Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold817.1
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: 725883
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.31
Warning! 29547 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:385 original size:75 final size:75
Alignment explanation
Indices: 262--410 Score: 289
Period size: 75 Copynumber: 2.0 Consensus size: 75
252 AAAAATAGAA
262 AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
1 AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
327 TGTATTTAAC
66 TGTATTTAAC
*
337 AATTCACCTTAGGGTTTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
1 AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
402 TGTATTTAA
66 TGTATTTAA
411 TCTACTAGTA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.19, C:0.11, G:0.20, T:0.49
Consensus pattern (75 bp):
AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
TGTATTTAAC
Found at i:898 original size:309 final size:309
Alignment explanation
Indices: 337--953 Score: 1171
Period size: 309 Copynumber: 2.0 Consensus size: 309
327 TGTATTTAAC
*
337 AATTCACCTTAGGGTTTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
1 AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
402 TGTATTTAATCTACTAGTATTAAAAAAAACAAAGAAAAATCCTTTGTATGGATAGAAAAAATCCC
66 TGTATTTAATCTACTAGTATTAAAAAAAACAAAGAAAAATCCTTTGTATGGATAGAAAAAATCCC
*
467 CCTTAATCTATTTTTCATTCGGCCTTTTATAGCCTATGTTTTACACTGTCTGTTTTTCCCTTTTT
131 CCTTAATCTATTTTTCATTCGGCCTTTTATAGCATATGTTTTACACTGTCTGTTTTTCCCTTTTT
*
532 GCTATTGTGTGTTCTGTTTTGTCCTTGCAGGGTGGTTGAACGGTGGCATGGAGAGCTGGGGCGCC
196 GCTATTGTGTGTTCTGTTTTGTCCTTGCAGGGTGGTTGAACGGTGGCATGAAGAGCTGGGGCGCC
597 AGGGTATGGTGCTGATGGCTGGTGTCAGAGGGCAGGTGCAAGTGGGAAA
261 AGGGTATGGTGCTGATGGCTGGTGTCAGAGGGCAGGTGCAAGTGGGAAA
646 AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
1 AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
* *
711 TGTATTTAATCTGCTAGTATTAAAAAAAACAAAGAAAAATCCTTTGTATTGATAGAAAAAATCCC
66 TGTATTTAATCTACTAGTATTAAAAAAAACAAAGAAAAATCCTTTGTATGGATAGAAAAAATCCC
* *
776 CCTTAATCTGTTTTTCATTCGTCCTTTTATAGCATATGTTTTACACTGTCTGTTTTTCCCTTTTT
131 CCTTAATCTATTTTTCATTCGGCCTTTTATAGCATATGTTTTACACTGTCTGTTTTTCCCTTTTT
841 GCTATTGTGTGTTCTGTTTTGTCCTTGCAGGGTGGTTGAACGGTGGCATGAAGAGCTGGGGCGCC
196 GCTATTGTGTGTTCTGTTTTGTCCTTGCAGGGTGGTTGAACGGTGGCATGAAGAGCTGGGGCGCC
906 AGGGTATGGTGCTGATGGCTGGTGTCAGAGGGCAGGTGCAAGTGGGAA
261 AGGGTATGGTGCTGATGGCTGGTGTCAGAGGGCAGGTGCAAGTGGGAA
954 GCCGAAAATG
Statistics
Matches: 301, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
309 301 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (309 bp):
AATTCACCTTAGGGATTTGGTTTGATTTGATGCTATTCTACTGCTTTGATGTTTGGAATTGTTCT
TGTATTTAATCTACTAGTATTAAAAAAAACAAAGAAAAATCCTTTGTATGGATAGAAAAAATCCC
CCTTAATCTATTTTTCATTCGGCCTTTTATAGCATATGTTTTACACTGTCTGTTTTTCCCTTTTT
GCTATTGTGTGTTCTGTTTTGTCCTTGCAGGGTGGTTGAACGGTGGCATGAAGAGCTGGGGCGCC
AGGGTATGGTGCTGATGGCTGGTGTCAGAGGGCAGGTGCAAGTGGGAAA
Found at i:3020 original size:27 final size:26
Alignment explanation
Indices: 2976--3027 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2966 CTCGCTGCAA
*
2976 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
3003 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
3028 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:3065 original size:67 final size:67
Alignment explanation
Indices: 2957--3132 Score: 316
Period size: 67 Copynumber: 2.6 Consensus size: 67
2947 GAGGAAGCGT
2957 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
3022 TA
66 TA
*
3024 TCTGGCAGCCTCGCTGCAATCTGATGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
3089 TA
66 TA
* * *
3091 TCTAGCAGCCTCGCTGCAATCTGGTGGCTTCACCACATATAT
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATAT
3133 ATATCTGTTC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 104 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
TA
Found at i:3162 original size:26 final size:27
Alignment explanation
Indices: 3133--3192 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
3123 CCACATATAT
*
3133 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
3159 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
3186 ATATCTG
1 ATATCTG
3193 GCAGCTTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:9502 original size:37 final size:37
Alignment explanation
Indices: 9452--9525 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
9442 ATACTAAGAA
9452 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
9489 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
9526 CGTGAAACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (37 bp):
TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
Found at i:14383 original size:27 final size:26
Alignment explanation
Indices: 14339--14389 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
14329 CTCGCTGCAA
*
14339 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
14366 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
14390 AGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:14458 original size:26 final size:27
Alignment explanation
Indices: 14429--14488 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
14419 CCACATATAT
*
14429 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
14455 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
14482 ATATCTG
1 ATATCTG
14489 GCAGCTTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:20798 original size:37 final size:37
Alignment explanation
Indices: 20748--21561 Score: 1628
Period size: 37 Copynumber: 22.0 Consensus size: 37
20738 ATACTAAGAA
20748 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
20785 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
20822 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
20859 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
20896 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
20933 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
20970 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21007 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21044 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21081 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21118 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21155 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21192 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21229 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21266 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21303 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21340 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21377 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21414 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21451 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21488 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21525 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
1 TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
21562 CGTGAAACTG
Statistics
Matches: 777, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 777 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (37 bp):
TGTAGATTATGAAACTACGTATACTCAAACTTTAGAT
Found at i:31133 original size:61 final size:60
Alignment explanation
Indices: 31057--31181 Score: 214
Period size: 61 Copynumber: 2.1 Consensus size: 60
31047 AATTTATCAA
*
31057 TTTTCCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTTCC
1 TTTTCCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCC
* *
31117 TTTNTCCTGCTGATTTCATGCCCTTGCTGTCCAGCCCAAATAAATTTTGGGTCTAATTGCC
1 TTT-TCCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCC
31178 TTTT
1 TTTT
31182 AAATCCTCTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 4 0.07
61 57 0.93
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.40
Consensus pattern (60 bp):
TTTTCCTGCTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCC
Found at i:41737 original size:120 final size:120
Alignment explanation
Indices: 41576--41884 Score: 410
Period size: 120 Copynumber: 2.6 Consensus size: 120
41566 TTTAGTAACT
*
41576 CACACAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACC
1 CACA-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACAAATGCCTTCGGGACTTAACC
41641 CGG-ATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCG
65 CGGAATTT-GTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCG
* * * * *
41697 CACAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACAAATGCCTTCGGGGCTTAACC
1 CACAAATGCCTTCGGGACATAACCCGG-ATTTAATAACTCGCACAAATGCCTTCGGGACTTAACC
*
41761 CGGAATTTGTATCTCGCACAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCG
65 CGGAATTTGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCG
* ** * * * * *
41817 CACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CACAAATGCCTTCGGGA-CATAACCCGGATTTAATAAC-TCGCACAAATGCCTTCGGGACTTAAC
41880 CCGGA
64 CCGGA
41885 CAGCATTCAA
Statistics
Matches: 166, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
119 5 0.03
120 141 0.85
121 20 0.12
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (120 bp):
CACAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACAAATGCCTTCGGGACTTAACCC
GGAATTTGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCG
Found at i:41844 original size:40 final size:40
Alignment explanation
Indices: 41540--41831 Score: 412
Period size: 40 Copynumber: 7.3 Consensus size: 40
41530 GCTCCTCGTT
* * * * * *
41540 CAAATGCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
