Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:132457 original size:167 final size:167
Alignment explanation
Indices: 132181--133006 Score: 920
Period size: 167 Copynumber: 5.0 Consensus size: 167
132171 TAACTCAAGG
* *
132181 CGAGAAGGGTTATCTGCCAACAAAGAGCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
1 CGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCAT
* * * *
132246 TTGTAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTACGCT
66 TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCT
132311 CAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGT
131 CAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGT
*
132348 CGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACGCTCAGCTCTAAGGCACATCAT
1 CGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCAT
** * * *
132413 TTGCAAAATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTTGACTACGCT
66 TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCT
* *
132478 CAGCTCCAAGGTACATCATTTGCAGTATAGCTTAAGT
131 CAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGT
* * * * * *
132515 CGAGAAGGGCTAGT-TG-C--CAAAGACCCTCGAGTTCGATTACACTCAGCT-TGAGGGTACATC
1 CGAGAAGGGTTA-TCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCT-AAGGCACATC
* * * * * * * * ** *
132575 ATTTACAGTATAACCCAAGGCTAGAAGAGTTATCTGTCTCCAAAAGACCTTCGAGTTCTACTACG
64 ATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* * * * * *
132640 CTCAGCTCTAAGGCATATCATTTGCAGCATAACATAAGT
129 CTCAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGT
* * *
132679 CGAGAAGGGTTATTTGCCAACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCTGAGGCACATC
1 CGAGAAGGGTTATCTGCCAA-C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
* * * * * * * *
132744 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTTGATTACA
64 ATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
* * ** * * *
132805 CTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGG
129 CTCAGC-TCCAAGGCACATCATTTACAGTATAGCTTAAGT
* * *
132845 CTAGAAGGGTTATCTGTCTCCA-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
1 CGAGAAGGGTTATCTG-C-CAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
* * * *
132909 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACG
64 ATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG
**
132973 CTCAGCTCTTAGGCACATCATTTACA-TAATAGCT
129 CTCAGCTCCAAGGCACATCATTTACAGT-ATAGCT
133007 CAAGGAAAGA
Statistics
Matches: 556, Mismatches: 87, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
163 2 0.00
164 131 0.24
165 93 0.17
166 42 0.08
167 195 0.35
168 31 0.06
169 61 0.11
170 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (167 bp):
CGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCAT
TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGT
Found at i:133572 original size:2 final size:2
Alignment explanation
Indices: 133565--133605 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
133555 CGGAGTTATT
133565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
133606 TTACTTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:133723 original size:36 final size:36
Alignment explanation
Indices: 133676--133984 Score: 224
Period size: 36 Copynumber: 8.8 Consensus size: 36
133666 AACGATTTTC
* * *
133676 GAAAATTTATATATTATATAGTTTTTGAAAATATTT
1 GAAAAATTATATAGTATATAGTTTTTAAAAATATTT
* * *
133712 -AAAAATATATATAATATATAG-TTTTGAAAACATTT
1 GAAAAAT-TATATAGTATATAGTTTTTAAAAATATTT
*
133747 -----A-TATAT--TATATAGTTTTTAAAACAT-TTC
1 GAAAAATTATATAGTATATAGTTTTTAAAA-ATATTT
* *
133775 GAAAACTTATATAGTATATAGTTTTTTAAAACATTTTT
1 GAAAAATTATATAGTATATAG-TTTTTAAAA-ATATTT
*
133813 GAAAAATTATATAGTATATAG-TTTTAAAACATTTTT
1 GAAAAATTATATAGTATATAGTTTTTAAAA-ATATTT
133849 GAAAAATTATATAGTATATAG-TTTTAAAAATATTTTT
1 GAAAAATTATATAGTATATAGTTTTTAAAAATA--TTT
* * *
133886 GAAAAATTATATAATATATAGTTTTAAAAACATTTTTT
1 GAAAAATTATATAGTATATAGTTTTTAAAA-A-TATTT
* * *
133924 G-GAAACT-TATA-TA-ATA-TTTTTAAAAACATTTT
1 GAAAAATTATATAGTATATAGTTTTTAAAAATA-TTT
* * *
133956 G-AAAACTATATAATATATAGTTTTGAAAA
1 GAAAAATTATATAGTATATAGTTTTTAAAA
133985 CTATATAATA
Statistics
Matches: 230, Mismatches: 20, Indels: 46
0.78 0.07 0.16
Matches are distributed among these distances:
27 7 0.03
28 9 0.04
29 6 0.03
31 1 0.00
32 10 0.04
33 12 0.05
34 10 0.04
35 25 0.11
36 76 0.33
37 39 0.17
38 33 0.14
39 1 0.00
40 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
GAAAAATTATATAGTATATAGTTTTTAAAAATATTT
Found at i:133753 original size:63 final size:63
Alignment explanation
Indices: 133680--133810 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 63
133670 ATTTTCGAAA
*
133680 ATTTATATATTATATAGTTTTTGAAAATATTT-AAAAATATATATAATATATAG-TTTTGAAAAC
1 ATTTATATATTATATAGTTTTT-AAAACATTTCAAAAAT-TATATAATATATAGTTTTTGAAAAC
* * *
133743 ATTTATATATTATATAGTTTTTAAAACATTTCGAAAACTTATATAGTATATAGTTTTTTAAAAC
1 ATTTATATATTATATAGTTTTTAAAACATTTC-AAAAATTATATAATATATAGTTTTTGAAAAC
133807 ATTT
1 ATTT
133811 TTGAAAAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 8 0.13
63 35 0.57
64 18 0.30
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (63 bp):
ATTTATATATTATATAGTTTTTAAAACATTTCAAAAATTATATAATATATAGTTTTTGAAAAC
Found at i:133757 original size:27 final size:27
Alignment explanation
Indices: 133719--133773 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
133709 TTTAAAAATA
133719 TATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
* *
133746 TATATATTATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
133773 T
1 T
133774 CGAAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (27 bp):
TATATAATATATAGTTTTGAAAACATT
Found at i:133934 original size:38 final size:37
Alignment explanation
Indices: 133733--133985 Score: 297
Period size: 37 Copynumber: 6.9 Consensus size: 37
133723 TAATATATAG
* *
133733 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA-
1 TTTTGAAAA-A-TTATATAATATATAGTTTTAAAAACAT
* * * *
133771 TTTCGAAAACTTATATAGTATATAGTTTTTTAAAACAT
1 TTTTGAAAAATTATATAATATATAG-TTTTAAAAACAT
*
133809 TTTTGAAAAATTATATAGTATATAGTTTT-AAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
* *
133845 TTTTGAAAAATTATATAGTATATAGTTTTAAAAATAT
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
133882 TTTTGAAAAATTATATAATATATAGTTTTAAAAACATT
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAACA-T
* *
133920 TTTTGGAAACTTATAT-A-ATAT--TTTTAAAAACA-
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
* *
133952 TTTTG-AAAACTATATAATATATAGTTTTGAAAAC
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAAC
133986 TATATAATAT
Statistics
Matches: 194, Mismatches: 13, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
31 8 0.04
32 6 0.03
33 4 0.02
34 11 0.06
35 9 0.05
36 54 0.28
37 56 0.29
38 46 0.24
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
Found at i:134022 original size:26 final size:24
Alignment explanation
Indices: 133952--134010 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
133942 TTTAAAAACA
133952 TTTTGAAAACTATATAATATATAG
1 TTTTGAAAACTATATAATATATAG
133976 TTTTGAAAACTATATAATATATAG
1 TTTTGAAAACTATATAATATATAG
134000 TTTTGAAAACT
1 TTTTGAAAACT
134011 TTTTTAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (24 bp):
TTTTGAAAACTATATAATATATAG
Found at i:134022 original size:31 final size:33
Alignment explanation
Indices: 133987--134069 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 33
133977 TTTGAAAACT
* *
133987 ATATAATATATAGTTTTGAAAACT-TTTTT-AA
1 ATATAATATATAGTTTTAAAAAATATTTTTGAA
134018 ATATAATATATAGTTTTAAAAAATATTTTTGAA
1 ATATAATATATAGTTTTAAAAAATATTTTTGAA
134051 ATATATATTATATAGTTTT
1 ATATA-A-TATATAGTTTT
134070 TATCATGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 22 0.48
32 5 0.11
33 7 0.15
34 1 0.02
35 11 0.24
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (33 bp):
ATATAATATATAGTTTTAAAAAATATTTTTGAA
Found at i:141317 original size:36 final size:36
Alignment explanation
Indices: 141270--141390 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 36
141260 TACCTATACA
* *
141270 ATAAGCGAAACCCATACAGCAAAACAAGTACGACAT
1 ATAAGCAAAACCCATACAGCAAAACAAGTACAACAT
* * *
141306 ATAAGCAAAACCCATACAGCAAAGCTAGTATAACAT
1 ATAAGCAAAACCCATACAGCAAAACAAGTACAACAT
* * * * *
141342 ATAAGCAAAATCCATACTGCAGAACTAA-TATAAGAT
1 ATAAGCAAAACCCATACAGCAAAAC-AAGTACAACAT
*
141378 ATAAGAAAAACCC
1 ATAAGCAAAACCC
141391 TTAATTGCTT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
36 70 0.99
37 1 0.01
ACGTcount: A:0.51, C:0.21, G:0.12, T:0.16
Consensus pattern (36 bp):
ATAAGCAAAACCCATACAGCAAAACAAGTACAACAT
Found at i:143944 original size:16 final size:16
Alignment explanation
Indices: 143909--143938 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
143899 ATAGACTTAA
143909 ATAAATCTTATTTTAC
1 ATAAATCTTATTTTAC
143925 ATAAAT-TTATTTTA
1 ATAAATCTTATTTTA
143939 TTATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAAATCTTATTTTAC
Found at i:145040 original size:21 final size:20
Alignment explanation
Indices: 145009--145049 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
144999 AAACTCAAGA
145009 AAAAAATAAAGATA-TAATAT
1 AAAAAATAAAGA-ACTAATAT
145029 AAAAAATAAAAGAACTAATAT
1 AAAAAAT-AAAGAACTAATAT
145050 TCCCGACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAAATAAAGAACTAATAT
Found at i:156300 original size:4 final size:4
Alignment explanation
Indices: 156291--158045 Score: 2975
Period size: 4 Copynumber: 452.5 Consensus size: 4
156281 TGAGCGGATC
156291 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
156339 TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA GACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156385 TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA CTACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA -TACA
156433 TACA TACA T-CA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156480 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156528 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156576 T--A TACA TAC- TACA TACA TACA TACA TACA TACA TACA -ACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156620 TACA TACA TACA TACA TACA TACA TACA TACA TACAA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TAC-A TACA TACA TACA
