Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 62
Found at i:2207489 original size:13 final size:13
Alignment explanation
Indices: 2207471--2207495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2207461 ATGACAGATT
2207471 AAAGAAATTTTTG
1 AAAGAAATTTTTG
2207484 AAAGAAATTTTT
1 AAAGAAATTTTT
2207496 TTAAAGGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AAAGAAATTTTTG
Found at i:2209872 original size:23 final size:23
Alignment explanation
Indices: 2209846--2209890 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2209836 CACCACAGCT
*
2209846 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2209869 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2209891 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2210128 original size:149 final size:149
Alignment explanation
Indices: 2209858--2210172 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
2209848 TATAATTGCA
*
2209858 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAA-TGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAA
2209922 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
2209987 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
2210007 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAAT
1 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAAT
*
2210072 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
2210137 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
*
2210156 CCGAAGGACCGCGTAGA
1 CCGAATGACCGCGTAGA
2210173 CCCTCGACTC
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 2 0.01
149 160 0.99
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:2210850 original size:18 final size:18
Alignment explanation
Indices: 2210829--2210863 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2210819 TCCCATCTAG
2210829 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2210847 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2210864 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2211470 original size:21 final size:21
Alignment explanation
Indices: 2211446--2211490 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2211436 TGTTGTTCGT
* *
2211446 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2211467 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2211488 TTG
1 TTG
2211491 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2212160 original size:23 final size:23
Alignment explanation
Indices: 2212134--2212178 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2212124 CACCACAGCT
*
2212134 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
2212157 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2212179 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2212416 original size:149 final size:149
Alignment explanation
Indices: 2212146--2212460 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
2212136 TATAATTGCA
*
2212146 CCGAAGTG-CCGCGTAGAATTGCATCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
2212210 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
2212275 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
2212295 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
2212360 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
2212425 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
2212444 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2212461 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 162 0.99
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:2213140 original size:18 final size:18
Alignment explanation
Indices: 2213119--2213153 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2213109 TCCCATCTAG
2213119 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2213137 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2213154 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2217049 original size:23 final size:23
Alignment explanation
Indices: 2217023--2217067 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2217013 CACCACAGCT
*
2217023 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2217046 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2217068 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2217305 original size:149 final size:149
Alignment explanation
Indices: 2217035--2217349 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
2217025 TATAATTGCA
2217035 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
2217099 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
2217164 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
2217184 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
2217249 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
2217314 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
2217333 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2217350 CCCTCGACTC
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 163 0.99
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:2218020 original size:18 final size:18
Alignment explanation
Indices: 2217999--2218033 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2217989 TCCCATCTAG
2217999 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2218017 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2218034 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2221940 original size:23 final size:23
Alignment explanation
Indices: 2221914--2221958 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2221904 CACCACAGCT
*
2221914 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2221937 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2221959 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2222771 original size:18 final size:18
Alignment explanation
Indices: 2222750--2222784 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2222740 TCCCATCTAG
2222750 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2222768 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2222785 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2223391 original size:21 final size:21
Alignment explanation
Indices: 2223367--2223411 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2223357 TGTTGTTCGT
* *
2223367 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2223388 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2223409 TTG
1 TTG
2223412 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2229555 original size:2 final size:2
Alignment explanation
Indices: 2229548--2229572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2229538 TATACTTATT
2229548 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2229573 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2232485 original size:2 final size:2
Alignment explanation
Indices: 2232480--2232506 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2232470 TATCCATCCT
2232480 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2232507 TTTTTTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2265784 original size:16 final size:18
Alignment explanation
Indices: 2265752--2265789 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2265742 AGAAAATTAG
2265752 AATCTGTGAAGGAATTGA
1 AATCTGTGAAGGAATTGA
*
2265770 AATCTGT-AA-GAATTGT
1 AATCTGTGAAGGAATTGA
2265786 AATC
1 AATC
2265790 CAATTCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 2 0.11
18 7 0.37
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (18 bp):
AATCTGTGAAGGAATTGA
Found at i:2266102 original size:37 final size:38
Alignment explanation
Indices: 2266027--2266104 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
2266017 AACTTGAACT
2266027 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
1 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
* *
2266065 CGACTCGACCCGAATATCACACTT-AAAAAACCTGACC
1 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
2266102 CGA
1 CGA
2266105 ACAAAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 15 0.39
38 23 0.61
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.13
Consensus pattern (38 bp):
CGACCCGACCCGAATATCACACTTAAAAAAACCCGACC
Found at i:2266384 original size:186 final size:182
Alignment explanation
Indices: 2266055--2266449 Score: 591
Period size: 186 Copynumber: 2.2 Consensus size: 182
2266045 ACACTTAAAA
* *
2266055 AAACCCG-ACCCGACTCGACCCGAATATCACACTTAAAAAACCTGACCCGAACAAAATAAAGTTT
1 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTT
* * *
2266119 CATCCGATCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCTGA
66 CATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGA
* * *
2266184 CCCGACCCGAATTATGTATAT-T-TTCGGGTCGGTCTGGTTTTTTTCACCCT
131 CCCGACCCGAATTATATATATATATTCGGGTCGGTCCGGGTTTTTTCACCCT
*
2266234 AAACCCGAACCTGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATA
1 AAACCCGAACCCGACCCGACCCGAATATCACACTT--AAAAA----ACCCGACCCGAACAAAATA
**
2266299 AAGTTTCATCCGACCCGACCCGAAATAATAAAAATTTATTTTTATTTAATAAAAACAATGACTTA
60 AAGTTTCATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTA
*
2266364 ATCCGACCC-AGCCTGAATTATATATATATATTCGGGTCGGTCCGGGTTTTTTCACCCT
125 ATCCGACCCGA-CCCGAATTATATATATATATTCGGGTCGGTCCGGGTTTTTTCACCCT
