Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 21
Found at i:2491430 original size:7 final size:7
Alignment explanation
Indices: 2491400--2491497 Score: 53
Period size: 7 Copynumber: 13.7 Consensus size: 7
2491390 AATAAAACGT
2491400 AAAAAT-
1 AAAAATA
2491406 AAAAATA
1 AAAAATA
2491413 AAAAAT-
1 AAAAATA
2491419 AAAAATA
1 AAAAATA
2491426 AAAAATA
1 AAAAATA
*
2491433 GTAAATAGTA
1 --AAA-AATA
2491443 AATAAATA
1 AA-AAATA
*
2491451 AAAGAAGA
1 AAA-AATA
2491459 GAAAAA-A
1 -AAAAATA
*
2491466 GAATAA-A
1 -AAAAATA
2491473 AAAAATA
1 AAAAATA
* *
2491480 AAAGAGA
1 AAAAATA
2491487 AAAAA-A
1 AAAAATA
2491493 AAAAA
1 AAAAA
2491498 AATGTTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
6 22 0.29
7 31 0.41
8 12 0.16
9 7 0.09
10 3 0.04
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2491430 original size:13 final size:13
Alignment explanation
Indices: 2491400--2491432 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2491390 AATAAAACGT
2491400 AAAAATAAAAATA
1 AAAAATAAAAATA
2491413 AAAAATAAAAATA
1 AAAAATAAAAATA
2491426 AAAAATA
1 AAAAATA
2491433 GTAAATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:2491484 original size:17 final size:16
Alignment explanation
Indices: 2491460--2491498 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2491450 AAAAGAAGAG
2491460 AAAAAAGA-ATAAAAAA
1 AAAAAAGAGA-AAAAAA
2491476 AATAAAAGAGAAAAAAA
1 AA-AAAAGAGAAAAAAA
2491493 AAAAAA
1 AAAAAA
2491499 ATGTTAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 14 0.67
18 1 0.05
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAA
Found at i:2491499 original size:17 final size:17
Alignment explanation
Indices: 2491460--2491499 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
2491450 AAAAGAAGAG
2491460 AAAAAAGAATAAAAAAA
1 AAAAAAGAATAAAAAAA
2491477 ATAAAAGAGAA-AAAAAAA
1 A-AAAA-AGAATAAAAAAA
2491495 AAAAA
1 AAAAA
2491500 TGTTAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (17 bp):
AAAAAAGAATAAAAAAA
Found at i:2492240 original size:23 final size:23
Alignment explanation
Indices: 2492214--2492268 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
2492204 TGGTTGTTTA
*
2492214 ATGGTATTTGATGTTTTGGATTT
1 ATGGTATTTGATGTTTTGAATTT
2492237 ATGGTATTTGATGTTTTGAATTT
1 ATGGTATTTGATGTTTTGAATTT
*
2492260 ATTGTATTT
1 ATGGTATTT
2492269 TCTTTTTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (23 bp):
ATGGTATTTGATGTTTTGAATTT
Found at i:2492552 original size:16 final size:15
Alignment explanation
Indices: 2492526--2492555 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2492516 ATGTGTGACC
2492526 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
2492541 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
2492556 AACAGCCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:2492737 original size:11 final size:11
Alignment explanation
Indices: 2492723--2492765 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
2492713 GGAAAAGAAT
*
2492723 AATAAATAACA
1 AATAAATAATA
2492734 AATAAATAATA
1 AATAAATAATA
2492745 AATAAAATAATA
1 AAT-AAATAATA
2492757 AATAAATAA
1 AATAAATAA
2492766 AGAAAAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAAATAATA
Found at i:2492754 original size:12 final size:12
Alignment explanation
Indices: 2492726--2492762 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2492716 AAAGAATAAT
*
2492726 AAATAACAAAT-
1 AAATAATAAATA
2492737 AAATAATAAATA
1 AAATAATAAATA
2492749 AAATAATAAATA
1 AAATAATAAATA
2492761 AA
1 AA
2492763 TAAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATAATAAATA
Found at i:2492823 original size:42 final size:41
Alignment explanation
Indices: 2492777--2493003 Score: 158
Period size: 39 Copynumber: 5.8 Consensus size: 41
2492767 GAAAAAAAGG
* * *
2492777 AAAAATATTTTTTTAAAACTATATTTTATATATGATTTTTTT
1 AAAAATATTTTTTTAAAACTATATATTATATAT-ATATTTTC
* * * *
2492819 AAAAATGTTTTTTCAAAACCATATAATATA-ATATATTTTC
1 AAAAATATTTTTTTAAAACTATATATTATATATATATTTTC
* *
2492859 AAAAA-AATATTTTAAAA-T-TATA-TAT-TATATATTTTC
1 AAAAATATTTTTTTAAAACTATATATTATATATATATTTTC
* * * *
2492895 -CAAA-ATGTTTTAAAAACTATATATTATATA-A-GTTTTC
1 AAAAATATTTTTTTAAAACTATATATTATATATATATTTTC
* **
2492932 AATAAA-GTTTTTAAAAAACTATATA--ATATATATATTTTC
1 AA-AAATATTTTTTTAAAACTATATATTATATATATATTTTC
* **
2492971 AAAAA-AGTTTTAAAAAATCTATATATTATATAT
1 AAAAATATTTTTTTAAAA-CTATATATTATATAT
2493004 TTTCAATTTT
Statistics
Matches: 148, Mismatches: 25, Indels: 25
0.75 0.13 0.13
Matches are distributed among these distances:
35 11 0.07
36 14 0.09
37 18 0.12
38 18 0.12
39 43 0.29
40 11 0.07
41 8 0.05
42 25 0.17
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (41 bp):
AAAAATATTTTTTTAAAACTATATATTATATATATATTTTC
Found at i:2492923 original size:35 final size:35
Alignment explanation
Indices: 2492844--2493163 Score: 278
Period size: 35 Copynumber: 8.9 Consensus size: 35
2492834 AAACCATATA
* * * *
2492844 ATATAATATATTTTCAAAAAAATATTTT-AAAATTAT
1 ATATTATATATTTTC--CAAAATGTTTTAAAAACTAT
2492880 ATATTATATATTTTCCAAAATGTTTTAAAAACTAT
1 ATATTATATATTTTCCAAAATGTTTTAAAAACTAT
*
2492915 ATATTATATAAGTTTT-CAATAAAGTTTTTAAAAAACTAT
1 ATATTATAT-A-TTTTCCAA-AATG-TTTT-AAAAACTAT
* *
2492954 ATAATATATATATTTTCAAAAAAGTTTTAAAAAATCTAT
1 AT-AT-TATATATTTTCCAAAATGTTTT-AAAAA-CTAT
*
2492993 ATATTATATATTTT-C--AAT-TTTTAAAAAATAT
1 ATATTATATATTTTCCAAAATGTTTTAAAAACTAT
* *
2493024 A-ATATATAAATGTTTTCAAAATGGTTTTAAAAACTAT
1 ATAT-TATATAT-TTTCCAAAAT-GTTTTAAAAACTAT
* *
2493061 ATATTATATATTTTCAAAAATGTTTCAAAAACTAT
1 ATATTATATATTTTCCAAAATGTTTTAAAAACTAT
* ** *
2493096 ATGTTATATAGTTTTAAAAAATG-TTTAAAACCTAT
1 ATATTATATA-TTTTCCAAAATGTTTTAAAAACTAT
* *
2493131 ATATTATATATATTTTCAAAACGTTTTAAAAAC
1 ATATTATATAT-TTTCCAAAATGTTTTAAAAAC
2493164 GTATTTTCAA
Statistics
Matches: 239, Mismatches: 24, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
30 2 0.01
31 10 0.04
32 8 0.03
33 5 0.02
34 12 0.05
35 68 0.28
36 45 0.19
37 36 0.15
38 18 0.08
39 25 0.10
40 5 0.02
41 5 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
ATATTATATATTTTCCAAAATGTTTTAAAAACTAT
Found at i:2493200 original size:2 final size:2
Alignment explanation
Indices: 2493189--2493217 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2493179 ATTTGGAAAC
2493189 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2493218 CGGACGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2494154 original size:167 final size:165
Alignment explanation
Indices: 2493650--2494284 Score: 824
Period size: 167 Copynumber: 3.9 Consensus size: 165
2493640 TATGCCTTTG
* * * * *
2493650 AATCGAACTCGAAGGTCTTGTGGTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGAT
1 AATCGAACTCAAAGGTCTT-TGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
* * *
2493715 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GT-TCTTTGGCAGATAACCCTTCTTGCCTTAA
65 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAGCCCTTCTTGCCTTGA
*
2493778 GCTACGCTGCAAATGATGTGCC-TTGAGCTGAGTGT
130 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * **
2493813 AATCGAACCCGAAGGTCTTTG--G-CAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
1 AATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* *
2493875 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTC--TTTGGCAGATAGCCCTTCTCGCCTTGAG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAGCCCTTCTTGCCTTGAG
2493938 CTA--CTGCAAATGATGTGCCTTTGAGCTGAGTGT
131 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * *
2493971 AATCGAACTAAAAGGTCTTTGTTGACAGATAACCCTTCTAGCATTGAGTTATGCTGCAAATGATG
1 AATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
*** * * *
2494036 TGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGTTGGTAGATAGCCATTCTTGCCTTG
66 TG-CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-TTGGCAGATAGCCCTTCTTGCCTTG
* *
2494101 ATCTATGCTGCAAATGATGTGCCTTTGAGCTGATTGT
129 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* *
2494138 AATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAGCTATGCTGCAAATGATG
1 AATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* * * * *
2494203 CGCCTTGGCA-CTGAGAGTAGTCGAACTCGAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTT
66 TGCCTTTG-AGCTGAGTGTAATCGAACTCGAAGGTC-TTT-TTGGCAGATAGCCCTTCTTGCCTT
*
2494267 GAGCTATGTTGCAAATGA
128 GAGCTATGCTGCAAATGA
2494285 ACACGATATC
Statistics
Matches: 415, Mismatches: 43, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
157 16 0.04
158 31 0.07
159 94 0.23
160 4 0.01
161 39 0.09
162 30 0.07
163 18 0.04
164 1 0.00
165 26 0.06
166 25 0.06
167 131 0.32
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
AATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGGCAGATAGCCCTTCTTGCCTTGAG
CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
Found at i:2494162 original size:83 final size:83
Alignment explanation
Indices: 2493650--2494284 Score: 765
Period size: 84 Copynumber: 7.8 Consensus size: 83
2493640 TATGCCTTTG
* * * * *
2493650 AATCGAACTCGAAGGTCTTGTGGTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGAT
1 AATCGAACTCGAAGGTCTT-TGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
2493715 GTGCCTTTGAGCTGAGTGT
65 GTGCCTTTGAGCTGAGTGT
* * * *
2493734 AATCGAACTCGAA-GT-TCT-TTGGCAGATAACCCTTCTTGCCTTAAGCTACGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
2493796 TGCC-TTGAGCTGAGTGT
66 TGCCTTTGAGCTGAGTGT
* * **
2493813 AATCGAACCCGAAGGTC--T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
*
2493875 TGCTTTTGAGCTGAGTGT
66 TGCCTTTGAGCTGAGTGT
* *
2493893 AATCGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTCGCCTTGAGCTA--CTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
2493953 TGCCTTTGAGCTGAGTGT
66 TGCCTTTGAGCTGAGTGT
** * * *
2493971 AATCGAACTAAAAGGTCTTTGTTGACAGATAACCCTTCTAGCATTGAGTTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
***
2494036 TGCCCTCAAAGCTGAGTGT
66 TG-CCTTTGAGCTGAGTGT
* * * * * *
2494055 AATCGAACTCGAGGGTCTTTGTTGGTAGATAGCCATTCTTGCCTTGATCTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
*
2494120 TGCCTTTGAGCTGATTGT
66 TGCCTTTGAGCTGAGTGT
* *
2494138 AATCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAGCTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* * *
2494203 CGCCTTGGCA-CTGAGAGT
66 TGCCTTTG-AGCTGAGTGT
* * * * * *
2494221 AGTCGAACTCGAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGA
1 AATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGA
2494285 ACACGATATC
Statistics
Matches: 472, Mismatches: 68, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
78 42 0.09
79 67 0.14
80 101 0.21
81 26 0.06
82 1 0.00
83 112 0.24
84 123 0.26
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
AATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
TGCCTTTGAGCTGAGTGT
Found at i:2494579 original size:125 final size:125
Alignment explanation
Indices: 2494286--2494881 Score: 887
Period size: 125 Copynumber: 4.8 Consensus size: 125
2494276 TGCAAATGAA
2494286 CACGATAT-CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCTC-TTCGTTGTGAAGTTGAGCCTT
1 CACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCC-CATTCGTTGTGAAGTTGAGCCTT
* *
2494349 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT-ATAAAGATGAATGTCACTGGTGAG
64 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTCAATGGTGAG
* *
2494410 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCTCATTCGTTGTGAAGTTGAGCCTTAA
1 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* *** *
2494475 ATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTTGCTGGTAAG
66 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTCAATGGTGAG
*
2494535 CATGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * *
2494600 ATTGGATATCTTTCATCGTGAAGTTGAAATCCAATC-TAAAAATGAATG-CAATGGTGAG
66 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTCAATGGTGAG
* * * * *
2494658 CACAATTCTCTTCGTCGTGAAGTTGAAACTGTGGATGGCCCTTTCGTTGTGAAGTTAAGCCTTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * **
2494723 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAATATAAATGTTGATGGTGAG
66 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTCAATGGTGAG
* *
2494783 CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCATTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * * *
2494848 CTTGAATATCCTTCGTTGTGAAGTTAAAATCCAA
66 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
2494882 GCTTGTATTG
Statistics
Matches: 427, Mismatches: 40, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
123 101 0.24
124 114 0.27
125 212 0.50
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (125 bp):
CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTCAATGGTGAG
Found at i:2494774 original size:248 final size:249
Alignment explanation
Indices: 2494286--2494881 Score: 937
Period size: 248 Copynumber: 2.4 Consensus size: 249
2494276 TGCAAATGAA
2494286 CACGATAT-CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCTC-TTCGTTGTGAAGTTGAGCCTT
1 CACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCC-CATTCGTTGTGAAGTTGAGCCTT
* * *
2494349 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATGAATGTCACTGGTGAGCACG
64 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAAATGAATGTCAATGGTGAGCACA
* *
2494414 ATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCTCATTCGTTGTGAAGTTGAGCCTTAAATTG
129 ATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTAAATTG
* *
2494479 GATATCATTCGTCGTGAAGTTGAAATCCAATCTTAAAGATGAATGTTGCTGGTAAG
194 GATATCATTCGTCGTGAAGTTGAAATCCAATCTTAAAGATAAATGTTGATGGTAAG
*
2494535 CATGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * *
2494600 ATTGGATATCTTTCATCGTGAAGTTGAAATCCAATCTAAAAATGAATG-CAATGGTGAGCACAAT
66 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAAATGAATGTCAATGGTGAGCACAAT
* * * *
2494664 TCTCTTCGTCGTGAAGTTGAAACTGTGGATGGCCCTTTCGTTGTGAAGTTAAGCCTTGAATTGGA
131 TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTAAATTGGA
* * *
2494729 TATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAATATAAATGTTGATGGTGAG
196 TATCATTCGTCGTGAAGTTGAAATCCAATCTTAAAGATAAATGTTGATGGTAAG
* *
2494783 CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCATTGA
1 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * * *
2494848 CTTGAATATCCTTCGTTGTGAAGTTAAAATCCAA
66 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
2494882 GCTTGTATTG
Statistics
Matches: 318, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
248 214 0.67
249 104 0.33
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (249 bp):
CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAAATGAATGTCAATGGTGAGCACAAT
TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTAAATTGGA
TATCATTCGTCGTGAAGTTGAAATCCAATCTTAAAGATAAATGTTGATGGTAAG
Found at i:2496451 original size:96 final size:95
Alignment explanation
Indices: 2496227--2496486 Score: 378
Period size: 96 Copynumber: 2.7 Consensus size: 95
2496217 AGCTAGATCT
* *
2496227 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTA-TATATATTA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTATATTA
*
2496291 TAATCACCTTTATCAGGCTAGCTGAATATTATCC
62 TAATCACCTTTACCAGGCTAGCTGAATATTATCC
* *
2496325 ATAAAGCTGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
*
2496390 CACCTTTACCAGGCTTAGCTGAATCTTATCC
66 CACCTTTACCAGGC-TAGCTGAATATTATCC
* * *
2496421 ATAAAGCCGGGGCATTTAACCGATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATATATAA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAA
2496486 T
65 T
2496487 TATAATTTGG
Statistics
Matches: 148, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
94 2 0.01
95 27 0.18
96 71 0.48
97 7 0.05
98 41 0.28
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
CACCTTTACCAGGCTAGCTGAATATTATCC
Found at i:2499120 original size:5 final size:6
Alignment explanation
Indices: 2499089--2499185 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
2499079 AAAGTGTTAG
*
2499089 ATAAAGA ATAAAA CATAAAA ATAAAA ATAAAAA ATAGTAA AT--AA ATCAAAGA
1 ATAAA-A ATAAAA -ATAAAA ATAAAA AT-AAAA ATA-AAA ATAAAA AT-AAA-A
*
2499141 ATAGAAA A-AAGA ATAAAA A-AAGAGA ATAAAA ATAAAA ATAAAA AT
1 ATA-AAA ATAAAA ATAAAA ATAA-A-A ATAAAA ATAAAA ATAAAA AT
2499186 GTTAAAAGTA
Statistics
Matches: 75, Mismatches: 3, Indels: 25
0.73 0.03 0.24
Matches are distributed among these distances:
4 4 0.05
5 5 0.07
6 31 0.41
7 28 0.37
8 7 0.09
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (6 bp):
ATAAAA
Found at i:2499120 original size:12 final size:12
Alignment explanation
Indices: 2499089--2499185 Score: 67
Period size: 13 Copynumber: 7.7 Consensus size: 12
2499079 AAAGTGTTAG
2499089 ATAAAGAATAAAA
1 ATAAA-AATAAAA
2499102 CATAAAAATAAAA
1 -ATAAAAATAAAA
*
2499115 ATAAAAAATAGTAA
1 AT-AAAAATA-AAA
2499129 AT--AAATCAAAGA
1 ATAAAAAT-AAA-A
*
2499141 ATAGAAAA-AAGA
1 ATA-AAAATAAAA
2499153 ATAAAAA-AAGAGA
1 ATAAAAATAA-A-A
2499166 ATAAAAATAAAA
1 ATAAAAATAAAA
2499178 ATAAAAAT
1 ATAAAAAT
2499186 GTTAAAAGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
11 11 0.16
12 19 0.28
13 25 0.36
14 11 0.16
15 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:2499130 original size:20 final size:19
Alignment explanation
Indices: 2499089--2499178 Score: 80
Period size: 19 Copynumber: 4.7 Consensus size: 19
2499079 AAAGTGTTAG
* *
2499089 ATAAAGAATAAAACATAAAA
1 ATAAA-AATAAAAAATAGAA
2499109 ATAAAAATAAAAAATAGTAA
1 ATAAAAATAAAAAATAG-AA
*
2499129 AT--AAATCAAAGAATAGAA
1 ATAAAAAT-AAAAAATAGAA
2499147 A-AAAGAATAAAAAA-AGAGA
1 ATAAA-AATAAAAAATAGA-A
2499166 ATAAAAATAAAAA
1 ATAAAAATAAAAA
2499179 TAAAAATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.17
19 34 0.58
20 15 0.25
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (19 bp):
ATAAAAATAAAAAATAGAA
Found at i:2499176 original size:19 final size:19
Alignment explanation
Indices: 2499108--2499178 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
2499098 AAAACATAAA
2499108 AATAAAAATAAAAAATAGTA-
1 AATAAAAATAAAAAA-AG-AG
* * *
2499128 AAT--AAATCAAAGAATAG
1 AATAAAAATAAAAAAAGAG
*
2499145 AAAAAAGAATAAAAAAAGAG
1 AATAAA-AATAAAAAAAGAG
2499165 AATAAAAATAAAAA
1 AATAAAAATAAAAA
2499179 TAAAAATGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 8 0.21
19 9 0.23
20 18 0.46
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (19 bp):
AATAAAAATAAAAAAAGAG
Found at i:2500465 original size:18 final size:17
Alignment explanation
Indices: 2500422--2500466 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2500412 AAAGGAAAAG
2500422 AATAATAAATAACAAAT
1 AATAATAAATAACAAAT
* *
2500439 AACTAATAAATAATACAT
1 AA-TAATAAATAACAAAT
2500457 AATACATAAA
1 AATA-ATAAA
2500467 GAAAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAATAAATAACAAAT
Found at i:2500563 original size:43 final size:42
Alignment explanation
Indices: 2500481--2500598 Score: 105
Period size: 43 Copynumber: 2.8 Consensus size: 42
2500471 GAAAAAAAGG
* * **
2500481 AAAAAATATTTTTTTAAAACTATATTTTATATATGATTTTTT
1 AAAAAATATTTTTTCAAAACCATATAATATATATGATTTTTT
* **
2500523 AAAACAATGTTTTTTCAAAACCATATAATATAATAT-ATTTTCA
1 AAAA-AATATTTTTTCAAAACCATATAATAT-ATATGATTTTTT
* ** *
2500566 AAAAAATATATTTT-AAAATTATATATTATATAT
1 AAAAAATATTTTTTCAAAACCATATAATATATAT
2500599 TTTCCAATAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
40 4 0.06
41 12 0.19
42 12 0.19
43 30 0.48
44 4 0.06
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (42 bp):
AAAAAATATTTTTTCAAAACCATATAATATATATGATTTTTT
Found at i:2500592 original size:15 final size:16
Alignment explanation
Indices: 2500554--2500583 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2500544 CATATAATAT
2500554 AATATATTTTCAAAAA
1 AATATATTTTCAAAAA
2500570 AATATATTTT-AAAA
1 AATATATTTTCAAAA
2500584 TTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATTTTCAAAAA
Found at i:2500631 original size:35 final size:35
Alignment explanation
Indices: 2500576--2500855 Score: 264
Period size: 35 Copynumber: 7.7 Consensus size: 35
2500566 AAAAAATATA
* *
2500576 TTTT-AAAATTATATATTATATATTTTCCAATATG
1 TTTTAAAAACTATATATTATATATTTTCCAAAATG
* *
2500610 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATAT
1 TTTTAAAAACTATATATTATAT-A-TTTTCCAAAAT-G
*
2500648 TTTTAAAAAACTATATAATATATATATATT-CAAAA-G
1 TTTT-AAAAACTATAT-AT-TATATATTTTCCAAAATG
2500684 TTTTTAAAAAAACTATATATTATATATTTT-CAAAATG
1 -TTTT--AAAAACTATATATTATATATTTTCCAAAATG
* *
2500721 TTTTTTTAAAAACTATATAATATATAAATGTTTTCAAAATG
1 ---TTTTAAAAACTATAT-AT-TATATAT-TTTCCAAAATG
* *
2500762 ATTTAAAAACTATATATTATATATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATTTTCCAAAATG
* * * *
2500797 TTTCAAAAAGTATATGTTATATAGTTTTCAAAAATG
1 TTTTAAAAACTATATATTATATA-TTTTCCAAAATG
2500833 -TTTAAAAACTATATATTATATAT
1 TTTTAAAAACTATATATTATATAT
2500856 ATATTTTCAA
Statistics
Matches: 209, Mismatches: 20, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
