Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008005.1 Hibiscus syriacus cultivar Beakdansim tig00110467_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: 1778185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 7
Found at i:1524550 original size:13 final size:13
Alignment explanation
Indices: 1524532--1524558 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1524522 TTACAGACAC
1524532 GCATATGAAGACT
1 GCATATGAAGACT
1524545 GCATATGAAGACT
1 GCATATGAAGACT
1524558 G
1 G
1524559 TTTCAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1528190 original size:15 final size:15
Alignment explanation
Indices: 1528172--1528211 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
1528162 ATGGTAACAC
1528172 AATAAAAACAATTAA
1 AATAAAAACAATTAA
1528187 AATAACAAA-AATTAA
1 AATAA-AAACAATTAA
1528202 AATAGAAAAC
1 AATA-AAAAC
1528212 CCAAAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (15 bp):
AATAAAAACAATTAA
Found at i:1531837 original size:26 final size:26
Alignment explanation
Indices: 1531801--1531853 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1531791 TCATAAAGTA
1531801 AACTTCGAAAAGGACATGAAAATGAG
1 AACTTCGAAAAGGACATGAAAATGAG
1531827 AACTTCGAAAAGGACATGAAAATGAG
1 AACTTCGAAAAGGACATGAAAATGAG
1531853 A
1 A
1531854 TCTTACAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.23, T:0.15
Consensus pattern (26 bp):
AACTTCGAAAAGGACATGAAAATGAG
Found at i:1535656 original size:31 final size:30
Alignment explanation
Indices: 1535612--1535686 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 30
1535602 TTTATTTGGA
* *
1535612 TTTAATGTCAAATTAATAATTTATATAAAG
1 TTTAAAGTAAAATTAATAATTTATATAAAG
* * * *
1535642 TTTAAGAGTTAAATTAATATTTTATGTAAAT
1 TTTAA-AGTAAAATTAATAATTTATATAAAG
1535673 TTTAAAGTAAAATT
1 TTTAAAGTAAAATT
1535687 GATATTATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 13 0.34
31 25 0.66
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTAAAGTAAAATTAATAATTTATATAAAG
Found at i:1535692 original size:30 final size:30
Alignment explanation
Indices: 1535612--1535701 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
1535602 TTTATTTGGA
* * *
1535612 TTTAATGTCAAATTAATAATTTATATAAAG
1 TTTAAAGTAAAATTAATATTTTATATAAAG
* * *
1535642 TTTAAGAGTTAAATTAATATTTTATGTAAAT
1 TTTAA-AGTAAAATTAATATTTTATATAAAG
* * *
1535673 TTTAAAGTAAAATTGATATTATATTTAAA
1 TTTAAAGTAAAATTAATATTTTATATAAA
1535702 AATCACTAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 25 0.50
31 25 0.50
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTAAAGTAAAATTAATATTTTATATAAAG
Found at i:1543652 original size:23 final size:24
Alignment explanation
Indices: 1543610--1543654 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1543600 AAATACTTTA
* *
1543610 AATTTTTTTTATGTATTTTTATTG
1 AATTTTTTTTATATAATTTTATTG
1543634 AATTTTTTTT-TATAATTTTAT
1 AATTTTTTTTATATAATTTTAT
1543655 AAATTCAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (24 bp):
AATTTTTTTTATATAATTTTATTG
Found at i:1543870 original size:30 final size:30
Alignment explanation
Indices: 1543790--1543879 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
1543780 TTTATTTGGA
* *
1543790 TTTAATGTCAAATTAATATTTTATATAAAG
1 TTTAAAGTAAAATTAATATTTTATATAAAG
* * *
1543820 TTTAAGAGTTAAATTAATATTTTATGTAAAT
1 TTTAA-AGTAAAATTAATATTTTATATAAAG
* * *
1543851 TTTAAAGTAAAATTGATATTATATTTAAA
1 TTTAAAGTAAAATTAATATTTTATATAAA
1543880 AATCACTAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 25 0.49
31 26 0.51
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTAAAGTAAAATTAATATTTTATATAAAG
Found at i:1550348 original size:21 final size:21
Alignment explanation
Indices: 1550324--1550371 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1550314 TCAACTACCA
1550324 TCACATAAATTATGGTGTATC
1 TCACATAAATTATGGTGTATC
1550345 TCACATAAATTATGGTGTATC
1 TCACATAAATTATGGTGTATC
*
1550366 TAACAT
1 TCACAT
1550372 CAATATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
TCACATAAATTATGGTGTATC
Found at i:1554409 original size:20 final size:20
Alignment explanation
Indices: 1554384--1554426 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1554374 TTATTATTGG
*
1554384 TACTGACCTCTTGGTATCGA
1 TACTGACCTCTAGGTATCGA
**
1554404 TACTGATTTCTAGGTATCGA
1 TACTGACCTCTAGGTATCGA
1554424 TAC
1 TAC
1554427 CACTGACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TACTGACCTCTAGGTATCGA
Found at i:1557254 original size:3 final size:3
Alignment explanation
Indices: 1557246--1557310 Score: 94
Period size: 3 Copynumber: 21.0 Consensus size: 3
1557236 GATTCATTTG
* *
1557246 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT AAT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
1557292 ATT ATAT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT
1557311 TAATAAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1560974 original size:43 final size:43
Alignment explanation
Indices: 1560907--1560992 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
1560897 TGGCTTTAGA
* *
1560907 GAAGTTAGGAGGGAAAGTTATCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
* *
1560950 GAAGTTAGGACTGAAAGATGTCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
1560993 TGATGCACAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (43 bp):
GAAGTTAGGACGGAAAGATATCCCCTATATGTAAAGTTTTGTT
Found at i:1561285 original size:15 final size:15
Alignment explanation
Indices: 1561249--1561287 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1561239 AATTTACATG
1561249 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
1561263 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
1561278 TTTGCATTTG
1 TTTACATTTG
1561288 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:1564660 original size:21 final size:18
Alignment explanation
Indices: 1564609--1564685 Score: 86
Period size: 17 Copynumber: 4.2 Consensus size: 18
1564599 TCCAGCAAAG
1564609 AAAGGAAAAAAG-AAAAA
1 AAAGGAAAAAAGAAAAAA
*
1564626 AGAGGAAAAAAGAAAAAA
1 AAAGGAAAAAAGAAAAAA
1564644 AAAGGAAAGACATAGAAAAAA
1 AAAGGAAA-A-A-AGAAAAAA
*
1564665 AAA-CAAAAAAGAAAAAGA
1 AAAGGAAAAAAGAAAAA-A
1564683 AAA
1 AAA
1564686 AAATTAAATC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
17 18 0.35
18 17 0.33
19 2 0.04
20 4 0.08
21 11 0.21
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (18 bp):
AAAGGAAAAAAGAAAAAA
Found at i:1567127 original size:114 final size:114
Alignment explanation
Indices: 1566922--1567144 Score: 374
Period size: 114 Copynumber: 2.0 Consensus size: 114
1566912 TGCCAGGTGA
1566922 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGA
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGA
* * *
1566987 TTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGC
* *
1567036 TCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGA
* * *
1567101 TTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
1567145 CTGCATGATC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGC
Found at i:1569715 original size:21 final size:22
Alignment explanation
Indices: 1569679--1569754 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
1569669 ATCTACACTC
1569679 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1569701 TTCAAAGAT-ATAGATTCCCTT
1 TTCAAAGATGATAGATTCTCTT
* * *
1569722 TTTAAAGATGACAGTTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1569744 TTCAAAGATGA
1 TTCAAAGATGA
1569755 AAGCTTTATC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.40
22 28 0.60
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1570360 original size:113 final size:113
Alignment explanation
Indices: 1570162--1571032 Score: 929
Period size: 113 Copynumber: 7.9 Consensus size: 113
1570152 GATTCAAATC
* * *
1570162 CATCA-TCTGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTC-GATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
1570226 AAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * *
1570275 CATCATTCGATGGATCAGCATGACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAATGA
1 CATCATTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1570340 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * *
1570388 CATCATTCGATGGATCAACATTATCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1570453 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * * * * * *
1570501 CATCACTAGATGGATCAACTTTTCCATAGAAAGTTCATAATGAGAAGAATTTATCT---------
1 CATCATTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * ** *
1570557 -GAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTT-GCTCAAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
* * * *
1570604 CATCACTT-GATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCA-TTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1570668 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* ** *
1570717 CATCATTCGAT-GATTTAGTATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTCGATGGA-TCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * * *
1570781 AAGGAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC--AAATC
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
* * * * * *
1570828 CATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
1 CATCA-TTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * *
1570892 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCGAC-TTTAG-TTTAA-T
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * * * *
1570938 CA--A--C-----ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAATGA
1 CATCATTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
**
1570994 AGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
1571033 GCATGACTCT
Statistics
Matches: 657, Mismatches: 76, Indels: 60
0.83 0.10 0.08
Matches are distributed among these distances:
101 78 0.12
102 1 0.00
103 87 0.13
104 6 0.01
108 1 0.00
109 3 0.00
110 4 0.01
111 86 0.13
112 13 0.02
113 371 0.56
114 7 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
Found at i:1570778 original size:329 final size:316
Alignment explanation
Indices: 1570306--1571032 Score: 938
Period size: 329 Copynumber: 2.2 Consensus size: 316
1570296 GACCAGTTCG
*
1570306 AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
1570371 AACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTATCAGGTCGAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAGA
* **
1570436 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGTTTGAAT
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT-G--CAAAT
* * * * *
1570500 TCATCACTAGATGGATCAACTTTTCCATAGAAAGTTCATAATGAGAAGAATTTATCT-GAAGAAG
193 CCATCACTAGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAGAAGAAG
* *
1570564 TTTATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCC
258 TTCATAATGAGAAGAATTTGTTCAA-CTTTAG-TCAAAT-CA--AC-------ATCAACTTTTCC
1570629 AGAAAA
311 AGAAAA
*
1570635 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* **
1570700 AACTTTTCGCTTGAATTCATCATTCGAT-GATTTAGTATTACCAGGTAGAGTTCATAATGAGAAG
66 AACTTTTCGCTTGAATTCATCATTCGATGGA-TCAACATTACCAGGTAGAGTTCATAATGAGAAG
* *
1570764 AACTCATCTGAAGAAGGAAGGAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCAAATCC
130 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCAAATCC
* *
1570829 ATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
195 ATCACTAGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT---------A
* ** *
1570894 GAAGAAGTTCATAATGAGAAGAATTTGTTCGACTTTAGTTTAATCAACATCAACTTTTCCAGAGA
251 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTAGTCAAATCAACATCAACTTTTCCAGAAA
1570959 A
316 A
* * **
1570960 AGTTCATAATGAGAAGAATTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1571025 AACCTTTT
66 AA-CTTTT
1571033 GCATGACTCT
Statistics
Matches: 355, Mismatches: 30, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
325 79 0.22
326 5 0.01
327 53 0.15
328 2 0.01
329 168 0.47
330 5 0.01
332 2 0.01
334 2 0.01
335 4 0.01
336 5 0.01
337 30 0.08
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (316 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCAAATCCA
TCACTAGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACTTTAGTCAAATCAACATCAACTTTTCCAGAAAA
Found at i:1570962 original size:101 final size:101
Alignment explanation
Indices: 1570841--1571024 Score: 314
Period size: 101 Copynumber: 1.8 Consensus size: 101
1570831 CACTTGATGG
*
1570841 ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1570906 AATGAGAAGAATTTGTTCGACTTTAGTTTAATCAAC
66 AATGAGAAGAATTTGTTCGACTTTAGTTTAATCAAC
* * * *
1570942 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAATGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
*
1571007 AATGAGAAGAGTTTGTTC
66 AATGAGAAGAATTTGTTC
1571025 AACCTTTTGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (101 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCGACTTTAGTTTAATCAAC
Found at i:1571093 original size:84 final size:83
Alignment explanation
Indices: 1570994--1571184 Score: 274
Period size: 84 Copynumber: 2.3 Consensus size: 83
1570984 TGAAGAATGA
** * *
1570994 AGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCATGACTCTATCACAGAATTAGATA
1 AGAA-AAGTTCATAATGAGAAGAAATTGTTCAACCTTTTGCATAACTCTATCACAGAAGTAGATA
*
1571059 GATCAACATCAACTTTTCC
65 GATCAACATCAACATTTCC
* ** *
1571078 AGAGAAAGTTCATAATGAGAAGAAATTGTTTAACCTTTTGTTTAACTCTATCACAGAAGTAGATG
1 AGA-AAAGTTCATAATGAGAAGAAATTGTTCAACCTTTTGCATAACTCTATCACAGAAGTAGATA
1571143 GATCAACATCAACATTTCC
65 GATCAACATCAACATTTCC
*
1571162 AGAAATGTTCATAATGAGAAGAA
1 AGAAAAGTTCATAATGAGAAGAA
1571185 CTCATCTGAA
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
83 19 0.20
84 76 0.79
85 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (83 bp):
AGAAAAGTTCATAATGAGAAGAAATTGTTCAACCTTTTGCATAACTCTATCACAGAAGTAGATAG
ATCAACATCAACATTTCC
Found at i:1571443 original size:3 final size:3
Alignment explanation
Indices: 1571435--1571499 Score: 94
Period size: 3 Copynumber: 21.0 Consensus size: 3
1571425 GATTCATTTG
* *
1571435 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT AAT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
1571481 ATT ATAT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT
1571500 TAATAAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1572234 original size:13 final size:13
Alignment explanation
Indices: 1572216--1572244 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1572206 CCACCGTTCA
1572216 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1572229 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1572242 CGG
1 CGG
1572245 AGTACGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:1573105 original size:114 final size:114
Alignment explanation
Indices: 1572968--1573173 Score: 258
Period size: 114 Copynumber: 1.8 Consensus size: 114
1572958 GTTTTAATAT
* * *
1572968 TTATTTATTTTTCAATATTAAG-AAAG-GCCAGTCTTAAAACAACTGGATGTCCATTTTCTGATA
1 TTATTTATTTTTCAATATGAAGAAAAGAG-CAGTCTTAAAACAACTAGAAG-CCATTTTCTGATA
*
1573031 TTTTTAAATAAATAAATATCATACTTTATAAATTATATATTAATTGTTTTAA
64 TTTCTAAATAAATAAATATCATA-TTTATAAATTATATATTAATTGTTTTAA
* * * *
1573083 TTATTT-TTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGACACCTAGAAGCCCTTTTCTGATAT
1 TTATTTATTTTTCAATAT-GAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCATTTTCTGATAT
* *
1573146 TTCTAAATAAGTAAATATCTTATTTATA
65 TTCTAAATAAATAAATATCATATTTATA
1573174 TATATTAATA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
113 11 0.14
114 40 0.51
115 26 0.33
116 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (114 bp):
TTATTTATTTTTCAATATGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCATTTTCTGATATT
TCTAAATAAATAAATATCATATTTATAAATTATATATTAATTGTTTTAA
Found at i:1573941 original size:28 final size:29
Alignment explanation
Indices: 1573901--1573963 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1573891 TATTCACTGC
1573901 ATGTTCTTA-TTTTTTTTTGAGAGAATTG
1 ATGTTCTTATTTTTTTTTTGAGAGAATTG
1573929 ATGTTCTTATTTTTTTTTTGAGAGAATTG
1 ATGTTCTTATTTTTTTTTTGAGAGAATTG
1573958 ATGTTC
1 ATGTTC
1573964 ATCTTTTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.57
Consensus pattern (29 bp):
ATGTTCTTATTTTTTTTTTGAGAGAATTG
Found at i:1574376 original size:18 final size:19
Alignment explanation
Indices: 1574351--1574387 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1574341 ACCTCGGTTC
1574351 AAATGAGA-A-TAGGGGAG
1 AAATGAGAGATTAGGGGAG
1574368 AAATGGAGAGATTAGGGGAG
1 AAAT-GAGAGATTAGGGGAG
1574388 GAAGAAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 1 0.06
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (19 bp):
AAATGAGAGATTAGGGGAG
Found at i:1576779 original size:31 final size:31
Alignment explanation
Indices: 1576744--1576806 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1576734 ATAACAAGTA
1576744 AGATAAGTAAACTTTATTTATTATTGTTTTC
1 AGATAAGTAAACTTTATTTATTATTGTTTTC
1576775 AGATAAGTAAACTTTATTTATTATTGTTTTC
1 AGATAAGTAAACTTTATTTATTATTGTTTTC
1576806 A
1 A
1576807 ATCTTACAAT
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:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (31 bp):
AGATAAGTAAACTTTATTTATTATTGTTTTC
Found at i:1576886 original size:18 final size:19
Alignment explanation
Indices: 1576849--1576886 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1576839 TCTTAAACTT
* *
1576849 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
1576868 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
1576886 T
1 T
1576887 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:1577043 original size:16 final size:16
Alignment explanation
Indices: 1577022--1577077 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
1577012 CGAGTTAAAA
*
1577022 TTCGGTTTGGATTAAT
1 TTCGGTTTGGGTTAAT
*
1577038 TTCGGTTCGGGTTAAT
1 TTCGGTTTGGGTTAAT
1577054 TTCGGTTTGGGTTAAT
1 TTCGGTTTGGGTTAAT
1577070 TTCGGTTT
1 TTCGGTTT
1577078 CACTAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.12, C:0.09, G:0.29, T:0.50
Consensus pattern (16 bp):
TTCGGTTTGGGTTAAT
Found at i:1577087 original size:32 final size:32
Alignment explanation
Indices: 1577017--1577087 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1577007 AGGATCGAGT
* **
1577017 TAAAATTCGGTTTGGATTAATTTCGGTTCGGG
1 TAAATTTCGGTTTGGATTAATTTCGGTTCGAC
* *
1577049 TTAATTTCGGTTTGGGTTAATTTCGGTTTC-AC
1 TAAATTTCGGTTTGGATTAATTTCGG-TTCGAC
1577081 TAAATTT
1 TAAATTT
1577088 TAGATCGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 29 0.91
33 3 0.09
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (32 bp):
