Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold91
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: 1327174
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 48727 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:150063 original size:52 final size:52
Alignment explanation
Indices: 149933--150106 Score: 203
Period size: 52 Copynumber: 3.4 Consensus size: 52
149923 GATTTCTCAT
* * *
149933 AATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACTAATTTTCC-AC
1 AATCGAGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCTTC
* * *
149984 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTC
* * *
150036 AATCGAGGATACTCCAACTCCAATTTTATTTCTAAAAACACCAATTTT--TTAC
1 AATCGAGGATACTCCAACCCCGATTTTATTT-TCAAAACACCAATTTTCCTT-C
*
150088 AATCGATGATACTCCAACC
1 AATCGAGGATACTCCAACC
150107 TCATTATTTC
Statistics
Matches: 107, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
51 44 0.41
52 48 0.45
53 15 0.14
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (52 bp):
AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTC
Found at i:150070 original size:103 final size:103
Alignment explanation
Indices: 149886--150106 Score: 275
Period size: 102 Copynumber: 2.1 Consensus size: 103
149876 TTACCTCCGA
* *** *
149886 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCATAATCGAGGATACTCCAAC
* *
149951 CCCGATTTTATTTCT-AAAACACTAATTTTCCACAATC
66 CCCAATTTTATTTCTAAAAACACCAATTTTCCACAATC
* * *
149988 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-TCCTTTAATCGAGGATACTCCA
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCT-C-ATAATCGAGGATACTCCA
* **
150052 ACTCCAATTTTATTTCTAAAAACACCAATTTTTTACAATC
64 ACCCCAATTTTATTTCTAAAAACACCAATTTTCCACAATC
**
150092 GATGATACTCCAACC
1 GGGGATACTCCAACC
150107 TCATTATTTC
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
101 1 0.01
102 37 0.37
103 31 0.31
104 32 0.32
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (103 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCATAATCGAGGATACTCCAAC
CCCAATTTTATTTCTAAAAACACCAATTTTCCACAATC
Found at i:150126 original size:28 final size:28
Alignment explanation
Indices: 150095--150169 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
150085 TACAATCGAT
* *
150095 GATACTCCAACCTCATTA-TTTC-ATCGGG
1 GATACTCCAACCCCATTACCTTCGA--GGG
*
150123 GATACTCCAACCCCGTTACCTTCGAGGG
1 GATACTCCAACCCCATTACCTTCGAGGG
150151 GATACTCCAACCCCATTAC
1 GATACTCCAACCCCATTAC
150170 TATCTCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 37 0.90
29 3 0.07
30 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (28 bp):
GATACTCCAACCCCATTACCTTCGAGGG
Found at i:155850 original size:2 final size:2
Alignment explanation
Indices: 155845--155878 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
155835 TCACACACAC
155845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155879 GATAATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:156073 original size:34 final size:34
Alignment explanation
Indices: 156030--156112 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
156020 GTATCATTCG
* *
156030 ATCAAAAACTATTTGTGTTCACTCAAAATCTTAA
1 ATCAAAAACTATTTGAGATCACTCAAAATCTTAA
**
156064 ATCAAAAACTATTTGAGATCTTTCAAAATCTTAA
1 ATCAAAAACTATTTGAGATCACTCAAAATCTTAA
* *
156098 ATTAAAACCTATTTG
1 ATCAAAAACTATTTG
156113 GGAATGACCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (34 bp):
ATCAAAAACTATTTGAGATCACTCAAAATCTTAA
Found at i:156170 original size:19 final size:19
Alignment explanation
Indices: 156146--156196 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
156136 TAATTTGATA
156146 ATTTATATATTTATATTAT
1 ATTTATATATTTATATTAT
*
156165 ATTTATATATTT-TATCAT
1 ATTTATATATTTATATTAT
156183 A-TTATA-A-TTATATT
1 ATTTATATATTTATATT
156197 TAAAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 4 0.14
17 5 0.17
18 6 0.21
19 12 0.41
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:156206 original size:29 final size:28
Alignment explanation
Indices: 156147--156216 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
156137 AATTTGATAA
*
156147 TTTATATATTTATATTATATTTATATAT
1 TTTATATATTTATATTATATTTAAATAT
156175 TTTATCATA-TTATAATTATATTTAAA-AT
1 TTTAT-ATATTTAT-ATTATATTTAAATAT
*
156203 TTT-TTTATTTATAT
1 TTTATATATTTATAT
156217 AAATTTTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 4 0.11
27 5 0.14
28 14 0.38
29 14 0.38
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTATATATTTATATTATATTTAAATAT
Found at i:156287 original size:11 final size:11
Alignment explanation
Indices: 156267--156309 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
156257 AAATATTTGT
*
156267 ATATTCATATC
1 ATATTTATATC
*
156278 GTATTTATATC
1 ATATTTATATC
156289 ATTATTTATATC
1 A-TATTTATATC
156301 ATA-TTATAT
1 ATATTTATAT
156310 TTTATATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 6 0.21
11 11 0.39
12 11 0.39
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (11 bp):
ATATTTATATC
Found at i:156298 original size:29 final size:28
Alignment explanation
Indices: 156266--156323 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
156256 AAAATATTTG
*
156266 TATATTCATATCGTA-TTTATATCATTATT
1 TATA-TCATATCATATTTTATATCA-TATT
*
156295 TATATCATATTATATTTTATATCATATT
1 TATATCATATCATATTTTATATCATATT
156323 T
1 T
156324 TAATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (28 bp):
TATATCATATCATATTTTATATCATATT
Found at i:156304 original size:17 final size:17
Alignment explanation
Indices: 156284--156321 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
156274 TATCGTATTT
156284 ATATCAT-TATTTATATC
1 ATATCATAT-TTTATATC
*
156301 ATATTATATTTTATATC
1 ATATCATATTTTATATC
156318 ATAT
1 ATAT
156322 TTTAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATCATATTTTATATC
Found at i:156325 original size:29 final size:29
Alignment explanation
Indices: 156259--156325 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
156249 AAATTTTAAA
*
156259 ATATTTGTATATTCATATCGTATTTATATC
1 ATATTT-TATATTCATATCATATTTATATC
*
156289 AT-TATTTATA-TCATATTATATTTTATATC
1 ATAT-TTTATATTCATATCATA-TTTATATC
156318 ATATTTTA
1 ATATTTTA
156326 ATAATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 8 0.25
29 19 0.59
30 5 0.16
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (29 bp):
ATATTTTATATTCATATCATATTTATATC
Found at i:159952 original size:10 final size:10
Alignment explanation
Indices: 159937--159961 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
159927 AGGCACCCAC
159937 AGAAAAGGAA
1 AGAAAAGGAA
159947 AGAAAAGGAA
1 AGAAAAGGAA
159957 AGAAA
1 AGAAA
159962 GAAGAGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AGAAAAGGAA
Found at i:159980 original size:7 final size:7
Alignment explanation
Indices: 159962--159996 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
159952 AGGAAAGAAA
159962 GAAGAGG
1 GAAGAGG
159969 AGAAGAGG
1 -GAAGAGG
*
159977 GAAGAAG
1 GAAGAGG
159984 GAAGAGG
1 GAAGAGG
159991 GAAGAG
1 GAAGAG
159997 AGAGTGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (7 bp):
GAAGAGG
Found at i:159981 original size:22 final size:22
Alignment explanation
Indices: 159947--159996 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
159937 AGAAAAGGAA
*
159947 AGAAAAGGAAAGAAAGAAGAGG
1 AGAAGAGGAAAGAAAGAAGAGG
* *
159969 AGAAGAGGGAAGAAGGAAGAGG
1 AGAAGAGGAAAGAAAGAAGAGG
159991 -GAAGAG
1 AGAAGAG
159997 AGAGTGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (22 bp):
AGAAGAGGAAAGAAAGAAGAGG
Found at i:163316 original size:29 final size:28
Alignment explanation
Indices: 163281--163356 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
163271 AGATCATTTT
*
163281 GTAATTTCATGCATTTTAGGATTGTCTTA
1 GTAATTTCATGCATTTTAGGATT-ACTTA
* * *
163310 GTCATTTTCAATG-ATTTAAGGATTACTTT
1 GT-AATTTC-ATGCATTTTAGGATTACTTA
163339 GTAATTTCATGCATTTTA
1 GTAATTTCATGCATTTTA
163357 AGCAATTTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
27 3 0.08
28 10 0.26
29 7 0.18
30 15 0.39
31 3 0.08
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (28 bp):
GTAATTTCATGCATTTTAGGATTACTTA
Found at i:163357 original size:29 final size:30
Alignment explanation
Indices: 163278--163358 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
163268 AAAAGATCAT
*
163278 TTTGTAATTTCATGCATTTT-AGGATTGTC
1 TTTGTAATTTCATGCATTTTAAGGATTGAC
* *
163307 TTAGTCATTTTCAATG-A-TTTAAGGATT-AC
1 TTTGT-AATTTC-ATGCATTTTAAGGATTGAC
163336 TTTGTAATTTCATGCATTTTAAG
1 TTTGTAATTTCATGCATTTTAAG
163359 CAATTTAGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
27 3 0.07
28 6 0.14
29 18 0.43
30 12 0.29
31 3 0.07
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (30 bp):
TTTGTAATTTCATGCATTTTAAGGATTGAC
Found at i:165008 original size:16 final size:17
Alignment explanation
Indices: 164979--165010 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
164969 AAAATAAAAT
164979 TTAAAGATTAAATATTC
1 TTAAAGATTAAATATTC
164996 TTAAAGA-TAAATATT
1 TTAAAGATTAAATATT
165011 AATTATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAAAGATTAAATATTC
Found at i:165784 original size:2 final size:2
Alignment explanation
Indices: 165777--165811 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
165767 CTTTAAGTTT
165777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
165812 TTTAAGAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:166386 original size:9 final size:8
Alignment explanation
Indices: 166339--166389 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 8
166329 TTATTTTTAA
166339 TAATATTAT
1 TAATATT-T
166348 TAAATAATTT
1 T-AAT-ATTT
166358 TAA-ATTT
1 TAATATTT
166365 TAA-ATTT
1 TAATATTT
166372 TAATATTT
1 TAATATTT
166380 ATAATATTT
1 -TAATATTT
166389 T
1 T
166390 TTTTACTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
7 14 0.37
8 5 0.13
9 11 0.29
10 5 0.13
11 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TAATATTT
Found at i:166951 original size:7 final size:8
Alignment explanation
Indices: 166905--166950 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
166895 TATTTTTCAT
166905 ATTAAAAA
1 ATTAAAAA
* *
166913 ATTGAATA
1 ATTAAAAA
*
166921 A--AAAAT
1 ATTAAAAA
166927 ATTAAAAA
1 ATTAAAAA
166935 ATTAAAAA
1 ATTAAAAA
166943 ATTAAAAA
1 ATTAAAAA
166951 TAAATAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
6 3 0.10
8 27 0.90
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
ATTAAAAA
Found at i:166958 original size:18 final size:18
Alignment explanation
Indices: 166917--166961 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
166907 TAAAAAATTG
*
166917 AATAAAAAATATTAAAAA
1 AATAAAAAATATAAAAAA
*
166935 ATTAAAAAAT-TAAAAATA
1 AATAAAAAATATAAAAA-A
166953 AATAAAAAA
1 AATAAAAAA
166962 GAAGTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAAAAAATATAAAAAA
Found at i:166970 original size:30 final size:30
Alignment explanation
Indices: 166905--166970 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
166895 TATTTTTCAT
*
166905 ATTAAAAAATTGAATAAAAAATATTAAAAA
1 ATTAAAAAATTGAATAAAAAATATAAAAAA
166935 ATTAAAAAATT-AA-AAATAAATA-AAAAAGA
1 ATTAAAAAATTGAATAAA-AAATATAAAAA-A
166964 AGTTAAA
1 A-TTAAA
166971 TTTTTATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 7 0.22
29 9 0.28
30 16 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (30 bp):
ATTAAAAAATTGAATAAAAAATATAAAAAA
Found at i:167628 original size:14 final size:14
Alignment explanation
Indices: 167609--167636 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
167599 CTTATTTTTT
167609 ATTATTTAAATAAA
1 ATTATTTAAATAAA
167623 ATTATTTAAATAAA
1 ATTATTTAAATAAA
167637 TTTAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATTTAAATAAA
Found at i:167672 original size:16 final size:16
Alignment explanation
Indices: 167653--167699 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
167643 TAATATAATT
