Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 90 of 171
Found at i:29400654 original size:22 final size:22
Alignment explanation
Indices: 29400626--29400670 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
29400616 CTCTTACTGA
29400626 TCAGCACTATGTGTGCTTCTGT
1 TCAGCACTATGTGTGCTTCTGT
*
29400648 TCAGCACTGTGTGTGCTTCTGT
1 TCAGCACTATGTGTGCTTCTGT
29400670 T
1 T
29400671 TCCCCAGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.42
Consensus pattern (22 bp):
TCAGCACTATGTGTGCTTCTGT
Found at i:29428542 original size:28 final size:28
Alignment explanation
Indices: 29428505--29428569 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
29428495 TTCAGGGAAA
29428505 TTTACTAAACTAGTAAGTATTTAATAAT
1 TTTACTAAACTAGTAAGTATTTAATAAT
29428533 TTTACTAAACTAGTAAGTATTTAATAAT
1 TTTACTAAACTAGTAAGTATTTAATAAT
29428561 TTTACTAAA
1 TTTACTAAA
29428570 TAATATGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (28 bp):
TTTACTAAACTAGTAAGTATTTAATAAT
Found at i:29432346 original size:23 final size:23
Alignment explanation
Indices: 29432318--29432384 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
29432308 ATTAACATTG
29432318 TTTGTGAACATGTTCGTTTAATA
1 TTTGTGAACATGTTCGTTTAATA
*
29432341 TTTGTGAACATGTTCGTTTAATG
1 TTTGTGAACATGTTCGTTTAATA
* *
29432364 TTCGTGAACATGTTCGATTAA
1 TTTGTGAACATGTTCGTTTAA
29432385 GCTAAATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.45
Consensus pattern (23 bp):
TTTGTGAACATGTTCGTTTAATA
Found at i:29432378 original size:12 final size:12
Alignment explanation
Indices: 29432311--29432379 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
29432301 ATTATTCATT
*
29432311 AACATTGTTTGTG
1 AACA-TGTTCGTG
*
29432324 AACATGTTCGTTT
1 AACATGTTCG-TG
*
29432337 AATAT-TT-GTG
1 AACATGTTCGTG
*
29432347 AACATGTTCGTT
1 AACATGTTCGTG
*
29432359 TA-ATGTTCGTG
1 AACATGTTCGTG
29432370 AACATGTTCG
1 AACATGTTCG
29432380 ATTAAGCTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
10 5 0.12
11 12 0.28
12 17 0.40
13 9 0.21
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:29438797 original size:13 final size:14
Alignment explanation
Indices: 29438774--29438822 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
29438764 ATATTTAATA
29438774 TAATAATAAATTAT
1 TAATAATAAATTAT
29438788 TAAT-ATAAATTAT
1 TAATAATAAATTAT
*
29438801 TATTTTAATAAATTATT
1 TA--ATAATAAATTA-T
29438818 TAATA
1 TAATA
29438823 TTACAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 11 0.38
14 4 0.14
15 3 0.10
16 8 0.28
17 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATAATAAATTAT
Found at i:29438971 original size:36 final size:35
Alignment explanation
Indices: 29438891--29438973 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
29438881 GAAAATATTT
* * *
29438891 ATATTAATATTTCAATAATAAATATATATTATAAT
1 ATATAAATATTTCAATAATAAATATATAGTATAAA
* *
29438926 TTATAAATATTT-AATAATAAAGGTTTATAGTATAAA
1 ATATAAATATTTCAATAATAAA--TATATAGTATAAA
*
29438962 ATATGAATATTT
1 ATATAAATATTT
29438974 TAATTATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 9 0.23
35 10 0.26
36 20 0.51
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (35 bp):
ATATAAATATTTCAATAATAAATATATAGTATAAA
Found at i:29439695 original size:29 final size:30
Alignment explanation
Indices: 29439663--29439724 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29439653 TAATAAAGAT
*
29439663 AAAA-TTACATTTTATCC-CTTAAAATAATA
1 AAAATTTA-ATTTAATCCTCTTAAAATAATA
* *
29439692 AAAATTTAATTTAATCCTTTTAAAATTATA
1 AAAATTTAATTTAATCCTCTTAAAATAATA
29439722 AAA
1 AAA
29439725 GTATAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTTAATTTAATCCTCTTAAAATAATA
Found at i:29444504 original size:16 final size:16
Alignment explanation
Indices: 29444477--29444514 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
29444467 TAAGTGTGTT
*
29444477 TAATAAAAAAAATGAAA
1 TAATTAAAAAAAT-AAA
29444494 TAATTAAAAAAATAAA
1 TAATTAAAAAAATAAA
29444510 TAATT
1 TAATT
29444515 TTTTTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAATTAAAAAAATAAA
Found at i:29449058 original size:9 final size:9
Alignment explanation
Indices: 29449044--29449084 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
29449034 AAACTTTTCA
*
29449044 TTTAAACTT
1 TTTAAAATT
29449053 TTTAAAATT
1 TTTAAAATT
29449062 TTTAAAA-T
1 TTTAAAATT
29449070 TTT-AAATT
1 TTTAAAATT
*
29449078 ATTAAAA
1 TTTAAAA
29449085 GTAAAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 3 0.11
8 7 0.25
9 18 0.64
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAAAATT
Found at i:29449076 original size:16 final size:17
Alignment explanation
Indices: 29449052--29449084 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29449042 CATTTAAACT
*
29449052 TTTTAAAATTTTTAAAA
1 TTTTAAAATTATTAAAA
29449069 TTTT-AAATTATTAAAA
1 TTTTAAAATTATTAAAA
29449085 GTAAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAAAATTATTAAAA
Found at i:29449468 original size:25 final size:25
Alignment explanation
Indices: 29449440--29449487 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
29449430 ACTGGGGTGG
29449440 GAACAATGCTTTTTACTCATCAGAA
1 GAACAATGCTTTTTACTCATCAGAA
*
29449465 GAACAATGCTTTTTACTTATCAG
1 GAACAATGCTTTTTACTCATCAG
29449488 GGAACTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (25 bp):
GAACAATGCTTTTTACTCATCAGAA
Found at i:29449893 original size:22 final size:22
Alignment explanation
Indices: 29449862--29449916 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
29449852 TTTTTGCTAT
*
29449862 TTTTTGAATTTTT-GAATTATTA
1 TTTTTAAATTTTTAGAATTA-TA
*
29449884 TTTTTAAATTTTTAGATTTATA
1 TTTTTAAATTTTTAGAATTATA
*
29449906 TTTTTTAATTT
1 TTTTTAAATTT
29449917 AAAATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTTTAAATTTTTAGAATTATA
Found at i:29454127 original size:52 final size:52
Alignment explanation
Indices: 29454049--29454392 Score: 544
Period size: 52 Copynumber: 6.6 Consensus size: 52
29454039 ATAAATGCAA
* *
29454049 AAGGTCCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACGAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
29454101 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
** *
29454153 AAGGTCTAATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
29454205 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
29454257 AAGGTCCGATGACTATGTGTCATCGTGAGAATATGAATCTTTTACGGATTAC
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * * *
29454309 GAGGTCCAATGACTATATGTGATCGTGAGTATATGAATCCTTTTCGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
29454361 GAGGTCTGATGACAATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
29454393 TAAATGTGAA
Statistics
Matches: 268, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 268 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:29461314 original size:24 final size:24
Alignment explanation
Indices: 29461287--29461361 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 24
29461277 TACGCTTGCT
29461287 AGCTTGCACATGTTTACGCTCGTC
1 AGCTTGCACATGTTTACGCTCGTC
** * *
29461311 AGCTTATATATGTGTTTACGCTCGCC
1 AGCTTGCACA--TGTTTACGCTCGTC
** *
29461337 AGCTTGCACACATTTACGTTCGTC
1 AGCTTGCACATGTTTACGCTCGTC
29461361 A
1 A
29461362 TTTTATATAT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
24 18 0.47
26 20 0.53
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.35
Consensus pattern (24 bp):
AGCTTGCACATGTTTACGCTCGTC
Found at i:29461353 original size:50 final size:50
Alignment explanation
Indices: 29461276--29461394 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
29461266 TCTCGTCAGC
* * ** *
29461276 TTACGCTTGCTAGCTTGCACATGTTTACGCTCGTCAGCTTATATATGTGT
1 TTACGCTCGCCAGCTTGCACACATTTACGCTCGTCAGCTTATATATGCGT
* **
29461326 TTACGCTCGCCAGCTTGCACACATTTACGTTCGTCATTTTATATATGCGT
1 TTACGCTCGCCAGCTTGCACACATTTACGCTCGTCAGCTTATATATGCGT
* * *
29461376 TTATGCTCACCAACTTGCA
1 TTACGCTCGCCAGCTTGCA
29461395 TACGTCCAGA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (50 bp):
TTACGCTCGCCAGCTTGCACACATTTACGCTCGTCAGCTTATATATGCGT
Found at i:29462932 original size:13 final size:13
Alignment explanation
Indices: 29462914--29462960 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
29462904 TTGACTCATA
29462914 AATATTAAATAAT
1 AATATTAAATAAT
*
29462927 AATATT-TATAGACTT
1 AATATTAAATA-A--T
29462942 AATATTAAATAAT
1 AATATTAAATAAT
29462955 AATATT
1 AATATT
29462961 TACAAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 3 0.11
13 14 0.50
15 8 0.29
16 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
AATATTAAATAAT
Found at i:29462969 original size:28 final size:28
Alignment explanation
Indices: 29462914--29462970 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
29462904 TTGACTCATA
* *
29462914 AATATTAAATAATAATATTTATAGACTT
1 AATATTAAATAATAATATTTACAAACTT
29462942 AATATTAAATAATAATATTTACAAACTT
1 AATATTAAATAATAATATTTACAAACTT
29462970 A
1 A
29462971 CTTTTCGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (28 bp):
AATATTAAATAATAATATTTACAAACTT
Found at i:29463128 original size:15 final size:15
Alignment explanation
Indices: 29463084--29463128 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
29463074 ATATTGGTGA
29463084 AAAAAAATTAATATT
1 AAAAAAATTAATATT
**
29463099 -AAAATTTTAATTATT
1 AAAAAAATTAA-TATT
29463114 AAAAAAATTAATATT
1 AAAAAAATTAATATT
29463129 GATTTAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAAAATTAATATT
Found at i:29463995 original size:51 final size:50
Alignment explanation
Indices: 29463910--29464007 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 50
29463900 ATGATATAAT
* *
29463910 AAAAATTTCCCTTAACTTTTACATATTATATCAATTTAGTCATAATTTTA
1 AAAAATTTCCCTTAAATTTTACATATTATATCAATTTAATCATAATTTTA
* *
29463960 AAAAATTTACCCTTAAATTTTACCA-A-TACTCTCAATTTAATCCTAATT
1 AAAAATTT-CCCTTAAATTTTA-CATATTA-TATCAATTTAATCATAATT
29464008 CTAAGATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
50 10 0.24
51 29 0.71
52 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (50 bp):
AAAAATTTCCCTTAAATTTTACATATTATATCAATTTAATCATAATTTTA
Found at i:29464075 original size:21 final size:19
Alignment explanation
Indices: 29464020--29464103 Score: 53
Period size: 21 Copynumber: 4.2 Consensus size: 19
29464010 AAGATATTTA
*
29464020 AATAACTATATAAAAAAACAT
1 AATAA-TAT-TAAAAAAATAT
*
29464041 AA-ACATTTTCAAAAAAATAT
1 AATA-ATATT-AAAAAAATAT
**
29464061 AATAATAAATTAAAAATTTAT
1 AATAAT--ATTAAAAAAATAT
* *
29464082 ATTAATATTAAATAAATAT
1 AATAATATTAAAAAAATAT
29464101 AAT
1 AAT
29464104 TTTATTAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
19 13 0.27
20 16 0.33
21 17 0.35
22 2 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAATATTAAAAAAATAT
Found at i:29466863 original size:91 final size:90
Alignment explanation
Indices: 29466686--29466935 Score: 344
Period size: 91 Copynumber: 2.8 Consensus size: 90
29466676 AGGAGAAAGT
* *
29466686 ACTGACAATT-TTAAC-TACAAACACTCGTGGTTTATCCACAACTTATATTGGTAGCTATTATCT
1 ACTGACAATTATTAACATGCAAACACTCGTGGTTTATCCACAACTTATACTGGTAGCTATTATCT
*
29466749 GCAAACTCATTGTGTATTCATAACC
66 GCAAACTCATTGTGTATTAATAACC
*
29466774 ACTGACAATGTATTAACATGCAAACACTCATGGTTTATCCACAACTTATACTGGTAGCTATTATC
1 ACTGACAAT-TATTAACATGCAAACACTCGTGGTTTATCCACAACTTATACTGGTAGCTATTATC
29466839 TGCAAACTCATTGTGTATTAATAACC
65 TGCAAACTCATTGTGTATTAATAACC
* * * * ** **
