Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001978.1 Hibiscus syriacus cultivar Beakdansim tig00004013_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: 2594977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1633919 original size:125 final size:124
Alignment explanation
Indices: 1633696--1633965 Score: 398
Period size: 125 Copynumber: 2.2 Consensus size: 124
1633686 TAGGATATGT
* * * *
1633696 TGGGGCACGACTGAACCCACATTATGTTGAGATGATAACTTTCAGACCAAGGAGGCATGAAGAAT
1 TGGGGCACGACTGAACCCACATTATGTTGAGATGACAACATTCAAACCAAGAAGGCATGAAGAAT
*
1633761 GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACTAGTATAAGATAATG
66 GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
* *
1633820 TGGGGGCATGACTGAACCCACATCT-TGTTGAGATGACAAGATTCAAACCAAGAAGGCATGAAGA
1 T-GGGGCACGACTGAACCCACAT-TATGTTGAGATGACAACATTCAAACCAAGAAGGCATGAAGA
* * ** *
1633884 ATGAGCTTTACAATTTGAGGTGATGTGGCATTTTGAAGGCTTGTACCAGTATAAGATAAGG
64 ATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
1633945 ATGGGGCACGACTGAACCCAC
1 -TGGGGCACGACTGAACCCAC
1633966 GTCAAGATAA
Statistics
Matches: 130, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
124 1 0.01
125 127 0.98
126 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (124 bp):
TGGGGCACGACTGAACCCACATTATGTTGAGATGACAACATTCAAACCAAGAAGGCATGAAGAAT
GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
Found at i:1633984 original size:125 final size:125
Alignment explanation
Indices: 1633736--1634013 Score: 371
Period size: 125 Copynumber: 2.2 Consensus size: 125
1633726 GATGATAACT
*
1633736 TTCAGACCAAGGAGGCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCC
1 TTCAGACCAAGAAGGCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCC
* * * ** * * **
1633801 GTACTAGTATAAGATAATGTGGGGGCATGACTGAACCCACATCTTGTTGAGATGACAAGA
66 GTACCAGTATAAGATAAGGTGGGGGCACGACTGAACCCACATCAAGATAAGAAAACAAGA
* * * **
1633861 TTCAAACCAAGAAGGCATGAAGAATGAGCTTTACAATTTGAGGTGATGTGGCATTTTGAAGGCTT
1 TTCAGACCAAGAAGGCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCC
*
1633926 GTACCAGTATAAGATAAGGAT-GGGGCACGACTGAACCCACGTCAAGATAAGAAAACAAGA
66 GTACCAGTATAAGATAAGG-TGGGGGCACGACTGAACCCACATCAAGATAAGAAAACAAGA
*
1633986 TTCAGACCAAGAAGCCATTG-AGAATGAG
1 TTCAGACCAAGAAGGCA-TGAAGAATGAG
1634014 TCTCGCAACT
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
125 130 0.98
126 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (125 bp):
TTCAGACCAAGAAGGCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCC
GTACCAGTATAAGATAAGGTGGGGGCACGACTGAACCCACATCAAGATAAGAAAACAAGA
Found at i:1635203 original size:214 final size:213
Alignment explanation
Indices: 1634735--1635203 Score: 751
Period size: 213 Copynumber: 2.2 Consensus size: 213
1634725 TGAAGCAAAC
* *
1634735 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGACTTTAGAGCAA
1 CCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGACTTTAGAGCAA
*
1634800 GATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
1634865 TAAAAATGATGTTTTAAGAAGATGAAATTTTTTAAAACTAAGAATGCGATTTTCAAAATTTCACA
131 TAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACA
1634930 ATTTATAAGTCCTTCGGG
196 ATTTATAAGTCCTTCGGG
* * * * * *
1634948 CTATAAGTAATTATTTCAAGCATGATGCTTAATTCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGACTTTAGAGCAA
1635013 GATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
1635078 TGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGATGAATGCGATTTTTAAAATTTCAC
131 T-AAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCAC
* **
1635143 GATTTATAAGTTTTTCGGG
195 AATTTATAAGTCCTTCGGG
*
1635162 CCATCAGTAAGTCTTTCAAG-AGTGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCAAGCA-TGATGCTTAAATCCTTCGGG
1635204 CATGATGTTT
Statistics
Matches: 231, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
213 123 0.53
214 108 0.47
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (213 bp):
CCATCAGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGACTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACA
ATTTATAAGTCCTTCGGG
Found at i:1640185 original size:27 final size:26
Alignment explanation
Indices: 1640125--1640212 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 26
1640115 AAACTTAACC
* *
1640125 TTTTATTAT-TATTTT-TTTATTCTA
1 TTTTATTTTCTATTTTATTTATTTTA
*
1640149 TTTTGTTTTTCTACTTTTATTTATTTTA
1 TTTT-ATTTTCTA-TTTTATTTATTTTA
1640177 TTTTATTTTCTA-TTTATTTATTATTA
1 TTTTATTTTCTATTTTATTTATT-TTA
1640203 TTATTATTTT
1 TT-TTATTTT
1640213 TTTTATTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.07
25 13 0.24
26 7 0.13
27 18 0.33
28 12 0.22
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (26 bp):
TTTTATTTTCTATTTTATTTATTTTA
Found at i:1640214 original size:29 final size:26
Alignment explanation
Indices: 1640134--1640213 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 26
1640124 CTTTTATTAT
* * *
1640134 TATTTTTTTATTCTATTTTGTTTTTC
1 TATTTATTTATTTTATTTTATTTTTC
1640160 TACTTTTATTTATTTTATTTTA-TTTTC
1 TA--TTTATTTATTTTATTTTATTTTTC
1640187 TATTTATTTATTATTATTATTATTTTT
1 TATTTATTTATT-TTATT-TTATTTTT
1640214 TTTATTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 10 0.22
26 7 0.15
27 10 0.22
28 19 0.41
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (26 bp):
TATTTATTTATTTTATTTTATTTTTC
Found at i:1640219 original size:29 final size:25
Alignment explanation
Indices: 1640125--1640219 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 25
1640115 AAACTTAACC
* * *
1640125 TTTTATTAT-TATTTTTTTATTCTA
1 TTTTATTTTCTATTTATTTATTTTA
*
1640149 TTTTGTTTTTCTACTTTTATTTATTTTA
1 TTTT-ATTTTCTA--TTTATTTATTTTA
1640177 TTTTATTTTCTATTTATTTATTATTA
1 TTTTATTTTCTATTTATTTATT-TTA
1640203 TTATTATTTT-T-TTTATT
1 TT-TTATTTTCTATTTATT
1640220 GTTTTACTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
24 4 0.07
25 19 0.32
26 8 0.13
27 14 0.23
28 15 0.25
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTATTTTCTATTTATTTATTTTA
Found at i:1640225 original size:29 final size:28
Alignment explanation
Indices: 1640131--1640225 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 28
1640121 AACCTTTTAT
* *
1640131 TATTATTTT-TTTATTCTATTTTGTTTTTC
1 TATT-TTTTATTTATTTTATTTT-ATTTTC
*
1640160 TA-CTTTTATTTATTTTATTTTATTTTC
1 TATTTTTTATTTATTTTATTTTATTTTC
*
1640187 TATTTATTTA-TTATTATTATTATT-TTTTT
1 TATTT-TTTATTTATT-TTATT-TTATTTTC
1640216 TATTGTTTTA
1 TATT-TTTTA
1640226 CTCAATTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 11 0.20
28 18 0.33
29 23 0.42
30 3 0.05
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (28 bp):
TATTTTTTATTTATTTTATTTTATTTTC
Found at i:1640329 original size:16 final size:17
Alignment explanation
Indices: 1640296--1640329 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1640286 ATTTATTTAA
*
1640296 TATTTTTTCTTTTGATT
1 TATTTTTGCTTTTGATT
1640313 TATTTTTGCTTTT-ATT
1 TATTTTTGCTTTTGATT
1640329 T
1 T
1640330 TTTCTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
TATTTTTGCTTTTGATT
Found at i:1643517 original size:27 final size:26
Alignment explanation
Indices: 1643487--1643578 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 26
1643477 AATCAAGAAC
* *
1643487 AAAAAGAGAAGAACAAAGAAAAAAAGC
1 AAAAAGA-AAAAACAAAGAAAAAAAGA
* *
1643514 AAAAAGAAAATAAAAAATAAAAAATA-A
1 AAAAAGAAAA-AACAAAGAAAAAA-AGA
1643541 AAAAAGAAAAAACAAAGGAAAATAAAGA
1 AAAAAGAAAAAACAAA-GAAAA-AAAGA
*
1643569 AAAAATAAAA
1 AAAAAGAAAA
1643579 CAAGACGCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 7 0.13
27 33 0.62
28 13 0.25
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAAACAAAGAAAAAAAGA
Found at i:1643562 original size:11 final size:10
Alignment explanation
Indices: 1643505--1643573 Score: 57
Period size: 11 Copynumber: 6.4 Consensus size: 10
1643495 AAGAACAAAG
1643505 AAAAAAAGCAA
1 AAAAAAAG-AA
*
1643516 AAAGAAAATAA
1 AAA-AAAAGAA
*
1643527 AAAATAAAAAA
1 AAAA-AAAGAA
1643538 TAAAAAAAGAA
1 -AAAAAAAGAA
*
1643549 AAAACAAAGGA
1 AAAA-AAAGAA
*
1643560 AAATAAAGAA
1 AAAAAAAGAA
1643570 AAAA
1 AAAA
1643574 TAAAACAAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 13 0.28
11 26 0.55
12 8 0.17
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:1644643 original size:32 final size:32
Alignment explanation
Indices: 1644596--1644689 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
1644586 GAATAATGGG
* *
1644596 GGCATCTTTGAAGATTCAACGTCAAATGTTGA
1 GGCATCTTTGGAGATTCAACATCAAATGTTGA
* * *
1644628 GGCATTTTTGGAGATTCAACATCGAATATTGA
1 GGCATCTTTGGAGATTCAACATCAAATGTTGA
*
1644660 GGCATCTTTGGGGATTCAACATCCAAATGT
1 GGCATCTTTGGAGATTCAACAT-CAAATGT
1644690 GAAATCACCA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 47 0.90
33 5 0.10
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATGTTGA
Found at i:1645843 original size:37 final size:36
Alignment explanation
Indices: 1645794--1645870 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 36
1645784 CATCTTTAGG
*
1645794 AACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1 AACAAATTTTGTCTCTCTTGACACAGTTTCCCTTGA
*
1645830 AACAAAGTTTTGTCTCTCTTGACACAGTTTCTCTTGA
1 AACAAA-TTTTGTCTCTCTTGACACAGTTTCCCTTGA
1645867 AACA
1 AACA
1645871 CCAACCTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 6 0.16
37 32 0.84
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (36 bp):
AACAAATTTTGTCTCTCTTGACACAGTTTCCCTTGA
Found at i:1645979 original size:33 final size:32
Alignment explanation
Indices: 1645923--1646013 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 32
1645913 CTGAAGACAA
1645923 TTTCTCTTG-AACACAAAAACCTTTGAAATCG
1 TTTCTCTTGAAACACAAAAACCTTTGAAATCG
*
1645954 TTTCTCTTGAAACACAAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACAC-AAAAACCTTTGAAATCG
*
1645987 TTTCTCTTGAAACACAAAGACCTTTGA
1 TTTCTCTTGAAACACAAAAACCTTTGA
1646014 GTTCGACTAC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 9 0.16
32 16 0.29
33 31 0.55
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (32 bp):
TTTCTCTTGAAACACAAAAACCTTTGAAATCG
Found at i:1647045 original size:28 final size:26
Alignment explanation
Indices: 1647001--1647088 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 26
1646991 AAATTTAACC
1647001 TTTTTTAATTTTTTTATTCTATTTCT
1 TTTTTTAATTTTTTTATTCTATTTCT
* *
1647027 TTTTTCTACTTTTATTTATTTTATTTCCT
1 TTTTT-TAATTTT-TTTATTCTATTT-CT
*
1647056 ATTTATTT-TTTATTTTTA-T-TATTTCT
1 -TTT-TTTAATT-TTTTTATTCTATTTCT
1647082 TTTTTTA
1 TTTTTTA
1647089 CTCAATTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
24 3 0.06
25 3 0.06
26 7 0.13
27 11 0.21
28 12 0.23
29 8 0.15
30 6 0.12
31 2 0.04
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTAATTTTTTTATTCTATTTCT
Found at i:1647214 original size:29 final size:28
Alignment explanation
Indices: 1647198--1647256 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1647188 TTTTTCTTCA
*
1647198 TTTTCCCTTTTGATTTATTTTATTTTAT
1 TTTTCCCATTTGATTTATTTTATTTTAT
* *
1647226 TTTTTCCATTTGATTTATTTAATATTTAT
1 TTTTCCCATTTGATTTATTTTAT-TTTAT
1647255 TT
1 TT
1647257 ATCATTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTCCCATTTGATTTATTTTATTTTAT
Found at i:1653190 original size:38 final size:38
Alignment explanation
Indices: 1653126--1653245 Score: 150
Period size: 38 Copynumber: 3.1 Consensus size: 38
1653116 CGAGTCAAAT
*
1653126 ATATGCACCGTAGTGATTACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTG-TTACACATAAGGTCGTGCCCACC
* *
1653165 ATATGCACCGAAGTGCTACACATAAGGTCGTGTCCACC
1 ATATGCACCGAAGTGTTACACATAAGGTCGTGCCCACC
* * * * **
1653203 ATTTACACCGAAGTGTTACACAAAAGGTCATGGTCACC
1 ATATGCACCGAAGTGTTACACATAAGGTCGTGCCCACC
1653241 ATATG
1 ATATG
1653246 AACTAAAGTT
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 55 0.80
39 14 0.20
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (38 bp):
ATATGCACCGAAGTGTTACACATAAGGTCGTGCCCACC
Found at i:1653618 original size:17 final size:16
Alignment explanation
Indices: 1653597--1653635 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1653587 TTTTAAAAGC
*
1653597 AATAAAATAAAG-AAA
1 AATAAAAGAAAGAAAA
1653612 AATATAAAGAAAGAAAA
1 AATA-AAAGAAAGAAAA
1653629 AATAAAA
1 AATAAAA
1653636 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (16 bp):
AATAAAAGAAAGAAAA
Found at i:1653626 original size:16 final size:15
Alignment explanation
Indices: 1653605--1653647 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
1653595 GCAATAAAAT
1653605 AAAGAAAAATATAAAG
1 AAAGAAAAA-ATAAAG
1653621 AAAGAAAAAATAAA-
1 AAAGAAAAAATAAAG
*
1653635 AAA-ATAAAATAAA
1 AAAGAAAAAATAAA
1653648 AAACTTAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 9 0.35
14 3 0.12
15 5 0.19
16 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (15 bp):
AAAGAAAAAATAAAG