167653 TTTATCTTAAATTAAA
1 TTTATCTTAAATTAAA
*
167669 TTTAAT-TAAAATTAAA
1 TTT-ATCTTAAATTAAA
*
167685 TTAATCTTTAAATTA
1 TTTATC-TTAAATTA
167700 CAAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 9 0.36
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATCTTAAATTAAA
Found at i:168393 original size:24 final size:22
Alignment explanation
Indices: 168349--168397 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
168339 TTTAAAAATT
*
168349 TTTAAATTTAATAAAATAATATA
1 TTTAAATATAATAAAATAATA-A
168372 TTTAAATAATAAT-AAATAAATAA
1 TTTAAAT-ATAATAAAAT-AATAA
168395 TTT
1 TTT
168398 TTAATTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAATATAATAAAATAATAA
Found at i:169178 original size:18 final size:18
Alignment explanation
Indices: 169157--169227 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 18
169147 ATATTTTAAT
169157 AATAATTATATTAATATA
1 AATAATTATATTAATATA
*
169175 AATAA-TAT-TT-TTAT-
1 AATAATTATATTAATATA
* * *
169189 AATAAATAGTATTATTTTA
1 AATAATTA-TATTAATATA
*
169208 AATAGTTAATATTAATATA
1 AATAATT-ATATTAATATA
169227 A
1 A
169228 TATTTAATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.12
15 5 0.12
16 3 0.07
17 5 0.12
18 8 0.20
19 14 0.34
20 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AATAATTATATTAATATA
Found at i:169187 original size:33 final size:32
Alignment explanation
Indices: 169140--169211 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
169130 TTGAAAAAAG
*
169140 TAAATTAATATTTTAATAATAATTA-TATTAATA
1 TAAA-TAATATTTT-ATAATAAATAGTATTAATA
* *
169173 TAAATAATATTTTTATAATAAATAGTATTATTT
1 TAAATAATA-TTTTATAATAAATAGTATTAATA
169206 TAAATA
1 TAAATA
169212 GTTAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 14 0.41
33 20 0.59
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TAAATAATATTTTATAATAAATAGTATTAATA
Found at i:170088 original size:2 final size:2
Alignment explanation
Indices: 170081--170107 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
170071 GCTTAATTTC
170081 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
170108 CATAGAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:171166 original size:16 final size:16
Alignment explanation
Indices: 171142--171172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
171132 ATTTGTTCTC
*
171142 CATATTATATAAATAA
1 CATAGTATATAAATAA
171158 CATAGTATATAAATA
1 CATAGTATATAAATA
171173 TATATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
CATAGTATATAAATAA
Found at i:174294 original size:27 final size:27
Alignment explanation
Indices: 174256--174329 Score: 148
Period size: 27 Copynumber: 2.7 Consensus size: 27
174246 TTTGATTGAA
174256 AATGGGGTTGGAGTGTCCCCTCGGAGG
1 AATGGGGTTGGAGTGTCCCCTCGGAGG
174283 AATGGGGTTGGAGTGTCCCCTCGGAGG
1 AATGGGGTTGGAGTGTCCCCTCGGAGG
174310 AATGGGGTTGGAGTGTCCCC
1 AATGGGGTTGGAGTGTCCCC
174330 GATGAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.43, T:0.23
Consensus pattern (27 bp):
AATGGGGTTGGAGTGTCCCCTCGGAGG
Found at i:176686 original size:67 final size:68
Alignment explanation
Indices: 176564--176690 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
176554 ATTGGGTTTT
* * *
176564 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
176629 AGA
66 AGA
* * * *
176632 AAAG-TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
176691 TGAAAAAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:176769 original size:49 final size:49
Alignment explanation
Indices: 176695--177228 Score: 696
Period size: 49 Copynumber: 10.9 Consensus size: 49
176685 AGATGATGAA
* *
176695 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
176745 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * *
176794 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA-TGGACTTAATGGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
176842 GCAA-GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * * * *
176891 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
176940 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * *
176989 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
177038 GCAA-GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * * * *
177087 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
177136 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * * *
177185 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
177229 GAAGGGTTGC
Statistics
Matches: 415, Mismatches: 64, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
48 43 0.10
49 366 0.88
50 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:176990 original size:98 final size:98
Alignment explanation
Indices: 176704--177228 Score: 921
Period size: 98 Copynumber: 5.4 Consensus size: 98
176694 AAAAGGATGT
* * * * *
176704 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
*
176769 GGCCAGCTACATTGGACTTAAAGATAAAGGTGC
66 GGCCAGCTACATTGGACTTAAAGATAAAAGTGC
176802 CAATATGCTGATTCAAGGCCAGCTATA-TGGACTTAATGGTGCAA-GTGCCAATGTGCTGAGTCA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTG-AAGGTGCCAATGTGCTGAGTCA
176865 AGGCCAGCTACATTGGACTTAAAGATAAAAGTGC
65 AGGCCAGCTACATTGGACTTAAAGATAAAAGTGC
*
176899 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
*
176964 GGCCAGCTACATTGGACTTAAAGATAAAGGTGC
66 GGCCAGCTACATTGGACTTAAAGATAAAAGTGC
176997 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGCAA-GTGCCAATGTGCTGAGTCA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTG-AAGGTGCCAATGTGCTGAGTCA
177061 AGGCCAGCTACATTGGACTTAAAGATAAAAGTGC
65 AGGCCAGCTACATTGGACTTAAAGATAAAAGTGC
*
177095 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
177160 GGCCAGCTACATTGGACTTAAAGATAAAAGTGC
66 GGCCAGCTACATTGGACTTAAAGATAAAAGTGC
*
177193 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
177229 GAAGGGTTGC
Statistics
Matches: 411, Mismatches: 11, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
97 94 0.23
98 315 0.77
99 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (98 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
GGCCAGCTACATTGGACTTAAAGATAAAAGTGC
Found at i:177272 original size:33 final size:35
Alignment explanation
Indices: 177228--177297 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
177218 TATTGGGCTT
177228 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
*
177262 AGAA-GGTTGCCATCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
177296 AG
1 AG
177298 GGTGAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:177344 original size:33 final size:33
Alignment explanation
Indices: 177302--178180 Score: 760
Period size: 34 Copynumber: 26.6 Consensus size: 33
177292 AGGAAGGGTG
* * *
177302 AAAGATGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
177335 CAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAA-G--AA
* * *
177372 AAAGGGTGCCACGAAGTTGTGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
177406 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
177440 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
*
177474 AAAGAGTGCCACGGAGTTGTGGGCTT-AAAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
177507 AAAGAGTGCCACGTAGTTGTGGGCTT-TAAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
177540 AAAGAGTGCCACGGAGTCGTGGACTT-AAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
177571 ---GGTGCCACAGAGTTGTGGGCTTAGAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAG-AA
*
177602 AGAAGGTGCCATGGAGTTGTGGGCTTTAAAAAGGGAA
1 A-AAGGTGCCACGGAGTTGTGGGC-TTAAAAA--GAA
177639 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
*
177674 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAA-AGAA
*
177710 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
177745 AAAGTGTGCCACAGAGTTGTGGGCTTTGAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
*
177780 GAAGGTGCCACGGAGTTGTGGGCTT--AAAG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
** * *
177810 TGAGGTGCCACGGAATTGTGGGCTTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
177841 ---GGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
*
177871 CAAGGTGCCACGGAGTTGTGGGCTTTAAAGAA-AA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAA-AAGAA
* * **
177905 AAAGAGTGCCACGAAGTTCTGGGCTTTAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
177940 AAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAAGAA
*
177974 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
*
178007 --A-GTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
178038 GAAGGTGCCATGGAGTTGTGGGCTT--AAAG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
** * *
178068 TGAGGTGCCACGGAATTGTGGGCTTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
178099 ---GGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
178129 CAAGGTGCCACGGAGTTGTGGGCTT-TAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
178161 AAA-ATGCCACTGAGTTGTGG
1 AAAGGTGCCACGGAGTTGTGG
178181 ACTTTGAGAC
Statistics
Matches: 724, Mismatches: 75, Indels: 96
0.81 0.08 0.11
Matches are distributed among these distances:
27 18 0.02
28 52 0.07
29 26 0.04
30 45 0.06
31 24 0.03
32 15 0.02
33 127 0.18
34 197 0.27
35 121 0.17
36 21 0.03
37 59 0.08
38 19 0.03
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
Found at i:177354 original size:71 final size:70
Alignment explanation
Indices: 177282--178157 Score: 715
Period size: 71 Copynumber: 13.2 Consensus size: 70
177272 CATCGACTTG
* ** * *
177282 TGTGGGCTTTAGGAAGGGTGAAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAACAAG-GTGCCA
1 TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCA
*
177345 CAGAGT
65 CGGAGT
* * * *
177351 TGTGGGCTTTAAAAAGGAAAAAAAGGGTGCCACGAAGTTGTGGGCTTAGAAGGAAAAAGAGTGCC
1 TGTGGGCTTT-AAAAGG-GAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCC
177416 ACGGAGT
64 ACGGAGT
* * * *
177423 TGTGGGC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCAC
177486 GGAGT
66 GGAGT
* * *
177491 TGTGGGC-TTAAAA-GG-AAAAGAGTGCCACGTAGTTGTGGGCTT-TAAAGGAAAAGAGTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCAC
177552 GGAGT
66 GGAGT
* * * *
177557 CGTGGAC-TTAAAA--G-----G-GTGCCAC-AGAGTTGTGGGCTT-AGAAGGAAAAGAAGGTGC
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAAGAAAAAG-A-GTGC
*
177611 CATGGAGT
63 CACGGAGT
*
177619 TGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCC
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGC-TTAAAAAGAAAAAGAGTGCC
177683 ACGGAGT
64 ACGGAGT
*
177690 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCAC-AGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGC
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGA-AGTTGTGGGC-TTAAAAAGAAAAAGAGTGC
*
177754 CACAGAGT
63 CACGGAGT
* * **
177762 TGTGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTT--AAAG-ATGAG-GTGCCA
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCA
*
177820 CGGAAT
65 CGGAGT
* * * *
177826 TGTGGGCTTTAAAA--G-----G-GTGCCACGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCAC
177882 GGAGT
66 GGAGT
** * ** *
177887 TGTGGGCTTT-AAAGAAAAAAAGAGTGCCACGAAGTTCTGGGCTTTAAAGGGAAAAAGGGTGCCA
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGC-TTAAAAAGAAAAAGAGTGCCA
177951 CGGAGT
65 CGGAGT
* *
177957 TGTGGGC-TTAGAA-GGAAAAAGAGTGCCAC-AGAGTTGTGGGCTT-----TAAAAAGAGTGCCA
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAAGAAAAAGAGTGCCA
178014 CGGAGT
65 CGGAGT
* * * **
178020 TGTGGGCTTTGAAAA--GAAGAAG-GTGCCATGGAGTTGTGGGCTT--AAAG-ATGAG-GTGCCA
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCA
*
178078 CGGAAT
65 CGGAGT
* * * *
178084 TGTGGGCTTTAAAA--G-----G-GTGCCACGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCAC
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCAC
178140 GGAGT
66 GGAGT
178145 TGTGGGCTTTAAA
1 TGTGGGCTTTAAA
178158 GAAAAAATGC
Statistics
Matches: 689, Mismatches: 71, Indels: 102
0.80 0.08 0.12
