Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_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: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1647300 original size:160 final size:158
Alignment explanation
Indices: 1646955--1647312 Score: 450
Period size: 158 Copynumber: 2.3 Consensus size: 158
1646945 TGTGATATAT
* * * *
1646955 GAGCATGTGATTCATATTTGATACAAAAA-GTGACTTAAAATAAATCACAAATTGAAGGAATAAT
1 GAGCATGTGATTCAAATTTGATAAAAAAATG-GACTTAAAATAAATCACAAATTGAAGAAATAAG
* ** *
1647019 GAGATCATTAAAAATTGAATTACTAAATTGAAAAATAAAAAATTATTATAAAAAAGAGGAATTGA
65 GAGATCATAAAAAATTGAAAGACTAAATTAAAAAATAAAAAATTATTATAAAAAAGAGGAATTGA
1647084 AAGTACAAATGTATTATACTATGATTTAG
130 AAGTACAAATGTATTATACTATGATTTAG
** * ****
1647113 GAGCATGTGGCTCAAATTTGATAAAAAAATGGACTTAAAATAAATGATGTTTTGAAGAAATAAGG
1 GAGCATGTGATTCAAATTTGATAAAAAAATGGACTTAAAATAAATCACAAATTGAAGAAATAAGG
* * * * * *
1647178 AGATTATAAAAAATTGAAAGACTAACTTAAAAAAATATAAAATTTGTTATCAAAAAGTGGAATTG
66 AGATCATAAAAAATTGAAAGACTAAATT-AAAAAATA-AAAAATTATTATAAAAAAGAGGAATTG
* * *
1647243 AAAGTACACATGTATTCTACTATGGTTTAG
129 AAAGTACAAATGTATTATACTATGATTTAG
*
1647273 GAGCATGTGATTCAAATTTGGT-AAAAAATGGACTTAAAAT
1 GAGCATGTGATTCAAATTTGATAAAAAAATGGACTTAAAAT
1647313 GAAGGAGGAA
Statistics
Matches: 170, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
158 75 0.44
159 26 0.15
160 69 0.41
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (158 bp):
GAGCATGTGATTCAAATTTGATAAAAAAATGGACTTAAAATAAATCACAAATTGAAGAAATAAGG
AGATCATAAAAAATTGAAAGACTAAATTAAAAAATAAAAAATTATTATAAAAAAGAGGAATTGAA
AGTACAAATGTATTATACTATGATTTAG
Found at i:1647727 original size:26 final size:26
Alignment explanation
Indices: 1647694--1647743 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1647684 GTAAATTAAA
*
1647694 TAAAAATTAAAATT-TACATTTTAAGT
1 TAAAAATT-AAATTATAAATTTTAAGT
1647720 TAAAAATTAAATTATAAATTTTAA
1 TAAAAATTAAATTATAAATTTTAA
1647744 AATGCAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAAAATTAAATTATAAATTTTAAGT
Found at i:1649321 original size:23 final size:22
Alignment explanation
Indices: 1649277--1649321 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1649267 TCAGGAGTTA
1649277 CAGGAGTTATCTGATTTAATTT
1 CAGGAGTTATCTGATTTAATTT
1649299 CAGGAGTTATAACTG-TTTAATTT
1 CAGGAGTTAT--CTGATTTAATTT
1649322 TTATGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
CAGGAGTTATCTGATTTAATTT
Found at i:1655600 original size:34 final size:34
Alignment explanation
Indices: 1655557--1655629 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1655547 TTAAATGTTT
*
1655557 TTAATATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* *
1655591 TTAAAATACAAATTATGGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
1655625 TTAAA
1 TTAAA
1655630 TTCAACTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:1667736 original size:32 final size:33
Alignment explanation
Indices: 1667695--1667758 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
1667685 TAGGTGTTAG
1667695 AAACTTTTCA-GTGATATATCACTTCATTTTAA
1 AAACTTTTCATGTGATATATCACTTCATTTTAA
*
1667727 AAACTTTTCATTGGTGATATATCACTTTATTT
1 AAACTTTTCA-T-GTGATATATCACTTCATTT
1667759 CAGAAAAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.36
35 18 0.64
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (33 bp):
AAACTTTTCATGTGATATATCACTTCATTTTAA
Found at i:1667868 original size:32 final size:34
Alignment explanation
Indices: 1667832--1667908 Score: 86
Period size: 36 Copynumber: 2.3 Consensus size: 34
1667822 ATAACTTCAC
*
1667832 TTTAGAAACTTTTCA-A-TGATATATCAATTTAT
1 TTTAGAAAATTTTCAGAGTGATATATCAATTTAT
* * *
1667864 TTTAGAAAAATTTTTAGTAGTGATATATTACTTTAT
1 TTTAG-AAAATTTTCAG-AGTGATATATCAATTTAT
1667900 TTTAGAAAA
1 TTTAGAAAA
1667909 AACGACCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 5 0.14
33 8 0.22
35 5 0.14
36 19 0.51
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (34 bp):
TTTAGAAAATTTTCAGAGTGATATATCAATTTAT
Found at i:1667953 original size:144 final size:144
Alignment explanation
Indices: 1667691--1668420 Score: 886
Period size: 142 Copynumber: 5.1 Consensus size: 144
1667681 CAATTAGGTG
* * * * *
1667691 TTAGAAACTTTTCAGTGATATATCACTTCATTTTA-AAAACTTTTCATTGGTGATATATCACTTT
1 TTAGAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTTAGTAGTGATATATCACTTT
* * *
1667755 ATTTCAG-AAAAACGTCCATTTCTCATAGACCATTTAATGCATATGGTGAC--AAACTTTTCAGT
66 ATTTCAGAAAAAACGTCCATTTCTCATAGACCATTTAATGCACA--ATGACAGAAACTTTTCAAT
1667817 GCCCAATAACTTCACT
129 GCCCAATAACTTCACT
* * * * *
1667833 TTAGAAACTTTTCAATGATATATCAATTTATTTTAGAAAAATTTTTAGTAGTGATATATTACTTT
1 TTAGAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTTAGTAGTGATATATCACTTT
* * *
1667898 ATTTTAGAAAAAACGACCATTTCTCATAGACTATTTAATGCACAATGACAGAAACTTTTCAATGC
66 ATTTCAGAAAAAACGTCCATTTCTCATAGACCATTTAATGCACAATGACAGAAACTTTTCAATGC
1667963 CCAATAACTTCACT
131 CCAATAACTTCACT
* * *
1667977 TAATAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTTCAATAGTGATATATCACTT
1 TTAGAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTT-AGTAGTGATATATCACTT
* * *
1668042 CATTTCAGAAAAAATGTCCATTTCTCATATG-CCATTTAATGCACAATGACAGAAAATTTTCAAT
65 TATTTCAGAAAAAACGTCCATTTCTCATA-GACCATTTAATGCACAATGACAGAAACTTTTCAAT
1668106 GCCCAATAACTTCACT
129 GCCCAATAACTTCACT
* * * *
1668122 TCAAAAACTTTTTAGTG-TATATCAATTCATTTCAGAAAACTTTTCAGTAGTGATATATCACTTT
1 TTAGAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTTAGTAGTGATATATCACTTT
* * ** * ** *
1668186 ATTTCAG-AAAAATGTCAATTTCTCATAGATTATTTAATGCACAATAATGGAAACTTTTCAGTGC
66 ATTTCAGAAAAAACGTCCATTTCTCATAGACCATTTAATGCACAATGACAGAAACTTTTCAATGC
*
1668250 CCAAAAACTTCACT
131 CCAATAACTTCACT
* * * * * *
1668264 TCAGAAACTTTTTAGCG-TATATAAATTCATTTAAGAAAA-TTTTTCAGTAGTGATATCTCACTT
1 TTAGAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTT-AGTAGTGATATATCACTT
* * * * *
1668327 CATTTCAAAAAAAAAGTTCATTTCTCATAGACCATTTAATGCACAATGACAAAAACTTTTCAATG
65 TATTTCAGAAAAAACGTCCATTTCTCATAGACCATTTAATGCACAATGACAGAAACTTTTCAATG
** * *
1668392 -ATATATTACTTCATT
130 CCCA-ATAACTTCACT
1668407 TTAGAAACTTTTCA
1 TTAGAAACTTTTCA
1668421 TAAACCTATT
Statistics
Matches: 510, Mismatches: 68, Indels: 19
0.85 0.11 0.03
Matches are distributed among these distances:
141 5 0.01
142 155 0.30
143 120 0.24
144 127 0.25
145 102 0.20
146 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (144 bp):
TTAGAAACTTTTCAGTGATATATCAATTCATTTCAGAAAACTTTTTAGTAGTGATATATCACTTT
ATTTCAGAAAAAACGTCCATTTCTCATAGACCATTTAATGCACAATGACAGAAACTTTTCAATGC
CCAATAACTTCACT
Found at i:1692391 original size:118 final size:114
Alignment explanation
Indices: 1692187--1692415 Score: 422
Period size: 118 Copynumber: 2.0 Consensus size: 114
1692177 CTGCACATTA
1692187 TATCTTTCAGCCGAACACACACAATCCCTAAAACCACTTTTCATAATTAAATCCAAAGCATCTCA