* * * *
41580 C-AATGCCTTCGGGACATAACCCGG-ATTTAATAACTCGCA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
* *
41619 CGAATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
*
41659 CAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
41699 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
41739 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
41779 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
41819 CAAATGCCTTCGG
1 CAAATGCCTTCGG
41832 ATCTTAGTCC
Statistics
Matches: 239, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
39 35 0.15
40 200 0.84
41 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
Found at i:41893 original size:41 final size:41
Alignment explanation
Indices: 41816--41893 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41806 TTTGTATCTC
* * *
41816 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41857 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41894 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:46097 original size:11 final size:11
Alignment explanation
Indices: 46081--46114 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
46071 GAATTAAGAG
46081 CTTTTTTTTCT
1 CTTTTTTTTCT
46092 CTTTTTTTTCT
1 CTTTTTTTTCT
46103 CTTTTTTTTCT
1 CTTTTTTTTCT
46114 C
1 C
46115 ATTCCCATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTTTTTCT
Found at i:55512 original size:34 final size:34
Alignment explanation
Indices: 55468--55558 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
55458 TACCACTAAA
* * ***
55468 TGTAATACCCCTTACTCATATTCAATGTTGAAAC
1 TGTAACACCCCTTACCCATATTCAATGCCAAAAC
*
55502 TGTAACACCCCTTACCCGTATTCAATGCCAAAAC
1 TGTAACACCCCTTACCCATATTCAATGCCAAAAC
55536 TGTAACACCCCTTACCCATATTC
1 TGTAACACCCCTTACCCATATTC
55559 GACGCCGGGA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.30
Consensus pattern (34 bp):
TGTAACACCCCTTACCCATATTCAATGCCAAAAC
Found at i:57527 original size:45 final size:45
Alignment explanation
Indices: 57462--57551 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
57452 CCAAAACATG
* * *
57462 TGTCACATACATCATGAACTCACACCT-CAACTCGATGAGTTCAGA
1 TGTCACATACATCATAAACTCA-AACTACAACTCAATGAGTTCAGA
**
57507 TGTCACATATGTCATAAACTCAAACTACAACTCAATGAGTTCAGA
1 TGTCACATACATCATAAACTCAAACTACAACTCAATGAGTTCAGA
57552 CCACATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.08
45 36 0.92
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (45 bp):
TGTCACATACATCATAAACTCAAACTACAACTCAATGAGTTCAGA
Found at i:61939 original size:42 final size:42
Alignment explanation
Indices: 61884--61979 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
61874 AACATGGCCA
* *
61884 AGACACACACCCGTGTTCTAGGCAGTGTAGCACACATGACTG
1 AGACACACGCCCGTGTTCTAGGCAGTGTAGCACACACGACTG
* *
61926 AGACACACGCCCGTGTTCTAGGCCGTGTAGCACACACGGCTG
1 AGACACACGCCCGTGTTCTAGGCAGTGTAGCACACACGACTG
*
61968 AGAGACACGCCC
1 AGACACACGCCC
61980 ATGTGCTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (42 bp):
AGACACACGCCCGTGTTCTAGGCAGTGTAGCACACACGACTG
Found at i:64615 original size:50 final size:50
Alignment explanation
Indices: 64553--64660 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 50
64543 TCTATTTCAA
* **
64553 TCCTTTTCATAATTTCATGACATAGTTCATTCCAGTACATACCTTTCCTT
1 TCCTTTTTATAATTTCATGACATAGTTCATTCCAACACATACCTTTCCTT
**
64603 TCCTTTTTATAATTTCATGACATAGTTCATTTGAACACATACCTTTCCTT
1 TCCTTTTTATAATTTCATGACATAGTTCATTCCAACACATACCTTTCCTT
64653 TCCTTTTT
1 TCCTTTTT
64661 CATGCCCGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.23, C:0.24, G:0.06, T:0.47
Consensus pattern (50 bp):
TCCTTTTTATAATTTCATGACATAGTTCATTCCAACACATACCTTTCCTT
Found at i:65808 original size:15 final size:16
Alignment explanation
Indices: 65788--65821 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
65778 TAGTTATTAC
*
65788 TTAATATTCAATT-TA
1 TTAATATTAAATTATA
65803 TTAATATTAAATTATA
1 TTAATATTAAATTATA
65819 TTA
1 TTA
65822 TATAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATATTAAATTATA
Found at i:68992 original size:23 final size:25
Alignment explanation
Indices: 68952--68997 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
68942 AGGACTAGCA
68952 CCCTAATCACATAATCAC-AGTAAC
1 CCCTAATCACATAATCACTAGTAAC
* *
68976 CCCTAATGACAT-GTCACTAGTA
1 CCCTAATCACATAATCACTAGTA
68998 TCCTATCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (25 bp):
CCCTAATCACATAATCACTAGTAAC
Found at i:69537 original size:21 final size:20
Alignment explanation
Indices: 69508--69548 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
69498 ACAAAACTTG
69508 TATAACTATCATCAAACATT
1 TATAACTATCATCAAACATT
*
69528 TATAATCTATCATCAATCATT
1 TATAA-CTATCATCAAACATT
69549 AAAATACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAACTATCATCAAACATT
Found at i:79174 original size:35 final size:35
Alignment explanation
Indices: 79135--79201 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
79125 CACATGTAAT
*
79135 CGAATACTA-AAATTTAATATAACCTCACATGTTGC
1 CGAATA-TACAAATTCAATATAACCTCACATGTTGC
* * *
79170 CGAATATACAAGTTCAATATAAGCTTACATGT
1 CGAATATACAAATTCAATATAACCTCACATGT
79202 ACTTACCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 25 0.93
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (35 bp):
CGAATATACAAATTCAATATAACCTCACATGTTGC
Found at i:81081 original size:23 final size:23
Alignment explanation
Indices: 81051--81095 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
81041 CTAAGACAAA
81051 TAAGTCAAGTATTTATCATTTTC
1 TAAGTCAAGTATTTATCATTTTC
81074 TAAGTCAAGTATTTATCATTTT
1 TAAGTCAAGTATTTATCATTTT
81096 TTGATAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (23 bp):
TAAGTCAAGTATTTATCATTTTC
Found at i:82158 original size:27 final size:27
Alignment explanation
Indices: 82128--82227 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
82118 ATATATTATT
* *
82128 AAATTTTAATAAAAATTCAAATATTAA
1 AAATTTTAATAAAAATTAAAAAATTAA
** *
82155 AAATTAGAAAAAAATATTAAAAAATATAA
1 AAATTTTAATAAAA-ATTAAAAAAT-TAA
** *
82184 AAATCGTAA-AAAAATTAAAAAATTGTA
1 AAATTTTAATAAAAATTAAAAAATT-AA
82211 AAATTTT-ATAAAAATTA
1 AAATTTTAATAAAAATTA
82228 TAAATATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
26 2 0.03
27 35 0.60
28 12 0.21
29 9 0.16
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AAATTTTAATAAAAATTAAAAAATTAA
Found at i:82176 original size:10 final size:10
Alignment explanation
Indices: 82146--82206 Score: 56
Period size: 10 Copynumber: 6.4 Consensus size: 10
82136 ATAAAAATTC
82146 AAATATTAAA
1 AAATATTAAA
* **
82156 AATTAGAAAA
1 AAATATTAAA
82166 AAATATTAAA
1 AAATATTAAA
82176 AAATA-T-AA
1 AAATATTAAA
**
82184 AAATCGTAAA
1 AAATATTAAA
82194 AAA-ATTAAA
1 AAATATTAAA
82203 AAAT
1 AAAT
82207 TGTAAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
8 6 0.15
9 9 0.23
10 24 0.62
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (10 bp):
AAATATTAAA
Found at i:82185 original size:20 final size:20
Alignment explanation
Indices: 82146--82186 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
82136 ATAAAAATTC
*
82146 AAATATTAAAAATTAGAAAA
1 AAATATTAAAAAATAGAAAA
*
82166 AAATATTAAAAAATATAAAA
1 AAATATTAAAAAATAGAAAA
82186 A
1 A
82187 TCGTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATATTAAAAAATAGAAAA
Found at i:82223 original size:19 final size:19
Alignment explanation
Indices: 82172--82231 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
82162 AAAAAAATAT
*
82172 TAAAAAA-TATAAAAATCG
1 TAAAAAATTATAAAAATTG
82190 TAAAAAAATTA-AAAAATTG
1 T-AAAAAATTATAAAAATTG
** *
82209 TAAAATTTTATAAAAATTA
1 TAAAAAATTATAAAAATTG
82228 TAAA
1 TAAA
82232 TATATAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.23
19 25 0.71
20 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTG
Found at i:82261 original size:9 final size:9
Alignment explanation
Indices: 82209--82268 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
82199 TAAAAAATTG
82209 TAAAATTTTA
1 TAAAA-TTTA
*
82219 TAAAAATTA
1 TAAAATTTA
*
82228 T-AAATATA
1 TAAAATTTA
*
82236 TAGAAATATA
1 TA-AAATTTA
*
82246 AAAAATTTA
1 TAAAATTTA
82255 TAAAATTTTA
1 TAAAA-TTTA
82265 TAAA
1 TAAA
82269 GTCGTACGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 6 0.15
9 14 0.34
10 21 0.51
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
TAAAATTTA
Found at i:83380 original size:17 final size:19
Alignment explanation
Indices: 83358--83392 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
83348 GAAAATTAGT
83358 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
83375 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
83393 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:84712 original size:51 final size:51
Alignment explanation
Indices: 84613--84745 Score: 149
Period size: 51 Copynumber: 2.6 Consensus size: 51
84603 CCATCAAATC
* * *
84613 TCTAAGAATATAATATCATATCTTCTAAGATTACATATCTTAGATAAGATA
1 TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
* ** * * * ** *
84664 TGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAGATC
1 TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
*
84715 TCTAAGATTATAATATCATATCTTTTAAGAT
1 TCTAAGATTATAATATCATATCTTATAAGAT
84746 CATGTTTCCA
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (51 bp):
TCTAAGATTATAATATCATATCTTATAAGATTACATATCATAGATAAGATA
Found at i:85346 original size:96 final size:96
Alignment explanation
Indices: 85176--85470 Score: 477
Period size: 96 Copynumber: 3.1 Consensus size: 96
85166 TCGCTTCTTT
*
85176 TTGCTCCTCTTAGCCCTCTTGG-TTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCT
1 TTGCTCCTCTTTGCCCTCTTGGCTTT-GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCT
*
85240 TATCTACTCCATCGTTCCCTACGATGACAGAC
65 TATCTGCTCCATCGTTCCCTACGATGACAGAC
85272 TTGCTCCTCTTTGCCCTCTTGGCTTTGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 TTGCTCCTCTTTGCCCTCTTGGCTTTGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
* *
85337 GTCTGCTCCATCGTTCCCTTCGATGACAGAC
66 ATCTGCTCCATCGTTCCCTACGATGACAGAC
*
85368 TTGCTCCTCTTTGCCCTCTTGGCTTTGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCGT
1 TTGCTCCTCTTTGCCCTCTTGGCTTTGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
* * *
85433 ATCTGCTCGATCATT-CCTATCGATAACAGAC
66 ATCTGCTCCATCGTTCCCTA-CGATGACAGAC
*
85464 TTCCTCC
1 TTGCTCC
85471 GACACTTTCG
Statistics
Matches: 186, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
95 3 0.02
96 180 0.97
97 3 0.02
ACGTcount: A:0.13, C:0.34, G:0.17, T:0.36
Consensus pattern (96 bp):
TTGCTCCTCTTTGCCCTCTTGGCTTTGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
ATCTGCTCCATCGTTCCCTACGATGACAGAC
Found at i:87073 original size:96 final size:96
Alignment explanation
Indices: 86909--87172 Score: 429
Period size: 96 Copynumber: 2.8 Consensus size: 96
86899 NNNNNNNNNN
* *
86909 GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTACTCCATCGTTCCCTGCGATGA
1 GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGCTCCATCGTTCCCTTCGATGA
86974 CAGACTTGCTCCTCTTAGCCCTCTTGGCTTC
66 CAGACTTGCTCCTCTTAGCCCTCTTGGCTTC
87005 GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGCTCCATCGTTCCCTTCGATGA
1 GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGCTCCATCGTTCCCTTCGATGA
*
87070 CAGACTTGCTCCTCTTTGCCCTCTTGGCTTC
66 CAGACTTGCTCCTCTTAGCCCTCTTGGCTTC
* * * * * * * *
87101 GGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCCGTATCTGCTCGATCATTACCATCGATAA
1 GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGCTCCATCGTTCCCTTCGATGA
87166 CAGACTT
66 CAGACTT
87173 CCTCGGACAC
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 157 1.00
ACGTcount: A:0.14, C:0.34, G:0.19, T:0.34
Consensus pattern (96 bp):
GGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGCTCCATCGTTCCCTTCGATGA
CAGACTTGCTCCTCTTAGCCCTCTTGGCTTC
Found at i:87870 original size:47 final size:47
Alignment explanation
Indices: 87801--87900 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
87791 TGGAACTTCT
*
87801 CCCATGTTCCAATCTCACATTGCCTTTTATCTGTGGTCCTACCTTGC
1 CCCATGTTCCAATCTCACATTGCCTTTTATCTGTGGTCCTACCTCGC
87848 CCCATGTTCCAATCTCACATTGCCTTTTATCTGTGGTCCTACCTCGC
1 CCCATGTTCCAATCTCACATTGCCTTTTATCTGTGGTCCTACCTCGC
87895 CACCAT
1 C-CCAT
87901 AAAAGCGCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 47 0.92
48 4 0.08
ACGTcount: A:0.16, C:0.36, G:0.12, T:0.36
Consensus pattern (47 bp):
CCCATGTTCCAATCTCACATTGCCTTTTATCTGTGGTCCTACCTCGC
Found at i:95258 original size:20 final size:21
Alignment explanation
Indices: 95220--95260 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
95210 AATATGATGT
95220 TTTAGATCCCAGAAAGTGAGA
1 TTTAGATCCCAGAAAGTGAGA
* *
95241 TTTAGA-CCTAGAACGTGAGA
1 TTTAGATCCCAGAAAGTGAGA
95261 AAAACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (21 bp):
TTTAGATCCCAGAAAGTGAGA
Found at i:96108 original size:55 final size:54
Alignment explanation
Indices: 95991--96284 Score: 319
Period size: 55 Copynumber: 5.4 Consensus size: 54
95981 GGATATCATA
* * * * *
95991 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAAT-CATG
1 TAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGG-ATTCCACG
* *
96045 TAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGAAAAGG-TTCCACG
1 TAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGG-CAAGGATTCCACG
* * * * *
96100 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAAT-CATG
1 TAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGG-ATTCCACG
* *
96154 TAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGAAAAGG-TTCCACG
1 TAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGG-CAAGGATTCCACG
* * * *
96209 TAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACC
1 TAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGGATTCCACG
**
96262 TAAGACCATATCAAGACATGGCA
1 TAAGACCATGCCAAGACATGGCA
96285 ATGGCAAGTT
Statistics
Matches: 201, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
52 4 0.02
53 35 0.17
54 72 0.36
55 82 0.41
56 8 0.04
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (54 bp):
TAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGGATTCCACG
Found at i:96182 original size:109 final size:109
Alignment explanation
Indices: 95991--96284 Score: 509
Period size: 109 Copynumber: 2.7 Consensus size: 109
95981 GGATATCATA
95991 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
1 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
96056 CAAGACATGGCATTGATGAGTTACTATAAGGAAAAGGTTCCACG
66 CAAGACATGGCATTGATGAGTTACTATAAGGAAAAGGTTCCACG
96100 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
1 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
96165 CAAGACATGGCATTGATGAGTTACTATAAGGAAAAGGTTCCACG
66 CAAGACATGGCATTGATGAGTTACTATAAGGAAAAGGTTCCACG
** * * * ** *
96209 TAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACCTAAGACCATAT
1 TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
96273 CAAGACATGGCA
66 CAAGACATGGCA
96285 ATGGCAAGTT
Statistics
Matches: 177, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
108 37 0.21
109 140 0.79
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (109 bp):
TAAGACCATGCCAAGGCATGGCATTAATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
CAAGACATGGCATTGATGAGTTACTATAAGGAAAAGGTTCCACG
Found at i:101514 original size:45 final size:45
Alignment explanation
Indices: 101454--101541 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
101444 CGATATCATT
*
101454 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
* *
101499 TCACCGGCATCATAGCCTGCTAGGTTCAAAGGCCCGAATAGTA
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCAAATAGTA
101542 CCGTACAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (45 bp):
TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
Found at i:105770 original size:11 final size:11
Alignment explanation
Indices: 105754--105787 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
105744 ATGTCAAATC
*
105754 ATCAAGAATAA
1 ATCAAGAACAA
105765 ATCAAGAACAA
1 ATCAAGAACAA
105776 ATCAAGAACAA
1 ATCAAGAACAA
105787 A
1 A
105788 ACTAGATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.65, C:0.15, G:0.09, T:0.12
Consensus pattern (11 bp):
ATCAAGAACAA
Found at i:106511 original size:25 final size:25
Alignment explanation
Indices: 106453--106504 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
106443 TTTTAGTAAT
* **
106453 TTAATTTTTTTTTCTTTATGTTCTT
1 TTAACTTTTTTTTCTTTATGTTCCA
*
106478 TTAACTTTTTTTTCTTTATTTTCCA
1 TTAACTTTTTTTTCTTTATGTTCCA
106503 TT
1 TT
106505 CTCTTTTGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.13, C:0.12, G:0.02, T:0.73
Consensus pattern (25 bp):
TTAACTTTTTTTTCTTTATGTTCCA
Found at i:110466 original size:15 final size:15
Alignment explanation
Indices: 110446--110496 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
110436 TTGTCTCGTG
110446 TTATATTTTAGTCAC
1 TTATATTTTAGTCAC
** *
110461 TTATA-TTT-GAAATT
1 TTATATTTTAGTCA-C
110475 TTATATTTTAGTCAC
1 TTATATTTTAGTCAC
110490 TTATATT
1 TTATATT
110497 ATTGTGTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (15 bp):
TTATATTTTAGTCAC
Found at i:111748 original size:11 final size:11
Alignment explanation
Indices: 111713--111742 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
111703 ATGAAGAAGG
111713 AAGAGAAGCAA
1 AAGAGAAGCAA
111724 AAGGAGAAGCAA
1 AA-GAGAAGCAA
111736 AAGAGAA
1 AAGAGAA
111743 TGAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.07, G:0.30, T:0.00
Consensus pattern (11 bp):
AAGAGAAGCAA
Found at i:118781 original size:40 final size:40
Alignment explanation
Indices: 118726--118866 Score: 194
Period size: 40 Copynumber: 3.5 Consensus size: 40
118716 TATTCGGATG
118726 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
118766 ATATCTGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
118806 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
118846 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
118867 ATACTTGGGT
Statistics
Matches: 87, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 13 0.15
40 74 0.85
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:132852 original size:22 final size:22
Alignment explanation
Indices: 132810--132854 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
132800 AAACTTGTCG
*
132810 TGTGTAAATATGATATGCGAAT
1 TGTGTAAATATGACATGCGAAT
132832 TGTGTAAATAT-ACATGTCGAAT
1 TGTGTAAATATGACATG-CGAAT
132854 T
1 T
132855 AAGTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (22 bp):
TGTGTAAATATGACATGCGAAT
Found at i:132860 original size:22 final size:22
Alignment explanation
Indices: 132813--132860 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
132803 CTTGTCGTGT
* **
132813 GTAAATATGATATGCGAATTGT
1 GTAAATATGACATGCGAATTAA
132835 GTAAATAT-ACATGTCGAATTAA
1 GTAAATATGACATG-CGAATTAA
132857 GTAA
1 GTAA
132861 TAAAGTGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (22 bp):
GTAAATATGACATGCGAATTAA
Found at i:137501 original size:42 final size:42
Alignment explanation
Indices: 137442--137542 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
137432 AAAGGGCCTC
* *
137442 CTCACATGAGTTGTGGATC-AGAATGTAAGCTACACGATGCTG