Matches are distributed among these distances:
58 41 0.06
60 37 0.05
61 53 0.08
62 16 0.02
63 55 0.08
64 53 0.08
65 10 0.01
66 37 0.05
67 27 0.04
68 86 0.12
69 69 0.10
70 35 0.05
71 98 0.14
72 61 0.09
73 2 0.00
74 9 0.01
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (70 bp):
TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCAC
GGAGT
Found at i:177598 original size:27 final size:27
Alignment explanation
Indices: 177539--177598 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
177529 GCTTTAAAGG
* *
177539 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACAGAGTCGTGGACTT
* *
177566 AAAAGGGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTCGTGGACTT
*
177593 AGAAGG
1 AAAAGG
177599 AAAAGAAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.37, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTCGTGGACTT
Found at i:178071 original size:258 final size:257
Alignment explanation
Indices: 177307--178164 Score: 1181
Period size: 258 Copynumber: 3.2 Consensus size: 257
177297 GGGTGAAAGA
* * *
177307 TGCCACGAAGTTGTGGACTTAAAAAGAACAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT--AAA-GAAAA
* *
177372 AAAGGGTGCCACGAAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
63 AAAGAGTGCCACGAAGTTGTGGGCTTTA-AAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTAGAA
* *
177436 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
127 GGAAAAAGAGTGCCACAGAGTTGTGGGCTT-----TAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* ** * * *
177500 -AAAAGGAA-AAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTCGTGGA
187 GAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGC-TTAAA-GATGAG-GTGCCACGGAATTGTGGG
177563 C-TTAAAAGGG
247 CTTTAAAAGGG
* * * * *
177573 TGCCACAGAGTTGTGGGCTTAGAAGGAAAAGAAGGTGCCATGGAGTTGTGGGCTTTAAA-AAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGG--AACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAA---
* *
177637 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GGTGCCACGGAGTTGTGGGCTTTG
61 AAAAAGAGTGCCACGAAGTTGTGGGCTTT-AAAGGAAAAAGGGTGCCACGGAGTTGTGGGC-TT-
* *
177701 AAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTG
123 AGAA-GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAG----A--GTGCCACGGAGTTGTG
177766 GGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGATGAGGTGCCACGGAATTGTGG
181 GGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGATGAGGTGCCACGGAATTGTGG
177831 GCTTTAAAAGGG
246 GCTTTAAAAGGG
177843 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAAA
*
177908 GAGTGCCACGAAGTTCTGGGCTTTAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGA
66 GAGTGCCACGAAGTTGTGGGCTTTAAA-GGAAAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGA
177973 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
130 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
*
178038 GAAGGTGCCATGGAGTTGTGGGCTTAAAGATGAGGTGCCACGGAATTGTGGGCTTTAAAAGGG
195 GAAGGTGCCACGGAGTTGTGGGCTTAAAGATGAGGTGCCACGGAATTGTGGGCTTTAAAAGGG
178101 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
178165 TGCCACTGAG
Statistics
Matches: 536, Mismatches: 33, Indels: 54
0.86 0.05 0.09
Matches are distributed among these distances:
258 155 0.29
260 1 0.00
264 39 0.07
265 12 0.02
266 59 0.11
267 63 0.12
268 66 0.12
269 23 0.04
270 65 0.12
271 23 0.04
272 23 0.04
273 7 0.01
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.20
Consensus pattern (257 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAAA
GAGTGCCACGAAGTTGTGGGCTTTAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGAA
AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
AAGGTGCCACGGAGTTGTGGGCTTAAAGATGAGGTGCCACGGAATTGTGGGCTTTAAAAGGG
Found at i:178169 original size:92 final size:93
Alignment explanation
Indices: 177708--178185 Score: 427
Period size: 92 Copynumber: 5.0 Consensus size: 93
177698 TTGAAAAGGG
* * *
177708 AAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGC-TT-
** *
177773 AAAAGAAGAAGGTGCCACGGAGTTGTGGGC-TT
63 -AAAGAA-AAAATGCCACAGAGTTGTGGGCTTT
* * *
177805 AAAGATGAGGTGCCACGGAATTGTGGGCTTTAAAA-G-----GGTGCCACGGAGTTGTGGACTTA
1 AAA-AAGA-GTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTT-
** *
177864 AAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
63 AAA-GAA-AAAATGCCACAGAGTTGTGGGCTTT
* * *
177897 AAAGAAAAAAAGAGTGCCACGAAGTTCTGGGCTTTAAAGGGAAAAAGGGTGCCACGGAGTTGTGG
1 ------AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAA-GGTGCCACGGAGTTGTGG
177962 GCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
59 GCTTA-AA-GAAAAA-A-TGCCACAGAGTTGTGGGCTTT
* *
178001 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAGGTGCCATGGAGTTGTGGGCTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAA
** ** * *
178065 AGATGAGGTGCCACGGAATTGTGGGCTTT
65 AGAAAAAATGCCACAGAGTTGTGGGCTTT
* * *
178094 -AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTAA
* *
178157 AGAAAAAATGCCACTGAGTTGTGGACTTT
65 AGAAAAAATGCCACAGAGTTGTGGGCTTT
178186 GAGACAAAAT
Statistics
Matches: 321, Mismatches: 37, Indels: 51
0.78 0.09 0.12
Matches are distributed among these distances:
90 8 0.02
91 53 0.17
92 68 0.21
93 20 0.06
95 3 0.01
96 24 0.07
97 29 0.09
98 39 0.12
99 27 0.08
102 3 0.01
103 27 0.08
104 20 0.06
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.22
Consensus pattern (93 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAA
GAAAAAATGCCACAGAGTTGTGGGCTTT
Found at i:178197 original size:30 final size:30
Alignment explanation
Indices: 178134--178217 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
178124 AGGAACAAGG
* * *
178134 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACTGAGTTGTGGACTTT-GAGAAAAAA
*
178165 TGCCACTGAGTTGTGGACTTTGAGACAAAA
1 TGCCACTGAGTTGTGGACTTTGAGAAAAAA
*
178195 TGCCACTGAGTCGTGGACTTTGA
1 TGCCACTGAGTTGTGGACTTTGA
178218 AAAGGTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 29 0.60
31 19 0.40
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (30 bp):
TGCCACTGAGTTGTGGACTTTGAGAAAAAA
Found at i:184306 original size:27 final size:27
Alignment explanation
Indices: 184268--184341 Score: 148
Period size: 27 Copynumber: 2.7 Consensus size: 27
184258 TTTGATTGAA
184268 AATGGGGTTGGAGTGTCCCCTCGGAGG
1 AATGGGGTTGGAGTGTCCCCTCGGAGG
184295 AATGGGGTTGGAGTGTCCCCTCGGAGG
1 AATGGGGTTGGAGTGTCCCCTCGGAGG
184322 AATGGGGTTGGAGTGTCCCC
1 AATGGGGTTGGAGTGTCCCC
184342 GATGAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.43, T:0.23
Consensus pattern (27 bp):
AATGGGGTTGGAGTGTCCCCTCGGAGG
Found at i:186544 original size:52 final size:51
Alignment explanation
Indices: 186466--186595 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 51
186456 CCCGAAATAT
* *
186466 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
186518 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
*
186570 GCAAATTGCCTGCATGTATCGATACA
1 GAAAATTGCCTGCATGTATCGATACA
186596 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (51 bp):
GAAAATTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:186608 original size:51 final size:50
Alignment explanation
Indices: 186466--186615 Score: 171
Period size: 52 Copynumber: 2.9 Consensus size: 50
186456 CCCGAAATAT
* * *
186466 GAAAAGTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGG
186518 GAAAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGG
*
186570 GCAAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
186616 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (50 bp):
GAAAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGG
Found at i:186622 original size:13 final size:13
Alignment explanation
Indices: 186604--186628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186594 CAAAGATCAG
186604 TGTATCGATACAA
1 TGTATCGATACAA
186617 TGTATCGATACA
1 TGTATCGATACA
186629 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:186710 original size:13 final size:13
Alignment explanation
Indices: 186692--186716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186682 AAAAAAAATA
186692 TGTATCGATACAT
1 TGTATCGATACAT
186705 TGTATCGATACA
1 TGTATCGATACA
186717 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:187128 original size:63 final size:63
Alignment explanation
Indices: 187041--187192 Score: 189
Period size: 63 Copynumber: 2.4 Consensus size: 63
187031 GTGTCTACAC
* * * * * * *
187041 ATACATAGTAAATTATATCGATACATTGAGCCCAACATCTATAATTTTAAATGTATTGTATCT
1 ATACATAGTGAATTATATCGATACATTGAGCCCAACAGCTAGAATTTCAAATGCATTATATCG
* * * *
187104 ATACATGGTGAATTGTATCGATACATTGAGCCTAACGGCTAGAATTTCAAATGCATTATATCG
1 ATACATAGTGAATTATATCGATACATTGAGCCCAACAGCTAGAATTTCAAATGCATTATATCG
187167 ATACATTA-TGAATTATATCGATACAT
1 ATACA-TAGTGAATTATATCGATACAT
187193 AAGAGGTGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
63 74 0.99
64 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (63 bp):
ATACATAGTGAATTATATCGATACATTGAGCCCAACAGCTAGAATTTCAAATGCATTATATCG
Found at i:189883 original size:56 final size:56
Alignment explanation
Indices: 189797--189907 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
189787 TTGATAATGG
189797 ATGCTCGAGGCATATGACCAAAGAAAAAAGCCTATTCACGAAGTTAAGATGAAAAT
1 ATGCTCGAGGCATATGACCAAAGAAAAAAGCCTATTCACGAAGTTAAGATGAAAAT
* *
189853 ATGCTCGAGGCATATGACCAGAGACAAAAGCCTATTCACGAAGTTAAGATGAAAA
1 ATGCTCGAGGCATATGACCAAAGAAAAAAGCCTATTCACGAAGTTAAGATGAAAA
189908 GATGGTGGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (56 bp):
ATGCTCGAGGCATATGACCAAAGAAAAAAGCCTATTCACGAAGTTAAGATGAAAAT
Found at i:195741 original size:13 final size:13
Alignment explanation
Indices: 195723--195747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195713 ATATTGCTTA
195723 GTATCGATACATT
1 GTATCGATACATT
195736 GTATCGATACAT
1 GTATCGATACAT
195748 GTTCTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:195764 original size:32 final size:33
Alignment explanation
Indices: 195704--195765 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
195694 CACCCAGACA
195704 TATCGATACATATTGCTTAGTATCGATACATTG
1 TATCGATACATATTGCTTAGTATCGATACATTG
* *
195737 TATCGATACATGTT-CTTTGTATCGATACA
1 TATCGATACATATTGCTTAGTATCGATACA
195766 CCATAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (33 bp):
TATCGATACATATTGCTTAGTATCGATACATTG
Found at i:195911 original size:25 final size:25
Alignment explanation
Indices: 195883--195937 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 25
195873 CTGTAATTTC
195883 AATTGTATTGTATCGATACATGGTG
1 AATTGTATTGTATCGATACATGGTG
195908 -A----ATTGTATCGATACATGGTG
1 AATTGTATTGTATCGATACATGGTG
195928 AATTGTATTG
1 AATTGTATTG
195938 ATACATTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
20 19 0.76
21 1 0.04
24 1 0.04
25 4 0.16
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (25 bp):
AATTGTATTGTATCGATACATGGTG
Found at i:195914 original size:20 final size:20
Alignment explanation
Indices: 195889--195943 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
195879 TTTCAATTGT
195889 ATTGTATCGATACATGGTGA
1 ATTGTATCGATACATGGTGA
195909 ATTGTATCGATACATGGTGA
1 ATTGTATCGATACATGGTGA
*
195929 ATTGTATTGATACAT
1 ATTGTATCGATACAT
195944 TGAGCCCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGGTGA
Found at i:195964 original size:83 final size:83
Alignment explanation
Indices: 195823--196003 Score: 247
Period size: 83 Copynumber: 2.2 Consensus size: 83
195813 TATTTATAAT
* * *** *
195823 TGAATTGCATCGATACATGGTAAATTGTATTGATACATTGAGCTCAGTGGCTGTAATTTCAATTG
1 TGAATTGTATCGATACATGGTAAATTGTATTGATACATTGAGCCCAACAGCTGTAATTTCAAATG
* *
195888 TATTGTATCGATACATGG
66 CATTGTATCAATACATGG
* *
195906 TGAATTGTATCGATACATGGTGAATTGTATTGATACATTGAGCCCAACAGTTAG-AATTTCAAAT
1 TGAATTGTATCGATACATGGTAAATTGTATTGATACATTGAGCCCAACAGCT-GTAATTTCAAAT
*
195970 GCATTGTATCAATACATTG
65 GCATTGTATCAATACATGG
195989 TGAATTGTATCGATA
1 TGAATTGTATCGATA
196004 TATAGAAACG