29466865 ACTAAC-ATCATATTAACATGCAAGCACTCGTGGTTTAACCACACCTTATACTGACAATTATTAT
1 ACTGACAAT--TATTAACATGCAAACACTCGTGGTTTATCCACAACTTATACTGGTAGCTATTAT
29466929 CTGCAAA
64 CTGCAAA
29466936 GTTTTTGTGT
Statistics
Matches: 144, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
88 9 0.06
89 1 0.01
90 7 0.05
91 127 0.88
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (90 bp):
ACTGACAATTATTAACATGCAAACACTCGTGGTTTATCCACAACTTATACTGGTAGCTATTATCT
GCAAACTCATTGTGTATTAATAACC
Found at i:29466970 original size:91 final size:91
Alignment explanation
Indices: 29466703--29466972 Score: 261
Period size: 91 Copynumber: 3.0 Consensus size: 91
29466693 ATTTTAACTA
* * * ** * * *
29466703 CAAACACTCGTGGTTTATCCACAACTTATATTGGTAGCTATTATCTGCAAACTCATTGTGTATTC
1 CAAACACTCATGGTTTAACCACAACTTATACTGACAACTATTATCTGCAAACTCATTGTGTACTA
* * **
29466768 ATAACCACTGACAATGTATTAACATG
66 ACAACCACTAACAGCGTATTAACATG
* ** * *
29466794 CAAACACTCATGGTTTATCCACAACTTATACTGGTAGCTATTATCTGCAAACTCATTGTGTATTA
1 CAAACACTCATGGTTTAACCACAACTTATACTGACAACTATTATCTGCAAACTCATTGTGTACTA
* * *
29466859 ATAACCACTAACATCATATTAACATG
66 ACAACCACTAACAGCGTATTAACATG
* * * * * ** *
29466885 CAAGCACTCGTGGTTTAACCACACCTTATACTGACAATTATTATCTGCAAAGTTTTTGTGTACTC
1 CAAACACTCATGGTTTAACCACAACTTATACTGACAACTATTATCTGCAAACTCATTGTGTACTA
* **
29466950 ACAACTACTAGTAGCGTATTAAC
66 ACAACCACTAACAGCGTATTAAC
29466973 CTACAACAGT
Statistics
Matches: 153, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
91 153 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (91 bp):
CAAACACTCATGGTTTAACCACAACTTATACTGACAACTATTATCTGCAAACTCATTGTGTACTA
ACAACCACTAACAGCGTATTAACATG
Found at i:29482432 original size:31 final size:30
Alignment explanation
Indices: 29482394--29482522 Score: 127
Period size: 31 Copynumber: 4.3 Consensus size: 30
29482384 ATACAATAAC
*
29482394 TAAATAAATTCTAACTAAGTAAATAAGTAAT
1 TAAATAAATT-TAACTAAGTAAATAAGTAAA
* *
29482425 TAAATAAATTTTAACTTAGTAAATAAGTAAC
1 TAAATAAA-TTTAACTAAGTAAATAAGTAAA
* * * * * *
29482456 TAGATAAATTTGACGATGTAAGTAAATAAA
1 TAAATAAATTTAACTAAGTAAATAAGTAAA
*
29482486 TAAATAAA--TAACTAGGTAAATAAGTAAA
1 TAAATAAATTTAACTAAGTAAATAAGTAAA
*
29482514 TAACTAAAT
1 TAAATAAAT
29482523 AAACAAAATA
Statistics
Matches: 79, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
28 22 0.28
30 22 0.28
31 33 0.42
32 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.31
Consensus pattern (30 bp):
TAAATAAATTTAACTAAGTAAATAAGTAAA
Found at i:29482485 original size:4 final size:4
Alignment explanation
Indices: 29482478--29482627 Score: 120
Period size: 4 Copynumber: 37.0 Consensus size: 4
29482468 ACGATGTAAG
* ** * *
29482478 TAAA TAAA TAAA TAAA TAAC TAGG TAAA TAAG TAAA TAAC TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * * *
29482526 CAAAA TAAA AAAA TAAA TAAC TAAA TACA TAAAA TAAA TAAA TAAC TAGA
1 -TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA
* * * * * **
29482576 TATA TAAA TAAT TAAC TAAT TAAA TAAA AAAA TACC TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
29482624 TAAA
1 TAAA
29482628 ATATTTTTAA
Statistics
Matches: 112, Mismatches: 32, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
4 106 0.95
5 6 0.05
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:29482507 original size:20 final size:20
Alignment explanation
Indices: 29482478--29482627 Score: 134
Period size: 20 Copynumber: 7.8 Consensus size: 20
29482468 ACGATGTAAG
29482478 TAAATAAATAAATAAATAAC
1 TAAATAAATAAATAAATAAC
** *
29482498 TAGGTAAATAAGTAAATAAC
1 TAAATAAATAAATAAATAAC
*
29482518 TAAATAAACAAA-ATAA-AA-
1 TAAATAAATAAATA-AATAAC
*
29482536 -AAATAAATAACTAAAT-AC
1 TAAATAAATAAATAAATAAC
*
29482554 -ATA-AAATAAATAAATAAC
1 TAAATAAATAAATAAATAAC
* * *
29482572 TAGATATATAAATAATTAAC
1 TAAATAAATAAATAAATAAC
* * *
29482592 TAATTAAATAAAAAAATACC
1 TAAATAAATAAATAAATAAC
29482612 TAAATAAATAAATAAA
1 TAAATAAATAAATAAA
29482628 ATATTTTTAA
Statistics
Matches: 101, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
17 23 0.23
18 5 0.05
19 5 0.05
20 68 0.67
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.25
Consensus pattern (20 bp):
TAAATAAATAAATAAATAAC
Found at i:29482542 original size:21 final size:22
Alignment explanation
Indices: 29482518--29482567 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
29482508 AGTAAATAAC
29482518 TAAATAAACAAAATA-AAAAAA
1 TAAATAAACAAAATACAAAAAA
* *
29482539 TAAAT-AACTAAATACATAAAA
1 TAAATAAACAAAATACAAAAAA
29482560 TAAATAAA
1 TAAATAAA
29482568 TAACTAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 15 0.60
22 2 0.08
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAATAAACAAAATACAAAAAA
Found at i:29482586 original size:29 final size:27
Alignment explanation
Indices: 29482503--29482586 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 27
29482493 ATAACTAGGT
* *
29482503 AAATAAGTAAATAACTAAATAAACAAAATA
1 AAATAAATAAATAACT-AAT-AA-TAAATA
*
29482533 AAA-AAATAAATAACT-A-AATACATA
1 AAATAAATAAATAACTAATAATAAATA
29482557 AAATAAATAAATAACTAGATATATAAATA
1 AAATAAATAAATAACTA-ATA-ATAAATA
29482586 A
1 A
29482587 TTAACTAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
24 7 0.16
25 14 0.31
27 2 0.04
28 1 0.02
29 18 0.40
30 3 0.07
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (27 bp):
AAATAAATAAATAACTAATAATAAATA
Found at i:29482969 original size:17 final size:17
Alignment explanation
Indices: 29482943--29482989 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
29482933 TAATAAAAGG
* *
29482943 AAAATTAAAAAGATAT-
1 AAAAATAAAAAAATATC
*
29482959 AAAAATAAAAAAATTTC
1 AAAAATAAAAAAATATC
29482976 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
29482990 TATAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAAAATATC
Found at i:29482988 original size:26 final size:26
Alignment explanation
Indices: 29482959--29483010 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
29482949 AAAAAGATAT
29482959 AAAAATA-AAAAAATTTCAAAAATAAA
1 AAAAATATAAAAAA-TTCAAAAATAAA
* * *
29482985 AAAATTATAAATAATTGAAAAATAAA
1 AAAAATATAAAAAATTCAAAAATAAA
29483011 TTTTATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (26 bp):
AAAAATATAAAAAATTCAAAAATAAA
Found at i:29489465 original size:31 final size:29
Alignment explanation
Indices: 29489430--29489499 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
29489420 ACCTCAAAAT
*
29489430 TATACATTAACTATGGTTTAATGTGCAATTG
1 TATACATTAACTATGATTT--TGTGCAATTG
* * * *
29489461 TATACATGAACTTTGATTTTGTGTAATTT
1 TATACATTAACTATGATTTTGTGCAATTG
29489490 TATACATTAA
1 TATACATTAA
29489500 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (29 bp):
TATACATTAACTATGATTTTGTGCAATTG
Found at i:29491060 original size:14 final size:14
Alignment explanation
Indices: 29491041--29491067 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29491031 AATCTGCCAT
29491041 TATTTTTAATATTC
1 TATTTTTAATATTC
29491055 TATTTTTAATATT
1 TATTTTTAATATT
29491068 TTGAGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTAATATTC
Found at i:29495552 original size:26 final size:26
Alignment explanation
Indices: 29495514--29495645 Score: 138
Period size: 26 Copynumber: 5.1 Consensus size: 26
29495504 ATTTTGAATA
* * *
29495514 GATATACTGAATTGGCTCGTAAGAGT
1 GATATACTAAACTGGCTCGTAAGAGC
*
29495540 GATATACTAAATTGGCTCGTAAGAGC
1 GATATACTAAACTGGCTCGTAAGAGC
* * * *
29495566 AATTTACTAAACTGGCTCCTAAGAGT
1 GATATACTAAACTGGCTCGTAAGAGC
* *
29495592 GATATACTAAACTAGCTTGTAAGAGC
1 GATATACTAAACTGGCTCGTAAGAGC
** * *
29495618 GATATACTGTACTAGATCGTAAGAGC
1 GATATACTAAACTGGCTCGTAAGAGC
29495644 GA
1 GA
29495646 ANNNNNNNNN
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 89 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (26 bp):
GATATACTAAACTGGCTCGTAAGAGC
Found at i:29496085 original size:161 final size:159
Alignment explanation
Indices: 29495747--29496054 Score: 404
Period size: 161 Copynumber: 1.9 Consensus size: 159
29495737 NNNNNNNNNN
* * *
29495747 AGAGGTTGCAACGTGTCACTTTTGGATTATTTCTGCATTTAGTCCTTTTTATTTTTTATTTGTTT
1 AGAGGCTGCCACGTGTCACTTTTGGATTATTTCTGCATTTAGTCCTTTTTATTTTTAATTTGTTT
* * *
29495812 TAATTTAATCCCAAATCAACTTTATTTTAATTACGAAATTGGCCCAATAATTTTTCAAGGTTTAT
66 TAATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATTTAT
* * *
29495877 AAACTAGTCCTTTGACTGTTTGACTGCACC
131 AAACTAGTCCCTTGACTGCTGGACT-CACC
* * *
29495907 AGAGGTTGCCACGTGTCATCTTTTTGATTATTTCTGTATTTAGTCCTTTTTATTTTTAATTTGTT
1 AGAGGCTGCCACGTGTCA-CTTTTGGATTATTTCTGCATTTAGTCCTTTTTATTTTTAATTTGTT
* * *
29495972 TTAATTTAATCCTTAAATCGACTTT-TATTTAATTACAAAATTGGTCCAAAAATTTTTCAAGATT
65 TTAATTTAATCC-CAAATCAACTTTAT-TTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATT
* *
29496036 T-TCAAATTGGTCCCTTGAC
128 TAT-AAACTAGTCCCTTGAC
29496055 CTCTGGATAC
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
160 17 0.13
161 57 0.44
162 57 0.44
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.46
Consensus pattern (159 bp):
AGAGGCTGCCACGTGTCACTTTTGGATTATTTCTGCATTTAGTCCTTTTTATTTTTAATTTGTTT
TAATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATTTAT
AAACTAGTCCCTTGACTGCTGGACTCACC
Found at i:29496222 original size:31 final size:30
Alignment explanation
Indices: 29496125--29496232 Score: 126
Period size: 30 Copynumber: 3.5 Consensus size: 30
29496115 CCCTAAATTG
*
29496125 TCCAGAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCAAAAACTTT
* * * **
29496156 CCCAAAATTATATTTTAACCCCGAAACTTT
1 TCCAAAATTACATTTTGACCCAAAAACTTT
* *
29496186 ACCAAAATTACGTTTTGACCCAAAAAACTTT
1 TCCAAAATTACATTTTGACCC-AAAAACTTT
29496217 TCCAAAATTACATTTT
1 TCCAAAATTACATTTT
29496233 TAACCCCGAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
30 39 0.62
31 24 0.38
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCAAAAACTTT
Found at i:29496282 original size:29 final size:29
Alignment explanation
Indices: 29496250--29496468 Score: 102
Period size: 29 Copynumber: 7.5 Consensus size: 29
29496240 GATTTCACCG
29496250 AAAATTACCATTTTACCCCCAAATCTTTT
1 AAAATTACCATTTTACCCCCAAATCTTTT
* ** ****
29496279 AAAATT-CCATTTTTAACCCCGATTTCACCG
1 AAAATTACCA-TTTT-ACCCCCAAATCTTTT
* *
29496309 AAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATTACCATTTTACCCCCAAATCTTTT
* * * ** * **
29496338 AAAATT-CCGTTTTTAAACCCGATTTCATCG
1 AAAATTACC-ATTTT-ACCCCCAAATCTTTT
**
29496368 AAAATTACCATTTTACCCCTGAATCTTTT
1 AAAATTACCATTTTACCCCCAAATCTTTT
* ** * ** ****
29496397 AAAATTTCGTTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTT-ACCCCCAAATCTTTT
*
29496427 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACCATTTTACCCCCAAATCTTTT
29496456 AAAATT-CCATTTT
1 AAAATTACCATTTT
29496469 TAACCTCGAT
Statistics
Matches: 126, Mismatches: 57, Indels: 15
0.64 0.29 0.08
Matches are distributed among these distances:
28 12 0.10
29 57 0.45
30 52 0.41
31 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAATCTTTT
Found at i:29496293 original size:59 final size:59
Alignment explanation
Indices: 29496220--29496623 Score: 621
Period size: 59 Copynumber: 6.9 Consensus size: 59
29496210 AAACTTTTCC
* *
29496220 AAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
*
29496279 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * * *
29496338 AAAATTCCGTTTTTAAACCCGATTTCATCGAAAATTACCATTTTACCCCTGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * *
