Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001577.1 Hibiscus syriacus cultivar Beakdansim tig00003137_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: 426047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:220067 original size:42 final size:40
Alignment explanation
Indices: 220005--220090 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 40
219995 AATTCATCAA
* * *
220005 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 TAAGTCTTTCGAGCAAGATGAT-AAATCCTCCGGGCCATTT
* *
220046 GTAAGTCTTTTGAGCAAGATGATAAGTCCTCCGGGCCATTT
1 -TAAGTCTTTCGAGCAAGATGATAAATCCTCCGGGCCATTT
220087 TAAG
1 TAAG
220091 CCTTCTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.10
41 15 0.38
42 20 0.51
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (40 bp):
TAAGTCTTTCGAGCAAGATGATAAATCCTCCGGGCCATTT
Found at i:220708 original size:161 final size:159
Alignment explanation
Indices: 220464--220775 Score: 516
Period size: 161 Copynumber: 1.9 Consensus size: 159
220454 AAATCGCACC
* *
220464 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTC
1 AGAAGATTGTTCAAGTTCTACTCCATGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTC
* *
220529 GAGTTCTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAAGCAGAAGATTGTTCGAGTTCTACTCC
66 GAGTTCTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAAGCAGAAGATTGTTCAAGTTCTACTCA
* *
220594 CTGAAGCAAGAGTGAGTGAACTCGTAAGT
131 CTGAAGCAAGAGGGAGAGAACTCGTAAGT
* *
220623 AGAAGATTGTTCAAGTTCTACACTCCATTAAGCAAGAGGGAGCGAACCCGTAGGCAGAGGATTGT
1 AGAAGATTGTTCAAGTTCT--ACTCCATGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGT
* *
220688 TCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTCAAGTTCTACT
64 TCGAGTTCTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAAGCAGAAGATTGTTCAAGTTCTACT
220753 CACTGAAGCAAGAGGGAGAGAAC
129 CACTGAAGCAAGAGGGAGAGAAC
220776 CCCCTGGTCG
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
159 18 0.13
161 123 0.87
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (159 bp):
AGAAGATTGTTCAAGTTCTACTCCATGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTC
GAGTTCTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAAGCAGAAGATTGTTCAAGTTCTACTCA
CTGAAGCAAGAGGGAGAGAACTCGTAAGT
Found at i:220797 original size:53 final size:53
Alignment explanation
Indices: 220463--220777 Score: 468
Period size: 53 Copynumber: 5.9 Consensus size: 53
220453 AAAATCGCAC
220463 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
220516 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
220569 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGTGAGTGAACTCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
220622 TAGAAGATTGTTCAAGTTCTACACTCCATTAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCT--ACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* *
220677 CAGAGGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
220730 CAGAAGATTGTTCAAGTTCTACTCACTGAAGCAAGAGGGAGAGAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
220778 CCTGGTCGAA
Statistics
Matches: 234, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
53 190 0.81
55 44 0.19
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:220957 original size:9 final size:9
Alignment explanation
Indices: 220943--221024 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
220933 TTTGTCTGGG
220943 ATTTTTATT
1 ATTTTTATT
220952 ATTTTTATT
1 ATTTTTATT
* *
220961 GTTTTATTTT
1 ATTTT-TATT
220971 ATTTTTATT
1 ATTTTTATT
* *
220980 ATTATAATT
1 ATTTTTATT
**
220989 ATTAATATT
1 ATTTTTATT
*
220998 ATATATTAATTT
1 AT-T-TTTA-TT
*
221010 AATTTTATT
1 ATTTTTATT
221019 ATTTTT
1 ATTTTT
221025 TAGGTCATTA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
9 39 0.71
10 11 0.20
11 2 0.04
12 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (9 bp):
ATTTTTATT
Found at i:220983 original size:3 final size:3
Alignment explanation
Indices: 220947--221005 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
220937 TCTGGGATTT
* * * *
220947 TTA TTA TTT TTA TTG TT- TTA TT- TTA TTT TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
220993 ATA TTA TATA TTA
1 TTA TTA T-TA TTA
221006 ATTTAATTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:224775 original size:18 final size:18
Alignment explanation
Indices: 224752--224792 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
224742 TAATGCAAAT
224752 CAAGTTAAAAGCGAACTA
1 CAAGTTAAAAGCGAACTA
224770 CAAGTTAAAAGCGAACTA
1 CAAGTTAAAAGCGAACTA
224788 CAAGT
1 CAAGT
224793 CACAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
CAAGTTAAAAGCGAACTA
Found at i:226318 original size:12 final size:12
Alignment explanation
Indices: 226301--226326 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
226291 GGACTTTTTC
226301 TCCCTCTTCTCT
1 TCCCTCTTCTCT
226313 TCCCTCTTCTCT
1 TCCCTCTTCTCT
226325 TC
1 TC
226327 TGAGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (12 bp):
TCCCTCTTCTCT
Found at i:226427 original size:40 final size:40
Alignment explanation
Indices: 226367--226512 Score: 256
Period size: 40 Copynumber: 3.6 Consensus size: 40
226357 AAAAAAACAG
* *
226367 TAATATCATATATGCAATAATCAAAAAATAATAATCAAAA
1 TAATCTCATATATGCAATAATCAAAAAACAATAATCAAAA
226407 TAATCTCATATATGCAATAATCAAAAAACAATAATCAAAA
1 TAATCTCATATATGCAATAATCAAAAAACAATAATCAAAA
**
226447 TAATCTCATATATGCAATAATCAAAATCCAATAATCAAAA
1 TAATCTCATATATGCAATAATCAAAAAACAATAATCAAAA
226487 TAATCTCATATATGCAATAATCAAAA
1 TAATCTCATATATGCAATAATCAAAA
226513 CTTACAATTT
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.27
Consensus pattern (40 bp):
TAATCTCATATATGCAATAATCAAAAAACAATAATCAAAA
Found at i:226480 original size:14 final size:13
Alignment explanation
Indices: 226381--226487 Score: 62
Period size: 14 Copynumber: 8.0 Consensus size: 13
226371 ATCATATATG
226381 CAATAATCAAAAAAT
1 CAATAATC--AAAAT
226396 -AATAATCAAAAT
1 CAATAATCAAAAT
* *
226408 -AAT-CTCATATAT
1 CAATAATCA-AAAT
*
226420 GCAATAATCAAAAAA
1 -CAATAATC-AAAAT
226435 CAATAATCAAAAT
1 CAATAATCAAAAT
* *
226448 -AAT-CTCATATAT
1 CAATAATCA-AAAT
226460 GCAATAATCAAAAT
1 -CAATAATCAAAAT
226474 CCAATAATCAAAAT
1 -CAATAATCAAAAT
226488 AATCTCATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
11 6 0.08
12 17 0.24
13 4 0.06
14 37 0.51
15 7 0.10
16 1 0.01
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (13 bp):
CAATAATCAAAAT
Found at i:226839 original size:23 final size:22
Alignment explanation
Indices: 226813--226859 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
226803 ATAAAGTACA
*
226813 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGC-TAT
**
226836 ATAATGTAATAGGTAGCGCTAT
1 ATAACATAATAGGTAGCGCTAT
226858 AT
1 AT
226860 TTACGTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (22 bp):
ATAACATAATAGGTAGCGCTAT
Found at i:227640 original size:23 final size:23
Alignment explanation
Indices: 227614--227676 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
227604 ATATAACCAC
227614 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
227637 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
227660 TACCTATTACATCATAT
1 TACCTATTACATTATAT
227677 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:228125 original size:38 final size:38
Alignment explanation
Indices: 228076--228154 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
228066 AGTTGTAGAT
*
228076 TTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGGA
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGA
* *
228114 TTTGATTTCCTTTTGTTTGGCACCATATGAGCTTTGGA
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGA
228152 TTT
1 TTT
228155 TGATGAGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.49
Consensus pattern (38 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGA
Found at i:228438 original size:18 final size:18
Alignment explanation
Indices: 228415--228451 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
228405 GCCGAAATAT
228415 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
228433 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
228451 A
1 A
228452 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:229098 original size:21 final size:22
Alignment explanation
Indices: 229073--229124 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
229063 ACACTTTACA
*
229073 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
229096 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
229119 ATATAA
1 ATATAA
229125 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:229109 original size:23 final size:23
Alignment explanation
Indices: 229083--229145 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
229073 ATATAACCAC
229083 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
229106 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
229129 TACCTATTACATCATAT
1 TACCTATTACATTATAT
229146 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:230096 original size:197 final size:199
Alignment explanation
Indices: 229751--231106 Score: 2490
Period size: 195 Copynumber: 6.9 Consensus size: 199
229741 TTTAAATTAG
* *
229751 TATCGACACAAACTATATTAGTGTCGACACATTTTTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
229816 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
229881 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
229945 CAAA
196 CAAA
*** *
229949 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230013 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
230078 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230143 CAAA
196 CAAA
*
230147 TATCGACACAAACTGTATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230212 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
230277 CGACAC-TTTT-TATATGGAACGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230340 CAAA
196 CAAA
230344 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230408 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
230472 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230535 CAAA
196 CAAA
*
230539 TATCGACAC-AACTATATTAGTGTCGAGACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230603 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
230668 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230733 CAAA
196 CAAA
230737 TATCGACACAAACTATA-TAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230799 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
230863 CGACACTTGTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230928 CAAA
196 CAAA