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 85 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (83 bp):
TGAATTGTATCGATACATGGTAAATTGTATTGATACATTGAGCCCAACAGCTGTAATTTCAAATG
CATTGTATCAATACATGG
Found at i:196425 original size:35 final size:34
Alignment explanation
Indices: 196378--196443 Score: 114
Period size: 35 Copynumber: 1.9 Consensus size: 34
196368 TAAGTGATTG
*
196378 AGAGGTTTTATCTTAGCCTTTGTAAAAGATAGGAA
1 AGAGGTTCTATCTTAGCCTTTG-AAAAGATAGGAA
196413 AGAGGTTCTATCTTAGCCTTTGAAAAGATAG
1 AGAGGTTCTATCTTAGCCTTTGAAAAGATAG
196444 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTTGAAAAGATAGGAA
Found at i:198057 original size:28 final size:28
Alignment explanation
Indices: 198024--198122 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
198014 AATAAAATTA
* *
198024 GGGTTGGAGTATCCTCTCAAAAATAATG
1 GGGTTGGAGTATCCCCTCGAAAATAATG
* ** *
198052 GGGTTGGAGTATCCCCGATGGTGAA-AATA
1 GGGTTGGAGTATCCCC--TCGAAAATAATG
*
198081 GGGTTGGAGTATCCCCTCGAAAATAACG
1 GGGTTGGAGTATCCCCTCGAAAATAATG
*
198109 GGATTGGAGTATCC
1 GGGTTGGAGTATCC
198123 TCGATGGTAG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
27 4 0.07
28 30 0.54
29 19 0.34
30 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCGAAAATAATG
Found at i:198093 original size:29 final size:31
Alignment explanation
Indices: 198043--198137 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 31
198033 TATCCTCTCA
*
198043 AAAATAATGGGGTTGGAGTATCCCCGATGGTG
1 AAAATAA-CGGGTTGGAGTATCCCCGATGGTG
*
198075 AAAAT-A-GGGTTGGAGTATCCCC--T--CG
1 AAAATAACGGGTTGGAGTATCCCCGATGGTG
*
198100 AAAATAACGGGATTGGAGTATCCTCGATGGTAG
1 AAAATAACGGG-TTGGAGTATCCCCGATGGT-G
198133 AAAAT
1 AAAAT
198138 TGGTATTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
25 6 0.12
26 1 0.02
27 4 0.08
28 12 0.23
29 16 0.31
30 1 0.02
31 1 0.02
32 5 0.10
33 6 0.12
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (31 bp):
AAAATAACGGGTTGGAGTATCCCCGATGGTG
Found at i:198116 original size:57 final size:58
Alignment explanation
Indices: 198017--198137 Score: 181
Period size: 57 Copynumber: 2.1 Consensus size: 58
198007 TTTTGGAAAT
* * *
198017 AAAATTAGGGTTGGAGTATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCGATGGT-G
1 AAAA-TAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGGTAG
* *
198075 AAAATAGGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCTCGATGGTAG
1 AAAATAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGGTAG
198133 AAAAT
1 AAAAT
198138 TGGTATTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 47 0.82
58 10 0.18
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (58 bp):
AAAATAGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGGTAG
Found at i:198214 original size:135 final size:136
Alignment explanation
Indices: 197945--198214 Score: 348
Period size: 136 Copynumber: 2.0 Consensus size: 136
197935 GATAAAAGCG
* * *
197945 GGGTTGGAGTATTCCCTTGAAAACAACAAGGTTGGAATATCCCCTATGGTGAAAAGTCGATATTT
1 GGGTTGGAGTATCCCCTCGAAAACAACAAGGTTGGAATATCCCCGATGGTGAAAAGTCGATATTT
* * * * * * *
198010 TGGAAATAAAATTAGGGTTGGAGTATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCGATGGTG
66 TAGAAATAAAACTAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGCTA
198075 AAAATA
131 AAAATA
* * * * * *
198081 GGGTTGGAGTATCCCCTCGAAAATAAC-GGGATTGGAGTATCCTCGATGGTAGAAAA-TTGGTAT
1 GGGTTGGAGTATCCCCTCGAAAACAACAAGG-TTGGAATATCCCCGATGGT-GAAAAGTCGATAT
*
198144 TTTAGAAATAAAACT-GAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCTCGATGC
64 TTTAGAAATAAAACTAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGC
198208 TAAAAAT
129 TAAAAAT
198215 TGGTGTTTTA
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
135 52 0.45
136 58 0.50
137 5 0.04
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (136 bp):
GGGTTGGAGTATCCCCTCGAAAACAACAAGGTTGGAATATCCCCGATGGTGAAAAGTCGATATTT
TAGAAATAAAACTAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGCTA
AAAATA
Found at i:198247 original size:78 final size:79
Alignment explanation
Indices: 198082--198629 Score: 615
Period size: 79 Copynumber: 7.0 Consensus size: 79
198072 GTGAAAATAG
* * *
198082 GGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCTCGATGGT-AGAAAATTGGTATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGA-AAAATTAGTGTTT
* *
198146 TAGAAATAAAACTGA
65 TGGAAATAAAACCGA
* * *
198161 -GTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCTCGATGCT-AAAAATTGGTGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTAGTGTTTT
* *
198224 AGAAGTAAAACCGA
66 GGAAATAAAACCGA
* * * *
198238 GGTTAGAGTATCCTCTCAAAAATAACGGGGTTGGAGTATCCTTGATGGTGAAAAATTAGTGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTAGTGTTTT
**
198303 GGAAATAAAATTGA
66 GGAAATAAAACCGA
* * ** * * * * *
198317 GGTTGGAGTATTCCCTTGAAAATAATAGGGTTGGAGTATTCTTGATGGTGGAAAATCAGTATTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTAGTGTTTT
198382 GGAAATAAAACC-A
66 GGAAATAAAACCGA
* * *
198395 GGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCGGT-GATGGTGAAAAATCAGTGTT
1 -GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATC-CTCGATGGTGAAAAATTAGTGTT
* * *
198459 TTGAAAATAAAA-TGT
64 TTGGAAATAAAACCGA
* * * * * * *
198474 GGTTGGAGTATCTCCTTGAAAATAATGGGGTTGGACTATCCACGATGGTGGAAAATTAGTATTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTAGTGTTTT
*
198539 GGAAATAAAATC-A
66 GGAAATAAAACCGA
* * * *
198552 GGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGGAAAATTGGTGTTT
1 -GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTAGTGTTT
198617 TGGAAATGAAAAC
65 TGGAAAT-AAAAC
198630 ATTAATGAAA
Statistics
Matches: 401, Mismatches: 59, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
77 25 0.06
78 156 0.39
79 215 0.54
80 5 0.01
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTAGTGTTTT
GGAAATAAAACCGA
Found at i:198554 original size:157 final size:157
Alignment explanation
Indices: 198075--198629 Score: 658
Period size: 157 Copynumber: 3.5 Consensus size: 157
198065 CCCGATGGTG
* *
198075 AAAAT-AGGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCTCGATGGT-AGAAAAT
1 AAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGA-AAAAT
* * * * ** *
198138 TGGTATTTT-AGAAATAAAACTGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCT
65 TAGTGTTTTGA-AAATAAAACTGGGTTGGAGTATCTCCTTGAAAATAATGGGGTTGGAGTATCCT
* * * * * *
198202 CGATGCT-AAAAATTGGTGTTTTAGAAGT
129 CGATGGTGGAAAATTAGTATTTTGGAAAT
* * * *
198230 AAAA-CCGAGGTTAGAGTATCCTCTCAAAAATAACGGGGTTGGAGTATCCTTGATGGTGAAAAAT
1 AAAATCAG-GGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAAT
* * * *
198294 TAGTGTTTTGGAAATAAAATTGAGGTTGGAGTAT-TCCCTTGAAAATAATAGGGTTGGAGTATTC
65 TAGTGTTTTGAAAATAAAACTG-GGTTGGAGTATCT-CCTTGAAAATAATGGGGTTGGAGTATCC
* *
198358 TTGATGGTGGAAAATCAGTATTTTGGAAAT
128 TCGATGGTGGAAAATTAGTATTTTGGAAAT
* * * *
198388 AAAACCAGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCGGT-GATGGTGAAAAAT
1 AAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATC-CTCGATGGTGAAAAAT
* * *
198452 CAGTGTTTTGAAAATAAAA-TGTGGTTGGAGTATCTCCTTGAAAATAATGGGGTTGGACTATCCA
65 TAGTGTTTTGAAAATAAAACTG-GGTTGGAGTATCTCCTTGAAAATAATGGGGTTGGAGTATCCT
198516 CGATGGTGGAAAATTAGTATTTTGGAAAT
129 CGATGGTGGAAAATTAGTATTTTGGAAAT
* *
198545 AAAATCAGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGGAAAATT
1 AAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATT
* *
198610 GGTGTTTTGGAAATGAAAAC
66 AGTGTTTTGAAAAT-AAAAC
198630 ATTAATGAAA
Statistics
Matches: 338, Mismatches: 49, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
155 5 0.01
156 67 0.20
157 173 0.51
158 90 0.27
159 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (157 bp):
AAAATCAGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATT
AGTGTTTTGAAAATAAAACTGGGTTGGAGTATCTCCTTGAAAATAATGGGGTTGGAGTATCCTCG
ATGGTGGAAAATTAGTATTTTGGAAAT
Found at i:201179 original size:13 final size:13
Alignment explanation
Indices: 201161--201186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
201151 TTTTAGGCAG
201161 GTATCGATACATT
1 GTATCGATACATT
201174 GTATCGATACATT
1 GTATCGATACATT
201187 TACTGTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:201865 original size:61 final size:60
Alignment explanation
Indices: 201711--202343 Score: 689
Period size: 61 Copynumber: 10.4 Consensus size: 60
201701 GGAGAGAGGC
* * **
201711 GTCCTGCTCTTTGAGGGCTAAAAGGTTCCACCAACTTGTGTGACCTTTAAAAGAAAAAAGAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG---AAA-AGGT
* * *
201775 GTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGT
* * * *
201836 GTCTTACTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-GT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGT
* * * * * * *
201895 GTCATTCTCTTTGAGGATTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAA-AGGAAGGAC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAGG-T
* * * * * * * * **
201956 ATCCTCCTTTTTGAAGACTGAAAGGTGCCACCAACTTGTATAGGCTTTAAAAGGGAAAGAC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGT
* *
202017 ATCCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGT
* * *
202078 GTTCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-GT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGT
* * * * * * *
202137 GTCCTACTCTTTGAGGACTAAAAGGTGCTACCAGCCTATATGGGCCTTAAAAAGAAAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGG-CTTTAAAAGAAAAGGT
* * *
202198 GTCCTGCTCTTTGAGGACTAAAAGGTGCGACTAACTTGTGTGGGCTTTAAAAGGAAA-GT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGT
* * * * *
202257 GTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACCTATGTGGGCTTTAAGAGGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAG-AAAAGGT
*
202319 ATCCTGCTCTTTGAGGACTAAAAGG
1 GTCCTGCTCTTTGAGGACTAAAAGG
202344 ATAAAAGGTT
Statistics
Matches: 484, Mismatches: 73, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
59 134 0.28
60 41 0.08
61 228 0.47
62 34 0.07
64 42 0.09
65 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (60 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGT
Found at i:201969 original size:120 final size:120
Alignment explanation
Indices: 201707--202343 Score: 781
Period size: 120 Copynumber: 5.2 Consensus size: 120
201697 AAAAGGAGAG
* * ** *
201707 AGGCGTCCTGCTCTTTGAGGGCTAAAAGGTTCCACCAACTTGTGTGACCTTTAAAAGAAAAAAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG---GAA-A
* * * *
201772 GGTGTCTTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAAGAAA
62 -GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAA
* * *
201832 AGGCGTCTTACTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGT
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGT
* * * * *
201897 CATTCTCTTTGAGGATTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAG-GA
66 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAA
* * * * * * *
201951 AGGACATCCTCCTTTTTGAAGACTGAAAGGTGCCACCAACTTGTATAGGCTTTAAAAGGGAAAGA
1 AGG-CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GGAAAG-
** * *
202016 CATCCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
63 TGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAA
* * *
202074 AGGTGTTCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGT
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGT
* * * * * *
202139 CCTACTCTTTGAGGACTAAAAGGTGCTACCAGCCTATATGGGCCTTAAAAAGAAA
66 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAA
* * *
202194 AGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCGACTAACTTGTGTGGGCTTTAAAAGGAAAGTGT
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGT
* * * *
202259 CCTGCTCTTTGAGGACTAAAAAGTGCCACCAACCTATGTGGGCTTTAAGAGGAAAA
66 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAG-AAA
*
202315 AGGCATCCTGCTCTTTGAGGACTAAAAGG
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGG
202344 ATAAAAGGTT
