Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 102 of 189
Found at i:28419921 original size:41 final size:41
Alignment explanation
Indices: 28419795--28419936 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 41
28419785 CAGTGCCTAT
*
28419795 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAA-CATTTCAGACTTTACGTCTAG
* * *
28419837 TAGGCTTAATGCCGGTGAAACAATATCAGACTTTACATCTAG
1 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTTTACGTCTAG
* * *
28419879 CAGGCTTAATGCCGGTGAAACATTTTAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACATTTCAGACTTTACGTCTAG
28419920 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
28419937 TACTGAATCA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 3 0.03
41 28 0.32
42 57 0.65
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (41 bp):
CAGGCTTAATGCCGGTGAAACATTTCAGACTTTACGTCTAG
Found at i:28421639 original size:70 final size:66
Alignment explanation
Indices: 28421534--28421665 Score: 174
Period size: 67 Copynumber: 1.9 Consensus size: 66
28421524 CCGAATAGAA
** *
28421534 AAAAGGAAAAACTACTTCGTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATTA
1 AAAAGGAAAAACTACTTCGTTTGATAAATGTTTACC-CAT-T-AAGTTAAAAGGCAAAACCATTA
28421599 AGTG
63 AGTG
* * *
28421603 AAAAGGCAAAACTACTTTGTTTTGATTAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGAAAAACTACTTCG-TTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
28421666 TATTGTTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 18 0.32
70 16 0.29
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (66 bp):
AAAAGGAAAAACTACTTCGTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTAAGT
G
Found at i:28425147 original size:79 final size:81
Alignment explanation
Indices: 28425011--28425195 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
28425001 TTGAATGATG
*
28425011 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28425075 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28425090 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28425152 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
28425170 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28425196 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:28425209 original size:40 final size:40
Alignment explanation
Indices: 28425012--28425195 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
28425002 TGAATGATGT
* * * *
28425012 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28425052 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28425092 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28425130 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28425171 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28425196 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28425217 original size:79 final size:79
Alignment explanation
Indices: 28425064--28425228 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28425054 GGACTAAGAT
* **
28425064 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28425129 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28425143 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28425206 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28425222 CCGAAGG
1 CCGAAGG
28425229 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28426383 original size:240 final size:240
Alignment explanation
Indices: 28425960--28426445 Score: 963
Period size: 240 Copynumber: 2.0 Consensus size: 240
28425950 AGCAGTGATG
28425960 TAGATTTGGAAAATCACTAAAAATAGTAGGAAGGGAATTAAATAGTGAATAAATTATGTAAACGA
1 TAGATTTGGAAAATCACTAAAAATAGTAGGAAGGGAATTAAATAGTGAATAAATTATGTAAACGA
28426025 ACCTTGATGAATCTATTTTCATAGGAAAGTAACGAAACGATCATATGGACAGTATGTTAAGAGAT
66 ACCTTGATGAATCTATTTTCATAGGAAAGTAACGAAACGATCATATGGACAGTATGTTAAGAGAT
*
28426090 ATTCAGGTTCTCGTAAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTTCGACTTTGGAAATTC
131 ATTCAGGTTCTCGCAAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTTCGACTTTGGAAATTC
28426155 ATTATAAATTAACCGGAGATAATTAGGAGTCATGCCATATATGTA
196 ATTATAAATTAACCGGAGATAATTAGGAGTCATGCCATATATGTA
28426200 TAGATTTGGAAAATCACTAAAAATAGTAGGAAGGGAATTAAATAGTGAATAAATTATGTAAACGA
1 TAGATTTGGAAAATCACTAAAAATAGTAGGAAGGGAATTAAATAGTGAATAAATTATGTAAACGA
28426265 ACCTTGATGAATCTATTTTCATAGGAAAGTAACGAAACGATCATATGGACAGTATGTTAAGAGAT
66 ACCTTGATGAATCTATTTTCATAGGAAAGTAACGAAACGATCATATGGACAGTATGTTAAGAGAT
28426330 ATTCAGGTTCTCGCAAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTTCGACTTTGGAAATTC
131 ATTCAGGTTCTCGCAAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTTCGACTTTGGAAATTC
28426395 ATTATAAATTAACCGGAGATAATTAGGAGTCATGCCATATATGTA
196 ATTATAAATTAACCGGAGATAATTAGGAGTCATGCCATATATGTA
28426440 TAGATT
1 TAGATT
28426446 CCTCTTTGAG
Statistics
Matches: 245, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 245 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (240 bp):
TAGATTTGGAAAATCACTAAAAATAGTAGGAAGGGAATTAAATAGTGAATAAATTATGTAAACGA
ACCTTGATGAATCTATTTTCATAGGAAAGTAACGAAACGATCATATGGACAGTATGTTAAGAGAT
ATTCAGGTTCTCGCAAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTTCGACTTTGGAAATTC
ATTATAAATTAACCGGAGATAATTAGGAGTCATGCCATATATGTA
Found at i:28428671 original size:10 final size:10
Alignment explanation
Indices: 28428656--28428680 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28428646 TATTTTTTCT
28428656 CATATTTATA
1 CATATTTATA
28428666 CATATTTATA
1 CATATTTATA
28428676 CATAT
1 CATAT
28428681 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (10 bp):
CATATTTATA
Found at i:28433023 original size:7 final size:6
Alignment explanation
Indices: 28432995--28433024 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
28432985 AATTTTTCAA
28432995 AAAAAG AAAAAG AAAAAG AAAAAG CAAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAA
28433025 AATAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:28434385 original size:42 final size:41
Alignment explanation
Indices: 28434337--28434474 Score: 125
Period size: 42 Copynumber: 3.2 Consensus size: 41
28434327 TTGCAGATCT
28434337 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCC-AGCC
* * * * * ** *
28434379 TATCTCCCTGAGCA-TCAGTGGAGTAGGTTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGT-AGTGGAGCAGATCG-AAGTCCCAG--CC
*
28434423 TATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCAAGCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCC-AGCC
28434465 TTATCTCCCT
1 -TATCTCCCT
28434475 GAGTAGCAGC
Statistics
Matches: 72, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
41 1 0.01
42 27 0.38
43 17 0.24
44 26 0.36
45 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAGCC
Found at i:28434465 original size:86 final size:87
Alignment explanation
Indices: 28434320--28434545 Score: 337
Period size: 86 Copynumber: 2.6 Consensus size: 87
28434310 GCGAAGCAGA
* *
28434320 TTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC-TATCT
1 TTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAAGCCTTATCT
* *
28434384 CCCTGAGCATCAGTGGAGTAGG
66 CCCTGAGCAGCAGCGGAGTAGG
* *
28434406 TTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCAAGCCTTATCT
1 TTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAAGCCTTATCT
*
28434471 CCCTGAGTAGCAGCGGAGTAGG
66 CCCTGAGCAGCAGCGGAGTAGG
* *
28434493 TTAAAAAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAG
1 TT---GAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
28434546 ACACTAGCCT
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 55 0.44
87 26 0.21
90 44 0.35
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAAGCCTTATCT
CCCTGAGCAGCAGCGGAGTAGG
Found at i:28434555 original size:90 final size:87
Alignment explanation
Indices: 28434326--28434556 Score: 338
Period size: 90 Copynumber: 2.6 Consensus size: 87
28434316 CAGATTGAAG
28434326 ATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC-TATCTCCCTGA
1 ATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTTATCTCCCTGA
* * *
28434390 GCATCAGTGGAGTAGGTTGAAA
66 GCAGCAGCGGAGTAGGTTAAAA
* * *
28434412 ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCAAGCCTTATCTCCCTGA
1 ATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTTATCTCCCTGA
*
28434477 GTAGCAGCGGAGTAGGTTAAAAAAA
66 GCAGCAGCGGAGTAGGTT---AAAA
* * *
28434502 ATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACACTAGCCTT
1 ATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTT
28434557 GCCTCCATCG
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
86 50 0.39
87 26 0.20
90 52 0.41
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (87 bp):
ATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTTATCTCCCTGA
GCAGCAGCGGAGTAGGTTAAAA
Found at i:28434763 original size:218 final size:217
Alignment explanation
Indices: 28434499--28435070 Score: 964
Period size: 218 Copynumber: 2.6 Consensus size: 217
28434489 TAGGTTAAAA
* * *
28434499 AAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACACTAGCCTTGCCTCCA
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCC-
*
28434564 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCCTGTACTGACAGTGAAGCAGAT
65 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
* *
28434629 TGAAAGAACCAATCTTATCTCCCTGGTCAGTAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
130 CGAAAAAACCAATCTTATCTCCCTGGTCAGTAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
28434694 TCTGGACAGTAGTGGAATAGGTT
195 TCTGGACAGTAGTGGAATAGGTT
28434717 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCT-CC
* * *
28434782 TCGGTGGTAGCGGAGCAGGCTAAAGATAGCAGATTTTGCCTCCCTATACTGACAGTGAAGCAGAT
65 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
* *
28434847 CGAAAAAACCAATCTTATCTCCCTGGTCAGTAGTGGAATAATTTGAGGATTGAGAATCCTATCTC
130 CGAAAAAACCAATCTTATCTCCCTGGTCAGTAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
28434912 TCTGGACAGTAGTGGAATAGGTT
195 TCTGGACAGTAGTGGAATAGGTT
** *
28434935 AAAATTTTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACATTAGCCTTGCCTCTC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTC-C
* * *
28435000 TCGGTGGCAGTGGAGCAGGTTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGTGAAGCAGAT
65 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
28435065 CGAAAA
130 CGAAAA
28435071 TTGTGAATCC
Statistics
Matches: 333, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
217 1 0.00
218 330 0.99
219 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (217 bp):
AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCT
CGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGATC
GAAAAAACCAATCTTATCTCCCTGGTCAGTAGTGAAATAAGTTGAGGATTGAGAATCCTATCTCT
CTGGACAGTAGTGGAATAGGTT
Found at i:28435204 original size:176 final size:175
Alignment explanation
Indices: 28434895--28435244 Score: 502
Period size: 176 Copynumber: 2.0 Consensus size: 175
28434885 TAATTTGAGG
* * **
28434895 ATTGAGAATCCTATCTCTCTGGACAGTAGTGGAATAGGTTAAAATTTTAGATCTTATCTCCCTAA
1 ATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAA
* ** * * **
28434960 GCAGTAGCGGAGCAGATCGAAGACATTAGCCTTGCCTCTCTCGGTGGCAGTGGAGCAGGTTAAAG
66 GCAGTAGCAGAGCAGATCGAAGACACCAACCTTGCCTCCCTCGGTCACAGTGGAGCAGGTTAAAG
*
28435025 ATAGCAGATATTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAA
131 ATAGCAGATATTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAA
* *
28435070 ATTGTGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAAATTACATATCTTATCTCCCTA
1 ATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTT-AAAATTACAGATCTTATCTCCCTA
* * * * * *
28435135 AGCAGTAGCAGAGCAGATCGAAGATACCAACCTTGCCTCCCTGGGTCATAGTGGATCATGTTGAA
65 AGCAGTAGCAGAGCAGATCGAAGACACCAACCTTGCCTCCCTCGGTCACAGTGGAGCAGGTTAAA
*
28435200 GATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAA
130 GATAGCAGATATTGCCTTCCTGTACCGACAGTGAAGCAGATCGAA
28435245 GATACCAGGC
Statistics
Matches: 153, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
175 37 0.24
176 116 0.76
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (175 bp):
ATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAA
GCAGTAGCAGAGCAGATCGAAGACACCAACCTTGCCTCCCTCGGTCACAGTGGAGCAGGTTAAAG
ATAGCAGATATTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAA
Found at i:28435241 original size:88 final size:88
Alignment explanation
Indices: 28435146--28435487 Score: 452
Period size: 88 Copynumber: 3.9 Consensus size: 88
28435136 GCAGTAGCAG
* ** * *
28435146 AGCAGATCGAAGATACCAACCTTGCCTCCCTGGGTCATAGTGGATCATGTTGAAGATAGCAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
28435211 TTGCCTTCCTGTACCGACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
* * * * *
28435234 AGCAGATCGAAGATACCAGGCTTGCCTCCCTGGGTTGTAGTAGAGTAGGTTGAAGATAACAAATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
** *
28435299 TTGTGTTCCTGTACCGATAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
*
28435322 AGCAGATCGAAGATACCAGCCTTGCCTCCTTGGGTTGTAGTGGAGCAGGTTGAAGATAGCCA-AT
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAG-CAGAT
**
28435386 CTTGCCTTCCTACACCGACAGTGA
65 CTTGCCTTCCTGTACCGACAGTGA
* * * * * *
28435410 AGCAGATCAAAGACACCAGCCTTGCTTCCCTGGGTTGTAGCGGAGCAGGCTGAAGATAGTAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
* *
28435475 TTGTCTTCATGTA
66 TTGCCTTCCTGTA
28435488 TTAGCGTGAA
Statistics
Matches: 218, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
87 1 0.00
88 215 0.99
89 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (88 bp):
AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATC
TTGCCTTCCTGTACCGACAGTGA
Found at i:28435248 original size:45 final size:45
Alignment explanation
Indices: 28435146--28435428 Score: 145
Period size: 44 Copynumber: 6.4 Consensus size: 45
28435136 GCAGTAGCAG
* * ** *
28435146 AGCAGATCGAAGATACCA-ACCTTGCCTCCCTGGGTC-ATAGTGG
1 AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACCGATAGTGA
* * * * *
28435189 ATCATG-TTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGA
1 AGCA-GATCGAAGATACCAGATCTTGCCTTCCTGGACCGATAGTGA
* * ***
28435234 AGCAGATCGAAGATACCAG-GCTTGCCTCCCTGGGTTG-TAGT-A
1 AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACCGATAGTGA
* * * * * ** *
28435276 GAGTAGGTTGAAGATAACAAATCTTGTGTTCCTGTACCGATAGTGA
1 -AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACCGATAGTGA
* *** *
28435322 AGCAGATCGAAGATACCAG-CCTTGCC-TCCTTGGGTTG-TAGTGG
1 AGCAGATCGAAGATACCAGATCTTGCCTTCC-TGGACCGATAGTGA
* * ** *
28435365 AGCAGGTTGAAGATAGCCA-ATCTTGCCTTCCTACACCGACAGTGA
1 AGCAGATCGAAGATA-CCAGATCTTGCCTTCCTGGACCGATAGTGA
* *
28435410 AGCAGATCAAAGACACCAG
1 AGCAGATCGAAGATACCAG
28435429 CCTTGCTTCC
Statistics
Matches: 166, Mismatches: 60, Indels: 26
0.66 0.24 0.10
Matches are distributed among these distances:
42 1 0.01
43 51 0.31
44 58 0.35
45 55 0.33
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (45 bp):
AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACCGATAGTGA
Found at i:28435518 original size:44 final size:44
Alignment explanation
Indices: 28435470--28435703 Score: 299
Period size: 44 Copynumber: 5.3 Consensus size: 44
28435460 TGAAGATAGT
* *
28435470 AGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
*** ** *
28435514 AGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGA-AAGC
1 AGATCTTGTCTTCATGTATTGG-CATGAAGTAGATCAAAGATAA-C
* * *
28435559 AGATCTTGTTTTCATGTATTGGCATGAAGTAGATCAAAGGTAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
* * * *
28435603 AGATCTTGTCTTCACGTATTGACATGAAGTAGATCGAAGATGAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
*
28435647 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
28435691 AGATCTTGTCTTC
1 AGATCTTGTCTTC
28435704 CCATACTGGT
Statistics
Matches: 160, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
44 124 0.77
45 36 0.22
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
Found at i:28435563 original size:89 final size:89
Alignment explanation
Indices: 28435461--28435731 Score: 393
Period size: 89 Copynumber: 3.1 Consensus size: 89
28435451 GGAGCAGGCT
* * * * *
28435461 GAAGATAGTAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTT
28435526 CCCATATTGGTGGTGAAGTAGATC
66 CCCATATTGGTGGTGAAGTAGATC
* *
28435550 GAAGAAAGCAGATCTTGTTTTCATGTATTGGCATGAAGTAGATCAAAGGTAGCAGATCTTGTCTT
1 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTT
* * ***
28435615 CACGTATT-GACATGAAGTAGATC
66 CCCATATTGGTGGTGAAGTAGATC
*
28435638 GAAG-ATGACAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
1 GAAGAAAG-CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
*
28435702 TCCCATACTGGTGGTGAAGTAGATC
65 TCCCATATTGGTGGTGAAGTAGATC
28435727 GAAGA
1 GAAGA
28435732 TCGCATCTAG
Statistics
Matches: 158, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
87 2 0.01
88 76 0.48
89 80 0.51
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (89 bp):
GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCTT
CCCATATTGGTGGTGAAGTAGATC
Found at i:28440164 original size:21 final size:21
Alignment explanation
Indices: 28440138--28440177 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28440128 CTAACAATAT
* *
28440138 ACCTTGTGGACCTCACAGTAC
1 ACCTTGCGAACCTCACAGTAC
28440159 ACCTTGCGAACCTCACAGT
1 ACCTTGCGAACCTCACAGT
28440178 GTAACCATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (21 bp):
ACCTTGCGAACCTCACAGTAC
Found at i:28441427 original size:90 final size:90
Alignment explanation
Indices: 28441270--28441441 Score: 245
Period size: 90 Copynumber: 1.9 Consensus size: 90
28441260 TTTATCTATT
* * * *
28441270 TATTATTGAACGTAGCTAAAGACGATGATGGGCCATCGAGAGGGAAAAGAAAGGCAAGATTCGTT
1 TATTATCGAACGTAGCTAAAGACGATGATGGGCCATCGAAAGGGAAAAGAAAGGCAAGAGTCATT
*
28441335 GACGAGCAACTGTGATTTGTGTTTG
66 GACAAGCAACTGTGATTTGTGTTTG
* * ** *
28441360 TATTATCGAATGTAGCTAAAGACGATGCTGGGCTGTCGAAAGGGAAAAGAAAGGCGAGAGTCATT
1 TATTATCGAACGTAGCTAAAGACGATGATGGGCCATCGAAAGGGAAAAGAAAGGCAAGAGTCATT
*
28441425 GACAAGTAACTGTGATT
66 GACAAGCAACTGTGATT
28441442 CCAATTTGCA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.24
Consensus pattern (90 bp):
TATTATCGAACGTAGCTAAAGACGATGATGGGCCATCGAAAGGGAAAAGAAAGGCAAGAGTCATT
GACAAGCAACTGTGATTTGTGTTTG
Found at i:28465919 original size:27 final size:27
Alignment explanation
Indices: 28465889--28466059 Score: 236
Period size: 27 Copynumber: 6.4 Consensus size: 27
28465879 GGTATAACAA
*
28465889 TCATTTTACCCTATGGGGATATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
**
28465916 TCATTTTACCCTATGGGGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCGG
**
28465943 TCATTTTACCCTATGGGGGTATTAAGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
28465970 TTATTTTACCCTAT-AGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
28465996 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
28466023 TCATTTTACCCTATAGTGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
28466050 TCATTTTACC
1 TCATTTTACC
28466060 TATTTTAGGG
Statistics
Matches: 126, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 21 0.17
27 105 0.83
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:28466013 original size:80 final size:81
Alignment explanation
Indices: 28465889--28466059 Score: 254
Period size: 80 Copynumber: 2.1 Consensus size: 81
28465879 GGTATAACAA
* * *
28465889 TCATTTTACCCTATGGGGATATTTCGGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCC
1 TCATTTTACCCTATAGGGATATTTCGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCC
*
28465954 TATGGGGGTATTAAGG
66 TATAGGGGTATTAAGG
* *
28465970 TTATTTTACCCTATAGGG-TATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCC
1 TCATTTTACCCTATAGGGATATTTCGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCC
* **
28466034 TATAGTGGTATTTTGG
66 TATAGGGGTATTAAGG
28466050 TCATTTTACC
1 TCATTTTACC
28466060 TATTTTAGGG
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 64 0.80
81 16 0.20
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (81 bp):
TCATTTTACCCTATAGGGATATTTCGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCC
TATAGGGGTATTAAGG
Found at i:28467198 original size:24 final size:24
Alignment explanation
Indices: 28467173--28467219 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
28467163 CCCAAATCCC
28467173 AATATTCTCTCCTCAAATCTCTCCA
1 AATATTC-CTCCTCAAATCTCTCCA
*
28467198 AATATTCCTCCTCAATTCTCTC
1 AATATTCCTCCTCAAATCTCTC
28467220 TATGACCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATTCCTCCTCAAATCTCTCCA
Found at i:28471492 original size:45 final size:46
Alignment explanation
Indices: 28471407--28471494 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
28471397 GAATGAATAT
*
28471407 AAATAGAGAAATGGAAAACATTAAAAAATGATTATGGTTTTCTTTG
1 AAATAGAGAAATGGAAAACATTAAAAAATGAATATGGTTTTCTTTG
* *** *
28471453 AAATAGAGAAAT-GAAATCATTTGGAAATGAATGTGGTTTTCT
1 AAATAGAGAAATGGAAAACATTAAAAAATGAATATGGTTTTCT
28471495 CAAAATTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 24 0.67
46 12 0.33
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (46 bp):
AAATAGAGAAATGGAAAACATTAAAAAATGAATATGGTTTTCTTTG
Found at i:28479476 original size:18 final size:18
Alignment explanation
Indices: 28479440--28479477 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28479430 AATATATATT
* *
28479440 TTAAAATATTTTAATTAA
1 TTAAAATATTTAAAATAA
28479458 TTAAAATATTTAAAATAA
1 TTAAAATATTTAAAATAA
28479476 TT
1 TT
28479478 GAGATCAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATATTTAAAATAA
Found at i:28484185 original size:29 final size:30
Alignment explanation
Indices: 28484139--28484195 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
28484129 AATCATTTGA
* *
28484139 TAAGGGGCGTAACTAAAAA-AATAAAAATG
1 TAAGGGGCGAAACAAAAAAGAATAAAAATG
* *
28484168 TAAGGGGTGAAACAAAAAAGGATAAAAA
1 TAAGGGGCGAAACAAAAAAGAATAAAAA
28484196 AAGAAAAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.58, C:0.05, G:0.23, T:0.14
Consensus pattern (30 bp):
TAAGGGGCGAAACAAAAAAGAATAAAAATG
Found at i:28489178 original size:21 final size:22
Alignment explanation
Indices: 28489136--28489178 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
28489126 TACTTCAAAC
*
28489136 CTTTCAAACATCTTAGAAAATT
1 CTTTCAAACATCTTACAAAATT
28489158 CTTT-AAACA-CTTACAATAATT
1 CTTTCAAACATCTTACAA-AATT
28489179 TTGCAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (22 bp):
CTTTCAAACATCTTACAAAATT
Found at i:28493822 original size:26 final size:27
Alignment explanation
Indices: 28493793--28493876 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 27
28493783 TGTAAATTAA
*
28493793 TAATAATAAATAAT-TT-AATCATATTT
1 TAATAATAAATAATATTAAAT-ATAATT
28493819 TAAT-AT-AATAATTATTAAATATAATT
1 TAATAATAAATAA-TATTAAATATAATT
28493845 TAATAA-AAATAATGA-T--ATATAATT
1 TAATAATAAATAAT-ATTAAATATAATT
28493869 TAATAATA
1 TAATAATA
28493877 TTCTTAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
24 19 0.38
25 4 0.08
26 17 0.34
27 10 0.20
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
TAATAATAAATAATATTAAATATAATT
Found at i:28493850 original size:24 final size:24