TAAATTTCGGTTTGGATTAATTTCGGTTCGAC
Found at i:1579895 original size:21 final size:20
Alignment explanation
Indices: 1579861--1579899 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1579851 TTGGTTAGTT
1579861 TAATTTGACTTAAAATCCTGA
1 TAATTTGACTT-AAATCCTGA
1579882 TAATTTGA-TATAAATCCT
1 TAATTTGACT-TAAATCCT
1579900 AAATTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATTTGACTTAAATCCTGA
Found at i:1582872 original size:16 final size:16
Alignment explanation
Indices: 1582853--1582899 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1582843 AAGAAGGGGA
1582853 AGAAGAAGGGGGAGGC
1 AGAAGAAGGGGGAGGC
**
1582869 AGAAGGCGGGGGAGG-
1 AGAAGAAGGGGGAGGC
1582884 AG--GAAGGGGGAGGC
1 AGAAGAAGGGGGAGGC
1582898 AG
1 AG
1582900 TTTTGTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.35
14 2 0.08
15 2 0.08
16 13 0.50
ACGTcount: A:0.32, C:0.06, G:0.62, T:0.00
Consensus pattern (16 bp):
AGAAGAAGGGGGAGGC
Found at i:1602247 original size:32 final size:33
Alignment explanation
Indices: 1602174--1602248 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
1602164 TTATTAAGAA
* * *
1602174 AAAATATTATTAATATTTTTTAATATATATATAC
1 AAAATTTTATTAATA-TTTTTAATATACAAATAC
*
1602208 AACATTTTATTAATA-TTTTAATATACAAAT-C
1 AAAATTTTATTAATATTTTTAATATACAAATAC
1602239 ATAAATTTTA
1 A-AAATTTTA
1602249 CTTACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.06
32 20 0.57
34 13 0.37
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (33 bp):
AAAATTTTATTAATATTTTTAATATACAAATAC
Found at i:1607879 original size:17 final size:17
Alignment explanation
Indices: 1607857--1607894 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1607847 AAAATAATAG
*
1607857 CAATATAAATCACTCAT
1 CAATATAAACCACTCAT
1607874 CAATATAAACCACTCAT
1 CAATATAAACCACTCAT
1607891 CAAT
1 CAAT
1607895 TCTGTCGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
CAATATAAACCACTCAT
Found at i:1608160 original size:9 final size:10
Alignment explanation
Indices: 1608131--1608163 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
1608121 TTTTTGAAAA
1608131 TTTAATATTAT
1 TTTAATA-TAT
1608142 TTTAATATAT
1 TTTAATATAT
1608152 TTT-ATATAT
1 TTTAATATAT
1608161 TTT
1 TTT
1608164 CTATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 6 0.27
11 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATATAT
Found at i:1613348 original size:194 final size:193
Alignment explanation
Indices: 1613007--1613724 Score: 984
Period size: 194 Copynumber: 3.7 Consensus size: 193
1612997 TGCAAAGAAA
* ** * * * *
1613007 TATCGATACATAACAATATAA-AAGGTTGAAGTTTGACAAAATCGGTTTCAATTTGACAAAACCA
1 TATCGATACATGACAATATAACAA-GTAAAAATATGACAAAATCGGTTTCAATATGACAAAACCG
* * * * * *
1613071 GTAGAA-A--TACCTGA-ATTATTGAAATTTGTATCGATACTTTTCTAAGTATATGCACCAAATT
65 GTA-AAGAGCTACC-GATA-TGTTG-AA--GGTATCGATACTTTTATAAGTATATGTATCATATT
* *
1613132 ATCGATACTTTATGAATTTAAAAGAATCT-CAATAATAGCGCCTATAAAGTATTGATACTTTATA
124 ATCGATACTTTAGGAATTTAAAAGAAT-TGCAATAATAGCGCCTATAAAGTATCGATACTTTATA
1613196 AACATG
188 AACATG
*
1613202 TATCGATACATGACAATATAGCAAGTAAAAATATGACAAAATCGGTTTCAATATGACAAAACCGG
1 TATCGATACATGACAATATAACAAGTAAAAATATGACAAAATCGGTTTCAATATGACAAAACCGG
* *
1613267 TAAAGAGTTACCAGATATGTTGAAGTTATCGATACTTTTATAAGTATATGTATCATATTATCGAT
66 TAAAGAGCTACC-GATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGAT
* * *
1613332 ACTTTAGGAATTTAAAAGAATTGCAATAATATCGCCTATAAAATATCGATATTTTATAAACATG
130 ACTTTAGGAATTTAAAAGAATTGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATG
* *
1613396 TATCGATACATAACAATATAACAGGTAAAAATATGACAAAA-CTGGTTTCAATATGACAAAACCG
1 TATCGATACATGACAATATAACAAGTAAAAATATGACAAAATC-GGTTTCAATATGACAAAACCG
* *
1613460 GTAAAGAGCTACCGAATATGTTGAAGGTATCGAAACTTTTATAAGTATATGTATCGTATTATCGA
65 GTAAAGAGCTACCG-ATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGA
* *
1613525 TACTTTAGGAATTTAAAAGAATTGCAATAATAGTGCTTATAAAGTATCGATACTTTATAAACATG
129 TACTTTAGGAATTTAAAAGAATTGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATG
*
1613590 TATCGATACATGACAATATAACAAGCT-AAAATATGACAAAACCGGTTTCAATATGACAAAACCG
1 TATCGATACATGACAATATAACAAG-TAAAAATATGACAAAATCGGTTTCAATATGACAAAACCG
* * *
1613654 GTAAAGCGCTACCGGATATGTTGAAGGTATCGATACTTTAATAAGTAAATGTATCATATTATCGA
65 GTAAAGAGCTACC-GATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGA
1613719 TACTTT
129 TACTTT
1613725 TAAAAGAAAA
Statistics
Matches: 472, Mismatches: 40, Indels: 23
0.88 0.07 0.04
Matches are distributed among these distances:
193 3 0.01
194 394 0.83
195 60 0.13
196 4 0.01
197 10 0.02
198 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (193 bp):
TATCGATACATGACAATATAACAAGTAAAAATATGACAAAATCGGTTTCAATATGACAAAACCGG
TAAAGAGCTACCGATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGATA
CTTTAGGAATTTAAAAGAATTGCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATG
Found at i:1619536 original size:16 final size:18
Alignment explanation
Indices: 1619515--1619548 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1619505 TTTAGTGGGT
1619515 TAAAAA-ATAAA-AAATA
1 TAAAAATATAAAGAAATA
1619531 TAAAAATATAAAGAAATA
1 TAAAAATATAAAGAAATA
1619549 AGAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAAAATATAAAGAAATA
Found at i:1621110 original size:53 final size:53
Alignment explanation
Indices: 1621028--1621132 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
1621018 TTGGGGTGGG
* *
1621028 GGTAATGCGATATTTCAACATGTAGGAGGTGGTCCTAATAATTTACCTCATAA
1 GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATAA
1621081 GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATA
1 GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATA
1621133 TTTGAAATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (53 bp):
GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATAA
Found at i:1627553 original size:17 final size:17
Alignment explanation
Indices: 1627531--1627569 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1627521 AGAAGTCTTG
1627531 GAGATTTTGGGAAATTA
1 GAGATTTTGGGAAATTA
* *
1627548 GAGATTTTGTGAAATTG
1 GAGATTTTGGGAAATTA
1627565 GAGAT
1 GAGAT
1627570 AGCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (17 bp):
GAGATTTTGGGAAATTA
Found at i:1629066 original size:13 final size:13
Alignment explanation
Indices: 1629048--1629077 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1629038 GGATAAAGTT
*
1629048 AAAACTCAACCAA
1 AAAACTCAAACAA
1629061 AAAACTCAAACAA
1 AAAACTCAAACAA
1629074 AAAA
1 AAAA
1629078 TAGATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.23, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAACTCAAACAA
Found at i:1629365 original size:23 final size:21
Alignment explanation
Indices: 1629343--1629385 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1629333 ACCAAGAAAG
1629343 AAGAC-GAAAAATGTGTCACA
1 AAGACAGAAAAATGTGTCACA
1629363 AAGACAGAAAAATGTGTCACA
1 AAGACAGAAAAATGTGTCACA
1629384 AA
1 AA
1629386 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (21 bp):
AAGACAGAAAAATGTGTCACA
Found at i:1631053 original size:24 final size:24
Alignment explanation
Indices: 1631026--1631072 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1631016 TATTATGTTT
* *
1631026 GTTTACATTCGTTCGTTTATATTC
1 GTTTACATCCATTCGTTTATATTC
*
1631050 GTTTACATCCATTCGTTTCTATT
1 GTTTACATCCATTCGTTTATATT
1631073 ATATTCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (24 bp):
GTTTACATCCATTCGTTTATATTC
Found at i:1634792 original size:3 final size:3
Alignment explanation
Indices: 1634784--1634914 Score: 217
Period size: 3 Copynumber: 43.7 Consensus size: 3
1634774 TTTTTATTCA
* *
1634784 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1634832 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1634880 TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1634915 AATATATTAA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1636429 original size:113 final size:113
Alignment explanation
Indices: 1636230--1636986 Score: 1261
Period size: 113 Copynumber: 6.7 Consensus size: 113
1636220 AGATTCAAAA
1636230 CCATCA-TCTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CCATCACT-TGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1636294 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* *
1636343 TCATCACTTGGTGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1636408 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * *
1636456 TCATCACTTGATGGATTATTTCTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1636521 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * * * *
1636569 TCATCACTTGATGGATTATTTCTGCCAGAGAATGTTCATAATGAGAAGAACTCATTTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1636634 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* ** *
1636682 CCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1636747 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* ** *
1636795 CCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAT---AAGAACTCATTTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1636857 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* **
1636905 CCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
1636970 AAGAAAAAGTTCATAAT
66 AAGAAGAAGTTCATAAT
1636987 CAAGAGCTTA
Statistics
