Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold393
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: 702984
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 6
Found at i:275466 original size:51 final size:51
Alignment explanation
Indices: 275367--275485 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
275357 ATTTGCTTAC
**
275367 ATGTATCGATACATTTGGGTCAAAAAACTTAGAATATATAGATATAATGAAGA
1 ATGTATCGATACATTTGGGTC-AAAAACCCAGAATATATAGATATAATGAA-A
* * *
275420 ATGTATCGATATATTTGGGTC-AAAACCCGGAATATATTGATATAATGAAA
1 ATGTATCGATACATTTGGGTCAAAAACCCAGAATATATAGATATAATGAAA
*
275470 ATATATCGATACATTT
1 ATGTATCGATACATTT
275486 TCATTCCAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 15 0.25
51 24 0.41
53 20 0.34
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (51 bp):
ATGTATCGATACATTTGGGTCAAAAACCCAGAATATATAGATATAATGAAA
Found at i:276276 original size:51 final size:52
Alignment explanation
Indices: 276207--276617 Score: 281
Period size: 52 Copynumber: 7.9 Consensus size: 52
276197 ATCAGACTCA
* * * * *
276207 ATGATAAGAGTGCCAATGTGTTGATTCACGGCCAGCAACATT-GACTTGAAG
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * * *
276258 ATGAGAAGAATGCCAATGTGCTGATTTAAGCCCAACGACATTGGACTTAAAG
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * ** *
276310 ATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAA
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* ** * * ** *
276362 ATGATAAGGGTGCTAATGTACTGATTCAAGGCCAGTGACATTGGGCTTAAA-
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * * * * * ** * ** *
276413 AGTGATAA-AGGTGCTAATATGCTGATTCGATGCCAATAATATCAGACTTAAAA
1 A-TGAGAAGA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * * * ** ** *
276466 ATAAAAAGAGTGCCAATGTACTGATTCAA-GCGGGTGACATTAGACTTAAAG
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * * ** ** * *
276517 ATAAGAAGGATGTCAACATATTGATTCAAGGCCAGCAATACTGGACTTAAAG
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * *
276569 ATGAGAAGAGTGCCAATGTGCTGATTCAAGGCAAGCGACATTGGACTTA
1 ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTA
276618 GAAAGAGATA
Statistics
Matches: 282, Mismatches: 72, Indels: 11
0.77 0.20 0.03
Matches are distributed among these distances:
51 72 0.26
52 208 0.74
53 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (52 bp):
ATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
Found at i:276411 original size:104 final size:104
Alignment explanation
Indices: 276228--276617 Score: 358
Period size: 104 Copynumber: 3.8 Consensus size: 104
276218 GCCAATGTGT
* * * * * * *
276228 TGATTCACGGCCAGCAACATT-GACTTGAAGATGAGAAGAATGCCAATGTGCTGATTTAAGCCCA
1 TGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAAGAGTGCCAATGTACTGATTCAAGGCCA
* * *
276292 ACGACATTGGACTTAAAGATGAGAAAAATGCTAATGTGC
66 GCGACATTGGACTTAAAGATGAGAAAGATGCTAATATGC
** * * *
276331 TGATTCAAGGCCAGTGACATTGGACTTAAAAATGATAAGGGTGCTAATGTACTGATTCAAGGCCA
1 TGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAAGAGTGCCAATGTACTGATTCAAGGCCA
* * * *
276396 GTGACATTGGGCTTAAA-AGTGATAAAGGTGCTAATATGC
66 GCGACATTGGACTTAAAGA-TGAGAAAGATGCTAATATGC
* * ** * ** * * **
276435 TGATTCGATGCCAATAATATCAGACTTAAAAATAAAAAGAGTGCCAATGTACTGATTCAA-GCGG
1 TGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAAGAGTGCCAATGTACTGATTCAAGGCCA
* * * * *
276499 GTGACATTAGACTTAAAGATAAGAAGGATGTCAACATAT--
66 GCGACATTGGACTTAAAGATGAGAAAGATG-CTA-ATATGC
* * * * *
276538 TGATTCAAGGCCAGCAATACTGGACTTAAAGATGAGAAGAGTGCCAATGTGCTGATTCAAGGCAA
1 TGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAAGAGTGCCAATGTACTGATTCAAGGCCA
276603 GCGACATTGGACTTA
66 GCGACATTGGACTTA
276618 GAAAGAGATA
Statistics
Matches: 227, Mismatches: 54, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
103 92 0.41
104 131 0.58
105 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (104 bp):
TGATTCAAGGCCAGCAACATTGGACTTAAAAATGAGAAGAGTGCCAATGTACTGATTCAAGGCCA
GCGACATTGGACTTAAAGATGAGAAAGATGCTAATATGC
Found at i:276591 original size:155 final size:156
Alignment explanation
Indices: 276227--276595 Score: 340
Period size: 155 Copynumber: 2.4 Consensus size: 156
276217 TGCCAATGTG
* * * * *
276227 TTGATTCACGGCCAGCAACATTGACTTGAAGATGAGAAGAATGCCAATGTGCTGATT-TAAGCCC
1 TTGATTCAAGGCCAGCAACATGGACTTAAAGATGAGAAGAGTGCCAATGTGCTGATTCGAAGCCC
* ** * * * *
276291 AACGACATTGGACTTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGTGACATTGGAC
66 AACAACATCAGACTTAAAAATGAGAAAAATGCCAATGTACTGATTCAAGGCCAGTGACATTAGAC
* * * **
276356 TTAAAAATGATAAGGGTGCTAATGTA
131 TTAAAAATAAGAAGGATGCTAACATA
* ** * * * * *
276382 CTGATTCAAGGCCAGTGACATTGGGCTTAAA-AGTGATAA-AGGTGCTAATATGCTGATTCGATG
1 TTGATTCAAGGCCAGCAACA-TGGACTTAAAGA-TGAGAAGA-GTGCCAATGTGCTGATTCGAAG
* * **
276445 -CCAATAATATCAGACTTAAAAAT-A-AAAAGAGTGCCAATGTACTGATTCAA-GCGGGTGACAT
63 CCCAACAACATCAGACTTAAAAATGAGAAAA-A-TGCCAATGTACTGATTCAAGGCCAGTGACAT
*
276506 TAGACTTAAAGATAAGAAGGATG-TCAACATA
126 TAGACTTAAAAATAAGAAGGATGCT-AACATA
*
276537 TTGATTCAAGGCCAGCAATACTGGACTTAAAGATGAGAAGAGTGCCAATGTGCTGATTC
1 TTGATTCAAGGCCAGCAACA-TGGACTTAAAGATGAGAAGAGTGCCAATGTGCTGATTC
276596 AAGGCAAGCG
Statistics
Matches: 166, Mismatches: 39, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
154 5 0.03
155 97 0.58
156 62 0.37
157 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.25
Consensus pattern (156 bp):
TTGATTCAAGGCCAGCAACATGGACTTAAAGATGAGAAGAGTGCCAATGTGCTGATTCGAAGCCC
AACAACATCAGACTTAAAAATGAGAAAAATGCCAATGTACTGATTCAAGGCCAGTGACATTAGAC
TTAAAAATAAGAAGGATGCTAACATA
Found at i:276721 original size:32 final size:31
Alignment explanation
Indices: 276685--276898 Score: 149
Period size: 32 Copynumber: 6.7 Consensus size: 31
276675 TAGAAGGAGA
* *
276685 TGCCACTAACTTATATGGGCTTTTGAAAGGGT
1 TGCCACCAACTTATGTGGGC-TTTGAAAGGGT
** * * * * *
276717 TGCCATAAATTTGTGTAGGCTTTTAAGAGGAT
1 TGCCACCAACTTATGTGGGCTTTGAA-AGGGT
* * **
276749 TGCCACCAACTTGTGTGGGCTTTTGGAAAAGAA
1 TGCCACCAACTTATGTGGGC-TTT-GAAAGGGT
* * *
276782 TGCCACCGACTTGTGTAGGCTTTGAAAGGGT
1 TGCCACCAACTTATGTGGGCTTTGAAAGGGT
* * *
276813 TGCCACCGACCTATGTGGACTTTGATAAGGGT
1 TGCCACCAACTTATGTGGGCTTTGA-AAGGGT
* * *
276845 TGCCATCAACTTTTGTGGGCTTTGAAAAGAGT
1 TGCCACCAACTTATGTGGGCTTTG-AAAGGGT
* * *
276877 TGCCACCGACTTGTGTGAGCTT
1 TGCCACCAACTTATGTGGGCTT
276899 CAAAAATGTT
Statistics
Matches: 143, Mismatches: 34, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
31 31 0.22
32 85 0.59
33 25 0.17
34 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (31 bp):
TGCCACCAACTTATGTGGGCTTTGAAAGGGT
Found at i:276816 original size:64 final size:64
Alignment explanation
Indices: 276727--276898 Score: 168
Period size: 64 Copynumber: 2.7 Consensus size: 64
276717 TGCCATAAAT
* * * *
276727 TTGTGTAGGCTTTTAAGAGGATTGCCACCAACTTGTGTGGGCTTTTGGA-AAAGAATGCCACCGA
1 TTGTGTAGGCTTTGAA-AGGGTTGCCACCGACTTGTGTGGGCTTTT-GATAAAGAATGCCACCAA
276791 C
64 C
* * * * ** *
276792 TTGTGTAGGCTTTGAAAGGGTTGCCACCGACCTATGTGGAC-TTTGATAAGGGTTGCCATCAAC
1 TTGTGTAGGCTTTGAAAGGGTTGCCACCGACTTGTGTGGGCTTTTGATAAAGAATGCCACCAAC
* * * *
276855 TTTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGAGCTT
1 TTGTGTAGGCTTTG-AAAGGGTTGCCACCGACTTGTGTGGGCTT
276899 CAAAAATGTT
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
62 2 0.02
63 26 0.30
64 42 0.49
65 16 0.19
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (64 bp):
TTGTGTAGGCTTTGAAAGGGTTGCCACCGACTTGTGTGGGCTTTTGATAAAGAATGCCACCAAC
Found at i:276912 original size:32 final size:32
Alignment explanation
Indices: 276869--277100 Score: 137
Period size: 32 Copynumber: 7.2 Consensus size: 32
276859 GTGGGCTTTG
*
276869 AAAAGAGTTGCCACCGACTTGTGTGAGCTTCAA
1 AAAAGA-TTGCCACCGACTTGTGTGAGCTTAAA
* * **
276902 AAATGTTTGCCACTAACTTGTGTG-GACTTAAA
1 AAAAGATTGCCACCGACTTGTGTGAG-CTTAAA
* * *
276934 AAAAGTTTTACCACCGACTTATGTG-GACTTAAAA
1 AAAAG-ATTGCCACCGACTTGTGTGAG-CTT-AAA
** * * *
276968 AAAAGATTGCCATTGACTTATGTGAACTTTAA
1 AAAAGATTGCCACCGACTTGTGTGAGCTTAAA
* * * * *
277000 AAAGGATTGCCATCAACTTGTGTGGGCTT-TA
1 AAAAGATTGCCACCGACTTGTGTGAGCTTAAA
** * * *
277031 AAAAGGGTGCCACAGACTTGTGTGGGCTTCAA
1 AAAAGATTGCCACCGACTTGTGTGAGCTTAAA
** * * *
277063 AAAAGGGTGCCACCGATTTGAGTGAGCTTTAGA
1 AAAAGATTGCCACCGACTTGTGTGAGC-TTAAA
277096 AAAAG
1 AAAAG
277101 GTTGTCACGG
Statistics
Matches: 157, Mismatches: 36, Indels: 12
0.77 0.18 0.06
Matches are distributed among these distances:
31 25 0.16
32 74 0.47
33 50 0.32
34 8 0.05
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (32 bp):
AAAAGATTGCCACCGACTTGTGTGAGCTTAAA
Found at i:276926 original size:96 final size:96
Alignment explanation
Indices: 276748--276930 Score: 219
Period size: 96 Copynumber: 1.9 Consensus size: 96
276738 TTTAAGAGGA
**
276748 TTGCCACCAACTTGTGTGGGCTTTTGGAAAAGAATGCCACCGACTTGTGTAGGCTTTGAAAGGGT
1 TTGCCACCAACTTGTGTGGGCTTTTGGAAAAGAATGCCACCGACTTGTGTAGGCTTAAAAAGGGT
*
276813 TGCCACCGACCTATGTGGACTTTGATAAGGG
66 TGCCACCAACCTATGTGGACTTTGATAAGGG
* * * *
276844 TTGCCATCAACTTTTGTGGGC-TTT-GAAAAGAGTTGCCACCGACTTGTGT-GAGCTTCAAAAAT
1 TTGCCACCAACTTGTGTGGGCTTTTGGAAAAGA-ATGCCACCGACTTGTGTAG-GCTT-AAAAAG
* * * *
276906 GTTTGCCACTAACTTGTGTGGACTT
63 GGTTGCCACCAACCTATGTGGACTT
276931 AAAAAAAGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
94 8 0.11
95 23 0.32
96 42 0.58
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (96 bp):
TTGCCACCAACTTGTGTGGGCTTTTGGAAAAGAATGCCACCGACTTGTGTAGGCTTAAAAAGGGT
TGCCACCAACCTATGTGGACTTTGATAAGGG
Found at i:276986 original size:33 final size:32
Alignment explanation
Indices: 276869--277011 Score: 117
Period size: 33 Copynumber: 4.4 Consensus size: 32
