Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006023.1 Hibiscus syriacus cultivar Beakdansim tig00014213_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: 1315283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:535981 original size:20 final size:20
Alignment explanation
Indices: 535952--536196 Score: 226
Period size: 20 Copynumber: 12.8 Consensus size: 20
535942 GCGATTTTCT
*
535952 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
535972 CGTGGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
535992 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
536012 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
536026 CTTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
536046 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
536066 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
536086 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
536106 CGTTGGGAT--T----TTTT
1 CGTTGCGATAGTCAAATTCG
* *
536120 CGTTGCGATAGTTAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
536140 CGTTGCGATAGTCATATTTG
1 CGTTGCGATAGTCAAATTCG
*
536160 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
536180 CGTTGTGATATTCAAAT
1 CGTTGCGATAGTCAAAT
536197 GAATGTGTAA
Statistics
Matches: 183, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
14 21 0.11
16 2 0.01
18 2 0.01
20 158 0.86
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:536034 original size:74 final size:74
Alignment explanation
Indices: 535908--536094 Score: 241
Period size: 74 Copynumber: 2.5 Consensus size: 74
535898 TTCAATCTGC
* * * * * *
535908 ATCATATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCC
1 ATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATTCAC
535973 GTGGCGATA
66 GTGGCGATA
* *
535982 ATCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATTTT-TGCTTTGCGATAGTCAAATTCA
1 ATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATAGTCAAATTCA
*
536046 CGTTGCGATA
65 CGTGGCGATA
* * * *
536056 GTTAAATTCGCGTTGCGATAGTCATATTCGCGTTACGAT
1 ATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
536095 AGTCAAATTC
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 1 0.01
74 97 0.99
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (74 bp):
ATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATTCAC
GTGGCGATA
Found at i:536074 original size:94 final size:94
Alignment explanation
Indices: 535952--536196 Score: 355
Period size: 94 Copynumber: 2.6 Consensus size: 94
535942 GCGATTTTCT
* * * *
535952 CGTTGCGATAGTCAAATTCCCGTGGCGATAATCAAATTCGCGTTGCGATAATCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAATCAAATTCGCGTTG
*
536017 CGATTTTTGCTTTGCGATAGTCAAATTCA
66 CGATTTTTGCGTTGCGATAGTCAAATTCA
* * *
536046 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATATTCGCGTTACGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAATCAAATTCGCGTTG
* * *
536111 GGATTTTTTCGTTGCGATAGTTAAATTCA
66 CGATTTTTGCGTTGCGATAGTCAAATTCA
* * * *
536140 CGTTGCGATAGTCATATTTGCGTTGCGATAGTCATATTCGCGTTGTGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAATCAAAT
536197 GAATGTGTAA
Statistics
Matches: 134, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 134 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAATCAAATTCGCGTTG
CGATTTTTGCGTTGCGATAGTCAAATTCA
Found at i:536124 original size:74 final size:74
Alignment explanation
Indices: 536046--536184 Score: 242
Period size: 74 Copynumber: 1.9 Consensus size: 74
536036 GTCAAATTCA
*
536046 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATATTCGCGTTACGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTTAAATTCACGTTGCGATAGTCATATTCGCGTTACGATAGTCAAATTCGCGTTG
536111 GGATTTTTT
66 GGATTTTTT
* * *
536120 CGTTGCGATAGTTAAATTCACGTTGCGATAGTCATATTTGCGTTGCGATAGTCATATTCGCGTTG
1 CGTTGCGATAGTTAAATTCACGTTGCGATAGTCATATTCGCGTTACGATAGTCAAATTCGCGTTG
536185 TGATATTCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (74 bp):
CGTTGCGATAGTTAAATTCACGTTGCGATAGTCATATTCGCGTTACGATAGTCAAATTCGCGTTG
GGATTTTTT
Found at i:539503 original size:20 final size:20
Alignment explanation
Indices: 539478--539625 Score: 183
Period size: 20 Copynumber: 7.3 Consensus size: 20
539468 AATTCAGTGA
539478 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
539498 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
** *
539518 TGCGATCACGT-ATTATCGCAT
1 TGCGAT-A-GTCAGAATCGCGT
539539 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
** * *
539559 TGCGATCACGT-ATTATTGCAT
1 TGCGAT-A-GTCAGAATCGCGT
539580 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
539600 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
539620 TGCGAT
1 TGCGAT
539626 TTACATATTC
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
19 4 0.04
20 73 0.68
21 27 0.25
22 4 0.04
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:539536 original size:41 final size:41
Alignment explanation
Indices: 539491--539605 Score: 212
Period size: 41 Copynumber: 2.8 Consensus size: 41
539481 GATAGTCAGA
*
539491 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
1 ATCGCATTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
539532 ATCGCATTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
1 ATCGCATTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
*
539573 ATTGCATTGCGATAGTCAGAATCGCGTTGCGAT
1 ATCGCATTGCGATAGTCAGAATCGCGTTGCGAT
539606 AGTCAGAATC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
Found at i:539541 original size:21 final size:21
Alignment explanation
Indices: 539511--539585 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
539501 GATAGTCAGA
*
539511 ATCGCGTTGCGATCACGTATT
1 ATCGCATTGCGATCACGTATT
**
539532 ATCGCATTGCGAT-A-GTCAGA
1 ATCGCATTGCGATCACGT-ATT
*
539552 ATCGCGTTGCGATCACGTATT
1 ATCGCATTGCGATCACGTATT
*
539573 ATTGCATTGCGAT
1 ATCGCATTGCGAT
539586 AGTCAGAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 25 0.58
22 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (21 bp):
ATCGCATTGCGATCACGTATT
Found at i:539544 original size:61 final size:61
Alignment explanation
Indices: 539478--539625 Score: 185
Period size: 61 Copynumber: 2.4 Consensus size: 61
539468 AATTCAGTGA
* **
539478 TGCGATAGTCAGAATCGCGTTGCGAT-A-GTCAGAATCGCGTTGCGATCACGT-ATTATCGCAT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGT-AGAATCGCATTGCGAT-A-GTCAGAATCGCAT
** * *
539539 TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATTGCATTGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGTAGAATCGCATTGCGATAGTCAGAATCGCAT
539600 TGCGATAGTCAGAATCGCGTTGCGAT
1 TGCGATAGTCAGAATCGCGTTGCGAT
539626 TTACATATTC
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
60 2 0.03
61 60 0.78
62 13 0.17
63 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATCACGTAGAATCGCATTGCGATAGTCAGAATCGCAT
Found at i:539665 original size:61 final size:61
Alignment explanation
Indices: 539477--539665 Score: 154
Period size: 61 Copynumber: 3.1 Consensus size: 61
539467 AAATTCAGTG
* * * * * **
539477 ATGCGATAGTCAGAATCGCGTTGCGATAGT-CAGAATCGCGTTGCGA-TCACGTATTATCGCA
1 ATGCGATAGTCAGAATCGCGTTGCGAT-TTACATATTCGCATTGCGATTCTC-TAAAATCGCA
* * ** * *
539538 TTGCGATAGTCAGAATCGCGTTGCGA-TCACGTATTATT-GCATTGCGATAGTC-AGAATCGCG
1 ATGCGATAGTCAGAATCGCGTTGCGATTTAC--A-TATTCGCATTGCGATTCTCTAAAATCGCA
* * *
539599 TTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTGCGATTTTCTAAAATCACA
1 ATGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTGCGATTCTCTAAAATCGCA
539660 ATGCGA
1 ATGCGA
539666 ATTTCGAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
59 4 0.04
60 14 0.14
61 68 0.67
62 12 0.12
63 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (61 bp):
ATGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTGCGATTCTCTAAAATCGCA
Found at i:539670 original size:21 final size:21
Alignment explanation
Indices: 539640--539686 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
539630 ATATTCGCAT
* *
539640 TGCGATTTTCTAAAATCACAA
1 TGCGAATTTCGAAAATCACAA
**
539661 TGCGAATTTCGAAAATCGTAA
1 TGCGAATTTCGAAAATCACAA
539682 TGCGA
1 TGCGA
539687 TGATCAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
TGCGAATTTCGAAAATCACAA
Found at i:539686 original size:102 final size:102
Alignment explanation
Indices: 539457--539706 Score: 249
Period size: 102 Copynumber: 2.5 Consensus size: 102
539447 TAAAACTTGT
* *
539457 TGCGAATTT-GAAATTCAGTGATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGC
1 TGCGAATTTCGAAAATC-GTAATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGC
* * * **
539521 GATCACGTATTATCGCATTGCGATAGTCAGAATCGCGT
65 GATCACATATTATCGCATTGCGATAGTCAAAATCACAA
** ** * * *
539559 TGCG-ATCACGTATTATTGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGC
1 TGCGAATTTCG-AAAATCGTAATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGC
* **
539623 GATTTACATA-T-TCGCATTGCGATTTTCTAAAATCACAA
65 GA-TCACATATTATCGCATTGCGATAGTC-AAAATCACAA
* *
539661 TGCGAATTTCGAAAATCGTAATGCGAT-GATCAAAATCGCTTTGCGA
1 TGCGAATTTCGAAAATCGTAATGCGATAG-TCAGAATCGCGTTGCGA