29496397 AAAATTTCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * *
29496456 AAAATTCCATTTTTAACCTCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * *
29496515 AAAATTTCATTTTTAACCCCGATTTCACCGAAAATTGCCATTTTACCCCTGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * * *
29496574 AAAATTCCATTTTTAATCTCGATTACACC-AAAATTACCATTTTGCCCCCG
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
29496624 GGTATCCATA
Statistics
Matches: 313, Mismatches: 32, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
58 18 0.06
59 295 0.94
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
Found at i:29500563 original size:86 final size:85
Alignment explanation
Indices: 29500386--29500590 Score: 218
Period size: 86 Copynumber: 2.4 Consensus size: 85
29500376 CTTAATAGTG
* * *
29500386 TAAAAAGCCCTCAAACTTTTTCAAAAAAAATAATTAAGCCCCTACTTTTTTTACTAAATTGGGTA
1 TAAAAAGCCCACAAACTTTTTCAAAAAAAACAATTAAGCCCCTACTTTTTTTACTAAATTGAGTA
29500451 CTTGAACTATCAAAAATGAA
66 CTTGAACTATCAAAAATGAA
* * *
29500471 TAAAAAAGCCCACAAACTTTTT-AAAAAGAAGCAATTAAGCCCCTA-TATTTTTTGCATTCAATT
1 T-AAAAAGCCCACAAACTTTTTCAAAAA-AAACAATTAAGCCCCTACT-TTTTTT--ACTAAATT
**
29500534 GAGTACTTGAACT-TTTAAAATGCATAA
61 GAGTACTTGAACTATCAAAAATG---AA
* * *
29500561 AAAAAAACCCTCAAACTTTTTCAAAAAAAA
1 TAAAAAGCCCACAAACTTTTTCAAAAAAAA
29500591 AAAAAACAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
85 7 0.07
86 40 0.40
87 7 0.07
88 18 0.18
89 20 0.20
90 7 0.07
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (85 bp):
TAAAAAGCCCACAAACTTTTTCAAAAAAAACAATTAAGCCCCTACTTTTTTTACTAAATTGAGTA
CTTGAACTATCAAAAATGAA
Found at i:29500766 original size:29 final size:29
Alignment explanation
Indices: 29500717--29500780 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
29500707 AATGATAAAA
*
29500717 AATAAAAAAATAAAAGTTA-TTAAATTTT
1 AATAAAAAAATAAAAGATATTTAAATTTT
29500745 AATAAAAAACTATAAAA-ATATTTAAATTTT
1 AATAAAAAA--ATAAAAGATATTTAAATTTT
29500775 -ATAAAA
1 AATAAAA
29500781 TTATAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 9 0.28
29 8 0.25
30 15 0.47
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
AATAAAAAAATAAAAGATATTTAAATTTT
Found at i:29501103 original size:11 final size:11
Alignment explanation
Indices: 29501089--29501164 Score: 59
Period size: 11 Copynumber: 7.1 Consensus size: 11
29501079 TTTTAATGCA
29501089 TTTTATAATTT
1 TTTTATAATTT
**
29501100 TTTTATAA-AA
1 TTTTATAATTT
* *
29501110 GTTTACAATTT
1 TTTTATAATTT
29501121 TTTTATAA-TT
1 TTTTATAATTT
* *
29501131 GTTTATGATTT
1 TTTTATAATTT
*
29501142 TTATA-AATTTT
1 TTTTATAA-TTT
29501153 TTTTATAATTT
1 TTTTATAATTT
29501164 T
1 T
29501165 ATATTTTTTA
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
10 15 0.32
11 30 0.64
12 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:29501114 original size:21 final size:21
Alignment explanation
Indices: 29501090--29501143 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
29501080 TTTAATGCAT
29501090 TTTATAATTTTTTTATAAAAG
1 TTTATAATTTTTTTATAAAAG
* **
29501111 TTTACAATTTTTTTATAATTG
1 TTTATAATTTTTTTATAAAAG
*
29501132 TTTATGATTTTT
1 TTTATAATTTTT
29501144 ATAAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.63
Consensus pattern (21 bp):
TTTATAATTTTTTTATAAAAG
Found at i:29501166 original size:21 final size:19
Alignment explanation
Indices: 29501121--29501205 Score: 73
Period size: 19 Copynumber: 4.3 Consensus size: 19
29501111 TTTACAATTT
* * * *
29501121 TTTTATAATTGTTTATGAT
1 TTTTATAATTTTTTTTAAA
29501140 TTTTATAAATTTTTTTTATAA
1 TTTTAT-AATTTTTTTTA-AA
29501161 TTTTAT-ATTTTTTATTAAAA
1 TTTTATAATTTTTT-TT-AAA
* *
29501181 TTTAATAATTTTTTATAAA
1 TTTTATAATTTTTTTTAAA
29501200 TTTTAT
1 TTTTAT
29501206 TTATTATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
19 21 0.39
20 18 0.33
21 15 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTTTAAA
Found at i:29501173 original size:51 final size:51
Alignment explanation
Indices: 29501089--29501209 Score: 122
Period size: 51 Copynumber: 2.4 Consensus size: 51
29501079 TTTTAATGCA
* * * *
29501089 TTTTAT-AATTTTTTTATAAAAGTTTACAATTTTT-TTATAATTGTTTATGA-T
1 TTTTATAAATTTTTTT-TATAAGTTTACAATTTTTATTA-AAAT-TTAATAATT
* * *
29501140 TTTTATAAATTTTTTTTATAATTTTATATTTTTTATTAAAATTTAATAATT
1 TTTTATAAATTTTTTTTATAAGTTTACAATTTTTATTAAAATTTAATAATT
*
29501191 TTTTATAAATTTTATTTAT
1 TTTTATAAATTTTTTTTAT
29501210 TATAGTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
50 5 0.08
51 42 0.71
52 12 0.20
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (51 bp):
TTTTATAAATTTTTTTTATAAGTTTACAATTTTTATTAAAATTTAATAATT
Found at i:29501182 original size:20 final size:21
Alignment explanation
Indices: 29501140--29501205 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 21
29501130 TGTTTATGAT
*
29501140 TTTTATAAATTTTTT-TTATAA
1 TTTTAT-AATTTTTTATTAAAA
29501161 TTTTAT-ATTTTTTATTAAAA
1 TTTTATAATTTTTTATTAAAA
*
29501181 TTTAATAATTTTTTA-T-AAA
1 TTTTATAATTTTTTATTAAAA
29501200 TTTTAT
1 TTTTAT
29501206 TTATTATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 15 0.38
20 11 0.28
21 14 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATAATTTTTTATTAAAA
Found at i:29501433 original size:85 final size:86
Alignment explanation
Indices: 29501325--29501483 Score: 198
Period size: 85 Copynumber: 1.8 Consensus size: 86
29501315 TCAAAAAGTT
** * * * *
29501325 TTTTTGATGCATTTGACAATTCAAGTATCCAATTGAGTG-AAAAAAT-TAGGGATTTAATTGCAT
1 TTTTTGATGCATTTGACAATTCAAACATCCAAGTGAGTGAAAAAAATGGAAGGACTTAATTGCAT
29501388 TTTTTGAAAGAGTTTGAGGGC
66 TTTTTGAAAGAGTTTGAGGGC
*
29501409 TTTTTGATGCATTTTGA-AAGTTCAAACATCTAAGTGAGTGCAAAAAAATGGAAGGACTTAATTG
1 TTTTTGATGCA-TTTGACAA-TTCAAACATCCAAGTGAGTG-AAAAAAATGGAAGGACTTAATTG
*
29501473 CTTTTTTTGAA
63 CATTTTTTGAA
29501484 CCATTAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
84 13 0.21
85 21 0.34
87 7 0.11
88 21 0.34
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (86 bp):
TTTTTGATGCATTTGACAATTCAAACATCCAAGTGAGTGAAAAAAATGGAAGGACTTAATTGCAT
TTTTTGAAAGAGTTTGAGGGC
Found at i:29501817 original size:26 final size:26
Alignment explanation
Indices: 29501781--29501882 Score: 98
Period size: 26 Copynumber: 3.8 Consensus size: 26
29501771 ATGTGGCACA
*
29501781 AAAAATTATAAAAAATAAAAATCAAT
1 AAAAATTATAAAAAATAAAAATTAAT
* **
29501807 AAAAATTATAAAATTATTAAATTTTAAT
1 AAAAATTATAAAA--AATAAAAATTAAT
* *
29501835 AAAAA-TATAAAAAACTAAAATTTATT
1 AAAAATTATAAAAAA-TAAAAATTAAT
*
29501861 AAAAATTAGAAAAAATATAAAA
1 AAAAATTATAAAAAATA-AAAA
29501883 AGCCTTAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
25 1 0.02
26 29 0.47
27 18 0.29
28 14 0.23
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (26 bp):
AAAAATTATAAAAAATAAAAATTAAT
Found at i:29501860 original size:36 final size:35
Alignment explanation
Indices: 29501815--29501883 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
29501805 ATAAAAATTA
**
29501815 TAAAATTATTAAATTTTA-ATAAAAATATAAAAAAC
1 TAAAATTATTAAAAATTAGA-AAAAATATAAAAAAC
29501850 TAAAATTTATTAAAAATTAGAAAAAATATAAAAA
1 TAAAA-TTATTAAAAATTAGAAAAAATATAAAAA
29501884 GCCTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 5 0.17
36 24 0.80
37 1 0.03
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (35 bp):
TAAAATTATTAAAAATTAGAAAAAATATAAAAAAC
Found at i:29502205 original size:90 final size:88
Alignment explanation
Indices: 29502012--29502206 Score: 212
Period size: 90 Copynumber: 2.2 Consensus size: 88
29502002 AAAATCAGGA
* * *
29502012 GCTTAATTATTTTTTTGAAAAAAGTTTGAAGTCTTTTTGACGCATTTTAAAAGTTCAAGTATCCA
1 GCTTAATTATTTTTTTGAAAAAAGTTTGAAGCCTCTTTGACACATTTTAAAAGTTCAAGTATCCA
* * * * *
29502077 ATTGAGTGTAAAATAAAAGTAGG
66 AGTAAGTGCAAAATAAAAATAAG
** * * * * *
29502100 GACTTAACTGCTTTTTTTG-ATAAAGTTTGAGGGCCTCTTTGATACATTTTGAAAGTTTAAGTAT
1 G-CTTAA-TTATTTTTTTGAAAAAAGTTTGA-AGCCTCTTTGACACATTTTAAAAGTTCAAGTAT
29502164 CCAAGTAAGTGCAAAATAAAAATAAAG
63 CCAAGTAAGTGCAAAATAAAAAT-AAG
29502191 GCTTAATTATTTTTTT
1 GCTTAATTATTTTTTT
29502207 AAATTAAAAG
Statistics
Matches: 86, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
88 1 0.01
89 23 0.27
90 59 0.69
91 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.39
Consensus pattern (88 bp):
GCTTAATTATTTTTTTGAAAAAAGTTTGAAGCCTCTTTGACACATTTTAAAAGTTCAAGTATCCA
AGTAAGTGCAAAATAAAAATAAG
Found at i:29502726 original size:14 final size:14
Alignment explanation
Indices: 29502707--29502737 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29502697 AGAATAAATC
29502707 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
29502721 TTTAATTAATTAAA
1 TTTAATTAAATAAA
29502735 TTT
1 TTT
29502738 TTTAAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:29526763 original size:21 final size:20
Alignment explanation
Indices: 29526735--29526782 Score: 87
Period size: 21 Copynumber: 2.4 Consensus size: 20
29526725 GCCAAATTCT
29526735 TCACTATTGACCCTGCCAAG
1 TCACTATTGACCCTGCCAAG
29526755 TCATCTATTGACCCTGCCAAG
1 TCA-CTATTGACCCTGCCAAG
29526776 TCACTAT
1 TCACTAT
29526783 CTGAGTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.29
Consensus pattern (20 bp):
TCACTATTGACCCTGCCAAG
Found at i:29536589 original size:17 final size:17
Alignment explanation
Indices: 29536517--29536610 Score: 50
Period size: 17 Copynumber: 5.5 Consensus size: 17
29536507 ACGAACTGTG
* *
29536517 TTTATATGCAAGATGT-
1 TTTATATGCGAGTTGTA
* * *
29536533 TTATATATGCTAATTATA
1 TT-TATATGCGAGTTGTA
*
29536551 TTTATACGCGAGCTATG-A
1 TTTATATGCGAG-T-TGTA
*
29536569 -TTATATGCTAGTTGTA
1 TTTATATGCGAGTTGTA
* **
29536585 TTTATAAGCGAGTTGGG
1 TTTATATGCGAGTTGTA
29536602 TTTATATGC
1 TTTATATGC
29536611 AAATTAAGTC
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
15 2 0.04
16 4 0.07
17 46 0.81
18 4 0.07
19 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.44
Consensus pattern (17 bp):
TTTATATGCGAGTTGTA
Found at i:29536607 original size:34 final size:34
Alignment explanation
Indices: 29536536--29536616 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
29536526 AAGATGTTTA
* *
29536536 TATATGCTAATTATATTTATACGCGAGCTATGAT
1 TATATGCTAATTATATTTATAAGCGAGCTAGGAT
* * * * *
29536570 TATATGCTAGTTGTATTTATAAGCGAGTTGGGTT
1 TATATGCTAATTATATTTATAAGCGAGCTAGGAT
*
29536604 TATATGCAAATTA
1 TATATGCTAATTA
29536617 AGTCAATGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (34 bp):
TATATGCTAATTATATTTATAAGCGAGCTAGGAT
Found at i:29539348 original size:7 final size:7
Alignment explanation
Indices: 29539336--29539360 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29539326 TCAAAGCTTG
29539336 AACCATA
1 AACCATA
29539343 AACCATA
1 AACCATA
29539350 AACCATA
1 AACCATA
29539357 AACC
1 AACC
29539361 CCAAATCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCATA
Found at i:29539430 original size:21 final size:21
Alignment explanation
Indices: 29539404--29539443 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29539394 TTTGATCAAG
29539404 TGTTTAAGGTTTAAGGTTTTA
1 TGTTTAAGGTTTAAGGTTTTA
* *
29539425 TGTTTAGGGTTTAGGGTTT
1 TGTTTAAGGTTTAAGGTTT
29539444 CAAGTGTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (21 bp):
TGTTTAAGGTTTAAGGTTTTA
Found at i:29539453 original size:21 final size:21
Alignment explanation
Indices: 29539411--29539460 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
29539401 AAGTGTTTAA
* * * *
29539411 GGTTTAAGGTTTTATGTTTAG
1 GGTTTAGGGTTTCAAGTGTAG
