTAATGTGAAACACATAATACCT
1 TCAAAATTAATTTTATATAATATAAATGATTAATATATCAAATTAATAT-AAACACATAATACCT
* * *
344507 TAATTATAATTATAACACGTGAAAGCATACGAACAA-A-ATACATACA-TGGACTATCATGTCTA
65 TAATTATAATTATAACACATGAAAGCATACGAACAAGATATACATACACT-AACTATCATATCTA
* * * * **
344569 CTTAGAGCTAATCGTTACCATTTTTTAAAGGTTTTTTATTCGGTAATCA
129 CTTAGAGCTAATCATCACC-CTTTGT-AAGGTTTTTTATTCACTAATCA
* * * * * * *
344618 TCAAATTTAATTTTATATAATATAAGTTATTAATACATTAAATTAATATAAATATATAATATATA
1 TCAAAATTAATTTTATATAATATAAATGATTAAT--A-T--ATCAA-ATTAATATA-AACACATA
** * * * * * * * *
344683 ATATATTAATTATAATTATAATACGTAAAAGTATACAAATAAG--ATACATATA-TGAACTAGCA
59 ATACCTTAATTATAATTATAACACATGAAAGCATACGAACAAGATATACATACACT-AACTATCA
344745 TATCTACTTAGAGCTAATCATCACCCT
123 TATCTACTTAGAGCTAATCATCACCCT
344772 CTTTTAGGAA
Statistics
Matches: 260, Mismatches: 58, Indels: 18
0.77 0.17 0.05
Matches are distributed among these distances:
173 1 0.00
174 36 0.14
175 46 0.18
176 85 0.33
179 1 0.00
181 6 0.02
182 85 0.33
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (175 bp):
TCAAAATTAATTTTATATAATATAAATGATTAATATATCAAATTAATATAAACACATAATACCTT
AATTATAATTATAACACATGAAAGCATACGAACAAGATATACATACACTAACTATCATATCTACT
TAGAGCTAATCATCACCCTTTGTAAGGTTTTTTATTCACTAATCA
Found at i:344680 original size:7 final size:7
Alignment explanation
Indices: 344661--344705 Score: 60
Period size: 6 Copynumber: 6.7 Consensus size: 7
344651 TACATTAAAT
344661 TAATATA
1 TAATATA
344668 -AATATA
1 TAATATA
344674 TAATATA
1 TAATATA
344681 TAATATA
1 TAATATA
344688 TTAAT-TA
1 -TAATATA
344695 TAAT-TA
1 TAATATA
344701 TAATA
1 TAATA
344706 CGTAAAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 16 0.46
7 15 0.43
8 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATATA
Found at i:344686 original size:20 final size:19
Alignment explanation
Indices: 344661--344705 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
344651 TACATTAAAT
344661 TAATATA-AATATATAATATA
1 TAATATATAAT-TATAAT-TA
344681 TAATATATTAATTATAATTA
1 TAATATA-TAATTATAATTA
344701 TAATA
1 TAATA
344706 CGTAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.61
21 6 0.26
22 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATATAATTATAATTA
Found at i:344704 original size:12 final size:14
Alignment explanation
Indices: 344661--344705 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
344651 TACATTAAAT
344661 TAATATA-AATATA
1 TAATATATAATATA
344674 TAATATATAATATA
1 TAATATATAATATA
344688 TTAAT-TATAAT-TA
1 -TAATATATAATATA
344701 TAATA
1 TAATA
344706 CGTAAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.14
13 9 0.31
14 12 0.41
15 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATATAATATA
Found at i:344762 original size:182 final size:178
Alignment explanation
Indices: 344267--344771 Score: 480
Period size: 182 Copynumber: 2.9 Consensus size: 178
344257 CATGATTATG
*
344267 TCAAATTTAATTTTATATAATATAAATTATTAATATATTAAATTAATATAAATATATAATACTTT
1 TCAAATTTAATTTTATATAATAT-AATTATTAATATATTAAATTAATATAAATATATAATA-TAT
* * * *
344332 AAT-TA-TAATTATGA-TAT-AT--G-AAAGTATATGTATAAGATATATATACACT-AACTATCA
64 AATATATTAATTATAATTATAATACGTAAAGTATACGAATAAGATACATAT--A-TGAACTATCA
* * * *
344389 TATTTACTTAGAGCTAATCATCACCCTTTGTAGGGTTTTTTCTTCACTAGTCA
126 TATCTACTTAGAGCTAATCATCACCCTTTGTAAGGTTTTTTATTCACTAATCA
* * * * * * * * * *
344442 TTAAAATTGATTTTATATAATATGAATGATTAATGTATCAAATT-A-AT--GT-GA-AACACATA
1 TCAAATTTAATTTTATATAATAT-AATTATTAATATATTAAATTAATATAAATATATAATATATA
** * * * * * * *
344501 ATACCTTAATTATAATTATAACACGTGAAAGCATACGAACAAAATACATACATGGACTATCATGT
65 ATATATTAATTATAATTATAATACGT-AAAGTATACGAATAAGATACATATATGAACTATCATAT
* * * * **
344566 CTACTTAGAGCTAATCGTTACCATTTTTTAAAGGTTTTTTATTCGGTAATCA
129 CTACTTAGAGCTAATCATCACC-CTTTGT-AAGGTTTTTTATTCACTAATCA
*
344618 TCAAATTTAATTTTATATAATATAAGTTATTAATACATTAAATTAATATAAATATATAATATATA
1 TCAAATTTAATTTTATATAATATAA-TTATTAATATATTAAATTAATATAAATATATAATATATA
* *
344683 ATATATTAATTATAATTATAATACGTAAAAGTATACAAATAAGATACATATATGAACTAGCATAT
65 ATATATTAATTATAATTATAATACGT-AAAGTATACGAATAAGATACATATATGAACTATCATAT
344748 CTACTTAGAGCTAATCATCACCCT
129 CTACTTAGAGCTAATCATCACCCT
344772 CTTTTAGGAA
Statistics
Matches: 251, Mismatches: 61, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
168 4 0.02
169 3 0.01
170 9 0.04
171 4 0.02
172 1 0.00
173 3 0.01
174 31 0.12
175 43 0.17
176 68 0.27
177 1 0.00
178 2 0.01
180 1 0.00
181 2 0.01
182 79 0.31
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (178 bp):
TCAAATTTAATTTTATATAATATAATTATTAATATATTAAATTAATATAAATATATAATATATAA
TATATTAATTATAATTATAATACGTAAAGTATACGAATAAGATACATATATGAACTATCATATCT
ACTTAGAGCTAATCATCACCCTTTGTAAGGTTTTTTATTCACTAATCA
Found at i:344988 original size:16 final size:15
Alignment explanation
Indices: 344940--345029 Score: 63
Period size: 16 Copynumber: 5.7 Consensus size: 15
344930 TCGAAATTAT
*
344940 CCGAACCCGAAATAG
1 CCGAACCCGAAAAAG
* *
344955 CTCGAACTCGAGAAAG
1 C-CGAACCCGAAAAAG
344971 CCGAAACCCGAAAAAG
1 CCG-AACCCGAAAAAG
* * *
344987 CCTGAATCCAAAAGAAC
1 CC-GAACCCGAAA-AAG
* *
345004 CCGAACTCGAAAGAAC
1 CCGAACCCGAAA-AAG
345020 CCGAACCCGA
1 CCGAACCCGA
345030 GATTGACCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
15 3 0.05
16 51 0.86
17 5 0.08
ACGTcount: A:0.42, C:0.32, G:0.19, T:0.07
Consensus pattern (15 bp):
CCGAACCCGAAAAAG
Found at i:345973 original size:24 final size:24
Alignment explanation
Indices: 345944--346001 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
345934 TGAGTTTACG
*
345944 TGAGCTTTTAAGTTTAGA-TGAGCA
1 TGAGCTTTTAAGTTTAGACGGA-CA
345968 TGAGCTTTTAAGTTTAGACGGACA
1 TGAGCTTTTAAGTTTAGACGGACA
345992 TGAGCTTTTA
1 TGAGCTTTTA
346002 GTTAAGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (24 bp):
TGAGCTTTTAAGTTTAGACGGACA
Found at i:346404 original size:16 final size:16
Alignment explanation
Indices: 346359--346409 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
346349 CCTGAACCCA
*
346359 AAAAAGCTCAAA-CTCA
1 AAAAAGCTCAAACCT-G
**
346375 AAAAAGCTTGAACCTG
1 AAAAAGCTCAAACCTG
*
346391 AAAAAGCTCAAACCCG
1 AAAAAGCTCAAACCTG
346407 AAA
1 AAA
346410 GAGCATGACC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 26 0.93
17 2 0.07
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAAGCTCAAACCTG
Found at i:346451 original size:16 final size:16
Alignment explanation
Indices: 346432--346467 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
346422 AATAAATTCC
* *
346432 AACCTGAATAAGCTCG
1 AACCTGAACAAGCCCG
346448 AACCTGAACAAGCCCG
1 AACCTGAACAAGCCCG
346464 AACC
1 AACC
346468 CAAACCTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.17, T:0.11
Consensus pattern (16 bp):
AACCTGAACAAGCCCG
Found at i:349962 original size:2 final size:2
Alignment explanation
Indices: 349944--349989 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
349934 TTAAAAATAA
*
349944 AT AT CAT AT AT -T A- AT AT AT AT AT AT AT AT AT AT GAT AT AA AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
349986 AT AT
1 AT AT
349990 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 2 0.05
2 32 0.84
3 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:353010 original size:18 final size:19
Alignment explanation
Indices: 352989--353037 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
352979 ATATAAAATT
352989 TTATATATTAATA-ATTTA
1 TTATATATTAATATATTTA
*
353007 TTATATATTTTTATATATTTA
1 TTATATA--TTAATATATTTA
353028 TTAT-TATTAA
1 TTATATATTAA
353038 ATTTATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.38
20 7 0.27
21 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATATTAATATATTTA
Found at i:353011 original size:28 final size:27
Alignment explanation
Indices: 352973--353025 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
352963 ATGTGTTTAT
352973 TAATTTATATAAAATTTTATATATTAA
1 TAATTTATATAAAATTTTATATATTAA
* *
353000 TAATTTATTATATATTTTTATATATT
1 TAATTTA-TATAAAATTTTATATATT
353026 TATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TAATTTATATAAAATTTTATATATTAA
Found at i:353022 original size:10 final size:11
Alignment explanation
Indices: 353002--353035 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
352992 TATATTAATA
353002 ATTTATTATAT
1 ATTTATTATAT
353013 ATTT-TTATAT
1 ATTTATTATAT
353023 ATTTATTAT-T
1 ATTTATTATAT
353033 ATT
1 ATT
353036 AAATTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTATTATAT
Found at i:353086 original size:24 final size:24
Alignment explanation
Indices: 352999--353087 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
352989 TTATATATTA
352999 ATAATTTATTATATATT--TTTAT
1 ATAATTTATTATATATTAATTTAT
353021 AT-ATTTATTAT-TATTAAATTTAT
1 ATAATTTATTATATATT-AATTTAT
* * * *
353044 GTTATTT-TTATGTTTTTAATTTAT
1 ATAATTTATTAT-ATATTAATTTAT
353068 ATAAATTT-TTATATATTAAT
1 AT-AATTTATTATATATTAAT
353088 AATTAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.07
21 9 0.17
22 2 0.04
23 10 0.19
24 18 0.33
25 11 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATAATTTATTATATATTAATTTAT
Found at i:353129 original size:32 final size:32
Alignment explanation
Indices: 353051--353129 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 32
353041 TATGTTATTT
* * * *
353051 TTATGTTTTTAATTTATATAAATTTTTATATA
1 TTATGTATTTATTTTATATAAAATTTGATATA
* * *
353083 TTAAT-AATTAATTTTATATAAAATTTGATATG
1 TT-ATGTATTTATTTTATATAAAATTTGATATA
353115 TTATGTATTTATTTT
1 TTATGTATTTATTTT
353130 GTATCGATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
31 2 0.06
32 32 0.89
33 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (32 bp):
TTATGTATTTATTTTATATAAAATTTGATATA
Found at i:353271 original size:16 final size:16
Alignment explanation
Indices: 353250--353280 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
353240 TTAATTTATA
353250 AAAAATATTTAAATAC
1 AAAAATATTTAAATAC