1 CTCACATGAGCTGTGGATCGA-AATCTAAGCTACACGATGCTG
137484 CTCACATGAGCTGTGGATCGAAATCTAAGCTACACGATGCTG
1 CTCACATGAGCTGTGGATCGAAATCTAAGCTACACGATGCTG
137526 CTCACATGAGCTGTGGA
1 CTCACATGAGCTGTGGA
137543 GTATTTGCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 55 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (42 bp):
CTCACATGAGCTGTGGATCGAAATCTAAGCTACACGATGCTG
Found at i:142128 original size:46 final size:46
Alignment explanation
Indices: 142078--142250 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
142068 TGGTTGAGCA
142078 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
142124 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
142169 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
142217 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
142251 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:142234 original size:93 final size:93
Alignment explanation
Indices: 142075--142245 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
142065 GGATGGTTGA
* *
142075 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
142140 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
142168 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
142233 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
142246 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:150778 original size:42 final size:42
Alignment explanation
Indices: 150719--150805 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
150709 GACACGGGCA
* *
150719 TGTCTATTGGCCGTGTGTGACACACGGGCTAGCACGTAGGCG
1 TGTCTACTGGCCGTGTGTGACACACGGGCTAGCACATAGGCG
*
150761 TGTCTACTGGCCGTGTGTGACACACGGGCTAGCACATGGGCG
1 TGTCTACTGGCCGTGTGTGACACACGGGCTAGCACATAGGCG
150803 TGT
1 TGT
150806 AGCCGGTCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (42 bp):
TGTCTACTGGCCGTGTGTGACACACGGGCTAGCACATAGGCG
Found at i:169531 original size:43 final size:42
Alignment explanation
Indices: 169483--169589 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
169473 GATTAACGAA
* *
169483 ATGTGATTATGTGTTAGACCATGTTTGGGACATTGGCATCATT
1 ATGTGATTATGTGTAAGACCATGTCTGGGA-ATTGGCATCATT
* * *
169526 ATGTGATTACGTGTAAAACCATGTCTGGGAATTGGCATCGTT
1 ATGTGATTATGTGTAAGACCATGTCTGGGAATTGGCATCATT
*
169568 ATTTGATT-TCGTGTAAGACCAT
1 ATGTGATTAT-GTGTAAGACCAT
169590 AGCTAGGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 29 0.53
43 26 0.47
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (42 bp):
ATGTGATTATGTGTAAGACCATGTCTGGGAATTGGCATCATT
Found at i:169575 original size:42 final size:42
Alignment explanation
Indices: 169486--169632 Score: 152
Period size: 43 Copynumber: 3.5 Consensus size: 42
169476 TAACGAAATG
* * * * *
169486 TGATTATGTGTTAGACCATGTTTGGGACATTGGCATCATTATG
1 TGATTACGTGTAAGACCATGTCTGGGA-ATTGGCATCGTTATT
*
169529 TGATTACGTGTAAAACCATGTCTGGGAATTGGCATCGTTATT
1 TGATTACGTGTAAGACCATGTCTGGGAATTGGCATCGTTATT
* ** *
169571 TGATTTCGTGTAAGACCATAG-CTAGGTTATTGGCATCGATATT
1 TGATTACGTGTAAGACCAT-GTCT-GGGAATTGGCATCGTTATT
* *
169614 TGATAACATGTAAGACCAT
1 TGATTACGTGTAAGACCAT
169633 AACTGGGATA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 32 0.36
43 56 0.64
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTGGGAATTGGCATCGTTATT
Found at i:175680 original size:47 final size:47
Alignment explanation
Indices: 175611--175762 Score: 295
Period size: 47 Copynumber: 3.2 Consensus size: 47
175601 TAGTATTAAT
175611 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
175658 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
175705 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
*
175752 AATGTGATAAG
1 TATGTGATAAG
175763 TCCCGAAGGG
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 104 1.00
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
Found at i:178296 original size:16 final size:17
Alignment explanation
Indices: 178275--178327 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 17
178265 AAGTTTATAT
178275 AATAAAT-TATTTTTAA
1 AATAAATATATTTTTAA
178291 AATAAATATAATTAATTTAA
1 AATAAATAT-ATT--TTTAA
* *
178311 AATATATCTATTTTTAA
1 AATAAATATATTTTTAA
178328 GTTATTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 7 0.23
17 6 0.19
18 3 0.10
19 3 0.10
20 12 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAAATATATTTTTAA
Found at i:178344 original size:17 final size:17
Alignment explanation
Indices: 178324--178366 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
178314 ATATCTATTT
* *
178324 TTAAGTTATTTATCAAA
1 TTAAGTTATATAACAAA
*
178341 TTAATTTATATAACAAA
1 TTAAGTTATATAACAAA
178358 TTAAAGTTA
1 TT-AAGTTA
178367 CATTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (17 bp):
TTAAGTTATATAACAAA
Found at i:181475 original size:16 final size:15
Alignment explanation
Indices: 181454--181484 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
181444 GTTCAAATTG
181454 TAAAAATAAAGTAAAA
1 TAAAAATAAAG-AAAA
181470 TAAAAATAAAGAAAA
1 TAAAAATAAAGAAAA
181485 CACAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAGAAAA
Found at i:187806 original size:43 final size:42
Alignment explanation
Indices: 187652--187808 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 42
187642 ATATCGAATA
*
187652 ATGCCAACGTCCCAGACGTGGTCTTACAT-GCTATCTCATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTAC-TCG-TAACTCATATCG
* * *
187695 ATGCC-ACTGTCCCAGACAG-GGTCTTCCACG-AA-TCAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACTCGTAACTCATAT-CG
* * * *
187736 ATGCCGATGTCCCAAACATGGTCTTACTCGTAACTACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACTCGTAACT-CATATCG
187779 ATGCCAACGTCCCAGACGTGGTCTTACTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACTCG
187809 AGAATACATA
Statistics
Matches: 91, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
40 5 0.05
41 25 0.27
42 5 0.05
43 51 0.56
44 5 0.05
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACTCGTAACTCATATCG
Found at i:189445 original size:22 final size:22
Alignment explanation
Indices: 189417--189461 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
189407 CCCGATACGC
189417 TCTATAATTTCATAGGGCCCAA
1 TCTATAATTTCATAGGGCCCAA
189439 TCTATAATTTCATAGGGCCCAA
1 TCTATAATTTCATAGGGCCCAA
189461 T
1 T
189462 GTATCTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (22 bp):
TCTATAATTTCATAGGGCCCAA
Found at i:190009 original size:160 final size:160
Alignment explanation
Indices: 189745--190064 Score: 597
Period size: 160 Copynumber: 2.0 Consensus size: 160
189735 GTAAGGTGCC
189745 ATTTTGATACTCGATTGAAAGCTATTATTGTATGCAAATTCAATCAAAGATAAGTATAGTTCTCG
1 ATTTTGATACTCGATTGAAAGCTATTATTGTATGCAAATTCAATCAAAGATAAGTATAGTTCTCG
189810 CGTACCTTCGATCTCGAGAATGCAACATCTCAACATATCCTCAAGTATCTAAATGACTCGTTCGG
66 CGTACCTTCGATCTCGAGAATGCAACATCTCAACATATCCTCAAGTATCTAAATGACTCGTTCGG
*
189875 ACTGGCCATCTATTTACGGATGGAAAGTAG
131 ACTGGCCATCAATTTACGGATGGAAAGTAG
189905 ATTTTGATACTCGATTGAAAGCTATTATTGTATGCAAATTCAATCAAAGATAAGTATAGTTC-CT
1 ATTTTGATACTCGATTGAAAGCTATTATTGTATGCAAATTCAATCAAAGATAAGTATAGTTCTC-
* *
189969 GCGTACCTTTGATCTCTAGAATGCAACATCTCAACATATCCTCAAGTATCTAAATGACTCGTTCG
65 GCGTACCTTCGATCTCGAGAATGCAACATCTCAACATATCCTCAAGTATCTAAATGACTCGTTCG
190034 GACTGGCCATCAATTTACGGATGGAAAGTAG
130 GACTGGCCATCAATTTACGGATGGAAAGTAG
190065 TGCTGAAATG
Statistics
Matches: 156, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
159 1 0.01
160 155 0.99
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (160 bp):
ATTTTGATACTCGATTGAAAGCTATTATTGTATGCAAATTCAATCAAAGATAAGTATAGTTCTCG
CGTACCTTCGATCTCGAGAATGCAACATCTCAACATATCCTCAAGTATCTAAATGACTCGTTCGG
ACTGGCCATCAATTTACGGATGGAAAGTAG
Found at i:194403 original size:35 final size:35
Alignment explanation
Indices: 194298--194403 Score: 88
Period size: 38 Copynumber: 2.9 Consensus size: 35
194288 TACAATCGTG
* * * * *
194298 GTGTCATTCCATAGAGTTAATAGACCATTGTTACG
1 GTGTCACTCCATAGAGTCAATAAACCATTGTCACA
* * * *
194333 GTATCACTCTAGT-GAGCCAGACTATAACCGTTGTCACA
1 GTGTCACTCCA-TAGAGTCA-A-TA-AACCATTGTCACA
194371 GTGTCACTCCATAGAGTCAATAAACCATTGTCA
1 GTGTCACTCCATAGAGTCAATAAACCATTGTCA
194404 TGGTATCACT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
35 22 0.42
36 4 0.08
37 4 0.08
38 23 0.43
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (35 bp):
GTGTCACTCCATAGAGTCAATAAACCATTGTCACA
Found at i:194413 original size:35 final size:35
Alignment explanation
Indices: 194305--194413 Score: 94
Period size: 35 Copynumber: 3.0 Consensus size: 35
194295 GTGGTGTCAT
* * *
194305 TCCATAGAGTTAATAGACCATTGTTACGGTATCAC
1 TCCATAGAGTCAATAAACCATTGTCACGGTATCAC
* * * * *
194340 TCTAGT-GAGCCAGACTATAACCGTTGTCACAGTGTCAC
1 TCCA-TAGAGTCA-A-TA-AACCATTGTCACGGTATCAC
*
194378 TCCATAGAGTCAATAAACCATTGTCATGGTATCAC
1 TCCATAGAGTCAATAAACCATTGTCACGGTATCAC
194413 T
1 T
194414 ATAGTGAGCC
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
35 24 0.44
36 4 0.07
37 4 0.07
38 23 0.42
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (35 bp):
TCCATAGAGTCAATAAACCATTGTCACGGTATCAC
Found at i:194458 original size:73 final size:73
Alignment explanation
Indices: 194298--194447 Score: 194
Period size: 73 Copynumber: 2.1 Consensus size: 73
194288 TACAATCGTG
* * * * * * *
194298 GTGTCATTCCATAGAGTTAATAGACCATTGTTACGGTATCACTCTAGTGAGCCAGACTATAACCG
1 GTGTCACTCCATAGAGTCAATAAACCATTGTCACGGTATCACTATAGTGAGCCAGACGATAACCA
*
194363 TTGTCACA
66 TCGTCACA
* *
194371 GTGTCACTCCATAGAGTCAATAAACCATTGTCATGGTATCACTATAGTGAGCCA-ATCGATAACT
1 GTGTCACTCCATAGAGTCAATAAACCATTGTCACGGTATCACTATAGTGAGCCAGA-CGATAACC
194435 ATCGTCACA
65 ATCGTCACA
194444 GTGT