1 TATCTTTCAGCCGAACACACACAATCCCTAAAACCACTTTTCATAATTAAATCCAAAGCATCTCA
1692252 CATGAGAAAATTACCGTTAACATGAATTATGTCAATTAATCTCATGTAT
66 CATGAGAAAATTACCGTTAACATGAATTATGTCAATTAATCTCATGTAT
1692301 TATCTTTCAGCCGAACACACACAATCCCTAAAACCATAACCTTTTCATAATTAAATCCAAAGCAT
1 TATCTTTCAGCCGAACACACACAATCCCTAAAACC---A-CTTTTCATAATTAAATCCAAAGCAT
1692366 CTCACATGAGAAAATTACCGTTAACATGAATTATGTCAATTAATCTCATG
62 CTCACATGAGAAAATTACCGTTAACATGAATTATGTCAATTAATCTCATG
1692416 AACAGGAACA
Statistics
Matches: 111, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
114 35 0.32
117 1 0.01
118 75 0.68
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (114 bp):
TATCTTTCAGCCGAACACACACAATCCCTAAAACCACTTTTCATAATTAAATCCAAAGCATCTCA
CATGAGAAAATTACCGTTAACATGAATTATGTCAATTAATCTCATGTAT
Found at i:1701134 original size:15 final size:17
Alignment explanation
Indices: 1701114--1701153 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1701104 GGTATTGGCT
1701114 TTCTTTT-G-TGTTTTG
1 TTCTTTTCGTTGTTTTG
1701129 TTCTTTTGCGTTGTTTTG
1 TTCTTTT-CGTTGTTTTG
1701147 TTCTTTT
1 TTCTTTT
1701154 TGCTGGAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
17 1 0.05
18 14 0.64
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.72
Consensus pattern (17 bp):
TTCTTTTCGTTGTTTTG
Found at i:1705247 original size:1 final size:1
Alignment explanation
Indices: 1705241--1705272 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
1705231 CATAAATTTC
*
1705241 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1705273 GCGTGGGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1708715 original size:6 final size:6
Alignment explanation
Indices: 1708704--1708741 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1708694 AACGAGTTCT
* *
1708704 TTCCTC TTCCTC TTCCTC TTCCTC TTCATC GTCCTC TT
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TT
1708742 TGTGAGGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.45, G:0.03, T:0.50
Consensus pattern (6 bp):
TTCCTC
Found at i:1710599 original size:23 final size:23
Alignment explanation
Indices: 1710557--1710625 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1710547 CACCACAGCT
* * *
1710557 CGTATAATTGCACCTAAGTGTCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1710580 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* * *
1710603 TGTAGAATAGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1710626 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1711918 original size:11 final size:11
Alignment explanation
Indices: 1711902--1711933 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1711892 TCACGATGGA
1711902 GAAGAAGAAGT
1 GAAGAAGAAGT
1711913 GAAGAAGAAGT
1 GAAGAAGAAGT
1711924 GAAGAAGAAG
1 GAAGAAGAAG
1711934 AGAAATCTGG
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:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (11 bp):
GAAGAAGAAGT
Found at i:1711920 original size:14 final size:12
Alignment explanation
Indices: 1711901--1711937 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1711891 CTCACGATGG
1711901 AGAAGAAGAAGT
1 AGAAGAAGAAGT
1711913 -GAAGAAGAAGT
1 AGAAGAAGAAGT
1711924 -GAAGAAGAAG-
1 AGAAGAAGAAGT
1711934 AGAA
1 AGAA
1711938 ATCTGGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.05
Consensus pattern (12 bp):
AGAAGAAGAAGT
Found at i:1712997 original size:19 final size:19
Alignment explanation
Indices: 1712973--1713016 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1712963 CACGGCACTG
*
1712973 TTCATATAGTATAGTACTA
1 TTCATACAGTATAGTACTA
*
1712992 TTCATACGGTATAGTACTA
1 TTCATACAGTATAGTACTA
1713011 TTCATA
1 TTCATA
1713017 AAACATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (19 bp):
TTCATACAGTATAGTACTA
Found at i:1716905 original size:64 final size:63
Alignment explanation
Indices: 1716837--1717045 Score: 235
Period size: 65 Copynumber: 3.2 Consensus size: 63
1716827 GTGCACCAAG
*
1716837 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGG-T
* * *
1716901 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG-
1 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATCCTGAGTGCATCGATGCATGGT
* * * * *
1716964 AGAATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCAT
1 TG--TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATATC-CTGAGTGCATCGATGCAT
1717027 GGT
61 GGT
*
1717030 TGATGCATCGGTGCAT
1 TG-TGCATCGATGCAT
1717046 CACCTCAAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 34 0.27
65 85 0.68
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGGT
Found at i:1716987 original size:17 final size:19
Alignment explanation
Indices: 1716949--1716995 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1716939 ATATTCAGAG
1716949 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1716968 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1716985 TGCATTCGATG
1 TGCA-TCGATG
1716996 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1717238 original size:20 final size:21
Alignment explanation
Indices: 1717215--1717254 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1717205 GAATCGAATA
1717215 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1717235 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1717255 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1718543 original size:20 final size:20
Alignment explanation
Indices: 1718518--1718572 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1718508 AACCCGACGG
*
1718518 ATGCATCGGTGCATGGTCT-T
1 ATGCATCGGTGCATGGT-TAA
* *
1718538 ATGCATCGATGCATTGTTAA
1 ATGCATCGGTGCATGGTTAA
1718558 ATGCATCGGTGCATG
1 ATGCATCGGTGCATG
1718573 AAGCACAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (20 bp):
ATGCATCGGTGCATGGTTAA
Found at i:1724404 original size:64 final size:64
Alignment explanation
Indices: 1724351--1724514 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
1724341 CGGTGCACCA
* *
1724351 AGTGTGCAACGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
1724415 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
1724480 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
1724515 CAATTAATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 31 0.36
65 54 0.64
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1724503 original size:17 final size:19
Alignment explanation
Indices: 1724465--1724511 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1724455 ATATTCAGAG
1724465 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1724484 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1724501 TGCATTCGATG
1 TGCA-TCGATG
1724512 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1724754 original size:20 final size:21
Alignment explanation