276859 GTGGGCTTTG
* * *
276869 AAAAGAGTTGCCACCGACTTGTGT-GAGCTTCAA
1 AAAAGA-TTGCCACTGACTTATGTGGA-CTTAAA
* * * *
276902 AAATGTTTGCCACTAACTTGTGTGGACTTAAA
1 AAAAGATTGCCACTGACTTATGTGGACTTAAA
* * *
276934 AAAAGTTTTACCACCGACTTATGTGGACTTAAAA
1 AAAAG-ATTGCCACTGACTTATGTGGACTT-AAA
* * *
276968 AAAAGATTGCCATTGACTTATGTGAACTTTAA
1 AAAAGATTGCCACTGACTTATGTGGACTTAAA
*
277000 AAAGGATTGCCA
1 AAAAGATTGCCA
277012 TCAACTTGTG
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
32 37 0.41
33 45 0.50
34 8 0.09
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (32 bp):
AAAAGATTGCCACTGACTTATGTGGACTTAAA
Found at i:277144 original size:31 final size:32
Alignment explanation
Indices: 277061--277540 Score: 255
Period size: 33 Copynumber: 15.2 Consensus size: 32
277051 TGTGGGCTTC
* * *
277061 AAAAAAGGGTGCCACCGATTTGAGTGAGCTTT-A
1 AAAAAAGGGTGCCACGGAGTTGTG-GA-CTTTAA
* * * *
277094 GAAAAAGGTTGTCACGGAGTTGTGGACTTT-T
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
* * * *
277125 GAAAAGGGGTGCCATGGAGTTGTAGACTTTAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
* *
277157 AAAAAATGGTGCTACGGAGTTGTGGACTTTAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
** * *
277189 AAGAAAAAAGTGCCACAGAGTTGTGGA-TGT--
1 AA-AAAAGGGTGCCACGGAGTTGTGGACTTTAA
* *
277219 AAAAAA-GGTGCCACGGAGTTATGAACTTT--
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
* * **
277248 AAAAAGGGGGGCCACAAAGTTGTGGACTTTAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
* * ** *
277280 GAAAAAATGGTGACATAGAGTTATGGACTTTAA
1 -AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
** ** *
277313 GAAAAAATAGTGGTATGGAGTTGTGGACTTT--
1 -AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
*
277344 -AAAAGGGGTGCCACGGAGTTGTGGAC-TTAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
* * *
277374 AAGGAAAAGGGTGCCAC-AACATTGTGGATTTTAA
1 AA--AAAAGGGTGCCACGGA-GTTGTGGACTTTAA
*
277408 TAGAAAAAGGGTGCCACAGAGTTGTGGAC-TT--
1 -A-AAAAAGGGTGCCACGGAGTTGTGGACTTTAA
* * * * *
277439 AAAAAA-GGTGTCACAGAATTGTAGACTTAAAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTT-TAA
* *
277471 AGAAAAAGGGTGCCAC-GAGTTGTAGATTTTTAA
1 A-AAAAAGGGTGCCACGGAGTTGTGGA-CTTTAA
* **
277504 AAAATA--GTGCCACAAAGTTGTGGAC-TTAA
1 AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
277533 AAGAAAAG
1 AA-AAAAG
277541 AAAAGATGAT
Statistics
Matches: 347, Mismatches: 73, Indels: 56
0.73 0.15 0.12
Matches are distributed among these distances:
28 34 0.10
29 43 0.12
30 31 0.09
31 38 0.11
32 38 0.11
33 127 0.37
34 33 0.10
35 2 0.01
36 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.28, T:0.24
Consensus pattern (32 bp):
AAAAAAGGGTGCCACGGAGTTGTGGACTTTAA
Found at i:277215 original size:33 final size:33
Alignment explanation
Indices: 277093--277605 Score: 232
Period size: 33 Copynumber: 16.2 Consensus size: 33
277083 AGTGAGCTTT
* *
277093 AGAAAAAGGTTGTCACGGAGTTGTGGACTTT---
1 AGAAAAAGG-TGCCACAGAGTTGTGGACTTTAAA
* * ** *
277124 TGAAAAGGGGTGCCATGGAGTTGTAGACTTTAAA
1 AGAAAA-AGGTGCCACAGAGTTGTGGACTTTAAA
* * *
277158 A-AAAATGGTGCTACGGAGTTGTGGACTTTAAA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
* *
277190 AGAAAAAAGTGCCACAGAGTTGTGGA-TGT---
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
* * *
277219 A-AAAAAGGTGCCACGGAGTTATGAACTTT--A
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
** * *
277249 A-AAAGGGGGGCCACAAAGTTGTGGACTTTAAGA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAA-A
* * * *
277282 A-AAAATGGTGACATAGAGTTATGGACTTTAAGA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAA-A
** **
277315 A-AAAATA-GTGGTATGGAGTTGTGGACTTTAAA
1 AGAAAA-AGGTGCCACAGAGTTGTGGACTTTAAA
* *
277347 AG----GGGTGCCACGGAGTTGTGGAC-TTAAA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
* * * *
277375 AGGAAAAGGGTGCCACA-ACATTGTGGATTTTAAT
1 A-GAAAAAGGTGCCACAGA-GTTGTGGACTTTAAA
277409 AGAAAAAGGGTGCCACAGAGTTGTGGAC-TT---
1 AGAAAAA-GGTGCCACAGAGTTGTGGACTTTAAA
* * * *
277439 A-AAAAAGGTGTCACAGAATTGTAGACTTAAAA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
* * *
277471 AGAAAAAGGGTGCCAC-GAGTTGTAGATTTTTAA
1 AGAAAAA-GGTGCCACAGAGTTGTGGACTTTAAA
* *
277504 A-AAATA-GTGCCACAAAGTTGTGGAC-TTAAA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
* **
277534 AGAAAAGAAAAGATG--ATGGAGTTGTGGACTTTAAA
1 AG---A-AAAAGGTGCCACAGAGTTGTGGACTTTAAA
* * *
277569 A-AAATA-GTGCAACAAAGTTGTGGAC-TTAAA
1 AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
277599 AGAAAAA
1 AGAAAAA
277606 AAAAGGATGC
Statistics
Matches: 368, Mismatches: 75, Indels: 78
0.71 0.14 0.15
Matches are distributed among these distances:
28 43 0.12
29 28 0.08
30 44 0.12
31 47 0.13
32 36 0.10
33 118 0.32
34 40 0.11
35 10 0.03
36 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.24
Consensus pattern (33 bp):
AGAAAAAGGTGCCACAGAGTTGTGGACTTTAAA
Found at i:277236 original size:124 final size:126
Alignment explanation
Indices: 277095--277371 Score: 314
Period size: 124 Copynumber: 2.2 Consensus size: 126
277085 TGAGCTTTAG
* * * ***
277095 AAAAAGGTTGTCACGGAGTTGTGGACTTTTGAAAAGGGGTGCCATGGAGTTGTAGACTTTAA-AA
1 AAAAAGG-TGCCACGGAGTTGTGGACTTTTAAAAAGGGGGGCCACAAAGTTGTAGACTTTAAGAA
*
277159 AAAATGGTG-C-TACGGAGTTGTGGACTTTAA-AAGAAAAAAGTGCCACAGAGTTGTGGA-TGTA
65 AAAATGGTGACATA--GAGTTATGGACTTTAAGAA-AAAAAAGTGCCACAGAGTTGTGGACTGTA
* * *
277220 AAAAAGGTGCCACGGAGTTATGAAC-TTTAAAAAGGGGGGCCACAAAGTTGTGGACTTTAAGAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTTTAAAAAGGGGGGCCACAAAGTTGTAGACTTTAAGAAA
* ** ** *
277284 AAATGGTGACATAGAGTTATGGACTTTAAGAAAAAATAGTGGTATGGAGTTGTGGACTTTA
66 AAATGGTGACATAGAGTTATGGACTTTAAGAAAAAAAAGTGCCACAGAGTTGTGGACTGTA
**
277345 AAAGGGGTGCCACGGAGTTGTGGACTT
1 AAAAAGGTGCCACGGAGTTGTGGACTT
277372 AAAAGGAAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
123 29 0.23
124 60 0.48
125 34 0.27
126 3 0.02
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (126 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTTTAAAAAGGGGGGCCACAAAGTTGTAGACTTTAAGAAA
AAATGGTGACATAGAGTTATGGACTTTAAGAAAAAAAAGTGCCACAGAGTTGTGGACTGTA
Found at i:277453 original size:28 final size:28
Alignment explanation
Indices: 277411--277471 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
277401 ATTTTAATAG
* * *
277411 AAAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAAAGGTGCCACAGAATTGTAGACTT
*
277439 AAAAAAGGTGTCACAGAATTGTAGACTT
1 AAAAAAGGTGCCACAGAATTGTAGACTT
277467 AAAAA
1 AAAAA
277472 GAAAAAGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (28 bp):
AAAAAAGGTGCCACAGAATTGTAGACTT
Found at i:277540 original size:62 final size:61
Alignment explanation
Indices: 277344--277605 Score: 192
Period size: 65 Copynumber: 4.1 Consensus size: 61
277334 TGTGGACTTT
* * * *
277344 AAAAGGGGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAAGGGTGCCACAACATTGTGGATTTTAA
1 AAAAAGGGTGCCAC-GAGTTGTGGATTTTAAAA--AATA--GTGCCACAA-ATTGTGGA-CTTAA
*
277408 TAG
59 AAG
* * * *
277411 AAAAAGGGTGCCACAGAGTTGTGGA-CTTAAAAAA-GGTGTCACAGAATTGTAGACTTAAAAAG
1 AAAAAGGGTGCCAC-GAGTTGTGGATTTTAAAAAATAGTGCCACA-AATTGTGGACTT-AAAAG
*
277473 AAAAAGGGTGCCACGAGTTGTAGATTTTTAAAAAATAGTGCCACAAAGTTGTGGACTTAAAAG
1 AAAAAGGGTGCCACGAGTTGTGGA-TTTTAAAAAATAGTGCCACAAA-TTGTGGACTTAAAAG
* * * * *
277536 AAAAGAAAAGATG--ATGGAGTTGTGGACTTTAAAAAAATAGTGCAACAAAGTTGTGGACTTAAA
1 --AA-AAAGGGTGCCA-CGAGTTGTGGA-TTTTAAAAAATAGTGCCACAAA-TTGTGGACTTAAA
277599 AG
60 AG
277601 AAAAA
1 AAAAA
277606 AAAAGGATGC
Statistics
Matches: 166, Mismatches: 19, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
61 11 0.07
62 35 0.21
63 18 0.11
64 17 0.10
65 49 0.30
66 6 0.04
67 30 0.18
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (61 bp):
AAAAAGGGTGCCACGAGTTGTGGATTTTAAAAAATAGTGCCACAAATTGTGGACTTAAAAG
Found at i:277577 original size:65 final size:65
Alignment explanation
Indices: 277487--277610 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
277477 AGGGTGCCAC
* * * *
277487 GAGTTGTAGATTTTTAAAAAATAGTGCCACAAAGTTGTGGACTTAAAAGAAAAGAAAAGATGATG
1 GAGTTGTAGACTTTAAAAAAATAGTGCAACAAAGTTGTGGACTTAAAAGAAAAAAAAAGATGATG
*
277552 GAGTTGTGGACTTTAAAAAAATAGTGCAACAAAGTTGTGGACTTAAAAGAAAAAAAAAG
1 GAGTTGTAGACTTTAAAAAAATAGTGCAACAAAGTTGTGGACTTAAAAGAAAAAAAAAG
277611 GATGCCACTA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (65 bp):
GAGTTGTAGACTTTAAAAAAATAGTGCAACAAAGTTGTGGACTTAAAAGAAAAAAAAAGATGATG
Found at i:277624 original size:37 final size:36
Alignment explanation
Indices: 277502--277632 Score: 107
Period size: 37 Copynumber: 3.8 Consensus size: 36
277492 GTAGATTTTT
*
277502 AAAAAATAG-TGCCACAAAGTTGTGGACTTAAAAGA
1 AAAAAAAAGATGCCACAAAGTTGTGGACTTAAAAGA
* *** *
277537 AAAGAAAAGATG--ATGGAGTTGTGGACTT----TA
1 AAAAAAAAGATGCCACAAAGTTGTGGACTTAAAAGA
* *
277567 AAAAAATAG-TGCAACAAAGTTGTGGACTTAAAAGA
1 AAAAAAAAGATGCCACAAAGTTGTGGACTTAAAAGA
* *
277602 AAAAAAAAGGATGCCACTAAGTTGTAGACTT
1 AAAAAAAA-GATGCCACAAAGTTGTGGACTT
277633 TGAAAAAAGA
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
29 2 0.03
30 8 0.11
31 13 0.18
34 13 0.18
35 15 0.21
36 3 0.04
37 17 0.24
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (36 bp):
AAAAAAAAGATGCCACAAAGTTGTGGACTTAAAAGA
Found at i:277645 original size:30 final size:30
Alignment explanation
Indices: 277604--277716 Score: 122
Period size: 30 Copynumber: 3.7 Consensus size: 30
277594 TTAAAAGAAA
* *
277604 AAAAAAGGATGCCACTAAGTTGTAGACTTTG
1 AAAAAA-GATGCCACTGAGTCGTAGACTTTG
*
277635 AAAAAAGATGCCACTGAGTCGTGGAC-TTG
1 AAAAAAGATGCCACTGAGTCGTAGACTTTG
* * *
277664 AAATAGAGATGCAACTGAGTCATAGACTTTG
1 AAA-AAAGATGCCACTGAGTCGTAGACTTTG
*
277695 -AAAAAGAATTCCACTGAGTCGT
1 AAAAAAG-ATGCCACTGAGTCGT