Alignment explanation
Indices: 28493823--28493890 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
28493813 ATATTTTAAT
28493823 ATAATAATTATTAAATATAATTTA
1 ATAATAATTATTAAATATAATTTA
* * * *
28493847 ATAAAAATAATGATATATAATTTA
1 ATAATAATTATTAAATATAATTTA
*
28493871 ATAAT-ATTCTT-AATATAATT
1 ATAATAATTATTAAATATAATT
28493891 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 8 0.23
23 3 0.09
24 24 0.69
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
ATAATAATTATTAAATATAATTTA
Found at i:28495835 original size:20 final size:21
Alignment explanation
Indices: 28495791--28495845 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
28495781 ACAGCATAAA
28495791 GATTTAAAGCATCAAACAAGT
1 GATTTAAAGCATCAAACAAGT
*
28495812 GATTTAAA-CATCAAATAA-T
1 GATTTAAAGCATCAAACAAGT
*
28495831 CGATTCAAAGCATCA
1 -GATTTAAAGCATCA
28495846 TTCAATCAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (21 bp):
GATTTAAAGCATCAAACAAGT
Found at i:28506832 original size:80 final size:81
Alignment explanation
Indices: 28506695--28506879 Score: 238
Period size: 80 Copynumber: 2.3 Consensus size: 81
28506685 GGTATAACAG
**
28506695 TCATTTTACCCTATACGGGTATTTCTATCATTTTACCCTATGGGGATATTTCGATCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCTATCATTTTACCCTATGGGGATATTTCGATCATTTTACCC
*
28506760 T-T-GGGTGTATTTTGA
66 TATAGGG-GTATTTCGA
28506775 TCGA-TTTACCCTATGGGGGTATTTCGT-TCGA-TTTACCCTATGAGGG-TATTTCGATCATTTT
1 TC-ATTTTACCCTATGGGGGTATTTC-TATC-ATTTTACCCTATG-GGGATATTTCGATCATTTT
28506836 ACCCTATAGGGGTATTTCGA
62 ACCCTATAGGGGTATTTCGA
* *
28506856 TCATTTTATCGTATGGGGGTATTT
1 TCATTTTACCCTATGGGGGTATTT
28506880 TGGTCATTCT
Statistics
Matches: 93, Mismatches: 5, Indels: 13
0.84 0.05 0.12
Matches are distributed among these distances:
80 55 0.59
81 35 0.38
82 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCTATCATTTTACCCTATGGGGATATTTCGATCATTTTACCC
TATAGGGGTATTTCGA
Found at i:28506887 original size:27 final size:27
Alignment explanation
Indices: 28506695--28506879 Score: 232
Period size: 27 Copynumber: 6.9 Consensus size: 27
28506685 GGTATAACAG
** *
28506695 TCATTTTACCCTATACGGGTATTTCTA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
28506722 TCATTTTACCCTATGGGGATATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
28506749 TCATTTTACCCT-TGGGTGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
28506775 TCGA-TTTACCCTATGGGGGTATTTCGT
1 TC-ATTTTACCCTATGGGGGTATTTCGA
*
28506802 TCGA-TTTACCCTATGAGGGTATTTCGA
1 TC-ATTTTACCCTATGGGGGTATTTCGA
*
28506829 TCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
28506856 TCATTTTATCGTATGGGGGTATTT
1 TCATTTTACCCTATGGGGGTATTT
28506880 TGGTCATTCT
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
26 22 0.16
27 116 0.84
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:28509171 original size:25 final size:25
Alignment explanation
Indices: 28509143--28509280 Score: 131
Period size: 25 Copynumber: 5.5 Consensus size: 25
28509133 TAGTACTTCA
28509143 CCACAAAGGCTTTTCACAAGATTAG
1 CCACAAAGGCTTTTCACAAGATTAG
* * **
28509168 CCACAAAGGCTTCTCAGATTA-TACG
1 CCACAAAGGCTTTTCACAAGATTA-G
* *
28509193 CCACAAAGGCTTTTCACAACATTTG
1 CCACAAAGGCTTTTCACAAGATTAG
** *
28509218 TAACAAAGGC--TTC-CTAGATAATACG
1 CCACAAAGGCTTTTCACAAGAT--TA-G
28509243 CCACAAAGGCTTTTCACAAGATTAG
1 CCACAAAGGCTTTTCACAAGATTAG
28509268 CCACAAAGGCTTT
1 CCACAAAGGCTTT
28509281 CTAGGTAACC
Statistics
Matches: 88, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
22 4 0.05
23 3 0.03
24 3 0.03
25 67 0.76
26 3 0.03
27 3 0.03
28 5 0.06
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
CCACAAAGGCTTTTCACAAGATTAG
Found at i:28509202 original size:50 final size:50
Alignment explanation
Indices: 28509143--28509284 Score: 214
Period size: 50 Copynumber: 2.8 Consensus size: 50
28509133 TAGTACTTCA
*
28509143 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTT-CTCAGATTATACG
1 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCT-AGATAATACG
* * **
28509193 CCACAAAGGCTTTTCACAACATTTGTAACAAAGGCTTCCTAGATAATACG
1 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAGATAATACG
*
28509243 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTTCTAG
1 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAG
28509285 GTAACCTGTC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 79 0.98
51 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (50 bp):
CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTCCTAGATAATACG
Found at i:28516051 original size:28 final size:28
Alignment explanation
Indices: 28516005--28516113 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 28
28515995 TTGGTAAAAA
* * **
28516005 TGGGCCCACACGTTTGTGTGTGCTTATG
1 TGGGCCCACACGCTCGTGTGTGCCCATG
28516033 TGGGCCCACACGCTCGTGTGTGCCCATG
1 TGGGCCCACACGCTCGTGTGTGCCCATG
* ** * *
28516061 TGGGTCCGTACGCCCGTGTGTGCCCGTG
1 TGGGCCCACACGCTCGTGTGTGCCCATG
* * * *
28516089 TGGACCCGCACACCCGTGTG-GCCCA
1 TGGGCCCACACGCTCGTGTGTGCCCA
28516114 CTCGGCCCAT
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 4 0.06
28 63 0.94
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.24
Consensus pattern (28 bp):
TGGGCCCACACGCTCGTGTGTGCCCATG
Found at i:28521411 original size:66 final size:66
Alignment explanation
Indices: 28521305--28521437 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
28521295 AACTACTTGG
28521305 ATCCTTCAACTTAAGATACAACCTAATCTGCAAAAATAAGCTACATTTTATAGTTAGGGCTGCTT
1 ATCCTTCAACTTAAGATACAACCTAATCTGCAAAAATAAGCTACATTTTATAGTTAGGGCTGCTT
28521370 C
66 C
28521371 ATCCTTCAACTTAAGATACAACCTAATCTGCAAAAATAAGCTACATTTTATAGTTAGGGCTGCTT
1 ATCCTTCAACTTAAGATACAACCTAATCTGCAAAAATAAGCTACATTTTATAGTTAGGGCTGCTT
28521436 C
66 C
28521437 A
1 A
28521438 AATTACTTAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (66 bp):
ATCCTTCAACTTAAGATACAACCTAATCTGCAAAAATAAGCTACATTTTATAGTTAGGGCTGCTT
C
Found at i:28533151 original size:21 final size:21
Alignment explanation
Indices: 28533125--28533173 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28533115 CATTGTTTCT
** *
28533125 AATCTCACTGCTACAATATCC
1 AATCTCACCACTACAATAACC
*
28533146 AATCTCACCACTACAATAACT
1 AATCTCACCACTACAATAACC
28533167 AATCTCA
1 AATCTCA
28533174 TCGCCACTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.33, G:0.02, T:0.27
Consensus pattern (21 bp):
AATCTCACCACTACAATAACC
Found at i:28534184 original size:47 final size:47
Alignment explanation
Indices: 28534130--28534227 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 47
28534120 GAGAGAAAGA
28534130 GACATAAGGTGGTGAGTGGGAAAGGCTTACTAAGGGGGAGAATAGGG
1 GACATAAGGTGGTGAGTGGGAAAGGCTTACTAAGGGGGAGAATAGGG
*
28534177 GACATAAGGTGGTGAGTGGGGAAGGCTTACTAAGGGGGAGAATAGGG
1 GACATAAGGTGGTGAGTGGGAAAGGCTTACTAAGGGGGAGAATAGGG
28534224 GACA
1 GACA
28534228 ATATGATGTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.32, C:0.07, G:0.45, T:0.16
Consensus pattern (47 bp):
GACATAAGGTGGTGAGTGGGAAAGGCTTACTAAGGGGGAGAATAGGG
Found at i:28537431 original size:15 final size:17
Alignment explanation
Indices: 28537411--28537442 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28537401 TATGGATTGA
28537411 GAATATT-TGT-TTTTG
1 GAATATTATGTGTTTTG
28537426 GAATATTATGTGTTTTG
1 GAATATTATGTGTTTTG
28537443 AAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (17 bp):
GAATATTATGTGTTTTG
Found at i:28551086 original size:67 final size:67
Alignment explanation
Indices: 28550996--28551163 Score: 185
Period size: 67 Copynumber: 2.5 Consensus size: 67
28550986 TTTTTTCTCA
* * * *
28550996 GCAGACTATCTTTATTGTCATAGTCAAGCTATGGACTTACACAGCACACCCCATATTTAATGTCA
1 GCAGACTATATTTGTTGCCATAGTCAAGCTATGGACTTACACAGCACACCACATATTTAATGTCA
28551061 TG
66 TG
* * * * * * *
28551063 GTAGACTATATTTGTTGCCATAGTCGAGCAATGGACTTACATAGTACACCACATGTTTAATGTCC
1 GCAGACTATATTTGTTGCCATAGTCAAGCTATGGACTTACACAGCACACCACATATTTAATGTCA
28551128 TG
66 TG
* * * *
28551130 GCGGACTCTATTGGTTGGCATAGTCTAA-CTATGG
1 GCAGACTATATTTGTTGCCATAGTC-AAGCTATGG
28551164 TCCTATAACT
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
67 81 0.99
68 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (67 bp):
GCAGACTATATTTGTTGCCATAGTCAAGCTATGGACTTACACAGCACACCACATATTTAATGTCA
TG
Found at i:28551289 original size:27 final size:27
Alignment explanation
Indices: 28551203--28551296 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
28551193 GTCACGACGA
* * * *
28551203 ACTATCCCGTGTTTGCTGTCCCAACGG
1 ACTATCCCATGTTTACTATCCCAACAG
* * * * * *
28551230 ACTATCCTATGTTTATTCTCTCGACAA
1 ACTATCCCATGTTTACTATCCCAACAG
*
28551257 AGTATCCCATGTTTACTATCCCAACAG
1 ACTATCCCATGTTTACTATCCCAACAG
*
28551284 ACTATCTCATGTT
1 ACTATCCCATGTT
28551297 ATTGTTTCGG
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (27 bp):
ACTATCCCATGTTTACTATCCCAACAG
Found at i:28552657 original size:14 final size:16
Alignment explanation
Indices: 28552638--28552670 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
28552628 TTACATAGAG
28552638 CTCACATA-T-CACAA
1 CTCACATATTCCACAA
28552652 CTCACATATTCCACAA
1 CTCACATATTCCACAA
28552668 CTC
1 CTC
28552671 TCACATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
CTCACATATTCCACAA
Found at i:28552658 original size:25 final size:25
Alignment explanation
Indices: 28552612--28552659 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28552602 TACTTTGTTG
* *
28552612 GCTCACACATAACCACTTACATAGA
1 GCTCACACATAACAACTCACATAGA
* *
28552637 GCTCACATATCACAACTCACATA
1 GCTCACACATAACAACTCACATA
28552660 TTCCACAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.33, G:0.06, T:0.21
Consensus pattern (25 bp):
GCTCACACATAACAACTCACATAGA
Found at i:28552870 original size:51 final size:51
Alignment explanation
Indices: 28552809--28553322 Score: 562
Period size: 51 Copynumber: 10.1 Consensus size: 51
28552799 TTTGCTTATA
* * * * * *
28552809 GAACTGAATATTATCAGCACGCACATACTTTTTTTATATAGTTAACACATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* *
28552860 GAACTTAATATAATCAACACGCACATACTTGGTTTAGACAGTTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* * *
28552911 GAACTTAATATAATCAACACGCGCATACTTTTTTTAGATAGTTCACAAATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* * * * * * *
28552962 GAGCTTAATATAATTAGCACACACATACTTGGTTTAGACAGTTCACACATA
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* * * * * * *
28553013 GAACTTAATATAACCAGCATGCACATACCTGGTTTAGACAATTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* * *
28553064 GAACTTAATATAATCAAAACGCACATACTTTGTTTAAATAGTTCACAAATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* * ** * * * *
28553115 GAGCTTAATATAATTAACATACACATACTTAGTTTAGACAATTCACAAATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* ** *
28553166 AAACTTAATATAATCAGTACACACATACTTTGTTTAGATAGTTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* * *
28553217 GAACTTAATATAATCAATACACATATACTTTGTTTAGATAGTTCACACATG
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
* ** * * * * *
28553268 GAACTTAATATAATTAGTACGCATATACGTAGTTTAGACAGTTCACAAAT-
1 GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
28553318 GAACT
1 GAACT
28553323 CTTCCTTGTG
Statistics
Matches: 393, Mismatches: 70, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
50 5 0.01
51 388 0.99
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (51 bp):
GAACTTAATATAATCAACACGCACATACTTTGTTTAGATAGTTCACACATG
Found at i:28553093 original size:153 final size:152
Alignment explanation
Indices: 28552815--28553322 Score: 665
