Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold84
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: 2025335
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 30794 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:408954 original size:13 final size:13
Alignment explanation
Indices: 408936--408964 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
408926 ACATTTGGTC
408936 ATGTATCGATACA
1 ATGTATCGATACA
408949 ATGTATCGATACA
1 ATGTATCGATACA
408962 ATG
1 ATG
408965 CAGTCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:409556 original size:22 final size:21
Alignment explanation
Indices: 409514--409557 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
409504 TTTTCTTTTC
*
409514 TCTCCCCCTTAATCAAAAATT
1 TCTCCCCCTTAATAAAAAATT
*
409535 TCTCCCCCTTAGTAAAATAATT
1 TCTCCCCCTTAATAAAA-AATT
409557 T
1 T
409558 GACAGTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.36
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:411401 original size:13 final size:13
Alignment explanation
Indices: 411383--411407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411373 ATAATCCCCT
411383 TGTATCGATACAA
1 TGTATCGATACAA
411396 TGTATCGATACA
1 TGTATCGATACA
411408 GAGAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:417395 original size:51 final size:51
Alignment explanation
Indices: 417323--417441 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
417313 TGAAAATAAT
* *
417323 GGGGTTGGAGTGTCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCC
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
* * **
417374 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGTT
1 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
417425 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
417442 TCAGAAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCC
Found at i:417498 original size:28 final size:28
Alignment explanation
Indices: 417425--417500 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
417415 AAATAAAGTT
*
417425 GGGGTTGGAGTATCCCCTCA-GAAATAAC
1 GGGGTTGGAGTATCCCC-GATGAAATAAC
*
417453 AGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
417481 GGGGTTGGAATATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
417501 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:417546 original size:51 final size:51
Alignment explanation
Indices: 417484--417599 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
417474 AAATAACGGG
* * *
417484 GTTGGAATATCCCCGATTGTGAAAAATTTGTGTTTTAAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
* * * * *
417535 GTTGGAGTATCCTCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
417586 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
417600 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
Found at i:417618 original size:79 final size:78
Alignment explanation
Indices: 417535--417836 Score: 388
Period size: 79 Copynumber: 3.8 Consensus size: 78
417525 TAAAATCGGA
* * * * * *
417535 GTTGGAGTATCCTCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTAT-AAAAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCC
*
417600 TCGAAAATAATGGG
65 TCGAAAATAACGGG
*
417614 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCT
1 GTTGGAGTATCCCCGATTAT-AAAAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCC
*
417679 TCGGAAATAACGGG
65 TCGAAAATAACGGG
* * * * *
417693 GTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAAAAATAAAACCGAGGTTGGAGTGTCCCC
1 GTTGGAGTATCCCCGATTAT-AAAAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCC
417758 TCGAAAATAACGGG
65 TCGAAAATAACGGG
* * * * * *
417772 GTTGGAGTATCCCCGATTGTAAAAAGTCGGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATAAAAA-TTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCC
417837 GATCATGGAA
Statistics
Matches: 195, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
78 4 0.02
79 191 0.98
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (78 bp):
GTTGGAGTATCCCCGATTATAAAAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCCT
CGAAAATAACGGG
Found at i:417697 original size:158 final size:158
Alignment explanation
Indices: 417535--417835 Score: 435
Period size: 158 Copynumber: 1.9 Consensus size: 158
417525 TAAAATCGGA
* * ** * * *
417535 GTTGGAGTATCCTCGATTGTG-GAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAGA-AATTAATATTTTAAAAATAAAACCGAGGTTGGAGTATCCC
* *
417599 CTCGAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAA-TTGATGTTTTAAAAATAAAACCG
65 CTCGAAAATAACGGGGTTGGAGTATCCCCGATTAT-AAAAAGTCGATGTTTTAAAAATAAAACCG
*
417663 GGGTTGGAGTATCCCTTCGGAAATAACGGG
129 GAGTTGGAGTATCCCTTCGGAAATAACGGG
*
417693 GTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAAAAATAAAACCGAGGTTGGAGTGTCCCC
1 GTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAAAAATAAAACCGAGGTTGGAGTATCCCC
* * * *
417758 TCGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAGTCGGTGTTTTGAAAATAAAATCGGA
66 TCGAAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAGTCGATGTTTTAAAAATAAAACCGGA
417823 GTTGGAGTATCCC
131 GTTGGAGTATCCC
417836 CGATCATGGA
Statistics
Matches: 126, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
157 5 0.04
158 119 0.94
159 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (158 bp):
GTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAAAAATAAAACCGAGGTTGGAGTATCCCC
TCGAAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAGTCGATGTTTTAAAAATAAAACCGGA
GTTGGAGTATCCCTTCGGAAATAACGGG
Found at i:417833 original size:51 final size:50
Alignment explanation
Indices: 417772--417940 Score: 193
Period size: 51 Copynumber: 3.3 Consensus size: 50
417762 AAATAACGGG
417772 GTTGGAGTATCCCCGATTGTAAAAAGTCGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAAAA-TCGGTGTTTTGAAAATAAAATCGGA
* *
417823 GTTGGAGTATCCCCGATCATG-GAAAATGGGTGTTTT-AGAAATAAAATCGGA
1 GTTGGAGTATCCCCGAT--TGTAAAAATCGGTGTTTTGA-AAATAAAATCGGA
* * * *
417874 GTTGGAGTATCCCCGTTTAAG-AAAAATTGATGTTTTGAAAATAAAA-CTGA
1 GTTGGAGTATCCCCGATT--GTAAAAATCGGTGTTTTGAAAATAAAATCGGA
417924 GATTGGAGTATCCCCGA
1 G-TTGGAGTATCCCCGA
417941 GATGAAAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
49 1 0.01
50 5 0.05
51 90 0.87
52 5 0.05
53 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTAAAAATCGGTGTTTTGAAAATAAAATCGGA
Found at i:420066 original size:20 final size:20
Alignment explanation
Indices: 420041--420112 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
420031 GTCTGACATG
*
420041 TGTATCGATACAATG-AGCAA
1 TGTATCGATACAATGCA-AAA
420061 TGTATCGATACAATGCAAAA
1 TGTATCGATACAATGCAAAA
420081 TGTATCGATACAATGCAAAA
1 TGTATCGATACAATGCAAAA
420101 TGTATCGATACA
1 TGTATCGATACA
420113 TCTGGGTAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAATGCAAAA
Found at i:420169 original size:13 final size:13
Alignment explanation
Indices: 420151--420176 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420141 ACAAAGATCG
420151 ATGTATCGATACA
1 ATGTATCGATACA
420164 ATGTATCGATACA
1 ATGTATCGATACA
420177 TTGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:428741 original size:55 final size:55
Alignment explanation
Indices: 428648--429051 Score: 454
Period size: 55 Copynumber: 7.0 Consensus size: 55
428638 GATGCCTTTT
*
428648 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
* **
428703 CCTTTCAAAGCCCACACAAGTTGGTGCCATTTTCCAGTCCTCAAAGAATAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
428758 CCTTTTAAAGCCCACACACGTTGGTGGCATTTTCCAATCCTCAAAAGAGCAGGATC-
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC-AAAGAGCAGGA-CG
* *
428814 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
428869 TTTTTTCTTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTTAAAGAGCAGGACG
1 -----CCTT-TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
428930 CCTTTTCTTTCAAAGCCCGCACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACG
1 -C----CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
428990 CCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCATGACG
1 CCTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACG
429051 C
1 C
429052 TCTCTCCTTT
Statistics
Matches: 302, Mismatches: 26, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
54 3 0.01
55 99 0.33
56 50 0.17
57 2 0.01
59 1 0.00
60 54 0.18
61 93 0.31
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:428976 original size:121 final size:117
Alignment explanation
Indices: 428617--429051 Score: 527
Period size: 121 Copynumber: 3.8 Consensus size: 117
428607 CTCCTTTCAC
* *
428617 TTTT-CAGTCCTCAAAGAACAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 TTTTCCAGTCCTCAAAGAACAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTT
* *
428681 T-CAGTCCTCAAAGAGCAGGACG-CCTTTCAAAGCCCACACAAGTTGGTGCCA