1 GTGT
194448 TGTTCTATAG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
72 1 0.02
73 65 0.98
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (73 bp):
GTGTCACTCCATAGAGTCAATAAACCATTGTCACGGTATCACTATAGTGAGCCAGACGATAACCA
TCGTCACA
Found at i:196447 original size:27 final size:27
Alignment explanation
Indices: 196405--196458 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
196395 ATTAACATCC
*
196405 AATATACATGCGTGCAAGCAACTCATT
1 AATATACATGCATGCAAGCAACTCATT
*
196432 AATATACATGTATGCAAGCAACTCATT
1 AATATACATGCATGCAAGCAACTCATT
196459 CTTTCACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (27 bp):
AATATACATGCATGCAAGCAACTCATT
Found at i:197506 original size:2 final size:2
Alignment explanation
Indices: 197499--197548 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
197489 ATCTACAATA
* *
197499 AG AG AG AG AG AG AG AG AG AG GG A- AG -G AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
197539 AG AA AG AG AG
1 AG AG AG AG AG
197549 GAATTTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:202254 original size:31 final size:31
Alignment explanation
Indices: 202219--202280 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
202209 GAATAAATGC
202219 CATGTGCAAGGCCAATGCATATTGATATGTT
1 CATGTGCAAGGCCAATGCATATTGATATGTT
202250 CATGTGCAAGGCCAATGCATATTGATATGTT
1 CATGTGCAAGGCCAATGCATATTGATATGTT
202281 TTACTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (31 bp):
CATGTGCAAGGCCAATGCATATTGATATGTT
Found at i:203492 original size:21 final size:21
Alignment explanation
Indices: 203451--203493 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
203441 GCACTCGATG
**
203451 AAGATAAGAAGCAAACTTACA
1 AAGATAAGAAGCAAAAATACA
203472 AAGATCAAGAA-CAAAAATACA
1 AAGAT-AAGAAGCAAAAATACA
203493 A
1 A
203494 TCATTTCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.63, C:0.14, G:0.12, T:0.12
Consensus pattern (21 bp):
AAGATAAGAAGCAAAAATACA
Found at i:206039 original size:25 final size:26
Alignment explanation
Indices: 205991--206041 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
205981 AAAAAAATTT
*
205991 AGACAACCCTAAAAACCAACGACTTC
1 AGACAACCCTAAAAACCAAAGACTTC
206017 AGACAACCC-AAAAACCAAAGACTTC
1 AGACAACCCTAAAAACCAAAGACTTC
206042 TTTTTGTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.49, C:0.33, G:0.08, T:0.10
Consensus pattern (26 bp):
AGACAACCCTAAAAACCAAAGACTTC
Found at i:209421 original size:12 final size:12
Alignment explanation
Indices: 209404--209429 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
209394 AATCGCCCAC
209404 GTGCCAGGCCGT
1 GTGCCAGGCCGT
209416 GTGCCAGGCCGT
1 GTGCCAGGCCGT
209428 GT
1 GT
209430 AACTGCCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.42, T:0.19
Consensus pattern (12 bp):
GTGCCAGGCCGT
Found at i:211507 original size:20 final size:20
Alignment explanation
Indices: 211482--211528 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
211472 AAAGCATACG
211482 CCCGTGTGCTTAGGGACACA
1 CCCGTGTGCTTAGGGACACA
211502 CCCGTGTGCTTAGGGACACA
1 CCCGTGTGCTTAGGGACACA
211522 CCCGTGT
1 CCCGTGT
211529 CCCTCGCCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.32, G:0.30, T:0.21
Consensus pattern (20 bp):
CCCGTGTGCTTAGGGACACA
Found at i:214472 original size:47 final size:48
Alignment explanation
Indices: 214354--214484 Score: 183
Period size: 47 Copynumber: 2.8 Consensus size: 48
214344 GTGCGAATGA
* ** *
214354 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTTAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAGAGAGAAGT
* *
214402 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTCCAG-GATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAGAGAGAAGT
* *
214449 TACCTTGATTTGGCTACGAGCCATGGTATAAGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
214485 TATCGATTGA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 38 0.51
48 36 0.49
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (48 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAGAGAGAAGT
Found at i:216231 original size:137 final size:137
Alignment explanation
Indices: 215985--216236 Score: 360
Period size: 137 Copynumber: 1.8 Consensus size: 137
215975 AAGCCACAAA
* * * * *
215985 TGGGTCTGCTTACACAAGCTGATGGTCAGAATGTAGCTACACGATGCCGCTCACACAAGCTGACG
1 TGGGTCTACTCACACAAGCTAACGGTCAGAATGTAGCTACACGATGCCGCTCACACAAGCTAACG
*
216050 AGTATCCACAACAAATATCGGAACTCAGCCATCAATAGGACATTCAGGACCAGTACCCTGAACAT
66 AGTATCCACAACAAATATCGGAACTCACCCATCAATAGGACATTCAGGACCAGTACCCTGAACAT
216115 GGTAACT
131 GGTAACT
* * *
216122 TGGGTCTACTCACACAAGCTAACGGTCAGAATGTAGCTACATGATGCTGCTCATACAAGCTAACG
1 TGGGTCTACTCACACAAGCTAACGGTCAGAATGTAGCTACACGATGCCGCTCACACAAGCTAACG
** * * * * *
216187 AGTATCCGTAACAAATGTTGGAACTTACCCTTCAGTAGGACATTCAGGAC
66 AGTATCCACAACAAATATCGGAACTCACCCATCAATAGGACATTCAGGAC
216237 TAACACCCGA
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 99 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (137 bp):
TGGGTCTACTCACACAAGCTAACGGTCAGAATGTAGCTACACGATGCCGCTCACACAAGCTAACG
AGTATCCACAACAAATATCGGAACTCACCCATCAATAGGACATTCAGGACCAGTACCCTGAACAT
GGTAACT
Found at i:217741 original size:24 final size:24
Alignment explanation
Indices: 217711--217760 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
217701 AAATATGAAT
217711 TTATTTGTTTTAAAATATTTTAAA
1 TTATTTGTTTTAAAATATTTTAAA
217735 TTATTTGTTTTAAAATATTTTAAA
1 TTATTTGTTTTAAAATATTTTAAA
217759 TT
1 TT
217761 TACTCCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATTTGTTTTAAAATATTTTAAA
Found at i:218926 original size:11 final size:11
Alignment explanation
Indices: 218910--218937 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
218900 CGTGACGTTG
218910 GGCCTTTTTCA
1 GGCCTTTTTCA
218921 GGCCTTTTTCA
1 GGCCTTTTTCA
218932 GGCCTT
1 GGCCTT
218938 CTTCGGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.29, G:0.21, T:0.43
Consensus pattern (11 bp):
GGCCTTTTTCA
Found at i:223693 original size:136 final size:136
Alignment explanation
Indices: 223542--223815 Score: 512
Period size: 136 Copynumber: 2.0 Consensus size: 136
223532 ACCAAAAGAA
* *
223542 GAGTATAAGATAAACAAACAATCAAAACCCAAAAATACAAAGTTCTGTCGAAATTCTCACAAATT
1 GAGTATAAGATAAACAAACAAACAAAACCCAAAAATACAAAGTTCTCTCGAAATTCTCACAAATT
223607 CTCTCTTAATTATGTTGTTGAATCTATTTCTCTAGGATTGCTAAAAGCCCTATTTATAGGCTAAA
66 CTCTCTTAATTATGTTGTTGAATCTATTTCTCTAGGATTGCTAAAAGCCCTATTTATAGGCTAAA
223672 ATTTGT
131 ATTTGT
* *
223678 GAGTATAAGATAAACACACAAACTAAACCCAAAAATACAAAGTTCTCTCGAAATTCTCACAAATT
1 GAGTATAAGATAAACAAACAAACAAAACCCAAAAATACAAAGTTCTCTCGAAATTCTCACAAATT
223743 CTCTCTTAATTATGTTGTTGAATCTATTTCTCTAGGATTGCTAAAAGCCCTATTTATAGGCTAAA
66 CTCTCTTAATTATGTTGTTGAATCTATTTCTCTAGGATTGCTAAAAGCCCTATTTATAGGCTAAA
223808 ATTTGT
131 ATTTGT
223814 GA
1 GA
223816 CTAATCTGAT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 134 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (136 bp):
GAGTATAAGATAAACAAACAAACAAAACCCAAAAATACAAAGTTCTCTCGAAATTCTCACAAATT
CTCTCTTAATTATGTTGTTGAATCTATTTCTCTAGGATTGCTAAAAGCCCTATTTATAGGCTAAA
ATTTGT
Found at i:233896 original size:43 final size:43
Alignment explanation
Indices: 233848--233998 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
233838 TATCCCAGAT
* * *
233848 ATGGTCTTACATGTTATCACATATCGATGCCAATGTCCTAGAG
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCTAGAC
* * *
233891 ATGGTCTTACACGAAATCATATAACGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCTAGAC
* * * * * *
233934 ATAGTCTTACACATAATCATA-ATACAATTCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACATAT-CGATGCCAATGTCCTAGAC
* *
233977 ATGGTCTTCCATGTAATCACAT
1 ATGGTCTTACACGTAATCACAT
233999 CTCGGCAATC
Statistics
Matches: 88, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 87 0.99
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCTAGAC
Found at i:247125 original size:9 final size:9
Alignment explanation
Indices: 247111--247179 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
247101 CAATAATTAT
247111 TAATTTTTA
1 TAATTTTTA
247120 TAATTTATTA
1 TAATTT-TTA
* *
247130 GAATCTTTAA
1 TAAT-TTTTA
247140 TAA-TTTTA
1 TAATTTTTA
*
247148 TATTTTTTA
1 TAATTTTTA
*
247157 CT-ATTCTTAA
1 -TAATT-TTTA
247167 TAATTTTTA
1 TAATTTTTA
247176 TAAT
1 TAAT
247180 ATTATGTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.13
9 21 0.46
10 17 0.37
11 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (9 bp):
TAATTTTTA
Found at i:248898 original size:14 final size:14
Alignment explanation
Indices: 248859--248899 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
248849 TTGTTTAATT
* * *
248859 AAAAATAGTTTCTG
1 AAAAATAATTTTTA
248873 AAAAATAATTTTTA
1 AAAAATAATTTTTA
248887 AAAAATAATTTTT
1 AAAAATAATTTTT
248900 TTAGAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:248902 original size:16 final size:16
Alignment explanation
Indices: 248873--248922 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
248863 ATAGTTTCTG
248873 AAAAATAA--TTTTTA
1 AAAAATAATTTTTTTA
248887 AAAAATAATTTTTTTA
1 AAAAATAATTTTTTTA
248903 GAAAATATAATATTTTTTA
1 -AAAA-ATAAT-TTTTTTA
248922 A
1 A
248923 TGTTTAGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.26
16 6 0.19
17 4 0.13
18 6 0.19
19 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAAAATAATTTTTTTA
Found at i:248912 original size:18 final size:17
Alignment explanation
Indices: 248876--248922 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
248866 GTTTCTGAAA
*
248876 AATAATTTTTAAAAAAT
1 AATATTTTTTAAAAAAT
248893 AAT-TTTTTTAGAAAATAT
1 AATATTTTTTA-AAAA-AT