539707 ATCTGGAAAC
Statistics
Matches: 116, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
101 17 0.15
102 88 0.76
103 11 0.09
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (102 bp):
TGCGAATTTCGAAAATCGTAATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCG
ATCACATATTATCGCATTGCGATAGTCAAAATCACAA
Found at i:544006 original size:17 final size:17
Alignment explanation
Indices: 543981--544022 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
543971 ATTTTTACCC
543981 ATTTTTTTCTAATTT-A
1 ATTTTTTTCTAATTTGA
*
543997 ATTATTTTTCTTATTTGA
1 ATT-TTTTTCTAATTTGA
544015 ATTTTTTT
1 ATTTTTTT
544023 GATTGATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 4 0.17
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTTTTCTAATTTGA
Found at i:544400 original size:67 final size:67
Alignment explanation
Indices: 544292--544490 Score: 380
Period size: 67 Copynumber: 3.0 Consensus size: 67
544282 ACTTAAATGC
*
544292 TTTATGATTCTATGTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGGCTTTTAATCTTAT
1 TTTATGATTCTATTTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGGCTTTTAATCTTAT
544357 GT
66 GT
544359 TTTATGATTCTATTTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGGCTTTTAATCTTAT
1 TTTATGATTCTATTTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGGCTTTTAATCTTAT
544424 GT
66 GT
*
544426 TTTATGATTCTATTTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGACTTTTAATCTTAT
1 TTTATGATTCTATTTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGGCTTTTAATCTTAT
544491 AAGGGCTCAT
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 130 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (67 bp):
TTTATGATTCTATTTATGCGCATATAACAAATGAATTTGAAAGCTTAAGTGGCTTTTAATCTTAT
GT
Found at i:545814 original size:60 final size:60
Alignment explanation
Indices: 545455--545803 Score: 488
Period size: 60 Copynumber: 5.8 Consensus size: 60
545445 TAGATTGGAG
* * *
545455 GCCAAGGAAGGATATGTACTATGAGGAGGAATTAAAGCCGAAGAAGGATGCAGAGCTGAA
1 GCCAAGTAAGGATATGTTCTATGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAA
* ** *
545515 GCCAAGTAAGGATATGTTCTACGAGGAGGCTTTAAAGCCGATA-AAGGAAGCAGAACTGAA
1 GCCAAGTAAGGATATGTTCTATGAGGAGGAATTAAAGCCGA-AGAAGGAAGCAGAGCTGAA
* * * *
545575 ACCGAGTAAGGATATGATCTGTGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAA
1 GCCAAGTAAGGATATGTTCTATGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAA
* *
545635 GCCAAGTAAGGATATGTTCTATGAGGA-GACATTAAAGCCGATGAAGGAAGCAGAACTGAA
1 GCCAAGTAAGGATATGTTCTATGAGGAGGA-ATTAAAGCCGAAGAAGGAAGCAGAGCTGAA
* * *
545695 ACCAAGTAAGGATATGATCTATGAGGAGGAATTAAAGCCGCAGAAGGAAGCAGAGCTGAA
1 GCCAAGTAAGGATATGTTCTATGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAA
* *
545755 GCCAAGTAAGGAGATGTTCTATGAGGA-GACATTAAAGCCGACGAAGGAA
1 GCCAAGTAAGGATATGTTCTATGAGGAGGA-ATTAAAGCCGAAGAAGGAA
545804 TCTGGACTGA
Statistics
Matches: 253, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
59 5 0.02
60 245 0.97
61 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.31, T:0.16
Consensus pattern (60 bp):
GCCAAGTAAGGATATGTTCTATGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAA
Found at i:545841 original size:120 final size:120
Alignment explanation
Indices: 545456--545819 Score: 577
Period size: 120 Copynumber: 3.0 Consensus size: 120
545446 AGATTGGAGG
* * *
545456 CCAAGGAAGGATATG-TACTATGAGGAGGAATTAAAGCCGAAGAAGGATGCAGAGCTGAAGCCAA
1 CCAAGTAAGGATATGAT-CTGTGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAAGCCAA
* * * *
545520 GTAAGGATATGTTCTACGAGGAGGCTTTAAAGCCGATAAAGGAAGCAGAACTGAAA
65 GTAAGGATATGTTCTATGAGGAGACATTAAAGCCGATGAAGGAAGCAGAACTGAAA
*
545576 CCGAGTAAGGATATGATCTGTGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAAGCCAAG
1 CCAAGTAAGGATATGATCTGTGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAAGCCAAG
545641 TAAGGATATGTTCTATGAGGAGACATTAAAGCCGATGAAGGAAGCAGAACTGAAA
66 TAAGGATATGTTCTATGAGGAGACATTAAAGCCGATGAAGGAAGCAGAACTGAAA
* *
545696 CCAAGTAAGGATATGATCTATGAGGAGGAATTAAAGCCGCAGAAGGAAGCAGAGCTGAAGCCAAG
1 CCAAGTAAGGATATGATCTGTGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAAGCCAAG
* * * * *
545761 TAAGGAGATGTTCTATGAGGAGACATTAAAGCCGACGAAGGAATCTGGACTGAAA
66 TAAGGATATGTTCTATGAGGAGACATTAAAGCCGATGAAGGAAGCAGAACTGAAA
545816 CCAA
1 CCAA
545820 TGAAAGTTGT
Statistics
Matches: 227, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
120 226 1.00
121 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.30, T:0.16
Consensus pattern (120 bp):
CCAAGTAAGGATATGATCTGTGAGGAGGAATTAAAGCCGAAGAAGGAAGCAGAGCTGAAGCCAAG
TAAGGATATGTTCTATGAGGAGACATTAAAGCCGATGAAGGAAGCAGAACTGAAA
Found at i:547735 original size:2 final size:2
Alignment explanation
Indices: 547730--547756 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
547720 AACTTAAAAT
547730 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
547757 TATTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:548417 original size:21 final size:21
Alignment explanation
Indices: 548366--548418 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
548356 ATTATGACTA
548366 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
548387 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
548408 TCGCAATGCGA
1 TCGCAATGCGA
548419 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:548433 original size:20 final size:21
Alignment explanation
Indices: 548408--548459 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
548398 TTTTCCCAAT
*
548408 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
548428 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
548449 TCGCAATGCGA
1 TCGCAATGCGA
548460 TACTCACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:548473 original size:20 final size:20
Alignment explanation
Indices: 548448--548521 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
548438 AATTTGGAAA
*
548448 ATCGCAATGCGATACTCACT
1 ATCGCAACGCGATACTCACT
* * **
548468 ATCGCAACGTGATAATACAAA
1 ATCGCAACGCGATACT-CACT
* *
548489 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTCACT
* *
548509 TTCGCAATGCGAT
1 ATCGCAACGCGAT
548522 TCTGTTGGGA
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTCACT
Found at i:548814 original size:34 final size:32
Alignment explanation
Indices: 548761--548830 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
548751 ACCTTACAAC
* *
548761 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
548793 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
548827 TCCC
1 TCCC
548831 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:549139 original size:21 final size:21
Alignment explanation
Indices: 549113--549154 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
549103 CCCAAAATAG
*
549113 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
549134 GGGAATCGATACTCCTTCATA
1 GGGAATCGATACCCCTTCATA
549155 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:549284 original size:19 final size:19
Alignment explanation
Indices: 549260--549326 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
549250 GAGCCTCGGG
*
549260 TTACTGTTCAAACT-GTGAT
1 TTACTGTTCAAA-TAGTAAT
549279 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAATAGTAAT
* *
549298 GTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAT
*
549317 TTACTATTCA
1 TTACTGTTCA
549327 TAAAAACATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
18 1 0.02
19 41 0.98
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:549414 original size:29 final size:31
Alignment explanation
Indices: 549382--549441 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
549372 AAATTTTGAA
*
549382 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
549411 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
549442 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:552292 original size:34 final size:31
Alignment explanation
Indices: 552239--552307 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
552229 ACCTTACAAC
* *
552239 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTA-AACATT
*
552271 TCCCTAGCTTTTACACGGGCTAAGCTAAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAAACATT
552304 TCCC
1 TCCC
552308 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 7 0.22
33 14 0.44
34 11 0.34
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.32
Consensus pattern (31 bp):
TCCCTAGTTTTACCGGGCTAAACTAAACATT
Found at i:552617 original size:21 final size:21
Alignment explanation
Indices: 552591--552632 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
552581 CCAAAATAGG
*
552591 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
552612 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
552633 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:552889 original size:29 final size:31
Alignment explanation
Indices: 552857--552916 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
552847 AAATTTTGAA
*
552857 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