65 TCCAATCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
428732 TTTTCCAGTCCTCAAAGAATAGGACGCC---T--TTT-AAAGCCCACACACGTTGGTGGCATTTT
1 TTTTCCAGTCCTCAAAGAACAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
*
428791 CCAATCCTCAAAAGAGCAGGA-TCCCTTTCAAAGCCCACACAAGTTGGTGGCA
66 CCAATCCTC-AAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
428843 TTTTCCAATCCTCAAAGAGCAGGATG-TTTTTTCTTCTCAAAGCCCACACAAGTTGGTGGCATTT
1 TTTTCCAGTCCTCAAAGAACAGGACGCCTTTTCCTT-TCAAAGCCCACACAAGTTGGTGGCATTT
* *
428907 TCCAATCCTTAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCGCACAAGTTGGTGGCA
65 TCCAATCCTCAAAGAGCAGGACGCC----CTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
428964 TTTTCCAGTCCTCAAA-AAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CT
1 TTTTCCAGTCCTCAAAGAA-CAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
* *
429027 TCCTAGTCCTCAAAGAGCATGACGC
65 TCC-AATCCTCAAAGAGCAGGACGC
429052 TCTCTCCTTT
Statistics
Matches: 274, Mismatches: 27, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
109 3 0.01
110 29 0.11
111 64 0.23
113 2 0.01
115 6 0.02
116 33 0.12
117 36 0.13
120 5 0.02
121 90 0.33
122 6 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (117 bp):
TTTTCCAGTCCTCAAAGAACAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
CCAATCCTCAAAGAGCAGGACGCCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:429051 original size:61 final size:60
Alignment explanation
Indices: 428617--429062 Score: 489
Period size: 61 Copynumber: 7.6 Consensus size: 60
428607 CTCCTTTCAC
* * *
428617 TTTT-CAGTCCTCAAAGAACAGGATGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
428677 CCTTT-CAGTCCTCAAAGAGCAGGACG-----CCTTTCAAAGCCCACACAAGTTGGTGCCA
1 -TTTTCCAGTCCTCAAAGAGCAGGACGCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
** *
428732 TTTTCCAGTCCTCAAAGAATAGGACGC--CT--TTT-AAAGCCCACACACGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
428787 TTTTCCAATCCTCAAAAGAGCAGGA----TC-CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTC-AAAGAGCAGGACGCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
428843 TTTTCCAATCCTCAAAGAGCAGGATGTTTTTTCTTCTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTCTCCTT-TCAAAGCCCACACAAGTTGGTGGCA
* * * *
428904 TTTTCCAATCCTTAAAGAGCAGGACGCCTT-TTCTTTCAAAGCCCGCACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
428964 TTTTCCAGTCCTCAAAAAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
429025 -CTTCCTAGTCCTCAAAGAGCATGACGCTCTCTCCTTTC
1 TTTTCC-AGTCCTCAAAGAGCAGGACGCT-TCTCCTTTC
429063 GCCTTTTTGT
Statistics
Matches: 337, Mismatches: 29, Indels: 38
0.83 0.07 0.09
Matches are distributed among these distances:
54 4 0.01
55 94 0.28
56 47 0.14
59 1 0.00
60 60 0.18
61 129 0.38
62 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (60 bp):
TTTTCCAGTCCTCAAAGAGCAGGACGCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:429212 original size:61 final size:60
Alignment explanation
Indices: 429090--429215 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 60
429080 GAGCAGGATG
* *
429090 CCTTTTAAAGCCCACACAGGTTGGTGGCACCTTCAGTCTTCAAAGAGTAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCTTCAAAGAGCAGGACGCCTTCT
*
429150 CCTTTTAAAGCCCATACAAGTTGGTGGCA-CTTCCTAGTCTTCAAAGAGCAGGACG-CTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C-AGTCTTCAAAGAGCAGGACGCCT-TCT
429211 CCTTT
1 CCTTT
429216 CGCCTTTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
59 3 0.05
60 30 0.50
61 27 0.45
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCTTCAAAGAGCAGGACGCCTTCT
Found at i:429249 original size:154 final size:154
Alignment explanation
Indices: 428936--429356 Score: 675
Period size: 154 Copynumber: 2.7 Consensus size: 154
428926 GACGCCTTTT
* * * ** *
428936 CTTTCAAAGCCCGCACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACGCCTTCTCCTTT
1 CTTTTAAAGCCCACACAGGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
*
429001 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCATGACGCTCTCTCCTTTCGCC
65 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCC
*
429066 TTTTTGTCCTCAAAGAGCAGGATGC
130 TTTTTATCCTCAAAGAGCAGGATGC
* *
429091 CTTTTAAAGCCCACACAGGTTGGTGGCACCTTCAGTCTTCAAAGAGTAGGACGCCTTCTCCTTTT
1 CTTTTAAAGCCCACACAGGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
* *
429156 AAAGCCCATACAAGTTGGTGGCACTTCCTAGTCTTCAAAGAGCAGGACGCTCTCTCCTTTCGCCT
66 AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCT
429221 TTTTATCCTCAAAGAGCAGGATGC
131 TTTTATCCTCAAAGAGCAGGATGC
*
429245 CTTTTAAAGCCCACACAAGG-TGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTT
1 CTTTTAAAGCCCACAC-AGGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
*
429309 TAAAGCCCACACAAGTTGGTGGCACTT-TTCAGTCCTCAAAGAGCAGGA
65 TAAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCCTCAAAGAGCAGGA
429357 TGCTTTCATT
Statistics
Matches: 246, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
153 1 0.00
154 215 0.87
155 30 0.12
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (154 bp):
CTTTTAAAGCCCACACAGGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCT
TTTTATCCTCAAAGAGCAGGATGC
Found at i:429375 original size:61 final size:59
Alignment explanation
Indices: 429226--429479 Score: 313
Period size: 61 Copynumber: 4.3 Consensus size: 59
429216 CGCCTTTTTA
* * *
429226 TCCTCAAAGAGCAGGATGC---CTTTT-AAAGCCCACACAAGGTGGTGGCAC-CTTCAG
1 TCCTCAAAGAGCAGGACGCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAG
429280 TCCTCAAAGAGCAGGACGCCTTCTTCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAG
1 TCCTCAAAGAGCAGGACG-C-T-TTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAG
* * * *
429341 TCCTCAAAGAGCAGGATGCTTTCATTTTGCAAAGCCGACACAAGTTGGTGGCACCTTCCAG
1 TCCTCAAAGAGCAGGACGCTTTC-TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAG
* * *
429402 TCCTCAAAGGGTAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAG
1 TCCTCAAAGAGCAGGACG-C-TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAG
429463 TCCTCAAAGAGCAGGAC
1 TCCTCAAAGAGCAGGAC
429480 ACACTTCTTT
Statistics
Matches: 172, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
54 17 0.10
55 1 0.01
58 3 0.02
59 5 0.03
60 29 0.17
61 108 0.63
62 5 0.03
63 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (59 bp):
TCCTCAAAGAGCAGGACGCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAG
Found at i:429442 original size:122 final size:115
Alignment explanation
Indices: 429226--429478 Score: 382
Period size: 122 Copynumber: 2.1 Consensus size: 115
429216 CGCCTTTTTA
429226 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGGTGGTGGCACCTTCAGTCCTCAAAGAG
1 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGGTGGTGGCACCTTCAGTCCTCAAAGAG
429291 CAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
66 CAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
* *
429341 TCCTCAAAGAGCAGGATGCTTTCATTTTGCAAAGCCGACACAAGTTGGTGGCACCTTCCAGTCCT
1 TCCTCAAAGAGCAGGATGC---C-TTTT--AAAGCCCACACAAGGTGGTGGCACCTT-CAGTCCT
* * *
429406 CAAAGGGTAGGACGCCTT-TTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAG
59 CAAAGAGCAGGACGCCTTCTTCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAG
429463 TCCTCAAAGAGCAGGA
1 TCCTCAAAGAGCAGGA
429479 CACACTTCTT
Statistics
Matches: 125, Mismatches: 5, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
115 19 0.15
118 1 0.01
119 4 0.03
121 32 0.26
122 69 0.55
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (115 bp):
TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGGTGGTGGCACCTTCAGTCCTCAAAGAG
CAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
Found at i:430431 original size:20 final size:20
Alignment explanation
Indices: 430385--430441 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
430375 ATAAATAGTA
*
430385 AATGTATCGATACATAAGTGT
1 AATGTATCGATACATTA-TGT
*
430406 --TGTATCGATACATTATTT
1 AATGTATCGATACATTATGT
*
430424 AATGTATCAATACATTAT
1 AATGTATCGATACATTAT
430442 ATCGATACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 15 0.48
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTATGT
Found at i:430519 original size:20 final size:19
Alignment explanation
Indices: 430490--430564 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
430480 TTTACCCAAA
*
430490 TGTATTGATACATTCTGCAT
1 TGTATCGATACATTCT-CAT
430510 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
* *
430530 TGTATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
430550 TGTATCGATACATTC
1 TGTATCGATACATTC
430565 GGGCATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.94
21 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:431133 original size:23 final size:24
Alignment explanation