* *
156669 TCCA TACA TA-A TACA TACA GACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156716 TACA TACA TACA TACA TACA TACA T--A TACA TACA TACA T--A TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156760 TACA T-CA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156806 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156854 TACA TACA TA-A TACA -ACA TACA TACA TACA TACA T-CA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156899 TACA TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TAC- TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
156944 TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
156991 TACAA TACC TACA TACA TACA TACA TACA TACA TACA TACA TACAA TACA
1 TAC-A TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-A TACA
157041 TACA TACA TA-A TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157088 TACA TACA TACA TACA TACA TACA TACA TACA TACA -ACA TAC- TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157134 TACA TACA TACA TACA T-C- TACA TACAA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TAC-A TACA TACA TACA TACA TACA
157181 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157229 TAC- -ACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157274 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T-CA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157321 TACA TACA TACA T-CA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157368 TAC- TACA T-CA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157414 TAC- TACA TACA TACA TACA TACA TACA TACA TAC- -ACA TAC- TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157458 TACA TACA TACA TACA TACA TACA TACA T-CA T-CA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157504 TAC- TACA TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157550 TACA -ACA TACA TAC- TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157596 TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TAC- -ACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
157640 T-CA TACA TACA TACA TACA TACA TACA CACA TACA TACA TACA TTACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA -TACA
157688 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157735 TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157781 TACA TACA -ACA TACA TACA TACA -ACA TAC- -ACA TACA T-CA -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157823 TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
157869 TACA TACA TACA TACA TACC TACA TACA TACA TAC- TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157916 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
157964 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
158012 TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
158046 TACCGACATC
Statistics
Matches: 1673, Mismatches: 12, Indels: 132
0.92 0.01 0.07
Matches are distributed among these distances:
2 25 0.01
3 105 0.06
4 1519 0.91
5 24 0.01
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:163525 original size:187 final size:187
Alignment explanation
Indices: 163210--163583 Score: 667
Period size: 187 Copynumber: 2.0 Consensus size: 187
163200 CGCTCATATG
* *
163210 GCCAAACCTTTGGTGCCATAGGTTTGGTTTTCCATCAGTATCTGCTACTGCAATGATATTCTCTA
1 GCCAAACCTTTGGTGCCATAGGTTTGGTTTTCCATCAGCATCTGCTACTACAATGATATTCTCTA
*
163275 AATTTGAGGCTACATAGAGAGTACCAGTCTTCTTACCACGAGCAATGATGAGTGCTCCTTTGGTA
66 AATTTGAGGCTACATAGAGAGTACCAGTCTTCTTACCACGAGCAATGACGAGTGCTCCTTTGGTA
163340 ATCTTCCATTCACAGCCTGAAAAGGTTGTGTTATATCATTCTCCATCAAGATGTCCT
131 ATCTTCCATTCACAGCCTGAAAAGGTTGTGTTATATCATTCTCCATCAAGATGTCCT
163397 GCCAAACCTTTGGTGCCATAGGTTTGGTTTTCCATCAGCATCTGCTACTACAATGATATTCTCTA
1 GCCAAACCTTTGGTGCCATAGGTTTGGTTTTCCATCAGCATCTGCTACTACAATGATATTCTCTA
* * * *
163462 AATTTGAGGTTATATAGAGAGTATCAGTCTTCTTACCATGAGCAATGACGAGTGCTCCTTTGGTA
66 AATTTGAGGCTACATAGAGAGTACCAGTCTTCTTACCACGAGCAATGACGAGTGCTCCTTTGGTA
* *
163527 ATCTTCCATTCACAGCCTGAAAAGGTTGTGTTATATCCTTCTCCATCAAGCTGTCCT
131 ATCTTCCATTCACAGCCTGAAAAGGTTGTGTTATATCATTCTCCATCAAGATGTCCT
163584 ATAGAAATCA
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
187 178 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (187 bp):
GCCAAACCTTTGGTGCCATAGGTTTGGTTTTCCATCAGCATCTGCTACTACAATGATATTCTCTA
AATTTGAGGCTACATAGAGAGTACCAGTCTTCTTACCACGAGCAATGACGAGTGCTCCTTTGGTA
ATCTTCCATTCACAGCCTGAAAAGGTTGTGTTATATCATTCTCCATCAAGATGTCCT
Found at i:169428 original size:44 final size:44
Alignment explanation
Indices: 169376--169474 Score: 189
Period size: 44 Copynumber: 2.2 Consensus size: 44
169366 GATCATTATC
169376 TATTCCATTCAATTAACAACACTGTGCAATACATATTATCCTTT
1 TATTCCATTCAATTAACAACACTGTGCAATACATATTATCCTTT
*
169420 TGTTCCATTCAATTAACAACACTGTGCAATACATATTATCCTTT
1 TATTCCATTCAATTAACAACACTGTGCAATACATATTATCCTTT
169464 TATTCCATTCA
1 TATTCCATTCA
169475 CTGAGTGGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.39
Consensus pattern (44 bp):
TATTCCATTCAATTAACAACACTGTGCAATACATATTATCCTTT
Found at i:169667 original size:2 final size:2
Alignment explanation
Indices: 169660--169685 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
169650 CCAAAGTATG
169660 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
169686 ATACTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:172242 original size:15 final size:15
Alignment explanation
Indices: 172222--172253 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
172212 ATCCCCTGTT
172222 AGGTTCGAGTGGGGG
1 AGGTTCGAGTGGGGG
172237 AGGTTCGAGTGGGGG
1 AGGTTCGAGTGGGGG
172252 AG
1 AG
172254 AAACAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.59, T:0.19
Consensus pattern (15 bp):
AGGTTCGAGTGGGGG
Found at i:173968 original size:3 final size:3
Alignment explanation
Indices: 173960--174034 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
173950 CATTTGTTTT
*
173960 TTA TTA TTA -TA TTA TTA TTA ATA TTA TT- TTA TT- TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
174004 TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
174035 CATTTCAGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
2 7 0.11
3 57 0.88
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:175202 original size:17 final size:17
Alignment explanation
Indices: 175180--175219 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
175170 ATTTTAGTCC
175180 TTAAATTAATAATAAGG
1 TTAAATTAATAATAAGG
175197 TTAAATTAATAATAAGG
1 TTAAATTAATAATAAGG
*
175214 TAAAAT
1 TTAAAT
175220 AGCATGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (17 bp):
TTAAATTAATAATAAGG
Found at i:175373 original size:25 final size:24
Alignment explanation
Indices: 175317--175394 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 24
175307 AATACTTTCA
* *
175317 TTTATTTTACAAATTTTATTACTT
1 TTTATTTTACAAATTTTATCACTG
**
175341 TTTAATTTTACTTATTTTAGTCACTG
1 TTT-ATTTTACAAATTTTA-TCACTG
*
175367 TTTATTTT--TAATTTTAT-A-TG
1 TTTATTTTACAAATTTTATCACTG
175387 TTTATTTT
1 TTTATTTT
175395 TAATATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 10 0.21
21 1 0.02
22 1 0.02
23 7 0.15
24 3 0.06
25 18 0.38
26 7 0.15
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTATTTTACAAATTTTATCACTG
Found at i:175589 original size:2 final size:2
Alignment explanation
Indices: 175582--175638 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
175572 ATAAATATCT
*
175582 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175624 TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA T
175639 TTTCTTAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:180398 original size:27 final size:29
Alignment explanation
Indices: 180342--180398 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
180332 AAAGTTATGG
**
180342 TTTTTTATAAACATAATAATATTTTTAAT
1 TTTTTTATAAACATAATAATATTTAAAAT
180371 TTTTTTATAAA-A-AATAA-ATTTCAAAAT
1 TTTTTTATAAACATAATAATATTT-AAAAT
180398 T
1 T
180399 ACCAAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.16
27 9 0.36
28 1 0.04
29 11 0.44
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTTTTATAAACATAATAATATTTAAAAT
Found at i:184468 original size:6 final size:6
Alignment explanation
Indices: 184457--184514 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
184447 CTGTAAACTG
*
184457 GGCACA GGCACA GGCACA GGCACA GGCACA GGCACA -G-ACA GGCAGA
1 GGCACA GGCACA GGCACA GGCACA GGCACA GGCACA GGCACA GGCACA
*
184503 GGCACA GACACA
1 GGCACA GGCACA
184515 ACTACTGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
4 3 0.06
5 2 0.04
6 42 0.89
ACGTcount: A:0.36, C:0.31, G:0.33, T:0.00
Consensus pattern (6 bp):
GGCACA
Found at i:184499 original size:16 final size:16
Alignment explanation
Indices: 184460--184512 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
184450 TAAACTGGGC
184460 ACAGGCACAGGCACAGG
1 ACAGGCACAGGCACA-G
184477 CACAGGCACAGGCACAG
1 -ACAGGCACAGGCACAG
*
184494 ACAGGCAGAGGCACAG
1 ACAGGCACAGGCACAG
184510 ACA
1 ACA
184513 CAACTACTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 18 0.53
17 1 0.03
18 15 0.44
ACGTcount: A:0.38, C:0.30, G:0.32, T:0.00
Consensus pattern (16 bp):
ACAGGCACAGGCACAG
Found at i:186130 original size:18 final size:18
Alignment explanation
Indices: 186093--186131 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
186083 ACCGGTCACA
*
186093 ACCCGACCCGACCCGCTG
1 ACCCGACCAGACCCGCTG
* *
186111 ACCCGACCAGATCCGTTG
1 ACCCGACCAGACCCGCTG
186129 ACC
1 ACC
186132 GGCATTGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCAGACCCGCTG
Found at i:188607 original size:24 final size:24
Alignment explanation
Indices: 188580--188670 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
188570 TCGATTTGAT
188580 TTCTGATCTGATA-TCTGA-TATGGA
1 TTCTGATCTGATACT-TGACT-TGGA
188604 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACTTGGA
188628 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACTTGGA
* *
188652 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
188671 GTGAATTATG
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
24 61 0.97
25 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACTTGGA
Found at i:188682 original size:24 final size:24
Alignment explanation
Indices: 188583--188687 Score: 115
Period size: 24 Copynumber: 4.4 Consensus size: 24
188573 ATTTGATTTC
*
188583 TGATCTGATA-TCTGA-TATGGATTC
1 TGATCTGATACT-TGACT-TGGATTA
*
188607 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACTTGGATTA
*
188631 TGATCTGATACTTGACTTGGATTT
1 TGATCTGATACTTGACTTGGATTA
* * *
188655 TGATATGATACTTGACGTGAATTA
1 TGATCTGATACTTGACTTGGATTA
*
188679 TGATTTGAT
1 TGATCTGAT
188688 TTTTGATATA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
24 71 0.97
25 2 0.03
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (24 bp):
TGATCTGATACTTGACTTGGATTA
Found at i:189683 original size:59 final size:56
Alignment explanation
Indices: 189598--189718 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 56
189588 AAATAATTTT
** * *
189598 TTTTTTACTTTTAATGTTTTAGGTTTGGACCAAAACATGGCCAATAATAAGTTAATTAA
1 TTTTTTACTTTTAATGTTAAAGGTTTGGACCAAAACAT-ACC--TAATAAATTAATTAA
*
189657 TTTTTTACTTTTAATGTTAAAGGTTTGGACCAAAACATACCTAATAAATTAATTAT
1 TTTTTTACTTTTAATGTTAAAGGTTTGGACCAAAACATACCTAATAAATTAATTAA
189713 TTTTTT
1 TTTTTT
189719 GATTTGATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
56 19 0.33
58 2 0.04
59 36 0.63
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (56 bp):
TTTTTTACTTTTAATGTTAAAGGTTTGGACCAAAACATACCTAATAAATTAATTAA
Found at i:191091 original size:37 final size:37
Alignment explanation
Indices: 191041--191151 Score: 213
Period size: 37 Copynumber: 3.0 Consensus size: 37
191031 AACTGAAAAC
*
191041 CAATTATCTGAATATGACAGCAAACACTATAGAGAGA
1 CAATTGTCTGAATATGACAGCAAACACTATAGAGAGA
191078 CAATTGTCTGAATATGACAGCAAACACTATAGAGAGA
1 CAATTGTCTGAATATGACAGCAAACACTATAGAGAGA
191115 CAATTGTCTGAATATGACAGCAAACACTATAGAGAGA
1 CAATTGTCTGAATATGACAGCAAACACTATAGAGAGA
191152 GCAGAATAAG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (37 bp):
CAATTGTCTGAATATGACAGCAAACACTATAGAGAGA
Found at i:191508 original size:6 final size:6
Alignment explanation
Indices: 191493--191521 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
191483 ACTTGGTTCC
191493 TAGC-T TAGCTT TAGCTT TAGCTT TAGCTT
1 TAGCTT TAGCTT TAGCTT TAGCTT TAGCTT
191522 CAGTCCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
TAGCTT
Found at i:194450 original size:34 final size:36
Alignment explanation
Indices: 194399--194506 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 36
194389 TGGCAATCAA
194399 CTTTGAAAAAATGGTTTTCAAAGTTTGGT-AATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
194435 CTTTG-AAAATAGTTTTTAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
194470 CTTTGAAAAATGGTTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
194507 GTTGAAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
34 20 0.32
35 11 0.18
36 11 0.18
37 20 0.32
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:196641 original size:38 final size:39
Alignment explanation
Indices: 196599--196696 Score: 144
Period size: 38 Copynumber: 2.5 Consensus size: 39
196589 ATTCGTGTTG
*
196599 CATTTCGCGTTGTGATAGTTGAAAATCGC-ACGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCTACGATTTTC
*
196637 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGC--TACGATTTTC
*
196678 TATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
196697 CTACAGTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 28 0.52
41 26 0.48
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCTACGATTTTC
Found at i:196687 original size:20 final size:20
Alignment explanation
Indices: 196629--196693 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
196619 GAAAATCGCA
*
196629 CGATTTTCCATTTCGCGTTG
1 CGATTTTCAATTTCGCGTTG
* * **
196649 CGATAGTTGAAAATCGCGTTG
1 CGAT-TTTCAATTTCGCGTTG
*
196670 CGATTTTCTATTTCGCGTTG
1 CGATTTTCAATTTCGCGTTG
196690 CGAT
1 CGAT
196694 AGTCTACAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (20 bp):
CGATTTTCAATTTCGCGTTG
Found at i:196713 original size:22 final size:21
Alignment explanation
Indices: 196685--196797 Score: 90
Period size: 22 Copynumber: 5.4 Consensus size: 21
196675 TTCTATTTCG
196685 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
** * *
196707 CGTTGCGATTTTCCA-AATTT
1 CGTTGCGATAGTCTACAGTTT
196727 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
** * *
196748 CGTTGCGATTTTCCA-AATTT
1 CGTTGCGATAGTCTACAGTTT
*
196768 -GTTGCAATAGTCTACAGTTTT
1 CGTTGCGATAGTCTACAG-TTT
196789 CGTTGCGAT
1 CGTTGCGAT
196798 TTTCCAAATT
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 21 0.31
20 6 0.09
21 10 0.15
22 30 0.45
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:196731 original size:41 final size:41
Alignment explanation
Indices: 196686--196819 Score: 241
Period size: 41 Copynumber: 3.3 Consensus size: 41
196676 TCTATTTCGC
196686 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTT
1 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTT
196727 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTT
1 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTT
* * *
196768 GTTGCAATAGTCTACAGTTTTCGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTT
196809 GTTGCGATAGT
1 GTTGCGATAGT
196820 TAAAAAAAAG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (41 bp):
GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTT
Found at i:196732 original size:19 final size:19
Alignment explanation
Indices: 196708--196816 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 19
196698 TACAGTTGTC
196708 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
** * *
196727 GTTGCGATAGTCTACAGTTGT
1 GTTGCGATTTTCCA-AATT-T
196748 CGTTGCGATTTTCCAAATTT
1 -GTTGCGATTTTCCAAATTT
* * * **
196768 GTTGCAATAGTCTACAGTTTT
1 GTTGCGAT--TTTCCAAATTT
*
196789 CGTTGCGATTTTCCAAATTC
1 -GTTGCGATTTTCCAAATTT
196809 GTTGCGAT
1 GTTGCGAT
196817 AGTTAAAAAA
Statistics
Matches: 65, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
19 26 0.40
20 10 0.15
21 11 0.17
22 18 0.28
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:197623 original size:20 final size:20
Alignment explanation
Indices: 197598--197669 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
197588 ACTGTAGACT
*
197598 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
197618 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
197638 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
197658 ATCGCAACGCGA
1 ATCGCAACGCGA
197670 TTTTCAACTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:197684 original size:21 final size:21
Alignment explanation
Indices: 197658--197711 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
197648 GAAATGAAAA
197658 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
197679 ATCGCAACGCGATTTTCATCT
1 ATCGCAACGCGATTTTCAACT
197700 ATCGCAACGCGA
1 ATCGCAACGCGA
197712 ATTTGCGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:200306 original size:21 final size:20
Alignment explanation
Indices: 200282--200342 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
200272 AACTTTGAAA
200282 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTT-GT
*
200303 AAAT-G-TTTC----TTTGA
1 AAATGGTTTTCAAAGTTTGT
200317 AAATGGTTTTCAAAGTTTAGT
1 AAATGGTTTTCAAAGTTT-GT
200338 AAATG
1 AAATG
200343 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (20 bp):
AAATGGTTTTCAAAGTTTGT
Found at i:200320 original size:35 final size:36
Alignment explanation
Indices: 200274--200373 Score: 157
Period size: 35 Copynumber: 2.8 Consensus size: 36
200264 TGACAACCAA
200274 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
200311 CTTTG-AAAATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
200346 CTTTGAAAAATGATTTTTCAAAGTTTGG
1 CTTTGAAAAATG-GTTTTCAAAGTTTGG
200374 AGGATGTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.59
36 6 0.10
37 18 0.31
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:200807 original size:113 final size:113
Alignment explanation
Indices: 200609--200831 Score: 383
Period size: 113 Copynumber: 2.0 Consensus size: 113
200599 GTCCGGAGAC
* * * *
200609 GTAAGCACAATTGGCTGAATTCCGTTATCAATTTCGGGTATTATTTTTCTGCTTTTATTTCGTAT
1 GTAAGCACAATTGGCTGAACTCCGTTATCAATTTCGCGTATTATTTTTCCGCTTTTATTTCGCAT
*
200674 TTTCACTAATCTGGTTATAGGGAAATTACTCGTACTCGGTTTATTGAT
66 TCTCACTAATCTGGTTATAGGGAAATTACTCGTACTCGGTTTATTGAT
*
200722 GTAAGTACAATTGGCTGAACTCCGTTATCAATTTCGCGTATTATTTTTCCGCTTTTATTTCGCAT
1 GTAAGCACAATTGGCTGAACTCCGTTATCAATTTCGCGTATTATTTTTCCGCTTTTATTTCGCAT
*
200787 TCTCACTAATCTGGTTATAGGGAAATTACTCGTACTTGGTTTATT
66 TCTCACTAATCTGGTTATAGGGAAATTACTCGTACTCGGTTTATT
200832 TCCTAACAGA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (113 bp):
GTAAGCACAATTGGCTGAACTCCGTTATCAATTTCGCGTATTATTTTTCCGCTTTTATTTCGCAT
TCTCACTAATCTGGTTATAGGGAAATTACTCGTACTCGGTTTATTGAT
Found at i:204334 original size:19 final size:17
Alignment explanation
Indices: 204293--204331 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
204283 CATTATGAAA
204293 ATTTTAAATTATTATAT
1 ATTTTAAATTATTATAT
* *
204310 ATTTTAAATTTTTACAT
1 ATTTTAAATTATTATAT
204327 ATTTT
1 ATTTT
204332 TTATTGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:204895 original size:16 final size:15
Alignment explanation
Indices: 204848--204933 Score: 68
Period size: 16 Copynumber: 5.5 Consensus size: 15
204838 TTTTTTAATA
* *
204848 TATATATATATATATT
1 TATATTTATAT-TTTT
204864 TAGTATTT-TA-TTTT
1 TA-TATTTATATTTTT
*
204878 TATTTTTAGTATTTTT
1 TATATTTA-TATTTTT
204894 TATATTTATATTTTT
1 TATATTTATATTTTT
*
204909 AAATATTTGAATATTTTT
1 -TATATTT--ATATTTTT
204927 TATATTT
1 TATATTT
204934 TGAATTCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.07
14 5 0.09
15 9 0.16
16 21 0.37
17 10 0.18
18 8 0.14