34 5 0.02
35 63 0.30
36 33 0.16
37 29 0.14
38 36 0.17
39 25 0.12
40 6 0.03
41 12 0.06
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATATTTTCCAAAATG
Found at i:2500770 original size:75 final size:73
Alignment explanation
Indices: 2500550--2500855 Score: 290
Period size: 75 Copynumber: 4.2 Consensus size: 73
2500540 AAACCATATA
* * * * * *
2500550 ATATAATATATTTTCAAAAAAATATATTTT--AAAATTATATATTATAT-AT-TTTCCAATATGT
1 ATATTATATATTTTC--AAAAATGT-TTTTAAAAAACTATATAATATATAATGTTTTCAAAATG-
2500611 TTTAAAAACTAT
62 TTTAAAAACTAT
* * * *
2500623 ATATTATATAAGTTTTCAAAAATATTTTTAAAAAACTATATAATATAT-ATATATTCAAAAGTTT
1 ATATTATAT-A-TTTTCAAAAATGTTTTTAAAAAACTATATAATATATAATGTTTTCAAAA-TGT
2500687 TTAAAAAAACTAT
63 TT--AAAAACTAT
*
2500700 ATATTATATATTTTC-AAAATGTTTTTTTAAAAACTATATAATATATAAATGTTTTCAAAATGAT
1 ATATTATATATTTTCAAAAATG-TTTTTAAAAAACTATATAATATAT-AATGTTTTCAAAATG-T
2500764 TTAAAAACTAT
63 TTAAAAACTAT
* * **
2500775 ATATTATATATTTTCAAAAATG--TTTCAAAAAGTATATGTTATAT-A-GTTTTCAAAAATGTTT
1 ATATTATATATTTTCAAAAATGTTTTTAAAAAACTATATAATATATAATGTTTTC-AAAATGTTT
2500836 AAAAACTAT
65 AAAAACTAT
2500845 ATATTATATAT
1 ATATTATATAT
2500856 ATATTTTCAA
Statistics
Matches: 203, Mismatches: 16, Indels: 31
0.81 0.06 0.12
Matches are distributed among these distances:
70 29 0.14
71 7 0.03
72 4 0.02
73 34 0.17
74 23 0.11
75 66 0.33
76 9 0.04
77 31 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (73 bp):
ATATTATATATTTTCAAAAATGTTTTTAAAAAACTATATAATATATAATGTTTTCAAAATGTTTA
AAAACTAT
Found at i:2505178 original size:43 final size:44
Alignment explanation
Indices: 2505105--2505242 Score: 133
Period size: 43 Copynumber: 3.2 Consensus size: 44
2505095 CGCATATACA
* * * *
2505105 TATTACGGCGTTTGTAATAAAAACGCCGCTAAATATTGA-CACC
1 TATTGCGGCGTTTGTAAGACAAACGCCGCTAAATATTCAGCACC
* * *
2505148 TATTGTGGCGTGTT-TAAGACAAACACCGCTAAATA-TCAGTACC
1 TATTGCGGCGT-TTGTAAGACAAACGCCGCTAAATATTCAGCACC
* * *
2505191 TATTGCGGCGTTTGTTAGACAAACGCCGCTATATA-TC-GTTACC
1 TATTGCGGCGTTTGTAAGACAAACGCCGCTAAATATTCAG-CACC
2505234 TATTGCGGC
1 TATTGCGGC
2505243 ATATTTTATT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
42 5 0.06
43 73 0.91
44 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
TATTGCGGCGTTTGTAAGACAAACGCCGCTAAATATTCAGCACC
Found at i:2505733 original size:16 final size:16
Alignment explanation
Indices: 2505712--2505746 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2505702 TGCCACTTTG
*
2505712 ATTTTTGGGGTGTACA
1 ATTTTTGGGATGTACA
2505728 ATTTTTGGGATGTACA
1 ATTTTTGGGATGTACA
2505744 ATT
1 ATT
2505747 ATTCGGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.46
Consensus pattern (16 bp):
ATTTTTGGGATGTACA
Found at i:2512249 original size:13 final size:13
Alignment explanation
Indices: 2512203--2512240 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
2512193 AGCATTGTGG
2512203 AAAGAAAATAATA
1 AAAGAAAATAATA
2512216 AAAGAAAATAATA
1 AAAGAAAATAATA
2512229 AAAGAAAATAAT
1 AAAGAAAATAAT
2512241 GAAACAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAGAAAATAATA
Found at i:2514605 original size:112 final size:109
Alignment explanation
Indices: 2514377--2514587 Score: 284
Period size: 112 Copynumber: 1.9 Consensus size: 109
2514367 ATGGGGCCCC
* * * **
2514377 AAAAAAGTATATATATAGTGGCGTTTTTTCAATAAACGCCACTATAGATGGACATATTGCGATGT
1 AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATGGACATATTGCGACAT
* *
2514442 TTTTTCAAAAAAATGCCACTATTATTACGCATGCCCAAAAAAATCCC
66 TTTTTCAAAAAAACGCCACTATTATTA-GCA--CCCAAAAAAATCCA
*
2514489 AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACAT
1 AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATGGACATATTGCGACAT
* *
2514554 TTTTTC-AAAAAACGCCATTATTGTT-GC-CCCAAAA
66 TTTTTCAAAAAAACGCCACTATTATTAGCACCCAAAA
2514588 TTGAATATAT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
106 7 0.08
109 2 0.02
111 16 0.18
112 65 0.72
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (109 bp):
AAAAAAGTATATATATAGTGGCATTTTTCCAATAAACACCACTATAGATGGACATATTGCGACAT
TTTTTCAAAAAAACGCCACTATTATTAGCACCCAAAAAAATCCA
Found at i:2520760 original size:64 final size:63
Alignment explanation
Indices: 2520692--2520872 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
2520682 TTGGAACACT
* ***
2520692 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
2520756 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
2520820 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
2520873 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:2520844 original size:19 final size:19
Alignment explanation
Indices: 2520820--2520870 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2520810 GAAAATATTC
2520820 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2520839 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2520858 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2520871 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2520912 original size:65 final size:64
Alignment explanation
Indices: 2520714--2520921 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 64
2520704 GCACCAAGTG
* *
2520714 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
2520778 -
64 A
*
2520778 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
2520840 GA
63 GA
* * * *
2520842 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
2520906 GA
63 GA
2520908 TGCATC-AGTGCATG
1 TGCATCGA-TGCATG
2520922 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 63 0.51
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:2523973 original size:51 final size:51
Alignment explanation
Indices: 2523918--2524020 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
2523908 TAATTATTAA
* *
2523918 AATATTTACAAT-ATATTTATTAATATTTTTAATAATAAATGT-TA-TATTTTT
1 AATA-TTACAATAATATTCATTAATA-TTATAATAATAAAT-TATATTATTTTT
* *
2523969 AATATTAGAATAATATTCATTTATATTATAATAATAAATTATATTATTTTT
1 AATATTACAATAATATTCATTAATATTATAATAATAAATTATATTATTTTT
2524020 A
1 A
2524021 TTTTGATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 1 0.02
50 21 0.47
51 23 0.51
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (51 bp):
AATATTACAATAATATTCATTAATATTATAATAATAAATTATATTATTTTT
Found at i:2524402 original size:167 final size:167
Alignment explanation
Indices: 2524126--2524428 Score: 545
Period size: 167 Copynumber: 1.8 Consensus size: 167
2524116 AATATAATAA
* * *
2524126 TCTAGTAATGTTTTTAATAGAAATACTTAAAATATATTCATTAATAATTTCAAAATGTAATATAG
1 TCTAGTAATGATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTCAAAATGTAATATAA
*
2524191 TATTCTTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTATC
66 TATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTATC
2524256 TTAATATTGTTATTTACAAAATTATAGAAATAATATT
131 TTAATATTGTTATTTACAAAATTATAGAAATAATATT
*
2524293 TCTAGTAAT-ATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTTCAAAATGTAGTATA
1 TCTAGTAATGATTTTAATAAAAATACTTAAAATATATTCATTAATAA-TTTCAAAATGTAATATA
2524357 ATATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
65 ATATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTAT
2524422 CTTAATA
130 CTTAATA
2524429 CAAAATTATA
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 35 0.27
167 95 0.73
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (167 bp):
TCTAGTAATGATTTTAATAAAAATACTTAAAATATATTCATTAATAATTTCAAAATGTAATATAA
TATTATTATTTTAATAAATAATTAATATAATTTATAATATTTTTATTTTAATAGAATATATTATC
TTAATATTGTTATTTACAAAATTATAGAAATAATATT
Found at i:2524515 original size:19 final size:17
Alignment explanation
Indices: 2524493--2524559 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
2524483 TTCAAAATTA
2524493 ATAAT-ATTAATTTTTT
1 ATAATAATTAATTTTTT
2524509 ATAATAATTAATATTATTT
1 ATAATAATTAAT-TT-TTT
* * *
2524528 ATTATATTTAA-TATTT
1 ATAATAATTAATTTTTT
*
2524544 ATAATAAATAATTTTT
1 ATAATAATTAATTTTT
2524560 AAAAACAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 16 0.40
17 10 0.25
18 2 0.05
19 12 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATAATTAATTTTTT
Found at i:2524539 original size:26 final size:25
Alignment explanation
Indices: 2524480--2524549 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 25
2524470 ATTATTTTGG
2524480 TATTTCAA-AATTAATAATATTAATT
1 TATTT-AATAATTAATAATATTAATT
* * *
2524505 TTTTATAATAATTAATATTATTTATT
1 TATT-TAATAATTAATAATATTAATT
*
2524531 ATATTTAAT-ATTTATAATA
1 -TATTTAATAATTAATAATA
2524550 AATAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
25 13 0.36
26 20 0.56
27 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTTAATAATTAATAATATTAATT
Found at i:2535589 original size:127 final size:127
Alignment explanation
Indices: 2535423--2535729 Score: 420
Period size: 127 Copynumber: 2.4 Consensus size: 127
2535413 TAGGAGAGGC
* * * *
2535423 TGAATCGAGGTTGATTTTCTTTACTGCTCTTCAGGAAGATTAAAT-TTAAAAAAGAATCTGCTTC
1 TGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTT-AAAAAGAATCTGCTTC
* * *
2535487 ACTTCTC-TTCAAGAAAATCAGATATGGAAACTTTGATTCATTTCACTATTCTTCAGGGAAAGT
65 ACTACTCATT-AAGAAAATCAGATATGGAAAATTTGATTCATTTCACTACTCTTCAGGGAAAGT
* * * *
2535550 TGAATCGAGGTTGATTTGCTTCACTGCTCTTTAGAAAGATCAAATCTTAAAAAGGATTTGTTTCA
1 TGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTTAAAAAGAATCTGCTTCA
*
2535615 CTAGTCATTAAGAAAATCAGATATGGAAAATTTGATTCATTTCACTACTCTTCAGGGAAAGT
66 CTACTCATTAAGAAAATCAGATATGGAAAATTTGATTCATTTCACTACTCTTCAGGGAAAGT
* * * * * *
2535677 TGAATTGAGATTGATTTGCTTCATTACTCTTCAAAAAGATCAAATCTGAAAAA
1 TGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTTAAAAA
2535730 CAAGGATCTG
Statistics
Matches: 159, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
127 155 0.97
128 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (127 bp):
TGAATCGAGGTTGATTTGCTTCACTGCTCTTCAGAAAGATCAAATCTTAAAAAGAATCTGCTTCA
CTACTCATTAAGAAAATCAGATATGGAAAATTTGATTCATTTCACTACTCTTCAGGGAAAGT
Found at i:2536460 original size:50 final size:51
Alignment explanation
Indices: 2536379--2536482 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 51
2536369 AGAAAAATTT
*
2536379 AAGTTGAAGAATGATACAACTGAAAAGTTGACTCATC-TCCGCGAGAAAGTC
1 AAGTTGAAGAATGACACAACTGAAAAGTTGACTCATCTTCC-CGAGAAAGTC
*
2536430 AAGTTG-AGAATGACATC-ACT-AAAAGGTTGACTCATCTTCCTGAGAAAGTC
1 AAGTTGAAGAATGACA-CAACTGAAAA-GTTGACTCATCTTCCCGAGAAAGTC
2536480 AAG
1 AAG
2536483 AATCATATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
49 4 0.08
50 34 0.71
51 10 0.21