Indices: 1724731--1724770 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1724721 GAATCGAATA
1724731 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1724751 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1724771 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1731601 original size:180 final size:180
Alignment explanation
Indices: 1731267--1731737 Score: 658
Period size: 180 Copynumber: 2.6 Consensus size: 180
1731257 GATCCAAATT
* * * * * * **
1731267 AAAAATGTGTCGATCCAAAACGATATAACATGTAAAACTATGACAAAACCTGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGA-TAAACCGGTATCAAAATGATA
* * * * * *
1731332 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTATTTTAATATAAGGATCGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
1731397 GTGAATTTAAAAGAAAAACAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 GTGAATTTAAAAGAAAAACAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTA
*
1731449 AAAAATATATCGATCCAAAACGATATACCAGGTAAAAATATGATAAACCGGTATCAAAATGATAA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAACCGGTATCAAAATGATAA
* *
1731514 AACTC-GTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAC-CGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * ** *
1731577 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTA
130 GTGAATTTAAAAGAAAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
*
1731628 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGAT-AAACCGGTATCAAAATGATA
* *
1731693 AAACCGGTAAAATGATACCAGATATATTGAAAGTGTCGATACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1731738 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
179 47 0.18
180 119 0.46
181 54 0.21
182 39 0.15
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (180 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAACCGGTATCAAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAAAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:1731681 original size:20 final size:19
Alignment explanation
Indices: 1731658--1731704 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1731648 CGATATAACA
1731658 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1731678 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1731698 GGTAAAA
1 GGTAAAA
1731705 TGATACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1731706 original size:17 final size:19
Alignment explanation
Indices: 1731667--1731709 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1731657 AGGTAAAAAT
1731667 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1731687 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1731704 ATGATA
1 ATGATA
1731710 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1733958 original size:21 final size:21
Alignment explanation
Indices: 1733928--1733992 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1733918 AAGACAATCA
* *
1733928 AGAGTTGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1733949 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1733970 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1733991 AG
1 AG
1733993 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1734068 original size:33 final size:33
Alignment explanation
Indices: 1734026--1734091 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1734016 AAATAGATGG
*
1734026 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1734059 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1734092 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1735906 original size:19 final size:19
Alignment explanation
Indices: 1735882--1735930 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1735872 AATGTAGGGT
1735882 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1735901 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1735920 TAATTTTGTAT
1 TAATTTTGTAT
1735931 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1736436 original size:200 final size:200
Alignment explanation
Indices: 1736043--1737801 Score: 3143
Period size: 200 Copynumber: 8.9 Consensus size: 200
1736033 AATTTACAAT
*
1736043 ATGGCCAACAGGGTGCAACTATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1736108 CGAAAACCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1736172 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1736237 AATGA
196 AATGA
*
1736242 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1736307 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1736372 ATGAGAGAATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTATCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1736437 AATGA
196 AATGA
1736442 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
1736506 CGAAAACC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATATCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1736570 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1736635 AATGA
196 AATGA
*
1736640 ATGGCCAACAGGGTGCAACCATATAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1736705 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1736770 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1736835 AATGA
196 AATGA
1736840 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
1736905 CGAAAACCAAAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1736970 ATGAGAGAATATGTCTAAATAATGTGTCG----------A-------T--AT-TTTTT-GTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1737014 AATGA
196 AATGA
*
1737019 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGCGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
1737084 CGAAAACCAAAAGTATAATGTATTATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1737149 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1737214 AATGA
196 AATGA
*
1737219 ATGGCCAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1737284 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1737349 ATGAGAGAAAATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1737414 AATGA
196 AATGA
*
1737419 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
1737484 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATTTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1737549 ATGAGAGAATATATCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
*
1737614 AATTA
196 AATGA
* * *
1737619 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* *
1737684 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1737749 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
1737802 CTAATTTAAA
Statistics
Matches: 1502, Mismatches: 34, Indels: 47
0.95 0.02 0.03
Matches are distributed among these distances:
179 167 0.11
180 5 0.00
181 2 0.00
183 1 0.00
189 1 0.00
190 1 0.00
196 1 0.00
198 164 0.11
199 161 0.11
200 999 0.67