29539432 GGTTTAGGGTTTCAAGTGTAG
1 GGTTTAGGGTTTCAAGTGTAG
*
29539453 GGTATAGG
1 GGTTTAGG
29539461 TTTAGGGTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.42
Consensus pattern (21 bp):
GGTTTAGGGTTTCAAGTGTAG
Found at i:29539516 original size:20 final size:21
Alignment explanation
Indices: 29539487--29539536 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
29539477 TATGTATAGG
29539487 TTTAAGGTTTAGGGTTCAAGA
1 TTTAAGGTTTAGGGTTCAAGA
**
29539508 TTT-AGGTTTAGGGTTTGAGA
1 TTTAAGGTTTAGGGTTCAAGA
29539528 TTTAAGGTT
1 TTTAAGGTT
29539537 CGAGGTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTCAAGA
Found at i:29539537 original size:34 final size:34
Alignment explanation
Indices: 29539485--29539556 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
29539475 TCTATGTATA
* * *
29539485 GGTTTAAGGTTTAGGGTTCAAGATTTAGGTTTAG
1 GGTTTAAGATTTAAGGTTCAAGATTCAGGTTTAG
* * * *
29539519 GGTTTGAGATTTAAGGTTCGAGGTTCATGTTTAG
1 GGTTTAAGATTTAAGGTTCAAGATTCAGGTTTAG
29539553 GGTT
1 GGTT
29539557 CAAAGTGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.04, G:0.33, T:0.42
Consensus pattern (34 bp):
GGTTTAAGATTTAAGGTTCAAGATTCAGGTTTAG
Found at i:29550612 original size:75 final size:76
Alignment explanation
Indices: 29550492--29550640 Score: 273
Period size: 75 Copynumber: 2.0 Consensus size: 76
29550482 AAATTAAGTT
*
29550492 TAAAGTTTAATAAACTAATGATTTAATTAAGAAAAAGTAGATTAATTAAATCTTAACGAGGTATA
1 TAAAGTTTAATAAACTAATGATTTAATTAAGAAAAACTAGATTAATTAAATCTTAACGAGGTATA
29550557 TAAGTAAAGGG
66 TAAGTAAAGGG
*
29550568 TAAAGTTTAATAAACTAATGA-TTAATTAAGAAAAACTAGATTAATTAAATCTTAATGAGGTATA
1 TAAAGTTTAATAAACTAATGATTTAATTAAGAAAAACTAGATTAATTAAATCTTAACGAGGTATA
29550632 TAAGTAAAG
66 TAAGTAAAG
29550641 TGAGTGGGAA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 50 0.70
76 21 0.30
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (76 bp):
TAAAGTTTAATAAACTAATGATTTAATTAAGAAAAACTAGATTAATTAAATCTTAACGAGGTATA
TAAGTAAAGGG
Found at i:29562677 original size:91 final size:91
Alignment explanation
Indices: 29562522--29562731 Score: 375
Period size: 91 Copynumber: 2.3 Consensus size: 91
29562512 TTACCGGTAT
* * *
29562522 ACGATGCTGCTCACACTAAGTTGATGAGGACTCGTAACATATGTGTTACCCTAGCCATCGATACG
1 ACGATGCTGCTCACACAAAGTTGACGAGGACTCGTAACATATGTGTTACCCTAGCCAGCGATACG
29562587 GTATCTATACATATAACTATTCCCTG
66 GTATCTATACATATAACTATTCCCTG
29562613 ACGATGCTGCTCACACAAAGTTGACGAGGACTCGTAACATATGTGTTACCCTAGCCAGCGATACG
1 ACGATGCTGCTCACACAAAGTTGACGAGGACTCGTAACATATGTGTTACCCTAGCCAGCGATACG
*
29562678 GTATCTATACATATAACTGTTCCCTG
66 GTATCTATACATATAACTATTCCCTG
*
29562704 ACGATGCTACTCACACAAAGTTGACGAG
1 ACGATGCTGCTCACACAAAGTTGACGAG
29562732 AATATGCAAA
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 114 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (91 bp):
ACGATGCTGCTCACACAAAGTTGACGAGGACTCGTAACATATGTGTTACCCTAGCCAGCGATACG
GTATCTATACATATAACTATTCCCTG
Found at i:29566430 original size:22 final size:23
Alignment explanation
Indices: 29566402--29566458 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
29566392 TTAATGCTTC
29566402 TTGTCTCAAGACAAAAAGGT-CA
1 TTGTCTCAAGACAAAAAGGTACA
* * *
29566424 TTGTCTCGAGACCATAAGGTACA
1 TTGTCTCAAGACAAAAAGGTACA
29566447 -TGTCTCAAGACA
1 TTGTCTCAAGACA
29566459 TGCTCAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (23 bp):
TTGTCTCAAGACAAAAAGGTACA
Found at i:29574915 original size:377 final size:377
Alignment explanation
Indices: 29574216--29574937 Score: 1099
Period size: 377 Copynumber: 1.9 Consensus size: 377
29574206 ATATATACAT
* * * * *
29574216 ATAATCACAATCAAGCATAATTTATGATAATTTGGCTATTGGGACTATGAAACGTATAGTGAGCT
1 ATAATCACAATCAAACACAATTTATGATAATTTGGCTATTGAGACTATAAAACATATAGTGAGCT
* * * *
29574281 CTATCATCACACATTTGATATGTGGATCTCCAACACACCAACACTGGATTCATAGAGTCGAAACA
66 CTATCATCACACATTGGATATGCGGATCTCCAACACACCAACACTAGACTCATAGAGTCGAAACA
* * *
29574346 TATCATATAAGTGAAGCATATAGCTAACACCCTCCAACACACCAAACATATCCTGTTGAATTGAG
131 TATCATATAAGTGAAGCATATAGCTAACACCCTCCAACACACCAAACAGATCCCGTTGAATGGAG
**
29574411 TTTAGCTCACATTCCCTTATCTCTCCAACATGTCCCTAACCCTCAGCACCCCACATATAACACAA
196 CATAGCTCACATTCCCTTATCTCTCCAACATGTCCCTAACCCTCAGCACCCCACATATAACACAA
* * *
29574476 ACGTGAGTACTTACAGTCCTATGGCATGCCAACTACATCTAAAGGTCTCATAAGACCACAAAGCC
261 ACGTAAGTACTTACAATCCTATGGCATGCCAACTACATCCAAAGGTCTCATAAGACCACAAAGCC
29574541 AAAATATCCACATTATTATTGCATATTTTTATCAGATATTCACTGCATATTC
326 AAAATATCCACATTATTATTGCATATTTTTATCAGATATTCACTGCATATTC
* *
29574593 ATAATCACAATCAAACACAATTTATGATAATTTGGTTGTTGAGACTATAAAACATATAGTGAGCT
1 ATAATCACAATCAAACACAATTTATGATAATTTGGCTATTGAGACTATAAAACATATAGTGAGCT
* *
29574658 CTATCATTACACATTGGATACT-CGGATCTCCAACACATCAACACTAGACTCATAGAGTCGAAAC
66 CTATCATCACACATTGGATA-TGCGGATCTCCAACACACCAACACTAGACTCATAGAGTCGAAAC
* * ** *
29574722 ATATCCTATAAGTTAAGCATATAGCTAACACTTTCCAACACACCATACAGATCCCGTTGAATGGA
130 ATATCATATAAGTGAAGCATATAGCTAACACCCTCCAACACACCAAACAGATCCCGTTGAATGGA
* *** *
29574787 GCATAGCTCACATTCCCTTATCTCTCCAACATGTCCTTGGGCCTCTA-CGCCCCACATATAACAC
195 GCATAGCTCACATTCCCTTATCTCTCCAACATGTCCCTAACCCTC-AGCACCCCACATATAACAC
* *
29574851 AAACGTAAGTACTCT-CAATCCTATGGCATGCCAACTATATCCAAAGGTCTCATAAGATCACAAA
259 AAACGTAAGTACT-TACAATCCTATGGCATGCCAACTACATCCAAAGGTCTCATAAGACCACAAA
29574915 GCCAAAATATCCACATTATTATT
323 GCCAAAATATCCACATTATTATT
29574938 ATTACTACTA
Statistics
Matches: 309, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
377 306 0.99
378 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (377 bp):
ATAATCACAATCAAACACAATTTATGATAATTTGGCTATTGAGACTATAAAACATATAGTGAGCT
CTATCATCACACATTGGATATGCGGATCTCCAACACACCAACACTAGACTCATAGAGTCGAAACA
TATCATATAAGTGAAGCATATAGCTAACACCCTCCAACACACCAAACAGATCCCGTTGAATGGAG
CATAGCTCACATTCCCTTATCTCTCCAACATGTCCCTAACCCTCAGCACCCCACATATAACACAA
ACGTAAGTACTTACAATCCTATGGCATGCCAACTACATCCAAAGGTCTCATAAGACCACAAAGCC
AAAATATCCACATTATTATTGCATATTTTTATCAGATATTCACTGCATATTC
Found at i:29575176 original size:23 final size:23
Alignment explanation
Indices: 29575149--29575603 Score: 561
Period size: 23 Copynumber: 20.2 Consensus size: 23
29575139 ATCTTAATTC
* *
29575149 TTTAAGAACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
29575172 TTTAATCAGAAATCATATT-A-A
1 TTTAAGCACAAATCACATTAATA
29575193 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
29575216 GTTAAG--C--AT---ATTAATA
1 TTTAAGCACAAATCACATTAATA
29575232 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
29575255 TTTGAGCATAAATCACATTACTA
1 TTTAAGCACAAATCACATTAATA
29575278 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29575301 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
29575324 TCTAAGTACATA-CACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29575346 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
29575369 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29575392 TTTAAGCATAGATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
29575415 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** *
29575438 TTTGGGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29575461 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
29575484 TTTAAGCACAAATCACTTTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29575507 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
29575530 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
29575553 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
29575576 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
29575599 TTTAA
1 TTTAA
29575604 TATTAATATT
Statistics
Matches: 370, Mismatches: 52, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
16 12 0.03
18 1 0.00
19 2 0.01
20 2 0.01
21 18 0.05
22 19 0.05
23 316 0.85
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:29575197 original size:21 final size:21
Alignment explanation
Indices: 29575149--29575736 Score: 286
Period size: 23 Copynumber: 26.5 Consensus size: 21
29575139 ATCTTAATTC
*
29575149 TTTAAGAACAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
* *
29575172 TTTAATCAGAAATCATATTAA
1 TTTAAGCACAAATCATATTAA
*
29575193 TTTAAGCACAAATCACATTAA
1 TTTAAGCACAAATCATATTAA
* *
29575214 TAGTTAAG--CATAT--TAAT-A
1 T--TTAAGCACAAATCATATTAA
*
29575232 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCATATT-A-A
* * *
29575255 TTTGAGCATAAATCACATTACTA
1 TTTAAGCACAAATCATATTA--A
*
29575278 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCATATT-A-A
*
29575301 TTTGAGCACAAATCATATTAA
1 TTTAAGCACAAATCATATTAA
* * *
29575322 TATCTAAGTACATA-CACATTAATA
1 T-T-TAAGCACAAATCATATT-A-A
*
29575346 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
29575369 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
* * *
29575392 TTTAAGCATAGATCACATTAA
1 TTTAAGCACAAATCATATTAA
*
29575413 TACTTAAGCACAAATCACATTAATA
1 T--TTAAGCACAAATCATATT-A-A
** * *
29575438 TTTGGGCATAAATCACATTAATA
1 TTTAAGCACAAATCATATT-A-A
*
29575461 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
29575484 TTTAAGCACAAATCACT-TTAATA
1 TTTAAGCACAAATCA-TATT-A-A
*
29575507 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
* *
29575530 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCATATT-A-A
*
29575553 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCATATT-A-A
*
29575576 TTTAAGCATAAATCATATTAA
1 TTTAAGCACAAATCATATTAA
* * *
29575597 TATT---TA-ATAT--TAAT-A
1 T-TTAAGCACAAATCATATTAA
* *
29575612 TTTGAGTACAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
* *
29575635 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCATATT-A-A
*
29575658 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATT-A-A
** * *
29575681 TTTAAGCTTAAATTACATTAA
1 TTTAAGCACAAATCATATTAA
29575702 TAATTAAGCACAAATCATATTAATA
1 T--TTAAGCACAAATCATATT-A-A
29575727 TTTAAGCACA
1 TTTAAGCACA
29575737 GATATAAGAA
Statistics
Matches: 462, Mismatches: 67, Indels: 72
0.77 0.11 0.12
Matches are distributed among these distances:
14 2 0.00
15 2 0.00
16 8 0.02
17 2 0.00
18 12 0.03
19 3 0.01
20 5 0.01
21 32 0.07
22 22 0.05
23 364 0.79
24 6 0.01
25 4 0.01
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (21 bp):
TTTAAGCACAAATCATATTAA
Found at i:29575228 original size:16 final size:16
Alignment explanation
Indices: 29575209--29575239 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29575199 CACAAATCAC
29575209 ATTAATAGTTAAGCAT
1 ATTAATAGTTAAGCAT
*
29575225 ATTAATATTTAAGCA
1 ATTAATAGTTAAGCA
29575240 CAAATCACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (16 bp):
ATTAATAGTTAAGCAT
Found at i:29575297 original size:46 final size:46
Alignment explanation
Indices: 29575222--29575736 Score: 649
Period size: 46 Copynumber: 11.4 Consensus size: 46
29575212 AATAGTTAAG
*
29575222 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCATAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* *
29575268 CACATTACTATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* * *
29575314 CATATTAATATCTAAGTACATA-CACATTAATATTTGAGCACAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* * * *
29575359 CATATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAGAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* * * *
29575405 CACATTAATACTTAAGCACAAATCACATTAATATTTGGGCATAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* * * *
29575451 CACATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* * * *