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (51 bp):
AAGTTGAAGAATGACACAACTGAAAAGTTGACTCATCTTCCCGAGAAAGTC
Found at i:2536496 original size:45 final size:44
Alignment explanation
Indices: 2536396--2536797 Score: 206
Period size: 45 Copynumber: 8.8 Consensus size: 44
2536386 AGAATGATAC
* *
2536396 AACTGAAAA-GTTGACTCATCTCCGCGAGAAAGTCAAGTTGAGAATGACAT
1 AACT-AAAAGGTTGACTCATCTTC-CGAGAAAGTC-A----AGAATCACAT
* *
2536446 CACTAAAAGGTTGACTCATCTTCCTGAGAAAGTCAAGAATCATAT
1 AACTAAAAGGTTGACTCATCTTCC-GAGAAAGTCAAGAATCACAT
* * * * *
2536491 TACTAAAAGGTTGACTCTTTTTTACGAGAAAGTCAAGAATGACAT
1 AACTAAAAGGTTGACTC-ATCTTCCGAGAAAGTCAAGAATCACAT
* * * * **
2536536 AACTAAAAGTTTGACTCCTGTTCGCGAGAAAGTCAATAAGGACA-
1 AACTAAAAGGTTGACTCATCTTC-CGAGAAAGTCAAGAATCACAT
* * * * **
2536580 ACACTGAAAGGTTAACTCCTCTTCAAGAGAAAGTCAAGAAGGACA-
1 A-ACTAAAAGGTTGACTCATCTTC-CGAGAAAGTCAAGAATCACAT
* ** * ** **
2536625 ACAATAAAATATTGACTCCTCTTTGTGAGAAAGTCAAGAAGGACA-
1 A-ACTAAAAGGTTGACTCATC-TTCCGAGAAAGTCAAGAATCACAT
* * * *
2536670 ACACTAAAAGATTGACTTC-TCTTTGCGAGAAAGTCATGAATAACAT
1 A-ACTAAAAGGTTGAC-TCATC-TTCCGAGAAAGTCAAGAATCACAT
* * * * **
2536716 CACCAAAAGGTTGACTCCTCTTCACAAGAAA-TCAAGAAGGACA-
1 AACTAAAAGGTTGACTCATCTTC-CGAGAAAGTCAAGAATCACAT
* *
2536759 ACACTAAAAGATTGACTTATCTTCACGAGAAAGTCAAGA
1 A-ACTAAAAGGTTGACTCATCTTC-CGAGAAAGTCAAGA
2536798 CTAAAAGATT
Statistics
Matches: 289, Mismatches: 51, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
44 42 0.15
45 208 0.72
46 8 0.03
49 6 0.02
50 25 0.09
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (44 bp):
AACTAAAAGGTTGACTCATCTTCCGAGAAAGTCAAGAATCACAT
Found at i:2536565 original size:90 final size:90
Alignment explanation
Indices: 2536436--2536797 Score: 363
Period size: 90 Copynumber: 4.0 Consensus size: 90
2536426 AGTCAAGTTG
* * ** * **
2536436 AGAATGACATCACTAAAAGGTTGACTCATCTTC-CTGAGAAAGTCAAGAATCATATTACTAAAAG
1 AGAATGACATAACTAAAAGGTTGACTCCTCTTCGC-GAGAAAGTCAAGAAGGACAACACTAAAAG
* * *
2536500 GTTGACTCT-TTTTTACGAGAAAGTCA
65 ATTGACT-TATCTTCACGAGAAAGTCA
* * * * *
2536526 AGAATGACATAACTAAAAGTTTGACTCCTGTTCGCGAGAAAGTCAATAAGGACAACACTGAAAGG
1 AGAATGACATAACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGA
* ** *
2536591 TTAACTCCTCTTCAAGAGAAAGTCA
66 TTGACTTATCTTCACGAGAAAGTCA
* * ** * *
2536616 AGAAGGACA-ACAATAAAATATTGACTCCTCTTTGTGAGAAAGTCAAGAAGGACAACACTAAAAG
1 AGAATGACATA-ACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAG
* **
2536680 ATTGACTTCTCTTTGCGAGAAAGTCA
65 ATTGACTTATCTTCACGAGAAAGTCA
* * * * * *
2536706 TGAATAACATCACCAAAAGGTTGACTCCTCTTCACAAGAAA-TCAAGAAGGACAACACTAAAAGA
1 AGAATGACATAACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGA
2536770 TTGACTTATCTTCACGAGAAAGTCA
66 TTGACTTATCTTCACGAGAAAGTCA
2536795 AGA
1 AGA
2536798 CTAAAAGATT
Statistics
Matches: 221, Mismatches: 47, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
89 48 0.22
90 172 0.78
91 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (90 bp):
AGAATGACATAACTAAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGA
TTGACTTATCTTCACGAGAAAGTCA
Found at i:2536633 original size:135 final size:134
Alignment explanation
Indices: 2536494--2536797 Score: 364
Period size: 135 Copynumber: 2.3 Consensus size: 134
2536484 ATCATATTAC
* * * * *
2536494 TAAAAGGTTGACTCTTTTTTACGAGAAAGTCAAGAATGACATA-ACTAAAAGTTTGACTCCTGTT
1 TAAAAGATTGACTCTTCTTTACGAGAAAGTCAAGAAGGACA-ACACTAAAAGATTGACTCCTCTT
* **
2536558 CGCGAGAAAGTCAAT-AAGGACAACACTGAAAGGTTAACTCCTCTTCA-AGAGAAAGTCAAGAAG
65 CGCGAGAAAGTC-ATGAAGAACAACACCAAAAGGTTAACTCCTCTTCACA-AGAAA-TCAAGAAG
2536621 GACAACAA
127 GACAACAA
* * ** * *
2536629 TAAAATATTGACTCCTCTTTGTGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTCTCTTT
1 TAAAAGATTGACTCTTCTTTACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTC
* * *
2536694 GCGAGAAAGTCATGAATAACATCACCAAAAGGTTGACTCCTCTTCACAAGAAATCAAGAAGGACA
66 GCGAGAAAGTCATGAAGAACAACACCAAAAGGTTAACTCCTCTTCACAAGAAATCAAGAAGGACA
*
2536759 ACAC
131 ACAA
*
2536763 TAAAAGATTGACT-TATCTTCACGAGAAAGTCAAGA
1 TAAAAGATTGACTCT-TCTTTACGAGAAAGTCAAGA
2536798 CTAAAAGATT
Statistics
Matches: 142, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
134 47 0.33
135 94 0.66
136 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (134 bp):
TAAAAGATTGACTCTTCTTTACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTC
GCGAGAAAGTCATGAAGAACAACACCAAAAGGTTAACTCCTCTTCACAAGAAATCAAGAAGGACA
ACAA
Found at i:2536859 original size:41 final size:41
Alignment explanation
Indices: 2536659--2536863 Score: 154
Period size: 44 Copynumber: 5.0 Consensus size: 41
2536649 GTGAGAAAGT
*
2536659 CAAGAAGGACAACACTAAAAGATTGACTTC-TCTTTGCGA-GAAA
1 CAAGAATGACAACACTAAAAGATTGAC-TCATC-TT-C-ACGAAA
* * * * * *
2536702 GTCATGAATAACATCACCAAAAGGTTGACTCCTCTTCACAAGAAA
1 --CAAGAATGACAACACTAAAAGATTGACTCATCTTCAC--GAAA
* * *
2536747 TCAAGAAGGACAACACTAAAAGATTGACTTATCTTCACGAGA
1 -CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAAA
*
2536789 -AAG--T--CAAGACTAAAAGATTGACTCATCTTCACGAAA
1 CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAAA
* * *
2536825 CAAGAATGACAACACTGAAAGATTGTCTCCTCTTCACGA
1 CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGA
2536864 GAAACTCAAG
Statistics
Matches: 128, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
36 29 0.23
37 3 0.02
39 1 0.01
40 3 0.02
41 26 0.20
42 4 0.03
43 1 0.01
44 34 0.27
45 27 0.21
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
CAAGAATGACAACACTAAAAGATTGACTCATCTTCACGAAA
Found at i:2536859 original size:77 final size:79
Alignment explanation
Indices: 2536720--2536873 Score: 213
Period size: 77 Copynumber: 2.0 Consensus size: 79
2536710 TAACATCACC
* * *
2536720 AAAAGGTTGACTCCTCTTCACAAGAAATCAAGAAGGACAACACTAAAAGATTGACTTATCTTCAC
1 AAAAGATTGACTCATCTTCAC-AGAAATCAAGAAGGACAACACTAAAAGATTGACTCATCTTCAC
*
2536785 GAGAAAGTCAAGACT
65 GAGAAACTCAAGACT
* * * *
2536800 AAAAGATTGACTCATCTTCAC-GAAA-CAAGAATGACAACACTGAAAGATTGTCTCCTCTTCACG
1 AAAAGATTGACTCATCTTCACAGAAATCAAGAAGGACAACACTAAAAGATTGACTCATCTTCACG
2536863 AGAAACTCAAG
66 AGAAACTCAAG
2536874 TTGAGGTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 43 0.65
78 4 0.06
80 19 0.29
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (79 bp):
AAAAGATTGACTCATCTTCACAGAAATCAAGAAGGACAACACTAAAAGATTGACTCATCTTCACG
AGAAACTCAAGACT
Found at i:2538264 original size:20 final size:20
Alignment explanation
Indices: 2538239--2538288 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2538229 GACCAACAAA
2538239 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* ** *
2538259 TTCGCAACCCAATTTCTAAT
1 TTCGCAACGCAAACTCCAAT
2538279 TTCGCAACGC
1 TTCGCAACGC
2538289 GAATCTGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:2538343 original size:60 final size:60
Alignment explanation
Indices: 2538279--2538506 Score: 214
Period size: 60 Copynumber: 3.8 Consensus size: 60
2538269 AATTTCTAAT
* * *
2538279 TTCGCAACGCGAATCTGTAAATCGCAACATAGAAGTCAAATTTGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
* * * ** ***
2538339 TTCGCAATGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCACAATGCGGTAGTCAAA
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
* * * *
2538399 TTCGCAACAC-AA-AAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACTCAAAAGTCAAA
1 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
* * *
2538459 TTCGCAATGCG-ATA-GTCAAATTCACAACGC-GAAAGTCAAATTCGCAAC
1 TTCGCAACGCGAATATGT-AAA-TCGCAACACAG-AAGTCAAATTCGCAAC
2538507 GCGAAACACA
Statistics
Matches: 137, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
58 2 0.01
59 5 0.04
60 129 0.94
61 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (60 bp):
TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:2538396 original size:80 final size:81
Alignment explanation
Indices: 2538312--2538512 Score: 264
Period size: 80 Copynumber: 2.5 Consensus size: 81
2538302 GCAACATAGA
* * ** *
2538312 AGTCAAATTTGCAACACAAAAGTCAAATTCGCAATGCGAATTTGT-AAA-TCGCAACACAGAAGT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAA-AAGTCAAATTCGCAACACAAAAGT
*
2538375 CAAATTCACAATGCGGT
65 CAAATTCACAATGCGAT
* *
2538392 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACAC-AAAAGTCAAATTCGCAACTCAAAAGTC
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAAGTCAAATTCGCAACACAAAAGTC
*
2538456 AAATTCGCAATGCGAT
66 AAATTCACAATGCGAT
* * *
2538472 AGTCAAATTCACAACGCGAAAGTCAAATTCGCAACGCGAAA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAA
2538513 CACAATATTA
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 2 0.02
79 5 0.05
80 95 0.90
81 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.19
Consensus pattern (81 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAAGTCAAATTCGCAACACAAAAGTC
AAATTCACAATGCGAT
Found at i:2538507 original size:20 final size:20
Alignment explanation
Indices: 2538311--2538512 Score: 185
Period size: 20 Copynumber: 10.1 Consensus size: 20
2538301 CGCAACATAG
* * *
2538311 AAGTCAAATTTGCAACACAA
1 AAGTCAAATTCGCAACGCGA
*
2538331 AAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
* *
2538351 ATTTGT-AAA-TCGCAACAC-A
1 A--AGTCAAATTCGCAACGCGA
* * *
2538370 GAAGTCAAATTCACAATGCGG
1 -AAGTCAAATTCGCAACGCGA
* * *
2538391 TAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
* *
2538411 AAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
* *
2538431 AAGTCAAATTCGCAACTCAA
1 AAGTCAAATTCGCAACGCGA
*
2538451 AAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
* *
2538471 TAGTCAAATTCACAACGCGA
1 AAGTCAAATTCGCAACGCGA
2538491 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
2538511 AA
1 AA
2538513 CACAATATTA
Statistics
Matches: 148, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
18 2 0.01
19 4 0.03
20 137 0.93
21 3 0.02
22 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:2538650 original size:22 final size:22
Alignment explanation
Indices: 2538622--2538672 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2538612 CTACGGCGAC
2538622 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
2538644 ATTCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
2538666 ATCCGTC
1 ATCCGTC
2538673 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:2539078 original size:19 final size:18
Alignment explanation
Indices: 2539056--2539136 Score: 80
Period size: 19 Copynumber: 4.5 Consensus size: 18
2539046 AAATCGCAAC
