Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2698
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: 473008
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
File 2 of 4
Found at i:173744 original size:20 final size:20
Alignment explanation
Indices: 173719--173756 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
173709 TTTTTTCTTC
173719 TTCTTT-TTTTTTGTTTTGAT
1 TTCTTTCTTTTTT-TTTTGAT
173739 TTCTTTCTTTTTTTTTTG
1 TTCTTTCTTTTTTTTTTG
173757 CAATTTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.03, C:0.08, G:0.08, T:0.82
Consensus pattern (20 bp):
TTCTTTCTTTTTTTTTTGAT
Found at i:173998 original size:5 final size:5
Alignment explanation
Indices: 173988--174019 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
173978 ACATGAAATC
173988 CAATG CAATG CAATG CAATG CAATG CAATG CA
1 CAATG CAATG CAATG CAATG CAATG CAATG CA
174020 GTGACACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (5 bp):
CAATG
Found at i:177755 original size:13 final size:13
Alignment explanation
Indices: 177737--177762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177727 CATTTTTTGG
177737 TGTATCGATACAT
1 TGTATCGATACAT
177750 TGTATCGATACAT
1 TGTATCGATACAT
177763 ACTTTGTGTA
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):
TGTATCGATACAT
Found at i:177777 original size:32 final size:33
Alignment explanation
Indices: 177717--177780 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
177707 TACAAGCTAA
**
177717 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
177750 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
177781 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:178350 original size:299 final size:299
Alignment explanation
Indices: 177812--178398 Score: 1156
Period size: 299 Copynumber: 2.0 Consensus size: 299
177802 TCCCAATGAC
*
177812 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATAGATACTTTGAATTGTGT
*
177877 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATAC
66 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
177942 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
131 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
178007 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
196 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
178072 TGAATAAAACACATTTTTGGTATTTTCAAAATTATAAAG
261 TGAATAAAACACATTTTTGGTATTTTCAAAATTATAAAG
178111 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATAGATACTTTGAATTGTGT
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATAGATACTTTGAATTGTGT
178176 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
66 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
178241 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
131 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
178306 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
196 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
178371 TGAATAAAACACATTTTTGGTATTTTCA
261 TGAATAAAACACATTTTTGGTATTTTCA
178399 GAATAATTCC
Statistics
Matches: 286, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
299 286 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (299 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATAGATACTTTGAATTGTGT
ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
TGAATAAAACACATTTTTGGTATTTTCAAAATTATAAAG
Found at i:178727 original size:20 final size:22
Alignment explanation
Indices: 178702--178742 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
178692 TTCTTTTCTT
178702 TCCCCCTTAA-AA-ATAATTTC
1 TCCCCCTTAATAAGATAATTTC
178722 TCCCCCTTAATAAGATAATTT
1 TCCCCCTTAATAAGATAATTT
178743 TAACAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (22 bp):
TCCCCCTTAATAAGATAATTTC
Found at i:182904 original size:51 final size:52
Alignment explanation
Indices: 182836--182955 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 52
182826 GAAAATTTAT
* *
182836 CTGCATGTATCGATACATTTAAT-GTGTATCGATACGTCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
182887 CTGCATGTATCGATACATTTTATAATGTATCGATATATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
182939 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
182956 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 22 0.34
52 42 0.66
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:182968 original size:52 final size:52
Alignment explanation
Indices: 182836--182975 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 52
182826 GAAAATTTAT
* *
182836 CTGCATGTATCGATACATTTA-AT-GTGTATCGATACGTCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*** * *
182887 CTGCATGTATCGATACATTTTATAATGTATCGATATATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
182939 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
182976 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
50 2 0.03
51 21 0.27
52 54 0.70
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:182982 original size:13 final size:13
Alignment explanation
Indices: 182964--182988 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
182954 CAAAGATCAG
182964 TGTATCGATACAA
1 TGTATCGATACAA
182977 TGTATCGATACA
1 TGTATCGATACA
182989 TATGAGTAAT
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:183073 original size:13 final size:13
Alignment explanation
Indices: 183055--183079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183045 AAAAAAAATA
183055 TGTATCGATACAT
1 TGTATCGATACAT
183068 TGTATCGATACA
1 TGTATCGATACA
183080 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:184075 original size:21 final size:20
Alignment explanation
Indices: 184029--184075 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
184019 TTTGAAGGTG
*
184029 ATTTTGATGAAAAACGATGT
1 ATTTTGATGAAAAACGAAGT
*
184049 AATTTGAAGTGAAAAAC-AAGT
1 ATTTTG-A-TGAAAAACGAAGT
184070 ATTTTG
1 ATTTTG
184076 CAAAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:184234 original size:20 final size:20
Alignment explanation
Indices: 184209--184261 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
184199 TATCGATACA
**
184209 ATGTATCGATACAAAGAATG
1 ATGTATCGATACAAAGAAAC
*
184229 ATGTATCGATACACAGAAAC
1 ATGTATCGATACAAAGAAAC
184249 ATGTATCGATACA
1 ATGTATCGATACA
184262 TTTTGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (20 bp):
ATGTATCGATACAAAGAAAC
Found at i:192355 original size:21 final size:21
Alignment explanation
Indices: 192326--192383 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
192316 ATATAAGTGG
*
192326 AAATTTATCGATACATTAAGT
1 AAATGTATCGATACATTAAGT
* * *
192347 AAATGTATCAATACATCATGT
1 AAATGTATCGATACATTAAGT
*
192368 -ATTGTATCGATACATT
1 AAATGTATCGATACATT
192384 TTGTTGGCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATGTATCGATACATTAAGT
Found at i:196985 original size:154 final size:154
Alignment explanation
Indices: 196770--197105 Score: 383
Period size: 154 Copynumber: 2.2 Consensus size: 154
196760 GAAAACTATG
* * *
196770 AAAATCCCCCTAGGGGATACTTTTGACATAAAAGTACTTGATACCCCTAAAAGACCAAAAAAAGA
1 AAAATACCCCTAGGGGATACCTTTGACATAAAAGTACCTGATACCCCTAAAAGACC-AAAAAAGA
*** * * * **
196835 TTTTAAAATGG-ATGAAATTATCCTAAATATCTA-CTCTCGGCATAAAAGCAGACCAGGTGATGA
65 TGAGAAAA-GGAATGAAACTATCCTAAATACCCACCT-TCGGCATAAAAGCAGACCAGGTGACAA
* * *
196898 CTTAGGAGTTTGTTCTAAAGAATTACA
128 CCTAGGAGTTGGTTCTAAAAAATTACA
* **
196925 AAAATACCCCTA-GGGATACCTTTGACATAAAAGTACCTGATACCCCT-AATGAACTTAAAAAGA
1 AAAATACCCCTAGGGGATACCTTTGACATAAAAGTACCTGATACCCCTAAAAG-ACCAAAAAAGA
* * * * *
196988 TGAGAAGAGGAAATGAAACTATCCTAAATGCCCACCTTTGGCGTAAAAGCAGACTAGGTGACAAC
65 TGAGAAAAGG-AATGAAACTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCAGGTGACAAC
**
197053 CTAGGAGTTGGTTCTAAAAAATTATG
129 CTAGGAGTTGGTTCTAAAAAATTACA
197079 AAAATACCCCTAGGGGATACCTTTGAC
1 AAAATACCCCTAGGGGATACCTTTGAC
197106 GTCGGCGTCC
Statistics
Matches: 152, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
152 2 0.01
153 14 0.09
154 109 0.72
155 27 0.18
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (154 bp):
AAAATACCCCTAGGGGATACCTTTGACATAAAAGTACCTGATACCCCTAAAAGACCAAAAAAGAT
GAGAAAAGGAATGAAACTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCAGGTGACAACCT
AGGAGTTGGTTCTAAAAAATTACA
Found at i:198792 original size:13 final size:12
Alignment explanation
Indices: 198757--198803 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
198747 TTCTCTATTT
198757 TCTTCTATTT-TC
1 TCTTCT-TTTCTC
*
198769 TCTTGCTTTTCTT
1 TCTT-CTTTTCTC
198782 TCTCTCTTTTCTC
1 TCT-TCTTTTCTC
198795 TCTTCTTTT
1 TCTTCTTTT
198804 TCCAGCAGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 13 0.43
13 16 0.53
14 1 0.03
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (12 bp):
TCTTCTTTTCTC
Found at i:198805 original size:26 final size:25
Alignment explanation
Indices: 198755--198803 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
198745 TTTTCTCTAT
198755 TTTCTTCTATTTTCTCTTGCTTTTC
1 TTTCTTCTATTTTCTCTTGCTTTTC
198780 TTTCTCTCT-TTTCTCTCTT-CTTTT
1 TTTCT-TCTATTT-TCTCTTGCTTTT
198804 TCCAGCAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTCTTCTATTTTCTCTTGCTTTTC
Found at i:199535 original size:167 final size:162
Alignment explanation
Indices: 199134--199856 Score: 713
Period size: 167 Copynumber: 4.4 Consensus size: 162
199124 TCAAAATTTA
* * * * * * * * *
199134 GAAAATAAATTGAATTTTTCAAAACTGAATTAAT-GGGAGTTCAATGACAATATTAGATGAGTTT
1 GAAAATGAA-TGAATTTTTGAAAACTAAATTAATATGAAG-TAAATGATAATATTTGATGAATTT
* * * * * * **
199198 TAAAAATTTTAAACCAAGAAAAATCCTCTCGAAAAAATTTGCAGAGAAGAAAACTCGGT-TTCTC
64 TAAAAA-TTAAAAACAAGAAAAATCCCCTCGAAAAAATTT-CTGAGTAGAAAACACCATATT-TC
* * *
199262 GAAAAAAGGAAAATTTCAACAAAAAAATCCAAAACTCAT
126 GAAAAAAGG--AGTTTCAAGAAAAAAATCAAAAACTCAT
* * * * * *
199301 GAAAATGAATTAATTTTTTAAAACTGAATTAATATGAA-TCAAATAATGATGTTTGATGAATTTT
1 GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAGT-AAATGATAATATTTGATGAATTTT
* * *
199365 AAAAACTAAAAATCGATAAAAATCCCCTCGAAAAAATTTCTGAGGTAGAAAACACCATATTTCAG
65 AAAAATTAAAAA-CAAGAAAAATCCCCTCGAAAAAATTTCTGA-GTAGAAAACACCATATTTC-G
* * *
199430 AAAAATAGGAGTTTCAAGGAAAACAATCAAAAATTAAT
127 AAAAA-AGGAGTTTCAA-GAAAAAAATCAAAAACTCAT
* * * *
199468 GAAAATGAAAGAATTTATAAAAACTAAATTAATATGAAGTAAA-GAATAATATTTTATGAATTTT
1 GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAGTAAATG-ATAATATTTGATGAATTTT
* * * * *
199532 AAAAATTAAAAACTAAGAAAAATCCCCTCAAAAAAATTTATGAAATAGAAAACA-TAGTATTTTG
65 AAAAATTAAAAAC-AAGAAAAATCCCCTCGAAAAAATTTCTG-AGTAGAAAACACCA-TATTTCG
* * *
199596 GAAAAAGTCAGTTTCAAGAAAAAAATAAAAAACTCAT
127 AAAAAAG-GAGTTTCAAGAAAAAAATCAAAAACTCAT
* *
199633 GAAAATGAATGAATTTTTGAAAAC-AGAATTAATATGAAGTAAATGATAATATTTTATGAATTTA
1 GAAAATGAATGAATTTTTGAAAACTA-AATTAATATGAAGTAAATGATAATATTTGATGAATTTT
* * * * * *
199697 AAAAATTAAAAACCAAGAAAAATTCGCTTGAAAAAATTTACGGAGTA-AAAAAACCGTATTTCGA
65 AAAAATTAAAAA-CAAGAAAAATCCCCTCGAAAAAATTT-CTGAGTAGAAAACACCATATTTCG-
*
199761 AAAAAAGGAGCTTCAAGAAAAAAATCAAAAACTCAT
127 AAAAAAGGAGTTTCAAGAAAAAAATCAAAAACTCAT
*
199797 GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATGATAATATTTGATGAA
1 GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAGTAAATGATAATATTTGATGAA
199857 ATAAATTTAT
Statistics
Matches: 462, Mismatches: 73, Indels: 45
0.80 0.13 0.08
Matches are distributed among these distances:
164 94 0.20
165 125 0.27
166 104 0.23
167 134 0.29
168 5 0.01
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (162 bp):
GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAGTAAATGATAATATTTGATGAATTTTA
AAAATTAAAAACAAGAAAAATCCCCTCGAAAAAATTTCTGAGTAGAAAACACCATATTTCGAAAA
AAGGAGTTTCAAGAAAAAAATCAAAAACTCAT
Found at i:204015 original size:48 final size:48
Alignment explanation
Indices: 203914--204067 Score: 193
Period size: 48 Copynumber: 3.2 Consensus size: 48
203904 TATGATCAAA
* * * * * * *
203914 GTATAGATACATCTAGATTTTTCCATAATGTATCGATACAATGCA-ACT
1 GTATCGATACATCTGGGTTTTT-CAGATTGTATCGATACAATGAATAAT
*