Found at i:1653628 original size:15 final size:15
Alignment explanation
Indices: 1653598--1653650 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1653588 TTTAAAAGCA
1653598 ATAAAATAAAGAAAAAT
1 ATAAAA-AAAG-AAAAT
* *
1653615 ATAAAGAAAGAAAAA
1 ATAAAAAAAGAAAAT
*
1653630 ATAAAAAAATAAAAT
1 ATAAAAAAAGAAAAT
1653645 A-AAAAA
1 ATAAAAA
1653651 CTTAGAGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 4 0.13
17 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (15 bp):
ATAAAAAAAGAAAAT
Found at i:1654264 original size:114 final size:115
Alignment explanation
Indices: 1654064--1654295 Score: 448
Period size: 114 Copynumber: 2.0 Consensus size: 115
1654054 ATCTTGATGT
1654064 AAGGAACACAGATCTAACCTCCGTTTTGCGAGGAACAGTCTCCAACTTGACAAAAAGGTCGTCAA
1 AAGGAACACAGATCTAACCTCCGTTTTGCGAGGAACAGTCTCCAACTTGACAAAAAGGTCGTCAA
1654129 TCATTCAACTTTCTCCATTCCGATTTACCACCGTCCCCCGTT-ATTATCA
66 TCATTCAACTTTCTCCATTCCGATTTACCACCGTCCCCCGTTAATTATCA
1654178 AAGGAACACAGATCTAACCTCCGTTTTGCGAGGAACAGTCTCCAACTTGACAAAAAGGTCGTCAA
1 AAGGAACACAGATCTAACCTCCGTTTTGCGAGGAACAGTCTCCAACTTGACAAAAAGGTCGTCAA
1654243 TCATTCAACTTTCTCCATTCCGATTTACCACCGTCCCCCGTTAGATTATCA
66 TCATTCAACTTTCTCCATTCCGATTTACCACCGTCCCCCGTTA-ATTATCA
1654294 AA
1 AA
1654296 ATTTTCAGGT
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
114 107 0.92
116 9 0.08
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (115 bp):
AAGGAACACAGATCTAACCTCCGTTTTGCGAGGAACAGTCTCCAACTTGACAAAAAGGTCGTCAA
TCATTCAACTTTCTCCATTCCGATTTACCACCGTCCCCCGTTAATTATCA
Found at i:1656102 original size:45 final size:47
Alignment explanation
Indices: 1655988--1656102 Score: 135
Period size: 48 Copynumber: 2.5 Consensus size: 47
1655978 ACCTTTTATC
1655988 CCATAAGCTCATAAGCTTATTTTTACCAAAATACATACCATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACATACCATTT-AATT
* ** * * *
1656036 CCATAAGCTCGTAAGCTTATTTTTTTCAATATACTTGCCA-TT-ATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACATACCATTTAATT
* *
1656081 TCGTAAGCTCATAAGCTTATTT
1 CCATAAGCTCATAAGCTTATTT
1656103 GCATCGTAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 22 0.38
47 2 0.03
48 34 0.59
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (47 bp):
CCATAAGCTCATAAGCTTATTTTTACCAAAATACATACCATTTAATT
Found at i:1656170 original size:40 final size:40
Alignment explanation
Indices: 1656115--1656196 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1656105 ATCGTAGTGC
*
1656115 TACACATATGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1656155 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1656195 TA
1 TA
1656197 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1663029 original size:40 final size:40
Alignment explanation
Indices: 1662985--1663106 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
1662975 ACCGTAGTGC
* *
1662985 TACACATAAGGTCTTGCCCACCAAATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1663025 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1663065 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1663105 TA
1 TA
1663107 TAAACCTACA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1666977 original size:47 final size:48
Alignment explanation
Indices: 1666881--1666977 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
1666871 TTTGATGGCT
*
1666881 AAAGTAGAAAATTAGGAAAAGTTTAAGGACCTAAATGGTAATTTTAAA
1 AAAGTAGAAAATTAGGAAAAGTTTAAGGACCTAAATGATAATTTTAAA
* * * *
1666929 AAAGTATAAACTTTGGAAAAGTTTAGGGA-CTAAA-GTATAATTTTAAA
1 AAAGTAGAAAATTAGGAAAAGTTTAAGGACCTAAATG-ATAATTTTAAA
1666976 AA
1 AA
1666978 GTTATGTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.02
47 17 0.40
48 25 0.58
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (48 bp):
AAAGTAGAAAATTAGGAAAAGTTTAAGGACCTAAATGATAATTTTAAA
Found at i:1677688 original size:24 final size:24
Alignment explanation
Indices: 1677633--1677736 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 24
1677623 CATCGAAGTG
* *
1677633 CCACATAGAATTTGTGCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*** *
1677657 CGGTGTAGAATTTTTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* * *
1677681 CCACGTAGTA-TTATCCCAAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* *
1677704 CCACATAG-ATCTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*
1677727 CCGCGTAGAA
1 CCACGTAGAA
1677737 CCCTCGACTC
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
22 1 0.02
23 34 0.57
24 25 0.42
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCGAAGGA
Found at i:1683851 original size:23 final size:24
Alignment explanation
Indices: 1683783--1683885 Score: 104
Period size: 24 Copynumber: 4.4 Consensus size: 24
1683773 CACTGAAGTG
*
1683783 CCACGTAGAATTTTTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* * * *
1683807 TCGCATAGAATTTGTCCAGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
1683831 CCACGTAGAA-TTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* * * *
1683854 CCACATAG-ATTTAT-CCTAAAGA
1 CCACGTAGAATTTGTCCCGAAGGA
1683876 CCACGTAGAA
1 CCACGTAGAA
1683886 CCCTGACTCT
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
22 14 0.22
23 23 0.37
24 26 0.41
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCGAAGGA
Found at i:1685703 original size:30 final size:28
Alignment explanation
Indices: 1685669--1685747 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 28
1685659 AAATCCAATA
*
1685669 TTTAACTTTTGAAAATTTACATTTTTAGTC
1 TTTAACTTTT-AAAATTTACA-CTTTAGTC
1685699 TTTAAACTTTTACAACA-TTACACTTTAGTC
1 TTT-AACTTTTA-AA-ATTTACACTTTAGTC
* *
1685729 TCTAAATTTTCAAAATTTA
1 TTTAACTTTT-AAAATTTA
1685748 TATTCCAGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
28 1 0.02
29 11 0.27
30 14 0.34
31 14 0.34
32 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (28 bp):
TTTAACTTTTAAAATTTACACTTTAGTC
Found at i:1692205 original size:22 final size:22
Alignment explanation
Indices: 1692121--1692206 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
1692111 GATTTTCTCC
* *
1692121 TATCATTGCTAAAGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
* * *
1692143 TATCAGTG-TGAATGTACTTTCG
1 TATCAGTGCT-AAGGCACTTTAG
* * *
1692165 TACCAGTACTGAGGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
*
1692187 TATCAGTGCTAAGGAACTTT
1 TATCAGTGCTAAGGCACTTT
1692207 TATTATTTAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (22 bp):
TATCAGTGCTAAGGCACTTTAG
Found at i:1694622 original size:50 final size:50
Alignment explanation
Indices: 1694539--1694634 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
1694529 AAGATAGATG
* **
1694539 AATATGCTCTATCAAGCCCTCCTAGTCGTAATGAAAAGG-AAAACTCGAC
1 AATATGCTCTATCAAGCCCTCCTAATCACAATGAAAAGGCAAAACTCGAC
*
1694588 AATATGGCTCTATCCAA-CCCTCCTAATCACAATGAGAAGGCAAAACT
1 AATAT-GCTCTAT-CAAGCCCTCCTAATCACAATGAAAAGGCAAAACT
1694635 GAGTCTGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 5 0.12
50 26 0.65
51 9 0.22
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.22
Consensus pattern (50 bp):
AATATGCTCTATCAAGCCCTCCTAATCACAATGAAAAGGCAAAACTCGAC
Found at i:1700531 original size:20 final size:20
Alignment explanation
Indices: 1700506--1700551 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1700496 CAACCAGAAA
1700506 AACCCTAGGGTACTCATTGT
1 AACCCTAGGGTACTCATTGT
1700526 AACCCTAGGGTACTCATTGT
1 AACCCTAGGGTACTCATTGT
1700546 AACCCT
1 AACCCT
1700552 GGGGCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
AACCCTAGGGTACTCATTGT
Found at i:1701411 original size:2 final size:2
Alignment explanation
Indices: 1701404--1701433 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1701394 TATGCTATTA
1701404 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
1701434 TATGGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1702745 original size:15 final size:15
Alignment explanation
Indices: 1702727--1702764 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1702717 CAACATATAA
1702727 TATCACCCTATCATG
1 TATCACCCTATCATG
1702742 TATCACCCTATCATG
1 TATCACCCTATCATG
1702757 TATCACCC
1 TATCACCC
1702765 ATGCAACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.32
Consensus pattern (15 bp):
TATCACCCTATCATG
Found at i:1709103 original size:35 final size:36
Alignment explanation
Indices: 1709051--1709122 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
1709041 TATTCTTTCC
1709051 ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
1 ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
*
1709087 ATGCAATTCAA-CCTTCACAAAAGAGTAGTGAAGCA
1 ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
1709122 A
1 A
1709123 GAACAGATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 25 0.71
36 10 0.29
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.18
Consensus pattern (36 bp):
ATGCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCA
Found at i:1712090 original size:21 final size:23
Alignment explanation
Indices: 1712056--1712099 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
1712046 TTTTCTCTTC
1712056 TTTCTCTTGATTTTTCTT-TTGTT
1 TTTCTCTTGATTTTT-TTGTTGTT
1712079 TTTCTC-TG-TTTTTTTGTTGTT
1 TTTCTCTTGATTTTTTTGTTGTT
1712100 GTTCGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 10 0.50
22 2 0.10
23 6 0.30
ACGTcount: A:0.02, C:0.11, G:0.11, T:0.75
Consensus pattern (23 bp):
TTTCTCTTGATTTTTTTGTTGTT
Found at i:1713396 original size:65 final size:65
Alignment explanation
Indices: 1713291--1713544 Score: 321
Period size: 65 Copynumber: 3.9 Consensus size: 65
1713281 AGGGATAATT
* ** * * * *
1713291 TGTTTTAAGAGAAAGGGTCTCAAGCGAGACAAAATATGTTTCAAGAGAAACAATCTCAAACTTTA
1 TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
* * * *
1713356 TGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATTTGTTTGAAGAAAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
* * * *
1713421 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAACTTTGTTTCAAGAGAAACAATCTTAAAGTTTA
1 TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
* * * *
1713486 TGTTTCAAGAGAAA-TTATCTTAAGAGAGACAAAACTTGTTTAAAGAGAAACAATCTCAA
1 TGTTTCAAGAGAAACTGA-CTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA
1713545 GTGAGATTAA
Statistics
Matches: 161, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
64 1 0.01
65 160 0.99
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
Found at i:1713525 original size:130 final size:130
Alignment explanation
Indices: 1713291--1713544 Score: 357
Period size: 130 Copynumber: 2.0 Consensus size: 130
1713281 AGGGATAATT
* * *
1713291 TGTTTTAAGAGAAAGGGTCTCAAGCGAGACAAAATATGTTTCAAGAGAAACAATCTCAAACTTTA
1 TGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATATGTTTCAAGAGAAACAATCTCAAACTTTA
* * *
1713356 TGTTTCAAGGGAAACTGACTCAAGAGAGACAAAATTTGTTTGAAGAAAAACAATCTCAAAGGTTA
66 TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAACTTGTTTAAAGAAAAACAATCTCAAAGGTTA
* * * * * *
1713421 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAACTTTGTTTCAAGAGAAACAATCTTAAAGTTTA
1 TGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATATGTTTCAAGAGAAACAATCTCAAACTTTA
* * *
1713486 TGTTTCAAGAGAAA-TTATCTTAAGAGAGACAAAACTTGTTTAAAGAGAAACAATCTCAA
66 TGTTTCAAGAGAAACTGA-CTCAAGAGAGACAAAACTTGTTTAAAGAAAAACAATCTCAA
1713545 GTGAGATTAA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
129 2 0.02
130 106 0.98
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (130 bp):
TGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATATGTTTCAAGAGAAACAATCTCAAACTTTA
TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAACTTGTTTAAAGAAAAACAATCTCAAAGGTTA
Found at i:1720887 original size:16 final size:17
Alignment explanation
Indices: 1720866--1720898 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1720856 CTCCTCAGGT
1720866 AGGAAAT-ATGTCCATA
1 AGGAAATGATGTCCATA
*
1720882 AGGAAATGATTTCCATA
1 AGGAAATGATGTCCATA
1720899 TTCTTCTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (17 bp):
AGGAAATGATGTCCATA
Found at i:1721389 original size:3 final size:3
Alignment explanation
Indices: 1721383--1721417 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1721373 TATTAATAAT
1721383 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1721418 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1721422 original size:3 final size:3
Alignment explanation
Indices: 1721416--1721441 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1721406 CAACAACAAC
1721416 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1721442 AAGTAGAACC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1723160 original size:163 final size:163
Alignment explanation
Indices: 1722890--1723213 Score: 594
Period size: 163 Copynumber: 2.0 Consensus size: 163