552886 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
552917 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:552975 original size:20 final size:20
Alignment explanation
Indices: 552950--552988 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
552940 TAGTTCAACA
552950 GATTCTGACTTTCGCAACGC
1 GATTCTGACTTTCGCAACGC
*
552970 GATTCTTACTTTCGCAACG
1 GATTCTGACTTTCGCAACG
552989 AGATCGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (20 bp):
GATTCTGACTTTCGCAACGC
Found at i:553383 original size:20 final size:20
Alignment explanation
Indices: 553358--553431 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
553348 CAACGGGGAA
*
553358 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
*
553378 ATCGCAACACGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
553398 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
553418 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
553432 TGAAAATCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:553479 original size:19 final size:19
Alignment explanation
Indices: 553438--553521 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
553428 GAAATGAAAA
553438 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
553454 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
553471 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
553490 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
553509 TAGCATTGCGATT
1 TCGCATTGCGATT
553522 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.18
16 3 0.05
17 3 0.05
19 44 0.72
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:555564 original size:20 final size:20
Alignment explanation
Indices: 555539--555611 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
555529 GAAGAATAGT
*
555539 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
555559 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
555579 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
555599 TGACTATCGCAAC
1 TTACTTTCGCAAC
555612 GCGGAAATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:555589 original size:40 final size:40
Alignment explanation
Indices: 555545--555630 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
555535 TAGTTTACTT
* *
555545 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
555585 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
555625 TCGCAA
1 TCGCAA
555631 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:555612 original size:20 final size:20
Alignment explanation
Indices: 555565--555651 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
555555 AAACTTACTT
*
555565 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
555585 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
555605 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
555625 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
555644 TCGCAACG
1 TCGCAACG
555652 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:555659 original size:14 final size:14
Alignment explanation
Indices: 555640--555698 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
555630 ATGCGAAATG
555640 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
555654 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
555673 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
555687 AAGATCGCAACG
1 AAAATCGCAACG
555699 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:555666 original size:33 final size:33
Alignment explanation
Indices: 555624--555715 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
555614 GGAAATGGCT
555624 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
555657 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
555690 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
555716 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:555764 original size:33 final size:33
Alignment explanation
Indices: 555727--555806 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
555717 GCGATTTGTG
555727 TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
*
555760 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
*
555793 TTTCACATTGCGAT
1 TTTCGCATTGCGAT
555807 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATCTTGTCGTTGCGATTTTCA
Found at i:555772 original size:19 final size:19
Alignment explanation
Indices: 555748--555806 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
555738 GATCTTGTCG
555748 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
555767 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
555781 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
555800 TTGCGAT
1 TTGCGAT
555807 AGCCATTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.19
15 3 0.09
16 4 0.12
17 3 0.09
18 3 0.09
19 13 0.41
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:555786 original size:14 final size:14
Alignment explanation
Indices: 555734--555790 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
555724 GTGTTTCGCA
*
555734 TTGCGATCTTGTCG
1 TTGCGATTTTGTCG
*
555748 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
555765 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
555781 TTGCGATTTT
1 TTGCGATTTT
555791 CATTTCACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
15 2 0.06
16 4 0.11
17 4 0.11
18 3 0.09
19 6 0.17
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:555813 original size:19 final size:20
Alignment explanation
Indices: 555791--555834 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
555781 TTGCGATTTT
555791 CATTT-CACATTGCGATAGC
1 CATTTCCACATTGCGATAGC
* * *
555810 CATTTCCGCGTTGCGATAGT
1 CATTTCCACATTGCGATAGC
555830 CATTT
1 CATTT
555835 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCACATTGCGATAGC
Found at i:555825 original size:20 final size:20
Alignment explanation
Indices: 555800--555845 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
555790 TCATTTCACA
555800 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
555820 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
555840 TTGCGA
1 TTGCGA
555846 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:556409 original size:18 final size:18
Alignment explanation
Indices: 556386--556433 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
556376 CGGGTCGATC
556386 AGGTGATGGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
* *
556404 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
556422 AGGTGATGGCTC
1 AGGTGATGGCTC
556434 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:558101 original size:22 final size:22
Alignment explanation
Indices: 558074--558117 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
558064 TATGGAGATA
*
558074 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
558096 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
558118 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:558403 original size:41 final size:41
Alignment explanation
Indices: 558284--558421 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
558274 CGCTTTGAAA
* * * *
558284 ATCGCATTGCGATTATGTATTATCTCGTTGCAAAAGTCAGT
1 ATCGCATTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
558325 ATCGCATTGCGAA---AGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGC-AATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* *
558365 ATCGCGTTGCAATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
558406 ATCGCATTGCGATTTT
1 ATCGCATTGCAATTTT
558422 CCCAATTCGC
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
39 4 0.05
40 29 0.36
41 45 0.56
42 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCAATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:558410 original size:20 final size:20
Alignment explanation
Indices: 558304--558417 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
558294 GATTATGTAT
* *
558304 TATCTCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
558324 TATCGCATTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
558344 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
558364 TATCGCGTTGC-AATTTTGT-AT
1 TATCGCGTTGCGAA---AGTCAG
*
558385 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
558405 TATCGCATTGCGA
1 TATCGCGTTGCGA
558418 TTTTCCCAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.05
20 58 0.75
21 12 0.16
22 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:558437 original size:41 final size:41
Alignment explanation
Indices: 558344--558439 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
558334 CGAAAGTAAG
* * ** *
558344 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCAATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAA
*
558385 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CCAA
*
558427 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
558440 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAA
Found at i:558451 original size:20 final size:21
Alignment explanation
Indices: 558407--558458 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
558397 ATAGTCAGTA
*