203962 CGTATCGATACATCTGGGTTTTTCAGATTGTATCGATATAATGAATAAT
1 -GTATCGATACATCTGGGTTTTTCAGATTGTATCGATACAATGAATAAT
**
204011 GTATCGATACATCTGGGTTTCACAGATTGTATCGATACAATGAATAAT
1 GTATCGATACATCTGGGTTTTTCAGATTGTATCGATACAATGAATAAT
204059 GTATCGATA
1 GTATCGATA
204068 TGTTGAATAA
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 72 0.77
49 21 0.23
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (48 bp):
GTATCGATACATCTGGGTTTTTCAGATTGTATCGATACAATGAATAAT
Found at i:204063 original size:20 final size:20
Alignment explanation
Indices: 204038--204124 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 20
204028 TTTCACAGAT
204038 TGTATCGATACAATGAATAA
1 TGTATCGATACAATGAATAA
***
204058 TGTATCGATATGTTGAATAA
1 TGTATCGATACAATGAATAA
*
204078 TGTATCGATAC---G--TAT
1 TGTATCGATACAATGAATAA
* * *
204093 TGTATCAATACAATTACTAA
1 TGTATCGATACAATGAATAA
204113 TGTATCGATACA
1 TGTATCGATACA
204125 TTTTCTATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 12 0.23
17 1 0.02
20 40 0.75
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACAATGAATAA
Found at i:206531 original size:20 final size:20
Alignment explanation
Indices: 206506--206546 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
206496 TCTAAGTAAA
206506 AATACTGAATGTATCGATAC
1 AATACTGAATGTATCGATAC
* *
206526 AATACTGTATGTATTGATAC
1 AATACTGAATGTATCGATAC
206546 A
1 A
206547 TATGGTTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (20 bp):
AATACTGAATGTATCGATAC
Found at i:206711 original size:20 final size:20
Alignment explanation
Indices: 206686--206755 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
206676 CACTCATTTA
206686 TATCGATACACATATAAATG
1 TATCGATACACATATAAATG
206706 TATCGATACA-AT-TCATAATG
1 TATCGATACACATAT-A-AATG
* * *
206726 TATAGATACATC-CATAATTG
1 TATCGATACA-CATATAAATG
206746 TATCGATACA
1 TATCGATACA
206756 TTGAGTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 35 0.85
21 1 0.02
22 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (20 bp):
TATCGATACACATATAAATG
Found at i:206756 original size:20 final size:19
Alignment explanation
Indices: 206702--206756 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
206692 TACACATATA
*
206702 AATGTATCGATACAATTCAT
1 AATGTATCGATAC-ATCCAT
*
206722 AATGTATAGATACATCCAT
1 AATGTATCGATACATCCAT
206741 AATTGTATCGATACAT
1 AA-TGTATCGATACAT
206757 TGAGTTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATCCAT
Found at i:208482 original size:15 final size:13
Alignment explanation
Indices: 208450--208475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208440 AATTTAGTCA
208450 TGTATCGATACAT
1 TGTATCGATACAT
208463 TGTATCGATACAT
1 TGTATCGATACAT
208476 CTTGTATGTA
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):
TGTATCGATACAT
Found at i:208612 original size:33 final size:33
Alignment explanation
Indices: 208557--208620 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
208547 TTCTTTGCAA
*
208557 GTATCGATACATTTGATCATGTATCAATACAAT
1 GTATCGATACATGTGATCATGTATCAATACAAT
* *
208590 GTATCGATAC-TGTGCATTATGTATCGATACA
1 GTATCGATACATGTG-ATCATGTATCAATACA
208621 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (33 bp):
GTATCGATACATGTGATCATGTATCAATACAAT
Found at i:209206 original size:27 final size:27
Alignment explanation
Indices: 209153--209208 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
209143 TTTCCTTTTC
*
209153 TCTCCCCCTTAAACAAATAAAAAAATT
1 TCTCCCCCTTAAACAAACAAAAAAATT
* *
209180 TCTCCCCCTTAATA-AAACAAGACAATT
1 TCTCCCCCTTAA-ACAAACAAAAAAATT
209207 TC
1 TC
209209 CTTTAATCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.27
Consensus pattern (27 bp):
TCTCCCCCTTAAACAAACAAAAAAATT
Found at i:211094 original size:13 final size:13
Alignment explanation
Indices: 211051--211086 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
211041 ATAAACCCTT
*
211051 TGTATCGATACAC
1 TGTATCGATACAA
211064 TGTATCGATACAA
1 TGTATCGATACAA
211077 TGTATCGATA
1 TGTATCGATA
211087 TAGAGTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:224861 original size:13 final size:13
Alignment explanation
Indices: 224843--224867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
224833 ATAATGCACA
224843 GTATCGATACATT
1 GTATCGATACATT
224856 GTATCGATACAT
1 GTATCGATACAT
224868 GACCACTGTA
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:224864 original size:33 final size:32
Alignment explanation
Indices: 224822--224884 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
224812 CACCTTCAGA
*
224822 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
224855 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
224885 TTGCCAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:224977 original size:32 final size:33
Alignment explanation
Indices: 224936--225003 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
224926 CCTTAACTAT
*
224936 TTGTATCGATACAT-A-CAAGTTCTATCGATACA
1 TTGTATCGATACATGACCAA-ATCTATCGATACA
*
224968 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATCTATCGATACA
225001 TTG
1 TTG
225004 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 15 0.47
34 3 0.09
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATCTATCGATACA
Found at i:228027 original size:34 final size:34
Alignment explanation
Indices: 227960--228946 Score: 831
Period size: 33 Copynumber: 30.8 Consensus size: 34
227950 TCTTTTCTCA
* * *
227960 AAGTCCACAACTTCGTGGTA-TCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
227993 AAGTCCACAACTCTGTGGCACTCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * ** * *
228027 AAGCCCAGAACTCTATGGCACTCTTTTTCATTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228061 AAGCCCACAACTCTGTGGCA-TCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228094 AAGTCCATAACTCTGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228121 AAGCCCACAACTCTGTGACACTCTTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTC-TTTTTCCTTTT
* *
228156 AAGCCCACAACTTCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228190 AAGCCCACAACTCCATGGCATTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228224 AAAGTCCAGAACTCCGTGGCA--C-----CATTTT
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228252 AAGTCCACATCTCCATGGCA-TCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
228285 AAGTCCACAACTCCGTGGCA-TATTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
228318 AAGTCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
228352 AAGTCCATAACTCCGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228379 AAGCCCACAACTCCGTGGTACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228413 AAGCCCACAACTCCGTGGCA-TCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
228446 AAGTCCACAACTTCGTGGCA-TC-TTTTCTCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTC-CTTTT
* *
228479 AAGTCCACAACTTCGTGGCA-TCTTATTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * *
228512 AAATCCACAACTCCATGGCA-TCATTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
228545 AAGTCCACAACTCCGTGGCA-TCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
** *
228578 AAGTCCATGACTCCGTGGCACTCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228612 ATGTCCACAACTCCGGGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228639 AAGTCCACGACTCCGTGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
228673 AAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228707 AAGTCCACAACTCTGTGGTA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228734 AAGTCCACAACTCCATGGCA-TCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228767 AAATCCACAACTCCATGGCA-TCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* ** **
228800 AAGTCCAGAACTCCAAGGCAC-CTTGCTCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
228833 AAGTCCACAACTCCGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228860 AAGTCCACAACTCCATGGTA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
228887 AAGTCCACAACTCCGTGGCA-TCTTTCTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * *
228920 AAGCCCACAAGTCAGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTT
228947 CAAAAGCCCA
Statistics
Matches: 799, Mismatches: 107, Indels: 95
0.80 0.11 0.09
Matches are distributed among these distances:
27 157 0.20
28 8 0.01
29 3 0.00
32 9 0.01
33 338 0.42
34 241 0.30
35 43 0.05
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:228132 original size:27 final size:27
Alignment explanation
Indices: 228060--228147 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 27
228050 TTTTTCATTC
228060 TAAGCCCACAACTCTGTGGCATCTTGTTCCTTT
1 TAAGCCCACAACTCTGTGGCA-C-----CCTTT
* *
228093 TAAGTCCATAACTCTGTGGCACCCTTT
1 TAAGCCCACAACTCTGTGGCACCCTTT
* *
228120 TAAGCCCACAACTCTGTGACACTCTTT
1 TAAGCCCACAACTCTGTGGCACCCTTT
228147 T
1 T
228148 TTCCTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 29 0.59
32 1 0.02
33 19 0.39
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.34
Consensus pattern (27 bp):
TAAGCCCACAACTCTGTGGCACCCTTT
Found at i:228343 original size:128 final size:127
Alignment explanation
Indices: 227986--228939 Score: 990
Period size: 128 Copynumber: 7.5 Consensus size: 127
227976 GGTATCTTTT
* * * **
227986 CCCTTTTAAGTCCACAACTCTGTGGCACTCTTTTTCTTTTTAAGCCCAGAACTCTATGGCACTCT
1 CCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA-TCT
* * * * * *
228051 TTTTCATTCTAAGCCCACAACTCTGTGGCATCTTGTTCCTTTTAAGTCCATAACTCTGTGGCA
65 TTTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * * *
228114 CCCTTTTAAGCCCACAACTCTGTGACACTCTTTTTTCCTTTTAAGCCCACAACTTCGTGGCACTC
1 CCCTTTTAAGTCCACAACTCCGTGGCACTC-TTTTTCCTTTTAAGCCCACAACTCCGTGGCA-TC
* ** *
228179 TTTTTCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAAGTCCAGAACTCCGTGGC
64 TTTTTCCTTTTAAGTCCACAACTCTGTGGCA-TCTTTTTCCTTTT-AAGTCCACAACTCCGTGGC
228244 A
127 A
* * * * * *
228245 CCATTTTAAGTCCACATCTCCATGGCA-TCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATATT
1 CCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCATCTT
*
228309 TTTCCTTTTAAGTCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCATAACTCCGTGGCA
66 TTTCCTTTTAAGTCCACAACTCTGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * *
228372 CCCTTTTAAGCCCACAACTCCGTGGTACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCATCTT
1 CCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCATCTT
* *
228437 GTTCCTTTTAAGTCCACAACT-TCGTGGCATC-TTTTCTCTTTTAAGTCCACAACTTCGTGGCA
66 TTTCCTTTTAAGTCCACAACTCT-GTGGCATCTTTTTC-CTTTTAAGTCCACAACTCCGTGGCA
* * * * *
228499 TCTTATTCCTTTTAAATCCACAACTCCATGGCA-TCATTTCCCTTTTAAGTCCACAACTCCGTGG
1 -C-----CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGG
* ** * * * *
228563 CATCTTGTTCCTTTTAAGTCCATGACTCCGTGGCACTCTTTTCCCTTTTATGTCCACAACTCCGG
60 CATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGT
228628 GGCA
124 GGCA
* * * *
228632 CCCTTTTAAGTCCACGACTCCGTGGCACCCTTTTCCCTTTTAAGCCCACAACTCTGTGGCACTCT
1 CCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA-TCT
* * *
228697 TTTTCTTTTTAAGTCCACAACTCTGTGGTA-C-----CCTTTTAAGTCCACAACTCCATGGCA
65 TTTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * * * **
228754 TCTTGTTCCTTTTAAATCCACAACTCCATGGCA-TCTTTTTCCTTTTAAGTCCAGAACTCCAAGG
1 -C-----CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGG
* ** * *
228818 CACCTTGCTCCTTTTAAGTCCACAACTCCGTGGCA-C-----CCTTTTAAGTCCACAACTCCATG
60 CATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTG
*
228877 GTA
125 GCA
* * * *
228880 CCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTCTCTTTTTAAGCCCACAAGTCAGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA
228940 CCCTTTTCAA
Statistics
Matches: 704, Mismatches: 99, Indels: 54
0.82 0.12 0.06
Matches are distributed among these distances:
120 49 0.07
122 23 0.03
123 1 0.00
125 1 0.00
126 58 0.08
127 117 0.17
128 182 0.26
129 111 0.16
130 14 0.02
131 39 0.06
132 59 0.08
133 46 0.07
134 4 0.01
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.35