353266 AAAAATATTTAAATA
1 AAAAATATTTAAATA
353281 ATTTCTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATATTTAAATAC
Found at i:353701 original size:14 final size:15
Alignment explanation
Indices: 353682--353716 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
353672 CTCAACGCGG
353682 ATAAAATTTAA-AAA
1 ATAAAATTTAATAAA
*
353696 ATAAAATTTAATTAA
1 ATAAAATTTAATAAA
353711 ATAAAA
1 ATAAAA
353717 AAATTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAATTTAATAAA
Found at i:353719 original size:18 final size:18
Alignment explanation
Indices: 353689--353723 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
353679 CGGATAAAAT
353689 TTAAAAAATAAAATTTAA
1 TTAAAAAATAAAATTTAA
353707 TTAAATAAA-AAAATTTA
1 TTAAA-AAATAAAATTTA
353724 TGTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAAATAAAATTTAA
Found at i:353750 original size:7 final size:7
Alignment explanation
Indices: 353731--353765 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
353721 TTATGTTAAA
353731 ATTAATGT
1 ATTAAT-T
353739 ATTAATT
1 ATTAATT
353746 ATTAATT
1 ATTAATT
353753 ATTAATT
1 ATTAATT
*
353760 TTTAAT
1 ATTAAT
353766 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
ATTAATT
Found at i:354138 original size:21 final size:21
Alignment explanation
Indices: 354114--354185 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
354104 TTTGATATGA
354114 TTATATAAGTTTAATTTATTT
1 TTATATAAGTTTAATTTATTT
*
354135 TTATTTGTAAAAGTTTAAATTTA-TT
1 TTA----TATAAGTTT-AATTTATTT
* *
354160 TTATTTAAGATATAATTTATTT
1 TTATATAAG-TTTAATTTATTT
354182 TTAT
1 TTAT
354186 TTGTAAGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
21 13 0.32
22 8 0.20
25 13 0.32
26 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATATAAGTTTAATTTATTT
Found at i:354148 original size:25 final size:25
Alignment explanation
Indices: 354120--354191 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
354110 ATGATTATAT
354120 AAGTTTAATTTATTTTTATTTGTAA
1 AAGTTTAATTTATTTTTATTTGTAA
354145 AAGTTTAAATTTA-TTTTA-TT-TAA
1 AAGTTT-AATTTATTTTTATTTGTAA
* *
354168 GA-TATAATTTATTTTTATTTGTAA
1 AAGTTTAATTTATTTTTATTTGTAA
354192 GATTAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 6 0.15
24 5 0.12
25 11 0.27
26 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (25 bp):
AAGTTTAATTTATTTTTATTTGTAA
Found at i:354253 original size:40 final size:40
Alignment explanation
Indices: 354124--354258 Score: 114
Period size: 40 Copynumber: 3.1 Consensus size: 40
354114 TTATATAAGT
354124 TTAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTATTTAAGA
1 TTAATTTATTTTTATTTGT-AAAGTTTAAATTTA-TTT-TTT---A
* **
354170 TATAATTTATTTTTATTTGT-AAGATT-AATTTAATTAAAGTTA
1 T-TAATTTATTTTTATTTGTAAAGTTTAAATTT-ATT--TTTTA
354212 TT-ATTTATTTTTATTTGTAATAGTTTAAATTTATTTTTTA
1 TTAATTTATTTTTATTTGTAA-AGTTTAAATTTATTTTTTA
354252 TTTAATT
1 -TTAATT
354259 ATATAAATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 22
0.73 0.06 0.22
Matches are distributed among these distances:
40 19 0.26
41 4 0.05
42 12 0.16
43 5 0.07
44 7 0.09
45 8 0.11
46 1 0.01
47 18 0.24
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (40 bp):
TTAATTTATTTTTATTTGTAAAGTTTAAATTTATTTTTTA
Found at i:356218 original size:29 final size:28
Alignment explanation
Indices: 356119--356721 Score: 426
Period size: 32 Copynumber: 20.2 Consensus size: 28
356109 GGTGAATTTA
*
356119 TGGGCTTTTG-AAGAGATGCCATTGACTTG
1 TGGGC-TTTGAAAG-GATGCCACTGACTTG
* * *
356148 TGGGCTTTGAAAAGAGTTGCCACCGAATTG
1 TGGGCTTTG-AAAG-GATGCCACTGACTTG
356178 TATGGGCTTTGAGAAGGATGCCACTGACTTG
1 --TGGGCTTTGA-AAGGATGCCACTGACTTG
* * *
356209 TGGGCTTTGAAAAGATGCCAATGATTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
356237 TGGGCTTTGAGAAGGATGCCATTGACTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
*
356266 TGGGCTTTGAGAAGGATGCCACTAACTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
* * *
356295 TAGGCTTTGAGAAGAATGCTACTGACTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
356324 TGGGCTTTGAAAGGATGCCACTG-CTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
356351 TGGGCTTTGAAAGGATGCCACTGATTTGTG
1 TGGGCTTTGAAAGGATGCCACTGA-CT-TG
*
356381 TGGGCTTTGAGAATGATGCCACTGACTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
* *
356410 TGGGCTTTGAAATGGGTTGCCAC-CAGCTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGA-C-T-TG
* *
356442 TGGGCTTTCAAATAGGTTGCCA-TCGACTTGTG
1 TGGGCTTT-GAA-AGGATGCCACT-GAC-T-TG
* *
356474 TGGGCTTTGAAATGGGTTGCCACCGACTTATG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
* * * *
356506 TGGGCTTTCAAATGGGTTGTCACCGACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
* *
356538 TGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
* *
356570 TGGGCTTTGAAATGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAAA--GGATGCCACTGAC-T-TG
** *
356602 TGGGCTTTGAAATAATGCCACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* ** *
356630 CGGGCTTAAAAATGGGTGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
** *
356659 TGGGCTTAAAAAGGATGCCAC-GAAGTTG
1 TGGGCTTTGAAAGGATGCCACTG-ACTTG
* *
356687 TGGACTTT-AGAAGGGTGCCACTGACTTG
1 TGGGCTTTGA-AAGGATGCCACTGACTTG
356715 TGGGCTT
1 TGGGCTT
356722 AAAAAAGATG
Statistics
Matches: 490, Mismatches: 58, Indels: 53
0.82 0.10 0.09
Matches are distributed among these distances:
27 29 0.06
28 91 0.19
29 130 0.27
30 45 0.09
31 29 0.06
32 162 0.33
33 3 0.01
34 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (28 bp):
TGGGCTTTGAAAGGATGCCACTGACTTG
Found at i:356335 original size:115 final size:115
Alignment explanation
Indices: 356114--356419 Score: 386
Period size: 115 Copynumber: 2.6 Consensus size: 115
356104 AGTCGGGTGA
* * * * *
356114 ATTTATGGGCTTT-TGAAGAGATGCCATTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGAA-TT
1 ATTTGTGGGCTTTGAGAAG-GATGCCATTGACTTGTGGGCTTTGAGAAG-GATGCCA-CTAACTT
*
356177 GTATGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCAATG
63 GTA--GGCTTTGAGAAGAATGCCACTGACTTGTGGGCTTTGAAAAGATGCCAATG
356232 ATTTGTGGGCTTTGAGAAGGATGCCATTGACTTGTGGGCTTTGAGAAGGATGCCACTAACTTGTA
1 ATTTGTGGGCTTTGAGAAGGATGCCATTGACTTGTGGGCTTTGAGAAGGATGCCACTAACTTGTA
* * *
356297 GGCTTTGAGAAGAATGCTACTGACTTGTGGGCTTTGAAAGGATGCCACTG
66 GGCTTTGAGAAGAATGCCACTGACTTGTGGGCTTTGAAAAGATGCCAATG
* * * * *
356347 -CTTGTGGGCTTTGA-AAGGATGCCACTGATTTGTGTGGGCTTTGAGAATGATGCCACTGACTTG
1 ATTTGTGGGCTTTGAGAAGGATGCCATTGA-CT-TGTGGGCTTTGAGAAGGATGCCACTAACTTG
*
356410 TGGGCTTTGA
64 TAGGCTTTGA
356420 AATGGGTTGC
Statistics
Matches: 169, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
113 13 0.08
114 14 0.08
115 84 0.50
116 3 0.02
117 11 0.07
118 40 0.24
119 4 0.02
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (115 bp):
ATTTGTGGGCTTTGAGAAGGATGCCATTGACTTGTGGGCTTTGAGAAGGATGCCACTAACTTGTA
GGCTTTGAGAAGAATGCCACTGACTTGTGGGCTTTGAAAAGATGCCAATG
Found at i:356677 original size:57 final size:57
Alignment explanation
Indices: 356579--356807 Score: 189
Period size: 56 Copynumber: 4.0 Consensus size: 57
356569 GTGGGCTTTG
* * * * *
356579 AAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATA-ATGCCACTAACTTGCGGGCTTAA
1 AAATGGG-TGCCACTGAC-T-TGTGGGC-TTAAAAAAGATGCCACGAACTTGCGGACTTAA
* * * *
356639 AAATGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGTTGTGGACTTTA
1 AAATGGGTGCCACTGACTTGTGGGCTTAAAAAAGATGCCACGAACTTGCGGACTTAA
* * * * *
356696 GAA-GGGTGCCACTGACTTGTGGGCTTAAAAAAGATGTCACAAAGTTGTGGACTT-A
1 AAATGGGTGCCACTGACTTGTGGGCTTAAAAAAGATGCCACGAACTTGCGGACTTAA
** * * * * * *
356751 AAA-GAATGTCACTGAGTTGTGGACTTAAAAGAG-TGCCACGAAGTTGTGGACTTAA
1 AAATGGGTGCCACTGACTTGTGGGCTTAAAAAAGATGCCACGAACTTGCGGACTTAA
356806 AA
1 AA
356808 GGGTACCATG
Statistics
Matches: 145, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
54 18 0.12
55 30 0.21
56 53 0.37
57 27 0.19
58 1 0.01
59 9 0.06
60 7 0.05
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (57 bp):
AAATGGGTGCCACTGACTTGTGGGCTTAAAAAAGATGCCACGAACTTGCGGACTTAA
Found at i:356761 original size:27 final size:27
Alignment explanation
Indices: 356712--356808 Score: 122
Period size: 27 Copynumber: 3.6 Consensus size: 27
356702 TGCCACTGAC
* *
356712 TTGTGGGCTTAAAAAAGATGTCACAAAG
1 TTGTGGACTTAAAAGA-ATGTCACAAAG
**
356740 TTGTGGACTTAAAAGAATGTCACTGAG
1 TTGTGGACTTAAAAGAATGTCACAAAG
* * *
356767 TTGTGGACTTAAAAGAGTGCCACGAAG
1 TTGTGGACTTAAAAGAATGTCACAAAG
356794 TTGTGGACTTAAAAG
1 TTGTGGACTTAAAAG
356809 GGTACCATGG
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
27 47 0.77
28 14 0.23
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (27 bp):
TTGTGGACTTAAAAGAATGTCACAAAG
Found at i:356822 original size:27 final size:27
Alignment explanation
Indices: 356646--357052 Score: 296
Period size: 28 Copynumber: 14.7 Consensus size: 27
356636 TAAAAATGGG
* * *
356646 TGCCACTGACTTGTGGGCTTAAAAAGGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGA
* * *
356674 TGCCACGAAGTTGTGGACTTTAGAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * * *
356702 TGCCACTGACTTGTGGGCTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGA
* ** *
356730 TGTCACAAAGTTGTGGACTTAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
356757 TGTCACTGAGTTGTGGACTTAAAA-GA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
356783 GTGCCACGAAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
356811 TACCATGGAGTTATGGACTTTAAAAGAA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * *
356839 CGCCACGGAGTTGAGGACGTGAAACA-GA
1 TGCCACGGAGTTGTGGAC-TTAAA-AGGA
** * *
356867 TGCCATAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
356894 TACCACGAAGTTGTGGACTTTAAAAGAA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
356922 TGCCACAGAGTTGTGGACTTGAAACGGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGA
* * * * *
356950 TGTCATGGAGTTATGGACTTGAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
