Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007173.1 Hibiscus syriacus cultivar Beakdansim tig00018827_pilon, whole genome shotgun sequence
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: 1357898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:538066 original size:16 final size:16
Alignment explanation
Indices: 538045--538079 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
538035 AAAAATAATT
538045 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
538061 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
538077 TAA
1 TAA
538080 ATACATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:538268 original size:15 final size:14
Alignment explanation
Indices: 538248--538294 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
538238 TTAATAGTAA
538248 AATAATAATAAATAT
1 AATAAT-ATAAATAT
538263 AATAATTATAAATAT
1 AATAA-TATAAATAT
*
538278 -AT-ATATATATAT
1 AATAATATAAATAT
538290 AATAA
1 AATAA
538295 CATTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 8 0.29
13 3 0.11
14 3 0.11
15 13 0.46
16 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:538301 original size:27 final size:25
Alignment explanation
Indices: 538247--538360 Score: 65
Period size: 26 Copynumber: 4.4 Consensus size: 25
538237 GTTAATAGTA
*
538247 AAATAATAATAAATATAATAATTAT
1 AAATAATAATAAATATAATAAATAT
*
538272 AAATATATATATATATATAATAACAT-T
1 AAATA-ATA-ATAAATATAATAA-ATAT
* * *
538299 AAAAAACATTAAA-ATAATATTAGA-AT
1 AAATAATAATAAATATAATA--A-ATAT
* *
538325 AAA-AATAATTAATATATATATATAT
1 AAATAATAATAAATATA-ATAAATAT
*
538350 AATTAATAATA
1 AAATAATAATA
538361 CGATTTATCA
Statistics
Matches: 66, Mismatches: 13, Indels: 19
0.67 0.13 0.19
Matches are distributed among these distances:
24 7 0.11
25 18 0.27
26 20 0.30
27 20 0.30
28 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (25 bp):
AAATAATAATAAATATAATAAATAT
Found at i:538809 original size:35 final size:36
Alignment explanation
Indices: 538739--538834 Score: 131
Period size: 35 Copynumber: 2.6 Consensus size: 36
538729 GTGCTTGTGG
* *
538739 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCATAGCAAAATTCT
*
538776 ATCCTATTTTAGGAG-TTGAATCATAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTCT
*
538811 ATCCTATTTTTGAGAGTTTGAATC
1 ATCCTATTTTAG-GAGTTTGAATC
538835 CTAGTAGGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
35 28 0.53
36 11 0.21
37 14 0.26
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTCT
Found at i:539607 original size:106 final size:105
Alignment explanation
Indices: 539299--539858 Score: 589
Period size: 109 Copynumber: 5.3 Consensus size: 105
539289 AATATTGTTC
* * * *
539299 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCT-GAAACGGAAAAATGTTTGTTGACA
** * * * *
539364 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
539405 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AAC-G--AAAT-CTTGTTGACAA
1 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAACGGAAAAATGTTTGTTGACAA
* *
539465 TCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * **
539505 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAA-CGGAAAAATGTTTGTTGACA
539570 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * ** * *
539611 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAA-TCGCGGATGAAAC-TAAAAAGTTGTTCG
1 CGAGT--C-CAATATCCTCCGCT-GTGAAGTTGAAATTGGC-TCTGAAACGGAAAAA--TGTTTG
539673 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
59 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** * * *
539720 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTT
1 CGAGT--C-CAATATCCTCCGCT-GTGAAGTTGAAATTGGCTCT-GAAACGGAAAAATGTTTGTT
*
539784 GACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
539829 CGAGTCCAATATCCTTCGCTGTGAAGTTGA
1 CGAGTCCAATATCCTCCGCTGTGAAGTTGA
539859 TTCGTTGTGA
Statistics
Matches: 389, Mismatches: 48, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
100 82 0.21
101 5 0.01
103 2 0.01
104 2 0.01
105 5 0.01
106 108 0.28
107 7 0.02
108 5 0.01
109 165 0.42
110 5 0.01
111 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (105 bp):
CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAACGGAAAAATGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:539802 original size:218 final size:205
Alignment explanation
Indices: 539299--539858 Score: 651
Period size: 206 Copynumber: 2.7 Consensus size: 205
539289 AATATTGTTC
* * **
539299 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGC-GTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
** * * * *
539364 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGA
65 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
* ** * *
539429 AGTTGAAATTGACTCTGAACGAAATCTTGTTGACAATCAGCCGTCCCTTCATTGTGAAGTTGAAC
130 AGTTGAAATCGACGATGAACAAAATCTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAAC
539494 TTGTGTTGTCT
195 TTGTGTTGTCT
* * * * *
539505 CGAGTCCAATATCCTTCGC-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGAC
1 CGAGTCCAATATCCTCCGCGTG-G-AGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGAC
*
539569 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-ACGATATCCTCCG-
64 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--CTA--ATATCCTCCGC
* * *
539632 TCGTGGAGTTGAAATCG-CGGATGAAACTAAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGT
125 T-GTGAAGTTGAAATCGAC-GATG-AAC--AAAA--TCTT-GTTGACAACCAGCCGTCCCTTCAT
539696 TGTGAAGTTGAACTTGTGTTGTCT
182 TGTGAAGTTGAACTTGTGTTGTCT
* * * *
539720 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTG
1 CGAGT--C-CAATATCCTCCG-CGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTG
* *
539785 ACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTG
62 ACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTG
539850 TGAAGTTGA
127 TGAAGTTGA
539859 TTCGTTGTGA
Statistics
Matches: 297, Mismatches: 36, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
204 2 0.01
206 92 0.31
207 1 0.00
208 3 0.01
209 24 0.08
210 3 0.01
212 3 0.01
214 3 0.01
215 68 0.23
216 2 0.01
217 2 0.01
218 90 0.30
219 2 0.01
220 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (205 bp):
CGAGTCCAATATCCTCCGCGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGAA
GTTGAAATCGACGATGAACAAAATCTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACT
TGTGTTGTCT
Found at i:539857 original size:324 final size:312
Alignment explanation
Indices: 539366--540192 Score: 879
Period size: 324 Copynumber: 2.6 Consensus size: 312
539356 TGTTGACAGT
* * * * * *
539366 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAG
1 CAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGGGTCCAATATCCTTCACTGTGAAG
* * * * * *
539431 TTGAAATTGACTCTG-AAC---GAAA-TCTTGTTGACAATCAGCCGTCCCTTCATTGTGAAGTTG
66 TTGAAATCGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
*
539491 AACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATT-TG-A
131 AACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTCTGAA
*
539554 A-AAATGT-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTG
196 AGAAAT-TATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-
* * *
539617 GCACGATATCCTCCG-TCGTGGAGTTGAAATCGCGGATGAAACTAAAAAGTTGTTCGTTGACAAC
259 GCA--ATATCCTCCGCT-GTGAAGTTGAAAT--CGGAT----CT-AAAA-TTATTCGTCGACAAC
* * * * * *
539681 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCC-TC-CGTCG
1 CAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGGGT--C-CAATATCCTTCAC-T-G
* * * * *
539744 TGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGCTGTG
61 TGAAGTTGAAATCGGCCCTGAAACTGGGAAATTA-TTGTTGACAACCAGCCGTCCCTTCGTTGTG
** *
539809 AAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGATTCGTTGTGAAGT-T
125 AAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA--AATTG-G--CTCT
539873 GAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAA
185 GAAATT----CTGAAA----GAAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAA
* * * * * *
539938 CTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTAAAATTATTTGTC
242 CTTGTGTTGTCTCGAGTGCAATATCCTCCGCTGTGAAGTTGAAATCGGATCTAAAATTATTCGTC
**
540003 GACAGT
307 GACAAC
* *
540009 CAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTGCCTTGGGTCCAATATCCTTCACTGTGAAG
1 CAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGGGTCCAATATCCTTCACTGTGAAG
*
540074 TTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
66 TTGAAATCGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
* *
540139 AACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTCGAAATTGACTCT
131 AACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
540193 AGCTAAAACC
Statistics
Matches: 430, Mismatches: 50, Indels: 59
0.80 0.09 0.11
Matches are distributed among these distances:
315 39 0.09
316 1 0.00
317 4 0.01
318 24 0.06
319 3 0.01
320 1 0.00
322 7 0.02
323 1 0.00
324 154 0.36
325 37 0.09
326 7 0.02
327 2 0.00
328 54 0.13
329 5 0.01
330 2 0.00
333 2 0.00
334 5 0.01
336 20 0.05
337 1 0.00
338 3 0.01
339 58 0.13
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (312 bp):
CAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGGGTCCAATATCCTTCACTGTGAAG
TTGAAATCGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
AACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTCTGAA
AGAAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC
AATATCCTCCGCTGTGAAGTTGAAATCGGATCTAAAATTATTCGTCGACAAC
Found at i:539867 original size:16 final size:16
Alignment explanation
Indices: 539843--539874 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
539833 TCCAATATCC
539843 TTCGCTGTGAAGTTGA
1 TTCGCTGTGAAGTTGA
*
539859 TTCGTTGTGAAGTTGA
1 TTCGCTGTGAAGTTGA
539875 AATTGGCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.09, G:0.31, T:0.41
Consensus pattern (16 bp):
TTCGCTGTGAAGTTGA
Found at i:539962 original size:121 final size:122
Alignment explanation
Indices: 539747--539979 Score: 396
Period size: 121 Copynumber: 1.9 Consensus size: 122
539737 TCCGTCGTGG
* * * *
539747 AGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAG
1 AGTTGAAATCGGCCCTGAAACTGGGAAATTATTTGTTGACAAACAGCCGTCCCTTCGCTGTGAAG
539812 TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGATTCGTTGTGA
66 TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGATTCGTTGTGA
* *
539869 AGTTGAAATTGGCCCTGAAACTGGGAAATTA-TTGTTGACAAACAGCCGTCCCTTCGTTGTGAAG
1 AGTTGAAATCGGCCCTGAAACTGGGAAATTATTTGTTGACAAACAGCCGTCCCTTCGCTGTGAAG
*
539933 TTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGA
66 TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA
539980 GATTGGCTCT
Statistics
Matches: 104, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
121 77 0.74
122 27 0.26
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (122 bp):
AGTTGAAATCGGCCCTGAAACTGGGAAATTATTTGTTGACAAACAGCCGTCCCTTCGCTGTGAAG
TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGATTCGTTGTGA
Found at i:540040 original size:98 final size:97
Alignment explanation
Indices: 539894--540193 Score: 357
Period size: 98 Copynumber: 3.0 Consensus size: 97
539884 TGAAACTGGG
*
539894 AAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAA
1 AAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
*
539959 TATCCTTCGCTGTGAAGTTGAGATTGGCTCTA
66 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTA
* ** * * * * * * * *
539991 AAATTATTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTGCCTTGGGTCCA
1 AAATTA-TTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
* *
540056 ATATCCTTCACTGTGAAGTTGAAATTGGCCCTGAAACTGGG
65 ATATCCTTCGCTGTGAAGTTGAAATTGG--CT----CT--A
*
540097 AAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
1 AAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
* *
540162 TATCCTTCGCTGTGAAGTCGAAATTGACTCTA
66 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTA
540194 GCTAAAACCT
Statistics
Matches: 164, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
97 6 0.04
98 72 0.44
99 2 0.01
100 2 0.01
103 2 0.01
104 2 0.01
105 72 0.44
106 6 0.04
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (97 bp):
AAATTATTGTTGACAAACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
TATCCTTCGCTGTGAAGTTGAAATTGGCTCTA
Found at i:540160 original size:105 final size:106
Alignment explanation
Indices: 539991--540187 Score: 270
Period size: 105 Copynumber: 1.9 Consensus size: 106
539981 ATTGGCTCTA
** * * *
539991 AAATTATTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTGCCTTGGGTCCA
1 AAATTATTTGTCGACAACCAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGAGTCCA
*
540056 ATATCCTTCACTGTGAAGTTGAAATTGGCCCTGAAACTGGG
66 ATATCCTTCACTGTGAAGTCGAAATTGGCCCTGAAACTGGG
* * * * * *
540097 AAATTA-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAATTATTTGTCGACAACCAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGAGTCCA
*
540161 ATATCCTTCGCTGTGAAGTCGAAATTG
66 ATATCCTTCACTGTGAAGTCGAAATTG
540188 ACTCTAGCTA
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
105 72 0.92
106 6 0.08
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (106 bp):
AAATTATTTGTCGACAACCAGCCGCCCCTTCGCTGTGAAATTGAACTTGTGCTGCCTCGAGTCCA
ATATCCTTCACTGTGAAGTCGAAATTGGCCCTGAAACTGGG
Found at i:540795 original size:65 final size:65
Alignment explanation
Indices: 540720--540866 Score: 258
Period size: 65 Copynumber: 2.3 Consensus size: 65
540710 AAATTTTGTT
540720 TCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTATC
1 TCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTATC
* *
540785 TCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTATC
* *
540850 TCAAGGGAGACAAAATT
1 TCAAGAGAGACGAAATT
540867 TTGTTTCGAG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 78 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTAAAGAGAAACTATC
Found at i:540882 original size:37 final size:37
Alignment explanation
Indices: 540831--541241 Score: 242
Period size: 37 Copynumber: 11.9 Consensus size: 37
540821 TCAATGTTTA
* *
540831 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
540868 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
540904 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
540932 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
540970 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
541006 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
541034 ATGTTTCAAGAGAAACTGTCTCAATG-GTGACAGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
541072 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
541108 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * * * *
541136 ATGTTTCAAGAGAAACTGTCTTAAGGGAGAAAAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
541174 TGTTTCAAGGGAAACTGTCTAAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
541210 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
541242 TGGTGAGCAT
Statistics
Matches: 278, Mismatches: 57, Indels: 78
0.67 0.14 0.19
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 38 0.14
30 11 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 8 0.03
36 81 0.29
37 116 0.42
38 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:540885 original size:102 final size:102
Alignment explanation
Indices: 540766--541223 Score: 763
Period size: 102 Copynumber: 4.5 Consensus size: 102
540756 TCAATGTTTA
* * *
540766 TGTTTAAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
540831 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
540868 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
540933 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
540970 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
541035 TGTTTCAAGAGAAACTGTCTCAATGGTGACAGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
541072 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
541137 TGTTTCAAGAGAAACTGTCTTAAGGGAGAAAAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * **
541174 TGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
541224 CTGTCTCAAG
Statistics
Matches: 333, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 333 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:541219 original size:36 final size:36
Alignment explanation
Indices: 541137--541241 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
541127 TCAATGTTTA
* * * *
541137 TGTTTCAAGAGAAACTGTCTTAAGGGAGAAAAAAATT
1 TGTTTCAAGGGAAACTGTCTAAAGAGAG-ACAAAATT
*
541174 TGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAATT
*
541210 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTAAAGAGAGACAA
541242 TGGTGAGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 37 0.60
37 25 0.40
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAATT
Found at i:542127 original size:22 final size:22
Alignment explanation
Indices: 542102--542152 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
542092 TTGTGTTTGG
542102 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
542124 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
542146 TCAAAGG
1 TCAAAGG
542153 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:542786 original size:14 final size:14
Alignment explanation
Indices: 542769--542847 Score: 78
Period size: 14 Copynumber: 5.8 Consensus size: 14
542759 CCTTTTTTTA
542769 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
542783 TTTTTGTTCTTGT-T
1 TTTTTGTTCTT-TCT
* *
542797 TTTTTCTTTTTTCT
1 TTTTTGTTCTTTCT
542811 TTTTT-TTC-TTC-
1 TTTTTGTTCTTTCT
542822 -TTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
542837 TTTTTGTTCTT
1 TTTTTGTTCTT
542848 GATTGGATCT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.07
12 6 0.11
13 3 0.06
14 32 0.59
15 4 0.07
16 5 0.09
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:542800 original size:27 final size:28
Alignment explanation
Indices: 542769--542848 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
542759 CCTTTTTTTA
542769 TTTTTGTTCTTTCTTTTTTGTTCTTGTT
1 TTTTTGTTCTTTCTTTTTTGTTCTTGTT
* *
542797 TTTTTCTTTTTTCTTTTTT-TTC---TT
1 TTTTTGTTCTTTCTTTTTTGTTCTTGTT
*
542821 CTTTTGCTTCTTTTCTTTTTTGTTCTTG
1 TTTTTG-TTC-TTTCTTTTTTGTTCTTG
542849 ATTGGATCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 6 0.15
25 2 0.05
26 10 0.24
27 6 0.15
28 17 0.41
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (28 bp):
TTTTTGTTCTTTCTTTTTTGTTCTTGTT
Found at i:542833 original size:21 final size:20
Alignment explanation
Indices: 542778--542839 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 20
542768 ATTTTTGTTC
*
542778 TTTCTT-TTTTGTTCTTGTT
1 TTTCTTCTTTTGTTCTTTTT
542797 TTT-TTCTTTT-TTCTTTTT
1 TTTCTTCTTTTGTTCTTTTT
542815 TTTCTTCTTTTGCTTCTTTTCT
1 TTTCTTCTTTTG-TTCTTTT-T
542837 TTT
1 TTT
542840 TTGTTCTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 12 0.32
19 14 0.38
21 7 0.19
22 4 0.11
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.81
Consensus pattern (20 bp):
TTTCTTCTTTTGTTCTTTTT
Found at i:547647 original size:16 final size:16
Alignment explanation
Indices: 547626--547663 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
547616 AAAAATAATT
547626 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
547642 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
547658 T-ATAAA
1 TAATAAA
547664 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:547858 original size:15 final size:15
Alignment explanation
Indices: 547838--547868 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
547828 TTAATAGTAA
547838 AATAATAATAAATAT
1 AATAATAATAAATAT
*
547853 AATAATTATAAATAT
1 AATAATAATAAATAT
547868 A
1 A
547869 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATAATAAATAT
Found at i:548392 original size:35 final size:36
Alignment explanation
Indices: 548322--548417 Score: 131
Period size: 35 Copynumber: 2.6 Consensus size: 36
548312 GTGCTTGTGG
* *
548322 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCATAGCAAAATTCT
*
548359 ATCCTATTTTAGGAG-TTGAATCATAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTCT
*
548394 ATCCTATTTTTGAGAGTTTGAATC
1 ATCCTATTTTAG-GAGTTTGAATC
548418 CTAGTAGGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
35 28 0.53
36 11 0.21
37 14 0.26
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTCT
Found at i:549221 original size:21 final size:21
Alignment explanation
Indices: 549179--549221 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
549169 TTTCTGGGTT
* * *
549179 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
549200 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
549221 A
1 A
549222 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:549281 original size:66 final size:68
Alignment explanation
Indices: 549201--549352 Score: 227
Period size: 67 Copynumber: 2.2 Consensus size: 68
549191 ACCCATTCAA
* *
549201 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGTATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
549265 -GG
66 GGG
* * *
549267 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