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TATATTTATATTTTT
Found at i:204899 original size:18 final size:18
Alignment explanation
Indices: 204856--204934 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 18
204846 TATATATATA
*
204856 TATATATTTAGTATTTTATT
1 TATATTTTTAGTA-TTT-TT
*
204876 TTTATTTTTAGTATTTTT
1 TATATTTTTAGTATTTTT
204894 TATA--TTTA-TA-TTTT
1 TATATTTTTAGTATTTTT
* * *
204908 TAAATATTTGAATATTTTT
1 TATAT-TTTTAGTATTTTT
204927 TATATTTT
1 TATATTTT
204935 GAATTCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 7 0.15
15 2 0.04
16 4 0.08
17 3 0.06
18 10 0.21
19 11 0.23
20 11 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (18 bp):
TATATTTTTAGTATTTTT
Found at i:207930 original size:229 final size:228
Alignment explanation
Indices: 207525--208011 Score: 857
Period size: 229 Copynumber: 2.1 Consensus size: 228
207515 GTAAATTATC
* * * * *
207525 TATCCTTTTTATAAAAGTGTCCATACTTATTTCATTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTACATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* *
207590 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAGCAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
207655 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
*
207720 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTAAAAAAAGTATA
*
207753 TATCATTTTTATAAAAGTGTACATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTACATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
207818 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
*
207883 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
207948 GAAACATAAATTACATAACTTTAAAAAAAGTATA
195 GAAACATAAATTACATAACTTTAAAAAAAGTATA
*
207982 TATCATTTTTATAAAAGTGTTCATACTTAT
1 TATCATTTTTATAAAAGTGTACATACTTAT
208012 AAAAGTAGGT
Statistics
Matches: 246, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
228 34 0.14
229 212 0.86
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTACATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:208313 original size:20 final size:19
Alignment explanation
Indices: 208290--208336 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
208280 CGATATACCA
208290 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
208310 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
208330 GGTAAAA
1 GGTAAAA
208337 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:208424 original size:181 final size:182
Alignment explanation
Indices: 208078--208550 Score: 707
Period size: 181 Copynumber: 2.6 Consensus size: 182
208068 GATCCAAATT
* * * *
208078 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
208142 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
208207 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
208260 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
208325 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
208389 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * *
208441 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
208506 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
208551 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 168 0.63
182 97 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:208494 original size:20 final size:19
Alignment explanation
Indices: 208471--208517 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
208461 CGATATAACA
208471 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
208491 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
208511 GGTAAAA
1 GGTAAAA
208518 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:208519 original size:17 final size:19
Alignment explanation
Indices: 208480--208522 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
208470 AGGTAAAAAT
208480 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
208500 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
208517 ATGATA
1 ATGATA
208523 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:210793 original size:21 final size:21
Alignment explanation
Indices: 210747--210799 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
210737 AAGACAATCA
* *
210747 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTCGAG
* *
210768 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
*
210789 AGAGTCAAAGA
1 AGAGTCGAAGA
210800 TACACTTGAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:210901 original size:33 final size:33
Alignment explanation
Indices: 210845--210910 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
210835 AAATAGATGG
*
210845 AGTGGTGAAAGAAGTATAAGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTATAAGTGTTAAGGGGTGA
**
210878 AGTGGTGAAAGAAGT-TGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAT-AAGTGTTAAGGGGTGA
210911 TATTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTATAAGTGTTAAGGGGTGA
Found at i:212726 original size:19 final size:19
Alignment explanation
Indices: 212702--212750 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
212692 AATGTAGGGT
212702 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
212721 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
212740 TATTTTTGTAT
1 TAATTTTGTAT
212751 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:213561 original size:199 final size:199
Alignment explanation
Indices: 213085--213816 Score: 1384
Period size: 199 Copynumber: 3.7 Consensus size: 199
213075 GTGCACCCAT
213085 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
213150 CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
213215 GTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
213279 ATAA
196 ATAA
213283 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
213348 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
213413 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
213478 ATAA
196 ATAA
213482 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
213547 CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
*
213612 GTGTCGATATTTTTTTTCCAAAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
213677 ATAA
196 ATAA
213681 AAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
* *
213745 CGGTACAAGTATACCG-GTTTATGAGAGAATATGTCTAAATAATGTGTCGACACGT--TATAGTT
66 CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC-TAATATAGTT
213807 TGTGTCGATA
130 TGTGTCGATA
213817 CTAATTTAAA
Statistics
Matches: 527, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
196 17 0.03
197 36 0.07
198 204 0.39
199 270 0.51
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (199 bp):
AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAATTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
ATAA
Found at i:215299 original size:6 final size:6
Alignment explanation
Indices: 215275--215363 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
215265 AGCGGTCGCA
* * * * * *
215275 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * *
215323 GGCGAT GAAGAT GATGACGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT GA
215364 TGATCCAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 58 0.91
8 1 0.02
9 5 0.08
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:215310 original size:3 final size:3
Alignment explanation
Indices: 215290--215367 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
215280 TGAAGCTGAC
* * * * * ** *
215290 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
215338 GAC GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
215368 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:215329 original size:36 final size:39
Alignment explanation
Indices: 215278--215359 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
215268 GGTCGCAGAA
215278 GATGAAGCTGACGATG-A-A-GATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
* *
215314 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
215353 GATGAAG
1 GATGAAG
215360 ATGATGATCC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 15 0.37
37 1 0.02
38 1 0.02
39 24 0.59
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (39 bp):
GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
Found at i:215367 original size:12 final size:12
Alignment explanation
Indices: 215278--215363 Score: 91
Period size: 12 Copynumber: 6.9 Consensus size: 12
215268 GGTCGCAGAA
*
215278 GATGAAGCTGAC
1 GATGAAGATGAC
215290 GATGAAGATGAC
1 GATGAAGATGAC
*
215302 GATGATGATGAC
1 GATGAAGATGAC
* *
215314 GATGAAGCTGGC
1 GATGAAGATGAC
215326 GATGAAGATGATGAC
1 GATG-A-A-GATGAC
* *
215341 GATGATGATGAT
1 GATGAAGATGAC
215353 GATGAAGATGA
1 GATGAAGATGA
215364 TGATCCAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
12 50 0.82
13 1 0.02
14 2 0.03
15 8 0.13
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:215367 original size:18 final size:18
Alignment explanation
Indices: 215278--215367 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
215268 GGTCGCAGAA
* * *
215278 GATGAAGCTGACGATGAA
1 GATGAAGATGATGATGAT
* *
215296 GATGACGATGATGATGAC
1 GATGAAGATGATGATGAT
* *
215314 GATGAAGCTGGCGATGAAGAT
1 GATGAAGAT---GATGATGAT
*
215335 GATGACGATGATGATGAT
1 GATGAAGATGATGATGAT
215353 GATGAAGATGATGAT
1 GATGAAGATGATGAT
215368 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
18 43 0.75
21 14 0.25
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.22
Consensus pattern (18 bp):
GATGAAGATGATGATGAT
Found at i:217330 original size:183 final size:182
Alignment explanation
Indices: 216865--217348 Score: 816
Period size: 178 Copynumber: 2.7 Consensus size: 182
216855 GCAATGCTAT
*
216865 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* * *
216930 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACA
*
216995 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
217048 CGGTATAAATATACC-----TATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
217108 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACA
* *
217173 TTTACACATCGGAACCTAGATTTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* *
217226 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