356977 TACCACGGAGTTGTGGACTTTAAAAGAA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * *
357005 CGCCACTGAGTTGTGGACTTGAAATGGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGA
*
357033 TGCTACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
357053 TGAAAAGAAA
Statistics
Matches: 286, Mismatches: 82, Indels: 22
0.73 0.21 0.06
Matches are distributed among these distances:
26 2 0.01
27 104 0.36
28 177 0.62
29 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:356889 original size:55 final size:54
Alignment explanation
Indices: 356764--357033 Score: 143
Period size: 55 Copynumber: 4.9 Consensus size: 54
356754 GAATGTCACT
* ** * * * *
356764 GAGTTGTGGACTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAGGGTACCATG
1 GAGTTATGGACTTAAAAGAACGCCACGAAGTTGAGGACTGAAAAGGATACCATA
* *
356818 GAGTTATGGACTTTAAAAGAACGCCACGGAGTTGAGGACGTGAAACA-GATGCCATA
1 GAGTTATGGAC-TTAAAAGAACGCCACGAAGTTGAGGAC-TGAAA-AGGATACCATA
**** * * * * *
356874 GAGTTATGGACTTAAAAGGGTACCACGAAGTTGTGGACTTTAAAAGAATGCCACA
1 GAGTTATGGACTTAAAAGAACGCCACGAAGTTGAGGAC-TGAAAAGGATACCATA
* * * * * * * * **
356929 GAGTTGTGGACTTGAAACGGATGTCATGGAGTT-ATGGACTTG-AAAGGGTACCACG
1 GAGTTATGGACTT-AAAAGAACGCCACGAAGTTGA-GGAC-TGAAAAGGATACCATA
* * *
356984 GAGTTGTGGACTTTAAAAGAACGCCACTG-AGTTGTGGACTTGAAATGGAT
1 GAGTTATGGAC-TTAAAAGAACGCCAC-GAAGTTGAGGAC-TGAAAAGGAT
357034 GCTACGGAGT
Statistics
Matches: 166, Mismatches: 40, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
54 11 0.07
55 106 0.64
56 48 0.29
57 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (54 bp):
GAGTTATGGACTTAAAAGAACGCCACGAAGTTGAGGACTGAAAAGGATACCATA
Found at i:357034 original size:83 final size:83
Alignment explanation
Indices: 356738--357052 Score: 402
Period size: 83 Copynumber: 3.8 Consensus size: 83
356728 GATGTCACAA
* * * *
356738 AGTTGTGGAC-TTAAAAGAATGTCACTGAGTTGTGGACTT-AAA-AGAGTGCCACGAAGTTGTGG
1 AGTTGTGGACTTTAAAAGAACGCCACTGAGTTGTGGACTTGAAACAGA-TGCCACGGAGTTATGG
*
356800 ACTTAAAAGGGTACCATGG
65 ACTTAAAAGGGTACCACGG
* * * * **
356819 AGTTATGGACTTTAAAAGAACGCCACGGAGTTGAGGACGTGAAACAGATGCCATAGAGTTATGGA
1 AGTTGTGGACTTTAAAAGAACGCCACTGAGTTGTGGACTTGAAACAGATGCCACGGAGTTATGGA
*
356884 CTTAAAAGGGTACCACGA
66 CTTAAAAGGGTACCACGG
* * * * *
356902 AGTTGTGGACTTTAAAAGAATGCCACAGAGTTGTGGACTTGAAACGGATGTCATGGAGTTATGGA
1 AGTTGTGGACTTTAAAAGAACGCCACTGAGTTGTGGACTTGAAACAGATGCCACGGAGTTATGGA
*
356967 CTTGAAAGGGTACCACGG
66 CTTAAAAGGGTACCACGG
** * *
356985 AGTTGTGGACTTTAAAAGAACGCCACTGAGTTGTGGACTTGAAATGGATGCTACGGAGTTGTGGA
1 AGTTGTGGACTTTAAAAGAACGCCACTGAGTTGTGGACTTGAAACAGATGCCACGGAGTTATGGA
357050 CTT
66 CTT
357053 TGAAAAGAAA
Statistics
Matches: 202, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
81 9 0.04
82 24 0.12
83 166 0.82
84 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (83 bp):
AGTTGTGGACTTTAAAAGAACGCCACTGAGTTGTGGACTTGAAACAGATGCCACGGAGTTATGGA
CTTAAAAGGGTACCACGG
Found at i:358384 original size:20 final size:19
Alignment explanation
Indices: 358335--358384 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
358325 TTTTTTTGGA
* *
358335 TTTTTGTTGTTCCCTTTTT
1 TTTTTGTTTTTCACTTTTT
* *
358354 ATTTTGCTTTTGCACTTTTT
1 TTTTTG-TTTTTCACTTTTT
358374 TTTTTGTTTTT
1 TTTTTGTTTTT
358385 TTTTCATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.04, C:0.12, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTTGTTTTTCACTTTTT
Found at i:366217 original size:16 final size:16
Alignment explanation
Indices: 366198--366250 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
366188 ATACAAGAAA
366198 AAGAAAGGTAAAGAGT
1 AAGAAAGGTAAAGAGT
*
366214 AAGAAAAGTAAA-AG-
1 AAGAAAGGTAAAGAGT
366228 AAGAAAGGTAAAGAGT
1 AAGAAAGGTAAAGAGT
366244 AAGAAAG
1 AAGAAAG
366251 TTGTTGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 11 0.33
15 4 0.12
16 18 0.55
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.09
Consensus pattern (16 bp):
AAGAAAGGTAAAGAGT
Found at i:366933 original size:15 final size:15
Alignment explanation
Indices: 366915--366953 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
366905 TATTTAAAAG
*
366915 TTAATAATTTATTAT
1 TTAATAATTTATTAA
* *
366930 TTAAAAATTTTTTAA
1 TTAATAATTTATTAA
366945 TTAATAATT
1 TTAATAATT
366954 GTTTAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATAATTTATTAA
Found at i:367112 original size:10 final size:10
Alignment explanation
Indices: 367079--367122 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
367069 CTTTTTCGCA
367079 ATGAACAGTG
1 ATGAACAGTG
*
367089 AT-ACATCTGTG
1 ATGA-A-CAGTG
367100 ATGAACAGTG
1 ATGAACAGTG
367110 ATGAACAGTG
1 ATGAACAGTG
367120 ATG
1 ATG
367123 TATCGATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 1 0.03
10 20 0.69
11 7 0.24
12 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.25
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:367138 original size:13 final size:13
Alignment explanation
Indices: 367120--367144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
367110 ATGAACAGTG
367120 ATGTATCGATACA
1 ATGTATCGATACA
367133 ATGTATCGATAC
1 ATGTATCGATAC
367145 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:368417 original size:30 final size:31
Alignment explanation
Indices: 368341--368432 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
368331 ACAGTTCAGA
* *
368341 ACAAAAACCACTATTCTTATTTGGTGGTACG
1 ACAAAAACCACTATTCTTATCTGGTGGCACG
368372 ACAAAAACCACTATTCTTATCTGGTGGCACG
1 ACAAAAACCACTATTCTTATCTGGTGGCACG
* * * *
368403 A-AGAAACCATTATTCTTAACCGGTGGCACG
1 ACAAAAACCACTATTCTTATCTGGTGGCACG
368433 GTTTGAAATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
30 25 0.45
31 30 0.55
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (31 bp):
ACAAAAACCACTATTCTTATCTGGTGGCACG
Found at i:369288 original size:14 final size:15
Alignment explanation
Indices: 369269--369297 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
369259 TTACGACTAT
369269 AAAATA-ATTTATTA
1 AAAATATATTTATTA
369283 AAAATATATTTATTA
1 AAAATATATTTATTA
369298 TGTCATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATATTTATTA
Found at i:370527 original size:75 final size:75
Alignment explanation
Indices: 370441--370745 Score: 311
Period size: 75 Copynumber: 4.1 Consensus size: 75
370431 GGTATTACAT
* * * *
370441 TACAAATAAAAATAAATTATACCATCAAAAATATAAACTCATATAATTATACAAAAAAAAACACA
1 TACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCGTATAATCATACCAAAAAAAACACA
*
370506 TTTAAA-TTT
66 TTTAAACTTC
* * * * *
370515 TGATAAATAAAAATAAATTATACCATCAAAAATTTAAACTTGTATAAGCATACCCAAAAAAACAT
1 T-ACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCGTATAATCATACCAAAAAAAACAC
370580 ATTTAAACTTC
65 ATTTAAACTTC
* * * * *
370591 TACAAATAAAAATAAATTATATCTTAAAAAATTTTAACTCGTATAATCATACC--AAAAAGCA-A
1 TACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCGTATAATCATACCAAAAAAAACACA
* *
370653 ATTAAACTTT
66 TTTAAACTTC
* * * * * *
370663 TACAAATAAAGATAAATAATATC-TTAAAAATTTAAA-TATGTATAATCAAACC-AAAAAAACA-
1 TACAAATAAAAATAAATTATACCATCAAAAATTTAAACT-CGTATAATCATACCAAAAAAAACAC
370724 ATAATTAAACTTC
65 AT--TTAAACTTC
370737 TACAAATAA
1 TACAAATAA
370746 TGAAAAATAA
Statistics
Matches: 196, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 23 0.12
72 38 0.19
73 7 0.04
74 18 0.09
75 106 0.54
76 3 0.02
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (75 bp):
TACAAATAAAAATAAATTATACCATCAAAAATTTAAACTCGTATAATCATACCAAAAAAAACACA
TTTAAACTTC
Found at i:370755 original size:74 final size:72
Alignment explanation
Indices: 370542--370757 Score: 240
Period size: 72 Copynumber: 2.9 Consensus size: 72
370532 TTATACCATC
* * * *
370542 AAAAATTTAAACTTGTATAAGCATACCCAAAAAAACATATTTAAACTTCTACAAATAAAAATAAA
1 AAAAATTTAAA-TTGTATAATCA-AACCAAAAAAACATAATTAAACTTCTACAAATAAGAA-AAA
*
370607 TTATATCTTA
63 TAATATCTTA
* * * * * *
370617 AAAAATTTTAACTCGTATAATCATACC-AAAAAGCA-AATTAAACTTTTACAAATAAAGATAAAT
1 AAAAA-TTTAAATTGTATAATCAAACCAAAAAAACATAATTAAACTTCTACAAAT-AAGAAAAAT
370680 AATATCTT-
64 AATATCTTA
370688 AAAAATTTAAATATGTATAATCAAACCAAAAAAACAATAATTAAACTTCTACAAATAATGAAAAA
1 AAAAATTTAAAT-TGTATAATCAAACCAAAAAAAC-ATAATTAAACTTCTACAAATAA-GAAAAA
370753 TAATA
63 TAATA
370758 CCCATGACCT
Statistics
Matches: 117, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
70 6 0.05
71 17 0.15
72 33 0.28
73 13 0.11
74 29 0.25
75 14 0.12
76 5 0.04
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (72 bp):
AAAAATTTAAATTGTATAATCAAACCAAAAAAACATAATTAAACTTCTACAAATAAGAAAAATAA
TATCTTA
Found at i:370790 original size:8 final size:7
Alignment explanation
Indices: 370767--370796 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
370757 ACCCATGACC
370767 TTTAATT
1 TTTAATT
370774 TTTAATT
1 TTTAATT
370781 TTTAATT
1 TTTAATT
*
370788 TTTTATT
1 TTTAATT
370795 TT
1 TT
370797 ATTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTAATT
Found at i:371037 original size:26 final size:27
Alignment explanation
Indices: 370988--371049 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
370978 CGATTTCTCG
*
370988 ACATTTGTTGATATGATAA-CTTTTTA
1 ACATGTGTTGATATGATAATCTTTTTA
* * *
371014 ACATGTGTTGATATGATGATTTTTTTT
1 ACATGTGTTGATATGATAATCTTTTTA
371041 ACATGTGTT
1 ACATGTGTT
371050 AGGAAATCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (27 bp):
ACATGTGTTGATATGATAATCTTTTTA
Found at i:371387 original size:2 final size:2
Alignment explanation
Indices: 371380--371410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
371370 AAATCCTTTC
371380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
371411 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:371652 original size:2 final size:2
Alignment explanation
Indices: 371647--371673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
371637 TTATATATCG
371647 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 A