Indices: 431084--431133 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
431074 ATTCCCGTAG
*
431084 CTCCAAAAACCACCACCAAAGAAC
1 CTCCAAAAACCACCACCAAACAAC
* *
431108 CTCCAAAAA-CACCCCCAAACAGC
1 CTCCAAAAACCACCACCAAACAAC
431131 CTC
1 CTC
431134 TTCCTTAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.44, C:0.46, G:0.04, T:0.06
Consensus pattern (24 bp):
CTCCAAAAACCACCACCAAACAAC
Found at i:432899 original size:51 final size:51
Alignment explanation
Indices: 432841--433005 Score: 165
Period size: 51 Copynumber: 3.2 Consensus size: 51
432831 TTCATCTCGA
** * *
432841 GGATACTCCAA-TCCCGATTTTATTTTCAAAACGTCAATTTTTCTTAATCGG
1 GGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTTCCATAATCGG
* * * * *
432892 TGATACTCAAACTCCGATTTT-TTTTCTAAAATACCCATTTTCCATGATCGG
1 GGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTCCATAATCGG
* * * *
432943 GGATACTCCAACTCCGATTTTATTTCCAAAACACTAACTTTT-TATAATCGA
1 GGATACTCCAACTCCGATTTTATTTTCAAAACACCAA-TTTTCCATAATCGG
432994 GGATACTCCAAC
1 GGATACTCCAAC
433006 CCCGTTATTT
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
50 5 0.05
51 78 0.85
52 9 0.10
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCCATAATCGG
Found at i:433077 original size:79 final size:79
Alignment explanation
Indices: 432941--433242 Score: 389
Period size: 79 Copynumber: 3.8 Consensus size: 79
432931 TTCCATGATC
* * * *
432941 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAACTTT-TTATAATCGAGGATACTCCAA
1 GGGGATACTCCAACGCCGATTTTATTTCTAAAACACCAA-TTTCTCATAATCGAGGATACTCCAA
433005 CCCCGTTA-TTTCTGA
65 CCCCGTTATTTTC-GA
* * ** *
433020 GGGGACACTCCAAC-CACGATTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACGC-CGATTTTATTTCTAAAACACCAATTTCTCATAATCGAGGATACTCCAA
433084 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * *
433099 GGGGATACTCCAACGCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGAGGATACTCCAAC
1 GGGGATACTCCAACGCCGATTTTATTTCTAAAACACCAATTTCTCATAATCGAGGATACTCCAAC
433164 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * *
433178 GGGGATACTCCAAC-CTCGGTTTTATTTCTAAAACACCAA-TTCTCTACAATCGGGGATACTCCA
1 GGGGATACTCCAACGC-CGATTTTATTTCTAAAACACCAATTTCTC-ATAATCGAGGATACTCCA
433241 AC
64 AC
433243 TCCGATTTTA
Statistics
Matches: 201, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
78 9 0.04
79 187 0.93
80 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACGCCGATTTTATTTCTAAAACACCAATTTCTCATAATCGAGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:433151 original size:158 final size:158
Alignment explanation
Indices: 432941--433242 Score: 450
Period size: 158 Copynumber: 1.9 Consensus size: 158
432931 TTCCATGATC
*
432941 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAACTTTTTATAATCGAGGATACTCCAAC
1 GGGGATACTCCAACGCCGATTTTATTTCCAAAACACTAACTTTTTATAATCGAGGATACTCCAAC
* ** *
433006 CCCGTTA-TTTCTGAGGGGACACTCCAACCACGATTTTATTTCTAAAATATTAATT-TCTCATAA
66 CCCGTTATTTTC-GAGGGGACACTCCAACCACGATTTTATTTCTAAAACACCAATTCTCT-ACAA
433069 TCGGGGATACTCCAACCCCGTTATTTTCGA
129 TCGGGGATACTCCAACCCCGTTATTTTCGA
* *
433099 GGGGATACTCCAACGCCGGTTTTATTTCTAAAACA-TCAA-TTTTTCATAATCGAGGATACTCCA
1 GGGGATACTCCAACGCCGATTTTATTTCCAAAACACT-AACTTTTT-ATAATCGAGGATACTCCA
* * *
433162 ACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTCTCTACAA
64 ACCCCGTTATTTTCGAGGGGACACTCCAACCACGATTTTATTTCTAAAACACCAATTCTCTACAA
433227 TCGGGGATACTCCAAC
129 TCGGGGATACTCCAAC
433243 TCCGATTTTA
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
157 6 0.05
158 117 0.90
159 7 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACGCCGATTTTATTTCCAAAACACTAACTTTTTATAATCGAGGATACTCCAAC
CCCGTTATTTTCGAGGGGACACTCCAACCACGATTTTATTTCTAAAACACCAATTCTCTACAATC
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:433254 original size:51 final size:51
Alignment explanation
Indices: 433178--433294 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
433168 TTATTTTCGA
*
433178 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAA-TTCTCTACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAATTTCTC-ACAATC
* * * *
433229 GGGGATACTCCAA-CTCCGATTTTATTTTTAAAACACTAATTTTTCACAGTC
1 GGGGATACTCCAACCT-CGATTTTATTTCTAAAACACCAATTTCTCACAATC
*
433280 GGGGATATTCCAACC
1 GGGGATACTCCAACC
433295 CCGTTATTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 2 0.04
51 50 0.88
52 5 0.09
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAATTTCTCACAATC
Found at i:433314 original size:28 final size:28
Alignment explanation
Indices: 433281--433353 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
433271 TTCACAGTCG
*
433281 GGGATATTCCAACCCCGTTATTTCATC-AA
1 GGGATACTCCAACCCCGTTATTTC--CGAA
433310 -GGATACTCCAACCCCGTTATTTCCGAA
1 GGGATACTCCAACCCCGTTATTTCCGAA
433337 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
433354 GCTTTATTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 1 0.02
27 2 0.05
28 38 0.93
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCGAA
Found at i:433385 original size:158 final size:158
Alignment explanation
Indices: 433150--433488 Score: 387
Period size: 158 Copynumber: 2.1 Consensus size: 158
433140 TTTCATAATC
* * * * *
433150 GAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACC
1 GAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAACACC
* * ** * * * *
433215 AATTCTCTACAATCGGGGATACTCCAACTCC-GATTTTATTTTTAAAACACTAATTTTTCACAGT
66 AATTCTCTACAATCAGGGATACTCCAACCCCAG-CCTAATTTCTAAAACACTAATTTCTCACAAT
* *
433279 CGGGGATATTCCAACCCCGTTATTTCATCA
130 CGGGGACACTCCAACCCCGTTATTT-ATCA
* **
433309 -AGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAATATT
1 GAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAACACC
* * * * *
433373 GATT-TCTCACAATCAGGGATACTTCAACCCCAGCCTAATTTCTAAAATATTGATTTCTCACAAT
66 AATTCTCT-ACAATCAGGGATACTCCAACCCCAGCCTAATTTCTAAAACACTAATTTCTCACAAT
* *
433437 CGGGGACACTCCAACCCCGTTATTTTTGA
130 CGGGGACACTCCAACCCCGTTATTTATCA
* *
433466 GGGGATACTTCAACCCCGTTATT
1 GAGGATACTCCAACCCCGTTATT
433489 ATCTCCAAAA
Statistics
Matches: 150, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
157 5 0.03
158 144 0.96
159 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (158 bp):
GAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAACACC
AATTCTCTACAATCAGGGATACTCCAACCCCAGCCTAATTTCTAAAACACTAATTTCTCACAATC
GGGGACACTCCAACCCCGTTATTTATCA
Found at i:433401 original size:51 final size:51
Alignment explanation
Indices: 433336--433455 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 51
433326 TTATTTCCGA
* *
433336 AGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC
1 AGGGATACTCCAACCCCGGCCTAATTTCCAAAATATTGATTTCTCACAATC
* * *
433387 AGGGATACTTCAACCCCAGCCTAATTTCTAAAATATTGATTTCTCACAATC
1 AGGGATACTCCAACCCCGGCCTAATTTCCAAAATATTGATTTCTCACAATC
* *
433438 GGGGACACTCCAACCCCG
1 AGGGATACTCCAACCCCG
433456 TTATTTTTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (51 bp):
AGGGATACTCCAACCCCGGCCTAATTTCCAAAATATTGATTTCTCACAATC
Found at i:439501 original size:79 final size:79
Alignment explanation
Indices: 439360--439706 Score: 207
Period size: 79 Copynumber: 4.4 Consensus size: 79
439350 CGGGCATAAC
* * * * *
439360 AACACGGTTGGAGTATCCCCGATTATGGAAAATCGGTATTCTGGAAATAACATCAGGGTTGGAGT
1 AACAGGGTTGGAGTATCCCCGATTATAGAAAATCGGCATTCTGAAAATAACATCAGGATTGGAGT
* *
439425 ATTCTCTC-AGAAAT
66 ATCCCCTCGA-AAAT
* * * *
439439 AACAGGGTTAGAGTATCCCTGATTATAGAAAATTGGCATTTTGAAAATATA-ATC-GAGATTGGA
1 AACAGGGTTGGAGTATCCCCGATTATAGAAAATCGGCATTCTGAAAATA-ACATCAG-GATTGGA
439502 GTATCCCCTCGAAAAT
64 GTATCCCCTCGAAAAT
* * * * * * * * *
439518 AACAGGGATGGAGTATCCCCAATTGTGGAAATTCGAAGC-TT-T-AGAAATAAAACCGGGGTTGG
1 AACAGGGTTGGAGTATCCCCGATTATAGAAAATCG--GCATTCTGA-AAATAACATCAGGATTGG
*
439580 AGTATCCCCGAC-AAAAT
63 AGTATCCCC-TCGAAAAT
* * * *** * *
439597 AACGGGGTTAGAGTATCCCCAATTAT-GAAAAATCAATATT-TTAGAAATAA-AGTC-GAGTTTG
1 AACAGGGTTGGAGTATCCCCGATTATAG-AAAATCGGCATTCTGA-AAATAACA-TCAG-GATTG
*
439658 GAGTATCCTCTCGAAAAT
62 GAGTATCCCCTCGAAAAT
* *
439676 AA-TGGGATTGGAGTATCCTCGATTAT-GAAAA
1 AACAGGG-TTGGAGTATCCCCGATTATAGAAAA
439707 ATTGATGTTT
Statistics
Matches: 214, Mismatches: 38, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
78 17 0.08
79 189 0.88
80 6 0.03
81 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (79 bp):
AACAGGGTTGGAGTATCCCCGATTATAGAAAATCGGCATTCTGAAAATAACATCAGGATTGGAGT
ATCCCCTCGAAAAT
Found at i:439659 original size:158 final size:157
Alignment explanation
Indices: 439435--439748 Score: 395
Period size: 158 Copynumber: 2.0 Consensus size: 157
439425 ATTCTCTCAG
** *
439435 AAATAACAGGGTTAGAGTATCCCTGATTATAGAAAATTGGCATTTTGAAAATATAATCGAGATTG
1 AAATAACAGGGTTAGAGTATCCCCAATTATAGAAAAAT-GCATTTTGAAAATATAATCGAGATTG
* *
439500 GAGTATCCCCTCGAAAATAACAGGGA-TGGAGTATCCCCAATTGTG-GAAATTCGAAGCTTTAGA
