Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:523633 original size:22 final size:21
Alignment explanation
Indices: 523591--523630 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
523581 GAGTTTGTTT
*
523591 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
523612 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
523631 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:525660 original size:64 final size:65
Alignment explanation
Indices: 525580--525737 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
525570 ACCAAGTGTT
* * *
525580 CATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGCGTGCATCGATGCATGGCTTGTG
1 CATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGCTTGTG
* ** ****
525644 CATCGATGTATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAATG
1 CATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGCTTGTG
* **
525709 CATCGGTGCATGGAATGCATTCGATGTTT
1 CATCGATGCATCAAATGCATTCGATGTTT
525738 CAATTAATTC
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 24 0.30
65 55 0.70
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGCTTGTG
Found at i:525726 original size:17 final size:19
Alignment explanation
Indices: 525688--525734 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
525678 ATATTCAGAG
525688 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
525707 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
525724 TGCATTCGATG
1 TGCA-TCGATG
525735 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:526571 original size:20 final size:20
Alignment explanation
Indices: 526540--526577 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
526530 AACTCCAATA
526540 ATGCATGCTAAATGCAACTAC
1 ATGCATGCTAAATG-AACTAC
526561 ATGCA-GCTAAATGAACT
1 ATGCATGCTAAATGAACT
526578 TGAAACCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCATGCTAAATGAACTAC
Found at i:531147 original size:13 final size:13
Alignment explanation
Indices: 531129--531189 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
531119 TGCGTCAAAA
531129 ATTTATGACGCGC
1 ATTTATGACGCGC
*
531142 ATTTATGACTCGC
1 ATTTATGACGCGC
* * *
531155 ATTTATAACACAC
1 ATTTATGACGCGC
531168 ATTTATGACGCGC
1 ATTTATGACGCGC
531181 ATTTATGAC
1 ATTTATGAC
531190 TTACATTGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:531196 original size:13 final size:13
Alignment explanation
Indices: 531129--531196 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
531119 TGCGTCAAAA
* *
531129 ATTTATGACGCGC
1 ATTTATGACTCAC
*
531142 ATTTATGACTCGC
1 ATTTATGACTCAC
* *
531155 ATTTATAACACAC
1 ATTTATGACTCAC
* *
531168 ATTTATGACGCGC
1 ATTTATGACTCAC
*
531181 ATTTATGACTTAC
1 ATTTATGACTCAC
531194 ATT
1 ATT
531197 GTGCGTCATT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (13 bp):
ATTTATGACTCAC
Found at i:536881 original size:42 final size:42
Alignment explanation
Indices: 536822--536955 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
536812 AAAGTGAGAT
** * * *
536822 TGAGGGTGCACAGGGTGAGGCTGATAATTCTAA-AACCGAGGG
1 TGAGGGTGCTGAGGGTGAGGTTGATAAGTCTAACAA-TGAGGG
*
536864 TGAGGGTGCTGAGGGTGAGGTTGATAAGTCTAACAATAAGGG
1 TGAGGGTGCTGAGGGTGAGGTTGATAAGTCTAACAATGAGGG
*
536906 TGAGGATGCTGAGGGTGAGGTTGATAAGTCTAACAATGAGGG
1 TGAGGGTGCTGAGGGTGAGGTTGATAAGTCTAACAATGAGGG
536948 TGAGGGTG
1 TGAGGGTG
536956 AGGGTGCTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 80 0.98
43 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.41, T:0.22
Consensus pattern (42 bp):
TGAGGGTGCTGAGGGTGAGGTTGATAAGTCTAACAATGAGGG
Found at i:541789 original size:18 final size:19
Alignment explanation
Indices: 541766--541811 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
541756 TTGCAATTCT
*
541766 TCATATGTTATTCGTT-AA
1 TCATATGTTATTAGTTAAA
*
541784 TCATAT-TTTTTAGTTAAA
1 TCATATGTTATTAGTTAAA
*
541802 TCGTATGTTA
1 TCATATGTTA
541812 CCCTCAAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (19 bp):
TCATATGTTATTAGTTAAA
Found at i:549315 original size:125 final size:125
Alignment explanation
Indices: 549090--549394 Score: 412
Period size: 125 Copynumber: 2.4 Consensus size: 125
549080 AATTTAGGAT
* * ** ** * *
549090 ATGTTGGGGCACGAGTAAACCCACATCGGGTTGAGATGATAAGATTCAGAAGAAGGAGGCATTAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGGAAGCATAAA
* * **
549155 GAATGAGCCTTATAATTTGAGGTGATGAGGTATTTTGAAGGCCTGTACCAGTATAAGATA
66 GAATGAGCCTTATAATTTGAGGTGATGAGGCATTTTGAAAGCCCATACCAGTATAAGATA
* *
549215 ATGTTGGGGCACGACTGAATCCACATCATGTTGAGATGATAAGATACAGACCAAGGAAGCATAAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGGAAGCATAAA
* * *
549280 GAATGAGTCTTATAATTTGAGGTGATGGGGCATTTTGAAAGCCCATACTAGTATAAGATA
66 GAATGAGCCTTATAATTTGAGGTGATGAGGCATTTTGAAAGCCCATACCAGTATAAGATA
* * * * *
549340 AGGTTGGGGCACGACTGAACCCATATCCTTTTGAGATGACAAGATTCAGACCAAG
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAG
549395 AAGTTATTGA
Statistics
Matches: 156, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
125 156 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGGAAGCATAAA
GAATGAGCCTTATAATTTGAGGTGATGAGGCATTTTGAAAGCCCATACCAGTATAAGATA
Found at i:550182 original size:35 final size:35
Alignment explanation
Indices: 550141--550295 Score: 186
Period size: 35 Copynumber: 4.3 Consensus size: 35
550131 GGGCAAGTCA
550141 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATC
* * *
550176 ATCTTAAGCCTTCACCGAAGAGTAGCGAATCAAAC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATC
* ** * *
550211 AATTTTAAGCCTTCAAAGAAGATTAGTGAAGC-ACC
1 -ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATC
*
550246 ATCTTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AAT-C
550283 ATCTATAAGCCTT
1 ATCT-TAAGCCTT
550296 TAGAGCAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
34 27 0.27
35 34 0.34
36 26 0.26
37 5 0.05
38 8 0.08
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (35 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATC
Found at i:550505 original size:42 final size:42
Alignment explanation
Indices: 550446--550564 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
550436 ATTTATAAGT
*
550446 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAA
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAA
550488 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAA
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAA
* * * *
550530 CCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATG
550565 AAAAGTCTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (42 bp):
CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAA
Found at i:550750 original size:256 final size:257
Alignment explanation
Indices: 550282--550756 Score: 801
Period size: 256 Copynumber: 1.9 Consensus size: 257
550272 GAAGCAAATC
*
550282 CATCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTTAGGCCATCCATAAGACCTTCGGGTAGGA
1 CATCTATAAGCCTTTAGAGCAAGATGAAAAGTCCTTTAGGCCATCCATAAGACCTTCGGGTAGGA
* * * *
550347 TGTTTTCAAATGAATTTGAAAATGAGAAAATGATATTTCAAGAAGATGCAATTTTTGAAAGCTAA
66 TGTTTTCAAATGAATTTGAAAATGAAAAAATGATATTTCAAGAAAATGCAATTTTTGAAAACAAA
*
550412 GAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
131 GAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCAT
550477 GATGCTTAAAACCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGT
196 GATGCTTAAAACCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGT
* *
550539 CATCTGTAAGCCTTTAGAGCAAGATGAAAAGT-CTTTCGGGCCATCCATAAGACCTTCGGGTAGG
1 CATCTATAAGCCTTTAGAGCAAGATGAAAAGTCCTTT-AGGCCATCCATAAGACCTTCGGGTAGG
* * *
550603 ATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAAATG-AATTTTTGAAAACAA
65 ATGTTTTCAAATGAATTTGAAAATGAAAAAATGATATTTCAAGAAAATGCAATTTTTGAAAACAA
* *
550667 ATAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTTGAGCCATCAGTAAGTCTTTCGAGCA
130 AGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCA
*
550732 TGATGCTTAAATCCTTCGGGTCATC
195 TGATGCTTAAAACCTTCGGGTCATC
550757 TATAAGCCTT
Statistics
Matches: 203, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
256 103 0.51
257 100 0.49
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (257 bp):
CATCTATAAGCCTTTAGAGCAAGATGAAAAGTCCTTTAGGCCATCCATAAGACCTTCGGGTAGGA
TGTTTTCAAATGAATTTGAAAATGAAAAAATGATATTTCAAGAAAATGCAATTTTTGAAAACAAA
GAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCAT
GATGCTTAAAACCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGT
Found at i:551196 original size:42 final size:41
Alignment explanation
Indices: 551129--551230 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 41
551119 TTCACAATTT
* * *
551129 ATAAGTCCTTCGGACCATCAT-TAAGTATTTCA-AGCATGATG
1 ATAAATCCTTCGGGCCATC-TGTAAGTATTT-AGAGCAAGATG
* * *
551170 CTTAAATCCTTCGGGTCATCTGTAAGTGTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCTGTAAGTATTTAGAGCAAGATG
*
551212 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
551231 CATAAAACCT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 18 0.37
42 31 0.63
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCTGTAAGTATTTAGAGCAAGATG
Found at i:551205 original size:216 final size:216
Alignment explanation
Indices: 550488--551448 Score: 1467
Period size: 217 Copynumber: 4.4 Consensus size: 216
550478 ATGCTTAAAA
* *
550488 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
* * *
550553 TAGAGCAAGATGAAAAGTCTTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAA
66 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
* *
550618 TTTGAAAATG-AAAAAATGATGTTTTAAGAAAATG-AATTTTTGAAAACAAATAATGTGATTTTC
131 TTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGTGATTTTC
550681 AAAATTTCACAATTTATAAGT
196 AAAATTTCACAATTTATAAGT
* * *
550702 CCTTTGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
* * * * * ** *
550767 TAGAGTAATATGATAAGTCATTCGAGCCATCCATAAAACGTTTAGGTAGGATGTTTTGACATGAA
66 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
* * *
550832 TTTGAAAATGGAAAAAATGATGTTTTATGAAGATGAAATTTTTTGAAAACTAAGAATGTGATTTT
131 TTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGAAA-TTTTTGAAAACAAAGAATGTGATTTT
550897 CAAAATTTCACAATTTATAAGT
195 CAAAATTTCACAATTTATAAGT
* * *
550919 CTTTCGGGCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATATGTAAGCCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
550984 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
66 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
* * *
551049 TTTGAAAATGAAAAAAATTATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTC
131 TTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGTGATTTTC
*
551114 AACATTTCACAATTTATAAGT
196 AAAATTTCACAATTTATAAGT
* * * * **
551135 CCTTCGGACCATCATTAAGTATTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTGTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
*
551200 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTATGATGTTTTCACATGAA
66 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
*
551265 TTTGAAAATAAAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGTGATTTT
131 TTTGAAAAT-GAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGTGATTTT
*
551330 CAAAATTTCACAATTTACAAGT
195 CAAAATTTCACAATTTATAAGT
* * * * * **
551352 CCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCTTTCGGGTCATTTATGATTCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
* *
551417 TCGAGCATGATGATGAAGTCCTTCGGGCCATC
66 TAGAGCAAGATGAT-AAGTCCTTCGGGCCATC
551449 ATTAAGTTTT
Statistics
Matches: 675, Mismatches: 67, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
214 125 0.19
215 22 0.03
216 177 0.26
217 334 0.49
218 17 0.03
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (216 bp):
CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTT
TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
TTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGTGATTTTC
AAAATTTCACAATTTATAAGT
Found at i:551310 original size:433 final size:431
Alignment explanation
Indices: 550488--551448 Score: 1467
Period size: 433 Copynumber: 2.2 Consensus size: 431
550478 ATGCTTAAAA
* * *
550488 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATATGTAAGCCTT
* * *
550553 TAGAGCAAGATGAAAAGTCTTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAA
66 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
* *
550618 TTTGAAAATGAAAAAATGATGTTTTAAGAAAATGAATTTTTGAAAACAAATAATGTGATTTTCAA
131 TTTGAAAATGAAAAAATGATGTTTTAAGAAAATGAATTTTTGAAAACAAAGAATGCGATTTTCAA
* * *
550683 AATTTCACAATTTATAAGTCCTTTGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTT
196 AATTTCACAATTTATAAGTCCTTGGAGCCATCAGTAAGTATTTCAAGCATGATGCTTAAATCCTT
* * * *
550748 CGGGTCATCTATAAGCCTTTAGAGTAATATGATAAGTCATTCGAGCCATCCATAAAACGTTTAGG
261 CGGGTCATCTATAAGCCTTTAGAGCAAGATGATAAGTCATTCGAGCCATCCATAAAACCTTCAGG
* ** *
550813 TAGGATGTTTTGACATGAATTTGAAAATGGAAAAAATGATGTTTTATGAAGATGAAATTTTTTGA
326 TAGGATGTTTTCACATGAATTTGAAAATAAAAAAAATGATGTTTTAAGAAGATGAAATTTTTTGA
* *
550878 AAACTAAGAATGTGATTTTCAAAATTTCACAATTTATAAGT
391 AAACAAAGAATGTGATTTTCAAAATTTCACAATTTACAAGT
* *
550919 CTTTCGGGCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATATGTAAGCCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATATGTAAGCCTT
550984 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
66 TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
* * *
551049 TTTGAAAATGAAAAAAATTATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTC
131 TTTGAAAATG-AAAAAATGATGTTTTAAGAAAATG-AATTTTTGAAAACAAAGAATGCGATTTTC
* *
551114 AACATTTCACAATTTATAAGTCCTTCGGA-CCATCATTAAGTATTTCAAGCATGATGCTTAAATC
194 AAAATTTCACAATTTATAAGTCCTT-GGAGCCATCAGTAAGTATTTCAAGCATGATGCTTAAATC
* ** * *
551178 CTTCGGGTCATCTGTAAGTGTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTC
258 CTTCGGGTCATCTATAAGCCTTTAGAGCAAGATGATAAGTCATTCGAGCCATCCATAAAACCTTC
* *
551243 GGGTATGATGTTTTCACATGAATTTGAAAATAAAAAAAAATGATGTTTTAAGAAGATGAAA-TTT
323 AGGTAGGATGTTTTCACATGAATTTGAAAAT-AAAAAAAATGATGTTTTAAGAAGATGAAATTTT
551307 TTGAAAACAAAGAATGTGATTTTCAAAATTTCACAATTTACAAGT
387 TTGAAAACAAAGAATGTGATTTTCAAAATTTCACAATTTACAAGT
* * * * * **
551352 CCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCTTTCGGGTCATTTATGATTCTT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATATGTAAGCCTT
* *
551417 TCGAGCATGATGATGAAGTCCTTCGGGCCATC
66 TAGAGCAAGATGAT-AAGTCCTTCGGGCCATC
551449 ATTAAGTTTT
Statistics
Matches: 479, Mismatches: 46, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
431 132 0.28
432 22 0.05
433 280 0.58
434 45 0.09
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (431 bp):
CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATATGTAAGCCTT
TAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAA
TTTGAAAATGAAAAAATGATGTTTTAAGAAAATGAATTTTTGAAAACAAAGAATGCGATTTTCAA
AATTTCACAATTTATAAGTCCTTGGAGCCATCAGTAAGTATTTCAAGCATGATGCTTAAATCCTT
CGGGTCATCTATAAGCCTTTAGAGCAAGATGATAAGTCATTCGAGCCATCCATAAAACCTTCAGG
TAGGATGTTTTCACATGAATTTGAAAATAAAAAAAATGATGTTTTAAGAAGATGAAATTTTTTGA
AAACAAAGAATGTGATTTTCAAAATTTCACAATTTACAAGT
Found at i:551417 original size:42 final size:42
Alignment explanation
Indices: 551354--551483 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 42
551344 TTACAAGTCC
* *
551354 TTCGGGCCATCAGTAAG-TCTTTTGAGCATGATGCTTAAATCT
1 TTCGGGCCAT-ATTAAGTTCTTTTGAGCATGATGATTAAATCT
* * * * * *
551396 TTCGGGTCAT-TTATGATTCTTTCGAGCATGATGATGAAGTCC
1 TTCGGGCCATATTAAG-TTCTTTTGAGCATGATGATTAAATCT
551438 TTCGGGCCATCATTAAGTT-TTTTGAGCATGATGATTAAATCT
1 TTCGGGCCAT-ATTAAGTTCTTTTGAGCATGATGATTAAATCT
551480 TTCG
1 TTCG
551484 AGTAATTTGT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
40 3 0.04
42 61 0.87
43 2 0.03
44 4 0.06
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
TTCGGGCCATATTAAGTTCTTTTGAGCATGATGATTAAATCT
Found at i:551518 original size:84 final size:84
Alignment explanation
Indices: 551348--551506 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
551338 CACAATTTAC
* * * * *
551348 AAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCTTTCGGGTCATTTATGAT
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGAGTAATTTATAAG
* * *
551413 TCTTTCGAGCATGATGATG
66 CCTTACAAGCATGATGATG
* * *
551432 AAGTCCTTCGGGCCATCATTAAGTTTTTTGAGCATGATGATTAAATCTTTCGAGTAATTTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGAGTAATTTATAAG
551497 CCTTCACAAG
66 CCTT-ACAAG
551507 AGAGTAGTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 60 0.95
85 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (84 bp):
AAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGAGTAATTTATAAG
CCTTACAAGCATGATGATG
Found at i:551554 original size:80 final size:80
Alignment explanation
Indices: 551444--551615 Score: 229
Period size: 80 Copynumber: 2.1 Consensus size: 80
551434 GTCCTTCGGG
* * * *
551444 CCATCATTAAGTTTTTTGAGCATGATGATTAAATCTTTCGAGTAATTTGTAAGCCTTCACA-AGA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGAGTAATTTATAAGCCTTCACAGA-A
551508 GAGTAGTGAAGCAAAT
65 GAGTAGTGAAGCAAAT
* * * * * * *
551524 CTATTAGTAAGTCTTTCGAGCATGATGATTAAATTTTTTGGGTCATTTATAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGAGTAATTTATAAGCCTTCACAGAAG
551589 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
551604 CCATCAGTAAGT
1 CCATCAGTAAGT
551616 GCCATACGTA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 77 0.99
81 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGAGTAATTTATAAGCCTTCACAGAAG
AGTAGTGAAGCAAAT
Found at i:553601 original size:29 final size:27
Alignment explanation
Indices: 553568--553649 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 27
553558 TTTGGTTTGT
553568 ATTTTGTTTGTATTCACGCGTCCATTAGC
1 ATTTTGTTTGTATTCA--CGTCCATTAGC
553597 ATTTTGTTTG---T----TCCATTAGC
1 ATTTTGTTTGTATTCACGTCCATTAGC
553617 ATTTTGTTTGTATTCACATGTCCATTAGC
1 ATTTTGTTTGTATTCAC--GTCCATTAGC
553646 ATTT
1 ATTT
553650 GAGTCATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 18
0.71 0.00 0.29
Matches are distributed among these distances:
20 19 0.43
23 1 0.02
26 1 0.02
29 23 0.52
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.50
Consensus pattern (27 bp):
ATTTTGTTTGTATTCACGTCCATTAGC
Found at i:553613 original size:20 final size:20
Alignment explanation
Indices: 553588--553627 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
553578 TATTCACGCG
553588 TCCATTAGCATTTTGTTTGT
1 TCCATTAGCATTTTGTTTGT
553608 TCCATTAGCATTTTGTTTGT
1 TCCATTAGCATTTTGTTTGT
553628 ATTCACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (20 bp):
TCCATTAGCATTTTGTTTGT
Found at i:556974 original size:14 final size:12
Alignment explanation
Indices: 556949--557021 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
556939 GATCAACATT
556949 TTTGCATCTGCA
1 TTTGCATCTGCA
556961 TTTGCATCTTTGCA
1 TTTGCATC--TGCA
*
556975 TTTTGTA-CTGCA
1 -TTTGCATCTGCA
556987 TTTGCATCTTTGCA
1 TTTGCATC--TGCA
* *
557001 TTTGCATATGAA
1 TTTGCATCTGCA
*
557013 TTCGCATCT
1 TTTGCATCT
557022 TTGGATTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 5 0.10
12 23 0.47
14 16 0.33
15 5 0.10
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (12 bp):
TTTGCATCTGCA
Found at i:557019 original size:26 final size:26
Alignment explanation
Indices: 556949--557029 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
556939 GATCAACATT
*
556949 TTTGCATCTGCATTTGCATCTTTGCA
1 TTTGCATATGCATTTGCATCTTTGCA
556975 TTTTG--TACTGCATTTGCATCTTTGCA
1 -TTTGCATA-TGCATTTGCATCTTTGCA
* * *
557001 TTTGCATATGAATTCGCATCTTTGGA
1 TTTGCATATGCATTTGCATCTTTGCA
557027 TTT
1 TTT
557030 TTATGTTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 5 0.11
26 36 0.77
27 6 0.13
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (26 bp):
TTTGCATATGCATTTGCATCTTTGCA
Found at i:559145 original size:6 final size:7
Alignment explanation
Indices: 559128--559154 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
559118 AAAATGAAGA
559128 AAAAAAT
1 AAAAAAT
559135 AAAAAAT
1 AAAAAAT
559142 AAAAAAT
1 AAAAAAT
559149 AAAAAA
1 AAAAAA
559155 GTGTGATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:559631 original size:15 final size:16
Alignment explanation
Indices: 559602--559637 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
559592 CGTCAATCAG
*
559602 AGAAACAAAAGAGAAA
1 AGAAACAAAAAAGAAA
559618 AGAAA-AAAAAAGAAA
1 AGAAACAAAAAAGAAA
559633 AGAAA
1 AGAAA
559638 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAAACAAAAAAGAAA
Found at i:561195 original size:52 final size:52
Alignment explanation
Indices: 561112--561255 Score: 227
Period size: 52 Copynumber: 2.8 Consensus size: 52
561102 GGTCCATATT
* * * *
561112 ATCCATGT-GGGTATATTGAAGGCTCATATCAGCATGAAAAAGACAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAAAAGTA
*
561163 GTCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAAAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAAAAGTA
*
561215 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGTATGAAAA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAA
561256 GGTTGGGATA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 7 0.08
52 78 0.92
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (52 bp):
ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAAAAGTA
Found at i:562971 original size:117 final size:117
Alignment explanation
Indices: 562819--563054 Score: 357
Period size: 117 Copynumber: 2.0 Consensus size: 117
562809 GATGTGAACT
* * * * *
562819 AACATTTTCAATAGAGATTTCATAATGAGATGAACTCATCCAATGAGGAATAAGAAGTTCATAAT
1 AACATTTTCAATAGAAATTTCATAATGACAAGAACTCATCCAATGAGGAAGAAAAAGTTCATAAT
* *
562884 AAGAAGAACTTGTTCGACCTTGGTTTGATTCCATCACAGAAGGAGATGGATC
66 AAGAAGAACTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGATGGATC
*
562936 AACATTTTCAATGGAAAGTTT-ATAATGACAAGAACTCATCCAATGAGGAAGAAAAAGTTCATAA
1 AACATTTTCAATAGAAA-TTTCATAATGACAAGAACTCATCCAATGAGGAAGAAAAAGTTCATAA
** *
563000 TGGGAAGAACTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGGTGGATC
65 TAAGAAGAACTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGATGGATC
563053 AA
1 AA
563055 TAATTCCATT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
117 104 0.97
118 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (117 bp):
AACATTTTCAATAGAAATTTCATAATGACAAGAACTCATCCAATGAGGAAGAAAAAGTTCATAAT
AAGAAGAACTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGATGGATC
Found at i:563097 original size:117 final size:117
Alignment explanation
Indices: 562827--563088 Score: 355
Period size: 117 Copynumber: 2.2 Consensus size: 117
562817 CTAACATTTT
* * * *
562827 CAATAGAGATTTCATAATGAG-ATGAACTCATCCAATGAGGAATAAGAAGTTCATAATAAGAAGA
1 CAATGGAGAGTTCATAATGAGAAT-AACTCATCCAATGAGGAAGAAAAAGTTCATAATAAGAAGA
* * * *
562891 ACTTGTTCGACCTTGGTTTGATTCCATCACAGAAGGAGATGGATCAACATTTT
65 ACTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGATGGATCAACAATTC
* * * * **
562944 CAATGGAAAGTTTATAATGACAAGAACTCATCCAATGAGGAAGAAAAAGTTCATAATGGGAAGAA
1 CAATGGAGAGTTCATAATGAGAATAACTCATCCAATGAGGAAGAAAAAGTTCATAATAAGAAGAA
* *
563009 CTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGGTGGATCAATAATTC
66 CTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGATGGATCAACAATTC
*
563061 CATTGGAGAGTTCATAATGAGAATAACT
1 CAATGGAGAGTTCATAATGAGAATAACT
563089 TGTTCAATGC
Statistics
Matches: 123, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
117 122 0.99
118 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (117 bp):
CAATGGAGAGTTCATAATGAGAATAACTCATCCAATGAGGAAGAAAAAGTTCATAATAAGAAGAA
CTTGTTCAACATTGGTTTGATTCCATCACAGAAGGAGATGGATCAACAATTC
Found at i:563290 original size:43 final size:43
Alignment explanation
Indices: 563242--563396 Score: 159
Period size: 43 Copynumber: 3.5 Consensus size: 43
563232 CGACCTAATT
563242 TCCTCATCACGTAGGAACTGTGTCAACCCCAGATAACCAACTA
1 TCCTCATCACGTAGGAACTGTGTCAACCCCAGATAACCAACTA
* * ** ** * *
563285 TCCTCATCACGTAGGAATTGTGTTATCACACTTAGATGGCCTACTG
1 TCCTCATCACGTAGGAACTGTGTCA--AC-CCCAGATAACCAACTA
* *
563331 TCCTCATCACGTAGGAACCGTTTCAACCCCAGATAACCAA-TCA
1 TCCTCATCACGTAGGAACTGTGTCAACCCCAGATAACCAACT-A
* *
563374 ACCTCATCACATAGGAACTGTGT
1 TCCTCATCACGTAGGAACTGTGT
563397 TATCACACTT
Statistics
Matches: 86, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
42 1 0.01
43 50 0.58
44 2 0.02
45 2 0.02
46 31 0.36
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACTGTGTCAACCCCAGATAACCAACTA
Found at i:563344 original size:46 final size:45
Alignment explanation
Indices: 563285--563432 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 45
563275 TAACCAACTA
563285 TCCTCATCACGTAGGAATTGTGTTATCACACTTAGATGGCCTACTG
1 TCCTCATCACGTAGGAA-TGTGTTATCACACTTAGATGGCCTACTG
** ** ** * *
563331 TCCTCATCACGTAGGAA-CCGTT-TCA-ACCCCAGATAACC-AATCA
1 TCCTCATCACGTAGGAATGTGTTATCACA-CTTAGATGGCCTACT-G
* * *
563374 ACCTCATCACATAGGAACTGTGTTATCACACTTAGATGGCCTACCG
1 TCCTCATCACGTAGGAA-TGTGTTATCACACTTAGATGGCCTACTG
563420 TCCTCATCACGTA
1 TCCTCATCACGTA
563433 AGAACCATGT
Statistics
Matches: 74, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
42 3 0.04
43 25 0.34
44 3 0.04
45 3 0.04
46 38 0.51
47 2 0.03
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (45 bp):
TCCTCATCACGTAGGAATGTGTTATCACACTTAGATGGCCTACTG
Found at i:563396 original size:89 final size:89
Alignment explanation
Indices: 563242--563534 Score: 340
Period size: 89 Copynumber: 3.3 Consensus size: 89
563232 CGACCTAATT
* * * *
563242 TCCTCATCACGTAGGAACTGTGTCAACCCCAGATAACCAACTATCCTCATCACGTAGGAATTGTG
1 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAACTAACCTCATCACATAGGAACTGTG
*
563307 TTATCACACTTAGATGGCCTACTG
66 TTATCACACTTAGATGGCCTACCG
*
563331 TCCTCATCACGTAGGAACCGTTTCAACCCCAGATAACCAA-TCAACCTCATCACATAGGAACTGT
1 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAACT-AACCTCATCACATAGGAACTGT
563395 GTTATCACACTTAGATGGCCTACCG
65 GTTATCACACTTAGATGGCCTACCG
* * * * * * * *
563420 TCCTCATCACGTAAGAACCATGTC-ACCCCAGATAACCAGCCATCCCCATAATATAGGAA-TCGT
1 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAACTAACCTCATCACATAGGAACT-GT
* * * ** *
563483 GTTATCATCCCTAATGATGGTCTGTCA
65 GTTATCA-CACTTA-GATGGCCTACCG
*
563510 TCCTCATCACGTAAGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
563535 TCCCTCGACC
Statistics
Matches: 176, Mismatches: 22, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
87 1 0.01
88 38 0.22
89 106 0.60
90 31 0.18
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (89 bp):
TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAACTAACCTCATCACATAGGAACTGTG
TTATCACACTTAGATGGCCTACCG
Found at i:563638 original size:46 final size:46
Alignment explanation
Indices: 563586--563712 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
563576 TCTTTGATAA
563586 CCAGAACTCTTCATCATGTATGAGCTGTGTTATCACCTTAAGATGG
1 CCAGAACTCTTCATCATGTATGAGCTGTGTTATCACCTTAAGATGG
* *
563632 CCAGAACTCTTCATCATGTATGAGCCGTTTTATCACCTTAAGATGG
1 CCAGAACTCTTCATCATGTATGAGCTGTGTTATCACCTTAAGATGG
* * * *
563678 CCAGAACTCTTCAACACGTATGAGTTGTGTCATCA
1 CCAGAACTCTTCATCATGTATGAGCTGTGTTATCA
563713 GCCGACTAGG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (46 bp):
CCAGAACTCTTCATCATGTATGAGCTGTGTTATCACCTTAAGATGG
Found at i:563793 original size:128 final size:128
Alignment explanation
Indices: 563636--563905 Score: 323
Period size: 128 Copynumber: 2.1 Consensus size: 128
563626 AGATGGCCAG
* * * * *
563636 AACTCTTCATCATGTATGAGCCGTTTTATCACCTTAAGATGGCCAGAACTCTTCAACACGT-ATG
1 AACTCTTCATCACGAACGAGCCATGTTATCACCTTAAGATGGCCAGAACTCTTCAACAC-TCATG
** * * * *
563700 AGTTGTGTCATCAGCC-GACTAGGTTTCCTTATTATGTAGGAG-CTATGTCAACCTT-GATAACC
65 AGCAGTGTCATC--CCTGACTAGATCTCCTCATTATGTAGGAGCCT-TGTCAACCTTAGACAACC
563762 AA
127 AA
* *
563764 AACTCTTCATCACGAACGAGCCATGTTATCACCTTTAGATGGCCAGAACTCTTCATCACTCATGA
1 AACTCTTCATCACGAACGAGCCATGTTATCACCTTAAGATGGCCAGAACTCTTCAACACTCATGA
* * **
563829 GCAGTGTCATCCCTGACTAGATCTCCTCATTATGTAGGAGCCTTTTCACCCTTAGACAACCCG
66 GCAGTGTCATCCCTGACTAGATCTCCTCATTATGTAGGAGCCTTGTCAACCTTAGACAACCAA
563892 AACTCTTCATCACG
1 AACTCTTCATCACG
563906 TATAAGCAGT
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
126 2 0.02
127 32 0.26
128 87 0.72
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (128 bp):
AACTCTTCATCACGAACGAGCCATGTTATCACCTTAAGATGGCCAGAACTCTTCAACACTCATGA
GCAGTGTCATCCCTGACTAGATCTCCTCATTATGTAGGAGCCTTGTCAACCTTAGACAACCAA
Found at i:564080 original size:3 final size:3
Alignment explanation
Indices: 564072--564132 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
564062 AAAATATTAA
564072 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
564120 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
564133 AAGTTATTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:567100 original size:59 final size:59
Alignment explanation
Indices: 566949--567492 Score: 772
Period size: 59 Copynumber: 9.2 Consensus size: 59
566939 TCCATGATTT
* * * * *
566949 GCACACAAAGTGCCCAACACGGAAATTCATACACTTAGTATGAATTTCTTAGCATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
** * * *
567008 -CACAAAAAGTGCCCAATACGGAAATTCATACACTTGGTATGAATTTCTTAACATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
* *
567066 GCACACGAAGTGCCTTATACGAAAATTCATACACTTAGTATGAATTTTTTAACATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
* *
567125 GCATACGAAGTGCCCTATACGAAAATTCATACACTTAGTATTAATTTCTTAACATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
*
567184 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTGTGAATTTCTTAACATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
* * * *
567243 GCACACGAAGTTCCCTATATGGAAATTCTTACACTTAGTATGAATTTCTTAACATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
* *
567302 GCACAAGAAGTGCCCTATAC-AGAAATTCATACACTTGGTATGAATTTCTTAACATTTTA
1 GCACACGAAGTGCCCTATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTA
* * * * * *
567361 GCATATGAAGTGCCCTATAAGGAAATTCATACACTTAGTTTGAATTTTTTAACATTTTA
1 GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
*
567420 GCACACGAAGTGCCCTATAC-AGAAATTCATACACTTAGTATGAATTTTTTAACATTTTA
1 GCACACGAAGTGCCCTATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTA
*
567479 GTACAC-AGAGTGCC
1 GCACACGA-AGTGCC
567493 TTTTGGTAAA
Statistics
Matches: 438, Mismatches: 42, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
58 55 0.13
59 383 0.87
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (59 bp):
GCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
Found at i:583352 original size:26 final size:25
Alignment explanation
Indices: 583321--583379 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
583311 ATTCTTCTCA
583321 AAAAATAATT-TTTTAAAAAAATAAT
1 AAAAATAATTGTTTTAAAAAAAT-AT
* *
583346 AATAAAT-GTTGTTTTAAATAAATAT
1 AA-AAATAATTGTTTTAAAAAAATAT
583371 AAAAATAAT
1 AAAAATAAT
583380 GTTGTAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 4 0.14
25 9 0.32
26 15 0.54
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
AAAAATAATTGTTTTAAAAAAATAT
Found at i:583380 original size:27 final size:26
Alignment explanation
Indices: 583331--583384 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
583321 AAAAATAATT
*
583331 TTTTAAAAAAATAATAATAAATGTTG
1 TTTTAAAAAAATAAAAATAAATGTTG
583357 TTTTAAATAAATATAAAAAT-AATGTTG
1 TTTTAAA-AAA-ATAAAAATAAATGTTG
583384 T
1 T
583385 AGTAAACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 11 0.44
28 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (26 bp):
TTTTAAAAAAATAAAAATAAATGTTG
Found at i:583395 original size:28 final size:28
Alignment explanation
Indices: 583334--583395 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
583324 AATAATTTTT
* **
583334 TAAA-AAA-ATAATAATAAATGTTGTTT
1 TAAATAAATATAAAAATAAATGTTGTAG
583360 TAAATAAATATAAAAAT-AATGTTGTAG