230932 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230997 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
231061 CGACACTTTGTTATATA-GGATCGACACTTTATGGGTGCACCCTGTT
131 CGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCCTGTT
231107 GGCCATATTG
Statistics
Matches: 1130, Mismatches: 17, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
195 284 0.25
196 225 0.20
197 278 0.25
198 208 0.18
199 135 0.12
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
CAAA
Found at i:230550 original size:195 final size:198
Alignment explanation
Indices: 229751--231106 Score: 2468
Period size: 197 Copynumber: 6.9 Consensus size: 198
229741 TTTAAATTAG
* *
229751 TATCGACACAAACTATATTAGTGTCGACACATTTTTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
229816 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
229881 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
229945 CAAA
195 CAAA
*** *
229949 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTAAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230013 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
230078 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230143 CAAA
195 CAAA
*
230147 TATCGACACAAACTGTATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230212 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
230277 CGACACTTTT-TATATGGAACGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAC
131 CGACACTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAC
230341 AAA
196 AAA
230344 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230408 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
230472 CGACACTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAC
131 CGACACTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAC
230536 AAA
196 AAA
*
230539 TATCGACAC-AACTATATTAGTGTCGAGACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230603 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
230668 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230733 CAAA
195 CAAA
230737 TATCGACACAAACTATA-TAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230799 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
230863 CGACACTTGTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
131 CGACACTT-TTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
230928 CAAA
195 CAAA
230932 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
230997 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
231061 CGACACTTTGT-TATATAGGATCGACACTTTATGGGTGCACCCTGTT
131 CGACACTTT-TATATAT-GGATCGACACTTTATGGGTGCACCCTGTT
231107 GGCCATATTG
Statistics
Matches: 1130, Mismatches: 15, Indels: 26
0.96 0.01 0.02
Matches are distributed among these distances:
194 2 0.00
195 282 0.25
196 225 0.20
197 284 0.25
198 209 0.18
199 128 0.11
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAC
AAA
Found at i:231246 original size:17 final size:17
Alignment explanation
Indices: 231224--231266 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
231214 ATTATATCAC
231224 ATACAAAAATAAATCGT
1 ATACAAAAATAAATCGT
* *
231241 ATACAAATTATAAATCTT
1 ATACAAA-AATAAATCGT
231259 ATACAAAA
1 ATACAAAA
231267 TTAACCCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (17 bp):
ATACAAAAATAAATCGT
Found at i:233095 original size:33 final size:33
Alignment explanation
Indices: 233058--233123 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
233048 CATCTTAATA
* *
233058 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
233091 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
233124 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:233197 original size:21 final size:21
Alignment explanation
Indices: 233157--233221 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
233147 CCCCTTATGC
* *
233157 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
233178 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
233199 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
233220 CT
1 CT
233222 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:235469 original size:17 final size:18
Alignment explanation
Indices: 235447--235489 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
235437 ATATATCCGG
235447 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
235464 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
235484 TATCAT
1 TATCAT
235490 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:235507 original size:20 final size:19
Alignment explanation
Indices: 235452--235498 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
235442 TCCGGTATCA
235452 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
235471 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
235492 TTTTACC
1 TTTTACC
235499 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:235646 original size:20 final size:20
Alignment explanation
Indices: 235620--235665 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
235610 CACTTTTAAA
235620 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
235639 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
235660 TTTACC
1 TTTACC
235666 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:237516 original size:28 final size:27
Alignment explanation
Indices: 237484--237549 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
237474 AATTTTATGA
237484 AAATATAAAAATCAA-GGATCCTAATTAT
1 AAATATAAAAA--AATGGATCCTAATTAT
* *
237512 AAATATAAAAAAATTGGGTGCTAATTAT
1 AAATATAAAAAAA-TGGATCCTAATTAT
237540 AAATATAAAA
1 AAATATAAAA
237550 GAATTCAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.06
28 32 0.94
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATATAAAAAAATGGATCCTAATTAT
Found at i:237758 original size:16 final size:17
Alignment explanation
Indices: 237726--237759 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
237716 AAATAATATT
237726 TTAACTTTTTTATAAAA
1 TTAACTTTTTTATAAAA
*
237743 TTAATTTTTTTA-AAAA
1 TTAACTTTTTTATAAAA
237759 T
1 T
237760 ATATAAACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAACTTTTTTATAAAA
Found at i:241626 original size:21 final size:22
Alignment explanation
Indices: 241602--241642 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
241592 CAACATCCTC
241602 AAGACACC-GGAAATCCCAAAT
1 AAGACACCGGGAAATCCCAAAT
* *
241623 AAGACGCCGGGAGATCCCAA
1 AAGACACCGGGAAATCCCAA
241643 GCAAGACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.41, C:0.29, G:0.22, T:0.07
Consensus pattern (22 bp):
AAGACACCGGGAAATCCCAAAT
Found at i:241648 original size:22 final size:21
Alignment explanation
Indices: 241601--241650 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
241591 CCAACATCCT
241601 CAAGACACCGGAAATCCCAAA
1 CAAGACACCGGAAATCCCAAA
* * * *
241622 TAAGACGCCGGGAGATCCCAAG
1 CAAGACACC-GGAAATCCCAAA
241644 CAAGACA
1 CAAGACA
241651 AAAAAATCTG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.42, C:0.30, G:0.22, T:0.06
Consensus pattern (21 bp):
CAAGACACCGGAAATCCCAAA
Found at i:245252 original size:13 final size:13
Alignment explanation
Indices: 245234--245264 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
245224 CCGGGTCAAG
245234 CTGAGCCAACTCA
1 CTGAGCCAACTCA
*
245247 CTGAGCCAACTCG
1 CTGAGCCAACTCA
245260 CTGAG
1 CTGAG
245265 TCAAACTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (13 bp):
CTGAGCCAACTCA
Found at i:247590 original size:23 final size:23
Alignment explanation
Indices: 247553--247597 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
247543 TAATTATGTC
**
247553 TTTATGACATGTTTATATATATT
1 TTTATGACACATTTATATATATT
*
247576 TTTATGACACATTTATCTATAT
1 TTTATGACACATTTATATATAT
247598 ATTTGATGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (23 bp):
TTTATGACACATTTATATATATT
Found at i:249891 original size:21 final size:22
Alignment explanation
Indices: 249866--249914 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
249856 TTAAACTTAA
*
249866 AAAATAAT-ATTAAATTATTA-T
1 AAAATAATCATTAAAAT-TTATT
249887 AAAATAATCATTAAAATTTATT
1 AAAATAATCATTAAAATTTATT
249909 AAAATA
1 AAAATA
249915 TAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAATCATTAAAATTTATT
Found at i:249910 original size:32 final size:32
Alignment explanation
Indices: 249873--249959 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 32
249863 TAAAAAATAA
*
249873 TATTAAATTATTATAAAATAATCATTAAAATT
1 TATTAAATTATTATAAAATAATCAATAAAATT
* * * **
249905 TATTAAAATATAAAAAAAT-ATCAATAATTTT
1 TATTAAATTATTATAAAATAATCAATAAAATT
* *
249936 TATCAAATTATTATAAAACAATCA
1 TATTAAATTATTATAAAATAATCA
249960 GTAATATTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
31 23 0.53
32 20 0.47
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (32 bp):
TATTAAATTATTATAAAATAATCAATAAAATT
Found at i:249917 original size:24 final size:20
Alignment explanation
Indices: 249865--249917 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 20
249855 GTTAAACTTA
249865 AAAAATAATATTAAATTATT
1 AAAAATAATATTAAATTATT
249885 ATAAAATAATCATTAAAATTTATT
1 A-AAAATAAT-ATT-AAA-TTATT
249909 AAAATATAA
1 AAAA-ATAA
249918 AAAAATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 3 0.11
23 6 0.21
24 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATAATATTAAATTATT
Found at i:250029 original size:30 final size:29
Alignment explanation
Indices: 249994--250061 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
249984 TATAATATCA
* *
249994 TAATAATTATTGTATAATAATTT-AAAATTT
1 TAATAATAATTGTATAAT--TTTAAAAAATT
*
250024 TAATAATAATTTTATAATTTTAAAAAATT
1 TAATAATAATTGTATAATTTTAAAAAATT
250053 TAATAATAA
1 TAATAATAA
250062 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 3 0.09
29 15 0.44
30 16 0.47
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
TAATAATAATTGTATAATTTTAAAAAATT
Found at i:250031 original size:19 final size:19
Alignment explanation
Indices: 250007--250055 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
249997 TAATTATTGT
250007 ATAATAATTTAAAATTTTA
1 ATAATAATTTAAAATTTTA
*
250026 ATAATAATTTTATAATTTTA
1 ATAATAA-TTTAAAATTTTA
250046 A-AA-AATTTAA
1 ATAATAATTTAA
250056 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 2 0.07
19 9 0.33
20 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATAATTTAAAATTTTA
Found at i:251175 original size:31 final size:32
Alignment explanation
Indices: 251140--251203 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
251130 ATAGTGTTGT
*
251140 TTTGGTTTATGAAGGTGG-AGAGAGGGATTGA
1 TTTGGTGTATGAAGGTGGAAGAGAGGGATTGA
* * *
251171 TTTGGTGTATGGAGGTGGAAGCGTGGGATTGA