Period size: 153 Copynumber: 3.3 Consensus size: 152
28552805 TATAGAACTG
* * * ** * * * * *
28552815 AATATTATCAGCACGCACATACTTTTTTTATATAGTTAACACATGGAACTTAATATAATCAACAC
1 AATATAATTAGCACACACATACTTAGTTTAGACAGTTCACAAAT-GAACTTAATATAATCAGCAC
* * *
28552880 GCACATACTTGGTTTAGACAGTTCACACATGGAACTTAATATAATCAACACGCGCATACTTTTTT
65 GCACATACTTGGTTTAGACAGTTCACACATGGAACTTAATATAATCAAAACGCACATACTTTGTT
28552945 TAGATAGTTCACAAATGGAGCTT
130 TAGATAGTTCACAAATGGAGCTT
* * * *
28552968 AATATAATTAGCACACACATACTTGGTTTAGACAGTTCACACATAGAACTTAATATAACCAGCAT
1 AATATAATTAGCACACACATACTTAGTTTAGACAGTTCACAAAT-GAACTTAATATAATCAGCAC
* *
28553033 GCACATACCTGGTTTAGACAATTCACACATGGAACTTAATATAATCAAAACGCACATACTTTGTT
65 GCACATACTTGGTTTAGACAGTTCACACATGGAACTTAATATAATCAAAACGCACATACTTTGTT
*
28553098 TAAATAGTTCACAAATGGAGCTT
130 TAGATAGTTCACAAATGGAGCTT
* * * *
28553121 AATATAATTAACATACACATACTTAGTTTAGACAATTCACAAATGAAACTTAATATAATCAGTAC
1 AATATAATTAGCACACACATACTTAGTTTAGACAGTTCACAAATG-AACTTAATATAATCAGCAC
* * * * * *
28553186 ACACATACTTTGTTTAGATAGTTCACACATGGAACTTAATATAATCAATACACATATACTTTGTT
65 GCACATACTTGGTTTAGACAGTTCACACATGGAACTTAATATAATCAAAACGCACATACTTTGTT
* *
28553251 TAGATAGTTCACACATGGAACTT
130 TAGATAGTTCACAAATGGAGCTT
* * * *
28553274 AATATAATTAGTACGCATATACGTAGTTTAGACAGTTCACAAATGAACT
1 AATATAATTAGCACACACATACTTAGTTTAGACAGTTCACAAATGAACT
28553323 CTTCCTTGTG
Statistics
Matches: 310, Mismatches: 44, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
152 5 0.02
153 305 0.98
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (152 bp):
AATATAATTAGCACACACATACTTAGTTTAGACAGTTCACAAATGAACTTAATATAATCAGCACG
CACATACTTGGTTTAGACAGTTCACACATGGAACTTAATATAATCAAAACGCACATACTTTGTTT
AGATAGTTCACAAATGGAGCTT
Found at i:28553212 original size:24 final size:24
Alignment explanation
Indices: 28553185--28553266 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
28553175 ATAATCAGTA
28553185 CACACATACTTTGTTTAGATAGTT
1 CACACATACTTTGTTTAGATAGTT
** * * *
28553209 CACACATGGAACTTAATATA-ATCAATA
1 CACACAT---ACTTTGTTTAGAT-AGTT
*
28553236 CACATATACTTTGTTTAGATAGTT
1 CACACATACTTTGTTTAGATAGTT
28553260 CACACAT
1 CACACAT
28553267 GGAACTTAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 22 0.54
25 2 0.05
26 2 0.05
27 15 0.37
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (24 bp):
CACACATACTTTGTTTAGATAGTT
Found at i:28553285 original size:27 final size:27
Alignment explanation
Indices: 28553204--28553285 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
28553194 TTTGTTTAGA
28553204 TAGTTCACACATGGAACTTAATATAAT
1 TAGTTCACACATGGAACTTAATATAAT
* * ** *
28553231 CA-AT-ACACAT--ATACTTTGTTTAGA-
1 TAGTTCACACATGGA-ACTTAATATA-AT
28553255 TAGTTCACACATGGAACTTAATATAAT
1 TAGTTCACACATGGAACTTAATATAAT
28553282 TAGT
1 TAGT
28553286 ACGCATATAC
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
23 1 0.03
24 8 0.21
25 8 0.21
26 8 0.21
27 12 0.32
28 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (27 bp):
TAGTTCACACATGGAACTTAATATAAT
Found at i:28553916 original size:43 final size:42
Alignment explanation
Indices: 28553848--28554155 Score: 370
Period size: 43 Copynumber: 7.3 Consensus size: 42
28553838 GTCGCTAACT
*
28553848 TTTA-CGGCGCTTTTCCACAAACGCCGCTATAAATCAAGACC
1 TTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACC
* *
28553889 TTTAGCGGCGCTTTTCTCACAAACGCCGCTATAGACCGTA-ACC
1 TTTAGCGGCGCTTTTC-CACAAACGCCGCTATAGATC-AAGACC
* *
28553932 TTTAGCGACGCTTTTACCACAAACGCCGCTATAGACCAAGACC
1 TTTAGCGGCGCTTTT-CCACAAACGCCGCTATAGATCAAGACC
** *
28553975 TTTAGCGGCGCTTTTCCCACAAACATCGCTATAGATCTAGACC
1 TTTAGCGGCGCTTTT-CCACAAACGCCGCTATAGATCAAGACC
* * * *
28554018 TTTAGGGGCGCTTTCCCAAAAACGCCGCTATAGATCAGGACC
1 TTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACC
* * * * *
28554060 TTTAACGGTGCTTTTCAACAAACGCCGCTATAGATCAGGATC
1 TTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACC
** * *
28554102 TTTAGCGGTACTTTTTCACAAACGCCGCTATAGAACAA-ACC
1 TTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACC
28554143 TTTAGCGGCGCTT
1 TTTAGCGGCGCTT
28554156 CTCGTAAAAC
Statistics
Matches: 228, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
41 17 0.07
42 101 0.44
43 108 0.47
44 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACC
Found at i:28558813 original size:22 final size:23
Alignment explanation
Indices: 28558775--28558820 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
28558765 AAATTAAAGG
28558775 AGTCAATAAAAACAAGAGATGTT
1 AGTCAATAAAAACAAGAGATGTT
*
28558798 AGTCAATAAAAA-AAGATATGTT
1 AGTCAATAAAAACAAGAGATGTT
28558820 A
1 A
28558821 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (23 bp):
AGTCAATAAAAACAAGAGATGTT
Found at i:28558830 original size:23 final size:23
Alignment explanation
Indices: 28558777--28558822 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
28558767 ATTAAAGGAG
*
28558777 TCAATAAAAACAAGAGATGTTAG
1 TCAATAAAAACAAGAGATGTTAA
*
28558800 TCAATAAAAA-AAGATATGTTAA
1 TCAATAAAAACAAGAGATGTTAA
28558822 T
1 T
28558823 TAATTAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (23 bp):
TCAATAAAAACAAGAGATGTTAA
Found at i:28559702 original size:41 final size:41
Alignment explanation
Indices: 28559604--28559703 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
28559594 GCTTTTTCAA
* * *
28559604 AGCATTAGTGGCGCTTTTTCAGAAACACCGCTAAAGACTCG
1 AGCATTAGTGGCGCTTTTCCAAAAACACCGCTAAAGACCCG
** *
28559645 AGCATTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGACCCG
1 AGCATTAGTGGCGCTTTTCCAAAAACACCGCTAAAGACCCG
*
28559686 AGCATTAGTGGTGCTTTT
1 AGCATTAGTGGCGCTTTT
28559704 TCAACTAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (41 bp):
AGCATTAGTGGCGCTTTTCCAAAAACACCGCTAAAGACCCG
Found at i:28559882 original size:40 final size:40
Alignment explanation
Indices: 28559775--28559886 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
28559765 TCCCAAAAAA
* * * * *
28559775 CGCCGCTAATGCTC-ATTTTTCGCGGCGCTTTCCTTGAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTTCGTAAAG
* * *
28559814 TGCCGCTAATGATCGATCTTTAGCGGCGTTTTTCGTAAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTTCGTAAAG
*
28559854 CGCCGGTAATGCTCGATTTTTAGCGGCGTTTTT
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTT
28559887 TATCCAAACG
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
39 12 0.20
40 48 0.80
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTTCGTAAAG
Found at i:28560822 original size:10 final size:10
Alignment explanation
Indices: 28560807--28560839 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
28560797 AAAAATATCA
28560807 TATTAATTTT
1 TATTAATTTT
28560817 TATTAA-TTT
1 TATTAATTTT
28560826 TATTAATTTT
1 TATTAATTTT
28560836 TATT
1 TATT
28560840 TTACTTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTAATTTT
Found at i:28563970 original size:9 final size:9
Alignment explanation
Indices: 28563956--28563986 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28563946 GTTAAACGAA
28563956 TCGAGTTAT
1 TCGAGTTAT
*
28563965 TCGAGTTAA
1 TCGAGTTAT
28563974 TCGAGTTAT
1 TCGAGTTAT
28563983 TCGA
1 TCGA
28563987 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28566777 original size:25 final size:25
Alignment explanation
Indices: 28566674--28566788 Score: 108
Period size: 25 Copynumber: 4.6 Consensus size: 25
28566664 GTATATGTAT
* *
28566674 GCTCATACGAGCTGTA-AACAGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
28566698 GCTCCT-CTGAGCTGAATAATGGTAA
1 GCTCATAC-GAGCTGAATAACGGTAA
* * * * *
28566723 GCTCCTCCAAGCTAAATAATGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
28566748 GCTCATACGAGCTGAGTAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
28566773 GCTCATAAGAGCTGAA
1 GCTCATACGAGCTGAA
28566789 ATTGGTAACC
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.01
24 12 0.16
25 60 0.81
26 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:28566851 original size:74 final size:74
Alignment explanation
Indices: 28566770--28566917 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
28566760 TGAGTAACGG
*
28566770 TAAGCTCATAAGAGCTGAAATTGGTAACCATAATGACATGTCATTTGTATCCTACGAATTTCTAA
1 TAAGCTCATAAGAGCTGAAATTGGTAACCATAATGACATGTCATTTGTATCCTACGAATTCCTAA
28566835 GGTTCAAAC
66 GGTTCAAAC
* *
28566844 TAAGCTCATAAGAGCTGAAATTGGTAACCCTAGTGACATGTCATTTGTATCCTACGAATTCCTAA
1 TAAGCTCATAAGAGCTGAAATTGGTAACCATAATGACATGTCATTTGTATCCTACGAATTCCTAA
28566909 GGTTCAAAC
66 GGTTCAAAC
28566918 AGGGCTCGGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (74 bp):
TAAGCTCATAAGAGCTGAAATTGGTAACCATAATGACATGTCATTTGTATCCTACGAATTCCTAA
GGTTCAAAC
Found at i:28573550 original size:50 final size:50
Alignment explanation
Indices: 28573439--28573685 Score: 259
Period size: 50 Copynumber: 4.8 Consensus size: 50
28573429 ATTTGGGTAA
28573439 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
* * *
28573495 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * * *
28573545 AGAGGTCACC-CGTAAGACCATGTCTGGGACATGGCATAGGCACCAATATG
1 AGAGATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * *
28573595 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGAATTGGCA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATG
* * *
28573644 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28573686 TGTTATTATC
Statistics
Matches: 165, Mismatches: 21, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
49 41 0.25
50 78 0.47
51 4 0.02
55 2 0.01
56 40 0.24
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:28577739 original size:25 final size:25
Alignment explanation
Indices: 28577649--28577764 Score: 101
Period size: 25 Copynumber: 4.6 Consensus size: 25
28577639 GCGAACACAC
*
28577649 CACAGCTCGTATGAGCTTCCCAATT
1 CACAGCTCGTATGAGCTTACCAATT
*
28577674 TACAGCTCGTGA-GAGCTTACCAATT
1 CACAGCTCGT-ATGAGCTTACCAATT
* * * *
28577699 CTCAACTCATATGAGCTTACCGATT
1 CACAGCTCGTATGAGCTTACCAATT
* * *
28577724 CACAGCTCGTGA-GAGCATATCGATT
1 CACAGCTCGT-ATGAGCTTACCAATT
* *
28577749 CATAGCTCATATGAGC
1 CACAGCTCGTATGAGC
28577765 ATATATGTAC
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.03
25 69 0.95
26 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCAATT
Found at i:28577758 original size:50 final size:50
Alignment explanation
Indices: 28577651--28577764 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 50
28577641 GAACACACCA
* * * *
28577651 CAGCTCGTATGAGCTTCCCAATTTACAGCTCGTGAGAGCTTACCAATTCT
1 CAGCTCATATGAGCTTACCAATTCACAGCTCGTGAGAGCATACCAATTCT
* * * *
28577701 CAACTCATATGAGCTTACCGATTCACAGCTCGTGAGAGCATATCGATTCAT
1 CAGCTCATATGAGCTTACCAATTCACAGCTCGTGAGAGCATACCAATTC-T
28577752 -AGCTCATATGAGC
1 CAGCTCATATGAGC
28577765 ATATATGTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 53 0.98
51 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (50 bp):
CAGCTCATATGAGCTTACCAATTCACAGCTCGTGAGAGCATACCAATTCT
Found at i:28600197 original size:17 final size:17
Alignment explanation
Indices: 28600175--28600215 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28600165 ATTTTCAATC
28600175 TTTTTTCTTCATTTTTA
1 TTTTTTCTTCATTTTTA
* *
28600192 TTTTTTTTTCGTTTTTA
1 TTTTTTCTTCATTTTTA
28600209 TTCTTTT
1 TT-TTTT
28600216 AAAATGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTTCTTCATTTTTA
Found at i:28601649 original size:107 final size:107
Alignment explanation
Indices: 28601417--28601842 Score: 611
Period size: 108 Copynumber: 4.0 Consensus size: 107
28601407 TATTCAAATA
* ** * *