65 GAGTATCCCCTCGAAAATAA-AGGGATTGGAGTATCCCCAATTATGAAAAATT-GAAGCTTTAGA
439563 AATAAAACCGGGGTTGGAGTATCCCCGACA
128 AATAAAACCGGGGTTGGAGTATCCCCGACA
* * *
439593 AAATAACGGGGTTAGAGTATCCCCAATTAT-GAAAAAT-CAATATTTTAGAAATA-AAGTCGAGT
1 AAATAACAGGGTTAGAGTATCCCCAATTATAGAAAAATGC-AT-TTTGA-AAATATAA-TCGAGA
* * * * * * *
439655 TTGGAGTATCCTCTCGAAAATAATGGGATTGGAGTATCCTCGATTATGAAAAATTGATGTTTTGG
62 TTGGAGTATCCCCTCGAAAATAAAGGGATTGGAGTATCCCCAATTATGAAAAATTGAAGCTTTAG
439720 AAATAAAACCGGGGTTGGAGTATCCCCGA
127 AAATAAAACCGGGGTTGGAGTATCCCCGA
439749 GACGAAAAAT
Statistics
Matches: 135, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
155 1 0.01
156 2 0.01
157 16 0.12
158 111 0.82
159 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (157 bp):
AAATAACAGGGTTAGAGTATCCCCAATTATAGAAAAATGCATTTTGAAAATATAATCGAGATTGG
AGTATCCCCTCGAAAATAAAGGGATTGGAGTATCCCCAATTATGAAAAATTGAAGCTTTAGAAAT
AAAACCGGGGTTGGAGTATCCCCGACA
Found at i:439707 original size:79 final size:78
Alignment explanation
Indices: 439483--439745 Score: 253
Period size: 79 Copynumber: 3.3 Consensus size: 78
439473 GGCATTTTGA
* * * * *
439483 AAATATAATCGAGATTGGAGTATCCCCTCGAAAATAACAGGGA-TGGAGTATCCCCAATTGTGGA
1 AAATAAAACCGAGGTTGGAGTAT-CCCTCGAAAATAA-AGGGATTGGAGTATCCCCAATTATGAA
* *
439547 AATTCGAA-GCTTTAG
64 AAATC-AATGTTTTAG
* * * *
439562 AAATAAAACCGGGGTTGGAGTATCCC-CGACAAAATAACGGGGTTAGAGTATCCCCAATTATGAA
1 AAATAAAACCGAGGTTGGAGTATCCCTCG--AAAATAAAGGGATTGGAGTATCCCCAATTATGAA
*
439626 AAATCAATATTTTAG
64 AAATCAATGTTTTAG
** * * * *
439641 AAATAAAGTCGAGTTTGGAGTATCCTCTCGAAAATAATGGGATTGGAGTATCCTCGATTATGAAA
1 AAATAAAACCGAGGTTGGAGTATCC-CTCGAAAATAAAGGGATTGGAGTATCCCCAATTATGAAA
** *
439706 AATTGATGTTTTGG
65 AATCAATGTTTTAG
*
439720 AAATAAAACCGGGGTTGGAGTATCCC
1 AAATAAAACCGAGGTTGGAGTATCCC
439746 CGAGACGAAA
Statistics
Matches: 149, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
77 2 0.01
78 9 0.06
79 135 0.91
80 1 0.01
81 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (78 bp):
AAATAAAACCGAGGTTGGAGTATCCCTCGAAAATAAAGGGATTGGAGTATCCCCAATTATGAAAA
ATCAATGTTTTAG
Found at i:439773 original size:50 final size:50
Alignment explanation
Indices: 439714--439809 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
439704 AAAATTGATG
* * *
439714 TTTTGGAAATAAAACCGGGGTTGGAGTATCCCCGAGACGAAAAATCAATA
1 TTTTAGAAATAAAACCAGGGTTGGAGTATCCCCAAGACGAAAAATCAATA
* * *
439764 TTTTAGAAATAAAGCCAGGGTTGGAGTATCTCCAAGATGAAAAATC
1 TTTTAGAAATAAAACCAGGGTTGGAGTATCCCCAAGACGAAAAATC
439810 TATAAATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (50 bp):
TTTTAGAAATAAAACCAGGGTTGGAGTATCCCCAAGACGAAAAATCAATA
Found at i:442123 original size:13 final size:13
Alignment explanation
Indices: 442105--442131 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
442095 ATTGAAAAAC
442105 GTATCGATACAAT
1 GTATCGATACAAT
442118 GTATCGATACAAT
1 GTATCGATACAAT
442131 G
1 G
442132 AACAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:442142 original size:20 final size:20
Alignment explanation
Indices: 442113--442168 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
442103 ACGTATCGAT
*
442113 ACAATGTATCGATACAATGA
1 ACAATATATCGATACAATGA
*
442133 ACAATATATCAATACAATGA
1 ACAATATATCGATACAATGA
* *
442153 ATAATACATCGATACA
1 ACAATATATCGATACA
442169 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (20 bp):
ACAATATATCGATACAATGA
Found at i:450800 original size:20 final size:20
Alignment explanation
Indices: 450775--450872 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
450765 TTTTAACTAG
450775 ATGTATCAATACATTGAAAA
1 ATGTATCAATACATTGAAAA
450795 ATGTATCAATACATCTGGGTAAAAAGACAAA
1 ATGTATCAATACAT-T--G-----A-A-A-A
* *
450826 ATGTATCGATACATTGAAGA
1 ATGTATCAATACATTGAAAA
*
450846 ATGTATCGATACATTGAAAA
1 ATGTATCAATACATTGAAAA
450866 ATGTATC
1 ATGTATC
450873 GATATATCTG
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
20 41 0.64
21 1 0.02
22 1 0.02
23 2 0.03
28 2 0.03
29 1 0.02
30 2 0.03
31 14 0.22
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (20 bp):
ATGTATCAATACATTGAAAA
Found at i:450873 original size:20 final size:20
Alignment explanation
Indices: 450823--450876 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
450813 GTAAAAAGAC
450823 AAAATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
*
450843 AGAATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
450863 AAAATGTATCGATA
1 AAAATGTATCGATA
450877 TATCTGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:451888 original size:20 final size:20
Alignment explanation
Indices: 451855--451916 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
451845 ACTATCTCTT
* *
451855 ATGAAATAACGCATTTGTTG
1 ATGAAAGAATGCATTTGTTG
451875 ATGAATA-AATGCATTTGTTGG
1 ATGAA-AGAATGCATTTGTT-G
*
451896 ATGAAAGAATGCATTTATTG
1 ATGAAAGAATGCATTTGTTG
451916 A
1 A
451917 ATGATGTCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.35
Consensus pattern (20 bp):
ATGAAAGAATGCATTTGTTG
Found at i:451900 original size:21 final size:21
Alignment explanation
Indices: 451855--451920 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
451845 ACTATCTCTT
* *
451855 ATGAAATAACGCATTTGTT-G
1 ATGAAAGAATGCATTTGTTGG
451875 ATGAATA-AATGCATTTGTTGG
1 ATGAA-AGAATGCATTTGTTGG
* *
451896 ATGAAAGAATGCATTTATTGA
1 ATGAAAGAATGCATTTGTTGG
451917 ATGA
1 ATGA
451921 TGTCGCAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (21 bp):
ATGAAAGAATGCATTTGTTGG
Found at i:453773 original size:7 final size:8
Alignment explanation
Indices: 453757--453781 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
453747 ATAATACAAC
453757 TTTTATTT
1 TTTTATTT
453765 TTTTATTT
1 TTTTATTT
453773 TTTTATTT
1 TTTTATTT
453781 T
1 T
453782 ACCATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:453899 original size:22 final size:22
Alignment explanation
Indices: 453865--453906 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
453855 GAAAAAAATG
453865 TTTTCAATCTTTTCACTTTTCTC
1 TTTTCAATCTTTTCA-TTTTCTC
*
453888 TTTT-AATTTTTTCATTTTC
1 TTTTCAATCTTTTCATTTTC
453907 CCAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCAATCTTTTCATTTTCTC
Found at i:454139 original size:17 final size:16
Alignment explanation
Indices: 454117--454165 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
454107 GTTAAGTGCA
454117 TATTTATAAAATTATAT
1 TATTTATAAAATT-TAT
*
454134 TATTTATTAAATTTAT
1 TATTTATAAAATTTAT
*
454150 T-TTTATCATAATTTAT
1 TATTTAT-AAAATTTAT
454166 AAAAATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 5 0.18
16 11 0.39
17 12 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATAAAATTTAT
Found at i:457376 original size:2 final size:2
Alignment explanation
Indices: 457366--457398 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
457356 TTTTATAATG
*
457366 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
457399 AAACTTCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:458595 original size:20 final size:20
Alignment explanation
Indices: 458537--458588 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
458527 TCAAGTCATA
*
458537 TAGGTCAAAAGCTAAGTCACC
1 TAGGTCAAAA-CTAAGTTACC
* *
458558 TATGTCAAAACTGAGTTACC
1 TAGGTCAAAACTAAGTTACC
458578 TAGGTCAAAAC
1 TAGGTCAAAAC
458589 CTAGTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
TAGGTCAAAACTAAGTTACC
Found at i:462794 original size:13 final size:13
Alignment explanation
Indices: 462753--462805 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
462743 GCTATTGCAA
462753 ACAATGTATCGAT
1 ACAATGTATCGAT
462766 ACAA--T-TC-AT
1 ACAATGTATCGAT
462775 -C-ATGTATCGAT
1 ACAATGTATCGAT
462786 ACAATGTATCGAT
1 ACAATGTATCGAT
462799 ACAATGT
1 ACAATGT
462806 GCCATGTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 21 0.62
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:462795 original size:33 final size:33
Alignment explanation
Indices: 462753--462822 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 33
462743 GCTATTGCAA
462753 ACAATGTATCGATACAAT-T-CATCATGTATCGAT
1 ACAATGTATCGATACAATGTGC--CATGTATCGAT
462786 ACAATGTATCGATACAATGTGCCATGTATCGAT
1 ACAATGTATCGATACAATGTGCCATGTATCGAT
462819 ACAA
1 ACAA
462823 ACAGTGGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
33 33 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTGCCATGTATCGAT
Found at i:462895 original size:19 final size:19
Alignment explanation
Indices: 462851--462906 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
462841 CTGCCAGTTT
**
462851 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
462871 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
462890 CATGTATCGATACAATG
1 CATGTATCGATACAATG
462907 TATTGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:471624 original size:13 final size:13