549332 GGGG
66 -GGG
*
549336 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
549353 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 22 0.29
67 37 0.48
69 18 0.23
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:549697 original size:34 final size:29
Alignment explanation
Indices: 549658--549729 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
549648 CATATTATGA
*
549658 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
549687 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
549716 TACATGACATGAAT
1 TACATGACATGAAT
549730 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:550168 original size:149 final size:149
Alignment explanation
Indices: 549898--550201 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
549888 GGGTAGAGGG
549898 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
549963 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
550028 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
550047 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
*
550112 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
550177 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
550196 TCTACG
1 TCTACG
550202 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:550224 original size:23 final size:23
Alignment explanation
Indices: 550180--550224 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
550170 ATTATTATAT
* *
550180 GGCACTACGGTGTAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
550203 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
550225 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:556297 original size:21 final size:21
Alignment explanation
Indices: 556255--556297 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
556245 TTTCTGGGTT
* * *
556255 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
556276 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
556297 A
1 A
556298 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:556357 original size:66 final size:67
Alignment explanation
Indices: 556277--556413 Score: 222
Period size: 67 Copynumber: 2.1 Consensus size: 67
556267 ACCCATTCAA
* *
556277 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGTATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
556341 GG
66 GG
* * *
556343 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
556408 GG
66 GG
556410 GGGG
1 GGGG
556414 GGGGGAACCG
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 22 0.34
67 43 0.66
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:556776 original size:34 final size:29
Alignment explanation
Indices: 556737--556808 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
556727 CATATTATGA
*
556737 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
556766 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
556795 TACATGACATGAAT
1 TACATGACATGAAT
556809 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:557247 original size:149 final size:149
Alignment explanation
Indices: 556977--557280 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
556967 GGGTAGAGGG
556977 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
557042 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
557107 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
557126 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
*
557191 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
557256 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
557275 TCTACG
1 TCTACG
557281 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:557303 original size:23 final size:23
Alignment explanation
Indices: 557259--557303 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
557249 ATTATTATAT
*
557259 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
557282 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
557304 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:558130 original size:95 final size:96
Alignment explanation
Indices: 557985--558185 Score: 253
Period size: 95 Copynumber: 2.1 Consensus size: 96
557975 ACTAACCCGA
* * *
557985 TATTGATACTTCTATACTATGGTACCGATACCCCCATCCAGTATCGATACCAAAATTAGGTTCGA
1 TATTGATACTTCTATACTATGGTACCGATACCCCCATCCAGTATCAATACCAAAATTAGATTCAA
* * *
558050 TGTTGTTTGGTATCGATA-CCCTTACCATGG
66 TATTGCTTGGTACCGATACCCCTTACCATGG
* * * * * *
558080 TATTGATA-TTATCATATTATGGTACCGATACCTCCTTTCGGTATCAATACCAAAATTAGATTCA
1 TATTGATACTTCT-ATACTATGGTACCGATACCCCCATCCAGTATCAATACCAAAATTAGATTCA
*
558144 ATATTGCTTGGTACCGATACCCCTTATCATGG
65 ATATTGCTTGGTACCGATACCCCTTACCATGG
*
558176 TATCGATACT
1 TATTGATACT
558186 ACCTCCTCGG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 3 0.03
95 67 0.75
96 18 0.20
97 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (96 bp):
TATTGATACTTCTATACTATGGTACCGATACCCCCATCCAGTATCAATACCAAAATTAGATTCAA
TATTGCTTGGTACCGATACCCCTTACCATGG
Found at i:559238 original size:29 final size:29
Alignment explanation
Indices: 559196--559262 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
559186 ATTTTCGTAC
*
559196 TGATACTATCTGAGTATCGATTCAAATAT
1 TGATACTCTCTGAGTATCGATTCAAATAT
*
559225 TGATACTCTCTGAGTATCGATTCAGATAT
1 TGATACTCTCTGAGTATCGATTCAAATAT
*
559254 CGATACTCT
1 TGATACTCT
559263 ATATGGAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (29 bp):
TGATACTCTCTGAGTATCGATTCAAATAT
Found at i:560676 original size:22 final size:22
Alignment explanation
Indices: 560651--560709 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
560641 CCTAATGAAT
560651 GTGGTTTTCAATGACCTCGAAA
1 GTGGTTTTCAATGACCTCGAAA
560673 GTGGTTTTCAATGACCTCGAAA
1 GTGGTTTTCAATGACCTCGAAA
560695 GTGGTTTTCAATGAC
1 GTGGTTTTCAATGAC
560710 AACGATCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (22 bp):
GTGGTTTTCAATGACCTCGAAA
Found at i:561199 original size:52 final size:52
Alignment explanation
Indices: 561142--561240 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
561132 TGCTGATTTG
*
561142 ATTTGATTGCTTAAGG-ATATAAAGACATTCATATTTGTTTTGGATTGTGCAA
1 ATTTGATTGCTT-AGGTATATAAAGACATTCATATTTGTTTTGCATTGTGCAA
561194 ATTTGATTGCTTAGGTATATAAAGACATTCATATTTGTTTTGCATTG
1 ATTTGATTGCTTAGGTATATAAAGACATTCATATTTGTTTTGCATTG
561241 ACATGTTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 3 0.07
52 42 0.93
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44
Consensus pattern (52 bp):
ATTTGATTGCTTAGGTATATAAAGACATTCATATTTGTTTTGCATTGTGCAA
Found at i:562234 original size:58 final size:56
Alignment explanation
Indices: 562144--562257 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 56
562134 AAACTATCAA
*
562144 GAAGTAACTTATCCAAGATGCATGTTATTAATGATTAAAAAAATGTATGTTATTAATG
1 GAAGTAACTTATCCAAGATGCATATTATTAATGATT--AAAAATGTATGTTATTAATG
* * *
562202 GAAGTAACTTATGCAATATGCATATTATTAATGATTAAAAATGTATTTTATTAATG
1 GAAGTAACTTATCCAAGATGCATATTATTAATGATTAAAAATGTATGTTATTAATG
562258 ATTAAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 19 0.37
58 33 0.63
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (56 bp):
GAAGTAACTTATCCAAGATGCATATTATTAATGATTAAAAATGTATGTTATTAATG
Found at i:562314 original size:33 final size:32
Alignment explanation
Indices: 562231--562333 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
562221 GCATATTATT
*
562231 AATGATTAAAAA-TGTATTTTATTAATGATTAAA
1 AATG-TTAAAAAGT-TATGTTATTAATGATTAAA
*
562264 AATTGTTAAAAATTTATGTTATTAATGATTAGAA
1 AA-TGTTAAAAAGTTATGTTATTAATGATTA-AA
* * *
562298 AATGTTAACAAGTTATG-TGTTATTGATTAAA
1 AATGTTAAAAAGTTATGTTATTAATGATTAAA
562329 AATGT
1 AATGT
562334 ATGTTATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
31 7 0.11
32 10 0.16
33 38 0.61
34 7 0.11
ACGTcount: A:0.44, C:0.01, G:0.13, T:0.43
Consensus pattern (32 bp):
AATGTTAAAAAGTTATGTTATTAATGATTAAA
Found at i:562375 original size:144 final size:144
Alignment explanation
Indices: 562182--562463 Score: 505
Period size: 144 Copynumber: 2.0 Consensus size: 144
562172 TAATGATTAA
*
562182 AAAAATGTATGTTATTAATGGAAGTAACTTATGCAATATGCATATTATTAATGATTAAAAA-TGT
1 AAAAATGTATGTTATTAATGAAAGTAACTTATGCAATATGCATATTATTAATGATTAAAAATTGT
*
562246 ATTTTATTAATGATTAAAAATTGTTAAAAATTTATGTTATTAATGATTAGAA-AATGTTAACAAG
66 ATTTTATTAATGATTAAAAATTGTTAAAAATGTAT-TTATTAATGATTA-AACAATGTTAACAAG
562310 TTATGTGTTATTGATT
129 TTATGTGTTATTGATT
*
562326 AAAAATGTATGTTATTAATGAAAGTAACTTATGCAATATTCATATTATTAATGATTAAAAATTGT
1 AAAAATGTATGTTATTAATGAAAGTAACTTATGCAATATGCATATTATTAATGATTAAAAATTGT
562391 ATTTTATTAATGATTAAAAATTGTTAAAAATGTATTTATTAATGATTAAACAATGTTAACAAGTT
66 ATTTTATTAATGATTAAAAATTGTTAAAAATGTATTTATTAATGATTAAACAATGTTAACAAGTT
562456 ATGTGTTA
131 ATGTGTTA
562464 CTTATAATTA
Statistics
Matches: 133, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
143 2 0.02
144 94 0.71
145 37 0.28
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.42
Consensus pattern (144 bp):
AAAAATGTATGTTATTAATGAAAGTAACTTATGCAATATGCATATTATTAATGATTAAAAATTGT
ATTTTATTAATGATTAAAAATTGTTAAAAATGTATTTATTAATGATTAAACAATGTTAACAAGTT
ATGTGTTATTGATT
Found at i:562432 original size:32 final size:34
Alignment explanation
Indices: 562375--562449 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 34
562365 TCATATTATT
562375 AATGATTAAAAATTGTATTTTATTAATGATTAAA-
1 AATG-TTAAAAATTGTATTTTATTAATGATTAAAC
562409 AATTGTTAAAAA-TGTA-TTTATTAATGATTAAAC
1 AA-TGTTAAAAATTGTATTTTATTAATGATTAAAC
562442 AATGTTAA
1 AATGTTAA
562450 CAAGTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
32 22 0.56
33 6 0.15
34 9 0.23
35 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (34 bp):
AATGTTAAAAATTGTATTTTATTAATGATTAAAC
Found at i:565670 original size:55 final size:55
Alignment explanation
Indices: 565610--565775 Score: 332
Period size: 55 Copynumber: 3.0 Consensus size: 55
565600 TACAATTGAT
565610 TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
1 TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
565665 TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
1 TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
565720 TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
1 TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
565775 T
1 T
565776 CTACAATTTG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 111 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (55 bp):
TTATATAGTTTTTAAGTGTATATTAACAAGTATTTTATACTATTCTCTTTTCTTC
Found at i:566465 original size:21 final size:21
Alignment explanation