Consensus pattern (127 bp):
CCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCATCTT
TTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:228376 original size:27 final size:27
Alignment explanation
Indices: 228346--228405 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
228336 CACTCTTTTT
* *
228346 CCTTTTAAGTCCATAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
228373 CCTTTTAAGCCCACAACTCCGTGGTAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
228400 TCTTTT
1 CCTTTT
228406 TCCTTCTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:228635 original size:27 final size:27
Alignment explanation
Indices: 228605--228906 Score: 118
Period size: 27 Copynumber: 10.0 Consensus size: 27
228595 GCACTCTTTT
*
228605 CCCTTTTATGTCCACAACTCCGGGGCA
1 CCCTTTTAAGTCCACAACTCCGGGGCA
* *
228632 CCCTTTTAAGTCCACGACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGGGGCA
* * *
228659 CCCTTTTCCCTTTTAAGCCCACAACTCTGTGGCA
1 -------CCCTTTTAAGTCCACAACTCCGGGGCA
* * *
228693 CTCTTTTTCTTTTTAAGTCCACAACTCTGTGGTA
1 C-C-----C-TTTTAAGTCCACAACTCCGGGGCA
**
228727 CCCTTTTAAGTCCACAACTCCATGGCA
1 CCCTTTTAAGTCCACAACTCCGGGGCA
* **
228754 TCTTGTTCCTTTTAAATCCACAACTCCATGGCA
1 -C-----CCTTTTAAGTCCACAACTCCGGGGCA
* **
228787 TCTTTTTCCTTTTAAGTCCAGAACTCCAAGGCA
1 -C-----CCTTTTAAGTCCACAACTCCGGGGCA
*
228820 CCTTGCTCCTTTTAAGTCCACAACTCCGTGGCA
1 -----C-CCTTTTAAGTCCACAACTCCGGGGCA
** *
228853 CCCTTTTAAGTCCACAACTCCATGGTA
1 CCCTTTTAAGTCCACAACTCCGGGGCA
*
228880 CCCTTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGGGGCA
228907 TCTTTCTCTT
Statistics
Matches: 227, Mismatches: 24, Indels: 48
0.76 0.08 0.16
Matches are distributed among these distances:
27 95 0.42
28 4 0.02
33 80 0.35
34 47 0.21
37 1 0.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.32
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGGGGCA
Found at i:228995 original size:29 final size:30
Alignment explanation
Indices: 228920--229044 Score: 159
Period size: 29 Copynumber: 4.3 Consensus size: 30
228910 TTCTCTTTTT
*
228920 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
228950 AAGCCCACAAGTCAGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
* * *
228979 AAGCCTACAAGTTAGTGGCA-ACC-TTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
* * *
229007 AAGCACACAAGTTAGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
229036 AAGCCCACA
1 AAGCCCACA
229045 CAAGTTGGTG
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
27 6 0.07
28 19 0.23
29 32 0.38
30 27 0.32
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCCTTTCAA
Found at i:229039 original size:57 final size:58
Alignment explanation
Indices: 228920--229044 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 58
228910 TTCTCTTTTT
* * *
228920 AAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCACCCCTTTCA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCACACAAGTCAGTGGCAACCCTTTCA
* * *
228979 AAGCCTACAAGTTAGTGGCAACC-TTCAAAAGCACACAAGTTAGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCACACAAGTCAGTGGCAACCCTTTC-A
229036 AAGCCCACA
1 AAGCCCACA
229045 CAAGTTGGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 10 0.17
57 28 0.48
59 20 0.34
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (58 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCACACAAGTCAGTGGCAACCCTTTCA
Found at i:229126 original size:39 final size:39
Alignment explanation
Indices: 229071--229231 Score: 171
Period size: 39 Copynumber: 3.9 Consensus size: 39
229061 TCTTCTAAGT
*
229071 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
229110 CCAATATCGCTGGCCTTGAATCAACATATTGGCACCTCCATCTTAAAG-
1 CCAATATCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAGC
*
229158 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
229197 CCAATATCGCTGGCCTTAAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
229232 CTTCATCTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 22
0.77 0.07 0.17
Matches are distributed among these distances:
38 3 0.03
39 61 0.60
41 1 0.01
42 2 0.02
45 2 0.02
46 1 0.01
48 29 0.28
49 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
Found at i:229219 original size:87 final size:88
Alignment explanation
Indices: 229071--229280 Score: 341
Period size: 87 Copynumber: 2.4 Consensus size: 88
229061 TCTTCTAAGT
* * *
229071 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTAAATCAACA
229136 TATTGGCACCTCCATCTTAAAG-
66 TATTGGCACCTCCATCTTAAAGA
*
229158 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTAAATCAGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTAAATCAACA
* *
229223 TATTGGCACCTTCATCTTTAAGA
66 TATTGGCACCTCCATCTTAAAGA
* *
229246 CCAATGTCGTTGGCCTTGAATAAGCACATTGGCAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
229281 CTTCATCTTT
Statistics
Matches: 114, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
87 81 0.71
88 33 0.29
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (88 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTAAATCAACA
TATTGGCACCTCCATCTTAAAGA
Found at i:229277 original size:49 final size:49
Alignment explanation
Indices: 229197--229526 Score: 367
Period size: 49 Copynumber: 6.6 Consensus size: 49
229187 TGGCACAAGC
* * * *
229197 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATCTTTAAGA
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
*
229246 CCAATGTCGTTGGCCTTGAATAAGCACATTGGCACCTTCATCTTTAAGA
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * *
229295 CCGATGTCGTTGGCCTTCAATTAGCACATTGGCACCTTAACCATCTTTAAGA
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGA
* * *
229347 CCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * * * *
229396 CCAATATCATTGGCCTTGAATCAGCACATTGGCATCTTTAACATTCCTAAGC
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATC-TT--TAAGA
** * *
229448 CCAATGTCGTTGGCCTTGTCTCAGGCACATTGGCA--TTCTTCTTTAAGT
1 CCAATGTCGTTGGCCTTGAATCA-GCACATTGGCACCTTCATCTTTAAGA
* * *
229496 CTAATGTCGATGGCCATGAATCAGCACATTG
1 CCAATGTCGTTGGCCTTGAATCAGCACATTG
229527 TCATTCTTCG
Statistics
Matches: 241, Mismatches: 33, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
47 8 0.03
48 22 0.09
49 124 0.51
50 4 0.02
51 3 0.01
52 69 0.29
53 11 0.05
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
Found at i:229379 original size:101 final size:100
Alignment explanation
Indices: 229197--229526 Score: 391
Period size: 101 Copynumber: 3.3 Consensus size: 100
229187 TGGCACAAGC
* * * *
229197 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTT--CATCTTTAAGACCAATGTCGTTGGC
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACATCTTTAAGACCAATGTCGTTGGC
*
229260 CTTGAATAAGCACATTGGCACCTTCATCTTTAAGA
66 CTTGAATAAGCACATTGGCACCTTCATCTTTAAGT
* * * *
229295 CCGATGTCGTTGGCCTTCAATTAGCACATTGGCACCTTAACCATCTTTAAGACCAATGTCGCTGG
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAA-CATCTTTAAGACCAATGTCGTTGG
*
229360 CCTTGAATTAGCACATTGGCACCTTCATCTTTAAGT
65 CCTTGAATAAGCACATTGGCACCTTCATCTTTAAGT
* * * * *
229396 CCAATATCATTGGCCTTGAATCAGCACATTGGCATCTTTAACAT-TCCTAAGCCCAATGTCGTTG
1 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-CCTTAACATCT-TTAAGACCAATGTCGTTG
** * *
229460 GCCTTGTCTCAGGCACATTGGCA--TTCTTCTTTAAGT
64 GCCTTGAAT-AAGCACATTGGCACCTTCATCTTTAAGT
* * *
229496 CTAATGTCGATGGCCATGAATCAGCACATTG
1 CCAATGTCGTTGGCCTTGAATCAGCACATTG
229527 TCATTCTTCG
Statistics
Matches: 198, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
98 32 0.16
100 39 0.20
101 111 0.56
102 16 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (100 bp):
CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACATCTTTAAGACCAATGTCGTTGGC
CTTGAATAAGCACATTGGCACCTTCATCTTTAAGT
Found at i:230317 original size:13 final size:13
Alignment explanation
Indices: 230299--230324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
230289 ACATAAGTGT
230299 TGTATCGATACAA
1 TGTATCGATACAA
230312 TGTATCGATACAA
1 TGTATCGATACAA
230325 AACTACTGCC
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):
TGTATCGATACAA
Found at i:234825 original size:16 final size:16
Alignment explanation
Indices: 234801--234834 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
234791 GATCAATCCT
234801 TATTCGTGATTGTAAC
1 TATTCGTGATTGTAAC
*
234817 TATTTGTGATTGTAAC
1 TATTCGTGATTGTAAC
234833 TA
1 TA
234835 AGTCTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (16 bp):
TATTCGTGATTGTAAC
Found at i:239784 original size:21 final size:21
Alignment explanation
Indices: 239737--239815 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
239727 AATTTGCCTA
* *
239737 CATGTATCAATACATT-GAAG
1 CATGTATCGATACATTACAAG
*
239757 AATGTATCGATACATTACAAG
1 CATGTATCGATACATTACAAG
239778 CATGTATCGATACATTACAAG
1 CATGTATCGATACATTACAAG
239799 CATGTATCGATAACATT
1 CATGTATCGAT-ACATT
239816 TACTTATGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.26
21 34 0.64
22 5 0.09
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (21 bp):
CATGTATCGATACATTACAAG
Found at i:240658 original size:52 final size:52
Alignment explanation
Indices: 240583--241044 Score: 270
Period size: 52 Copynumber: 8.8 Consensus size: 52
240573 CTTAACAAAT
* * *
240583 GTGCCAATATGCAGATTCAAGGCTTGTGACATTGGACTTAAAGATGATAAGA
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGATAAGA
* * * * * *
240635 GTGCTATTGTGCTGATTCAAGGCTAATGACATTGGATTTAAAGATGGTAAGC
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGATAAGA
* * ** *
240687 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGG-CTTTGGACAGAAGGTTTTGAAAA
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATT-GGAC-TT----A-AAGATGAT-AAGA
* * * * ** * * *
240746 GTGACAACGTGCTGATTCAAGGCCAATGATGTTGGGCTTAAAGGTGATAAAA
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGATAAGA
* * ** * *
240798 GGTGCTAATGTGCTGATTCAAGGCCAACGAC-TTAGG-CTTAAAGGTGATAAGG
1 -GTGCCAATGTGCTGATTCAAGGCTAGTGACATT-GGACTTAAAGATGATAAGA
* * * * * * *
240850 GTGCCAATGTGCTGATTCAAGGCTAGCGAC-TTGGGCTCAATGGTGATGAGG
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGATAAGA
* * * ** * * *
240901 GTTCTAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAATAACAAG-
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGATAAGA
* * * * * ** * **
240952 GATGTCAATATGCTAATTTAAGGCCAGCAATATCAGACTTAAA-ATTGATAAGA
1 G-TGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGA-TGATAAGA
* *
241005 GTGCCAATGTGCTAATTCAAGGCTAGTGACATTGGGCTTA
1 GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTA
241045 GAAAGAAATG
Statistics
Matches: 318, Mismatches: 76, Indels: 32
0.75 0.18 0.08
Matches are distributed among these distances:
50 2 0.01
51 70 0.22
52 168 0.53
53 38 0.12
54 1 0.00
57 1 0.00
58 9 0.03
59 29 0.09
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (52 bp):
GTGCCAATGTGCTGATTCAAGGCTAGTGACATTGGACTTAAAGATGATAAGA
Found at i:240867 original size:51 final size:51
Alignment explanation
Indices: 240754--241027 Score: 219
Period size: 51 Copynumber: 5.3 Consensus size: 51
240744 AAGTGACAAC
* * * * *
240754 GTGCTGATTCAAGGCCAATGATGTTGGGCTTAAAGGTGATAAAAGGTGCTAAT
1 GTGCTGATTCAAGGCCAACGA-CTTAGGCTTAAAGGTGAT-AAGGGTGCCAAT
240807 GTGCTGATTCAAGGCCAACGACTTAGGCTTAAAGGTGATAAGGGTGCCAAT
1 GTGCTGATTCAAGGCCAACGACTTAGGCTTAAAGGTGATAAGGGTGCCAAT
* * * * * * * *
240858 GTGCTGATTCAAGGCTAGCGACTTGGGCTCAATGGTGATGAGGGTTCTAAT
1 GTGCTGATTCAAGGCCAACGACTTAGGCTTAAAGGTGATAAGGGTGCCAAT
** * * * *
240909 GTGCTGATTCAAGGCCAACGACATT-GGACTTAAAAATAACAAGGATGTCAAT
1 GTGCTGATTCAAGGCCAACGAC-TTAGG-CTTAAAGGTGATAAGGGTGCCAAT
* * * * * * ** *
240961 ATGCTAATTTAAGGCCAGC-AATATCAGACTTAAAATTGATAAGAGTGCCAAT
1 GTGCTGATTCAAGGCCAACGACT-T-AGGCTTAAAGGTGATAAGGGTGCCAAT
*
241013 GTGCTAATTCAAGGC
1 GTGCTGATTCAAGGC
241028 TAGTGACATT
Statistics
Matches: 176, Mismatches: 40, Indels: 11
0.78 0.18 0.05
Matches are distributed among these distances:
50 1 0.01
51 77 0.44
52 77 0.44
53 21 0.12