1 TTTGGTGTATGAAGGTGGAAGAGAGGGATTGA
251203 T
1 T
251204 GGGTCTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.33
Consensus pattern (32 bp):
TTTGGTGTATGAAGGTGGAAGAGAGGGATTGA
Found at i:253950 original size:10 final size:10
Alignment explanation
Indices: 253935--253972 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
253925 ATCCTAATCA
253935 AATTTATTTT
1 AATTTATTTT
253945 AATTTATTTT
1 AATTTATTTT
*
253955 AATCTA-TTT
1 AATTTATTTT
*
253964 GATTTATTT
1 AATTTATTT
253973 GTGTATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (10 bp):
AATTTATTTT
Found at i:254543 original size:27 final size:27
Alignment explanation
Indices: 254512--254573 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
254502 TTTAACATTT
** *
254512 CCGGTAAAGTGCCTAACAATAACAAAA
1 CCGGTAAAGCACCCAACAATAACAAAA
* *
254539 TCGGTAAAGCACCCAATAATAACAAAA
1 CCGGTAAAGCACCCAACAATAACAAAA
254566 CCGGTAAA
1 CCGGTAAA
254574 AATAATAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.15
Consensus pattern (27 bp):
CCGGTAAAGCACCCAACAATAACAAAA
Found at i:255707 original size:17 final size:17
Alignment explanation
Indices: 255685--255717 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
255675 AAAAACATAA
*
255685 GTATATCAATCAATATG
1 GTATATCAAACAATATG
255702 GTATATCAAACAATAT
1 GTATATCAAACAATAT
255718 AGTAATTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (17 bp):
GTATATCAAACAATATG
Found at i:261606 original size:18 final size:18
Alignment explanation
Indices: 261583--261628 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
261573 GCCCAAATCT
261583 CAATACTTTCTTTCAAGG
1 CAATACTTTCTTTCAAGG
261601 CAATACTTTCTTTCAAGG
1 CAATACTTTCTTTCAAGG
*
261619 CGATACTTTC
1 CAATACTTTC
261629 AGAAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (18 bp):
CAATACTTTCTTTCAAGG
Found at i:270866 original size:13 final size:13
Alignment explanation
Indices: 270848--270876 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
270838 ATTTGGGGGC
270848 ATGCCAAATGAAG
1 ATGCCAAATGAAG
270861 ATGCCAAATGAAG
1 ATGCCAAATGAAG
270874 ATG
1 ATG
270877 TCCTGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.17
Consensus pattern (13 bp):
ATGCCAAATGAAG
Found at i:277565 original size:24 final size:24
Alignment explanation
Indices: 277519--277565 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
277509 TGTTCCCCAT
* *
277519 CCTGCCACTGAAGATGCTCACCAG
1 CCTGCCACTGAAGAGGCTAACCAG
* *
277543 CCTGCCAGTGAAGAGGTTAACCA
1 CCTGCCACTGAAGAGGCTAACCA
277566 ACCTACCGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (24 bp):
CCTGCCACTGAAGAGGCTAACCAG
Found at i:282521 original size:13 final size:13
Alignment explanation
Indices: 282503--282531 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
282493 CACCGTTGCG
282503 GCCAAAAATTGAA
1 GCCAAAAATTGAA
282516 GCCAAAAATTGAA
1 GCCAAAAATTGAA
282529 GCC
1 GCC
282532 CTTGCACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (13 bp):
GCCAAAAATTGAA
Found at i:283847 original size:14 final size:14
Alignment explanation
Indices: 283828--283857 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
283818 GCATTTATTA
283828 ATTATTTTAAATAC
1 ATTATTTTAAATAC
283842 ATTATTTTAAATAC
1 ATTATTTTAAATAC
283856 AT
1 AT
283858 CTCTAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATTTTAAATAC
Found at i:292182 original size:233 final size:232
Alignment explanation
Indices: 291761--294070 Score: 2103
Period size: 233 Copynumber: 9.9 Consensus size: 232
291751 AAGAAAAATG
*
291761 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* *
291826 ACCTAGTAAACTATTTCCAAAATTTATAAG-TCATTCGGGTCATCAGTAAGTCTTTTGAGCATGA
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTTC-TTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * *
291890 TGCTTAAATCATTCGGGTCATCTGTATGTCATTCGAGCAAGATGATAAGT-CTATCGGGCCATCC
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCT-TCGGGCCATCC
* *
291954 ATAAGACCTTCGGGCATAATTTTTTCACGTGTCTCTCAAA
194 ATAAGACCTTCGGGCA-AATGTTTTCACATGTCTCTCAAA
* ***
291994 AAAAGAGAAATAATTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* * * *
292059 ACTTAGTAAACTATTTCTAAAATTTATAAGTTCTTTGGGCCATCAGTAAGTCTTTCAAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * *
292124 GCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGCAAGATGATAAATCCTTCGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
* * * *
292189 AAGACCTTCGGGCAGGATATTTTTACATGTCTCTCGAA
196 AAGACCTTCGGGCA-AATGTTTTCACATGTCTCTCAAA
*
292227 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTCTGAAAAGTAAGAAATGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* * * *
292292 ACCCAGTAAACTACTTCCAAAATTTATAAG-TCTTTCGGGCCATTAGTAAGTCTTTTGAGCATGA
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTTC-TTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * * *
292356 TGCTTACATCATTCAGGTCATCTTTAAGTCTTTCGAGCAAGATGATAAGCCCTTCGGGCCATCCA
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* * *
292421 TAAGACCTTCGGGGAAGATGTTTCCACATGTTTCTCAAA
195 TAAGACCTTCGGGCAA-ATGTTTTCACATGTCTCTCAAA
** * * * * * * * *
292460 AAAAAATAAAGGTTTTTTATTTAAATCTAAAAATTGAAATTTTTGAATAGTGAGAAAGGTTTATT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* * *
292525 ACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTTGGGCCATCCGTAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* *
292590 TCTTAAATCCTTCGGGTCTTCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
* *
292655 AAGACATTCGGGTAAGATGTTTTCACATGTCTCTCAAA
196 AAGACCTTCGGGCAA-ATGTTTTCACATGTCTCTCAAA
* * * *
292693 AAATGAGAAAGATTTCTTATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAATATTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* * * * *
292758 ACCTTGTAAACTATTTCCAAAATTTATAAGTTATTCGGGTCATTAGTAAGTCTTTTGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * *
292823 GCTTAAGTTCATCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGG-----C--
131 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
**
292881 ---A------GG---ATGTTTTCACACATCTCTCAAA
196 AAGACCTTCGGGCAAATGTTTTCACATGTCTCTCAAA
* * *
292906 AAATGAGAAAGGTTTCTCATTTAAATATGAAAAATTGAAAATTATT-AAAAGTAAGAAAAGTTTC
1 AAATGAGAAAGGTTTCTCATTTAAATCTG-AAAATTG-AAATTTTTGAAAAGTAAGAAATGTTTC
* * * * * * * *
292970 TTACTTAGTAAACTA--T-GAAAATTAAGAAAAGTTTCTT----AC-TTAGTAAACTATTTTC-A
64 TTACCTAGTAAACTATTTCCAAAATT--TATAAG-TTCTTCGGGCCATCAGT-AAGT-CTTTCGA
* * * * * ** * * * * * * *
293026 --AAGTTG-GTAACTACTTCGGGAAATCAGTAAGTCTTTTGAGCATGATGCTTAAATCATTTGGG
124 GCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG-ATAAGTCCTTCGGG
* ** * * * * *
293088 TCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTC-GA-GCCATC-CATAA
188 CCATCCATAAGACCTTCGGGC-A-A--AT--GT-TTTCACATGTC-TCTCA-AA
** * * * ** *
293139 GACCTTCGAGCATGATGTTTTCACATATCTCTCGAAAAATGAGAAAGGTTTCTCATTTAAATCTG
1 -A-AAT-GAG-A--AAGGTTTCTC--AT-T-T----AAATCTGAAA--------ATTGAAAT-T-
* * * * * **
293204 AAAATTGAAAATTTTGAAAAGTAAGAAAAGTTTCTTTCCTAGTAAACTATTTCCAAAGTTGGTAA
42 ---TTTGAAAA----G-TAAG-AA---ATGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAA
* * * *
293269 GTCCTTTGGGCCATAAGTAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCTGTAAGTC
95 GTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTC
* * *
293334 TTTCGAGTAAGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCACGTG
160 TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAA-ATGTTTTCACATG
* *
293399 TCTTTCGAA
224 TCTCTCAAA
* * * * *
293408 AAATGAGAAAGGTTTCTCATTTAAGTATGAAATTTGAATTTTTTTGAAAAGTAAGAAAGGTTTCT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAA-ATTTTTGAAAAGTAAGAAATGTTTCT
* *
293473 TACCTAGTAAATTATTTCTAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
65 TACCTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * *
293538 TGCTTAATTCATTC-GGACATCTGTAAGTCTTTCGAGCAGGATGATAAGTCCTTCGGGCCATCCA
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* * * *
293602 TAAGACCTTTGGTCAGGATGTTTTCACATGTCTCTCGAA
195 TAAGACCTTCGGGCA-AATGTTTTCACATGTCTCTCAAA
* * *
293641 AAATGATAAAGATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* ** * * *
293706 ACCTAGTAAACTATTTCCAAAGTTGGTTAGATCTTCGGCCCATCAGTAAGTCTTTCGAGCATGAT
66 ACCTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * * * * * *
293771 G-TTGAAATCCTTTGGGTCTTATGTTAGTTTTTCGAGCAAGATGATAAGTCATTCGGGTCGTCCA
131 GCTT-AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
* * * * * * * **
293835 TAAGATCTTCGTGTAGGATGTTTTCACATTTTTGTTGAA
195 TAAGACCTTCGGGCA-AATGTTTTCACATGTCTCTCAAA
* * *
293874 AAATGAGAAATGTTTCTCATTTAAATCTG-AAATTGAAATTTTTGAAAAGTAAGAAAAGTTTATT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
* * * *
293938 ACCTAGTAAACTATTTCC-AAATTTGGTAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCAAGA
66 ACCTAGTAAACTATTTCCAAAATTT-ATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* * * * * * * *
294002 TGATTAAATCCTTCGGGTCATTTATAAGCCTCTCGAACAAGAAGATAAGTCTTTCGGGCCATCCA
130 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
294067 TAAG
195 TAAG
294071 TCGTTTGGGC
Statistics
Matches: 1692, Mismatches: 286, Indels: 199
0.78 0.13 0.09
Matches are distributed among these distances:
207 31 0.02
208 14 0.01
209 5 0.00
210 5 0.00
211 9 0.01
212 1 0.00
213 51 0.03
214 40 0.02
215 7 0.00
217 2 0.00
223 1 0.00
224 1 0.00
228 1 0.00
231 8 0.00
232 232 0.14
233 987 0.58
234 84 0.05
235 1 0.00
236 3 0.00
237 3 0.00
238 3 0.00
239 8 0.00
241 2 0.00
242 1 0.00
243 8 0.00
246 3 0.00
247 10 0.01
248 1 0.00
253 4 0.00
254 4 0.00
255 7 0.00
258 3 0.00
259 5 0.00
260 1 0.00
261 2 0.00
263 8 0.00
264 3 0.00
265 3 0.00
266 3 0.00
267 1 0.00
268 29 0.02
269 9 0.01
270 4 0.00
271 12 0.01
272 6 0.00
273 5 0.00
274 29 0.02
275 32 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (232 bp):
AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
ACCTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
AAGACCTTCGGGCAAATGTTTTCACATGTCTCTCAAA
Found at i:292191 original size:41 final size:42
Alignment explanation
Indices: 292095--292191 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
292085 TAAGTTCTTT
* *
292095 GGGCCAT-CAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTC
1 GGGCCATCCA-TAAGTCTTTCAAGCAAGATGCATAAATCCTTC
* * * *
292137 GAGTCATCTATAAGTCTTTCGAGCAAGATG-ATAAATCCTTC
1 GGGCCATCCATAAGTCTTTCAAGCAAGATGCATAAATCCTTC
292178 GGGCCATCCATAAG
1 GGGCCATCCATAAG
292192 ACCTTCGGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 21 0.47
42 23 0.51
43 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (42 bp):