Alignment explanation
Indices: 471584--471636 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
471574 CCATTACAAG
471584 CAATGTATCGATA
1 CAATGTATCGATA
471597 CAA--T-TC-AT-
1 CAATGTATCGATA
471605 C-ATGTATCGATA
1 CAATGTATCGATA
*
471617 CAATGTATCAATA
1 CAATGTATCGATA
471630 CAATGTA
1 CAATGTA
471637 CCATGTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:471624 original size:33 final size:33
Alignment explanation
Indices: 471584--471652 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
471574 CCATTACAAG
* *
471584 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCAATACAATGT-ACCATGTATCGATA
*
471617 CAATGTATCAATACAATGTACCATGTATCTATA
1 CAATGTATCAATACAATGTACCATGTATCGATA
471650 CAA
1 CAA
471653 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (33 bp):
CAATGTATCAATACAATGTACCATGTATCGATA
Found at i:471710 original size:20 final size:20
Alignment explanation
Indices: 471685--471735 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
471675 CAGTTTCATA
***
471685 TATCGATACAATTGTCCATG
1 TATCGATACAATTAAACATG
471705 TATCGATACAA-TAAACATG
1 TATCGATACAATTAAACATG
471724 TATCGATACAAT
1 TATCGATACAAT
471736 GTATCAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (20 bp):
TATCGATACAATTAAACATG
Found at i:474188 original size:18 final size:18
Alignment explanation
Indices: 474165--474200 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
474155 TTAACCTGTG
*
474165 GATGTATTAATAAATTAA
1 GATGTACTAATAAATTAA
*
474183 GATGTACTAATACATTAA
1 GATGTACTAATAAATTAA
474201 TGAAATGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
GATGTACTAATAAATTAA
Found at i:480108 original size:32 final size:33
Alignment explanation
Indices: 480067--480128 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
480057 TAGCCAAACT
*
480067 TGTATCGATACACAAAATA-TGTATCGATATAA
1 TGTATCGATACACAAAAAATTGTATCGATATAA
*
480099 TGTATCGATACATAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
480129 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATATAA
Found at i:482362 original size:21 final size:21
Alignment explanation
Indices: 482329--482378 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
482319 TTGCAAGTTG
*
482329 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
482351 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
482372 AAATAAA
1 AAATAAA
482379 AATTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:484196 original size:15 final size:15
Alignment explanation
Indices: 484176--484206 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
484166 TAAAAATATC
*
484176 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
484191 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
484206 C
1 C
484207 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:486276 original size:13 final size:13
Alignment explanation
Indices: 486258--486282 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486248 CATTTTTCTT
486258 TGTATCGATACAC
1 TGTATCGATACAC
486271 TGTATCGATACA
1 TGTATCGATACA
486283 GGGGGATTAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:488855 original size:13 final size:13
Alignment explanation
Indices: 488837--488862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488827 TACACAAAAT
488837 ATGTATCGATACA
1 ATGTATCGATACA
488850 ATGTATCGATACA
1 ATGTATCGATACA
488863 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:488862 original size:32 final size:33
Alignment explanation
Indices: 488821--488882 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
488811 GCCAAACTTT
*
488821 TATCGATACACAAAATA-TGTATCGATACAATG
1 TATCGATACACAAAAAATTGTATCGATACAATG
488853 TATCGATACACAAAAAATTGTATCGATACA
1 TATCGATACACAAAAAATTGTATCGATACA
488883 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (33 bp):
TATCGATACACAAAAAATTGTATCGATACAATG
Found at i:492949 original size:13 final size:13
Alignment explanation
Indices: 492931--492956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
492921 CAATTTTTTG
492931 TGTATCGATACAT
1 TGTATCGATACAT
492944 TGTATCGATACAT
1 TGTATCGATACAT
492957 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:493040 original size:20 final size:20
Alignment explanation
Indices: 492995--493067 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
492985 CTGCCAAGAA
***
492995 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
493016 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
493036 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
493056 ATGTATCGATAC
1 ATGTATCGATAC
493068 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:493068 original size:20 final size:20
Alignment explanation
Indices: 493015--493070 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
493005 ACATCTTTTT
*
493015 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
493035 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
493054 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
493071 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:493704 original size:21 final size:21
Alignment explanation
Indices: 493663--493706 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
493653 CTCCCCTTTA
* *
493663 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
493684 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
493705 TC
1 TC
493707 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:495529 original size:13 final size:13
Alignment explanation
Indices: 495511--495538 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
495501 ATAATCACCC
495511 TGTATCGATACAA
1 TGTATCGATACAA
495524 TGTATCGATACAA
1 TGTATCGATACAA
495537 TG
1 TG
495539 AAAAATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:495547 original size:20 final size:20
Alignment explanation
Indices: 495522--495560 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
495512 GTATCGATAC
495522 AATGTATCGATACAATGAAA
1 AATGTATCGATACAATGAAA
*
495542 AATGTATCGATACATTGAA
1 AATGTATCGATACAATGAA
495561 TTTCCAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:497624 original size:15 final size:15
Alignment explanation
Indices: 497604--497634 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
497594 ATTTCGTTTG
*
497604 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
497619 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
497634 G
1 G
497635 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:499467 original size:21 final size:21
Alignment explanation
Indices: 499438--499482 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
499428 AAGTTTTCAT
*
499438 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
499458 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
499480 TTT
1 TTT
499483 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:501703 original size:13 final size:13
Alignment explanation
Indices: 501685--501710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
501675 CAATTTTTTG
501685 TGTATCGATACAT
1 TGTATCGATACAT
501698 TGTATCGATACAT
1 TGTATCGATACAT
501711 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:506809 original size:21 final size:22
Alignment explanation
Indices: 506780--506823 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
506770 AACTATTACA
506780 ACATATGTATCGATACATTCAT
1 ACATATGTATCGATACATTCAT
506802 ACAT-TGTATCGATACATTCAT
1 ACATATGTATCGATACATTCAT
506823 A
1 A
506824 ACAAAACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
ACATATGTATCGATACATTCAT
Found at i:512609 original size:49 final size:48
Alignment explanation
Indices: 512549--512915 Score: 178
Period size: 49 Copynumber: 7.5 Consensus size: 48
512539 GTTATGATGA
* * *
512549 AAAGTACAAAACCAACCCTAAAAGACTTAATTTTGGTCGATTTTAATAG
1 AAAGTATAAAACTAACCCTAAAAGACTTAATTTTGGT-GATTTTGATAG
** * ** * *
512598 AAAGTATAAAACTAATGC-ACAAAGACTTGATTTTGGACAATTTTGACAA
1 AAAGTATAAAACTAACCCTA-AAAGACTTAATTTTGG-TGATTTTGATAG
*** * * * * * *
512647 AAAGTATAAAACTAATTGTAAAATACTTAGTTATGGTAATTTTTGACAA
1 AAAGTATAAAACTAACCCTAAAAGACTTAATTTTGGTGA-TTTTGATAG
** * * * * * *
512696 AAAGTATAAAA-TAAACATTTAAAGGCATGATTTTGCTTGATTTTAATAG
1 AAAGTATAAAACT-AACCCTAAAAGACTTAATTTTG-GTGATTTTGATAG
* * ** *
512745 TAAGTACT-AAACCAAAACTAAAAGACTTAATTTTGGTTGGTTTTGAT-G
1 AAAGTA-TAAAACTAACCCTAAAAGACTTAATTTTGG-TGATTTTGATAG
* * * *
512793 AAAGTACAAAAC-AACCCTAAGAA-ACTTTATTTTAGTTAGTTTTGAT-G
1 AAAGTATAAAACTAACCCTAA-AAGACTTAATTTTGGTGA-TTTTGATAG
* * *
512840 AAAAGTACAAAACTAACCCTAAAAGA-TTCAATTTTGGTTAGTTTTAAT-G
1 -AAAGTATAAAACTAACCCTAAAAGACTT-AATTTTGGTGA-TTTTGATAG
512889 AAA-TATTCAAAACTAACCCTAAAAGAC
1 AAAGTA-T-AAAACTAACCCTAAAAGAC
512916 GTAGTTTTCT
Statistics
Matches: 244, Mismatches: 55, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
46 1 0.00
47 26 0.11