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (51 bp):
GTGCTGATTCAAGGCCAACGACTTAGGCTTAAAGGTGATAAGGGTGCCAAT
Found at i:241405 original size:33 final size:33
Alignment explanation
Indices: 241326--241661 Score: 113
Period size: 31 Copynumber: 10.5 Consensus size: 33
241316 CCAACTCGTG
* ** * *
241326 TGGGCTTTTGGAAAG-GTTGCCACCAACTTGTG
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
* * * * *
241358 TGGCCTTTTAAAAAGAGTTGCCATTGATTTTCTG
1 TGGGCTTTTGAAAAGAGTTGCCACTGA-CTTCTA
*
241392 TGGGC-TTTGAAAAGGGTTGCCACTGACTTCTA
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
* ** * *
241424 TGGGCTTTTGAAAAGA--TACCACCAACTTGTG
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
* * * * * *
241455 TGAGCTTTAG-AAAG-GTTACCACCGACTTGTG
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
* * * ** *
241486 TAGGCTTTTAAAAAGGGTTGCCA-TCGACTAGTG
1 TGGGCTTTTGAAAAGAGTTGCCACT-GACTTCTA
* * * * *
241519 TGAGC-TTTG-AAAGGGTTGCCA-TCGATTTATG
1 TGGGCTTTTGAAAAGAGTTGCCACT-GACTTCTA
* * * * *
241550 TGGGC-TTTAAAAAGGGTTGCCACTAACTTGTG
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
* ** * *
241582 TGGGCTTTTG-AAAG-GATGCCACCAACTTGTG
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
** * * * *
241613 TATGCTTTTGAAAAAAGTTGCCACCGACTTATG
1 TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
241646 TGGGCTTTTGAAAAGA
1 TGGGCTTTTGAAAAGA
241662 TGCTATGCTT
Statistics
Matches: 238, Mismatches: 53, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
30 4 0.02
31 87 0.37
32 57 0.24
33 82 0.34
34 8 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (33 bp):
TGGGCTTTTGAAAAGAGTTGCCACTGACTTCTA
Found at i:241475 original size:31 final size:32
Alignment explanation
Indices: 241442--241658 Score: 156
Period size: 31 Copynumber: 6.8 Consensus size: 32
241432 TGAAAAGATA
*
241442 CCACCAACTTGTGTGAGCTTTAGAAA-GGTTA
1 CCACCAACTTGTGTGAGCTTTAGAAAGGGTTG
* *
241473 CCACCGACTTGTGT-AGGCTTTTAAAAAGGGTTG
1 CCACCAACTTGTGTGA-GC-TTTAGAAAGGGTTG
* * *
241506 CCATCGACTAGTGTGAGCTTT-GAAAGGGTTG
1 CCACCAACTTGTGTGAGCTTTAGAAAGGGTTG
* * * * * *
241537 CCATCGATTTATGTGGGCTTTAAAAAGGGTTG
1 CCACCAACTTGTGTGAGCTTTAGAAAGGGTTG
* * * *
241569 CCACTAACTTGTGTGGGCTTTTGAAA-GGATG
1 CCACCAACTTGTGTGAGCTTTAGAAAGGGTTG
* **
241600 CCACCAACTTGTGT-ATGCTTTTGAAAAAAGTTG
1 CCACCAACTTGTGTGA-GCTTTAG-AAAGGGTTG
* * * *
241633 CCACCGACTTATGTGGGCTTTTGAAA
1 CCACCAACTTGTGTGAGCTTTAGAAA
241659 AGATGCTATG
Statistics
Matches: 151, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.01
31 65 0.43
32 44 0.29
33 40 0.26
34 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (32 bp):
CCACCAACTTGTGTGAGCTTTAGAAAGGGTTG
Found at i:241648 original size:64 final size:64
Alignment explanation
Indices: 241324--241658 Score: 272
Period size: 64 Copynumber: 5.2 Consensus size: 64
241314 TGCCAACTCG
* ** *
241324 TGTGGGCTTTTGGAAAGGTTGCCACCAACTTGTGT-GGCCTTTTAAAAAGAGTTGCCATTGATTT
1 TGTGGGCTTTT-GAAAGGTTGCCACCGACTTGTGTAGG-CTTTTAAAAAGAGTTGCCACCGA-CT
*
241388 TC
63 TA
* * * * * * *
241390 TGTGGGC-TTTGAAAAGGGTTGCCACTGACTTCTATGGGCTTTTGAAAAGA--TACCACCAACTT
1 TGTGGGCTTTTG-AAA-GGTTGCCACCGACTTGTGTAGGCTTTTAAAAAGAGTTGCCACCGACTT
*
241452 G
64 A
* * * * *
241453 TGTGAGCTTTAGAAAGGTTACCACCGACTTGTGTAGGCTTTTAAAAAGGGTTGCCATCGAC-TA
1 TGTGGGCTTTTGAAAGGTTGCCACCGACTTGTGTAGGCTTTTAAAAAGAGTTGCCACCGACTTA
* * * * * * **
241516 GTGTGAGC-TTTGAAAGGGTTGCCATCGATTTATGTGGGC-TTTAAAAAGGGTTGCCACTAACTT
1 -TGTGGGCTTTTGAAA-GGTTGCCACCGACTTGTGTAGGCTTTTAAAAAGAGTTGCCACCGACTT
*
241579 G
64 A
* * *
241580 TGTGGGCTTTTGAAAGGATGCCACCAACTTGTGTATGCTTTTGAAAAA-AGTTGCCACCGACTTA
1 TGTGGGCTTTTGAAAGGTTGCCACCGACTTGTGTAGGCTTTT-AAAAAGAGTTGCCACCGACTTA
241644 TGTGGGCTTTTGAAA
1 TGTGGGCTTTTGAAA
241659 AGATGCTATG
Statistics
Matches: 211, Mismatches: 46, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
62 27 0.13
63 59 0.28
64 79 0.37
65 11 0.05
66 33 0.16
67 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (64 bp):
TGTGGGCTTTTGAAAGGTTGCCACCGACTTGTGTAGGCTTTTAAAAAGAGTTGCCACCGACTTA
Found at i:241756 original size:33 final size:31
Alignment explanation
Indices: 241668--241767 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
241658 AAGATGCTAT
* *
241668 GCTTTGGAAAGGTTGCCACCGACTTGTGTGG
1 GCTTTGGAAAGGTTACCACCAACTTGTGTGG
* *
241699 GCTTTTGAAAGGATACCACCAACTTGTGTGG
1 GCTTTGGAAAGGTTACCACCAACTTGTGTGG
*
241730 GCTTTGGAAAAGGGTTACCACTAACTTGTGTGG
1 GCTTTGG-AAA-GGTTACCACCAACTTGTGTGG
241763 GCTTT
1 GCTTT
241768 AAAAGGGTGC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 33 0.55
32 3 0.05
33 24 0.40
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (31 bp):
GCTTTGGAAAGGTTACCACCAACTTGTGTGG
Found at i:241799 original size:28 final size:28
Alignment explanation
Indices: 241764--241827 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
241754 CTTGTGTGGG
* * *
241764 CTTTAAAAGGGTGCGAC-GAAGTTGCGAA
1 CTTTAAAAAGGTGCCACAG-AGTTACGAA
*
241792 CTTTAAAAAGGTGCCACAGAGTTATGAA
1 CTTTAAAAAGGTGCCACAGAGTTACGAA
241820 CTTTAAAA
1 CTTTAAAA
241828 TAATGCCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (28 bp):
CTTTAAAAAGGTGCCACAGAGTTACGAA
Found at i:241897 original size:30 final size:29
Alignment explanation
Indices: 241758--242748 Score: 633
Period size: 30 Copynumber: 33.8 Consensus size: 29
241748 CACTAACTTG
* *
241758 TGTGGGCTTT-AAAAGGGTGCGACGAAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* * *
241786 TGCGAACTTT-AAAAAGGTGCCAC-AGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGA-AGT
* * *** *
241814 TATGAACTTT-AAAATAATGCCACGAAAT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* * *
241842 TATTGACTTT-AAAAGAGGTGTCACGAAGT
1 TGTGGACTTTGAAAAG-GGTGCCACGAAGT
* *
241871 TGTGGACTATGAGAAGGGGTGCCACGAAGT
1 TGTGGACTTTGA-AAAGGGTGCCACGAAGT
*
241901 TATGGACTTTGAAAAGGG-GCACCACGAAGT
1 TGTGGACTTTGAAAAGGGTG--CCACGAAGT
* * *
241931 TATAGACTTT-AAGAAGGGTGCCA-TAGAG-
1 TGTGGACTTTGAA-AAGGGTGCCACGA-AGT
*
241959 TGTGGACTTTGAAAAGGGGTGCCAC-AGAGC
1 TGTGGACTTTGAAAA-GGGTGCCACGA-AGT
* * **
241989 TATGGACTTTGAGAAGGGTGCCATAAAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* *
242018 TGTAGACTTTGAAAAAGGGTGCCACGGAGT
1 TGTGGACTTTG-AAAAGGGTGCCACGAAGT
*
242048 TATGGACTTTGAAAAGGGTGCCACGAAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* ** * * *
242077 TATGGACTTTGAAAAATGTGTCATGGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* * ** * *
242106 TGTTGACTTTAAAAAATTGTGCC-CTAAAAT
1 TGTGGACTTT-GAAAAGGGTGCCAC-GAAGT
* ** *
242136 TGTGGACTTAGAAAAAAGTGCCACGGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
*
242165 TGTGGGCTTTGAAAAAGGGTGCCACCG-AGT
1 TGTGGACTTTG-AAAAGGGTGCCA-CGAAGT
*
242195 TGTGGACTTTGGAAAAGGGTGCCATTG-AGT
1 TGTGGACTTT-GAAAAGGGTGCCA-CGAAGT
* *
242225 TGTAGACTTT-AAAAGGGTGCCACGGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* *
242253 TGTGGACTTTGGAAAGGGGTGCCATTG-AGT
1 TGTGGACTTT-GAAAAGGGTGCCA-CGAAGT
* *
242283 TGTGGACTTTCAAAAGGGTGCCACGGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* *
242312 TGTGGACTTT-AAAAAGGTGCCACGGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* * *
242340 TGTGGACTCT-AAAAGGGTGCCACAAAAT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* *** *
242368 TGTAGACTTT-AAAAGGGTGTTGCGGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* * * * *
242396 TATGGAGTTTGGAAAGGGTTGCCATGGAGT
1 TGTGGACTTTGAAAAGGG-TGCCACGAAGT
* *
242426 TGTGGACTTTGAAAAGGGGGCTAC-AGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGA-AGT
*
242455 TGTGGACTTTGAAAAAGGGTGCCACAAAGT
1 TGTGGACTTTG-AAAAGGGTGCCACGAAGT
* ** *
242485 TGTGGACTTTAAGAAAGGGCACCATTG-AGT
1 TGTGGACTTTGA-AAAGGGTGCCA-CGAAGT
* * *
242515 TATGGACTTTGAAAAGGGTGGCATGGAGTGGAGT
1 TGTGGACTTTGAAAAGGGTGCCA-CGA----AGT
* * * * *
242549 TCTGTACTTTAGAAAAAGGTGCCATGGAGT
1 TGTGGACTTT-GAAAAGGGTGCCACGAAGT
* * ** * *
242579 TATGAACAATAAAAAGGGTGCCACAAAGT
1 TGTGGACTTTGAAAAGGGTGCCACGAAGT
* **
242608 TGCGGACTTTGAAAAAGGGTGCCATAAAGT
1 TGTGGACTTTG-AAAAGGGTGCCACGAAGT
* *
242638 TGTGGACTTTGAAAAAGGATGCCACAAAGT
1 TGTGGACTTTG-AAAAGGGTGCCACGAAGT
* * *
242668 TGTGGGCTTTTAAAAGGGTGCCA-AAGAGT
1 TGTGGACTTTGAAAAGGGTGCCACGA-AGT
* *
242697 TGT-GAGCTTTAAAAAGGGTGTCACGATA-T
1 TGTGGA-CTTTGAAAAGGGTGCCACGA-AGT
242726 TGTGGACTTTGAAAAGGGTGCCA
1 TGTGGACTTTGAAAAGGGTGCCA
242749 TGGAGTTATA
Statistics
Matches: 761, Mismatches: 157, Indels: 89
0.76 0.16 0.09
Matches are distributed among these distances:
27 2 0.00
28 160 0.21
29 259 0.34
30 308 0.40
31 9 0.01
34 12 0.02
35 11 0.01
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (29 bp):
TGTGGACTTTGAAAAGGGTGCCACGAAGT
Found at i:241976 original size:58 final size:59
Alignment explanation
Indices: 241846--242770 Score: 432
Period size: 59 Copynumber: 15.7 Consensus size: 59
241836 CGAAATTATT
* * * * * ** *
241846 GACTTT-AAAAGAGGTGTCACGAAGTTGTGGACTATGAGAAGGGGTGCCACGAAGTTATG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTTAAGAA-GGGTGCCATAAAGTTGTG
** * *
241905 GACTTTGAAAAGGGGCACCACGAAGTTATAGACTTTAAGAAGGGTGCCATAGAG-TGTG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTTAAGAAGGGTGCCATAAAGTTGTG
* * *
241963 GACTTTGAAAAGGGGTGCCAC-AGAGCTATGGACTTTGAGAAGGGTGCCATAAAGTTGTA
1 GACTTTGAAAAGGGGTGCCACGA-AGTTATGGACTTTAAGAAGGGTGCCATAAAGTTGTG
* * ** *
242022 GACTTTGAAAAAGGGTGCCACGGAGTTATGGACTTTGAA-AAGGGTGCCACGAAGTTATG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTT-AAGAAGGGTGCCATAAAGTTGTG
** * * * * * * ** * *
242081 GACTTTGAAAA-ATGTGTCATGGAGTTGTTGACTTTAAAAAATTGTGCCCTAAAATTGTG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTT-AAGAAGGGTGCCATAAAGTTGTG
* ** * * * * ***
242140 GACTTAGAAAA-AAGTGCCACGGAGTTGTGGGCTTTGAAAAAGGGTGCCACCGAGTTGTG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTT-AAGAAGGGTGCCATAAAGTTGTG
* * * ***
242199 GACTTTGGAAAA-GGGTGCCATTG-AGTTGTAGACTTTAA-AAGGGTGCCACGGAGTTGTG
1 GACTTT-GAAAAGGGGTGCCA-CGAAGTTATGGACTTTAAGAAGGGTGCCATAAAGTTGTG
* * * ***
242257 GACTTTGGAAAGGGGTGCCATTG-AGTTGTGGACTTTCAA-AAGGGTGCCACGGAGTTGTG
1 GACTTTGAAAAGGGGTGCCA-CGAAGTTATGGACTTT-AAGAAGGGTGCCATAAAGTTGTG
* * * * * * *
242316 GACTTT-AAAA-AGGTGCCACGGAGTTGTGGACTCTAA-AAGGGTGCCACAAAATTGTA
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTTAAGAAGGGTGCCATAAAGTTGTG
*** * * * **
242372 GACTTT-AAAA-GGGTGTTGCGGAGTTATGGAGTTT-GGAAAGGGTTGCCATGGAGTTGTG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTTAAG-AAGGG-TGCCATAAAGTTGTG
* * * *
242430 GACTTTGAAAAGGGG-GCTAC-AGAGTTGTGGACTTTGAAAAAGGGTGCCACAAAGTTGTG
1 GACTTTGAAAAGGGGTGCCACGA-AGTTATGGACTTT-AAGAAGGGTGCCATAAAGTTGTG
* ** * * * *
242489 GACTTT-AAGAAAGGGCACCATTG-AGTTATGGACTTTGAA-AAGGGTGGCATGGAGTGGAGTTC
1 GACTTTGAA-AAGGGGTGCCA-CGAAGTTATGGACTTT-AAGAAGGGTGCCAT--A---AAGTTG
242551 TG
58 TG
* * * * * ** * * *
242553 TACTTTAGAAAA-AGGTGCCATGGAGTTATGAACAATAAAAAGGGTGCCACAAAGTTGCG
1 GACTTT-GAAAAGGGGTGCCACGAAGTTATGGACTTTAAGAAGGGTGCCATAAAGTTGTG
* ** * * * *
242612 GACTTTGAAAAAGGGTGCCATAAAGTTGTGGACTTTGAAAAAGGATGCCACAAAGTTGTG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTT-AAGAAGGGTGCCATAAAGTTGTG
* * * * * * * *
242672 GGCTTTTAAAA-GGGTGCCA-AAGAGTTGT-GAGCTTTAAAAAGGGTGTCACGATA-TTGTG
1 GACTTTGAAAAGGGGTGCCACGA-AGTTATGGA-CTTTAAGAAGGGTGCCA-TAAAGTTGTG
* * * *
242730 GACTTTGAAAA-GGGTGCCATGGAGTTATAGATTTTAA-AAGG
1 GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTTAAGAAGG
242771 TTACCCCATT
Statistics
Matches: 689, Mismatches: 138, Indels: 80
0.76 0.15 0.09
Matches are distributed among these distances:
56 46 0.07
57 33 0.05
58 190 0.28
59 270 0.39
60 104 0.15
61 2 0.00
62 1 0.00
63 4 0.01
64 35 0.05
65 2 0.00
66 2 0.00
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (59 bp):
GACTTTGAAAAGGGGTGCCACGAAGTTATGGACTTTAAGAAGGGTGCCATAAAGTTGTG
Found at i:241982 original size:88 final size:85
Alignment explanation
Indices: 241764--242748 Score: 522
Period size: 88 Copynumber: 11.2 Consensus size: 85
241754 CTTGTGTGGG
* * * * * *