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1737029 original size:179 final size:179
Alignment explanation
Indices: 1736813--1737387 Score: 819
Period size: 179 Copynumber: 3.1 Consensus size: 179
1736803 TTTTTTAGTT
*
1736813 TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATA
1 TGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATA
*
1736878 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATATAATTTTTCAA
66 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
1736943 TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
131 TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
1736992 TGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATA
1 TGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATA
* *
1737057 TATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTATTATGTAATTTTTCAA
66 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
1737122 TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
131 TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
* * *** *
1737171 TGTGTCGACACTTTTTTAGTTTGTGTC-GATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGC
1 TGTGTCG--A--TATTT--TTTGT-CCAGA-ATGAATGG-CC------AA----C-AG--GGTGC
*
1737235 AACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTAT
44 AACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTAT
*
1737300 AATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAAATGTCT
109 AATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCT
1737365 AAATAA
174 AAATAA
*
1737371 TGTGTCGACACTTTTTT
1 TGTGTCGATA-TTTTTT
1737388 AGTTTGTGTT
Statistics
Matches: 357, Mismatches: 16, Indels: 30
0.89 0.04 0.07
Matches are distributed among these distances:
179 182 0.51
181 1 0.00
183 4 0.01
185 7 0.02
186 6 0.02
187 2 0.01
193 2 0.01
195 3 0.01
197 4 0.01
198 2 0.01
200 144 0.40
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (179 bp):
TGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATA
TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
TCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
Found at i:1737198 original size:400 final size:380
Alignment explanation
Indices: 1736613--1737787 Score: 1958
Period size: 379 Copynumber: 3.0 Consensus size: 380
1736603 TTTTTTAGTT
* *
1736613 TGTGTCGATA-TTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATATAGTGTCGATCCAT
1 TGTGTCGATATTTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCAT
*
1736677 ATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
66 ATATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
*
1736742 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTT
131 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATATCTAAATAATGTGTCGACACTTTT
1736807 TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGA
196 TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGA
*
1736872 TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATATAATT
261 TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATT
1736937 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
326 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
*
1736992 TGTGTCGATATTTTTT-GTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCAT
1 TGTGTCGATATTTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCAT
*
1737056 ATATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTATTATGTAATTTTTCA
66 ATATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
*
1737121 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTT
131 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATATCTAAATAATGTGTCGACACTTTT
*
1737186 TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAATGTCGA
196 TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGA
1737251 TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATT
261 TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATT
*
1737316 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAAATGTCTAAATAA
326 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
1737371 TGTGTCGACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
1 TGTGTCG----------A--------T-AT-TTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
*
1737436 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATA
46 ACCATAAAGTGTCGATCCATATATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAAAGTATA
*
1737501 ATGTAATATGTAATTTTTCAATTTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATATCTA
111 ATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATATCTA
* * *
1737566 AATAATGTGTCGACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAGAATTAATGGCAAACAGG
176 AATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGG
* *
1737631 GTGCAACCGTAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAAAAACATCGAAAACCAAAA
241 GTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAA
* * *
1737696 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGAGAGAATAG
306 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAT
1737761 GTCTAAATAA
371 GTCTAAATAA
*
1737771 TGTGTCGACACTTTTTT
1 TGTGTCGATA-TTTTTT
1737788 AGTTTGTGTC
Statistics
Matches: 751, Mismatches: 22, Indels: 44
0.92 0.03 0.05
Matches are distributed among these distances:
379 374 0.50
380 5 0.01
381 6 0.01
382 1 0.00
389 1 0.00
390 1 0.00
397 1 0.00
398 2 0.00
399 5 0.01
400 355 0.47
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (380 bp):
TGTGTCGATATTTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCAT
ATATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATATCTAAATAATGTGTCGACACTTTT
TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGA
TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATT
TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
Found at i:1737311 original size:579 final size:579
Alignment explanation
Indices: 1736043--1737801 Score: 2930
Period size: 579 Copynumber: 3.0 Consensus size: 579
1736033 AATTTACAAT
*
1736043 ATGGCCAACAGGGTGCAACTATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1736108 CGAAAACCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1736172 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
*
1736237 AATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAA
196 AATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
1736302 AACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
*
1736367 GTTTTATGAGAGAATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTATCGATATTTTTGG
326 GTTTTATGAGAGAATATGTC----TAA-A--T--A-A------T-G--TG--TCGATATTTTTTG
1736432 TCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATC
370 TCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
1736496 CCAAAAACATCGAAAACC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTA
435 CCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTA
*
1736560 TATCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATT
500 TACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATT
1736625 TTTGGTCCAGAATGA
565 TTTGGTCCAGAATGA
*
1736640 ATGGCCAACAGGGTGCAACCATATAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1736705 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1736770 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
1736835 AATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
196 AATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
*
1736900 AACATCGAAAACCAAAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
1736965 GTTTTATGAGAGAATATGTCTAAATAATGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAG
326 GTTTTATGAGAGAATATGTCTAAATAATGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAG
*
1737030 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGCGTCGATCCCAAAAACATCGAAAACCAAA
391 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
*
1737095 AGTATAATGTATTATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
456 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
1737160 TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
521 TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
*
1737219 ATGGCCAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1737284 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1737349 ATGAGAGAAAATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAG
131 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
*
1737414 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
196 AATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
*
1737479 AACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATTTAACCGGTACAAGTATACCG
261 AACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
*
1737544 GTTTTATGAGAGAATATATCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTTGATATTTTTGG
326 GTTTTATGAGAGAATATGTCTAAATAATGTGTCG----------A--------T-AT-TTTTT-G
* * * *
1737609 TCCAGAATTAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAATGTCGATC
370 TCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
*
1737674 CCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTA
435 CCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTA
* *
1737739 TACTGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
500 TACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
1737802 CTAATTTAAA
Statistics
Matches: 1113, Mismatches: 25, Indels: 45
0.94 0.02 0.04
Matches are distributed among these distances:
577 62 0.06
578 31 0.03
579 477 0.43
581 1 0.00
582 1 0.00
588 1 0.00
589 2 0.00
591 1 0.00
593 1 0.00
594 3 0.00
597 94 0.08
598 249 0.22
599 5 0.00
600 185 0.17
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (579 bp):
ATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
AACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
GTTTTATGAGAGAATATGTCTAAATAATGTGTCGATATTTTTTGTCCAGAATGAATGGCCAACAG
GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
Found at i:1740545 original size:183 final size:183
Alignment explanation
Indices: 1740237--1740997 Score: 1378
Period size: 183 Copynumber: 4.2 Consensus size: 183
1740227 CAAAGTTTTC
** *
1740237 ACACTTTTTAATATTGTGTATGTACTTTATGTCCAGAATGGAAGAAAAATGTGTTGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
1740302 CAAAAAGTGTCGACATTTACACGTCGGAACCCAGAATTATAATATAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1740367 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
**
1740420 ACACTTTTTAATATTGTGTATGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1740485 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1740550 AACCGGTATAAATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1740603 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
1740668 CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTTTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1740733 AACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * *
1740786 ATACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1740851 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
1740916 AATCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1740969 ACACTTTTTAATATTGTGTCGGTACTTTA
1 ACACTTTTTAATATTGTGTCGGTACTTTA
1740998 CAATAGGAGT
Statistics
Matches: 559, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 559 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1743769 original size:22 final size:22
Alignment explanation
Indices: 1743725--1743769 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1743715 ATTACATAAC
*
1743725 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
1743747 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATCGAAC-CTT
1743769 T
1 T
1743770 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:1743812 original size:23 final size:23
Alignment explanation
Indices: 1743786--1743835 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1743776 AATAGGTAAA
*
1743786 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1743809 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1743832 ATAT
1 ATAT
1743836 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1744181 original size:22 final size:22
Alignment explanation
Indices: 1744137--1744181 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1744127 ATTACATAAC
*
1744137 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
1744159 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATCGAAC-CTT
1744181 T
1 T
1744182 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:1744230 original size:23 final size:23
Alignment explanation
Indices: 1744199--1744248 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1744189 ATAGGTAAAA
*
1744199 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1744222 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1744245 ATAT
1 ATAT
1744249 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1744474 original size:414 final size:414
Alignment explanation
Indices: 1743528--1745201 Score: 2953
Period size: 414 Copynumber: 4.0 Consensus size: 414
1743518 ATATTATTAT
1743528 TAAATTAAAAACAATAAACATATATATTACATATTTATTATT-T-TTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
*
1743591 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
1743656 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
1743721 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGT-AA
196 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
1743785 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
261 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
*