1722880 GTGTGGAGCC
*
1722890 CAGACTCTGAGAAATGGGTTGAAGCCCTGAGATCTGAGATGGATTCCTCAGTAAAACAAGTATGG
1 CAGACTCTAAGAAATGGGTTGAAGCCCTGAGATCTGAGATGGATTCCTCAGTAAAACAAGTATGG
*
1722955 ACTTTGGTTGAACCACCAGAAAGGGTCAAACCTGTAAGGTGTAAATGTGTTTTCAAGATAAAAAC
66 ACTTTGGTTGAACCACCAGAAAGGGTCAAACCTGTAAGGTGTAAATGGGTTTTCAAGATAAAAAC
*
1723020 CGACATGGATGGTAATCTACCAGCATACAAGTA
131 CGACATGGATGGTAATCTACCAACATACAAGTA
*
1723053 CAGACTCTAAGAAATGGGTTGAAGCCCTGAGATCTGAGATGGATTCCTCAGTAAACCAAGTATGG
1 CAGACTCTAAGAAATGGGTTGAAGCCCTGAGATCTGAGATGGATTCCTCAGTAAAACAAGTATGG
1723118 ACTTTGGTTGAACCACCAGAAAGGGTCAAACCTGTAAGGTGTAAATGGGTTTTCAAGATAAAAAC
66 ACTTTGGTTGAACCACCAGAAAGGGTCAAACCTGTAAGGTGTAAATGGGTTTTCAAGATAAAAAC
* *
1723183 CGACATGGATGGTAATGTACCAATATACAAG
131 CGACATGGATGGTAATCTACCAACATACAAG
1723214 GGGCGATTGG
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 155 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (163 bp):
CAGACTCTAAGAAATGGGTTGAAGCCCTGAGATCTGAGATGGATTCCTCAGTAAAACAAGTATGG
ACTTTGGTTGAACCACCAGAAAGGGTCAAACCTGTAAGGTGTAAATGGGTTTTCAAGATAAAAAC
CGACATGGATGGTAATCTACCAACATACAAGTA
Found at i:1725645 original size:17 final size:17
Alignment explanation
Indices: 1725604--1725647 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1725594 CCGGAATTTA
1725604 TGTTAAAAG-CTAGAAAG
1 TGTT-AAAGTCTAGAAAG
1725621 TGTTAAAGTCTAGAAAG
1 TGTTAAAGTCTAGAAAG
1725638 TGTTAAAGTC
1 TGTTAAAGTC
1725648 CGATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30
Consensus pattern (17 bp):
TGTTAAAGTCTAGAAAG
Found at i:1729095 original size:19 final size:18
Alignment explanation
Indices: 1729063--1729098 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1729053 TTTATCGCAC
1729063 TTAAATTAAAATATATAA
1 TTAAATTAAAATATATAA
*
1729081 TTAAGATTAATATATATA
1 TTAA-ATTAAAATATATA
1729099 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTAAATTAAAATATATAA
Found at i:1737297 original size:53 final size:53
Alignment explanation
Indices: 1737159--1738287 Score: 1530
Period size: 53 Copynumber: 21.0 Consensus size: 53
1737149 CAAAAACAAT
*
1737159 ACCCTCAATCTTCATCAATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
1737211 ACTCGAACAATCTTCA-AAGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 AC-C-CACAATCTTCATCA-ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1737266 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
1737319 ACCCACAATCTTCAACGATCACGTATGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1737372 ACCAACAATCTTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
1737425 ACTCGAACAATCTTCAACGATTGTGTCTGCCCCCTATTTCTTTAGAGAGTATAAG
1 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1737480 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
1737533 ACTCGAACAATCTTCAAT-GATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 AC-C-CACAATCTTC-ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1737588 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1737641 ACCCACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
1737694 ACCAACAATCTTTATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
1737747 ACTCGAACAAACTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGATAGTATAA-
1 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1737801 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
1737854 ACTCGAACAATCTTCAACGATTGCGTCTGCACCCTATTTCTTCAGAGAGGATAAG
1 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1737909 ACCCACAATCTTCATCAATCGCGTATGCCCCCTATTTTTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1737962 ACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCATAGAGTATAAG
1 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
1738017 ACTCGAACAATCTTCA-AAGATTGCGTCTGCCCCCTATTTATTTAGAGAGTATAAG
1 AC-C-CACAATCTTCATCA-ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1738072 ACCCACAATCTTCATAAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * * * * *
1738125 AATCGAACAATCTTCAACGATTGTGTTTGCCCCCTATTTCTTCAGAGAGTATAAG
1 -A-CCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1738180 ACCCACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1738233 ACCCACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1738286 AC
1 AC
1738288 TCGAACAATC
Statistics
Matches: 952, Mismatches: 103, Indels: 43
0.87 0.09 0.04
Matches are distributed among these distances:
52 47 0.05
53 522 0.55
54 36 0.04
55 345 0.36
56 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (53 bp):
ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:1737488 original size:108 final size:108
Alignment explanation
Indices: 1737159--1738300 Score: 1696
Period size: 108 Copynumber: 10.6 Consensus size: 108
1737149 CAAAAACAAT
*
1737159 ACCCTCAATCTTCATCAATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* *
1737223 TTCAAAGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1737266 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* *
1737329 TTCAACGATCACGTATGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1737372 ACCAACAATCTTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * *
1737437 TTCAACGATTGTGTCTGCCCCCTATTTCTTTAGAGAGTATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1737480 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * *
1737545 TTCAATGATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1737588 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1737651 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
1737694 ACCAACAATCTTTATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAAC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* *
1737759 TTCAACGATTGCGTCTGCCCCCTATTTCTTCAGATAGTATAA-
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1737801 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * *
1737866 TTCAACGATTGCGTCTGCACCCTATTTCTTCAGAGAGGATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1737909 ACCCACAATCTTCATCAATCGCGTATGCCCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * *
1737974 TTCATCAATCGCGTCTGCCCCCTATTTCTTCATAGAGTATAAG
66 TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
1738017 ACTCGAACAATCTTCA-AAGATTGCGTCTGCCCCCTATTTATTTAGAGAGTATAAGAC-C-CACA
1 AC-C-CACAATCTTCATCA-ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
* *
1738079 ATCTTCATA-AATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
63 ATCTTCA-ACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * * * * * *
1738125 AATCGAACAATCTTCAACGATTGTGTTTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 -A-CCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
1738188 TCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
64 TCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
1738233 ACCCACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1738298 TTC
66 TTC
1738301 TTTTGCTTCA
Statistics
Matches: 951, Mismatches: 68, Indels: 31
0.91 0.06 0.03
Matches are distributed among these distances:
106 245 0.26
107 132 0.14
108 525 0.55
109 4 0.00
110 45 0.05
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (108 bp):
ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:1738300 original size:161 final size:161
Alignment explanation
Indices: 1737159--1738287 Score: 1598
Period size: 161 Copynumber: 7.0 Consensus size: 161
1737149 CAAAAACAAT
* *
1737159 ACCCTCAATCTTCATCAATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* *
1737223 TTCA-AAGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCG
66 TTCATCA-ATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCG
1737287 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
130 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
1737319 ACCCACAATCTTCAACGATCACGTATGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-AACAATC
1 ACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * * * *
1737382 TTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATT
66 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATC
* *
1737447 GTGTCTGCCCCCTATTTCTTTAGAGAGTATAAG
129 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1737480 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * *
1737545 TTCAAT-GATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCG
66 TTC-ATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCG
1737609 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
130 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1737641 ACCCACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-AACAATC
1 ACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * * * * * *
1737704 TTTATCAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAACTTCAACGATT
66 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATC
*
1737769 GCGTCTGCCCCCTATTTCTTCAGATAGTATAA-
129 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1737801 ACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
1 ACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
* * * * *
1737866 TTCAACGATTGCGTCTGCACCCTATTTCTTCAGAGAGGATAAGACCCACAATCTTCATCAATCGC
66 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGC
* *
1737931 GTATGCCCCCTATTTTTTCAGAGAGTATAAG
131 GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
1737962 ACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCATAGAGTATAAGACTCGAACAA
1 AC-C-CACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
1738027 TCTTCA-AAGATTGCGTCTGCCCCCTATTTATTTAGAGAGTATAAGACCCACAATCTTCATA-AA
64 TCTTCATCA-ATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCA-ACAA
*
1738090 TCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
127 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * * * * *
1738125 AATCGAACAATCTTCAACGATTGTGTTTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 -A-CCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
** *
1738188 TCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACGATC
64 TCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATC
1738253 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
129 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1738286 AC
1 AC
1738288 TCGAACAATC
Statistics
Matches: 863, Mismatches: 85, Indels: 43
0.87 0.09 0.04
Matches are distributed among these distances:
158 2 0.00
159 92 0.11
160 123 0.14
161 357 0.41
162 50 0.06
163 235 0.27
164 3 0.00
165 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (161 bp):
ACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC
TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGC
GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:1743356 original size:13 final size:12
Alignment explanation
Indices: 1743334--1743383 Score: 75
Period size: 13 Copynumber: 4.1 Consensus size: 12
1743324 AAACAAATAC
1743334 ATGC-AATGCAA
1 ATGCAAATGCAA
1743345 ATGCTAAATGCAA
1 ATGC-AAATGCAA
1743358 ATGCAAATGCTAA
1 ATGCAAATGC-AA
1743371 ATGCAAATGCAA
1 ATGCAAATGCAA
1743383 A
1 A
1743384 AGGTGTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.11
12 9 0.25
13 23 0.64
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (12 bp):
ATGCAAATGCAA
Found at i:1743359 original size:6 final size:6
Alignment explanation
Indices: 1743334--1743383 Score: 75
Period size: 6 Copynumber: 8.2 Consensus size: 6
1743324 AAACAAATAC
1743334 ATGC-A ATGCAA ATGCTAA ATGCAA ATGCAA ATGCTAA ATGCAA ATGCAA
1 ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA
1743383 A
1 A
1743384 AGGTGTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.10
6 26 0.62
7 12 0.29
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (6 bp):
ATGCAA
Found at i:1743362 original size:19 final size:19
Alignment explanation
Indices: 1743334--1743383 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1743324 AAACAAATAC
1743334 ATGC-AATGCAAATGCTAA
1 ATGCAAATGCAAATGCTAA
1743352 ATGCAAATGCAAATGCTAA
1 ATGCAAATGCAAATGCTAA
1743371 ATGCAAATGCAAA
1 ATGCAAATGCAAA
1743384 AGGTGTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.13
19 27 0.87
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (19 bp):
ATGCAAATGCAAATGCTAA
Found at i:1750288 original size:23 final size:24
Alignment explanation
Indices: 1750248--1750292 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1750238 TGGTTGAGGT
1750248 AATAAAAATATGTAAAGGTAAACA
1 AATAAAAATATGTAAAGGTAAACA
*
1750272 AATAAAAAT-TGTCAAGGTAAA
1 AATAAAAATATGTAAAGGTAAA
1750293 TAAAAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.22
Consensus pattern (24 bp):
AATAAAAATATGTAAAGGTAAACA
Found at i:1756254 original size:42 final size:41
Alignment explanation
Indices: 1756207--1756301 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 41
1756197 ATTTTGTTCT
* * *