277717 GGACCTTTAG
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.13
30 50 0.74
31 9 0.13
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (30 bp):
AAAAAAGATGCCACTGAGTCGTAGACTTTG
Found at i:278908 original size:48 final size:48
Alignment explanation
Indices: 278838--278979 Score: 184
Period size: 45 Copynumber: 3.0 Consensus size: 48
278828 ATTTAGTTTT
*
278838 TTTTTTTTA-CATAGGATTGGGTGAGTCTTGAAGCTTATGTCACACCAAG
1 TTTTTTTTACCA-A-GATTGGGTGAGTCTTGAAGCTTATGTCTCACCAAG
*
278887 TTTTTTTTACCAAGATTGGGTGAGTCTTGAAGTTTATGTCTCACC-A-
1 TTTTTTTTACCAAGATTGGGTGAGTCTTGAAGCTTATGTCTCACCAAG
* * * *
278933 -TTTTTTTCCCAAGATTGGGTGAGCCTCGAAGCTTGTGTCTCACCAAG
1 TTTTTTTTACCAAGATTGGGTGAGTCTTGAAGCTTATGTCTCACCAAG
278980 GGTTTTTTGC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
45 39 0.47
46 1 0.01
47 1 0.01
48 30 0.36
49 10 0.12
50 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (48 bp):
TTTTTTTTACCAAGATTGGGTGAGTCTTGAAGCTTATGTCTCACCAAG
Found at i:295182 original size:24 final size:23
Alignment explanation
Indices: 295151--295195 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
295141 CAATTAATTC
295151 ATTATTTATATAAAGTAAAAATAT
1 ATTATTTA-ATAAAGTAAAAATAT
* *
295175 ATTATTTAATGAATTAAAAAT
1 ATTATTTAATAAAGTAAAAAT
295196 TGAATGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
ATTATTTAATAAAGTAAAAATAT
Found at i:295405 original size:2 final size:2
Alignment explanation
Indices: 295400--295428 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
295390 ACACACACAC
295400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
295429 AGGATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295876 original size:17 final size:18
Alignment explanation
Indices: 295856--295891 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
295846 TTTAATGAAT
*
295856 AAATATT-ATTAATAAAA
1 AAATATTAATGAATAAAA
295873 AAATATTAATGAATAAAA
1 AAATATTAATGAATAAAA
295891 A
1 A
295892 TTCTTGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATATTAATGAATAAAA
Found at i:295881 original size:14 final size:16
Alignment explanation
Indices: 295847--295892 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 16
295837 TTAAGTTTAT
*
295847 TTAATGAATAAATATTA
1 TTAATGAATAAA-AATA
295864 TTAAT-AA-AAAAATA
1 TTAATGAATAAAAATA
295878 TTAATGAATAAAAAT
1 TTAATGAATAAAAAT
295893 TCTTGATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 8 0.31
17 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
TTAATGAATAAAAATA
Found at i:296579 original size:23 final size:24
Alignment explanation
Indices: 296523--296580 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
296513 ATATATTTTA
*
296523 TAATTAAATTTAAATAAAAATATT
1 TAATTAAATTAAAATAAAAATATT
* *
296547 T--TTATTATTAAAATAATAAT-TT
1 TAATTA-AATTAAAATAAAAATATT
296569 TAATTAAATTAA
1 TAATTAAATTAA
296581 TTTGAATAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
22 6 0.22
23 17 0.63
24 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATTAAATTAAAATAAAAATATT
Found at i:302440 original size:14 final size:14
Alignment explanation
Indices: 302418--302447 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
302408 ATATTTAACA
302418 ATAAGTTTTTTATT
1 ATAAGTTTTTTATT
*
302432 ATAATTTTTTTATT
1 ATAAGTTTTTTATT
302446 AT
1 AT
302448 TATCATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
ATAAGTTTTTTATT
Found at i:302449 original size:17 final size:17
Alignment explanation
Indices: 302423--302460 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
302413 TAACAATAAG
*
302423 TTTT-TTATTATAATTT
1 TTTTATTATTATAATTA
*
302439 TTTTATTATTATCATTA
1 TTTTATTATTATAATTA
302456 TTTTA
1 TTTTA
302461 AATTTAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTATTATAATTA
Found at i:302503 original size:3 final size:3
Alignment explanation
Indices: 302495--302572 Score: 65
Period size: 3 Copynumber: 26.7 Consensus size: 3
302485 AGTTTTAATT
* * * * *
302495 TTA TTA TTA -TA ATA TT- TAA TTA -TA TTA TTA TAA TAAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
302538 TTA TTGA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
302573 GATAGTTTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
2 6 0.09
3 54 0.84
4 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:302512 original size:21 final size:21
Alignment explanation
Indices: 302488--302568 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
302478 TTTAATTAGT
302488 TTTAATTTTATTATTATAATA
1 TTTAATTTTATTATTATAATA
*
302509 TTTAATTATATTATTATAATA
1 TTTAATTTTATTATTATAATA
** *
302530 AATAA--TTATTATTGATATTA
1 TTTAATTTTATTATT-ATAATA
*
302550 TTATTATTATTATTATTAT
1 TT-TAATT-TTATTATTAT
302569 TATTGATAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 7 0.15
20 5 0.11
21 25 0.53
23 2 0.04
24 8 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
TTTAATTTTATTATTATAATA
Found at i:302989 original size:18 final size:19
Alignment explanation
Indices: 302968--303011 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
302958 TTATTATTAA
*
302968 AATATTTATTTTTAT-ATT
1 AATATTTATGTTTATAATT
*
302986 AATACTTATGTTTATAATT
1 AATATTTATGTTTATAATT
303005 AA-ATTTA
1 AATATTTA
303012 AATAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
AATATTTATGTTTATAATT
Found at i:303816 original size:9 final size:9
Alignment explanation
Indices: 303804--303914 Score: 65
Period size: 9 Copynumber: 12.3 Consensus size: 9
303794 TCATATTATC
303804 TTTATATAT
1 TTTATATAT
303813 TTTATATAT
1 TTTATATAT
*
303822 TATA-ATTATT
1 TTTATA-TA-T
*
303832 TTTAAAATAT
1 TTT-ATATAT
303842 TTTATAT-T
1 TTTATATAT
* *
303850 TATATAAAT
1 TTTATATAT
*
303859 TTTA-AAAT
1 TTTATATAT
303867 ATTTATATAT
1 -TTTATATAT
303877 TTT-T-TA-
1 TTTATATAT
303883 TTTATATTAT
1 TTTATA-TAT
303893 TTT-TAATAT
1 TTTAT-ATAT
303902 TTTATATTAT
1 TTTATA-TAT
303912 TTT
1 TTT
303915 TAACATATAA
Statistics
Matches: 81, Mismatches: 7, Indels: 27
0.70 0.06 0.23
Matches are distributed among these distances:
6 3 0.04
7 3 0.04
8 12 0.15
9 38 0.47
10 21 0.26
11 3 0.04
12 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTATATAT
Found at i:303861 original size:27 final size:28
Alignment explanation
Indices: 303809--303878 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
303799 TTATCTTTAT
* *
303809 ATATTTTATATATTATAATTATTTTTAAA
1 ATATTTTATAT-TTATAATAAATTTTAAA
303838 ATATTTTATATTTAT-ATAAATTTTAAA
1 ATATTTTATATTTATAATAAATTTTAAA
303865 ATATTTATATATTT
1 ATATTT-TATATTT
303879 TTTATTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 16 0.42
28 11 0.29
29 11 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTTTATATTTATAATAAATTTTAAA
Found at i:303914 original size:18 final size:18
Alignment explanation
Indices: 303796--303914 Score: 79
Period size: 18 Copynumber: 6.6 Consensus size: 18
303786 TAATTTATTC
303796 ATATTATCTTTATATATTTT
1 ATATTAT-TTTA-ATATTTT
*
303816 ATA-TATTATAATTATTTTT
1 ATATTATTTTAA-TA-TTTT
* *
303835 AAAATATTTT-ATA-TTT
1 ATATTATTTTAATATTTT
* *
303851 ATATAAATTTTAAAATATTT
1 ATAT-TATTTTAATAT-TTT
*
303871 ATA-TATTTT-TTA-TTT
1 ATATTATTTTAATATTTT
303886 ATATTATTTTTAATATTTT
1 ATATTA-TTTTAATATTTT
303905 ATATTATTTT
1 ATATTATTTT
303915 TAACATATAA
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
15 6 0.08
16 7 0.09
17 11 0.14
18 20 0.26
19 19 0.25
20 14 0.18
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTATTTTAATATTTT
Found at i:303915 original size:35 final size:35
Alignment explanation
Indices: 303838--303915 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
303828 TATTTTTAAA
*
303838 ATATTTTATATTTATATAAATTTTAAAATATTTAT
1 ATATTTTTTATTTATATAAATTTTAAAATATTTAT
* * *
303873 ATATTTTTTATTTATATTATTTTTAATAT-TTTAT
1 ATATTTTTTATTTATATAAATTTTAAAATATTTAT
303907 ATTATTTTT
1 A-TATTTTT
303916 AACATATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 6 0.16
35 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (35 bp):
ATATTTTTTATTTATATAAATTTTAAAATATTTAT
Found at i:303931 original size:22 final size:19
Alignment explanation
Indices: 303841--303922 Score: 68
Period size: 19 Copynumber: 4.6 Consensus size: 19
303831 TTTTAAAATA
* *
303841 TTTT-ATAT-TTATATAAA
1 TTTTAATATATTATATTAT
*
303858 TTTTAAAATATT-TATATAT
1 TTTTAATATATTATAT-TAT
303877 TTTT--TAT-TTATATTAT
1 TTTTAATATATTATATTAT
*
303893 TTTTAATATTTTATATTAT
1 TTTTAATATATTATATTAT
*
303912 TTTTAACATAT
1 TTTTAATATAT
303923 AATTATATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
16 9 0.17
17 9 0.17
18 9 0.17
19 25 0.48
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAATATATTATATTAT
Found at i:303931 original size:62 final size:64
Alignment explanation
Indices: 303798--303937 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 64
303788 ATTTATTCAT
* *
303798 ATTATCTTTATATATTTTATATATTATAATTATTTTTAAAATATTTTATATTTATATAAATTTTA
1 ATTATATTTATATATTTTATATATTATAATTATTTTT-AAATATTTTATATTTATATAAATTATA
* * * *
303863 A-AATATTTATATATTTTTTAT-TTAT-ATTATTTTT-AATATTTTATATTATTTTTAACA-TAT
1 ATTATATTTATATATTTTATATATTATAATTATTTTTAAATATTTTATATT-TATATAA-ATTAT
303923 A
64 A
*
303924 ATTATATTCATATA
1 ATTATATTTATATA
303938 CTTAAATTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
60 13 0.20
61 9 0.14
62 20 0.31
63 4 0.06
64 17 0.27
65 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (64 bp):
ATTATATTTATATATTTTATATATTATAATTATTTTTAAATATTTTATATTTATATAAATTATA
Found at i:306483 original size:25 final size:25
Alignment explanation
Indices: 306451--306498 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
306441 GGAAACTTCC
*
306451 TTTTCCTTTTCAAATTGTGTTTTCT
1 TTTTCCTTTTCAAATTGGGTTTTCT