2539056 GCGATTTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
2539075 GCGATTTTCATTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
*
2539094 GCGA---T-TTTCTCGTT
1 GCGATTTTATTTCGCGTT
2539108 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-A-TTTCGCGTT
*
2539128 GCGAATTTA
1 GCGATTTTA
2539137 AGTTTCAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
14 12 0.23
16 1 0.02
17 1 0.02
19 22 0.42
20 16 0.31
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:2539083 original size:14 final size:14
Alignment explanation
Indices: 2539084--2539116 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2539074 TGCGATTTTC
2539084 ATTT-CGCGTTGCG
1 ATTTTCGCGTTGCG
*
2539097 ATTTTCTCGTTGCG
1 ATTTTCGCGTTGCG
2539111 ATTTTC
1 ATTTTC
2539117 ATTTTCGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2539113 original size:33 final size:34
Alignment explanation
Indices: 2539066--2539131 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
2539056 GCGATTTTAG
2539066 TTTCGCGTTGCGATTTTCA-TTTCGCGTTGCGAT
1 TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGAT
*
2539099 TTTCTCGTTGCGATTTTCATTTTCGCGTTGCGA
1 TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGA
2539132 ATTTAAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGAT
Found at i:2539142 original size:20 final size:19
Alignment explanation
Indices: 2539066--2539135 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 19
2539056 GCGATTTTAG
*
2539066 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGAATTTCA
2539085 TTTCGCGTTGCG-A--T--
1 TTTCGCGTTGCGAATTTCA
* *
2539099 TTTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGAATTTCA
2539118 TTTTCGCGTTGCGAATTT
1 -TTTCGCGTTGCGAATTT
2539136 AAGTTTCAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 11 0.28
16 1 0.03
17 1 0.03
19 12 0.30
20 15 0.38
ACGTcount: A:0.10, C:0.20, G:0.21, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGAATTTCA
Found at i:2540385 original size:21 final size:21
Alignment explanation
Indices: 2540361--2540410 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2540351 GTTAGGGGAG
* *
2540361 TTACGTGTTGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
*
2540382 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
2540403 TTACGTGA
1 TTACGTGA
2540411 AGATAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:2540835 original size:21 final size:21
Alignment explanation
Indices: 2540809--2540914 Score: 65
Period size: 21 Copynumber: 5.0 Consensus size: 21
2540799 GAAGCCCGAT
*
2540809 GCACCTATCATCATTCAAGAG
1 GCACCTATCATCGTTCAAGAG
*
2540830 GCACCT-CCTATCGTTCAAGAG
1 GCACCTATC-ATCGTTCAAGAG
* * *
2540851 GC-CCTTCTCATC-ATCGAAGAA
1 GCACC-TATCATCGTTC-AAGAG
* ** *
2540872 GCCCCTCCCACCGTTCAAGAG
1 GCACCTATCATCGTTCAAGAG
* *
2540893 GCCCCAATCATCGTTCAAGAG
1 GCACCTATCATCGTTCAAGAG
2540914 G
1 G
2540915 TCCCGCCCGC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.08
21 56 0.85
22 5 0.08
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (21 bp):
GCACCTATCATCGTTCAAGAG
Found at i:2540879 original size:42 final size:42
Alignment explanation
Indices: 2540816--2540896 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
2540806 GATGCACCTA
* * *
2540816 TCATCATTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCTTC
1 TCATCATTCAAGAAGCACCTCCCACCGTTCAAGAGGCCCTTC
*
2540858 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCC
1 TCATCATTC-AAGAAGCACCTCCCACCGTTCAAGAGGCCC
2540897 CAATCATCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.21
Consensus pattern (42 bp):
TCATCATTCAAGAAGCACCTCCCACCGTTCAAGAGGCCCTTC
Found at i:2540904 original size:42 final size:42
Alignment explanation
Indices: 2540815--2540934 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
2540805 CGATGCACCT
* * * **
2540815 ATCATCATTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCTT
1 ATCATCATTCAAGAAGCACCTCCCACCGTTCAAGAGGCCCCA
* *
2540857 CTCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCA
1 ATCATCATTC-AAGAAGCACCTCCCACCGTTCAAGAGGCCCCA
* * * *
2540899 ATCATCGTTCAAGAGGTC-CCGCCCGCCGTTCAAGAG
1 ATCATCATTCAAGAAG-CACCTCCCACCGTTCAAGAG
2540935 CCCGATTCAT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.03
42 58 0.92
43 3 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCATCATTCAAGAAGCACCTCCCACCGTTCAAGAGGCCCCA
Found at i:2542391 original size:66 final size:65
Alignment explanation
Indices: 2542227--2542402 Score: 255
Period size: 66 Copynumber: 2.6 Consensus size: 65
2542217 TGGCGTACAC
*
2542227 TTTTTTTGCTTGTTTAATTGAATTTTACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTTGCTTGTTTAATTG-A-TTT---TTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
2542292 AATTA
61 AATTA
* * *
2542297 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
2542361 A
65 A
2542362 TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTT
2542403 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
64 18 0.18
65 19 0.19
66 39 0.39
67 3 0.03
68 1 0.01
69 19 0.19
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:2542893 original size:18 final size:18
Alignment explanation
Indices: 2542870--2542905 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2542860 AAGCCGGTTG
*
2542870 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2542888 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2542906 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2543879 original size:18 final size:18
Alignment explanation
Indices: 2543856--2543892 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2543846 CGAAATTTAT
2543856 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2543874 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2543892 A
1 A
2543893 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2544318 original size:23 final size:24
Alignment explanation
Indices: 2544276--2544323 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2544266 CATTATTTTC
*
2544276 CAAATAATGTACCCATAACAATGTT
1 CAAATAA-GTACCCACAACAATGTT
2544301 CAAATAA-TACCCACAACAATGTT
1 CAAATAAGTACCCACAACAATGTT
2544324 TAATTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
25 7 0.32
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (24 bp):
CAAATAAGTACCCACAACAATGTT
Found at i:2544577 original size:20 final size:20
Alignment explanation
Indices: 2544528--2544577 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2544518 GCAATGCTTA
*
2544528 TTTCGCGTTACGAATTTAAC
1 TTTCGCGTTGCGAATTTAAC
**
2544548 TTTCATGTTGCGAATTTAAC
1 TTTCGCGTTGCGAATTTAAC
2544568 TTTCGCGTTG
1 TTTCGCGTTG
2544578 ATCGCAACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAC
Found at i:2544886 original size:18 final size:18
Alignment explanation
Indices: 2544863--2544898 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2544853 AAGCCGGTTG
2544863 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
2544881 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
2544899 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:2548107 original size:19 final size:19
Alignment explanation
Indices: 2548060--2548110 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
2548050 TACCCAAAAT
*
2548060 ATTTGTGTTACGAAACTAA
1 ATTTGTGTTGCGAAACTAA
* * *
2548079 A-ATATGTTGCGAAATTAA
1 ATTTGTGTTGCGAAACTAA
2548097 ATTTGTGTTGCGAA
1 ATTTGTGTTGCGAA
2548111 TTTGAAATTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (19 bp):
ATTTGTGTTGCGAAACTAA
Found at i:2548168 original size:20 final size:20
Alignment explanation
Indices: 2548143--2548289 Score: 100
Period size: 20 Copynumber: 7.3 Consensus size: 20
2548133 CAAATTCCGC
2548143 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
2548163 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
* * ***
2548183 GTTACG-ATTT-ACAAATTCAC
1 GTTGCGAATTTGAC--TTTTGT
* * * * *
2548203 ATTGCGAAATTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
**
2548223 GTTGCGAAACTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* ***
2548243 GTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGACTTTTGT
*
2548263 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
2548283 GTTGCGA
1 GTTGCGA
2548290 TTTATAGATT
Statistics
Matches: 94, Mismatches: 29, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 83 0.88
21 3 0.03
22 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:2548208 original size:60 final size:60
Alignment explanation
Indices: 2548144--2548289 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
2548134 AAATTCCGCG
**
2548144 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTATGTGTTACG-ATTT-ACAAATTCACA
1 TTGCGAATTTGACTTTTGTGTTGCGAAACTGACTTATGTGTTACGAATTTGAC-AA-TCACA
* * * * * * * *
2548204 TTGCGAAATTGACTATCGCGTTGCGAAACTGACTTTTGTGTTGCGAATTTGACTATCACG
1 TTGCGAATTTGACTTTTGTGTTGCGAAACTGACTTATGTGTTACGAATTTGACAATCACA
*
2548264 TTGCGAATTTGACTTCTGTGTTGCGA
1 TTGCGAATTTGACTTTTGTGTTGCGA
2548290 TTTATAGATT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
60 62 0.90
61 5 0.07
62 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.40
Consensus pattern (60 bp):
TTGCGAATTTGACTTTTGTGTTGCGAAACTGACTTATGTGTTACGAATTTGACAATCACA
Found at i:2548248 original size:40 final size:40
Alignment explanation
Indices: 2548204--2548289 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
2548194 CAAATTCACA
* *
2548204 TTGCGAAATTGACTATCGCGTTGCGAAACTGACTTTTGTG
1 TTGCGAAATTGACTATCACGTTGCGAAACTGACTTCTGTG
* **
2548244 TTGCGAATTTGACTATCACGTTGCGAATTTGACTTCTGTG
1 TTGCGAAATTGACTATCACGTTGCGAAACTGACTTCTGTG
2548284 TTGCGA
1 TTGCGA
2548290 TTTATAGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
TTGCGAAATTGACTATCACGTTGCGAAACTGACTTCTGTG
Found at i:2548758 original size:76 final size:73
Alignment explanation
Indices: 2548607--2548818 Score: 293
Period size: 75 Copynumber: 2.9 Consensus size: 73
2548597 ATTTTAAACA
* * *
2548607 TTATATTTTATCTTTTCTTTATGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAG
1 TTATATTTTATCTTTT-TTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAG
*
2548672 GATATTATTT
65 AATATTA-TT
2548682 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTA
2548747 GAATATTATT
64 GAATATTATT
* * * *
2548757 TTAAATATTA--TTTTTTTAGTTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
2548819 AGATGTTTTA
Statistics
Matches: 126, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
71 5 0.04
72 41 0.33