558407 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
558428 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
558448 TCGCATTGCGA
1 TCGCATTGCGA
558459 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:558500 original size:21 final size:22
Alignment explanation
Indices: 558448--558500 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
558438 ATTTACTTAT
*
558448 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
558469 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
558490 TCGCATTGCGA
1 TCGCATTGCGA
558501 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:558889 original size:27 final size:27
Alignment explanation
Indices: 558829--558890 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
558819 GTTAATTCGG
*** * *
558829 TCGGTTAACGGTTAATTTTTTTTGAAT
1 TCGGTTAACGGTTAATTCGGTTCGAAA
*
558856 TCAGTTAACGGTTAATTCGGTTCGAAA
1 TCGGTTAACGGTTAATTCGGTTCGAAA
558883 TCGGTTAA
1 TCGGTTAA
558891 TTAACCGAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (27 bp):
TCGGTTAACGGTTAATTCGGTTCGAAA
Found at i:559731 original size:16 final size:16
Alignment explanation
Indices: 559698--559742 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
559688 GATTTTAGTT
*
559698 TTTAAGGATTT-A-AG
1 TTTAAGGATTTGAGAA
559712 TTTAAGGATTTGAGAA
1 TTTAAGGATTTGAGAA
*
559728 TTTAAGGGTTTGAGA
1 TTTAAGGATTTGAGA
559743 CGACGATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 11 0.41
15 1 0.04
16 15 0.56
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
TTTAAGGATTTGAGAA
Found at i:559949 original size:62 final size:62
Alignment explanation
Indices: 559852--559975 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
559842 AATGTTTTTT
* * *
559852 AAATAAAAATTTCAAACAAAATATAAACTCAACATGTGTCGGATAACTTTTTTTTTAAACGA
1 AAATAAAAATTTCAAACAAAATATAAACTCAACATGTGTCAGATAACTTTTTCTTAAAACGA
*
559914 AAATAAAAATTTCAAACAAAATATAAACTCAACATGTGTTAGATAACTTTTTCTTAAAACGA
1 AAATAAAAATTTCAAACAAAATATAAACTCAACATGTGTCAGATAACTTTTTCTTAAAACGA
559976 CTATGACATG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (62 bp):
AAATAAAAATTTCAAACAAAATATAAACTCAACATGTGTCAGATAACTTTTTCTTAAAACGA
Found at i:562644 original size:27 final size:27
Alignment explanation
Indices: 562613--562669 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
562603 AAATACTATT
*
562613 TTTTTCTTTTTTCCCCTTCATTTTCTCA
1 TTTTT-TTTTTACCCCTTCATTTTCTCA
***
562641 TTTTTTTTTTATTTCTTCATTTTCTCA
1 TTTTTTTTTTACCCCTTCATTTTCTCA
562668 TT
1 TT
562670 GTATCATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTTTTTTACCCCTTCATTTTCTCA
Found at i:568208 original size:19 final size:19
Alignment explanation
Indices: 568184--568222 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
568174 GCAGCAAAAG
568184 ATCCCAACCATGTCCCATT
1 ATCCCAACCATGTCCCATT
568203 ATCCCAACCATGTCCCATT
1 ATCCCAACCATGTCCCATT
568222 A
1 A
568223 AGTAATCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.41, G:0.05, T:0.26
Consensus pattern (19 bp):
ATCCCAACCATGTCCCATT
Found at i:569046 original size:3 final size:3
Alignment explanation
Indices: 569038--569063 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
569028 TGTCCTCTCT
569038 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
569064 ATTTAGGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:570743 original size:2 final size:2
Alignment explanation
Indices: 570736--570806 Score: 94
Period size: 2 Copynumber: 36.5 Consensus size: 2
570726 GGTCCAATTA
* *
570736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT GA- AT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
570776 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 A
570807 ATCGTTATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.05
2 59 0.95
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:573362 original size:2 final size:2
Alignment explanation
Indices: 573349--573392 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
573339 TTTTAAGAAA
573349 AT AT AT -T A- 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
573389 AT AT
1 AT AT
573393 TTATTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573429 original size:23 final size:21
Alignment explanation
Indices: 573389--573430 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
573379 ATATATATAT
*
573389 ATATTTATTTTTATAAATAAG
1 ATATTTATTTTTAGAAATAAG
573410 ATATTTATTTACTTAGAAATA
1 ATATTTATTT--TTAGAAATA
573431 TCAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAG
Found at i:573643 original size:21 final size:22
Alignment explanation
Indices: 573619--573662 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
573609 AGTCAATTTC
573619 TTAATA-TTAAAAAAATAAATA
1 TTAATATTTAAAAAAATAAATA
* *
573640 TTAATATTTAAACAAATATATA
1 TTAATATTTAAAAAAATAAATA
573662 T
1 T
573663 ATTTATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATATTTAAAAAAATAAATA
Found at i:576174 original size:237 final size:236
Alignment explanation
Indices: 575699--576969 Score: 2136
Period size: 237 Copynumber: 5.4 Consensus size: 236
575689 GAATTAAGGC
* * * *
575699 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCGTTA
1 AAGGTTGAACAA-TTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
** * * * *
575763 TGAACACT-TCTGGAAATATTGATGCTGATATATCTCCTTCTGTAATAGAATCAAGCA-AAAGGT
65 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAA-GT
*
575826 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAC
129 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* ** * * *
575890 TTTCTCTGAAAAAGTTGATGCATCGAGTGATGAATTCGAGCAA
194 TTTATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
* * *
575933 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAA-TTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
*
575998 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCTTTCTGTGATAGAATCGAGCACAAAGTT
65 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
576063 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
130 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
576128 TTATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
195 TTATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
* * *
576170 AAGGTTAAACCAATTCTTCTTATTATGAATTTCTTCTTCATTCTTCGGATGAATTCTTCTCATTA
1 AAGGTTGAA-CAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
576235 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
65 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
*
576300 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACT
130 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
576365 TTATCTGGGAATACTGATCCATCGAGTGATGAATTCGAGCAA
195 TTATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
576407 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
1 AAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
*
576472 TGAACTTTATCTGGAAATGTTGATGCTGGTCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
65 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
*
576537 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACT
130 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
576602 TTATCTGGGAATACTGATCCATCGAGTGATGAATTCGAGCAA
195 TTATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
576644 AAGGTTGAACCAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
1 AAGGTTGAA-CAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
*
576709 TGAACTTTATCTGGAAATGTTGATGCTGGTCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
65 TGAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTT
576774 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
130 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
576839 TTATCTGGGAATGCTGATCTATCGAGTGATGAATTCGAGCAA
195 TTATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
* * *
576881 AAGGTTGATCAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTA
*
576946 TGAACTTTATATGGAAATGTTGAT
65 TGAACTTTATCTGGAAATGTTGAT
576970 CCATTAAGCG
Statistics
Matches: 994, Mismatches: 35, Indels: 13
0.95 0.03 0.01
Matches are distributed among these distances:
234 36 0.04
235 33 0.03
236 83 0.08
237 838 0.84
238 4 0.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (236 bp):
AAGGTTGAACAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTAT
GAACTTTATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCACAAAGTTG
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
TATCTGGGAATGCTGATCCATCGAGTGATGAATTCGAGCAA
Found at i:576988 original size:113 final size:113
Alignment explanation
Indices: 576760--576989 Score: 345
Period size: 113 Copynumber: 2.0 Consensus size: 113
576750 TGTGATAGAA
*
576760 TCGAGCACAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCACAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * * *
576825 TCTCATTATGAACTTTATCTGGGAATGCTGATCTATCGAGTGATGAAT
66 TCTCATTATGAACTTTATATGGAAATGCTGATCCATCAAGCGATGAAT
* *
576873 TCGAGCA-AAAGGTTGATCAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCGAGCACAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
* * *