306476 TTTTCCTTTTCAAATTGGGTTTT
1 TTTTCCTTTTCAAATTGGGTTTT
306499 TATTTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.62
Consensus pattern (25 bp):
TTTTCCTTTTCAAATTGGGTTTTCT
Found at i:308224 original size:19 final size:19
Alignment explanation
Indices: 308178--308227 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
308168 CCTAATTTGA
*
308178 AAATAAAAAAT-TAAATAT
1 AAATAAAAAATATAAAAAT
* * *
308196 ATACATAAAATATAAAAAT
1 AAATAAAAAATATAAAAAT
308215 AAATAAAAAATAT
1 AAATAAAAAATAT
308228 CACATTATAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAAAAATATAAAAAT
Found at i:308283 original size:17 final size:17
Alignment explanation
Indices: 308177--308281 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 17
308167 ACCTAATTTG
308177 AAAATAAAAAATTAAATAT
1 AAAATAAAAAA-TAAA-AT
* *
308196 ATACATAAAATATAAAA-
1 A-AAATAAAAAATAAAAT
308213 ATAAATAAAAAATATCACATTAT
1 A-AAATAAAAAATA--A-A--AT
* *
308236 AAAACAGATAAATAAAAT
1 AAAATA-AAAAATAAAAT
308254 AAAATAAAAAATAAAAT
1 AAAATAAAAAATAAAAT
*
308271 GAAAACAAAAA
1 -AAAATAAAAA
308282 TATACCAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
17 22 0.32
18 17 0.25
19 6 0.09
20 10 0.15
21 1 0.01
22 5 0.07
23 7 0.10
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:309357 original size:13 final size:13
Alignment explanation
Indices: 309339--309364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
309329 TACACCAAGT
309339 ATGTATCGATACA
1 ATGTATCGATACA
309352 ATGTATCGATACA
1 ATGTATCGATACA
309365 CAAAAAAAAT
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:312249 original size:21 final size:19
Alignment explanation
Indices: 312215--312253 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
312205 TTAATAAGAC
*
312215 CATGATGATTTGATACCTAA
1 CATGATCATTTGAT-CCTAA
312235 CATGATCATTTTGATCCTA
1 CATGATCA-TTTGATCCTA
312254 GTTTTAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (19 bp):
CATGATCATTTGATCCTAA
Found at i:313286 original size:20 final size:20
Alignment explanation
Indices: 313261--313389 Score: 87
Period size: 20 Copynumber: 6.8 Consensus size: 20
313251 CTGTCAAGGA
*
313261 AATGTATCAATACATTATTC
1 AATGTATCGATACATTATTC
*
313281 AATGTATCGATATATT-TTGC
1 AATGTATCGATACATTATT-C
* **
313301 ATTGTATCGATACATTGCTC
1 AATGTATCGATACATTATTC
*
313321 ATTGTATCGATAC---ATT-
1 AATGTATCGATACATTATTC
* **
313337 -A--TATCTATACATTGCTC
1 AATGTATCGATACATTATTC
*
313354 ATTGTATCGATACATT-TTAC
1 AATGTATCGATACATTATT-C
313374 AATGTATCGATACATT
1 AATGTATCGATACATT
313390 CAGGCATTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
13 8 0.10
16 1 0.01
17 1 0.01
19 3 0.04
20 70 0.83
21 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:313352 original size:33 final size:33
Alignment explanation
Indices: 313300--313369 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
313290 ATATATTTTG
*
313300 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTATATCGATACATTGCTCATTGTATCGATA
*
313333 CATTATATCTATACATTGCTCATTGTATCGATA
1 CATTATATCGATACATTGCTCATTGTATCGATA
313366 CATT
1 CATT
313370 TTACAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (33 bp):
CATTATATCGATACATTGCTCATTGTATCGATA
Found at i:315745 original size:51 final size:51
Alignment explanation
Indices: 315670--315900 Score: 236
Period size: 51 Copynumber: 4.6 Consensus size: 51
315660 AAATTTCTAG
* * * * *
315670 ATTTTTCAT-CTCGGGGATACTCCAATCCCGGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
* * *
315720 ATTTTTCTTAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
* * * ** *
315771 ATTTTCCATAATCGGGAAAACTCCAACTTCGATTTTATTTCCAAAACACCG
1 ATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
* * * * * * *
315822 ACTTTTCACAACCGAGGATACTCCAACCCCAATTTTATTTCTAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
*
315873 ATTTTT--T-ATCGGGGATACTCTAACCCCG
1 ATTTTTCATAATCGGGGATACTCCAACCCCG
315901 TTATTTCCGA
Statistics
Matches: 145, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
48 17 0.12
50 8 0.06
51 120 0.83
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
Found at i:315985 original size:79 final size:80
Alignment explanation
Indices: 315837--316115 Score: 279
Period size: 79 Copynumber: 3.6 Consensus size: 80
315827 TCACAACCGA
* * ** * *
315837 GGATACTCCAAC-CCCAATTTTATTTCTAAAACATCAATTT-T--TTATCGGGGATACTCTAACC
1 GGATACTCCAACTCCCGATTTTATTTCTAAATCATCAATTTCTCACAATCAGGGATACTCCAACC
315898 CCGTTATTTCCGAGG
66 CCGTTATTTCCGAGG
* * * * *
315913 GGATACTCCAACT-CCGGTTTTGTTTTTAAAAT-ATTAATTTCTCATAATCAGGGATACTCCAAC
1 GGATACTCCAACTCCCGATTTTATTTCT-AAATCATCAATTTCTCACAATCAGGGATACTCCAAC
* *
315976 CCCGTTATTTCTGAAG
65 CCCGTTATTTCCGAGG
* * * *
315992 GGATACT-CAAATCCCGATTTTATTTCTAAATCATCAATTTTTCACAATCGGGGATACTTCAACC
1 GGATACTCCAACTCCCGATTTTATTTCTAAATCATCAATTTCTCACAATCAGGGATACTCCAACC
*
316056 CCGTTATTTTCGAGG
66 CCGTTATTTCCGAGG
* * *
316071 GGATACTCCAAC-CCCG-TTATTATCTTCAAAATCTTAAATTTCTCA
1 GGATACTCCAACTCCCGATT-TTAT-TTCTAAATCATCAATTTCTCA
316116 TCGGGAGATG
Statistics
Matches: 165, Mismatches: 28, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
76 29 0.18
77 4 0.02
78 10 0.06
79 102 0.62
80 20 0.12
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (80 bp):
GGATACTCCAACTCCCGATTTTATTTCTAAATCATCAATTTCTCACAATCAGGGATACTCCAACC
CCGTTATTTCCGAGG
Found at i:317466 original size:68 final size:68
Alignment explanation
Indices: 317355--317484 Score: 224
Period size: 68 Copynumber: 1.9 Consensus size: 68
317345 GCATATTTTT
* *
317355 CTCTTTTTTCTTCCTTTCAAACTTTTAGATTTCCTATAATACTTTTATGAATCTTGAATATTAAC
1 CTCTCTTTTCTTCCTTTCAAACTTTTAGATTTCCTATAATACTTTTATGAATCTCGAATATTAAC
317420 TTC
66 TTC
* *
317423 CTCTCTTTTCTTCTTTTCAAACTTTTAGATTTCCTATATTACTTTTATGAATCTCGAATATT
1 CTCTCTTTTCTTCCTTTCAAACTTTTAGATTTCCTATAATACTTTTATGAATCTCGAATATT
317485 GACTATTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (68 bp):
CTCTCTTTTCTTCCTTTCAAACTTTTAGATTTCCTATAATACTTTTATGAATCTCGAATATTAAC
TTC
Found at i:318839 original size:80 final size:79
Alignment explanation
Indices: 318733--318921 Score: 202
Period size: 79 Copynumber: 2.4 Consensus size: 79
318723 GTTGTAGTGT
* * ** * *
318733 TCCCTT-GAAAATAATGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TCAGAAGAAAAA
1 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTCAG-AGAAAAA
*
318796 AATCGGGATTGGAGTA
64 AACCGGGATTGGAGTA
** * * *
318812 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAG
1 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCAGAGAAAAAAA
*
318877 CCGGGGTTGGAGTA
66 CCGGGATTGGAGTA
* * *
318891 TCCCCTCGGAAGTAACGGGGTTGGAGTATCC
1 TCCCTTCGAAAATAACGGGGTTGGAGTATCC
318922 TTGATAAGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 53 0.58
80 39 0.42
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (79 bp):
TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCAGAGAAAAAAA
CCGGGATTGGAGTA
Found at i:319092 original size:52 final size:52
Alignment explanation
Indices: 318937--319330 Score: 264
Period size: 52 Copynumber: 7.5 Consensus size: 52
318927 AAGATAACGA
* ** * *
318937 GGTTGGATTATCATCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTTGGAAATAAAACCGG
* ** *
318989 AGTTGGAGTATCCCCGATTAAAGGAAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGG-AAAAATTGGTGTTTTGGAAATAAAACCGG
* * *
319043 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGGAAATAAAACCGG
* * *** * * *
319095 GGTTGGAGTATCCCCGATTAT-GAAGAATCAATATTTTGGAAATAAAGTCGGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGGAAATAAA-ACCGG
* * * *** * *
319147 GGTTGGAGTATCCCC--TCG-GAAATAACAGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGGAA-AA-A---TTGGTGT-T-TTGGA-AATAAAACCGG
* *
319202 GGTTGGAGTATCCCCGATTGT-GAAAATTTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTG--TTTTGGAAATAAAACCGG
* * * * * *
319255 AGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTCTCGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGGAAATAAAACCGG
* *
319307 AGTTGGAATATCCCCGATTGTGGA
1 GGTTGGAGTATCCCCGATTGTGGA
319331 GAATTGAGAA
Statistics
Matches: 264, Mismatches: 57, Indels: 42
0.73 0.16 0.12
Matches are distributed among these distances:
50 3 0.01
51 22 0.08
52 126 0.48
53 26 0.10
54 46 0.17
55 29 0.11
56 3 0.01
57 7 0.03
58 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGGAAATAAAACCGG
Found at i:319207 original size:27 final size:28
Alignment explanation
Indices: 319145--319219 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
319135 AATAAAGTCG
***
319145 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
* *
319173 AGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
319200 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
319220 TGTGAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:321691 original size:13 final size:13
Alignment explanation
Indices: 321673--321697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
321663 CAAAGATCCT
321673 TGTATCGATACAA
1 TGTATCGATACAA
321686 TGTATCGATACA
1 TGTATCGATACA
321698 CAGAAAAATG
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:321761 original size:19 final size:18
Alignment explanation
Indices: 321737--321804 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
321727 CAGTAGCTAA
321737 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
321756 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
321771 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
321788 TTATGTGTCGATACAAA
1 TTATGTATCGATACAAA
321805 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:321777 original size:13 final size:13
Alignment explanation