48 35 0.14
49 178 0.73
50 4 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (48 bp):
AAAGTATAAAACTAACCCTAAAAGACTTAATTTTGGTGATTTTGATAG
Found at i:512835 original size:47 final size:48
Alignment explanation
Indices: 512762--512915 Score: 199
Period size: 49 Copynumber: 3.2 Consensus size: 48
512752 TAAACCAAAA
*
512762 CTAAAAGACTTAATTTTGGTTGGTTTTGATGAAAGTACAAAAC-AACC
1 CTAAAAGACTTAATTTTGGTTAGTTTTGATGAAAGTACAAAACTAACC
* *
512809 CTAAGAA-ACTTTATTTTAGTTAGTTTTGATGAAAAGTACAAAACTAACC
1 CTAA-AAGACTTAATTTTGGTTAGTTTTGATG-AAAGTACAAAACTAACC
*
512858 CTAAAAGA-TTCAATTTTGGTTAGTTTTAATGAAA-TATTCAAAACTAACC
1 CTAAAAGACTT-AATTTTGGTTAGTTTTGATGAAAGTA--CAAAACTAACC
512907 CTAAAAGAC
1 CTAAAAGAC
512916 GTAGTTTTCT
Statistics
Matches: 93, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
47 27 0.29
48 21 0.23
49 45 0.48
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (48 bp):
CTAAAAGACTTAATTTTGGTTAGTTTTGATGAAAGTACAAAACTAACC
Found at i:514436 original size:21 final size:20
Alignment explanation
Indices: 514383--514441 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
514373 CAACATTTTT
*
514383 TAAGCTAATGTATTGATATA
1 TAAGCTAATGTATTGATAAA
514403 TCAA--TGAATTGTATTGATAAAA
1 T-AAGCT-AA-TGTATTGAT-AAA
514425 TAAGCTAATGTATTGAT
1 TAAGCTAATGTATTGAT
514442 CCATCAGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 22 0.69
22 5 0.16
23 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (20 bp):
TAAGCTAATGTATTGATAAA
Found at i:514587 original size:17 final size:18
Alignment explanation
Indices: 514553--514592 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
514543 TTTAATTTTC
*
514553 TAAATGTGTTCATTTTAT
1 TAAATGTGTTCATCTTAT
514571 TAAATGTGTTCA-CTTAT
1 TAAATGTGTTCATCTTAT
514588 TAAAT
1 TAAAT
514593 TTAGTGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (18 bp):
TAAATGTGTTCATCTTAT
Found at i:519970 original size:77 final size:78
Alignment explanation
Indices: 519755--519993 Score: 234
Period size: 78 Copynumber: 3.1 Consensus size: 78
519745 TATAAAGTTG
* * * * *
519755 TAATGCAAAAATGACTAAAGTTACTTTAAAGACACACCTTTGACAT-AGAAGTGCTAATATGATC
1 TAATGCAAAAATAACTAAAATAACCTTAAAGACATA-CTTTGACATGA-AAGTGCTAATATGATC
*
519819 CTAAAGACTTAGATT
64 CTAAAGACTCAGATT
* * * * * * * *
519834 CAATGCAAAAA-AAGCTCAAATGAGCTTATAGACATATTTTGACATGAAAGTCCTAATATGATCT
1 TAATGCAAAAATAA-CTAAAATAACCTTAAAGACATACTTTGACATGAAAGTGCTAATATGATCC
*
519898 TAGAGACTCA-ATTT
65 TAAAGACTCAGA-TT
* *
519912 TAATGCAAAAATTACTAAAATAACCTTAAAGGCATA-TTTGACATGAAAGTGCTAATATGATCCT
1 TAATGCAAAAATAACTAAAATAACCTTAAAGACATACTTTGACATGAAAGTGCTAATATGATCCT
* * *
519976 AAAAACTAAGGTT
66 AAAGACTCAGATT
519989 TAATG
1 TAATG
519994 TGGAATTTAT
Statistics
Matches: 128, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
77 40 0.31
78 61 0.48
79 27 0.21
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (78 bp):
TAATGCAAAAATAACTAAAATAACCTTAAAGACATACTTTGACATGAAAGTGCTAATATGATCCT
AAAGACTCAGATT
Found at i:521629 original size:19 final size:19
Alignment explanation
Indices: 521604--521687 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
521594 ATTTCAATGA
*
521604 TTTGTATCGATACATGAGT
1 TTTGTATCGATACATAAGT
*
521623 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
521638 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
521655 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
521674 TTTGTATCGATACA
1 TTTGTATCGATACA
521688 ATGTATTGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 1 0.02
19 43 0.75
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:521643 original size:13 final size:13
Alignment explanation
Indices: 521625--521649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
521615 ACATGAGTGT
521625 TGTATCGATACAA
1 TGTATCGATACAA
521638 TGTATCGATACA
1 TGTATCGATACA
521650 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:521647 original size:32 final size:32
Alignment explanation
Indices: 521606--521668 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
521596 TTCAATGATT
*
521606 TGTATCGATACATGAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
521638 TGTATCGATACATAAGTTTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
521669 TAAGTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:521816 original size:52 final size:52
Alignment explanation
Indices: 521736--521885 Score: 230
Period size: 52 Copynumber: 2.9 Consensus size: 52
521726 ATACATTACT
***
521736 CAAATGTATCGATACACTGAT-CTTTGTATCGATACATGCAGGCAAATTTGCC
1 CAAATGTATCGATACACT-ATGAAATGTATCGATACATGCAGGCAAATTTGCC
**
521788 CAAATGTATCGATACACTATGAAATGTATCGATACATAAAGGCAAATTTGCC
1 CAAATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCC
*
521840 CAGATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAA
1 CAAATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAA
521886 ATTTCATATT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (52 bp):
CAAATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCC
Found at i:529074 original size:20 final size:20
Alignment explanation
Indices: 529028--529074 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
529018 ACAAGGGGGG
*
529028 AAGGTATTACTATAATTTTC
1 AAGGTATTACTATAATGTTC
**
529048 ATTGTATTGA-TATAATGTTC
1 AAGGTATT-ACTATAATGTTC
529068 AAGGTAT
1 AAGGTAT
529075 CAATACAATG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (20 bp):
AAGGTATTACTATAATGTTC
Found at i:536208 original size:13 final size:13
Alignment explanation
Indices: 536190--536215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536180 TACACAAAGT
536190 ATGTATCGATACA
1 ATGTATCGATACA
536203 ATGTATCGATACA
1 ATGTATCGATACA
536216 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:536213 original size:32 final size:33
Alignment explanation
Indices: 536172--536235 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
536162 TAGCCAAACT
**
536172 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
536204 TGTATCGATACATAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
536236 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:540283 original size:15 final size:15
Alignment explanation
Indices: 540263--540293 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
540253 TAAAAATGTC
*
540263 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
540278 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
540293 C
1 C
540294 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:544956 original size:13 final size:13
Alignment explanation
Indices: 544938--544963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
544928 TACACAAAGT
544938 ATGTATCGATACA
1 ATGTATCGATACA
544951 ATGTATCGATACA
1 ATGTATCGATACA
544964 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:544961 original size:32 final size:33
Alignment explanation
Indices: 544920--544983 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
544910 TAGCCAAACT
**
544920 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
544952 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
544984 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:545050 original size:20 final size:19
Alignment explanation
Indices: 545016--545055 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
545006 AGCTATATTT
*
545016 TCAAATATTTATCGATACA
1 TCAAAAATTTATCGATACA
545035 TCAAAAATTGTATCGATACA
1 TCAAAAATT-TATCGATACA
545055 T
1 T
545056 TCACACGGGA
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:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (19 bp):
TCAAAAATTTATCGATACA
Found at i:547831 original size:73 final size:73
Alignment explanation
Indices: 547738--547877 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 73
547728 ACATATCCTT
* * ** * *
547738 AAGTACATCTTTGATATGAAAATATCTTGATAACTTTAAAAGACTCGATAATGGGATGAAATAAC
1 AAGTACATCTTCGACATGAAAATATCTTGATAACCCTAAAAGACTCGATAATGAGATGAAACAAC
547803 TAGCAATA
66 TAGCAATA
* * * * * *
547811 AAGTGCATCTTCGACATGAAAGTATCTTGGTGACCCTAAGAGACTTGATAATGAGATGAAACAAC
1 AAGTACATCTTCGACATGAAAATATCTTGATAACCCTAAAAGACTCGATAATGAGATGAAACAAC
547876 TA
66 TA
547878 TCGCATCCTA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 55 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (73 bp):
AAGTACATCTTCGACATGAAAATATCTTGATAACCCTAAAAGACTCGATAATGAGATGAAACAAC
TAGCAATA
Found at i:554869 original size:24 final size:24
Alignment explanation
Indices: 554840--554888 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
554830 TTAGCATGTG
554840 CTAGTCTCAAAAGTAATTACTTTA
1 CTAGTCTCAAAAGTAATTACTTTA
554864 CTAGTCTCAAAAGTAATTACTTTA
1 CTAGTCTCAAAAGTAATTACTTTA
554888 C
1 C
554889 AATCATACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (24 bp):
CTAGTCTCAAAAGTAATTACTTTA
Found at i:560642 original size:19 final size:19