Statistics
Matches: 441, Mismatches: 66, Indels: 14
0.85 0.13 0.03
Matches are distributed among these distances:
119 4 0.01
120 246 0.56
121 43 0.10
122 94 0.21
123 4 0.01
125 50 0.11
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (120 bp):
AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGT
CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAA
Found at i:202046 original size:242 final size:239
Alignment explanation
Indices: 201779--202342 Score: 736
Period size: 242 Copynumber: 2.3 Consensus size: 239
201769 AGAGGTGTCT
* *
201779 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAAGAAAAGGCGTCTTACT
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCTTGCT
*
201844 CTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGTCATTCTCTTTGA
65 CTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGTCATACTCTTTGA
* * * * * * *
201909 GGATTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAG-GAAGGACATCCTCCTTTTTGAAGA
130 GGACTAAAAGGTGCCACCAACCTATATGGGCCTTAAAAAGAAAAGG-CATCCTCCTCTTTGAAGA
*
201973 CTGAAAGGTGCCACCAACTTGTATAGGCTTTAAAAGGGAAAGACATCC
194 CTAAAAGGTGCCACCAACTTGTATAGGCTTTAAAA-GGAAAG-CATCC
* *
202021 TGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGTGT-TCTGC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCT-TGC
* * *
202085 TTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGTCCTACTCTTTG
64 TCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGTCATACTCTTTG
* * ** * *
202150 AGGACTAAAAGGTGCTACCAGCCTATATGGGCCTTAAAAAGAAAAGGTGTCCTGCTCTTTGAGGA
129 AGGACTAAAAGGTGCCACCAACCTATATGGGCCTTAAAAAGAAAAGGCATCCTCCTCTTTGAAGA
* * * * **
202215 CTAAAAGGTGCGACTAACTTGTGTGGGCTTTAAAAGGAAAGTGTCC
194 CTAAAAGGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAGCATCC
* * * * * *
202261 TGCTCTTTGAGGACTAAAAAGTGCCACCAACCTATGTGGGCTTTAAGAGGAAAAAGGCATCCTGC
1 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AAG-AAAAGGCGTCTTGC
202326 TCTTTGAGGACTAAAAG
64 TCTTTGAGGACTAAAAG
202343 GATAAAAGGT
Statistics
Matches: 279, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
239 2 0.01
240 45 0.16
241 33 0.12
242 195 0.70
243 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (239 bp):
TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTTGCTC
TTTGAGGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGTGTCATACTCTTTGAG
GACTAAAAGGTGCCACCAACCTATATGGGCCTTAAAAAGAAAAGGCATCCTCCTCTTTGAAGACT
AAAAGGTGCCACCAACTTGTATAGGCTTTAAAAGGAAAGCATCC
Found at i:212829 original size:20 final size:20
Alignment explanation
Indices: 212804--212850 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
212794 CAAATCTTTT
212804 TCAAAATTCATCT-TTTTGCA
1 TCAAAATTC-TCTATTTTGCA
* *
212824 TCAAAACTCTCTATTTTTCA
1 TCAAAATTCTCTATTTTGCA
212844 TCAAAAT
1 TCAAAAT
212851 CTTCAACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (20 bp):
TCAAAATTCTCTATTTTGCA
Found at i:215395 original size:13 final size:13
Alignment explanation
Indices: 215377--215401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
215367 ATATTGCTTA
215377 GTATCGATACATT
1 GTATCGATACATT
215390 GTATCGATACAT
1 GTATCGATACAT
215402 GTTCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:215416 original size:32 final size:33
Alignment explanation
Indices: 215356--215418 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
215346 CACACCCAGA
*
215356 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCATAGTATCGATACAT
*
215389 TGTATCGATACATGTT-CATAGTATCGATAC
1 TGTATCGATACATATTGCATAGTATCGATAC
215419 GCCTTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATATTGCATAGTATCGATACAT
Found at i:216775 original size:50 final size:50
Alignment explanation
Indices: 216700--216801 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
216690 GTTTATGGTT
216700 TCAGTGGGCTCCTCATGAGGTAATACTTATTTTTCTTCTTGCTCAATCAA
1 TCAGTGGGCTCCTCATGAGGTAATACTTATTTTTCTTCTTGCTCAATCAA
*
216750 TCAGTGGGCTCCTCATGAGGTAATACTTATTTTTCTTTTTGCTCAATCAA
1 TCAGTGGGCTCCTCATGAGGTAATACTTATTTTTCTTCTTGCTCAATCAA
216800 TC
1 TC
216802 TTAATAGTCC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (50 bp):
TCAGTGGGCTCCTCATGAGGTAATACTTATTTTTCTTCTTGCTCAATCAA
Found at i:223677 original size:4 final size:4
Alignment explanation
Indices: 223668--223705 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
223658 AAACAAAACA
223668 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
223706 GCACCACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:224166 original size:28 final size:28
Alignment explanation
Indices: 224130--224200 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
224120 ATAAAATCGA
* * *
224130 GGTTAGAGTATCCCCTTGAAAATAATGG
1 GGTTGGAGTATCCCCTCGAAAATAACGG
*
224158 GGTTGGAGTATCCTCTCGAAAATAACGG
1 GGTTGGAGTATCCCCTCGAAAATAACGG
224186 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
224201 AATGGTGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCGAAAATAACGG
Found at i:224406 original size:79 final size:79
Alignment explanation
Indices: 224158--224404 Score: 288
Period size: 79 Copynumber: 3.1 Consensus size: 79
224148 AAAATAATGG
**
224158 GGTTGGAGTATCCTCTC-GAAAATAACGGGGTTGGAGTATCCCCAATGGTGAAAAATCGGTGTTT
1 GGTTGGAGTATCCTCTCAGAAAATAACAAGGTTGGAGTATCCCCAATGGTGAAAAATCGGTGTTT
* *
224222 TGAAATAAAACTAA
66 GGAAATAAAACTGA
* * **
224236 GGTTGGAGTATCCTC-CAGAAAATAA-TAGGATTGGAGTATCCCCAATGGTAAAAAATTAGTGTT
1 GGTTGGAGTATCCTCTCAGAAAATAACAAGG-TTGGAGTATCCCCAATGGTGAAAAATCGGTG-T
* *
224299 TTGGGAATAAAACTGG
64 TTGGAAATAAAACTGA
* * * * *
224315 GGTTGGAGTATTCTCTCAG-AAATAACAAGGTTGAAGTATCCTCGATGGTGGAAAATCGGTGTTT
1 GGTTGGAGTATCCTCTCAGAAAATAACAAGGTTGGAGTATCCCCAATGGTGAAAAATCGGTGTTT
224379 GGAAAATAAAA-TCGA
66 GG-AAATAAAACT-GA
224394 GGTTGGAGTAT
1 GGTTGGAGTAT
224405 TCCTGATAGT
Statistics
Matches: 142, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
77 3 0.02
78 57 0.40
79 76 0.54
80 6 0.04
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCTCTCAGAAAATAACAAGGTTGGAGTATCCCCAATGGTGAAAAATCGGTGTTT
GGAAATAAAACTGA
Found at i:224421 original size:51 final size:52
Alignment explanation
Indices: 224342--224455 Score: 126
Period size: 51 Copynumber: 2.2 Consensus size: 52
224332 AGAAATAACA
* * * * *
224342 AGGTTGAAGTA-TCCTCGATGGTGGAAAATCGGTG-TTTGGAAAATAAAATCG
1 AGGTTGGAGTATTCCTCGATAGTGAAAAATCAGTGTTTTGG-AAATAAAACCG
*
224393 AGGTTGGAGTATTCCT-GATAGTGAAAAATTAGTGTTTTGGAAATAAAACCG
1 AGGTTGGAGTATTCCTCGATAGTGAAAAATCAGTGTTTTGGAAATAAAACCG
* *
224444 GGGTTAGAGTAT
1 AGGTTGGAGTAT
224456 CCCGAAAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
51 44 0.83
52 9 0.17
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (52 bp):
AGGTTGGAGTATTCCTCGATAGTGAAAAATCAGTGTTTTGGAAATAAAACCG
Found at i:224519 original size:77 final size:79
Alignment explanation
Indices: 224413--224596 Score: 214
Period size: 79 Copynumber: 2.4 Consensus size: 79
224403 ATTCCTGATA
* * * *
224413 GTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTAT-C-C-CGAAAAATAATGAGG-T
1 GTGAAAAATCAGTGTTTTGGAAATAAAACCAGAGTTAGAGTATCCTCTCG-AAAATAACG-GGAT
**
224474 TAGACTATCTTCGATG
64 TAGACTATCCCCGATG
* * * *
224490 GTGAAAAATCAATGTTTTGAAAATAAAACCAGAGTTGGAGTATCCTCTCGAAAATAACGGGATTG
1 GTGAAAAATCAGTGTTTTGGAAATAAAACCAGAGTTAGAGTATCCTCTCGAAAATAACGGGATTA
*
224555 GAGTATCCCCGATG
66 GACTATCCCCGATG
*
224569 GTGAAAAATCGGTGTTTTGGAAATAAAA
1 GTGAAAAATCAGTGTTTTGGAAATAAAA
224597 ACATTAATAA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
77 37 0.42
78 3 0.03
79 47 0.53
80 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (79 bp):
GTGAAAAATCAGTGTTTTGGAAATAAAACCAGAGTTAGAGTATCCTCTCGAAAATAACGGGATTA
GACTATCCCCGATG
Found at i:224527 original size:128 final size:130
Alignment explanation
Indices: 224286--224532 Score: 315
Period size: 128 Copynumber: 1.9 Consensus size: 130
224276 CCCAATGGTA
* * * * *
224286 AAAAATTAGTGTTTTGGGAATAAAACTGGGGTTGGAGTATTCTCTCAGAAATAACAAGGTTGAAG
1 AAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTATTCTCTCAAAAATAACAAGGTTGAAC
* ** *
224351 TATCCTCGATGGTGGAAAATCGGTGTTTGGAAAATAAAATCGAGGTTGGAGTATTCCTGATAGTG
66 TATCCTCGATGGTGAAAAATCAATGTTTGGAAAATAAAACCGAGGTTGGAGTATTCCTGATAGTG
**
224416 AAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTA-TC-C-CGAAAAATAATGAGGTT-AG
1 AAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTATTCTCTC-AAAAATAACAAGGTTGA-
* *
224477 ACTATCTTCGATGGTGAAAAATCAATGTTTTGAAAATAAAACC-AGAGTTGGAGTAT
64 ACTATCCTCGATGGTGAAAAATCAATGTTTGGAAAATAAAACCGAG-GTTGGAGTAT
224533 CCTCTCGAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
127 4 0.04
128 59 0.58
129 2 0.02
130 36 0.36
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (130 bp):
AAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTATTCTCTCAAAAATAACAAGGTTGAAC
TATCCTCGATGGTGAAAAATCAATGTTTGGAAAATAAAACCGAGGTTGGAGTATTCCTGATAGTG
Found at i:224547 original size:207 final size:208
Alignment explanation
Indices: 224186--224596 Score: 474
Period size: 207 Copynumber: 2.0 Consensus size: 208
224176 AAAATAACGG
* * * *
224186 GGTTGGAGTATCCCCAATGGTGAAAAATCGGTGTTTTGAAATAAAACTAAGGTTGGAGTATCCTC
1 GGTTGGAGTATCCCCAATAGTGAAAAATCAGTGTTTTGAAATAAAACCAAGGTTAGAGTATCCTC
* * * * ** ** *
224251 CAGAAAATAATAGGATTGGAGTATCCCCAATGGTAAAAAATTAGTGTTTTGGGAATAAAACTGGG
66 CAGAAAATAATAGGATTAGACTATCCCCAATGGTAAAAAATCAATGTTTTGAAAATAAAACCAGA
* * *
224316 GTTGGAGTATTCTCTCAGAAATAACAAGG-TTGAAGTATCCTCGATGGTGGAAAATCGGTG-TTT
131 GTTGGAGTATCCTCTCAGAAATAAC-AGGATTGAAGTATCCCCGATGGTGAAAAATCGGTGTTTT
224379 GGAAAATAAAATCGA
195 GG-AAATAAAATCGA
* ** * **
224394 GGTTGGAGTATTCCTGATAGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTATCC-
1 GGTTGGAGTATCCCCAATAGTGAAAAATCAGTGTTTT-GAAATAAAACCAAGGTTAGAGTATCCT
* ** * *
224458 CGA-AAAATAATGAGG-TTAGACTATCTTCGATGGTGAAAAATCAATGTTTTGAAAATAAAACCA
65 CCAGAAAATAAT-AGGATTAGACTATCCCCAATGGTAAAAAATCAATGTTTTGAAAATAAAACCA
* *
224521 GAGTTGGAGTATCCTCTC-GAAAATAACGGGATTGGAGTATCCCCGATGGTGAAAAATCGGTGTT
129 GAGTTGGAGTATCCTCTCAG-AAATAACAGGATTGAAGTATCCCCGATGGTGAAAAATCGGTGTT
224585 TTGGAAATAAAA
193 TTGGAAATAAAA
224597 ACATTAATAA
Statistics
Matches: 169, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
206 3 0.02
207 103 0.61
208 41 0.24
209 22 0.13
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (208 bp):
GGTTGGAGTATCCCCAATAGTGAAAAATCAGTGTTTTGAAATAAAACCAAGGTTAGAGTATCCTC
CAGAAAATAATAGGATTAGACTATCCCCAATGGTAAAAAATCAATGTTTTGAAAATAAAACCAGA
GTTGGAGTATCCTCTCAGAAATAACAGGATTGAAGTATCCCCGATGGTGAAAAATCGGTGTTTTG
GAAATAAAATCGA
Found at i:224585 original size:79 final size:77
Alignment explanation
Indices: 224391--224596 Score: 227
Period size: 77 Copynumber: 2.6 Consensus size: 77
224381 AAAATAAAAT
* * * * * *
224391 CGAGGTTGGAGTATTCCTGATAGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTAGAGTAT
1 CGAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTGGAAATAAAACCAGAGTTAGAGTAT
224456 CCCGAAAAATAA
66 CCCGAAAAATAA
* * * ** * * *
224468 TGAGGTTAGACTATCTTCGATGGTGAAAAATCAATGTTTTGAAAATAAAACCAGAGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTGGAAATAAAACCAGAGTTAGAGTAT
224533 CCTCTCG-AAAATAA
66 -C-C-CGAAAAATAA
*
224547 CG-GGATTGGAGTATCCCCGATGGTGAAAAATCGGTGTTTTGGAAATAAAA
1 CGAGG-TTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTGGAAATAAAA
224597 ACATTAATAA
Statistics
Matches: 103, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
77 51 0.50
78 3 0.03
79 47 0.46
80 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (77 bp):
CGAGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTGGAAATAAAACCAGAGTTAGAGTAT
CCCGAAAAATAA
Found at i:231045 original size:21 final size:21
Alignment explanation
Indices: 231021--231062 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
231011 CACTTGAACC
231021 TTTCTTCTTCAAGTGAGGTCT
1 TTTCTTCTTCAAGTGAGGTCT
* **
231042 TTTCTTTTTCTTGTGAGGTCT
1 TTTCTTCTTCAAGTGAGGTCT