Matches: 622, Mismatches: 18, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
110 110 0.18
113 511 0.82
114 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
Found at i:1637238 original size:3 final size:3
Alignment explanation
Indices: 1637230--1637355 Score: 207
Period size: 3 Copynumber: 41.7 Consensus size: 3
1637220 TTTTTATCCA
*
1637230 TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1637276 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1637324 TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1637356 AATATATTAA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
3 111 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1637854 original size:27 final size:27
Alignment explanation
Indices: 1637824--1637876 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1637814 AGAACGAGAC
1637824 AGAGAAACAGAAAAAAAAAAAGAAAAG
1 AGAGAAACAGAAAAAAAAAAAGAAAAG
* * * *
1637851 AGAGATATAGAAAAAAACAGAGAAAA
1 AGAGAAACAGAAAAAAAAAAAGAAAA
1637877 TACAAACTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (27 bp):
AGAGAAACAGAAAAAAAAAAAGAAAAG
Found at i:1638702 original size:18 final size:19
Alignment explanation
Indices: 1638667--1638707 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1638657 TAGGAATTAG
*
1638667 ATTTAGTTTTATT-TTTTT
1 ATTTAGTTTTATTGTTTTC
1638685 ATTTA-TTTTATATGTTTTC
1 ATTTAGTTTTAT-TGTTTTC
1638704 ATTT
1 ATTT
1638708 TACTGCTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (19 bp):
ATTTAGTTTTATTGTTTTC
Found at i:1641242 original size:16 final size:16
Alignment explanation
Indices: 1641214--1641250 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1641204 CAATTATATC
1641214 TATTTCAAGTTCAATT
1 TATTTCAAGTTCAATT
1641230 TATTT-AAGATTCAATT
1 TATTTCAAG-TTCAATT
1641246 TATTT
1 TATTT
1641251 TTGGAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TATTTCAAGTTCAATT
Found at i:1641896 original size:83 final size:83
Alignment explanation
Indices: 1641757--1643123 Score: 2518
Period size: 83 Copynumber: 16.5 Consensus size: 83
1641747 TGCTCAATAT
*
1641757 CATCTTCTGGAAGTGTTCTTTGAGTTATCAGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1641822 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1641840 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCTATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
* *
1641905 AGATGAATTTGTTAATAG
66 AGATGAATGTGTTCATAG
*
1641923 CATCTTCTGGAAGTGTTCTTTGCGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1641988 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642006 CATCTTCTGGAAGTGTTCTTTCAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642071 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642089 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642154 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642172 CATCTTCTGGAAGTGTTCTTTGAGTTATCAGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642237 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642255 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCTATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
* *
1642320 AGATGAATTTGTTAATAG
66 AGATGAATGTGTTCATAG
1642338 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642403 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
1642421 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642486 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642504 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642569 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642587 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642652 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
* *
1642670 CATCTTCTGGAAGTGTTCTTCGAGTTATCTGATCTGGTTGGACAGAACCTATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642735 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
1642753 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642818 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642836 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
1642901 AGATGAATGTGTTCATAG
66 AGATGAATGTGTTCATAG
*
1642919 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
* * *
1642984 AGATGAATTTGCTAATAG
66 AGATGAATGTGTTCATAG
*
1643002 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTAAATTTGGA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
* * *
1643067 AGATGAATTTGCTAATAG
66 AGATGAATGTGTTCATAG
1643085 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1643124 TGGTAGGAAC
Statistics
Matches: 1251, Mismatches: 33, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 1251 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (83 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTGGA
AGATGAATGTGTTCATAG
Found at i:1643973 original size:113 final size:113
Alignment explanation
Indices: 1643774--1644530 Score: 1261
Period size: 113 Copynumber: 6.7 Consensus size: 113
1643764 AGATTCAAAA
1643774 CCATCA-TCTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CCATCACT-TGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1643838 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* *
1643887 TCATCACTTGGTGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1643952 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * *
1644000 TCATCACTTGATGGATTATTTCTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1644065 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * * * *
1644113 TCATCACTTGATGGATTATTTCTGCCAGAGAATGTTCATAATGAGAAGAACTCATTTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1644178 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* ** *
1644226 CCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1644291 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* ** *
1644339 CCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAT---AAGAACTCATTTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1644401 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* **
1644449 CCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
1644514 AAGAAAAAGTTCATAAT
66 AAGAAGAAGTTCATAAT
1644531 CAAGAGCTTA
Statistics
Matches: 622, Mismatches: 18, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
110 110 0.18
113 511 0.82
114 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CCATCACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
Found at i:1644782 original size:3 final size:3
Alignment explanation
Indices: 1644774--1644913 Score: 235
Period size: 3 Copynumber: 46.7 Consensus size: 3
1644764 TTTTTATCCA
* *
1644774 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1644822 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1644870 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1644914 AATATATTAA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 127 1.00
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1646265 original size:18 final size:19
Alignment explanation
Indices: 1646230--1646270 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1646220 TAGGAATTAG
*
1646230 ATTTAGTTTTATT-TTTTT
1 ATTTAGTTTTATTGTTTTC
1646248 ATTTA-TTTTATATGTTTTC
1 ATTTAGTTTTAT-TGTTTTC
1646267 ATTT
1 ATTT
1646271 TACTGCTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (19 bp):
ATTTAGTTTTATTGTTTTC
Found at i:1649023 original size:12 final size:12
Alignment explanation
Indices: 1649006--1649079 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
1648996 AGGAAAGTCT
*
1649006 CAGATACGGATA
1 CAGATACGAATA
* * *
1649018 CAGATATGGACA
1 CAGATACGAATA
*
1649030 CGGATACGAATA
1 CAGATACGAATA
*
1649042 CAAATAC-ATATA
1 CAGATACGA-ATA
*
1649054 CGGATACGAATA
1 CAGATACGAATA
* *
1649066 CAAATACAAATA
1 CAGATACGAATA
1649078 CA
1 CA
1649080 AATATCAAGT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
11 1 0.02
12 45 0.96
13 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (12 bp):
CAGATACGAATA
Found at i:1649042 original size:6 final size:6
Alignment explanation
Indices: 1649033--1649083 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
1649023 ATGGACACGG
* * ** *
1649033 ATACGA ATACAA ATACAT ATACGG ATACGA ATACAA ATACAA ATACAA
1 ATACAA ATACAA ATACAA ATACAA ATACAA ATACAA ATACAA ATACAA
1649081 ATA
1 ATA
1649084 TCAAGTATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.20
Consensus pattern (6 bp):
ATACAA
Found at i:1649042 original size:24 final size:24
Alignment explanation
Indices: 1649008--1649073 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
1648998 GAAAGTCTCA
* * **
1649008 GATACGGATACAGATATGGACACG
1 GATACGAATACAAATACAGACACG
* *
1649032 GATACGAATACAAATACATATACG
1 GATACGAATACAAATACAGACACG
1649056 GATACGAATACAAATACA
1 GATACGAATACAAATACA
1649074 AATACAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (24 bp):
GATACGAATACAAATACAGACACG
Found at i:1649072 original size:30 final size:30
Alignment explanation
Indices: 1649015--1649079 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1649005 TCAGATACGG
* * *
1649015 ATACAGATATGGACACGGATACGAATACAA
1 ATACAGATACGGACACGAATACAAATACAA
* *
1649045 ATACATATACGGATACGAATACAAATACAA
1 ATACAGATACGGACACGAATACAAATACAA
1649075 ATACA
1 ATACA
1649080 AATATCAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (30 bp):