Alignment explanation
Indices: 560618--560673 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
560608 TTTATCGATA
* *
560618 CATTGTATCAATACATGTT
1 CATTGTATCGATACATGCT
*
560637 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
560656 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
560674 AAACTAGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:569615 original size:19 final size:20
Alignment explanation
Indices: 569573--569623 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
569563 CATCTAGATA
569573 TATCGATACAT-TACACTTTG
1 TATCGATACATGTACAC-TTG
*
569593 TATCGATACATGTTCAC-TG
1 TATCGATACATGTACACTTG
569612 TATCGATACATG
1 TATCGATACATG
569624 AAACTGGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
20 11 0.38
21 4 0.14
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (20 bp):
TATCGATACATGTACACTTG
Found at i:574438 original size:28 final size:27
Alignment explanation
Indices: 574401--574453 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
574391 ATTCGATTGG
574401 AAAAATCTAATT-ACAAATTCTACATGT
1 AAAAATCTAATTGA-AAATTCTACATGT
574428 AAAAATACTAATTGAAAATTCTACAT
1 AAAAAT-CTAATTGAAAATTCTACAT
574454 ATGATTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 6 0.25
28 17 0.71
29 1 0.04
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (27 bp):
AAAAATCTAATTGAAAATTCTACATGT
Found at i:574669 original size:25 final size:27
Alignment explanation
Indices: 574628--574704 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 27
574618 GTGTAATTAA
* * *
574628 AAAGTTTAGTTAGAA-TTCTGTGTA-G
1 AAAGTTTAATTAAAATTTCTATGTACG
*
574653 AAAGTTTAATTAAAATTTTTATGTACG
1 AAAGTTTAATTAAAATTTCTATGTACG
*
574680 AAAGTTTAATTAAAAATTTATATGT
1 AAAGTTTAATT-AAAATTTCTATGT
574705 GAAAATTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 13 0.30
26 7 0.16
27 12 0.27
28 12 0.27
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (27 bp):
AAAGTTTAATTAAAATTTCTATGTACG
Found at i:574699 original size:26 final size:26
Alignment explanation
Indices: 574648--574700 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
574638 TAGAATTCTG
*
574648 TGTAGAAAGTTTAATTAAAATTTTTA
1 TGTAGAAAGTTTAATTAAAATATTTA
574674 TGTACGAAAGTTTAATTAAAA-ATTTA
1 TGTA-GAAAGTTTAATTAAAATATTTA
574700 T
1 T
574701 ATGTGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (26 bp):
TGTAGAAAGTTTAATTAAAATATTTA
Found at i:574704 original size:28 final size:27
Alignment explanation
Indices: 574648--574861 Score: 125
Period size: 26 Copynumber: 7.9 Consensus size: 27
574638 TAGAATTCTG
*
574648 TGTAGAAAGTTTAATT-AAAATTTTTA
1 TGTAGAAAGTTTAATTAAAAATTTATA
574674 TGTACGAAAGTTTAATTAAAAATTTATA
1 TGTA-GAAAGTTTAATTAAAAATTTATA
* * * *
574702 TGT-GAAA-ATTAATTTGAAAATCTACA
1 TGTAGAAAGTTTAA-TTAAAAATTTATA
* * * *
574728 TATA-AAAGCTTAATTGAAAATTCA-A
1 TGTAGAAAGTTTAATTAAAAATTTATA
* *
574753 GTGT-GAAAATTTAATTAAAAATTCTACA
1 -TGTAGAAAGTTTAATTAAAAATT-TATA
* * * *
574781 TGGAAAAAAGTTTTCAATAAAAAATTTATG
1 T-GTAGAAAG-TTT-AATTAAAAATTTATA
* * *
574811 TGTAAAAAGTTTGATAAAAAATTTTATA
1 TGTAGAAAGTTTAATTAAAAA-TTTATA
* * *
574839 TGCACAAAGTTTAATTTAAAATT
1 TGTAGAAAGTTTAATTAAAAATT
574862 CTATTTGTGG
Statistics
Matches: 146, Mismatches: 28, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
25 5 0.03
26 49 0.34
27 28 0.19
28 38 0.26
29 10 0.07
30 6 0.04
31 10 0.07
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (27 bp):
TGTAGAAAGTTTAATTAAAAATTTATA
Found at i:574772 original size:38 final size:38
Alignment explanation
Indices: 574679--574773 Score: 95
Period size: 38 Copynumber: 2.4 Consensus size: 38
574669 TTTTATGTAC
* * *
574679 GAAAGTTTAATTAAAAATTTATATGTGAAAATTAATTT
1 GAAAATTTAATTAAAAACTTATATGTGAAAATTAATGT
* *
574717 GAAAATCTACATATAAAAGCTTA-AT-TGAAAATTCAAGTGT
1 GAAAATTTA-AT-TAAAAACTTATATGTGAAAATT-AA-TGT
574757 GAAAATTTAATTAAAAA
1 GAAAATTTAATTAAAAA
574774 TTCTACATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
38 20 0.43
39 8 0.17
40 18 0.39
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (38 bp):
GAAAATTTAATTAAAAACTTATATGTGAAAATTAATGT
Found at i:578807 original size:13 final size:13
Alignment explanation
Indices: 578789--578816 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
578779 TACAAAACTT
578789 ATGTATCGATACA
1 ATGTATCGATACA
578802 ATGTATCGATACA
1 ATGTATCGATACA
578815 AT
1 AT
578817 ACTTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:578812 original size:32 final size:33
Alignment explanation
Indices: 578771--578835 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
578761 TAGCTTAAAT
578771 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
*
578803 TGTATCGATACAATACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
578836 ATCATTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:583575 original size:104 final size:103
Alignment explanation
Indices: 583372--583592 Score: 273
Period size: 104 Copynumber: 2.1 Consensus size: 103
583362 CCAATACATT
* * * * *
583372 CAGAATACTTTGGACATTTTGAGCCATTTTTAACCTTTGCTTATTGACCTAATATCTGGTTTGAA
1 CAGAATACTTTAGACATTTCGAGCCATTTTCAACCTTTGCTCATTGACCTAATATCTAGTTTGAA
* *
583437 CATGTTTTGTTATAGCAAAATTCATGCCAAATTCACAC
66 CATGTTTTGTTACACCAAAATTCATGCCAAATTCACAC
* * * * * *
583475 TAGAATGCTTTAGATATTTCGAGTCATTTTCAGCCTTTGCTCATTGACCTAATGTTCTAGTTTGA
1 CAGAATACTTTAGACATTTCGAGCCATTTTCAACCTTTGCTCATTGACCTAAT-ATCTAGTTTGA
* *
583540 ACATGTTTT-TTCACACCAAAATTCATGCTAGATTCACAC
65 ACATGTTTTGTT-ACACCAAAATTCATGCCAAATTCACAC
583579 CAGAATACATTTAG
1 CAGAATAC-TTTAG
583593 TTAACTTTGG
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
103 46 0.47
104 47 0.48
105 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (103 bp):
CAGAATACTTTAGACATTTCGAGCCATTTTCAACCTTTGCTCATTGACCTAATATCTAGTTTGAA
CATGTTTTGTTACACCAAAATTCATGCCAAATTCACAC
Found at i:589364 original size:17 final size:16
Alignment explanation
Indices: 589340--589386 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
589330 ATTAAGATAG
589340 TTTAT-AAATTAATAAT
1 TTTATAAAATTAA-AAT
589356 TTTACTAAAATTAAAATT
1 TTTA-TAAAATTAAAA-T
*
589374 TTTAGAAAATTAA
1 TTTATAAAATTAA
589387 GGTAATATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 11 0.41
18 12 0.44
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTATAAAATTAAAAT
Found at i:592637 original size:22 final size:22
Alignment explanation
Indices: 592583--592640 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
592573 TTCTAGCATT
592583 ATTTTGGCCTTAAAACAATCTTC
1 ATTTTGGCC-TAAAACAATCTTC
*
592606 A-TTTGAGCCTCAAACAATCTT-
1 ATTTTG-GCCTAAAACAATCTTC
592627 AGTTTTGGCCTAAA
1 A-TTTTGGCCTAAA
592641 TTTTCTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.70
23 8 0.27
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (22 bp):
ATTTTGGCCTAAAACAATCTTC
Found at i:596802 original size:78 final size:78
Alignment explanation
Indices: 596694--596866 Score: 238
Period size: 78 Copynumber: 2.2 Consensus size: 78
596684 GATACTTGCC
* ** *
596694 GAAAGTATGCTTTAGAGATAAGTCTGTCATTTCAGATCATTACTAAGTCTTTTAAGGTCATCGAG
1 GAAAGTATGCTTTAGGGATAAGTCCATCATTTCAGATCATTACTAAGCCTTTTAAGGTCATCGAG
596759 ATACTTTCATGTT
66 ATACTTTCATGTT
* * * * * *
596772 GAAGGTATGCTTTAGGGATAGGTCCATCATTTTATATCATTACTAAGCCTTTTAAGGTTATTGAG
1 GAAAGTATGCTTTAGGGATAAGTCCATCATTTCAGATCATTACTAAGCCTTTTAAGGTCATCGAG
596837 ATACTTTCATGTT
66 ATACTTTCATGTT
* *
596850 GAAAGTATACCTTAGGG
1 GAAAGTATGCTTTAGGG
596867 GATATTTTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (78 bp):
GAAAGTATGCTTTAGGGATAAGTCCATCATTTCAGATCATTACTAAGCCTTTTAAGGTCATCGAG
ATACTTTCATGTT
Found at i:596919 original size:79 final size:79
Alignment explanation
Indices: 596828--596985 Score: 246
Period size: 79 Copynumber: 2.0 Consensus size: 79
596818 GCCTTTTAAG
** * *
596828 GTTATTGAGATACTTTCATGTTGAAAGTATACCTTA-GGGGATATTTTAATAATTTCATCTCAAA
1 GTTATTGAGATACTTTCAAATCGAAAGTATACCTTAGGGGGAT-TTTCAATAATTTCATCTCAAA
596892 ACTAAGTCTATTAGA
65 ACTAAGTCTATTAGA
*
596907 GTTATTGAGATACTTTCAAATCGAAAGTATACCTTAGGGGGCTTTTCAATAATTTCATCTCAAAA
1 GTTATTGAGATACTTTCAAATCGAAAGTATACCTTAGGGGGATTTTCAATAATTTCATCTCAAAA
*
596972 CTAATTCTATTAGA
66 CTAAGTCTATTAGA
596986 ATTGTTGTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
79 67 0.93
80 5 0.07
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (79 bp):
GTTATTGAGATACTTTCAAATCGAAAGTATACCTTAGGGGGATTTTCAATAATTTCATCTCAAAA
CTAAGTCTATTAGA
Found at i:597822 original size:20 final size:19
Alignment explanation
Indices: 597796--597868 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
597786 CTGCCAGTTT
*
597796 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
597816 TATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
597835 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