GGGCCATCCATAAGTCTTTCAAGCAAGATGCATAAATCCTTC
Found at i:292850 original size:42 final size:42
Alignment explanation
Indices: 292784--292865 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
292774 CCAAAATTTA
* *
292784 TAAGTTATTCGGGTCATTAGTAAGTCTTTTGAGCATGATGCT
1 TAAGTTATTCGGGTCATTAGTAAGTCTTTCGAGCAAGATGCT
292826 TAAGTTCA-TCGGGTCATCTA-TAAGTCTTTCGAGCAAGATG
1 TAAGTT-ATTCGGGTCAT-TAGTAAGTCTTTCGAGCAAGATG
292866 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (42 bp):
TAAGTTATTCGGGTCATTAGTAAGTCTTTCGAGCAAGATGCT
Found at i:292871 original size:21 final size:21
Alignment explanation
Indices: 292845--292886 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
292835 CGGGTCATCT
*
292845 ATAAGTCTTTCGAGCAAGATG
1 ATAAGTCCTTCGAGCAAGATG
* *
292866 ATAAGTCCTTCGGGCAGGATG
1 ATAAGTCCTTCGAGCAAGATG
292887 TTTTCACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCAAGATG
Found at i:293003 original size:35 final size:35
Alignment explanation
Indices: 292952--293020 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
292942 GAAAATTATT
292952 AAAAGTAAGAAAAGTTTCTTACTTAGTAAACTATG
1 AAAAGTAAGAAAAGTTTCTTACTTAGTAAACTATG
*
292987 AAAATTAAGAAAAGTTTCTTACTTAGTAAACTAT
1 AAAAGTAAGAAAAGTTTCTTACTTAGTAAACTAT
293021 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (35 bp):
AAAAGTAAGAAAAGTTTCTTACTTAGTAAACTATG
Found at i:293583 original size:948 final size:948
Alignment explanation
Indices: 292037--293827 Score: 2583
Period size: 948 Copynumber: 1.9 Consensus size: 948
292027 TTGAAATTTT
* * * * * **
292037 TGAAAAGTAAGAAATGTTTCTTACTTAGTAAACTATTTCTAAAATTTATAAGTTCTTTGGGCCAT
1 TGAAAAGTAAGAAAAGTTTCTTACTTAGTAAACTATTTCTAAAATTGATAACTACTTCGGGAAAT
*
292102 CAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGCAAGATG
66 CAGTAAGTCTTTCAAGCATGATGCTTAAATCATTCGAGTCATCTATAAGTCTTTCGAGCAAGATG
* * * *
292167 ATAAATCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATATTTTTACATGTCTCTCGAAAAATG
131 ATAAATCCTTCGAGCCATCCATAAGACCTTCGAGCAGGATATTTTCACATATCTCTCGAAAAATG
*
292232 AGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTCTGAAAAGTAAGAAATGTTTCTTACCCA
196 AGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTCTGAAAAGTAAGAAAAGTTTCTTACCCA
* * *
292297 GTAAACTACTTCCAAAATTTATAAGTCTTTCGGGCCATTAGTAAGTCTTTTGAGCATGATGCTTA
261 GTAAACTACTTCCAAAATTGATAAGTCTTTCGGGCCATAAGTAAGTCTTTCGAGCATGATGCTTA
* *
292362 CATCATTCAGGTCATCTTTAAGTCTTTCGAGCAAGATGATAAGCCCTTCGGGCCATCCATAAGAC
326 AATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGCCCTTCGGGCCATCCATAAGAC
* * * * *
292427 CTTCGGGGAAGATGTTTCCACATGTTTCTCAAAAAAAAATAAAGGTTTTTTATTTAAATCTAAAA
391 CTTCGGGCAAGATGTTTCCACATGTTTCTCAAAAAAAAAGAAAGGTTTCTCATTTAAATATAAAA
* *
292492 ATTGAAATTTTTGAATAGTGAGAAAGGTTTATTACCTAGTAAACTATTTCCAAAATTTATAAGTC
456 ATTGAAATTTTTGAAAAGTAAGAAAGGTTTATTACCTAGTAAACTATTTCCAAAATTTATAAGTC
* * * * * *
292557 CTTTGGGCCATCCGTAAGTCTTTCGAGCATGATTCTTAAATCCTTCGGGTCTTCTGTAAGTCTTT
521 CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGACATCTGTAAGTCTTT
292622 CGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACATTCGGGT-AAGATGTTTTCACATGTC
586 CGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACATT-GGGTCAAGATGTTTTCACATGTC
*
292686 TCTCAAAAAATGAGAAAGATTTCTTATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAT
650 TCTCAAAAAATGAGAAAGATTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAA-
* * * ** * *
292751 A-TTTCTTACCTTGTAAACTATTTCCAAAATTTATAAGTTATTCGGGTCATTAGTAAGTCTTTTG
714 AGTTTCTTACCTAGTAAACTATTTCCAAAATTGATAAGATATTCGGCCCATCAGTAAGTCTTTCG
* * * *
292815 AGCATGATGCTT-AAGTTCATCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGG
779 AGCATGATG-TTGAAATCCATCGGGTCATATATAAGTCTTTCGAGCAAGATGATAAGTCATTCGG
292879 GCAGGATGTTTTCACACATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAAATTGA
843 GCAGGATGTTTTCACACATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAAATTGA
292944 AAATTATTAAAAGTAAGAAAAGTTTCTTACTTAGTAAACTA
908 AAATTATTAAAAGTAAGAAAAGTTTCTTACTTAGTAAACTA
* * *
292985 TGAAAATTAAGAAAAGTTTCTTACTTAGTAAACTATTT-TCAAAGTTGGTAACTACTTCGGGAAA
1 TGAAAAGTAAGAAAAGTTTCTTACTTAGTAAACTATTTCT-AAAATTGATAACTACTTCGGGAAA
** * * *
293049 TCAGTAAGTCTTTTGAGCATGATGCTTAAATCATTTGGGTCATCTGTAAGTCTTTCGAGCAAGAT
65 TCAGTAAGTCTTTCAAGCATGATGCTTAAATCATTCGAGTCATCTATAAGTCTTTCGAGCAAGAT
* * * *
293114 GATAAGTCTTTCGAGCCATCCATAAGACCTTCGAGCATGATGTTTTCACATATCTCTCGAAAAAT
130 GATAAATCCTTCGAGCCATCCATAAGACCTTCGAGCAGGATATTTTCACATATCTCTCGAAAAAT
*
293179 GAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAAATTT-TGAAAAGTAAGAAAAGTTTCTTTCC
195 GAGAAAGGTTTCTCATTTAAATCTGAAAATTG-AAATTTCTGAAAAGTAAGAAAAGTTTCTTACC
* * * *
293243 TAGTAAACTATTTCCAAAGTTGGTAAGTCCTTT-GGGCCATAAGTAAGTCTTTCGAGCATGATGC
259 CAGTAAACTACTTCCAAAATTGATAAGT-CTTTCGGGCCATAAGTAAGTCTTTCGAGCATGATGC
* * * *
293307 TTAAATTC-TTCGGGTCATCTGTAAGTCTTTCGAGTAAGATGATAAGTCTTTCGGGCCATCCATA
323 TTAAA-TCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGCCCTTCGGGCCATCCATA
* * * ** *
293371 AGACCTTCGGGCAAGATGTTTTCACGTGTCTT-TCGAAAAATGAGAAAGGTTTCTCATTTAAGTA
387 AGACCTTCGGGCAAGATGTTTCCACATGT-TTCTCAAAAAAAAAGAAAGGTTTCTCATTTAAATA
* * * * * *
293435 TGAAATTTGAATTTTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAATTATTTCTAAAATTTA
451 TAAAAATTGAA-ATTTTTGAAAAGTAAGAAAGGTTTATTACCTAGTAAACTATTTCCAAAATTTA
* *
293500 TAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAATTCATTC-GGACATCTGTAA
515 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGACATCTGTAA
* * * *
293564 GTCTTTCGAGCAGGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGTCAGGATGTTTTCAC
580 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACATTGGGTCAAGATGTTTTCAC
* * *
293629 ATGTCTCTCGAAAAATGATAAAGATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
645 ATGTCTCTCAAAAAATGAGAAAGATTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAA
* * * *
293694 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAGTTGGTTAGATCTTCGGCCCATCAGTAAGTCT
710 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGATAAGATATTCGGCCCATCAGTAAGTCT
* * * * * *
293759 TTCGAGCATGATGTTGAAATCCTTTGGGTCTTATGTTAGTTTTTCGAGCAAGATGATAAGTCATT
775 TTCGAGCATGATGTTGAAATCCATCGGGTCATATATAAGTCTTTCGAGCAAGATGATAAGTCATT
293824 CGGG
840 CGGG
293828 TCGTCCATAA
Statistics
Matches: 739, Mismatches: 95, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
947 7 0.01
948 625 0.85
949 107 0.14
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (948 bp):
TGAAAAGTAAGAAAAGTTTCTTACTTAGTAAACTATTTCTAAAATTGATAACTACTTCGGGAAAT
CAGTAAGTCTTTCAAGCATGATGCTTAAATCATTCGAGTCATCTATAAGTCTTTCGAGCAAGATG
ATAAATCCTTCGAGCCATCCATAAGACCTTCGAGCAGGATATTTTCACATATCTCTCGAAAAATG
AGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTCTGAAAAGTAAGAAAAGTTTCTTACCCA
GTAAACTACTTCCAAAATTGATAAGTCTTTCGGGCCATAAGTAAGTCTTTCGAGCATGATGCTTA
AATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGCCCTTCGGGCCATCCATAAGAC
CTTCGGGCAAGATGTTTCCACATGTTTCTCAAAAAAAAAGAAAGGTTTCTCATTTAAATATAAAA
ATTGAAATTTTTGAAAAGTAAGAAAGGTTTATTACCTAGTAAACTATTTCCAAAATTTATAAGTC
CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGACATCTGTAAGTCTTT
CGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACATTGGGTCAAGATGTTTTCACATGTCT
CTCAAAAAATGAGAAAGATTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAG
TTTCTTACCTAGTAAACTATTTCCAAAATTGATAAGATATTCGGCCCATCAGTAAGTCTTTCGAG
CATGATGTTGAAATCCATCGGGTCATATATAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCA
GGATGTTTTCACACATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAAATTGAAAA
TTATTAAAAGTAAGAAAAGTTTCTTACTTAGTAAACTA
Found at i:294609 original size:133 final size:133
Alignment explanation
Indices: 294391--294677 Score: 416
Period size: 133 Copynumber: 2.2 Consensus size: 133
294381 GCGAATCGAA
* * *
294391 CTCGATTCAATTTTCCCTGAGTGACAGTGGAATAAATCAACTCCCCCAGATCTGATTTTTACTCA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATAAATCAACT-CCCCAGATCTAATTTTCACTCA
* *
294456 AGAAGAAGCAGAACGAATCCCTTTCTTTCAAGATTTGATATTCCTTGAGTAACAGTAGAACAAGT
65 AGAAGAAGCAGAACGAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGT
*
294521 CTGC
130 CTAC
* * *
294525 CTCGATTCAATCTTCCCTGAGTGACAGTGGAGTGAATCAACGT-CCCAGATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATAAATCAAC-TCCCCAGATCTAATTTTCACTCA
* *
294589 AGAAGAAGCGGAAC-ATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
65 AGAAGAAGCAGAACGA-ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAG
*
294653 TTTAC
129 TCTAC
*
294658 CTCTATTCAATCTTCCCTGA
1 CTCGATTCAATCTTCCCTGA
294678 AGAATAGTGG
Statistics
Matches: 138, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
132 1 0.01
133 98 0.71
134 38 0.28
135 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAGTGACAGTGGAATAAATCAACTCCCCAGATCTAATTTTCACTCAA
GAAGAAGCAGAACGAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGTC
TAC
Found at i:300632 original size:11 final size:11
Alignment explanation
Indices: 300616--300649 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
300606 GAGTCGATTC
300616 GAAATTAATGA
1 GAAATTAATGA
300627 GAAATTAATGA
1 GAAATTAATGA
300638 GAAATTAATGA
1 GAAATTAATGA
300649 G
1 G
300650 TAACGGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (11 bp):
GAAATTAATGA
Found at i:301945 original size:21 final size:22
Alignment explanation
Indices: 301890--301945 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
301880 TTTCAACTAT
301890 CCTTAAGTCTATCAAAAGTAGG
1 CCTTAAGTCTATCAAAAGTAGG
* *
301912 ACTTCTA-TCTATCAAAAGTA-G
1 CCTT-AAGTCTATCAAAAGTAGG
301933 CCTTAAGTCTATC
1 CCTTAAGTCTATC
301946 CCGAATCATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 10 0.36
22 16 0.57
23 1 0.04
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (22 bp):
CCTTAAGTCTATCAAAAGTAGG
Found at i:305960 original size:19 final size:20
Alignment explanation
Indices: 305936--305976 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
305926 CAAAACTTGC
305936 ATGA-GGGTATCGGTACCCT
1 ATGAGGGGTATCGGTACCCT
305955 ATGAGGGGGGTATCGGTACCCT
1 ATGA--GGGGTATCGGTACCCT
305977 CTGGGCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
22 15 0.79
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.24
Consensus pattern (20 bp):
ATGAGGGGTATCGGTACCCT
Found at i:308629 original size:23 final size:23
Alignment explanation
Indices: 308602--308659 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
308592 CCTCAGGGGA
308602 GGTATCGATACCCATTCAAAGAG
1 GGTATCGATACCCATTCAAAGAG
* * *
308625 GGTATCGGTACCCTTTCAAAGGG
1 GGTATCGATACCCATTCAAAGAG
308648 GGTATCGATACC
1 GGTATCGATACC