Indices: 566441--566490 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
566431 TGGAAATATT
** *
566441 CATTTTAGGTAGCGAAATTAA
1 CATTTTAGGTAGAAAAAATAA
566462 CATTTTCA-GTAGAAAAAATAA
1 CATTTT-AGGTAGAAAAAATAA
566483 CATTTTAG
1 CATTTTAG
566491 ATAGTGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (21 bp):
CATTTTAGGTAGAAAAAATAA
Found at i:566763 original size:20 final size:19
Alignment explanation
Indices: 566711--566767 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
566701 AATTATAGTC
* *
566711 ATAATATTAAATTATAATT
1 ATAATATTAAAATATAAGT
**
566730 ATAATACAATAAATATAAGT
1 ATAATATTA-AAATATAAGT
566750 ATAATATTACAAATATAA
1 ATAATATTA-AAATATAA
566768 ATATTACGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAATATTAAAATATAAGT
Found at i:568722 original size:5 final size:5
Alignment explanation
Indices: 568712--568755 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
568702 GGTTACAGAG
568712 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
568756 TCCTTCTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:569362 original size:64 final size:63
Alignment explanation
Indices: 569246--569386 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
569236 CATATTCAAT
* *
569246 GTGCATCGATGCACTCTTTAAAGAAGAAACATCAAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * ** * * *
569309 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTGATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCAAAGGCAATTGGTGCATCGATGCATAGGTA
*
569373 GTGCATCAATGCAC
1 GTGCATCGATGCAC
569387 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 18 0.28
64 47 0.72
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:569422 original size:20 final size:20
Alignment explanation
Indices: 569394--569431 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
569384 CACATGTTAA
*
569394 AGAATGCATCGATGCACTGT
1 AGAACGCATCGATGCACTGT
569414 AGAACGCATCGATGCACT
1 AGAACGCATCGATGCACT
569432 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (20 bp):
AGAACGCATCGATGCACTGT
Found at i:570433 original size:31 final size:31
Alignment explanation
Indices: 570375--570439 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
570365 AGAGTCGAGG
*
570375 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATGGACA
* * *
570406 GTTTACCTAGGT-TCTTCGGGACCTATGGATA
1 GTTTACCTAGGTCT-TTCGAGACATATGGACA
570437 GTT
1 GTT
570440 ATCGAGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGACA
Found at i:570491 original size:29 final size:30
Alignment explanation
Indices: 570425--570496 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
570415 GGTTCTTCGG
* * *
570425 GACCTATGGATAGTTATCGAGGTTCTTTAT
1 GACCTCTGGATAGTTATCGAGGGTATTTAT
* *
570455 GACCTCTGGATAGTTGTCG-GGGTATTTGT
1 GACCTCTGGATAGTTATCGAGGGTATTTAT
*
570484 GACCTCTGAATAG
1 GACCTCTGGATAG
570497 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (30 bp):
GACCTCTGGATAGTTATCGAGGGTATTTAT
Found at i:572029 original size:21 final size:21
Alignment explanation
Indices: 572003--572042 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
571993 TGGGGTTACC
572003 AAAGTTATGAGGATCCAATCT
1 AAAGTTATGAGGATCCAATCT
*
572024 AAAGTTATGAGGATGCAAT
1 AAAGTTATGAGGATCCAAT
572043 GAAGATTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
AAAGTTATGAGGATCCAATCT
Found at i:573511 original size:64 final size:63
Alignment explanation
Indices: 573414--573554 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
573404 CATATTCAAT
* * *
573414 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* ** * * *
573477 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTGATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
573541 GTGCATCGATGCAC
1 GTGCATCGATGCAC
573555 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:573587 original size:20 final size:22
Alignment explanation
Indices: 573542--573599 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
573532 GCATGGGTAG
573542 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
573566 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
573586 TGCATCGATGCACT
1 TGCATCGATGCACT
573600 TCAAGGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:574438 original size:15 final size:15
Alignment explanation
Indices: 574418--574447 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
574408 TATCCTTACA
574418 CATACATGTGGTATG
1 CATACATGTGGTATG
574433 CATACATGTGGTATG
1 CATACATGTGGTATG
574448 TGAAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
CATACATGTGGTATG
Found at i:574581 original size:31 final size:31
Alignment explanation
Indices: 574543--574637 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
574533 AGAGTCGAGG
*
574543 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
574574 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
* * *
574605 G-TTACCGAGGTTCTT-GATGACCTATGGATA
1 GTTTACCTAGGTTCTTCGA-GACATATGGACA
574635 GTT
1 GTT
574638 GTCGGGGTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.02
30 25 0.45
31 27 0.49
32 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:574616 original size:30 final size:30
Alignment explanation
Indices: 574557--574637 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
574547 ACCTATGTCT
* *
574557 TTCGAGACATATGGACAGTTTACCTAGGTTC
1 TTCGAGACCTATGGACAG-TTACCGAGGTTC
*
574588 TTCGGGACCTATGGACAGTTACCGAGGTTC
1 TTCGAGACCTATGGACAGTTACCGAGGTTC
*
574618 TT-GATGACCTATGGATAGTT
1 TTCGA-GACCTATGGACAGTT
574638 GTCGGGGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 1 0.02
30 27 0.61
31 16 0.36
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (30 bp):
TTCGAGACCTATGGACAGTTACCGAGGTTC
Found at i:577224 original size:31 final size:30
Alignment explanation
Indices: 577170--577263 Score: 116
Period size: 31 Copynumber: 3.1 Consensus size: 30
577160 CCAACTTAAT
* * *
577170 GGAATACCTTGGGCCATAAAGCCTACCCAA
1 GGAATACCTAGGGCCTTAGAGCCTACCCAA
577200 GGAATACCTAAGGGCCTTAGAGCCTACCCAA
1 GGAATACCT-AGGGCCTTAGAGCCTACCCAA
* * *
577231 GGAGTACCTTGGGGCCTAAGAGCCTACCCAA
1 GGAATACC-TAGGGCCTTAGAGCCTACCCAA
577262 GG
1 GG
577264 GTCACCACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 9 0.16
31 46 0.82
32 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (30 bp):
GGAATACCTAGGGCCTTAGAGCCTACCCAA
Found at i:579550 original size:21 final size:21
Alignment explanation
Indices: 579512--579562 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
579502 ACATAGTATT
579512 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
579532 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
579553 ACATATAGAA
1 AAATA-AGAA
579563 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:581270 original size:106 final size:107
Alignment explanation
Indices: 581112--581318 Score: 326
Period size: 106 Copynumber: 1.9 Consensus size: 107
581102 GTTCTGGAAC
** *
581112 TGGGAAATTGTTTTGTTGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
1 TGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGGGCTGTCTCGA
*
581177 GTCCAATGCCCTTCAATGTGAAGTTGAAATTGGCTCCAAAAT
66 GTCCAATACCCTTCAATGTGAAGTTGAAATTGGCTCCAAAAT
* *
581219 TGGGAAATTG-TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGGGTTGTCTTGA
1 TGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGGGCTGTCTCGA
* **
581283 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 GTCCAATACCCTTCAATGTGAAGTTGAAATTGGCTC
581319 TAGCTAAAAC
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 81 0.89
107 10 0.11
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (107 bp):
TGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGGGCTGTCTCGA
GTCCAATACCCTTCAATGTGAAGTTGAAATTGGCTCCAAAAT
Found at i:581812 original size:67 final size:67
Alignment explanation
Indices: 581632--581824 Score: 215
Period size: 67 Copynumber: 2.8 Consensus size: 67
581622 GTCTTAAAAA
* * * * * * * *
581632 AGACAGAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTATTTCATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTAA
581697 AGGG
64 AGGG
* * * * * *
581701 AGACAAAATTTTGTTTTAAAGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTAAA
1 AGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTAAA
581766 GGG
65 GGG
* *
581769 AGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
581825 ATTTTCAAAG
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
67 43 0.42
68 28 0.27
69 10 0.10
70 22 0.21
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTAAAG
GG
Found at i:581847 original size:33 final size:35
Alignment explanation
Indices: 581779--581929 Score: 215
Period size: 36 Copynumber: 4.4 Consensus size: 35
581769 AGACGAAATT
* *
581779 TGTTTCAAGGGAAACAATCTCAAAGG----TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTCTTTTTG
*
581810 TGTTTCAAGAGAAACATTTTCAAAGG-T-TTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTCTTTTTG
581843 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TTCTTTTTG
581879 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TTCTTTTTG
581915 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
581930 TGTATCAAGG
Statistics
Matches: 111, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
31 23 0.21
33 30 0.27
35 1 0.01
36 57 0.51
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTCTTTTTG
Found at i:581884 original size:36 final size:36
Alignment explanation
Indices: 581805--581929 Score: 220
Period size: 36 Copynumber: 3.6 Consensus size: 36
581795 ATCTCAAAGG
*
581805 TTTTGTGTTTCAAGAGAAACATTTTCAAAGG--T-T
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
581838 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
581874 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
581910 TTTTGTGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
581930 TGTATCAAGG
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
33 30 0.34
35 1 0.01
36 57 0.65
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (36 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
Found at i:582070 original size:36 final size:36
Alignment explanation
Indices: 581970--582084 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 36
581960 CAATGATTGA
*
581970 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
582007 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
582044 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
582080 TGTTT
1 TGTTT
582085 AATGTAAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 24 0.35
37 28 0.41
38 17 0.25