231063 CTTGTTTGGA
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:0.10, C:0.17, G:0.19, T:0.55
Consensus pattern (21 bp):
TTTCTTCTTCAAGTGAGGTCT
Found at i:233467 original size:14 final size:14
Alignment explanation
Indices: 233456--233493 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
233446 AATTTTAAGC
233456 AAATATTTTTAATT
1 AAATATTTTTAATT
233470 AAATATTTTTAATT
1 AAATATTTTTAATT
233484 AAATATTTTT
1 AAATATTTTT
233494 CACAAATGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AAATATTTTTAATT
Found at i:233500 original size:13 final size:14
Alignment explanation
Indices: 233448--233493 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
233438 ACATACTAAA
*
233448 TTTTAAGCAAATAT
1 TTTTAATCAAATAT
*
233462 TTTTAATTAAATAT
1 TTTTAATCAAATAT
*
233476 TTTTAATTAAATAT
1 TTTTAATCAAATAT
233490 TTTT
1 TTTT
233494 CACAAATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (14 bp):
TTTTAATCAAATAT
Found at i:234132 original size:51 final size:50
Alignment explanation
Indices: 234056--234154 Score: 180
Period size: 51 Copynumber: 2.0 Consensus size: 50
234046 GCTCAAGTAG
234056 GAGCCATATATGATTTTATTTTCATGTGAAAAAAACATTTTTGGTAGTTAA
1 GAGCCATATATGATTTTATTTTCATGTG-AAAAAACATTTTTGGTAGTTAA
*
234107 GAGCCATGTATGATTTTATTTTCATGTGAAAAAACATTTTTGGTAGTT
1 GAGCCATATATGATTTTATTTTCATGTGAAAAAACATTTTTGGTAGTT
234155 TCATGTCATG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 20 0.43
51 27 0.57
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (50 bp):
GAGCCATATATGATTTTATTTTCATGTGAAAAAACATTTTTGGTAGTTAA
Found at i:237854 original size:14 final size:14
Alignment explanation
Indices: 237835--237884 Score: 77
Period size: 13 Copynumber: 3.7 Consensus size: 14
237825 GAGGTCCCTT
237835 AAAAAAAAAACAAC
1 AAAAAAAAAACAAC
*
237849 AAAAAACAAACAAC
1 AAAAAAAAAACAAC
237863 -AAAAAAAAAC-AC
1 AAAAAAAAAACAAC
237875 AAAAAAAAAA
1 AAAAAAAAAA
237885 TGTGCAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 2 0.06
13 18 0.55
14 13 0.39
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAC
Found at i:239218 original size:31 final size:30
Alignment explanation
Indices: 239180--239326 Score: 172
Period size: 32 Copynumber: 4.7 Consensus size: 30
239170 ATACCTTTTT
*
239180 AAAGTCCACGACTAAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTC
* *
239211 AAAGTCCACGACTCAGTGGCATCCTTTTCTTT
1 AAAGTCCACGACTCAGTGGCAT-CTCTTC-TC
239243 AAAGTCCACGACTCAGTGGCATC-CTTCTC
1 AAAGTCCACGACTCAGTGGCATCTCTTCTC
*
239272 TTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 ---AAAGTCCACGACTCAGTGGCATCTCT-TCTC
*
239305 AAAGGCCACGACTCAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
239327 TTTTTCTTTA
Statistics
Matches: 102, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.01
30 26 0.25
31 25 0.25
32 46 0.45
33 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTC
Found at i:239249 original size:63 final size:62
Alignment explanation
Indices: 239177--239325 Score: 198
Period size: 62 Copynumber: 2.4 Consensus size: 62
239167 CAAATACCTT
*
239177 TTTAAAGTCCACGACTAAGTGGCAATCTCTTCTC-AAAGTCCACGACTCAGTGGCATCCTTT-TC
1 TTTAAAGTCCACGACTCAGTGGCAATC-CTTCTCTAAAGTCCACGACTCAGTGGCAT--TTTGTC
239240 TTTAAAGTCCACGACTCAGTGGC-ATCCTTCTCTTTAAAGTCCACGACTCAGTGGCATTTTGTC
1 TTTAAAGTCCACGACTCAGTGGCAATCCTTCTC--TAAAGTCCACGACTCAGTGGCATTTTGTC
* *
239303 -TCAAAGGCCACGACTCAGTGGCA
1 TTTAAAGTCCACGACTCAGTGGCA
239326 TTTTTTCTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
61 6 0.08
62 26 0.33
63 24 0.31
64 22 0.28
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (62 bp):
TTTAAAGTCCACGACTCAGTGGCAATCCTTCTCTAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:239375 original size:34 final size:34
Alignment explanation
Indices: 239303--239862 Score: 423
Period size: 34 Copynumber: 16.9 Consensus size: 34
239293 GCATTTTGTC
* * * *
239303 TCAAAGGCCACGACTCAGTGGCA-TTTTTTC-TT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
*
239335 T-AAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
*
239368 TCAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTT
239405 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TT
*
239440 T-AAAGCCCACAACTCTGTGGCACTCTTTTTCTCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-C-TTTT-TCTTT
*
239476 TCAAAGCCCACGACTCCGTGGCA-C----TC-TT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
239504 T-AAAGCCCACAACTCCGTGGCA-C----TCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* *
239532 TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * * *
239566 TTAAAGCCCACAGCTCTGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * **
239600 TCAAAGTCCACGACTTAGTGGCA--TTTTGTC---
1 TCAAAGCCCACAACTCCGTGGCACCTTTT-TCTTT
* * *
239630 TCAAAGTCCACGACTCCGTGGCACTCTTTTTC-CT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
* * *
239664 TCTAAGCCCACAACTCTGTGGCACTCTTTTTC-CT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
*
239698 TCTAAGCCCACAACTCCGTGGCACC-----CTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * *
239727 T--AAGCCCATAACTCCATGGCACTTTTTTCATCTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC-T-TT
* *
239761 T--AAGTCCACAACTCCGTGGCACCTTTTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
239793 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1 TC----AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTT
* *
239834 T--AAGTCCACAACTCCGTGGCATCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC
239863 CCTTCCTAAA
Statistics
Matches: 446, Mismatches: 41, Indels: 82
0.78 0.07 0.14
Matches are distributed among these distances:
27 42 0.09
28 7 0.02
29 25 0.06
30 22 0.05
31 18 0.04
32 16 0.04
33 12 0.03
34 183 0.41
35 29 0.07
36 13 0.03
37 49 0.11
38 20 0.04
39 6 0.01
41 4 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (34 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
Found at i:239418 original size:71 final size:70
Alignment explanation
Indices: 239336--239879 Score: 430
Period size: 71 Copynumber: 8.1 Consensus size: 70
239326 TTTTTTCTTT
* *
239336 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCC
239401 CTTTTC
65 CTTTTC
* *
239407 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
239472 CTTTTC
65 CTTTTC
*
239478 AAAGCCCACGACTCCGTGGCA-C----TC-TTTAAAGCCCACAACTCCGTGGCACTC----T---
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
239530 TTTT-
66 TTTTC
* * * *
239534 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAGCTCTGTGGCAC-CTTCTT--
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
239596 CTTTTC
65 CTTTTC
* * ** * * *
239602 AAAGTCCACGACTTAGTGGCA--TTTTGTC--TCAAAGTCCACGACTCCGTGGCACTCTTTTT-C
1 AAAGCCCACAACTCCGTGGCACCTTTT-TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
239662 C--TTC
65 CTTTTC
* * *
239666 TAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCA--------C
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
239722 CCTTTT-
64 CCTTTTC
* * * * *
239728 -AAGCCCATAACTCCATGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCA-C-TCTTTT
**
239791 TTTCTTTT-
62 TCCCTTTTC
*
239799 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
239862 CCC-TTCC
63 CCCTTTTC
239869 TAAAGCCCACA
1 -AAAGCCCACA
239880 CAAGTTGGTG
Statistics
Matches: 387, Mismatches: 42, Indels: 88
0.75 0.08 0.17
Matches are distributed among these distances:
56 20 0.05
57 5 0.01
59 1 0.00
60 7 0.02
61 43 0.11
62 1 0.00
63 25 0.06
64 64 0.17
65 5 0.01
66 8 0.02
67 11 0.03
68 35 0.09
69 2 0.01
70 8 0.02
71 100 0.26
72 22 0.06
73 28 0.07
74 1 0.00
75 1 0.00
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (70 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
TTTTC
Found at i:239508 original size:27 final size:28
Alignment explanation
Indices: 239470--239555 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 28
239460 CACTCTTTTT
*
239470 CTCTTTTCAAAGCCCACGACTCCGTGGCA
1 CTCTTTT-AAAGCCCACAACTCCGTGGCA
239499 CTC-TTTAAAGCCCACAACTCCGTGGCA
1 CTCTTTTAAAGCCCACAACTCCGTGGCA
239526 CTCTTTTTAAAGCCCACAACTCCGTGGCA
1 CTC-TTTTAAAGCCCACAACTCCGTGGCA
239555 C
1 C
239556 CTTCTTCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
27 23 0.43
28 3 0.06
29 28 0.52
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.24
Consensus pattern (28 bp):
CTCTTTTAAAGCCCACAACTCCGTGGCA
Found at i:239556 original size:127 final size:127
Alignment explanation
Indices: 239401--239727 Score: 376
Period size: 127 Copynumber: 2.5 Consensus size: 127
239391 CTCTTTTTCC
*
239401 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACTCT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCTGTGGCAC-CT
*
239466 TTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCT-T-T-AAAGCCCACAACTCCGTGGCACT
64 TTTT-TCTTTTCAAAGCCCACGACTCAGTGGCACTCTGTCTCAAAGCCCACAACTCCGTGGCACT
* *
239528 CTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAGCTCTGTGGCACC-T
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCTGTGGCACCTT
* * * * * * *
239592 TCTTCTTTTCAAAGTCCACGACTTAGTGGCATTTTGTCTCAAAGTCCACGACTCCGTGGCACT
65 TTTTCTTTTCAAAGCCCACGACTCAGTGGCACTCTGTCTCAAAGCCCACAACTCCGTGGCACT
* * * *
239655 CTTTTTCCTTCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGG
1 C--TTT--TT-AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCTGTGG
*
239719 CACCCTTTT
59 CACCTTTTT
239728 AAGCCCATAA
Statistics
Matches: 170, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
124 27 0.16
125 4 0.02
126 2 0.01
127 79 0.46
128 1 0.01
129 3 0.02
131 2 0.01
132 40 0.24
133 11 0.06
134 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (127 bp):
CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCTTT
TTTCTTTTCAAAGCCCACGACTCAGTGGCACTCTGTCTCAAAGCCCACAACTCCGTGGCACT
Found at i:239719 original size:98 final size:99
Alignment explanation
Indices: 239209--239879 Score: 465
Period size: 98 Copynumber: 6.8 Consensus size: 99
239199 CAATCTCTTC
* * * * * * *
239209 TCAAAGTCCACGACTCAGTGGCATCCTTTTCTTTAAAGTCCACGACTCAGTGGCATCCTTC-TCT
1 TCAAAGCCCACAACTCCGTGGCA-CTTTTTCTTTAAAGCCCACAACTCCGTGGCA-CCTTCTTCT
* * * *
239273 -TT-AAAGTCCACGACTCAGTGGCA-T-TTTGT-C-
64 CTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCT
* * * * *
239303 TCAAAGGCCACGACTCAGTGGCATTTTTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACTTTTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTCT
239368 TCAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
66 TCAAAGCCCACAACTCTGTGGCACTCTTTTT-CC--T
* *
239405 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCA-CTTTTTC--TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT
* *
239470 CTCTTTTCAAAGCCCACGACTCCGTGGCACTC----T--T
62 CTC--TTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCT
* *
239504 T-AAAGCCCACAACTCCGTGGCAC-TCTT-TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACTTTTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTCT
* * * *
239566 TTAAAGCCCACAGCTCTGTGGCAC-CTTCTTCTTT
66 TCAAAGCCCACAACTCTGTGGCACTCTTTTTC-CT
* * ** * * * *
239600 TCAAAGTCCACGACTTAGTGGCA-TTTTGTC-TCAAAGTCCACGACTCCGTGGCACTCTTTTTC-
1 TCAAAGCCCACAACTCCGTGGCACTTTT-TCTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCT
*
239662 CTTCTAAGCCCACAACTCTGTGGCACTCTTTTTCCT
64 CTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCT
* * * * * * *
239698 TCTAAGCCCACAACTCCGTGGCAC----CCTTTTAAGCCCATAACTCCATGGCACTTTTTTCATC
1 TCAAAGCCCACAACTCCGTGGCACTTTTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TC
* * * * *
239759 TT-TAAGTCCACAACTCCGTGGCACCTTTTTTTTTTCTT
65 TTCAAAGCCCACAACTCTGTGGCA-C---TCTTTTTCCT
* * * * *
239797 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 TCAAAGCCCACAACTCCGTGGCA--CTTTTT--CTTTAAAGCCCACAACTCCGTGGCACCTTCTT
*
239862 CCCTTCCTAAAGCCCACA
62 CTCTT-C-AAAGCCCACA
239880 CAAGTTGGTG
Statistics
Matches: 459, Mismatches: 70, Indels: 81
0.75 0.11 0.13