ATACAGATACGGACACGAATACAAATACAA
Found at i:1649078 original size:24 final size:24
Alignment explanation
Indices: 1649029--1649078 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1649019 AGATATGGAC
*
1649029 ACGGATACGAATACAAATACATAT
1 ACGGATACGAATACAAATACAAAT
1649053 ACGGATACGAATACAAATACAAAT
1 ACGGATACGAATACAAATACAAAT
1649077 AC
1 AC
1649079 AAATATCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
ACGGATACGAATACAAATACAAAT
Found at i:1652404 original size:16 final size:16
Alignment explanation
Indices: 1652383--1652417 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1652373 AATCCATTAA
1652383 TAATTTTAAACCCAAT
1 TAATTTTAAACCCAAT
* *
1652399 TAATTTTAAGCTCAAT
1 TAATTTTAAACCCAAT
1652415 TAA
1 TAA
1652418 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATTTTAAACCCAAT
Found at i:1652601 original size:14 final size:14
Alignment explanation
Indices: 1652584--1652612 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1652574 GTTCAGTTGT
1652584 TCATGTTCGTTCGG
1 TCATGTTCGTTCGG
1652598 TCATGTTCGTTCGG
1 TCATGTTCGTTCGG
1652612 T
1 T
1652613 TAAAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.28, T:0.45
Consensus pattern (14 bp):
TCATGTTCGTTCGG
Found at i:1656101 original size:21 final size:21
Alignment explanation
Indices: 1656056--1656099 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1656046 TTGGTAAAAA
* *
1656056 TTTATCTAAAATATTATTATT
1 TTTATCTAAAACATTAATATT
1656077 TTTAT-TAAAACATTAATATT
1 TTTATCTAAAACATTAATATT
1656097 TTT
1 TTT
1656100 TAATATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATCTAAAACATTAATATT
Found at i:1657748 original size:21 final size:21
Alignment explanation
Indices: 1657722--1657852 Score: 174
Period size: 21 Copynumber: 6.2 Consensus size: 21
1657712 GTTTCCAGAT
* *
1657722 TCGCAACGCAAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1657743 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
1657764 TCGCAATGCGATA-GTCAACTA
1 TCGCAATGCGA-ACTTCGACTA
*
1657785 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1657806 TCGTAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1657827 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
1657848 TCGCA
1 TCGCA
1657853 CAACAAGGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
20 1 0.01
21 93 0.98
22 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1658467 original size:42 final size:42
Alignment explanation
Indices: 1658408--1658631 Score: 394
Period size: 42 Copynumber: 5.3 Consensus size: 42
1658398 CGTTGCGATT
*
1658408 TTGGACTATCGCAACGAACTTGGAATAAATCACAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
1658450 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
1658492 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
1658534 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* *
1658576 TTCGACTATTGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1658618 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1658632 TGTGAATATG
Statistics
Matches: 171, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 171 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:1659607 original size:61 final size:60
Alignment explanation
Indices: 1659483--1659621 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 60
1659473 TAAATTTTCT
**
1659483 AATTTC-TCCCCTAAACTATGACTATTAGTCTAAATTAGTCCTTAAACTTTTGAACATAAC
1 AATTTCATCCCC-AAACTATGACTATTAGTCTAAATTAGTCCCCAAACTTTTGAACATAAC
* * **
1659543 AATTTCATCCCCAAACTATGAC-ATTCATTCTAAATTGGTCCCCAAACTTTTTGAACATTCC
1 AATTTCATCCCCAAACTATGACTATT-AGTCTAAATTAGTCCCCAAAC-TTTTGAACATAAC
*
1659604 AATTTCAT-CTCAAACTAT
1 AATTTCATCCCCAAACTAT
1659622 ATGTATATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.04
60 42 0.61
61 24 0.35
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (60 bp):
AATTTCATCCCCAAACTATGACTATTAGTCTAAATTAGTCCCCAAACTTTTGAACATAAC
Found at i:1659837 original size:60 final size:59
Alignment explanation
Indices: 1659772--1659905 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 59
1659762 TAATGTTTGG
*
1659772 GGACTAATTTAGAAATAAGGTCATAGTTTAGGGATGAAACTGAAATGTTCAAAAGTTTAA
1 GGACTAATTTA-AAATAAGGTCATAGTTTAGGGATGAAACTGAAATATTCAAAAGTTTAA
* * * * *
1659832 GGACTAATTTAAAATGAGAGTCATAGTTTAAGGATGAAATTGGAATATTCAATAGTTTAA
1 GGACTAATTTAAAATAAG-GTCATAGTTTAGGGATGAAACTGAAATATTCAAAAGTTTAA
*
1659892 GGACCAATTTAAAA
1 GGACTAATTTAAAA
1659906 AGAAGATTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.09
60 60 0.91
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (59 bp):
GGACTAATTTAAAATAAGGTCATAGTTTAGGGATGAAACTGAAATATTCAAAAGTTTAA
Found at i:1660980 original size:24 final size:25
Alignment explanation
Indices: 1660933--1660981 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1660923 ATTGATGATC
1660933 TAATTTTATAAATCTTTAAATCTTA
1 TAATTTTATAAATCTTTAAATCTTA
*
1660958 TAATTTTA-AACTC-TTAAATTCTTA
1 TAATTTTATAAATCTTTAAA-TCTTA
1660982 CAATAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 9 0.41
25 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATTTTATAAATCTTTAAATCTTA
Found at i:1663542 original size:20 final size:20
Alignment explanation
Indices: 1663519--1663582 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
1663509 TAGTATTTAG
1663519 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
1663539 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
1663559 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
1663578 TTAAA
1 ATAAA
1663583 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:1663552 original size:19 final size:20
Alignment explanation
Indices: 1663528--1663577 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1663518 GATAAATTTA
*
1663528 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1663547 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1663568 TT-ATAATTTT
1 TTAATAATTTT
1663578 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1663580 original size:31 final size:30
Alignment explanation
Indices: 1663495--1663581 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1663485 TTCGATAATA
* *
1663495 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
1663526 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
1663557 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
1663582 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:1664171 original size:19 final size:19
Alignment explanation
Indices: 1664149--1664236 Score: 54
Period size: 20 Copynumber: 4.4 Consensus size: 19
1664139 AAAGTTTAAA
1664149 AAATTATAAAATATTTATT
1 AAATTATAAAATATTTATT
* *
1664168 AAATTTATTAAAAGA-TTATA
1 AAA-TTA-TAAAATATTTATT
*
1664188 AAATTATTAATAA-GTTTATCT
1 AAATTA-TAA-AATATTTAT-T
*
1664209 AAATACTATAAAATAATTATT
1 AAAT--TATAAAATATTTATT
*
1664230 ATATTAT
1 AAATTAT
1664237 CGAACTTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
19 13 0.24
20 16 0.30
21 16 0.30
22 7 0.13
23 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATTATAAAATATTTATT
Found at i:1664179 original size:31 final size:31
Alignment explanation
Indices: 1664144--1664230 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
1664134 TGAATAAAGT
1664144 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* * *
1664175 TTAAAAGATTATAAAAT-TATTAATAAGTTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
1664206 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
1664231 TATTATCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:1664186 original size:20 final size:21
Alignment explanation
Indices: 1664163--1664212 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
1664153 TATAAAATAT
1664163 TTATTAAATTTATTAA-AAGA
1 TTATTAAATTTATTAATAAGA
* *
1664183 TTA-TAAAATTATTAATAAGT
1 TTATTAAATTTATTAATAAGA
1664203 TTATCTAAAT
1 TTAT-TAAAT
1664213 ACTATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
22 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTATTAAATTTATTAATAAGA
Found at i:1667622 original size:19 final size:19
Alignment explanation
Indices: 1667546--1667624 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
1667536 TAACAATATA
* *
1667546 TAGTATATAATTTAGAAAA
1 TAGTATATAATTTTGAAAT
* * *
1667565 TATTATACAATTTTAAAAT
1 TAGTATATAATTTTGAAAT
*
1667584 ACTATATATATAAGTTTTGAAAT
1 --TA-GTATATAA-TTTTGAAAT
1667607 TAGTATATAATTTTGAAA
1 TAGTATATAATTTTGAAA
1667625 ATAATATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
19 22 0.47
20 7 0.15
21 4 0.09
22 6 0.13
23 8 0.17
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (19 bp):
TAGTATATAATTTTGAAAT
Found at i:1667637 original size:24 final size:24
Alignment explanation
Indices: 1667564--1667649 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
1667554 AATTTAGAAA
* *
1667564 ATATTATACAATTTT-AAAATACT
1 ATATTATATAATTTTGAAAATAAT
1667587 ATA-TATATAAGTTTTG---A-AAT
1 ATATTATATAA-TTTTGAAAATAAT
*
1667607 -TAGTATATAATTTTGAAAATAAT
1 ATATTATATAATTTTGAAAATAAT
*
1667630 ATATTATATAGTTTTGAAAA
1 ATATTATATAATTTTGAAAA
1667650 AAAAAACATT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
19 7 0.14
20 9 0.18
21 1 0.02
22 7 0.14
23 10 0.20
24 17 0.33
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (24 bp):
ATATTATATAATTTTGAAAATAAT
Found at i:1667643 original size:43 final size:41