1756207 TGATTAAGTCCTCTAGGCTATCAGTAAGTCTTCCGAGCATGA
1 TGATTAAGTCCTCGAGGC-ATCAGTAAGTCTACCGAGCAAGA
* * * *
1756249 TGATTAAATTCTTCGAGTCATCTGTAAGTCTACCGAGCAAGA
1 TGATT-AAGTCCTCGAGGCATCAGTAAGTCTACCGAGCAAGA
1756291 TGA-TAAGTCCT
1 TGATTAAGTCCT
1756302 TTGGGCCATC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
40 5 0.12
41 1 0.02
42 28 0.65
43 9 0.21
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
TGATTAAGTCCTCGAGGCATCAGTAAGTCTACCGAGCAAGA
Found at i:1758547 original size:182 final size:182
Alignment explanation
Indices: 1758161--1758634 Score: 698
Period size: 182 Copynumber: 2.6 Consensus size: 182
1758151 GATCTAAATT
* * * * * **
1758161 AAAAATGTATCGATCCACAACGATATAGCAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
1758226 AAACTGGTAAAGCGGTATCGAATATATTTAAAGTGTCGGTACTTTGATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTGATATAAGGATCGACACTTC
* *
1758291 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * * *
1758343 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCCAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
1758408 AAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTGATATAAGGATCGACACTTC
1758472 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
1758524 AAAAATGTATTGATCAAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
1758589 AAAACCAGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
1758635 CATAAGTACA
Statistics
Matches: 261, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 81 0.31
182 180 0.69
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTGATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:1758578 original size:20 final size:19
Alignment explanation
Indices: 1758555--1758601 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1758545 CGATATAACA
1758555 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1758575 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
1758595 AGTAAAA
1 GGTAAAA
1758602 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1760869 original size:21 final size:21
Alignment explanation
Indices: 1760843--1760883 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1760833 AAGACAATCA
1760843 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
1760864 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
1760884 GAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:1760962 original size:33 final size:33
Alignment explanation
Indices: 1760920--1760983 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1760910 AAATAGATGG
*
1760920 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTTA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTTA
*
1760953 AGTGGTGAAAGAAGTCGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
1760984 GATCTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.02, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTTA
Found at i:1762782 original size:182 final size:182
Alignment explanation
Indices: 1762125--1763511 Score: 2326
Period size: 182 Copynumber: 7.7 Consensus size: 182
1762115 TTTTACCTTT
* * * *
1762125 TTTAAAAGAAAAGAAGTGATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
1762190 AACAATATAACAGGTAAAAATACGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
** *
1762255 ATGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
1762307 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
1762371 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAT
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1762436 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATC-A-ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
1762486 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATAATTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
1762550 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
1762615 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
1762668 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTTTTGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * **
1762733 AACAATATAATAGGTATTAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1762798 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * *
1762848 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTTTCGATAATTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
1762912 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATAACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
1762977 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
1763030 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATATATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
1763095 AACAATATAACAAGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1763160 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
1763212 TTTAAAATAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
** *
1763277 AACAATATAACAAATAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTGAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* * *
1763342 CGGATATGTTGAAAGCGTCGATAATTTATTATAAGTATCGAAACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
1763394 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * * **
1763458 TAATAATATAACGTGTAAAAATATGATAAAACTGGTCTATAAATGA-AAAA-AGGT
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
1763512 GAACGCATAT
Statistics
Matches: 1140, Mismatches: 55, Indels: 22
0.94 0.05 0.02
Matches are distributed among these distances:
178 4 0.00
179 22 0.02
180 323 0.28
181 155 0.14
182 628 0.55
183 8 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:1762858 original size:362 final size:361
Alignment explanation
Indices: 1762126--1763511 Score: 2321
Period size: 362 Copynumber: 3.8 Consensus size: 361
1762116 TTTACCTTTT
* * * * *
1762126 TTAAAAGAAAAGAAGTGATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
1 TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAATTTATAAAAATGTATCGATCCATA
* * *
1762191 ACAATATAACAGGTAAAAATACGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACA
66 ACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACC
* *
1762256 TGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG-
131 GGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGA
*
1762320 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
196 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAG
* *
1762385 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTATCGGTTATGTTGAAA
261 TAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
*
1762450 GTGTCGATAATTTATTATAAGTATCAACTTTTGGAA
326 GTGTCGATAATTTATTATAAGTATCGACTTTTGGAA
*
1762486 TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATAATTTATAAAAATGTATCGATCCAT
1 TTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
*
1762551 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTAC
65 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1762616 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
130 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
* * * *
1762681 AAGTTATAGCGCCAATAAAGTTTTGATACTTTATAAAAATGTATCGATCCATAACAATATAATAG
195 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAA
*
1762746 GTATTAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
260 GTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
1762811 AGTGTCGATAATTTATTATAAGTATCGACTTTTGGAA
325 AGTGTCGATAATTTATTATAAGTATCGACTTTTGGAA
* *
1762848 TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTTTCGATAATTTATAAAAATGTATCGATCCAT
1 TTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
*
1762913 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATAACAAAACAGGTAAAGCGCTAC
65 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1762978 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
130 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
*
1763043 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAA
195 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAA
1763108 GTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
260 GTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
1763173 AGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
325 AGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
* *
1763212 TTTAAAATAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 -TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
** *
1763277 AACAATATAACAAATAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTGAAGCGCTAC
65 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* * *
1763342 CGGATATGTTGAAAGCGTCGATAATTTATTATAAGTATCGAAACTTTTGGAA-TTAATAAGAGAA
130 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAA
* *
1763406 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACG
194 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
* * * * **
1763471 TGTAAAAATATGATAAAACTGGTCTATAAATGA-AAAA-AGGT
259 AGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
1763512 GAACGCATAT
Statistics
Matches: 971, Mismatches: 49, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
360 4 0.00
361 178 0.18
362 505 0.52
363 8 0.01
364 272 0.28
365 4 0.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (361 bp):
TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAATTTATAAAAATGTATCGATCCATA
ACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACC
GGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGA
AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAG
TAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
GTGTCGATAATTTATTATAAGTATCGACTTTTGGAA
Found at i:1763176 original size:544 final size:543
Alignment explanation
Indices: 1762125--1763495 Score: 2354
Period size: 544 Copynumber: 2.5 Consensus size: 543
1762115 TTTTACCTTT
* * * *
1762125 TTTAAAAGAAAAGAAGTGATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
1762190 AACAATATAACAGGTAAAAATACGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
** *
1762255 ATGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAA-AAGAGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA-ACTTTTGGAA-TTAATAAGAGAA
1762319 G-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
194 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
* *
1762383 TGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTATCGGTTATGTTGA
259 TGTAAAAATATGACAAAACCGGTCTCGAAATAACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
1762448 AAGTGTCGATAATTTATTATAAGTATCAACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCA
324 AAGTGTCGATAATTTATTATAAGTATCAACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCA
* * *
1762513 ATAACGTGTCGATAATTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACA
389 ATAAAGTGTCGATAATTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAATATGACA
*
1762578 AAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTT
454 AAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTT
1762643 ATTATAAGTATCGACACTTTTGGAA
519 ATTATAAGTATCGACACTTTTGGAA
* *
1762668 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTTTTGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* **
1762733 AACAATATAATAGGTATTAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1762798 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG-ACTTTTGGAATTAATAAGAGAAGA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAATTAATAAGAGAAGA
* * *
1762862 AGTTATAGCGCCAATAACGTTTCGATAATTTATAAAAATGTATCGATCCATAACAATATAACATG
196 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
1762927 TAAAAATATGACAAAACCGGTCTCGAAATAACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
261 TAAAAATATGACAAAACCGGTCTCGAAATAACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
1762992 GTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGCC
326 GTGTCGATAATTTATTATAAGTATC-A-ACTTTTGGAA-TTAATAAGAGAAGAAGTTATAGCGCC
* *
1763056 AATAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAATAATATGAC
388 AATAAAGTGTCGATAATTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAATATGAC
1763121 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
453 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
1763186 TATTATAAGTATCGACACTTTTGGAA
518 TATTATAAGTATCGACACTTTTGGAA
*
1763212 TTTAAAATAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
** *
1763277 AACAATATAACAAATAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTGAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
1763342 CGGATATGTTGAAAGCGTCGATAATTTATTATAAGTATCGAAACTTTTGGAATTAATAAGAGAAG
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG-AACTTTTGGAATTAATAAGAGAAG
* *
1763407 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACGT
195 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAT
* *