2266422 AAACCCGAACCCGACCCGACCCGAATAT
1 AAACCCGAACCCGACCCGACCCGAATAT
2266450 ATGAATTAGA
Statistics
Matches: 193, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
179 7 0.04
180 25 0.13
182 5 0.03
185 1 0.01
186 101 0.52
187 1 0.01
188 53 0.27
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.25
Consensus pattern (182 bp):
AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTT
CATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGA
CCCGACCCGAATTATATATATATATTCGGGTCGGTCCGGGTTTTTTCACCCT
Found at i:2266796 original size:2 final size:2
Alignment explanation
Indices: 2266789--2266813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2266779 CCAAAGCCTT
2266789 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 T
2266814 CACTTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2268599 original size:19 final size:20
Alignment explanation
Indices: 2268557--2268609 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 20
2268547 TAAGGAAATA
2268557 TAAATAAATTTTATTATATTG
1 TAAAT-AATTTTATTATATTG
2268578 TAAATAATTTT-TTACT-TTG
1 TAAATAATTTTATTA-TATTG
2268597 TAAATAATTTTAT
1 TAAATAATTTTAT
2268610 CTTAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.57
20 8 0.27
21 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TAAATAATTTTATTATATTG
Found at i:2273227 original size:46 final size:47
Alignment explanation
Indices: 2273167--2273256 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
2273157 CCGAATAAAT
* *
2273167 GCATGCGAACTAGATATCGTGCGGTTAGG-TTTATTTTTTTGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
* *
2273213 GCATGCTAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
2273257 TAACAAAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 26 0.67
47 13 0.33
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:2282909 original size:20 final size:19
Alignment explanation
Indices: 2282877--2282963 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 19
2282867 TAAAGATGAG
2282877 AAAAAGA-AGAAAAGAAGAAA
1 AAAAAGAGA-AAAAGAA-AAA
*
2282897 AAAATGAGAAAAA-AATAAA
1 AAAAAGAGAAAAAGAA-AAA
2282916 AAAAA-AG--AAAGAAAAA
1 AAAAAGAGAAAAAGAAAAA
2282932 TAAAAAGAGAAAAATGAAAAA
1 -AAAAAGAGAAAAA-GAAAAA
2282953 AAAAAGAGAAA
1 AAAAAGAGAAA
2282964 TAAAAGGAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
16 6 0.11
17 7 0.12
18 4 0.07
19 9 0.16
20 24 0.42
21 7 0.12
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAGAGAAAAAGAAAAA
Found at i:2282916 original size:18 final size:18
Alignment explanation
Indices: 2282877--2282968 Score: 80
Period size: 18 Copynumber: 5.1 Consensus size: 18
2282867 TAAAGATGAG
* *
2282877 AAAAAGAAGA-AAAGAAG
1 AAAAAAAAGAGAAAGAAA
*
2282894 AAAAAAATGAGAAA-AAA
1 AAAAAAAAGAGAAAGAAA
*
2282911 ATAAAAAAAAAGAAAGAAA
1 A-AAAAAAAGAGAAAGAAA
* *
2282930 AATAAAAAGAGAAAAATGAA
1 AAAAAAAAGAGAAAGA--AA
*
2282950 AAAAAAAAGAGAAATAAA
1 AAAAAAAAGAGAAAGAAA
2282968 A
1 A
2282969 GGAGGGTTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
17 11 0.18
18 29 0.48
19 4 0.07
20 16 0.27
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAAAAGAGAAAGAAA
Found at i:2282927 original size:36 final size:36
Alignment explanation
Indices: 2282877--2282968 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
2282867 TAAAGATGAG
* *
2282877 AAAAAGAAGAAAAGAAGAAA-AAAATGAGAAAAA-AATA
1 AAAAAAAAG-AAAGAA-AAATAAAAAGAGAAAAATAA-A
2282914 AAAAAAAAGAAAGAAAAATAAAAAGAGAAAAATGAAA
1 AAAAAAAAGAAAGAAAAATAAAAAGAGAAAAAT-AAA
*
2282951 AAAAAAAGAGAAATAAAA
1 AAAAAAA-AGAAAGAAAA
2282969 GGAGGGTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
35 3 0.06
36 18 0.38
37 16 0.33
38 11 0.23
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (36 bp):
AAAAAAAAGAAAGAAAAATAAAAAGAGAAAAATAAA
Found at i:2282934 original size:65 final size:65
Alignment explanation
Indices: 2282823--2282971 Score: 153
Period size: 65 Copynumber: 2.3 Consensus size: 65
2282813 ATTTCGCTTG
* * * * *
2282823 AAGAAGAAATAAAAGGAAAAAAACGAAAAATGAAAAAATAATAATAAAGATGAGAAAAA-GAAGA
1 AAGAAGAAATAAAAGGAAAAAAACGAAAAATAAAAAAAGAAAAATAAA-AAGAGAAAAATGAAAA
2282887 A
65 A
*
2282888 AAGAAGAAA-AAAATGAGAAAAAAA-TAAAAA-AAAAGAAAGAAAAATAAAAAGAGAAAAATGAA
1 AAGAAGAAATAAAA-G-GAAAAAAACGAAAAATAAAA-AAAGAAAAATAAAAAGAGAAAAATG-A
2282950 AAAA
62 AAAA
*
2282954 AAAAGAGAAATAAAAGGA
1 AAGA-AGAAATAAAAGGA
2282972 GGGTTCAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
64 16 0.23
65 27 0.39
66 17 0.24
67 6 0.09
68 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (65 bp):
AAGAAGAAATAAAAGGAAAAAAACGAAAAATAAAAAAAGAAAAATAAAAAGAGAAAAATGAAAAA
Found at i:2282968 original size:14 final size:13
Alignment explanation
Indices: 2282875--2282968 Score: 54
Period size: 12 Copynumber: 7.5 Consensus size: 13
2282865 AATAAAGATG
*
2282875 AGAAAAAGAAGAAA
1 AGAAAAAAAAG-AA
*
2282889 AGAAGAAAAA-AA
1 AGAAAAAAAAGAA
* * *
2282901 TGAGAAAAAA-AT
1 AGAAAAAAAAGAA
2282913 A-AAAAAAAAGAA
1 AGAAAAAAAAGAA
*
2282925 AGAAAAATAA-AA
1 AGAAAAAAAAGAA
* *
2282937 AGAGAAAAATGAA
1 AGAAAAAAAAGAA
2282950 A-AAAAAAAGAGAA
1 AGAAAAAAA-AGAA
*
2282963 ATAAAA
1 AGAAAA
2282969 GGAGGGTTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
11 7 0.12
12 27 0.45
13 14 0.23
14 12 0.20
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:2284336 original size:51 final size:51
Alignment explanation
Indices: 2284276--2284788 Score: 918
Period size: 51 Copynumber: 10.0 Consensus size: 51
2284266 AAGCAAATTC
2284276 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
2284327 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
2284378 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
2284429 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
2284480 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
2284531 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGAAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
2284582 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
2284633 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
2284684 GTTCGTTGAAGATTGAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * * *
2284735 GTTTGTTGAAGATTTTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 GTTCGTTGAAGA----TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
2284789 CGTTTTCCAA
Statistics
Matches: 450, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
51 414 0.92
55 36 0.08
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (51 bp):
GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
Found at i:2284812 original size:55 final size:55
Alignment explanation
Indices: 2284290--2284847 Score: 273
Period size: 51 Copynumber: 10.7 Consensus size: 55
2284280 GTTGAAGATT
* * * * **
2284290 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTTGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * **
2284341 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTTGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * * **
2284392 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * * **
2284443 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * * **
2284494 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * * * **
2284545 GAGTCCTATACTCTCTGAATGAATAGGAAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * * **
2284596 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * * * **
2284647 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
* * * ** * *
2284698 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAGTTTGTTGAAGATTTTTT
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
2284753 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTT-TCCAAGGATTGTTC
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAA-GATTGTTC
* * * * *
2284808 GAGTCTTATACGCCTTGAAAGAAAAGGGAGCAGACCCGTT
1 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTT
2284848 ATTTGAAGAT
Statistics
Matches: 485, Mismatches: 17, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
51 401 0.83
54 5 0.01
55 79 0.16
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (55 bp):
GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTCCAAGATTGTTC
Found at i:2299756 original size:3 final size:3
Alignment explanation
Indices: 2299741--2299874 Score: 133
Period size: 3 Copynumber: 44.7 Consensus size: 3
2299731 ATCCCTTCTT
* * * * *
2299741 TGC TGC AGC TGC TGC TGC GGC TGC TGC TGC TGC TGT TGT TGT TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * * * *
2299789 TGC TGC TGC TGT TGT TGC TGT TGC TGC TGC TGT TGC TGC TGC TGC TGT
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * * * *
2299837 TGT TGT TGC TGC TGC TGC TGA TGT TGT TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
2299875 AGCATGCCTC
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 114 1.00
ACGTcount: A:0.01, C:0.23, G:0.34, T:0.41
Consensus pattern (3 bp):
TGC
Found at i:2299766 original size:21 final size:21
Alignment explanation
Indices: 2299741--2299874 Score: 169
Period size: 21 Copynumber: 6.4 Consensus size: 21
2299731 ATCCCTTCTT
* **
2299741 TGCTGCAGCTGCTGCTGCGGC
1 TGCTGCTGCTGCTGCTGTTGC
* *
2299762 TGCTGCTGCTGCTGTTGTTGT
1 TGCTGCTGCTGCTGCTGTTGC
*