Indices: 321759--321783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
321749 ACAATACTTA
321759 TGTATCGATACAT
1 TGTATCGATACAT
321772 TGTATCGATACA
1 TGTATCGATACA
321784 AAACTTATGT
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):
TGTATCGATACAT
Found at i:321781 original size:32 final size:32
Alignment explanation
Indices: 321740--321802 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
321730 TAGCTAATTA
*
321740 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
321772 TGTATCGATACAAAACTTATGTGTCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
321803 AATTGTTGAA
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:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:322727 original size:55 final size:54
Alignment explanation
Indices: 322643--323300 Score: 1023
Period size: 55 Copynumber: 12.0 Consensus size: 54
322633 ATAAAGTGTA
* * * * *
322643 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
322698 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGCATGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
322753 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
322808 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTTTGAAAGGTA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
322863 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
322918 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
322973 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGGGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
323028 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
323083 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
323138 TCCTGCTCTTTGAGAACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
323193 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
323248 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
323301 AAAAAGCATC
Statistics
Matches: 565, Mismatches: 27, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
54 9 0.02
55 544 0.96
56 12 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:330032 original size:17 final size:17
Alignment explanation
Indices: 330010--330043 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
330000 ATATCGATTC
*
330010 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
330027 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
330044 CTTACCTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:336860 original size:80 final size:79
Alignment explanation
Indices: 336756--336963 Score: 240
Period size: 79 Copynumber: 2.6 Consensus size: 79
336746 GAGATAATAA
* * * *
336756 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
336820 A-TCAGAAGAAAAAAAT
64 ATTCAG-AGAAAAAAAC
* *
336836 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
** * * *
336901 TTTGGGAATAAAGC
66 TCAGAGAAAAAAAC
* * *
336915 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
336964 GAGATAACGA
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 57 0.52
80 52 0.48
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TCAGAGAAAAAAAC
Found at i:336971 original size:28 final size:28
Alignment explanation
Indices: 336915--336991 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
336905 GGAATAAAGC
***
336915 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAGTAA
336943 CGGGGTTGGAGTATCCCCGATG-AGATAA
1 CGGGGTTGGAGTATCCCCGATGAAG-TAA
* * *
336971 CGAGGTTAGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
336992 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAGTAA
Found at i:337038 original size:52 final size:51
Alignment explanation
Indices: 336974--337365 Score: 274
Period size: 52 Copynumber: 7.4 Consensus size: 51
336964 GAGATAACGA
* * *
336974 GGTTAGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATCGG
* * * *
337026 AGTTGGAGTATCCCCTATTAAAG-GAAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTG-AAAAATTGGTGTTTTGGAAATAAAATCGG
* * *
337080 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGG
* * *** * *
337132 GGTTGGAGTATCCCCGATTATGAAGAATCAATATTTTGGAAATAAAGTCGAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCG-G
* * * *** * *
337184 GGTTAGAGTATCCCC--TCG-GAAATAACAAGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTG--A-AA-AA--TTGGTGT-T-TTGGA-AATAAAATCGG
*
337239 GGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG--TTTTGGAAATAAAATCGG
* * * * *
337292 AGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTCTCGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGG
* *
337344 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
337366 GAGAATTGAG
Statistics
Matches: 263, Mismatches: 53, Indels: 49
0.72 0.15 0.13
Matches are distributed among these distances:
49 1 0.00
50 1 0.00
51 27 0.10
52 119 0.45
53 27 0.10
54 46 0.17
55 30 0.11
56 4 0.02
57 5 0.02
58 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGG
Found at i:339743 original size:13 final size:13
Alignment explanation
Indices: 339725--339749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339715 CAAAGATCCT
339725 TGTATCGATACAA
1 TGTATCGATACAA
339738 TGTATCGATACA
1 TGTATCGATACA
339750 CAGAAAAATG
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:339813 original size:19 final size:18
Alignment explanation
Indices: 339789--339856 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
339779 CAGTAGCTAA
339789 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
339808 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
339823 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
339840 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
339857 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:339829 original size:13 final size:13
Alignment explanation
Indices: 339811--339835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339801 ACAATACTTA
339811 TGTATCGATACAT
1 TGTATCGATACAT
339824 TGTATCGATACA
1 TGTATCGATACA
339836 AAACTTATGT
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):
TGTATCGATACAT
Found at i:339833 original size:32 final size:32
Alignment explanation
Indices: 339792--339854 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
339782 TAGCTAATTA
*
339792 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
339824 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
339855 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:342052 original size:12 final size:12
Alignment explanation
Indices: 342022--342046 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
342012 TATCGCATAA
342022 TCTTTTTTTCTT
1 TCTTTTTTTCTT
342034 TCTTTTTTTCTT
1 TCTTTTTTTCTT
342046 T
1 T
342047 TATTTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:346721 original size:15 final size:16
Alignment explanation
Indices: 346698--346736 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
346688 GTTTAAAGTT
346698 AGTTCTTTTTC-GAAA
1 AGTTCTTTTTCTGAAA
*
346713 AGTTTTTTTTCTGAAA
1 AGTTCTTTTTCTGAAA
*
346729 AATTCTTT
1 AGTTCTTT
346737 CTTAGAAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (16 bp):
AGTTCTTTTTCTGAAA
Found at i:348494 original size:2 final size:2
Alignment explanation
Indices: 348487--348542 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
348477 AAAATGATTC
348487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
348529 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
348543 CAAAACAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351666 original size:16 final size:16
Alignment explanation
Indices: 351645--351675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
351635 ATACTCACCA
*
351645 AAATAAAAAATAAGTG
1 AAATAAAAAAAAAGTG
351661 AAATAAAAAAAAAGT
1 AAATAAAAAAAAAGT
351676 TTCCTAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAATAAAAAAAAAGTG
Found at i:351819 original size:18 final size:18
Alignment explanation
Indices: 351778--351838 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
351768 TCAATATCAC
*
351778 AAATTAATTAAAATTAACT
1 AAATTAA-TAAAATTAATT
* *
351797 CAATTAATAATATTAATT
1 AAATTAATAAAATTAATT
*
351815 TAATTAA-AAAATTAAATT
1 AAATTAATAAAATT-AATT
351833 AAATTA
1 AAATTA
351839 TAATTATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 5 0.14
18 24 0.69
19 6 0.17
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTAATAAAATTAATT
Found at i:352962 original size:2 final size:2
Alignment explanation
Indices: 352955--352981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
352945 CCCTAACCCC
352955 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
352982 AGAGAGAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:353807 original size:18 final size:18
Alignment explanation
Indices: 353767--353808 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
353757 ATGAATGTGT
*
353767 TTTATTATAAATATTTAA
1 TTTATTATAAATATATAA
*
353785 ATTATATATAAATA-ATAA
1 TTTAT-TATAAATATATAA
353803 TTTATT
1 TTTATT
353809 TTTATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATTATAAATATATAA
Found at i:354487 original size:6 final size:6
Alignment explanation
Indices: 354476--354504 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
354466 AATAGACGAT
354476 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
354505 TGATAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:354649 original size:21 final size:21
Alignment explanation
Indices: 354623--354684 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
354613 TAATTATACC
*
354623 AATATAATATAAAAAAATTAA
1 AATATAATATAAATAAATTAA
*
354644 AATATAATATAAATAATTTAA
1 AATATAATATAAATAAATTAA
*
354665 AAT-TTATATAATATAAATTA