Matches are distributed among these distances:
89 1 0.00
90 21 0.05
92 12 0.03
93 54 0.12
94 31 0.07
95 55 0.12
96 10 0.02
97 24 0.05
98 84 0.18
99 44 0.10
101 1 0.00
102 20 0.04
103 6 0.01
104 1 0.00
105 24 0.05
106 10 0.02
107 28 0.06
108 25 0.05
109 8 0.02
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.33
Consensus pattern (99 bp):
TCAAAGCCCACAACTCCGTGGCACTTTTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTCT
TCAAAGCCCACAACTCTGTGGCACTCTTTTTCCT
Found at i:239754 original size:27 final size:27
Alignment explanation
Indices: 239695--239748 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
239685 CACTCTTTTT
* *
239695 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
*
239722 CCTTTTAAGCCCATAACTCCATGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
239749 TTTTTTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.41, G:0.13, T:0.22
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCATGGCAC
Found at i:239770 original size:61 final size:61
Alignment explanation
Indices: 239661--239854 Score: 176
Period size: 61 Copynumber: 3.0 Consensus size: 61
239651 CACTCTTTTT
* **
239661 CCTTCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCAC
* *
239722 CCTTTTAAGCCCATAACTCCATGGCACT-TTTTTCATCTT-TAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCACTCTTTTTC--CTTCTAAGCCCACAACTCCGTGGCAC
* * *
239783 CTTTTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTC
1 C----------CTTTT-AAGCCCACAACTCCATGGCACTCTTTTT-CCTTCTAAGCCCACAACTC
239848 CGTGGCA
54 CGTGGCA
239855 TCTTTTTCCC
Statistics
Matches: 110, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
60 6 0.05
61 46 0.42
62 3 0.03
71 5 0.05
72 23 0.21
73 26 0.24
74 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (61 bp):
CCTTTTAAGCCCACAACTCCATGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCAC
Found at i:239846 original size:73 final size:71
Alignment explanation
Indices: 239723--239861 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 71
239713 CCGTGGCACC
*
239723 CTTTTAAGCCCATAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTT
1 CTTTTAAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTT
239788 TTTTTT
66 TTTTTT
* * *
239794 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTT-AAGCCCACAACTCCATGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCT
239858 TTTT
63 TTTT
239862 CCCTTCCTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
71 5 0.08
72 21 0.34
73 35 0.57
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.40
Consensus pattern (71 bp):
CTTTTAAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTT
TTTTTT
Found at i:239892 original size:73 final size:71
Alignment explanation
Indices: 239728--239879 Score: 191
Period size: 73 Copynumber: 2.1 Consensus size: 71
239718 GCACCCTTTT
* * ***
239728 AAGCCCATAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCCCT
*
239793 TCTTTTA
66 TC-TCTA
* *
239800 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTTTCC
239864 CTTC-CTA
64 CTTCTCTA
239871 AAGCCCACA
1 AAGCCCACA
239880 CAAGTTGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
71 11 0.16
72 21 0.30
73 38 0.54
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.36
Consensus pattern (71 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCCCT
TCTCTA
Found at i:239907 original size:33 final size:35
Alignment explanation
Indices: 239864--239933 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
239854 ATCTTTTTCC
*
239864 CTTCCTAAAGCCCACACAAGTTGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
239898 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
239932 CT
1 CT
239934 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:240052 original size:49 final size:49
Alignment explanation
Indices: 239933--240683 Score: 951
Period size: 49 Copynumber: 15.7 Consensus size: 49
239923 GCAACCCTTC
* * * *
239933 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTT
* *
239985 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
240034 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * * *
240077 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
240126 TAAGTCCAATGTAGCTGGCCCTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
240169 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
**
240218 TAAGTCCAATGTAGCTGGCCTTGACGCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
240267 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
240310 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* **
240359 TAAGTCCAATGTAGCTAGCCTTGACGCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
240408 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
240456 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
240505 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
240553 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
240596 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
240648 TAAATTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
240684 ACATCCTTTT
Statistics
Matches: 613, Mismatches: 58, Indels: 56
0.84 0.08 0.08
Matches are distributed among these distances:
43 153 0.25
45 2 0.00
47 3 0.00
48 90 0.15
49 290 0.47
50 2 0.00
52 73 0.12
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:240139 original size:92 final size:92
Alignment explanation
Indices: 239982--240639 Score: 800
Period size: 92 Copynumber: 7.0 Consensus size: 92
239972 CATTTTCCAT
* *
239982 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
240047 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * * *
240074 CTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
*
240139 GCTGGCCCTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
240166 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
**
240231 GCTGGCCTTGACGCAGCACATTGGCACCTTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
*
240262 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
* *
240321 TCGCTGGCCTTGAATCAGCATATTGGCATCATC
64 TAGCTGGCCTTGAATCAGCACATTGG---CA-C
* **
240354 ATCTTTAAGTCCAATGTAGCTAGCCTTGACGCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
240419 TAGCTGGCCTTGAATCAGCACATTGGCACCTC
64 TAGCTGGCCTTGAATCAGCACATTGGCA---C
*
240451 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
240516 TAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
64 TAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
240550 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CATCTTTAAGTCCAATATA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
240609 GCTGGCCTTGAATCAGCATATCGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
240636 CTTT
1 CTTT
240640 TCCATCTTTA
Statistics
Matches: 509, Mismatches: 35, Indels: 50
0.86 0.06 0.08
Matches are distributed among these distances:
86 7 0.01
91 40 0.08
92 246 0.48
94 1 0.00
95 4 0.01
96 2 0.00
97 130 0.26
98 76 0.15
99 1 0.00
102 2 0.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (92 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:240219 original size:141 final size:141
Alignment explanation
Indices: 239933--240683 Score: 1003
Period size: 141 Copynumber: 5.3 Consensus size: 141
239923 GCAACCCTTC
* * * *
239933 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTTTAAGTCCAATGTA
* *
239998 GCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
63 GCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAG
*
240063 CACATTGG---CA-C--CTT
122 CATATTGGCATCATCATCTT
* * * * * *
240077 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
240142 GGCCCTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
240207 ATCATCATCTT
131 ATCATCATCTT
**
240218 TAAGTCCAATGTAGCTGGCCTTGACGCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
240283 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
240348 ATCATCATCTT
131 ATCATCATCTT
* **
240359 TAAGTCCAATGTAGCTAGCCTTGACGCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* * *
240424 GGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACA
66 GGCCTTGAATCAGCACATTGGCA---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
* *
240489 TTGGCACCTTCATCTT
126 TTGGCATCATCATCTT
*
240505 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
240569 GGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
**
240634 ACCTTTTCCATCTT
131 A--TCAT-CATCTT
* *
240648 TAAATTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
240684 ACATCCTTTT
Statistics
Matches: 555, Mismatches: 38, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
135 37 0.07
138 2 0.00
139 1 0.00
140 39 0.07
141 265 0.48
142 4 0.01
143 40 0.07
144 38 0.07
145 45 0.08
146 84 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (141 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
ATCATCATCTT
Found at i:241611 original size:13 final size:13
Alignment explanation
Indices: 241593--241617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
241583 CATAAAATGT
241593 TGTATCGATACAA
1 TGTATCGATACAA
241606 TGTATCGATACA
1 TGTATCGATACA
241618 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:241615 original size:33 final size:34
Alignment explanation
Indices: 241573--241643 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
241563 TTCAACGATT
241573 TGTATCGATACATA-AAATGTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
*** *
241606 TGTATCGATACATATTTTTTTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
241640 TGTA
1 TGTA
241644 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (34 bp):
TGTATCGATACATATAAATGTTGTATCGATACAA
Found at i:241701 original size:13 final size:13
Alignment explanation
Indices: 241683--241707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
241673 ATTACTCACA
241683 TGTATCGATACAT
1 TGTATCGATACAT
241696 TGTATCGATACA
1 TGTATCGATACA
241708 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:241844 original size:52 final size:52
Alignment explanation
Indices: 241716--241836 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
241706 CACTGATCTT
*
241716 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
241768 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
241820 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
241837 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:248382 original size:13 final size:13
Alignment explanation
Indices: 248361--248394 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
248351 TAAAAATTAA
*
248361 ATAAAATATATAT
1 ATAATATATATAT
*
248374 ATAATATATATGT
1 ATAATATATATAT
248387 ATAATATA
1 ATAATATA
248395 ATAAAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:249009 original size:56 final size:56
Alignment explanation
Indices: 248938--249064 Score: 211
Period size: 56 Copynumber: 2.3 Consensus size: 56
248928 AAGCTGCTGC
* * *
248938 AAACAGTAGCAATGAAGAATGTAATGAAGACACCAACGTGTTGCAATGAAGAGAAG
1 AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
248994 AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
1 AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
*
249050 AAACGGCAGC-ATGAA
1 AAACGGTAGCAATGAA
249065 ATCAAAGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 5 0.07
56 62 0.93
ACGTcount: A:0.46, C:0.14, G:0.26, T:0.13
Consensus pattern (56 bp):
AAACGGTAGCAATGAAGAAAGTAATGAAGACACCAACGTGCTGCAATGAAGAGAAG
Found at i:249327 original size:19 final size:19
Alignment explanation
Indices: 249282--249325 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
249272 AAATTGCAGC
249282 AAAAAAAATAGAAGAGAAG
1 AAAAAAAATAGAAGAGAAG
*
249301 AAAAAAAAT-GAAG-GAGG
1 AAAAAAAATAGAAGAGAAG
249318 AAAAAAAA
1 AAAAAAAA
249326 AAAGCAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 4 0.17
19 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAAAAATAGAAGAGAAG
Found at i:249541 original size:20 final size:21