371674 AAGAATGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:372776 original size:7 final size:7
Alignment explanation
Indices: 372753--372807 Score: 64
Period size: 7 Copynumber: 8.1 Consensus size: 7
372743 TTAACAAGTG
372753 AAATTTA
1 AAATTTA
372760 ATATATTTA
1 A-A-ATTTA
372769 AAATTT-
1 AAATTTA
372775 AAATTT-
1 AAATTTA
372781 AAA--TA
1 AAATTTA
372786 AAATTTA
1 AAATTTA
372793 AAATTTA
1 AAATTTA
372800 AAATTTA
1 AAATTTA
372807 A
1 A
372808 TATTATAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 9 0.21
7 22 0.51
8 2 0.05
9 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:372789 original size:17 final size:18
Alignment explanation
Indices: 372767--372801 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
372757 TTAATATATT
372767 TAAAATTT-AAATTTAAA
1 TAAAATTTAAAATTTAAA
372784 TAAAATTTAAAATTTAAA
1 TAAAATTTAAAATTTAAA
372802 ATTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTTAAAATTTAAA
Found at i:373063 original size:77 final size:77
Alignment explanation
Indices: 372970--373129 Score: 236
Period size: 77 Copynumber: 2.1 Consensus size: 77
372960 TTCTTTTCAC
* *
372970 TTCTATATGTTGTTTTTAGTTGTTATTTAAT-GAAAACTT-GCTGCACTGTTATTCAATGCATTA
1 TTCTATATGTTGTTTTTAGTTGTTATTTAATAG-AAACTTAACCGCACTG-TATTCAATGCATTA
373033 CAAGAAAATTGATT
64 CAAGAAAATTGATT
* * *
373047 TTCTATATGTTGTTTTTAGTTTTTATTTAATAGAAACTTAACCGTACTGTATTCAATGCATTCCA
1 TTCTATATGTTGTTTTTAGTTGTTATTTAATAGAAACTTAACCGCACTGTATTCAATGCATTACA
373112 AGAAAATTGATT
66 AGAAAATTGATT
373124 TT-TATA
1 TTCTATA
373130 CCTATTTACA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
76 4 0.05
77 65 0.86
78 7 0.09
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (77 bp):
TTCTATATGTTGTTTTTAGTTGTTATTTAATAGAAACTTAACCGCACTGTATTCAATGCATTACA
AGAAAATTGATT
Found at i:373368 original size:20 final size:20
Alignment explanation
Indices: 373323--373370 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
373313 ATTTACATAT
373323 TTATT-AATAAAAATATTAA
1 TTATTAAATAAAAATATTAA
* *
373342 TTTTTAAATAAAATATATTTA
1 TTATTAAATAAAA-ATATTAA
373363 -TATTAAAT
1 TTATTAAAT
373371 TTATATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTAAATAAAAATATTAA
Found at i:373901 original size:50 final size:51
Alignment explanation
Indices: 373847--373964 Score: 148
Period size: 50 Copynumber: 2.3 Consensus size: 51
373837 AAAGAAAATA
* * * *
373847 TATCGATACATTTTTTATTATATCGATACATTCTAGG-TTTGATCTAAACG
1 TATCGATACATTTTTCATTATACCAATACATTCTAGGTTTTGACCTAAACG
* * *
373897 TATCGATATATTTTTCATTGTACCAATACATTCTAGGTTTTGACCTAAATG
1 TATCGATACATTTTTCATTATACCAATACATTCTAGGTTTTGACCTAAACG
* *
373948 TATCAATACATTCTTCA
1 TATCGATACATTTTTCA
373965 ATGTATCGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 32 0.56
51 25 0.44
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (51 bp):
TATCGATACATTTTTCATTATACCAATACATTCTAGGTTTTGACCTAAACG
Found at i:376500 original size:96 final size:96
Alignment explanation
Indices: 376319--376506 Score: 227
Period size: 96 Copynumber: 2.0 Consensus size: 96
376309 TGTCCATCGA
** * *
376319 GGATACTCCAACCACATTCTTCCAAGGGGATACTCCAACTCCACTTTTAAACTTCTCAATAGTTA
1 GGATACTCCAACCACATTCTTCCAAGAAGATACTCCAACCCCACTTTTAAACTTCTCAAGAGTTA
*
376384 AATATTATTTTTGTTCAAATTATCATCGTCG
66 AATATTATTTTTCTTCAAATTATCATCGTCG
* ** * * *
376415 GGATACTCCAACCCCATTCTTCCAAGAAGATACTCTTACCCCGCTTTTAAAC-TCGTTAAGATTT
1 GGATACTCCAACCACATTCTTCCAAGAAGATACTCCAACCCCACTTTTAAACTTC-TCAAGAGTT
* *
376479 AAATCTTATTTTCTCTT-AAATTGTCATC
65 AAATATTATTTT-TCTTCAAATTATCATC
376507 ATTGGGGACA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
95 2 0.03
96 72 0.94
97 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (96 bp):
GGATACTCCAACCACATTCTTCCAAGAAGATACTCCAACCCCACTTTTAAACTTCTCAAGAGTTA
AATATTATTTTTCTTCAAATTATCATCGTCG
Found at i:378013 original size:13 final size:13
Alignment explanation
Indices: 377995--378020 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
377985 CTATTTATGA
377995 TGTATCGATACAC
1 TGTATCGATACAC
378008 TGTATCGATACAC
1 TGTATCGATACAC
378021 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:378128 original size:21 final size:22
Alignment explanation
Indices: 378096--378151 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
378086 CGTGAACAGT
378096 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
*
378118 ATGAA-AGTGATATATCGATAC
1 ATGAACAGTGATGTATCGATAC
378139 ATGAACAGTGATG
1 ATGAACAGTGATG
378152 AATAGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:378158 original size:10 final size:10
Alignment explanation
Indices: 378139--378169 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
378129 ATATCGATAC
378139 ATGAACAGTG
1 ATGAACAGTG
*
378149 ATGAATAGTG
1 ATGAACAGTG
378159 ATGAACAGTG
1 ATGAACAGTG
378169 A
1 A
378170 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:378267 original size:53 final size:53
Alignment explanation
Indices: 378194--378329 Score: 227
Period size: 53 Copynumber: 2.5 Consensus size: 53
378184 TACTTCCAAT
* *
378194 GTATTGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACCA
1 GTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACCA
* *
378247 GTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCCT
1 GTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACCA
378300 GTATCGATACATATTTGTGTGTATCGATAC
1 GTATCGATACATA-TTGTGTGTATCGATAC
378330 TATGCAATTT
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 62 0.79
54 16 0.21
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (53 bp):
GTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACCA
Found at i:378362 original size:20 final size:20
Alignment explanation
Indices: 378299--378369 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
378289 GCCAATGTCC
**
378299 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
378319 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
378339 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
378359 TGTATCGATAC
1 TGTATCGATAC
378370 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:378948 original size:8 final size:8
Alignment explanation
Indices: 378935--378964 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
378925 GATTGATGTC
378935 TATTCTTT
1 TATTCTTT
378943 TATTCTTT
1 TATTCTTT
378951 TATTCTTGT
1 TATTCTT-T
378960 TATTC
1 TATTC
378965 ATTTCTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (8 bp):
TATTCTTT
Found at i:379688 original size:20 final size:21
Alignment explanation
Indices: 379646--379698 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
379636 TTCTACAATT
379646 TGTATCGATACAACAAGTCAA
1 TGTATCGATACAACAAGTCAA
* * *
379667 TGTATCGATA-TATAAGTGAA
1 TGTATCGATACAACAAGTCAA
*
379687 TGTATTGATACA
1 TGTATCGATACA
379699 TTTTTGAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAACAAGTCAA
Found at i:385506 original size:70 final size:71
Alignment explanation
Indices: 385432--385586 Score: 226
Period size: 70 Copynumber: 2.2 Consensus size: 71
385422 CTTCCACAAT
* *
385432 TTGTATCGATACATTATTCATTGTTTCGATACATTCTAGGTTTTACCCAGATATATCAATACATT
1 TTGTATCGATACATTATTCATTGTATCGATAAATTCTAGGTTTTACCCAGATATATCAATACATT
385497 GT-T-AA
66 -TCTCAA
* * * *
385502 TTGTATCGATACATTGTTCATTGTATCGATAAATTCTGGGTTTTACCTAGATGTATCAATACATT
1 TTGTATCGATACATTATTCATTGTATCGATAAATTCTAGGTTTTACCCAGATATATCAATACATT
385567 TCTCAA
66 TCTCAA
385573 -TGTATCGATACATT
1 TTGTATCGATACATT
385587 CAGGCATTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
69 1 0.01
70 74 0.96
71 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (71 bp):
TTGTATCGATACATTATTCATTGTATCGATAAATTCTAGGTTTTACCCAGATATATCAATACATT
TCTCAA
Found at i:385513 original size:20 final size:20
Alignment explanation
Indices: 385485--385532 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
385475 TACCCAGATA
*
385485 TATCAATACATTGTTAATTG
1 TATCGATACATTGTTAATTG
*
385505 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTAATTG
385525 TATCGATA
1 TATCGATA
385533 AATTCTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
TATCGATACATTGTTAATTG
Found at i:388125 original size:79 final size:78
Alignment explanation
Indices: 387905--388161 Score: 250
Period size: 79 Copynumber: 3.3 Consensus size: 78
387895 ATTCATGTTT
* * * * * * **
387905 TTATTTCCGAGAGGATACTACAACCCCGGTTTTATTTTCAAAAC-TCTAATTTTTCACAACCGGG
1 TTATTTCTGAGGGGATACTCCAA-CCCAGTTTTATTTCCAAAACATC-AATTTTCCACAATTGGG
387969 GATACTTCAAGCCCG
64 GATACTTCAAGCCCG
* * * * * *
387984 TTATGTCTAAGGGGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATTGGGG
1 TTATTTCTGAGGGGATACTCCAACCCAG-TTTTATTTCCAAAACATCAATTTTCCACAATTGGGG
*
388049 ATAC-TCTAGCCCTG
65 ATACTTCAAGCCC-G
* *
388063 TTATTTCTGAGGGGATACTCCAACCCTAGTTTTATTTCCAAAACATCGATTTTCCACCATTGGGG
1 TTATTTCTGAGGGGATACTCCAACCC-AGTTTTATTTCCAAAACATCAATTTTCCACAATTGGGG
** *
388128 ATACCCCAA-CCTCA
65 ATACTTCAAGCC-CG
*
388142 TTATTTCTGAGGGGGTACTC
1 TTATTTCTGAGGGGATACTC
388162 TGACTACGTT
Statistics
Matches: 146, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
78 11 0.08
79 130 0.89
80 5 0.03
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (78 bp):
TTATTTCTGAGGGGATACTCCAACCCAGTTTTATTTCCAAAACATCAATTTTCCACAATTGGGGA
TACTTCAAGCCCG
Found at i:393384 original size:12 final size:12
Alignment explanation
Indices: 393363--393393 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
393353 CTCTTCTACA
393363 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
393375 AAAAACAAAAAC
1 AAAAAAAAAAAC
393387 AAAAAAA
1 AAAAAAA
393394 CCTGGGTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:394409 original size:30 final size:30
Alignment explanation
Indices: 394348--394409 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
394338 GTAACCTTTC
* * *
394348 TTCAAAGTCTACGACTTCGTGACATCTCTT
1 TTCAAAGTCCACGACTTCGTGACACCCCTT