1 AATATAATATAA-ATAAATTA
354685 TTAATATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.19
21 29 0.81
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATATAATATAAATAAATTAA
Found at i:354681 original size:16 final size:16
Alignment explanation
Indices: 354656--354707 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
354646 TATAATATAA
*
354656 ATAATTTAAAATTTAT
1 ATAATATAAAATTTAT
*
354672 ATAATATAAATTATTA-
1 ATAATATAAAAT-TTAT
354688 AT-ATATTAAAATTTAT
1 ATAATA-TAAAATTTAT
354704 ATAA
1 ATAA
354708 AATATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.21
16 19 0.66
17 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATATAAAATTTAT
Found at i:354712 original size:21 final size:22
Alignment explanation
Indices: 354687--354736 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
354677 ATAAATTATT
* *
354687 AATATATTAA-AATTTATATAA
1 AATATATTAATAACTTAAATAA
354708 AATATA-TAATAACTTAAATAA
1 AATATATTAATAACTTAAATAA
354729 AATTATAT
1 AA-TATAT
354737 ATGGTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATATTAATAACTTAAATAA
Found at i:355187 original size:2 final size:2
Alignment explanation
Indices: 355180--355212 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
355170 TGAAATTTGA
355180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
355213 CACGATTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:355957 original size:73 final size:68
Alignment explanation
Indices: 355879--356076 Score: 189
Period size: 73 Copynumber: 2.8 Consensus size: 68
355869 ATTTTTGATA
* *
355879 TAATTATATGAGTTTAAGTTTTATAACATATGATTTATTTTTATTTGTAGAAGTTTAAATTTATT
1 TAATTATA-GAGTTTAAATTTTATAA-ATATGATTTATTTTTATTTGTAAAAGTTTAAA--T-TT
*
355944 TTTTAGTT
61 TTTTAGGT
* * * ** * *
355952 TAATTACACAAGTTTAAATTTTCTATGGTATGATTTATTTTTATTTTTAAAAGTTTTAATTTTTT
1 TAATTATA-GAGTTTAAATTTTATA-AATATGATTTATTTTTATTTGTAAAAGTTTAAATTTTTT
*
356017 TGGGT
64 TAGGT
* *
356022 TAATTATAGAACTTTAAAATTTTTTAAAGTATGATTTATTTTTATTTGTAAAAGT
1 TAATTATAG-AGTTT-AAATTTTATAAA-TATGATTTATTTTTATTTGTAAAAGT
356077 AATTTAATTT
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
70 19 0.19
71 35 0.34
73 48 0.47
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (68 bp):
TAATTATAGAGTTTAAATTTTATAAATATGATTTATTTTTATTTGTAAAAGTTTAAATTTTTTTA
GGT
Found at i:356061 original size:71 final size:70
Alignment explanation
Indices: 355907--356088 Score: 211
Period size: 73 Copynumber: 2.5 Consensus size: 70
355897 TTTTATAACA
* * * *
355907 TATGATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTAGTTTAATTACACAAGTTTAAATT
1 TATGATTTATTTTTATTTGTAAAAGTTTTAA--T-TTTTTTAGGTTAATTACACAACTTTAAATT
**
355972 TTCTATGG
63 TTCTAAAG
* * * *
355980 TATGATTTATTTTTATTTTTAAAAGTTTTAATTTTTTTGGGTTAATTATAGAACTTTAAAATTTT
1 TATGATTTATTTTTATTTGTAAAAGTTTTAATTTTTTTAGGTTAATTACACAACTTT-AAATTTT
*
356045 TTAAAG
65 CTAAAG
356051 TATGATTTATTTTTATTTGTAAAAGTAATTTAATTTTT
1 TATGATTTATTTTTATTTGTAAAAGT--TTTAATTTTT
356089 GAGATATTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
70 20 0.21
71 36 0.38
73 38 0.40
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (70 bp):
TATGATTTATTTTTATTTGTAAAAGTTTTAATTTTTTTAGGTTAATTACACAACTTTAAATTTTC
TAAAG
Found at i:356089 original size:71 final size:70
Alignment explanation
Indices: 355907--356089 Score: 199
Period size: 71 Copynumber: 2.6 Consensus size: 70
355897 TTTTATAACA
* * * * *
355907 TATGATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTAGTTTAATTACACAAGTTTAAATT
1 TATGATTTATTTTTATTTGTAAAAG--T-AATTTAATTTTTGGGTTAATTACACAACTTTAAATT
**
355972 TTCTATGG
63 TTCTAAAG
* * *
355980 TATGATTTATTTTTATTTTTAAAAGT--TTTAATTTTTTTGGGTTAATTATAGAACTTTAAAATT
1 TATGATTTATTTTTATTTGTAAAAGTAATTTAA--TTTTTGGGTTAATTACACAACTTT-AAATT
*
356043 TTTTAAAG
63 TTCTAAAG
356051 TATGATTTATTTTTATTTGTAAAAGTAATTTAATTTTTG
1 TATGATTTATTTTTATTTGTAAAAGTAATTTAATTTTTG
356090 AGATATTTTA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
68 4 0.04
70 19 0.20
71 42 0.45
73 28 0.30
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (70 bp):
TATGATTTATTTTTATTTGTAAAAGTAATTTAATTTTTGGGTTAATTACACAACTTTAAATTTTC
TAAAG
Found at i:360709 original size:30 final size:30
Alignment explanation
Indices: 360637--360710 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
360627 TTTAAAGTCT
* *
360637 ACAACTTTGTGGCATCTCTTCTCAAAGTCC
1 ACAACTCTGTGGCATCTCTTCTCAAAGACC
** * *
360667 ATGACTCAGTGGCATCTCTTTTCAGAA-ACC
1 ACAACTCTGTGGCATCTCTTCTCA-AAGACC
360697 ACAACTCTGTGGCA
1 ACAACTCTGTGGCA
360711 CGCCTTTTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (30 bp):
ACAACTCTGTGGCATCTCTTCTCAAAGACC
Found at i:360788 original size:59 final size:59
Alignment explanation
Indices: 360697--360810 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
360687 TTCAGAAACC
* * *
360697 ACAACTCTGTGGCACGCCTTTTAAGTCTACAACTCCGTGACACTTTTTTCTTCAAATTTT
1 ACAACTCTGTGACACGCCTTTTAAGTCCACAACTCCGTGACACCTTTTT-TTCAAATTTT
* * *
360757 ACAACTCTGTGACAC-CTTTTTAAGTCCACAACTCTGTGGCACCTTTTTTTCAAA
1 ACAACTCTGTGACACGCCTTTTAAGTCCACAACTCCGTGACACCTTTTTTTCAAA
360811 GTCCACAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 6 0.12
59 28 0.58
60 14 0.29
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (59 bp):
ACAACTCTGTGACACGCCTTTTAAGTCCACAACTCCGTGACACCTTTTTTTCAAATTTT
Found at i:360835 original size:30 final size:29
Alignment explanation
Indices: 360773--360880 Score: 105
Period size: 31 Copynumber: 3.6 Consensus size: 29
360763 CTGTGACACC
*
360773 TTTTT-AAGTCCACAAC-TCTGTGGCACCTT
1 TTTTTAAAGTCCACAACTTC-GTGCCA-CTT
*
360802 TTTTTCAAAGTCCACAACTTCGTGTCACTTT
1 TTTTT-AAAGTCCACAACTTCGTGCCAC-TT
* *
360833 TTTTTAAAGTCCACAATTTCGTGACCCCCTT
1 TTTTTAAAGTCCACAACTTCGTG--CCACTT
360864 TTTTT-AAGTCCACAACT
1 TTTTTAAAGTCCACAACT
360881 CTATGGCACC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
29 5 0.07
30 29 0.43
31 30 0.44
32 4 0.06
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTTTAAAGTCCACAACTTCGTGCCACTT
Found at i:360836 original size:59 final size:60
Alignment explanation
Indices: 360695--360895 Score: 164
Period size: 60 Copynumber: 3.4 Consensus size: 60
360685 TTTTCAGAAA
* * * * * *
360695 CCACAACTCTGTGGCACGCCTTTTAAGTCTACAACTCCGTGACACTTTTTTCTTCAAATT
1 CCACAACTCTGTGACACTCTTTTTAAGTCCACAACTCCGTGACACCTTTTTCTTCAAAGT
** * *
360755 TTACAACTCTGTGACAC-CTTTTTAAGTCCACAACTCTGTGGCACCTTTTT-TTCAAAGT
1 CCACAACTCTGTGACACTCTTTTTAAGTCCACAACTCCGTGACACCTTTTTCTTCAAAGT
* * * * *
360813 CCACAACT-TCGTGTCACTTTTTTTTAAAGTCCACAATTTCGTGACCCCCTTTTT-TT--AAGT
1 CCACAACTCT-GTGACAC-TCTTTTT-AAGTCCACAACTCCGTGA-CACCTTTTTCTTCAAAGT
* *
360873 CCACAACTCTATGGCAC-CTTTTT
1 CCACAACTCTGTGACACTCTTTTT
360896 TTAGCCCACA
Statistics
Matches: 114, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
57 1 0.01
58 24 0.21
59 28 0.25
60 36 0.32
61 15 0.13
62 10 0.09
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (60 bp):
CCACAACTCTGTGACACTCTTTTTAAGTCCACAACTCCGTGACACCTTTTTCTTCAAAGT
Found at i:360896 original size:30 final size:31
Alignment explanation
Indices: 360773--360897 Score: 134
Period size: 30 Copynumber: 4.1 Consensus size: 31
360763 CTGTGACACC
360773 TTTTTAAGTCCACAACTCT-GTGGCACCTTT
1 TTTTTAAGTCCACAACTCTCGTGGCACCTTT
* *
360803 TTTTCAAAGTCCACAACT-TCGTGTCA-CTTT
1 TTTT-TAAGTCCACAACTCTCGTGGCACCTTT
* * * *
360833 TTTTTAAAGTCCACAA-TTTCGTGACCCCCTT
1 TTTTT-AAGTCCACAACTCTCGTGGCACCTTT
*
360864 TTTTTAAGTCCACAACTCT-ATGGCACCTTT
1 TTTTTAAGTCCACAACTCTCGTGGCACCTTT
360894 TTTT
1 TTTT
360898 AGCCCACATA
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
29 1 0.01
30 50 0.64
31 27 0.35
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTTTAAGTCCACAACTCTCGTGGCACCTTT
Found at i:361010 original size:32 final size:31
Alignment explanation
Indices: 360898--361013 Score: 99
Period size: 32 Copynumber: 3.6 Consensus size: 31
360888 ACCTTTTTTT
* *
360898 AGCCCACATAAGTCAGTGGCAACCTCTTTCAAA
1 AGCCCACACAAGTCAGTGGAAACC-CTTTC-AA
* **
360931 AGCCTACACAAGTTGGTGGCAATACCCTTT-AA
1 AGCCCACACAAGTCAGTGG-AA-ACCCTTTCAA
* * *
360963 AGGCCAAACAAGTCAGTGGTAACCCTTTCGAA
1 AGCCCACACAAGTCAGTGGAAACCCTTTC-AA
*
360995 AGCCCACATAAGTCAGTGG
1 AGCCCACACAAGTCAGTGG
361014 CATCTTCTTC
Statistics
Matches: 65, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
30 7 0.11
31 1 0.02
32 34 0.52
33 15 0.23
34 5 0.08
35 3 0.05
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (31 bp):
AGCCCACACAAGTCAGTGGAAACCCTTTCAA
Found at i:366255 original size:21 final size:20
Alignment explanation
Indices: 366208--366261 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
366198 TATTTTAGAC
366208 ATGTATCGATACATTCCCTT
1 ATGTATCGATACATTCCCTT
* *
366228 ATATATCAATACATTACCC-T
1 ATGTATCGATACATT-CCCTT
366248 ATTGTATCGATACA
1 A-TGTATCGATACA
366262 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCCCTT
Found at i:367317 original size:53 final size:52
Alignment explanation
Indices: 367257--367431 Score: 219
Period size: 53 Copynumber: 3.3 Consensus size: 52
367247 CACTTTCGAA
367257 GGGATACTCCAACCCCATTTTTATTTCCCAAACATCGAATTTTTTTCATCTTG
1 GGGATACTCCAACCCCATTTTTATTTCCCAAACATCGAATTTTTTT-ATCTTG
*
367310 GGGATACTCCAACCCCATTTTTATTTCCCAAACATC-AATTTTTTTTTTTCATATG
1 GGGATACTCCAACCCCATTTTTATTTCCCAAACATCGAA--TTTTTTTATC-T-TG
* ** * *
367365 GAGGACACTCCAACCCCATTTTTATTTTTCAAACACCGAA-TTTTTTATCTCG
1 G-GGATACTCCAACCCCATTTTTATTTCCCAAACATCGAATTTTTTTATCTTG
*
367417 GGGATACTCTAACCC
1 GGGATACTCCAACCC
367432 TATTAGTTCC
Statistics
Matches: 107, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
51 12 0.11
52 4 0.04
53 39 0.36
54 16 0.15
55 3 0.03