217291 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGT
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
217349 GTCGGTAATT
Statistics
Matches: 283, Mismatches: 11, Indels: 14
0.92 0.04 0.05
Matches are distributed among these distances:
178 166 0.59
179 3 0.01
183 113 0.40
184 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (182 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACAT
TTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:219848 original size:25 final size:25
Alignment explanation
Indices: 219820--219884 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
219810 TTATCATTAA
219820 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
**** *
219845 ATTTAGGTATGTTTGTTAATTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
219870 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
219885 TCTTTTCAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:220250 original size:23 final size:23
Alignment explanation
Indices: 220219--220291 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
220209 ATAGGTAAAC
*
220219 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
220242 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
220265 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
220288 ATAT
1 ATAT
220292 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:221032 original size:39 final size:39
Alignment explanation
Indices: 220989--221075 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
220979 TTCGATGCTC
*
220989 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
221028 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
221067 ATCAAAATC
1 ATCAAAATC
221076 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:222829 original size:65 final size:67
Alignment explanation
Indices: 222689--222829 Score: 214
Period size: 65 Copynumber: 2.1 Consensus size: 67
222679 TTAATTTTTT
* * * *
222689 TTACATTTCTGCTAAGCCAACCAAACACAAAATGTAACATTCTCAGTAATCTTATTCCATGGTAA
1 TTACATTCCTGCTAAGCCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCATGGTAA
222754 TC
66 TC
*
222756 TTACATTCCTGCTAAGCCAACCAAAC-CAAAATGCAACATTCCCAG-AATCCTATTCCCTGGTAA
1 TTACATTCCTGCTAAGCCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCATGGTAA
222819 TC
66 TC
*
222821 TTATATTCC
1 TTACATTCC
222830 CATGGGTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 26 0.38
66 17 0.25
67 25 0.37
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.30
Consensus pattern (67 bp):
TTACATTCCTGCTAAGCCAACCAAACACAAAATGCAACATTCCCAGTAATCCTATTCCATGGTAA
TC
Found at i:227116 original size:55 final size:55
Alignment explanation
Indices: 227015--227156 Score: 176
Period size: 55 Copynumber: 2.6 Consensus size: 55
227005 ACATTCAAAT
* * * * * *
227015 GATCTATGTAGAAAGACATCCTATGAATGAAGAAATTTGAACCTGATTGAAGAAC
1 GATCCATGAAGAAAGACATCCGATGAATGAAGAAATGTGAAACTGATTAAAGAAC
* * * * *
227070 GATTCATGAAGATAGACATCCGATAAATGAAGACATGTGAAACTGATTAAAGACC
1 GATCCATGAAGAAAGACATCCGATGAATGAAGAAATGTGAAACTGATTAAAGAAC
*
227125 GATCCATGAAGAAATACATCCGATGAATGAAG
1 GATCCATGAAGAAAGACATCCGATGAATGAAG
227157 TTTGAAGTTG
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 72 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (55 bp):
GATCCATGAAGAAAGACATCCGATGAATGAAGAAATGTGAAACTGATTAAAGAAC
Found at i:227496 original size:6 final size:6
Alignment explanation
Indices: 227485--227510 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
227475 ATTAACACCT
227485 TTTGCA TTTGCA TTTGCA TTTGCA TT
1 TTTGCA TTTGCA TTTGCA TTTGCA TT
227511 CTTATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTGCA
Found at i:237107 original size:2 final size:2
Alignment explanation
Indices: 237100--237128 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
237090 GTACCCAATA
237100 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
237129 GTGTATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:239304 original size:37 final size:37
Alignment explanation
Indices: 239183--239369 Score: 243
Period size: 37 Copynumber: 5.1 Consensus size: 37
239173 TGGAGCAATT
* *
239183 CATCTTAAGCCTTCACCAAATAGTAGTGAAGC-AATC
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
239219 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AATC
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
* * * * * * *
239255 AATCTAAAGCCTTTACCAAAGAATAGTGAACCAAAAC
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
* * *
239292 CATCTTAAGCCTTCACCGGAGAATAGTGAAACAAATC
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
*
239329 CATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
1 CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
239366 CATC
1 CATC
239370 AGTAAGTCTT
Statistics
Matches: 129, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 60 0.47
37 69 0.53
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (37 bp):
CATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATC
Found at i:239843 original size:215 final size:214
Alignment explanation
Indices: 239365--240279 Score: 1544
Period size: 215 Copynumber: 4.3 Consensus size: 214
239355 TGAAGCAAAT
*
239365 CCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
239430 GATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
239495 TAAAAAAAT-AGTGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCAATTTTCAAAATTTC
131 T-GAAAAATGA-TGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTC
*
239559 ACAATTTATAAGTCCTTTGGG
194 ACAATTTATAAGTCCTTCGGG
* *
239580 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGATCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
239645 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
239710 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTTAAAATGAAGAATGCGATTTTTAAAATTTCAC
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCAC
*
239775 GATTTATAAGTCCTTCGGG
196 AATTTATAAGTCCTTCGGG
* *
239794 CCATCAATAAGTCTTTCGAGCATGATGCTAAAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
1 CCATCAGTAAGTCTTTCGAGCATGATGCT-TAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
239859 AGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
65 AGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
*
239924 ATGAAAAATGATGTTTTAAGAAGATGTAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCA
130 ATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCA
*
239989 CGATTTATAAGTCCTTCGGG
195 CAATTTATAAGTCCTTCGGG
* * *
240009 CCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCTTTCGGGTCATCTATAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
240074 GATGATAAGTCCTTCGGGTCATCCATAAAACCTTCGGGTAGGATGTTTTCACAAGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
240139 TGAAAAATAATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCAC
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCAC
240204 AATTTATAAGTCCTTCGGG
196 AATTTATAAGTCCTTCGGG
* * * *
240223 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATTTTTAAGCCTT
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
240280 CACAAGAGAG
Statistics
Matches: 661, Mismatches: 37, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
214 329 0.50
215 332 0.50
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (214 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCAC
AATTTATAAGTCCTTCGGG
Found at i:240092 original size:41 final size:41
Alignment explanation
Indices: 239995--240101 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
239985 TTCACGATTT
* * *
239995 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGC
1 ATAAGTCCTTCGGGTCATCA-TAAGCCTTTAGAGCATAATGC
* * *
240037 TTAAATCTTTCGGGTCATCTATAAGCCTTTAGAGCA-AGATG-
1 ATAAGTCCTTCGGGTCATC-ATAAGCCTTTAGAGCATA-ATGC
240078 ATAAGTCCTTCGGGTCATCCATAA
1 ATAAGTCCTTCGGGTCAT-CATAA
240102 AACCTTCGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
ATAAGTCCTTCGGGTCATCATAAGCCTTTAGAGCATAATGC
Found at i:240171 original size:429 final size:429
Alignment explanation
Indices: 239365--240279 Score: 1564
Period size: 429 Copynumber: 2.1 Consensus size: 429
239355 TGAAGCAAAT
* *
239365 CCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
239430 GATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAA
66 GATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
239495 TAAAAAAATAGTGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCAATTTTCAAAATTTCA
131 TAAAAAAATAGTGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCAATTTTCAAAATTTCA
* *
239560 CAATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGATCA
196 CAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCATTCGGATCA
*
239625 TCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATG
261 TCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATG
* * * *
239690 TTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTTAAAATGAAGAA
326 TTTTCACAAGAATTTGAAAATGAAAAATAATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAA
* *
239755 TGCGATTTTTAAAATTTCACGATTTATAAGTCCTTCGGG
391 TGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
*
239794 CCATCAATAAGTCTTTCGAGCATGATGCTAAAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
1 CCATCAATAAGTCTTTCGAGCATGATGCT-TAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
*
239859 AGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
65 AGATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
* * *
239924 AT-GAAAAAT-GATGTTTTAAGAAGATGTAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT
130 ATAAAAAAATAG-TGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCAATTTTCAAAATTT
* * *
239987 CACGATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCTTTCGGGT
194 CACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCATTCGGAT
*
240052 CATCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGTCATCCATAAAACCTTCGGGTAGGA
259 CATCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGA
*
240117 TGTTTTCACAAGAATTTGAAAATGAAAAATAATGTTTTAAGAAGATGGAATTTTTGAAAACGAAG