308660 TAGCACACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (23 bp):
GGTATCGATACCCATTCAAAGAG
Found at i:312499 original size:22 final size:21
Alignment explanation
Indices: 312457--312496 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
312447 AAGACTATTT
312457 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
312478 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
312497 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:314582 original size:11 final size:11
Alignment explanation
Indices: 314566--314591 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
314556 AACTATTTTT
314566 GGATCGTTTAA
1 GGATCGTTTAA
314577 GGATCGTTTAA
1 GGATCGTTTAA
314588 GGAT
1 GGAT
314592 TAAAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.35
Consensus pattern (11 bp):
GGATCGTTTAA
Found at i:318871 original size:15 final size:15
Alignment explanation
Indices: 318820--318871 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
318810 ATGTTTTATA
* *
318820 TGAAAATGATCTATG
1 TGAAAATGTTCTAAG
* * *
318835 AGAAAACGTGCTAAG
1 TGAAAATGTTCTAAG
*
318850 TGAAAATGTTCTACG
1 TGAAAATGTTCTAAG
318865 TGAAAAT
1 TGAAAAT
318872 ACCCTATGTG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:319040 original size:25 final size:24
Alignment explanation
Indices: 319012--319106 Score: 109
Period size: 24 Copynumber: 3.9 Consensus size: 24
319002 TTCTACGCGA
*
319012 TCCTTCGGGACTAATTTATACGTGG
1 TCCTTCGGGAC-AAATTATACGTGG
*
319037 TCCTTCGGGACAAATTCTACGTGG
1 TCCTTCGGGACAAATTATACGTGG
* * *
319061 TCCTTCGGGAAAAATTCTACGCGG
1 TCCTTCGGGACAAATTATACGTGG
* *
319085 TCCTTCGAGACATATCTATACG
1 TCCTTCGGGACAAAT-TATACG
319107 GCACTTCAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 45 0.74
25 16 0.26
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (24 bp):
TCCTTCGGGACAAATTATACGTGG
Found at i:319062 original size:24 final size:24
Alignment explanation
Indices: 319002--319096 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
318992 GAGTCGAGGG
* *
319002 TTCTACGCGATCCTTCGGGACTAAT
1 TTCTACGCGGTCCTTCGGGAC-AAA
* *
319027 TTATACGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* *
319051 TTCTACGTGGTCCTTCGGGAAAAA
1 TTCTACGCGGTCCTTCGGGACAAA
*
319075 TTCTACGCGGTCCTTCGAGACA
1 TTCTACGCGGTCCTTCGGGACA
319097 TATCTATACG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
24 43 0.70
25 18 0.30
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:320054 original size:18 final size:18
Alignment explanation
Indices: 320031--320069 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
320021 CCAAAACGCA
320031 AAAATGGTATCGATACTT
1 AAAATGGTATCGATACTT
320049 AAAATGGTATCGATACTT
1 AAAATGGTATCGATACTT
320067 AAA
1 AAA
320070 GGAGTACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (18 bp):
AAAATGGTATCGATACTT
Found at i:326197 original size:131 final size:131
Alignment explanation
Indices: 325963--326224 Score: 470
Period size: 131 Copynumber: 2.0 Consensus size: 131
325953 AGATGGATCG
*
325963 AGATTTTAAAAGATTATGATGTGATGACTGATTATCATCCAAGAAAAGCTAATATGGTAGTTGAT
1 AGATTTTAAAAGATTATGATGTGATGACTGATTATCATCCAAGAAAAGCTAATATGGTAGCTGAT
* *
326028 GCACTTAGTCGAAAGACTTTTGCAGCTCTGCGAGCTTTGGATGCACGTATATCAATAAAAGAATA
66 GCACTTAGTCGAAAGACTTGTGCAGCTCTACGAGCTTTGGATGCACGTATATCAATAAAAGAATA
326093 T
131 T
*
326094 AGATTTTAAAAGATTATGATGTGATGACTGATTATCATCCAAGAAAAGCTAATGTGGTAGCTGAT
1 AGATTTTAAAAGATTATGATGTGATGACTGATTATCATCCAAGAAAAGCTAATATGGTAGCTGAT
* *
326159 GCACTTAGTCGAAAGACTTGTGTAGCTCTACGAGCTTTGGATGCACGTATATCAGTAAAAGAATA
66 GCACTTAGTCGAAAGACTTGTGCAGCTCTACGAGCTTTGGATGCACGTATATCAATAAAAGAATA
326224 T
131 T
326225 GGCACCTTAA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 125 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (131 bp):
AGATTTTAAAAGATTATGATGTGATGACTGATTATCATCCAAGAAAAGCTAATATGGTAGCTGAT
GCACTTAGTCGAAAGACTTGTGCAGCTCTACGAGCTTTGGATGCACGTATATCAATAAAAGAATA
T
Found at i:333829 original size:81 final size:81
Alignment explanation
Indices: 333700--334814 Score: 1655
Period size: 81 Copynumber: 13.8 Consensus size: 81
333690 TATTTAGTCT
* * * *
333700 TTCATCTAACTAGCATAATTGACACTTTTCTGCCAAATCCACAGCTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
333765 CAACGGTATTTAACCG
66 CAACGGTATTTAACCG
* * * *
333781 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGAACAACTAGGCCATAAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* **
333846 CAATGGTATTTAACTA
66 CAACGGTATTTAACCG
333862 TTCATCTAACT-GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
333926 CAACGGTATTTAACCG
66 CAACGGTATTTAACCG
* * * *
333942 TTCATCTAACTGGTATAATTGACACATTTCTACCAAATGCAAAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
334007 CAATGGTATTTAACCG
66 CAACGGTATTTAACCG
* * *
334023 TTCATCTAACTGGCATAATTGAAACGTTTCTGCCAAATACACAGCT-GTGCCATTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAG-GCCATTAATCTTTTAC
*
334087 TCAACGGTATTTAATCG
65 TCAACGGTATTTAACCG
* *
334104 TTCATCTAACTGGCATAATTGGCACCTTTCTGCCAAATGCACAGCTATGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
334169 CAACGGTATTTAACCA
66 CAACGGTATTTAACCG
* * * *
334185 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAACGCATAACTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
334250 TAACGGTATTTAACC-
66 CAACGGTATTTAACCG
* * *
334265 AT-ATCTAACTGGAATAATTAACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
334329 CAACGGTATTTAGCCG
66 CAACGGTATTTAACCG
* * *
334345 TTCATCTAACTTGCATAGTTGACACCTTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
*
334410 CAACAGTATTTAACCG
66 CAACGGTATTTAACCG
* * * * **
334426 TTCATATAACTGACATAATTGACACCTTTCTGCCAAATGCACATCTAGGCAATTCTTCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
334491 CAACGGTATTTAACCG
66 CAACGGTATTTAACCG
** * *
334507 TTCATCTAACCAGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATTTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
334572 CAACGGTATTTAACCG
66 CAACGGTATTTAACCG
* * **
334588 TTCATCTAACTGGCATAATTGACACATTTCTACCAAATGCACAGCTAATCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* **
334653 CAAGGGTATTTAATAG
66 CAACGGTATTTAACCG
* * *
334669 TTCATCTAACTGGCATAATTGACATCTTTCTGCCAAATGCACATCTAAGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
334734 CAACGGTATTTAACCAG
66 CAACGGTATTTAACC-G
**
334751 -TCATCTAACTAACATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
334815 TTAGAATTGT
Statistics
Matches: 926, Mismatches: 102, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
79 69 0.07
80 76 0.08
81 780 0.84
82 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
CAACGGTATTTAACCG
Found at i:335044 original size:57 final size:57
Alignment explanation
Indices: 334975--335232 Score: 401
Period size: 57 Copynumber: 4.5 Consensus size: 57
334965 AAATTCATAT
* * * * *
334975 AATTGCTTAACTTTTTACACACAAAGTGCCCATGTAGAAATTCATAAACTAATCATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTAATTATG
* *
335032 AATTTTTTAACTTTTTGCACACAAAGTGCCCATATGGAATTTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTAATTATG
* * *
335089 AATTTTTTAACTTTTTGTACACAATGTGCCCATATGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTAATTATG
335146 AATTTCTTAACTTTTTGCACACAAAGCT-CCCATATGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAG-TGCCCATATGGAAATTCATAAACTAATTATG
*
335203 AATTTCTTCACTTTTTGCACACAAAGTGCC
1 AATTTCTTAACTTTTTGCACACAAAGTGCC
335233 TATTGGGTAA
Statistics
Matches: 185, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
56 1 0.01
57 183 0.99
58 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (57 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTAATTATG
Found at i:337283 original size:2 final size:2
Alignment explanation
Indices: 337276--337308 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
337266 CCAGAAAAAC
337276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
337309 TTCTGACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:340961 original size:15 final size:16
Alignment explanation
Indices: 340943--340993 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
340933 TGTTTTATAT
*
340943 GAAAATGTTCTATG-A
1 GAAAATGTTCTAAGTA
*
340958 GAAAATGTGCTAAGTA
1 GAAAATGTTCTAAGTA
*
340974 -AAAATGTTCTACGT-
1 GAAAATGTTCTAAGTA
340988 GAAAAT
1 GAAAAT
340994 ACCCTATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 29 0.97
16 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (16 bp):
GAAAATGTTCTAAGTA
Found at i:341160 original size:25 final size:24
Alignment explanation
Indices: 341124--341194 Score: 97
Period size: 25 Copynumber: 2.9 Consensus size: 24
341114 GAGTCGAGGG
341124 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* * *
341148 TTTCTATGTGGTCTTTCGGGACAAA
1 -TTCTACGCGGTCCTTCGGGACAAA
*
341173 TTCTACGCGGTCCTTTGGGACA
1 TTCTACGCGGTCCTTCGGGACA
341195 TATCTATCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 18 0.46
25 21 0.54
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.32
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:343205 original size:575 final size:572
Alignment explanation
Indices: 341842--343435 Score: 1920
Period size: 575 Copynumber: 2.8 Consensus size: 572
341832 TACACGCTTT
* * ** *
341842 GTAACTATCAAATAAAATATT-CTTATTTCTAAAAATAAACTTTAGAAAAATGATAGTATAGAGA
1 GTAACTGTCAAATAAAATATTCCTT-TTTCTCAAAATAAACAATAGAAAAAAGATAGTATAGAGA
* * ** * * * * * *
341906 AGTAAGGTCAATCCGCATAGACTTTAGAGTTTCCAATTTCGAATTATTTTGATATGGATTAAATG
65 AGTAGGGTCAATCTGCAGGGACTTTGGAGTTTCCAATTCCGAATTGTTTTGATATAGATGAAA-C
* *
341971 GAAAAATAAAG-AAAATTGGGGTTATCA-AGTAAAAATAAAAGAAACG-AGAATCTT-AAAAAAA
129 AAAAAATAAAGAAAAAAT-GGGTTATCATA-TAAAAATAAAAGAAACGAAG-ATCTTGAAAAAAA
* *
342032 TGAC----AATAAAACAAGGTAATTTTTTAAAAGAAATCAAATAGATGAAATAGCCTCAAGCTTC
191 AGACGAAAAATAAAACAAGGTAAATTTTTAAAAGAAATCAAATAGATGAAATAGCCTCAAGCTTC
* * * * *
342093 GCTTTGCCTCAATTCCAATTAATCATCGAAAGAGATTTTACTTTAGGTAACATGTCGGTTACATT
256 GCTTTGCCTCAATTCCAATTAATCATCGAAAGAGATTTTACTTCAAGAAACATGTCAGTTACAGT
* * *
342158 CTTCAAGGCCCAACCCTTGTAACTTACTTTTTTCTCTGGTAAAACGATATTACAAAGTCTATCTC
321 CTTCAAGGCACAACCCTTGTAACTTACTTTTCTCTCTAGTAAAACGATATT-CAAAGTCTATCT-
* * ** * *
342223 CAAAATTCAGTCCTTGTTGGACTAACCACAATTATCACTTTTAGTTTCACTACAACTTTAAGCGA
384 C-TAATTCAGTCCTTGTTGGACTAACCACAACTATCACTTTTAGGATCAATACAACTTTAAGCAA
* * * ** * *** *
342288 CCTGGTCGATCTTGGGTCTTTAGTACGTTTAATTTTCTGGAAGCAACCTGGTTATAGATCAAAAT
448 CCTAGTCAATCTCGGGTCTGCAGTACGTTAAATTTTCTGGAAGCAACCTGAAGATAGATCAAAAC
* *
342353 AAAAATGAGACTAGTAACTTTTTCGTAGTCCCCGACAATAGCGCCAATTTGACACGGGTC
513 AAAAATGAGACTAGTAACTTTATCGTAGTCCCCGACAACAGCGCCAATTTGACACGGGTC