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:582196 original size:36 final size:36
Alignment explanation
Indices: 582156--582224 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
582146 ATAGAAATTG
*
582156 TCTCAA-AGGAGACAAAATTTATTTCAAGGGAAACTA
1 TCTCAAGA-GAGACAAAATTCATTTCAAGGGAAACTA
582192 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
582225 TGTTTTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACTA
Found at i:582298 original size:37 final size:37
Alignment explanation
Indices: 582240--582492 Score: 140
Period size: 37 Copynumber: 7.4 Consensus size: 37
582230 TCAATGTTTA
* *
582240 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
582277 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
582311 TATTTCAAGGGAAA-TGCTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
582339 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
582377 TGTTCCAAGGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
582405 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * * *
582443 TGTTTCAAGGGAAAATATCTTAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
**
582479 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
582493 TGTTTTCAAT
Statistics
Matches: 164, Mismatches: 27, Indels: 51
0.68 0.11 0.21
Matches are distributed among these distances:
28 5 0.03
29 34 0.21
30 4 0.02
31 1 0.01
32 2 0.01
33 1 0.01
34 21 0.13
35 2 0.01
36 16 0.10
37 72 0.44
38 6 0.04
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:582347 original size:100 final size:101
Alignment explanation
Indices: 582115--582390 Score: 448
Period size: 100 Copynumber: 2.7 Consensus size: 101
582105 ATTTTGTTTT
* * * *
582115 AAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAATTGTCTCAAAGGAGACAAAA-TTTATT
1 AAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTT
582179 TCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
65 TCAAGGGAAACTATCTCAAGAGAGAC-AAATTCATTTC
582217 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTT
*
582282 CAAGGGAAACTATCTCAAGAGAGAC-AATTTATTTC
66 CAAGGGAAACTATCTCAAGAGAGACAAATTCATTTC
* * *
582317 AAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTC
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTT
582382 CAAGGGAAA
66 CAAGGGAAA
582391 TGTTTTCAAT
Statistics
Matches: 165, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
100 80 0.48
101 46 0.28
102 39 0.24
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTT
CAAGGGAAACTATCTCAAGAGAGACAAATTCATTTC
Found at i:582406 original size:166 final size:166
Alignment explanation
Indices: 582177--582560 Score: 592
Period size: 166 Copynumber: 2.3 Consensus size: 166
582167 ACAAAATTTA
* * *
582177 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TTCAAGGGAAATGTTTTCAATGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TTGTTCAAGGGAAATGTTTTCAATGTTTAT
* *
582241 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
65 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAATATCTCAAGAGAGA
*
582306 C-AATTTATTTCAAGGGAAATGCTTTCAATGTTTATG
130 CAAATTCATTTCAAGGGAAATGCTTTCAATGTTTATG
*
582342 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT-CAAGGGAAATGTTTTCAATGTTTAT
*
582407 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAATATCTTAAGAGAGA
65 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAATATCTCAAGAGAGA
*
582472 CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
130 C-AAATTCATTTCAAGGGAAATGCTTTCAATGTTTATG
* * *
582510 TTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTT-TG-TTCAAGGGAAA
582561 CTATCTCAAG
Statistics
Matches: 200, Mismatches: 12, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
164 1 0.00
165 33 0.17
166 88 0.44
168 63 0.31
169 3 0.01
170 10 0.05
171 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (166 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTATG
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAATATCTCAAGAGAGAC
AAATTCATTTCAAGGGAAATGCTTTCAATGTTTATG
Found at i:582411 original size:66 final size:65
Alignment explanation
Indices: 582277--582456 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 65
582267 GACAAAATTT
* * *
582277 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
582339 A
65 A
*
582340 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
582405 A
65 A
582406 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
582457 ATATCTTAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 7 0.06
66 71 0.66
67 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:582518 original size:102 final size:105
Alignment explanation
Indices: 582340--582581 Score: 348
Period size: 102 Copynumber: 2.3 Consensus size: 105
582330 TCAATGTTTA
* * * *
582340 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
*
582405 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-
66 ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
* *
582443 TGTTTCAAGGGAAAATATCTTAAGAGAGACAAAATTCAT-TT-CAAGGGAAATGTTTTCAATGTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT-ATGTTCCAAGGGAAATGTTTTCAATGTT
*
582506 TATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTC
65 TATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
* * *
582547 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
582582 CTTGTTTTAA
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
102 56 0.46
103 36 0.29
104 31 0.25
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (105 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
Found at i:584088 original size:183 final size:183
Alignment explanation
Indices: 583780--584129 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
583770 GGTTTAACTA
583780 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
** * ** *
583845 AGTGTCCGATTAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
583910 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
583963 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
*
584028 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
584093 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
584130 CGGATTTAAT
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:588008 original size:21 final size:21
Alignment explanation
Indices: 587970--588020 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
587960 ACATAGTATT
587970 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
587990 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
588011 ACATATAGAA
1 AAATA-AGAA
588021 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:592477 original size:2 final size:2
Alignment explanation
Indices: 592470--592500 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
592460 TTGTTTTAGT
592470 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
592501 TACTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:602338 original size:44 final size:44
Alignment explanation
Indices: 602288--602446 Score: 189
Period size: 44 Copynumber: 3.6 Consensus size: 44
602278 TTGGCTTGTT
602288 CATCACATAAGGAGTTGGATCAGCATCACCACTTCGCTCGATTC
1 CATCACATAAGGAGTTGGATCAGCATCACCACTTCGCTCGATTC
* * ** * *
602332 CATCACATAAGGAGTTGTATCGGTGTCATCACCTTGGCTCG--TC
1 CATCACATAAGGAGTTGGATCAGCATCACCA-CTTCGCTCGATTC
* *
602375 CATCATATAAGGAGTTGGATC-GACATCACCATTTCGCTCGATTC
1 CATCACATAAGGAGTTGGATCAG-CATCACCACTTCGCTCGATTC
* *
602419 CGTCACATAAGGAGTTGGATCAACATCA
1 CATCACATAAGGAGTTGGATCAGCATCA
602447 TCTTGGTCGA
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
42 8 0.09
43 26 0.28
44 52 0.55
45 8 0.09
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (44 bp):
CATCACATAAGGAGTTGGATCAGCATCACCACTTCGCTCGATTC
Found at i:602419 original size:87 final size:87
Alignment explanation
Indices: 602273--602435 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 87
602263 AAGAACTTGT
* *
602273 TCACCTTGGCTTGTTCATCACATAAGGAGTTGGATCAGCATCACCACTTCGCTCGATTCCATCAC
1 TCACCTTGGCTCGTCCATCACATAAGGAGTTGGATCAGCATCACCACTTCGCTCGATTCCATCAC
602338 ATAAGGAGTTGTATCGGTGTCA
66 ATAAGGAGTTGTATCGGTGTCA
* * *
602360 TCACCTTGGCTCGTCCATCATATAAGGAGTTGGATC-GACATCACCATTTCGCTCGATTCCGTCA
1 TCACCTTGGCTCGTCCATCACATAAGGAGTTGGATCAG-CATCACCACTTCGCTCGATTCCATCA
602424 CATAAGGAGTTG
65 CATAAGGAGTTG
602436 GATCAACATC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 1 0.01
87 69 0.99
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (87 bp):
TCACCTTGGCTCGTCCATCACATAAGGAGTTGGATCAGCATCACCACTTCGCTCGATTCCATCAC
ATAAGGAGTTGTATCGGTGTCA
Found at i:603506 original size:12 final size:12
Alignment explanation
Indices: 603489--603513 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
603479 TGACCTGATC
603489 CGGGATAAGACT
1 CGGGATAAGACT
603501 CGGGATAAGACT
1 CGGGATAAGACT
603513 C
1 C
603514 ACATTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (12 bp):
CGGGATAAGACT
Found at i:603841 original size:2 final size:2
Alignment explanation
Indices: 603834--603872 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
603824 AAGCTAAATA
603834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
603873 TAAATATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:610207 original size:17 final size:18
Alignment explanation
Indices: 610182--610218 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
610172 AAAAACATGT
*
610182 TTTCTATTAAAAAAATTA
1 TTTCTATTAAAAAAAATA
610200 TTTC-ATTAAAAAAAATA
1 TTTCTATTAAAAAAAATA
610217 TT
1 TT
610219 CACGATCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTCTATTAAAAAAAATA
Found at i:616572 original size:2 final size:2
Alignment explanation
Indices: 616565--616595 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
616555 TTAACCACAG
616565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
616596 CAATTCCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:618316 original size:20 final size:20
Alignment explanation
Indices: 618293--618355 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
618283 ATCTAAATTC
618293 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
618313 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
618336 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
618356 AATAACAAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:618507 original size:24 final size:27
Alignment explanation
Indices: 618446--618499 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
618436 CCAATATATA
*
618446 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
618473 GAAGCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