Alignment explanation
Indices: 1667543--1667649 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 41
1667533 TCATAACAAT
* * *
1667543 ATATAGTATATAATTTAGAAAATATTATACAATTTTAAAATA
1 ATATA-TATATAGTTTTGAAAATAGTATACAATTTTAAAATA
* * *
1667585 CTATATATATAAGTTTTGAAATTAGTATATAATTTTGAAAATA
1 ATATATATAT-AGTTTTGAAAATAGTATACAATTTT-AAAATA
1667628 ATATATTATATAGTTTTGAAAA
1 ATATA-TATATAGTTTTGAAAA
1667650 AAAAAACATT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 5 0.09
42 24 0.44
43 20 0.37
44 5 0.09
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (41 bp):
ATATATATATAGTTTTGAAAATAGTATACAATTTTAAAATA
Found at i:1667736 original size:37 final size:38
Alignment explanation
Indices: 1667616--1667737 Score: 125
Period size: 37 Copynumber: 3.3 Consensus size: 38
1667606 TTAGTATATA
*
1667616 ATTTTGAAAATAATATATTATATAGTTTTGAAAAAAAAAAC
1 ATTTTGAAAATAATATATTATATAGTTTTG---AGAAAAAC
* *
1667657 ATTTTG---A-AA-ATAGTATATAGTTTTGAGAAATA-
1 ATTTTGAAAATAATATATTATATAGTTTTGAGAAAAAC
1667689 A-TTTGAAAAATAATATATTATATAGTTTTG-GAAAAAC
1 ATTTTG-AAAATAATATATTATATAGTTTTGAGAAAAAC
1667726 ATTTTGAAAATA
1 ATTTTGAAAATA
1667738 GTATGTAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
31 4 0.06
32 1 0.01
33 5 0.07
35 1 0.01
36 22 0.32
37 24 0.35
38 5 0.07
41 6 0.09
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (38 bp):
ATTTTGAAAATAATATATTATATAGTTTTGAGAAAAAC
Found at i:1667797 original size:68 final size:69
Alignment explanation
Indices: 1667618--1667813 Score: 238
Period size: 69 Copynumber: 2.8 Consensus size: 69
1667608 AGTATATAAT
*
1667618 TTTG-AAAATAATATATTATATAGTTTTGAAAAAAAAAACATTTTGAAAATAGTATATAGTTTTG
1 TTTGAAAAATAATATATTATATAGTTTTG----GAAAAACATTTTGAAAATAGTATATAGTTTTG
* *
1667682 AGAAATAA
62 AAAAACAA
*
1667690 TTTGAAAAATAATATATTATATAGTTTTGGAAAAACATTTTGAAAATAGTATGTAGTTTT-AAAA
1 TTTGAAAAATAATATATTATATAGTTTTGGAAAAACATTTTGAAAATAGTATATAGTTTTGAAAA
1667754 ACAA
66 ACAA
* * *
1667758 TTTGAAAAACATTATATATTATATAG-TTTGG-AAAACATTTAGAAAAATAGTCTATA
1 TTTG-AAAA-ATAATATATTATATAGTTTTGGAAAAACATTTTG-AAAATAGTATATA
1667814 CAATAGTTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 11
0.85 0.06 0.08
Matches are distributed among these distances:
68 20 0.18
69 49 0.44
70 15 0.13
72 4 0.04
73 24 0.21
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (69 bp):
TTTGAAAAATAATATATTATATAGTTTTGGAAAAACATTTTGAAAATAGTATATAGTTTTGAAAA
ACAA
Found at i:1668876 original size:10 final size:10
Alignment explanation
Indices: 1668837--1668877 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1668827 ATAATTTATA
1668837 ATTTATTTTT
1 ATTTATTTTT
1668847 ATTTTATTTTT
1 A-TTTATTTTT
1668858 ATTTA-TTTT
1 ATTTATTTTT
*
1668867 ATTGATTTTT
1 ATTTATTTTT
1668877 A
1 A
1668878 ATTTGGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 8 0.29
10 10 0.36
11 10 0.36
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1668877 original size:15 final size:14
Alignment explanation
Indices: 1668839--1668877 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1668829 AATTTATAAT
1668839 TTATTTTTATTTTA
1 TTATTTTTATTTTA
*
1668853 TTTTTATTTATTTTA
1 TTATT-TTTATTTTA
1668868 TTGATTTTTA
1 TT-ATTTTTA
1668878 ATTTGGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.19
15 15 0.71
16 2 0.10
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:1671064 original size:19 final size:20
Alignment explanation
Indices: 1671023--1671062 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1671013 TTTAATTAGC
1671023 TTAGTTTAGGTCCTTAAACT
1 TTAGTTTAGGTCCTTAAACT
*
1671043 TTAG-TTAGTTCCTT-AACT
1 TTAGTTTAGGTCCTTAAACT
1671061 TT
1 TT
1671063 TAAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (20 bp):
TTAGTTTAGGTCCTTAAACT
Found at i:1672069 original size:13 final size:13
Alignment explanation
Indices: 1672041--1672096 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1672031 CATGCATCTC
*
1672041 TTTAGTTACCTTTA
1 TTTAGTTA-TTTTA
1672055 TTTAGTTATTTTA
1 TTTAGTTATTTTA
*
1672068 TTTA-TTATCTCTA
1 TTTAGTTAT-TTTA
1672081 TTTAGTT-TTATTA
1 TTTAGTTATT-TTA
1672094 TTT
1 TTT
1672097 TTTATGCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.14
13 21 0.58
14 10 0.28
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.66
Consensus pattern (13 bp):
TTTAGTTATTTTA
Found at i:1672084 original size:26 final size:27
Alignment explanation
Indices: 1672053--1672107 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1672043 TAGTTACCTT
1672053 TATTTAGTTATT-TTATTTATTAT-CTC
1 TATTTAGTT-TTATTATTTATTATGCTC
*
1672079 TATTTAGTTTTATTATTTTTTATGCTC
1 TATTTAGTTTTATTATTTATTATGCTC
1672106 TA
1 TA
1672108 ATTGATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 19 0.73
27 5 0.19
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTAGTTTTATTATTTATTATGCTC
Found at i:1672822 original size:85 final size:86
Alignment explanation
Indices: 1672727--1672925 Score: 310
Period size: 86 Copynumber: 2.3 Consensus size: 86
1672717 CCGCAAGATC
* *
1672727 TGAACCAATCCAACGGTCCAGACTACAAGC-AAATAGGGTTCATTCATAACCTTAGCCAAGTCAG
1 TGAACCAATCCAATGGTCCAGACTACAAGCAAAATAGGGTTCATTCATAACCTTAGCCAAGTCAA
*
1672791 ATCGTGCAACCGCATCGGATA
66 ATCGTGCAACCACATCGGATA
* * *
1672812 TGAACCAATCCAATAGTCCATACTATAAGCAAAATAGGGTTCATTCATAACCTTAGCCAAGTCAA
1 TGAACCAATCCAATGGTCCAGACTACAAGCAAAATAGGGTTCATTCATAACCTTAGCCAAGTCAA
*
1672877 ATCGTGCAACCACATCGGATC
66 ATCGTGCAACCACATCGGATA
* *
1672898 TGAACCAATCCAATGATCCAGATTACAA
1 TGAACCAATCCAATGGTCCAGACTACAA
1672926 AAACAAAAGA
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
85 26 0.26
86 75 0.74
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.22
Consensus pattern (86 bp):
TGAACCAATCCAATGGTCCAGACTACAAGCAAAATAGGGTTCATTCATAACCTTAGCCAAGTCAA
ATCGTGCAACCACATCGGATA
Found at i:1673738 original size:9 final size:9
Alignment explanation
Indices: 1673726--1673759 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1673716 TAATATTTTG
1673726 TATTTAATT
1 TATTTAATT
*
1673735 TATTTAA-G
1 TATTTAATT
1673743 TATTTAATT
1 TATTTAATT
1673752 TATTTAAT
1 TATTTAAT
1673760 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1673765 original size:17 final size:17
Alignment explanation
Indices: 1673725--1673763 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1673715 TTAATATTTT
1673725 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1673742 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1673759 -TATTT
1 GTATTT
1673764 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1679219 original size:16 final size:16
Alignment explanation
Indices: 1679200--1679230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1679190 ATTTTTTTGA
*
1679200 AATAATTATAATAAAC
1 AATAAGTATAATAAAC
1679216 AATAAGTATAATAAA
1 AATAAGTATAATAAA
1679231 AAATTATCAC
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:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAGTATAATAAAC
Found at i:1680724 original size:31 final size:32
Alignment explanation
Indices: 1680689--1680752 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
1680679 TTTGATGTTT
*
1680689 TAATTTACTAAGTTAAGTCCTTA-AACATTTA
1 TAATTAACTAAGTTAAGTCCTTAGAACATTTA
* * *
1680720 TAATTAACTCAGTTTAGTCCTTAGAATATTTA
1 TAATTAACTAAGTTAAGTCCTTAGAACATTTA
1680752 T
1 T
1680753 TTTATTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (32 bp):
TAATTAACTAAGTTAAGTCCTTAGAACATTTA
Found at i:1681732 original size:17 final size:17
Alignment explanation
Indices: 1681712--1681745 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1681702 CAACATCTTT
1681712 TTCAAAACCGCATCATA
1 TTCAAAACCGCATCATA
1681729 TTCAAAACCGCATCATA
1 TTCAAAACCGCATCATA
1681746 ATTTCTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
TTCAAAACCGCATCATA
Found at i:1683782 original size:2 final size:2
Alignment explanation
Indices: 1683775--1683801 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1683765 ACAAAAATAA
1683775 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 A
1683802 AATAAAAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1686554 original size:2 final size:2
Alignment explanation
Indices: 1686547--1686572 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1686537 TCTTTCACAG
1686547 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
1686573 GCACATCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1696683 original size:3 final size:3
Alignment explanation
Indices: 1696677--1696717 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1696667 GGTCTTTTTT
**
1696677 TTA TTA TTA TTA TCG TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1696718 TAATTTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1704604 original size:36 final size:38
Alignment explanation
Indices: 1704564--1704642 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1704554 AAAAAGTGTC
* *
1704564 GTCTCACTAGAGAC-AGTTT-TCTTAAAAACAAATTTT
1 GTCTCACTAGAGACAACTTTCTCTTAAAAACAAATTAT
* * *
1704600 GTCTCGCTTGAGACAACTTTCTCTTTAAAACAAATTAT
1 GTCTCACTAGAGACAACTTTCTCTTAAAAACAAATTAT
1704638 GTCTC
1 GTCTC
1704643 GCCTGAGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 12 0.33
37 4 0.11
38 20 0.56
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (38 bp):