* * * *
342413 GTAATTGTCAAATAAAAATATTCCTATTTCTCAAAATAAACAATGGAAAAAAGATAATATAGAGA
1 GTAACTGTCAAAT-AAAATATTCCTTTTTCTCAAAATAAACAATAGAAAAAAGATAGTATAGAGA
* * *
342478 AGTAGGGTCGATCTGCAGGGACTTTGGAGTTTTCAATTCTGAATTGTTTTGATATAGATGAAACA
65 AGTAGGGTCAATCTGCAGGGACTTTGGAGTTTCCAATTCCGAATTGTTTTGATATAGATGAAAC-
* *
342543 AAAAAATAAA-AGAAAATGGGGATATCATAT---AA-AAAAGAAACGAAGATCTTGAAAAATAAA
129 AAAAAATAAAGAAAAAAT-GGGTTATCATATAAAAATAAAAGAAACGAAGATCTTGAAAAA-AAA
*
342603 TGATGAAAAATAAAACAAGGT-AATTTTTAAAAGAAATCAAATAGATGAAAATAGCCTCAAGCTT
192 -GACGAAAAATAAAACAAGGTAAATTTTTAAAAGAAATCAAATAGATG-AAATAGCCTCAAGCTT
342667 CGCTTTGCCTCAATTCCAATTAATCATCGAAAGAGATTTTACTTCAAGAAACATGTCAGTTACAG
255 CGCTTTGCCTCAATTCCAATTAATCATCGAAAGAGATTTTACTTCAAGAAACATGTCAGTTACAG
* * * * *
342732 TCTTCAAGGCTCAACTCTTGTAACTTACTTTTCTCTATCGTAAAATGATATTCAGAAGTCTATCT
320 TCTTCAAGGCACAACCCTTGTAACTTACTTTTCTCTCTAGTAAAACGATATTCA-AAGTCTATCT
* * ** *
342797 CTGGAATTCAGTCCTTATTGGACTAATCACGGCTATCTCTTTTAGCGAT-AATACAACTTTAAGC
384 CT--AATTCAGTCCTTGTTGGACTAACCACAACTATCACTTTTAG-GATCAATACAACTTTAAGC
*
342861 AACCTAGTCAATCTCGGGTCTGCAGTTCGTTAAA-TTTCTTGGAAGCAACCTGAAGATAGATCAA
446 AACCTAGTCAATCTCGGGTCTGCAGTACGTTAAATTTTC-TGGAAGCAACCTGAAGATAGATCAA
* *
342925 AACAAAAATTAGACTAGTAACTTTATCGCT-GTCCCCGACAACGGCGCCAATTTGACACGGGTC
510 AACAAAAATGAGACTAGTAACTTTATCG-TAGTCCCCGACAACAGCGCCAATTTGACACGGGTC
*
342988 GTAACTGTCAAATAAAATATTCCTTTTTCTCAAAATAAACAATAGAAAAAAGATAGTATGGAGAA
1 GTAACTGTCAAATAAAATATTCCTTTTTCTCAAAATAAACAATAGAAAAAAGATAGTATAGAGAA
** * * * *
343053 GTAGGGTTTATATGTAGGGACTTTGGTGTTTCCAATTCCGAATTGTTTTGATCTAGATGAAA-AA
66 GTAGGGTCAATCTGCAGGGACTTTGGAGTTTCCAATTCCGAATTGTTTTGATATAGATGAAACAA
343117 ATAAATAAAGAAAAAAT-GGTTATCATATAAAAATAAAAGAAACGAAGATCTTGAAAAAAAAGAC
131 A-AAATAAAGAAAAAATGGGTTATCATATAAAAATAAAAGAAACGAAGATCTTGAAAAAAAAGAC
* * ** * *
343181 GAAAAATAAAACAAGGTAAATTTTTTAGAAGAAATCAAATATATGAAATAGTATTATGCTTCGCT
195 GAAAAATAAAACAAGGTAAA-TTTTTAAAAGAAATCAAATAGATGAAATAGCCTCAAGCTTCGCT
* * * * *
343246 TTGACTCAA-TCCTAATTAATTATCGAAAGATATTTTACTTCACGAAATATGTCAGTTACAGTCT
259 TTGCCTCAATTCC-AATTAATCATCGAAAGAGATTTTACTTCAAGAAACATGTCAGTTACAGTCT
* * * *
343310 ACAAGGCACAACCCTTGTAACTTATTTTTCTCTCTAGTAAACCGATATTCCCAAGTCTATCTTCA
323 TCAAGGCACAACCCTTGTAACTTACTTTTCTCTCTAGTAAAACGATATT-CAAAGTCTATC-TC-
* * * * *
343375 TAATTCAGTCCTTGCTGGACTAACCA-AGACTATC-GTCGTTAGCACCAATACAACTTTAAGC
385 TAATTCAGTCCTTGTTGGACTAACCACA-ACTATCACT-TTTAGGATCAATACAACTTTAAGC
343436 GCTAGAAAAG
Statistics
Matches: 877, Mismatches: 111, Indels: 66
0.83 0.11 0.06
Matches are distributed among these distances:
568 15 0.02
569 9 0.01
570 2 0.00
571 13 0.01
572 128 0.15
573 10 0.01
574 164 0.19
575 484 0.55
576 51 0.06
577 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (572 bp):
GTAACTGTCAAATAAAATATTCCTTTTTCTCAAAATAAACAATAGAAAAAAGATAGTATAGAGAA
GTAGGGTCAATCTGCAGGGACTTTGGAGTTTCCAATTCCGAATTGTTTTGATATAGATGAAACAA
AAAATAAAGAAAAAATGGGTTATCATATAAAAATAAAAGAAACGAAGATCTTGAAAAAAAAGACG
AAAAATAAAACAAGGTAAATTTTTAAAAGAAATCAAATAGATGAAATAGCCTCAAGCTTCGCTTT
GCCTCAATTCCAATTAATCATCGAAAGAGATTTTACTTCAAGAAACATGTCAGTTACAGTCTTCA
AGGCACAACCCTTGTAACTTACTTTTCTCTCTAGTAAAACGATATTCAAAGTCTATCTCTAATTC
AGTCCTTGTTGGACTAACCACAACTATCACTTTTAGGATCAATACAACTTTAAGCAACCTAGTCA
ATCTCGGGTCTGCAGTACGTTAAATTTTCTGGAAGCAACCTGAAGATAGATCAAAACAAAAATGA
GACTAGTAACTTTATCGTAGTCCCCGACAACAGCGCCAATTTGACACGGGTC
Found at i:346789 original size:68 final size:67
Alignment explanation
Indices: 346714--346880 Score: 185
Period size: 68 Copynumber: 2.5 Consensus size: 67
346704 TCAAAATTTG
* * *
346714 TTCGGTTCGATTAATTATTTTCAAATAAATTTCGATTCGATTAAT-GGTTAAAGAAAAAAATCGG
1 TTCGGTTCGGTTAATAATTTTCAAATTAATTT-GATTCGATTAATAGGTTAAA-AAAAAAATCGG
346778 TTAA
64 TTAA
* * * ** * *
346782 TTTGGTTCGGTTAATAATGTTT-AAATTAATTTGGTTCGGTTAATAATTTTCAAAAAAAATTCGG
1 TTCGGTTCGGTTAATAAT-TTTCAAATTAATTTGATTCGATTAAT-AGGTTAAAAAAAAAATCGG
346846 TTAA
64 TTAA
*
346850 TTCGATTCGGTTAATAATTTTCAAATTAATT
1 TTCGGTTCGGTTAATAATTTTCAAATTAATT
346881 CGGTTCAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
67 13 0.16
68 63 0.76
69 7 0.08
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (67 bp):
TTCGGTTCGGTTAATAATTTTCAAATTAATTTGATTCGATTAATAGGTTAAAAAAAAAATCGGTT
AA
Found at i:346793 original size:14 final size:14
Alignment explanation
Indices: 346774--346825 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
346764 AAGAAAAAAA
346774 TCGGTTAATTTGGT
1 TCGGTTAATTTGGT
* *
346788 TCGGTTAATAATGTT
1 TCGGTTAAT-TTGGT
***
346803 TAAATTAATTTGGT
1 TCGGTTAATTTGGT
346817 TCGGTTAAT
1 TCGGTTAAT
346826 AATTTTCAAA
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.48
Consensus pattern (14 bp):
TCGGTTAATTTGGT
Found at i:346879 original size:29 final size:29
Alignment explanation
Indices: 346846--346904 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
346836 AAAAATTCGG
*
346846 TTAATTCGATTCGGTTAATAATTTTCAAA
1 TTAATTCGATTCAGTTAATAATTTTCAAA
*
346875 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGATTCAGTTAATAATTTTCAAA
346904 T
1 T
346905 AGTTTTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (29 bp):
TTAATTCGATTCAGTTAATAATTTTCAAA
Found at i:346886 original size:68 final size:67
Alignment explanation
Indices: 346767--346903 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 67
346757 ATGGTTAAAG
* * * *
346767 AAAAAAATCGGTTAATTTGGTTCGGTTAATAATGTTTAAATTAATTTGGTTCGGTTAATAATTTT
1 AAAAAAATCGGTTAATTCGATTCGGTTAATAATGTTTAAATTAATTCGGTTCAGTTAATAATTTT
346832 CA
66 CA
346834 AAAAAAATTCGGTTAATTCGATTCGGTTAATAAT-TTTCAAATTAATTCGGTTCAGTTAATAATT
1 AAAAAAA-TCGGTTAATTCGATTCGGTTAATAATGTTT-AAATTAATTCGGTTCAGTTAATAATT
346898 TTCA
64 TTCA
346902 AA
1 AA
346904 TAGTTTTTGG
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
67 10 0.16
68 54 0.84
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (67 bp):
AAAAAAATCGGTTAATTCGATTCGGTTAATAATGTTTAAATTAATTCGGTTCAGTTAATAATTTT
CA
Found at i:349329 original size:84 final size:84
Alignment explanation
Indices: 349188--349351 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 84
349178 CTTCAAATCG
* *
349188 ATTTGAATTACCCAGACAAAATTAAGGCATTACAGATTTATGATCAAGATAATAGAAGAACATAT
1 ATTTGAATTACCCAGACAAAATTAAGGCATTACAGATTTATGATCAAGACAAGAGAAGAACATAT
*
349253 AGTAAAATCAAGTCCTTCA
66 AATAAAATCAAGTCCTTCA
* * * * *
349272 ATTTGAATTATCCAGACAAAGTTAGGGCATTACAGGTTTATGATCAAGACAAGAGAAGAACATGT
1 ATTTGAATTACCCAGACAAAATTAAGGCATTACAGATTTATGATCAAGACAAGAGAAGAACATAT
349337 AATAAAATCAAGTCC
66 AATAAAATCAAGTCC
349352 AAAAGATAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (84 bp):
ATTTGAATTACCCAGACAAAATTAAGGCATTACAGATTTATGATCAAGACAAGAGAAGAACATAT
AATAAAATCAAGTCCTTCA
Found at i:351169 original size:16 final size:16
Alignment explanation
Indices: 351148--351202 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
351138 AGTTTACATA
351148 TTAATTTCATTTTATT
1 TTAATTTCATTTTATT
*
351164 TTAATTTCGGTCTTTATAT
1 TTAATTTC-AT-TTTAT-T
*
351183 TTAATGTGCATTTTATT
1 TTAAT-TTCATTTTATT
351200 TTA
1 TTA
351203 GTCCCAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 10 0.31
19 7 0.22
20 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (16 bp):
TTAATTTCATTTTATT
Found at i:363736 original size:16 final size:16
Alignment explanation
Indices: 363717--363788 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 16
363707 AAAAGGGAAC
363717 AAAT-AAAAAGATAAAA
1 AAATGAAAAAGA-AAAA
363733 AAATGAAAAAGAAAAA
1 AAATGAAAAAGAAAAA
363749 AAATGAAAAAAAAATGAAAAA
1 AAATG----AAAAA-GAAAAA
363770 AAATGAAAAATGAAAAA
1 AAATGAAAAA-GAAAAA
363787 AA
1 AA
363789 GAAATGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.26
17 21 0.42
20 5 0.10
21 11 0.22
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAATGAAAAAGAAAAA
Found at i:363742 original size:10 final size:10
Alignment explanation
Indices: 363738--363800 Score: 69
Period size: 10 Copynumber: 6.3 Consensus size: 10
363728 TAAAAAAATG
363738 AAAAA-GAAA
1 AAAAATGAAA
363747 AAAAATGAAAA
1 AAAAATG-AAA
363758 AAAAATGAAA
1 AAAAATGAAA
363768 AAAAATGAAA
1 AAAAATGAAA
363778 AATGAAA--AAA
1 AA--AAATGAAA
*
363788 AGAAATGAAA
1 AAAAATGAAA
363798 AAA
1 AAA
363801 TGAAAAGAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 3 0.07
9 5 0.11
10 25 0.54
11 10 0.22
12 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:363760 original size:11 final size:11
Alignment explanation
Indices: 363744--363800 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
363734 AATGAAAAAG
363744 AAAAAAAATGA
1 AAAAAAAATGA
363755 AAAAAAAATG-
1 AAAAAAAATGA
363765 AAAAAAAATGA
1 AAAAAAAATGA
**
363776 AAAATGAA--A
1 AAAAAAAATGA
*
363785 AAAAGAAATGA
1 AAAAAAAATGA
363796 AAAAA
1 AAAAA
363801 TGAAAAGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.18
10 10 0.26
11 21 0.55
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.09
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:363767 original size:21 final size:20
Alignment explanation
Indices: 363738--363800 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
363728 TAAAAAAATG
363738 AAAAAGAAAAAAAATGAAAA
1 AAAAAGAAAAAAAATGAAAA
363758 AAAAATGAAAAAAAATGAAAA
1 AAAAA-GAAAAAAAATGAAAA
* *
363779 ATGAAA-AAAAGAAATGAAAA
1 A-AAAAGAAAAAAAATGAAAA
363799 AA
1 AA
363801 TGAAAAGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 19 0.50
21 16 0.42
22 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (20 bp):
AAAAAGAAAAAAAATGAAAA
Found at i:363771 original size:37 final size:37
Alignment explanation
Indices: 363721--363806 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 37
363711 GGGAACAAAT
363721 AAAAA-GATAAAAAAATGAAAAA-GAAAAAAAATGAAA-A
1 AAAAATGA-AAAAAAATGAAAAATG-AAAAAAA-GAAAGA
363758 AAAAATGAAAAAAAATGAAAAATGAAAAAAAGAAATGA
1 AAAAATGAAAAAAAATGAAAAATGAAAAAAAGAAA-GA
363796 AAAAATGAAAA
1 AAAAATGAAAA
363807 GAGAAAAGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
36 4 0.09
37 26 0.58
38 15 0.33
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (37 bp):
AAAAATGAAAAAAAATGAAAAATGAAAAAAAGAAAGA
Found at i:363800 original size:28 final size:25
Alignment explanation
Indices: 363738--363813 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 25
363728 TAAAAAAATG
363738 AAAAAG-AAAAAAAATG--AAA-AA
1 AAAAAGAAAAAAAAATGAAAAAGAA
*
363759 AAAATG-AAAAAAAATGAAAAATGAA
1 AAAAAGAAAAAAAAATGAAAAA-GAA
363784 AAAAAGAAATGAAAAAATGAAAAGAGAA
1 AAAAAGAAA--AAAAAATGAAAA-AGAA
363812 AA
1 AA
363814 GGAGGGTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 15 0.33
23 3 0.07
25 7 0.16
26 2 0.04
28 17 0.38