618500 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:623744 original size:18 final size:18
Alignment explanation
Indices: 623713--623755 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
623703 GCTTGAGATA
* *
623713 ACCTAAAGAAAATAGAAT
1 ACCTAAAGAAAATAAAAC
**
623731 ACCTAAAGGCAATAAAAC
1 ACCTAAAGAAAATAAAAC
623749 ACCTAAA
1 ACCTAAA
623756 AATAATCCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAC
Found at i:623997 original size:10 final size:10
Alignment explanation
Indices: 623982--624011 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
623972 GCCATTGTCA
623982 TAGCATTTAG
1 TAGCATTTAG
623992 TAGCATTTAG
1 TAGCATTTAG
*
624002 TTGCATTTAG
1 TAGCATTTAG
624012 GTCATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (10 bp):
TAGCATTTAG
Found at i:628765 original size:43 final size:44
Alignment explanation
Indices: 628717--628911 Score: 145
Period size: 43 Copynumber: 4.5 Consensus size: 44
628707 ACATAACTCA
* * *
628717 TACGTGATGAAGAGTTCTGGTTATC-AAGGGTTGACACGGCTCC
1 TACGTGATGAGGAGATCTGGTTATCTAAGGGATGACACGGCTCC
* * *
628760 TACGTGATGAGGAGATCTGG---TC--AGGTGATGACATGACTCA
1 TACGTGATGAGGAGATCTGGTTATCTAAGG-GATGACACGGCTCC
* * * * ** * * *
628800 TATGTGATGAAGAGTTCTCGCCATCTAAGAATGATAACACGGTTCC
1 TACGTGATGAGGAGATCTGGTTATCTAAG--GGATGACACGGCTCC
* *
628846 TACGCGATGAGGACG-GCTGGTTATCTAAGGG-TGACACGGCTCC
1 TACGTGATGAGGA-GATCTGGTTATCTAAGGGATGACACGGCTCC
628889 TACGTGATGAGGAGATCTGGTTA
1 TACGTGATGAGGAGATCTGGTTA
628912 CGTGATGAGA
Statistics
Matches: 114, Mismatches: 28, Indels: 20
0.70 0.17 0.12
Matches are distributed among these distances:
39 3 0.03
40 28 0.25
42 1 0.01
43 49 0.43
44 1 0.01
45 2 0.02
46 29 0.25
47 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (44 bp):
TACGTGATGAGGAGATCTGGTTATCTAAGGGATGACACGGCTCC
Found at i:629060 original size:125 final size:126
Alignment explanation
Indices: 628609--629205 Score: 585
Period size: 125 Copynumber: 4.7 Consensus size: 126
628599 GATCGTCTAA
* * * * *
628609 GGGTTGACACGGCTCCTACGTAATGAGGAGATATGGTCAGGGGATGACACTGCTCATACTTGATG
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATATGGTAAGGTGATGACACTGCTCAT--TTGTTC
* * **** * * *
628674 AAGAGTTCTTGGCCATCTTTAGGAAGGGTAATAACATAACTCATACGTGATGAAGA-GTTCTGGT
64 ATGAG-TCTTGGCCATC--T---AAGGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGT
*
628738 TATCAA
122 TATC-T
* * *
628744 GGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGTGATGACA-TGACTCATATGTGAT
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATATGGTAAGGTGATGACACTG-CTCAT-T-TGTT
* * * ** *
628808 GAAGAGT-TCTCGCCATCTAAGAATGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCT
63 CATGAGTCT-TGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
* * * * *
628872 AAGGG-TGACACGGCTCCTACGTGATGAGGAGATCTGGTTACGTGATGAGACTGCTCATCTGTTC
1 --GGGTTGACACGGCTCCTACGTGATGAGGAGATATGGTAAGGTGATGACACTGCTCATTTGTTC
* *
628936 ATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGATGGTTGGTTATCT
64 ATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
* *
628999 GGG-TGACATGGCTCCTACATGATGAGGAGATATGGTAAGGTGATGACACTGCTCATTTGTTCAT
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATATGGTAAGGTGATGACACTGCTCATTTGTTCAT
** * * **
629063 GAGTCTTTTCCATCTAAGGGTGATAACATGGTTCCTACATGATGAGGACAACTGGTTATCT
66 GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
** * * * * *
629124 GGGTTGACACAACTCTTACATAATGAGGAGATATGATCAA-GTGATGACACTACTCATTTGTTCA
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATATGGT-AAGGTGATGACACTGCTCATTTGTTCA
629188 TGAGTCTTGGCCATCTAA
65 TGAGTCTTGGCCATCTAA
629206 AGGATTTTGG
Statistics
Matches: 398, Mismatches: 54, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
125 113 0.28
126 66 0.17
127 59 0.15
128 1 0.00
129 79 0.20
130 6 0.02
132 1 0.00
133 1 0.00
134 11 0.03
135 61 0.15
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (126 bp):
GGGTTGACACGGCTCCTACGTGATGAGGAGATATGGTAAGGTGATGACACTGCTCATTTGTTCAT
GAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
Found at i:629586 original size:23 final size:23
Alignment explanation
Indices: 629528--629593 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
629518 TGCCTCAACA
629528 TTTGAAGGGGAACCGA-TCCCCC
1 TTTGAAGGGGAACCGATTCCCCC
**
629550 CATG-A-GGGAACCGATTCCCCC
1 TTTGAAGGGGAACCGATTCCCCC
*
629571 TTTGAAGGGGAGCCGATTCCCCC
1 TTTGAAGGGGAACCGATTCCCCC
629594 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 9 0.25
21 9 0.25
22 3 0.08
23 15 0.42
ACGTcount: A:0.21, C:0.33, G:0.27, T:0.18
Consensus pattern (23 bp):
TTTGAAGGGGAACCGATTCCCCC
Found at i:629614 original size:44 final size:43
Alignment explanation
Indices: 629528--629614 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
629518 TGCCTCAACA
* *
629528 TTTGAAGGGGAACCGATCCCCCCATGAGGGAACCGATTCCCCC
1 TTTGAAGGGGAACCGATCCCCCCAAGAGGGAACCGATACCCCC
* *
629571 TTTGAAGGGGAGCCGATTCCCCCCACAG-GGGAATCGATACCCCC
1 TTTGAAGGGGAACCGA-TCCCCCCA-AGAGGGAACCGATACCCCC
629615 CTGGGGTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 15 0.39
44 22 0.58
45 1 0.03
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.16
Consensus pattern (43 bp):
TTTGAAGGGGAACCGATCCCCCCAAGAGGGAACCGATACCCCC
Found at i:640008 original size:41 final size:42
Alignment explanation
Indices: 639963--640066 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
639953 CCTATCCTAA
* ** * **
639963 GTCATATAAATTAGTTATGGTTTCACATGA-TTCTGTCAAAG
1 GTCATATCAATTAGTTATGACTTCACATGAGGTCTACCAAAG
*
640004 GTCATATCAATTAGTTATGACTTCACATTAGGTCTACCAAAG
1 GTCATATCAATTAGTTATGACTTCACATGAGGTCTACCAAAG
*
640046 GTCATAGCAATTAGTTATGAC
1 GTCATATCAATTAGTTATGAC
640067 AGTTTCATGT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
41 26 0.48
42 28 0.52
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (42 bp):
GTCATATCAATTAGTTATGACTTCACATGAGGTCTACCAAAG
Found at i:641091 original size:43 final size:43
Alignment explanation
Indices: 641030--641113 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
641020 TTTGTTTAGC
* *
641030 GAGACAAGACACTAGATCTCTTAAGTAAATCAACAGCTCGAGT
1 GAGACAAGACACTAGATCTCTTAAGCAAATCAACAACTCGAGT
641073 GAGACAAGACACTAGATCTCTTAAGCAAATCAACAACTCGA
1 GAGACAAGACACTAGATCTCTTAAGCAAATCAACAACTCGA
641114 ATTTAGTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.19
Consensus pattern (43 bp):
GAGACAAGACACTAGATCTCTTAAGCAAATCAACAACTCGAGT
Found at i:641788 original size:3 final size:3
Alignment explanation
Indices: 641780--641870 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
641770 CACTTGCTTC
641780 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
641828 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
641871 GTAGTAGTAG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:642603 original size:14 final size:14
Alignment explanation
Indices: 642584--642615 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
642574 ATATTTATAC
642584 ATTTTTATAATTAT
1 ATTTTTATAATTAT
642598 ATTTTTATAATTAT
1 ATTTTTATAATTAT
642612 ATTT
1 ATTT
642616 AATGTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTTATAATTAT
Found at i:650847 original size:21 final size:22
Alignment explanation
Indices: 650823--650871 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
650813 GGAGGGAACT
650823 GATTCCCCC-CAAGGGCGTACC
1 GATTCCCCCACAAGGGCGTACC
*
650844 GATTCCCCCACAAGGGGGTACC
1 GATTCCCCCACAAGGGCGTACC
650866 GATTCC
1 GATTCC
650872 TCCCTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.16
Consensus pattern (22 bp):
GATTCCCCCACAAGGGCGTACC
Found at i:651085 original size:10 final size:10
Alignment explanation
Indices: 651070--651094 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
651060 GCCATTGATC
651070 AACAACAAGA
1 AACAACAAGA
651080 AACAACAAGA
1 AACAACAAGA
651090 AACAA
1 AACAA
651095 GAATCAAGAG
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:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:656679 original size:22 final size:22
Alignment explanation
Indices: 656649--656728 Score: 74
Period size: 23 Copynumber: 3.7 Consensus size: 22
656639 TAGTGCAGGA
* *
656649 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTGAAAG
* *
656671 GGAACCGATTCCCCCTTTGAATG
1 GGAACCGATACCCCC-TTGAAAG
* *
656694 GGAACTGATTCCCCC-T-AAAG
1 GGAACCGATACCCCCTTGAAAG
*
656714 GGAATCGATACCCCC
1 GGAACCGATACCCCC
656729 CACGGGGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.31
21 1 0.02
22 13 0.27
23 20 0.41
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (22 bp):
GGAACCGATACCCCCTTGAAAG
Found at i:656690 original size:23 final size:23
Alignment explanation
Indices: 656649--656709 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
656639 TAGTGCAGGA
* *
656649 GGAATCGATACCCCC-TTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
*
656671 GGAACCGATTCCCCCTTTGAATG
1 GGAACCGATTCCCCCTTTGAAGG
*
656694 GGAACTGATTCCCCCT
1 GGAACCGATTCCCCCT
656710 AAAGGGAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (23 bp):
GGAACCGATTCCCCCTTTGAAGG
Found at i:658642 original size:18 final size:18
Alignment explanation
Indices: 658614--658648 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
658604 TGAATGTTTG
658614 AATGTTTGGATTTATTATT
1 AATGTTTGGATTT-TTATT
658633 AATG-TTGGATTTTTAT
1 AATGTTTGGATTTTTAT
658649 GTTTTGGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (18 bp):
AATGTTTGGATTTTTATT
Found at i:660488 original size:18 final size:18
Alignment explanation
Indices: 660456--660502 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
660446 TGATAAAACT
*
660456 TAACCTATACCCCTATCC
1 TAACCCATACCCCTATCC
* *
660474 TATCCCATACTCCTATCC
1 TAACCCATACCCCTATCC
660492 TAACCCATACC
1 TAACCCATACC
660503 TTGTAATAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28
Consensus pattern (18 bp):
TAACCCATACCCCTATCC
Found at i:664078 original size:19 final size:20
Alignment explanation
Indices: 664034--664083 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
664024 AACATTTAAT
*
664034 AATAATAATAATTTATTCTCA
1 AATAATAAT-ATTTATTATCA
*
664055 AATAATAATATTT-TTATTA
1 AATAATAATATTTATTATCA
664074 AATAATAATA
1 AATAATAATA
664084 ACATCATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 14 0.52
20 4 0.15
21 9 0.33
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAATAATATTTATTATCA
Found at i:664596 original size:3 final size:3
Alignment explanation
Indices: 664588--664612 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