28601417 AAAATTTCAAAATAAGGTAATATTTTGTGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTAG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * *
28601482 ATTTCGCTTTTTTCGTTCGACCAAATAGGTAAAATATCCTTTT
66 GTTTCG-ATTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
* *
28601525 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCAAACATGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
28601590 GTTTCGATTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
66 GTTTCGATTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
* * *
28601632 AGAATTTCAAAATAAGGCAATATTTTACGTTTTGGAAATTCGAAAAAACGTGCCCTAACGCGCTG
1 AAAATTTCAAAATAAGGCAATATTTTACG-TTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* **
28601697 GGTTTCGATTTTTCGCTCGACCAAATAGCTAAAATATCCTTCA
65 GGTTTCGATTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
* * * *
28601740 AAAATTTCAAAATAAGACAATATTTTGCTTTTGAAAATTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* ** *
28601805 GTTTCGATTTCTCGTTAAACCAAATAGC-CAAATATCCT
66 GTTTCGATTTTTCGTTCGACCAAATAGCTAAAATATCCT
28601843 CTTATACCTT
Statistics
Matches: 287, Mismatches: 30, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
106 9 0.03
107 119 0.41
108 159 0.55
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (107 bp):
AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
Found at i:28601790 original size:215 final size:214
Alignment explanation
Indices: 28601419--28601842 Score: 618
Period size: 215 Copynumber: 2.0 Consensus size: 214
28601409 TTCAAATAAA
* * * *
28601419 AATTTCAAAATAAGGTAATATTTTGTGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTAGAT
1 AATTTCAAAATAAGGCAATATTTTGTGTTTGGAAATTCGAAAAAACGTGCCCTAACGCGCTAGAT
* * * ** *
28601484 TTCGCTTTTTTCGTTCGACCAAATAGGTAAAATATCCTTTTAAAATTTCAAAATAAGGCAATATT
66 TTCGCATTTTTCGCTCGACCAAATAGCTAAAATATCCTTCAAAAATTTCAAAATAAGACAATATT
* * **
28601549 TTACGTTTGGAAATTCGAGAAAACGTGCCCAAACATGCTGGGTTTCGATTTTTCGTTCGACCAAA
131 TTACGTTTGAAAATTCGAGAAAACGTGCCCAAACATGCTGGGTTTCGATTTCTCGTTAAACCAAA
28601614 TAGCTAAAATATCCTTTTAG
196 TAGC-AAAATATCCTTTTAG
*
28601634 AATTTCAAAATAAGGCAATATTTTACGT-TTTGGAAATTCGAAAAAACGTGCCCTAACGCGCTGG
1 AATTTCAAAATAAGGCAATATTTT--GTGTTTGGAAATTCGAAAAAACGTGCCCTAACGCGCTAG
*
28601698 GTTTCG-ATTTTTCGCTCGACCAAATAGCTAAAATATCCTTCAAAAATTTCAAAATAAGACAATA
64 ATTTCGCATTTTTCGCTCGACCAAATAGCTAAAATATCCTTCAAAAATTTCAAAATAAGACAATA
* * * *
28601762 TTTTGCTTTTGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTAAACCA
129 TTTTACGTTTGAAAATTCGAGAAAACGTGCCCAAACATGCTGGGTTTCGATTTCTCGTTAAACCA
*
28601827 AATAGCCAAATATCCT
194 AATAGCAAAATATCCT
28601843 CTTATACCTT
Statistics
Matches: 186, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
214 9 0.05
215 138 0.74
216 37 0.20
217 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (214 bp):
AATTTCAAAATAAGGCAATATTTTGTGTTTGGAAATTCGAAAAAACGTGCCCTAACGCGCTAGAT
TTCGCATTTTTCGCTCGACCAAATAGCTAAAATATCCTTCAAAAATTTCAAAATAAGACAATATT
TTACGTTTGAAAATTCGAGAAAACGTGCCCAAACATGCTGGGTTTCGATTTCTCGTTAAACCAAA
TAGCAAAATATCCTTTTAG
Found at i:28603284 original size:19 final size:19
Alignment explanation
Indices: 28603260--28603306 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28603250 CTCTTTTTCT
*
28603260 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
28603279 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
28603298 TATGCATTA
1 TTTGCATTA
28603307 GAGTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:28607523 original size:9 final size:9
Alignment explanation
Indices: 28607509--28607712 Score: 108
Period size: 9 Copynumber: 23.7 Consensus size: 9
28607499 ATAATGTAAT
28607509 TAAGTTATG
1 TAAGTTATG
*
28607518 TAAGTTGTG
1 TAAGTTATG
28607527 T-A-TTAT-
1 TAAGTTATG
*
28607533 TAAAGTTAAG
1 T-AAGTTATG
28607543 T-A-TTATG
1 TAAGTTATG
*
28607550 TAAGTTATT
1 TAAGTTATG
28607559 TAAGTTATG
1 TAAGTTATG
**
28607568 TAAGTGGTG
1 TAAGTTATG
28607577 T-A-TTATG
1 TAAGTTATG
*
28607584 TAAGTTAAG
1 TAAGTTATG
28607593 TAAGTTATG
1 TAAGTTATG
* *
28607602 TAGGCTATG
1 TAAGTTATG
28607611 T-A-TTATG
1 TAAGTTATG
* *
28607618 CAAGTTATT
1 TAAGTTATG
* *
28607627 TATGTAAGTGG
1 TAAGTTA-T-G
**
28607638 TGTGTTATG
1 TAAGTTATG
*
28607647 TAAGTTATA
1 TAAGTTATG
28607656 TAAGTTATG
1 TAAGTTATG
* *
28607665 TAGGCTATG
1 TAAGTTATG
*
28607674 T-A-TTATC
1 TAAGTTATG
*
28607681 TAAGTT-TT
1 TAAGTTATG
*
28607689 TAAGTTATA
1 TAAGTTATG
28607698 TAAGTTATG
1 TAAGTTATG
*
28607707 CAAGTT
1 TAAGTT
28607713 TCTATATAAG
Statistics
Matches: 143, Mismatches: 37, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
6 1 0.01
7 20 0.14
8 15 0.10
9 99 0.69
10 3 0.02
11 5 0.03
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28607527 original size:29 final size:31
Alignment explanation
Indices: 28607485--28607555 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
28607475 TATTATGATA
*
28607485 TATGTATGTTGTGTATAATGT-AA-TTAAG-T
1 TATGTAAGTTGTGTATAAT-TAAAGTTAAGAT
*
28607514 TATGTAAGTTGTGTATTATTAAAGTTAAGTAT
1 TATGTAAGTTGTGTATAATTAAAGTTAAG-AT
28607546 TATGTAAGTT
1 TATGTAAGTT
28607556 ATTTAAGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 19 0.53
30 5 0.14
32 11 0.31
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (31 bp):
TATGTAAGTTGTGTATAATTAAAGTTAAGAT
Found at i:28607538 original size:25 final size:24
Alignment explanation
Indices: 28607507--28607603 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
28607497 GTATAATGTA
* *
28607507 ATTAAGTTATGTAAGTTGTGTATT
1 ATTAAGTTAAGTAAGTTATGTATT
28607531 ATTAAAGTTAAGT-A-TTATGTAAGTT
1 ATT-AAGTTAAGTAAGTTATGT-A-TT
* **
28607556 ATTTAAGTTATGTAAGTGGTGTATT
1 A-TTAAGTTAAGTAAGTTATGTATT
28607581 ATGTAAGTTAAGTAAGTTATGTA
1 AT-TAAGTTAAGTAAGTTATGTA
28607604 GGCTATGTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
23 5 0.09
24 6 0.10
25 39 0.67
26 4 0.07
27 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (24 bp):
ATTAAGTTAAGTAAGTTATGTATT
Found at i:28607585 original size:34 final size:33
Alignment explanation
Indices: 28607542--28607702 Score: 145
Period size: 34 Copynumber: 4.9 Consensus size: 33
28607532 TTAAAGTTAA
*
28607542 GTATTATGTAAGTTATTTAAGTTATGTAAGTGGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGT-AT
** *
28607576 GTATTATGTAAGTTAAGTAAGTTATGTAGGCTAT
1 GTATTATGTAAGTTATTTAAGTTATGTAAG-TAT
* *
28607610 GTATTATGCAAGTTA--T---TTATGTAAGTGGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGT-AT
* * *
28607639 GTGTTATGTAAGTTATATAAGTTATGTAGGCTAT
1 GTATTATGTAAGTTATTTAAGTTATGTAAG-TAT
* *
28607673 GTATTATCTAAGTT-TTTAAGTTATATAAGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGT
28607703 TATGCAAGTT
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.01
29 22 0.21
31 1 0.01
32 2 0.02
33 12 0.12
34 63 0.61
35 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.45
Consensus pattern (33 bp):
GTATTATGTAAGTTATTTAAGTTATGTAAGTAT
Found at i:28607686 original size:63 final size:62
Alignment explanation
Indices: 28607563--28607690 Score: 206
Period size: 63 Copynumber: 2.0 Consensus size: 62
28607553 GTTATTTAAG
28607563 TTATGTAAGTGGTGTATTATGTAAGTTAAGTAAGTTATGTAGGCTATGTATTATGCAAGTTAT
1 TTATGTAAGTGGTGTATTATGTAAGTTAAGTAAGTTATGTAGGCTATGTATTATGCAAGTT-T
*
28607626 TTATGTAAGTGGTGTGTTATGTAAGTTATA-TAAGTTATGTAGGCTATGTATTAT-CTAAGTTT
1 TTATGTAAGTGGTGTATTATGTAAGTTA-AGTAAGTTATGTAGGCTATGTATTATGC-AAGTTT
28607688 TTA
1 TTA
28607691 AGTTATATAA
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
62 5 0.08
63 56 0.90
64 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (62 bp):
TTATGTAAGTGGTGTATTATGTAAGTTAAGTAAGTTATGTAGGCTATGTATTATGCAAGTTT
Found at i:28607724 original size:63 final size:63
Alignment explanation
Indices: 28607579--28607712 Score: 152
Period size: 63 Copynumber: 2.2 Consensus size: 63
28607569 AAGTGGTGTA
* * * **
28607579 TTATGTAAGTTA-AGTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTATGTAAGTGGTGTG
1 TTATGCAAGTTATA-TAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTAAGTGATAAG
* *
28607642 TTATGTAAGTTATATAAGTTATGTAGGCTATGTATTAT-CTAAGTT-TTTAAGTTA-T-ATAAG
1 TTATGCAAGTTATATAAGTTATGTAGGCTATGTATTATGC-AAGTTATTTAAGTAAGTGATAAG
28607702 TTATGCAAGTT
1 TTATGCAAGTT
28607713 TCTATATAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
60 12 0.19
61 1 0.02
62 8 0.13
63 41 0.65
64 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.45
Consensus pattern (63 bp):
TTATGCAAGTTATATAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTAAGTGATAAG
Found at i:28607735 original size:12 final size:12
Alignment explanation
Indices: 28607703--28607736 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28607693 TTATATAAGT
28607703 TATGCAAGTTTC
1 TATGCAAGTTTC
**
28607715 TATATAAGTTTC
1 TATGCAAGTTTC
28607727 TATGCAAGTT
1 TATGCAAGTT
28607737 ATGTAGGTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (12 bp):
TATGCAAGTTTC
Found at i:28607810 original size:16 final size:16
Alignment explanation
Indices: 28607786--28607948 Score: 72
Period size: 16 Copynumber: 10.0 Consensus size: 16
28607776 AATAAAAATT
*
28607786 TTATTTAAGTTATGTA
1 TTATGTAAGTTATGTA
28607802 TTATGTAAG---TGTA
1 TTATGTAAGTTATGTA
*
28607815 -TATATAAGTTATGATA
1 TTATGTAAGTTATG-TA
* *
28607831 TGATTGATAAATT-TG-A
1 TTA-TG-TAAGTTATGTA
28607847 GTTATGTAAGTTATGATA
1 -TTATGTAAGTTATG-TA
* *
28607865 TGATTTATAAGTTATGTA
1 T--TATGTAAGTTATGTA
* *
28607883 TAATGTAAGTTATGAAA
1 TTATGTAAGTTATG-TA
28607900 GTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
*
28607916 TTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
* *
28607933 TTATGCAAGTCATGTA
1 TTATGTAAGTTATGTA
28607949 GGCTATGTAT
Statistics
Matches: 109, Mismatches: 20, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
12 7 0.06
13 4 0.04
15 7 0.06
16 50 0.46
17 8 0.07
18 17 0.16
19 16 0.15
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.46
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:28607858 original size:9 final size:9
Alignment explanation
Indices: 28607846--28607999 Score: 76
Period size: 9 Copynumber: 17.7 Consensus size: 9
28607836 GATAAATTTG
28607846 AGTTATGTA
1 AGTTATGTA
28607855 AGTTATGATA
1 AGTTATG-TA
* *
28607865 TGATT-TATA
1 AG-TTATGTA
28607874 AGTTATGT-
1 AGTTATGTA
*
28607882 A-TAATGTA
1 AGTTATGTA
*
28607890 AGTTATGAA
1 AGTTATGTA
28607899 AGTTATGT-
1 AGTTATGTA
28607907 A-TTATGTA
1 AGTTATGTA
*
28607915 ATTTATGTA
1 AGTTATGTA
*
28607924 AGTTGTGT-
1 AGTTATGTA
*
28607932 A-TTATGCA
1 AGTTATGTA
*
28607940 AGTCATGTA
1 AGTTATGTA
* *
28607949 GGCTATGT-
1 AGTTATGTA
*
28607957 A-TTATGTC
1 AGTTATGTA
28607965 AGTTAT-TA
1 AGTTATGTA
*
28607973 TGTTATTATGTA
1 AG---TTATGTA
*
28607985 AGTTATGAA
1 AGTTATGTA
28607994 AGTTAT
1 AGTTAT
28608000 ATATAAGTTA
Statistics
Matches: 107, Mismatches: 23, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
7 20 0.19
8 11 0.10
9 63 0.59
10 4 0.04
11 6 0.06
12 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (9 bp):
AGTTATGTA
Found at i:28607862 original size:34 final size:35
Alignment explanation
Indices: 28607811--28607897 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 35
28607801 ATTATGTAAG
*
28607811 TGTAT-ATATAAGTTATGATATGATTGATAAATT-
1 TGTATAATGTAAGTTATGATATGATTGATAAATTA
* * *
28607844 TG-AGTTATGTAAGTTATGATATGATTTATAAGTTA
1 TGTA-TAATGTAAGTTATGATATGATTGATAAATTA
28607879 TGTATAATGTAAGTTATGA
1 TGTATAATGTAAGTTATGA
28607898 AAGTTATGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 1 0.02
33 3 0.07
34 25 0.54
35 16 0.35
36 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (35 bp):