1763472 GTAAAAATATGATAAAACTGGTCT
260 GTAAAAATATGACAAAACCGGTCT
1763496 ATAAATGAAA
Statistics
Matches: 779, Mismatches: 42, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
540 4 0.01
541 18 0.02
542 150 0.19
543 158 0.20
544 340 0.44
545 4 0.01
546 105 0.13
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (543 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAATTAATAAGAGAAGA
AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
TAAAAATATGACAAAACCGGTCTCGAAATAACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
GTGTCGATAATTTATTATAAGTATCAACTTTTGGAATTAATAAGAGAAGAAGTTATAGCGCCAAT
AAAGTGTCGATAATTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTAT
TATAAGTATCGACACTTTTGGAA
Found at i:1763739 original size:87 final size:87
Alignment explanation
Indices: 1763644--1763806 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
1763634 AAATAGGTCA
1763644 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1763709 CCGATTAAATACCTATTTTATT
66 CCGATTAAATACCTATTTTATT
* * *
1763731 ATATAAGCGTTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
1763796 TCGGTTAAATA
66 CCGATTAAATA
1763807 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGATTAAATACCTATTTTATT
Found at i:1763778 original size:23 final size:23
Alignment explanation
Indices: 1763728--1763772 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1763718 TACCTATTTT
* *
1763728 ATTATATAAGCGTTATCTATTAC
1 ATTATATAAGCGTTACCTAATAC
1763751 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGTTACCTAATA
1763773 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGTTACCTAATAC
Found at i:1764361 original size:50 final size:50
Alignment explanation
Indices: 1764298--1764393 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
1764288 GATCATCTGC
** *
1764298 ACCTTATTTGAGCTGGCGCCATGTAATGACATATGCGGATCGTCATTCGG
1 ACCTTATCCGAGCTGGCGCCACGTAATGACATATGCGGATCGTCATTCGG
* *
1764348 ACCTTATCCGAGCTGGCGCCACGTAATGACATGTGCGGATTGTCAT
1 ACCTTATCCGAGCTGGCGCCACGTAATGACATATGCGGATCGTCAT
1764394 CCGCTCCTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (50 bp):
ACCTTATCCGAGCTGGCGCCACGTAATGACATATGCGGATCGTCATTCGG
Found at i:1768050 original size:3 final size:3
Alignment explanation
Indices: 1768042--1768089 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
1768032 CTTCTCATTT
*
1768042 TCA TCA TCA TCA TCA -CTA TCA CCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA TCA TCA TCA TCA
1768087 TCA
1 TCA
1768090 AGAGCAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.02
3 39 0.95
4 1 0.02
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:1770195 original size:39 final size:39
Alignment explanation
Indices: 1770138--1770216 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
1770128 TTTATAACTG
*
1770138 AAAATAATAAAAAGTTAATATAATATAATTTAATAAAAT
1 AAAATAATAAAAAGTTAATATAATATAATATAATAAAAT
* * *
1770177 AAAATAATAAATCA-TTAATTTATTATAATATAATAAAAT
1 AAAATAATAAA-AAGTTAATATAATATAATATAATAAAAT
1770216 A
1 A
1770217 TTTTACCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (39 bp):
AAAATAATAAAAAGTTAATATAATATAATATAATAAAAT
Found at i:1773934 original size:21 final size:21
Alignment explanation
Indices: 1773908--1773947 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1773898 CAGAACCCCA
*
1773908 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1773929 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1773948 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1777839 original size:22 final size:21
Alignment explanation
Indices: 1777797--1777836 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1777787 GAGTTTGTTT
*
1777797 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1777818 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1777837 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1779842 original size:76 final size:77
Alignment explanation
Indices: 1779756--1779964 Score: 266
Period size: 76 Copynumber: 2.8 Consensus size: 77
1779746 CCATTGTACA
* * *
1779756 AGGGGGGAATCGGTACCCCCT-TGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
** *
1779820 ACAAAACTGTTT
66 ACAAAACCATTC
* *
1779832 AGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
* *
1779895 GCCAAACCATTC
66 ACAAAACCATTC
**
1779907 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
1779965 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
74 21 0.18
75 45 0.39
76 48 0.42
77 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
ACAAAACCATTC
Found at i:1782035 original size:137 final size:137
Alignment explanation
Indices: 1781790--1782042 Score: 328
Period size: 137 Copynumber: 1.8 Consensus size: 137
1781780 TCACATCAAA
* * *
1781790 TAATAAAATTTAAGTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATTATTATGAAAAA
1 TAATAAAATTTAAGTTTTTGTAATAAATTATTTTTGCAATTATATATTTTAATCATTATGAAAAA
* * * ** ** *
1781855 TTATACTATCAGAACCATTTCTCCCTATTTTTTATTGTCAAAATGTTATATAGTAACAAAATATA
66 TTATACTATCAGAAACATTTATCCCTAATTTTTAGCGAAAAAATATTATATAGTAACAAAATATA
1781920 TTGTAAT
131 TTGTAAT
* *
1781927 TAATAAAATTTAAGTTTTTTTTAATTAATTA-TTTTGCAATTATATATTTTAATCATTATGAAAA
1 TAATAAAATTTAAG-TTTTTGTAATAAATTATTTTTGCAATTATATATTTTAATCATTATGAAAA
* * * * *
1781991 CTTATACTATCAGAAATATTTATTCTTAATTTTTGGCGAAAAAATATTATAT
65 ATTATACTATCAGAAACATTTATCCCTAATTTTTAGCGAAAAAATATTATAT
1782043 TGTGACAAGT
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
137 83 0.86
138 14 0.14
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.47
Consensus pattern (137 bp):
TAATAAAATTTAAGTTTTTGTAATAAATTATTTTTGCAATTATATATTTTAATCATTATGAAAAA
TTATACTATCAGAAACATTTATCCCTAATTTTTAGCGAAAAAATATTATATAGTAACAAAATATA
TTGTAAT
Found at i:1784806 original size:32 final size:33
Alignment explanation
Indices: 1784770--1784902 Score: 94
Period size: 33 Copynumber: 4.1 Consensus size: 33
1784760 TTCGTCACAA
*
1784770 TATTTTGTCAAAATAAAAAATTGTGACAAAT-T
1 TATTTTATCAAAATAAAAAATTGTGACAAATAT
* * * *
1784802 TATTTAATCAAAAT-AACAATTCATAACAAATAT
1 TATTTTATCAAAATAAAAAATT-GTGACAAATAT
* * ** *
1784835 TAATTTCTCATTATAAAAAATTGTGACAAATAA
1 TATTTTATCAAAATAAAAAATTGTGACAAATAT
* * * *
1784868 TATTCTT-TTACAATAACAAATTGTAACAAA-AT
1 TATT-TTATCAAAATAAAAAATTGTGACAAATAT
1784900 TAT
1 TAT
1784903 CTAATCACAG
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
31 6 0.08
32 23 0.30
33 39 0.51
34 8 0.11
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (33 bp):
TATTTTATCAAAATAAAAAATTGTGACAAATAT
Found at i:1785479 original size:2 final size:2
Alignment explanation
Indices: 1785472--1785533 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1785462 TTTCTTGTAG
1785472 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1785513 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1785534 TATGTTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1785567 original size:6 final size:5
Alignment explanation
Indices: 1785472--1785571 Score: 51
Period size: 6 Copynumber: 18.2 Consensus size: 5
1785462 TTTCTTGTAG
*
1785472 TATAT ATATAT ATATAT ATATAT ATATAT ATATAT AATA- TATAT ATATAT
1 TATAT -TATAT -TATAT -TATAT -TATAT -TATAT TATAT TATAT -TATAT
* * *
1785522 ATATAT ATATAT TATGTT TATTT TCTAT T-TAT TATCAT TAATAT TATAT
1 -TATAT -TATAT TAT-AT TATAT TATAT TATAT TAT-AT T-ATAT TATAT
1785571 T
1 T
1785572 TTGTAATTGC
Statistics
Matches: 83, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
4 7 0.08
5 18 0.22
6 56 0.67
7 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:1795954 original size:41 final size:41
Alignment explanation
Indices: 1795850--1795964 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 41
1795840 TTTCTAAAAT
* * * *
1795850 TGATAAGT-CTGTCTGGCCATCAGTAAGCCTTTTGAGCATGA
1 TGATAAGTCCT-TCGGGCCATCTGTAAGCCTTTCGAGCAAGA
* * * *
1795891 TGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGA
1 TGA-TAAGTCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGA
*
1795933 TGATAAGTCCTTCGGGCCATCTATAAGACCTT
1 TGATAAGTCCTTCGGGCCATCTGTAAG-CCTT
1795965 CGGGCTGGAT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 23 0.40
42 33 0.57
43 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
TGATAAGTCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGA
Found at i:1796003 original size:196 final size:196
Alignment explanation
Indices: 1795669--1796022 Score: 622
Period size: 196 Copynumber: 1.8 Consensus size: 196
1795659 AGTCCTTCAC
*
1795669 GCCATCAGTAAGTTATTCGAGCATGATGATTAAATCCTTCGGGTCATATTTAAGTCTTTCGAGCA
1 GCCATCAGTAAGTTATTCGAGCATGATGATTAAATCCTTCGGGTCATATGTAAGTCTTTCGAGCA
* *
1795734 AGAGGATAAGTCTTTTGGGCCATCTATAAGACCTTCGGGCTGGATGTTTTCACTTGATTTTCAAA
66 AGAGGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCTGGATGTTTTCACTTGATTTTCAAA
1795799 AAATGAGAAAGCGATTTCCAAAGTTTCTTACCAGTAGACTATTTCTAAAATTGATAAGTCTGTCT
131 AAATGAGAAAGCGATTTCCAAAGTTTCTTACCAGTAGACTATTTCTAAAATTGATAAGTCTGTCT
1795864 G
196 G
* *
1795865 GCCATCAGTAAGCCTT-TT-GAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAG
1 GCCATCAGTAAG--TTATTCGAGCATGATGATTAAATCCTTCGGGTCATATGTAAGTCTTTCGAG
*
1795928 CAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCTGGATGTTTTCACTTGATTTTCA
64 CAAGAGGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCTGGATGTTTTCACTTGATTTTCA
1795993 AAAAATGAGAAAGCGATTTCCAAAGTTTCT
129 AAAAATGAGAAAGCGATTTCCAAAGTTTCT
1796023 CGTTTATTAT
Statistics
Matches: 150, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
196 146 0.97
197 2 0.01
198 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (196 bp):
GCCATCAGTAAGTTATTCGAGCATGATGATTAAATCCTTCGGGTCATATGTAAGTCTTTCGAGCA
AGAGGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCTGGATGTTTTCACTTGATTTTCAAA
AAATGAGAAAGCGATTTCCAAAGTTTCTTACCAGTAGACTATTTCTAAAATTGATAAGTCTGTCT
G
Found at i:1796222 original size:20 final size:20
Alignment explanation
Indices: 1796193--1796247 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1796183 GAGCAAGATG
*
1796193 ATAAGTCCTTCGGGCCATCT
1 ATAAGACCTTCGGGCCATCT
1796213 ATAAGACCTTCGGGCCATCT
1 ATAAGACCTTCGGGCCATCT
*
1796233 ATAAGACCTTGGGGC
1 ATAAGACCTTCGGGC
1796248 AAGATGCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (20 bp):
ATAAGACCTTCGGGCCATCT
Found at i:1796355 original size:20 final size:20
Alignment explanation
Indices: 1796312--1796349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1796302 CTCATTTAAT
1796312 AAAAAAACACAAAAAGAAAA
1 AAAAAAACACAAAAAGAAAA
*
1796332 AAAAGAACACAAAAAGAA
1 AAAAAAACACAAAAAGAA
1796350 GGAAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAAACACAAAAAGAAAA
Found at i:1796868 original size:2 final size:2
Alignment explanation
Indices: 1796850--1797139 Score: 251
Period size: 2 Copynumber: 146.5 Consensus size: 2
1796840 TTTTGAATAA
*
1796850 AT AT A- AT AT AG 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
*
1796891 AT AT AT AT AT AT AT AT AT AT AT AT AT CT 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
* * * * *
1796933 AT AT AA AT AG AT AT AT A- AT AT AGT TT TT A- AG AT AT A- AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
* * ** * * * *
1796974 AT AT AT AT GGT AT AT CAT -T TT GG A- AA AT AT AT AGT TT TT TT
1 AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
1797015 AA 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
* *
1797057 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AGT -T TT GAA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT
* *
1797099 -T TT AT AT AA AT AT AT -T A- AT AT GAT 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
1797139 A
1 A
1797140 GTCTTACACA
Statistics
Matches: 242, Mismatches: 27, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
1 11 0.05
2 222 0.92
3 9 0.04
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1797163 original size:6 final size:6
Alignment explanation
Indices: 1797152--1797196 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
1797142 CTTACACATT
*
1797152 TTTATA TTTATA TTTATA -TTAT- TATTATG TTTAT- TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA T-TTATA TTTATA TTTATA TTTAT
1797197 TATCATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 9 0.26
6 25 0.71
7 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:1797179 original size:17 final size:16
Alignment explanation
Indices: 1797153--1797215 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
1797143 TTACACATTT
1797153 TTATATTTATATTTATA
1 TTATA-TTATATTTATA
* *
1797170 TTATTATTATGTTTATT
1 TTA-TATTATATTTATA
1797187 TTATATT-TA-TTATCA
1 TTATATTATATTTAT-A
1797202 TTAATATTATATTT
1 TT-ATATTATATTT
1797216 TGTAATTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 9 0.24
17 17 0.46
18 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATATTATATTTATA
Found at i:1797184 original size:23 final size:23
Alignment explanation
Indices: 1797153--1797199 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1797143 TTACACATTT
1797153 TTATATTTATATTTATA-TTATTA
1 TTATATTTAT-TTTATATTTATTA
*
1797176 TTATGTTTATTTTATATTTATTA
1 TTATATTTATTTTATATTTATTA
1797199 T
1 T
1797200 CATTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTATATTTATTTTATATTTATTA
Found at i:1797979 original size:23 final size:24
Alignment explanation
Indices: 1797928--1797979 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1797918 ACAATAAAAT
* * *
1797928 ATTAGGTAGCTCTTATATAATGTA
1 ATTAGGTAACGCTTATATAATGAA
1797952 A-TAGGTAACGCTTATATAAT-AA
1 ATTAGGTAACGCTTATATAATGAA
1797974 ATTAGG
1 ATTAGG
1797980 CATTTAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 21 0.88
24 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (24 bp):
ATTAGGTAACGCTTATATAATGAA
Found at i:1798051 original size:87 final size:87
Alignment explanation
Indices: 1797893--1798055 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 87
1797883 TATGTTATAT
* * * *
1797893 CATTTAACCGAAAATATTATCAAGTACAATAAAATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGAAATAAGT
1797958 AACGCTTATATAATAAATTAGG
66 AACGCTTATATAATAAATTAGG
*
1797980 CATTTAACC-AGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGAAATAAG
1 CATTTAACCGA-AAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGAAATAAG
*
1798044 TAGCGCTTATAT
65 TAACGCTTATAT
1798056 TGACCTATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 68 0.99
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGAAATAAGT
AACGCTTATATAATAAATTAGG
Found at i:1798473 original size:199 final size:196
Alignment explanation
Indices: 1798056--1798578 Score: 622
Period size: 199 Copynumber: 2.6 Consensus size: 196
1798046 GCGCTTATAT
* *
1798056 TGACCTATTTTCTAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACAT
1 TGACCTATTTTCTAA-TAAAACCGGTATATTTATACAGGT-ACATTGTAAATTTACCTATTACAT
* ** * * *
1798120 TATAATTATCGGTTTCGATGTTTTTTGGATTAATACAATTT--TAAATGTATCAAAACTTTATGC
64 TATAATTATCGGTTTCGATG-TTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGC
* * * * *
1798183 ATGCACCTCGTTGGGCATTCATTCTGGAAAAACGTATTGACACAAACTTAAAAAGTGTCGATACA
127 ATGCACCCCGTTGGACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
*
1798248 TTATT
192 TTATC
* * * * * *
1798253 TAGACATATTTTCTCATAAAACCGGTATATTTCTGTCGGGTACATTGTAAATTTACCTATCACAT
1 T-GACCTATTTTCTAATAAAACCGGTATATTTAT-ACAGGTACATTGTAAATTTACCTATTACAT
* * * *
1798318 TGTAATTATTGGTTTCGATGTTTGTGGGATCGATACTTTTAATAAATGTATCGACATTTTATGCG
64 TATAATTATCGGTTTCGATGTTT-TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCA
* * * * * *
1798383 TGTACCCCGTTTGACATTCATTATGGACAAAAAGTATCGGCAC-AATTTAAATAGTGTCGATACT
128 TGCACCCCGTTGGACATTCATTATGGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
1798447 TTATGC
192 TTAT-C
* *
1798453 TGACCTATTTTCTTATAAAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATT
1 TGACCTATTTTCTAATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTATTACATT
*
1798518 ATAATTATCGGTTTCAATGTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTAT
65 ATAATTATCGGTTTCGATGTT-TTGGGATCGATACTTTTAATAAATGTATCGACACTTTAT
1798579 ATTCTGGACA
Statistics
Matches: 276, Mismatches: 40, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
197 8 0.03
198 76 0.28
199 178 0.64
200 14 0.05
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (196 bp):
TGACCTATTTTCTAATAAAACCGGTATATTTATACAGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGC
ACCCCGTTGGACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTAT
C
Found at i:1798702 original size:177 final size:177
Alignment explanation
Indices: 1798406--1798750 Score: 487
Period size: 177 Copynumber: 1.9 Consensus size: 177
1798396 ACATTCATTA
* * * * *
1798406 TGGACAAAAAGTATCGGCACAATTTAAATAGTGTCGATACTTTATGCTGACCTATTTTCTTATAA
1 TGGACAAAAAGTATCGACACAATTCAAAAAGTGTCGATACATTATGCTGACCTATTTTCTAATAA
1798471 AACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAT
66 AACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAT
1798536 GTTATTGGGATCGATACTTTTA-ATAAATGTATCGACACTTTATATTC
131 GTTATTGGGATCGATACTTTTAGA-AAATGTATCGACACTTTATATTC
* * * *
1798583 TGGACAATAAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACTTGTTTTCTAAT-
1 TGGACAAAAAGTATCGACAC-AATTCAAAAAGTGTCGATACATTATGCTGACCTATTTTCTAATA
* * * * * * **
1798647 TAACCTGTATATTTATATCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTTGA
65 AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAA
* *
1798712 TGTTTTTGGGGTCGATACTTTTAGAAAATGTATCGACAC
130 TGTTATTGGGATCGATACTTTTAGAAAATGTATCGACAC
1798751 CTATTTAGTT
Statistics
Matches: 147, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
177 110 0.75
178 37 0.25
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (177 bp):
TGGACAAAAAGTATCGACACAATTCAAAAAGTGTCGATACATTATGCTGACCTATTTTCTAATAA
AACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAT
GTTATTGGGATCGATACTTTTAGAAAATGTATCGACACTTTATATTC
Found at i:1802760 original size:199 final size:196
Alignment explanation
Indices: 1802260--1803021 Score: 798
Period size: 199 Copynumber: 3.8 Consensus size: 196
1802250 AACGTAATTT
* * *
1802260 AAAAACGTATCGACACAAATTTAAAACTGTCGATACACTATGTTAACCTATTTTCTCATAAAACT
1 AAAAATGTATCGACACAAATTTAAAAGTGTCGATACAATATGTTAACCTATTTTCTCATAAAACT
* *
1802325 GGTGTATTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTTTTGGTTTCGATGTTT
66 -GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATA-ATTTTGGTTTCGATG-TT
* * *
1802390 TTTGGATAGATACTTTTTATAAATGTATCGACACTTTATGCGTGTACCCCGTTTTGCATTCATTA
128 TTTGGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTA
1802455 TAGAC
192 TAGAC
* * * *
1802460 AAAAATGTATCGACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTTATAAAAC
1 AAAAATGTATCGACACAAAT-TTAAAAGTGTCGATACAATATGTTAACCTATTTTCTCATAAAA-
* *
1802525 CGGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATG-T
64 CTGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATT-TTGGTTTCGATGTT
*
1802589 TTTGAGATCGAAACTTTTTTAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATT
128 TTTG-GATCGATAC-TTTTTAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATT
*
1802654 ATGGAC
191 ATAGAC
* **
1802660 -AAAATGTATCGACACAAATTTAAACAGTTTTAATACAATATG-TATACCTATTTTCTCATAAAA
1 AAAAATGTATCGACACAAATTTAAA-AGTGTCGATACAATATGTTA-ACCTATTTTCTCATAAAA
* * * *
1802723 CATGTATATTTATACTGGTTACATTGTATATTTACCTATTACATTTTAATTTTCGATTTCGATGT
64 C-TGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTT-GGTTTCGATG-
* * * * ** *
1802788 TTTTTGGATCGATACAATTTT-AAATGTATCAACACTTTTATGCGTGAAGCTTG-TTGAGCA--A
126 TTTTTGGATCGATAC-TTTTTAAAATGTATCGACAC-TTTATGCGTGCACCCCGTTTG-GCATTC
*** *
1802849 AGGCTCGGAC
188 ATTAT-AGAC
* ** ** * *
1802859 AAAAA-ATATCGACACAAATTTAAAAGGTGTTAATACTTTATGCTAACCTATTTGCTCAT--AA-
1 AAAAATGTATCGACACAAATTTAAAA-GTGTCGATACAATATGTTAACCTATTTTCTCATAAAAC
* * * * *
1802920 ---ATACTTATACCGGTAACATTGTAAATTTACCTATTACATTATAATTTTCAGTTGC-ATTACT
65 TGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTT-GGTTTCGA-T-GT
1802981 TTTTGGATCGATACTTTTTATAAATGTATCGACACTTTATG
127 TTTTGGATCGATACTTTTTA-AAATGTATCGACACTTTATG
1803022 GGAAACTTTA
Statistics
Matches: 485, Mismatches: 56, Indels: 50
0.82 0.09 0.08
Matches are distributed among these distances:
191 5 0.01
192 69 0.14
193 13 0.03
197 2 0.00
198 11 0.02
199 171 0.35
200 109 0.22
201 104 0.21
202 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (196 bp):
AAAAATGTATCGACACAAATTTAAAAGTGTCGATACAATATGTTAACCTATTTTCTCATAAAACT
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTGGTTTCGATGTTTTT
GGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTATAGA
C
Found at i:1806472 original size:200 final size:199
Alignment explanation
Indices: 1806121--1807280 Score: 1499
Period size: 200 Copynumber: 5.8 Consensus size: 199
1806111 TTTTAAAATG
* * *
1806121 GTATCGACACAAATTT-AACAATTGTTGATACTTTATGTAGACCTATTCTCACATAAAACCGGTA
1 GTATCGACACAAATTTCAA-AAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
* *
1806185 TATTTATACCGGTTACATTACAAAATTACCTATTAGATTATAATTATGGGTTTCGATGTCTCCGG
65 TA-TTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGG
* * * *
1806250 GATC-A-ACATTTTTAAAAAATGTATCAACACTTTATGGGTGCACCCTTTTGGGCATTCCTTATG
129 GATCGATAC-TTTTT-AAAAATGTATCAACACTTTATGCGTGCACCATTTTGGGCATTCATTCTG
*
1806313 GACAAACA
192 GACAAAAA
* * * *
1806321 GTATCGACACAAATTCCAGAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGATAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* ** * * *
1806386 AGTTATACTGGTTACATTTTAAATTTGCCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
66 A-TTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGG
* * * * *
1806451 ATGGATAATTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTTGGCATTCATTCTGG
130 ATCGATACTTTTTAAAAATGTATCAACACTTTATGCGTGCACCA--TTTTGGGCATTCATTCTGG
*
1806516 ACAAAAT
193 ACAAAAA
* * *
1806523 GTATCGACACATAA-TTAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAAACGGTA
1 GTATCGACACA-AATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
*
1806587 TATTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGG-TTCGATGTCTCTGG
65 TA-TTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGG
* * * *
1806651 GATCGACACTTTTTAAAAATGTATCGAA-ACTTTATGTGTTCACCATTTTGGGCATTCATTTTGG
129 GATCGATACTTTTTAAAAATGTATC-AACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGG
1806715 A-AAGAAA
193 ACAA-AAA
*
1806722 GTATCGACAGC-AATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
1 GTATCGACA-CAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
*
1806786 TATTAATACCGGTTACATTACAAAATTACCTATTAGATTATAATTATGGGTTTCGATGTCTCTGG
65 TATT-ATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGG
* * * * * *
1806851 GATCGACACTTTTAAAAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCCTTCTGGA
129 GATCGATACTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGA
*
1806916 CAAATA
194 CAAAAA
* * * * **
1806922 GTATCAACACAAATTCCAGAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACTAGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* ** * * * * *
1806987 AGTTATACCAGTTACATTGTAAATTTACGTATTGCATTATAATTATGGGTTTCGTTGTTTCTGGG
66 A-TTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGG
* * *
1807052 ATCGATATTTTTTTATAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGA
130 ATCGATA-CTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGA
1807117 CAAAAA
194 CAAAAA
* * *
1807123 GTATCGACACCAATTTCAAAAGCGTCGATACATTATGTAGACCTATTCTCACATATAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * * * *
1807188 ATTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGA
66 ATTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGA
* *
1807253 TCGATACTTTTTATAAATGTATCGACAC
131 TCGATACTTTTTAAAAATGTATCAACAC
1807281 ATCTACTTAC
Statistics
Matches: 832, Mismatches: 111, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
198 6 0.01
199 142 0.17
200 390 0.47
201 171 0.21
202 121 0.15
203 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
ATTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGA
TCGATACTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACA
AAAA
Found at i:1806873 original size:401 final size:396
Alignment explanation
Indices: 1806115--1807280 Score: 1570
Period size: 401 Copynumber: 2.9 Consensus size: 396
1806105 CGCAATTTTT
* * * * * *
1806115 AAAATGGTATCGACACAAATTTAACAATTGTTGATACTTTATGTAGACCTATTCTCACATAAAAC
1 AAAATAGTATCGACACAAA-TTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAA
* *
1806180 CGGTATATTTATACCGGTTACATTACAAAATTACCTATTAGATTATAATTATGGGTTTCGATGTC
65 CGGTATATTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTC
* * * * * *
1806245 TCCGGGATCAACATTTTTAAAAAATGTATCAACACTTTATGGGTGCACCCTTTTGGGCATTCCTT
130 TCTGGGATCGACATTTTT-AAAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATT
* * *
1806310 ATGGACAAACAGTATCGACACAAATTCCAGAAGTGTCGATACATTATGTAGACCTATTCTCTCAT
194 ATGGACAAAAAGTATCGACAC-AATTTCA-AAGTGTCGATACATTATGTAGACCTATTCTCACAT
* * ** * *
1806375 AAAACCGATATAGTTATACTGGTTACATTTTAAATTTGCCTATTACATTATAATTATGGGTTTCG
257 AAAACCGGTATA-TTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCG
* * * *
1806440 ATGTTTCTGGGATGGATAATTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTTGGC
321 ATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACC--CTTTTGGGC
1806505 ATTCATTCTGGAC
384 ATTCATTCTGGAC
*
1806518 AAAAT-GTATCGACACATAATTAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAAA
1 AAAATAGTATCGACACA-AATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAA
1806582 CGGTATATTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGG-TTCGATGTC
65 CGGTATATTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTC
*
1806646 TCTGGGATCGACACTTTTTAAAAATGTATCGAA-ACTTTATGTGTTCACCATTTTGGGCATTCAT
130 TCTGGGATCGACA-TTTTTAAAAATGTATC-AACACTTTATGCGTTCACCATTTTGGGCATTCAT
*
1806710 TTTGGA-AAGAAAGTATCGACAGCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCAC
193 TATGGACAA-AAAGTATCGACA-CAATTTCAAA-GTGTCGATACATTATGTAGACCTATTCTCAC
*
1806774 ATAAAACCGGTATATTAATACCGGTTACATTACAAAATTACCTATTAGATTATAATTATGGGTTT
255 ATAAAACCGGTATATT-ATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTT
* * * * *
1806839 CGATGTCTCTGGGATCGACACTTTTAAAAAATGTATCGACACTTTATGGGTGCACCCTTTTGGGC
319 CGATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGC
*
1806904 ATTCCTTCTGGAC
384 ATTCATTCTGGAC
* * * *
1806917 -AAATAGTATCAACACAAATTCCAGAAGTGTCGATACATTATGTAGACCTATTCTCTCAT-AAAA
1 AAAATAGTATCGACACAAATT-AAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAA
* * * ** * * * *
1806980 CTAGTATAGTTATACCAGTTACATTGTAAATTTACGTATTGCATTATAATTATGGGTTTCGTTGT
65 C-GGTATATTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
* * *
1807045 TTCTGGGATCGATATTTTTTTATAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCA
129 CTCTGGGATCGACA--TTTTTAAAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCA
* *
1807110 TTCTGGACAAAAAGTATCGACACCAATTTCAAAAGCGTCGATACATTATGTAGACCTATTCTCAC
192 TTATGGACAAAAAGTATCGACA-CAATTTC-AAAGTGTCGATACATTATGTAGACCTATTCTCAC
* * * *
1807175 ATATAACCGGTATATTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTT
255 ATAAAACCGGTATATTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTC
*
1807240 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACAC
320 GATGTTTCTGGGATCGATACTTTTTATAAATGTATCGACAC
1807281 ATCTACTTAC
Statistics
Matches: 681, Mismatches: 67, Indels: 33
0.87 0.09 0.04
Matches are distributed among these distances:
398 13 0.02
399 109 0.16
400 108 0.16
401 328 0.48
402 116 0.17
403 7 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (396 bp):
AAAATAGTATCGACACAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAAC
GGTATATTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCT
CTGGGATCGACATTTTTAAAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATTAT
GGACAAAAAGTATCGACACAATTTCAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAA
CCGGTATATTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
TCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
CTGGAC
Found at i:1807325 original size:15 final size:15
Alignment explanation
Indices: 1807297--1807335 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1807287 TTACCTATTT
* *
1807297 TTTGGAAACATTACG
1 TTTGGGAACATTACA
*
1807312 TTTGGGAACTTTACA
1 TTTGGGAACATTACA
1807327 TTTGGGAAC
1 TTTGGGAAC
1807336 CATACTGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (15 bp):
TTTGGGAACATTACA
Found at i:1807671 original size:19 final size:19
Alignment explanation
Indices: 1807647--1807695 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1807637 TTACGTTCAC
*
1807647 ATACAAAATTATATATCAT
1 ATACAAAATTATAAATCAT
*
1807666 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
1807685 ATACAAAATTA
1 ATACAAAATTA
1807696 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:1809262 original size:18 final size:18
Alignment explanation
Indices: 1809235--1809291 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1809225 TCCTCCTCAT
*
1809235 TTCCTACATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
1809253 TTCCTCCATCTTTCCTTC
1 TTCCTCCATCTTTTCTTC
*
1809271 TTCCTCTATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
1809289 TTC
1 TTC
1809292 ATATTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:1809475 original size:65 final size:65
Alignment explanation
Indices: 1809396--1809520 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 65
1809386 ACTACCCCCT
* * **
1809396 TCACCCTCGTAAGTTCACTCCTCAATTCCACAACCTCCTTCACCACTCCATCAATTTTTCACCCG
1 TCACCATCGTAAGTTCACCCCTCAACACCACAACCTCCTTCACCACTCCATCAATTTTTCACCCG
* * * * *
1809461 TCACCATCTTAAGTTCACCCCTCAACACCTCAACTTCTTTCACCACTCCATCTATTTTTC
1 TCACCATCGTAAGTTCACCCCTCAACACCACAACCTCCTTCACCACTCCATCAATTTTTC
1809521 CTTCCACTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.23, C:0.42, G:0.03, T:0.32
Consensus pattern (65 bp):
TCACCATCGTAAGTTCACCCCTCAACACCACAACCTCCTTCACCACTCCATCAATTTTTCACCCG
Found at i:1809566 original size:21 final size:21
Alignment explanation
Indices: 1809541--1809584 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1809531 CCCCTTATGC
1809541 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
*
1809562 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
1809583 CT
1 CT
1809585 TGATTGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:1812295 original size:182 final size:181
Alignment explanation
Indices: 1811984--1812476 Score: 675
Period size: 182 Copynumber: 2.7 Consensus size: 181
1811974 TACGCGTACT
* * * * *
1811984 TATTAAAGTATCGACACTTTCAATATATCTGGTAGCACTTTACCGGTTTTGT-CATTACGAGAAC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTC-TTACCGGTTTTGTCCTTTA-GAGACC
* * *
1812048 GGTTTTGTCATATTTTTACTTGTTATATCGTTATGAATCGATACATTTTTATAAAGTATCGACAC
64 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACAC
* *
1812113 TTTATAGGAGTTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
129 TTTATAGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
1812166 TATTAAAGTATCGACACATTCAATATATCCGGTCGCTCTATACCGATTATGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCT-TACCGGTTTTGTCCTTTAGAGACCG
* *
1812231 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTACCGACACT
65 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
* * *
1812296 TTATAGGTGCTAAAACTGATTCTCTTTTAAATTCATAAAGTGTTGATACTTA
130 TTATAGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * *
1812348 TATTAAAGTATCGACACTTTCAATATATCCAGTATCGCT-TTACTGGTTTTATCTTTTCGAGACT
1 TATTAAAGTATCGACACTTTCAATATATCC-G-GTCGCTCTTACCGGTTTTGTCCTTTAGAGACC
* * *
1812412 AGTTTTGTCATATTTTTACCTGTTATATTGATGTGGATCGATACATTTTTTATAAAGTATCGACA
64 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACA-TTTTTATAAAGTATCGACA
1812477 TAAACAGACA
Statistics
Matches: 274, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
181 1 0.00
182 245 0.89
183 23 0.08
184 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTTACCGGTTTTGTCCTTTAGAGACCGG
TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTT
TATAGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:1816452 original size:138 final size:138
Alignment explanation
Indices: 1816115--1816457 Score: 370
Period size: 138 Copynumber: 2.5 Consensus size: 138
1816105 TGAATGCATG
** * * * * *
1816115 AGGGTCCATTTTGATTATCCGATTCAATAATTTATTAAAATCAATTATGA-TTAATGTTAAAGCC
1 AGGGTCCAAATTGATTATTCGATTC-ATAA-TTGTTAAAATTAATTA-GAGTTAATATTAGAGCC
** * **
1816179 TTCACTTTAGATTTTTCACATTTTAGTCCTTTAATTTAGGGAATAATTTGATTTGGCCTTCACAT
63 TTCACTTTAGATTTTTCACACATTAGTCCATTAATTTAGGGAATAATTCAATTTGGCCTTCACAT
* **
1816244 TAACATGCCTG
128 TAAAATGCCCA
* ** * * * *
1816255 AGGGTCCAAAATGATTATTCGATTCCATAATTGACATAATTCATGAGGGTTAATGATTAGAGCCT
1 AGGGTCCAAATTGATTATTCGATT-CATAATTGTTAAAATTAATTAGAGTTAAT-ATTAGAGCCT
*
1816320 TCGA-TTTAGA-TTTTCACACATTAGT-CATTAATTTAGGGAATAATTCAATTTGGCCTTCGCAT
64 TC-ACTTTAGATTTTTCACACATTAGTCCATTAATTTAGGGAATAATTCAATTTGGCCTTCACAT
1816382 TAAAATGCCCA
128 TAAAATGCCCA
*
1816393 AGGGTCCAAGTTGATTATTCGATTCATCAATTGGTTAAAATTAATTAGAGTTAATATTAGAGCCT
1 AGGGTCCAAATTGATTATTCGATTCAT-AATT-GTTAAAATTAATTAGAGTTAATATTAGAGCCT
1816458 CTATTTCCAT
Statistics
Matches: 166, Mismatches: 31, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
137 3 0.02
138 78 0.47
139 43 0.26
140 40 0.24
141 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (138 bp):
AGGGTCCAAATTGATTATTCGATTCATAATTGTTAAAATTAATTAGAGTTAATATTAGAGCCTTC
ACTTTAGATTTTTCACACATTAGTCCATTAATTTAGGGAATAATTCAATTTGGCCTTCACATTAA
AATGCCCA
Found at i:1830892 original size:24 final size:24
Alignment explanation
Indices: 1830847--1830894 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1830837 TCCACCACTC
* **
1830847 TCATTCAAAAAGAAATTTAAATAT
1 TCATTCAAAAACAAATACAAATAT
*
1830871 TCATTCAAATACAAATACAAATAT
1 TCATTCAAAAACAAATACAAATAT
1830895 AATTATTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.31
Consensus pattern (24 bp):
TCATTCAAAAACAAATACAAATAT
Found at i:1837082 original size:16 final size:17
Alignment explanation
Indices: 1837055--1837087 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1837045 CGCCGCATGC
1837055 TTCCCATTTTTCTCTTT
1 TTCCCATTTTTCTCTTT
1837072 TTCCC-TTTTTCTCTTT
1 TTCCCATTTTTCTCTTT
1837088 GCAGCAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCCCATTTTTCTCTTT
Found at i:1840894 original size:2 final size:2
Alignment explanation
Indices: 1840887--1840935 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1840877 TCAATCTACA
1840887 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
1840929 AT AT AT A
1 AT AT AT A
1840936 ATTTATGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1841130 original size:26 final size:26
Alignment explanation
Indices: 1841092--1841142 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1841082 AGTGATGCTC
1841092 AATGCGCGCCATAAATACGAGTCATA
1 AATGCGCGCCATAAATACGAGTCATA
* * * *
1841118 AATGCGTGTCATAAATGCGCGTCAT
1 AATGCGCGCCATAAATACGAGTCAT
1841143 TTGATATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (26 bp):
AATGCGCGCCATAAATACGAGTCATA
Found at i:1841134 original size:13 final size:13
Alignment explanation
Indices: 1841101--1841142 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1841091 CAATGCGCGC
*
1841101 CATAAATACGAGT
1 CATAAATGCGAGT
*
1841114 CATAAATGCGTGT
1 CATAAATGCGAGT
*
1841127 CATAAATGCGCGT
1 CATAAATGCGAGT
1841140 CAT
1 CAT
1841143 TTGATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (13 bp):
CATAAATGCGAGT
Found at i:1852065 original size:12 final size:12
Alignment explanation
Indices: 1852050--1852076 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1852040 GCTATGAACA
1852050 CACTAATGACTC
1 CACTAATGACTC
1852062 CACTAATGACTC
1 CACTAATGACTC
1852074 CAC
1 CAC
1852077 CTTGCTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.22
Consensus pattern (12 bp):
CACTAATGACTC
Found at i:1863083 original size:24 final size:24
Alignment explanation
Indices: 1863001--1863083 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
1862991 ATTTCTGACT
* **
1863001 TGAATTATGTTCTGATACATGACC
1 TGAATTATGTTCTGATATATGTTC
* * * *
1863025 TGAATTCTGTTCTGAT-TTTTTATA
1 TGAATTATGTTCTGATATATGT-TC
* *
1863049 TGGATTCTGTTCTGATATATGTTC
1 TGAATTATGTTCTGATATATGTTC
1863073 TGAATTATGTT
1 TGAATTATGTT
1863084 TAGATTTATG
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.91
25 3 0.07
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTATGTTCTGATATATGTTC
Found at i:1864177 original size:94 final size:93
Alignment explanation
Indices: 1864016--1864198 Score: 269
Period size: 94 Copynumber: 2.0 Consensus size: 93
1864006 TTTCTGGAAA
* *
1864016 CTTTGGGGTATGTTGAACCAGCTAGGGTAGATTTGTTTAAACATTTACTTATAAAGGTAATCCAT
1 CTTTGGGGTATGTTGAACCAGCTAGGATAGATTTGTTTAAACATTTACTTAGAAAGGTAATCCAT
* *
1864081 TTTCAATGATCCGGAAAAACTATTTTGAG
66 TTTCAACGATCC-AAAAAACTATTTTGAG
** * *
1864110 CTTTGGGGTATGTTGAACCATTTAGGATAGATTTGTTTGAACGA-TTAGTTAGAAAGGTAATCCA
1 CTTTGGGGTATGTTGAACCAGCTAGGATAGATTTGTTTAAAC-ATTTACTTAGAAAGGTAATCCA
1864174 TTTTCAACGATCCAAAAAACTATTT
65 TTTTCAACGATCCAAAAAACTATTT
1864199 CGATTGTTGA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 11 0.14
94 68 0.85
95 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (93 bp):
CTTTGGGGTATGTTGAACCAGCTAGGATAGATTTGTTTAAACATTTACTTAGAAAGGTAATCCAT
TTTCAACGATCCAAAAAACTATTTTGAG
Found at i:1864220 original size:94 final size:94
Alignment explanation
Indices: 1864028--1864221 Score: 205
Period size: 94 Copynumber: 2.1 Consensus size: 94
1864018 TTGGGGTATG
* * *
1864028 TTGAACCAGCTAGGGTAGATTTGTTTAAACATTTACTTATAAAGGTAATCCATTTTCAATGATCC
1 TTGAACCAGCTAGGATAGATTTGTTTAAACATTTACTTAGAAAGGTAATCCATTTTCAACGATCC
* * **** *
1864093 GGAAAAACTATTTTGAGCTTTGGGGTATG
66 GAAAAAACTATTTCGAGCTTTGAACCATA
** * *
1864122 TTGAACCATTTAGGATAGATTTGTTTGAACGA-TTAGTTAGAAAGGTAATCCATTTTCAACGATC
1 TTGAACCAGCTAGGATAGATTTGTTTAAAC-ATTTACTTAGAAAGGTAATCCATTTTCAACGATC
*
1864186 C-AAAAAACTATTTCGA-TTGTTGAACCACTA
65 CGAAAAAACTATTTCGAGCT-TTGAACCA-TA
1864216 TTGAAC
1 TTGAAC
1864222 GGTAGAAAGA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
92 1 0.01
93 17 0.21
94 63 0.77
95 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (94 bp):