324 TGTTTTCACAAGAATTTGAAAATGAAAAATAATGTTTTAAGAAGATGAAATTTTTGAAAACGAAG
*
240182 AATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
389 AATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
* * *
240223 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATTTTTAAGCCTT
1 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
240280 CACAAGAGAG
Statistics
Matches: 457, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
428 25 0.05
429 333 0.73
430 99 0.22
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (429 bp):
CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TAAAAAAATAGTGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCAATTTTCAAAATTTCA
CAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCATTCGGATCA
TCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATG
TTTTCACAAGAATTTGAAAATGAAAAATAATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAA
TGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
Found at i:242761 original size:2 final size:2
Alignment explanation
Indices: 242754--242779 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
242744 GTATATTAAC
242754 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
242780 GGTATAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242877 original size:2 final size:2
Alignment explanation
Indices: 242870--242908 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
242860 TAAGTGATTT
242870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
242909 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:243484 original size:16 final size:16
Alignment explanation
Indices: 243463--243494 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
243453 CCTTAATTTG
243463 TTTTTTTAATTAAAAT
1 TTTTTTTAATTAAAAT
*
243479 TTTTTTTATTTAAAAT
1 TTTTTTTAATTAAAAT
243495 GACAACGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTTAATTAAAAT
Found at i:246692 original size:2 final size:2
Alignment explanation
Indices: 246685--246732 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
246675 CTCTCAAGCT
246685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
246727 TA TA TA
1 TA TA TA
246733 ATTCATACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:249555 original size:29 final size:29
Alignment explanation
Indices: 249510--249567 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
249500 ATTTTATGTT
* * **
249510 AGGGGTGAACTTTAACTTTTAAAATTTTA
1 AGGGGTAAACTTAAACTCATAAAATTTTA
249539 AGGGGTAAACTTAAACTCATAAAATTTTA
1 AGGGGTAAACTTAAACTCATAAAATTTTA
249568 GGAGGGCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (29 bp):
AGGGGTAAACTTAAACTCATAAAATTTTA
Found at i:249751 original size:32 final size:32
Alignment explanation
Indices: 249715--249778 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
249705 ATACAGTCCT
249715 CCAACATTTAGTCCGTTTGTAAAATGGTCCCC
1 CCAACATTTAGTCCGTTTGTAAAATGGTCCCC
* *
249747 CCAACATTTAGTCTGTTTGTAATATGGTCCCC
1 CCAACATTTAGTCCGTTTGTAAAATGGTCCCC
249779 GACCATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (32 bp):
CCAACATTTAGTCCGTTTGTAAAATGGTCCCC
Found at i:259158 original size:40 final size:40
Alignment explanation
Indices: 259106--259185 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
259096 AACATCTGAC
259106 TATACATGGTACTAGTGCATGAGAATGATTATGGATCCTA
1 TATACATGGTACTAGTGCATGAGAATGATTATGGATCCTA
259146 TATACATGGTACTAGTGCATGAGAATGATTATGGATCCTA
1 TATACATGGTACTAGTGCATGAGAATGATTATGGATCCTA
259186 CAAACACAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (40 bp):
TATACATGGTACTAGTGCATGAGAATGATTATGGATCCTA
Found at i:260838 original size:14 final size:14
Alignment explanation
Indices: 260819--260850 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
260809 CGTTCGTGAA
260819 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
260833 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
260847 CGTT
1 CGTT
260851 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:260867 original size:24 final size:24
Alignment explanation
Indices: 260820--260870 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
260810 GTTCGTGAAC
* *
260820 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
260844 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
260868 GTT
1 GTT
260871 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:261394 original size:11 final size:11
Alignment explanation
Indices: 261378--261443 Score: 96
Period size: 11 Copynumber: 5.9 Consensus size: 11
261368 GTCGAGCTCA
261378 GAATCGAGCTT
1 GAATCGAGCTT
*
261389 GAATCGAGCAT
1 GAATCGAGCTT
261400 GAATCGAGCTT
1 GAATCGAGCTT
*
261411 GAATTGAGCTT
1 GAATCGAGCTT
261422 AGAATCGAGCTT
1 -GAATCGAGCTT
*
261434 CAATCGAGCT
1 GAATCGAGCT
261444 CGAGTCTCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
11 39 0.80
12 10 0.20
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (11 bp):
GAATCGAGCTT
Found at i:261405 original size:22 final size:23
Alignment explanation
Indices: 261369--261442 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
261359 TGGGGCAATG
261369 TCGAGC-TCAGAATCGAGCTTGAA
1 TCGAGCAT-AGAATCGAGCTTGAA
261392 TCGAGCAT-GAATCGAGCTTGAA
1 TCGAGCATAGAATCGAGCTTGAA
* * *
261414 TTGAGCTTAGAATCGAGCTTCAA
1 TCGAGCATAGAATCGAGCTTGAA
261437 TCGAGC
1 TCGAGC
261443 TCGAGTCTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.44
23 24 0.53
24 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (23 bp):
TCGAGCATAGAATCGAGCTTGAA
Found at i:261676 original size:16 final size:15
Alignment explanation
Indices: 261655--261705 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
261645 GTCTCCAACG
261655 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTT-A
*
261671 TTTATGTTCGTGTTTG
1 TTTATGTTCGTG-TTA
261687 TTTATGTTCGT-TTA
1 TTTATGTTCGTGTTA
261701 TTTAT
1 TTTAT
261706 TAAATGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
16 23 0.72
17 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.63
Consensus pattern (15 bp):
TTTATGTTCGTGTTA
Found at i:268197 original size:150 final size:150
Alignment explanation
Indices: 267926--268226 Score: 602
Period size: 150 Copynumber: 2.0 Consensus size: 150
267916 CTGGGGTAGG
267926 AGTAAGTCCTTCCCGCCGGGGTGCCAACACAATCTTTTTTCCCTTGATGCTAAGGGAATATGTAT
1 AGTAAGTCCTTCCCGCCGGGGTGCCAACACAATCTTTTTTCCCTTGATGCTAAGGGAATATGTAT
267991 TCTTCCGTCCATCATGAATGACACTGCGATCATACTGCCAAGGTCGACCCAACAATATATGACAC
66 TCTTCCGTCCATCATGAATGACACTGCGATCATACTGCCAAGGTCGACCCAACAATATATGACAC
268056 GCATCCATAGACACAACATC
131 GCATCCATAGACACAACATC
268076 AGTAAGTCCTTCCCGCCGGGGTGCCAACACAATCTTTTTTCCCTTGATGCTAAGGGAATATGTAT
1 AGTAAGTCCTTCCCGCCGGGGTGCCAACACAATCTTTTTTCCCTTGATGCTAAGGGAATATGTAT
268141 TCTTCCGTCCATCATGAATGACACTGCGATCATACTGCCAAGGTCGACCCAACAATATATGACAC
66 TCTTCCGTCCATCATGAATGACACTGCGATCATACTGCCAAGGTCGACCCAACAATATATGACAC
268206 GCATCCATAGACACAACATC
131 GCATCCATAGACACAACATC
268226 A
1 A
268227 CACCAGGCAT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 151 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (150 bp):
AGTAAGTCCTTCCCGCCGGGGTGCCAACACAATCTTTTTTCCCTTGATGCTAAGGGAATATGTAT
TCTTCCGTCCATCATGAATGACACTGCGATCATACTGCCAAGGTCGACCCAACAATATATGACAC
GCATCCATAGACACAACATC
Found at i:269367 original size:15 final size:15
Alignment explanation
Indices: 269349--269378 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
269339 CCACGGTGCT
269349 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
269364 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
269379 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:270514 original size:26 final size:26
Alignment explanation
Indices: 270478--270530 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
270468 GTTCTGAGGG
270478 TATGAAACTAGTGTGGGATAAAACTA
1 TATGAAACTAGTGTGGGATAAAACTA
270504 TATGAAACTAGTGTGGGATAAAACTA
1 TATGAAACTAGTGTGGGATAAAACTA
270530 T
1 T
270531 CTTCTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (26 bp):
TATGAAACTAGTGTGGGATAAAACTA
Found at i:280094 original size:21 final size:20
Alignment explanation
Indices: 280070--280333 Score: 155
Period size: 21 Copynumber: 12.7 Consensus size: 20
280060 CATATTCGCA
280070 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT-GCG
* *
280091 TTGCGATAGTCGAAGTTCGCT
1 TTGCGATAGTCCAAGTT-GCG
* *
280112 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTGCG
* *
280133 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTGCG
* * *
280154 TTGCGATTTATTCCAA-ATGAG
1 TTGCGA--TAGTCCAAGTTGCG
*
280175 TTGCGATAGTCTAAGTTCGCG
1 TTGCGATAGTCCAAGTT-GCG
*
280196 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA--TAGTCCAAGTTGCG
*
280217 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT-GCG
* *
280238 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTGCG
*
280259 TTACGATAGTCCAAGTT-CG
1 TTGCGATAGTCCAAGTTGCG
* *
280278 TTGTGATAGTCAAAGTTCGCG
1 TTGCGATAGTCCAAGTT-GCG
* *
280299 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTGCG
280320 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
280334 AATCGCAACG
Statistics
Matches: 198, Mismatches: 30, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
19 47 0.24
20 2 0.01
21 116 0.59
23 33 0.17
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTGCG
Found at i:280135 original size:42 final size:42
Alignment explanation
Indices: 280089--280277 Score: 256
Period size: 42 Copynumber: 4.5 Consensus size: 42
280079 TCCAAGTTCG
* *
280089 CGTTGCGATAGTCGAAGTTCGCTTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
280131 CGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATG
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
280173 AGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
280215 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
280257 CGTTACGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
280278 TTGTGATAGT
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
40 8 0.06
42 111 0.87
44 8 0.06
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:280178 original size:84 final size:83
Alignment explanation