2299783 TGCTGCTGCTGCTGCTGTTGT
1 TGCTGCTGCTGCTGCTGTTGC
*
2299804 TGCTGTTGCTGCTGCTGTTGC
1 TGCTGCTGCTGCTGCTGTTGC
* *
2299825 TGCTGCTGCTGTTGTTGTTGC
1 TGCTGCTGCTGCTGCTGTTGC
* *
2299846 TGCTGCTGCTGATGTTGTTGC
1 TGCTGCTGCTGCTGCTGTTGC
2299867 TGCTGCTG
1 TGCTGCTG
2299875 AGCATGCCTC
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 101 1.00
ACGTcount: A:0.01, C:0.23, G:0.34, T:0.41
Consensus pattern (21 bp):
TGCTGCTGCTGCTGCTGTTGC
Found at i:2307808 original size:20 final size:17
Alignment explanation
Indices: 2307783--2307823 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 17
2307773 AGTTAGGTTT
2307783 TTTTTATAAACATAATAACA
1 TTTTTATAAA-A-AATAA-A
2307803 TTTTTATAAAAAATAAA
1 TTTTTATAAAAAATAAA
2307820 TTTT
1 TTTT
2307824 AAAATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 1 0.05
20 10 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTTATAAAAAATAAA
Found at i:2312784 original size:2 final size:2
Alignment explanation
Indices: 2312763--2312816 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
2312753 TCAATTGGTA
* * *
2312763 AT AT AA AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2312805 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2312817 TGAATAGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2315487 original size:2 final size:2
Alignment explanation
Indices: 2315482--2315507 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2315472 ATTTTTTAAA
2315482 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
2315508 TAATAATTAA
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:2316222 original size:20 final size:20
Alignment explanation
Indices: 2316197--2316261 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
2316187 TACAAAATTG
*
2316197 AAAAGATAAATAGATTTAAT
1 AAAAGATAAATAGGTTTAAT
2316217 AAAAGATAAATAGGTTTAAT
1 AAAAGATAAATAGGTTTAAT
*
2316237 AAAAGATATATAGGTTTAAT
1 AAAAGATAAATAGGTTTAAT
2316257 AAAAG
1 AAAAG
2316262 GGTAAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAAGATAAATAGGTTTAAT
Found at i:2319639 original size:19 final size:19
Alignment explanation
Indices: 2319615--2319676 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
2319605 AACACGGAAA
2319615 TCGGTTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
*
2319634 TCGGTTTTTT---TAACGGT
1 TCGGTTTTTTCGGT-TCGGT
*
2319651 TCGGGTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
2319670 TCGGTTT
1 TCGGTTT
2319677 ATCGGTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.37
19 20 0.57
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.52
Consensus pattern (19 bp):
TCGGTTTTTTCGGTTCGGT
Found at i:2319828 original size:12 final size:12
Alignment explanation
Indices: 2319811--2319835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2319801 TGAAGCCTTT
2319811 AAACCGAACCGA
1 AAACCGAACCGA
2319823 AAACCGAACCGA
1 AAACCGAACCGA
2319835 A
1 A
2319836 CCGTTTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:2324919 original size:2 final size:2
Alignment explanation
Indices: 2324912--2324947 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2324902 TTCAGCCATG
2324912 TA TA TA TA TA TA TA TA -A 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 T
2324948 GAAAATCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2324934 original size:17 final size:17
Alignment explanation
Indices: 2324912--2324944 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2324902 TTCAGCCATG
2324912 TATATATATATATATAA
1 TATATATATATATATAA
2324929 TATATATATATATATA
1 TATATATATATATATA
2324945 TATGAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:2332719 original size:15 final size:16
Alignment explanation
Indices: 2332688--2332720 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2332678 AAAAATTTAT
*
2332688 TTTTATATCTTTTAAA
1 TTTTATATCTTTCAAA
2332704 TTTTATATC-TTCAAA
1 TTTTATATCTTTCAAA
2332719 TT
1 TT
2332721 CATTCATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATATCTTTCAAA
Found at i:2333712 original size:31 final size:31
Alignment explanation
Indices: 2333649--2333712 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2333639 TGGTGACCCA
* * *
2333649 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAATGACCAT
*
2333680 ATCTTAATTAAATAAAAACAAAAATTACCAT
1 ATCTTAATTAAATAAAAACAAAAATGACCAT
2333711 AT
1 AT
2333713 ATTATGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAATGACCAT
Found at i:2347388 original size:73 final size:75
Alignment explanation
Indices: 2347264--2347412 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 75
2347254 AATGCCAAAG
*
2347264 ACAAATGACAGGCATATCTTGCAGCACAGATACACTTGCTACTTACAGGAATAAGTACAAAGCTA
1 ACAAATGACAGGCATATCTTGCAGCACAGATAAACTTGCTACTTACAGGAATAAGTACAAAGCTA
2347329 ATATGAAGAA
66 ATATGAAGAA
* *
2347339 ACAAATGACA-G-ATATCTTGCAGCACAGATAAATTTGCTACTTACCGGAATAAGTACAAAGCTA
1 ACAAATGACAGGCATATCTTGCAGCACAGATAAACTTGCTACTTACAGGAATAAGTACAAAGCTA
2347402 ATATGAAGAA
66 ATATGAAGAA
2347412 A
1 A
2347413 TTATAAGTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 60 0.85
74 1 0.01
75 10 0.14
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (75 bp):
ACAAATGACAGGCATATCTTGCAGCACAGATAAACTTGCTACTTACAGGAATAAGTACAAAGCTA
ATATGAAGAA
Found at i:2351428 original size:17 final size:16
Alignment explanation
Indices: 2351397--2351430 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2351387 CACGTGAGGA
2351397 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2351413 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2351430 T
1 T
2351431 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2357814 original size:19 final size:21
Alignment explanation
Indices: 2357777--2357819 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2357767 TAACTTTTTC
2357777 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
2357797 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
2357817 TTT
1 TTT
2357820 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:2357825 original size:19 final size:20
Alignment explanation
Indices: 2357776--2357825 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2357766 TTAACTTTTT
*
2357776 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
2357796 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
2357815 CTTTTACCTTT
1 CTTTTACCTTT
2357826 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:2361670 original size:17 final size:16
Alignment explanation
Indices: 2361639--2361672 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2361629 CACGTGAGGA
2361639 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2361655 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2361672 T
1 T
2361673 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2367169 original size:21 final size:21
Alignment explanation
Indices: 2367136--2367204 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
2367126 GTCCTCATCC
*
2367136 GAGTAGGACTGACTACC-CTTG
1 GAGTTGGACTGAC-ACCTCTTG
*
2367157 GAGTTGGATTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
2367178 GAGTTGGACTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
*
2367199 AAGTTG
1 GAGTTG
2367205 AACTAAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 3 0.07
21 40 0.93
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
GAGTTGGACTGACACCTCTTG
Found at i:2367291 original size:21 final size:21
Alignment explanation
Indices: 2367262--2367324 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
2367252 GTTCTCATCC
*
2367262 GAGTAGGACTGACTACCT-TTG
1 GAGTTGGACTGAC-ACCTCTTG
2367283 GAGTTGGACTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
2367304 GAGTTGGACTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
2367325 AATTTGAACC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 4 0.10
21 36 0.90
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
GAGTTGGACTGACACCTCTTG
Found at i:2367311 original size:126 final size:126
Alignment explanation
Indices: 2367086--2367356 Score: 425
Period size: 126 Copynumber: 2.2 Consensus size: 126
2367076 CAAAACTGAG
* * *
2367086 AACTGACGTTGAGCTATGGGATTGACTCGATAAGGTGGATGTCCTCATCCGAGTAGGACTGACTA
1 AACTGAAGTTGAGCTATGGAACTGACTCGATAAGGTGGATGTCCTCATCCGAGTAGGACTGACTA
* *
2367151 CCCTTGGAGTTGGATTGACACCTCTTGGAGTTGGACTGACACCTCTTGAAGTTGAACTAAA
66 CCCTTGGAGTTGGACTGACACCTCTTGGAGTTGGACTGACACCTCTTGAAGTTGAACCAAA
* * *
2367212 AACTGAAGTTGAGCTATGGAACTGACTTGATGAGGTGGATGTTCTCATCCGAGTAGGACTGACTA
1 AACTGAAGTTGAGCTATGGAACTGACTCGATAAGGTGGATGTCCTCATCCGAGTAGGACTGACTA
* * * *
2367277 CCTTTGGAGTTGGACTGACACCTCTTGGAGTTGGACTGACACCTCTTGAATTTGAACCGAG
66 CCCTTGGAGTTGGACTGACACCTCTTGGAGTTGGACTGACACCTCTTGAAGTTGAACCAAA
*
2367338 AACTGAAGATGAGCTATGG
1 AACTGAAGTTGAGCTATGG
2367357 GATCGACTAT
Statistics
Matches: 132, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 132 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (126 bp):
AACTGAAGTTGAGCTATGGAACTGACTCGATAAGGTGGATGTCCTCATCCGAGTAGGACTGACTA
CCCTTGGAGTTGGACTGACACCTCTTGGAGTTGGACTGACACCTCTTGAAGTTGAACCAAA
Found at i:2367489 original size:81 final size:81
Alignment explanation
Indices: 2367386--2367549 Score: 222
Period size: 81 Copynumber: 2.0 Consensus size: 81