*
394378 TTCAAAGTCCACGAC-TCTGTGGCACCCCTT
1 TTCAAAGTCCACGACTTC-GTGACACCCCTT
394408 TT
1 TT
394410 AGCATTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.34
Consensus pattern (30 bp):
TTCAAAGTCCACGACTTCGTGACACCCCTT
Found at i:394544 original size:61 final size:61
Alignment explanation
Indices: 394416--395365 Score: 883
Period size: 61 Copynumber: 15.6 Consensus size: 61
394406 TTTTAGCATT
* * * * * ** *
394416 TTTAGTCCTTAAAGAGTAGGATGCC-TTTCCTTTTCAAGCCCATATGAGTTAGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * ** * *
394476 TTTAGTCCTCAAAGAGCAAGATGCCTTTTTGTTTTCAAA-CCCACACAAGTTGGCGACACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCC
* * **
394537 TTTAGTCCTCAAAGAGCATGACGTCTTTTCCTTTTAAAGCCCACATGAGTTGGTGGCA---
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * * * * *
394595 TTCAATCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAGGTTAGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * * *
394656 TTTAGTCCTCAAAGAGCAAGATGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAACT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * * *
394717 TTTAGTCCTCGAAGAGCAAGACACTTCTTTT-CTGTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGC--CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * *
394779 TTTAGTCCTCAAAGAGCACGACGTCTTTTCCTTTTGAAG-CCACACAAGTTGGTGGCA-CC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * *
394838 TTTCAGTCCTCGAAGAGCAGGACACTTCTTTT--TAGTTAAAGCCCACACAAGTTGGTGGCA-CC
1 TTT-AGTCCTCAAAGAGCAGGACGC--CTTTTCCT-TTTAAAGCCCACACAAGTTGGTGGCACCC
* ** *
394900 TTTCAGTCCTCAAAGAGTAGGACGTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTT-AGTCCTCAAAGAGCAGGACG-CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * *
394963 TTTAGTCCTCAAAGAGCAGGACACTTCTTTT-CTGTTAAAGCCCACAAAAGTTAGTGGCA-CC
1 TTTAGTCCTCAAAGAGCAGGACGC--CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * ** **
395024 TTTCAGTCCTCAAAGAGCAGGACGTCTTTT-CTTTTGAAGCCCACACGGGTTGGTGGCACTT
1 TTT-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* *
395085 TTTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCA-CC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * * * * *
395145 TTTCGATCTTTAAAGAGCAGGATGTCTTTTCCTTTTAACGCCCACACAAGTTGGTGGCACCT
1 TTTAG-TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * * * * *
395207 TTTAGTCCTCGAAA-AGTAGGACACTTTTTTTCTGTTAAAGCCCATACAAGTTGGTGGCA-CT
1 TTTAGTCCTC-AAAGAGCAGGACGC-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* * * * * * **
395268 TTTCAGTTCTCAAAGAGTAGGATGCCCTTTCCTTTTAAAGCCTACACGAGTTGGTGGCA-TT
1 TTT-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
* *
395329 TTTCAGTCCTCAAAGAGCATGACAGTCTTTTCCTTTT
1 TTT-AGTCCTCAAAGAGCAGGAC-GCCTTTTCCTTTT
395366 CTCCTTTGTC
Statistics
Matches: 731, Mismatches: 129, Indels: 58
0.80 0.14 0.06
Matches are distributed among these distances:
58 48 0.07
59 4 0.01
60 121 0.17
61 298 0.41
62 246 0.34
63 14 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (61 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCC
Found at i:394882 original size:184 final size:185
Alignment explanation
Indices: 394415--395365 Score: 951
Period size: 184 Copynumber: 5.2 Consensus size: 185
394405 CTTTTAGCAT
* * * * * * **
394415 TTTTAGTCCTTAAAGAGTAGGATG-CCTTTCCTTTTCAAGCCCATATGAGTTAGTGGCACCCTTT
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA-CCTTT
* ** * * * * * * *
394479 -AGTCCTCAAAGAGCAAGATGCCT-TTTTGTTTTCAAA-CCCACACAAGTTGGCGACACCCTTTA
65 CAGTCCTCAAAGAGCAGGACACTTCTTTTCTGTT-AAAGCCCACACAAGTTGGTGGCAACTTTTA
* * * **
394541 GTCCTCAAAGAGCATGAC-GTCTTTTCCTTTTAAAGCCCACATGAGTTGGTGGCA--
129 GTCCTCAAAGAGTAGGACACTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * * *
394595 -TTCAATCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAGGTTAGTGGCACCTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACCTTTC
* *
394659 AGTCCTCAAAGAGCA--AGA-TGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAACTTTTA
66 AGTCCTCAAAGAGCAGGACACT-TCTTTT-CTGTTAAAGCCCACACAAGTTGGTGGCAACTTTTA
* * * *
394721 GTCCTCGAAGAGCAAGACACTTCTTTT-CTGTTAAAGCCCACACAAGTTGGTGGCACC
129 GTCCTCAAAGAGTAGGACAC-TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
394778 TTTTAGTCCTCAAAGAGCACGACGTCTTTTCCTTTTGAAG-CCACACAAGTTGGTGGCACCTTTC
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACCTTTC
* * *
394842 AGTCCTCGAAGAGCAGGACACTTCTTTT-TAGTTAAAGCCCACACAAGTTGGTGGCACCTTTCAG
66 AGTCCTCAAAGAGCAGGACACTTCTTTTCT-GTTAAAGCCCACACAAGTTGGTGGCAACTTTTAG
** *
394906 TCCTCAAAGAGTAGGACGTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
130 TCCTCAAAGAGTAGGACACTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
394962 TTTTAGTCCTCAAAGAGCAGGACACTTCTTTT-CTGTTAAAGCCCACAAAAGTTAGTGGCACCTT
1 TTTTAGTCCTCAAAGAGCAGG--ACGTCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACCTT
* * * **
395026 TCAGTCCTCAAAGAGCAGG--ACGTCTTTTCTTTTGAAGCCCACACGGGTTGGTGGC-ACTTTTT
64 TCAGTCCTCAAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCAAC-TTTT
* *
395088 AGTCCTCAAAGAGTAGGACGC-CTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACC
128 AGTCCTCAAAGAGTAGGACACTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * *
395145 -TTTCGATCTTTAAAGAGCAGGATGTCTTTTCCTTTTAACGCCCACACAAGTTGGTGGCACCTTT
1 TTTTAG-TCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACCTTT
* * * *
395209 TAGTCCTCGAAA-AGTAGGACACTTTTTTTCTGTTAAAGCCCATACAAGTTGGTGGC-ACTTTTC
65 CAGTCCTC-AAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCAACTTTT-
* ** * * * *
395272 AGTTCTCAAAGAGTAGGATGC-CCTTTCCTTTTAAAGCCTACACGAGTTGGTGGCA-T
128 AGTCCTCAAAGAGTAGGACACTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
395328 TTTTCAGTCCTCAAAGAGCATGACAGTCTTTTCCTTTT
1 TTTT-AGTCCTCAAAGAGCAGGAC-GTCTTTTCCTTTT
395366 CTCCTTTGTC
Statistics
Matches: 649, Mismatches: 92, Indels: 55
0.82 0.12 0.07
Matches are distributed among these distances:
178 2 0.00
179 32 0.05
180 85 0.13
181 32 0.05
182 51 0.08
183 96 0.15
184 274 0.42
185 30 0.05
186 47 0.07
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (185 bp):
TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACCTTTC
AGTCCTCAAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCAACTTTTAGT
CCTCAAAGAGTAGGACACTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:394885 original size:122 final size:123
Alignment explanation
Indices: 394415--395360 Score: 1046
Period size: 122 Copynumber: 7.8 Consensus size: 123
394405 CTTTTAGCAT
* * * * * * ** * *
394415 TTTTAGTCCTTAAAGAGTAGGATG-CCTTTCCTTTTCAAGCCCATATGAGTTAGTGGCACCCTTT
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* ** * * * * *
394479 AGTCCTCAAAGAGCAAGATGCCT-TTTTGTTTTCAAA-CCCACACAAGTTGGCGACACC
66 AGTCCTCAAAGAGCAGGACACTTCTTTTCTGTT-AAAGCCCACACAAGTTGGTGGCACC
* * ** *
394536 CTTTAGTCCTCAAAGAGCATGACGTCTTTTCCTTTTAAAGCCCACATGAGTTGGTGGCA---TTC
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * ** * * *
394598 AATCCTCAAAGAGTAGGATGC--CTTTTCCTTTTAAAGCCCACACAGGTTAGTGGCACC
66 AGTCCTCAAAGAGCAGGACACTTCTTTT-CTGTTAAAGCCCACACAAGTTGGTGGCACC
* * *
394655 TTTTAGTCCTCAAAGAGCAAGATGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAACTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
394720 AGTCCTCGAAGAGCAAGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCACC
66 AGTCCTCAAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCACC
* * *
394778 TTTTAGTCCTCAAAGAGCACGACGTCTTTTCCTTTTGAAG-CCACACAAGTTGGTGGCACCTTTC
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
*
394842 AGTCCTCGAAGAGCAGGACACTTCTTTT-TAGTTAAAGCCCACACAAGTTGGTGGCACC
66 AGTCCTCAAAGAGCAGGACACTTCTTTTCT-GTTAAAGCCCACACAAGTTGGTGGCACC
* * *
394900 TTTCAGTCCTCAAAGAGTAGGACGTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 TTTTAGTCCTCAAAGAGCAGGACG-TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
394965 TAGTCCTCAAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACAAAAGTTAGTGGCACC
65 TAGTCCTCAAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCACC
* * ** *
395024 TTTCAGTCCTCAAAGAGCAGGACGTCTTTT-CTTTTGAAGCCCACACGGGTTGGTGGCACTTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * *
395088 AGTCCTCAAAGAGTAGGACGC--CTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACC
66 AGTCCTCAAAGAGCAGGACACTTCTTTT-CTGTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
395145 -TTTCGATCTTTAAAGAGCAGGATGTCTTTTCCTTTTAACGCCCACACAAGTTGGTGGCACCTTT
1 TTTTAG-TCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
395209 TAGTCCTCGAAA-AGTAGGACACTTTTTTTCTGTTAAAGCCCATACAAGTTGGTGGCA-C
65 TAGTCCTC-AAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * * * *
395267 TTTTCAGTTCTCAAAGAGTAGGATGCCCTTTCCTTTTAAAGCCTACACGAGTTGGTGGCA-TTTT
1 TTTT-AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
395331 TCAGTCCTCAAAGAGCATGACA-GTCTTTTC
65 T-AGTCCTCAAAGAGCAGGACACTTCTTTTC
395361 CTTTTCTCCT
Statistics
Matches: 714, Mismatches: 88, Indels: 45
0.84 0.10 0.05
Matches are distributed among these distances:
118 7 0.01
119 95 0.13
120 8 0.01
121 67 0.09
122 253 0.35
123 174 0.24
124 109 0.15
125 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (123 bp):
TTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
AGTCCTCAAAGAGCAGGACACTTCTTTTCTGTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:395423 original size:45 final size:44
Alignment explanation
Indices: 395361--395752 Score: 255
Period size: 45 Copynumber: 9.1 Consensus size: 44
395351 CAGTCTTTTC
*
395361 CTTTTCTCCTTTGTCCTCAAAGAGCATGACACATTTCATTTCCTT
1 CTTTTC-CCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT
* * *
395406 CTTTTCCCTTTTATCCTCAAAGAGTAGGACGCACTTT-ATTTCC-T
1 CTTTTCCC-TTTGTCCTCAAAGAGCAGGACACA-TTTCATTTCCTT
** * * * * * *
395450 -TTTTCCC-TTACCCTCAAAAAGTAGGGCGCACCTT-ATTCCCTT
1 CTTTTCCCTTTGTCCTCAAAGAGCAGGACACA-TTTCATTTCCTT
* * * * *