Indices: 280090--280326 Score: 270
Period size: 84 Copynumber: 2.8 Consensus size: 83
280080 CCAAGTTCGC
*
280090 GTTGCGATAGTCGAAGTTCGCTTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGT
1 GTTGCGATAGTCCAAGTTCGC-TTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGT
280155 TGCGATTTATTCCAAATGA
65 TGCGATTTATTCCAAATGA
* * * * *
280174 GTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAGTTCGC
1 GTTGCGATAGTCCAAGTTCGC-TTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT--C
**
280237 GTTGCGATTTATTCCAAATTC
63 GTTGCGATTTATTCCAAATGA
* * *
280258 GTTACGATAGTCCAAGTTCG-TTGTGA--TAGT-CAAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCCAAGTTCGCTTGCGATTTATTCCAAA-TT--CGTTGCGATTTATTCCAAATTC
280319 GTTGCGAT
63 GTTGCGAT
280327 AGTCCAAAAT
Statistics
Matches: 130, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
79 3 0.02
80 5 0.04
82 30 0.23
84 92 0.71
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (83 bp):
GTTGCGATAGTCCAAGTTCGCTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTT
GCGATTTATTCCAAATGA
Found at i:283850 original size:60 final size:60
Alignment explanation
Indices: 283785--283938 Score: 197
Period size: 59 Copynumber: 2.6 Consensus size: 60
283775 TTATATCAGC
* *
283785 CCTTAAACTTTTGAATATTTTAATTTTATCCCCAAACTATGACTCTCATTCTAAATTAGT
1 CCTTAAACTTTTGAATATTCTAATTTTATCCCCAAACTATGACCCTCATTCTAAATTAGT
* * * * *
283845 CCTTAAACTTTTAAACATTCTAA-TTTATCCCTAAACTATGACCCTCTTTCTAAATTGGT
1 CCTTAAACTTTTGAATATTCTAATTTTATCCCCAAACTATGACCCTCATTCTAAATTAGT
* *
283904 CAC-T-AACTTTTGAATATTCCAATTTCATCCCCAAA
1 C-CTTAAACTTTTGAATATTCTAATTTTATCCCCAAA
283939 TTCATCCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
58 15 0.19
59 44 0.55
60 21 0.26
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
CCTTAAACTTTTGAATATTCTAATTTTATCCCCAAACTATGACCCTCATTCTAAATTAGT
Found at i:283886 original size:59 final size:59
Alignment explanation
Indices: 283751--283934 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 59
283741 TTGAATCATA
* * * * * *
283751 TATCCCTAAACTATAACTTTCAATT-TATATCAGCCCTTAAACTTTTGAATATTTTAATTT
1 TATCCCTAAACTATGACTCTC-ATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAA-TT
* * *
283811 TATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATT
1 TATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATT
* * * *
283870 TATCCCTAAACTATGACCCTCTTTCTAAATTGGTCAC-T-AACTTTTGAATATTCCAATT
1 TATCCCTAAACTATGACTCTCATTCTAAATTAGTC-CTTAAACTTTTGAATATTCTAATT
283928 TCATCCC
1 T-ATCCC
283935 CAAATTCATC
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
58 18 0.17
59 42 0.40
60 45 0.43
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (59 bp):
TATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATT
Found at i:286479 original size:2 final size:2
Alignment explanation
Indices: 286474--286503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
286464 AAAATGAGTT
286474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
286504 ACTTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:290522 original size:27 final size:27
Alignment explanation
Indices: 290492--290551 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
290482 ATATAAAAAC
*
290492 AATTTATTAATCTAA-TAATCATAATTA
1 AATTTATTAATCTAACAAAT-ATAATTA
*
290519 AATTTATTAGTCTAACAAATATAATTA
1 AATTTATTAATCTAACAAATATAATTA
290546 ATATTT
1 A-ATTT
290552 TCCTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTTATTAATCTAACAAATATAATTA
Found at i:292834 original size:3 final size:3
Alignment explanation
Indices: 292826--292914 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
292816 TTTTTATCCA
* *
292826 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
292874 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
292915 AATATATATT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:294339 original size:19 final size:20
Alignment explanation
Indices: 294312--294350 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
294302 TTTATTGTTA
294312 TTTATTATATT-ATTAAATAT
1 TTTATTATATTCA-TAAATAT
294332 TTTA-TATATTCATAAATAT
1 TTTATTATATTCATAAATAT
294351 ATATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTATATTCATAAATAT
Found at i:295011 original size:6 final size:7
Alignment explanation
Indices: 294990--295014 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
294980 TGTCTCTATT
294990 AATTAAA
1 AATTAAA
294997 AATTAAA
1 AATTAAA
295004 AATTAAA
1 AATTAAA
295011 AATT
1 AATT
295015 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:298462 original size:14 final size:15
Alignment explanation
Indices: 298432--298464 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
298422 TTATTATTTT
298432 ATTTATTAAGATAAA
1 ATTTATTAAGATAAA
*
298447 ATTTATTAA-TTAAA
1 ATTTATTAAGATAAA
298461 ATTT
1 ATTT
298465 GAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTATTAAGATAAA
Found at i:305255 original size:19 final size:19
Alignment explanation
Indices: 305208--305256 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
305198 AAGAGAATCA
*
305208 TTACAAAGAATACTGAAAC
1 TTACAAAGATTACTGAAAC
305227 TTACAAAGATTACTGAAAC
1 TTACAAAGATTACTGAAAC
305246 TTACAAAGATT
1 TTACAAAGATT
305257 GGCACGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (19 bp):
TTACAAAGATTACTGAAAC
Found at i:305764 original size:9 final size:9
Alignment explanation
Indices: 305750--305824 Score: 66
Period size: 9 Copynumber: 8.3 Consensus size: 9
305740 ATGCTTGAAG
305750 AAAAAAGAA
1 AAAAAAGAA
305759 AAAAAAGAA
1 AAAAAAGAA
*
305768 AAGAAAGAA
1 AAAAAAGAA
*
305777 AATAAA-AA
1 AAAAAAGAA
*
305785 AAGAAAGAA
1 AAAAAAGAA
305794 AAGAAAA-AA
1 AA-AAAAGAA
*
305803 TAGAAAATGAA
1 -A-AAAAAGAA
305814 AAAAAA-AA
1 AAAAAAGAA
305822 AAA
1 AAA
305825 GGGGGTCAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
8 12 0.22
9 32 0.58
10 8 0.15
11 3 0.05
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:305786 original size:22 final size:22
Alignment explanation
Indices: 305758--305800 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
305748 AGAAAAAAGA
305758 AAAAAAAGAAA-AGAAAGAAAAT
1 AAAAAAAGAAAGA-AAAGAAAAT
305780 AAAAAAAGAAAGAAAAGAAAA
1 AAAAAAAGAAAGAAAAGAAAA
305801 AATAGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAGAAAAGAAAAT
Found at i:305786 original size:31 final size:31
Alignment explanation
Indices: 305750--305824 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
305740 ATGCTTGAAG
305750 AAAAAAGAAAAAAAAGAAAAGAA-AGAAAATA
1 AAAAAAGAAAAAAAAGAAAA-AATAGAAAATA
* *
305781 AAAAAAGAAAGAAAAGAAAAAATAGAAAATG
1 AAAAAAGAAAAAAAAGAAAAAATAGAAAATA
305812 AAAAAA-AAAAAAA
1 AAAAAAGAAAAAAA
305825 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.20
31 32 0.80
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (31 bp):
AAAAAAGAAAAAAAAGAAAAAATAGAAAATA
Found at i:305809 original size:26 final size:25
Alignment explanation
Indices: 305747--305825 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 25
305737 ATTATGCTTG
305747 AAGAAAA-AAGAAAAAAAAGAAAAGA
1 AAGAAAAGAA-AAAAAAAAGAAAAGA
*
305772 AAGAAAATAAAAAAAGAAAGAAAAGA
1 AAGAAAAGAAAAAAA-AAAGAAAAGA
305798 AA-AAATAGAAAATGAAAAAA-AAAA-A
1 AAGAAA-AGAAAA--AAAAAAGAAAAGA
305823 AAG
1 AAG
305826 GGGGTCAAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
25 18 0.38
26 23 0.49
27 3 0.06
28 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (25 bp):
AAGAAAAGAAAAAAAAAAGAAAAGA
Found at i:305814 original size:24 final size:22
Alignment explanation
Indices: 305751--305824 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
305741 TGCTTGAAGA
*
305751 AAAAAGAAAAAAAAGAAAAGAAAG
1 AAAAA-AAAAAAAATAAAA-AAAG
* *
305775 AAAATAAAAAAAGA-AAGAAAAG
1 AAAA-AAAAAAAAATAAAAAAAG
* * *
305797 AAAAAATAGAAAATGAAAAAA-
1 AAAAAAAAAAAAATAAAAAAAG
305818 AAAAAAA
1 AAAAAAA
305825 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
21 12 0.30
22 13 0.32
23 3 0.08
24 11 0.28
25 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (22 bp):
AAAAAAAAAAAAATAAAAAAAG
Found at i:307061 original size:83 final size:82
Alignment explanation
Indices: 306861--307237 Score: 655
Period size: 83 Copynumber: 4.6 Consensus size: 82
306851 AATAGAACAA
** *
306861 ATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
*
306926 ATCATTGAGTTTAGAAG
66 AGCATTGAGTTTAGAAG
306943 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
307008 AAGCATTGAGTTTAGAAG
65 AAGCATTGAGTTTAGAAG
* *
307026 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAAAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
* *
307091 AAGCATTGAATTTGGAAG
65 AAGCATTGAGTTTAGAAG
307109 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
*
307174 ATCATTGAGTTTAGAAG
66 AGCATTGAGTTTAGAAG
307191 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
307238 GTTTGGTATG
Statistics
Matches: 281, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 123 0.44
83 158 0.56
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (82 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
AGCATTGAGTTTAGAAG
Found at i:307182 original size:165 final size:165
Alignment explanation
Indices: 306861--307237 Score: 657
Period size: 165 Copynumber: 2.3 Consensus size: 165
306851 AATAGAACAA
** * *
306861 ATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTGGAAAGAACA
* *
306926 ATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
66 AGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
306991 TCTGGTTGGACAGAATCAAGCATTGAGTTTAGAAG
131 TCTGGTTGGACAGAATCAAGCATTGAGTTTAGAAG
*
307026 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAAAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTGGAAAGAA-C
*
307091 AAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
65 AAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
307156 ATCTGGTTGGACAGAA-CAATCATTGAGTTTAGAAG
130 ATCTGGTTGGACAGAATCAAGCATTGAGTTTAGAAG
307191 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
307238 GTTTGGTATG
Statistics
Matches: 202, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