576937 TTCTCATTATGAACTTTATATGGAAATGTTGATCCATTAAGCGATGGAT
65 TTCTCATTATGAACTTTATATGGAAATGCTGATCCATCAAGCGATGAAT
576986 TCGA
1 TCGA
576990 ATCTTTGCTA
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 3 0.03
113 102 0.97
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (113 bp):
TCGAGCACAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTATATGGAAATGCTGATCCATCAAGCGATGAAT
Found at i:577372 original size:21 final size:22
Alignment explanation
Indices: 577342--577400 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
577332 GAATCCAATA
*
577342 AATCTTTCATCTTT-A-AAAGAG
1 AATCTATCATCTTTGAGAAA-AG
* *
577363 AATCTATCATCTTTGAGGAAAT
1 AATCTATCATCTTTGAGAAAAG
577385 AATCTATCATCTTTGA
1 AATCTATCATCTTTGA
577401 AGAGTGTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.39
22 18 0.55
23 2 0.06
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
AATCTATCATCTTTGAGAAAAG
Found at i:577836 original size:54 final size:54
Alignment explanation
Indices: 577772--577922 Score: 214
Period size: 54 Copynumber: 2.8 Consensus size: 54
577762 TAACTGGTTC
* * * *
577772 GTAAAACATTTGATAACATATTCAT-CATCTCATGTGGTTTCTGCTCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCATCTC-TGTGGATTCTGCACAGATGTTT
*
577826 GTAAAACATTTGACAACACATTCATCCATTTCTGTGGATTCTGCACAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCATCTCTGTGGATTCTGCACAGATGTTT
* * *
577880 GTAAAACATTTGGCAATACATTCATCCATTTCTGTGGATTCTG
1 GTAAAACATTTGACAACACATTCATCCATCTCTGTGGATTCTG
577923 TATAGATTTC
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 84 0.94
55 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCATCTCTGTGGATTCTGCACAGATGTTT
Found at i:583237 original size:19 final size:19
Alignment explanation
Indices: 583172--583228 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
583162 TTTATTTATT
*
583172 GCACAAAAAGCAGAGAAAG
1 GCACAAAAAGCGGAGAAAG
*
583191 GCACAAAAAGTGGAGAAAG
1 GCACAAAAAGCGGAGAAAG
583210 GCACAAAAAGCGGAGAAAG
1 GCACAAAAAGCGGAGAAAG
583229 AAACAAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.54, C:0.14, G:0.30, T:0.02
Consensus pattern (19 bp):
GCACAAAAAGCGGAGAAAG
Found at i:584774 original size:6 final size:7
Alignment explanation
Indices: 584757--584797 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
584747 ATAAAAGTAT
584757 AAATGCA
1 AAATGCA
584764 AAATG-A
1 AAATGCA
584770 AAATGCA
1 AAATGCA
*
584777 AAGATACA
1 AA-ATGCA
584785 AAATGC-
1 AAATGCA
584791 AAATGCA
1 AAATGCA
584798 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 12 0.41
7 11 0.38
8 6 0.21
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:586370 original size:24 final size:27
Alignment explanation
Indices: 586343--586410 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 27
586333 TGAAAATAAA
*
586343 ATAAAGATTT-AAAA-AATAA-TATAT
1 ATAAAAATTTGAAAATAATAAGTATAT
*
586367 ATAAATATTATGAAAATAATAAGTATAT
1 ATAAAAATT-TGAAAATAATAAGTATAT
586395 ATAAAAATTTTGAAAA
1 ATAAAAA-TTTGAAAA
586411 GAAAGATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 8 0.22
25 1 0.03
26 4 0.11
27 5 0.14
28 17 0.46
29 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (27 bp):
ATAAAAATTTGAAAATAATAAGTATAT
Found at i:586393 original size:28 final size:26
Alignment explanation
Indices: 586353--586410 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
586343 ATAAAGATTT
*
586353 AAAAAATAATATATATAAATATTATG
1 AAAAAATAATATATATAAAAATTATG
*
586379 AAAATAATAAGTATATATAAAAATTTTG
1 AAAA-AATAA-TATATATAAAAATTATG
586407 AAAA
1 AAAA
586411 GAAAGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 5 0.18
28 19 0.68
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAAAATAATATATATAAAAATTATG
Found at i:587169 original size:21 final size:22
Alignment explanation
Indices: 587145--587188 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
587135 AGTACATTTC
587145 TTAATA-TTAAAAAAATAAATA
1 TTAATATTTAAAAAAATAAATA
* *
587166 TTAATATTTAAACAAATATATA
1 TTAATATTTAAAAAAATAAATA
587188 T
1 T
587189 ATTTATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATATTTAAAAAAATAAATA
Found at i:587316 original size:19 final size:19
Alignment explanation
Indices: 587294--587354 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
587284 TAAAGTAATG
587294 AAATTAAATAAATAAAAAT
1 AAATTAAATAAATAAAAAT
**
587313 AAATCGAATAAATTAAAATAT
1 AAATTAAATAAA-TAAAA-AT
* * *
587334 AAAGTAAAGAACT-AAAAT
1 AAATTAAATAAATAAAAAT
587352 AAA
1 AAA
587355 AGATATTGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 5 0.15
19 13 0.39
20 6 0.18
21 9 0.27
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATTAAATAAATAAAAAT
Found at i:592259 original size:32 final size:31
Alignment explanation
Indices: 592223--592298 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
592213 TGGGGCCGTG
*
592223 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
592255 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
592286 GAGCCTACCTAAG
1 GGGCCTACCTAAG
592299 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:592282 original size:63 final size:63
Alignment explanation
Indices: 592176--592298 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
592166 ACCTAAGGGA
* ** ** *
592176 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTTGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
592239 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
592299 TGTCACATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:593972 original size:141 final size:141
Alignment explanation
Indices: 593718--593999 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 141
593708 TCTTGAGTCA
593718 TTTCCATTCCAGGGGTATTTTGGTCATTTTACAGATCCAATGTATTTCCATCATTTCCTTACGTC
1 TTTCCATTCCAGGGGTATTTTGGTCATTTTACAGATCCAATGTATTTCCATCATTTCCTTACGTC
593783 TGATCTTATTATTTAATTTAATCTTATCACTTACTTCAGTCCTTTCAAACAATTCTGACCAAATA
66 TGATCTTATTATTTAATTTAATCTTATCACTTACTTCAGTCCTTTCAAACAATTCTGACCAAATA
593848 GCACATTCGAT
131 GCACATTCGAT
593859 TTTCCATTCCAGGGGTATTTTGGTCATTTTACAGATCCAATGTATTTCCATCATTTCCTTACGTC
1 TTTCCATTCCAGGGGTATTTTGGTCATTTTACAGATCCAATGTATTTCCATCATTTCCTTACGTC
593924 TGATCTTATTATTTAATTTAATCTTATCACTTACTTCAGTCCTTTCAAACAATTCTGACCAAATA
66 TGATCTTATTATTTAATTTAATCTTATCACTTACTTCAGTCCTTTCAAACAATTCTGACCAAATA
593989 GCACATTCGAT
131 GCACATTCGAT
594000 AAATCATTCT
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (141 bp):
TTTCCATTCCAGGGGTATTTTGGTCATTTTACAGATCCAATGTATTTCCATCATTTCCTTACGTC
TGATCTTATTATTTAATTTAATCTTATCACTTACTTCAGTCCTTTCAAACAATTCTGACCAAATA
GCACATTCGAT
Found at i:594228 original size:16 final size:16
Alignment explanation
Indices: 594207--594239 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
594197 GGCATTTTCG
594207 TAATTTCTTAACCAGA
1 TAATTTCTTAACCAGA
594223 TAATTTCTTAACCAGA
1 TAATTTCTTAACCAGA
594239 T
1 T
594240 CGGAGTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (16 bp):
TAATTTCTTAACCAGA
Found at i:595711 original size:20 final size:19
Alignment explanation
Indices: 595631--595722 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 19
595621 CTCAGTTTCC
*
595631 AAATTCGCAACGCGAATCTGT
1 AAATTCGCAACACGAAT-T-T
595652 AAA-TCGCAACACTGAATTT
1 AAATTCGCAACAC-GAATTT
* * *
595671 CAAATTCACAACTCGATTTT
1 -AAATTCGCAACACGAATTT
595691 AAATTTCGCAACACGAATTT
1 AAA-TTCGCAACACGAATTT
*
595711 AATTTCGCAACA
1 AAATTCGCAACA
595723 GGTTTTATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.22
20 32 0.54
21 14 0.24
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (19 bp):
AAATTCGCAACACGAATTT
Found at i:595897 original size:14 final size:16
Alignment explanation
Indices: 595878--595914 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
595868 TCCCCATCTC
595878 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
595892 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
595908 TAATTTT
1 TAATTTT
595915 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:599003 original size:18 final size:18
Alignment explanation
Indices: 598980--599015 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
598970 AAGCAAAAGG
598980 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
598998 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
599016 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:599319 original size:49 final size:49
Alignment explanation
Indices: 599251--599364 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 49
599241 AATTTCGCAA
* * * * * *
599251 CGCAAAAATTGCAATGCGAATTTGACTTTTACGTTGCGAATTTGACTTT
1 CGCAACAATCGCAACGCGAATTTGACTTTCACGTTGCGAATTTAACTAT
* *
599300 CGCAACAATCGCAACGCGAATTTTACTTTCGCGTTGCGAATTTAACTAT
1 CGCAACAATCGCAACGCGAATTTGACTTTCACGTTGCGAATTTAACTAT
* *
599349 CGTAACAATCGAAACG
1 CGCAACAATCGCAACG
599365 AGAAAATCGC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (49 bp):
CGCAACAATCGCAACGCGAATTTGACTTTCACGTTGCGAATTTAACTAT
Found at i:599511 original size:25 final size:25
Alignment explanation
Indices: 599473--599522 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
599463 AAATCAATTA