664578 AAACATCAAT
664588 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
664613 ATAGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:664623 original size:18 final size:16
Alignment explanation
Indices: 664588--664634 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
664578 AAACATCAAT
664588 ATAATAAT-AATAATA
1 ATAATAATAAATAATA
664603 ATAATAATAAATAGATAA
1 ATAATAATAAATA-AT-A
*
664621 ATAAAAATAAATAA
1 ATAATAATAAATAA
664635 ATTTAGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 3 0.11
18 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:664629 original size:24 final size:23
Alignment explanation
Indices: 664585--664710 Score: 70
Period size: 23 Copynumber: 5.6 Consensus size: 23
664575 GAAAAACATC
*
664585 AATATAATAAT-AATAATAATAAT
1 AATA-AATAATAAATAAAAATAAT
664608 AATAAATAGATAAATAAAAATAAAT
1 AATAAATA-ATAAATAAAAAT-AAT
* * *
664633 AAATTTAGTAA-AAAGAAAAATAAT
1 -AA-TAAATAATAAATAAAAATAAT
* * * *
664657 AA-AAACAAAGAAAGAGAAATAA-
1 AATAAA-TAATAAATAAAAATAAT
664679 AAT-AA-AA-AAATAAAAA-AAT
1 AATAAATAATAAATAAAAATAAT
664698 AATAAATAATAAA
1 AATAAATAATAAA
664711 AAGAAAAAAG
Statistics
Matches: 81, Mismatches: 10, Indels: 25
0.70 0.09 0.22
Matches are distributed among these distances:
18 2 0.02
19 10 0.12
20 4 0.05
21 3 0.04
22 13 0.16
23 19 0.23
24 11 0.14
25 12 0.15
26 3 0.04
27 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (23 bp):
AATAAATAATAAATAAAAATAAT
Found at i:664680 original size:28 final size:26
Alignment explanation
Indices: 664649--664721 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 26
664639 AGTAAAAAGA
664649 AAAATAATAAAAACAAAGAAAGAGAAAT
1 AAAATAATAAAAACAAA-AAAGA-AAAT
* *
664677 AAAATAA-AAAAATAAAAAA-ATAAT
1 AAAATAATAAAAACAAAAAAGAAAAT
*
664701 -AAATAATAAAAAGAAAAAAGA
1 AAAATAATAAAAACAAAAAAGA
664722 CGTTAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.15
24 14 0.35
25 2 0.05
26 3 0.08
27 8 0.20
28 7 0.17
ACGTcount: A:0.79, C:0.01, G:0.07, T:0.12
Consensus pattern (26 bp):
AAAATAATAAAAACAAAAAAGAAAAT
Found at i:664710 original size:18 final size:18
Alignment explanation
Indices: 664588--664712 Score: 66
Period size: 17 Copynumber: 6.9 Consensus size: 18
664578 AAACATCAAT
*
664588 ATAAT-AATAATAATAATA
1 ATAATAAATAATAA-AAAA
664606 ATAATAAATAGATAAATAAAA
1 ATAATAAATA-AT-AA-AAAA
* *
664627 ATAAATAAAT-TTAGTAAAA
1 AT-AATAAATAATA-AAAAA
* *
664646 AGAA-AAATAATAAAAAC
1 ATAATAAATAATAAAAAA
* * *
664663 A-AAGAAAGAGA-AATAAA
1 ATAATAAATA-ATAAAAAA
664680 ATAA-AAA-AATAAAAAA
1 ATAATAAATAATAAAAAA
664696 ATAATAAATAATAAAAA
1 ATAATAAATAATAAAAA
664713 GAAAAAAGAC
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
15 1 0.01
16 12 0.14
17 23 0.27
18 20 0.24
19 10 0.12
20 3 0.04
21 8 0.10
22 7 0.08
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.21
Consensus pattern (18 bp):
ATAATAAATAATAAAAAA
Found at i:664779 original size:4 final size:4
Alignment explanation
Indices: 664766--664803 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
664756 AGTGAGGGAA
664766 AAAT -AAT AAAT AAAT AAAT AAAT AAAT GAAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAA
664804 AAACATAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.19
4 21 0.68
5 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:666589 original size:83 final size:82
Alignment explanation
Indices: 666347--666714 Score: 326
Period size: 83 Copynumber: 4.4 Consensus size: 82
666337 ATATGTCATC
* * * * * * *
666347 GAGCTGAATGGAATCGAACTCGATGGTTTTTTATTGAAAAATAACCCTTCTAGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGG-TCTTTGTTG-AAGATAACCCTTCTAGCCTTGAGTTATA
* * *
666412 CTGTAAAATTTGATATGTCTTT
64 CTG-CAAA--TGATGTGCCTTT
* * * *
666434 GAGCTGAATTTAATCGAACTTGAAGGTCTTTTGTTGGAAGATAACCCTTCTCGTCTTGAGTTATA
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTT-GAAGATAACCCTTCTAGCCTTGAGTTATA
*
666499 ATGCAAATGATGTGCCTTT
64 CTGCAAATGATGTGCCTTT
* *
666518 GAGTTGAATGTAATCGAACTCGAAGGTCTTCGTTGACAGATAACCCTTCTAGCCTTGAGTTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA-AGATAACCCTTCTAGCCTTGAGTTATAC
* *
666583 TGCAAATGATGTGTCTTG
65 TGCAAATGATGTGCCTTT
** * * * ** * *
666601 GAGCTGAGCGTAGTTGAACTCTAAGGTCTTTAAT--AGATAACCCTTCCAGCCTTGAGTTATGCT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAAGATAACCCTTCTAGCCTTGAGTTATACT
* *
666664 GCAAATGATGTGCCCTC
66 GCAAATGATGTGCCTTT
* * * * *
666681 GAAGCTGAGTGTAGTCGAACGCAAAGGTTTTTGT
1 G-AGCTGAATGTAATCGAACTCGAAGGTCTTTGT
666715 GTTTCAAGAG
Statistics
Matches: 232, Mismatches: 45, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
80 42 0.18
81 25 0.11
82 2 0.01
83 71 0.31
84 35 0.15
86 4 0.02
87 52 0.22
88 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (82 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAAGATAACCCTTCTAGCCTTGAGTTATACT
GCAAATGATGTGCCTTT
Found at i:666784 original size:32 final size:33
Alignment explanation
Indices: 666702--666827 Score: 157
Period size: 34 Copynumber: 3.8 Consensus size: 33
666692 TAGTCGAACG
**
666702 CAAAGG-TTTTTGTGTTTCAAGAGAAACATTTTT
1 CAAAGGTTTTTTGTGTTTCAAGAGAAA-AGATTT
*
666735 CAAAGGTTTTTTTTGTTTCAAGAGAAAAGATTT
1 CAAAGGTTTTTTGTGTTTCAAGAGAAAAGATTT
* * *
666768 -AATGGTTTTTTGTGTTTCAAAAGAAACGATTT
1 CAAAGGTTTTTTGTGTTTCAAGAGAAAAGATTT
*
666800 CAAAGGTTTTTTTTTGTTTCAAGAGAAA
1 CAAAGG-TTTTTTGTGTTTCAAGAGAAA
666828 CTGTCTCCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
32 28 0.35
33 14 0.17
34 38 0.47
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (33 bp):
CAAAGGTTTTTTGTGTTTCAAGAGAAAAGATTT
Found at i:666855 original size:37 final size:36
Alignment explanation
Indices: 666812--667243 Score: 409
Period size: 36 Copynumber: 12.2 Consensus size: 36
666802 AAGGTTTTTT
*
666812 TTTGTTTCAAGAGAAACTGTCTCCAAG-GAGGCAAAA
1 TTTGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAA
*
666848 TTTTGTTTCAAGAGAAACATAT-TCAA-AG-G------
1 -TTTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA
666877 TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TT--TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
666915 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
666952 TTTGTTTCAAGAGAAACTGTCTCAAGAGATACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
666988 CTTAG-TTCTAAAAGAAACTGTCCCAAGAGAGACAAAA
1 -TTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * **
667025 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
667062 TTTGTTTCAAGAAAAAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAAG-AGAAAC-TGTCTCAAGAGAGACAAAA
667092 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA
* *
667128 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
667164 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
667200 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACACAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAA
667237 TTTGTTT
1 TTTGTTT
667244 TGAGTAAATT
Statistics
Matches: 334, Mismatches: 31, Indels: 60
0.79 0.07 0.14
Matches are distributed among these distances:
28 4 0.01
29 8 0.02
30 32 0.10
31 3 0.01
32 3 0.01
34 2 0.01
35 1 0.00
36 148 0.44
37 125 0.37
38 6 0.02
39 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:666875 original size:71 final size:67
Alignment explanation
Indices: 666780--667215 Score: 191
Period size: 73 Copynumber: 6.2 Consensus size: 67
666770 TGGTTTTTTG
* ** *
666780 TGTTTCAAAAGAAACGATTTCAAAGGTTTTTTTTTGTTTCAAGAGAAACTGTCTCCAAG-GAGGC
1 TGTTTCAAGAGAAACGATTTCAAAGG----TTGGTGTTTCAAGAGAAACTGTCT-CAAGAGAGAC
*
666844 AAAATTT
61 AAAACTT
666851 TGTTTCAAGAGAAAC-ATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACGAT-TTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
666915 CTT
65 CTT
* *
666918 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT--TGTTTCAAGAGAAACTGTCTCAAGAG
1 TGTTTCAAGAGAAAC-GATTTCAA-AG-G------TTGGTGTTTCAAGAGAAACTGTCTCAAGAG
*
666980 ATACAAAACTT
57 AGACAAAACTT
* * ** **** * * *
666991 AG-TTCTAAAAGAAACTG-TCCCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TGTTTC-AAGAGAAAC-GATTTCAA-AG-G----TTGGT-GTTTCAAGAGAAACTGTCTCAAGAG
**
667054 AGATGAAA-TT
57 AGACAAAACTT
* * *
667064 TGTTTCAAGAAAAAAC-ATATTCAAAGATT-TTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAG-AGAAACGAT-TTCAAAGGTTGGTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAA
667126 AA-TT
63 AACTT
* * * *
667130 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAATAT-TTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGAGAAAC-GATTTCAA-AG-G----T-TGGTGTTTCAAGAGAAACTGTCTCAAGAGA
*
667193 GATAAAA-TT
58 GACAAAACTT
667202 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
667216 TTGTCTCAAG
Statistics
Matches: 294, Mismatches: 40, Indels: 61
0.74 0.10 0.15
Matches are distributed among these distances:
65 9 0.03
66 44 0.15
67 52 0.18
68 3 0.01
69 1 0.00
70 2 0.01
71 26 0.09
72 51 0.17
73 66 0.22
74 38 0.13
75 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACGATTTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
TT
Found at i:666974 original size:73 final size:72
Alignment explanation
Indices: 666881--667243 Score: 404
Period size: 73 Copynumber: 5.1 Consensus size: 72
666871 CAAAGGTTGG
*
666881 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
666946 ACAAAATT
65 ACAAAATT
* * * *
666954 TGTTTCAAGAGAAACTGTCTCAAGAGATACAAAACTTAG-TTCTAAAAGAAACTGTCCCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTC-AAGAGAAACTGTCTCAAGAGA
667018 GACAAAACTT
64 GACAAAA-TT
* * * * ** * *
667028 AGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAGAAAAAACATAT-TC-A-A-A
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-AGAAAC-TGTCTCAAGAGA
*
667089 G----ATTT
64 GACAAAATT
*
667094 TGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
667158 ACAATATT
65 ACAAAATT
* * *
667166 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
*
667231 CACAACTT
66 CA-AAATT
667239 TGTTT
1 TGTTT
667244 TGAGTAAATT
Statistics
Matches: 240, Mismatches: 34, Indels: 32
0.78 0.11 0.10
Matches are distributed among these distances:
64 2 0.01
65 7 0.03
66 40 0.17
67 2 0.01
68 2 0.01
71 2 0.01
72 68 0.28
73 77 0.32
74 38 0.16
75 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (72 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAATT
Found at i:667137 original size:21 final size:20
Alignment explanation
Indices: 667113--667213 Score: 60
Period size: 21 Copynumber: 5.4 Consensus size: 20
667103 GAAAACTGTC
667113 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGA-AAAATTTGTT