GTCTCACTAGAGACAACTTTCTCTTAAAAACAAATTAT
Found at i:1705115 original size:27 final size:27
Alignment explanation
Indices: 1704942--1705102 Score: 252
Period size: 27 Copynumber: 5.9 Consensus size: 27
1704932 AAGACAATTT
1704942 CTTTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
*
1704969 CTCTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
*
1704996 CTCTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
1705023 CTTTTGAATAAAAATCTTTGAGTTTGTTC
1 CTTTTG-A-AAAAATCTTTGAGTTTGTTC
*
1705052 CTTTTGAATAAATATCTTTGAG-TTGTTT
1 CTTTTGAA-AAA-ATCTTTGAGTTTGTTC
1705080 CTTTTGAAAAAATCTTTGAGTTT
1 CTTTTGAAAAAATCTTTGAGTTT
1705103 ATTTCTTTGG
Statistics
Matches: 126, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
26 9 0.07
27 64 0.51
28 18 0.14
29 35 0.28
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (27 bp):
CTTTTGAAAAAATCTTTGAGTTTGTTC
Found at i:1706105 original size:27 final size:28
Alignment explanation
Indices: 1706067--1706127 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1706057 TAAAAACATC
1706067 ATCTTTGAGTTT-ATT-TTCTTGAAACAA
1 ATCTTTGAGTTTGATTCTT-TTGAAACAA
* *
1706094 ATCTTTGGGTTTGCTTCTTTTGAAACAA
1 ATCTTTGAGTTTGATTCTTTTGAAACAA
1706122 ATCTTT
1 ATCTTT
1706128 AATTTGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 11 0.37
28 17 0.57
29 2 0.07
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (28 bp):
ATCTTTGAGTTTGATTCTTTTGAAACAA
Found at i:1706139 original size:28 final size:28
Alignment explanation
Indices: 1706083--1706147 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
1706073 GAGTTTATTT
**
1706083 TCTTGAAACAAATCTTTGGGTTTGCTTC
1 TCTTGAAACAAATCTTTGAATTTGCTTC
* *
1706111 TTTTGAAACAAATCTTT-AATTTGGTTTC
1 TCTTGAAACAAATCTTTGAATTT-GCTTC
1706139 TCTTGAAAC
1 TCTTGAAAC
1706148 CATAACTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (28 bp):
TCTTGAAACAAATCTTTGAATTTGCTTC
Found at i:1706266 original size:43 final size:44
Alignment explanation
Indices: 1706205--1706538 Score: 260
Period size: 43 Copynumber: 7.7 Consensus size: 44
1706195 TCATCCCTAG
* *
1706205 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCA-ACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
* * * * *
1706248 ACCAG-CCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATA
* * * * * **
1706294 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
*
1706335 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
* * * * *
1706378 ACCAG-CCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATA
* * * * * **
1706424 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
*
1706465 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
*
1706508 ACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGT
1706539 TATCACCTTA
Statistics
Matches: 225, Mismatches: 49, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
40 8 0.04
41 58 0.26
42 3 0.01
43 80 0.36
44 4 0.02
45 10 0.04
46 60 0.27
47 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (44 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
Found at i:1706352 original size:41 final size:40
Alignment explanation
Indices: 1706173--1706627 Score: 180
Period size: 43 Copynumber: 10.6 Consensus size: 40
1706163 TGGCTAGCCG
* * ** * *
1706173 TCCTTATCATGTAGGAATCGTGTCATCCCTAGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGAAC
* * ** *
1706213 TCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAG---ACCAGAAC
* * * *
1706255 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA---CCAGAAC
* * *
1706302 TCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGACCAGAAC
* ** *
1706343 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAG---ACCAGAAC
* * * *
1706385 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA---CCAGAAC
* * *
1706432 TCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGACCAGAAC
* ** *
1706473 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAG---ACCAGAAC
* * *
1706515 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA---CC-AGAAC
* * * * **
1706563 TCTTCATCACGTATGAGCAGTGTCAACCCTC-GACCAGATT
1 TCCTCATCACGTAGGAGCCGTGTCATCCC-CAGACCAGAAC
* *
1706603 TCCTCATCACGTAGGAACCATGTCA
1 TCCTCATCACGTAGGAGCCGTGTCA
1706628 CCCTTAGACG
Statistics
Matches: 312, Mismatches: 67, Indels: 72
0.69 0.15 0.16
Matches are distributed among these distances:
40 56 0.18
41 60 0.19
42 3 0.01
43 87 0.28
44 11 0.04
45 1 0.00
46 64 0.21
47 29 0.09
48 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGAAC
Found at i:1706654 original size:130 final size:130
Alignment explanation
Indices: 1706191--1706627 Score: 754
Period size: 130 Copynumber: 3.4 Consensus size: 130
1706181 ATGTAGGAAT
* *
1706191 CGTGTCA-TCCCTAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
1 CGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
1706255 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
66 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
1706320 CGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
1 CGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
1706385 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
66 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
1706450 CGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
1 CGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
* *
1706515 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGAG
66 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAG
1706580 C
130 C
* * * * *
1706581 AGTGTCA-ACCCTC-GACCAGATTTCCTCATCACGTAGGAACCATGTCA
1 CGTGTCATTCCC-CAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1706628 CCCTTAGACG
Statistics
Matches: 296, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
129 7 0.02
130 259 0.88
131 30 0.10
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (130 bp):
CGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
Found at i:1706830 original size:3 final size:3
Alignment explanation
Indices: 1706824--1706858 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1706814 TCTTTTTTTT
**
1706824 TTA TTA TTA TCG TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1706859 TAATTTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1718297 original size:10 final size:9
Alignment explanation
Indices: 1718279--1718305 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1718269 GCTCTTAAAC
1718279 TTATTTTTT
1 TTATTTTTT
1718288 TTATTTTTT
1 TTATTTTTT
1718297 TTATTTTTT
1 TTATTTTTT
1718306 CGTAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTATTTTTT
Found at i:1718861 original size:23 final size:23
Alignment explanation
Indices: 1718818--1718861 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1718808 TTAAGCATTG
*
1718818 TATTAGTTTGTAAGAATTTATAC
1 TATTAGTTTGTAAGAAGTTATAC
* *
1718841 TATTATTTTGTAATAAGTTAT
1 TATTAGTTTGTAAGAAGTTAT
1718862 TTTGTATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (23 bp):
TATTAGTTTGTAAGAAGTTATAC
Found at i:1719621 original size:16 final size:16
Alignment explanation
Indices: 1719600--1719630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1719590 AATTCTAAAT
*
1719600 CGAAATTGATCCGAAC
1 CGAAATTGACCCGAAC
1719616 CGAAATTGACCCGAA
1 CGAAATTGACCCGAA
1719631 AATATAAAAC
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:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (16 bp):
CGAAATTGACCCGAAC
Found at i:1726079 original size:43 final size:43
Alignment explanation
Indices: 1725998--1726088 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
1725988 AACAAAAAAT
*
1725998 GCCGCAAAAGGTCAAGACCTATAGCAACGTTTTCGAAACAAAC
1 GCCGCAAAAGGTCAAGACCTATAGCAACATTTTCGAAACAAAC
** *** *
1726041 GCCGCAAAAGGTCAAGTTCTATAGTGGCATTTTGGAAACAAAC
1 GCCGCAAAAGGTCAAGACCTATAGCAACATTTTCGAAACAAAC
*
1726084 ACCGC
1 GCCGC
1726089 TAATTAACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (43 bp):
GCCGCAAAAGGTCAAGACCTATAGCAACATTTTCGAAACAAAC
Found at i:1733756 original size:59 final size:59
Alignment explanation
Indices: 1733651--1733778 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
1733641 GTAGTGCTAA
* * * ** *
1733651 CCCGAGTATGACACATAAAGTCGTGTCCACCATCTGTACTATGTATCCTTAAGTACAAT
1 CCCGAATATGACACATAAAGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAAT
* * ** *
1733710 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATT
1 CCCGAATATGACACATAAAGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAAT
1733769 CCCGAATATG
1 CCCGAATATG
1733779 TAGCCTGCTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (59 bp):
CCCGAATATGACACATAAAGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAAT
Found at i:1737925 original size:22 final size:22
Alignment explanation
Indices: 1737897--1737941 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1737887 ATGACATTAA
1737897 AGATTTTCGTTACATAAAGTAT
1 AGATTTTCGTTACATAAAGTAT
1737919 AGATTTTCGTTACATAAAGTAT
1 AGATTTTCGTTACATAAAGTAT
1737941 A
1 A
1737942 TTATTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (22 bp):
AGATTTTCGTTACATAAAGTAT
Found at i:1738328 original size:40 final size:42
Alignment explanation
Indices: 1738222--1738337 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
1738212 GATGAAAAAT
* * *
1738222 TTTGTCACTAGTCTTAGTTGGTGATTTGTGACGTTAATTGTT