248911 AATATTTTTTAA
1 AATATTTTTTAA
248923 TGTTTAGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 7 0.27
18 6 0.23
19 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AATATTTTTTAAAAAAT
Found at i:258828 original size:40 final size:40
Alignment explanation
Indices: 258576--258821 Score: 449
Period size: 40 Copynumber: 6.2 Consensus size: 40
258566 AACCCAAGTA
* *
258576 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
258615 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
258655 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
258695 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
258735 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
258775 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
258815 CCTTCGG
1 CCTTCGG
258822 ATCTTAGTCC
Statistics
Matches: 202, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
39 13 0.06
40 189 0.94
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:265269 original size:40 final size:40
Alignment explanation
Indices: 265193--265446 Score: 312
Period size: 40 Copynumber: 6.1 Consensus size: 40
265183 AACCCAAGTA
* * ** *
265193 CCTTCGGGATTTAG-CCAGATATAACAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
265232 CCTTCGGGACTTAGCCTGGATATAGTAACTCGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
265272 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
265312 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTCCGGG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA----T----G
*
265360 CTACCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 ---CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
265403 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
265443 CCTT
1 CCTT
265447 TGGATCCTAG
Statistics
Matches: 190, Mismatches: 13, Indels: 23
0.84 0.06 0.10
Matches are distributed among these distances:
39 13 0.07
40 136 0.72
43 1 0.01
44 1 0.01
47 1 0.01
48 1 0.01
51 37 0.19
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:265388 original size:51 final size:51
Alignment explanation
Indices: 265312--265410 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
265302 CGCACAAATG
265312 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTCCGGGCTA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTCCGGGCTA
* *
265363 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATGCCTTCGGG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTCCGGG
265411 ACTTAGCCCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (51 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTCCGGGCTA
Found at i:265427 original size:91 final size:91
Alignment explanation
Indices: 265272--265445 Score: 321
Period size: 91 Copynumber: 1.9 Consensus size: 91
265262 CGGACAAATG
265272 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
265337 TAACTCGCACAAATGCCTCCGGGCTA
66 TAACTAGCACAAATGCCTCCGGGCTA
*
265363 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
265428 TCACTAGCACAAATGCCT
66 TAACTAGCACAAATGCCT
265446 TTGGATCCTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (91 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTAGCACAAATGCCTCCGGGCTA
Found at i:265459 original size:22 final size:22
Alignment explanation
Indices: 265431--265474 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
265421 GATATAGTCA
*
265431 CTAGCACAAATGCCTTTGGATC
1 CTAGCACAAATGCCTTCGGATC
265453 CTAGCACAAATGCCTTCGGATC
1 CTAGCACAAATGCCTTCGGATC
265475 TTAGTCCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (22 bp):
CTAGCACAAATGCCTTCGGATC
Found at i:272909 original size:15 final size:15
Alignment explanation
Indices: 272889--272940 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
272879 ACTACAAAAC
272889 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
272904 ATTTATAATTGAGATAAAT
1 ATTTATTATT-A-AT--AT
*
272923 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
272938 ATT
1 ATT
272941 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 14 0.47
16 1 0.03
17 3 0.10
18 1 0.03
19 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:273064 original size:24 final size:24
Alignment explanation
Indices: 273037--273087 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
273027 TTTATTAAAA
* *
273037 TAATAATTTGTATTAATAATTTAT
1 TAATAAATTATATTAATAATTTAT
273061 TAATAAATTATATTAATAATTTAT
1 TAATAAATTATATTAATAATTTAT
273085 TAA
1 TAA
273088 ATGGTTAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATAAATTATATTAATAATTTAT
Found at i:278840 original size:38 final size:38
Alignment explanation
Indices: 278797--278872 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
278787 TTCATCCTTT
278797 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
**
278835 TTCATTTCTTTTGGCTTAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
278873 GGAGTTCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:280155 original size:40 final size:40
Alignment explanation
Indices: 280061--280205 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
280051 TACTCGAATG
*
280061 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
280102 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
280142 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
280182 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
280206 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:288106 original size:40 final size:41
Alignment explanation
Indices: 288010--288114 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 41
288000 TGAATGATGT
*
288010 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
* * * *
288050 CCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTATAA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGTGACCATAA
*
288090 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
288115 AACGAGGAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 46 0.84
41 8 0.15
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
Found at i:311816 original size:18 final size:18
Alignment explanation
Indices: 311793--311827 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
311783 CCTTCGTCCT
* *
311793 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
311811 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
311828 CTGCCTAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:322335 original size:46 final size:47
Alignment explanation
Indices: 322240--322356 Score: 150
Period size: 46 Copynumber: 2.5 Consensus size: 47
322230 GGTGTGAGCC
* * *
322240 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACATCGCATCGACATCGAGACGAGTGCT
*
322288 AGTGTAAGACATGTCTGGGACA-CGCATCGACCTCGAGAC-A-TAAGCT
1 AGTGTAAGACATGTCTGGGACATCGCATCGACATCGAGACGAGT--GCT
322334 AGTGTAAGACATGTCTGGGACAT
1 AGTGTAAGACATGTCTGGGACAT
322357 GTATTGGCTA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
44 1 0.02
45 1 0.02
46 38 0.61
47 13 0.21
48 9 0.15
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATCGCATCGACATCGAGACGAGTGCT
Found at i:326162 original size:21 final size:21
Alignment explanation
Indices: 326138--326177 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
326128 ACATGTAAAG
326138 CACATCAACATAACTCACAAT
1 CACATCAACATAACTCACAAT
326159 CACATCAACATAACTCACA
1 CACATCAACATAACTCACA
326178 TTACATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (21 bp):
CACATCAACATAACTCACAAT
Found at i:333899 original size:13 final size:14
Alignment explanation
Indices: 333872--333900 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
333862 CAAAGGGTGA
333872 TGGTGATTCGAAAT
1 TGGTGATTCGAAAT
333886 TGGTGATT-GAAAT
1 TGGTGATTCGAAAT
333899 TG
1 TG
333901 ACATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.03, G:0.31, T:0.38
Consensus pattern (14 bp):
TGGTGATTCGAAAT
Found at i:335094 original size:17 final size:18
Alignment explanation
Indices: 335062--335096 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
335052 TAAAGTTTTT
335062 TTTTAAATAGTTTCACTA
1 TTTTAAATAGTTTCACTA
*
335080 TTTTAAA-ATTTTCACTA
1 TTTTAAATAGTTTCACTA
335097 CATGATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTAAATAGTTTCACTA
Found at i:337531 original size:21 final size:20
Alignment explanation
Indices: 337475--337532 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
337465 TTATCAAATG
*
337475 TATATAAACATTAAAA-AAA
1 TATATAAAAATTAAAATAAA
337494 -ATATAAGAAA-TAGAAATAAA
1 TATATAA-AAATTA-AAATAAA
337514 TATATTAAAAATTAAAATA
1 TATA-TAAAAATTAAAATA
337533 TATAATCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
18 8 0.25
19 5 0.16
20 3 0.09
21 11 0.34
22 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (20 bp):
TATATAAAAATTAAAATAAA
Found at i:337688 original size:11 final size:10
Alignment explanation
Indices: 337648--337708 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 10
337638 GAAAAACTTG
337648 TAAAAATTTT
1 TAAAAATTTT
* *
337658 AAAAAATTGTA
1 TAAAAATT-TT
*
337669 AAAAGAATTATT
1 TAAA-AATT-TT
337681 TAAAAA-TTT
1 TAAAAATTTT
337690 TAAAAATTTAT
1 TAAAAATTT-T
337701 TAAAAATT
1 TAAAAATT
337709 ATAACAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.19
10 10 0.24
11 16 0.38
12 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TAAAAATTTT
Found at i:337703 original size:20 final size:20
Alignment explanation
Indices: 337627--337727 Score: 78
Period size: 20 Copynumber: 4.9 Consensus size: 20
337617 AATAGTATTA
* * *
337627 TAAAAATGTTAGAAAAACTTG
1 TAAAAAT-TTATAAAAAATTT
337648 TAAAAATTT-TAAAAAATTGT
1 TAAAAATTTATAAAAAATT-T
* * *
337668 AAAAAGAATTATTTAAAAATTT