165 123 0.61
166 79 0.39
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (165 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGATTGGAAAGAACA
AGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
TCTGGTTGGACAGAATCAAGCATTGAGTTTAGAAG
Found at i:308284 original size:113 final size:113
Alignment explanation
Indices: 308081--308865 Score: 1378
Period size: 113 Copynumber: 7.0 Consensus size: 113
308071 CAAAGATTCA
* * *
308081 AATCTATCATTTGAAAGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
308146 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
308194 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
308259 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
308307 AATCCATCATTTGAGGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
308372 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
308420 AATCCATCATTTGATG-GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGA-GAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
308484 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
308533 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
308598 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
308646 AATCCATCATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
308711 AGGAAGAAGAAGTTCATAATTAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
308759 AATTCATCAATTGATG-GATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGA-GAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
308822 AAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
308866 GCATAATTCT
Statistics
Matches: 652, Mismatches: 17, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
112 71 0.11
113 579 0.89
114 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGAGAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:309192 original size:3 final size:3
Alignment explanation
Indices: 309184--309278 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
309174 TTTTTATCCA
*
309184 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
309232 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
309279 AATATATTAA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:310748 original size:20 final size:20
Alignment explanation
Indices: 310725--310765 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
310715 TTTATTGTTA
310725 TTTTATTATATT-ATTAAATAT
1 TTTTA-TATATTCA-TAAATAT
310746 TTTTATATATTCATAAATAT
1 TTTTATATATTCATAAATAT
310766 ATATATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATATATTCATAAATAT
Found at i:313365 original size:21 final size:20
Alignment explanation
Indices: 313335--313375 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
313325 CCTAATTTAG
*
313335 TATCGGTACTACCCTCTACAA
1 TATCGATACTACCCT-TACAA
313356 TATCGATACTACCCTTACAA
1 TATCGATACTACCCTTACAA
313376 AATAGCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.29
Consensus pattern (20 bp):
TATCGATACTACCCTTACAA
Found at i:323834 original size:43 final size:43
Alignment explanation
Indices: 323768--323993 Score: 206
Period size: 43 Copynumber: 5.3 Consensus size: 43
323758 TGGTAACAAA
*** * **
323768 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTT-GGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TTCCAAC
* *
323811 AAACGCCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
323854 AAACGTCGCAATAGGTGTTAATATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
323897 AAACGCCGCAATAGGTCTTCAGATTTAGCGGCGTTTTTCTC-AC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTC-CAAC
* * * * * * **
323940 AAACACCGCAAAAGAT-CTGGTATATAGCGGCGTTTTTTAGAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTTTCCAAC
323983 AAACGCCGCAA
1 AAACGCCGCAA
323994 AATATCATAT
Statistics
Matches: 151, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
42 13 0.09
43 137 0.91
44 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Found at i:323994 original size:43 final size:43
Alignment explanation
Indices: 323895--324034 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 43
323885 CGTTTTTCCC
* * * * * *
323895 ACAAACGCCGCAATAGGTCTTCAGATTTAGCGGCGTTTTTCT--C
1 ACAAACGCCGCAAAAGATCAT-ATATATAGCGGCGTTTTT-TAGA
* *
323938 ACAAACACCGCAAAAGATC-TGGTATATAGCGGCGTTTTTTAGA
1 ACAAACGCCGCAAAAGATCAT-ATATATAGCGGCGTTTTTTAGA
* * *
323981 ACAAACGCCGCAAAATATCATATCTATAGCGGCG-TTTTAAGA
1 ACAAACGCCGCAAAAGATCATATATATAGCGGCGTTTTTTAGA
324023 TACAAACGCCGC
1 -ACAAACGCCGC
324035 TAATTACCTC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 23 0.29
43 55 0.69
44 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (43 bp):
ACAAACGCCGCAAAAGATCATATATATAGCGGCGTTTTTTAGA
Found at i:324172 original size:21 final size:21
Alignment explanation
Indices: 324146--324204 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
324136 ATTTTCCAAT
*
324146 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
324167 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
324188 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
324205 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:326944 original size:39 final size:39
Alignment explanation
Indices: 326901--326988 Score: 158
Period size: 39 Copynumber: 2.3 Consensus size: 39
326891 ACTCCCCCTT
326901 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACAC
1 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACAC
*
326940 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACAT
1 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACAC
*
326979 ACTTAAACAC
1 ACTTTAACAC
326989 ACTTCTTCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (39 bp):
ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACAC
Found at i:329734 original size:2 final size:2
Alignment explanation
Indices: 329729--329756 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
329719 GTGTGTGTGT
329729 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
329757 TAAAGGGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:330600 original size:41 final size:44
Alignment explanation
Indices: 330552--330632 Score: 116
Period size: 41 Copynumber: 1.9 Consensus size: 44
330542 CGATTGTTAT
*
330552 AAACGCCATTAATAA-AC-AAT-TTTTGCGGCGTTT-TTATTTAA
1 AAACGCCAATAA-AATACAAATATTTTGCGGCGTTTGTTATTTAA
330593 AAACGCCAATAAAATACAAATATTTTGCGGCGTTTGTTAT
1 AAACGCCAATAAAATACAAATATTTTGCGGCGTTTGTTAT
330633 AAGAACGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
40 2 0.06
41 13 0.37
42 3 0.09
43 13 0.37
44 4 0.11
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (44 bp):
AAACGCCAATAAAATACAAATATTTTGCGGCGTTTGTTATTTAA
Found at i:330964 original size:52 final size:52
Alignment explanation
Indices: 330900--331058 Score: 291
Period size: 52 Copynumber: 3.1 Consensus size: 52
330890 TAACAATAAA
* *
330900 ATACATTATAATTTAGAAACATTAAAATACTTATACATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
330952 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
331004 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
331056 ATA
1 ATA
331059 TTGTTCAGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:331284 original size:24 final size:24
Alignment explanation
Indices: 331252--331302 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
331242 TTTAGTGCTT
331252 CACTTGAAACAGATAACGACCCTC
1 CACTTGAAACAGATAACGACCCTC
331276 CACTTGAAACAGATAACGACCCTC
1 CACTTGAAACAGATAACGACCCTC
331300 CAC
1 CAC
331303 CTACAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.35, G:0.12, T:0.16
Consensus pattern (24 bp):
CACTTGAAACAGATAACGACCCTC
Found at i:332202 original size:42 final size:42
Alignment explanation
Indices: 332156--332293 Score: 131
Period size: 42 Copynumber: 3.3 Consensus size: 42
332146 TTTATACAAA
* *
332156 AAACGCCGCTATTTTACTACTCTATTGCGGCATTTTTGGTAT
1 AAACGCCGCTATTTTACTACTATATTGCGGCATTTTTGCTAT
* * * *
332198 AAACGACGCTAAATGTTA--AATATATTGCGGCATTTTAGCTA-
1 AAACGCCGCT--ATTTTACTACTATATTGCGGCATTTTTGCTAT
** * *
332239 AAACGCCGCTA-CATATCTACTATATTGCGGCGTTTTTACTAT
1 AAACGCCGCTATTTTA-CTACTATATTGCGGCATTTTTGCTAT
332281 AAACGCCGCTATT
1 AAACGCCGCTATT
332294 GTTTAACCTT
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
41 28 0.37
42 39 0.52
44 5 0.07
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (42 bp):
AAACGCCGCTATTTTACTACTATATTGCGGCATTTTTGCTAT
Found at i:336284 original size:23 final size:23
Alignment explanation
Indices: 336249--336316 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
336239 ATTATTATAT
*
336249 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
336272 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
336295 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
336317 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:342541 original size:24 final size:24
Alignment explanation
Indices: 342513--342619 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
342503 AAACAGAGAT
*
342513 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
342537 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
342561 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
342585 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
342609 ATCAGAAATCA
1 ATCAGAAATCA
342620 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:342619 original size:48 final size:48
Alignment explanation
Indices: 342513--342621 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
342503 AAACAGAGAT
* * * *
342513 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
342561 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
342609 ATCAGAAATCAGA
1 ATCAGAAATCAGA
342622 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:343769 original size:18 final size:18
Alignment explanation
Indices: 343748--343783 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
343738 CTTCCATCCG
*
343748 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
343766 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
343784 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Done.