2367376 TTGATGAGGT
* ** * * *
2367386 GGATGTCCTCATCCGGGTTGGACTAAGTACTCTTGGAGCTGAGCTGAGGACTGAAGTTGAG-CTA
1 GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGCTGAACTGAGAACTGAAGTTGAGAC-A
**
2367450 TGGGATTGACTTGATGA
65 TGGGATTGACAGGATGA
* *
2367467 GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGTTGAACTGAGAATTGAAGTTGAGACAT
1 GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGCTGAACTGAGAACTGAAGTTGAGACAT
2367532 GGGATTGACAGGATGA
66 GGGATTGACAGGATGA
2367548 GG
1 GG
2367550 CGGATATTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 71 0.99
82 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.27
Consensus pattern (81 bp):
GGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGCTGAACTGAGAACTGAAGTTGAGACAT
GGGATTGACAGGATGA
Found at i:2367568 original size:33 final size:34
Alignment explanation
Indices: 2367531--2367615 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 34
2367521 AGTTGAGACA
2367531 TGGGATTGAC-AGGATGAGGCGGATATTGAGCTT
1 TGGGATTGACTAGGATGAGGCGGATATTGAGCTT
* *
2367564 TGGGATTG-CTTGGATGAGGCGGATGTTGAGCTT
1 TGGGATTGACTAGGATGAGGCGGATATTGAGCTT
2367597 TGGGATTGACTA-GATGAGG
1 TGGGATTGACTAGGATGAGG
2367616 TCGATGTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 1 0.02
33 44 0.94
34 2 0.04
ACGTcount: A:0.21, C:0.08, G:0.41, T:0.29
Consensus pattern (34 bp):
TGGGATTGACTAGGATGAGGCGGATATTGAGCTT
Found at i:2367805 original size:33 final size:33
Alignment explanation
Indices: 2367738--2367805 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
2367728 GAGAATTGAA
*
2367738 GTTGAGCTACGGAATTGACTGAATGAGTTAGAT
1 GTTGAGCTACGGAATTGACTGAATGAGGTAGAT
* * * * *
2367771 GTTGAGCTATGGGATTGATTGGATGAGGTGGAT
1 GTTGAGCTACGGAATTGACTGAATGAGGTAGAT
2367804 GT
1 GT
2367806 CCTCATTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.06, G:0.37, T:0.32
Consensus pattern (33 bp):
GTTGAGCTACGGAATTGACTGAATGAGGTAGAT
Found at i:2368040 original size:84 final size:84
Alignment explanation
Indices: 2367899--2368065 Score: 280
Period size: 84 Copynumber: 2.0 Consensus size: 84
2367889 TCCCACTCGT
* * * * *
2367899 AGTTGGACTGAGAACTGGAGTTGAGCTATGGGATTGACTTGATGAGGTGGATGTCCTCATCCGAG
1 AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
2367964 TTGGACTGACTACCCTTGG
66 TTGGACTGACTACCCTTGG
2367983 AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
1 AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
*
2368048 TTGGACTGACTCCCCTTG
66 TTGGACTGACTACCCTTG
2368066 AAGTATGATT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (84 bp):
AGTTGGACTGAGAACCGGAGTCGAGCTATGAGATTGACTTGATGAGGTAGAAGTCCTCATCCGAG
TTGGACTGACTACCCTTGG
Found at i:2368050 original size:147 final size:147
Alignment explanation
Indices: 2367771--2368056 Score: 366
Period size: 147 Copynumber: 1.9 Consensus size: 147
2367761 TGAGTTAGAT
* *
2367771 GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATTCGAGTTGGGCTGACAACCCTTGC
1 GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTGC
* * * * * * *
2367836 AGTTGAATTGATAACTGATGTTGAGCTATAGGATAGACTCGATGTGGTGGATGTCCCACTCGTAG
66 AGTTGAACTGAGAACGGATGTCGAGCTATAGGATAGACTCGATGAGGTAGAAGTCCCACTCGTAG
2367901 TTGGACTGAGAACTGGA
131 TTGGACTGAGAACTGGA
*
2367918 GTTGAGCTATGGGATTGACTT-GATGAGGTGGATGTCCTCATCCGAGTTGGACTGACTACCCTTG
1 GTTGAGCTATGGGATTGA-TTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTG
* * * *
2367982 GAGTTGGACTGAGAACCGGA-GTCGAGCTAT-GAGATTGACTTGATGAGGTAGAAGTCCTCA-TC
65 CAGTTGAACTGAGAA-CGGATGTCGAGCTATAG-GATAGACTCGATGAGGTAGAAGTCC-CACT-
2368044 CG-AGTTGGACTGA
126 CGTAGTTGGACTGA
2368057 CTCCCCTTGA
Statistics
Matches: 120, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
146 1 0.01
147 110 0.92
148 9 0.08
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (147 bp):
GTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTGC
AGTTGAACTGAGAACGGATGTCGAGCTATAGGATAGACTCGATGAGGTAGAAGTCCCACTCGTAG
TTGGACTGAGAACTGGA
Found at i:2368093 original size:42 final size:42
Alignment explanation
Indices: 2368047--2368184 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 42
2368037 CCTCATCCGA
*
2368047 GTTGGACTGACTCCCCTTGAAGTATGATTGGCTCCTCTTGCG
1 GTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCG
* ** * *
2368089 GTTGGAGTTGGACT--GATTGAAGTATGACTGGATCCTCTTACTGTTGG
1 GTTGGA-CT-GACTCCCCTTGAAGTATGACTGGCTCCTC-T--TG--CG
*
2368136 AGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCA
1 -GTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCG
2368179 GTTGGA
1 GTTGGA
2368185 GTGGAAGGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
42 31 0.42
43 2 0.03
44 4 0.05
45 4 0.05
46 4 0.05
47 3 0.04
48 26 0.35
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.33
Consensus pattern (42 bp):
GTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCG
Found at i:2368102 original size:48 final size:48
Alignment explanation
Indices: 2368045--2368186 Score: 197
Period size: 48 Copynumber: 3.1 Consensus size: 48
2368035 GTCCTCATCC
* *
2368045 GAGTTGGACTGACTCCCCTTGAAGTATGATTGGCTCCTCTTGCGGTTG
1 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
* * *
2368093 GAGTTGGACTGA------TTGAAGTATGACTGGATCCTCTTACTGTTG
1 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
2368135 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
1 GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
2368183 GAGT
1 GAGT
2368187 GGAAGGTCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
42 38 0.47
48 43 0.53
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (48 bp):
GAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTG
Found at i:2371237 original size:45 final size:45
Alignment explanation
Indices: 2371173--2371267 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
2371163 TACTTCATAC
*
2371173 AAAAATAAATATTTAAATTATATATTCAATTAATTTATGATGTCT
1 AAAAATAAATATTTAAATTATATATTAAATTAATTTATGATGTCT
* * * *
2371218 AAAAATATATATTTAAATTATATCTTAAATTAATTTTTGATGTTT
1 AAAAATAAATATTTAAATTATATATTAAATTAATTTATGATGTCT
2371263 AAAAA
1 AAAAA
2371268 GTTTTTCCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (45 bp):
AAAAATAAATATTTAAATTATATATTAAATTAATTTATGATGTCT
Found at i:2373264 original size:12 final size:11
Alignment explanation
Indices: 2373241--2373274 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2373231 ATCGGATGGA
*
2373241 CTCGAATCGAG
1 CTCGACTCGAG
2373252 CTCGAGCTCGAG
1 CTCGA-CTCGAG
2373264 CTCGACTCGAG
1 CTCGACTCGAG
2373275 TTCTTAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (11 bp):
CTCGACTCGAG
Found at i:2373556 original size:31 final size:29
Alignment explanation
Indices: 2373521--2373610 Score: 76
Period size: 31 Copynumber: 3.0 Consensus size: 29
2373511 GCTGTTCATG
* *
2373521 AGCTTCAGTTCAGAATTTCGAGTTCGAGTCT
1 AGCTTCAATTCAG-ATTTCGAG-TCGAGTCA
*
2373552 AGCTTAAAATT-AG-TGTTCGAGTCGAGTCA
1 AGCTT-CAATTCAGAT-TTCGAGTCGAGTCA
*
2373581 AGCTTCATTTCAGAGTTTTCGAGTCGAGTC
1 AGCTTCAATTCAGA--TTTCGAGTCGAGTC
2373611 GAACTCAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.06
29 15 0.31
30 6 0.12
31 20 0.42
32 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (29 bp):
AGCTTCAATTCAGATTTCGAGTCGAGTCA
Found at i:2386316 original size:126 final size:124
Alignment explanation
Indices: 2386068--2386296 Score: 307
Period size: 126 Copynumber: 1.8 Consensus size: 124
2386058 AGTAGAAACT
2386068 ATAAAAGAGCATCTCAGTTTTACTAGCTGAGTGAGAATATAGTGTTGAATTGAACTCAGTTGCAC
1 ATAAAAGAGCATCTCAGTTTTACTAGCTGAGTGAGAATATAGTGTTGAATTGAACTCAGTTGCAC
* * * **
2386133 AATATGATGCGTGTAGCTTATTCAATGGTGATGGGGAACATTGTAGACTGTAGTTGTATC
66 AATATGACGCATGCAGCTTATTCAATGGTGATAAGGAACATTGTAGACTGTA-TTGTATC
* * * * **
2386193 ATAAACGAGGATCTCAAG-TTTACTAGCTTATTGAGAATATAGTGTTGAATTCGAGTTCAGTTGC
1 ATAAAAGAGCATCTC-AGTTTTACTAGCTGAGTGAGAATATAGTGTTGAATT-GAACTCAGTTGC
* *
2386257 ACAATATGACGCATGCAGCTTGTTCAATGGTGGTAAGGAA
64 ACAATATGACGCATGCAGCTTATTCAATGGTGATAAGGAA
2386297 TAGCTTAGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
125 44 0.49
126 45 0.51
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (124 bp):
ATAAAAGAGCATCTCAGTTTTACTAGCTGAGTGAGAATATAGTGTTGAATTGAACTCAGTTGCAC
AATATGACGCATGCAGCTTATTCAATGGTGATAAGGAACATTGTAGACTGTATTGTATC
Found at i:2388283 original size:29 final size:31
Alignment explanation
Indices: 2388250--2388328 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
2388240 ATCATAAGTG
*
2388250 TTAATGTGATATTATCATATGT-T-TAAATC
1 TTAATGTGATATTATCATATGTATATAAATA
* * *
2388279 TTAATATGATATTTTCAAATGTATATAAATA
1 TTAATGTGATATTATCATATGTATATAAATA
* *
2388310 TTAACGTGACATATATCAT
1 TTAATGTGATAT-TATCAT
2388329 TGCGTGTTCC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 19 0.50
30 1 0.03
31 14 0.37
32 4 0.11
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (31 bp):
TTAATGTGATATTATCATATGTATATAAATA
Found at i:2394486 original size:60 final size:60
Alignment explanation
Indices: 2394399--2394511 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
2394389 TTTAGGGATC
* * * * * *
2394399 AATTTAGAATGAGAATCATAATTTGAGGATG-AATGTGGAATGTTTAAAAGTTTGGACACA
1 AATTTAGAATCAGAATCACAATGTGAGGAGGAAAT-TAGAATGTTCAAAAGTTTGGACACA
* *
2394459 AATTTAGAATCAGAGTCGCAATGTGAGGAGGAAATTAGAATGTTCAAAAGTTT