73 3 0.02
75 46 0.37
76 31 0.25
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.59
Consensus pattern (73 bp):
TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGA
ATATTATT
Found at i:2548812 original size:72 final size:74
Alignment explanation
Indices: 2548624--2548818 Score: 270
Period size: 72 Copynumber: 2.6 Consensus size: 74
2548614 TTATCTTTTC
* * * * * *
2548624 TTTATGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATT
1 TTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTAAATA
2548689 TTATCTTTGT
66 TTA-CTTTGT
2548699 TTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTA-TTTTAAAT
1 TTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTAAAT
2548763 ATTA-TTT-T
65 ATTACTTTGT
* *
2548771 TTTAGTTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
2548819 AGATGTTTTA
Statistics
Matches: 110, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
71 5 0.05
72 41 0.37
73 3 0.03
75 31 0.28
76 30 0.27
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (74 bp):
TTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTAAATA
TTACTTTGT
Found at i:2549536 original size:13 final size:13
Alignment explanation
Indices: 2549486--2549535 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2549476 GAAACCCCCC
2549486 TTTTA-TTTTTACT
1 TTTTATTTTTTA-T
**
2549499 TTTTAATTCATTAT
1 TTTT-ATTTTTTAT
2549513 TTTTATTTTTTAT
1 TTTTATTTTTTAT
2549526 TTTT-TTTTTT
1 TTTTATTTTTT
2549536 TTATAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 6 0.19
13 15 0.48
14 6 0.19
15 4 0.13
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:2556881 original size:75 final size:73
Alignment explanation
Indices: 2556776--2556979 Score: 268
Period size: 75 Copynumber: 2.8 Consensus size: 73
2556766 ATTTTAAACA
*
2556776 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTAT-TTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
* *
2556841 GGATATTAGTT
64 GAATATTA-AT
* *
2556852 TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAATATTTTAATTAGGATTTAG
1 TTATATTTTAT-TTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAG
2556917 AATATTAAT
65 AATATTAAT
* * * * *
2556926 TTAAATATTA--TTTTTTAAGTATTTTAGTTTAAATAGGTTTAAGTGTTTTAATTA
1 TTATATTTTATTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTA
2556980 GTATTTAAGA
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
71 40 0.34
74 9 0.08
75 53 0.46
76 14 0.12
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (73 bp):
TTATATTTTATTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGA
ATATTAAT
Found at i:2558286 original size:3 final size:3
Alignment explanation
Indices: 2558278--2558322 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
2558268 TTCTCCTTTT
* *
2558278 TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC TTT TTC TT- TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2558323 CATTTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:2558317 original size:27 final size:26
Alignment explanation
Indices: 2558268--2558373 Score: 80
Period size: 27 Copynumber: 4.1 Consensus size: 26
2558258 ACTTGATATG
* *
2558268 TTCTCCTTTT-TTCTTCTTCTTCTTC
1 TTCTTCTTTTCTTCTTCTTTTTCTTC
2558293 TTCTTCTTATTCTTCTTCTTTTTCTT-
1 TTCTTCTT-TTCTTCTTCTTTTTCTTC
* *
2558319 TTC-TCATTTTTCTTTCTTTTTTTTCCTTT
1 TTCTTC--TTTTC-TTCTTCTTTTT-CTTC
2558348 TTCTATCTTTTC-TCTT-TTTTT-TTC
1 TTCT-TCTTTTCTTCTTCTTTTTCTTC
2558372 TT
1 TT
2558374 GAATATGAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
24 4 0.06
25 9 0.13
26 13 0.19
27 29 0.43
28 3 0.04
29 8 0.12
31 2 0.03
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (26 bp):
TTCTTCTTTTCTTCTTCTTTTTCTTC
Found at i:2558347 original size:10 final size:10
Alignment explanation
Indices: 2558277--2558373 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 10
2558267 GTTCTCCTTT
*
2558277 TTTCTTCTTC
1 TTTCTTTTTC
*
2558287 -TTCTTCTTC
1 TTTCTTTTTC
*
2558296 -TTCTTATTC
1 TTTCTTTTTC
*
2558305 -TTCTTCTT-
1 TTTCTTTTTC
2558313 TTTC-TTTTC
1 TTTCTTTTTC
2558322 --TCATTTTTC
1 TTTC-TTTTTC
2558331 TTTCTTTTT-
1 TTTCTTTTTC
2558340 TTTCCTTTTTC
1 TTT-CTTTTTC
*
2558351 TATCTTTTCTC
1 TTTCTTTT-TC
*
2558362 TTTTTTTTTC
1 TTTCTTTTTC
2558372 TT
1 TT
2558374 GAATATGAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 35 0.49
10 20 0.28
11 12 0.17
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:2560404 original size:17 final size:17
Alignment explanation
Indices: 2560382--2560421 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2560372 CGAATAAAAC
2560382 CTACCCTCGCAGGTTGA
1 CTACCCTCGCAGGTTGA
2560399 CTACCCTCGCAGGTTGA
1 CTACCCTCGCAGGTTGA
2560416 CTACCC
1 CTACCC
2560422 ATACATGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.40, G:0.20, T:0.23
Consensus pattern (17 bp):
CTACCCTCGCAGGTTGA
Found at i:2561190 original size:8 final size:8
Alignment explanation
Indices: 2561179--2561209 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2561169 AAAAATGACA
2561179 AAAATAAT
1 AAAATAAT
2561187 AAAATAAT
1 AAAATAAT
*
2561195 GAAATAAT
1 AAAATAAT
2561203 AAAATAA
1 AAAATAA
2561210 AGAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:2562238 original size:32 final size:32
Alignment explanation
Indices: 2562197--2562268 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
2562187 AGATGGAGAA
*
2562197 GGGGTTTTGTCGATTATAAAAGGGATAAACAT
1 GGGGTTTTGTCGATTATAAAAGGAATAAACAT
* *
2562229 GGGGTTTTGTCGGTTATAAAATGAATAAACAT
1 GGGGTTTTGTCGATTATAAAAGGAATAAACAT
2562261 GGGGTTTT
1 GGGGTTTT
2562269 AAGTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.35
Consensus pattern (32 bp):
GGGGTTTTGTCGATTATAAAAGGAATAAACAT
Found at i:2562588 original size:16 final size:14
Alignment explanation
Indices: 2562576--2562617 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2562566 GATAAAATAA
2562576 AAATGAAATAAAAT
1 AAATGAAATAAAAT
*
2562590 AAATTAAATTAAAAT
1 AAATGAAA-TAAAAT
2562605 GAAATGAAATAAA
1 -AAATGAAATAAA
2562618 GCATGCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 10 0.42
16 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (14 bp):
AAATGAAATAAAAT
Found at i:2562604 original size:25 final size:25
Alignment explanation
Indices: 2562570--2562617 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2562560 GCATCTGATA
2562570 AAATAAAAATGAAATAAAATAAATT
1 AAATAAAAATGAAATAAAATAAATT
* *
2562595 AAATTAAAATGAAATGAAATAAA
1 AAATAAAAATGAAATAAAATAAA
2562618 GCATGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (25 bp):
AAATAAAAATGAAATAAAATAAATT
Found at i:2562642 original size:12 final size:12
Alignment explanation
Indices: 2562625--2562662 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2562615 AAAGCATGCT
2562625 AAAAATAAAACG
1 AAAAATAAAACG
*
2562637 AAAAATAAAATG
1 AAAAATAAAACG
2562649 -AAAATAAAACG
1 AAAAATAAAACG
2562660 AAA
1 AAA
2562663 TAGGTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (12 bp):
AAAAATAAAACG
Found at i:2562652 original size:11 final size:11
Alignment explanation
Indices: 2562569--2562662 Score: 52
Period size: 11 Copynumber: 8.3 Consensus size: 11
2562559 AGCATCTGAT
2562569 AAAATAAAAATG
1 AAAAT-AAAATG
2562581 -AAATAAAAT-
1 AAAATAAAATG
* *
2562590 -AAATTAAATT
1 AAAATAAAATG
*
2562600 AAAATGAAATG
1 AAAATAAAATG
2562611 -AAATAAAGCATG
1 AAAATAAA--ATG
*
2562623 CTAAAAATAAAACG
1 ---AAAATAAAATG
2562637 AAAAATAAAATG
1 -AAAATAAAATG
*
2562649 AAAATAAAACG
1 AAAATAAAATG
2562660 AAA
1 AAA
2562663 TAGGTTGCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
9 8 0.12
10 11 0.16
11 25 0.37
12 14 0.21
14 2 0.03
16 7 0.10
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:2575241 original size:23 final size:23
Alignment explanation
Indices: 2575203--2575260 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2575193 TCATGTTCAT
*
2575203 GAACATATAAACGAACACGTTCGC
1 GAACAT-TAAATGAACACGTTCGC
* *
2575227 GAACATTAAATGAACATGTTCGT
1 GAACATTAAATGAACACGTTCGC
*
2575250 GAACAATAAAT
1 GAACATTAAAT
2575261 AAACGAACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (23 bp):
GAACATTAAATGAACACGTTCGC
Found at i:2583320 original size:4 final size:4
Alignment explanation
Indices: 2583311--2583344 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2583301 AAAGGAAAAC
2583311 AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
2583345 CAGCAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:2593423 original size:16 final size:15
Alignment explanation
Indices: 2593402--2593432 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2593392 TAGAGGTACG
2593402 TTTTTTAATTTTAATT
1 TTTTTTAA-TTTAATT
2593418 TTTTTTAATTTAATT
1 TTTTTTAATTTAATT
2593433 ATCTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTAATTTAATT
Found at i:2594417 original size:24 final size:24
Alignment explanation
Indices: 2594382--2594436 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2594372 GCTGAGAGTA
*
2594382 ATGATGATGATGACGAT-AACAATG
1 ATGATGACGATGACGATCAA-AATG
*
2594406 ATGATGACGATGACGATCAAGATG
1 ATGATGACGATGACGATCAAAATG
2594430 ATGATGA
1 ATGATGA
2594437 TCAAGATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (24 bp):
ATGATGACGATGACGATCAAAATG
Found at i:2594438 original size:15 final size:15
Alignment explanation
Indices: 2594414--2594451 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2594404 TGATGATGAC
2594414 GATGACGATCAAGAT
1 GATGACGATCAAGAT
*
2594429 GATGATGATCAAGAT
1 GATGACGATCAAGAT
*
2594444 GACGACGA
1 GATGACGA
2594452 CGATGATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.18
Consensus pattern (15 bp):
GATGACGATCAAGAT
Found at i:2597093 original size:59 final size:60
Alignment explanation
Indices: 2597015--2597164 Score: 169
Period size: 59 Copynumber: 2.5 Consensus size: 60
2597005 ATGCATCTCT
* * * *
2597015 ATATTGAGGTTTTAA-AAGTTGACAGATGAATATCTCCCCCTGAAACTGGAAG-GATATCC
1 ATATTGAGG-TTAAAGAAGTTGGCAGATGAATATCTCCCACTGAAACTGGAAGACATATCC
* * * * *
2597074 ATATTGAGGTTGAAGAAGTTGGCAGATGAATGTCTCCCATTGGAACTGGAAGACATATCT
1 ATATTGAGGTTAAAGAAGTTGGCAGATGAATATCTCCCACTGAAACTGGAAGACATATCC
** *
2597134 ATATTGACATCAAAGAAGTTGGCAGATGAAT
1 ATATTGAGGTTAAAGAAGTTGGCAGATGAAT
2597165 GTCACCCTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 4 0.05
59 41 0.53
60 32 0.42
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (60 bp):
ATATTGAGGTTAAAGAAGTTGGCAGATGAATATCTCCCACTGAAACTGGAAGACATATCC
Found at i:2597157 original size:60 final size:59