1 TAAAA-ATTTA-TAAAAAATTT
* *
337690 TAAAAATTTATTAAAAATTA
1 TAAAAATTTATAAAAAATTT
*
337710 TAACAATTTATAAAAAAT
1 TAAAAATTTATAAAAAAT
337728 AAAAAGAAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 7 0.11
20 31 0.48
21 14 0.22
22 5 0.08
23 8 0.12
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAAAATTTATAAAAAATTT
Found at i:338334 original size:10 final size:10
Alignment explanation
Indices: 338321--338460 Score: 75
Period size: 10 Copynumber: 14.7 Consensus size: 10
338311 TAAAATTATT
338321 ATAATTTTAA
1 ATAATTTTAA
**
338331 ATAATTTTTT
1 ATAATTTTAA
* *
338341 ACAATTTTTA
1 ATAATTTTAA
*
338351 ATCATTTT--
1 ATAATTTTAA
*
338359 ATAATTTTTA
1 ATAATTTTAA
* *
338369 ATGATTTTCAC
1 ATAATTTT-AA
338380 A-AATTTTAA
1 ATAATTTTAA
338389 AT--TTTTAA
1 ATAATTTTAA
* *
338397 ATATTTTTTAC
1 ATA-ATTTTAA
338408 A-AATTTTAA
1 ATAATTTTAA
338417 AT-ATTTTAA
1 ATAATTTTAA
*
338426 A-ATATTTT-T
1 ATA-ATTTTAA
*
338435 ATAATTTTTA
1 ATAATTTTAA
338445 ATAATTTTAA
1 ATAATTTTAA
338455 A-AATTT
1 ATAATTT
338461 AAACAAGTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
8 15 0.15
9 27 0.27
10 51 0.51
11 7 0.07
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.56
Consensus pattern (10 bp):
ATAATTTTAA
Found at i:338364 original size:18 final size:18
Alignment explanation
Indices: 338337--338388 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
338327 TTAAATAATT
338337 TTTTACAATTTTTAATCA
1 TTTTACAATTTTTAATCA
* *
338355 TTTTATAATTTTTAATGA
1 TTTTACAATTTTTAATCA
*
338373 TTTTCACAAATTTTAA
1 TTTT-ACAATTTTTAA
338389 ATTTTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTACAATTTTTAATCA
Found at i:338385 original size:28 final size:27
Alignment explanation
Indices: 338354--338434 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 27
338344 ATTTTTAATC
338354 ATTTTATAATTTTTAATGA-TTTTCACAA
1 ATTTTA-AATTTTTAAT-ATTTTTCACAA
*
338382 ATTTTAAATTTTTAAATATTTTTTACAA
1 ATTTTAAATTTTT-AATATTTTTCACAA
338410 ATTTTAAATATTTTAAAATATTTTT
1 ATTTTAAAT-TTTT--AATATTTTT
338435 ATAATTTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 8 0.17
28 26 0.54
29 4 0.08
30 10 0.21
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (27 bp):
ATTTTAAATTTTTAATATTTTTCACAA
Found at i:338434 original size:20 final size:19
Alignment explanation
Indices: 338387--338483 Score: 67
Period size: 20 Copynumber: 4.9 Consensus size: 19
338377 CACAAATTTT
*
338387 AAATTTTTAAATATTTTTTAC
1 AAATTTTTAAATA--TTTTAA
338408 AAA-TTTTAAATATTTTAA
1 AAATTTTTAAATATTTTAA
338426 AATATTTTTATAAT-TTTTAA
1 AA-ATTTTTA-AATATTTTAA
* *
338446 TAA-TTTTAAA-AATTTAA
1 AAATTTTTAAATATTTTAA
338463 ACAAGTTTTTACAAGTATTTT
1 A-AA-TTTTTA-AA-TATTTT
338484 TTTTACTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
17 7 0.11
18 14 0.23
19 2 0.03
20 26 0.43
21 8 0.13
23 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (19 bp):
AAATTTTTAAATATTTTAA
Found at i:338440 original size:28 final size:29
Alignment explanation
Indices: 338372--338460 Score: 105
Period size: 28 Copynumber: 3.1 Consensus size: 29
338362 ATTTTTAATG
*
338372 ATTTTCACAAATTTTAAAT-TTTT-AAAT
1 ATTTTTACAAATTTTAAATATTTTAAAAT
338399 ATTTTTTACAAATTTTAAATATTTTAAAAT
1 A-TTTTTACAAATTTTAAATATTTTAAAAT
* *
338429 ATTTTTA-TAATTTTTAATAATTTTAAAA-
1 ATTTTTACAAATTTTAAAT-ATTTTAAAAT
338457 ATTT
1 ATTT
338461 AAACAAGTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
27 1 0.02
28 30 0.55
29 19 0.35
30 5 0.09
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTTACAAATTTTAAATATTTTAAAAT
Found at i:338443 original size:38 final size:35
Alignment explanation
Indices: 338310--338463 Score: 121
Period size: 38 Copynumber: 4.1 Consensus size: 35
338300 TAAAAAAAGA
* * * *
338310 TTAAAATTATTATAATTTTAAATAATTTTTTACAATT
1 TTAAATTTTTTATAATTTTTAATAA--TTTTAAAATT
* * *
338347 TTTAATCATTTTATAATTTTTAATGATTTTCACAAATT
1 TTAAAT-TTTTTATAATTTTTAATAATTTT-A-AAATT
* *
338385 TTAAATTTTTAAATATTTTTTACA-AATTTTAAATATT
1 TTAAATTTTT-TATAATTTTTA-ATAATTTTAAA-ATT
*
338422 TTAAAATATTTTTATAATTTTTAATAATTTTAAAAAT
1 TT-AAAT-TTTTTATAATTTTTAATAATTTTAAAATT
338459 TTAAA
1 TTAAA
338464 CAAGTTTTTA
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
36 9 0.10
37 19 0.20
38 60 0.65
39 5 0.05
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (35 bp):
TTAAATTTTTTATAATTTTTAATAATTTTAAAATT
Found at i:338608 original size:21 final size:20
Alignment explanation
Indices: 338584--338623 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
338574 TTTTCTAGAT
338584 TATATATATTCTAAATTTTTA
1 TATATATATT-TAAATTTTTA
* *
338605 TATATTTATTTCAATTTTT
1 TATATATATTTAAATTTTT
338624 TTTAATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATATATTTAAATTTTTA
Found at i:339003 original size:28 final size:28
Alignment explanation
Indices: 338972--339044 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
338962 CCAGAAAAGC
*
338972 TGTTTTTACATATATTTATATTTTAAAT
1 TGTTTTTACATATATTTATACTTTAAAT
*
339000 TGTTTTTTTA-ATAAATTTATACTTTAAAT
1 TG--TTTTTACATATATTTATACTTTAAAT
339029 TGTTTTTACATATATT
1 TGTTTTTACATATATT
339045 GCAATGATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 6 0.15
28 8 0.21
29 19 0.49
30 6 0.15
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (28 bp):
TGTTTTTACATATATTTATACTTTAAAT
Found at i:340323 original size:21 final size:20
Alignment explanation
Indices: 340307--340352 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
340297 ATTATCCAAC
340307 CAAATAAATTCAATATCTAA
1 CAAATAAATTCAATATCTAA
*
340327 CATAATAAATTTAATATCTAA
1 CA-AATAAATTCAATATCTAA
340348 CAAAT
1 CAAAT
340353 TCAAGACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAATAAATTCAATATCTAA
Found at i:342128 original size:13 final size:13
Alignment explanation
Indices: 342112--342172 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
342102 ACCAAATTTT
342112 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
342125 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
342138 TCCACAGCACTTC
1 TCAAAAGCACTTC
*
342151 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
342164 TTAAAAGCA
1 TCAAAAGCA
342173 TTGCCAAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:342172 original size:26 final size:26
Alignment explanation
Indices: 342108--342172 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
342098 TTAAACCAAA
342108 TTTTTCAAAAGCACTTCTCAAAAGCAC
1 TTTTT-AAAAGCACTTCTCAAAAGCAC
** *
342135 TTTTCCACAGCACTTCTCAAAAGCAC
1 TTTTTAAAAGCACTTCTCAAAAGCAC
342161 TTTTTAAAAGCA
1 TTTTTAAAAGCA
342173 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTTTAAAAGCACTTCTCAAAAGCAC
Found at i:348550 original size:20 final size:18
Alignment explanation
Indices: 348527--348586 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 18
348517 TCAATTCTCT
348527 TGTTTGCACATTGGTGCCC
1 TGTTT-CACATTGGTGCCC
348546 ATGTTT-ACACTTCGGTGCCTC
1 -TGTTTCACA-TT-GGTGCC-C
*
348567 TGTATTCACATTTGTGCCC
1 TGT-TTCACATTGGTGCCC
348586 T
1 T
348587 TATCCAGCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 19 0.56
21 5 0.15
22 3 0.09
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (18 bp):
TGTTTCACATTGGTGCCC
Found at i:350577 original size:24 final size:23
Alignment explanation
Indices: 350550--350596 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
350540 ACGCATCTAT
*
350550 TCATGAGCATCCTGATATAGGCTC
1 TCATGAGCATCCTGACAT-GGCTC
*
350574 TCATGAGCTTCCTGACATGGCTC
1 TCATGAGCATCCTGACATGGCTC
350597 GCTTGAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (23 bp):
TCATGAGCATCCTGACATGGCTC
Found at i:351216 original size:11 final size:11
Alignment explanation
Indices: 351200--351225 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
351190 CATAAAGGTT
351200 AGAGATCGGTC
1 AGAGATCGGTC
351211 AGAGATCGGTC
1 AGAGATCGGTC
351222 AGAG
1 AGAG
351226 CATCATCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (11 bp):
AGAGATCGGTC
Found at i:354487 original size:24 final size:25
Alignment explanation
Indices: 354447--354493 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
354437 ATATGCATAT
*
354447 TAAGCTACATGATTTGC-AATTAAC
1 TAAGCTACATAATTTGCTAATTAAC
354471 TAAGCTA-ATAATCTTGCTAATTA
1 TAAGCTACATAAT-TTGCTAATTA
354494 TCTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (25 bp):
TAAGCTACATAATTTGCTAATTAAC
Found at i:357709 original size:823 final size:823
Alignment explanation
Indices: 356124--357769 Score: 3292
Period size: 823 Copynumber: 2.0 Consensus size: 823
356114 GTCCGAGTTC
356124 GAGAGATGTAACTAGGCATCTTAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACAC
1 GAGAGATGTAACTAGGCATCTTAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACAC
356189 CCGAGCTCGTTGAGTTCAGTCCAAGTTCACTTATGGGTGGGTTACATGGTAGCTTGGCTACACAT
66 CCGAGCTCGTTGAGTTCAGTCCAAGTTCACTTATGGGTGGGTTACATGGTAGCTTGGCTACACAT
356254 ATATTCTGCCGGCTATTGAGTTTGTCTAACTGTTGGCATGGCACTTATGTGCATGCATTCCGTGT
131 ATATTCTGCCGGCTATTGAGTTTGTCTAACTGTTGGCATGGCACTTATGTGCATGCATTCCGTGT
356319 ATCCGATTACATTCCGAGTGTTCAATGGGTAATTTGGCAAAGTATTCGTTGATGATCCCAATGAG
196 ATCCGATTACATTCCGAGTGTTCAATGGGTAATTTGGCAAAGTATTCGTTGATGATCCCAATGAG
356384 ATAACCCATTGGTGAGTATGTCTTTGAGTTATGTTACAAGTTGTACATGTATGTACACTAAACTT
261 ATAACCCATTGGTGAGTATGTCTTTGAGTTATGTTACAAGTTGTACATGTATGTACACTAAACTT
356449 ATGTGTGATGCCTTGACATGTGATGATCTATGATGTATATAGTATTTGGTGAATATTATGAAAAT
326 ATGTGTGATGCCTTGACATGTGATGATCTATGATGTATATAGTATTTGGTGAATATTATGAAAAT
356514 GACATGATTTGGAATAAGTCCTTGATACTTGATGACATTGAGATTATGGATTTATGCTTATGAAG
391 GACATGATTTGGAATAAGTCCTTGATACTTGATGACATTGAGATTATGGATTTATGCTTATGAAG