1 AATTTAGAATCAGAATCACAATGTGAGGAGGAAATTAGAATGTTCAAAAGTTT
2394512 AAGGACCAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 41 0.93
61 3 0.07
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (60 bp):
AATTTAGAATCAGAATCACAATGTGAGGAGGAAATTAGAATGTTCAAAAGTTTGGACACA
Found at i:2394873 original size:38 final size:37
Alignment explanation
Indices: 2394812--2394889 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 37
2394802 AACTTAACGT
2394812 TAAATTTTAAACCAGATACTAAAATGAAACAAAAA-C
1 TAAATTTTAAACCAGATACTAAAATGAAACAAAAAGC
* *
2394848 TAAATTTTTAACGACGAGTACTAAAATGAAACAAAAAGC
1 TAAATTTTAAACCA-GA-TACTAAAATGAAACAAAAAGC
2394887 TAA
1 TAA
2394890 CCTTTAGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 12 0.32
37 2 0.05
38 19 0.51
39 4 0.11
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.23
Consensus pattern (37 bp):
TAAATTTTAAACCAGATACTAAAATGAAACAAAAAGC
Found at i:2395218 original size:2 final size:2
Alignment explanation
Indices: 2395211--2395236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2395201 ATCCACCTGC
2395211 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
2395237 GTCATCCCAC
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:2397427 original size:112 final size:112
Alignment explanation
Indices: 2397230--2397453 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
2397220 AAAAATGCAT
*
2397230 CCATGAATCATGATCCAAATTACGTAAAAGACGAGTTGTTATTTTTACGTAAAAAATGCAGTCTT
1 CCATGAATCAAGATCCAAATTACGTAAAAGACGAGTTGTTATTTTTACGTAAAAAATGCAGTCTT
*
2397295 CTAGACAGAAACCTATGCAACCATGAACTCTTCTATCTTATAAATGA
66 CTAGACAGAAACCTACGCAACCATGAACTCTTCTATCTTATAAATGA
*
2397342 CCATGAATCAAGATCCAAATTACGTAAAAGATGAGTTGTTATTTTTACGTAAAAAATGCAGTCTT
1 CCATGAATCAAGATCCAAATTACGTAAAAGACGAGTTGTTATTTTTACGTAAAAAATGCAGTCTT
2397407 CTAGACAGAAACCTACGCAACCATGAACTCTTCTATCTTATAAATGA
66 CTAGACAGAAACCTACGCAACCATGAACTCTTCTATCTTATAAATGA
2397454 TAAATTATTT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (112 bp):
CCATGAATCAAGATCCAAATTACGTAAAAGACGAGTTGTTATTTTTACGTAAAAAATGCAGTCTT
CTAGACAGAAACCTACGCAACCATGAACTCTTCTATCTTATAAATGA
Found at i:2410555 original size:23 final size:23
Alignment explanation
Indices: 2410529--2410572 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2410519 CACCACAGCT
*
2410529 CGTATAATTGCACCGAAGTGCTG
1 CGTAGAATTGCACCGAAGTGCTG
*
2410552 CGTAGAATTGCACCGTAGTGC
1 CGTAGAATTGCACCGAAGTGC
2410573 CTATAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCTG
Found at i:2412275 original size:21 final size:21
Alignment explanation
Indices: 2412251--2412295 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2412241 TGTTGTTCGT
* *
2412251 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2412272 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2412293 TTG
1 TTG
2412296 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2413953 original size:29 final size:29
Alignment explanation
Indices: 2413919--2413990 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2413909 CATATTATGA
**
2413919 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
2413948 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2413977 TACATGACATGAAT
1 TACATGACATGAAT
2413991 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:2414060 original size:29 final size:28
Alignment explanation
Indices: 2414006--2414060 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2413996 GAAAAGTTAT
*
2414006 ATGCCTATGTGATAAGGTATGTAAATGA
1 ATGCCTATGTGATAAGGTATGGAAATGA
*
2414034 ATGCCTATGTGTTAAAGGTATGGAAAT
1 ATGCCTATGTGAT-AAGGTATGGAAAT
2414061 ACTATGTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (28 bp):
ATGCCTATGTGATAAGGTATGGAAATGA
Found at i:2414304 original size:22 final size:22
Alignment explanation
Indices: 2414277--2414318 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2414267 ATGGACATAA
2414277 TCTACGGGCACTTCGGTGCAAT
1 TCTACGGGCACTTCGGTGCAAT
2414299 TCTACGGGCACTTCGGTGCA
1 TCTACGGGCACTTCGGTGCA
2414319 TTTATACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.26
Consensus pattern (22 bp):
TCTACGGGCACTTCGGTGCAAT
Found at i:2414326 original size:22 final size:22
Alignment explanation
Indices: 2414279--2414326 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2414269 GGACATAATC
*
2414279 TACGGGCACTTCGGTGCAATTC
1 TACGGGCACTTCGGTGCAATTA
*
2414301 TACGGGCACTTCGGTGCATTTA
1 TACGGGCACTTCGGTGCAATTA
2414323 TACG
1 TACG
2414327 AGCTGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (22 bp):
TACGGGCACTTCGGTGCAATTA
Found at i:2420155 original size:22 final size:22
Alignment explanation
Indices: 2420110--2420155 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2420100 ATAAGTCTAG
* * *
2420110 ATTCCATATTTTGATATATTAC
1 ATTCCATATTATGATACATGAC
2420132 ATTCCATATTATGATACATGAC
1 ATTCCATATTATGATACATGAC
2420154 AT
1 AT
2420156 GAATTTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (22 bp):
ATTCCATATTATGATACATGAC
Found at i:2420205 original size:25 final size:25
Alignment explanation
Indices: 2420136--2420210 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
2420126 TATTACATTC
*
2420136 CATATTATGATACATGACATGAATT
1 CATATTATGTTACATGACATGAATT
** *
2420161 TGTA-AATGTATTACATGACATGAATT
1 CATATTATG--TTACATGACATGAATT
2420187 CATATTATGTTACATGACATGAAT
1 CATATTATGTTACATGACATGAAT
2420211 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
24 3 0.08
25 17 0.43
26 17 0.43
27 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (25 bp):
CATATTATGTTACATGACATGAATT
Found at i:2420267 original size:30 final size:31
Alignment explanation
Indices: 2420225--2420284 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2420215 AGAAAAAGTT
*
2420225 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
2420256 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
2420285 ACTCTACGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:2420568 original size:22 final size:22
Alignment explanation
Indices: 2420495--2420560 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
2420485 TTATGGACAT
2420495 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2420517 AATTCTACGGGCACTTC-GTGC
1 AATTCTACGGGCACTTCGGTGC
2420538 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2420560 A
1 A
2420561 TTTATACGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.49
22 22 0.51
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2431854 original size:2 final size:2
Alignment explanation
Indices: 2431847--2431871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2431837 AAATAATAAA
2431847 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2431872 AATAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2433311 original size:20 final size:20
Alignment explanation
Indices: 2433288--2433329 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2433278 GAATCCTTCG
2433288 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
*
2433308 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
2433328 TC
1 TC
2433330 AGAGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:2433587 original size:193 final size:195
Alignment explanation
Indices: 2433374--2433995 Score: 933
Period size: 208 Copynumber: 3.1 Consensus size: 195
2433364 GCCAAAGATA
* *
2433374 CTTCGTTGTGAAGCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
2433439 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
** *** *
2433504 -AA-GTTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATC
131 AAATGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* *
2433567 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTAAAGT
1 CTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
2433632 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAG
66 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
2433697 AAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
131 AAA----TGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
2433762 TATC
192 TATC
*
2433766 CTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGATGTTTGTTGACAACCAGCGGTCCCTTCG
1 CTTCATTGTGAAGTTGAAATTGG----GAAA-T----TGTTTATTGACAACCAGCGGTCCCTTCG
*
2433831 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
57 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
* *
2433896 GAAATTGGGAAATGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
122 GAAATTGAGAAATG----TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
2433961 GGAGTCCAATATC
183 GGAGTCCAATATC
2433974 CTTCATTGTGAAGTTGAAATTG
1 CTTCATTGTGAAGTTGAAATTG
2433996 ACTCTGGGTA
Statistics
Matches: 392, Mismatches: 18, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
193 127 0.32
194 2 0.01
199 76 0.19
203 4 0.01
204 3 0.01
208 180 0.46
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (195 bp):
CTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
AAATGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
Found at i:2433801 original size:105 final size:105
Alignment explanation
Indices: 2433581--2434001 Score: 711
Period size: 105 Copynumber: 4.0 Consensus size: 105
2433571 GTTGTGAAGT
* *
2433581 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