* *
667134 TCAAG-G-G--AAA-CTGTC
1 TCAAGAGAGAAAAATTTGTT
*
667149 TCAAGAGAGACAATATTTGTT
1 TCAAGAGAGA-AAAATTTGTT
* *
667170 TCAAG-G-G--AAA-CTGTC
1 TCAAGAGAGAAAAATTTGTT
667185 TCAAGAGAGATAAAATTTGTT
1 TCAAGAGAGA-AAAATTTGTT
667206 TCAAGAGA
1 TCAAGAGA
667214 AATTGTCTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
15 16 0.28
16 7 0.12
17 2 0.03
19 2 0.03
20 7 0.12
21 24 0.41
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (20 bp):
TCAAGAGAGAAAAATTTGTT
Found at i:667210 original size:138 final size:140
Alignment explanation
Indices: 666952--667211 Score: 366
Period size: 138 Copynumber: 1.9 Consensus size: 140
666942 AGAGACAAAA
*
666952 TTTGTTTCAAGAGAAACTGTCTCAAGAGATACAAAACTTAGTTCTAAAAGAAACTGTCCCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCCCAAGAG
* *
667017 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAGAAAAAACAT
66 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAAAAAACAT
667082 ATTCAAAGAT
131 ATTCAAAGAT
* ** *
667092 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAG
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCCCAAG
* * * **
667154 AGAGACAATA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGA
64 AGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGA
667212 GAAATTGTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
138 43 0.41
139 30 0.28
140 33 0.31
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (140 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCCCAAGAG
AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAAAAAACAT
ATTCAAAGAT
Found at i:668523 original size:95 final size:94
Alignment explanation
Indices: 668360--668545 Score: 277
Period size: 95 Copynumber: 2.0 Consensus size: 94
668350 ATATGTAAAT
* * *
668360 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCTGAGGCGTTTAACCAATTACCTTAGAGGG
1 ACCTTTATCAGGCTACCTGAATATTATCCATAAAGCTGAGGCGTTTAACCAATTACCTTAGAGGG
*
668425 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAAATCAAGCTTTATTGTATA-TATAATC
* *
668455 ACCTTTATCAGGCTACCTGAATATTATCCATAAAG-TCGGGGCGTTTAACCAATT-GCTCTAGAG
1 ACCTTTATCAGGCTACCTGAATATTATCCATAAAGCT-GAGGCGTTTAACCAATTACCT-TAGAG
668518 GGACAAATCAAGCTTTATTGTATATATA
64 GGACAAATCAAGCTTTATTGTATATATA
668546 TTATAATCTG
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
94 7 0.08
95 76 0.92
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (94 bp):
ACCTTTATCAGGCTACCTGAATATTATCCATAAAGCTGAGGCGTTTAACCAATTACCTTAGAGGG
ACAAATCAAGCTTTATTGTATATATAATC
Found at i:671154 original size:4 final size:4
Alignment explanation
Indices: 671145--671201 Score: 68
Period size: 4 Copynumber: 14.8 Consensus size: 4
671135 GTGAGGGAAA
671145 AAAT AAAT -AAT AAA- ATAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
671191 GAAAT -AAT AAA
1 -AAAT AAAT AAA
671202 AAACATAGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
3 10 0.21
4 33 0.70
5 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:675415 original size:18 final size:17
Alignment explanation
Indices: 675394--675445 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
675384 ATAAATTAAG
675394 AAATAAATATAAATAAAT
1 AAATAAAT-TAAATAAAT
* *
675412 AAATGAAGTTTAATAAATT
1 AAAT-AAATTAAATAAA-T
675431 AAATTAAATTAAATA
1 AAA-TAAATTAAATA
675446 GTATTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 11 0.41
19 15 0.56
20 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
AAATAAATTAAATAAAT
Found at i:676736 original size:18 final size:18
Alignment explanation
Indices: 676681--676780 Score: 116
Period size: 18 Copynumber: 5.6 Consensus size: 18
676671 TATTTAATTG
*
676681 TTTC-TCTT-TATTCTTC
1 TTTCTTCTTCTATTTTTC
* *
676697 ATTTCTTCCTTATTTTTTTC
1 -TTTCTT-CTTCTATTTTTC
*
676717 TTTCTTCTACT-TTATTTC
1 TTTCTTCTTCTATT-TTTC
676735 TTTCTTCTTCTATTTTTC
1 TTTCTTCTTCTATTTTTC
676753 TTTCTTCTTCTATTTTTC
1 TTTCTTCTTCTATTTTTC
676771 TTTCTTCTTC
1 TTTCTTCTTC
676781 CCGGTGCCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.08
18 50 0.68
19 11 0.15
20 6 0.08
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTCTTCTATTTTTC
Found at i:677062 original size:39 final size:39
Alignment explanation
Indices: 677008--677082 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
676998 GCATGGCAGG
* *
677008 GGAGAGACGCATGACTCCCAATGCGTCTTTGGGGGTAGA
1 GGAGAGACGCATGACTCCCAATGCGTATTTAGGGGTAGA
* *
677047 GGAGAGACGCATGACTCTCGATGCGTATTTAGGGGT
1 GGAGAGACGCATGACTCCCAATGCGTATTTAGGGGT
677083 TGGGCAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (39 bp):
GGAGAGACGCATGACTCCCAATGCGTATTTAGGGGTAGA
Found at i:677539 original size:25 final size:27
Alignment explanation
Indices: 677489--677540 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
677479 TTATAGTCTG
*
677489 CATTATCTCAAGAATTTTTTTTCCAATA
1 CATTATCTCAAGAA-TTTTTTGCCAATA
677517 CATTATCTCAA-AA-TTTTTGCCAAT
1 CATTATCTCAAGAATTTTTTGCCAAT
677541 GATGTAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 10 0.43
27 2 0.09
28 11 0.48
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (27 bp):
CATTATCTCAAGAATTTTTTGCCAATA
Found at i:678371 original size:2 final size:2
Alignment explanation
Indices: 678364--678404 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
678354 CTAAAGTTGT
678364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
678405 GTATTTGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:684871 original size:22 final size:23
Alignment explanation
Indices: 684826--684876 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
684816 ATTGAATGTA
684826 ACAACTTGAATATGTTAAACATT
1 ACAACTTGAATATGTTAAACATT
* *
684849 ACAACTTGGATATG-TAAATATT
1 ACAACTTGAATATGTTAAACATT
684871 ACAACT
1 ACAACT
684877 CAAACATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (23 bp):
ACAACTTGAATATGTTAAACATT
Found at i:684949 original size:56 final size:56
Alignment explanation
Indices: 684876--685688 Score: 402
Period size: 56 Copynumber: 14.5 Consensus size: 56
684866 ATATTACAAC
* * * *
684876 TCAAACATCCATTTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGTTAA
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
* * * * *
684932 TCAGAA-ATCCATCTTTGAATGTACCAACTTGGATAAGTTAAGCCGTTACAACACTAT
1 TCA-AACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAA-ACATTACAACGCTAT
* * * * *
684989 ACAATCTTCCATCTTTGAAAGTAACAACTTGGTTAAGTTAAAC-TCTACAACACTAT
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACAT-TACAACGCTAT
* *
685045 TCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTGT
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
* ** * *
685101 TCAAACTTCCATCATTGAACATAACAACTTGGATAAGTTAGACATTGCAACGCTAT
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
* * ** * *
685157 TCAAACTTCCATTTTTGAATGTAACAACTTGGATAAGATAAATTTTTAGTATGTAAGC-A-
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAA-CATTA-CA---ACGCTAT
** * * * * * **
685216 TCAAACTAT-TTTGTTAAGACAT-T-ACAACATT--AT---TCAAAC-TTCCATCTTTGATT
1 TCAAACT-TCCATCTT-TGA-ATGTAACAAC-TTGGATAAGTTAAACATTACAACGCT-A-T
* * ** * ** * ** * ** * ** ** *
685269 GTAAAAATTTGGATAAGTTAAAACTCT-ACAACGCTATTCA-AATTTCCATATTTGAA-TATAA
1 -T-CAAACTTCCAT--CTTTGAA-TGTAACAA--CT-TGGATAAGTTAAACATTACAACGCTAT
** ** * ** * * * *
685330 T-AAA-TTGGATAAGTTAAACATTAGAACGTTTTGGATAAGTTAAACATTAGAACGTTAT
1 TCAAACTTCCAT-CTTTGAATGTAACAAC---TTGGATAAGTTAAACATTACAACGCTAT
* * *
685388 TCAAACTTGCATTTTTGAATGTAACAACTTGGATAAG-------TTACAACGTTAT
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
* *
685437 TCAAACTTCAATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGTTAT
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
* * *
685493 AT-AAACTTCCATTTTTGAATGTAACAACTTGGATAAGTTAAGAGATTACAACACTAT
1 -TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAA-ACATTACAACGCTAT
* * * *
685550 TTAAACTTTCAAT-TTTGAATGTAACAACTTTGATAAGTTAAACATTACAACACTAT
1 TCAAAC-TTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
* * * * * *
685606 TTAAACTTTCATTTTTGAATGTAACAACTTGGATAAGTTAAACATTTCAACACTTT
1 TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
**
685662 TTGAACTTCCATCTTTGAATGTAACAA
1 TCAAACTTCCATCTTTGAATGTAACAA
685689 ATAAGTTAAA
Statistics
Matches: 593, Mismatches: 110, Indels: 108
0.73 0.14 0.13
Matches are distributed among these distances:
49 45 0.08
51 1 0.00
52 1 0.00
53 2 0.00
54 3 0.01
55 15 0.03
56 337 0.57
57 118 0.20
58 15 0.03
59 29 0.05
60 13 0.02
61 6 0.01
62 1 0.00
63 4 0.01
64 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (56 bp):
TCAAACTTCCATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTAT
Found at i:685299 original size:57 final size:57
Alignment explanation
Indices: 685238--685347 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
685228 GTTAAGACAT
* * * *
685238 TACAACATTATTCAAACTTCCATCTTTGATTGTAA-AAATTTGGATAAGTTAAAACTC
1 TACAACACTATTCAAACTTCCATATTTGAATATAATAAA-TTGGATAAGTTAAAACTC
* *
685295 TACAACGCTATTCAAATTTCCATATTTGAATATAATAAATTGGATAAGTTAAA
1 TACAACACTATTCAAACTTCCATATTTGAATATAATAAATTGGATAAGTTAAA
685348 CATTAGAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 43 0.93
58 3 0.07
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (57 bp):
TACAACACTATTCAAACTTCCATATTTGAATATAATAAATTGGATAAGTTAAAACTC
Found at i:685370 original size:26 final size:26
Alignment explanation
Indices: 685334--685385 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
685324 ATATAATAAA
685334 TTGGATAAGTTAAACATTAGAACGTT
1 TTGGATAAGTTAAACATTAGAACGTT
685360 TTGGATAAGTTAAACATTAGAACGTT
1 TTGGATAAGTTAAACATTAGAACGTT
685386 ATTCAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (26 bp):
TTGGATAAGTTAAACATTAGAACGTT
Found at i:685420 original size:82 final size:83
Alignment explanation
Indices: 685276--685427 Score: 209
Period size: 82 Copynumber: 1.8 Consensus size: 83
685266 ATTGTAAAAA
* *
685276 TTTGGATAAGTTAAAACTCTACAACGCTATTCAAATTTCCATATTTGAATATAATAAATTGGATA
1 TTTGGATAAGTTAAAACTCTACAACGCTATTCAAACTTCCATATTTGAATATAACAAATTGGATA
685341 AGTTAAACATTAGAACGT
66 AGTTAAACATTAGAACGT
* * * * * *
685359 TTTGGATAAGTT-AAACAT-TAGAACGTTATTCAAACTTGCATTTTTGAATGTAACAACTTGGAT
1 TTTGGATAAGTTAAAAC-TCTACAACGCTATTCAAACTTCCATATTTGAATATAACAAATTGGAT
685422 AAGTTA
65 AAGTTA
685428 CAACGTTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 47 0.78
83 13 0.22
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (83 bp):
TTTGGATAAGTTAAAACTCTACAACGCTATTCAAACTTCCATATTTGAATATAACAAATTGGATA
AGTTAAACATTAGAACGT
Done.