29575497 CACT-TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAAT
1 CA-TATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
* * *
29575543 CACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
*
29575589 CATATTAATATTT-------AAT---ATTAATATTTGAGTACAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
*
29575625 CATATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
** * * *
29575671 CATATTAATATTTAAGCTTAAATTACATTAATAATTAAGCACAAAT
1 CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
29575717 CATATTAATATTTAAGCACA
1 CATATTAATATTTAAGCACA
29575737 GATATAAGAA
Statistics
Matches: 409, Mismatches: 47, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
36 30 0.07
39 3 0.01
43 3 0.01
45 42 0.10
46 331 0.81
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.35
Consensus pattern (46 bp):
CATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAAT
Found at i:29575309 original size:69 final size:69
Alignment explanation
Indices: 29575225--29575734 Score: 639
Period size: 69 Copynumber: 7.6 Consensus size: 69
29575215 AGTTAAGCAT
* * *
29575225 ATTAATATTTAAGCACAAATCACATTAATATTTGAGCATAAATCACATTACTATTTAAGCACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
29575290 TCAC
66 TCAC
* * * *
29575294 ATTAATATTTGAGCACAAATCATATTAATATCTAAG--TACATACACATTAATATTTGAGCACAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAAT-CACATTAATATTTAAGCACAA
*
29575357 ATCAT
65 ATCAC
* *
29575362 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAGATCACATTAATACTTAAGCACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
29575427 TCAC
66 TCAC
** * * *
29575431 ATTAATATTTGGGCATAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
29575496 TCAC
66 TCAC
* * * *
29575500 TTTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
29575565 TCAC
66 TCAC
* * *
29575569 ATTAATATTTAAGCATAAATCATATTAATA-TT-----T-AAT---ATTAATATTTGAGTACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
*
29575624 TCAT
66 TCAC
* * * * * **
29575628 ATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAATCATATTAATATTTAAGCTTAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
*
29575693 TTAC
66 TCAC
*
29575697 ATTAATAATTAAGCACAAATCATATTAATATTTAAGCA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCA
29575735 CAGATATAAG
Statistics
Matches: 381, Mismatches: 47, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
59 49 0.13
60 2 0.01
62 3 0.01
66 3 0.01
67 4 0.01
68 59 0.15
69 257 0.67
70 4 0.01
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (69 bp):
ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCACAAA
TCAC
Found at i:29575608 original size:13 final size:13
Alignment explanation
Indices: 29575590--29575614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29575580 AGCATAAATC
29575590 ATATTAATATTTA
1 ATATTAATATTTA
29575603 ATATTAATATTT
1 ATATTAATATTT
29575615 GAGTACAAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTAATATTTA
Found at i:29575609 original size:36 final size:36
Alignment explanation
Indices: 29575569--29575639 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
29575559 CACAAATCAC
*
29575569 ATTAATATTTAAGCATAAATCATATTAATATTTAAT
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAT
* *
29575605 ATTAATATTTGAGTACAAATCATATTAATATTTAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAA
29575640 GCATAAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
ATTAATATTTAAGCACAAATCATATTAATATTTAAT
Found at i:29575623 original size:59 final size:59
Alignment explanation
Indices: 29575546--29575660 Score: 194
Period size: 59 Copynumber: 1.9 Consensus size: 59
29575536 AACAAATCAC
*
29575546 ATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAAT
1 ATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTAAT
* * *
29575605 ATTAATATTTGAGTACAAATCATATTAATATTTAAGCATAAATCACATTAATATTT
1 ATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTT
29575661 GAGCACAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (59 bp):
ATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCACATTAATATTTAAT
Found at i:29575632 original size:82 final size:82
Alignment explanation
Indices: 29575521--29575685 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
29575511 AGCACAAATC
*
29575521 ATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATA
1 ATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCACA
29575586 AATCATATTAATATTTA
66 AATCATATTAATATTTA
* * * * *
29575603 ATATTAATATTTGAGTACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTGAGCACA
1 ATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCACA
29575668 AATCATATTAATATTTA
66 AATCATATTAATATTTA
29575685 A
1 A
29575686 GCTTAAATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (82 bp):
ATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCACA
AATCATATTAATATTTA
Found at i:29575678 original size:105 final size:105
Alignment explanation
Indices: 29575501--29575708 Score: 335
Period size: 105 Copynumber: 2.0 Consensus size: 105
29575491 ACAAATCACT
29575501 TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
* *
29575566 CACATTAATATTTAAGCATAAATCATATTAATATTTAATA
66 CACATTAATATTTAAGCATAAATCACATTAATAATTAATA
* * * *
29575606 TTAATATTTGAGTACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
* * *
29575671 CATATTAATATTTAAGCTTAAATTACATTAATAATTAA
66 CACATTAATATTTAAGCATAAATCACATTAATAATTAA
29575709 GCACAAATCA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 94 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (105 bp):
TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
CACATTAATATTTAAGCATAAATCACATTAATAATTAATA
Found at i:29575700 original size:128 final size:128
Alignment explanation
Indices: 29575226--29575731 Score: 539
Period size: 128 Copynumber: 3.8 Consensus size: 128
29575216 GTTAAGCATA
* * * *
29575226 TTAATATTTAAGCACAAATCACATTAATATTTGAGCATAAATCACATTACTATTTAAGCACAAAT
1 TTAATATTTAAGCACAAATCACATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
* * *
29575291 CACATTAATATTTGAGCACAAATCATATTAATATCTAAGTACATACACATTAATATTTGAGCACA
66 CACATTAATAATTAAGCACAAATCATATTAATAT-T---TA-AT----ATTAATATTTAAGCACA
29575356 AATCA-T
122 AATCACT
* * * * *
29575362 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAGATCACATTAATACTTAAGCACAAA
1 -TTAATATTTAAGCACAAATCACATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAA
* ** * *
29575427 TCACATTAATATTTGGGCATAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAAGCA
65 TCACATTAATAATTAAGCACAAATCATATTAATA-TT-----T--A--ATATTAATATTTAAGCA
29575492 CAAATCACT
120 CAAATCACT
* *
29575501 TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
1 TTAATATTTAAGCACAAATCACATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
* * * *
29575566 CACATTAATATTTAAGCATAAATCATATTAATATTTAATATTAATATTTGAGTACAAATCA-T
66 CACATTAATAATTAAGCACAAATCATATTAATATTTAATATTAATATTTAAGCACAAATCACT
* * * * **
29575628 ATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAATCATATTAATATTTAAGCTTAAA
1 -TTAATATTTAAGCACAAATCACATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAA
*
29575693 TTACATTAATAATTAAGCACAAATCATATTAATATTTAA
65 TCACATTAATAATTAAGCACAAATCATATTAATATTTAA
29575732 GCACAGATAT
Statistics
Matches: 328, Mismatches: 33, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
127 1 0.00
128 114 0.35
130 1 0.00
132 1 0.00
137 93 0.28
138 112 0.34
139 2 0.01
141 1 0.00
142 3 0.01
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (128 bp):
TTAATATTTAAGCACAAATCACATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAAT
CACATTAATAATTAAGCACAAATCATATTAATATTTAATATTAATATTTAAGCACAAATCACT
Found at i:29575724 original size:151 final size:151
Alignment explanation
Indices: 29575454--29575734 Score: 463
Period size: 151 Copynumber: 1.9 Consensus size: 151
29575444 CATAAATCAC
* *
29575454 ATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCACTTTAATATTTGAGCACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAA
*
29575519 TCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCA
66 TCATATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCA
29575584 TAAATCATATTAATATTTAAT
131 TAAATCATATTAATATTTAAT
* * *
29575605 ATTAATATTTGAGTACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTGAGCACAAA
1 ATTAATATTTAAGCACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAA
*** * *
29575670 TCATATTAATATTTAAGCTTAAATTACATTAATAATTAAGCACAAATCATATTAATATTTAAGCA
66 TCATATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCA
29575735 CAGATATAAG
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
151 119 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (151 bp):
ATTAATATTTAAGCACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAA
TCATATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCA
TAAATCATATTAATATTTAAT
Found at i:29575770 original size:151 final size:151
Alignment explanation
Indices: 29575297--29575720 Score: 245
Period size: 151 Copynumber: 2.9 Consensus size: 151
29575287 AAATCACATT
* * * * *
29575297 AATATTTGAGCACAAATCATATTAATATCTAAGTACATA-CACATTAATATTTGAGCACAAATCA
1 AATATTAGAGTACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAATCA
* * * * * *
29575361 TATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAGATCACATTAATACTTAAGCACAA
66 TATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCACAA
29575426 ATC------ACA-TTAAT---
131 ATCATAAGAACACTTAATAGG
* * * * * * *
29575437 -AT-TT-GGGCATAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAAGCACAAATCA
1 AATATTAGAGTACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAATCA
* * * * *
29575499 CT-TTAATATTTGAGCACAAATCATATTAATATTTAAGAACAAATCACATTAATATTTAAGCACA
66 -TATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCACA
* ** * * *
29575563 AATCACATTAATA-TTTA-AGC
130 AATCATAAGAACACTTAATAGG
* * * * * * * * * * *
29575583 ATAAATCATATTA-ATATTTAATATTAATATTTGAGTACAAATCATATTAATATTTAAGCATAAA
1 A-ATATTAGAGTACA-A-ATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAA
* * * * * ** * *
29575647 TCACATTAATATTTGAGCACAAATCATATTAATATTTAAGCTTAAATTACATTAATAATTAAGCA
63 TCATATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCA
29575712 CAAATCATA
128 CAAATCATA
29575721 TTAATATTTA
Statistics
Matches: 230, Mismatches: 36, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
137 25 0.11
138 86 0.37
139 3 0.01
144 5 0.02
148 1 0.00
149 2 0.01
150 2 0.01
151 106 0.46
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (151 bp):
AATATTAGAGTACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTGAGCACAAATCA
TATTAATATTTAAGAACAAATCACATTAATAATTAAGCACAAATCACATTAATATTTAAGCACAA
ATCATAAGAACACTTAATAGG
Found at i:29579246 original size:14 final size:14
Alignment explanation
Indices: 29579227--29579255 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29579217 TTTATCCTTT
29579227 GATCCAAATGGCTC
1 GATCCAAATGGCTC
29579241 GATCCAAATGGCTC
1 GATCCAAATGGCTC
29579255 G
1 G
29579256 GTGGATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (14 bp):
GATCCAAATGGCTC
Found at i:29579515 original size:11 final size:12
Alignment explanation
Indices: 29579489--29579519 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
29579479 CAAGTTCCTT
29579489 TTCTTCTTTCTC
1 TTCTTCTTTCTC
29579501 TTCTTCTTT-TC
1 TTCTTCTTTCTC
29579512 TTCTTCTT