* *
599473 AACATTGTTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
599498 AACATTATTATGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
599523 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:599516 original size:14 final size:13
Alignment explanation
Indices: 599483--599523 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
599473 AACATTGTTG
599483 TGGGTACATTATT
1 TGGGTACATTATT
*
599496 T--GAACATTATT
1 TGGGTACATTATT
599507 ATGGGTACATTATT
1 -TGGGTACATTATT
599521 TGG
1 TGG
599524 AAAATAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 9 0.39
12 1 0.04
13 4 0.17
14 9 0.39
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (13 bp):
TGGGTACATTATT
Found at i:599952 original size:24 final size:23
Alignment explanation
Indices: 599890--599953 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
599880 TTTCAAATTC
* *
599890 ATTTAATATATAATTGGAGTTTGA
1 ATTTAATATA-AATTTGAGCTTGA
* *
599914 ATTTAAATTTCAATTTGAGCTTGA
1 ATTT-AATATAAATTTGAGCTTGA
599938 ATTTCAATATAAATTT
1 ATTT-AATATAAATTT
599954 CGGCTCCACT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (23 bp):
ATTTAATATAAATTTGAGCTTGA
Found at i:600930 original size:18 final size:18
Alignment explanation
Indices: 600896--600931 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
600886 AAGCAAAAGG
**
600896 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
600914 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
600932 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:601490 original size:64 final size:64
Alignment explanation
Indices: 601411--601568 Score: 273
Period size: 64 Copynumber: 2.5 Consensus size: 64
601401 AATTTAAAAC
*
601411 AACAAATCAATTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACAT-ATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTT-CATCATCAATTA
*
601475 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCATCATCAATTA
601539 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
601569 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
63 2 0.02
64 84 0.93
65 4 0.04
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCATCATCAATTA
Found at i:602935 original size:21 final size:20
Alignment explanation
Indices: 602909--603026 Score: 101
Period size: 21 Copynumber: 5.7 Consensus size: 20
602899 GTGAATCGGG
*
602909 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGG-C
* **
602930 CTCTTGAATGATGACAAGGGC
1 CTCTTGAACGATG-GGAGGGC
* * *
602951 CTCTTGAATGGTAGGAGTGGC
1 CTCTTGAACGATGGGAG-GGC
*
602972 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGA-GGGC
*
602993 CTCTTGAACGATAGGAGGCGC
1 CTCTTGAACGATGGGAGG-GC
*
603014 CTCTTGAATGATG
1 CTCTTGAACGATG
603027 ACAGGTGAAT
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.05
21 68 0.88
22 5 0.06
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGATGGGAGGGC
Found at i:602975 original size:42 final size:41
Alignment explanation
Indices: 602909--603029 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 41
602899 GTGAATCGGG
*
602909 CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGACAAGGGC
1 CTCTTGAACGGTAGGAGGG-CCTCTTGAATGATGACAAGGGC
* * * *
602951 CTCTTGAATGGTAGGAGTGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTAGGAG-GGCCTCTTGAATGATGACAAGGGC
*
602993 CTCTTGAACGATAGGAGGCGCCTCTTGAATGATGACA
1 CTCTTGAACGGTAGGAGG-GCCTCTTGAATGATGACA
603030 GGTGAATCAG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.96
43 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGCCTCTTGAATGATGACAAGGGC
Found at i:603450 original size:63 final size:63
Alignment explanation
Indices: 603356--603476 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
603346 ACCACGTAGC
* *
603356 GCACCATTGTCATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCGTACCTCATCACACCAT
1 GCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG-ACCTCATCACACCAT
* ** **
603419 GCACCATTGTCTTCACGTAAAGTA-CCGACCTCATGACGCAAAGCACCGACCTCATCAC
1 GCACCATTGTCATCACGTAAAACATCC-ACCTCACCACGCAAAGCACCGACCTCATCAC
603477 GTAACTCTCC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
62 2 0.04
63 43 0.88
64 4 0.08
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.19
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCGACCTCATCACACCAT
Found at i:605262 original size:20 final size:20
Alignment explanation
Indices: 605139--605272 Score: 162
Period size: 20 Copynumber: 6.8 Consensus size: 20
605129 AGTAGTTTCT
* * *
605139 GAAAATTAAATTCGCAACAC
1 GAAAATGAAAATCGCAACGC
*
605159 GAAAATGAAAATTGCAACGC
1 GAAAATGAAAATCGCAACGC
*
605179 GAACATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
605199 GAACATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
* *
605219 GAACATGAAAATCGCAACGT
1 GAAAATGAAAATCGCAACGC
* *
605239 GAAAATGAAAATCGTAATGC
1 GAAAATGAAAATCGCAACGC
*
605259 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
605273 GTTGCGATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
19 7 0.07
20 94 0.93
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.15
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:605663 original size:20 final size:21
Alignment explanation
Indices: 605638--605686 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
605628 TCTGAGAGAT
605638 GGAGAT-AGAC-GAATTTCGCC
1 GGAGATGAGACAG-ATTTCGCC
*
605658 GGAGATGGAGACAGATTTCGTC
1 GGAGAT-GAGACAGATTTCGCC
605680 GGAGATG
1 GGAGATG
605687 GGGAAGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 17 0.68
23 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACAGATTTCGCC
Found at i:605828 original size:19 final size:20
Alignment explanation
Indices: 605806--605843 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
605796 AATATTGTGT
605806 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
605825 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
605844 CGCGCTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:605894 original size:20 final size:20
Alignment explanation
Indices: 605869--605915 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
605859 TGACTTCTGT
605869 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
605889 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
605909 GTTGCGA
1 GTTGCGA
605916 ATTTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:608078 original size:36 final size:36
Alignment explanation
Indices: 607988--608084 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 36
607978 AAACACATAC
*
607988 AAACATACATTTTCCATGTACATAATATACAAATTT
1 AAACATACATTTTCCATGTAAATAATATACAAATTT
*
608024 AATCTGTACATACATTTTCCATGTAAATACTCATACAAATTT
1 AA-----ACATACATTTTCCATGTAAATAAT-ATACAAATTT
608066 -AACATACATTTTCCATGTA
1 AAACATACATTTTCCATGTA
608085 CAAGTCCAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
36 20 0.38
41 23 0.43
42 10 0.19
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (36 bp):
AAACATACATTTTCCATGTAAATAATATACAAATTT
Found at i:609184 original size:26 final size:25
Alignment explanation
Indices: 609146--609209 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
609136 TTTTTAAGAT
* *
609146 TATATATTGTTTTAGTTTTTTAATGTAA
1 TATATAAT-TTTTA-TTTTTAAAT-TAA
609174 -ATATAATTTTTATTTTTAAATTAA
1 TATATAATTTTTATTTTTAAATTAA
609198 TTATATAATTTT
1 -TATATAATTTT
609210 AAATTTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 3 0.09
25 8 0.25
26 15 0.47
27 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (25 bp):
TATATAATTTTTATTTTTAAATTAA
Found at i:610482 original size:50 final size:50
Alignment explanation
Indices: 610420--610522 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
610410 AGGAAATATT
610420 ATAATTTTGAATGTATAAGAACACCAAATATTTATAAATGCAAAATATAG
1 ATAATTTTGAATGTATAAGAACACCAAATATTTATAAATGCAAAATATAG
610470 ATAATTTTGAATGTATAAGAACACCAAATATTTATAAATGCAAAATATAG
1 ATAATTTTGAATGTATAAGAACACCAAATATTTATAAATGCAAAATATAG
610520 ATA
1 ATA
610523 TAAATATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (50 bp):
ATAATTTTGAATGTATAAGAACACCAAATATTTATAAATGCAAAATATAG
Found at i:610575 original size:17 final size:18
Alignment explanation
Indices: 610553--610591 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
610543 AATAGTTTAT
610553 ATTTTATCTAATTTAA-A
1 ATTTTATCTAATTTAATA
*
610570 ATTTTATTTAATTTAATA
1 ATTTTATCTAATTTAATA
610588 ATTT
1 ATTT
610592 ATATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTATCTAATTTAATA
Found at i:612123 original size:11 final size:11
Alignment explanation
Indices: 612107--612131 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
612097 CACACGTAGA
612107 ATTTTATTAAT
1 ATTTTATTAAT
612118 ATTTTATTAAT
1 ATTTTATTAAT
612129 ATT
1 ATT
612132 ATTTTCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTATTAAT
Found at i:613283 original size:187 final size:187
Alignment explanation
Indices: 612955--613334 Score: 577
Period size: 187 Copynumber: 2.0 Consensus size: 187
612945 TTATACGGAG
*
612955 AAAATATGATTTTATATGGGATTCAAAACTATGTCGTTTTGATGTAAACTTATTTTTTTCAAAAT