395492 CTTTTCCCTTAGTCTTCAAAGAGCAGG----A-TGCCTTT--TC
1 CTTTTCCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT
* * *
395529 CTTTTCACCTTTGTCCTCAAAGAGCAAGACATATTTCATTTCTTT
1 CTTTTC-CCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT
* * *
395574 CTTTTCCCTTTGTCCTCAAAGAGCATGACACACTTCATTTTCTT
1 CTTTTCCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT
* *
395618 -TTTTCCTCTTTTGTCCTCAAAGAGTAGGACACACTTT-ATTTTCTT
1 CTTTTCC-C-TTTGTCCTCAAAGAGCAGGACACA-TTTCATTTCCTT
* * *
395663 -TTTT--CTTTGTCCTCAAAGAGCAAGG-CGCACCTT-ATTCCCTT
1 CTTTTCCCTTTGTCCTCAAAGAGC-AGGACACA-TTTCATTTCCTT
* * * * *
395704 CTTTTCCCTTAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTCTT
1 CTTTTCCCTTTGTCCTCAAAGAGCAGGACA-CATTTCATTTCCTT
395749 CTTT
1 CTTT
395753 GAAAGCTCAA
Statistics
Matches: 277, Mismatches: 46, Indels: 48
0.75 0.12 0.13
Matches are distributed among these distances:
37 7 0.03
38 19 0.07
39 2 0.01
40 1 0.00
41 55 0.20
42 10 0.04
43 28 0.10
44 67 0.24
45 83 0.30
46 5 0.02
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (44 bp):
CTTTTCCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT
Found at i:395497 original size:43 final size:43
Alignment explanation
Indices: 395402--395502 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 43
395392 CATTTCATTT
* * * *
395402 CCTTCTTTTCCCTTTTATCCTCAAAGAGTAGGACGCACTTTATTT
1 CCTTCTTTTCCC--TTACCCTCAAAAAGTAGGACGCACCTTATTC
*
395447 CC-T-TTTTCCCTTACCCTCAAAAAGTAGGGCGCACCTTATTC
1 CCTTCTTTTCCCTTACCCTCAAAAAGTAGGACGCACCTTATTC
395488 CCTTCTTTTCCCTTA
1 CCTTCTTTTCCCTTA
395503 GTCTTCAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
41 28 0.57
42 1 0.02
43 17 0.35
44 1 0.02
45 2 0.04
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.40
Consensus pattern (43 bp):
CCTTCTTTTCCCTTACCCTCAAAAAGTAGGACGCACCTTATTC
Found at i:395613 original size:212 final size:213
Alignment explanation
Indices: 395361--395746 Score: 605
Period size: 212 Copynumber: 1.8 Consensus size: 213
395351 CAGTCTTTTC
*
395361 CTTTTCTCCTTTGTCCTCAAAGAGCATGACACATTTCATTTCCTTCTTTTCC-CTTTTATCCTCA
1 CTTTTCTCCTTTGTCCTCAAAGAGCATGACACACTTCATTTCCTT-TTTTCCTCTTTTATCCTCA
* * *
395425 AAGAGTAGGACGCACTTTATTTCCTTTTTCCCTTACCCTCAAAAAGTAGGGCGCACCTTATTCCC
65 AAGAGTAGGACACACTTTATTTCCTTTTTCCCTTACCCTCAAAAAGCAAGGCGCACCTTATTCCC
* * **
395490 TTCTTTTCCCTTAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCA
130 TTCTTTTCCCTTAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCA
395555 AGACATATTTCATTTCTTT
195 AGACATATTTCATTTCTTT
* *
395574 CTTTTC-CCTTTGTCCTCAAAGAGCATGACACACTTCATTTTCTTTTTTCCTCTTTTGTCCTCAA
1 CTTTTCTCCTTTGTCCTCAAAGAGCATGACACACTTCATTTCCTTTTTTCCTCTTTTATCCTCAA
* * * ** *
395638 AGAGTAGGACACACTTTATTTTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCGCACCTTATTCCCT
66 AGAGTAGGACACACTTTATTTCCTTTTTCCCTTACCCTCAAAAAGCAAGGCGCACCTTATTCCCT
395703 TCTTTTCCCTTAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTC
131 TCTTTTCCCTTAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTC
395747 TTCTTTGAAA
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
211 6 0.04
212 144 0.92
213 6 0.04
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (213 bp):
CTTTTCTCCTTTGTCCTCAAAGAGCATGACACACTTCATTTCCTTTTTTCCTCTTTTATCCTCAA
AGAGTAGGACACACTTTATTTCCTTTTTCCCTTACCCTCAAAAAGCAAGGCGCACCTTATTCCCT
TCTTTTCCCTTAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCAA
GACATATTTCATTTCTTT
Found at i:395664 original size:168 final size:166
Alignment explanation
Indices: 395333--395684 Score: 420
Period size: 168 Copynumber: 2.1 Consensus size: 166
395323 GGCATTTTTC
* * * * *
395333 AGTCCTCAAAGAGCATGACAGTCTTTTCCTTTTCTCCTTTGTCCTCAAAGAGCATGACACATTTC
1 AGTCCTCAAAGAGCAGGA-TGCCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCAAGACACATTTC
* * *
395398 ATTTCCTTCTTTTCCCTTTTATCCTCAAAGAGTAGGACGCACTTTATTTCCTTTTTCCCTTACCC
65 ATTTCCTTCTTTTCCCTTTTATCCTCAAAGAGCAGGACACACTTCATTTCCTTTTTCCCTTACCC
* *
395463 TCAAAAAGTAGGGCGCACCTTATTCCCTTCTTTTCCCTT
130 TCAAAAAGTAGGACACACCTTATT--CTTCTTTTCCCTT
* *
395502 AGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCAAGACATATTTCA
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCAAGACACATTTCA
* * * * *
395567 TTTCTTTCTTTTCCC-TTTGTCCTCAAAGAGCATGACACACTTCATTTTCTTTTTTCCTCTTTTG
66 TTTCCTTCTTTTCCCTTTTATCCTCAAAGAGCAGGACACACTTCA-TTTCCTTTTTCC-C--TTA
* * * **
395631 TCCTCAAAGAGTAGGACACACTTTATT-TTCTTTTTTCTT
127 CCCTCAAAAAGTAGGACACACCTTATTCTTCTTTTCCCTT
*
395670 TGTCCTCAAAGAGCA
1 AGTCCTCAAAGAGCA
395685 AGGCGCACCT
Statistics
Matches: 155, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
167 24 0.15
168 90 0.58
169 17 0.11
171 24 0.15
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.40
Consensus pattern (166 bp):
AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCACCTTTGTCCTCAAAGAGCAAGACACATTTCA
TTTCCTTCTTTTCCCTTTTATCCTCAAAGAGCAGGACACACTTCATTTCCTTTTTCCCTTACCCT
CAAAAAGTAGGACACACCTTATTCTTCTTTTCCCTT
Found at i:395698 original size:41 final size:41
Alignment explanation
Indices: 395571--395753 Score: 126
Period size: 41 Copynumber: 4.4 Consensus size: 41
395561 ATTTCATTTC
** * *
395571 TTTCTTTTCCCTTTGTCCTCAAAGAGCATGACACA-CTTCAT
1 TTTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCACACCTT-AT
* *
395612 TTTCTTTTTTCCTCTTTTGTCCTCAAAGAG-TAGGACACACTTTAT
1 TTTC-TTTTT--TC-TTTGTCCTCAAAGAGCAAGG-CACACCTTAT
*
395657 TTTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCGCACCTTAT
1 TTTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCACACCTTAT
** * *
395698 TCCCTTCTTTTCCCTTAGTCCTCAAAAAGC-AGG-ACACC-T-T
1 T---TTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCACACCTTAT
*
395738 TTCCTTTTCTTCTTTG
1 TTTCTTTT-TTCTTTG
395754 AAAGCTCAAG
Statistics
Matches: 113, Mismatches: 18, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
37 6 0.05
38 4 0.04
40 2 0.02
41 29 0.26
42 13 0.12
43 3 0.03
44 29 0.26
45 25 0.22
46 2 0.02
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (41 bp):
TTTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCACACCTTAT
Found at i:395748 original size:86 final size:86
Alignment explanation
Indices: 395571--395738 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 86
395561 ATTTCATTTC
* ** *
395571 TTTCTTTTCCCTTTGTCCTCAAAGAGCATGACACACTTCATTTTCTTTTTTCCTCTTTTGTCCTC
1 TTTCTTTTCCCTTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTTTTTCCTCTTTAGTCCTC
* *
395636 AAAGAGTAGGACACACTTTAT
66 AAAAAGCAGGACACACTTTAT
** * *
395657 TTTCTTTTTTCTTTGTCCTCAAAGAGCAAGGCGCACCTT-ATTCCCTTCTTTTCC-C-TTAGTCC
1 TTTCTTTTCCCTTTGTCCTCAAAGAGCAAGACACA-CTTCATTCCCTT-TTTTCCTCTTTAGTCC
395719 TCAAAAAGCAGGACAC-CTTT
64 TCAAAAAGCAGGACACACTTT
395739 TCCTTTTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 4 0.06
85 20 0.29
86 37 0.53
87 9 0.13
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.40
Consensus pattern (86 bp):
TTTCTTTTCCCTTTGTCCTCAAAGAGCAAGACACACTTCATTCCCTTTTTTCCTCTTTAGTCCTC
AAAAAGCAGGACACACTTTAT
Found at i:396556 original size:20 final size:20
Alignment explanation
Indices: 396531--396581 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
396521 CAGTTTCATT
**
396531 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATG
*
396551 TATCGATACGA-TGAACATG
1 TATCGATACAATTGAACATG
*
396570 TATCAATACAAT
1 TATCGATACAAT
396582 GTATCGATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:399102 original size:13 final size:13
Alignment explanation
Indices: 399084--399123 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
399074 ATAGTAACCC
*
399084 ATGTATCAATACA
1 ATGTATCGATACA
*
399097 ATGTATGGATACA
1 ATGTATCGATACA
399110 ATGTATCGATACA
1 ATGTATCGATACA
399123 A
1 A
399124 AGAATATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:401280 original size:117 final size:117
Alignment explanation
Indices: 401074--401288 Score: 403
Period size: 117 Copynumber: 1.8 Consensus size: 117
401064 AAAGCAACAA
401074 AATCACAAGTGTTTCTAAGAGATGATCTAGTTCTTACCCCATGACTTAGATTACCGATTATCTCA
1 AATCACAAGTGTTTCTAAGAGATGATCTAGTTCTTACCCCATGACTTAGATTACCGATTATCTCA
401139 CCTTCTTGCACATAAGTCAACTCTCTCAGATGTCTAGTTCTTACCCCATAGG
66 CCTTCTTGCACATAAGTCAACTCTCTCAGATGTCTAGTTCTTACCCCATAGG
* *
401191 AATCACAAGTGTTTCTAAGAGATGATCTAGTTTTTACCCCATGACTTGGATTACCGATTATCTCA
1 AATCACAAGTGTTTCTAAGAGATGATCTAGTTCTTACCCCATGACTTAGATTACCGATTATCTCA
*
401256 CCTTCTTGCACATAAGTCAACTCTCTCGGATGT
66 CCTTCTTGCACATAAGTCAACTCTCTCAGATGT
401289 TTCTTTTCGA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 95 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (117 bp):
AATCACAAGTGTTTCTAAGAGATGATCTAGTTCTTACCCCATGACTTAGATTACCGATTATCTCA
CCTTCTTGCACATAAGTCAACTCTCTCAGATGTCTAGTTCTTACCCCATAGG
Found at i:405386 original size:20 final size:20
Alignment explanation
Indices: 405361--405434 Score: 123
Period size: 20 Copynumber: 3.7 Consensus size: 20
405351 GTTAGAAGCA
*
405361 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
405381 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
405401 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
405421 ATGTATCGATACAA
1 ATGTATCGATACAA
405435 ATAGTGGTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
20 51 0.98
21 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:405489 original size:20 final size:20
Alignment explanation
Indices: 405463--405517 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
405453 CTGCCAGTTT
*
405463 CATGTATCGATACAATTG-T
1 CATGTATCGATACAATTGAA
405482 CTATGTATCGATACAA-TGAA
1 C-ATGTATCGATACAATTGAA
405502 CATGTATCGATACAAT
1 CATGTATCGATACAAT
405518 GTATCGATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:405521 original size:13 final size:13
Alignment explanation
Indices: 405503--405529 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
405493 TACAATGAAC
405503 ATGTATCGATACA
1 ATGTATCGATACA