1 TAAATAAATATAAAAATAAATGTTGTAG
583387 TAAACTAAA
1 TAAA-TAAA
583396 AATGATTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 4 0.13
27 15 0.50
28 11 0.37
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (28 bp):
TAAATAAATATAAAAATAAATGTTGTAG
Found at i:587984 original size:25 final size:25
Alignment explanation
Indices: 587933--587984 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
587923 AAAATTGACT
* **
587933 TTTTAAAAAATAATAATAAATGTTG
1 TTTTAAAAAATAATAAAAAATAATG
587958 TTTTAAATAAAT-ATAAAAAATAATG
1 TTTTAAA-AAATAATAAAAAATAATG
587983 TT
1 TT
587985 GTAGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
TTTTAAAAAATAATAAAAAATAATG
Found at i:595689 original size:25 final size:28
Alignment explanation
Indices: 595659--595725 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
595649 TCTTGGCTTG
595659 TTTTA-TCTTTT-TGAATTTCTTT-TTC
1 TTTTATTCTTTTCTGAATTTCTTTCTTC
* *
595684 TTTTATTCTTTTCTGAGTTTTTTTCTTC
1 TTTTATTCTTTTCTGAATTTCTTTCTTC
595712 TTTT-TGTCTTTTCT
1 TTTTAT-TCTTTTCT
595726 TTTCTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 5 0.14
26 6 0.17
27 10 0.28
28 15 0.42
ACGTcount: A:0.07, C:0.13, G:0.06, T:0.73
Consensus pattern (28 bp):
TTTTATTCTTTTCTGAATTTCTTTCTTC
Found at i:606095 original size:22 final size:22
Alignment explanation
Indices: 606069--606110 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
606059 TTTCAAAAGG
606069 TATTA-TTTTCCTATTCGAAAAC
1 TATTACTTTT-CTATTCGAAAAC
606091 TATTACTTTTCTATTCGAAA
1 TATTACTTTTCTATTCGAAA
606111 GCAGAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (22 bp):
TATTACTTTTCTATTCGAAAAC
Found at i:607328 original size:21 final size:21
Alignment explanation
Indices: 607304--607370 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
607294 TTCGAATTTG
607304 ATTTGATAAAATTCGATTAAT
1 ATTTGATAAAATTCGATTAAT
* * *
607325 ATTTG-TAGTAATTAGAGT-AT
1 ATTTGATA-AAATTCGATTAAT
* *
607345 GATTTAATAAAAATCGATTAAT
1 -ATTTGATAAAATTCGATTAAT
607367 ATTT
1 ATTT
607371 AGATTGAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 4 0.12
21 26 0.76
22 4 0.12
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (21 bp):
ATTTGATAAAATTCGATTAAT
Found at i:607348 original size:42 final size:42
Alignment explanation
Indices: 607281--607370 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
607271 GATACTAGGT
* * * * *
607281 ATATTTGTAGTTATTCGAATTTGATTTGATAAAATTCGATTA
1 ATATTTGTAGTAATTAGAATATGATTTAATAAAAATCGATTA
*
607323 ATATTTGTAGTAATTAGAGTATGATTTAATAAAAATCGATTA
1 ATATTTGTAGTAATTAGAATATGATTTAATAAAAATCGATTA
607365 ATATTT
1 ATATTT
607371 AGATTGAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (42 bp):
ATATTTGTAGTAATTAGAATATGATTTAATAAAAATCGATTA
Found at i:607957 original size:2 final size:2
Alignment explanation
Indices: 607952--607999 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
607942 ATTTTTTTAA
607952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
607994 AT AT AT
1 AT AT AT
608000 TAAACATATA
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):
AT
Found at i:614987 original size:19 final size:19
Alignment explanation
Indices: 614963--615001 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
614953 ACGAAGCCTT
*
614963 TTGATTCTGGTTATGTATG
1 TTGATTATGGTTATGTATG
* *
614982 TTGATTATTGTTCTGTATG
1 TTGATTATGGTTATGTATG
615001 T
1 T
615002 GTTCGATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.56
Consensus pattern (19 bp):
TTGATTATGGTTATGTATG
Found at i:615513 original size:104 final size:104
Alignment explanation
Indices: 615183--615610 Score: 659
Period size: 104 Copynumber: 4.1 Consensus size: 104
615173 TGCTTGGAAA
* * * *
615183 GTAGGATATTTGTTAGTGTAGCTCTTGTTCATAATTTCATACAGTTTATATACATATATATATAT
1 GTAGGTTATTTGTTAGTGTAGTTCTTGTTCATAATTTCATACAGTTTATATAC--ATATATGTAC
*
615248 ATATATATACAATTCGTGTTCGACATGGTATGTTTCAGTTT
64 ATATATATACAATTCGTGTTCGACATGGTATGTTTCGGTTT
* *
615289 GTAGGATATTTGTTAGTGTAGTTCTTGTTCATAATTTCATACGGTTTATATACATATATGTAC--
1 GTAGGTTATTTGTTAGTGTAGTTCTTGTTCATAATTTCATACAGTTTATATACATATATGTACAT
615352 --ATATACAATTCGTGTTCGACATGGTATGTTTCGGTTT
66 ATATATACAATTCGTGTTCGACATGGTATGTTTCGGTTT
* * *
615389 GTAGGTTATTTGTTAGTGTAGTTCTCGTTCATAATTGCATACAGTTTATATACATATATTTACAT
1 GTAGGTTATTTGTTAGTGTAGTTCTTGTTCATAATTTCATACAGTTTATATACATATATGTACAT
*
615454 ATATATAAAATTCGTGTTCGACATGGTATGTTTCGGTTT
66 ATATATACAATTCGTGTTCGACATGGTATGTTTCGGTTT
* *
615493 GTAGGTTTTTTGTTAGTGTAGTTCTTTTTCATAATTTCATACAGTTTATATACATATATGTACAT
1 GTAGGTTATTTGTTAGTGTAGTTCTTGTTCATAATTTCATACAGTTTATATACATATATGTACAT
*
615558 ATATATACAATTCGTGTTCGACATGGTATGTTGT-GGTTA
66 ATATATACAATTCGTGTTCGACATGGTATGTT-TCGGTTT
*
615597 GTAGGATATTTGTT
1 GTAGGTTATTTGTT
615611 CTTGTACTTC
Statistics
Matches: 297, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
100 94 0.32
104 151 0.51
105 1 0.00
106 51 0.17
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.46
Consensus pattern (104 bp):
GTAGGTTATTTGTTAGTGTAGTTCTTGTTCATAATTTCATACAGTTTATATACATATATGTACAT
ATATATACAATTCGTGTTCGACATGGTATGTTTCGGTTT
Found at i:615542 original size:204 final size:207
Alignment explanation
Indices: 615182--615610 Score: 686
Period size: 204 Copynumber: 2.1 Consensus size: 207
615172 TTGCTTGGAA
* *
615182 AGTAGGATATTTGTTAGTGTAGCTCTTGTTCATAATTTCATACAGTTTATATACATATATATATA
1 AGTAGGATATTTGTTAGTGTAGCTCTCGTTCATAATTGCATACAGTTTATATACATATATATATA
* *
615247 TATATATATACAATTCGTGTTCGACATGGTATGTTTCAGTTTGTAGGATATTTGTTAGTGTAGTT
66 CATATATATAAAATTCGTGTTCGACATGGTATGTTTCAGTTTGTAGGATATTTGTTAGTGTAGTT
*
615312 CTTGTTCATAATTTCATACGGTTTATATACATATATGTAC-ATATACAATTCGTGTTCGACATGG
131 CTTGTTCATAATTTCATACAGTTTATATACATATATGTACAATATACAATTCGTGTTCGACATGG
615376 TATGTT-TCGGTT
196 TATGTTGT-GGTT
* * *
615388 TGTAGGTTATTTGTTAGTGTAGTTCTCGTTCATAATTGCATACAGTTTATATACATATAT-T-TA
1 AGTAGGATATTTGTTAGTGTAGCTCTCGTTCATAATTGCATACAGTTTATATACATATATATATA
* * *
615451 CATATATATAAAATTCGTGTTCGACATGGTATGTTTCGGTTTGTAGGTTTTTTGTTAGTGTAGTT
66 CATATATATAAAATTCGTGTTCGACATGGTATGTTTCAGTTTGTAGGATATTTGTTAGTGTAGTT
*
615516 CTTTTTCATAATTTCATACAGTTTATATACATATATGTACATATATATACAATTCGTGTTCGACA
131 CTTGTTCATAATTTCATACAGTTTATATACATATATGTAC--A-ATATACAATTCGTGTTCGACA
615581 TGGTATGTTGTGGTT
193 TGGTATGTTGTGGTT
615596 AGTAGGATATTTGTT
1 AGTAGGATATTTGTT
615611 CTTGTACTTC
Statistics
Matches: 204, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
204 100 0.49
205 1 0.00
206 55 0.27
208 47 0.23
209 1 0.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (207 bp):
AGTAGGATATTTGTTAGTGTAGCTCTCGTTCATAATTGCATACAGTTTATATACATATATATATA
CATATATATAAAATTCGTGTTCGACATGGTATGTTTCAGTTTGTAGGATATTTGTTAGTGTAGTT
CTTGTTCATAATTTCATACAGTTTATATACATATATGTACAATATACAATTCGTGTTCGACATGG
TATGTTGTGGTT
Found at i:620235 original size:22 final size:21
Alignment explanation
Indices: 620203--620275 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
620193 AATTTTTAAA
620203 ATTTAAATAATCAAAATCAGT
1 ATTTAAATAATCAAAATCAGT
***
620224 ATTTAAAATAATTTTTAA--A--
1 ATTT-AAATAA-TCAAAATCAGT
620243 ATTTAAATAATCAAAATCAGT
1 ATTTAAATAATCAAAATCAGT
620264 ATTTAAAATAAT
1 ATTT-AAATAAT
620276 TTTATAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
17 3 0.08
18 6 0.15
19 5 0.13
21 9 0.23
22 13 0.33
23 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTTAAATAATCAAAATCAGT
Found at i:620240 original size:40 final size:40
Alignment explanation
Indices: 620191--620292 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
620181 TTATTATTTG
620191 ATAATTTTTAAAATTTAAATAATCAAAATCAGTATTTAAA
1 ATAATTTTTAAAATTTAAATAATCAAAATCAGTATTTAAA
620231 ATAATTTTTAAAATTTAAATAATCAAAATCAGTATTTAAA
1 ATAATTTTTAAAATTTAAATAATCAAAATCAGTATTTAAA
* *
620271 ATAATTTTATAACATGTAAATA
1 ATAATTTT-TAAAATTTAAATA
620293 TGAATTTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
40 48 0.81
41 11 0.19
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (40 bp):
ATAATTTTTAAAATTTAAATAATCAAAATCAGTATTTAAA
Found at i:620725 original size:12 final size:12
Alignment explanation
Indices: 620708--620740 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
620698 TAATCTAATT
620708 GAAAAAATTATA
1 GAAAAAATTATA
620720 GAAAAAATTATA
1 GAAAAAATTATA
*
620732 AAAAAAATT
1 GAAAAAATT
620741 GGTTAACCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
GAAAAAATTATA
Found at i:622152 original size:555 final size:549
Alignment explanation
Indices: 620994--622503 Score: 1881
Period size: 552 Copynumber: 2.7 Consensus size: 549
620984 TAACTAAATA
* * * *
620994 TTCAATTTTTCT-AAAATCATACCTAATGTTTAATTTTTGTTTCATTTTAGTACCTTGTTCAAAA
1 TTCAATTTTTTTCAAAATCATACCTAATGTTTAGTTTTTGTTTCATTTTAGTACCTCGTTAAAAA
* * *
621058 CTTAATGTTAAGTTTTGAAAAAAATTGAATGCATTATATTTTTAACGGCGCAGTACTAAAATTA-
66 CTTAATGTTAAGTTTTGAAAAAAATTGAATGCGTTAAATTTTTAACGGCGCAATACTAAAA-TAG
* *
621122 AACAAAAACAAAGCGTTA-GATATGATTTTGAAAAAATTAAAAGTTTAGATACTAAAATAAATAA
130 AA-AAAAACAAA-AGTTATG-TATGATTTTGAAAAAATTAAAAGTTTAGATACTAAAATAGATAA
* * * *
621186 AAACTGATAGTTTAGGTACTAAACGCATAATGTACCCAATTTTATTTATAAGTCTAAACTATAA-
192 AAACTAATAATTTAGATACTAAACGCATAATTTA-CCAATTTTATTTATAAGTCTAAACTATAAT
* * *
621250 TCCTATTAAATGTTACATCAACTTTTTCACTTGTCGTTCATATATTGAGACTAACATGAAAATCT
256 TCC-GTTAAATGTTACATCAACTTTTTCACCTGTCGTTCATATACTGAGACTAACATGAAAAT-T
* *
621315 -AATTATGTTTGATTAATAAAAAATTTATATTTACATGTTATAAAATTATGTTTAAATAATCATT
319 AAATTATGTTTGATTAATAATAAATTTATATTTACATG-TATAAAATTATGATTAAATAATCATT
* *
621379 TTGA-TGATTGAATTTTTAAAAGCTATAAAATAATAATTAATTTATTAACTTTTTAAGTTTATTA
383 TTAATTG-TTGAATTTTTAAAAGCTATAAAATAATAATAAATTTATTAACTTTTTAAGTTTATTA
* ** * *
621443 TAATATTATAATGACTATTTTATAATAGTATGTAAATTTTATTGGGTAAACTACGTGTTTAGTAT
447 TAATATTATAATAACTATTTTATAATAGTAACTAAATTTTATTGGGCAAACTACATGTTTAGTAT
* *
621508 CTAAACTAACAGTTTTGATCCGTTTTAATACTTAAACT
512 ATAAACTAACAGTTTTGATCCATTTTAATACTTAAACT
* *** * *
621546 TTTAA-TTTTTTCAAAATCATACCTACCATTTAGTTTTTGTTTCATTTTAGTACCTGGTTGAAAA
1 TTCAATTTTTTTCAAAATCATACCTAATGTTTAGTTTTTGTTTCATTTTAGTACCTCGTTAAAAA
* ** *
621610 CTTAATGTTAAGTTTTTAACCAAATTGAACGCGTTAAATTTTTAACGGCGCAATACTAAAATAGA
66 CTTAATGTTAAGTTTTGAAAAAAATTGAATGCGTTAAATTTTTAACGGCGCAATACTAAAATAGA
* *
621675 ATAAAAACAAAATGTTATGTATGATTTTGAAAAAATTAAAAGTTTAGGTACTAAAATAGATTAAA
131 A-AAAAACAAAA-GTTATGTATGATTTTGAAAAAATTAAAAGTTTAGATACTAAAATAGATAAAA
* * *
621740 ACTAATAATATAGATACTACACACATAATTTACTCAATTTTATTTATAAGTCTAAACTAATAATT
194 ACTAATAATTTAGATACTAAACGCATAATTTAC-CAATTTTATTTATAAGTCTAAACT-ATAATT
* * *
621805 CCGTTAAATGTTACATCAACTTCTTTCACCTCTCGTTCATATACCGAGACTAACATAAAAATTAA