1 TTCTTCTT
29579520 CTTGATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:29586240 original size:296 final size:296
Alignment explanation
Indices: 29585706--29586299 Score: 1035
Period size: 296 Copynumber: 2.0 Consensus size: 296
29585696 TGAGTAATTT
* *
29585706 TCATATCTTAATATAGAAGCATTTTGATTCCCCCAAGGTTGTTGAGATCGGTTGTTGTATGAGTT
1 TCATATCTGAATATAGAAGCATTTTGATTCCCCCAAGGTTGTTGAAATCGGTTGTTGTATGAGTT
* *
29585771 ACCAAATGAACCTCCCTTGATGTTATTAACGTAGAAAGCATTTTCTGTATGTTGTGGGTAGTCCT
66 ACCAAATGAACCTCCCTTGATGTTATTAACGTAGAAAGCATTTTCTGCATGTTGTGGGCAGTCCT
* ** *
29585836 CATAATTATGATTGTCCCCGCAAATTTCAAAAGAAAATATGGGTGCATCCAATTTTTGGGCCACT
131 CATAATTATGATTGTCCCCGCAAATTTCAAAAGAAAATATCGACGCATCCAATTTCTGGGCCACT
* * *
29585901 TGAATAGGAGCAACGTCATTTGTTCCCTTTATATTCTTTATAATATTGGCCAATGAGGATACTTG
196 TGAATAAGAGCAACGTCATTTGTTCCCTTCATATTCTTTATAATATTGGCCAATGAGGATACCTG
29585966 CACTGACAAAGCAGAAATATCATCTAACTCAAGAAC
261 CACTGACAAAGCAGAAATATCATCTAACTCAAGAAC
*
29586002 TCATATCTGAATATAGAAGCATTTTGATTCCCTCAAGGTTGTTGAAATCGGTTGTTGTATGAGTT
1 TCATATCTGAATATAGAAGCATTTTGATTCCCCCAAGGTTGTTGAAATCGGTTGTTGTATGAGTT
*
29586067 ACCAAATGAACCTCCCTTGATGTTATTATCGTAGAAAGCATTTTCTGCATGTTGTGGGCAGTCCT
66 ACCAAATGAACCTCCCTTGATGTTATTAACGTAGAAAGCATTTTCTGCATGTTGTGGGCAGTCCT
* **
29586132 TATAATTATGATTGTCGTCGCAAATTTCAAAAGAAAATATCGACGCATCCAATTTCTGGGCCACT
131 CATAATTATGATTGTCCCCGCAAATTTCAAAAGAAAATATCGACGCATCCAATTTCTGGGCCACT
29586197 TGAATAAGAGCAACGTCATTTGTTCCCTTCATATTCTTTATAATATTGGCCAATGAGGATACCTG
196 TGAATAAGAGCAACGTCATTTGTTCCCTTCATATTCTTTATAATATTGGCCAATGAGGATACCTG
*
29586262 CACTGACAAAGTAGAAATATCATCTAACTCAAGAAC
261 CACTGACAAAGCAGAAATATCATCTAACTCAAGAAC
29586298 TC
1 TC
29586300 CAGTGATAGT
Statistics
Matches: 281, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
296 281 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (296 bp):
TCATATCTGAATATAGAAGCATTTTGATTCCCCCAAGGTTGTTGAAATCGGTTGTTGTATGAGTT
ACCAAATGAACCTCCCTTGATGTTATTAACGTAGAAAGCATTTTCTGCATGTTGTGGGCAGTCCT
CATAATTATGATTGTCCCCGCAAATTTCAAAAGAAAATATCGACGCATCCAATTTCTGGGCCACT
TGAATAAGAGCAACGTCATTTGTTCCCTTCATATTCTTTATAATATTGGCCAATGAGGATACCTG
CACTGACAAAGCAGAAATATCATCTAACTCAAGAAC
Found at i:29591200 original size:27 final size:27
Alignment explanation
Indices: 29591134--29591221 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
29591124 AGCCACATGC
29591134 AGAGTATTACTCTTTCAAGCCAAAAAT
1 AGAGTATTACTCTTTCAAGCCAAAAAT
* * * *
29591161 AGACTATCACTCTTTCGAA-CTAGAAAT
1 AGAGTATTACTCTTTC-AAGCCAAAAAT
* ** *
29591188 AGAGTATTGCTCTTTTGAGCCAAAAAA
1 AGAGTATTACTCTTTCAAGCCAAAAAT
29591215 AGAGTAT
1 AGAGTAT
29591222 CGCTTTTTTG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
26 1 0.02
27 44 0.94
28 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (27 bp):
AGAGTATTACTCTTTCAAGCCAAAAAT
Found at i:29591230 original size:27 final size:27
Alignment explanation
Indices: 29591188--29591267 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
29591178 AACTAGAAAT
* *
29591188 AGAGTATTGCTCTTTTGAGCCAAAAAA
1 AGAGTATCGCTTTTTTGAGCCAAAAAA
*
29591215 AGAGTATCGCTTTTTTGAGCCAGAATCAA
1 AGAGTATCGCTTTTTTGAGCCA-AA-AAA
*
29591244 A-A-TATCGCTCTTTCTGAGCCAAAA
1 AGAGTATCGCT-TTTTTGAGCCAAAA
29591268 TCAAAATATC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 29 0.64
28 13 0.29
29 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (27 bp):
AGAGTATCGCTTTTTTGAGCCAAAAAA
Found at i:29591264 original size:28 final size:28
Alignment explanation
Indices: 29591219--29591301 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
29591209 AAAAAAAGAG
*
29591219 TATCGCT-TTTTTGAGCCAGAATCAAAA
1 TATCGCTCTTTCTGAGCCAGAATCAAAA
*
29591246 TATCGCTCTTTCTGAGCCAAAATCAAAA
1 TATCGCTCTTTCTGAGCCAGAATCAAAA
*
29591274 TATCGCTCTTTCCGAGCCAGAATCAAAA
1 TATCGCTCTTTCTGAGCCAGAATCAAAA
29591302 AAAAATTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 7 0.14
28 44 0.86
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (28 bp):
TATCGCTCTTTCTGAGCCAGAATCAAAA
Found at i:29591778 original size:21 final size:21
Alignment explanation
Indices: 29591754--29591794 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29591744 ATTAGGGCCG
* *
29591754 TAAATATTTTTATTAAATATT
1 TAAATAGTCTTATTAAATATT
*
29591775 TAAATAGTCTTATTATATAT
1 TAAATAGTCTTATTAAATAT
29591795 GAATTGAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAAATAGTCTTATTAAATATT
Found at i:29595843 original size:129 final size:126
Alignment explanation
Indices: 29595616--29595873 Score: 426
Period size: 129 Copynumber: 2.0 Consensus size: 126
29595606 TCATGCTGCA
* * *
29595616 CAAGTTAAAGCAAACTACGGAGTTATTGAATTAGACGTATCAACTCTAAGTGCACAAGTATCTTC
1 CAAGTTAAAGCAAACCACAGAGTTATCGAATTAGACGTATCAACTCTAAGTGCACAAGTATCTTC
* * *
29595681 GTTAGCAAATATGATAAAGAACATGAAGGGGACCAGTGAAGTTGCTCCCATTCAAGTTACC
66 ATTAGAAAATATGATAAAGAACATGAAGGGGACCAGTGAAGTTGCTCCCAATCAAGTTACC
29595742 CAAGTTAAAGCAAACCACAGAGTTATCGAATTAGACGTTATATCAACTCTAAGTGCACAAGTATC
1 CAAGTTAAAGCAAACCACAGAGTTATCGAATTAGACG---TATCAACTCTAAGTGCACAAGTATC
*
29595807 TTCATTAGAAAATATGATAAAGAACATGAAGGGGACCAGTGAAGTTGCTTCCAATCAAGTTACC
63 TTCATTAGAAAATATGATAAAGAACATGAAGGGGACCAGTGAAGTTGCTCCCAATCAAGTTACC
29595871 CAA
1 CAA
29595874 CAACTGGATG
Statistics
Matches: 122, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
126 34 0.28
129 88 0.72
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (126 bp):
CAAGTTAAAGCAAACCACAGAGTTATCGAATTAGACGTATCAACTCTAAGTGCACAAGTATCTTC
ATTAGAAAATATGATAAAGAACATGAAGGGGACCAGTGAAGTTGCTCCCAATCAAGTTACC
Found at i:29606104 original size:16 final size:15
Alignment explanation
Indices: 29606074--29606129 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
29606064 ATTATTTATC
29606074 TAAAACTCTTTTAAT
1 TAAAACTCTTTTAAT
*
29606089 TAAAATTCTATTTAAT
1 TAAAACTCT-TTTAAT
*
29606105 T---A-TCTTTTATT
1 TAAAACTCTTTTAAT
29606116 TAAAACTCTTTTAA
1 TAAAACTCTTTTAA
29606130 GTAATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 1 0.03
14 1 0.03
15 15 0.45
16 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAACTCTTTTAAT
Found at i:29606141 original size:52 final size:52
Alignment explanation
Indices: 29606085--29606189 Score: 160
Period size: 52 Copynumber: 2.0 Consensus size: 52
29606075 AAAACTCTTT
* *
29606085 TAATTAAAATTCTA-TTTAATTATCT-TTTATTTAAAACTCTTTTAAGTAATAA
1 TAATT-AAATTCTATTTTAATTAT-TATTTATCTAAAACTCTTTTAAATAATAA
29606137 TAATTAAATTCTATTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
1 TAATTAAATTCTATTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
29606189 T
1 T
29606190 TAGATTCTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
51 9 0.18
52 40 0.82
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (52 bp):
TAATTAAATTCTATTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
Found at i:29606179 original size:26 final size:25
Alignment explanation
Indices: 29606087--29606181 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
29606077 AACTCTTTTA
*
29606087 ATTAAAATTCTATTTAATTATCT-TTT
1 ATTAAAACTCT-TTTAATTAT-TATTT
* * * *
29606113 ATTTAAAACTCTTTTAAGTAATAATA
1 A-TTAAAACTCTTTTAATTATTATTT
* *
29606139 ATTAAATTCTATTTTAATTATTATTT
1 ATTAAA-ACTCTTTTAATTATTATTT
29606165 ATCTAAAACTCTTTTAA
1 AT-TAAAACTCTTTTAA
29606182 ATAATAATTA
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
25 6 0.12
26 33 0.63
27 13 0.25
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTAAAACTCTTTTAATTATTATTT
Found at i:29608498 original size:23 final size:24
Alignment explanation
Indices: 29608454--29608498 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
29608444 GTTTTTAGGT
** *
29608454 CATGTGGTATCTAATGAGGGTATC
1 CATGTGGTATCTAAAAAAGGTATC
29608478 CATGTGG-ATCTAAAAAAGGTA
1 CATGTGGTATCTAAAAAAGGTA
29608499 GAAGCTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (24 bp):
CATGTGGTATCTAAAAAAGGTATC
Found at i:29609091 original size:646 final size:646
Alignment explanation
Indices: 29607861--29609152 Score: 2530
Period size: 646 Copynumber: 2.0 Consensus size: 646
29607851 ACCAACGTCC
29607861 ATTGTTCCTTACCGCATGGAACCTAAAAAGTTGACAGAGTTAAAAGCCTAGCTTTAGGAATTTTT
1 ATTGTTCCTTACCGCATGGAACCTAAAAAGTTGACAGAGTTAAAAGCCTAGCTTTAGGAATTTTT
29607926 AGACTGGGGATTTATAAACTCTAGTGTTTCATCTTGTAACGCACAGGTATTGTTCATTAAGAAGA
66 AGACTGGGGATTTATAAACTCTAGTGTTTCATCTTGTAACGCACAGGTATTGTTCATTAAGAAGA
29607991 AAAATGGAACACTATAATTATGTATTGATTACAGACAACTGAATAAACTAACCGTAAAGAATAAG
131 AAAATGGAACACTATAATTATGTATTGATTACAGACAACTGAATAAACTAACCGTAAAGAATAAG
29608056 TATCCTCTGTCAAAGATCGATTATCTGTTTGATTAGTTTAGGGGTGAAACTGTGTTCTCTAAAAT
196 TATCCTCTGTCAAAGATCGATTATCTGTTTGATTAGTTTAGGGGTGAAACTGTGTTCTCTAAAAT
29608121 TGACTTGAGATCTAGGTATTACCAACTTAAGGTGAAAGAATCCAATGTACCCAAGACTGCATTAA
261 TGACTTGAGATCTAGGTATTACCAACTTAAGGTGAAAGAATCCAATGTACCCAAGACTGCATTAA
29608186 GGACTCGTTATGATCATTATGAGTTCCTAGTTATGTCATTTAGATTGACTAATGTATCGACTGCA
326 GGACTCGTTATGATCATTATGAGTTCCTAGTTATGTCATTTAGATTGACTAATGTATCGACTGCA
*
29608251 TTTATGGATTCATGGACCATGTCTTTTAGCCTTTCCTTGATCAATTTGTCGTTGTGTTCATCGAA
391 TTTATGGATTCATGAACCATGTCTTTTAGCCTTTCCTTGATCAATTTGTCGTTGTGTTCATCGAA
29608316 AACATATTGGTATATTCTAAGTCAAAATTTGAGCATGATGAGCATTTGAGGGTAGCTTTGCAGAT
456 AACATATTGGTATATTCTAAGTCAAAATTTGAGCATGATGAGCATTTGAGGGTAGCTTTGCAGAT
29608381 TCTTTATAAGAAGAAGCTTTTTCCTAAGCTTAGTATGTGTGAGTTCTGGTTAAAGGAGTTTCTGT
521 TCTTTATAAGAAGAAGCTTTTTCCTAAGCTTAGTATGTGTGAGTTCTGGTTAAAGGAGTTTCTGT
29608446 TTTTAGGTCATGTGGTATCTAATGAGGGTATCCATGTGGATCTAAAAAAGGTAGAAGCTAT
586 TTTTAGGTCATGTGGTATCTAATGAGGGTATCCATGTGGATCTAAAAAAGGTAGAAGCTAT
*
29608507 ATTGTTCCTTACCGCATGGAACCTAAAAAGTTGACAGAGTTAAAAGTCTAGCTTTAGGAATTTTT
1 ATTGTTCCTTACCGCATGGAACCTAAAAAGTTGACAGAGTTAAAAGCCTAGCTTTAGGAATTTTT
*
29608572 GGACTGGGGATTTATAAACTCTAGTGTTTCATCTTGTAACGCACAGGTATTGTTCATTAAGAAGA
66 AGACTGGGGATTTATAAACTCTAGTGTTTCATCTTGTAACGCACAGGTATTGTTCATTAAGAAGA
29608637 AAAATGGAACACTATAATTATGTATTGATTACAGACAACTGAATAAACTAACCGTAAAGAATAAG
131 AAAATGGAACACTATAATTATGTATTGATTACAGACAACTGAATAAACTAACCGTAAAGAATAAG
29608702 TATCCTCTGTCAAAGATCGATTATCTGTTTGATTAGTTTAGGGGTGAAACTGTGTTCTCTAAAAT
196 TATCCTCTGTCAAAGATCGATTATCTGTTTGATTAGTTTAGGGGTGAAACTGTGTTCTCTAAAAT
*
29608767 TGACTTGAGATCTAGGTATTACCAACTTAAGGTGAAAGAATCCAATGTACCCAAGACTGCATTTA
261 TGACTTGAGATCTAGGTATTACCAACTTAAGGTGAAAGAATCCAATGTACCCAAGACTGCATTAA
29608832 GGACTCGTTATGATCATTATGAGTTCCTAGTTATGTCATTTAGATTGACTAATGTATCGACTGCA
326 GGACTCGTTATGATCATTATGAGTTCCTAGTTATGTCATTTAGATTGACTAATGTATCGACTGCA
29608897 TTTATGGATTCATGAACCATGTCTTTTAGCCTTTCCTTGATCAATTTGTCGTTGTGTTCATCGAA
391 TTTATGGATTCATGAACCATGTCTTTTAGCCTTTCCTTGATCAATTTGTCGTTGTGTTCATCGAA
29608962 AACATATTGGTATATTCTAAGTCAAAATTTGAGCATGATGAGCATTTGAGGGTAGCTTTGCAGAT
456 AACATATTGGTATATTCTAAGTCAAAATTTGAGCATGATGAGCATTTGAGGGTAGCTTTGCAGAT
*
29609027 TCTTTATAAGAAGAAGCTTTTTGCTAAGCTTAGTATGTGTGAGTTCTGGTTAAAGGAGTTTCTGT
521 TCTTTATAAGAAGAAGCTTTTTCCTAAGCTTAGTATGTGTGAGTTCTGGTTAAAGGAGTTTCTGT
*
29609092 TTTTTGGTCATGTGGTATCTAATGAGGGTATCCATGTGGATCTAAAAAAGGTAGAAGCTAT
586 TTTTAGGTCATGTGGTATCTAATGAGGGTATCCATGTGGATCTAAAAAAGGTAGAAGCTAT
29609153 CTTAGATTGG
Statistics
Matches: 640, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
646 640 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (646 bp):
ATTGTTCCTTACCGCATGGAACCTAAAAAGTTGACAGAGTTAAAAGCCTAGCTTTAGGAATTTTT