29 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (25 bp):
AAAAAGAAAAAAAAATGAAAAAGAA
Found at i:363801 original size:21 final size:19
Alignment explanation
Indices: 363729--363806 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 19
363719 ATAAAAAGAT
363729 AAAAAAATGAAAAA-G--A
1 AAAAAAATGAAAAATGAAA
**
363745 AAAAAAATGAAAAAAAAATGA
1 AAAAAAATGAAAAATGAA--A
363766 AAAAAAATGAAAAATGAAA
1 AAAAAAATGAAAAATGAAA
363785 AAAAGAAATGAAAAAATGAAA
1 AAAA-AAATG-AAAAATGAAA
363806 A
1 A
363807 GAGAAAAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
16 14 0.27
19 5 0.10
20 5 0.10
21 28 0.54
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (19 bp):
AAAAAAATGAAAAATGAAA
Found at i:364933 original size:136 final size:136
Alignment explanation
Indices: 364687--364996 Score: 494
Period size: 136 Copynumber: 2.3 Consensus size: 136
364677 GGTGAACCAG
* *
364687 CATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
364752 AGAAGAGCTTGTTCGACCTATCACTAGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
364817 GATCAG
131 GATCAA
* *
364823 TATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * * *
364888 AGAAGAGCTTGTTCGACTTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGTTTGATG
66 AGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
364953 GATCAA
131 GATCAA
* *
364959 CATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATC
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATC
364997 AAACGAAGAA
Statistics
Matches: 158, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 158 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:365025 original size:19 final size:17
Alignment explanation
Indices: 364976--365025 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
364966 AGTGAAGAGT
364976 TCAT-AATGAGAAGAAC
1 TCATCAATGAGAAGAAC
364992 TCATCAA--ACGAAGAAC
1 TCATCAATGA-GAAGAAC
365008 TCATCCAATGAGAGAGAA
1 TCAT-CAATGAGA-AGAA
365026 TAAGTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 1 0.04
16 15 0.54
17 5 0.18
18 2 0.07
19 5 0.18
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (17 bp):
TCATCAATGAGAAGAAC
Found at i:366682 original size:16 final size:16
Alignment explanation
Indices: 366661--366715 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
366651 AGTTTACATA
366661 TTAATTTCATTTTATT
1 TTAATTTCATTTTATT
*
366677 TTAATTTCGGTCTTTATAT
1 TTAATTTC-AT-TTTAT-T
*
366696 TTAATGTGCATTTTATT
1 TTAAT-TTCATTTTATT
366713 TTA
1 TTA
366716 GTCCCAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 10 0.31
19 7 0.22
20 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (16 bp):
TTAATTTCATTTTATT
Found at i:376247 original size:24 final size:24
Alignment explanation
Indices: 376220--376269 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
376210 TATATCAAAA
376220 ATCAAAACATAA-TCCAGGTCAAGT
1 ATCAAAACA-AATTCCAGGTCAAGT
* * *
376244 ATCAGATCAAATTCCATGTCAAGT
1 ATCAAAACAAATTCCAGGTCAAGT
376268 AT
1 AT
376270 TCGATTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCAAAACAAATTCCAGGTCAAGT
Found at i:376293 original size:19 final size:19
Alignment explanation
Indices: 376266--376305 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
376256 TCCATGTCAA
* * *
376266 GTATTCGATTAGAATCTAG
1 GTATCCGATCAGAATCCAG
376285 GTATCCGATCAGAATCCAG
1 GTATCCGATCAGAATCCAG
376304 GT
1 GT
376306 CAGGTATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (19 bp):
GTATCCGATCAGAATCCAG
Found at i:381204 original size:18 final size:19
Alignment explanation
Indices: 381181--381216 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
381171 TTAAAGCTCG
381181 AACTCAA-AAAAATTCAAA
1 AACTCAACAAAAATTCAAA
*
381199 AACTCAACTAAAATTCAA
1 AACTCAACAAAAATTCAA
381217 GACTCGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (19 bp):
AACTCAACAAAAATTCAAA
Found at i:381221 original size:18 final size:20
Alignment explanation
Indices: 381189--381226 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
381179 CGAACTCAAA
381189 AAAATTCAAAAACTC-AACT
1 AAAATTCAAAAACTCGAACT
*
381208 AAAATTC-AAGACTCGAACT
1 AAAATTCAAAAACTCGAACT
381227 CGATTAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATTCAAAAACTCGAACT
Found at i:381241 original size:11 final size:11
Alignment explanation
Indices: 381225--381267 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
381215 AAGACTCGAA
381225 CTCGATTAAAG
1 CTCGATTAAAG
* *
381236 CTCGATTCAGG
1 CTCGATTAAAG
*
381247 CTCGATTCAAG
1 CTCGATTAAAG
*
381258 TTCGATTAAA
1 CTCGATTAAA
381268 ACTCAATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (11 bp):
CTCGATTAAAG
Found at i:381263 original size:33 final size:33
Alignment explanation
Indices: 381226--381290 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
381216 AGACTCGAAC
* * *
381226 TCGATTAAAGCTCGATTCAGGCTCGATTCAAGT
1 TCGATTAAAACTCAATTCAGGCTCAATTCAAGT
381259 TCGATTAAAACTCAATTCAGGCTCAATTCAAG
1 TCGATTAAAACTCAATTCAGGCTCAATTCAAG
381291 CTAAGTGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (33 bp):
TCGATTAAAACTCAATTCAGGCTCAATTCAAGT
Found at i:382518 original size:7 final size:7
Alignment explanation
Indices: 382503--382604 Score: 57
Period size: 7 Copynumber: 14.6 Consensus size: 7
382493 GGGTTAAGGA
*
382503 TTTAGGG
1 TTTATGG
382510 TTTATGG
1 TTTATGG
382517 TTTA-GAG
1 TTTATG-G
* *
382524 TTTAAGA
1 TTTATGG
382531 TTTATGG
1 TTTATGG
382538 TTTA-GAG
1 TTTATG-G
382545 TTTATGG
1 TTTATGG
*
382552 TTTAAGG
1 TTTATGG
*
382559 TTTGA-GA
1 TTT-ATGG
*
382566 TTTAGGG
1 TTTATGG
*
382573 TTTATAG
1 TTTATGG
**
382580 TTTATTA
1 TTTATGG
*
382587 TTTATGA
1 TTTATGG
*
382594 TTTAGGG
1 TTTATGG
382601 TTTA
1 TTTA
382605 GGATTTAGGG
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
6 3 0.04
7 69 0.92
8 3 0.04
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (7 bp):
TTTATGG
Found at i:382518 original size:21 final size:21
Alignment explanation
Indices: 382494--382615 Score: 97
Period size: 21 Copynumber: 5.8 Consensus size: 21
382484 CACATAATCG
*
382494 GGTTAAGGATTTAGGGTTTAT
1 GGTTTAGGATTTAGGGTTTAT
* *
382515 GGTTTA-GAGTTTAAGATTTAT
1 GGTTTAGGA-TTTAGGGTTTAT
* *
382536 GGTTTA-GAGTTTATGGTTTAA
1 GGTTTAGGA-TTTAGGGTTTAT
382557 GGTTT-GAGATTTAGGGTTTAT
1 GGTTTAG-GATTTAGGGTTTAT
* ** * * *
382578 AGTTTATTATTTATGATTTAG
1 GGTTTAGGATTTAGGGTTTAT
382599 GGTTTAGGATTTAGGGT
1 GGTTTAGGATTTAGGGT
382616 GTAATATAAC
Statistics
Matches: 78, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
20 2 0.03
21 74 0.95
22 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
GGTTTAGGATTTAGGGTTTAT
Found at i:382520 original size:14 final size:14
Alignment explanation
Indices: 382503--382615 Score: 70
Period size: 14 Copynumber: 8.1 Consensus size: 14
382493 GGGTTAAGGA
* *
382503 TTTAGGGTTTATGG
1 TTTATGGTTTAGGG
* *
382517 TTTA-GAGTTTAAGA
1 TTTATG-GTTTAGGG
*
382531 TTTATGGTTTAGAG
1 TTTATGGTTTAGGG
*
382545 TTTATGGTTTAAGG
1 TTTATGGTTTAGGG
*
382559 TTTGA-GATTTAGGG
1 TTT-ATGGTTTAGGG
* ***
382573 TTTATAGTTTATTA
1 TTTATGGTTTAGGG
*
382587 TTTATGATTTAGGG
1 TTTATGGTTTAGGG
382601 TTTA-GGATTTAGGG
1 TTTATGG-TTTAGGG
382615 T
1 T
382616 GTAATATAAC
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
13 3 0.04
14 69 0.93
15 2 0.03
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (14 bp):
TTTATGGTTTAGGG
Found at i:382539 original size:28 final size:28
Alignment explanation
Indices: 382496--382605 Score: 98
Period size: 28 Copynumber: 3.9 Consensus size: 28
382486 CATAATCGGG
* * *
382496 TTAAGGATTTAGGGTTTATGGTTTAGAGT
1 TTAA-GATTTATGATTTAGGGTTTAGAGT
* *
382525 TTAAGATTTATGGTTTAGAGTTTATG-GT
1 TTAAGATTTATGATTTAGGGTTTA-GAGT
* *
382553 TTAAGGTTTGA-GATTTAGGGTTTATAGT
1 TTAAGATTT-ATGATTTAGGGTTTAGAGT
**
382581 TTATTATTTATGATTTAGGGTTTAG
1 TTAAGATTTATGATTTAGGGTTTAG
382606 GATTTAGGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.02
28 59 0.89
29 6 0.09
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (28 bp):
TTAAGATTTATGATTTAGGGTTTAGAGT
Found at i:386117 original size:5 final size:5
Alignment explanation
Indices: 386107--386134 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
386097 ACCAAACATC
386107 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
386135 GATGAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:388343 original size:27 final size:27
Alignment explanation
Indices: 388308--388383 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
388298 CTCAGAGAAT
388308 GGGGGGCACGAGAAAGGGAGAGGGAGC
1 GGGGGGCACGAGAAAGGGAGAGGGAGC
388335 GGGGGGCACGAGAAAGGGAGAGGGAGC
1 GGGGGGCACGAGAAAGGGAGAGGGAGC
* *
388362 GGGCGACACGAGAAA-GGAGAGG
1 GGGGGGCACGAGAAAGGGAGAGG
388384 AGCACGGAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 7 0.15
27 40 0.85
ACGTcount: A:0.32, C:0.12, G:0.57, T:0.00
Consensus pattern (27 bp):
GGGGGGCACGAGAAAGGGAGAGGGAGC
Found at i:392925 original size:118 final size:117
Alignment explanation
Indices: 392716--393170 Score: 518
Period size: 118 Copynumber: 3.8 Consensus size: 117
392706 TCTGAGCTAT
* * * * * *
392716 AAGTTTTTCTCATTATAAACTT-TTC-GCTCACTTCGGACGAGTTCTTCTTATTATGAACTTTTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCGGACGAGTTCTTCTCATTATGAAC-TCTC
* * * * * *
392779 CACTGGGAATGATGATCTATCTCTTTCTGTGATAGAATCTAACTAAGGTTGAAC
64 CATTGGAAATGTTGATCCATCTCCTTCTGTGATAGAATCGAACTAAGGTTGAAC
* * * *
392833 AAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTCGGACGAGTTATTCTCATTATAAACTTTTCC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAAC-TCTCC
* *
392898 GTTGGAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACTAAGGTTGAAC
65 ATTGGAAATGTTGATCCATCTCCTTCTGTGATAGAATCGAACTAAGGTTGAAC
* * * * *
392951 AAGTTCTTTTCATTTTGAACTTCTTCTTCCTATTCGAATGAGTTCTTCTCATTATGAACTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCA
* * * * * *
393016 TTGAAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAAC
66 TTG-GAA-----ATGTTGATCCATCTCCTTCTGTGATAGAATCGAAC-TAAGGTTGAAC
*
393075 AAGTTCTTCTCATTATGATCTTCTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCA
* *
393140 TTGGAAATGTTGATCCACCTCTTTCTGTGAT
66 TTGGAAATGTTGATCCATCTCCTTCTGTGAT
393171 GGATTTGAAT
Statistics
Matches: 285, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
117 27 0.09
118 154 0.54
123 32 0.11
124 72 0.25
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (117 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCA
TTGGAAATGTTGATCCATCTCCTTCTGTGATAGAATCGAACTAAGGTTGAAC
Found at i:394166 original size:4 final size:4
Alignment explanation
Indices: 394152--394192 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