257 CCGTTAAATGTTACATCAACTT-TTTCACCTGTCGTTCATATACTGAGACTAACATGAAAATTAA
*
621870 ATTATGTTTGATTAATAATAAATTTATATTTACATGATATAAAATTATGCTTAAATAATCATTTT
321 ATTATGTTTGATTAATAATAAATTTATATTTACATG-TATAAAATTATGATTAAATAATCATTTT
* *
621935 CATTGTTGAATTTTTAAATA-TTATAAAATAATAATCAAATTTATTAACTTTTTAAGTTTATTAT
385 AATTGTTGAATTTTTAAA-AGCTATAAAATAATAAT-AAATTTATTAACTTTTTAAGTTTATTAT
*
621999 AATATTATAATAATTATTTTATAATAGTAACTAAATTTTATTGGGCAAACTACATGTTTAGTATA
448 AATATTATAATAACTATTTTATAATAGTAACTAAATTTTATTGGGCAAACTACATGTTTAGTATA
* * *
622064 TAAACTATCAGTTTTGGTCTATTTTAATACTTAAACT
513 TAAACTAACAGTTTTGATCCATTTTAATACTTAAACT
* *
622101 TTCAATTTTTTTCAAAACCATACCTAATGTTTAGTTTGT-TTTCATTTTAGTATCC-CGTTAAAA
1 TTCAATTTTTTTCAAAATCATACCTAATGTTTAGTTTTTGTTTCATTTTAGTA-CCTCGTTAAAA
** ** * * *
622164 ACTTAACATTAAGTTTTGAAGAAAAAAATTGAATAAGTTAAATTTTTAACAGTGCGATACTAAAA
65 ACTTAATGTTAAGTTTT---GAAAAAAATTGAATGCGTTAAATTTTTAACGGCGCAATACTAAAA
* *
622229 T-GAAACAAAA-ATAAGTATTTGGTATGATTTTGAAAAAATT-AAAGTTTAGATACTAAAAT-GA
127 TAGAAA-AAAACAAAAGT-TAT-GTATGATTTTGAAAAAATTAAAAGTTTAGATACTAAAATAG-
* * * * * * *
622290 ATCAAAATTAATAATTTAAATATTAAACGCATAATTTACC-----CATTTATAAGTCCAACCTGA
188 ATAAAAACTAATAATTTAGATACTAAACGCATAATTTACCAATTTTATTTATAAGTCTAAACT-A
* * * * * * *
622350 TAATCCCGTTAAATGTTATATCAACTTATTTCAACTGTGGTACATATACTAAGAATAACATGAAA
252 TAATTCCGTTAAATGTTACATCAACTT-TTTCACCTGTCGTTCATATACTGAGACTAACATGAAA
* *
622415 A-TATAATTATGTTTGACTAATAATAAATTTATATTTATATGTAATAAAATTATGATTAAATAAT
316 ATTA-AATTATGTTTGATTAATAATAAATTTATATTTACATGT-ATAAAATTATGATTAAATAAT
* * *
622479 TATTTTAATTATTGAATTATTAAAA
379 CATTTTAATTGTTGAATTTTTAAAA
622504 ATTTAATAAA
Statistics
Matches: 834, Mismatches: 101, Indels: 49
0.85 0.10 0.05
Matches are distributed among these distances:
549 4 0.00
550 146 0.18
551 8 0.01
552 211 0.25
553 25 0.03
554 128 0.15
555 163 0.20
556 86 0.10
557 26 0.03
558 37 0.04
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (549 bp):
TTCAATTTTTTTCAAAATCATACCTAATGTTTAGTTTTTGTTTCATTTTAGTACCTCGTTAAAAA
CTTAATGTTAAGTTTTGAAAAAAATTGAATGCGTTAAATTTTTAACGGCGCAATACTAAAATAGA
AAAAAACAAAAGTTATGTATGATTTTGAAAAAATTAAAAGTTTAGATACTAAAATAGATAAAAAC
TAATAATTTAGATACTAAACGCATAATTTACCAATTTTATTTATAAGTCTAAACTATAATTCCGT
TAAATGTTACATCAACTTTTTCACCTGTCGTTCATATACTGAGACTAACATGAAAATTAAATTAT
GTTTGATTAATAATAAATTTATATTTACATGTATAAAATTATGATTAAATAATCATTTTAATTGT
TGAATTTTTAAAAGCTATAAAATAATAATAAATTTATTAACTTTTTAAGTTTATTATAATATTAT
AATAACTATTTTATAATAGTAACTAAATTTTATTGGGCAAACTACATGTTTAGTATATAAACTAA
CAGTTTTGATCCATTTTAATACTTAAACT
Found at i:622931 original size:29 final size:30
Alignment explanation
Indices: 622867--622933 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
622857 GGGAGGAACC
*
622867 CAAAATTTAAAAAATTGTAATTTTAACCTT
1 CAAAATTTAAAAAATTGTAATTTTAACCCT
** *
622897 TGAAATTTAAAAAAATT-TAA-TTTGACCCT
1 CAAAATTT-AAAAAATTGTAATTTTAACCCT
622926 CAAAATTT
1 CAAAATTT
622934 TTAGAAATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
29 13 0.43
30 9 0.30
31 8 0.27
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (30 bp):
CAAAATTTAAAAAATTGTAATTTTAACCCT
Found at i:625998 original size:16 final size:16
Alignment explanation
Indices: 625977--626007 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
625967 AACTGATATG
625977 ATATTTACCTAACTTT
1 ATATTTACCTAACTTT
*
625993 ATATTTACCTGACTT
1 ATATTTACCTAACTT
626008 ATAAGAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTTACCTAACTTT
Found at i:628916 original size:26 final size:26
Alignment explanation
Indices: 628885--628958 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 26
628875 TAATGCACCG
628885 TTATGCATTTCATTTATGGCATCCTT
1 TTATGCATTTCATTTATGGCATCCTT
* *
628911 TTATGC----C-TTAAT-GCA-CC-G
1 TTATGCATTTCATTTATGGCATCCTT
628929 TTATGCATTTCATTTATGGCATCCTT
1 TTATGCATTTCATTTATGGCATCCTT
628955 TTAT
1 TTAT
628959 ACCTTAATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 6 0.17
19 2 0.06
20 3 0.08
21 4 0.11
22 2 0.06
23 4 0.11
24 3 0.08
25 2 0.06
26 10 0.28
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (26 bp):
TTATGCATTTCATTTATGGCATCCTT
Found at i:628937 original size:44 final size:44
Alignment explanation
Indices: 628847--628990 Score: 243
Period size: 44 Copynumber: 3.2 Consensus size: 44
628837 TATTCATTAT
* * *
628847 TTTCATTTATGACTTCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTTATGCC-TTAATGCACCGTTATGCA
628892 TTTCATTTATGGCATCCTTTTATGCCTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTTATGCCTTAATGCACCGTTATGCA
*
628936 TTTCATTTATGGCATCCTTTTATACCTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTTATGCCTTAATGCACCGTTATGCA
628980 TTTCATTTATG
1 TTTCATTTATG
628991 AATTCGTTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 72 0.76
45 23 0.24
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (44 bp):
TTTCATTTATGGCATCCTTTTATGCCTTAATGCACCGTTATGCA
Found at i:630381 original size:51 final size:52
Alignment explanation
Indices: 630277--630387 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 52
630267 GTCGATCTTA
* * * * *
630277 TCATGGAACTGTGGTGATGGTGGAATATTTACCAGAATGCTGGTTATTTGCT
1 TCATGGAAATGAGGTGATGGTCGAATATTCACCAGAATGCAGGTTATTTGCT
630329 TCATGGAAATGAGGTGATGGTCGAATA-TCACCAGAATGCAGGTTATTTGCT
1 TCATGGAAATGAGGTGATGGTCGAATATTCACCAGAATGCAGGTTATTTGCT
630380 TCATGGAA
1 TCATGGAA
630388 CCGAGTTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 30 0.56
52 24 0.44
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (52 bp):
TCATGGAAATGAGGTGATGGTCGAATATTCACCAGAATGCAGGTTATTTGCT
Found at i:631399 original size:23 final size:23
Alignment explanation
Indices: 631369--631445 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
631359 CAGCAACTGA
* *
631369 CAAGCATCACTGTATCAATTCAG
1 CAAGCATCATTGCATCAATTCAG
* *
631392 CAAGCATCATTACATCAATTTAG
1 CAAGCATCATTGCATCAATTCAG
*
631415 CAAGCATTATTGCATCAATTCAG
1 CAAGCATCATTGCATCAATTCAG
631438 CAAGCATC
1 CAAGCATC
631446 CTTTATTCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (23 bp):
CAAGCATCATTGCATCAATTCAG
Found at i:631563 original size:20 final size:19
Alignment explanation
Indices: 631538--631605 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
631528 AACCCTTAGA
*
631538 AATATCAAGCAGAATAAACC
1 AATATCAAACAGAATAAA-C
*
631558 AATATCAAACATAAGTAAAC
1 AATATCAAACAGAA-TAAAC
* * *
631578 AATATAAAACATAATCAAGC
1 AATATCAAACAGAAT-AAAC
631598 AATATCAA
1 AATATCAA
631606 GAAGAATCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 36 0.88
21 4 0.10
ACGTcount: A:0.59, C:0.16, G:0.06, T:0.19
Consensus pattern (19 bp):
AATATCAAACAGAATAAAC
Found at i:633995 original size:64 final size:66
Alignment explanation
Indices: 633927--634048 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 66
633917 CCCTACTTAA
* *
633927 GGTATCGGTACCCTCATGGCATTCTGTAATT-TT-TCGTTCAAGGGGGTATAAGTACCCAACAGG
1 GGTATCGGTACCCTCATGACATTCTGTAATTCTTCTCGTTCAAGAGGGTATAAGTACCCAACAGG
633990 G
66 G
* ** *
633991 GGTATCGGTACCCTTATGACATTCTGTAATTCTTCTCGTTTGAGAGGGTATCAGTACC
1 GGTATCGGTACCCTCATGACATTCTGTAATTCTTCTCGTTCAAGAGGGTATAAGTACC
634049 TGTTGAATGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 29 0.58
65 2 0.04
66 19 0.38
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (66 bp):
GGTATCGGTACCCTCATGACATTCTGTAATTCTTCTCGTTCAAGAGGGTATAAGTACCCAACAGG
G
Found at i:636462 original size:35 final size:35
Alignment explanation
Indices: 636423--636500 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
636413 TAATGATACC
* *
636423 AAATCGTGAGAGCGAATACCACTGCAACTATTTCT
1 AAATCATGAGAGCGAATACCACTGCAACCATTTCT
* *
636458 AAATCATGAGAGTGAATACCACTGCAGCCATTTCT
1 AAATCATGAGAGCGAATACCACTGCAACCATTTCT
636493 AAATCATG
1 AAATCATG
636501 GGTGGGGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (35 bp):
AAATCATGAGAGCGAATACCACTGCAACCATTTCT
Found at i:640096 original size:23 final size:23
Alignment explanation
Indices: 640039--640100 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
640029 CTTGTATAAA
640039 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * * *
640062 TACACTGGAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
640085 TGCACCGAAGTGCCAC
1 TGCACCGAAGTGCCAC
640101 ATAAGATGTC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:643242 original size:24 final size:24
Alignment explanation
Indices: 643214--643279 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
643204 TCAGGTTCAG
643214 GTTCGGGTTCGGGTTTGGATTT-A
1 GTTCGGGTTCGGGTTTGGATTTGA
** *
643237 GATTCGAATTCAGGTTTGGATTTGA
1 G-TTCGGGTTCGGGTTTGGATTTGA
* *
643262 GTTTGGGTTTGGGTTTGG
1 GTTCGGGTTCGGGTTTGG
643280 GATAGGGTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.03
24 30 0.91
25 2 0.06
ACGTcount: A:0.12, C:0.06, G:0.38, T:0.44
Consensus pattern (24 bp):
GTTCGGGTTCGGGTTTGGATTTGA
Found at i:643280 original size:6 final size:6
Alignment explanation
Indices: 643249--643353 Score: 77
Period size: 6 Copynumber: 17.7 Consensus size: 6
643239 TTCGAATTCA
* * * * *
643249 GGTTTG GATTTG AGTTTG GGTTTG GGTTTG GGATAG GGTTTG GGTTTA
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* * * ** * * *
643297 AGATGG GGTTCA AGTTTG GGTTTG GGTTT- GGTTTC GGTTCG GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
*
643344 GGTTCG GGTT
1 GGTTTG GGTT
643354 AAGGTTAGAG
Statistics
Matches: 73, Mismatches: 25, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
5 5 0.07
6 68 0.93
ACGTcount: A:0.09, C:0.04, G:0.44, T:0.44
Consensus pattern (6 bp):
GGTTTG
Found at i:643335 original size:17 final size:17
Alignment explanation
Indices: 643310--643350 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
643300 TGGGGTTCAA
* *
643310 GTTTGGGTTTGGGTTTG
1 GTTTCGGTTCGGGTTTG
643327 GTTTCGGTTCGGGTTTG
1 GTTTCGGTTCGGGTTTG
*
643344 GGTTCGG
1 GTTTCGG
643351 GTTAAGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.07, G:0.46, T:0.46
Consensus pattern (17 bp):
GTTTCGGTTCGGGTTTG
Found at i:643725 original size:111 final size:111
Alignment explanation
Indices: 643519--643725 Score: 319
Period size: 111 Copynumber: 1.9 Consensus size: 111
643509 GTTTGGGGAA
* * * * *
643519 GAACACAGATGAACCATGGTTTAATTTTTGGGTGTTTGATCAAAAAAATAGGAATGAGTTTAGGT
1 GAACACAAATGAACAATGGTTGAATTTTTGGGTGTTTGATCAAAAAAACAGAAATGAGTTTAGGT
*
643584 TTTGGTGTTTGTGAAGATCAAATAATGGTTTGGGGAAGAATTGGAT
66 TTTGGTGTTTGTGAAGATCAAAGAATGGTTTGGGGAAGAATTGGAT
*
643630 GAACACAAATGAACAATGGTTGAATTTTTGGGTGTTTGATCAAAAAAACATGAAATG-GTTTGGG
1 GAACACAAATGAACAATGGTTGAATTTTTGGGTGTTTGATCAAAAAAACA-GAAATGAGTTTAGG