2433646 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
* * *
2433687 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
2433752 TGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
*
2433792 TGAAATTGAG--ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
**
2433855 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
* *
2433895 TGAAATTGGGAAATGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
2433960 TGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTC
66 TGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
2434000 TG
1 TG
2434002 GGTAAAACCT
Statistics
Matches: 297, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
103 99 0.33
105 187 0.63
106 11 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
Found at i:2445704 original size:2 final size:2
Alignment explanation
Indices: 2445697--2445735 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2445687 AAATAATAAA
*
2445697 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2445736 AATAAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2450631 original size:60 final size:61
Alignment explanation
Indices: 2450567--2450704 Score: 185
Period size: 60 Copynumber: 2.3 Consensus size: 61
2450557 AATGTTGAAA
*
2450567 AGAAAATCGCAACGGTC-A-AAAGAAAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGG-CGATAAAGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
** * * *
2450627 AGAAAATCGCAAC-GCGATTGAGAAAATCGCAACGCGATTCCAGGAATCGCAATGCGATTG
1 AGAAAATCGCAACGGCGATAAAGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
2450687 AGAAAATCGCAAC-GCGAT
1 AGAAAATCGCAACGGCGAT
2450705 TCCAAGAATC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
58 1 0.01
59 2 0.03
60 67 0.96
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (61 bp):
AGAAAATCGCAACGGCGATAAAGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
Found at i:2450705 original size:60 final size:60
Alignment explanation
Indices: 2450587--2450705 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
2450577 AACGGTCAAA
*
2450587 AGAAAATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAAAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTGAGAAAATCGCAACGCGATTG
* * *
2450647 AGAAAATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAAAATCGCAACGCGATT
1 AGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTGAGAAAATCGCAACGCGATT
2450706 CCAAGAATCG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17
Consensus pattern (60 bp):
AGAAAATCGCAACGCGATTCAAAGAATCGCAACGCGATTGAGAAAATCGCAACGCGATTG
Found at i:2450706 original size:40 final size:40
Alignment explanation
Indices: 2450591--2450718 Score: 179
Period size: 40 Copynumber: 3.2 Consensus size: 40
2450581 GTCAAAAGAA
* * *
2450591 AATCGCAATGCGATTCA-AAGAATCGCAACGCGATT-GAGAA
1 AATCGCAATGCGATTGAGAA-AATCGCAACGCGATTCCAG-G
*
2450631 AATCGCAACGCGATTGAGAAAATCGCAACGCGATTCCAGG
1 AATCGCAATGCGATTGAGAAAATCGCAACGCGATTCCAGG
*
2450671 AATCGCAATGCGATTGAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAATGCGATTGAGAAAATCGCAACGCGATTCCAGG
2450711 AATCGCAA
1 AATCGCAA
2450719 AACGGCAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 76 0.95
41 4 0.05
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAAAATCGCAACGCGATTCCAGG
Found at i:2450718 original size:20 final size:20
Alignment explanation
Indices: 2450529--2450705 Score: 166
Period size: 20 Copynumber: 8.8 Consensus size: 20
2450519 ATGCGAAACA
*
2450529 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
* * **
2450549 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTGAG
**
2450569 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
* *
2450589 AAAATCGCAATGCGATTCA-
1 AAAATCGCAACGCGATTGAG
2450608 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTGAG
2450629 AAAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTGAG
*
2450649 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-GAG
* *
2450670 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
2450689 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
2450706 CCAAGAATCG
Statistics
Matches: 131, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 118 0.90
21 7 0.05
22 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:2450722 original size:22 final size:20
Alignment explanation
Indices: 2450591--2450718 Score: 118
Period size: 20 Copynumber: 6.4 Consensus size: 20
2450581 GTCAAAAGAA
* *
2450591 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
2450611 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
* *
2450631 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
2450651 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
2450671 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
2450691 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
2450711 AATCGCAA
1 AATCGCAA
2450719 AACGGCAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 87 0.96
21 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:2451319 original size:6 final size:6
Alignment explanation
Indices: 2451310--2451358 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
2451300 CGCCGCCGTC
2451310 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
2451358 T
1 T
2451359 AATATGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2454094 original size:20 final size:20
Alignment explanation
Indices: 2454069--2454237 Score: 79
Period size: 20 Copynumber: 8.4 Consensus size: 20
2454059 GATTTTCCAG
2454069 AATCGCAACGAGAATATGAA
1 AATCGCAACGAGAATATGAA
* *
2454089 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGAGAATATGA-A
* * * * *
2454109 AATCGTAACGCGATTCTGAC
1 AATCGCAACGAGAATATGAA
* * * * **
2454129 TATTGCAACTAGTATCCGTAA
1 AATCGCAACGAGAATATG-AA
* * * ** *
2454150 AATCTCAACGCGTATCCGTA
1 AATCGCAACGAGAATATGAA
* *
2454170 AATCGCAACGAGAATACGTA
1 AATCGCAACGAGAATATGAA
* * * *
2454190 AATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATATGAA
*
2454210 AATCGCAACGAGAATATGTA
1 AATCGCAACGAGAATATGAA
2454230 AATCGCAA
1 AATCGCAA
2454238 TACGTATCCG
Statistics
Matches: 113, Mismatches: 33, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
19 1 0.01
20 97 0.86
21 15 0.13
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGAGAATATGAA
Found at i:2454202 original size:40 final size:40
Alignment explanation
Indices: 2454149--2454300 Score: 232
Period size: 40 Copynumber: 3.8 Consensus size: 40
2454139 AGTATCCGTA
*
2454149 AAATCTCAACGCGTATCCGTAAATCGCAACGAGAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
* *
2454189 AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATATGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
** *
2454229 AAATCGCAATACGTATCCGTAAATCGCAACGACAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
*
2454269 AAAATCGCAACGCGTATCCGTAAATCGTAACG
1 -AAATCGCAACGCGTATCCGTAAATCGCAACG
2454301 CGATTTTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 72 0.72
41 28 0.28
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
Found at i:2454245 original size:101 final size:101
Alignment explanation
Indices: 2454069--2454303 Score: 237
Period size: 101 Copynumber: 2.3 Consensus size: 101
2454059 GATTTTCCAG
* * * * * * * *
2454069 AATCGCAACGAGAATATGAAAATCGCAACGCGAACATATAAATCGTAACGCGATTCTGACTATTG
1 AATCGCAACGAGAATACGTAAATCGCAACGCGAACATATAAATCGCAACGAGAATATGACAATCG
* * *
2454134 CAACTAGTATCCGTAAAATCTCAACG-CGTATCCGT-A
66 CAACTAGTATCCGT-AAATCGCAACGAC-AATACGTAA
* *
2454170 AATCGCAACGAGAATACGTAAATCGCAACGCGTATC-TGTAAATCGCAACGAGAATATGTA-AAT
1 AATCGCAACGAGAATACGTAAATCGCAACGCG-AACATATAAATCGCAACGAGAATATG-ACAAT
2454233 CGCAA-TACGTATCCGTAAATCGCAACGACAATACGTAA
64 CGCAACTA-GTATCCGTAAATCGCAACGACAATACGTAA
* * * *
2454271 AATCGCAACGCGTATCCGTAAATCGTAACGCGA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGA
2454304 TTTTTAAAGC
Statistics
Matches: 112, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
100 18 0.16
101 91 0.81
102 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (101 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGAACATATAAATCGCAACGAGAATATGACAATCG
CAACTAGTATCCGTAAATCGCAACGACAATACGTAA
Found at i:2454300 original size:20 final size:20
Alignment explanation
Indices: 2454140--2454302 Score: 166
Period size: 20 Copynumber: 8.1 Consensus size: 20
2454130 ATTGCAACTA
*
2454140 GTATCCGTAAAATCTCAACGC
1 GTATCCGT-AAATCGCAACGC
*
2454161 GTATCCGTAAATCGCAACGA
1 GTATCCGTAAATCGCAACGC
* *
2454181 GAATACGTAAATCGCAACGC
1 GTATCCGTAAATCGCAACGC
* *
2454201 GTATCTGTAAATCGCAACGA
1 GTATCCGTAAATCGCAACGC
* ** **
2454221 GAATATGTAAATCGCAATAC
1 GTATCCGTAAATCGCAACGC
2454241 GTATCCGTAAATCGCAACGAC
1 GTATCCGTAAATCGCAACG-C
* *
2454262 -AATACGTAAAATCGCAACGC
1 GTATCCGT-AAATCGCAACGC
*
2454282 GTATCCGTAAATCGTAACGC
1 GTATCCGTAAATCGCAACGC
2454302 G
1 G
2454303 ATTTTTAAAG
Statistics
Matches: 115, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
20 90 0.78
21 25 0.22
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
GTATCCGTAAATCGCAACGC
Found at i:2454899 original size:33 final size:33
Alignment explanation
Indices: 2454841--2454933 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