597856 -ATGTATCGATACA
1 CATGTATCGATACA
597869 TCTGGATGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.38
20 27 0.60
21 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:597841 original size:19 final size:20
Alignment explanation
Indices: 597796--597849 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
597786 CTGCCAGTTT
*
597796 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
* *
597816 TATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
597835 CATGTATCGATACAA
1 CATGTATCGATACAA
597850 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:598447 original size:17 final size:17
Alignment explanation
Indices: 598427--598460 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
598417 TATTTAAAAC
598427 TTTATAAAACAAATTTA
1 TTTATAAAACAAATTTA
598444 TTTATAAAACAAATTTA
1 TTTATAAAACAAATTTA
598461 ACAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATAAAACAAATTTA
Found at i:598466 original size:26 final size:26
Alignment explanation
Indices: 598434--598486 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
598424 AACTTTATAA
598434 AACAAATTTATTTATAAAACAAATTT
1 AACAAATTTATTTATAAAACAAATTT
*
598460 AACAAATTTATTTATAAAATAAATTT
1 AACAAATTTATTTATAAAACAAATTT
598486 A
1 A
598487 TTTAAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AACAAATTTATTTATAAAACAAATTT
Found at i:600341 original size:13 final size:13
Alignment explanation
Indices: 600322--600361 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
600312 ATAGTAACCC
600322 ATGTATCGATACA
1 ATGTATCGATACA
* *
600335 TTGTATCGATATA
1 ATGTATCGATACA
600348 ATGTATCGATACA
1 ATGTATCGATACA
600361 A
1 A
600362 AGATCCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:600778 original size:13 final size:13
Alignment explanation
Indices: 600760--600784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
600750 ATAATGCATA
600760 GTATCGATACATT
1 GTATCGATACATT
600773 GTATCGATACAT
1 GTATCGATACAT
600785 GACCAAATAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:600884 original size:13 final size:13
Alignment explanation
Indices: 600866--600890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
600856 CTTAACTGTT
600866 TGTATCGATACAA
1 TGTATCGATACAA
600879 TGTATCGATACA
1 TGTATCGATACA
600891 GGTGATTGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:600917 original size:66 final size:66
Alignment explanation
Indices: 600811--600943 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
600801 ACTTGCAAAG
*
600811 AATGTATCGATACAGGTGATTGGCAGTAGCTTGGCAGTAGCCACCCTTAACTGTTTGTATCGATA
1 AATGTATCGATACAGGTGATTGGCAATAGCTTGGCAGTAGCCACCCTTAACTGTTTGTATCGATA
600876 C
66 C
* *
600877 AATGTATCGATACAGGTGATTGGCAATAGCTTGGTAGTAGCCACCCTTAAGTGTTTGTATCGATA
1 AATGTATCGATACAGGTGATTGGCAATAGCTTGGCAGTAGCCACCCTTAACTGTTTGTATCGATA
600942 C
66 C
600943 A
1 A
600944 CACAAGATGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (66 bp):
AATGTATCGATACAGGTGATTGGCAATAGCTTGGCAGTAGCCACCCTTAACTGTTTGTATCGATA
C
Found at i:600968 original size:13 final size:13
Alignment explanation
Indices: 600950--600975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
600940 TACACACAAG
600950 ATGTATCGATACA
1 ATGTATCGATACA
600963 ATGTATCGATACA
1 ATGTATCGATACA
600976 TCCCAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:607158 original size:13 final size:13
Alignment explanation
Indices: 607140--607175 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
607130 GCATTTTTAA
*
607140 TATCGATACATTG
1 TATCGATACAGTG
607153 TATCGATACAGTG
1 TATCGATACAGTG
607166 TATCGATACA
1 TATCGATACA
607176 AAGGATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:609642 original size:13 final size:13
Alignment explanation
Indices: 609624--609648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
609614 ATAATGCACA
609624 GTATCGATACATT
1 GTATCGATACATT
609637 GTATCGATACAT
1 GTATCGATACAT
609649 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:609661 original size:20 final size:21
Alignment explanation
Indices: 609636--609688 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
609626 ATCGATACAT
*
609636 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
* *
609656 TGTATCAATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
609677 TGTATCGATACA
1 TGTATCGATACA
609689 GGTCATTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:609767 original size:13 final size:13
Alignment explanation
Indices: 609749--609773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
609739 ACACACAAGT
609749 TGTATCGATACAA
1 TGTATCGATACAA
609762 TGTATCGATACA
1 TGTATCGATACA
609774 TCCCAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:616895 original size:52 final size:52
Alignment explanation
Indices: 616747--616875 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
616737 TAAAATATGA
*
616747 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
616799 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
616851 AAATTTGTCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
616876 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:616902 original size:13 final size:13
Alignment explanation
Indices: 616884--616908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
616874 CAAAGATCAG
616884 TGTATCGATACAA
1 TGTATCGATACAA
616897 TGTATCGATACA
1 TGTATCGATACA
616909 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:616985 original size:19 final size:19
Alignment explanation
Indices: 616961--617025 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
616951 AGCGATACAT
616961 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
616980 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
* *
616993 TGTGTCGATACAACACTTA
1 TGTATCGATACAAAACTTA
617012 TGTATCGATACAAA
1 TGTATCGATACAAA
617026 TTGTTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:616994 original size:32 final size:32
Alignment explanation
Indices: 616953--617023 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
616943 AGCTTCGTAG
616953 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
616985 CGATACATTGTGTCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
617017 CGATACA
1 CGATACA
617024 AATTGTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:618403 original size:33 final size:33
Alignment explanation
Indices: 618361--618451 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
618351 TTAGGGATAA
*
618361 TGTATCGATACAAT-T-CTTCATGTATCGATACAC
1 TGTATCGATACAATGTGC--CATGTATCAATACAC
*
618394 TGTATCGATATAATGTGCCATGTATCAATACAC
1 TGTATCGATACAATGTGCCATGTATCAATACAC
* *
618427 TGTATCGATATAATATGCCATGTAT
1 TGTATCGATACAATGTGCCATGTAT
618452 TGATACAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 51 0.96
34 1 0.02
35 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCAATACAC
Found at i:618458 original size:33 final size:33
Alignment explanation
Indices: 618379--618458 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
618369 TACAATTCTT
*
618379 CATGTATCGATACACTGTATCGATATAATGTGC
1 CATGTATCGATACACTGTATCGATATAATATGC
*
618412 CATGTATCAATACACTGTATCGATATAATATGC
1 CATGTATCGATACACTGTATCGATATAATATGC
*
618445 CATGTATTGATACA
1 CATGTATCGATACA
618459 AATAGTGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (33 bp):
CATGTATCGATACACTGTATCGATATAATATGC
Found at i:620072 original size:8 final size:8
Alignment explanation
Indices: 620061--620130 Score: 70
Period size: 8 Copynumber: 8.5 Consensus size: 8
620051 AAATACATTT
*
620061 TAAACAAA
1 TAAAAAAA
620069 TAAAAAAA
1 TAAAAAAA
620077 TAAAAAAA
1 TAAAAAAA
620085 TTAGAAAAAA
1 -TA-AAAAAA
**
620095 GGAAAAAA
1 TAAAAAAA
*
620103 T-ATAAAA
1 TAAAAAAA
620110 TATAAAAAA
1 TA-AAAAAA
620119 TAAAAAAA
1 TAAAAAAA
620127 TAAA
1 TAAA
620131 TGTAAGTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.12
8 31 0.60
9 9 0.17
10 6 0.12
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:620170 original size:14 final size:13
Alignment explanation
Indices: 620151--620182 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
620141 AGAAAATAGG
*
620151 TTAAAAATTTGGT
1 TTAAAAAATTGGT
620164 TTAAAAAATTGGT
1 TTAAAAAATTGGT
620177 TTAAAA
1 TTAAAA
620183 GAAAATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
TTAAAAAATTGGT
Found at i:622457 original size:11 final size:11
Alignment explanation
Indices: 622441--622479 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
622431 TAAGGTGGTT
622441 TTTTTCACTTG
1 TTTTTCACTTG
622452 TTTTTCACTTG
1 TTTTTCACTTG
622463 -TTTTCTACTTTG
1 TTTTTC-AC-TTG
622475 TTTTT
1 TTTTT
622480 GCTCATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 13 0.52
12 3 0.12
13 4 0.16
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTCACTTG
Done.