643694 TTTTGGTGTTTGTGAAGATCAAAGGAA-GGTTT
65 TTTTGGTGTTTGTGAAGATCAAA-GAATGGTTT
643726 TTGGGATGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
111 80 0.92
112 7 0.08
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.34
Consensus pattern (111 bp):
GAACACAAATGAACAATGGTTGAATTTTTGGGTGTTTGATCAAAAAAACAGAAATGAGTTTAGGT
TTTGGTGTTTGTGAAGATCAAAGAATGGTTTGGGGAAGAATTGGAT
Found at i:643765 original size:111 final size:110
Alignment explanation
Indices: 643541--643767 Score: 282
Period size: 111 Copynumber: 2.0 Consensus size: 110
643531 ACCATGGTTT
* *
643541 AATTTTTGGGTGTTTGATCAAAAAAATAGGAATGAGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
1 AATTTTTGGGTGTTTGATCAAAAAAACAGAAATGAGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
* ** * *
643606 TAATGGTTTGGGGAAGAATTGGATGAACACAAATGAACAATGGTTG
66 GAATGGTTTGGGGAAGAAACGGATGAACAAAAATGAACAAT-GATG
*
643652 AATTTTTGGGTGTTTGATCAAAAAAACATGAAATG-GTTTGGGTTTTGGTGTTTGTGAAGATCAA
1 AATTTTTGGGTGTTTGATCAAAAAAACA-GAAATGAGTTTAGGTTTTGGTGTTTGTGAAGATCAA
* *
643716 AGGAA-GGTTTTTGGGATGAACACGGATGAA-AAAAATGAACACAT-ATG
65 A-GAATGG-TTTGGGGAAGAA-ACGGATGAACAAAAATGAACA-ATGATG
643763 AATTT
1 AATTT
643768 CTAGAGAGAA
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
111 65 0.64
112 27 0.27
113 9 0.09
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (110 bp):
AATTTTTGGGTGTTTGATCAAAAAAACAGAAATGAGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
GAATGGTTTGGGGAAGAAACGGATGAACAAAAATGAACAATGATG
Found at i:644130 original size:33 final size:32
Alignment explanation
Indices: 644077--644165 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 32
644067 TATATATGTT
644077 TATATTAATATATAAG-TTATATATACTAATGA-AC
1 TATA-TAATATAT-AGTTTATATATAC-AAT-ATAC
*
644111 TATATAATATATAGTTTATATATACCATATAC
1 TATATAATATATAGTTTATATATACAATATAC
* *
644143 TTTAT-ATATATAGTTTTTATATA
1 TATATAATATATAGTTTATATATA
644166 TAGTTCATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 18 0.36
32 10 0.20
33 18 0.36
34 4 0.08
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATAATATATAGTTTATATATACAATATAC
Found at i:644134 original size:18 final size:18
Alignment explanation
Indices: 644064--644152 Score: 64
Period size: 18 Copynumber: 5.1 Consensus size: 18
644054 TTCTTTCAAT
644064 TAATATATATGTTTATAT-
1 TAATATATA-GTTTATATA
644082 TAATATATAAG-TTATATA
1 TAATATAT-AGTTTATATA
* *
644100 TACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
644115 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
** *
644133 TACCATATACTTTATATA
1 TAATATATAGTTTATATA
644151 TA
1 TA
644153 TAGTTTTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.02
15 9 0.16
16 2 0.04
17 9 0.16
18 34 0.60
19 2 0.04
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (18 bp):
TAATATATAGTTTATATA
Found at i:644168 original size:13 final size:13
Alignment explanation
Indices: 644137--644175 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
644127 TATATATACC
*
644137 ATATACTTTATAT
1 ATATAGTTTATAT
*
644150 ATATAGTTTTTAT
1 ATATAGTTTATAT
*
644163 ATATAGTTCATAT
1 ATATAGTTTATAT
644176 GTAAACTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (13 bp):
ATATAGTTTATAT
Found at i:644198 original size:18 final size:18
Alignment explanation
Indices: 644177--644223 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
644167 AGTTCATATG
644177 TAAACTATATA-GTAAATA
1 TAAACTATATATGT-AATA
*
644195 TAAACTATATATGTAGTA
1 TAAACTATATATGTAATA
*
644213 TATACTATATA
1 TAAACTATATA
644224 AATAGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAACTATATATGTAATA
Found at i:644260 original size:15 final size:15
Alignment explanation
Indices: 644242--644275 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
644232 ATTAATTAAT
644242 ATATTC-TACCATATA
1 ATATTCATA-CATATA
644257 ATATTCATACATATA
1 ATATTCATACATATA
644272 ATAT
1 ATAT
644276 ATACTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTCATACATATA
Found at i:644260 original size:17 final size:17
Alignment explanation
Indices: 644238--644277 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
644228 GTTTATTAAT
644238 TAATATATTC-TACCATA
1 TAATATATTCATA-CATA
644255 T-A-ATATTCATACATA
1 TAATATATTCATACATA
644270 TAATATAT
1 TAATATAT
644278 ACTTTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 11 0.55
16 4 0.20
17 5 0.25
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATATTCATACATA
Found at i:644302 original size:15 final size:14
Alignment explanation
Indices: 644287--644327 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
644277 TACTTTGAAT
644287 TTATATAATATAAA
1 TTATATAATATAAA
*
644301 TTATACAAATATAAA
1 TTATA-TAATATAAA
*
644316 TTATATTATATA
1 TTATATAATATA
644328 GTATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:644423 original size:7 final size:7
Alignment explanation
Indices: 644413--644501 Score: 71
Period size: 7 Copynumber: 13.1 Consensus size: 7
644403 TATAGTTTAT
644413 ATATATA
1 ATATATA
644420 ATATATA
1 ATATATA
*
644427 GTATATA
1 ATATATA
644434 A-ATATA
1 ATATATA
644440 A-ACTATA
1 ATA-TATA
*
644447 GTATATA
1 ATATATA
644454 ATATATA
1 ATATATA
644461 A-ATATA
1 ATATATA
644467 A-ACTATA
1 ATA-TATA
* *
644474 GTTTAT-
1 ATATATA
644480 ATATATA
1 ATATATA
*
644487 GTATATA
1 ATATATA
*
644494 GTATATA
1 ATATATA
644501 A
1 A
644502 ATAATTTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
6 18 0.27
7 48 0.72
8 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:644424 original size:20 final size:20
Alignment explanation
Indices: 644369--644500 Score: 77
Period size: 20 Copynumber: 5.9 Consensus size: 20
644359 ATTTATCAAC
644369 TATAATATATAGTTTACGTATAAA
1 TATAATATATAGTTTA--TAT--A
644393 CTATAATTTATATAGTTTATATA
1 -TATAA--TATATAGTTTATATA
* *
644416 TATAATATATAGTATATAAA
1 TATAATATATAGTTTATATA
644436 TATAA-ACTATAGTATATAATATA
1 TATAATA-TATAGT-T-T-ATATA
*
644459 TAAATATAAACTATAGTTTATATA
1 T--ATA-ATA-TATAGTTTATATA
* *
644483 TATAGTATATAGTATATA
1 TATAATATATAGTTTATA
644501 AATAATTTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
19 1 0.01
20 34 0.38
21 1 0.01
22 9 0.10
23 6 0.07
24 6 0.07
25 12 0.13
26 2 0.02
27 19 0.21
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (20 bp):
TATAATATATAGTTTATATA
Found at i:644493 original size:27 final size:26
Alignment explanation
Indices: 644302--644486 Score: 134
Period size: 27 Copynumber: 7.2 Consensus size: 26
644292 TAATATAAAT
* * *
644302 TATACAAATATAAATTATATTATATA
1 TATATAAATATAAACTATAGTATATA
*
644328 GTATATAAATATCAACTATAGTATATA
1 -TATATAAATATAAACTATAGTATATA
** *
644355 T-TATATTTATCAACTATA--ATATA
1 TATATAAATATAAACTATAGTATATA
* **
644378 TAGTTTACGTATAAACTATA--AT-T-
1 TA-TATAAATATAAACTATAGTATATA
** * *
644401 TATATAGTTTATATA-TATAATATATA
1 TATATA-AATATAAACTATAGTATATA
644427 GTATATAAATATAAACTATAGTATATAA
1 -TATATAAATATAAACTATAGTATAT-A
*
644455 TATATAAATATAAACTATAGTTTATA
1 TATATAAATATAAACTATAGTATATA
644481 TATATA
1 TATATA
644487 GTATATAGTA
Statistics
Matches: 129, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
22 7 0.05
23 13 0.10
24 3 0.02
25 31 0.24
26 13 0.10
27 61 0.47
28 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (26 bp):
TATATAAATATAAACTATAGTATATA
Found at i:644606 original size:31 final size:31
Alignment explanation
Indices: 644562--644659 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
644552 GCTACTAAAC
*
644562 TATATATA-T-TATATAGTTTACGTAGTTTA
1 TATATATAGTATATATAGTTTACATAGTTTA
*
644591 TATATATAGTATATATAGTTTACATGGTTTA
1 TATATATAGTATATATAGTTTACATAGTTTA
* *
644622 TATA-AGTTAGTATATATTGTTTATATATAGTTTA
1 TATATA--TAGTATATATAG-TT-TACATAGTTTA
644656 TATA
1 TATA
644660 CTATTATCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.14
30 2 0.03
31 22 0.38
32 11 0.19
33 2 0.03
34 13 0.22
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (31 bp):
TATATATAGTATATATAGTTTACATAGTTTA
Found at i:644609 original size:22 final size:23
Alignment explanation
Indices: 644566--644612 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
644556 CTAAACTATA
* *
644566 TATATTATATAGTTTACGTAGTT
1 TATATTATATAGTATACATAGTT
*
644589 TATA-TATATAGTATATATAGTT
1 TATATTATATAGTATACATAGTT
644611 TA
1 TA
644613 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (23 bp):
TATATTATATAGTATACATAGTT
Found at i:644648 original size:11 final size:11
Alignment explanation
Indices: 644584--644659 Score: 61
Period size: 11 Copynumber: 7.0 Consensus size: 11
644574 ATAGTTTACG
644584 TAGTTTATATA
1 TAGTTTATATA
*
644595 TA-TAGTATATA
1 TAGT-TTATATA
*
644606 TAG-TT-TACA
1 TAGTTTATATA
*
644615 TGGTTTATATA
1 TAGTTTATATA
644626 -AGTTAGTATATA
1 TAGTT--TATATA
*
644638 TTGTTTATATA
1 TAGTTTATATA
644649 TAGTTTATATA
1 TAGTTTATATA
644660 CTATTATCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
9 5 0.10
10 7 0.14
11 29 0.58
12 6 0.12
13 3 0.06
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (11 bp):
TAGTTTATATA
Found at i:644728 original size:2 final size:2
Alignment explanation
Indices: 644715--644987 Score: 77
Period size: 2 Copynumber: 133.5 Consensus size: 2
644705 ACTCTAAACC
*
644715 AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AA ACT AT AT AGT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * * *
644758 TT AT AT AT A- AT -T CAT AT A- AT TT AT AA AT AA ACT AT AT A- AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
644798 TT AT AT -T A- AT AA ACT AT GT AGT TT AT AT AT AGT -T CA- AT AGT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT A-T AT -AT AT A-T
* * * * *
644839 -T CAT AT AT AA ACT AT AT AGT TT AT AC AT GGT AT AT AT AGT TT AT
1 AT -AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT AT A-T AT AT
* *
644883 AC AT A- AT AT AT AT AT AT AT AT AT AT AT AGT TT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* * * * *
644926 AT A- AC A- AT AT AA AT AT AA ACT AT AT AGT TT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* *
644968 AT AT CT AT AT TT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
644988 GTTGTTTCAA
Statistics
Matches: 196, Mismatches: 43, Indels: 64
0.65 0.14 0.21
Matches are distributed among these distances:
1 13 0.07
2 163 0.83
3 20 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:644762 original size:20 final size:20
Alignment explanation
Indices: 644739--644962 Score: 137
Period size: 20 Copynumber: 11.4 Consensus size: 20
644729 TATATATATA
644739 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
* *
644759 TATATAT-AATTCATATAATT
1 TATATATAAACT-ATATAGTT