394142 TTTTATTTTC
*
394152 TCTT T-TT TCTT TCTT TCTT TCTT T-TT TC-T TCTT TTTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
394193 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 9 0.28
4 23 0.72
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TCTT
Found at i:394176 original size:18 final size:18
Alignment explanation
Indices: 394152--394192 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
394142 TTTTATTTTC
394152 TCTTTTTTCTTTCTTTCTT
1 TCTTTTTTC-TTCTTTCTT
*
394171 TCTTTTTTCTTCTTTTTT
1 TCTTTTTTCTTCTTTCTT
394189 TCTT
1 TCTT
394193 CAAGCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TCTTTTTTCTTCTTTCTT
Found at i:406731 original size:154 final size:154
Alignment explanation
Indices: 406476--406780 Score: 522
Period size: 154 Copynumber: 2.0 Consensus size: 154
406466 AGAGTATCAT
* *
406476 CATTTGTCTCAATATATGGAACATTACTTGTAACATAAGCATTGATTTCTTCCTCAGTTCCCAAA
1 CATTTGTCTCAATATATGGAACATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
*
406541 CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGGAACAACTCCTGC
66 CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTGC
406606 AGAATGAATCCATGGCCTCCCAAA
131 AGAATGAATCCATGGCCTCCCAAA
* *
406630 CATTTGTCTCAATATATGGAGCATTACTTGTAATAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
1 CATTTGTCTCAATATATGGAACATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
* *
406695 CATTTCAATTAA-TAGTCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTG
66 CATATCAATTAACCA-TCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTG
*
406759 CATAATGAATCCATGGCCTCCC
130 CAGAATGAATCCATGGCCTCCC
406781 CTGTAAGCAA
Statistics
Matches: 142, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
153 1 0.01
154 141 0.99
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (154 bp):
CATTTGTCTCAATATATGGAACATTACTTGTAACAGAAGCATTGATTTCTTCCTCAGCTCCCAAA
CATATCAATTAACCATCAATAACAAACTTCAGTTTTTGATGTAAAGAAGAAGAAACAACTCCTGC
AGAATGAATCCATGGCCTCCCAAA
Found at i:414011 original size:2 final size:2
Alignment explanation
Indices: 414004--414031 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
413994 TGAGTCTTTC
414004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
414032 TCATGTGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:417422 original size:14 final size:15
Alignment explanation
Indices: 417403--417449 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
417393 GGTCTGTAAT
417403 TATTTATTT-ATATA
1 TATTTATTTAATATA
417417 TATTTATTTAATATA
1 TATTTATTTAATATA
* *
417432 TATTAATAATAATATA
1 TATTTAT-TTAATATA
417448 TA
1 TA
417450 ATATAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.31
15 11 0.38
16 9 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:417443 original size:3 final size:3
Alignment explanation
Indices: 417425--417532 Score: 150
Period size: 3 Copynumber: 36.0 Consensus size: 3
417415 TATATTTATT
*
417425 TAA TATA TAT TAA TAA TAA TATA TAA T-A TAA TAA T-A TAAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA
417471 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
417518 TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA
417533 ATAAGTAATG
Statistics
Matches: 95, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
2 6 0.06
3 81 0.85
4 8 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:418017 original size:113 final size:112
Alignment explanation
Indices: 417675--418305 Score: 795
Period size: 113 Copynumber: 5.6 Consensus size: 112
417665 ATTGAATAAA
* * * * *
417675 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATG-ACTTTCTGCTGG-GATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATAATCCATC
* *
417737 AAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAATGATGAATTCAGA-AAAAAG-TTGAACAAATTCTTCTCATTATGAAC
* * * * *
417786 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT-ATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCC
* *
417849 ATCAAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAGA-AAAAAG-TTGAACAAATTCTTCTCATTATGAAC
417901 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
*
417966 ATTTGATGAATTCAGAAAAAAGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCAGAAAAAAGTTGAACAAATTCTTCTCATTATGAAC
418014 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
* *
418079 ATTTGATGAATTCAGAAAAAGGTTGAACAAATTCTTCTCATTATGAA-
66 A-ATGATGAATTCAGAAAAAAGTTGAACAAATTCTTCTCATTATGAAC
* *
418126 --CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATC-
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
* * * * * *
418188 AGTGATAGAATT-AGGCAGAAGGTTTAAC-AATTCTTCTCATTATGAAT
66 AATGAT-GAATTCA-GAAAAAAGTTGAACAAATTCTTCTCATTATGAAC
* *
418235 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTTGAAATG-TCAATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAT-AATCCATC
418299 AAATGAT
65 AAATGAT
418306 AGATTTGAAT
Statistics
Matches: 478, Mismatches: 24, Indels: 35
0.89 0.04 0.07
Matches are distributed among these distances:
108 23 0.05
109 17 0.04
110 61 0.13
111 63 0.13
112 30 0.06
113 162 0.34
114 26 0.05
115 94 0.20
116 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
AATGATGAATTCAGAAAAAAGTTGAACAAATTCTTCTCATTATGAAC
Found at i:419138 original size:82 final size:83
Alignment explanation
Indices: 418939--419652 Score: 1142
Period size: 83 Copynumber: 8.7 Consensus size: 83
418929 AGTTCTTACC
* * * *
418939 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419004 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
* * * *
419022 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTC-CAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419086 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
419104 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419169 TCAA-GATTGGTTCTG-T
66 TCAATGATTGGTTCTGCT
* * * * **
419185 CCAACCA-ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAA
1 -AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAA
419249 TTCAATGATTGGTTCTGCT
65 TTCAATGATTGGTTCTGCT
*
419268 AAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419333 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
* * **
419351 AAA-C----CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCCAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419411 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
*
419429 AAACC-GGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419493 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
*
419511 AAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
419576 TCAATGATTGGTTCTGCT
66 TCAATGATTGGTTCTGCT
**
419594 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
419653 TCAGTTAATG
Statistics
Matches: 591, Mismatches: 30, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
78 73 0.12
79 1 0.00
81 58 0.10
82 186 0.31
83 273 0.46
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
TCAATGATTGGTTCTGCT
Found at i:419506 original size:243 final size:244
Alignment explanation
Indices: 418938--419652 Score: 1150
Period size: 243 Copynumber: 2.9 Consensus size: 244
418928 TAGTTCTTAC
418938 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
1 CAAACCA-ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
* *
419003 TTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
65 TTCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
* * *
419068 GCATATTCATCTTC-CAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACAC
130 ACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACC--A-CAGATAACTCAAAGAACAC
*
419132 TTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAAGATTGGTTCTGT
192 TTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAAGATTGGTTCTGT
* *
419185 CCAACCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAAT
1 CAAACCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
419250 TCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAA
66 TCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAA
419315 CAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAA-C-CAGATAACTCAAAGAACACTTCC
131 CAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACCACAGATAACTCAAAGAACACTTCC
* * *
419378 AGAAGATGCTATTAATACATTCATCTTCCCAATTCAATGATTGGTTCTG-
196 AGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA-GATTGGTTCTGT
** * * * *
419427 CTAAACCGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAA
1 C-AAACCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
419492 TTCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
65 TTCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
419557 ACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACAC
130 ACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACC--A-CAGATAACTCAAAGAACAC
**
419622 TTCCAGAAGATGCTATTGGCAAATTCATCTT
192 TTCCAGAAGATGCTATTAACAAATTCATCTT
419653 TCAGTTAATG
Statistics
Matches: 437, Mismatches: 23, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
242 57 0.13
243 171 0.39
244 1 0.00
246 132 0.30
247 30 0.07
248 46 0.11
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (244 bp):
CAAACCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
TCAATGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAA
CAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACCACAGATAACTCAAAGAACACTTCC
AGAAGATGCTATTAACAAATTCATCTTCCAAATTCAAGATTGGTTCTGT
Found at i:420784 original size:10 final size:10
Alignment explanation
Indices: 420769--420806 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
420759 TTGACCCCTC
*
420769 TTTTTTCTCT
1 TTTTTTTTCT
420779 TTTTTTTTCTT
1 TTTTTTTTC-T
420790 TTTTTTTTCT
1 TTTTTTTTCT
420800 TTTTTTT
1 TTTTTTT
420807 CTTCAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:420786 original size:12 final size:11
Alignment explanation
Indices: 420769--420806 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
420759 TTGACCCCTC
420769 TTTTTTCTCTTT
1 TTTTTTCT-TTT
420781 TTTTTTCTTTT
1 TTTTTTCTTTT
420792 TTTTTTCTTTT
1 TTTTTTCTTTT
420803 TTTT
1 TTTT
420807 CTTCAAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:420806 original size:9 final size:9
Alignment explanation
Indices: 420767--420809 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
420757 CCTTGACCCC
*
420767 TCTTTTTTC
1 TCTTTTTTT
420776 TCTTTTTTTT
1 TC-TTTTTTT
420786 TCTTTTTTTTT
1 TC--TTTTTTT
420797 TCTTTTTTT
1 TCTTTTTTT
420806 TCTT
1 TCTT
420810 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 13 0.42
10 8 0.26
11 10 0.32
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TCTTTTTTT
Done.