TGTATAATGTAAGTTATGATATGATTGATAAATTA
Found at i:28607913 original size:25 final size:25
Alignment explanation
Indices: 28607873--28607999 Score: 113
Period size: 25 Copynumber: 5.3 Consensus size: 25
28607863 TATGATTTAT
*
28607873 AAGTTATGTATAATGTAAGTTATGA
1 AAGTTATGTATTATGTAAGTTATGA
* *
28607898 AAGTTATGTATTATGTAATTTATGT
1 AAGTTATGTATTATGTAAGTTATGA
* * * *
28607923 AAGTTGTGTATTATGCAAGTCATGT
1 AAGTTATGTATTATGTAAGTTATGA
* * *
28607948 AGGCTATGTATTATGTCAG-T-T--
1 AAGTTATGTATTATGTAAGTTATGA
28607969 -A-TTATGTTATTATGTAAGTTATGA
1 AAGTTATG-TATTATGTAAGTTATGA
28607993 AAGTTAT
1 AAGTTAT
28608000 ATATAAGTTA
Statistics
Matches: 79, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.05
20 10 0.13
21 1 0.01
22 1 0.01
23 1 0.01
25 58 0.73
26 4 0.05
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (25 bp):
AAGTTATGTATTATGTAAGTTATGA
Found at i:28607981 original size:20 final size:19
Alignment explanation
Indices: 28607952--28607990 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
28607942 TCATGTAGGC
*
28607952 TATGTATTATGTCAGTTAT
1 TATGTATTATGTAAGTTAT
28607971 TATGTTATTATGTAAGTTAT
1 TATG-TATTATGTAAGTTAT
28607991 GAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (19 bp):
TATGTATTATGTAAGTTAT
Found at i:28608084 original size:23 final size:22
Alignment explanation
Indices: 28608056--28608100 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
28608046 ATGTATATAA
*
28608056 ATATTAATAAGTTATTAAGTTAT
1 ATATTAAAAAGTTA-TAAGTTAT
*
28608079 ATATTAAAAATTTATAAGTTAT
1 ATATTAAAAAGTTATAAGTTAT
28608101 GTAAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
ATATTAAAAAGTTATAAGTTAT
Found at i:28608096 original size:30 final size:30
Alignment explanation
Indices: 28608049--28608109 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28608039 ATTAAAAATG
* *
28608049 TATATAAATATTAATAAGTTAT-TAAGTTA
1 TATATAAAAATTAATAAGTTATGTAAATTA
*
28608078 TATATTAAAAATTTATAAGTTATGTAAATTA
1 TATA-TAAAAATTAATAAGTTATGTAAATTA
28608109 T
1 T
28608110 GCAAGTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 16 0.59
31 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TATATAAAAATTAATAAGTTATGTAAATTA
Found at i:28609807 original size:22 final size:22
Alignment explanation
Indices: 28609782--28609831 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
28609772 AGTGCCTACA
28609782 CTAAAAAAGGTTCAAAGTTGCC
1 CTAAAAAAGGTTCAAAGTTGCC
*
28609804 CTAAAAAAGTTTCAAAGTTGCC
1 CTAAAAAAGGTTCAAAGTTGCC
28609826 CTAAAA
1 CTAAAA
28609832 TAAACTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (22 bp):
CTAAAAAAGGTTCAAAGTTGCC
Found at i:28610691 original size:105 final size:106
Alignment explanation
Indices: 28610558--28610816 Score: 344
Period size: 105 Copynumber: 2.4 Consensus size: 106
28610548 AAAATATTAT
*
28610558 TTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTT-TCAAAT
1 TTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTATTTGGTTTTTAT-AAAT
* * *
28610622 TGATTTAC-TTTTTGTGGCATTTTTATGGAAAACACCGCAAC
65 TGATTTACTTTTTTGCGGCATTTTTACGAAAAACACCGCAAC
* * * *
28610663 TTCAATTTGAACAAAATGATGCCGTTTTGTTATGCACAAAATTTTTTATTTGGTTTTTATAAATT
1 TTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTATTTGGTTTTTATAAATT
* * * *
28610728 GATTTACTTTTTTGCGGCATTTTTACGAAAAACGCTGCTAT
66 GATTTACTTTTTTGCGGCATTTTTACGAAAAACACCGCAAC
* *
28610769 TTCATTTTGAACAAAAACGGCGTCGTTTTGCTATGCA-AATAATTTTTT
1 TTCATTTTGAAC-AAAATGACGTCGTTTTGCTATGCACAA-AATTTTTT
28610817 TATAATTTTT
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
105 65 0.49
106 40 0.30
107 27 0.20
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (106 bp):
TTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTATTTGGTTTTTATAAATT
GATTTACTTTTTTGCGGCATTTTTACGAAAAACACCGCAAC
Found at i:28610826 original size:106 final size:105
Alignment explanation
Indices: 28610555--28610826 Score: 307
Period size: 106 Copynumber: 2.6 Consensus size: 105
28610545 CGCAAAATAT
** *
28610555 TATTTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAA-TTTTTTATTTTGTTTTTTCA
1 TATTTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTTATAAT-TTTTATCA
* * *
28610619 AATTGATTTACTTTTTGTGGCATTTTTATGGAAAACACCGC
65 AATTGATTTACTTTTTGCGGCATTTTTACGAAAAACACCGC
* * * * * * * **
28610660 AACTTCAATTTGAACAAAATGATGCCGTTTTGTTATGCACAAAATTTTTTATTTGGTTTTTAT-A
1 TATTTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTT-TATAATTTTTATCA
* *
28610724 AATTGATTTACTTTTTTGCGGCATTTTTACGAAAAACGCTGC
65 AATTGATTTAC-TTTTTGCGGCATTTTTACGAAAAACACCGC
* *
28610766 TATTTCATTTTGAACAAAAACGGCGTCGTTTTGCTATGCA-AATAATTTTTTTATAATTTTT
1 TATTTCATTTTGAAC-AAAATGACGTCGTTTTGCTATGCACAA-AATTTTTTTATAATTTTT
28610827 TTATTTTCTT
Statistics
Matches: 136, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
105 50 0.37
106 56 0.41
107 30 0.22
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (105 bp):
TATTTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTTTTTATAATTTTTATCAA
ATTGATTTACTTTTTGCGGCATTTTTACGAAAAACACCGC
Found at i:28611068 original size:355 final size:352
Alignment explanation
Indices: 28610343--28611044 Score: 979
Period size: 355 Copynumber: 2.0 Consensus size: 352
28610333 TCGGTATGCT
* * * * *
28610343 AAAAATTATTTATTTTGTTTTTTATAAATTGCTTTACTTTTTTCCGGCGTTTTTATGAAAAACGC
1 AAAATTTATTTA-TTTGGTTTTTATAAATTGATTTACTTTTTTCCGGCATTTTTACGAAAAACGC
*
28610408 CGCTATTTCATTTTGAACAAAAACGGCGCCGTTTTTCTATGCAAATAAAATTTTTATAATTTATT
65 CGCTATTTCATTTTGAACAAAAACGGCGCCGTTTTGCTATGCAAATAAAATTTTTATAATTTATT
28610473 TATTTTCTTTGCGGCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTCATA
130 TATTTTCTTTGCGGCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTCATA
*
28610538 AAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATTTT
195 AAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCAC-AAA---T
* * *
28610603 TTATTTTGTTTTTTCAAATTGATTTACTTTTTGTGGCATTTTTATGGAAAACACCGCAACTTCAA
256 TTATTTTGTTTTATCAAATTGATTTACTTTTTGCGGCATTTTTATAGAAAACACCGCAACTTCAA
* * *
28610668 TTTGAACAAAATGATGCCGTTTTGTTATGCAC
321 TTTGAACAAAACGACGCCGTTTTGCTATGCAC
* *
28610700 AAAATTT-TTTATTTGGTTTTTATAAATTGATTTACTTTTTTGCGGCATTTTTACGAAAAACGCT
1 AAAATTTATTTATTTGGTTTTTATAAATTGATTTACTTTTTTCCGGCATTTTTACGAAAAACGCC
* ** *
28610764 GCTATTTCATTTTGAACAAAAACGGCGTCGTTTTGCTATGCAAATAATTTTTTTATAATTTTTTT
66 GCTATTTCATTTTGAACAAAAACGGCGCCGTTTTGCTATGCAAATAAAATTTTTATAATTTATTT
* *
28610829 ATTTTCTTTGGGGCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTT-GTGA
131 ATTTTCTTTGCGGCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTCAT-A
*
28610893 AAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTCTGCAC-AA-TT-T
195 AAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAATTTAT
* ** * * * **
28610955 TTT-TTTTAT-AAATTGATTTATTTTTTTGCGGTGTTTTTATTAG-AAACGCCGCTATTTCGTTT
260 TTTGTTTTATCAAATTGATTTA-CTTTTTGCGGCATTTTTA-TAGAAAACACCGCAACTTCAATT
* *
28611017 TGATCAAAAACGGCGCCGTTTTGCTATG
323 TGAAC-AAAACGACGCCGTTTTGCTATG
28611045 TAAATAATTT
Statistics
Matches: 309, Mismatches: 32, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
346 11 0.04
347 37 0.12
348 24 0.08
349 2 0.01
353 2 0.01
354 1 0.00
355 222 0.72
356 4 0.01
357 6 0.02
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.44
Consensus pattern (352 bp):
AAAATTTATTTATTTGGTTTTTATAAATTGATTTACTTTTTTCCGGCATTTTTACGAAAAACGCC
GCTATTTCATTTTGAACAAAAACGGCGCCGTTTTGCTATGCAAATAAAATTTTTATAATTTATTT
ATTTTCTTTGCGGCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTCATAA
AAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAATTTATT
TTGTTTTATCAAATTGATTTACTTTTTGCGGCATTTTTATAGAAAACACCGCAACTTCAATTTGA
ACAAAACGACGCCGTTTTGCTATGCAC
Found at i:28611126 original size:135 final size:131
Alignment explanation
Indices: 28610978--28611321 Score: 318
Period size: 137 Copynumber: 2.5 Consensus size: 131
28610968 TGATTTATTT
* * * * * *
28610978 TTTTGCGGTGTTTTTATTAGAAACGCCGC-TATTTCGTTTTGATCAAAAACGGCGCCGTTTTGCT
1 TTTTGCGGCGTTTTTATTAAAAACGCCGCATATTTCATTTTCAAC-AAAACGACGCCGTTTTGCT
* * *
28611042 ATGTAAATAATTTTTTAT-AATTTATTTATTTTTTTGCGGCATTTTTATATAAAACGCCGCTA-T
65 AT-T---TAATTTTCTATAAATTGATTTA-TTTTTTGCGGCATTTTTATAGAAAACGCCGCTATT
28611105 TGCTTATC
125 TG-TTATC
* *
28611113 TTTTGCGGCGTTTTTGTTAAAAACGCCGCAAAATATTATTTCATTTTCAACAAAATGACGCCGTT
1 TTTTGCGGCGTTTTTATTAAAAACGCCGC-----A-TATTTCATTTTCAACAAAACGACGCCGTT
** *
28611178 TTGCTATTTTGTTTTCTATAAATTGATTTATTTTTTGTGGCATTTTTATAGAAAACGCCGCTATT
60 TTGCTATTTAATTTTCTATAAATTGATTTATTTTTTGCGGCATTTTTATAGAAAACGCCGCTATT
28611243 TGTTATC
125 TGTTATC
* * * *
28611250 TTTTGCGGCGTTTTGCA-TAAAAATGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGT
1 TTTTGCGGCGTTTT-TATTAAAAACGCCGC-----A-TATTTCATTTTCAACAAAACGACGCCGT
28611314 TTTGCTAT
59 TTTGCTAT
28611322 GCTAAATTTT
Statistics
Matches: 181, Mismatches: 18, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
135 26 0.14
137 111 0.61
138 12 0.07
140 1 0.01
141 19 0.10
142 12 0.07
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (131 bp):
TTTTGCGGCGTTTTTATTAAAAACGCCGCATATTTCATTTTCAACAAAACGACGCCGTTTTGCTA
TTTAATTTTCTATAAATTGATTTATTTTTTGCGGCATTTTTATAGAAAACGCCGCTATTTGTTAT
C
Found at i:28611154 original size:239 final size:233
Alignment explanation
Indices: 28610711--28611243 Score: 784
Period size: 239 Copynumber: 2.2 Consensus size: 233
28610701 AAATTTTTTA
* * * *
28610711 TTTGGTTTTTATAAATTGATTTACTTTTTTGCGGCATTTTTACGAAAAACGCTGCTATTTCATTT
1 TTTGTTTTTTATAAATTGATTTA-TTTTTTGCGGCATTTTTA-TAGAAACGCCGCTATTTCATTT
* * *
28610776 TGAACAAAAACGGCGTCGTTTTGCTATGCAAATAATTTTTTTATAATTTTTTTATTTTCTTTGGG
64 TGAACAAAAACGGCGCCGTTTTGCTATGCAAATAATTTTTTTATAATTTATTTATTTTCTTTGCG
*
28610841 GCGTTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTGTGAAAAACGCCGCAAA
129 GCATTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTGTGAAAAACGCCGCAAA
*
28610906 ATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTCTGCACAAT
194 ATATTATTTCATTTTCAACAAAATGACGCCGTTTTG--CT-----AT
** *
28610953 TTT-TTTTTTATAAATTGATTTATTTTTTTGCGGTGTTTTTATTAGAAACGCCGCTATTTCGTTT
1 TTTGTTTTTTATAAATTGATTTA-TTTTTTGCGGCATTTTTA-TAGAAACGCCGCTATTTCATTT
* *
28611017 TGATCAAAAACGGCGCCGTTTTGCTATGTAAATAA-TTTTTTATAATTTATTTATTTT-TTTGCG
64 TGAACAAAAACGGCGCCGTTTTGCTATGCAAATAATTTTTTTATAATTTATTTATTTTCTTTGCG
*
28611080 GCATTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTGTTAAAAACGCCGCAAA
129 GCATTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTGTGAAAAACGCCGCAAA
28611145 ATATTATTTCATTTTCAACAAAATGACGCCGTTTTGCTAT
194 ATATTATTTCATTTTCAACAAAATGACGCCGTTTTGCTAT
* *
28611185 TTTGTTTTCTATAAATTGATTTATTTTTTGTGGCATTTTTATAGAAAACGCCGCTATTT
1 TTTGTTTTTTATAAATTGATTTATTTTTTGCGGCATTTTTATAG-AAACGCCGCTATTT
28611244 GTTATCTTTT
Statistics
Matches: 268, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
231 3 0.01
232 34 0.13
233 18 0.07
237 2 0.01
239 103 0.38
240 21 0.08
241 84 0.31
242 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (233 bp):
TTTGTTTTTTATAAATTGATTTATTTTTTGCGGCATTTTTATAGAAACGCCGCTATTTCATTTTG
AACAAAAACGGCGCCGTTTTGCTATGCAAATAATTTTTTTATAATTTATTTATTTTCTTTGCGGC
ATTTTTATATAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTGTGAAAAACGCCGCAAAAT
ATTATTTCATTTTCAACAAAATGACGCCGTTTTGCTAT
Found at i:28611226 original size:137 final size:137
Alignment explanation
Indices: 28611052--28611321 Score: 429
Period size: 137 Copynumber: 2.0 Consensus size: 137
28611042 ATGTAAATAA
* * *
28611052 TTTTTTATAATTTATTTATTTTTTTGCGGCATTTTTATATAAAACGCCGCTA-TTGCTTATCTTT