* *
644779 TATAAATAAACTATATAATT
1 TATATATAAACTATATAGTT
*
644799 TATATTAATAAACTATGTAGTT
1 TATA-T-ATAAACTATATAGTT
**
644821 TATATAT-AGTTCA-ATAGTT
1 TATATATAAACT-ATATAGTT
*
644840 CATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
* **
644860 TATACATGGTA-TATATAGTT
1 TATATAT-AAACTATATAGTT
*
644880 TATACAT-AA-TATATA---
1 TATATATAAACTATATAGTT
*
644895 TATATATATA-TATATAGTT
1 TATATATAAACTATATAGTT
* * * *
644914 TATATATAGTA-TATAACAATA
1 TATATATA-AACTAT-ATAGTT
*
644935 TAAATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
644955 TGTATATA
1 TATATATA
644963 TATATATATC
Statistics
Matches: 159, Mismatches: 30, Indels: 30
0.73 0.14 0.14
Matches are distributed among these distances:
15 6 0.04
16 7 0.04
18 7 0.04
19 25 0.16
20 79 0.50
21 18 0.11
22 17 0.11
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:644936 original size:32 final size:34
Alignment explanation
Indices: 644869--644942 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
644859 TTATACATGG
*
644869 TATATATAGTTTATACATAATATATATATATATA
1 TATATATAGTTTATACATAATATATATACATATA
* *
644903 TATATATAGTTTATATATAGTATATA-ACA-ATA
1 TATATATAGTTTATACATAATATATATACATATA
*
644935 TAAATATA
1 TATATATA
644943 AACTATATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 10 0.28
33 2 0.06
34 24 0.67
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (34 bp):
TATATATAGTTTATACATAATATATATACATATA
Found at i:650034 original size:2 final size:2
Alignment explanation
Indices: 650027--650056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
650017 TATAATTTAA
650027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
650057 TTTTAATTTT
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):
AT
Found at i:651192 original size:60 final size:60
Alignment explanation
Indices: 651113--651225 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
651103 GTCCCTCGAT
* * *
651113 TATAGGGTGATGTTCTGTTGAGT-TCATCGACTATTAAACGCTACAAAATGATCCATCTAC
1 TATAGGGTGATGTTCTGTTGAATCTC-TCAACTATTAAAAGCTACAAAATGATCCATCTAC
* * *
651173 TATAGGGTGTTGCTT-TGTTGAATCTCTCAATTATTAAAAGTTACAAAATGATC
1 TATAGGGTGATG-TTCTGTTGAATCTCTCAACTATTAAAAGCTACAAAATGATC
651226 ACCCGACTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 41 0.91
61 4 0.09
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (60 bp):
TATAGGGTGATGTTCTGTTGAATCTCTCAACTATTAAAAGCTACAAAATGATCCATCTAC
Found at i:651553 original size:59 final size:59
Alignment explanation
Indices: 651442--651555 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
651432 CTAAATAGTT
* * *
651442 GAATGACCATTTTATAACTTTTAATAGTTGGGGGACTCAAGAAAATAACACCCTAAATC
1 GAATGACCATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAACACCCTAAATC
* * * *
651501 GAATGACTATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGCATCACCCTA
1 GAATGACCATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAACACCCTA
651556 TTGTCGAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (59 bp):
GAATGACCATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAACAACACCCTAAATC
Found at i:662382 original size:16 final size:17
Alignment explanation
Indices: 662348--662387 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
662338 TTATATGAAC
*
662348 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
662365 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
662381 TGATATG
1 TGATATG
662388 CCACATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:662941 original size:23 final size:23
Alignment explanation
Indices: 662907--662994 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
662897 AAATCTTAAA
*
662907 TGGCA-TTACGGTGCATTTCTACG
1 TGGCACTT-CGGTGCAATTCTACG
662930 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
662953 TGGTC-CTTCGAG-ACAAATTCTACG
1 TGG-CACTTCG-GTGC-AATTCTACG
662977 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
662995 TATATGAGCT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 34 0.61
24 22 0.39
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:663642 original size:21 final size:23
Alignment explanation
Indices: 663616--663661 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
663606 TGTAGCAGTA
*
663616 CTGTAGC-AGGGTATCGG-TTCC
1 CTGTAGCAAGGGAATCGGTTTCC
663637 CTGTAGCAAGGGAATCGGTTTCC
1 CTGTAGCAAGGGAATCGGTTTCC
663660 CT
1 CT
663662 CTGACAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.28
Consensus pattern (23 bp):
CTGTAGCAAGGGAATCGGTTTCC
Found at i:667657 original size:12 final size:12
Alignment explanation
Indices: 667640--667664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
667630 AAGAGTTGAT
667640 AAGTTAAATTTG
1 AAGTTAAATTTG
667652 AAGTTAAATTTG
1 AAGTTAAATTTG
667664 A
1 A
667665 CTTGTCATCA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AAGTTAAATTTG
Found at i:668397 original size:16 final size:17
Alignment explanation
Indices: 668363--668402 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
668353 TTATATGAAC
*
668363 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
668380 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
668396 TGATATG
1 TGATATG
668403 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:668979 original size:23 final size:23
Alignment explanation
Indices: 668945--668990 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
668935 AAATCTTAAA
*
668945 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
668968 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
668991 CAGTCCTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:669683 original size:21 final size:23
Alignment explanation
Indices: 669657--669699 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
669647 AGCAGTACTA
*
669657 TAGCA-GGGTATCGG-TTCCCTG
1 TAGCAGGGGAATCGGTTTCCCTG
669678 TAGCAGGGGAATCGGTTTCCCT
1 TAGCAGGGGAATCGGTTTCCCT
669700 CTGACAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.16, C:0.23, G:0.33, T:0.28
Consensus pattern (23 bp):
TAGCAGGGGAATCGGTTTCCCTG
Found at i:670757 original size:21 final size:21
Alignment explanation
Indices: 670732--670819 Score: 113
Period size: 21 Copynumber: 4.2 Consensus size: 21
670722 TGTCCCGTAT
670732 GACCACATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
* * * *
670753 AACCAAATATATGTCCCGAAG
1 GACCACATATATGTTCCAAAG
*
670774 GACCGCATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
* *
670795 GACCACATATATGTCCCGAAG
1 GACCACATATATGTTCCAAAG
670816 GACC
1 GACC
670820 GCGTAAAACC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
GACCACATATATGTTCCAAAG
Found at i:670820 original size:42 final size:42
Alignment explanation
Indices: 670722--670821 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
670712 CTCGTAGAAT
* * *
670722 TGTCCCGTATGACCACATATATGTTCCAAAGAACCAAATATA
1 TGTCCCGAAGGACCGCATATATGTTCCAAAGAACCAAATATA
* *
670764 TGTCCCGAAGGACCGCATATATGTTCCAAAGGACCACATATA
1 TGTCCCGAAGGACCGCATATATGTTCCAAAGAACCAAATATA
670806 TGTCCCGAAGGACCGC
1 TGTCCCGAAGGACCGC
670822 GTAAAACCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (42 bp):
TGTCCCGAAGGACCGCATATATGTTCCAAAGAACCAAATATA
Found at i:671248 original size:13 final size:12
Alignment explanation
Indices: 671227--671274 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
671217 CATATAACTT
671227 ATATAACATATAC
1 ATAT-ACATATAC
671240 ATATCACATA-AC
1 ATAT-ACATATAC
671252 ATATACATATCAC
1 ATATACATAT-AC
671265 ATA-ACATATA
1 ATATACATATA
671275 ATACCAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.19
12 12 0.38
13 14 0.44
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATACATATAC
Found at i:671252 original size:18 final size:18
Alignment explanation
Indices: 671229--671274 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
671219 TATAACTTAT
671229 ATAACATATACATATCAC
1 ATAACATATACATATCAC
671247 ATAACATATACATATCAC
1 ATAACATATACATATCAC
671265 ATAACATATA
1 ATAACATATA
671275 ATACCAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAACATATACATATCAC
Found at i:671271 original size:5 final size:6
Alignment explanation
Indices: 671227--671274 Score: 55
Period size: 7 Copynumber: 7.8 Consensus size: 6
671217 CATATAACTT
671227 ATATAAC ATATAC ATATCAC ATA-AC ATATAC ATATCAC ATA-AC ATATA
1 ATAT-AC ATATAC ATAT-AC ATATAC ATATAC ATAT-AC ATATAC ATATA
671275 ATACCAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 10 0.27
6 13 0.35
7 14 0.38
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (6 bp):
ATATAC
Found at i:674791 original size:23 final size:22
Alignment explanation
Indices: 674765--674808 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
674755 ATAAACATTT
*
674765 CATATAATATTATCATACAAAAC
1 CATATAAAATT-TCATACAAAAC
*
674788 CATATAAAATTTCATATAAAA
1 CATATAAAATTTCATACAAAA
674809 AATATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
CATATAAAATTTCATACAAAAC
Found at i:674805 original size:12 final size:12
Alignment explanation
Indices: 674754--674808 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
674744 CCTAACAATT
674754 TATAAACATTTCA
1 TATAAA-ATTTCA
*
674767 TATAATATTATCA
1 TATAAAATT-TCA
* *
674780 TACAAAA--CCA
1 TATAAAATTTCA
674790 TATAAAATTTCA
1 TATAAAATTTCA
674802 TATAAAA
1 TATAAAA
674809 AATATATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
10 8 0.24
12 12 0.36
13 13 0.39
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (12 bp):
TATAAAATTTCA
Found at i:674850 original size:18 final size:18
Alignment explanation
Indices: 674827--674868 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
674817 CATGCACATA
674827 TATCATCATCAACATTAT
1 TATCATCATCAACATTAT
* * *
674845 TATCATTATCCATATTAT
1 TATCATCATCAACATTAT
674863 TATCAT
1 TATCAT
674869 TAATTCCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (18 bp):
TATCATCATCAACATTAT
Found at i:675135 original size:23 final size:23
Alignment explanation
Indices: 675109--675172 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
675099 ACCACATATA
* * *
675109 TGTCCCGAAGGACCTCGTAGAAT
1 TGTCCCGAAGAACCACATAGAAT
675132 TGTCCCGAAGAACCACATAGAAT
1 TGTCCCGAAGAACCACATAGAAT
*
675155 TGTCCTGTAAG-ACCACAT
1 TGTCCCG-AAGAACCACAT
675173 TTATGTTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 33 0.92
24 3 0.08
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
TGTCCCGAAGAACCACATAGAAT
Found at i:675242 original size:21 final size:21
Alignment explanation
Indices: 675098--675251 Score: 105
Period size: 21 Copynumber: 7.1 Consensus size: 21
675088 TGTCCTGAAA
*
675098 GACCACATATATGTCCCGAAG