Alignment explanation
Indices: 2597030--2597180 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 59
2597020 GAGGTTTTAA
* * ** * * ** **
2597030 AAGTTGACAGATGAATATCTCCCCCTGAAACTGGAAGGATATCCATATTGAGGTTGAAG
1 AAGTTGGCAGATGAATGTCTCCCATTGGAACTGGAAGCATATCCATATTGACATCAAAG
*
2597089 AAGTTGGCAGATGAATGTCTCCCATTGGAACTGGAAGACATATCTATATTGACATCAAAG
1 AAGTTGGCAGATGAATGTCTCCCATTGGAACTGGAAG-CATATCCATATTGACATCAAAG
*
2597149 AAGTTGGCAGATGAATGTCACCCTATT-GAACT
1 AAGTTGGCAGATGAATGTCTCCC-ATTGGAACT
2597181 TGATGGAATG
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 32 0.41
60 43 0.55
61 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (59 bp):
AAGTTGGCAGATGAATGTCTCCCATTGGAACTGGAAGCATATCCATATTGACATCAAAG
Found at i:2598047 original size:30 final size:30
Alignment explanation
Indices: 2598009--2598090 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
2597999 GCAATCGAAG
* *
2598009 GCGGTGCACCAAACGCGCCTTATGGGAGGT
1 GCGGTGCACCAAATGCGCCTTATGGGAGGC
*
2598039 GTGGTGCACCAAATGCGCCTTATGGGAGGC
1 GCGGTGCACCAAATGCGCCTTATGGGAGGC
*
2598069 GCGGTGCACCAAATGCACCTTA
1 GCGGTGCACCAAATGCGCCTTA
2598091 CCCTAAGTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (30 bp):
GCGGTGCACCAAATGCGCCTTATGGGAGGC
Found at i:2599503 original size:16 final size:16
Alignment explanation
Indices: 2599479--2599513 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2599469 GACGATTAAA
* *
2599479 TTTATTTTAATCTATT
1 TTTAATTTAATATATT
2599495 TTTAATTTAATATATT
1 TTTAATTTAATATATT
2599511 TTT
1 TTT
2599514 CTCACCAATT
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:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:2599750 original size:18 final size:18
Alignment explanation
Indices: 2599724--2599770 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2599714 TTTATATATC
*
2599724 TTAACTTAAATTCACATA
1 TTAAATTAAATTCACATA
* *
2599742 TTAAATTAATTTTACATA
1 TTAAATTAAATTCACATA
2599760 TTAACATTAAA
1 TTAA-ATTAAA
2599771 AATATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAATTCACATA
Found at i:2599791 original size:30 final size:29
Alignment explanation
Indices: 2599757--2599874 Score: 148
Period size: 29 Copynumber: 4.0 Consensus size: 29
2599747 TTAATTTTAC
*
2599757 ATATTAACATTAAAAATATATTTTATTTTT
1 ATATTAAC-TTAAAAATATATTTTATTCTT
2599787 ATATTAAC-TAATCAAATATATTTTATTCTT
1 ATATTAACTTAA--AAATATATTTTATTCTT
* * *
2599817 GTCTTAACCTAAAAATATATTTTATTCTT
1 ATATTAACTTAAAAATATATTTTATTCTT
* *
2599846 ATTTTAACTTAAAAATATATTTTAGTCTT
1 ATATTAACTTAAAAATATATTTTATTCTT
2599875 TACCTTAGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
28 3 0.04
29 42 0.54
30 30 0.38
31 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATTAACTTAAAAATATATTTTATTCTT
Found at i:2599889 original size:30 final size:30
Alignment explanation
Indices: 2599760--2599890 Score: 144
Period size: 30 Copynumber: 4.4 Consensus size: 30
2599750 ATTTTACATA
*
2599760 TTAACATTAAAAATATATTTTATT-TTTATA
1 TTAAC-TTAAAAATATATTTTATTCTTTATC
*
2599790 TTAAC-TAATCAAATATATTTTATTC-TTGTC
1 TTAACTTAA--AAATATATTTTATTCTTTATC
* *
2599820 TTAACCTAAAAATATATTTTATTC-TTATT
1 TTAACTTAAAAATATATTTTATTCTTTATC
* *
2599849 TTAACTTAAAAATATATTTTAGTCTTTACC
1 TTAACTTAAAAATATATTTTATTCTTTATC
*
2599879 TTAGCTTAAAAA
1 TTAACTTAAAAA
2599891 ACATGAATGA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
28 3 0.03
29 40 0.46
30 41 0.47
31 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (30 bp):
TTAACTTAAAAATATATTTTATTCTTTATC
Found at i:2599890 original size:59 final size:58
Alignment explanation
Indices: 2599760--2599874 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 58
2599750 ATTTTACATA
* *
2599760 TTAACATTAAAAATATATTTTATTTTTATATTAACTAATCAAATATATTTTATTCTTGTC
1 TTAAC-TTAAAAATATATTTTATTCTTATATTAACTAA-CAAATATATTTTAGTCTTGTC
* *
2599820 TTAACCTAAAAATATATTTTATTCTTATTTTAACTTAA-AAATATATTTTAGTCTT
1 TTAACTTAAAAATATATTTTATTCTTATATTAAC-TAACAAATATATTTTAGTCTT
2599875 TACCTTAGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 16 0.32
59 26 0.52
60 8 0.16
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (58 bp):
TTAACTTAAAAATATATTTTATTCTTATATTAACTAACAAATATATTTTAGTCTTGTC
Found at i:2600761 original size:30 final size:29
Alignment explanation
Indices: 2600727--2600830 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 29
2600717 AAATATATTT
2600727 TATTCTTATCTTAATTTATTACATAAGTTA
1 TATTCTTATCTTAATTTATTACATAA-TTA
* *
2600757 TATTCTTAACTT-ATATTATTAAATATATTA
1 TATTCTTATCTTAAT-TTATTACATA-ATTA
* *
2600787 TATTCTTACCTTAAATTATTAAACATAATTA
1 TATTCTTATCTTAATTTATT--ACATAATTA
*
2600818 -ATTCTTATTTTAA
1 TATTCTTATCTTAA
2600831 CTTAAAACAC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.03
30 50 0.81
31 6 0.10
32 4 0.06
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.52
Consensus pattern (29 bp):
TATTCTTATCTTAATTTATTACATAATTA
Found at i:2600878 original size:30 final size:29
Alignment explanation
Indices: 2600818--2600945 Score: 86
Period size: 31 Copynumber: 4.4 Consensus size: 29
2600808 AACATAATTA
* * * *
2600818 ATTCTTATTTTAACTTAAAACACATCTTTT
1 ATTCTTATCTTAACTAAAAAAATAT-TTTT
2600848 ATTCTTATCTTAACTTAAAAAAATATTTTT
1 ATTCTTATCTTAAC-TAAAAAAATATTTTT
* * *
2600878 ATT-TTAAC-T-AC-AGAAATATA-TTTT
1 ATTCTTATCTTAACTAAAAAAATATTTTT
* * *
2600902 ATTTTTATCTTAACTACAAAAAACATATTAT
1 ATTCTTATCTTAACTA-AAAAAATAT-TTTT
*
2600933 ATTTTTATCTTAA
1 ATTCTTATCTTAA
2600946 ATTTAAAATA
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
24 7 0.09
25 11 0.14
26 1 0.01
27 4 0.05
28 2 0.03
29 9 0.12
30 20 0.26
31 24 0.31
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (29 bp):
ATTCTTATCTTAACTAAAAAAATATTTTT
Found at i:2600879 original size:24 final size:23
Alignment explanation
Indices: 2600847--2600903 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
2600837 ACACATCTTT
*
2600847 TATTCTTATCTTAACTTAAAAAAA
1 TATTTTTATCTTAAC-TAAAAAAA
* * *
2600871 TATTTTTATTTTAACTACAGAAA
1 TATTTTTATCTTAACTAAAAAAA
2600894 TATATTTTAT
1 TAT-TTTTAT
2600904 TTTTATCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTTTTATCTTAACTAAAAAAA
Found at i:2600885 original size:54 final size:56
Alignment explanation
Indices: 2600822--2600930 Score: 136
Period size: 54 Copynumber: 2.0 Consensus size: 56
2600812 TAATTAATTC
* *
2600822 TTATTTTAACTTA-A-AACACATCTTTTATTCTTATCTTAACT-TAAAAAA-ATATTT
1 TTATTTTAAC-TACAGAA-ACATATTTTATTCTTATCTTAACTACAAAAAACATATTT
* *
2600876 TTATTTTAACTACAGAAATATATTTTATTTTTATCTTAACTACAAAAAACATATT
1 TTATTTTAACTACAGAAACATATTTTATTCTTATCTTAACTACAAAAAACATATT
2600931 ATATTTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 2 0.04
54 32 0.68
55 8 0.17
56 5 0.11
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (56 bp):
TTATTTTAACTACAGAAACATATTTTATTCTTATCTTAACTACAAAAAACATATTT
Found at i:2600936 original size:31 final size:30
Alignment explanation
Indices: 2600870--2600945 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
2600860 ACTTAAAAAA
* * *
2600870 ATATTTTTATTTTAACTACAGAAATATATT
1 ATATTTTTATCTTAACTACAAAAACATATT
*
2600900 TTATTTTTATCTTAACTACAAAAAACATATT
1 ATATTTTTATCTTAACTAC-AAAAACATATT
2600931 ATATTTTTATCTTAA
1 ATATTTTTATCTTAA
2600946 ATTTAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.50
Consensus pattern (30 bp):
ATATTTTTATCTTAACTACAAAAACATATT
Found at i:2601040 original size:30 final size:30
Alignment explanation
Indices: 2600967--2601092 Score: 105
Period size: 30 Copynumber: 4.2 Consensus size: 30
2600957 TATCATAATG
* * *
2600967 AAATATAAATATTTAAGTTAAGATAAGAAT-
1 AAATATATAT-TTTAAATTAAAATAAGAATA
* * * *
2600997 AATTATATTTTTTAATTTAAAATAAGATTA
1 AAATATATATTTTAAATTAAAATAAGAATA
* *
2601027 AAATATATATTTTAAAATAAAATAAAAATA
1 AAATATATATTTTAAATTAAAATAAGAATA
** *
2601057 AAATATAT-TTTTCGATTATCAA-AAGAATA
1 AAATATATATTTTAAATTA-AAATAAGAATA
2601086 AAATATA
1 AAATATA
2601093 ATTAATAAGT
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
29 36 0.47
30 41 0.53
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
AAATATATATTTTAAATTAAAATAAGAATA
Found at i:2601122 original size:25 final size:23
Alignment explanation
Indices: 2601085--2601149 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
2601075 TCAAAAGAAT
2601085 AAAATATAATTAATAAGTTAAGATA
1 AAAATATAATTAAT-A-TTAAGATA
** *
2601110 AAAATATTTTTAATATTAAGATGT
1 AAAATATAATTAATATTAAGAT-A
2601134 AAAAT-TAATTCAATAT
1 AAAATATAATT-AATAT
2601150 GTGAATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 10 0.30
24 11 0.33
25 12 0.36
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (23 bp):
AAAATATAATTAATATTAAGATA
Found at i:2627523 original size:15 final size:15
Alignment explanation
Indices: 2627505--2627533 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2627495 TTAAATTTAT
2627505 TTTCAATTTTATTTG
1 TTTCAATTTTATTTG
2627520 TTTCAATTTTATTT
1 TTTCAATTTTATTT
2627534 ATTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTCAATTTTATTTG
Found at i:2631861 original size:44 final size:44
Alignment explanation
Indices: 2631812--2631938 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
2631802 TTAAATATTA
2631812 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
**
2631856 TATTTTAAT-TAAGTTTTAGG-A---TA--TT--AT---TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
*
2631888 TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
2631932 TATTTTA
1 TATTTTA
2631939 ATTAGGATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
31 2 0.03
32 14 0.22
33 6 0.09
36 4 0.06
38 4 0.06
40 4 0.06
43 6 0.09
44 22 0.34
45 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (44 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
Found at i:2631903 original size:76 final size:75
Alignment explanation
Indices: 2631809--2632024 Score: 326
Period size: 76 Copynumber: 2.9 Consensus size: 75
2631799 ATTTTAAATA
*
2631809 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
2631874 GGATATTATTT
66 GGATATTA-TT
* *
2631885 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
2631950 GGATATTATT
66 GGATATTATT
* * * * * *
2631960 TTAAATATTATTTTTGTTTTAGGTATTTTAGTTTATATA-GTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTT
2632024 A
65 A
2632025 AGATGTTTTA
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 5 0.04
75 55 0.42
76 70 0.54
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.58
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GGATATTATT