56 31 0.29
57 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (52 bp):
GGGATACTCCAACCCCATTTTTATTTCCCAAACATCGAATTTTTTTATCTTG
Found at i:367546 original size:81 final size:81
Alignment explanation
Indices: 367452--367628 Score: 232
Period size: 81 Copynumber: 2.2 Consensus size: 81
367442 CAGAGAATAA
* *
367452 TCTAACCCCATTTTTACTTCTA-AAACATAGAATTTCTTCATCT-TTGAGAATACTCCAATCCCA
1 TCTAACCCCATTTTTACTTCTAGAAACATA-AATTTCTTCATCTCTGGAG-ATACTCCAACCCCA
367515 CCATTTCCGAGGGGATAC
64 CCATTTCCGAGGGGATAC
* * * *
367533 TCTAACCCCATTTTCACTTCTAGAACCTTAAATTTCTTCATCTCTGGAGATACTCCAACCCCATC
1 TCTAACCCCATTTTTACTTCTAGAAACATAAATTTCTTCATCTCTGGAGATACTCCAACCCCACC
* *
367598 ATTTCTGAGGGGCTAC
66 ATTTCCGAGGGGATAC
* *
367614 TCTAACTCCGTTTTT
1 TCTAACCCCATTTTT
367629 GTTTTCCAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 74 0.89
82 9 0.11
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (81 bp):
TCTAACCCCATTTTTACTTCTAGAAACATAAATTTCTTCATCTCTGGAGATACTCCAACCCCACC
ATTTCCGAGGGGATAC
Found at i:371806 original size:32 final size:33
Alignment explanation
Indices: 371765--371827 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
371755 TAGCCAAACT
*
371765 TGTATCGAT-ACATAAAATATGTATCGATATAA
1 TGTATCGATAACAAAAAATATGTATCGATATAA
371797 TGTATCGATACACAAAAAATATGTATCGATA
1 TGTATCGATA-ACAAAAAATATGTATCGATA
371828 CATTGGCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 9 0.32
34 19 0.68
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (33 bp):
TGTATCGATAACAAAAAATATGTATCGATATAA
Found at i:374061 original size:21 final size:21
Alignment explanation
Indices: 374028--374077 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
374018 TTGCAAGTTG
*
374028 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
374050 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
374071 AAATAAA
1 AAATAAA
374078 AACTTGCATA
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:375894 original size:15 final size:15
Alignment explanation
Indices: 375874--375904 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
375864 TAAAAATATC
*
375874 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
375889 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
375904 C
1 C
375905 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:378001 original size:13 final size:13
Alignment explanation
Indices: 377983--378020 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
377973 CATTTTTCTT
377983 TGTATCGATACAA
1 TGTATCGATACAA
*
377996 TGTATCGATACAC
1 TGTATCGATACAA
378009 TGTATCGATACA
1 TGTATCGATACA
378021 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:378175 original size:20 final size:20
Alignment explanation
Indices: 378132--378177 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
378122 AAATCTTTTG
378132 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
378153 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
378173 CAAAA
1 CAAAA
378178 CCAGAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:379830 original size:29 final size:29
Alignment explanation
Indices: 379788--379855 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
379778 GAGAGAATAG
* *
379788 ATGTATGTATGTGCAAATAAATTTTTGAT
1 ATGTGTGTAAGTGCAAATAAATTTTTGAT
379817 ATGTGTGTAAGTGCAAATAAATTTTTGAT
1 ATGTGTGTAAGTGCAAATAAATTTTTGAT
379846 ATGTGTGTAA
1 ATGTGTGTAA
379856 ATTACCTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.43
Consensus pattern (29 bp):
ATGTGTGTAAGTGCAAATAAATTTTTGAT
Found at i:380620 original size:19 final size:19
Alignment explanation
Indices: 380596--380660 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
380586 TAGCCAAACT
380596 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
380615 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
380628 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
380649 TGTATCGATACA
1 TGTATCGATACA
380661 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:380632 original size:13 final size:13
Alignment explanation
Indices: 380614--380639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
380604 TACACAAAAT
380614 ATGTATCGATACA
1 ATGTATCGATACA
380627 ATGTATCGATACA
1 ATGTATCGATACA
380640 CAAAAAATAT
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:380637 original size:32 final size:33
Alignment explanation
Indices: 380596--380660 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
380586 TAGCCAAACT
380596 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
380628 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
380661 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:382395 original size:19 final size:20
Alignment explanation
Indices: 382371--382423 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
382361 AGCGATATAT
382371 TGTATCGATACAATACT-TA
1 TGTATCGATACAATACTGTA
* *
382390 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-ATACTGTA
382411 TGTATCGATACAA
1 TGTATCGATACAA
382424 ATTGTTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTGTA
Found at i:383269 original size:23 final size:24
Alignment explanation
Indices: 383229--383273 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
383219 ATATGATACG
* *
383229 TTTAACATATTTATTATATTTATA
1 TTTAAAATATTTAATATATTTATA
383253 TTTAAAAT-TTTAATATATTTA
1 TTTAAAATATTTAATATATTTA
383274 ATAAATCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAAAATATTTAATATATTTATA
Found at i:388146 original size:20 final size:20
Alignment explanation
Indices: 388097--388149 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
388087 TTAACATTTT
* *
388097 ATATAAAAATAATTTTAAAA
1 ATATAATAATAATATTAAAA
*
388117 ATATAATAATAATATTAATA
1 ATATAATAATAATATTAAAA
* *
388137 ATTTATTAATAAT
1 ATATAATAATAAT
388150 TATTTTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAATAATAATATTAAAA
Found at i:388264 original size:16 final size:16
Alignment explanation
Indices: 388243--388304 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
388233 TTTAAATTTT
388243 AATATATTATAATATA
1 AATATATTATAATATA
**
388259 AATATAAAATAATAT-
1 AATATATTATAATATA
*
388274 AATACATTATAAATAGATAA
1 AATATATTAT-AAT--AT-A
388294 AATATATTATA
1 AATATATTATA
388305 TTTTACATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
15 7 0.20
16 16 0.46
18 2 0.06
19 1 0.03
20 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
AATATATTATAATATA
Found at i:388286 original size:20 final size:21
Alignment explanation
Indices: 388261--388304 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
388251 ATAATATAAA
*
388261 TATAAAATA-ATATAATACAT
1 TATAAAATAGATAAAATACAT
*
388281 TAT-AAATAGATAAAATATAT
1 TATAAAATAGATAAAATACAT
388301 TATA
1 TATA
388305 TTTTACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TATAAAATAGATAAAATACAT
Found at i:388564 original size:21 final size:21
Alignment explanation
Indices: 388539--388581 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
388529 AATCTTAAGT
388539 AAAATAAAT-TATAAATATATA
1 AAAATAAATATA-AAATATATA
**
388560 AAAATTTATATAAAATATATA
1 AAAATAAATATAAAATATATA
388581 A
1 A
388582 TAGGTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATAAATATAAAATATATA
Found at i:388727 original size:31 final size:28
Alignment explanation
Indices: 388690--388776 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
388680 TTTAAATACC
*
388690 AAATAATTATATAATATTAATATAATATAAA
1 AAATAATTA-A-AATA-TAATAAAATATAAA
*
388721 AAATAATTAAAATATGATAAAATATAAA
1 AAATAATTAAAATATAATAAAATATAAA
* *
388749 ATAT-ATT--AACATAATAAAAATATAAA
1 AAATAATTAAAATATAAT-AAAATATAAA
388775 AA
1 AA
388777 TATGTAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
25 6 0.12
26 11 0.22
27 3 0.06
28 15 0.31
29 4 0.08
30 1 0.02
31 9 0.18
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (28 bp):
AAATAATTAAAATATAATAAAATATAAA
Found at i:388749 original size:26 final size:25
Alignment explanation
Indices: 388707--388785 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 25
388697 TATATAATAT
* *
388707 TAATATAATATAAAAAATAATTAAAA
1 TAATAAAATATAAAATAT-ATTAAAA
*
388733 TATGATAAAATATAAAATATATTAACA
1 TA--ATAAAATATAAAATATATTAAAA
388760 TAATAAAAATATAAAA-ATATGTAAAA
1 TAAT-AAAATATAAAATATAT-TAAAA
388786 ATTTATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 6 0.13
26 17 0.38
27 8 0.18
28 14 0.31
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (25 bp):
TAATAAAATATAAAATATATTAAAA
Found at i:388785 original size:17 final size:18
Alignment explanation
Indices: 388713--388800 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 18
388703 ATATTAATAT
* *
388713 AATATAAAAAATAATTAA
1 AATATATAAAATAATAAA
388731 AATATGATAAAAT-AT-AA
1 AATAT-ATAAAATAATAAA
*
388748 AATATATTAACATAATAAA
1 AATATA-TAAAATAATAAA
*
388767 AATATA-AAAATATGTAAA
1 AATATATAAAATA-ATAAA
388785 AATTTATATAAAATAA
1 AA--TATATAAAATAA
388801 ATTATTAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 17 0.30
18 15 0.26
19 14 0.25
20 4 0.07
21 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (18 bp):
AATATATAAAATAATAAA
Found at i:388787 original size:10 final size:8
Alignment explanation
Indices: 388713--388779 Score: 53
Period size: 9 Copynumber: 7.6 Consensus size: 8
388703 ATATTAATAT
388713 AATATAAAA
1 AATAT-AAA
*
388722 AATAATTAA
1 AAT-ATAAA
388731 AATATGATAA
1 AATAT-A-AA
388741 AATATAAA
1 AATATAAA
*
388749 ATATATTAA
1 A-ATATAAA
*
388758 CATAATAAA
1 AAT-ATAAA
388767 AATATAAA
1 AATATAAA
388775 AATAT
1 AATAT
388780 GTAAAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
8 17 0.36
9 21 0.45
10 9 0.19
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (8 bp):