2454831 CTAAACTTAA
**
2454841 AATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AATCGCAACACG-AAATGAAAATCGCAACGAGAG
*
2454875 AATCGCAACACGAAATGAAAATCGCAACGAGAT
1 AATCGCAACACGAAATGAAAATCGCAACGAGAG
* **
2454908 AATCGCAACTCGAAACCAAAATCGCA
1 AATCGCAACACGAAATGAAAATCGCA
2454934 TTGTGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.77
34 12 0.23
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.12
Consensus pattern (33 bp):
AATCGCAACACGAAATGAAAATCGCAACGAGAG
Found at i:2454982 original size:33 final size:33
Alignment explanation
Indices: 2454938--2455039 Score: 159
Period size: 33 Copynumber: 3.1 Consensus size: 33
2454928 ATCGCATTGT
*
2454938 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
*
2454971 GATTTTAATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
* * *
2455004 GATTTTCATTTCGTGTTGCGATTCTTTCGCTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
2455037 GAT
1 GAT
2455040 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:2455023 original size:19 final size:18
Alignment explanation
Indices: 2454938--2455026 Score: 59
Period size: 19 Copynumber: 5.2 Consensus size: 18
2454928 ATCGCATTGT
*
2454938 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCG-GTTGC
*
2454957 GA--TTC-TCTC-GTTGC
1 GATTTTCATTTCGGTTGC
*
2454971 GATTTTAATTTCGCGTTGC
1 GATTTTCATTTCG-GTTGC
*
2454990 GA--TTC-TCTC-GTTGC
1 GATTTTCATTTCGGTTGC
2455004 GATTTTCATTTCGTGTTGC
1 GATTTTCATTTCG-GTTGC
2455023 GATT
1 GATT
2455027 CTTTCGCTGC
Statistics
Matches: 53, Mismatches: 7, Indels: 20
0.66 0.09 0.25
Matches are distributed among these distances:
14 13 0.25
16 11 0.21
17 11 0.21
19 18 0.34
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (18 bp):
GATTTTCATTTCGGTTGC
Found at i:2455047 original size:33 final size:33
Alignment explanation
Indices: 2454944--2455059 Score: 106
Period size: 33 Copynumber: 3.5 Consensus size: 33
2454934 TTGTGATTTT
* * ***
2454944 CATTTCGCATTGCGATTCTCTCGTTGCGATTTT
1 CATTTCGCGTTGCGATTCTCTCGCTGCGATAGC
* * ***
2454977 AATTTCGCGTTGCGATTCTCTCGTTGCGATTTT
1 CATTTCGCGTTGCGATTCTCTCGCTGCGATAGC
* *
2455010 CATTTCGTGTTGCGATTCTTTCGCTGCGATAGC
1 CATTTCGCGTTGCGATTCTCTCGCTGCGATAGC
*
2455043 CATTTCCGCATTGCGAT
1 CATTT-CGCGTTGCGAT
2455060 AGTCATTCTC
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 62 0.87
34 9 0.13
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
CATTTCGCGTTGCGATTCTCTCGCTGCGATAGC
Found at i:2455048 original size:66 final size:69
Alignment explanation
Indices: 2454938--2455088 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 69
2454928 ATCGCATTGT
* *** *
2454938 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTT-CGCGTTGC-G-ATTCTCTCG
1 GATTTTCATTTCGCATTGCGATTCTCTCGCTGCGATAGCAATTTCCGCATTGCAGCATTCTCTCG
2455000 TTGC
66 TTGC
** * *
2455004 GATTTTCATTTCGTGTTGCGATTCTTTCGCTGCGATAGCCATTTCCGCATTGCGATAGTCATTCT
1 GATTTTCATTTCGCATTGCGATTCTCTCGCTGCGATAGCAATTTCCGCATTGC---AG-CATTCT
2455069 CTCGTTGC
62 CTCGTTGC
2455077 GATTTTCATTTC
1 GATTTTCATTTC
2455089 AACCAAAAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
66 36 0.52
67 7 0.10
71 1 0.01
73 25 0.36
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (69 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGCTGCGATAGCAATTTCCGCATTGCAGCATTCTCTCG
TTGC
Found at i:2457179 original size:94 final size:94
Alignment explanation
Indices: 2456777--2457156 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
2456767 TAGATTACTT
* * *
2456777 AGTAAATTTATTCGGTTGCTGCTAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2456842 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
2456871 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2456936 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
2456965 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGACGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2457030 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
2457059 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2457124 AATTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2457152 AGTAA
1 AGTAA
2457157 TGTAATCCAT
Statistics
Matches: 271, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 245 0.90
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2457266 original size:17 final size:17
Alignment explanation
Indices: 2457244--2457289 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 17
2457234 AAAAATGACT
2457244 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
2457261 ATCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
*
2457275 ATCGCAACGAGAAAT
1 ATCGCAACGCGAAAT
2457290 TAAAATCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
16 3 0.13
17 7 0.30
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:2457278 original size:14 final size:14
Alignment explanation
Indices: 2457259--2457286 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2457249 AACGCGAAAT
2457259 GAATCGCAACGAGA
1 GAATCGCAACGAGA
2457273 GAATCGCAACGAGA
1 GAATCGCAACGAGA
2457287 AATTAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.29, T:0.07
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:2457282 original size:31 final size:33
Alignment explanation
Indices: 2457244--2457317 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
2457234 AAAAATGACT
* *
2457244 ATCGCAACGCGAAA-T-GAATCGCAACGAGAGA
1 ATCGCAACGAGAAATTAAAATCGCAACGAGAGA
2457275 ATCGCAACGAGAAATTAAAATCGCAACGAGAGA
1 ATCGCAACGAGAAATTAAAATCGCAACGAGAGA
2457308 ATTC-CAACGA
1 A-TCGCAACGA
2457318 CAAAATCGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 13 0.34
32 1 0.03
33 22 0.58
34 2 0.05
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAAATTAAAATCGCAACGAGAGA
Found at i:2457420 original size:20 final size:20
Alignment explanation
Indices: 2457380--2457466 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
2457370 AATTCTCTCG
* **
2457380 TTGCGATAATCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
2457400 TCGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
2457420 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2457440 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2457460 TTGCGAT
1 TTGCGAT
2457467 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2457991 original size:18 final size:19
Alignment explanation
Indices: 2457952--2457993 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2457942 ATCACCTGTC
2457952 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2457973 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2457991 ATC
1 ATC
2457994 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:2459430 original size:14 final size:14
Alignment explanation
Indices: 2459411--2459446 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2459401 ATTGTTTAAT
2459411 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2459425 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2459439 TGATTTGT
1 TGATTTGT
2459447 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2459609 original size:33 final size:34
Alignment explanation
Indices: 2459548--2459611 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
2459538 AAAACAGACT
** *
2459548 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCACAACGAGAGA
*
2459582 ATCGCAATGC-GAAATGAAAATCACAACGAG
1 ATCGCAACGCGGAAATGAAAATCACAACGAG
2459612 TTCGCGTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 17 0.65
34 9 0.35
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCACAACGAGAGA
Found at i:2459676 original size:19 final size:19
Alignment explanation
Indices: 2459612--2459697 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
2459602 TCACAACGAG
* *
2459612 TTCGCGTTGGGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
2459632 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
2459648 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2459665 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2459684 TTCGCATTGCGATT
1 TTCGCATTGCGATT
2459698 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 3 0.05
18 4 0.07
19 27 0.47
20 10 0.18
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:2459698 original size:52 final size:53
Alignment explanation
Indices: 2459612--2459730 Score: 168
Period size: 52 Copynumber: 2.2 Consensus size: 53
2459602 TCACAACGAG
* * **
2459612 TTCGCGTTGGGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCAATAGTCAT
* *
2459665 TTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCAATAGTCAT
1 TTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCAATAGTCAT
2459717 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2459731 AGTCAATTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 32 0.55
53 26 0.45
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (53 bp):
TTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCAATAGTCAT
Found at i:2459727 original size:20 final size:20
Alignment explanation
Indices: 2459702--2459790 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
2459692 GCGATTCTCT
*
2459702 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
2459722 CGTTGCGATAGTCAATTCTA
1 CGTTGCGATAGTCATTTCCG
*