1 TTTTCTATAATTGATTTATTTTTTTGCGGCATTTTTATAGAAAACGCCGCTATTTG-TTATCTTT
*
28611116 TGCGGCGTTTTTG-TTAAAAACGCCGCAAAATATTATTTCATTTTCAACAAAATGACGCCGTTTT
65 TGCGGCG-TTTTGCATAAAAACGCCGCAAAATATTATTTCATTTTCAACAAAATGACGCCGTTTT
28611180 GCTATTTTG
129 GCTATTTTG
*
28611189 TTTTCTATAAATTGATTTA-TTTTTTGTGGCATTTTTATAGAAAACGCCGCTATTTGTTATCTTT
1 TTTTCTAT-AATTGATTTATTTTTTTGCGGCATTTTTATAGAAAACGCCGCTATTTGTTATCTTT
* *
28611253 TGCGGCGTTTTGCATAAAAATGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTG
65 TGCGGCGTTTTGCATAAAAACGCCGCAAAATATTATTTCATTTTCAACAAAATGACGCCGTTTTG
28611318 CTAT
130 CTAT
28611322 GCTAAATTTT
Statistics
Matches: 123, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
136 5 0.04
137 106 0.86
138 12 0.10
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (137 bp):
TTTTCTATAATTGATTTATTTTTTTGCGGCATTTTTATAGAAAACGCCGCTATTTGTTATCTTTT
GCGGCGTTTTGCATAAAAACGCCGCAAAATATTATTTCATTTTCAACAAAATGACGCCGTTTTGC
TATTTTG
Found at i:28611676 original size:15 final size:15
Alignment explanation
Indices: 28611643--28611684 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
28611633 CCCTAACTCT
**
28611643 TAACCCCT-AACGTC
1 TAACCCCTAAACCCC
28611657 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
*
28611672 TAACCCTTAAACC
1 TAACCCCTAAACC
28611685 ATAGTCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.33, C:0.45, G:0.02, T:0.19
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:28611693 original size:15 final size:14
Alignment explanation
Indices: 28611661--28611727 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
28611651 AACGTCTAAC
*
28611661 CCCTAAACCCCTAA-
1 CCCTAAA-CCATAAT
*
28611675 CCCTTAAACCATAGT
1 CCC-TAAACCATAAT
*
28611690 CCCTAATCCATAAT
1 CCCTAAACCATAAT
*
28611704 CCCTAAACCCATACT
1 CCCTAAA-CCATAAT
28611719 CCCTAAACC
1 CCCTAAACC
28611728 TTAAAATATG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 24 0.55
15 20 0.45
ACGTcount: A:0.34, C:0.43, G:0.01, T:0.21
Consensus pattern (14 bp):
CCCTAAACCATAAT
Found at i:28611706 original size:14 final size:14
Alignment explanation
Indices: 28611615--28611724 Score: 53
Period size: 14 Copynumber: 7.6 Consensus size: 14
28611605 TCGACCCCTG
* *
28611615 AATCCCTAAACCTT
1 AATCCCTAACCCAT
* *
28611629 AAATCCCTAACTCTT
1 -AATCCCTAACCCAT
* *
28611644 AACCCCTAACGTC-T
1 AATCCCTAAC-CCAT
* *
28611658 AACCCCTAAACCCCT
1 AATCCCT-AACCCAT
*
28611673 AA-CCCTTAAACCAT
1 AATCCC-TAACCCAT
* *
28611687 AGTCCCTAATCCAT
1 AATCCCTAACCCAT
28611701 AATCCCTAAACCCAT
1 AATCCCT-AACCCAT
*
28611716 ACTCCCTAA
1 AATCCCTAA
28611725 ACCTTAAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
14 42 0.54
15 36 0.46
ACGTcount: A:0.35, C:0.40, G:0.02, T:0.24
Consensus pattern (14 bp):
AATCCCTAACCCAT
Found at i:28611997 original size:14 final size:14
Alignment explanation
Indices: 28611980--28612006 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28611970 AACCCTTAAA
28611980 CCATAATCCCTAAT
1 CCATAATCCCTAAT
28611994 CCATAATCCCTAA
1 CCATAATCCCTAA
28612007 ACCCATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:28612250 original size:115 final size:114
Alignment explanation
Indices: 28612105--28612666 Score: 601
Period size: 115 Copynumber: 4.9 Consensus size: 114
28612095 TTTTTTTTTT
* * * *
28612105 GCGGCGCTTTCCTAAAAAACGCCGCTAAATCCCCCAAAAGCTCAAAAAACGGCGTCATTGGGCTT
1 GCGGCGCTTTCCTAAAAAACGCCACTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * * *
28612170 ATGTCTTTTTCCGGCGCTTTCTCACAAACGCCGCTAAAGCCCTGAGCATTA
65 A-GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * * *
28612221 GTGGCGC-TTCCTAAAAAATGCCACTAAATCCGCAAAAGCTCAAAAAAACGGCGTCGTTGGGCTT
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCCCGAAAGCTC-AGAAAACGGCGTCGTTGGGCTT
* *
28612285 AGTTTATTTTGCGGCGCTTCCTCAAAAACGTCGCTAAAGCCCTCAGCATTA
65 AGTTT-TTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
** ** * ** * *
28612336 GCAACGCTTTATTAAGAAACGCCACTAAATCTACGAAAGCTCAGAAAACGACGTCATTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * * *
28612401 GTTTATTTTGCGACGCTTTATCAAAAACGCCACAAAAGCCCTGAGCATTA
66 GTTT-TTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * * * *
28612451 GCGGCGC-TTCCTAAAAATCGCCACTAAATCCGCGAATGCTCAGAAAACAGCATTGTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
28612515 GTTTTTTTTGCGGTGC-TTCATCAAAAACGCCGCTAAAGCCCTCAGTATTA
66 G-TTTTTTTGCGGCGCTTTC-TCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * * * * *
28612565 GCGGCGCTTTCTTAAGAAACGCCGCTAAGTCCCCGAAAGCTCAGAAAATGGTG-CTGTTGAGCTT
1 GCGGCGCTTTCCTAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTC-GTTGGGCTT
* *
28612629 ATGTCTTTTTGCGGCGCTTTCTCAAAAACGCCACTAAA
65 A-GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
28612667 TCTGCGAAAG
Statistics
Matches: 369, Mismatches: 68, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
113 2 0.01
114 102 0.28
115 228 0.62
116 37 0.10
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCCTAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTCAGCATTA
Found at i:28612641 original size:229 final size:230
Alignment explanation
Indices: 28612105--28612662 Score: 714
Period size: 229 Copynumber: 2.4 Consensus size: 230
28612095 TTTTTTTTTT
* * * * *
28612105 GCGGCGCTTTCCTAAAAAACGCCGCTAAATCCCCCAAAAGCTCAAAAAACGGCG-TCATTGGGCT
1 GCGGCGCTTTCTTAAGAAACGCCGCTAAAT-CCCCGAAAGCTCAGAAAACGGTGCT-ATTGGGCT
* * * * *
28612169 TATGTCTTTTTCCGGCGCTTTCTCACAAACGCCGCTAAAGCCCTGAGCATTAGTGGCGCTTCCTA
64 TATGTCTTTTTGCGGCGCTTTCTCAAAAACGCCACAAAAGCCCTGAGCATTAGCGGCGCTTCCTA
* *
28612234 AAAAATGCCACTAAATCCGCAAAAGCTCAAAAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGG
129 AAAAATGCCACTAAATCCGCAAAAGCTCAAAAAAACAGCATCGTTGGGCTTAGTTTATTTTGCGG
* *
28612299 CGCTTCCTCAAAAACGTCGCTAAAGCCCTCAGCATTA
194 CGCTTCATCAAAAACGCCGCTAAAGCCCTCAGCATTA
** * * **
28612336 GCAACGCTTTATTAAGAAACGCCACTAAATCTACGAAAGCTCAGAAAACGACGT-C-ATTGGGCT
1 GCGGCGCTTTCTTAAGAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACG--GTGCTATTGGGCT
* * *
28612399 TA-GTTTATTTTGCGACGCTTTATCAAAAACGCCACAAAAGCCCTGAGCATTAGCGGCGCTTCCT
64 TATGTCT-TTTTGCGGCGCTTTCTCAAAAACGCCACAAAAGCCCTGAGCATTAGCGGCGCTTCCT
* * * * *
28612463 -AAAAATCGCCACTAAATCCGCGAATGCTC-AGAAAACAGCATTGTTGGGCTTAGTTTTTTTTGC
128 AAAAAAT-GCCACTAAATCCGCAAAAGCTCAAAAAAACAGCATCGTTGGGCTTAGTTTATTTTGC
* *
28612526 GGTGCTTCATCAAAAACGCCGCTAAAGCCCTCAGTATTA
192 GGCGCTTCATCAAAAACGCCGCTAAAGCCCTCAGCATTA
* * * *
28612565 GCGGCGCTTTCTTAAGAAACGCCGCTAAGTCCCCGAAAGCTCAGAAAATGGTGCTGTTGAGCTTA
1 GCGGCGCTTTCTTAAGAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGCTATTGGGCTTA
28612630 TGTCTTTTTGCGGCGCTTTCTCAAAAACGCCAC
66 TGTCTTTTTGCGGCGCTTTCTCAAAAACGCCAC
28612663 TAAATCTGCG
Statistics
Matches: 276, Mismatches: 43, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
227 2 0.01
228 1 0.00
229 149 0.54
230 99 0.36
231 24 0.09
232 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (230 bp):
GCGGCGCTTTCTTAAGAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGCTATTGGGCTTA
TGTCTTTTTGCGGCGCTTTCTCAAAAACGCCACAAAAGCCCTGAGCATTAGCGGCGCTTCCTAAA
AAATGCCACTAAATCCGCAAAAGCTCAAAAAAACAGCATCGTTGGGCTTAGTTTATTTTGCGGCG
CTTCATCAAAAACGCCGCTAAAGCCCTCAGCATTA
Found at i:28612696 original size:73 final size:72
Alignment explanation
Indices: 28612565--28612737 Score: 202
Period size: 73 Copynumber: 2.4 Consensus size: 72
28612555 CTCAGTATTA
* * * *
28612565 GCGGCGCTTTCTTAAGAAACGCCGCTAAGTCCCCGAAAGCTCAGAAAATGGTGCTGTTGAGCTTA
1 GCGGCGCTTTCTCAA-AAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCTGTTGAGCTTA
*
28612630 TGTCTTTTT
65 GGT-TTTTT
* ** * * *
28612639 GCGGCGCTTTCTCAAAAACGCCACTAAATCTGCGAAAGCTCAGAATACGGCGTTGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCTGTTGAGCTTAG
28612704 GTTTTTT
66 GTTTTTT
* * *
28612711 GTGGCACTTTCTGAAAAACGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
28612738 TGCTTTTTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 28 0.33
73 42 0.50
74 14 0.17
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCTGTTGAGCTTAG
GTTTTTT
Found at i:28618824 original size:21 final size:22
Alignment explanation
Indices: 28618798--28618852 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
28618788 AACAACGATG
**
28618798 GCGGTGAGATTAGG-TCCTGTA
1 GCGGTGAGATTAGGATAATGTA
28618819 GCGGTGAGATT-GGATAATGTA
1 GCGGTGAGATTAGGATAATGTA
*
28618840 GCAGTGAGATTAG
1 GCGGTGAGATTAG
28618853 AAACAGCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATAATGTA
Found at i:28619062 original size:19 final size:18
Alignment explanation
Indices: 28619016--28619054 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
28619006 TTATTATTAA
28619016 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
28619034 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
28619051 ATAT
1 ATAT
28619055 TAAATTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:28619068 original size:19 final size:16
Alignment explanation
Indices: 28619016--28619069 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 16
28619006 TTATTATTAA
28619016 ATATAATTTAATAAAAAT
1 ATATAATTT-A-AAAAAT
28619034 ATATAATTTAATAAAAT
1 ATATAATTTAA-AAAAT
28619051 ATATTAAATTTACAAAAAT
1 ATA-T-AATTTA-AAAAAT
28619070 TCAATCACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.03
17 9 0.28
18 10 0.31
19 11 0.34
20 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATTTAAAAAAT
Found at i:28628572 original size:17 final size:19
Alignment explanation
Indices: 28628528--28628573 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 19
28628518 ATATAAATTT
28628528 AAAG-GTTAAAAAAGAAGA
1 AAAGAGTTAAAAAAGAAGA
28628546 AAA-A-TT-AAAAA-AA-A
1 AAAGAGTTAAAAAAGAAGA
28628560 AAAGAGTTAAAAAA
1 AAAGAGTTAAAAAA
28628574 TTGGAAAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
14 4 0.17
15 3 0.12
16 7 0.29
17 7 0.29
18 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAGAGTTAAAAAAGAAGA
Found at i:28634883 original size:20 final size:20
Alignment explanation
Indices: 28634858--28634897 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28634848 AATATTTTCC
*
28634858 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28634878 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28634898 TCATTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28638983 original size:16 final size:16
Alignment explanation
Indices: 28638941--28638983 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28638931 AAAAAAGGAA
*
28638941 AGAATGGAGAGAGGGG
1 AGAAGGGAGAGAGGGG
*
28638957 AGAAGGAAGAGAGGGG
1 AGAAGGGAGAGAGGGG
28638973 A-AAGGG-GAGAG
1 AGAAGGGAGAGAG
28638984 CTCCGGTCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (16 bp):
AGAAGGGAGAGAGGGG
Found at i:28643064 original size:18 final size:19
Alignment explanation
Indices: 28643022--28643064 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
28643012 TATAAACTTC
28643022 TATTTATAATTTATTAGAA
1 TATTTATAATTTATTAGAA
* * *
28643041 TTTTTAT-ATTTTTTATAA
1 TATTTATAATTTATTAGAA
28643059 TATTTA
1 TATTTA
28643065 AAAAATTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTATAATTTATTAGAA
Found at i:28643127 original size:17 final size:17
Alignment explanation
Indices: 28643067--28643127 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
28643057 AATATTTAAA
*
28643067 AAATTTACATGTTTTTAT
1 AAATTTA-ATATTTTTAT
*
28643085 -AATATTAATAACTTTATAT
1 AAAT-TTAAT-A-TTTTTAT
28643104 AAAATTTAATATTTTTAT
1 -AAATTTAATATTTTTAT
28643122 AAATTT
1 AAATTT