1743850 CCTTTTTATAAAAGTGTCCATACTTTTTTCA-TGTGGAAAACATTAATTTATGGTTATCTTTTGA
326 CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
1743914 GTGAGTTTTAAGATATTAATTTAA
391 GTGAGTTTTAAGATATTAATTTAA
1743938 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1744003 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
1744068 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
1744133 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
196 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
1744198 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
261 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
*
1744263 CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTATGGTTATCTTTTGA
326 CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
1744328 GTGAGTTTTAAGATATTAATTTAA
391 GTGAGTTTTAAGATATTAATTTAA
1744352 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1744417 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
1744482 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
* *
1744547 TAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAA
196 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
1744612 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
261 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
*
1744677 CCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
326 CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
*
1744742 GTGAGTTTTAAGATATTAATTTAG
391 GTGAGTTTTAAGATATTAATTTAA
*
1744766 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAACATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
*
1744831 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
*
1744896 TATTAAATTAATATTGTAGGTGGAAAATATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTAC
*
1744961 ATAACTTT-AAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
195 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAA
1745025 AAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTA
260 AAATATGATGTAATAGGTAG--C-------------------GC--TTATATAATGTAATAGGTA
* * * *
1745090 GTGCTTATATTATAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAA
302 GTGCTTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAA
*
1745155 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAAATATTAATTTA
367 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTA
1745202 GTAATTATAT
Statistics
Matches: 1220, Mismatches: 16, Indels: 29
0.96 0.01 0.02
Matches are distributed among these distances:
410 42 0.03
411 1 0.00
412 211 0.17
413 98 0.08
414 709 0.58
415 31 0.03
416 1 0.00
435 2 0.00
437 125 0.10
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (414 bp):
TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTAT
CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
GTGAGTTTTAAGATATTAATTTAA
Found at i:1744644 original size:23 final size:23
Alignment explanation
Indices: 1744613--1744662 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1744603 ATAGGTAAAA
*
1744613 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1744636 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1744659 ATAT
1 ATAT
1744663 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1745058 original size:23 final size:23
Alignment explanation
Indices: 1745027--1745099 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1745017 ATAGGTAAAA
* *
1745027 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
1745050 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1745073 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1745096 ATAT
1 ATAT
1745100 TATAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1751988 original size:31 final size:31
Alignment explanation
Indices: 1751950--1752019 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
1751940 AAAGCAGCAT
1751950 GTGGAGGAGTAATCAGAGATTTGAATGGAAA
1 GTGGAGGAGTAATCAGAGATTTGAATGGAAA
1751981 GTGGAGGAGTAATCAGAGATTTGAATGGAAA
1 GTGGAGGAGTAATCAGAGATTTGAATGGAAA
*
1752012 ATGGAGGA
1 GTGGAGGA
1752020 TCGACTTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.39, C:0.03, G:0.37, T:0.21
Consensus pattern (31 bp):
GTGGAGGAGTAATCAGAGATTTGAATGGAAA
Found at i:1752505 original size:19 final size:18
Alignment explanation
Indices: 1752460--1752507 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1752450 TTGTTTAGAA
1752460 AATAAAATTAAAAAAATC
1 AATAAAATTAAAAAAATC
* * *
1752478 AAAATAAATTGATAAACATC
1 AATA-AAATT-AAAAAAATC
1752498 AATAAAATTA
1 AATAAAATTA
1752508 TTGTGGCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (18 bp):
AATAAAATTAAAAAAATC
Found at i:1754080 original size:2 final size:2
Alignment explanation
Indices: 1754075--1754127 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1754065 TTTTTCATGA
1754075 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
1754117 AT AT AT AT AT A
1 AT AT AT AT AT A
1754128 AGGAAAAGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1758314 original size:4 final size:4
Alignment explanation
Indices: 1758305--1758331 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1758295 TCAACATTTA
1758305 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
1758332 CTTGGTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1760662 original size:32 final size:32
Alignment explanation
Indices: 1760609--1760672 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1760599 TTCAAAGAAA
1760609 AAATAAAATGATTAATTTAAAGGTTT-GTGATCC
1 AAATAAAAT-ATTAATTTAAA-GTTTAGTGATCC
1760642 AAATAAAAT-TTGAATTTAAAGTTTAGTGATC
1 AAATAAAATATT-AATTTAAAGTTTAGTGATC
1760673 TAAAATGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 6 0.21
32 14 0.48
33 9 0.31
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.38
Consensus pattern (32 bp):
AAATAAAATATTAATTTAAAGTTTAGTGATCC
Found at i:1761385 original size:29 final size:29
Alignment explanation
Indices: 1761343--1761405 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1761333 TAATTTAATA
1761343 AATAAAATAAAAATTTGAAG-GCTAAAAAG
1 AATAAAATAAAAATTT-AAGTGCTAAAAAG
* * *
1761372 AATATAATAAAAATTTAAGTGTTAAAATG
1 AATAAAATAAAAATTTAAGTGCTAAAAAG
1761401 AATAA
1 AATAA
1761406 CTGATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (29 bp):
AATAAAATAAAAATTTAAGTGCTAAAAAG
Found at i:1762237 original size:25 final size:25
Alignment explanation
Indices: 1762209--1762262 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
1762199 TACCATATTT
*
1762209 GCAAGAAAACCTTGACATCCCTGAA
1 GCAAGAAAACCCTGACATCCCTGAA
1762234 GCAAGAAAACCCTGACATCCCTGAA
1 GCAAGAAAACCCTGACATCCCTGAA
1762259 GCAA
1 GCAA
1762263 CAATTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.30, G:0.17, T:0.13
Consensus pattern (25 bp):
GCAAGAAAACCCTGACATCCCTGAA