2459742 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
2459762 TGTTGTGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
2459782 CGTTGCGAT
1 CGTTGCGAT
2459791 TTCCGCGTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 53 0.96
21 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2459753 original size:40 final size:41
Alignment explanation
Indices: 2459704--2459780 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
2459694 GATTCTCTCG
2459704 TTGCAATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTACA
1 TTGCAATAGTCATTTCCGCGTTGCGATAGTCATATTCTACA
* * *
2459744 TTGCGATAGTCATTTCCGTGTTGTGATAGTCATATTC
1 TTGCAATAGTCATTTCCGCGTTGCGATAGTCATATTC
2459781 GCGTTGCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (41 bp):
TTGCAATAGTCATTTCCGCGTTGCGATAGTCATATTCTACA
Found at i:2459788 original size:40 final size:40
Alignment explanation
Indices: 2459702--2459790 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
2459692 GCGATTCTCT
*
2459702 CGTTGCAATAGTCATTTCCGCGTTGCGATAGTCAATTCTA
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATTCTA
* * * *
2459742 CATTGCGATAGTCATTTCCGTGTTGTGATAGTCATATTC-G
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTA
2459782 CGTTGCGAT
1 CGTTGCGAT
2459791 TTCCGCGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATTCTA
Found at i:2462258 original size:24 final size:24
Alignment explanation
Indices: 2462224--2462277 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2462214 CTGAAAAATC
2462224 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2462248 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2462272 ATCAAA
1 ATCAAA
2462278 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2462291 original size:24 final size:24
Alignment explanation
Indices: 2462224--2462291 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2462214 CTGAAAAATC
* * *
2462224 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2462248 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2462272 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2462292 TAGTACTCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2463152 original size:20 final size:20
Alignment explanation
Indices: 2463129--2463260 Score: 106
Period size: 20 Copynumber: 6.6 Consensus size: 20
2463119 TTGCGATAGT
* *
2463129 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
2463149 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
2463169 TAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
2463189 C-GTATTCGCATTGCAATTTA
1 CAG-AATCGCATTGCGATTTA
* **
2463209 CATAATCGCATTATGATTTA
1 CAGAATCGCATTGCGATTTA
* *
2463229 C-GTAATCACGTTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
* *
2463249 CATATTCGCATT
1 CAGAATCGCATT
2463261 ACGAATTAGG
Statistics
Matches: 88, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 87 0.99
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:2463218 original size:40 final size:40
Alignment explanation
Indices: 2463139--2463260 Score: 147
Period size: 40 Copynumber: 3.0 Consensus size: 40
2463129 CAGAATCTCG
* *
2463139 TTGCGATTTACAG-ATTCGCATTGCGATTTATAGATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACATATTCGCA
* *
2463179 TTGCGATTTACGTATTCGCATTGCAATTTACATAATCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACATATTCGCA
** * * *
2463219 TTATGATTTACGTAATCACGTTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACATATTCGCA
2463259 TT
1 TT
2463261 ACGAATTAGG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
39 1 0.01
40 69 0.99
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACATATTCGCA
Found at i:2463218 original size:60 final size:59
Alignment explanation
Indices: 2463139--2463260 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 59
2463129 CAGAATCTCG
* * * * *
2463139 TTGCGATTTACAGATTCGCATTGCGATTTA-TAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCAATTTACAGAATCGCATTACGATTTACTA-A-TCACATTGCGATTTACATATTCGCA
* * *
2463199 TTGCAATTTACATAATCGCATTATGATTTACGTAATCACGTTGCGATTTACATATTCGCA
1 TTGCAATTTACAGAATCGCATTACGATTTAC-TAATCACATTGCGATTTACATATTCGCA
2463259 TT
1 TT
2463261 ACGAATTAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
60 49 0.94
61 1 0.02
62 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (59 bp):
TTGCAATTTACAGAATCGCATTACGATTTACTAATCACATTGCGATTTACATATTCGCA
Found at i:2463378 original size:19 final size:19
Alignment explanation
Indices: 2463354--2463390 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2463344 CGATACCGAA
2463354 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
*
2463373 GATCGCGTTGCGATTTAT
1 GATCGCGTTGCGAATTAT
2463391 GGATACACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:2463444 original size:20 final size:20
Alignment explanation
Indices: 2463357--2463589 Score: 159
Period size: 20 Copynumber: 11.6 Consensus size: 20
2463347 TACCGAAGAT
*
2463357 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
*
2463376 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* * * *
2463396 CACGTTGTGATTTTATGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2463416 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* ** *
2463437 CGCATTGCGATTTACATATT
1 CGCGTTGCGATTTACGGATA
* **
2463457 CTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
2463477 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
2463497 CTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2463517 CGCGTTGCAATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
2463537 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2463558 CGCGTTACGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
2463579 CTCGTTACGAT
1 CGCGTTGCGAT
2463590 AGTCAGAATC
Statistics
Matches: 164, Mismatches: 41, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
19 16 0.10
20 98 0.60
21 50 0.30
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2463477 original size:40 final size:40
Alignment explanation
Indices: 2463357--2463589 Score: 245
Period size: 41 Copynumber: 5.8 Consensus size: 40
2463347 TACCGAAGAT
* * *
2463357 CGCGTTGCGAATTATCG-A-TCGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTA-CGTATTCTCGTTGCGATTTACGGATA
* * * *
2463396 CACGTTGTGATTTTATGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * **
2463437 CGCATTGCGATTTACATATTCTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
2463477 CGCGTTGCGATTTACGTATTCTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * *
2463517 CGCGTTGCAATTTTACGTATTGTCATTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * * *
2463558 CGCGTTACGATTTTACGGATACTCGTTACGAT
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGAT
2463590 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
39 9 0.06
40 73 0.46
41 77 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:2463537 original size:121 final size:119
Alignment explanation
Indices: 2463353--2463570 Score: 303
Period size: 121 Copynumber: 1.8 Consensus size: 119
2463343 GCGATACCGA
* * ** *
2463353 AGATCGCGTTGCGAATTATCGATCGCGTTGCGATTTATGGATACACGTTGTGATTTTATGTATTG
1 AGATCGCGTTGCGAATTATCGATCGCGTTACGATTTACGGATACACGTTGCAATTTTACGTATTG
* *
2463418 TCGTTGCGATTTACGGATACGCATTGCGATTTACATATTCTCGTTGCGATTTAT
66 TCATTGCGATTTACGGATACGCATTACGATTTACATATTCTCGTTGCGATTTAT
* * *
2463472 AGATACGCGTTGCGATTTA-CGTATTCTCGTTACGATTTACGGATACGCGTTGCAATTTTACGTA
1 AGAT-CGCGTTGCGAATTATCG-A-TCGCGTTACGATTTACGGATACACGTTGCAATTTTACGTA
*
2463536 TTGTCATTGCGATTTACGGATACGCGTTACGATTT
63 TTGTCATTGCGATTTACGGATACGCATTACGATTT
2463571 TACGGATACT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
119 6 0.07
120 14 0.16
121 65 0.76
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (119 bp):
AGATCGCGTTGCGAATTATCGATCGCGTTACGATTTACGGATACACGTTGCAATTTTACGTATTG
TCATTGCGATTTACGGATACGCATTACGATTTACATATTCTCGTTGCGATTTAT
Found at i:2463752 original size:20 final size:19
Alignment explanation
Indices: 2463700--2463753 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
2463690 ATTCTTCATA
2463700 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* ** *
2463719 AACTGATTTACGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
2463740 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
2463754 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:2470883 original size:24 final size:24
Alignment explanation
Indices: 2470851--2470931 Score: 135
Period size: 24 Copynumber: 3.4 Consensus size: 24
2470841 TTTATAGTGT
*
2470851 ATCGATGCATCCCTTAACATGTGC
1 ATCGATGCATCCCTTAACTTGTGC
2470875 ATCGATGCATCCCTTAACTTGTGC
1 ATCGATGCATCCCTTAACTTGTGC
* *
2470899 TTCGATTCATCCCTTAACTTGTGC
1 ATCGATGCATCCCTTAACTTGTGC
2470923 ATCGATGCA
1 ATCGATGCA
2470932 CTATCCCATG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.33
Consensus pattern (24 bp):
ATCGATGCATCCCTTAACTTGTGC
Found at i:2471753 original size:23 final size:22
Alignment explanation
Indices: 2471709--2471753 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2471699 AATCTCATAG
*
2471709 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
2471731 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
2471754 AAAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Done.