AGACTGGGGATTTATAAACTCTAGTGTTTCATCTTGTAACGCACAGGTATTGTTCATTAAGAAGA
AAAATGGAACACTATAATTATGTATTGATTACAGACAACTGAATAAACTAACCGTAAAGAATAAG
TATCCTCTGTCAAAGATCGATTATCTGTTTGATTAGTTTAGGGGTGAAACTGTGTTCTCTAAAAT
TGACTTGAGATCTAGGTATTACCAACTTAAGGTGAAAGAATCCAATGTACCCAAGACTGCATTAA
GGACTCGTTATGATCATTATGAGTTCCTAGTTATGTCATTTAGATTGACTAATGTATCGACTGCA
TTTATGGATTCATGAACCATGTCTTTTAGCCTTTCCTTGATCAATTTGTCGTTGTGTTCATCGAA
AACATATTGGTATATTCTAAGTCAAAATTTGAGCATGATGAGCATTTGAGGGTAGCTTTGCAGAT
TCTTTATAAGAAGAAGCTTTTTCCTAAGCTTAGTATGTGTGAGTTCTGGTTAAAGGAGTTTCTGT
TTTTAGGTCATGTGGTATCTAATGAGGGTATCCATGTGGATCTAAAAAAGGTAGAAGCTAT
Found at i:29609144 original size:23 final size:24
Alignment explanation
Indices: 29609100--29609144 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
29609090 GTTTTTTGGT
** *
29609100 CATGTGGTATCTAATGAGGGTATC
1 CATGTGGTATCTAAAAAAGGTATC
29609124 CATGTGG-ATCTAAAAAAGGTA
1 CATGTGGTATCTAAAAAAGGTA
29609145 GAAGCTATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (24 bp):
CATGTGGTATCTAAAAAAGGTATC
Found at i:29622459 original size:198 final size:198
Alignment explanation
Indices: 29622121--29622904 Score: 1397
Period size: 198 Copynumber: 4.0 Consensus size: 198
29622111 AATGGACGCA
* *
29622121 ATAATTGAAAGGTGCAAGCTTGATTTAGGTCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
1 ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
* *
29622186 AAGAGAGCTTTATTATCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
66 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
* *
29622251 GTCCCTGTTACTTCACATAGACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATGCAAG
131 GTCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATACAAG
29622316 TTT
196 TTT
*
29622319 ATAATTGAAAGGTGCAAGCTTGATTTAGATCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
1 ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
29622384 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
66 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
*
29622449 GTCCCTGTTACTTCCCATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATACAAG
131 GTCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATACAAG
29622514 TTT
196 TTT
* * *
29622517 ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTCATTACTT
1 ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
* * *
29622582 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAATTATTTCAAACCTAGCGC
66 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
*
29622647 GTCCCTTTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATACAAG
131 GTCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATACAAG
29622712 TTT
196 TTT
*
29622715 ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTCATAACTC
1 ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
* * *
29622780 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAATTATTTCAAACCTAGCGC
66 AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
29622845 GTCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTAT
131 GTCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTAT
29622905 GCATGTTTTT
Statistics
Matches: 568, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
198 568 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (198 bp):
ATAATTGAAAGGTGCAAGCTTGATTTAGATATTAGCCCGATTAAATTAAAGGTTTTTAATAACTC
AAGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCC
GTCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATACAAG
TTT
Found at i:29627071 original size:41 final size:41
Alignment explanation
Indices: 29627026--29627146 Score: 109
Period size: 41 Copynumber: 3.0 Consensus size: 41
29627016 CCAATTGAGT
*
29627026 CTCACCTCTAAAGGCGTCTTATTTTGCTTCACCAAATTAAC
1 CTCACCTCTAAAGGCATCTTATTTTGCTTCACCAAATTAAC
* * * * * ** *
29627067 CTCACCTTTATAGGCATCGTGTTTTCCTTCATTAAA-TAAGG
1 CTCACCTCTAAAGGCATCTTATTTTGCTTCACCAAATTAA-C
* * **
29627108 CTTAGCTCTAAAGGCATCTTATTTCACTTCACCAAATTA
1 CTCACCTCTAAAGGCATCTTATTTTGCTTCACCAAATTA
29627147 GAATTACATT
Statistics
Matches: 59, Mismatches: 19, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
40 3 0.05
41 54 0.92
42 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (41 bp):
CTCACCTCTAAAGGCATCTTATTTTGCTTCACCAAATTAAC
Found at i:29629207 original size:3 final size:3
Alignment explanation
Indices: 29629199--29629223 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29629189 TTTATTCAGT
29629199 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
29629224 CATTTTGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29639823 original size:20 final size:21
Alignment explanation
Indices: 29639790--29639830 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
29639780 CCCAAAAATG
29639790 TTTTAAACACCATTCAAACAT
1 TTTTAAACACCATTCAAACAT
29639811 TTTTAAACA-CATTCAAACAT
1 TTTTAAACACCATTCAAACAT
29639831 ATGTCTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTTAAACACCATTCAAACAT
Found at i:29651196 original size:19 final size:19
Alignment explanation
Indices: 29651164--29651211 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29651154 GTACGGGATT
*
29651164 ATGTGCCAAG-ATGCACTTC
1 ATGTGCC-AGTATGCAATTC
*
29651183 ATGTGCCAGTATGCAATTT
1 ATGTGCCAGTATGCAATTC
*
29651202 ACGTGCCAGT
1 ATGTGCCAGT
29651212 TTGCCCTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (19 bp):
ATGTGCCAGTATGCAATTC
Found at i:29653757 original size:19 final size:17
Alignment explanation
Indices: 29653733--29653796 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
29653723 ACTCTATGCT
29653733 ATTTTTAAAATTTTAATGA
1 ATTTTTAAAATTTT-AT-A
* * *
29653752 ATTTTTTATATTTTTTA
1 ATTTTTAAAATTTTATA
*
29653769 ATTTTTGAATATTTTCATA
1 ATTTTT-AAAATTTT-ATA
29653788 ATTTTTAAA
1 ATTTTTAAA
29653797 TTATTTATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 7 0.19
18 10 0.27
19 20 0.54
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTTTAAAATTTTATA
Found at i:29653798 original size:27 final size:26
Alignment explanation
Indices: 29653732--29653798 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
29653722 TACTCTATGC
*
29653732 TATTTTTAAAATTTTAATGAATTTTTTA
1 TATTTTT-AAATTTT-ATGAATTTTTCA
*
29653760 TATTTTTTAATTTT-TGAATATTTTCA
1 TATTTTTAAATTTTATGAAT-TTTTCA
29653786 TAATTTTTAAATT
1 T-ATTTTTAAATT
29653799 ATTTATTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 5 0.15
26 6 0.18
27 16 0.47
28 7 0.21
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (26 bp):
TATTTTTAAATTTTATGAATTTTTCA
Found at i:29657290 original size:22 final size:19
Alignment explanation
Indices: 29657264--29657317 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 19
29657254 CAATGTTTGG
29657264 AAAGGAAGAAAATTTAAAT
1 AAAGGAAGAAAATTTAAAT
29657283 CCAAAAGGAA-AAAA---AAAT
1 ---AAAGGAAGAAAATTTAAAT
29657301 AAAGGAAGAAAATTTAA
1 AAAGGAAGAAAATTTAA
29657318 GGGGAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
15 7 0.25
16 4 0.14
18 4 0.14
19 2 0.07
21 4 0.14
22 7 0.25
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAGGAAGAAAATTTAAAT
Found at i:29657499 original size:2 final size:2
Alignment explanation
Indices: 29657492--29657528 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29657482 AAAAGCACAA
29657492 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29657529 TTTAACAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29658891 original size:18 final size:18
Alignment explanation
Indices: 29658850--29658891 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29658840 TTTTTCTAAT
*
29658850 AAAAAAATCATAAAAATT
1 AAAAAAATCATAAAAATA
**
29658868 GTAAAAATCATAAAAATA
1 AAAAAAATCATAAAAATA
29658886 AAAAAA
1 AAAAAA
29658892 TAAAAAATGT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAATCATAAAAATA
Found at i:29658918 original size:19 final size:20
Alignment explanation
Indices: 29658894--29658933 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29658884 TAAAAAAATA
*
29658894 AAAAATGTT-AAAATTTTAT
1 AAAAATATTAAAAATTTTAT
29658913 AAAAATATTAAAAATTTTAT
1 AAAAATATTAAAAATTTTAT
29658933 A
1 A
29658934 TAAACTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAAATATTAAAAATTTTAT
Found at i:29658947 original size:22 final size:20
Alignment explanation
Indices: 29658903--29658949 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
29658893 AAAAAATGTT
*
29658903 AAAATTTTATAAAAATATTA
1 AAAATTTTATAAAAATATAA
*
29658923 AAAATTTTATATAAACTTATAA
1 AAAATTTTATA-AAA-ATATAA
29658945 AAAAT
1 AAAAT
29658950 CATAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 3 0.13
22 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTTATAAAAATATAA
Found at i:29658961 original size:29 final size:29
Alignment explanation
Indices: 29658939--29658994 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29658929 TTATATAAAC
29658939 TTATAAAAAATCATAAATATTATAAAAGC
1 TTATAAAAAATCATAAATATTATAAAAGC
* * *
29658968 TTATAAAACATCCTAAAAATTATAAAA
1 TTATAAAAAATCATAAATATTATAAAA
29658995 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (29 bp):
TTATAAAAAATCATAAATATTATAAAAGC
Found at i:29659457 original size:29 final size:26
Alignment explanation
Indices: 29659423--29659616 Score: 70
Period size: 29 Copynumber: 6.8 Consensus size: 26
29659413 TTTTTATACT
29659423 TTTATAATATTTATAAGTCTTTATGA-T
1 TTTATAATATTTATAAGT-TTTAT-ATT
*
29659450 TTTATATATCTTTTATAAG-TTTATATTT
1 TTTATA-AT-ATTTATAAGTTTTATA-TT
* *
29659478 TTTAAAATATTTTTAATGTGTTTTATTATT
1 TTTATAATATTTATAA---GTTTTA-TATT
* * *
29659508 TTTATAATTTATTAGAATTTATTATAAGTT
1 TTTATAATAT-TTATAAGTT-TTAT-A-TT
* * * *
29659538 TATATAATTTTTATTATTTTTATAATT
1 TTTATAATATTTATAAGTTTTAT-ATT
* * *
29659565 TATTAGAATTTATTATAAGCTTATATAATT
1 T-TTATAATAT-TTATAAG-TTTTAT-ATT
29659595 TTTATAA-ACTTATATAAGTTTT
1 TTTATAATA-TT-TATAAGTTTT
29659617 GAATATCAAC
Statistics
Matches: 129, Mismatches: 20, Indels: 35
0.70 0.11 0.19
Matches are distributed among these distances:
26 7 0.05
27 16 0.12
28 28 0.22
29 37 0.29
30 35 0.27
31 6 0.05
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (26 bp):
TTTATAATATTTATAAGTTTTATATT
Found at i:29659464 original size:19 final size:19
Alignment explanation
Indices: 29659413--29659475 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
29659403 TTTATAGAGG
29659413 TTTT-TATA-CTTTTATAA
1 TTTTATATATCTTTTATAA
*
29659430 TATTTATA-AGTC-TTTATGA
1 T-TTTATATA-TCTTTTATAA
29659449 TTTTATATATCTTTTATAA
1 TTTTATATATCTTTTATAA
*
29659468 GTTTATAT
1 TTTTATAT
29659476 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 1 0.03
18 12 0.32
19 23 0.62
20 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATATATCTTTTATAA
Found at i:29659479 original size:27 final size:25
Alignment explanation
Indices: 29659415--29659489 Score: 62
Period size: 29 Copynumber: 2.8 Consensus size: 25
29659405 TATAGAGGTT
*
29659415 TTTATACTTTTATAATATTTATAAG
1 TTTATATTTTTATAATATTTATAAG
*
29659440 TCTT-TATGATTTTATATATCTTTTATAAG
1 T-TTATAT--TTTTATA-AT-ATTTATAAG
*
29659469 TTTATATTTTTTAAAATATTT
1 TTTATA-TTTTTATAATATTT
29659490 TTAATGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
25 3 0.08
26 5 0.13
27 9 0.23
28 10 0.26
29 11 0.28
30 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTATATTTTTATAATATTTATAAG
Found at i:29659512 original size:9 final size:9
Alignment explanation
Indices: 29659413--29659601 Score: 107
Period size: 9 Copynumber: 20.0 Consensus size: 9