241764 CTTT-AAAAGGGTGCGAC-GAAGTTGCGAACTTT-AAAAAGGTGCCACAGAGTTATGAACTTT-A
1 CTTTGAAAAGGGTGCCACAG-AGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTTGA
*** * * *
241825 AAATAATGCCACGAAATTATTGA
65 AAA-GGGGCCACG-AGTTGTAGA
* * * *
241848 CTTT-AAAAGAGGTGTCAC-GAAGTTGTGGACTATGAGAAGGGGTGCCACGAAGTTATGGACTTT
1 CTTTGAAAAG-GGTGCCACAG-AGTTGTGGACTTTGA-AAAGGGTGCCACGGAGTTATGGACTTT
*
241911 GAAAAGGGGCACCACGAAGTTATAGA
63 GAAAAGGGG--CCACG-AGTTGTAGA
* * *
241937 CTTT-AAGAAGGGTGCCATAGAG-TGTGGACTTTGAAAAGGGGTGCCACAGAGCTATGGACTTTG
1 CTTTGAA-AAGGGTGCCACAGAGTTGTGGACTTTGAAAA-GGGTGCCACGGAGTTATGGACTTTG
* **
242000 AGAAGGGTGCCATAAAGTTGTAGA
64 AAAAGGG-GCCA-CGAGTTGTAGA
* * *
242024 CTTTGAAAAAGGGTGCCACGGAGTTATGGACTTTGAAAAGGGTGCCACGAAGTTATGGACTTTGA
1 CTTTG-AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTTG-
* * * * *
242089 AAAATGTGTCATGGAGTTGTTGA
64 AAAAGGGGCCA-CGAGTTGTAGA
* ** * * * ** * *
242112 CTTTAAAAAATTGTGCC-CTAAAATTGTGGACTTAGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
1 CTTT-GAAAAGGGTGCCAC-AGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTTG
*
242176 AAAAAGGGTGCCACCGAGTTGTGGA
64 -AAAAGGG-GCCA-CGAGTTGTAGA
** * *
242201 CTTTGGAAAAGGGTGCCATTGAGTTGTAGACTTT-AAAAGGGTGCCACGGAGTTGTGGACTTTGG
1 CTTT-GAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTT-G
* * *
242265 AAAGGGGTGCCATTGAGTTGTGGA
64 AAAAGGG-GCCA-CGAGTTGTAGA
* * * * *
242289 CTTTCAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAAGGTGCCACGGAGTTGTGGACTCT-AA
1 CTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTTGAA
* *
242352 AAGGGTGCCACAAAATTGTAGA
66 AAGGG-GCCAC-GAGTTGTAGA
*** * * * * * *
242374 CTTT-AAAAGGGTGTTGCGGAGTTATGGAGTTTGGAAAGGGTTGCCATGGAGTTGTGGACTTTGA
1 CTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGG-TGCCACGGAGTTATGGACTTTGA
* *
242438 AAAGGGGGCTACAGAGTTGTGGA
65 AAA-GGGGCCAC-GAGTTGTAGA
* * ** **
242461 CTTTGAAAAAGGGTGCCACAAAGTTGTGGACTTTAAGAAAGGGCACCATTGAGTTATGGACTTTG
1 CTTTG-AAAAGGGTGCCACAGAGTTGTGGACTTTGA-AAAGGGTGCCACGGAGTTATGGACTTTG
* * * *
242526 AAAAGGGTGGCATGGAGTGGAGTTCTGTA
64 AAAAGGG-GCCA-CGAGT--TG-T-AG-A
* ** * * ** * ** **
242555 CTTTAGAAAAAGGTGCCATGGAGTTATGAACAATAAAAAGGGTGCCACAAAGTTGCGGACTTTGA
1 CTTT-GAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTTG-
** *
242620 AAAAGGGTGCCATAAAGTTGTGGA
64 AAAAGGG-GCCA-CGAGTTGTAGA
* * * * ** * *
242644 CTTTGAAAAAGGATGCCACAAAGTTGTGGGCTTTTAAAAGGGTGCCAAAGAGTTGT-GAGCTTTA
1 CTTTG-AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGA-CTTTG
* * *
242708 AAAAGGGTGTCACGATATTGTGGA
64 AAAAGGG-GCCACGA-GTTGTAGA
242732 CTTTGAAAAGGGTGCCA
1 CTTTGAAAAGGGTGCCA
242749 TGGAGTTATA
Statistics
Matches: 705, Mismatches: 156, Indels: 77
0.75 0.17 0.08
Matches are distributed among these distances:
84 32 0.05
85 45 0.06
86 20 0.03
87 124 0.18
88 226 0.32
89 178 0.25
90 11 0.02
91 2 0.00
92 2 0.00
93 22 0.03
94 42 0.06
95 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (85 bp):
CTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGGGTGCCACGGAGTTATGGACTTTGAA
AAGGGGCCACGAGTTGTAGA
Found at i:242407 original size:143 final size:146
Alignment explanation
Indices: 241846--242755 Score: 607
Period size: 147 Copynumber: 6.2 Consensus size: 146
241836 CGAAATTATT
* * * * * *
241846 GACTTT-AAAAGAGGTGTCACGAAGTTGTGGACTATGAGAAGGGGTGCCAC-GAAGTTATGGACT
1 GACTTTGAAAAG-GGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAG-AGTTGTGGACT
* * * * ** * *
241909 TTGAAAAGGG-GCACCACGAAGTTATAGACTTTAAGAAGGGTGCCATAGAG-TGTGGACTTTGAA
64 CTGAAAAGGGTG--CCACAAAATTGTAGACTTTAA-AAGGGTGCCACGGAGTTATGGACTTTGGA
** * *
241972 AAGGGGTGCCACAGAGCTATG
126 AAGGGGTGCCATGGAGTTGTG
* *** * * * *
241993 GACTTTGAGAAGGGTGCCATAAAGTTGTAGACTTTGAAAAAGGGTGCCACGGAGTTATGGACTTT
1 GACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAGAGTTGTGGACTCT
* * * * ** * * * * ** **
242058 GAAAAGGGTGCCACGAAGTTATGGACTTTGAAAAATGTGTCATGGAGTTGTTGACTTTAAAAAAT
66 GAAAAGGGTGCCACAAAATTGTAGACTTT-AAAAGGGTGCCACGGAGTTATGGACTTTGGAAAGG
* * ** *
242123 TGTGCCCTAAAATTGTG
130 GGTGCCATGGAGTTGTG
* ** * * *
242140 GACTTAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAAGGGTGCCACCGAGTTGTGGACTTT
1 GACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAGAGTTGTGGACTCT
*** * *
242205 GGAAAAGGGTGCCATTGAGTTGTAGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTGGAAAGG
66 -GAAAAGGGTGCCACAAAATTGTAGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTGGAAAGG
*
242270 GGTGCCATTGAGTTGTG
130 GGTGCCATGGAGTTGTG
* *
242287 GACTTTCAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAA-GGTGCCACGGAGTTGTGGACTCT
1 GACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAGAGTTGTGGACTCT
*** *
242350 -AAAAGGGTGCCACAAAATTGTAGACTTTAAAAGGGTGTTGCGGAGTTATGGAGTTTGGAAAGGG
66 GAAAAGGGTGCCACAAAATTGTAGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTGGAAAGGG
*
242414 TTGCCATGGAGTTGTG
131 GTGCCATGGAGTTGTG
* * * * *
242430 GACTTTGAAAAGGGGGCTACAGAGTTGTGGACTTTGAAAAAGGGTGCCACAAAGTTGTGGACTTT
1 GACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAGAGTTGTGGACTCT
* ** *** * * * * * * * *
242495 AAGAAAGGGCACCATTGAGTTATGGACTTTGAAAAGGGTGGCATGGAGTGGAGTTCTGTACTTTA
66 GA-AAAGGGTGCCACAAAATTGTAGACTTT-AAAAGGGT-GC---CA-CGGAGTTATGGACTTTG
** *
242560 GAAAAAGGTGCCATGGAGTTATG
124 GAAAGGGGTGCCATGGAGTTGTG
* ** * ** * * * *
242583 AACAATAAAAAGGGTGCCACAAAGTTGCGGACTTTGAAAAAGGGTGCCATAAAGTTGTGGACTTT
1 GACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAGAGTTGTGGACTCT
* * * * ** * *
242648 GAAAAAGGATGCCACAAAGTTGTGGGCTTTTAAAAGGGTGCCAAAGAGTTGT-GAGCTTT-AAAA
66 G-AAAAGGGTGCCACAAAATTGTAGAC-TTTAAAAGGGTGCCACGGAGTTATGGA-CTTTGGAAA
* * * *
242711 AGGGTGTCA-CGATATTGTG
128 GGGGTGCCATGGA-GTTGTG
*
242730 GACTTTGAAAAGGGTGCCATGGAGTT
1 GACTTTGAAAAGGGTGCCACGGAGTT
242756 ATAGATTTTA
Statistics
Matches: 608, Mismatches: 135, Indels: 40
0.78 0.17 0.05
Matches are distributed among these distances:
143 100 0.16
144 5 0.01
145 41 0.07
146 37 0.06
147 258 0.42
148 48 0.08
149 2 0.00
152 2 0.00
153 111 0.18
154 4 0.01
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (146 bp):
GACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAAGGGTGCCACAGAGTTGTGGACTCT
GAAAAGGGTGCCACAAAATTGTAGACTTTAAAAGGGTGCCACGGAGTTATGGACTTTGGAAAGGG
GTGCCATGGAGTTGTG
Found at i:242558 original size:34 final size:35
Alignment explanation
Indices: 242511--242578 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
242501 GGGCACCATT
* *
242511 GAGTTATGGACTTT-GAAAAGGGTGGCATGGAGTG
1 GAGTTATGGACTTTAGAAAAAGGTGCCATGGAGTG
* *
242545 GAGTTCTGTACTTTAGAAAAAGGTGCCATGGAGT
1 GAGTTATGGACTTTAGAAAAAGGTGCCATGGAGT
242579 TATGAACAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (35 bp):
GAGTTATGGACTTTAGAAAAAGGTGCCATGGAGTG
Found at i:247322 original size:20 final size:22
Alignment explanation
Indices: 247282--247322 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
247272 TAGCCTTTGA
*
247282 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
247304 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
247323 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:247545 original size:20 final size:20
Alignment explanation
Indices: 247520--247644 Score: 97
Period size: 20 Copynumber: 5.8 Consensus size: 20
247510 TTTTACCCAG
247520 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
247540 ATGTATCGATACACTTTGTCTTTTACCCA
1 ATGTATCGATACA-----T-TTTT---CA
* *
247569 GATGTATCAAAACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
247590 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
247610 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
247630 ACGTATCGATACATT
1 ATGTATCGATACATT
247645 CTGTCTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
20 58 0.70
21 2 0.02
24 4 0.05
25 2 0.02
26 4 0.05
29 2 0.02
30 11 0.13
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:249387 original size:13 final size:13
Alignment explanation
Indices: 249369--249394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
249359 CAATTTTTTG
249369 TGTATCGATACAT
1 TGTATCGATACAT
249382 TGTATCGATACAT
1 TGTATCGATACAT
249395 ACTTTGGTGT
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):
TGTATCGATACAT
Found at i:249391 original size:33 final size:33
Alignment explanation
Indices: 249349--249413 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
249339 TACAAGCCAA
* *
249349 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
249382 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
249414 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:252225 original size:338 final size:338
Alignment explanation
Indices: 251609--252287 Score: 1117
Period size: 338 Copynumber: 2.0 Consensus size: 338
251599 TCAAGGGGAT
* *
251609 CATATTGAAATAATATCGAGTCAAAACCAATGAAACCAATGTCAAGTCAAAGTGTAGCTAATAAA
1 CATATTGAAATAATATCGAGTCAAAACCAATGAAACCAATGCCAAGTCAAAGTGAAGCTAATAAA
* *
251674 GTACTGATTTTTTACGTCACGAGGAGGTTCGTACCTCTTTGTGCGTAACCAACTCTTGAACCAAT
66 GTACCGATTTTTTACGTCACGAGGAGGTTCGTACCTCTTTGTACGTAACCAACTCTTGAACCAAT
* * *
251739 CGACGAATATTTGAAGTACGTAGATCATGAGATCGATGTCTCATGTTTTGTAACTCAATACATAG
131 CGACGAATATTTGAAGTACGTAGACCATGAGATCGATGTCTCATGTTTCGTAACTCAATACATAC
* * *
251804 GTTTCAATAGGCATCCGATCGTGCCTAGCCCGAAATGATCAATGGCAACTCTAACATTTTGGTCA
196 GTTTCAATAGGCATCCGATCATGCCTAACCCGAAATGATCAATGGCAACTCTAAAATTTTGGTCA
* * *
251869 TTTCTTGATGACCGTCGAGGATCAGTTAGATGAGCTATTCATCTATCAATCATCTCTTTTTCAGC
261 TTTCGTAATGACCGTCGAGGATCAGTTAGATGAGCTATTCATCTATCAATCATCTCTTTTTCAAC
251934 ACATATCTCTTAC
326 ACATATCTCTTAC
* * *
251947 CATATTGAAATAATATCGAGTCGAAACCAATGAAACCAATGCCAAGTCAAAGTGAAGCTAGTAAG
1 CATATTGAAATAATATCGAGTCAAAACCAATGAAACCAATGCCAAGTCAAAGTGAAGCTAATAAA
* *
252012 GTACCGATTTTTTACGTCACGAGGAGGTTCTTACCTTTTTGTACGTAACCAACTCTTGAACCAAT
66 GTACCGATTTTTTACGTCACGAGGAGGTTCGTACCTCTTTGTACGTAACCAACTCTTGAACCAAT
* *
252077 CGACGAATCTTTGAAGTACGTAGACCATGAGATCGATGTCTTGA-GTTTCGTAACTCAATACATA
131 CGACGAATATTTGAAGTACGTAGACCATGAGATCGATGTC-TCATGTTTCGTAACTCAATACATA
* *
252141 CGTTTCAATAGGCATCCGATCATGCCTAACCCGAAATGATCATTGGCAACTCTAAAATTTTGGTT
195 CGTTTCAATAGGCATCCGATCATGCCTAACCCGAAATGATCAATGGCAACTCTAAAATTTTGGTC
* * *
252206 ATTTCGTAATGATCGTCGAGGATCAGTTAGATGGGCTATTCATCTATCAATCTTCTCTTTTTCAA
260 ATTTCGTAATGACCGTCGAGGATCAGTTAGATGAGCTATTCATCTATCAATCATCTCTTTTTCAA
252271 CACATATCTCTTAC
325 CACATATCTCTTAC
252285 CAT
1 CAT
252288 GCCATAGAAA
Statistics
Matches: 315, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
338 313 0.99
339 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (338 bp):
CATATTGAAATAATATCGAGTCAAAACCAATGAAACCAATGCCAAGTCAAAGTGAAGCTAATAAA
GTACCGATTTTTTACGTCACGAGGAGGTTCGTACCTCTTTGTACGTAACCAACTCTTGAACCAAT
CGACGAATATTTGAAGTACGTAGACCATGAGATCGATGTCTCATGTTTCGTAACTCAATACATAC
GTTTCAATAGGCATCCGATCATGCCTAACCCGAAATGATCAATGGCAACTCTAAAATTTTGGTCA
TTTCGTAATGACCGTCGAGGATCAGTTAGATGAGCTATTCATCTATCAATCATCTCTTTTTCAAC
ACATATCTCTTAC
Found at i:255542 original size:20 final size:20
Alignment explanation
Indices: 255514--255589 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
255504 CATTGTTCAT
255514 GTATCGATACATTGTGATTA
1 GTATCGATACATTGTGATTA
* **
255534 GTATTGATACATCACTG-TTCA
1 GTATCGATACAT-TGTGATT-A
* * *
255555 TGTATTGATACATTATGAATA
1 -GTATCGATACATTGTGATTA
255576 GTATCGATACATTG
1 GTATCGATACATTG
255590 AGTCAACGGC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
20 25 0.57
21 6 0.14
22 13 0.30
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTGTGATTA
Found at i:255562 original size:22 final size:22
Alignment explanation
Indices: 255501--255567 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
255491 ATCAATCTAT
* *
255501 CATCATTGTTCATGTATCGATA
1 CATCACTGTTCATGTATTGATA
**
255523 CAT-TGTGATT-A-GTATTGATA
1 CATCACTG-TTCATGTATTGATA
255543 CATCACTGTTCATGTATTGATA
1 CATCACTGTTCATGTATTGATA
255565 CAT
1 CAT
255568 TATGAATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 13 0.36
21 6 0.17
22 17 0.47