Alignment explanation
Indices: 249516--249554 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
249506 AAAAAAGAAA
249516 ACAGC-AAACATCAAGCAAAG
1 ACAGCAAAACATCAAGCAAAG
249536 ACAGCAAAACATCAAGCAA
1 ACAGCAAAACATCAAGCAA
249555 TAGTAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.26, G:0.13, T:0.05
Consensus pattern (21 bp):
ACAGCAAAACATCAAGCAAAG
Found at i:249640 original size:23 final size:22
Alignment explanation
Indices: 249600--249642 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
249590 CAATAAACAT
*
249600 CAAGAAAGCAGCAACAGCAAAG
1 CAAGAAAGAAGCAACAGCAAAG
*
249622 CAAGAAATGAAGCAGCAGCAA
1 CAAGAAA-GAAGCAACAGCAA
249643 CTTTGCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.53, C:0.21, G:0.23, T:0.02
Consensus pattern (22 bp):
CAAGAAAGAAGCAACAGCAAAG
Found at i:252072 original size:16 final size:17
Alignment explanation
Indices: 252040--252072 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
252030 ATCTTTGCTC
*
252040 AAAGGAGAATCGAGCAA
1 AAAGGACAATCGAGCAA
252057 AAAGGACAAT-GAGCAA
1 AAAGGACAATCGAGCAA
252073 GTAATATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.12, G:0.27, T:0.06
Consensus pattern (17 bp):
AAAGGACAATCGAGCAA
Found at i:256508 original size:20 final size:21
Alignment explanation
Indices: 256429--256507 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
256419 AAATGTCCAA
*
256429 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
256449 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
256474 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
256494 TTGTATCGATACAT
1 ATGTATCGATACAT
256508 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:256512 original size:13 final size:13
Alignment explanation
Indices: 256494--256532 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
256484 ACATTTTTCT
256494 TTGTATCGATACA
1 TTGTATCGATACA
256507 TTGTATCGATACA
1 TTGTATCGATACA
*
256520 CTGTATCGATACA
1 TTGTATCGATACA
256533 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:258966 original size:20 final size:20
Alignment explanation
Indices: 258943--259015 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
258933 ACAATTCAAA
258943 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
258963 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
258984 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
259004 GTATCGATACAT
1 GTATCGATACAT
259016 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:258987 original size:21 final size:21
Alignment explanation
Indices: 258961--259036 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
258951 ACATGTTGCA
258961 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
258982 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
259002 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
259023 ATGTATCGATACAT
1 ATGTATCGATACAT
259037 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:258994 original size:41 final size:41
Alignment explanation
Indices: 258943--259036 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
258933 ACAATTCAAA
*
258943 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
258984 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
259025 GTATCGATACAT
1 GTATCGATACAT
259037 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:259093 original size:13 final size:13
Alignment explanation
Indices: 259075--259100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
259065 TACAGCAAGT
259075 ATGTATCGATACA
1 ATGTATCGATACA
259088 ATGTATCGATACA
1 ATGTATCGATACA
259101 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:266746 original size:21 final size:21
Alignment explanation
Indices: 266722--266763 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
266712 CACTTGAACC
266722 TTTCTTCTTCAAGTGAGGTCT
1 TTTCTTCTTCAAGTGAGGTCT
* **
266743 TTTCTTTTTCTTGTGAGGTCT
1 TTTCTTCTTCAAGTGAGGTCT
266764 CTTTGTTTGG
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:0.10, C:0.17, G:0.19, T:0.55
Consensus pattern (21 bp):
TTTCTTCTTCAAGTGAGGTCT
Found at i:269185 original size:15 final size:15
Alignment explanation
Indices: 269160--269198 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
269150 AATTTTAAGC
269160 AAATA-TTTTTAATT
1 AAATATTTTTTAATT
269174 AAATATTTTTTAATT
1 AAATATTTTTTAATT
269189 AAATATTTTT
1 AAATATTTTT
269199 CACAAATGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATATTTTTTAATT
Found at i:269843 original size:50 final size:49
Alignment explanation
Indices: 269768--269864 Score: 176
Period size: 50 Copynumber: 2.0 Consensus size: 49
269758 GCTCAAGTAG
269768 GAGCCATATATGATTTTATTTCATGTGAAAAAAACATTTTTGGTAGTTAA
1 GAGCCATATATGATTTTATTTCATGTG-AAAAAACATTTTTGGTAGTTAA
*
269818 GAGCCATGTATGATTTTATTTCATGTGAAAAAACATTTTTGGTAGTT
1 GAGCCATATATGATTTTATTTCATGTGAAAAAACATTTTTGGTAGTT
269865 TCATGTCATG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 20 0.43
50 26 0.57
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (49 bp):
GAGCCATATATGATTTTATTTCATGTGAAAAAACATTTTTGGTAGTTAA
Found at i:273557 original size:14 final size:14
Alignment explanation
Indices: 273538--273587 Score: 77
Period size: 13 Copynumber: 3.7 Consensus size: 14
273528 GAGGTCCCTT
273538 AAAAAAAAAACAAC
1 AAAAAAAAAACAAC
*
273552 AAAAAACAAACAAC
1 AAAAAAAAAACAAC
273566 -AAAAAAAAAC-AC
1 AAAAAAAAAACAAC
273578 AAAAAAAAAA
1 AAAAAAAAAA
273588 TGTGCAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 2 0.06
13 18 0.55
14 13 0.39
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAC
Found at i:274921 original size:31 final size:30
Alignment explanation
Indices: 274883--275029 Score: 172
Period size: 32 Copynumber: 4.7 Consensus size: 30
274873 ATACCTTTTT
*
274883 AAAGTCCACGACTAAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTC
* *
274914 AAAGTCCACGACTCAGTGGCATCCTTTTCTTT
1 AAAGTCCACGACTCAGTGGCAT-CTCTTC-TC
274946 AAAGTCCACGACTCAGTGGCATC-CTTCTC
1 AAAGTCCACGACTCAGTGGCATCTCTTCTC
*
274975 TTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 ---AAAGTCCACGACTCAGTGGCATCTCT-TCTC
*
275008 AAAGGCCACGACTCAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
275030 TTTTTCTTTA
Statistics
Matches: 102, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.01
30 26 0.25
31 25 0.25
32 46 0.45
33 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTC
Found at i:274952 original size:63 final size:62
Alignment explanation
Indices: 274880--275028 Score: 198
Period size: 62 Copynumber: 2.4 Consensus size: 62
274870 CAAATACCTT
*
274880 TTTAAAGTCCACGACTAAGTGGCAATCTCTTCTC-AAAGTCCACGACTCAGTGGCATCCTTT-TC
1 TTTAAAGTCCACGACTCAGTGGCAATC-CTTCTCTAAAGTCCACGACTCAGTGGCAT--TTTGTC
274943 TTTAAAGTCCACGACTCAGTGGC-ATCCTTCTCTTTAAAGTCCACGACTCAGTGGCATTTTGTC
1 TTTAAAGTCCACGACTCAGTGGCAATCCTTCTC--TAAAGTCCACGACTCAGTGGCATTTTGTC
* *
275006 -TCAAAGGCCACGACTCAGTGGCA
1 TTTAAAGTCCACGACTCAGTGGCA
275029 TTTTTTCTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
61 6 0.08
62 26 0.33
63 24 0.31
64 22 0.28
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (62 bp):
TTTAAAGTCCACGACTCAGTGGCAATCCTTCTCTAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:275078 original size:34 final size:34
Alignment explanation
Indices: 275006--275564 Score: 423
Period size: 34 Copynumber: 16.9 Consensus size: 34
274996 GCATTTTGTC
* * * *
275006 TCAAAGGCCACGACTCAGTGGCA-TTTTTTC-TT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
*
275038 T-AAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
*
275071 TCAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTT
275108 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TT
*
275143 T-AAAGCCCACAACTCTGTGGCACTCTTTTTCTCTTT
1 TCAAAGCCCACAACTCCGTGGCAC-C-TTTT-TCTTT
*
275179 TCAAAGCCCACGACTCCGTGGCA-C----TC-TT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
275207 T-AAAGCCCACAACTCCGTGGCA-C----TCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* *
275235 TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * * *
275269 TTAAAGCCCACAGCTCTGTGGCACCTTCTTCTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * *
275303 TCAAAGTCCACGACTCAGTGGCA--TTTTGTC---
1 TCAAAGCCCACAACTCCGTGGCACCTTTT-TCTTT
* * *
275333 TCAAAGTCCACGACTCCGTGGCACTCTTTTTC-CT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
* * *
275367 TCTAAG-CCACAACTCTGTGGCACTCTTTTTC-CT
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTT
*
275400 TCTAAGCCCACAACTCCGTGGCACC-----CTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
* * *
275429 T--AAGCCCATAACTCCATGGCACTTTTTTCATCTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC-T-TT
* *
275463 T--AAGTCCACAACTCCGTGGCACCTTTTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
275495 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1 TC----AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTT
* *
275536 T--AAGTCCACAACTCCGTGGCATCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC
275565 CCTTCCTAAA
Statistics
Matches: 447, Mismatches: 38, Indels: 84
0.79 0.07 0.15
Matches are distributed among these distances:
27 42 0.09
28 7 0.02
29 25 0.06
30 23 0.05
31 18 0.04
32 16 0.04
33 43 0.10
34 152 0.34
35 29 0.06
36 13 0.03
37 49 0.11
38 20 0.04
39 6 0.01
41 4 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (34 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
Found at i:275121 original size:71 final size:70
Alignment explanation
Indices: 275039--275581 Score: 430
Period size: 71 Copynumber: 8.1 Consensus size: 70
275029 TTTTTTCTTT
* *
275039 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCC
275104 CTTTTC
65 CTTTTC
* *
275110 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
275175 CTTTTC
65 CTTTTC
*
275181 AAAGCCCACGACTCCGTGGCA-C----TC-TTTAAAGCCCACAACTCCGTGGCACTC----T---
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
275233 TTTT-
66 TTTTC
* * * *
275237 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAAGCCCACAGCTCTGTGGCAC-CTTCTT--
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
275299 CTTTTC
65 CTTTTC
* * * * * *
275305 AAAGTCCACGACTCAGTGGCA--TTTTGTC--TCAAAGTCCACGACTCCGTGGCACTCTTTTT-C
1 AAAGCCCACAACTCCGTGGCACCTTTT-TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
275365 C--TTC
65 CTTTTC
* * *
275369 TAAG-CCACAACTCTGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCA--------C
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
275424 CCTTTT-
64 CCTTTTC
* * * * *
275430 -AAGCCCATAACTCCATGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCA-C-TCTTTT
**
275493 TTTCTTTT-
62 TCCCTTTTC
*
275501 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
*
275564 CCC-TTCC
63 CCCTTTTC
275571 TAAAGCCCACA
1 -AAAGCCCACA
275582 CAAGTTGGTG
Statistics
Matches: 388, Mismatches: 39, Indels: 90
0.75 0.08 0.17
Matches are distributed among these distances:
56 20 0.05
57 5 0.01
59 1 0.00
60 12 0.03
61 37 0.10
62 3 0.01
63 37 0.10
64 51 0.13
65 6 0.02
66 12 0.03
67 24 0.06
68 18 0.05
69 2 0.01
70 8 0.02
71 100 0.26
72 22 0.06
73 28 0.07
74 1 0.00
75 1 0.00
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (70 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
TTTTC
Found at i:275211 original size:27 final size:28
Alignment explanation
Indices: 275173--275258 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 28
275163 CACTCTTTTT
*
275173 CTCTTTTCAAAGCCCACGACTCCGTGGCA
1 CTCTTTT-AAAGCCCACAACTCCGTGGCA
275202 CTC-TTTAAAGCCCACAACTCCGTGGCA
1 CTCTTTTAAAGCCCACAACTCCGTGGCA
275229 CTCTTTTTAAAGCCCACAACTCCGTGGCA
1 CTC-TTTTAAAGCCCACAACTCCGTGGCA
275258 C
1 C
275259 CTTCTTCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
27 23 0.43
28 3 0.06
29 28 0.52
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.24
Consensus pattern (28 bp):
CTCTTTTAAAGCCCACAACTCCGTGGCA
Done.