29659403 TTTATAGAGG
29659413 TTTTTAT-A
1 TTTTTATAA
*
29659421 CTTTTATAA
1 TTTTTATAA
*
29659430 TATTTATAA
1 TTTTTATAA
* *
29659439 GTCTTTATGA
1 -TTTTTATAA
29659449 -TTTTATATA
1 TTTTTATA-A
29659458 TCTTTTATAA
1 T-TTTTATAA
* *
29659468 -GTTTATAT
1 TTTTTATAA
*
29659476 TTTTTAAAA
1 TTTTTATAA
29659485 TATTTT-TAA
1 T-TTTTATAA
*
29659494 TGTGTTTTATTA
1 --T-TTTTATAA
29659506 TTTTTATAA
1 TTTTTATAA
*
29659515 TTTATTAGAA
1 TTT-TTATAA
29659525 TTTATTATAA
1 TTT-TTATAA
*
29659535 GTTTATATAA
1 -TTTTTATAA
*
29659545 TTTTTATTA
1 TTTTTATAA
29659554 TTTTTATAA
1 TTTTTATAA
*
29659563 TTTATTAGAA
1 TTT-TTATAA
29659573 TTTATTATAA
1 TTT-TTATAA
* *
29659583 GCTTATATAA
1 -TTTTTATAA
29659593 TTTTTATAA
1 TTTTTATAA
29659602 ACTTATATAA
Statistics
Matches: 139, Mismatches: 28, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
8 17 0.12
9 52 0.37
10 51 0.37
11 17 0.12
12 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29659528 original size:10 final size:10
Alignment explanation
Indices: 29659500--29659601 Score: 99
Period size: 10 Copynumber: 10.6 Consensus size: 10
29659490 TTAATGTGTT
*
29659500 TTATTATTT-
1 TTATAATTTA
29659509 TTATAATTTA
1 TTATAATTTA
*
29659519 TTAGAATTTA
1 TTATAATTTA
29659529 TTATAAGTTTA
1 TTATAA-TTTA
29659540 -TATAATTT-
1 TTATAATTTA
*
29659548 TTATTATTT-
1 TTATAATTTA
29659557 TTATAATTTA
1 TTATAATTTA
*
29659567 TTAGAATTTA
1 TTATAATTTA
*
29659577 TTATAAGCTTA
1 TTATAA-TTTA
29659588 -TATAATTT-
1 TTATAATTTA
29659596 TTATAA
1 TTATAA
29659602 ACTTATATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
9 33 0.42
10 38 0.49
11 7 0.09
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (10 bp):
TTATAATTTA
Found at i:29659528 original size:26 final size:26
Alignment explanation
Indices: 29659499--29659580 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
29659489 TTTAATGTGT
29659499 TTTATTATTTTTATAATTTATTAGAA
1 TTTATTATTTTTATAATTTATTAGAA
* *
29659525 TTTATTA----TA-AGTTTATATA-ATT
1 TTTATTATTTTTATAATTTAT-TAGA-A
29659547 TTTATTATTTTTATAATTTATTAGAA
1 TTTATTATTTTTATAATTTATTAGAA
29659573 TTTATTAT
1 TTTATTAT
29659581 AAGCTTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
21 7 0.16
22 11 0.25
26 19 0.43
27 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTATTATTTTTATAATTTATTAGAA
Found at i:29659553 original size:48 final size:48
Alignment explanation
Indices: 29659498--29659599 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 48
29659488 TTTTAATGTG
*
29659498 TTTTATTATTTTTATAATTTATTAGAATTTATTATAAGTTTATATAAT
1 TTTTATTATTTTTATAATTTATTAGAATTTATTATAAGCTTATATAAT
29659546 TTTTATTATTTTTATAATTTATTAGAATTTATTATAAGCTTATATAAT
1 TTTTATTATTTTTATAATTTATTAGAATTTATTATAAGCTTATATAAT
29659594 TTTTAT
1 TTTTAT
29659600 AAACTTATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (48 bp):
TTTTATTATTTTTATAATTTATTAGAATTTATTATAAGCTTATATAAT
Found at i:29659601 original size:19 final size:18
Alignment explanation
Indices: 29659510--29659616 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 18
29659500 TTATTATTTT
* *
29659510 TATAATTTATTAGAATTTA
1 TATAATTT-TTATAACTTA
* * *
29659529 TTATAAGTTTATATAATTTT
1 -TATAA-TTTTTATAACTTA
* *
29659549 TATTATTTTTATAATTTA
1 TATAATTTTTATAACTTA
*
29659567 TTAGAATTTATTATAAGCTTA
1 -TATAATTT-TTATAA-CTTA
29659588 TATAATTTTTATAAACTTA
1 TATAATTTTTAT-AACTTA
29659607 TATAAGTTTT
1 TATAA-TTTT
29659617 GAATATCAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
18 11 0.15
19 23 0.32
20 31 0.44
21 6 0.08
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (18 bp):
TATAATTTTTATAACTTA
Found at i:29665504 original size:20 final size:19
Alignment explanation
Indices: 29665452--29665492 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
29665442 AAACTTGATA
29665452 TATCACAAAAATATCAAAT
1 TATCACAAAAATATCAAAT
29665471 TATCACAAAAATATCAAAT
1 TATCACAAAAATATCAAAT
29665490 TAT
1 TAT
29665493 TGATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (19 bp):
TATCACAAAAATATCAAAT
Found at i:29671157 original size:22 final size:22
Alignment explanation
Indices: 29671144--29671198 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
29671134 TATTTTAATC
29671144 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
29671166 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
29671189 TTAAAATTTA
1 TT-AAATTTA
29671199 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:29671174 original size:6 final size:6
Alignment explanation
Indices: 29671127--29671199 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
29671117 CATTTGAAAA
* * *
29671127 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
29671172 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
29671200 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:29671174 original size:17 final size:17
Alignment explanation
Indices: 29671147--29671214 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
29671137 TTTAATCTTA
*
29671147 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
29671163 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
29671181 AATTTAATTTAAAATTT-
1 AATTTAATTT-AAATTTC
29671198 AATATT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
29671215 AAAAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 16 0.36
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:29671184 original size:12 final size:12
Alignment explanation
Indices: 29671127--29671199 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
29671117 CATTTGAAAA
29671127 TTAAATTT--AT
1 TTAAATTTAAAT
*
29671137 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
29671150 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
29671160 TTCAATTTAAAT
1 TTAAATTTAAAT
*
29671172 TTAAATTTGAAT
1 TTAAATTTAAAT
29671184 TT-AATTTAAAAT
1 TTAAATTT-AAAT
29671196 TTAA
1 TTAA
29671200 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:29671200 original size:12 final size:11
Alignment explanation
Indices: 29671124--29671200 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
29671114 AACCATTTGA
*
29671124 AAATTAAATTT
1 AAATTTAATTT
*
29671135 -ATTTTAATCTT
1 AAATTTAAT-TT
*
29671146 AAATTTACTTT
1 AAATTTAATTT
*
29671157 AAATTCAATTT
1 AAATTTAATTT
29671168 AAATTTAAATTT
1 AAATTT-AATTT
*
29671180 GAATTTAATTT
1 AAATTTAATTT
29671191 AAAATTTAAT
1 -AAATTTAAT
29671201 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:29671329 original size:12 final size:14
Alignment explanation
Indices: 29671301--29671344 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
29671291 ATTTTTCGGT
29671301 CCAATTACAATGGC
1 CCAATTACAATGGC
29671315 CCAATTA-AA-GGC
1 CCAATTACAATGGC
29671327 CCAATTACAATGGC
1 CCAATTACAATGGC
29671341 CCAA
1 CCAA
29671345 ATAGGCCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.36
13 4 0.14
14 14 0.50
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.18
Consensus pattern (14 bp):
CCAATTACAATGGC
Found at i:29671421 original size:18 final size:17
Alignment explanation
Indices: 29671398--29671434 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
29671388 CCCCACGTGC
29671398 CTCTGCTGCCACCACCAG
1 CTCT-CTGCCACCACCAG
29671416 --CTCTGCCACCACCAG
1 CTCTCTGCCACCACCAG
29671431 CTCT
1 CTCT
29671435 ATCCACCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 5
0.77 0.00 0.23
Matches are distributed among these distances:
15 13 0.76
16 2 0.12
17 2 0.12
ACGTcount: A:0.16, C:0.51, G:0.14, T:0.19
Consensus pattern (17 bp):
CTCTCTGCCACCACCAG
Found at i:29671423 original size:15 final size:15
Alignment explanation
Indices: 29671403--29671434 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29671393 CGTGCCTCTG
29671403 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
29671418 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
29671433 CT
1 CT
29671435 ATCCACCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.53, G:0.12, T:0.16
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:29673125 original size:30 final size:30
Alignment explanation
Indices: 29673053--29673267 Score: 319
Period size: 30 Copynumber: 7.3 Consensus size: 30
29673043 GCTTATAGGT
29673053 CCCC-AAACTTTTCCAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
* * *
29673082 -CCCTAAA-TTTTCCAAAATTATATTTCGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
*
29673110 CCCCAAAACTTTTCCAAAATTACATTTTAA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
* *
29673140 CCCCAAAACTTTTCCAAAATTATATTTTAA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
*
29673170 CCTCAAAACTTTTCCAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
**
29673200 CCCTTAAACTTTTCCAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
29673230 CCCCAAAACTTTTCCAAAATTACATTTTGA
1 CCCCAAAACTTTTCCAAAATTACATTTTGA
*
29673260 CCCAAAAA
1 CCCCAAAA
29673268 ATCTCCTAAA
Statistics
Matches: 167, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
28 22 0.13
29 9 0.05
30 136 0.81
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
CCCCAAAACTTTTCCAAAATTACATTTTGA
Found at i:29673373 original size:30 final size:30
Alignment explanation
Indices: 29673280--29673375 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 30
29673270 CTCCTAAATC
** *
29673280 CCATTTTTAACTACGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATATCACCAAAA-TTA
* * * ***
29673311 CCA-TTTTACCCCCGAAACCTTTAAAATT-
1 CCATTTTTAACCCCGATATCACCAAAATTA
29673339 CCATTTTTAACCCCGATATCACCAAAATTA
1 CCATTTTTAACCCCGATATCACCAAAATTA
29673369 CCATTTT
1 CCATTTT
29673376 GCCCCCGGGT
Statistics
Matches: 48, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
28 3 0.06
29 21 0.44
30 21 0.44
31 3 0.06
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
CCATTTTTAACCCCGATATCACCAAAATTA
Found at i:29685377 original size:68 final size:68
Alignment explanation
Indices: 29685265--29685933 Score: 1101
Period size: 68 Copynumber: 9.9 Consensus size: 68
29685255 CTGCAGGTCT
*
29685265 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
29685330 GAG
66 GAG
*
29685333 CAGCGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
29685398 GAG
66 GAG
*
29685401 CAACGTCAT-CCCTTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTGAAGTA
1 CAACGTCATCCCCTT-GAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA
29685465 AGAG
65 AGAG
* **
29685469 CAGCGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATATCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
29685534 GAG
66 GAG
29685537 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
29685602 GGG
66 GAG
*
29685605 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
29685670 GAG
66 GAG
* * * *
29685673 CAACGTCAT-CCCTCGAAATTGAAGTGGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
29685737 GAG
66 GAG
* * *
29685740 CAACGTCAT-CCCTCGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
29685804 GAG
66 GAG
* * *
29685807 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
*
29685872 GCG
66 GAG
* * * *
29685875 CAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAGCACGTCTTTATCTCTGAAATTG
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTG
29685934 TTGAAATAAG
Statistics
Matches: 570, Mismatches: 28, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
67 131 0.23
68 434 0.76
69 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAG
Done.