1 AAAATATGATTTTATACGGGATTCAAAACTATGTCGTTTTGATGTAAACTTATTTTTTTCAAAAT
** * * * * *
613020 GATGTCATTTTGATTTCTTGTGACATGTCATAACGTCGTTAACTATTTAATGGCAGAGTGACTAA
66 GACATCATTTTGATTTCGTGTGACATGACATAACGCCGTTAACTATTTAACGGCAGAGTGACCAA
* *
613085 AATAGGAGCAATTCTGAAGTTCAATGATTAAATTGAAAAACTTTTAAAGTGCAGTGATC
131 AATAAGAGCAATTCTGAAATTCAATGATTAAATT--AAAACTTTTAAAGTGCAGTGATC
*
613144 AAAATATGATTTTATACGGGATTCAAAACTATGTCGTTTTGATGT-AA-TTTTTTTTTTCAAAAT
1 AAAATATGATTTTATACGGGATTCAAAACTATGTCGTTTTGATGTAAACTTATTTTTTTCAAAAT
*
613207 GACATCATTTTGATTTCGTGTGTCATGACATAACGCCGTTAACTATTTAACGGC-GAAGTGACCA
66 GACATCATTTTGATTTCGTGTGACATGACATAACGCCGTTAACTATTTAACGGCAG-AGTGACCA
* **
613271 AAATAAGAGCAATTCTGAAATTCAATGATTAAATTAAAATTTTTAAAGTTTAGTGATC
130 AAATAAGAGCAATTCTGAAATTCAATGATTAAATTAAAACTTTTAAAGTGCAGTGATC
613329 AAAATA
1 AAAATA
613335 GAAGAGGGAG
Statistics
Matches: 175, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
185 26 0.15
186 1 0.01
187 102 0.58
188 2 0.01
189 44 0.25
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (187 bp):
AAAATATGATTTTATACGGGATTCAAAACTATGTCGTTTTGATGTAAACTTATTTTTTTCAAAAT
GACATCATTTTGATTTCGTGTGACATGACATAACGCCGTTAACTATTTAACGGCAGAGTGACCAA
AATAAGAGCAATTCTGAAATTCAATGATTAAATTAAAACTTTTAAAGTGCAGTGATC
Found at i:613483 original size:29 final size:29
Alignment explanation
Indices: 613441--613498 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
613431 TTAACAATTA
613441 TCAGATTTCATTTTTACCATTGATGTTTT
1 TCAGATTTCATTTTTACCATTGATGTTTT
*
613470 TCAGATTTCATTTTTTCCATTGATGTTTT
1 TCAGATTTCATTTTTACCATTGATGTTTT
613499 GATTTAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (29 bp):
TCAGATTTCATTTTTACCATTGATGTTTT
Found at i:613870 original size:22 final size:20
Alignment explanation
Indices: 613842--613887 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
613832 TTTTAAAAAT
613842 ATATTTTATTTTAACTTATTA-A
1 ATATTTT-TTTT-A-TTATTATA
613864 ATATTTTTTTTATTATTATA
1 ATATTTTTTTTATTATTATA
613884 ATAT
1 ATAT
613888 AAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 4 0.17
22 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTTTTTATTATTATA
Found at i:613874 original size:26 final size:26
Alignment explanation
Indices: 613808--613877 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
613798 TTTACTTAAA
* *
613808 TTAACAATATTTTATATTCTTAACTT
1 TTAAAAATATTTTTTATTCTTAACTT
*
613834 TTAAAAATATATTTTATT-TTAACTT
1 TTAAAAATATTTTTTATTCTTAACTT
* *
613859 ATTAAATATTTTTTTTATT
1 -TTAAAAATATTTTTTATT
613878 ATTATAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.59
Consensus pattern (26 bp):
TTAAAAATATTTTTTATTCTTAACTT
Found at i:614123 original size:31 final size:29
Alignment explanation
Indices: 614081--614270 Score: 125
Period size: 28 Copynumber: 6.7 Consensus size: 29
614071 TTTAAAGTAG
614081 TAAT-AAA-ATATATTTTTAAGTGAAGATAA
1 TAATAAAATATATATTTTTAA-T-AAGATAA
**
614110 TAATAAAATATATATTTTT-ATATTATAA
1 TAATAAAATATATATTTTTAATAAGATAA
**
614138 TAATAAAATATATATTTTT-ATATTATAA
1 TAATAAAATATATATTTTTAATAAGATAA
*
614166 TAATAATA-ATATA-TTTTAATTTAAGAT-A
1 TAATAAAATATATATTTTTAA--TAAGATAA
** * *
614194 TTTTAAATTATATATTTTTACATTAAAATAA
1 TAATAAAATATATATTTTTA-A-TAAGATAA
* *
614225 AAAT-AAA-ATATA--TTTAATAAGGTAA
1 TAATAAAATATATATTTTTAATAAGATAA
*
614250 GACA-AAAATATATATTTTTAA
1 TA-ATAAAATATATATTTTTAA
614271 AATTTAAGGT
Statistics
Matches: 130, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
25 7 0.05
26 9 0.07
27 15 0.12
28 45 0.35
29 24 0.18
30 17 0.13
31 13 0.10
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (29 bp):
TAATAAAATATATATTTTTAATAAGATAA
Found at i:614195 original size:34 final size:28
Alignment explanation
Indices: 614106--614239 Score: 139
Period size: 28 Copynumber: 4.8 Consensus size: 28
614096 TTAAGTGAAG
614106 ATAATAATAAAATATATATTTTTATATT
1 ATAATAATAAAATATATATTTTTATATT
614134 ATAATAATAAAATATATATTTTTATATT
1 ATAATAATAAAATATATATTTTTATATT
* *
614162 ATAATAATAATA-ATATATTTTAAT-TT
1 ATAATAATAAAATATATATTTTTATATT
* * *
614188 A-AGATATTTTAAATTATATATTTTTACATT
1 ATA-ATA--ATAAAATATATATTTTTATATT
* * *
614218 AAAATAAAAATAAAATATATTT
1 ATAATAATAA-AATATATATTT
614240 AATAAGGTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 13
0.79 0.10 0.12
Matches are distributed among these distances:
25 1 0.01
26 6 0.07
27 11 0.12
28 44 0.50
29 19 0.22
30 6 0.07
31 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATAATAATAAAATATATATTTTTATATT
Found at i:617444 original size:2 final size:2
Alignment explanation
Indices: 617437--617481 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
617427 TACGACTTAC
617437 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
617479 AT A
1 AT A
617482 CTGATGAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:624363 original size:29 final size:29
Alignment explanation
Indices: 624322--624390 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
624312 AAATTATATT
* * *
624322 TTTAGTC-CTTAAACTTTTATAATTTATAC
1 TTTAGTCAC-TAAACTTTAAAAATTTACAC
*
624351 TTTAGTCACTAAAGTTTAAAAATTTACAC
1 TTTAGTCACTAAACTTTAAAAATTTACAC
*
624380 CTTAGTCACTA
1 TTTAGTCACTA
624391 GTCCAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 33 0.97
30 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTAGTCACTAAACTTTAAAAATTTACAC
Found at i:629347 original size:43 final size:44
Alignment explanation
Indices: 629255--629410 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 44
629245 TCCTCTGTTA
* * * * * * *
629255 TGTGCAAGGTTAAGTCTTTACCGTTACCACAGGCTCATTTACTG
1 TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
* *
629299 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
* * * *
629342 TGTGCAAGGGTAAG-CTTTATAGTTTCCCCAGGCTCTTTTGCTA
1 TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
* *
629385 AGTGCAAGGGTAAGACCTTACCGTTT
1 TGTGCAAGGGTAAGACCTTACAGTTT
629411 TTGCATGTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 73 0.78
44 21 0.22
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (44 bp):
TGTGCAAGGGTAAGACCTTACAGTTTCCCCAGGCTCATTTGCTG
Found at i:629433 original size:87 final size:87
Alignment explanation
Indices: 629255--629442 Score: 198
Period size: 87 Copynumber: 2.1 Consensus size: 87
629245 TCCTCTGTTA
* * **
629255 TGTGCAAGGTTAAGTCTTTACCGTTACCACAGGCTCATTTACTGTGTGCAAGGGTAAGCCTTACA
1 TGTGCAAGGGTAAGTCTTTACAGTTACCACAGGCTCATTTACTAAGTGCAAGGGTAAGCCTTACA
* *
629320 GTTTCCCCAGGTTCCTTTGCTG
66 GTTTCCCCAGGTTCCTCTACTG
* * * * *
629342 TGTGCAAGGGTAAG-CTTTATAGTTTCCCCAGGCTCTTTTGCTAAGTGCAAGGGTAAGACCTTAC
1 TGTGCAAGGGTAAGTCTTTACAGTTACCACAGGCTCATTTACTAAGTGCAAGGGTAAG-CCTTAC
* *** * *
629406 CGTTTTTGCATGTTCCTCTACTT
65 AGTTTCCCCAGGTTCCTCTACTG
629429 TGTGCACAGGGTAA
1 TGTGCA-AGGGTAA
629443 ATATGTTTTA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
86 35 0.43
87 40 0.49
88 7 0.09
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (87 bp):
TGTGCAAGGGTAAGTCTTTACAGTTACCACAGGCTCATTTACTAAGTGCAAGGGTAAGCCTTACA
GTTTCCCCAGGTTCCTCTACTG
Found at i:631671 original size:43 final size:43
Alignment explanation
Indices: 631582--631866 Score: 417
Period size: 43 Copynumber: 6.6 Consensus size: 43
631572 TCCTCTACTA
* * * * *
631582 TGTGCAAGGGTAAGTCCTTACCGTTACCGCAGGCTCATTTGCTG
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
631626 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
631669 TGTGCAAGGGTAAGCCTTACAGTTTCCCGAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* *
631712 TGTGCAAGGGTAAGCCTTACAATTTCCCTAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
631755 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * * * *
631798 TGTGCAAGGGTAAGCTTTATAGTTTCCCCAGGATCTTTTGCTA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
631841 TGTGCAAGGGTAAGACCTTACCGTTT
1 TGTGCAAGGGTAAG-CCTTACAGTTT
631867 TTGCATGCTC
Statistics
Matches: 220, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 198 0.90
44 22 0.10
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
Found at i:632924 original size:18 final size:18
Alignment explanation
Indices: 632897--632943 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
632887 AGTTCCAACA
* *
632897 CCATTAATATTTCTAG-T
1 CCATTGATATTTCCAGCT
632914 CCCATTGATATTTCCAGCT
1 -CCATTGATATTTCCAGCT
632933 CCATTGATATT
1 CCATTGATATT
632944 ATTAGCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (18 bp):
CCATTGATATTTCCAGCT
Found at i:644799 original size:2 final size:2
Alignment explanation
Indices: 644792--644826 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
644782 ATTTATCCTT
644792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
644827 GTTATCCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:645075 original size:13 final size:14
Alignment explanation
Indices: 645054--645098 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
645044 GGAAAAATAG
*
645054 AAGATATAAT-AAA
1 AAGAAATAATAAAA
645067 AAGAAATAATAAAA
1 AAGAAATAATAAAA
645081 AAGAAA-AGA-AAAA
1 AAGAAATA-ATAAAA
645094 AAGAA
1 AAGAA
645099 GACAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (14 bp):