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (22 bp):
CATCACTGTTCATGTATTGATA
Found at i:255565 original size:42 final size:42
Alignment explanation
Indices: 255501--255587 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
255491 ATCAATCTAT
* * * *
255501 CATCATTGTTCATGTATCGATACATTGTGATTAGTATTGATA
1 CATCACTGTTCATGTATCGATACATTATGAATAGTATCGATA
*
255543 CATCACTGTTCATGTATTGATACATTATGAATAGTATCGATA
1 CATCACTGTTCATGTATCGATACATTATGAATAGTATCGATA
255585 CAT
1 CAT
255588 TGAGTCAACG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (42 bp):
CATCACTGTTCATGTATCGATACATTATGAATAGTATCGATA
Found at i:256098 original size:35 final size:36
Alignment explanation
Indices: 256027--256098 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
256017 TGAAGTGATT
*
256027 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAGGGA
*
256063 GAGAGGTTCTATCTTAG-CTCGTG-AAAAGATTGGGA
1 GAGAGGTTCTATCTTAGCCT-GTGAAAAAGATAGGGA
256098 G
1 G
256099 GTTTTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 14 0.42
36 19 0.58
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAGGGA
Found at i:260816 original size:13 final size:13
Alignment explanation
Indices: 260798--260823 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
260788 TACACCAAGT
260798 ATGTATCGATACA
1 ATGTATCGATACA
260811 ATGTATCGATACA
1 ATGTATCGATACA
260824 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:260821 original size:32 final size:33
Alignment explanation
Indices: 260780--260843 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
260770 TAGCCAAACT
* **
260780 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
260812 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
260844 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:261343 original size:34 final size:35
Alignment explanation
Indices: 261280--261346 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
261270 CTAAGTGATT
261280 GAGAGGTTCTATCTTAGCCCTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCCTTG-AAAAGATAGAGA
261316 GAGAGGTTTCTATCTTAG-CCTTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCCTTGAAAAGATAG
261347 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 11 0.37
37 11 0.37
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCCTTGAAAAGATAGAGA
Found at i:262512 original size:20 final size:20
Alignment explanation
Indices: 262484--262559 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
262474 CATTGTTCAT
262484 GTATCGATACATTGTGAATA
1 GTATCGATACATTGTGAATA
* **
262504 GTATTGATACATCACTGTTCAT-
1 GTATCGATACAT---TGTGAATA
* *
262526 GTATTGATACATTATGAATA
1 GTATCGATACATTGTGAATA
262546 GTATCGATACATTG
1 GTATCGATACATTG
262560 AGTCCAACGG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 4 0.09
20 23 0.52
22 12 0.27
23 5 0.11
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTGTGAATA
Found at i:262532 original size:22 final size:21
Alignment explanation
Indices: 262471--262537 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
262461 CATCACTATT
*
262471 CATCATTGTTCATGTATCGATA
1 CATCA-TGTTCATGTATTGATA
**
262493 CAT--TGTGAATAGTATTGATA
1 CATCATGTTCAT-GTATTGATA
262513 CATCACTGTTCATGTATTGATA
1 CATCA-TGTTCATGTATTGATA
262535 CAT
1 CAT
262538 TATGAATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
22 15 0.42
23 5 0.14
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
CATCATGTTCATGTATTGATA
Found at i:262535 original size:42 final size:42
Alignment explanation
Indices: 262471--262557 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
262461 CATCACTATT
* * *
262471 CATCATTGTTCATGTATCGATACATTGTGAATAGTATTGATA
1 CATCACTGTTCATGTATCGATACATTATGAATAGTATCGATA
*
262513 CATCACTGTTCATGTATTGATACATTATGAATAGTATCGATA
1 CATCACTGTTCATGTATCGATACATTATGAATAGTATCGATA
262555 CAT
1 CAT
262558 TGAGTCCAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (42 bp):
CATCACTGTTCATGTATCGATACATTATGAATAGTATCGATA
Found at i:263065 original size:35 final size:36
Alignment explanation
Indices: 262994--263065 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
262984 TGAAGTGATT
*
262994 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAGGGA
*
263030 GAGAGGTTCTATCTTAG-CTCGTG-AAAAGATTGGGA
1 GAGAGGTTCTATCTTAGCCT-GTGAAAAAGATAGGGA
263065 G
1 G
263066 GTTTTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 14 0.42
36 19 0.58
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAGGGA
Found at i:265661 original size:13 final size:13
Alignment explanation
Indices: 265643--265667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
265633 ATAATGCACA
265643 GTATCGATACATT
1 GTATCGATACATT
265656 GTATCGATACAT
1 GTATCGATACAT
265668 GACCAAATGT
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:272016 original size:20 final size:20
Alignment explanation
Indices: 271981--272022 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
271971 CAAATTTCCT
271981 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
272003 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
272022 A
1 A
272023 ACAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:274327 original size:13 final size:13
Alignment explanation
Indices: 274309--274333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274299 ATAATGCACA
274309 GTATCGATACATT
1 GTATCGATACATT
274322 GTATCGATACAT
1 GTATCGATACAT
274334 GACCAAATGT
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:274452 original size:13 final size:13
Alignment explanation
Indices: 274434--274459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
274424 GCACACAATA
274434 TGTATCGATACAT
1 TGTATCGATACAT
274447 TGTATCGATACAT
1 TGTATCGATACAT
274460 CCCAAAATGT
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):
TGTATCGATACAT
Found at i:274475 original size:33 final size:32
Alignment explanation
Indices: 274414--274480 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
274404 CCTTAACTGT
* *
274414 TTGTATCGATGCACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
274446 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
274479 TT
1 TT
274481 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:277197 original size:77 final size:77
Alignment explanation
Indices: 277109--277260 Score: 295
Period size: 77 Copynumber: 2.0 Consensus size: 77
277099 TTTGGTATTA
277109 GTTGCATGAATAACAAAAAGGGAAAGAATAGATTTGGCCTAATAGAAAGGGGGAGAAAAGAGATG
1 GTTGCATGAATAACAAAAAGGGAAAGAATAGATTTGGCCTAATAGAAAGGGGGAGAAAAGAGATG
277174 TTTCACAAAGGG
66 TTTCACAAAGGG
*
277186 GTTGCATGAATAACAAAAAGGGAGAGAATAGATTTGGCCTAATAGAAAGGGGGAGAAAAGAGATG
1 GTTGCATGAATAACAAAAAGGGAAAGAATAGATTTGGCCTAATAGAAAGGGGGAGAAAAGAGATG
277251 TTTCACAAAG
66 TTTCACAAAG
277261 CGGGAGAATT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.44, C:0.08, G:0.30, T:0.18
Consensus pattern (77 bp):
GTTGCATGAATAACAAAAAGGGAAAGAATAGATTTGGCCTAATAGAAAGGGGGAGAAAAGAGATG
TTTCACAAAGGG
Found at i:278024 original size:13 final size:13
Alignment explanation
Indices: 278006--278030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277996 ATTTTGCTTA
278006 GTATCGATACATT
1 GTATCGATACATT
278019 GTATCGATACAT
1 GTATCGATACAT
278031 AAAACTAGCA
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:278073 original size:10 final size:10
Alignment explanation
Indices: 278058--278088 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
278048 AATCTCATTT
278058 TCACTGTTCA
1 TCACTGTTCA
*
278068 TCACTGTTAA
1 TCACTGTTCA
278078 TCACTGTTCA
1 TCACTGTTCA
278088 T
1 T
278089 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:278144 original size:52 final size:52
Alignment explanation
Indices: 278066--278164 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
278056 TTTCACTGTT
*
278066 CATCACTGTTAATCACTGTTCATGTATCGATACATTATGAATAGTATTGACA
1 CATCACTGTTAATCACAGTTCATGTATCGATACATTATGAATAGTATTGACA
* *
278118 CATCACTGTTCATCACAGTTCATGTATCGATATATTATGAATAGTAT
1 CATCACTGTTAATCACAGTTCATGTATCGATACATTATGAATAGTAT
278165 CGATACATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (52 bp):
CATCACTGTTAATCACAGTTCATGTATCGATACATTATGAATAGTATTGACA
Found at i:278653 original size:36 final size:33
Alignment explanation
Indices: 278613--278701 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 33
278603 GTGATTGAGA
*
278613 GGTTCTATCTTAGCCTTTGAAAAAGATTGGGATAG
1 GGTTCTATCTTAGCCTTTGAAAAAGATAGGG--AG
*
278648 CGGTTCTATCTTAG-CTCGTG-AAAAGATAGGGAG
1 -GGTTCTATCTTAGCCT-TTGAAAAAGATAGGGAG
*
278681 GTTTCTATCTTAGCC-TTGAAA
1 GGTTCTATCTTAGCCTTTGAAA
278702 GATAGTGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
31 2 0.04
32 14 0.30
33 3 0.07
35 12 0.26
36 15 0.33
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (33 bp):
GGTTCTATCTTAGCCTTTGAAAAAGATAGGGAG
Found at i:280212 original size:34 final size:35
Alignment explanation
Indices: 280174--280239 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
280164 CCTTACAACA
280174 CTATCTTTT-CGAAA-GCTAAGATAGAACCTCTTCC
1 CTATCTTTTAC-AAAGGCTAAGATAGAACCTCTTCC
280208 CTATCTTTTACAAAGGCTAAGATAGAACCTCT
1 CTATCTTTTACAAAGGCTAAGATAGAACCTCT
280240 CAATCACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (35 bp):
CTATCTTTTACAAAGGCTAAGATAGAACCTCTTCC
Found at i:280685 original size:43 final size:43
Alignment explanation
Indices: 280637--280738 Score: 141
Period size: 43 Copynumber: 2.4 Consensus size: 43
280627 TACAATTCAT
* * * *
280637 AATGTATTGATACAATATATTTAAAATTCTAGCCGTTAGGCTG
1 AATGTATCGATACAATACATTTAAAATTATAGCCGTTAGGCTA
* * *
280680 AATGTATCGATACAATACATTTGAAATTATAGCTGTTGGGCTA
1 AATGTATCGATACAATACATTTAAAATTATAGCCGTTAGGCTA
280723 AATGTATCGATACAAT
1 AATGTATCGATACAAT
280739 TTACCATGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (43 bp):
AATGTATCGATACAATACATTTAAAATTATAGCCGTTAGGCTA
Found at i:283332 original size:21 final size:22
Alignment explanation
Indices: 283308--283354 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
283298 TTTGATGCGT
283308 AAATAAAGAAATTTGA-G-TTGG
1 AAATAAAG-AATTTGACGATTGG
* *
283329 AAATGATGAATTTGACGATTGG
1 AAATAAAGAATTTGACGATTGG
283351 AAAT
1 AAAT
283355 CTAGGGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (22 bp):
AAATAAAGAATTTGACGATTGG
Found at i:283457 original size:19 final size:19
Alignment explanation
Indices: 283433--283469 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
283423 ATATAGTCGA
283433 AATGTATCGATACAATTTT
1 AATGTATCGATACAATTTT
283452 AATGTATCGATACAATTT
1 AATGTATCGATACAATTT
283470 CTTTATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (19 bp):
AATGTATCGATACAATTTT
Found at i:283478 original size:19 final size:19
Alignment explanation
Indices: 283437--283482 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
283427 AGTCGAAATG
*
283437 TATCGATACAATTTTAATG
1 TATCGATACAATTTTAATA
*
283456 TATCGATACAATTTCT-TTA
1 TATCGATACAATTT-TAATA
283475 TATCGATA
1 TATCGATA
283483 GATCTAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (19 bp):
TATCGATACAATTTTAATA
Found at i:285805 original size:3 final size:3
Alignment explanation
Indices: 285790--285821 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
285780 CATCAAAGGC
*
285790 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
285822 AGAAGTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:290625 original size:20 final size:19
Alignment explanation
Indices: 290600--290674 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 19
290590 TTACAAGCCA
290600 ATGTATCGATACAT-TTGGT
1 ATGTATCGATACATCTT-GT
290619 CATGTATCGATACATCTTGT
1 -ATGTATCGATACATCTTGT
*
290639 ATGTATCGATCGATACATATTGT
1 ATG--T--ATCGATACATCTTGT
290662 ATGTATCGATACA
1 ATGTATCGATACA
290675 AACAGTTAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
19 12 0.24
20 16 0.33
21 4 0.08
23 17 0.35
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATCTTGT
Found at i:290654 original size:23 final size:23
Alignment explanation