AATATAAA
Found at i:388843 original size:26 final size:26
Alignment explanation
Indices: 388814--388891 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 26
388804 ATTAATTTAT
* *
388814 TAAATTTATATAAATACATAATATCA
1 TAAATTTATATAAATACATAAAATAA
* **
388840 TAAATTTA-ATTAATTTA-AAAATAA
1 TAAATTTATATAAATACATAAAATAA
388864 TATAATTTAATATAAATACATAAAATAA
1 TA-AATTT-ATATAAATACATAAAATAA
388892 AAAAACAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
24 7 0.17
25 11 0.28
26 9 0.22
27 6 0.15
28 7 0.17
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAATTTATATAAATACATAAAATAA
Found at i:388905 original size:26 final size:26
Alignment explanation
Indices: 388872--388922 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
388862 AATATAATTT
*
388872 AATATAAATACA-TAAAATAAAAAAAC
1 AATATAAAGACATTAAAA-AAAAAAAC
*
388898 AATATAAAGATATTAAAAAAAAAAA
1 AATATAAAGACATTAAAAAAAAAAA
388923 GCTACGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (26 bp):
AATATAAAGACATTAAAAAAAAAAAC
Found at i:395031 original size:20 final size:22
Alignment explanation
Indices: 395008--395051 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
394998 GGCTCTCGTT
*
395008 AAAAAATTT-TCC-CTTTGATA
1 AAAAAATTTCTCCTCCTTGATA
395028 AAAAAATTTCTCCTCCTTGATA
1 AAAAAATTTCTCCTCCTTGATA
395050 AA
1 AA
395052 CGGTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 9 0.43
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAAAATTTCTCCTCCTTGATA
Found at i:395616 original size:3 final size:3
Alignment explanation
Indices: 395602--395635 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
395592 GGTCAAAGGC
*
395602 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
395636 GTGACTCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:402715 original size:20 final size:20
Alignment explanation
Indices: 402690--402754 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
402680 ACCACTGTTT
402690 GTATCGATACATGGCACATG
1 GTATCGATACATGGCACATG
402710 GTATCGATACAT------T-
1 GTATCGATACATGGCACATG
402723 GTATCGATACATGGCACATG
1 GTATCGATACATGGCACATG
402743 GTATCGATACAT
1 GTATCGATACAT
402755 TGTATCGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
19 1 0.03
20 24 0.63
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGGCACATG
Found at i:402726 original size:13 final size:13
Alignment explanation
Indices: 402705--402767 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
402695 GATACATGGC
*
402705 ACATGGTATCGAT
1 ACATTGTATCGAT
402718 ACATTGTATCGAT
1 ACATTGTATCGAT
*
402731 ACA-TG----G-C
1 ACATTGTATCGAT
*
402738 ACATGGTATCGAT
1 ACATTGTATCGAT
402751 ACATTGTATCGAT
1 ACATTGTATCGAT
402764 ACAT
1 ACAT
402768 GATGAATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
12 3 0.08
13 31 0.79
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:402788 original size:33 final size:33
Alignment explanation
Indices: 402688--402768 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
402678 CTACCACTGT
402688 TTGTATCGATACATGGCACATGGTATCGATACA
1 TTGTATCGATACATGGCACATGGTATCGATACA
402721 TTGTATCGATACATGGCACATGGTATCGATACA
1 TTGTATCGATACATGGCACATGGTATCGATACA
402754 TTGTATCGATACATG
1 TTGTATCGATACATG
402769 ATGAATTGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGGCACATGGTATCGATACA
Found at i:407952 original size:52 final size:52
Alignment explanation
Indices: 407857--407999 Score: 136
Period size: 52 Copynumber: 2.8 Consensus size: 52
407847 ATATAATTGT
* * *
407857 TAGTTAATATGGACTTGAACTT-TATA-GAGCTTGACT-TTTTTATA-TAGATG-
1 TAGTTAATATGAACTT-AAATTCTATAGGA-CTTGACTCTCTTTATACTAG-TGC
* * * *
407907 TCAGTTAATGTGGACATTAAGTTTTATAGGACTTGA-TCTCTTTATACTAGTGC
1 T-AGTTAATATGAAC-TTAAATTCTATAGGACTTGACTCTCTTTATACTAGTGC
407960 TAGTTAATATGAACTTAAATTCTATAGGACTTGACTCTCT
1 TAGTTAATATGAACTTAAATTCTATAGGACTTGACTCTCT
408000 ATACAAATGC
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
50 1 0.01
51 35 0.45
52 36 0.46
53 6 0.08
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (52 bp):
TAGTTAATATGAACTTAAATTCTATAGGACTTGACTCTCTTTATACTAGTGC
Found at i:408313 original size:62 final size:63
Alignment explanation
Indices: 408210--408329 Score: 206
Period size: 62 Copynumber: 1.9 Consensus size: 63
408200 TCATTCTGTC
*
408210 CTTATTCATCAATAAATAATAATTCATTGGTTTGGTTCAATGTTTGGGCTATTACATGTAATG
1 CTTATTCATCAAGAAATAATAATTCATTGGTTTGGTTCAATGTTTGGGCTATTACATGTAATG
* *
408273 CTTATTCATCAAGGAATAGTAATT-ATTGGTTTGGTTCAATGTTTGGGCTATTACATG
1 CTTATTCATCAAGAAATAATAATTCATTGGTTTGGTTCAATGTTTGGGCTATTACATG
408330 CAATTCCTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 33 0.61
63 21 0.39
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (63 bp):
CTTATTCATCAAGAAATAATAATTCATTGGTTTGGTTCAATGTTTGGGCTATTACATGTAATG
Found at i:408477 original size:14 final size:14
Alignment explanation
Indices: 408458--408490 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
408448 TTACTCTTTT
408458 ATATTATTTATTA-A
1 ATATTA-TTATTAGA
408472 ATATTATTATTAGA
1 ATATTATTATTAGA
408486 ATATT
1 ATATT
408491 TAATATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATTATTATTAGA
Found at i:408506 original size:33 final size:33
Alignment explanation
Indices: 408465--408676 Score: 99
Period size: 31 Copynumber: 6.4 Consensus size: 33
408455 TTTATATTAT
408465 TTATTAAATATTATTATTAGAATATTTAATATA
1 TTATTAAATATTATTATTAGAATATTTAATATA
*
408498 TTATT-AA-A-TATTATTAG-ATATTTACTATA
1 TTATTAAATATTATTATTAGAATATTTAATATA
* * *
408527 TTATTTAGAGTATT-TTAATAAAATATTATCAAATATAATTA
1 TTA-TTA-AATATTATTATTAGAATATT-T---A-AT-A-TA
*
408568 TTATTAAATATTATAAATATATA-AAT-TTTATTATA
1 TTATTAAATATTAT---TAT-TAGAATATTTAATATA
*
408603 TTATTAAA-A-TATTATAAAGTAAT-TTTAATATA
1 TTATTAAATATTATTAT-TAG-AATATTTAATATA
* * * * *
408635 TTATT-AATAATCTTATCAAAATA-TTAATTTA
1 TTATTAAATATTATTATTAGAATATTTAATATA
408666 TTATT-AATATT
1 TTATTAAATATT
408677 TTTACATATG
Statistics
Matches: 141, Mismatches: 15, Indels: 48
0.69 0.07 0.24
Matches are distributed among these distances:
29 14 0.10
30 16 0.11
31 23 0.16
32 21 0.15
33 19 0.13
34 7 0.05
35 11 0.08
36 1 0.01
37 1 0.01
38 2 0.01
39 6 0.04
40 5 0.04
41 6 0.04
42 2 0.01
43 5 0.04
44 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (33 bp):
TTATTAAATATTATTATTAGAATATTTAATATA
Found at i:408518 original size:20 final size:20
Alignment explanation
Indices: 408476--408519 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
408466 TATTAAATAT
*
408476 TATTATTAGAATATTTAATA
1 TATTATTAGAATATTTAAGA
*
408496 TATTATTA-AATATTATTAGA
1 TATTATTAGAATATT-TAAGA
408516 TATT
1 TATT
408520 TACTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
TATTATTAGAATATTTAAGA
Found at i:408589 original size:27 final size:26
Alignment explanation
Indices: 408538--408619 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 26
408528 TATTTAGAGT
* *
408538 ATTTTAATAAAATATTATCAA-ATATA
1 ATTTT-ATTAAATATTATAAATATATA
408564 ATTATTATTAAATATTATAAATATATAA
1 ATT-TTATTAAATATTATAAATATAT-A
*
408592 ATTTTATTATATTATTA-AAATATTATA
1 ATTTTATTA-AATATTATAAATA-TATA
408619 A
1 A
408620 AGTAATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 16 0.33
27 19 0.40
28 13 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTTATTAAATATTATAAATATATA
Found at i:408592 original size:8 final size:9
Alignment explanation
Indices: 408547--408643 Score: 58
Period size: 9 Copynumber: 10.6 Consensus size: 9
408537 TATTTTAATA
408547 AAATATTAT
1 AAATATTAT
*
408556 CAA-A-TAT
1 AAATATTAT
*
408563 AATTATTATT
1 AAATATTA-T
408573 AAATATTAT
1 AAATATTAT
408582 AAATA-TAT
1 AAATATTAT
*
408590 AAATTTTAT
1 AAATATTAT
*
408599 -TATATTATT
1 AAATATTA-T
408608 AAAATATTAT
1 -AAATATTAT
*
408618 AAAGTAATTTT
1 AAA-T-ATTAT
408629 AATATATTAT
1 AA-ATATTAT
*
408639 TAATA
1 AAATA
408644 ATCTTATCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 20
0.68 0.11 0.20
Matches are distributed among these distances:
7 4 0.06
8 14 0.21
9 20 0.30
10 15 0.22
11 13 0.19
12 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (9 bp):
AAATATTAT
Found at i:408616 original size:11 final size:11
Alignment explanation
Indices: 408600--408660 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
408590 AAATTTTATT
408600 ATATTATTAAA
1 ATATTATTAAA
408611 ATATTA-TAAA
1 ATATTATTAAA
* *
408621 GTAATT-TTAAT
1 AT-ATTATTAAA
408632 ATATTATTAATA
1 ATATTATTAA-A
* *
408644 ATCTTATCAAA
1 ATATTATTAAA
408655 ATATTA
1 ATATTA
408661 ATTTATTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
10 8 0.21
11 23 0.59
12 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (11 bp):
ATATTATTAAA
Found at i:408748 original size:28 final size:28
Alignment explanation
Indices: 408716--408770 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
408706 TAACATTTAT
*
408716 ATATTTTACATCTTTT-TTATATTATTAA
1 ATATTTTACAT-TTTTAATATATTATTAA
*
408744 ATATTTTATATTTTTAATATATTATTA
1 ATATTTTACATTTTTAATATATTATTA
408771 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTTTACATTTTTAATATATTATTAA
Found at i:408782 original size:28 final size:28
Alignment explanation
Indices: 408733--408815 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
408723 ACATCTTTTT
** **
408733 TATATTATTAAATATTTTATATTTTTAA
1 TATATTATTAAATATTAAATATTAATAA
**
408761 TATATTATTATTTATTAAATATTAATAA
1 TATATTATTAAATATTAAATATTAATAA
* * *
408789 AATATTATTAAATTTTATATGATTAAT
1 TATATTATTAAATATTAAAT-ATTAAT
408816 TATTATCATA
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 37 0.86
29 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
TATATTATTAAATATTAAATATTAATAA
Done.