AAGAAATAATAAAA
Found at i:645089 original size:5 final size:5
Alignment explanation
Indices: 645079--645165 Score: 51
Period size: 5 Copynumber: 17.8 Consensus size: 5
645069 GAAATAATAA
* * *
645079 AAAAG AAAAG AAAAA AAGAAG ACAAAT AAAAG AAAAG -AAAG -AAAG AAGAG
1 AAAAG AAAAG AAAAG AA-AAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
645129 -AGAG AAAAG AAATCA- AAAAG AAAA- AGAAG -AAAG AAAA
1 AAAAG AAAAG AAA--AG AAAAG AAAAG AAAAG AAAAG AAAA
645166 CATATCAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 19 0.29
5 35 0.54
6 9 0.14
7 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:645094 original size:27 final size:27
Alignment explanation
Indices: 645064--645127 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
645054 AAGATATAAT
*
645064 AAAAAGAA-ATAATAAAAAAGAAAAGAA
1 AAAAAGAAGACAA-AAAAAAGAAAAGAA
*
645091 AAAAAGAAGACAAATAAAAGAAAAGAA
1 AAAAAGAAGACAAAAAAAAGAAAAGAA
*
645118 AGAAAGAAGA
1 AAAAAGAAGA
645128 GAGAGAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 30 0.91
28 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.05
Consensus pattern (27 bp):
AAAAAGAAGACAAAAAAAAGAAAAGAA
Found at i:645127 original size:11 final size:10
Alignment explanation
Indices: 645064--645165 Score: 58
Period size: 11 Copynumber: 10.4 Consensus size: 10
645054 AAGATATAAT
*
645064 AAAAAGAAAT
1 AAAAAGAAAG
645074 AATAAA-AAAG
1 AA-AAAGAAAG
645084 -AAAAG-AA-
1 AAAAAGAAAG
645091 AAAAAG-AAG
1 AAAAAGAAAG
645100 ACAAATA-AAAG
1 A-AAA-AGAAAG
645111 -AAAAGAAAG
1 AAAAAGAAAG
*
645120 AAAGAAGAGAG
1 AAA-AAGAAAG
*
645131 AGAAAAGAAATC
1 A-AAAAGAAA-G
645143 AAAAAGAAA-
1 AAAAAGAAAG
*
645152 AAGAAGAAAG
1 AAAAAGAAAG
645162 AAAA
1 AAAA
645166 CATATCAAAC
Statistics
Matches: 73, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
8 13 0.18
9 17 0.23
10 13 0.18
11 27 0.37
12 3 0.04
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:645136 original size:27 final size:27
Alignment explanation
Indices: 645079--645140 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
645069 GAAATAATAA
*
645079 AAAAGAAAAGAAAAAAAGAAGACAAAT
1 AAAAGAAAAGAAAAAAAGAAGACAAAG
* * *
645106 AAAAGAAAAGAAAGAAAGAAGAGAGAG
1 AAAAGAAAAGAAAAAAAGAAGACAAAG
645133 AAAAGAAA
1 AAAAGAAA
645141 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAAAGAAGACAAAG
Found at i:645163 original size:29 final size:29
Alignment explanation
Indices: 645091--645174 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
645081 AAGAAAAGAA
* *
645091 AAAAAGAAGACAAATAAAAGAAA--AGAAAG
1 AAAAAGAAG--AAAGAAAAGAAATCAAAAAG
*
645120 AAAGAAG-AGAGAGAAAAGAAATCAAAAAG
1 AAA-AAGAAGAAAGAAAAGAAATCAAAAAG
* *
645149 AAAAAGAAGAAAGAAAACATATCAAA
1 AAAAAGAAGAAAGAAAAGAAATCAAA
645175 CACTTTAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
27 10 0.22
28 3 0.07
29 29 0.64
30 3 0.07
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.05
Consensus pattern (29 bp):
AAAAAGAAGAAAGAAAAGAAATCAAAAAG
Found at i:647371 original size:54 final size:54
Alignment explanation
Indices: 647116--647380 Score: 173
Period size: 54 Copynumber: 4.8 Consensus size: 54
647106 CCCGGCTAAC
** * * * ** *
647116 ATGATTTTTTTAGAAACTAAGCCTAATTTTCA-GGGTTTCTTGGTTTTTTTTAAA
1 ATGATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTT-GATTACTTTCAA
* * * * *
647170 ATGAGTTTTATTTAAAGAAGCTATGTCC-GATTTTC-GGAAGTTTCTTGATAATTTTGAA
1 ATGA---TT-TTTAAAGAAGCTAAG-CCTGATTTTCAGG-GGTTTCTTGATTACTTTCAA
* * * *
647228 ATAAGTTTTCAAA-AGAGCTAAGCCGGATTTTCAGGGGTTTCTTGA-TATTTTCAA
1 ATGA-TTTTTAAAGA-AGCTAAGCCTGATTTTCAGGGGTTTCTTGATTACTTTCAA
* * * * *
647282 ATGATTTTTTAGGAAACTAAACCTGATTTTCAGGGGTTTCTTGATTACTTTC-G
1 ATGATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATTACTTTCAA
* * *
647335 ATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGCTTCTTGAT
1 ATG-ATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGAT
647381 GATAACCGTA
Statistics
Matches: 165, Mismatches: 33, Indels: 26
0.74 0.15 0.12
Matches are distributed among these distances:
53 35 0.21
54 59 0.36
55 27 0.16
56 4 0.02
57 2 0.01
58 29 0.18
59 9 0.05
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (54 bp):
ATGATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATTACTTTCAA
Found at i:649097 original size:88 final size:88
Alignment explanation
Indices: 648868--649130 Score: 228
Period size: 88 Copynumber: 3.0 Consensus size: 88
648858 AATCAACATT
* * * * * *
648868 TCCAGTGGAAGGGTTCATAATGAGAAGAACTCATCCAATAAGGGAGAATAAG-TCATAATGAGAA
1 TCCAGTGG-AGAGCTCATAATGAGAAAAACTCATCC-A-ACGAGAGAAAAAGTTCATAATGAGAA
* * ** *
648932 AAACTTGTTCAACCTTGGCAT-AACATT
63 GAACTTATTCAACCTCAGC-TCAAC-TA
* * * * *
648959 TCTAGTGGAGAGCTCATAATGAGAATAATTCATCCAACGAGGGAAAAAGTTCATACTGA-AAGAA
1 TCCAGTGGAGAGCTCATAATGAGAAAAACTCATCCAACGAGAGAAAAAGTTCATAATGAGAAGAA
* *
649023 TTTATTCAACCTTAGCTCAACTA
66 CTTATTCAACCTCAGCTCAACTA
* * * *
649046 TCCAGTGGAGAGTTTATAATGAGAAAAAACTCATCC-GCGGAGAGAAGAAGTTCATAATGAGAAG
1 TCCAGTGGAGAGCTCATAATGAG-AAAAACTCATCCAAC-GAGAGAAAAAGTTCATAATGAGAAG
*
649110 AACTTGTTCAACCTCAGCTCA
64 AACTTATTCAACCTCAGCTCA
649131 TTTCCATCAC
Statistics
Matches: 140, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
87 23 0.16
88 57 0.41
89 30 0.21
90 23 0.16
91 7 0.05
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (88 bp):
TCCAGTGGAGAGCTCATAATGAGAAAAACTCATCCAACGAGAGAAAAAGTTCATAATGAGAAGAA
CTTATTCAACCTCAGCTCAACTA
Found at i:654430 original size:27 final size:26
Alignment explanation
Indices: 654386--654438 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
654376 TTCCAGAAGG
654386 TGCTGACTAGATCCTCTAGAAAACTAC
1 TGCTGACTAGATCCTCTAG-AAACTAC
*
654413 TGCTGACTGGA-CCTTCTAGAAACTAC
1 TGCTGACTAGATCC-TCTAGAAACTAC
654439 CACGTCGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (26 bp):
TGCTGACTAGATCCTCTAGAAACTAC
Found at i:656149 original size:16 final size:17
Alignment explanation
Indices: 656128--656160 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
656118 AAATTTTGTC
656128 ATATTTA-ATAATTTAT
1 ATATTTACATAATTTAT
656144 ATATTTACTATAATTTA
1 ATATTTAC-ATAATTTA
656161 AAAAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTACATAATTTAT
Found at i:658071 original size:10 final size:10
Alignment explanation
Indices: 658049--658096 Score: 82
Period size: 10 Copynumber: 5.0 Consensus size: 10
658039 AAAGAGTGGG
658049 AGAGAGCTC-
1 AGAGAGCTCT
658058 AGAGAGCTCT
1 AGAGAGCTCT
658068 AGAGAGCTCT
1 AGAGAGCTCT
658078 -GAGAGCTCT
1 AGAGAGCTCT
658087 AGAGAGCTCT
1 AGAGAGCTCT
658097 CTCAGGGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
9 18 0.49
10 19 0.51
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (10 bp):
AGAGAGCTCT
Found at i:658096 original size:19 final size:19
Alignment explanation
Indices: 658049--658096 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
658039 AAAGAGTGGG
*
658049 AGAGAGCTCAGAGAGCTCT
1 AGAGAGCTCTGAGAGCTCT
658068 AGAGAGCTCTGAGAGCTCT
1 AGAGAGCTCTGAGAGCTCT
658087 AGAGAGCTCT
1 AGAGAGCTCT
658097 CTCAGGGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (19 bp):
AGAGAGCTCTGAGAGCTCT
Found at i:660733 original size:18 final size:18
Alignment explanation
Indices: 660710--660752 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
660700 TTTATTTTTA
660710 ATATTGTGAGGGTAAACT
1 ATATTGTGAGGGTAAACT
660728 ATATTGTGAGGGTAAACT
1 ATATTGTGAGGGTAAACT
*
660746 ACATTGT
1 ATATTGT
660753 TCACCACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (18 bp):
ATATTGTGAGGGTAAACT
Found at i:662828 original size:12 final size:12
Alignment explanation
Indices: 662811--662849 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
662801 ACAATAATTA
662811 AAATATATACAT
1 AAATATATACAT
*
662823 AAATATACACAT
1 AAATATATACAT
* *
662835 ACATATATACTT
1 AAATATATACAT
662847 AAA
1 AAA
662850 AATGTAAGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATATACAT
Found at i:665215 original size:32 final size:31
Alignment explanation
Indices: 665164--665245 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
665154 CAAATATAGG
**
665164 TGTTTTGTTTCAAGGGAAACAGA-TGCAAAGA
1 TGTTTTGTTTCAAAAGAAACAGACT-CAAAGA
*
665195 TAGTTTTGTTTCAAAAGAAACATACTCAAAGA
1 T-GTTTTGTTTCAAAAGAAACAGACTCAAAGA
*
665227 T-TTTGTTTTTCAAAAGAAA
1 TGTTT-TGTTTCAAAAGAAA
665246 TTGTCTCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 3 0.07
31 14 0.32
32 26 0.59
33 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (31 bp):
TGTTTTGTTTCAAAAGAAACAGACTCAAAGA
Found at i:665458 original size:32 final size:32
Alignment explanation
Indices: 665422--665489 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
665412 GATCGTTCAT
665422 TGTTAAATCCCCAAAGATG-CCTCAACATTCGA
1 TGTTAAATCCCCAAAGATGCCCT-AACATTCGA
*
665454 TGTTAAATCTCCAAAGATGCCCTAACATTCGA
1 TGTTAAATCCCCAAAGATGCCCTAACATTCGA
665486 TGTT
1 TGTT
665490 TCTTGCTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 31 0.91
33 3 0.09
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (32 bp):
TGTTAAATCCCCAAAGATGCCCTAACATTCGA
Done.