Indices: 290624--290671 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
290614 TTGGTCATGT
*
290624 ATCGATACATCTTGTATGTATCG
1 ATCGATACATATTGTATGTATCG
290647 ATCGATACATATTGTATGTATCG
1 ATCGATACATATTGTATGTATCG
290670 AT
1 AT
290672 ACAAACAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (23 bp):
ATCGATACATATTGTATGTATCG
Found at i:290720 original size:19 final size:19
Alignment explanation
Indices: 290696--290738 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
290686 GTAGTTACTG
*
290696 CCAATCACCTGTATCGATA
1 CCAATCACCTATATCGATA
290715 CCAATCACCTATATCGATA
1 CCAATCACCTATATCGATA
290734 -CAATC
1 CCAATC
290739 TTTGCAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.35, C:0.33, G:0.07, T:0.26
Consensus pattern (19 bp):
CCAATCACCTATATCGATA
Found at i:290770 original size:19 final size:20
Alignment explanation
Indices: 290746--290795 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
290736 ATCTTTGCAA
*
290746 GTATCGATACAGTG-GTCAT
1 GTATCGATACAGTGCATCAT
* *
290765 GTATCGATACTGTGCATTAT
1 GTATCGATACAGTGCATCAT
290785 GTATCGATACA
1 GTATCGATACA
290796 TCTGAAGGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (20 bp):
GTATCGATACAGTGCATCAT
Found at i:298689 original size:52 final size:52
Alignment explanation
Indices: 298619--298739 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
298609 GAAAATTTAT
* *
298619 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACAACTGGGCAAATTTGC
*
298671 CTGCATGTATCGATACATTTTATAATGTATCGATACAACTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACAACTGGGCAAATTTGC
298723 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
298740 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACAACTGGGCAAATTTGC
Found at i:298752 original size:52 final size:51
Alignment explanation
Indices: 298619--298760 Score: 205
Period size: 52 Copynumber: 2.7 Consensus size: 51
298609 GAAAATTTAT
*
298619 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACAACTGGGCAAATTTGC
* *
298671 CTGCATGTATCGATACATTTTATAATGTATCGATACAACTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACAACTGGGCAAATTTGC
*
298723 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACAA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACAA
298761 TGTATCGATA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACAACTGGGCAAATTTGC
Found at i:298766 original size:13 final size:13
Alignment explanation
Indices: 298748--298772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
298738 CAAAGATCAG
298748 TGTATCGATACAA
1 TGTATCGATACAA
298761 TGTATCGATACA
1 TGTATCGATACA
298773 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:299654 original size:49 final size:49
Alignment explanation
Indices: 299599--300208 Score: 584
Period size: 49 Copynumber: 12.3 Consensus size: 49
299589 GCGGCTAGCG
* *
299599 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTTAAGGCCAGCG
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * * * * *
299648 ACATTGGACTTAAAGATGAAGGTGAGAAAAGTATGCCAATATGTTAATTCACGGCCAACG
1 ATATTGGACTTAAAGAT-AA----AG----G--TGCCAATATGCTGATTCAAGGCCAGCT
* * *
299708 ATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGAT-----AAAGG-TGCCAATATGCTGATTCAAGGCCAGCT
*
299763 ATATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
299815 ATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAACT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * * * * *
299858 ACATTGGACTTAAAGGTGAA-CTGCCAATGTTCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * * * *
299906 ACATTGGACTTAAAGATGAAGGTGCCAATGTGCTAAGTCAAGGCCAGCT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
*
299955 ACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * *
300004 ATATTGGACTTAATGGTGAAGGTGCCAATATGCTGAGTT-AAGGCCAGCT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGA-TTCAAGGCCAGCT
*
300053 ACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * * *
300102 ATTTTGGACTT--A-AT---GGTGCTAATGTGCTGAATCAAGGCCAGCT
1 ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * *
300145 ACATTGGACTTAAAGA-ATAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
1 ATATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCT
300194 ATATTGGACTTAAAG
1 ATATTGGACTTAAAG
300209 GAAGATGCCA
Statistics
Matches: 474, Mismatches: 56, Indels: 62
0.80 0.09 0.10
Matches are distributed among these distances:
43 73 0.15
44 1 0.00
45 1 0.00
46 4 0.01
47 1 0.00
48 46 0.10
49 222 0.47
50 4 0.01
51 1 0.00
52 33 0.07
53 7 0.01
54 2 0.00
55 36 0.08
56 1 0.00
58 1 0.00
60 39 0.08
64 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (49 bp):
ATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
Found at i:300251 original size:33 final size:33
Alignment explanation
Indices: 300214--300399 Score: 227
Period size: 33 Copynumber: 5.7 Consensus size: 33
300204 TAAAGGAAGA
* *
300214 TGCCACCAACTTGTGTGGGCTTTTGAAGAAAGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAAGT
* ***
300247 TGCCACCGACTTGTGTGGGCTTTTG-AGGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAAGT
*
300279 TGCCACCGACTTGTGTGGGCTTTAG-AGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAA-AGT
300312 TGCCACCGACTTGTGTGGGCTTTAGAA-AAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAA-GT
* **
300345 TGCCACCGACTTGTGTGGGCTTTAGAGGGGA-T
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAAAGT
*
300377 TGCCACCAACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
300400 GGGAAGGGTG
Statistics
Matches: 137, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
32 53 0.39
33 82 0.60
34 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGAAAGT
Found at i:300318 original size:65 final size:66
Alignment explanation
Indices: 300214--300399 Score: 254
Period size: 65 Copynumber: 2.8 Consensus size: 66
300204 TAAAGGAAGA
* * * * ***
300214 TGCCACCAACTTGTGTGGGCTTTTGAAGAA-AGTTGCCACCGACTTGTGTGGGCTTTTG-AGGGG
1 TGCCACCGACTTGTGTGGGCTTTAG-AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAG
300277 GT
65 GT
300279 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGG
1 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGG
300344 T
66 T
*
300345 TGCCACCGACTTGTGTGGGCTTTAGAG--GGGATTGCCACCAACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGG-TTGCCACCGACTTGTGTGGGCTTT
300400 GGGAAGGGTG
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
64 7 0.06
65 72 0.65
66 31 0.28
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (66 bp):
TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGG
T
Found at i:300383 original size:98 final size:97
Alignment explanation
Indices: 300214--300408 Score: 311
Period size: 98 Copynumber: 2.0 Consensus size: 97
300204 TAAAGGAAGA
* * *
300214 TGCCACCAACTTGTGTGGGCTTTTGAAGAAAGTTGCCACCGACTTGTGTGGGCTTTTGAGGGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAAAGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGAT
*
300279 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
66 TGCCACCAACTTGTGTGGGCTTT-GAGAAGGGT
*
300312 TGCCACCGACTTGTGTGGGCTTTAGAA-AAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGA
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAAA-GTTGCCACCGACTTGTGTGGGCTTTAGAGGGGA
*
300376 TTGCCACCAACTTGTGTGGGCTTTGGGAAGGGT
65 TTGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
300409 GAGAGATGCC
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 11 0.12
98 79 0.88
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (97 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAGAAAGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGAT
TGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
Found at i:300452 original size:33 final size:33
Alignment explanation
Indices: 300423--300809 Score: 293
Period size: 34 Copynumber: 12.2 Consensus size: 33
300413 GATGCCACAA
* *
300423 AGTTGTGGACTTAAAAGGAACAAGGTGCCACGA
1 AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
*
300456 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCAACGG
1 AGTTGTGGAC-TTAAAA-GGAAAAAG-GTGCCACGG
* * ** *
300492 AGTTATGGGCTTTGAA--AAGAAGGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
** * *
300523 AGCCGTGGACATAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAG-GTGCCACGG
* *
300557 AGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
* *
300590 AGTTGTGGGCTTAGAAGGAAAAA---G--AC--
1 AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
*
300616 ----GTGGACTTAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAG-GTGCCACGG
*
300646 AGTTGTGGGCTTAAAA-G-----GGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
*
300673 AGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAG-GTGCCACGG
*
300707 AGTTGTGGGCTTAAAA-G-----GGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
*
300734 AGTTGTGGACTTAGAAAAGAAAAAGGTGCCACGG
1 AGTTGTGGACTTA-AAAGGAAAAAGGTGCCACGG
* * * *
300768 AGTCGTGGGCTTAAAAGGAAAAAAAGTGCCACAG
1 AGTTGTGGACTTAAAAGG-AAAAAGGTGCCACGG
*
300802 AATTGTGG
1 AGTTGTGG
300810 GCTTTAGAGA
Statistics
Matches: 282, Mismatches: 39, Indels: 65
0.73 0.10 0.17
Matches are distributed among these distances:
22 18 0.06
26 1 0.00
27 44 0.16
28 10 0.04
29 1 0.00
30 1 0.00
31 18 0.06
32 5 0.02
33 52 0.18
34 106 0.38
35 11 0.04
36 15 0.05
ACGTcount: A:0.35, C:0.13, G:0.35, T:0.18
Consensus pattern (33 bp):
AGTTGTGGACTTAAAAGGAAAAAGGTGCCACGG
Found at i:300531 original size:67 final size:65
Alignment explanation
Indices: 300444--300614 Score: 173
Period size: 67 Copynumber: 2.6 Consensus size: 65
300434 TAAAAGGAAC
* ** * *
300444 AAGGTGCCACGAAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCAACGGAGTTATGGGCTTTGAAA
1 AAGGTGCCACGGAGCCGTGGAC-ATAAAA-GGAAAAAGAGTGCAACGGAGTTATGGGC-TTAAAA
300509 AG-
63 AGA
* * *
300511 AAGGTGCCACGGAGCCGTGGACATAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGA
1 AAGGTGCCACGGAGCCGTGGACATAAAAGGAAAAAGAGTGCAACGGAGTTATGGGCTTAAAAAG-
300576 AA
65 -A
** * * *
300578 AAGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGA
1 AAGGTGCCACGGAGCCGTGGACATAAAAGGAAAAAGA
300615 CGTGGACTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 7 0.08
65 26 0.29
66 4 0.04
67 52 0.58
ACGTcount: A:0.36, C:0.12, G:0.35, T:0.17
Consensus pattern (65 bp):
AAGGTGCCACGGAGCCGTGGACATAAAAGGAAAAAGAGTGCAACGGAGTTATGGGCTTAAAAAGA
Found at i:300553 original size:34 final size:34
Alignment explanation
Indices: 300423--300614 Score: 187
Period size: 33 Copynumber: 5.7 Consensus size: 34
300413 GATGCCACAA
* * * *
300423 AGTTGTGGACTTAAAAGGAACAAG-GTGCCACGA
1 AGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGG
* * *
300456 AGTTGTGGACTTTAAAAGGGAAAAAGAGTGCAACGG
1 AGTTGTGGGC-TTAGAA-GGAAAAAGAGTGCCACGG
* * *
300492 AGTTATGGGCTTTGAA--AAGAAG-GTGCCACGG
1 AGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGG
** * *
300523 AGCCGTGGACATAGAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGG
* *
300557 AGTTGTGGGCTTAAAAAGAAAAAG-GTGCCACGG
1 AGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGG
300590 AGTTGTGGGCTTAGAAGGAAAAAGA
1 AGTTGTGGGCTTAGAAGGAAAAAGA
300615 CGTGGACTTA
Statistics
Matches: 128, Mismatches: 24, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
31 18 0.14
32 5 0.04
33 46 0.36
34 33 0.26
35 11 0.09
36 15 0.12
ACGTcount: A:0.36, C:0.12, G:0.34, T:0.18
Consensus pattern (34 bp):
AGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGG
Found at i:300557 original size:65 final size:65
Alignment explanation
Indices: 300474--300614 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 65
300464 ACTTTAAAAG
*
300474 GGAAAAAGAGTGCAACGGAGTTATGGGCTTTGAAAAG-AAGGTGCCACGGAGCCGTGGACATAGA
1 GGAAAAAGAGTGCAACGGAGTTATGGGC-TTAAAAAGAAAGGTGCCACGGAGCCGTGGACATAGA
300538 A
65 A
* * ** * *
300539 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAG
1 GGAAAAAGAGTGCAACGGAGTTATGGGCTTAAAAAG--AAAGGTGCCACGGAGCCGTGGACATAG
300604 AA
64 AA
300606 GGAAAAAGA
1 GGAAAAAGA