405516 ATGTATCGATACA
1 ATGTATCGATACA
405529 A
1 A
405530 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:405980 original size:44 final size:43
Alignment explanation
Indices: 405839--406203 Score: 246
Period size: 44 Copynumber: 8.5 Consensus size: 43
405829 GTCCTAACAT
* **
405839 CCTTTGTCCTCAAAGAGCAGGACACTATTTCATTTCCTTCTTTTC
1 CCTTTGTCCTCAAAGAGTAGGACAC-ACCTCATTTCCTT-TTTTC
* * ** *
405884 CCTTTTGTCCTCAAA-ATGCAGGACATA-CTTTTTTCCCTTTTT-
1 CC-TTTGTCCTCAAAGA-GTAGGACACACCTCATTTCCTTTTTTC
* ***
405926 CCTTTGTCCTCAAAGAGAAGGGTGCACCTCATTTCCTTATTTTC
1 CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTT-TTTTC
** * *
405970 CCTTTGTCCTCAAAGAGTAGGATGCACTTCATTTCCTTATTTC
1 CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTTTTTTC
** * * * *
406013 TTTTTTGTCCTCAAAGTGTAGAACACACTTTATTTCC-TTTTT-
1 -CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTTTTTTC
* * * *
406055 CCTTTGTCCTCAAAGAGCAGGGCATACCTTATTTCCTTCTTTTC
1 CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTT-TTTTC
* * * ** *
406099 CCTTAGTCCTCAAAAAGAAGG--ATGCCT--TTTCCTTTTCT-
1 CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTTTTTTC
* **
406137 CCTTTGTCCTCAAAGAGTAGGGCACATTTCATTTCCTTCTTTTC
1 CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTT-TTTTC
* * *
406181 CTTTTGTCTTCAAAGGGTAGGAC
1 CCTTTGTCCTCAAAGAGTAGGAC
406204 GCTTTCTCCT
Statistics
Matches: 254, Mismatches: 50, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
38 18 0.07
39 3 0.01
40 9 0.04
41 45 0.18
42 24 0.09
43 23 0.09
44 108 0.43
45 4 0.02
46 20 0.08
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (43 bp):
CCTTTGTCCTCAAAGAGTAGGACACACCTCATTTCCTTTTTTC
Found at i:406043 original size:129 final size:131
Alignment explanation
Indices: 405839--406123 Score: 360
Period size: 129 Copynumber: 2.2 Consensus size: 131
405829 GTCCTAACAT
* ** * *
405839 CCTTTGTCCTCAAAGAGCAGGACACTATTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAATGCA
1 CCTTTGTCCTCAAAGAGAAGGATGCTACTTCATTTCCTTCATTTCCCTTTTGTCCTCAAAATGCA
* * **
405904 GGACATACTTT-TTTCCCTTTTTCCTTTGTCCTCAAAGAGAAGGGTGCACCTCATTTCCTTATTT
66 GAACACACTTTATTT-CCTTTTTCCTTTGTCCTCAAAGAGAAGGGCACACCTCATTTCCTTATTT
405968 TC
130 TC
* ** * *
405970 CCTTTGTCCTCAAAGAGTAGGATGC-ACTTCATTTCCTT-ATTTCTTTTTTGTCCTCAAAGTGTA
1 CCTTTGTCCTCAAAGAGAAGGATGCTACTTCATTTCCTTCATTTCCCTTTTGTCCTCAAAATGCA
* * * *
406033 GAACACACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCATACCTTATTTCCTTCTTTT
66 GAACACACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGAAGGGCACACCTCATTTCCTTATTTT
406098 C
131 C
* *
406099 CCTTAGTCCTCAAAAAGAAGGATGC
1 CCTTTGTCCTCAAAGAGAAGGATGC
406124 CTTTTCCTTT
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
129 96 0.72
130 15 0.11
131 22 0.17
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (131 bp):
CCTTTGTCCTCAAAGAGAAGGATGCTACTTCATTTCCTTCATTTCCCTTTTGTCCTCAAAATGCA
GAACACACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGAAGGGCACACCTCATTTCCTTATTTT
C
Found at i:406214 original size:82 final size:80
Alignment explanation
Indices: 405965--406214 Score: 222
Period size: 82 Copynumber: 3.0 Consensus size: 80
405955 CATTTCCTTA
* *
405965 TTTTC-CCTTTGTCCTCAAAGAGTAGGATGCAC-TTCATTTCCTT-ATTTCTTTTTTGTCCTCAA
1 TTTTCTCCTTTGTCCTCAAAGAGTAGG--GCACATTCATTTCCTTCTTTTC-CTTTTGTCCTCAA
* * *
406027 AGTGTAGAACACACTTTATTTCC
63 AGAGTAG--GACGC--T-TTTCC
* * * *
406050 TTTT-TCCTTTGTCCTCAAAGAGCAGGGCATACCTT-ATTTCCTTCTTTTCCCTTAGTCCTCAAA
1 TTTTCTCCTTTGTCCTCAAAGAGTAGGGC--ACATTCATTTCCTTCTTTTCCTTTTGTCCTCAAA
* * *
406113 AAGAAGGATGCCTTTTCC
64 GAGTAGGACG-CTTTTCC
*
406131 TTTTCTCCTTTGTCCTCAAAGAGTAGGGCACATTTCATTTCCTTCTTTTCCTTTTGTCTTCAAAG
1 TTTTCTCCTTTGTCCTCAAAGAGTAGGGCACA-TTCATTTCCTTCTTTTCCTTTTGTCCTCAAAG
*
406196 GGTAGGACGCTTTCTCC
65 AGTAGGACGCTTT-TCC
406213 TT
1 TT
406215 GCAAAGCCCA
Statistics
Matches: 135, Mismatches: 20, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
80 2 0.01
81 15 0.11
82 60 0.44
83 3 0.02
84 1 0.01
85 48 0.36
86 6 0.04
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (80 bp):
TTTTCTCCTTTGTCCTCAAAGAGTAGGGCACATTCATTTCCTTCTTTTCCTTTTGTCCTCAAAGA
GTAGGACGCTTTTCC
Found at i:406736 original size:20 final size:20
Alignment explanation
Indices: 406711--406762 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
406701 TGAGGACGAA
406711 TATCGATACATTATTCATTG
1 TATCGATACATTATTCATTG
*
406731 TATCGATACATTGTTCATTG
1 TATCGATACATTATTCATTG
*
406751 TATCGGTACATT
1 TATCGATACATT
406763 CTAGGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TATCGATACATTATTCATTG
Found at i:409334 original size:79 final size:79
Alignment explanation
Indices: 409151--409430 Score: 301
Period size: 79 Copynumber: 3.5 Consensus size: 79
409141 ATTCATGTTT
** * * * * * *
409151 TTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAGCACAAATTTTTCACAATCGGGG
1 TTATTTCTGAGGGGATACTCCAACCTTGATTTTATTTCCAAAACACCAATTTTCCACAATTGGGG
409216 ATACTCCAACCCCG
66 ATACTCCAACCCCG
* * * *
409230 TTATGTCCGAAGGGATACTCCAACCTTGATTTTATTTCCAAAACACCAATTTTCCACAATTAGGG
1 TTATTTCTGAGGGGATACTCCAACCTTGATTTTATTTCCAAAACACCAATTTTCCACAATTGGGG
* *
409295 ATACTCTAGCCCCG
66 ATACTCCAACCCCG
* * * **
409309 TTATTTCTGAGGGGATACTCCAACCTT-AGTTTTACTTCCAAAACATCGATTTTCCACCGTTGGG
1 TTATTTCTGAGGGGATACTCCAACCTTGA-TTTTATTTCCAAAACACCAATTTTCCACAATTGGG
* *
409373 GATACCCCAACCTCG
65 GATACTCCAACCCCG
* * * * * *
409388 TTATTTCTAAGGGGGTACTTCAACTTTGTTTTTATCTCCAAAA
1 TTATTTCTGAGGGGATACTCCAACCTTGATTTTATTTCCAAAA
409431 TATTAAATTT
Statistics
Matches: 165, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
78 1 0.01
79 164 0.99
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TTATTTCTGAGGGGATACTCCAACCTTGATTTTATTTCCAAAACACCAATTTTCCACAATTGGGG
ATACTCCAACCCCG
Found at i:411770 original size:49 final size:50
Alignment explanation
Indices: 411560--411759 Score: 199
Period size: 52 Copynumber: 3.9 Consensus size: 50
411550 AATGACATTG
* * *
411560 GACTTAAAAATTAGAAAAATGCCACTGTGCTGATTCAAGGCCAGCGATATTA
1 GACTTAAAGA-TA-AAAAATGCCAATATGCTGATTCAAGGCCAGCGATATTA
* * * * **
411612 GGCTTAGCAATGATAAAAAA-ACCAATATGATGATTCAAAGCCAGCGATATCG
1 GACTTA--AA-GATAAAAAATGCCAATATGCTGATTCAAGGCCAGCGATATTA
* *
411664 GACTTAAAGATAACAAATGTGCCAATATGCTGATTCAAGGCTAGCGATATTA
1 GACTTAAAGATAA-AAA-ATGCCAATATGCTGATTCAAGGCCAGCGATATTA
*
411716 GACTT-AAGA-AAAAAAGTGCCAATGTGCTGATTCAAGGCCAGCGA
1 GACTTAAAGATAAAAAA-TGCCAATATGCTGATTCAAGGCCAGCGA
411760 CATTGAACTT
Statistics
Matches: 121, Mismatches: 20, Indels: 17
0.77 0.13 0.11
Matches are distributed among these distances:
49 34 0.28
50 7 0.06
51 4 0.03
52 66 0.55
53 5 0.04
54 4 0.03
55 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (50 bp):
GACTTAAAGATAAAAAATGCCAATATGCTGATTCAAGGCCAGCGATATTA
Found at i:411925 original size:29 final size:28
Alignment explanation
Indices: 411878--411955 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 28
411868 GCTACCTTCG
* *
411878 ACTTGCGGGCTTTAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTAAAAGGGTGCCACCA
* *
411906 ACTTGTGGGCTTTGGAAAGGTTGCCACCA
1 ACTTGTGGGCTTT-AAAAGGGTGCCACCA
*
411935 ACTTGTGGACTTTAAAAGGGT
1 ACTTGTGGGCTTTAAAAGGGT
411956 TAAAGATGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 18 0.43
29 24 0.57
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (28 bp):
ACTTGTGGGCTTTAAAAGGGTGCCACCA
Found at i:412130 original size:30 final size:30
Alignment explanation
Indices: 412035--412132 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
412025 CTTGTGTGGG
* *
412035 CTTTAAAAAGAGATGCCA-CGAACTTGCTTGAG
1 CTTTAAAAAGAGATGCCATAGAA-TTG--TGAA
* * *
412067 CTTTAAAAAGAGATGCCATGGAATGGTGGA
1 CTTTAAAAAGAGATGCCATAGAATTGTGAA
*
412097 CTTTAAAAAGAGATGCCATAGAGTTGTGAA
1 CTTTAAAAAGAGATGCCATAGAATTGTGAA
412127 CTTTAA
1 CTTTAA
412133 GATGGTTGCC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
30 34 0.60
32 20 0.35
33 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (30 bp):
CTTTAAAAAGAGATGCCATAGAATTGTGAA
Found at i:412606 original size:14 final size:13
Alignment explanation
Indices: 412583--412625 Score: 68
Period size: 14 Copynumber: 3.2 Consensus size: 13
412573 TGTGATGGTA
412583 ATGTGAATGCATG
1 ATGTGAATGCATG
412596 ATGTGGAATGCATG
1 ATGT-GAATGCATG
412610 ATGTTGAATGCATG
1 ATG-TGAATGCATG
412624 AT
1 AT
412626 ATGTGAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.14
14 23 0.82
15 1 0.04
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (13 bp):
ATGTGAATGCATG
Found at i:415002 original size:21 final size:21
Alignment explanation
Indices: 414978--415021 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
414968 TTTTTGCCGA
*
414978 AATGTATCGATACATGCTTTT
1 AATGTATCGATACAAGCTTTT
* *
414999 AATGTATTGATACAAGGTTTT
1 AATGTATCGATACAAGCTTTT
415020 AA
1 AA
415022 CGGTCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (21 bp):
AATGTATCGATACAAGCTTTT
Found at i:415198 original size:20 final size:20
Alignment explanation
Indices: 415151--415206 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
415141 CATAAGTAAA
415151 TGTATCGATACATACTTATAAT
1 TGTATCGATACAT--TTATAAT
* *
415173 TATATCGATACATTTATCAT
1 TGTATCGATACATTTATAAT
415193 TGTATCGATACATT
1 TGTATCGATACATT
415207 CTGGGGTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 19 0.61
22 12 0.39
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTATAAT
Found at i:417739 original size:28 final size:28
Alignment explanation
Indices: 417699--417800 Score: 116
Period size: 28 Copynumber: 3.6 Consensus size: 28
417689 TTTTACCACC
417699 GGGGATACTCCAACCCCATTATTTCTGA
1 GGGGATACTCCAACCCCATTATTTCTGA
*
417727 GGGGATACTCCAACCCTAGTTTTATTTCT-A
1 GGGGATACTCCAACCCCA---TTATTTCTGA
**** *
417757 AAACACACTCCAACCCCATTATTTCTGA
1 GGGGATACTCCAACCCCATTATTTCTGA
417785 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