1 GACCACATATATGTTCCGAAG
* * * *
675119 GACCTCGTAGAATTGTCCCGAAG
1 GACCACATA-TA-TGTTCCGAAG
* *
675142 AACCACATAGAAT-TGTCCTGTAA-
1 GACCACATA-TATGT-TCC-G-AAG
* *
675165 GACCACATTTATGTTCCAAAG
1 GACCACATATATGTTCCGAAG
* * *
675186 GATCAAATATATGTCCCGAAG
1 GACCACATATATGTTCCGAAG
*
675207 GACCTCATATATGTTCCGAAG
1 GACCACATATATGTTCCGAAG
* *
675228 GACCACATATATGTTTCAAAG
1 GACCACATATATGTTCCGAAG
675249 GAC
1 GAC
675252 GGCGTAGAAC
Statistics
Matches: 103, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.02
21 62 0.60
22 9 0.09
23 28 0.27
24 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (21 bp):
GACCACATATATGTTCCGAAG
Found at i:679420 original size:20 final size:20
Alignment explanation
Indices: 679383--679421 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
679373 AGATTGAGTG
* * *
679383 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
679403 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
679422 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:683395 original size:31 final size:31
Alignment explanation
Indices: 683357--683419 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
683347 TACTTGTCTA
683357 ATTTTAAATCGTTTTCCTTTCTTTAAAGGAC
1 ATTTTAAATCGTTTTCCTTTCTTTAAAGGAC
683388 ATTTTAAATCGTTTTCCTTTCTTTAAAGGAC
1 ATTTTAAATCGTTTTCCTTTCTTTAAAGGAC
683419 A
1 A
683420 AGTATGTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (31 bp):
ATTTTAAATCGTTTTCCTTTCTTTAAAGGAC
Found at i:685513 original size:20 final size:20
Alignment explanation
Indices: 685484--685531 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
685474 TTACCTTATG
*
685484 GTATCAATCTTGTTCATACA
1 GTATCGATCTTGTTCATACA
685504 GTATCGATCTTGTTCATACA
1 GTATCGATCTTGTTCATACA
685524 GTATCGAT
1 GTATCGAT
685532 ACCCAGACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (20 bp):
GTATCGATCTTGTTCATACA
Found at i:688274 original size:2 final size:2
Alignment explanation
Indices: 688269--688305 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
688259 GTATGAAGAA
688269 AT AT AT AT 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 A
688306 AAAAATCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:688673 original size:31 final size:29
Alignment explanation
Indices: 688638--688701 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
688628 AAGTGATGCA
* *
688638 TTTAAACTCTTAAATTTTACTTTATTTATAT
1 TTTAAACACTTAAATTTTA-TTT-TTTAAAT
*
688669 TTTAATCACTTAAATTTTATTTTTTAAAT
1 TTTAAACACTTAAATTTTATTTTTTAAAT
688698 TTTA
1 TTTA
688702 TCACTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 10 0.33
30 3 0.10
31 17 0.57
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTAAACACTTAAATTTTATTTTTTAAAT
Found at i:688714 original size:28 final size:31
Alignment explanation
Indices: 688649--688715 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 31
688639 TTAAACTCTT
* *
688649 AAATTTTACTTTATTTATATTTTAATCACTT
1 AAATTTTACTTTATTTAAATTTTAATCACTC
688680 AAATTTTA-TTT-TTTAAATTTT-ATCACTC
1 AAATTTTACTTTATTTAAATTTTAATCACTC
*
688708 AATTTTTA
1 AAATTTTA
688716 AATTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 13 0.39
29 9 0.27
30 3 0.09
31 8 0.24
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (31 bp):
AAATTTTACTTTATTTAAATTTTAATCACTC
Found at i:688721 original size:28 final size:29
Alignment explanation
Indices: 688662--688722 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
688652 TTTTACTTTA
* * **
688662 TTTATATTTTAATCACTTAAATTTTATTT
1 TTTAAATTTTAATCACTCAAATTTTAAAT
*
688691 TTTAAATTTT-ATCACTCAATTTTTAAAT
1 TTTAAATTTTAATCACTCAAATTTTAAAT
688719 TTTA
1 TTTA
688723 TTTTAACTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTAAATTTTAATCACTCAAATTTTAAAT
Found at i:690284 original size:13 final size:13
Alignment explanation
Indices: 690266--690290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
690256 TTACATTTCA
690266 GGAAAACGTTTTT
1 GGAAAACGTTTTT
690279 GGAAAACGTTTT
1 GGAAAACGTTTT
690291 CTGTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
GGAAAACGTTTTT
Found at i:690580 original size:22 final size:21
Alignment explanation
Indices: 690554--690609 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 21
690544 TATTGAAATA
690554 AAAATATAATATTATATATATT
1 AAAATATAATATTATAT-TATT
690576 AAAATATAATATTATATTATT
1 AAAATATAATATTATATTATT
690597 AGAAATATTAATA
1 A-AAATA-TAATA
690610 AATGTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.16
22 22 0.69
23 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAATATAATATTATATTATT
Found at i:690903 original size:42 final size:42
Alignment explanation
Indices: 690840--690935 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
690830 TTTCTCCAAC
* *
690840 CAAACACTAAAAAAACATTTTCCGAAAAACGAATTACGTGGAA
1 CAAACAC-AAAAAAACATTTTCCGAAAAACAAATTACGTGAAA
* * * *
690883 TAAACACAGAAAAATATTTTCCGAAAAATAAATTACGTGAAA
1 CAAACACAAAAAAACATTTTCCGAAAAACAAATTACGTGAAA
690925 CAAACACAAAA
1 CAAACACAAAA
690936 TTTCGAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 39 0.87
43 6 0.13
ACGTcount: A:0.55, C:0.17, G:0.09, T:0.19
Consensus pattern (42 bp):
CAAACACAAAAAAACATTTTCCGAAAAACAAATTACGTGAAA
Found at i:696796 original size:16 final size:16
Alignment explanation
Indices: 696777--696843 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
696767 TGATCATTAA
696777 ATTTT-TAAATATTATT
1 ATTTTATAAA-ATTATT
696793 ATTTTATAAAATTA-T
1 ATTTTATAAAATTATT
*
696808 -TTTTA-AAATTTATCT
1 ATTTTATAAAATTAT-T
*
696823 AATTATTATAAAATAATT
1 -ATT-TTATAAAATTATT
696841 ATT
1 ATT
696844 AAATTAATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
13 6 0.15
14 5 0.12
15 2 0.05
16 9 0.22
17 9 0.22
18 4 0.10
19 6 0.15
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATAAAATTATT
Found at i:696814 original size:29 final size:33
Alignment explanation
Indices: 696776--696847 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
696766 TTGATCATTA
696776 AATTTTTAAATA-TTAT-T-ATT-TTATAAAAT
1 AATTTTTAAATATTTATCTAATTATTATAAAAT
*
696805 TATTTTTAAA-ATTTATCTAATTATTATAAAAT
1 AATTTTTAAATATTTATCTAATTATTATAAAAT
*
696837 AATTATTAAAT
1 AATTTTTAAAT
696848 TAATCATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 1 0.03
29 13 0.37
30 1 0.03
31 3 0.09
32 17 0.49
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
AATTTTTAAATATTTATCTAATTATTATAAAAT
Found at i:698664 original size:70 final size:69
Alignment explanation
Indices: 698510--698695 Score: 234
Period size: 70 Copynumber: 2.7 Consensus size: 69
698500 AATATCCGGG
* * * *
698510 ATTCGAATAACATAACATACAAGATACGAACACATGAATTTGAAC-AT-TGTCTTTGAATATGTA
1 ATTCAAATAACATAACATACAAGATATGAACACATGAATTCGAACAATATGTCTTTGAACATGTA
698573 GGTA
66 GGTA
* * * * *
698577 AGTCGAAA-AACATAACATTCAAGACATGAACACATGAATTCAAACAATATAGTCTTTGAGCATG
1 ATTC-AAATAACATAACATACAAGATATGAACACATGAATTCGAACAATAT-GTCTTTGAACATG
698641 TAGGTA
64 TAGGTA
* *
698647 ATTCAAATAACAAAACATACAAGATATGAACACATGGATTCGAACAATA
1 ATTCAAATAACATAACATACAAGATATGAACACATGAATTCGAACAATA
698696 ATTAAAATGG
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
67 35 0.35
68 4 0.04
69 4 0.04
70 56 0.57
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (69 bp):
ATTCAAATAACATAACATACAAGATATGAACACATGAATTCGAACAATATGTCTTTGAACATGTA
GGTA
Found at i:699319 original size:30 final size:30
Alignment explanation
Indices: 699138--699339 Score: 124
Period size: 30 Copynumber: 6.7 Consensus size: 30
699128 AATCCCCACT
* * *
699138 CCTTTCCCATTGCTACCACCAAAGG-CTCCT
1 CCTTTCCCAATGCCACCACC-AAGGCCTCCA
* * **
699168 CCTTTCCCAATGACACCACCAAAGCCTTTA
1 CCTTTCCCAATGCCACCACCAAGGCCTCCA
* ** * *
699198 CCTTTGCTGATGCCACCACCAAGGCCGCCT
1 CCTTTCCCAATGCCACCACCAAGGCCTCCA
* *
699228 CCTTTCCCAA-GTCCACCACCAATGCCCTTGC-
1 CCTTTCCCAATG-CCACCACCAA-GGCC-TCCA
* * ** *
699259 CC-TTACCAAAGCCACCACCAAGTACACCA
1 CCTTTCCCAATGCCACCACCAAGGCCTCCA
*
699288 CCTTTTCCAATGCCACCACCAAGGCCTCCA
1 CCTTTCCCAATGCCACCACCAAGGCCTCCA
* ** *
699318 CCCTTGTCAATTCCACCACCAA
1 CCTTTCCCAATGCCACCACCAA
699340 ATCCAATGCC
Statistics
Matches: 129, Mismatches: 36, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
28 1 0.01
29 8 0.06
30 113 0.88
31 6 0.05
32 1 0.01
ACGTcount: A:0.25, C:0.45, G:0.10, T:0.21
Consensus pattern (30 bp):
CCTTTCCCAATGCCACCACCAAGGCCTCCA
Found at i:699498 original size:30 final size:30
Alignment explanation
Indices: 699462--699531 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
699452 CTTACCAATC
**
699462 CCACCACCAAGTCCCCCATCC-TTTCCAAAG
1 CCACCACCAAGTCAACCA-CCTTTTCCAAAG
* * *
699492 CCACCACCGAGTCAACCACCTTTTCCTATG
1 CCACCACCAAGTCAACCACCTTTTCCAAAG
699522 CCACCACCAA
1 CCACCACCAA
699532 AGCCTCCTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.27, C:0.49, G:0.07, T:0.17
Consensus pattern (30 bp):
CCACCACCAAGTCAACCACCTTTTCCAAAG
Found at i:699498 original size:48 final size:48
Alignment explanation
Indices: 699385--699499 Score: 203
Period size: 48 Copynumber: 2.4 Consensus size: 48
699375 AGGCCCCTAC
* **
699385 CCTTTTCAAAGCCACCAAACTTACCAATCCCACCACCAAGTCCCCCAT
1 CCTTTCCAAAGCCACCACCCTTACCAATCCCACCACCAAGTCCCCCAT
699433 CCTTTCCAAAGCCACCACCCTTACCAATCCCACCACCAAGTCCCCCAT
1 CCTTTCCAAAGCCACCACCCTTACCAATCCCACCACCAAGTCCCCCAT
699481 CCTTTCCAAAGCCACCACC
1 CCTTTCCAAAGCCACCACC
699500 GAGTCAACCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.29, C:0.50, G:0.04, T:0.17
Consensus pattern (48 bp):
CCTTTCCAAAGCCACCACCCTTACCAATCCCACCACCAAGTCCCCCAT
Found at i:699577 original size:24 final size:24
Alignment explanation
Indices: 699550--699596 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
699540 CCTTTCCCAA
* *
699550 CTCCATCACCAAACCCTTCACCAG
1 CTCCACCACCAAACCCTCCACCAG
* *
699574 CTCCACCTCCAAGCCCTCCACCA
1 CTCCACCACCAAACCCTCCACCA
699597 CCAGCACCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.55, G:0.04, T:0.15
Consensus pattern (24 bp):
CTCCACCACCAAACCCTCCACCAG
Found at i:701454 original size:2 final size:2
Alignment explanation
Indices: 701449--701496 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
701439 ACACACACAC
701449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
701491 AT AT AT
1 AT AT AT
701497 CACACACACA
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):
AT
Found at i:701502 original size:2 final size:2
Alignment explanation
Indices: 701497--701532 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
701487 ATATATATAT
701497 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
701533 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.