300615 CGTGGACTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 7 0.11
65 26 0.39
67 33 0.50
ACGTcount: A:0.37, C:0.12, G:0.35, T:0.16
Consensus pattern (65 bp):
GGAAAAAGAGTGCAACGGAGTTATGGGCTTAAAAAGAAAGGTGCCACGGAGCCGTGGACATAGAA
Found at i:300624 original size:22 final size:22
Alignment explanation
Indices: 300594--300636 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
300584 CCACGGAGTT
*
300594 GTGGGCTTAGAAGGAAAAAGAC
1 GTGGACTTAGAAGGAAAAAGAC
300616 GTGGACTTAGAAGGAAAAAGA
1 GTGGACTTAGAAGGAAAAAGA
300637 GTGCCACGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.35, T:0.14
Consensus pattern (22 bp):
GTGGACTTAGAAGGAAAAAGAC
Found at i:300635 original size:89 final size:89
Alignment explanation
Indices: 300526--300790 Score: 312
Period size: 89 Copynumber: 3.0 Consensus size: 89
300516 GCCACGGAGC
*
300526 CGTGGACATAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGA
1 CGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGA
300591 GTTGTGGGCTTAGAAGGAAAAAGA
66 GTTGTGGGCTTAGAAGGAAAAAGA
300615 CGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAAAG-----GGTGCCACGGA
1 CGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGA
*
300674 GTTGTGGACTTAGAAGGAAAAAGA
66 GTTGTGGGCTTAGAAGGAAAAAGA
* ** * * *
300698 -GTGCCACGGAGTT-GTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAAAGAAAAAGGT
1 CGT-----GGACTTAGAAGG--AAAAAGAGTGCCACGGAGTTGTGGGCTTA-AAAAGAAAAAGGT
* *
300761 GCCACGGAGTCGTGGGCTTAAAAGGAAAAA
58 GCCACGGAGTTGTGGGCTTAGAAGGAAAAA
300791 AAGTGCCACA
Statistics
Matches: 151, Mismatches: 11, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
82 2 0.01
83 34 0.23
86 3 0.02
87 5 0.03
88 30 0.20
89 42 0.28
90 5 0.03
95 30 0.20
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.17
Consensus pattern (89 bp):
CGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGA
GTTGTGGGCTTAGAAGGAAAAAGA
Found at i:300669 original size:27 final size:27
Alignment explanation
Indices: 300631--300785 Score: 139
Period size: 27 Copynumber: 5.2 Consensus size: 27
300621 CTTAGAAGGA
*
300631 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
300658 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
300685 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 -------AAAAGGGTGCCACGGAGTTGTGGGCTT
*
300719 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
300746 AGAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTT
1 --AAAAG-----GGTGCCACGGAGTTGTGGGCTT
300780 AAAAGG
1 AAAAGG
300786 AAAAAAAGTG
Statistics
Matches: 106, Mismatches: 8, Indels: 28
0.75 0.06 0.20
Matches are distributed among these distances:
27 51 0.48
29 5 0.05
32 5 0.05
34 45 0.42
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.19
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTT
Found at i:300689 original size:61 final size:60
Alignment explanation
Indices: 300542--300785 Score: 318
Period size: 61 Copynumber: 4.1 Consensus size: 60
300532 CATAGAAGGA
* * *
300542 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
* *** ** *
300602 AGAA--G-G--AAAAAGACGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTT
*
300658 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTT
*
300719 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAG-AAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
300780 AAAAGG
1 AAAAGG
300786 AAAAAAAGTG
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
55 20 0.12
56 24 0.15
57 1 0.01
58 2 0.01
59 1 0.01
60 3 0.02
61 100 0.62
62 9 0.06
ACGTcount: A:0.33, C:0.13, G:0.36, T:0.18
Consensus pattern (60 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
Found at i:300871 original size:156 final size:156
Alignment explanation
Indices: 300693--301028 Score: 373
Period size: 156 Copynumber: 2.1 Consensus size: 156
300683 TTAGAAGGAA
* **
300693 AAAGAG-TGCCACGGAGTT-GTGGGCTTAAAAGGGT-GCCACGGAGTTGTGGACTTAGAAAAGAA
1 AAAGAGATGCCACTGA-TTCGTGGGCTTAAAAGGGTCGCCACAAAGTTGTGGACTT--AAAAGAA
* *
300755 AAAG-GTGCCACGGAGTCGTGGGCTTAAAAGGAAAAAAAGTGCCAC-AGAATTGTGGGCTTT-AG
63 AAAGAGTGCCACGGAGTCGTGGGCTTAAAA-GAAAAAAA-TGCCACTA-AATCGTGGACTTTGAG
*
300817 AGAAAAGATGCCACTAAGTCCTGGACTTTG-G
125 ACAAAAGATGCCACTAAGTCCTGGACTTTGAG
*
300848 AAAGAGATGCCACTGATTCGTGGGCTTAAAAGGGTGCGCCACAAAGTTGTGGACTTAAAAGGAAA
1 AAAGAGATGCCACTGATTCGTGGGCTTAAAAGGGT-CGCCACAAAGTTGTGGACTTAAAAGAAAA
* * *** ** *
300913 AGAGTGCCACGGAGTTGTGTGCTTTGCAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAA
65 AGAGTGCCACGGAGTCGTGGGCTTAAAAGAAAAAAATGCCACTAAATCGTGGACTTTGAGACAAA
* *
300978 AGATGCCACTGAGTCGTGGACTTTGAAG
130 AGATGCCACTAAGTCCTGGACTTTG-AG
*
301006 AAA-AGGATGCCACTGAGTCGTGG
1 AAAGA-GATGCCACTGATTCGTGG
301029 ACTTTGAGAA
Statistics
Matches: 153, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
155 24 0.16
156 70 0.46
157 21 0.14
158 38 0.25
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (156 bp):
AAAGAGATGCCACTGATTCGTGGGCTTAAAAGGGTCGCCACAAAGTTGTGGACTTAAAAGAAAAA
GAGTGCCACGGAGTCGTGGGCTTAAAAGAAAAAAATGCCACTAAATCGTGGACTTTGAGACAAAA
GATGCCACTAAGTCCTGGACTTTGAG
Found at i:301011 original size:64 final size:63
Alignment explanation
Indices: 300785--301069 Score: 230
Period size: 64 Copynumber: 4.6 Consensus size: 63
300775 GGCTTAAAAG
* * * * * *
300785 GAAAAAAAGTGCCACAGAATTGTGGGCTTTAGAGAAAA-GATGCCACTAAGTCCTGGACTTTG-
1 GAAAAAGAGTGCCACTGAGTCGTGGACTTTA-AGAAAAGGATGCCACTAAGTCGTGGACTTTGA
* * * * * * **
300847 GAAAGAGA-TGCCACTGATTCGTGGGC-TT---AAAAGGGTGCGCCACAAAGTTGTGGACTTAAA
1 GAAAAAGAGTGCCACTGAGTCGTGGACTTTAAGAAAAGGAT--GCCACTAAGTCGTGGACTT-TG
300907 A
63 A
* * * *
300908 GGAAAAGAGTGCCACGGAGTTGTGTG-CTTTGCAGAAAAGGATGCCACTAAGTCGTGGACTTTGA
1 GAAAAAGAGTGCCACTGAGTCGTG-GACTTT-AAGAAAAGGATGCCACTAAGTCGTGGACTTTGA
*
300972 GACAAAAGA-TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGA
1 GA-AAAAGAGTGCCACTGAGTCGTGGACTTT-AAGAAAAGGATGCCACTAAGTCGTGGACTTTGA
* * *
301036 G-AAGAGATTGCCACTAAGTCGTGGACTTTAAGAA
1 GAAAAAGAGTGCCACTGAGTCGTGGACTTTAAGAA
301070 GGTATTTGAA
Statistics
Matches: 180, Mismatches: 28, Indels: 30
0.76 0.12 0.13
Matches are distributed among these distances:
56 4 0.02
57 2 0.01
59 16 0.09
60 2 0.01
61 21 0.12
62 29 0.16
63 24 0.13
64 52 0.29
65 23 0.13
67 7 0.04
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.22
Consensus pattern (63 bp):
GAAAAAGAGTGCCACTGAGTCGTGGACTTTAAGAAAAGGATGCCACTAAGTCGTGGACTTTGA
Found at i:301056 original size:31 final size:30
Alignment explanation
Indices: 300806--301069 Score: 196
Period size: 32 Copynumber: 8.5 Consensus size: 30
300796 CCACAGAATT
*
300806 GTGGGCTTTAGAGAAAAGATGCCACTAAGTC
1 GTGGACTTT-GAGAAAAGATGCCACTAAGTC
* * *
300837 CTGGACTTTG-GAAAGAGATGCCACTGATTC
1 GTGGACTTTGAGAAA-AGATGCCACTAAGTC
* * * * *
300867 GTGGGC-TT-A-AAAGGGTGCGCCACAAAGTT
1 GTGGACTTTGAGAAAAGAT--GCCACTAAGTC
** ** *
300896 GTGGACTTAAAAGGAAAAGAGTGCCACGGAGTT
1 GTGGACTT-TGA-GAAAAGA-TGCCACTAAGTC
300929 GTGTG-CTTTGCAGAAAAGGATGCCACTAAGTC
1 GTG-GACTTTG-AGAAAA-GATGCCACTAAGTC
*
300961 GTGGACTTTGAGACAAAAGATGCCACTGAGTC
1 GTGGACTTTGAG--AAAAGATGCCACTAAGTC
*
300993 GTGGACTTTGAAGAAAAGGATGCCACTGAGTC
1 GTGGACTTTG-AGAAAA-GATGCCACTAAGTC
*
301025 GTGGACTTTGAGAAGAGATTGCCACTAAGTC
1 GTGGACTTTGAGAAAAGA-TGCCACTAAGTC
*
301056 GTGGACTTTAAGAA
1 GTGGACTTTGAGAA
301070 GGTATTTGAA
Statistics
Matches: 187, Mismatches: 27, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.01
28 3 0.02
29 18 0.10
30 21 0.11
31 43 0.23
32 70 0.37
33 24 0.13
34 5 0.03
35 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (30 bp):
GTGGACTTTGAGAAAAGATGCCACTAAGTC
Found at i:302054 original size:26 final size:28
Alignment explanation
Indices: 302025--302084 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
302015 CTTTCTCTTC
302025 TCTTTTTTTTCTCTT-T-CTTTGTTTCT
1 TCTTTTTTTTCTCTTGTGCTTTGTTTCT
* *
302051 TCTTTTTTTTCTTTTGTGTTTTGTTTCT
1 TCTTTTTTTTCTCTTGTGCTTTGTTTCT
302079 T-TTTTT
1 TCTTTTT
302085 GGAAAAGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 14 0.47
27 6 0.20
28 10 0.33
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (28 bp):
TCTTTTTTTTCTCTTGTGCTTTGTTTCT
Found at i:308887 original size:13 final size:13
Alignment explanation
Indices: 308869--308893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308859 CATAAAATGT
308869 TGTATCGATACAA
1 TGTATCGATACAA
308882 TGTATCGATACA
1 TGTATCGATACA
308894 TTTTTTTTTG
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:309046 original size:52 final size:52
Alignment explanation
Indices: 308990--309114 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
308980 CACTGATCTT
*
308990 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
309042 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
309094 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAAGCAA
309115 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:315396 original size:19 final size:20
Alignment explanation
Indices: 315372--315421 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
315362 ATCTTTGCAA
*
315372 GTATCGATACAGTG-GTCAT
1 GTATCGATACAGTGCATCAT
* *
315391 GTATCGATACTGTGCATTAT
1 GTATCGATACAGTGCATCAT
315411 GTATCGATACA
1 GTATCGATACA
315422 TCTGAAGGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (20 bp):
GTATCGATACAGTGCATCAT
Found at i:316401 original size:13 final size:13
Alignment explanation
Indices: 316383--316409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
316373 TACATGGCAT
316383 AATGTATCGATAC
1 AATGTATCGATAC
316396 AATGTATCGATAC
1 AATGTATCGATAC
316409 A
1 A
316410 TGATGAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:316402 original size:33 final size:33
Alignment explanation
Indices: 316365--316429 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
316355 TACCACTATT
316365 TGTATCGATACATGGCAT-AA-TGTATCGATACAA
1 TGTATCGATACAT-G-ATGAATTGTATCGATACAA
316398 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATCGATACA
316430 TTGTCCCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 2 0.07
32 3 0.10
33 25 0.83
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:318023 original size:15 final size:15
Alignment explanation
Indices: 318003--318037 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
317993 AACCATCAAA
318003 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
318018 GATGATGATGATAAT
1 GATGATGAAGATAAT
318033 GATGA
1 GATGA
318038 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:321166 original size:15 final size:16
Alignment explanation
Indices: 321143--321173 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
321133 AAAGGTTTTC
321143 AAAA-TTTTTAATAGA
1 AAAAGTTTTTAATAGA
321158 AAAAGTTTTTAATAGA
1 AAAAGTTTTTAATAGA
321174 GGAAATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
AAAAGTTTTTAATAGA
Found at i:323034 original size:20 final size:21
Alignment explanation
Indices: 323011--323063 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
323001 CAGATTGCAT
**
323011 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
323031 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
323052 TGTATCGATACA
1 TGTATCGATACA
323064 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:333102 original size:21 final size:20
Alignment explanation
Indices: 333058--333110 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
333048 CAGATTGCAT
**
333058 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
333078 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
333099 TGTATGGATACA
1 TGTATCGATACA
333111 AGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:339183 original size:13 final size:13
Alignment explanation
Indices: 339165--339200 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
339155 ACATTCTCTC
*
339165 TATCGATACATTG
1 TATCGATACACTG
339178 TATCGATACACTG
1 TATCGATACACTG
*
339191 TATCAATACA
1 TATCGATACA
339201 AGGGGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (13 bp):
TATCGATACACTG
Done.