1 TTTGTCACTAATCTTAGTTGGTGATTTGTGACGATAATTGTA
*
1738264 TTTGTCACTAATCTTAGTTGGTGATTTATGACGATAATTG-A
1 TTTGTCACTAATCTTAGTTGGTGATTTGTGACGATAATTGTA
*
1738305 TTT-TCACTAATCTTAGTTAGTGATTTGTGACGA
1 TTTGTCACTAATCTTAGTTGGTGATTTGTGACGA
1738338 CAATACTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 28 0.41
41 3 0.04
42 37 0.54
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (42 bp):
TTTGTCACTAATCTTAGTTGGTGATTTGTGACGATAATTGTA
Found at i:1742602 original size:105 final size:104
Alignment explanation
Indices: 1742421--1742642 Score: 257
Period size: 105 Copynumber: 2.1 Consensus size: 104
1742411 GAGTTATTTT
* * * *
1742421 TAATAGTATCGAATATATGGTCACTAAAAACACTTACTATGACAACATTGGTGATCACAAAATAA
1 TAATAGTATCAAACATATGGTCACTAAAAACACTTACTATGACAACATTGATGACCACAAAATAA
* * *
1742486 ACTTTTAGTGTCAAATAAA-TTTATCACAGTTTATATTGA
66 ACTTTTAGTGTCAAA-AAAGATCATCACAGTTTATATTAA
* * * * * * *
1742525 TAATAGTATCAAACATTTGGTCACTAAAAAATACTTAGTGTGACAATATTGATGGCCATAAAATA
1 TAATAGTATCAAACATATGGTCACT-AAAAACACTTACTATGACAACATTGATGACCACAAAATA
* *
1742590 TATTTTTAGTGTCAAAAAAGATCATCACAGTTTATATTAA
65 AACTTTTAGTGTCAAAAAAGATCATCACAGTTTATATTAA
* *
1742630 TAATTGTGTCAAA
1 TAATAGTATCAAA
1742643 TAGATGATCA
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
104 25 0.26
105 73 0.74
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (104 bp):
TAATAGTATCAAACATATGGTCACTAAAAACACTTACTATGACAACATTGATGACCACAAAATAA
ACTTTTAGTGTCAAAAAAGATCATCACAGTTTATATTAA
Found at i:1743733 original size:31 final size:30
Alignment explanation
Indices: 1743692--1743799 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 30
1743682 TAGGTCCCAA
*
1743692 AGAACCTAGGTAAAATGTTCATATATTCCTT
1 AGAACATAGGTAAAATGTTCATAT-TTCCTT
* * * * *
1743723 AGAACATAGGTATACTATTCATATGTCCTG
1 AGAACATAGGTAAAATGTTCATATTTCCTT
* * *
1743753 AAAGACATAGGTAATTATG-TCAATATGTTCCGT
1 AGA-ACATAGGTAA-AATGTTC-ATAT-TTCCTT
1743786 AGAACATAGGTAAA
1 AGAACATAGGTAAA
1743800 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
30 6 0.11
31 31 0.54
32 15 0.26
33 5 0.09
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (30 bp):
AGAACATAGGTAAAATGTTCATATTTCCTT
Found at i:1744138 original size:24 final size:24
Alignment explanation
Indices: 1744106--1744155 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1744096 CATGGTCACA
1744106 ATTCATATAA-CACTTATATTACAT
1 ATTCATATAATCACTTATATTA-AT
* *
1744130 ATTCCTATAATTACTTATATTAAT
1 ATTCATATAATCACTTATATTAAT
1744154 AT
1 AT
1744156 CACATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTCATATAATCACTTATATTAAT
Found at i:1744163 original size:25 final size:25
Alignment explanation
Indices: 1744109--1744163 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1744099 GGTCACAATT
1744109 CATATAACACTTATATTACATATTC
1 CATATAACACTTATATTACATATTC
*
1744134 C-TATAATTACTTATATTA-ATA-TC
1 CATATAA-CACTTATATTACATATTC
1744157 ACATATA
1 -CATATA
1744164 TAATAAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
25 15 0.58
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (25 bp):
CATATAACACTTATATTACATATTC
Found at i:1744721 original size:63 final size:63
Alignment explanation
Indices: 1744650--1744806 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 63
1744640 CCCTTAACAT
* * *
1744650 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCAATG-TTCTAATCTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCAATGTTTCCAATCTTAAGGG
* * * ** * * *
1744713 GTGTATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAAGGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCAATGTTTCCAATCTTAAGGG
*
1744777 GTGCATCGATGCACTTCCTGTGCATCGATA
1 GTGCATCGATGCAC-TCCTATGCATCGATA
1744807 TACACTGAAC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
62 2 0.03
63 37 0.48
64 35 0.45
65 3 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCAATGTTTCCAATCTTAAGGG
Found at i:1748434 original size:24 final size:24
Alignment explanation
Indices: 1748402--1748451 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1748392 CATGGTCACA
1748402 ATTCATATAA-CACTTATATTACAT
1 ATTCATATAATCACTTATATTA-AT
* *
1748426 ATTCCTATAATTACTTATATTAAT
1 ATTCATATAATCACTTATATTAAT
1748450 AT
1 AT
1748452 CACATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTCATATAATCACTTATATTAAT
Found at i:1748459 original size:25 final size:25
Alignment explanation
Indices: 1748405--1748459 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1748395 GGTCACAATT
1748405 CATATAACACTTATATTACATATTC
1 CATATAACACTTATATTACATATTC
*
1748430 C-TATAATTACTTATATTA-ATA-TC
1 CATATAA-CACTTATATTACATATTC
1748453 ACATATA
1 -CATATA
1748460 TAAAAAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
25 15 0.58
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (25 bp):
CATATAACACTTATATTACATATTC
Found at i:1751021 original size:37 final size:37
Alignment explanation
Indices: 1750940--1751021 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
1750930 ATCTAGCCCG
* *
1750940 AACCCAACCCAATTTTTTTTAGATAAAACTCGAACCC
1 AACCCGACCCAATTTTTTTTACATAAAACTCGAACCC
* * * * *
1750977 AAACCGACCCGATTTTTTTTACATAAACCTTGAACTC
1 AACCCGACCCAATTTTTTTTACATAAAACTCGAACCC
*
1751014 GACCCGAC
1 AACCCGAC
1751022 TCAAAATAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.27
Consensus pattern (37 bp):
AACCCGACCCAATTTTTTTTACATAAAACTCGAACCC
Found at i:1751970 original size:23 final size:23
Alignment explanation
Indices: 1751943--1751989 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1751933 TAATACAGTC
1751943 TTCCAAACCTCATATACAAAAAA
1 TTCCAAACCTCATATACAAAAAA
*
1751966 TTCCAAACCTCGTATACAAAAAA
1 TTCCAAACCTCATATACAAAAAA
1751989 T
1 T
1751990 GAGGAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (23 bp):
TTCCAAACCTCATATACAAAAAA
Found at i:1754664 original size:27 final size:25
Alignment explanation
Indices: 1754623--1754673 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1754613 CATTATTGTT
1754623 ATTTTTTTAAAATAA-ATTTAAATCA
1 ATTTTTTTAAAATAAGA-TTAAATCA
1754648 ATTTTTTTAAATGATAAGATTAAATC
1 ATTTTTTTAAA--ATAAGATTAAATC
1754674 GAGTTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 11 0.48
27 11 0.48
28 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
ATTTTTTTAAAATAAGATTAAATCA
Found at i:1758921 original size:2 final size:2
Alignment explanation
Indices: 1758914--1758942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1758904 TATAATACTC
1758914 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 A
1758943 ATAAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1759120 original size:4 final size:4
Alignment explanation
Indices: 1759111--1759144 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1759101 CCCTACCATA
*
1759111 TATG TATG TATG TATG TTTG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
1759145 CACCAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:1759594 original size:21 final size:21
Alignment explanation
Indices: 1759570--1759620 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1759560 TTTTATTAAA
1759570 AATAAAAATATCCATAATTAC
1 AATAAAAATATCCATAATTAC
1759591 AATAAAAATATCCATAATTAC
1 AATAAAAATATCCATAATTAC
*
1759612 AATAGAAAT
1 AATAAAAAT
1759621 TTACAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAAAAATATCCATAATTAC
Found at i:1765079 original size:29 final size:29
Alignment explanation
Indices: 1765046--1765102 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1765036 TAGAATGGGT
* *
1765046 GAACTTGAACTTTTAAAATTTTAGGGGAA
1 GAACTTGAACTTATAAAATTCTAGGGGAA
1765075 GAACTTGAACTTATAAAATTCTAGGGGA
1 GAACTTGAACTTATAAAATTCTAGGGGA
1765103 CGAAACCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (29 bp):
GAACTTGAACTTATAAAATTCTAGGGGAA
Found at i:1766353 original size:24 final size:23
Alignment explanation
Indices: 1766314--1766362 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
1766304 AATAAATTCG
*
1766314 TGAACATTAAATGAACATGTTCA
1 TGAACATTAAACGAACATGTTCA
1766337 TGAACATATAAACGAACATGTTCA
1 TGAACAT-TAAACGAACATGTTCA
1766361 TG
1 TG
1766363 GACACCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (23 bp):
TGAACATTAAACGAACATGTTCA
Found at i:1766918 original size:57 final size:57
Alignment explanation
Indices: 1766857--1766981 Score: 196
Period size: 57 Copynumber: 2.2 Consensus size: 57
1766847 GTGAATATGT
* * * *
1766857 AATTCGCAACGCTGATTACCGATTTAGGTAAACAATACTATCACAACGTGATTTTCA
1 AATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCACAACGCGATTTACA
* *
1766914 AATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTACA
1 AATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCACAACGCGATTTACA
1766971 AATTCGCAACG
1 AATTCGCAACG
1766982 AGATTTTCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (57 bp):
AATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCACAACGCGATTTACA
Found at i:1766979 original size:20 final size:20
Alignment explanation
Indices: 1766954--1766995 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1766944 AACAGTACTA
*
1766954 TCGCAACGCGATTTACAAAT
1 TCGCAACGAGATTTACAAAT
*
1766974 TCGCAACGAGATTTTCAAAT
1 TCGCAACGAGATTTACAAAT
1766994 TC
1 TC
1766996 ACCAATGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (20 bp):
TCGCAACGAGATTTACAAAT
Done.