Found at i:1764626 original size:23 final size:23
Alignment explanation
Indices: 1764600--1764668 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1764590 CACCACAACT
*
1764600 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1764623 CGTAGAATTGCACCAAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1764646 CGTAGAAATGTACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1764669 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1770861 original size:31 final size:31
Alignment explanation
Indices: 1770759--1770865 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 31
1770749 TTAGGGACTG
* *
1770759 AGAGCCTACCCAAGAAAGTTCTCGGGGCCAC
1 AGAGCCTACCCAAGAAAGATCTCAGGGCCAC
* * * * * *
1770790 GGGGCCTACCTAAGAAAAATCTCA-AGTCAC
1 AGAGCCTACCCAAGAAAGATCTCAGGGCCAC
*
1770820 A-AGGCCTACCCAAGAATGATCTCAGGGCCAC
1 AGA-GCCTACCCAAGAAAGATCTCAGGGCCAC
1770851 AGAGCCTACCCAAGA
1 AGAGCCTACCCAAGA
1770866 GTCACATTAG
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
30 22 0.38
31 35 0.60
32 1 0.02
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.13
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAGATCTCAGGGCCAC
Found at i:1777866 original size:18 final size:18
Alignment explanation
Indices: 1777843--1777883 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1777833 CGATCAACGA
1777843 GTCAGACAGTCGGGTCGG
1 GTCAGACAGTCGGGTCGG
1777861 GTCAGACAGTCGGGTCGG
1 GTCAGACAGTCGGGTCGG
1777879 GTCAG
1 GTCAG
1777884 GTTGGGTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (18 bp):
GTCAGACAGTCGGGTCGG
Found at i:1782066 original size:19 final size:17
Alignment explanation
Indices: 1782011--1782088 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 17
1782001 TTTTTGTGTC
*
1782011 TATTTTTATCTTATTTTT
1 TATTTTT-TTTTATTTTT
* *
1782029 TATTTATTTCTATTATTT
1 TATTTTTTTTTATT-TTT
1782047 TATTTTTGTTTTATGTTTT
1 TATTTTT-TTTTAT-TTTT
1782066 TATGTTTTTTTATATTTTT
1 TAT-TTTTTTT-TATTTTT
1782085 TATT
1 TATT
1782089 ATATTTTCCC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.10
18 16 0.32
19 21 0.42
20 8 0.16
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.77
Consensus pattern (17 bp):
TATTTTTTTTTATTTTT
Found at i:1782082 original size:36 final size:36
Alignment explanation
Indices: 1782011--1782083 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1782001 TTTTTGTGTC
*
1782011 TATTTTTATCTTATTTTTTATTTATTTCTATTATTT
1 TATTTTTATCTTATTTTTTATGTATTTCTATTATTT
* * * *
1782047 TATTTTTGTTTTATGTTTTTATGTTTTTTTA-TATTT
1 TATTTTTATCTTAT-TTTTTATGTATTTCTATTATTT
1782083 T
1 T
1782084 TTATTATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 18 0.58
37 13 0.42
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.77
Consensus pattern (36 bp):
TATTTTTATCTTATTTTTTATGTATTTCTATTATTT
Found at i:1795379 original size:34 final size:34
Alignment explanation
Indices: 1795333--1795422 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
1795323 ACAAGATGGG
*
1795333 ATTTCAACTTCACAACGAAGGACGTCCAATTAAA
1 ATTTCAACTTCACAACGAAGGACATCCAATTAAA
* * *
1795367 ATTTCAATTTCACAACGAAGGACATCCCATTCAA
1 ATTTCAACTTCACAACGAAGGACATCCAATTAAA
*
1795401 AGTTCAACTTCACAACGAAGGA
1 ATTTCAACTTCACAACGAAGGA
1795423 GTCATCCACG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.23
Consensus pattern (34 bp):
ATTTCAACTTCACAACGAAGGACATCCAATTAAA
Found at i:1797608 original size:5 final size:5
Alignment explanation
Indices: 1797587--1797721 Score: 90
Period size: 5 Copynumber: 27.6 Consensus size: 5
1797577 TTGTGTCTGT
*
1797587 TTTTA TCTTA -TTT- TTTTA TTTTA TTTTA -TTTA TTTCTA --TTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA
* * *
1797633 TTTTTA TTTTTT TTTTG TTTTA TGTTT- TTTTA TTTTTTA TTTTG TTTTA
1 -TTTTA -TTTTA TTTTA TTTTA T-TTTA TTTTA --TTTTA TTTTA TTTTA
* * *
1797682 -TTTA -TTTA TTGTA -TTTA TTTTA TTTTA TTATA TTATA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1797722 CCCTTTTTGA
Statistics
Matches: 106, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
3 2 0.02
4 24 0.23
5 60 0.57
6 15 0.14
7 5 0.05
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1797610 original size:18 final size:17
Alignment explanation
Indices: 1797587--1797721 Score: 89
Period size: 18 Copynumber: 7.7 Consensus size: 17
1797577 TTGTGTCTGT
1797587 TTTTATCTTATTTTTTTA
1 TTTTAT-TTATTTTTTTA
* *
1797605 TTTTATTTTATTTATTTC
1 TTTTA-TTTATTTTTTTA
* *
1797623 TATTATTT-TATTTTTA
1 TTTTATTTATTTTTTTA
1797639 TTTT-TTT-TTTGTTTTA
1 TTTTATTTATTT-TTTTA
*
1797655 TGTTTTTTTA-TTTTTTA
1 T-TTTATTTATTTTTTTA
* *
1797672 TTTTGTTTTATTTATTTA
1 TTTT-ATTTATTTTTTTA
*
1797690 TTGTATTTATTTTATTTTA
1 TTTTATTTA-TTT-TTTTA
*
1797709 TTATATTATATTT
1 TTTTATT-TATTT
1797722 CCCTTTTTGA
Statistics
Matches: 94, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
15 5 0.05
16 17 0.18
17 21 0.22
18 35 0.37
19 14 0.15
20 2 0.02
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTTATTTTTTTA
Found at i:1797663 original size:27 final size:26
Alignment explanation
Indices: 1797599--1797702 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 26
1797589 TTATCTTATT
* *
1797599 TTTTTATTTTATTTTATTTATTTCTATTA
1 TTTTT-TTTTATTTT-TTT-TTTGTTTTA
1797628 TTTTATTTTTATTTTTTTTTTGTTTTA
1 TTTT-TTTTTATTTTTTTTTTGTTTTA
*
1797655 TGTTTTTTTATTTTTTATTTTGTTTTA
1 TTTTTTTTTATTTTTT-TTTTGTTTTA
*
1797682 TTTATTTATTGTATTTATTTT
1 TTT-TTT-TT-TATTTTTTTT
1797703 ATTTTATTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
26 12 0.18
27 22 0.34
28 6 0.09
29 17 0.26
30 8 0.12
ACGTcount: A:0.15, C:0.01, G:0.04, T:0.80
Consensus pattern (26 bp):
TTTTTTTTTATTTTTTTTTTGTTTTA
Found at i:1797707 original size:27 final size:26
Alignment explanation
Indices: 1797600--1797721 Score: 80
Period size: 28 Copynumber: 4.7 Consensus size: 26
1797590 TATCTTATTT
1797600 TTTTATTTTATTTTATTTATT-TCTATTA
1 TTTTATTTTA-TTTATTTATTGT-T-TTA
* *
1797628 TTTTATTTTTATTTTTTTTTTGTTTTA
1 TTTTA-TTTTATTTATTTATTGTTTTA
1797655 TGTTT-TTTTATTT-TTTATTTTGTTTTA
1 T-TTTATTTTATTTATTTA--TTGTTTTA
1797682 -TTTA-TTTATTGTATTTA---TTTTA
1 TTTTATTTTATT-TATTTATTGTTTTA
*
1797704 TTTTATTATATTATATTT
1 TTTTATTTTATT-TATTT
1797722 CCCTTTTTGA
Statistics
Matches: 79, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
22 5 0.06
23 4 0.05
24 10 0.13
25 12 0.15
26 9 0.11
27 16 0.20
28 17 0.22
29 6 0.08
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTATTTTATTTATTTATTGTTTTA
Found at i:1802154 original size:19 final size:19
Alignment explanation
Indices: 1802130--1802187 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
1802120 TATGGATTAG
*
1802130 GCTATGAATTTGAAAATAA
1 GCTATGAATATGAAAATAA
*
1802149 GCTATGAATATGACAATAA
1 GCTATGAATATGAAAATAA
* * *
1802168 GATATGAGTCTGAAAATAA
1 GCTATGAATATGAAAATAA