356579 CATAATTATGTGTTCTTACCATTATGAATGAAATGGTATTGTATGGATTTGGTGAATAATAGTAA
456 CATAATTATGTGTTCTTACCATTATGAATGAAATGGTATTGTATGGATTTGGTGAATAATAGTAA
356644 TGAATGAGTAAATTTAGCCTTGGCAGTTTTGGGTTACTGCAGTGGTGCAACTTTGGAAATTCACC
521 TGAATGAGTAAATTTAGCCTTGGCAGTTTTGGGTTACTGCAGTGGTGCAACTTTGGAAATTCACC
356709 ATTAATTATGGAAATTGAATTAGGGGCTGAATAAAATATAAGGCTAAATACCAATGAATCTAGTT
586 ATTAATTATGGAAATTGAATTAGGGGCTGAATAAAATATAAGGCTAAATACCAATGAATCTAGTT
356774 TCACATAGATGAAACGGTATATGCAATCGGAATTTATATTATGAGATATTTAAATTGTTGTGAGA
651 TCACATAGATGAAACGGTATATGCAATCGGAATTTATATTATGAGATATTTAAATTGTTGTGAGA
356839 CAGAGTCTGAATGACTTCGTGATCCCCTGTTTCAATTTGAGAAAATTATTAAACATTGTATAAAA
716 CAGAGTCTGAATGACTTCGTGATCCCCTGTTTCAATTTGAGAAAATTATTAAACATTGTATAAAA
356904 ATAATTATGGGTTTTAATTTATATTATTAAAATCCTTAATGAG
781 ATAATTATGGGTTTTAATTTATATTATTAAAATCCTTAATGAG
356947 GAGAGATGTAACTAGGCATCTTAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACAC
1 GAGAGATGTAACTAGGCATCTTAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACAC
357012 CCGAGCTCGTTGAGTTCAGTCCAAGTTCACTTATGGGTGGGTTACATGGTAGCTTGGCTACACAT
66 CCGAGCTCGTTGAGTTCAGTCCAAGTTCACTTATGGGTGGGTTACATGGTAGCTTGGCTACACAT
357077 ATATTCTGCCGGCTATTGAGTTTGTCTAACTGTTGGCATGGCACTTATGTGCATGCATTCCGTGT
131 ATATTCTGCCGGCTATTGAGTTTGTCTAACTGTTGGCATGGCACTTATGTGCATGCATTCCGTGT
357142 ATCCGATTACATTCCGAGTGTTCAATGGGTAATTTGGCAAAGTATTCGTTGATGATCCCAATGAG
196 ATCCGATTACATTCCGAGTGTTCAATGGGTAATTTGGCAAAGTATTCGTTGATGATCCCAATGAG
357207 ATAACCCATTGGTGAGTATGTCTTTGAGTTATGTTACAAGTTGTACATGTATGTACACTAAACTT
261 ATAACCCATTGGTGAGTATGTCTTTGAGTTATGTTACAAGTTGTACATGTATGTACACTAAACTT
357272 ATGTGTGATGCCTTGACATGTGATGATCTATGATGTATATAGTATTTGGTGAATATTATGAAAAT
326 ATGTGTGATGCCTTGACATGTGATGATCTATGATGTATATAGTATTTGGTGAATATTATGAAAAT
357337 GACATGATTTGGAATAAGTCCTTGATACTTGATGACATTGAGATTATGGATTTATGCTTATGAAG
391 GACATGATTTGGAATAAGTCCTTGATACTTGATGACATTGAGATTATGGATTTATGCTTATGAAG
357402 CATAATTATGTGTTCTTACCATTATGAATGAAATGGTATTGTATGGATTTGGTGAATAATAGTAA
456 CATAATTATGTGTTCTTACCATTATGAATGAAATGGTATTGTATGGATTTGGTGAATAATAGTAA
357467 TGAATGAGTAAATTTAGCCTTGGCAGTTTTGGGTTACTGCAGTGGTGCAACTTTGGAAATTCACC
521 TGAATGAGTAAATTTAGCCTTGGCAGTTTTGGGTTACTGCAGTGGTGCAACTTTGGAAATTCACC
357532 ATTAATTATGGAAATTGAATTAGGGGCTGAATAAAATATAAGGCTAAATACCAATGAATCTAGTT
586 ATTAATTATGGAAATTGAATTAGGGGCTGAATAAAATATAAGGCTAAATACCAATGAATCTAGTT
357597 TCACATAGATGAAACGGTATATGCAATCGGAATTTATATTATGAGATATTTAAATTGTTGTGAGA
651 TCACATAGATGAAACGGTATATGCAATCGGAATTTATATTATGAGATATTTAAATTGTTGTGAGA
357662 CAGAGTCTGAATGACTTCGTGATCCCCTGTTTCAATTTGAGAAAATTATTAAACATTGTATAAAA
716 CAGAGTCTGAATGACTTCGTGATCCCCTGTTTCAATTTGAGAAAATTATTAAACATTGTATAAAA
357727 ATAATTATGGGTTTTAATTTATATTATTAAAATCCTTAATGAG
781 ATAATTATGGGTTTTAATTTATATTATTAAAATCCTTAATGAG
357770 TATATTCTCT
Statistics
Matches: 823, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
823 823 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (823 bp):
GAGAGATGTAACTAGGCATCTTAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACAC
CCGAGCTCGTTGAGTTCAGTCCAAGTTCACTTATGGGTGGGTTACATGGTAGCTTGGCTACACAT
ATATTCTGCCGGCTATTGAGTTTGTCTAACTGTTGGCATGGCACTTATGTGCATGCATTCCGTGT
ATCCGATTACATTCCGAGTGTTCAATGGGTAATTTGGCAAAGTATTCGTTGATGATCCCAATGAG
ATAACCCATTGGTGAGTATGTCTTTGAGTTATGTTACAAGTTGTACATGTATGTACACTAAACTT
ATGTGTGATGCCTTGACATGTGATGATCTATGATGTATATAGTATTTGGTGAATATTATGAAAAT
GACATGATTTGGAATAAGTCCTTGATACTTGATGACATTGAGATTATGGATTTATGCTTATGAAG
CATAATTATGTGTTCTTACCATTATGAATGAAATGGTATTGTATGGATTTGGTGAATAATAGTAA
TGAATGAGTAAATTTAGCCTTGGCAGTTTTGGGTTACTGCAGTGGTGCAACTTTGGAAATTCACC
ATTAATTATGGAAATTGAATTAGGGGCTGAATAAAATATAAGGCTAAATACCAATGAATCTAGTT
TCACATAGATGAAACGGTATATGCAATCGGAATTTATATTATGAGATATTTAAATTGTTGTGAGA
CAGAGTCTGAATGACTTCGTGATCCCCTGTTTCAATTTGAGAAAATTATTAAACATTGTATAAAA
ATAATTATGGGTTTTAATTTATATTATTAAAATCCTTAATGAG
Found at i:358792 original size:28 final size:28
Alignment explanation
Indices: 358761--358816 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
358751 AGAAGGTTGA
*
358761 ATCATCTATCGATTAAATGAGGTCTTAG
1 ATCATCCATCGATTAAATGAGGTCTTAG
*
358789 ATCATCCATTGATTAAATGAGGTCTTAG
1 ATCATCCATCGATTAAATGAGGTCTTAG
358817 CTTTACCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (28 bp):
ATCATCCATCGATTAAATGAGGTCTTAG
Found at i:360132 original size:22 final size:21
Alignment explanation
Indices: 360093--360136 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
360083 ACATGTCGAA
360093 TTTTGGGGCTAGAAGTTTTGAG
1 TTTTGGGGCTAGAAG-TTTGAG
*
360115 TTTTGGTGGCTAG-GGTTTGAG
1 TTTTGG-GGCTAGAAGTTTGAG
360136 T
1 T
360137 GTGAGGTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.14, C:0.05, G:0.39, T:0.43
Consensus pattern (21 bp):
TTTTGGGGCTAGAAGTTTGAG
Found at i:361907 original size:14 final size:15
Alignment explanation
Indices: 361878--361916 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
361868 CTGTATTCTG
361878 TTTGT-CTGAATGCA
1 TTTGTGCTGAATGCA
361892 TTTGTGCTGAAT-CA
1 TTTGTGCTGAATGCA
361906 TTTGTG-TGAAT
1 TTTGTGCTGAAT
361917 TTATGTACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.21
14 13 0.54
15 6 0.25
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (15 bp):
TTTGTGCTGAATGCA
Found at i:363596 original size:43 final size:43
Alignment explanation
Indices: 363548--363655 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
363538 GATTAACGAG
363548 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCATT
1 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCATT
* ** * *
363591 ATGTGATTACGTGTAAGACTGTGTCTGGGACATTGGCATCGTT
1 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCATT
* * *
363634 ATTTGATTTTCTGTAAGACCAT
1 ATGTGATTATGTGTAAGACCAT
363656 AGTTGGGCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (43 bp):
ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCATT
Found at i:381844 original size:40 final size:40
Alignment explanation
Indices: 381748--382050 Score: 425
Period size: 40 Copynumber: 7.6 Consensus size: 40
381738 TATTCAAATG
* * *
381748 ATATCCGGGCTAAGTCCAGAAGGCATTTGAT--TATTCGAAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTG-TGCTAGT-GACT
* *
381788 GATATCCGGGCTAAGTCCAGAAGGCATTTGTGCAAGTGACT
1 -ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
381829 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
381869 ATATCCGGGCTAAGTGCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
381909 ATATCCGAGCTAAGTCCCGAAGGCATTTGTGCTAGTAACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
381949 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
381989 ATATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
382029 ATAT-CTGGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
382051 TACTTGGGTT
Statistics
Matches: 242, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
39 15 0.06
40 191 0.79
41 34 0.14
42 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:389114 original size:44 final size:44
Alignment explanation
Indices: 389051--389137 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
389041 AGAAATAAGA
389051 TTTTTGTTTCTTATTAAATTGGATGTATCTTGTTGTATGAGTGG
1 TTTTTGTTTCTTATTAAATTGGATGTATCTTGTTGTATGAGTGG
*
389095 TTTTTGTTTCTTGTTAAATTGGATGTATCTTGTTGTATGAGTG
1 TTTTTGTTTCTTATTAAATTGGATGTATCTTGTTGTATGAGTG
389138 CTTGAACAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.17, C:0.05, G:0.23, T:0.55
Consensus pattern (44 bp):
TTTTTGTTTCTTATTAAATTGGATGTATCTTGTTGTATGAGTGG
Found at i:389970 original size:40 final size:40
Alignment explanation
Indices: 389915--390136 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
389905 TATTCAAATG
389915 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
389955 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
389995 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTAACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
390035 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
390075 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
390115 ATAT-CTGGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
390137 TACTTGGGTT
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 15 0.09
40 153 0.90
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:391842 original size:94 final size:94
Alignment explanation
Indices: 391681--391859 Score: 340
Period size: 94 Copynumber: 1.9 Consensus size: 94
391671 GGGTGTTACA
* *
391681 CATAGACCATGACCGAATGGCATTTAAACACAAGTCAACAAGATCTCATGATTTCAAATCAAACT
1 CATAGACCATGACCAAATGCCATTTAAACACAAGTCAACAAGATCTCATGATTTCAAATCAAACT
391746 CTTAACAAGAATGCACAATGGCAAACACC
66 CTTAACAAGAATGCACAATGGCAAACACC
391775 CATAGACCATGACCAAATGCCATTTAAACACAAGTCAACAAGATCTCATGATTTCAAATCAAACT
1 CATAGACCATGACCAAATGCCATTTAAACACAAGTCAACAAGATCTCATGATTTCAAATCAAACT
391840 CTTAACAAGAATGCACAATG
66 CTTAACAAGAATGCACAATG
391860 CCGAACCCTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (94 bp):
CATAGACCATGACCAAATGCCATTTAAACACAAGTCAACAAGATCTCATGATTTCAAATCAAACT
CTTAACAAGAATGCACAATGGCAAACACC
Found at i:398999 original size:40 final size:40
Alignment explanation
Indices: 398867--398992 Score: 200
Period size: 40 Copynumber: 3.2 Consensus size: 40
398857 AACCCAAGTA
* * *
398867 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
* *
398906 CCTTCGAGACTTAGCCCGGATATAGTAATTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
398946 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
398986 CCTTCGG
1 CCTTCGG
398993 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 12 0.15
40 67 0.85
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Done.