TTGAACCAGCTAGGATAGATTTGTTTAAACATTTACTTAGAAAGGTAATCCATTTTCAACGATCC
GAAAAAACTATTTCGAGCTTTGAACCATA
Found at i:1871054 original size:2 final size:2
Alignment explanation
Indices: 1871049--1871102 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
1871039 AATTTTTTCA
1871049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1871089 AT TT AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
1871103 GTCTTTACGT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1871109 original size:16 final size:16
Alignment explanation
Indices: 1871050--1871109 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1871040 ATTTTTTCAA
*
1871050 TATATA-TATATATAT
1 TATATAGTATTTATAT
*
1871065 ATATATA-TATATATAT
1 -TATATAGTATTTATAT
*
1871081 TATATATTATTTATAT
1 TATATAGTATTTATAT
*
1871097 TATATAGTCTTTA
1 TATATAGTATTTA
1871110 CGTATTCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
15 6 0.15
16 34 0.85
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATAGTATTTATAT
Found at i:1871252 original size:2 final size:2
Alignment explanation
Indices: 1871245--1871284 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1871235 GTTTCCATTC
1871245 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
1871285 TAATTTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1872684 original size:25 final size:25
Alignment explanation
Indices: 1872650--1872715 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
1872640 TTTTAGGGAG
1872650 TATGTTACTCATTTTAAGTTCCATA
1 TATGTTACTCATTTTAAGTTCCATA
1872675 TATGTTACTCATTTTAAGTTCCATA
1 TATGTTACTCATTTTAAGTTCCATA
1872700 TATGTTACTCATTTTA
1 TATGTTACTCATTTTA
1872716 TGAGTGAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (25 bp):
TATGTTACTCATTTTAAGTTCCATA
Found at i:1884365 original size:2 final size:2
Alignment explanation
Indices: 1884358--1884390 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1884348 GTGTTATAGT
1884358 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 T
1884391 GTAAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1894346 original size:11 final size:11
Alignment explanation
Indices: 1894330--1894361 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1894320 CTTGTATCCA
1894330 ATTTTCTTTTC
1 ATTTTCTTTTC
1894341 ATTTTCTTTTC
1 ATTTTCTTTTC
1894352 ATTTTCTTTT
1 ATTTTCTTTT
1894362 GGCGTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTCTTTTC
Found at i:1897196 original size:28 final size:26
Alignment explanation
Indices: 1897165--1897258 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 26
1897155 ACTGAAATAT
1897165 AGAGGTGCTCAGTCACTTTTAACTACAC
1 AGAGGTG-TCAGTCACTTTTAA-TACAC
*
1897193 AGAGGTGTCAGT-TCTTGATTGAAGTACA-
1 AGAGGTGTCAGTCACTT--TT-AA-TACAC
* *
1897221 A-AGGTGCTCAATCAATTTTAGATACAC
1 AGAGGTG-TCAGTCACTTTTA-ATACAC
1897248 AGAGGTGTCAG
1 AGAGGTGTCAG
1897259 CTCTCGATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
26 8 0.15
27 17 0.33
28 19 0.37
29 8 0.15
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (26 bp):
AGAGGTGTCAGTCACTTTTAATACAC
Found at i:1897240 original size:55 final size:55
Alignment explanation
Indices: 1897167--1897287 Score: 163
Period size: 55 Copynumber: 2.2 Consensus size: 55
1897157 TGAAATATAG
* * * * *
1897167 AGGTGCTCAGTCACTTTTA-ACTACACAGAGGTGTCAGTTCTTGATTGAAGTACAA
1 AGGTGCTCAATCAATTTTAGA-TACACAGAGGTGTCAGCTCTCGATTGAAGAACAA
* *
1897222 AGGTGCTCAATCAATTTTAGATACACAGAGGTGTCAGCTCTCGATTGATGAACAG
1 AGGTGCTCAATCAATTTTAGATACACAGAGGTGTCAGCTCTCGATTGAAGAACAA
1897277 AGGTGCTCAAT
1 AGGTGCTCAAT
1897288 TGTTAATTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 57 0.98
56 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (55 bp):
AGGTGCTCAATCAATTTTAGATACACAGAGGTGTCAGCTCTCGATTGAAGAACAA
Found at i:1904988 original size:16 final size:15
Alignment explanation
Indices: 1904964--1904993 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1904954 AAAATTTAGG
1904964 ATTTTTTTTATTTTT
1 ATTTTTTTTATTTTT
1904979 ATTTTATTTTATTTT
1 ATTTT-TTTTATTTT
1904994 GTAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTTTTTATTTTT
Found at i:1908615 original size:23 final size:23
Alignment explanation
Indices: 1908585--1908633 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1908575 TGGTGGTTGG
*
1908585 TTTAAAGG-ATGTTTAGACTTTAT
1 TTTAAAGGTATATTTA-ACTTTAT
*
1908608 TTTAAAGGTATATTTAAGTTTAT
1 TTTAAAGGTATATTTAACTTTAT
1908631 TTT
1 TTT
1908634 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTAAAGGTATATTTAACTTTAT
Found at i:1917797 original size:21 final size:21
Alignment explanation
Indices: 1917758--1917838 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
1917748 ATTTTCCTGA
1917758 AAAAATGATCGAT-CCTTTTT
1 AAAAATGATCGATCCCTTTTT
*
1917778 AATAATGATCGATCCCTTTTT
1 AAAAATGATCGATCCCTTTTT
* * *
1917799 AAAAAAGGTTCGATCCCTTTTG
1 -AAAAATGATCGATCCCTTTTT
*
1917821 AAAAATGATCAATCCCTT
1 AAAAATGATCGATCCCTT
1917839 GGAAAAGGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 12 0.24
21 22 0.43
22 17 0.33
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAAATGATCGATCCCTTTTT
Found at i:1917819 original size:43 final size:42
Alignment explanation
Indices: 1917757--1917838 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
1917747 TATTTTCCTG
* * * *
1917757 AAAAAATGATCGATCCTTTTTAATAATGATCGATCCCTTTTT
1 AAAAAAGGATCGATCCTTTTGAAAAATGATCAATCCCTTTTT
*
1917799 AAAAAAGGTTCGATCCCTTTTGAAAAATGATCAATCCCTT
1 AAAAAAGGATCGAT-CCTTTTGAAAAATGATCAATCCCTT
1917839 GGAAAAGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 12 0.35
43 22 0.65
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (42 bp):
AAAAAAGGATCGATCCTTTTGAAAAATGATCAATCCCTTTTT
Found at i:1929014 original size:21 final size:20
Alignment explanation
Indices: 1928989--1929027 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1928979 TATCAAGGTC
*
1928989 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
1929010 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
1929028 TGATGAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:1950824 original size:409 final size:412
Alignment explanation
Indices: 1949868--1951042 Score: 1875
Period size: 409 Copynumber: 2.9 Consensus size: 412
1949858 AATTCATCTC
* * *
1949868 TAATTTATTAAATTAAGTTAAAATTAGAACCAAATTGATTAAATGTAAAAATATTGAAGATCAAA
1 TAATTTATTAAATTAAGTTGAAATTAGGACCAAATTGATTAAATGTAAAAATATTGAGGATCAAA
* * * ** * * *
1949933 TGTGTAATTATACCAATTTTGTTAAATGACACATCAGCACCTCCATTAAATATTAGCGGCATATG
66 TTTGTAATTATACTAATTATGTTAGCTGACACGTCAGCACCTCCATTAAATATTAACGGCATGTG
* * *
1949998 TCTTGAATGAAACTAATTAAATAGTTAAGTGATCATATTGATGCAATTTTGAAAATGGTGGTCAT
131 TCTTGAATGAAACCAATTAAATAGTTAAGTGCTCATATTGACGCAATTTTGAAAATGGTGGTCAT
* *
1950063 TCAAGTAGTCCGTCCTAACATAAATGGCTAATATTTAATAAATCAATAGCATAACTGATAAAAAT
196 TCAAGTAGTCTGTCCTAACATAAATGACTAATATTTAATAAATCAATAGCATAACTGATAAAAAT
*
1950128 GTA----TTT-TTTTCTGAGCAAACATAAAAATATAAAATTT-ATCAATTTGATAATTTATCTAA
261 GTATTTTTTTATTTTGTGAGCAAACATAAAAATAT-AAATTTGATCAATTTGATAATTTATCTAA
1950187 ATATTAGACTTAATTTTTCCTAGAGGTCGAATCAATATATATATATATATATATATACACATATA
325 ATATTAGACTTAATTTTTCCTAGAGGTCGAATC-A-ATATATATATATATATATATA-ACA-ATA
1950252 CATAGAGAGAGAGATTGAAAATAAATT
386 CATAGAGAGAGAGATTGAAAATAAATT
*
1950279 TAATTTATTAAATTAAGTTGAAATTAGGATCAAATTGATTAAATGTAAAAATATTGAGGATCAAA
1 TAATTTATTAAATTAAGTTGAAATTAGGACCAAATTGATTAAATGTAAAAATATTGAGGATCAAA
* * *
1950344 TTTGTAATTATACTAATTATTTTAGCTGACACGTCAGCACCTCCATTAAATATTAACGACATGTT
66 TTTGTAATTATACTAATTATGTTAGCTGACACGTCAGCACCTCCATTAAATATTAACGGCATGTG
*
1950409 TCTTGAATGAAACCAATTAAATAGTTAAGTGCTCATATTAACGCAATTTTGAAAATGGTGGTCAT
131 TCTTGAATGAAACCAATTAAATAGTTAAGTGCTCATATTGACGCAATTTTGAAAATGGTGGTCAT
*
1950474 TCAAGTAGTCTGCCCTAACATAAATGACTAATATTTAATAAATCAATAGCATAACTGATAAAAAT
196 TCAAGTAGTCTGTCCTAACATAAATGACTAATATTTAATAAATCAATAGCATAACTGATAAAAAT
1950539 GTATTTTTTTTATTTTGTGAGCAAACATAAAAATATAAATTTGATCAATTTGATAATTTATCTAA
261 GTA-TTTTTTTATTTTGTGAGCAAACATAAAAATATAAATTTGATCAATTTGATAATTTATCTAA
1950604 ATATTAGACTTAATTTTTCCTAGAGGTCGAATC-A-ATATATATATATATATAT-AC-ATACATA
325 ATATTAGACTTAATTTTTCCTAGAGGTCGAATCAATATATATATATATATATATAACAATACATA
*
1950665 TAGAGAGAGATTGAAAATAAATT
390 GAGAGAGAGATTGAAAATAAATT
*
1950688 TAATTTATTAAATTAAGTTGAAATTAGGACCAAATTAATTAAATGTAAAAATATTGAGGATCAAA
1 TAATTTATTAAATTAAGTTGAAATTAGGACCAAATTGATTAAATGTAAAAATATTGAGGATCAAA
1950753 TTTGTAATTATACTAATTATGTTAGCTGACACGTCAGCACCTCCATTAAATATTAACGGCATGTG
66 TTTGTAATTATACTAATTATGTTAGCTGACACGTCAGCACCTCCATTAAATATTAACGGCATGTG
1950818 TCTTGAATGAAACCAATTAAATAGTTAAGTGCTCATATTGACGCAATTTTGAAAATGGTGGTCAT
131 TCTTGAATGAAACCAATTAAATAGTTAAGTGCTCATATTGACGCAATTTTGAAAATGGTGGTCAT
* * * * *
1950883 TCGAGCAGTCTGTCCTAGCATAAATGACTAATATTTAATAAATCGATAGCATAACTGATAAAACT
196 TCAAGTAGTCTGTCCTAACATAAATGACTAATATTTAATAAATCAATAGCATAACTGATAAAAAT
* * *
1950948 ATATATTTTTTATTTTGTGAGCAAACATAAAAAAAATATAAAATTGATCAATTTTATAATTTATC
261 GTAT-TTTTTTATTTTGTGAGCAAACAT---AAAAATATAAATTTGATCAATTTGATAATTTATC
* *
1951013 TAAATATTTGACTTAATTTTTCCTGGAGGT
322 TAAATATTAGACTTAATTTTTCCTAGAGGT
1951043 TGTATGTGTG
Statistics
Matches: 712, Mismatches: 41, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
408 1 0.00
409 302 0.42
411 243 0.34
412 60 0.08
413 18 0.03
414 1 0.00
416 9 0.01
417 78 0.11
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (412 bp):
TAATTTATTAAATTAAGTTGAAATTAGGACCAAATTGATTAAATGTAAAAATATTGAGGATCAAA
TTTGTAATTATACTAATTATGTTAGCTGACACGTCAGCACCTCCATTAAATATTAACGGCATGTG
TCTTGAATGAAACCAATTAAATAGTTAAGTGCTCATATTGACGCAATTTTGAAAATGGTGGTCAT
TCAAGTAGTCTGTCCTAACATAAATGACTAATATTTAATAAATCAATAGCATAACTGATAAAAAT
GTATTTTTTTATTTTGTGAGCAAACATAAAAATATAAATTTGATCAATTTGATAATTTATCTAAA
TATTAGACTTAATTTTTCCTAGAGGTCGAATCAATATATATATATATATATATAACAATACATAG
AGAGAGAGATTGAAAATAAATT
Found at i:1951313 original size:5 final size:5
Alignment explanation
Indices: 1951303--1951327 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1951293 AACTATAGGG
1951303 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
1951328 GGGTAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:1953585 original size:23 final size:24
Alignment explanation
Indices: 1953559--1953618 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1953549 ATGTATTTAT
* *
1953559 AAAT-TTTATATTAAATTATTCT-A
1 AAATATTTAT-TTAAAATATTATGA
*
1953582 AAATGTTTATTTAAAATATTATGA
1 AAATATTTATTTAAAATATTATGA
1953606 AAATATTTATTTA
1 AAATATTTATTTA
1953619 TTTTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (24 bp):
AAATATTTATTTAAAATATTATGA
Found at i:1954173 original size:20 final size:20
Alignment explanation
Indices: 1954150--1954219 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 20
1954140 AAAAAAGTGA
1954150 TAATTTAGGTACAAAACATG
1 TAATTTAGGTACAAAACATG
* *
1954170 TAATATATCTA-GTAAAAAAAAAGTG
1 T-A-AT-T-TAGGT-ACAAAACA-TG
1954195 ATAATTTAGGTACAAAACATG
1 -TAATTTAGGTACAAAACATG
1954216 TAAT
1 TAAT
1954220 ATATCCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
20 5 0.13
21 3 0.08
22 10 0.26
23 6 0.16
24 10 0.26
25 3 0.08
26 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (20 bp):
TAATTTAGGTACAAAACATG
Found at i:1954188 original size:23 final size:24
Alignment explanation
Indices: 1954155--1954224 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
1954145 AGTGATAATT
*
1954155 TAGGTACAAAACATGTAATATATC
1 TAGGTAAAAAACATGTAATATATC
* * * *
1954179 TA-GTAAAAAAAAAGTGATA-ATT
1 TAGGTAAAAAACATGTAATATATC
*
1954201 TAGGTACAAAACATGTAATATATC
1 TAGGTAAAAAACATGTAATATATC
1954225 CTTTTAATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (24 bp):
TAGGTAAAAAACATGTAATATATC
Found at i:1954194 original size:46 final size:46
Alignment explanation
Indices: 1954137--1954224 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
1954127 ACTAAAAGTA
1954137 AAAAAAAAAGTGATAATTTAGGTACAAAACATGTAATATATCTAGT
1 AAAAAAAAAGTGATAATTTAGGTACAAAACATGTAATATATCTAGT
1954183 AAAAAAAAAGTGATAATTTAGGTACAAAACATGTAATATATC
1 AAAAAAAAAGTGATAATTTAGGTACAAAACATGTAATATATC
1954225 CTTTTAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.27
Consensus pattern (46 bp):
AAAAAAAAAGTGATAATTTAGGTACAAAACATGTAATATATCTAGT
Found at i:1954560 original size:32 final size:31
Alignment explanation
Indices: 1954524--1954591 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1954514 ATTTTTGTAT
* *
1954524 TAGTTTGAGA-AAATTTTATTATCATTTTATAA
1 TAGTTTG-GATAAATTTAATAATCATTTT-TAA
1954556 TAG-TTGGATAAATTTAATAATCATTTTTAA
1 TAGTTTGGATAAATTTAATAATCATTTTTAA
*
1954586 AAGTTT
1 TAGTTT
1954592 AATAGCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 7 0.23
31 21 0.68
32 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (31 bp):
TAGTTTGGATAAATTTAATAATCATTTTTAA
Done.