28643128 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
17 11 0.31
18 9 0.26
19 7 0.20
20 5 0.14
21 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATTTAATATTTTTAT
Found at i:28653001 original size:15 final size:15
Alignment explanation
Indices: 28652955--28653002 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
28652945 TTACTTTCTC
28652955 CCCAAAACTTTTACT
1 CCCAAAACTTTTACT
***
28652970 CCCTCCTACTTTT-CT
1 CCC-AAAACTTTTACT
28652985 CCCAAAACTTTTACT
1 CCCAAAACTTTTACT
28653000 CCC
1 CCC
28653003 CTTCTATCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 6 0.24
15 13 0.52
16 6 0.24
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (15 bp):
CCCAAAACTTTTACT
Found at i:28659595 original size:19 final size:19
Alignment explanation
Indices: 28659559--28659598 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28659549 ATTCCAAATA
** *
28659559 TAATATTATTTTATATATT
1 TAATATTAAATTAAATATT
28659578 TAATATTAAATTAAATATT
1 TAATATTAAATTAAATATT
28659597 TA
1 TA
28659599 TCTTAATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATTAAATTAAATATT
Found at i:28659692 original size:69 final size:69
Alignment explanation
Indices: 28659577--28659706 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 69
28659567 TTTTATATAT
*
28659577 TTAATATTAAATTAAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTAATTATCGT
1 TTAATATTAAATTAAATATTTATCTTAATAGTATTATATTAATTTAATATTAAAGTAATTATCGT
28659642 AATA
66 AATA
* * * * *
28659646 TTAA-ATTTAATTTAATATTTATCTTGATAAGTATTATATTGATTTAATATTAAAGTGATTA
1 TTAATATTAAATTAAATATTTATCTTAAT-AGTATTATATTAATTTAATATTAAAGTAATTA
28659707 AGAATAATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 21 0.39
69 33 0.61
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (69 bp):
TTAATATTAAATTAAATATTTATCTTAATAGTATTATATTAATTTAATATTAAAGTAATTATCGT
AATA
Found at i:28662749 original size:15 final size:15
Alignment explanation
Indices: 28662729--28662758 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28662719 TTCACTGTTA
*
28662729 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
28662744 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
28662759 CCATTAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:28673932 original size:18 final size:17
Alignment explanation
Indices: 28673906--28673944 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28673896 ATTTTCCTTC
28673906 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
28673923 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
28673941 CACA
1 CACA
28673945 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:28675252 original size:10 final size:10
Alignment explanation
Indices: 28675239--28675281 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
28675229 TTTAAAATTT
28675239 AAAAATTT-A
1 AAAAATTTAA
*
28675248 AAAAATTCAA
1 AAAAATTTAA
28675258 AAAAATTTAA
1 AAAAATTTAA
28675268 AAAAATTTAA
1 AAAAATTTAA
28675278 AAAA
1 AAAA
28675282 TATGAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:28675253 original size:9 final size:9
Alignment explanation
Indices: 28675232--28675292 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
28675222 TTAATTTTTT
28675232 AAAATTT-A
1 AAAATTTAA
28675240 AAAATTTAA
1 AAAATTTAA
*
28675249 AAAATTCAAA
1 AAAATT-TAA
28675259 AAAATTTAAA
1 AAAATTT-AA
28675269 AAAATTTAA
1 AAAATTTAA
* *
28675278 AAAATATGA
1 AAAATTTAA
28675287 AAAATT
1 AAAATT
28675293 AATATTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
8 7 0.16
9 21 0.47
10 17 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTTAA
Found at i:28675289 original size:19 final size:18
Alignment explanation
Indices: 28675239--28675294 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
28675229 TTTAAAATTT
28675239 AAAAATTTAAAAAATTCAA
1 AAAAATTTAAAAAATT-AA
*
28675258 AAAAATTTAAAAAAATTTA
1 AAAAATTT-AAAAAATTAA
* *
28675277 AAAAATATGAAAAATTAA
1 AAAAATTTAAAAAATTAA
28675295 TATTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 8 0.25
19 16 0.50
20 8 0.25
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATTTAAAAAATTAA
Found at i:28681704 original size:32 final size:31
Alignment explanation
Indices: 28681646--28681712 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
28681636 AGGTTTTAAT
*
28681646 GTAATTATGATAATTTTTAAAGGTTAACTAA
1 GTAATTATGATAATTGTTAAAGGTTAACTAA
* *
28681677 GTAATT-TGATAATTAAGTTAAATGTTAATTAA
1 GTAATTATGATAATT--GTTAAAGGTTAACTAA
28681709 GTAA
1 GTAA
28681713 AAGATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.26
31 6 0.19
32 17 0.55
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.42
Consensus pattern (31 bp):
GTAATTATGATAATTGTTAAAGGTTAACTAA
Found at i:28682375 original size:40 final size:40
Alignment explanation
Indices: 28682331--28682442 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 40
28682321 AATTATTGTA
* * *
28682331 TGATTACACATATGTGCCCTTGTTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTCGGCAACCC
*
28682371 TGATTGCACATATGTGCCCTTGTTTGTACTTTGGCAACCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTCGGCAACCC
* *
28682411 TGATTGCACATATATACCCTTGTTTGTACTTC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTC
28682443 TGTATCCCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (40 bp):
TGATTGCACATATGTGCCCTTGTTTGTACTTCGGCAACCC
Found at i:28682458 original size:40 final size:39
Alignment explanation
Indices: 28682331--28682466 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 39
28682321 AATTATTGTA
* *
28682331 TGATTACACATATGTGCCCTTGTTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTCTGTA-CCC
*
28682371 TGATTGCACATATGTGCCCTTGTTTGTACTT-TGGCAACCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTCT-G-TACCC
* *
28682411 TGATTGCACATATATACCCTTGTTTGTACTTCTGTATCCC
1 TGATTGCACATATGTGCCCTTGTTTGTACTTCTGTA-CCC
*
28682451 -AAGTTGCACATATGTG
1 TGA-TTGCACATATGTG
28682467 TCTCTAATTG
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
39 2 0.02
40 78 0.95
41 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (39 bp):
TGATTGCACATATGTGCCCTTGTTTGTACTTCTGTACCC
Found at i:28696225 original size:4 final size:4
Alignment explanation
Indices: 28696216--28696258 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
28696206 TAAAAGCTGT
* *
28696216 TTTA TTTA -TTA TTTA ATAA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTT
28696259 CATTCTGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.85
5 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:28696455 original size:19 final size:17
Alignment explanation
Indices: 28696433--28696476 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28696423 CATTATCTGT
*
28696433 TTTTTTTGTGTTCTTGTTA
1 TTTTTTTGT-TGCTT-TTA
*
28696452 TTTTATTGTTGCTTTTA
1 TTTTTTTGTTGCTTTTA
28696469 TTTTTTTG
1 TTTTTTTG
28696477 GCACTTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.07, C:0.05, G:0.14, T:0.75
Consensus pattern (17 bp):
TTTTTTTGTTGCTTTTA
Found at i:28696587 original size:15 final size:16
Alignment explanation
Indices: 28696549--28696592 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
28696539 CCTTATTTAT
**
28696549 TTTATTATTCTTATAA
1 TTTATTATTAATATAA
28696565 TTTGATTATTAATA-AA
1 TTT-ATTATTAATATAA
28696581 TTTATTATTAAT
1 TTTATTATTAAT
28696593 TACATTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 8 0.32
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTATTATTAATATAA
Found at i:28700542 original size:18 final size:18
Alignment explanation
Indices: 28700519--28700559 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28700509 AAATATTGTG
28700519 AATAACTCTGGGGATGAT
1 AATAACTCTGGGGATGAT
28700537 AATAACTCTGGGGATGAT
1 AATAACTCTGGGGATGAT
28700555 AATAA
1 AATAA
28700560 AGACCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (18 bp):
AATAACTCTGGGGATGAT
Found at i:28706431 original size:4 final size:4
Alignment explanation
Indices: 28706422--28706456 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
28706412 TACAAGTTGT
28706422 TTTA TTTA -TTA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTT
28706457 CATTCTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 23 0.79
5 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:28708521 original size:30 final size:29
Alignment explanation
Indices: 28708459--28708526 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
28708449 AACATTTTAA
*
28708459 AATAAAAAATAATTACTTAGTAATTATAT
1 AATAAAAAATAATTACTGAGTAATTATAT
* *
28708488 AATAAAAAATAATTACTCGA-TAGTTAATGT
1 AATAAAAAATAATTACT-GAGTAATT-ATAT
28708518 AATAAAAAA
1 AATAAAAAA
28708527 AATAGGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (29 bp):
AATAAAAAATAATTACTGAGTAATTATAT
Found at i:28726154 original size:6 final size:6
Alignment explanation
Indices: 28726145--28726171 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28726135 CCTATTGACA
28726145 TAGGAG TAGGAG TAGGAG TAGGAG TAG
1 TAGGAG TAGGAG TAGGAG TAGGAG TAG
28726172 AGGTAGGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.19
Consensus pattern (6 bp):
TAGGAG
Found at i:28728363 original size:63 final size:62
Alignment explanation
Indices: 28728294--28728441 Score: 165
Period size: 62 Copynumber: 2.4 Consensus size: 62
28728284 GGCCGTGTGG
* *
28728294 CAGGCCGTGTAACTCACTATTTTTGAAT-TTGAG-GCACACGGGCTAAGGACACAAGCGTGTGTC
1 CAGGCCGTGTAACTCACTGTTTTT-AATATTG-GTG-ACACGGACTAAGGACACAAGCGTGTGTC
* * * * ** *
28728357 CAGGCCGTGTAAGTCACTGTTTGTATTATTGGTGACACGGACTAGGGACACGGGTGTGTGTC
1 CAGGCCGTGTAACTCACTGTTTTTAATATTGGTGACACGGACTAAGGACACAAGCGTGTGTC
*
28728419 CAGGCCGTGCAACTCACTGTTTT
1 CAGGCCGTGTAACTCACTGTTTT
28728442 GGATTTAGGG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
62 46 0.65
63 25 0.35
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (62 bp):
CAGGCCGTGTAACTCACTGTTTTTAATATTGGTGACACGGACTAAGGACACAAGCGTGTGTC
Found at i:28728468 original size:62 final size:62
Alignment explanation
Indices: 28728349--28728489 Score: 144
Period size: 62 Copynumber: 2.3 Consensus size: 62
28728339 AGGACACAAG
* * * * * * *
28728349 CGTGTGTCCAGGCCGTGTAAGTCACTGTTTGTATTATTGGTGACACGGACTAGGGACACGGG
1 CGTGTGTCCAGGCCGTGCAACTCACTGTTTGGATTATGGGTCACACGGACCAGGGACACGGA
* *
28728411 TGTGTGTCCAGGCCGTGCAACTCACTGTTTTGGATT-TAGGGTCACAC-GAGCCA-GGACATGGA
1 CGTGTGTCCAGGCCGTGCAACTCACTG-TTTGGATTAT-GGGTCACACGGA-CCAGGGACACGGA
*
28728473 CGTGTGTCCATGCCGTG
1 CGTGTGTCCAGGCCGTG
28728490 TGAGGGGTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
62 49 0.75
63 16 0.25
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (62 bp):
CGTGTGTCCAGGCCGTGCAACTCACTGTTTGGATTATGGGTCACACGGACCAGGGACACGGA
Found at i:28729664 original size:14 final size:14
Alignment explanation
Indices: 28729645--28729671 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28729635 TATTTTATAC
28729645 TATAAAATATTTAT
1 TATAAAATATTTAT
28729659 TATAAAATATTTA
1 TATAAAATATTTA
28729672 CAAATTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAAAATATTTAT
Found at i:28746551 original size:9 final size:9
Alignment explanation
Indices: 28746518--28746559 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
28746508 TAAAAATCTA
28746518 TAAAAAATAT
1 TAAAAAAT-T
* *
28746528 TTAAAATTT
1 TAAAAAATT
28746537 TAAAAAATT
1 TAAAAAATT
28746546 TAAAAAA-T
1 TAAAAAATT
28746554 TAAAAA
1 TAAAAA
28746560 GTTGTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.25
9 15 0.54
10 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAAATT
Done.