417801 AGTTTTATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
27 8 0.14
28 29 0.50
30 13 0.22
31 8 0.14
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTCTGA
Found at i:417769 original size:30 final size:29
Alignment explanation
Indices: 417733--417819 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
417723 CTGAGGGGAT
417733 ACTCCAACCCTAGTTTTATTTCTAAAACAC
1 ACTCCAACCC-AGTTTTATTTCTAAAACAC
**** *
417763 ACTCCAACCCCA---TTATTTCTGAGGGGAT
1 ACTCCAA-CCCAGTTTTATTTCT-AAAACAC
417791 ACTCCAACCCAGTTTTATTTCTAAAACAC
1 ACTCCAACCCAGTTTTATTTCTAAAACAC
417820 TGATTTTCCA
Statistics
Matches: 42, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
27 12 0.29
28 9 0.21
29 2 0.05
30 16 0.38
31 3 0.07
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (29 bp):
ACTCCAACCCAGTTTTATTTCTAAAACAC
Found at i:417778 original size:58 final size:57
Alignment explanation
Indices: 417705--417819 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 57
417695 CACCGGGGAT
417705 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACAC
1 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCC-AGTTTTATTTCTAAAACAC
417763 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCAGTTTTATTTCTAAAACAC
1 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCAGTTTTATTTCTAAAACAC
417820 TGATTTTCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 19 0.33
58 38 0.67
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (57 bp):
ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCAGTTTTATTTCTAAAACAC
Found at i:417892 original size:78 final size:78
Alignment explanation
Indices: 417763--417975 Score: 277
Period size: 78 Copynumber: 2.7 Consensus size: 78
417753 TCTAAAACAC
* ** *
417763 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACC-CAGTTTTATTTCTAAAACA-CTGATTT
1 ACTCCAA-CCCATTATTTTTGAGGGGATACTCCAACCTTGGTTTTATTTCTAAAACATC-GACTT
417826 TCCACCATCAGGGAT
64 TCCACCATCAGGGAT
* *
417841 ACTCCAACCCATTATTTTTGAGGGAATAATCCAACCTTGGTTTTATTTCTAAAACATCGACTTTC
1 ACTCCAACCCATTATTTTTGAGGGGATACTCCAACCTTGGTTTTATTTCTAAAACATCGACTTTC
*
417906 CACCATCGGGGAT
66 CACCATCAGGGAT
* ** * *
417919 ACTCCAACCTTATTATTTTCAAGGGGATGCTCCAACCTTGATTTTATTTCTAAAACA
1 ACTCCAACC-CATTATTTTTGAGGGGATACTCCAACCTTGGTTTTATTTCTAAAACA
417976 GTAACCAACT
Statistics
Matches: 118, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
77 26 0.22
78 51 0.43
79 41 0.35
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (78 bp):
ACTCCAACCCATTATTTTTGAGGGGATACTCCAACCTTGGTTTTATTTCTAAAACATCGACTTTC
CACCATCAGGGAT
Found at i:417894 original size:135 final size:137
Alignment explanation
Indices: 417626--417896 Score: 393
Period size: 135 Copynumber: 2.0 Consensus size: 137
417616 CATCAAGGAT
* * * * *
417626 ACTCCAACCCTATTATTTTTGAGGGGATACTCTAATCCCGGTTTTATTTTTAAAACACTAATTTT
1 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAATCCCAGTTTTATTTCTAAAACACTAATTTT
** * * *
417691 TTACCACCGGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCTAGTTTTATTTCT
66 CCACCACCAGGGATACTCCAACCCCATTATTTCTGAGGGAATAATCCAACCCTAGTTTTATTTCT
417756 AAAACAC
131 AAAACAC
*
417763 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAA-CCCAGTTTTATTTCTAAAACACTGATTTT
1 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAATCCCAGTTTTATTTCTAAAACACTAATTTT
* * * *
417827 CCACCATCAGGGATACTCCAA-CCCATTATTTTTGAGGGAATAATCCAACCTTGGTTTTATTTCT
66 CCACCACCAGGGATACTCCAACCCCATTATTTCTGAGGGAATAATCCAACCCTAGTTTTATTTCT
417891 AAAACA
131 AAAACA
417897 TCGACTTTCC
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
135 44 0.37
136 43 0.36
137 32 0.27
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (137 bp):
ACTCCAACCCCATTATTTCTGAGGGGATACTCCAATCCCAGTTTTATTTCTAAAACACTAATTTT
CCACCACCAGGGATACTCCAACCCCATTATTTCTGAGGGAATAATCCAACCCTAGTTTTATTTCT
AAAACAC
Found at i:417993 original size:108 final size:108
Alignment explanation
Indices: 417871--418082 Score: 293
Period size: 108 Copynumber: 2.0 Consensus size: 108
417861 AGGGAATAAT
* * * *
417871 CCAACCTTGGTTTTATTTCTAAAACATCGACTTTCCACCATCGGGGATACTCCAACCTTATTATT
1 CCAACCTTGATTTTATTTCTAAAACACCGACTTTCCACCATCAGGGATACTCCAACCCTATTA-T
* * *
417936 TTC-AAGGGGATGCTCCAACCTTGATTTTATTTCTAAAACAGTAA
65 TTCGAA-AGGATACTCCAACCCTGATTTTATTTCTAAAACAGTAA
* * *
417980 CCAA-CTTGATTTTATTTCTAAAACACCGATTTTTCACCATCAGGGATACTCCAACCCTGTTATT
1 CCAACCTTGATTTTATTTCTAAAACACCGACTTTCCACCATCAGGGATACTCCAACCCTATTATT
*
418044 TCGAAAGGATATTCCAACCCTGATTTTATTTCTAAAACA
66 TCGAAAGGATACTCCAACCCTGATTTTATTTCTAAAACA
418083 TTGATTTTCC
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 34 0.37
108 53 0.58
109 4 0.04
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (108 bp):
CCAACCTTGATTTTATTTCTAAAACACCGACTTTCCACCATCAGGGATACTCCAACCCTATTATT
TCGAAAGGATACTCCAACCCTGATTTTATTTCTAAAACAGTAA
Found at i:418122 original size:107 final size:108
Alignment explanation
Indices: 418010--418228 Score: 273
Period size: 108 Copynumber: 2.0 Consensus size: 108
418000 AAACACCGAT
* *
418010 TTTTCACCATCAGGGATACTCCAA-CCC--TGTTATTTCGAAAGGATATTCCAACCCTGATTTTA
1 TTTTCACCATCAAGGATACTCCAATCCCATTG-T-TTTCGAAAGGATACTCCAACCCTGATTTTA
* * * *
418072 TTTCTAAAACATTGATTTTCCACAATCGGAGATACTCCAACCCTA
64 TTTCCAAAACATCGATTTTCCACAATCGGAGATACTCAAACCCCA
* * *
418117 TTTTCACCATTAAGGATACTCCAATCCCATTGTTTTCGAAGGGATACTCCAACCTTGATTTTATT
1 TTTTCACCATCAAGGATACTCCAATCCCATTGTTTTCGAAAGGATACTCCAACCCTGATTTTATT
* ** * *
418182 TCCAAAATATCGATTTTTTACCATCGGGGATACTCAAACCCCA
66 TCCAAAACATCGATTTTCCACAATCGGAGATACTCAAACCCCA
418225 TTTT
1 TTTT
418229 TATTTACAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
107 22 0.23
108 70 0.74
109 1 0.01
110 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (108 bp):
TTTTCACCATCAAGGATACTCCAATCCCATTGTTTTCGAAAGGATACTCCAACCCTGATTTTATT
TCCAAAACATCGATTTTCCACAATCGGAGATACTCAAACCCCA
Found at i:418176 original size:186 final size:183
Alignment explanation
Indices: 417763--418222 Score: 448
Period size: 186 Copynumber: 2.5 Consensus size: 183
417753 TCTAAAACAC
* * ** *
417763 ACTCCAACCCCATTATTTCTGAGGGGATACTCCAACCCAG-TTTTATTTCTAAAACACTGATTTT
1 ACTCCAA-CCCATTTTTTC-GAAGGGATACTCCAACCTTGATTTTATTTCTAAAACACCGATTTT
* * * * *
417827 CCACCATCAGGGATACTCCAACCCATTATTTTTGAGGGAATAATCCAACCTTGGTTTTATTTCTA
64 TCACCATCAGGGATACTCCAACCCATTATTTTCGAAGGAATAATCCAACCCTGATTTTATTTCTA
* * * ** *
417892 AAACATCGACTTTCCACCATCGGGGATACTCCAACCTTATTATTTTCAAGGGGAT
129 AAACATCGACTTTCCACAATCGGAGATACTCCAACCCTATTATTACCAAGAGGAT
* * * *** *
417947 GCTCCAACCTTGATTTTATTTCTAAAACAGTA-ACCAA-CTTGATTTTATTTCTAAAACACCGAT
1 ACTCCAACC--CA-TTT-TTTCGAAGGGA-TACTCCAACCTTGATTTTATTTCTAAAACACCGAT
* *
418010 TTTTCACCATCAGGGATACTCCAACCCTGTTA-TTTCGAAAGG-ATATTCCAACCCTGATTTTAT
61 TTTTCACCATCAGGGATACTCCAACCC-ATTATTTTCG-AAGGAATAATCCAACCCTGATTTTAT
* *
418073 TTCTAAAACATTGATTTTCCACAATCGGAGATACTCCAACCCTATT-TTCACCATTA-AGGAT
124 TTCTAAAACATCGACTTTCCACAATCGGAGATACTCCAACCCTATTATT-ACCA--AGAGGAT
* * *
418134 ACTCCAATCCCATTGTTTTCGAAGGGATACTCCAACCTTGATTTTATTTCCAAAATATCGATTTT
1 ACTCCAA-CCCATT-TTTTCGAAGGGATACTCCAACCTTGATTTTATTTCTAAAACACCGATTTT
* * *
418199 TTACCATCGGGGATACTCAAACCC
64 TCACCATCAGGGATACTCCAACCC
418223 CATTTTTATT
Statistics
Matches: 221, Mismatches: 40, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
183 2 0.01
184 8 0.04
185 18 0.08
186 168 0.76
187 22 0.10
188 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (183 bp):
ACTCCAACCCATTTTTTCGAAGGGATACTCCAACCTTGATTTTATTTCTAAAACACCGATTTTTC
ACCATCAGGGATACTCCAACCCATTATTTTCGAAGGAATAATCCAACCCTGATTTTATTTCTAAA
ACATCGACTTTCCACAATCGGAGATACTCCAACCCTATTATTACCAAGAGGAT
Found at i:418255 original size:50 final size:51
Alignment explanation
Indices: 418175--418273 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 51
418165 CCAACCTTGA
* * * *
418175 TTTTATTTCCAAAATATCGATTTTTTACCATCGGGGATACTCAAACCCCAT
1 TTTTATTTACAAAATATCAATTTCTCACCATCGGGGATACTCAAACCCCAT
*
418226 TTTTATTTAC-AAATATCAATTTCTCACCATCGGGGATACTCTAACCCC
1 TTTTATTTACAAAATATCAATTTCTCACCATCGGGGATACTCAAACCCC
418274 GTTGTGTTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 34 0.79
51 9 0.21
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (51 bp):
TTTTATTTACAAAATATCAATTTCTCACCATCGGGGATACTCAAACCCCAT
Found at i:420363 original size:4 final size:4
Alignment explanation
Indices: 420354--420387 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
420344 ATTGAGGTGC
* *
420354 TTAT TTAT TTAT TTAT TTGT TTGT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
420388 TGTTTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:420380 original size:16 final size:18
Alignment explanation
Indices: 420361--420397 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
420351 TGCTTATTTA
420361 TTTATTTA-TTTG-TTTG
1 TTTATTTATTTTGTTTTG
420377 TTTATTTATTTTGTTTTG
1 TTTATTTATTTTGTTTTG
420395 TTT
1 TTT
420398 TGTACAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTATTTATTTTGTTTTG
Found at i:428255 original size:15 final size:14
Alignment explanation
Indices: 428237--428283 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
428227 ATGCATATAA
428237 ATTTTATATTTTCTT
1 ATTTTATATTTT-TT
428252 ATTTTATA-TTTTT
1 ATTTTATATTTTTT
*
428265 ATTTT-TATTTATT
1 ATTTTATATTTTTT
428278 -TTTTAT
1 ATTTTAT
428284 TATTAATGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 6 0.21
13 12 0.41
14 3 0.10
15 8 0.28
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTATATTTTTT
Found at i:428264 original size:23 final size:23
Alignment explanation
Indices: 428238--428284 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
428228 TGCATATAAA
428238 TTTTATATTTT-CTTATTTTATAT
1 TTTTAT-TTTTACTTATTTTATAT
* *
428261 TTTTATTTTTATTTATTTTTTAT
1 TTTTATTTTTACTTATTTTATAT
428284 T
1 T
428285 ATTAATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTATTTTTACTTATTTTATAT
Done.