Found at i:2643015 original size:39 final size:39
Alignment explanation
Indices: 2642972--2643076 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
2642962 TTCAAAAAAT
2642972 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
* ** *
2643011 AATTTGGAATGTT-ATGGTGGTA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTAAT-GTGAAATAATTTAAGAAATTAAG
*
2643049 AATTTTGAATGTTAGA-GTGAAATAATTT
1 AATTTAGAATGTTA-ATGTGAAATAATTT
2643077 GAGATTTTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
38 33 0.60
39 21 0.38
40 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:2645918 original size:17 final size:17
Alignment explanation
Indices: 2645898--2645947 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
2645888 ACTCGAGCTC
2645898 GATTCAAGCTCGAACTT
1 GATTCAAGCTCGAACTT
2645915 GATTCAAGCTCGAACTT
1 GATTCAAGCTCGAACTT
*
2645932 GATTCAAGCTCAAACT
1 GATTCAAGCTCGAACT
2645948 CGAATTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (17 bp):
GATTCAAGCTCGAACTT
Found at i:2651998 original size:6 final size:6
Alignment explanation
Indices: 2651987--2652013 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2651977 GACACGTATT
2651987 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
2652014 TGAGACGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2658725 original size:31 final size:31
Alignment explanation
Indices: 2658689--2658889 Score: 192
Period size: 31 Copynumber: 6.4 Consensus size: 31
2658679 TCTTCCGGGG
*
2658689 ACATATGGACAGTATAACTATGTTCTACGGA
1 ACATATGGACAGTATACCTATGTTCTACGGA
* * *
2658720 ACATATGGAGAGAATTACCTATG-TCTTTCAGG-
1 ACATATGGACAGTA-TACCTATGTTC-TAC-GGA
2658752 ACATATGGACAGTATACCTATGTTCTACGGA
1 ACATATGGACAGTATACCTATGTTCTACGGA
* ** *
2658783 ACATATGGACAGAATTACCTATG-TCTTTTGGG
1 ACATATGGACAGTA-TACCTATGTTC-TACGGA
**
2658815 ACATATGGACAGTATACCTATGTTCTAAAGA
1 ACATATGGACAGTATACCTATGTTCTACGGA
* * * * *
2658846 ACATATGGACAATTTACCTAGGTTCTTCGGG
1 ACATATGGACAGTATACCTATGTTCTACGGA
*
2658877 ACCTATGGACAGT
1 ACATATGGACAGT
2658890 TGCCGAGGTT
Statistics
Matches: 137, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.01
31 84 0.61
32 49 0.36
33 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTTCTACGGA
Found at i:2658766 original size:63 final size:63
Alignment explanation
Indices: 2658666--2658889 Score: 326
Period size: 63 Copynumber: 3.6 Consensus size: 63
2658656 CAAGAGTCGA
* * *
2658666 AGAATTACCTATGTCTTCCGGGGACATATGGACAGTATAACTATGTTCTACGGAACATATGGAG
1 AGAATTACCTATGTCTTTC-GGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
*
2658730 AGAATTACCTATGTCTTTCAGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* **
2658793 AGAATTACCTATGTCTTTTGGGACATATGGACAGTATACCTATGTTCTAAAGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* * *
2658856 A-ATTTACCTAGGT-TCTTCGGGACCTATGGACAGT
1 AGAATTACCTATGTCT-TTCGGGACATATGGACAGT
2658890 TGCCGAGGTT
Statistics
Matches: 147, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
61 1 0.01
62 27 0.18
63 101 0.69
64 18 0.12
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (63 bp):
AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
Found at i:2662433 original size:31 final size:31
Alignment explanation
Indices: 2662398--2662580 Score: 138
Period size: 31 Copynumber: 5.8 Consensus size: 31
2662388 GTCTTTCGGG
2662398 ACATATGAACAGTATACCTATGTTCTACGGA
1 ACATATGAACAGTATACCTATGTTCTACGGA
* * * *
2662429 ACATATGGATAAAAT-TACCTATG-TCTTTCGGG
1 ACATAT-GA-ACAGTATACCTATGTTC-TACGGA
*
2662461 ACATATGAACAGTATACCTATGTTCTACGAA
1 ACATATGAACAGTATACCTATGTTCTACGGA
* * * *
2662492 ACATATGGACAGAATTACCTATG-TCTTTCGGG
1 ACATATGAACAGTA-TACCTATGTTC-TACGGA
* * * **
2662524 ACATATGGACAATATACCTATCTTCTAAAGA
1 ACATATGAACAGTATACCTATGTTCTACGGA
* * * *
2662555 ACGTATGGACAGTTTACCTAGGTTCT
1 ACATATGAACAGTATACCTATGTTCT
2662581 TTGGGACCTA
Statistics
Matches: 118, Mismatches: 26, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
30 3 0.03
31 65 0.55
32 47 0.40
33 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (31 bp):
ACATATGAACAGTATACCTATGTTCTACGGA
Found at i:2662451 original size:32 final size:32
Alignment explanation
Indices: 2662412--2662565 Score: 127
Period size: 32 Copynumber: 4.9 Consensus size: 32
2662402 ATGAACAGTA
*
2662412 TACCTATGTTCTACGGAACATATGGATAAAAT
1 TACCTATGTTCTACGGAACATATGGACAAAAT
* * * **
2662444 TACCTATG-TCTTTCGGGACATATGAACAGTA-
1 TACCTATGTTC-TACGGAACATATGGACAAAAT
* *
2662475 TACCTATGTTCTACGAAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAAAAT
* * *
2662507 TACCTATG-TCTTTCGGGACATATGGACAATA-
1 TACCTATGTTC-TACGGAACATATGGACAAAAT
* ** *
2662538 TACCTATCTTCTAAAGAACGTATGGACA
1 TACCTATGTTCTACGGAACATATGGACA
2662566 GTTTACCTAG
Statistics
Matches: 95, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
31 46 0.48
32 49 0.52
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (32 bp):
TACCTATGTTCTACGGAACATATGGACAAAAT
Found at i:2662456 original size:63 final size:63
Alignment explanation
Indices: 2662378--2662550 Score: 283
Period size: 63 Copynumber: 2.7 Consensus size: 63
2662368 AGAGTCAAAG
* * *
2662378 AATTACTTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTACGGAACATATGGATAA
1 AATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTACGAAACATATGGACAA
*
2662441 AATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTACGAAACATATGGACAG
1 AATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTACGAAACATATGGACAA
* * *
2662504 AATTACCTATGTCTTTCGGGACATATGGACAATATACCTATCTTCTA
1 AATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTA
2662551 AAGAACGTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 103 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (63 bp):
AATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTACGAAACATATGGACAA
Found at i:2662562 original size:63 final size:63
Alignment explanation
Indices: 2662376--2662602 Score: 282
Period size: 63 Copynumber: 3.6 Consensus size: 63
2662366 CAAGAGTCAA
* ** *
2662376 AGAATTACTTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTACGGAACATATGGAT
1 AGAATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTAAAGAACATATGGAC
* *
2662439 AAAATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCT-ACGAAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTAAAG-AACATATGGAC
* * * *
2662502 AGAATTACCTATGTCTTTCGGGACATATGGACAATATACCTATCTTCTAAAGAACGTATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTAAAGAACATATGGAC
* * * *
2662565 AG-TTTACCTAGGTTCTTT-GGGACCTATGGACAGT-TACC
1 AGAATTACCTATG-TCTTTCGGGACATATGAACAGTATACC
2662603 GAGGTTCTTT
Statistics
Matches: 146, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
61 4 0.03
62 23 0.16
63 117 0.80
64 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (63 bp):
AGAATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTAAAGAACATATGGAC
Found at i:2662619 original size:30 final size:31
Alignment explanation
Indices: 2662558--2662624 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
2662548 CTAAAGAACG
* *
2662558 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
*
2662589 TATGGACAG-TTACCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
*
2662619 TCTGGA
1 TATGGA
2662625 TAGGTCCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:2665454 original size:17 final size:17
Alignment explanation
Indices: 2665426--2665475 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
2665416 GGAGTTGTTG
*
2665426 TGGTTA-GGTTGTTAGT
1 TGGTTAGGGTTGTTAGC
2665442 TGGTTAGGGTTGTTAGC
1 TGGTTAGGGTTGTTAGC
2665459 TGGTTAGGGTTGTTAGC
1 TGGTTAGGGTTGTTAGC
2665476 AGTCATGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 6 0.19
17 26 0.81
ACGTcount: A:0.12, C:0.04, G:0.40, T:0.44
Consensus pattern (17 bp):
TGGTTAGGGTTGTTAGC
Found at i:2666229 original size:21 final size:20
Alignment explanation
Indices: 2666188--2666234 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
2666178 GGATTTATTT
2666188 TATTTTTATTTTATAAATTA
1 TATTTTTATTTTATAAATTA
*
2666208 TCTTTTTATTTT-TAAATGTTA
1 TATTTTTATTTTATAAA--TTA
2666229 TATTTT
1 TATTTT
2666235 AGGCTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 11 0.48
21 8 0.35
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTTTATTTTATAAATTA
Found at i:2674137 original size:21 final size:21
Alignment explanation
Indices: 2674113--2674152 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2674103 TCCAAACATT
2674113 TTGATTATCAGTCGTCCAAAA
1 TTGATTATCAGTCGTCCAAAA
2674134 TTGATTATCAGTCGTCCAA
1 TTGATTATCAGTCGTCCAA
2674153 CATAATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (21 bp):
TTGATTATCAGTCGTCCAAAA
Found at i:2674626 original size:5 final size:5
Alignment explanation
Indices: 2674616--2674641 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2674606 AACCTTAACA
2674616 AGGCC AGGCC AGGCC AGGCC AGGCC A
1 AGGCC AGGCC AGGCC AGGCC AGGCC A
2674642 TGCATACTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.38, T:0.00
Consensus pattern (5 bp):
AGGCC
Found at i:2680967 original size:3 final size:3
Alignment explanation
Indices: 2680961--2680992 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2680951 AAAAATCAAT
*
2680961 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2680993 TCATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:2681201 original size:20 final size:21
Alignment explanation
Indices: 2681166--2681204 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2681156 TTTGGTGTTG
*
2681166 AAAACATTAATAATGTTGAAA
1 AAAAAATTAATAATGTTGAAA
2681187 AAAAAATTAAT-ATGTTGA
1 AAAAAATTAATAATGTTGA
2681205 TTGTCTGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAAATTAATAATGTTGAAA
Found at i:2682134 original size:47 final size:46
Alignment explanation
Indices: 2682064--2682177 Score: 115
Period size: 47 Copynumber: 2.4 Consensus size: 46
2682054 AAACGGAGAT
* * *
2682064 ATCAGAAATCAAAACAGATTTCAGATCA-GATATCAGAA-AGAATCTA
1 ATCAGAAATC-AAACAAAATTCAGATAATG-TATCAGAACAGAATCTA
* *
2682110 GATCAGAAATCGAAACAAAATTCAGGTAATGTATCAGAACAGAATTTA
1 -ATCAGAAATC-AAACAAAATTCAGATAATGTATCAGAACAGAATCTA
*
2682158 AGTCAGAAATCAAATAAAAT
1 A-TCAGAAATCAAACAAAAT
2682178 ATTTATATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
47 40 0.70
48 17 0.30
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (46 bp):
ATCAGAAATCAAACAAAATTCAGATAATGTATCAGAACAGAATCTA
Done.