1802187 G
1 G
1802188 TCATGAGTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:1802212 original size:19 final size:19
Alignment explanation
Indices: 1802140--1802212 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
1802130 GCTATGAATT
* * *
1802140 TGAAAATAAGCTATGAATA
1 TGAAAATAAGTTATGAGTC
* *
1802159 TGACAATAAGATATGAGTC
1 TGAAAATAAGTTATGAGTC
*
1802178 TGAAAATAAGTCATGAGTC
1 TGAAAATAAGTTATGAGTC
*
1802197 TGGAAAA-ACGTTATGA
1 T-GAAAATAAGTTATGA
1802213 TTTAAAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 39 0.89
20 5 0.11
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (19 bp):
TGAAAATAAGTTATGAGTC
Found at i:1809506 original size:44 final size:44
Alignment explanation
Indices: 1809443--1809532 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
1809433 GAAAGTGTCG
1809443 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
1 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
1809487 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
1 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
1809531 AT
1 AT
1809533 CAGTGACCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (44 bp):
ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
Found at i:1809737 original size:21 final size:21
Alignment explanation
Indices: 1809686--1809738 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1809676 ATTATGACTA
1809686 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1809707 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1809728 TCGCAATGCGA
1 TCGCAATGCGA
1809739 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1809752 original size:82 final size:81
Alignment explanation
Indices: 1809666--1809862 Score: 243
Period size: 81 Copynumber: 2.4 Consensus size: 81
1809656 GTTTCCAGAT
* * *
1809666 TCGCAACGCGATTATGACTATCGCAATGCGATTTTCC-AATTTCGCGTTGCGATTTTCCCAATTC
1 TCGCAATGCGATTATGACTATCGCAATGCGATTTTCCTAA-TTCGCATTGCGA-TTTACCAATTC
*
1809730 GCAATGCGAATAAGTAAA
64 ACAATGCGAATAAGTAAA
* * **
1809748 TCGCAATGCGATAATGACTATCGCAATGCAATTTTCCTAATTCGCATTGCGATTTACGTATTCAC
1 TCGCAATGCGATTATGACTATCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACCAATTCAC
** *
1809813 GTTGCGAATACGTAAA
66 AATGCGAATAAGTAAA
* * *
1809829 TCGCAATGCGAATCTTACTATCGCAATGCGATTT
1 TCGCAATGCGATTATGACTATCGCAATGCGATTT
1809863 ACATAGCGCC
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
81 51 0.52
82 45 0.46
83 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (81 bp):
TCGCAATGCGATTATGACTATCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACCAATTCAC
AATGCGAATAAGTAAA
Found at i:1809838 original size:20 final size:20
Alignment explanation
Indices: 1809815--1809859 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1809805 GTATTCACGT
1809815 TGCGAATACGTA-AATCGCAA
1 TGCGAAT-CGTACAATCGCAA
* *
1809835 TGCGAATCTTACTATCGCAA
1 TGCGAATCGTACAATCGCAA
1809855 TGCGA
1 TGCGA
1809860 TTTACATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TGCGAATCGTACAATCGCAA
Found at i:1809859 original size:40 final size:38
Alignment explanation
Indices: 1809728--1809859 Score: 104
Period size: 40 Copynumber: 3.3 Consensus size: 38
1809718 TTTTCCCAAT
* *
1809728 TCGCAATGCGAATAAGTAAATCGCAATGCGATAATGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAT--TTACTA
* * * *
1809768 TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACGTA
1 TCGCAATGCGAA--TACGTAAATCGCAATGCGATTTAC-TA
* **
1809808 TTCACGTTGCGAATACGTAAATCGCAATGCGAATCTTACTA
1 -TCGCAATGCGAATACGTAAATCGCAATGCG-AT-TTACTA
1809849 TCGCAATGCGA
1 TCGCAATGCGA
1809860 TTTACATAGC
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
39 5 0.07
40 33 0.48
41 25 0.36
42 6 0.09
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (38 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTTACTA
Found at i:1810126 original size:27 final size:27
Alignment explanation
Indices: 1810069--1810121 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1810059 CATCGCCGGC
* *
1810069 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
1810096 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
1810122 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:1810435 original size:19 final size:19
Alignment explanation
Indices: 1810371--1810455 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
1810361 TAGTTTCGAG
1810371 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
1810391 AAT-AACTATCGCAA--CG-
1 AATGAA-AATCGCAACGCGA
*
1810407 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
1810424 AATGAAAATCGCAACGCAA
1 AATGAAAATCGCAACGCGA
**
1810443 AACCAAAATCGCA
1 AATGAAAATCGCA
1810456 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
14 7 0.14
15 2 0.04
16 2 0.04
17 1 0.02
18 2 0.04
19 27 0.53
20 10 0.20
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:1810473 original size:19 final size:19
Alignment explanation
Indices: 1810451--1810582 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
1810441 AAAACCAAAA
*
1810451 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1810470 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1810489 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
**
1810506 T---GTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
1810522 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1810541 TCCGCGTTACGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1810561 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1810581 TC
1 TC
1810583 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 2 0.02
19 51 0.53
20 30 0.31
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1810540 original size:52 final size:53
Alignment explanation
Indices: 1810456--1810557 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
1810446 CAAAATCGCA
** ** *
1810456 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCTTG
1 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTCTTG
1810508 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTC
1810558 ATTATCTCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 30 0.68
53 14 0.32
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.43
Consensus pattern (53 bp):
TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTCTTG
Found at i:1812415 original size:17 final size:17
Alignment explanation
Indices: 1812385--1812417 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1812375 GTTGCTGCCA
1812385 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
1812402 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
1812418 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:1812439 original size:92 final size:90
Alignment explanation
Indices: 1812269--1812454 Score: 266
Period size: 92 Copynumber: 2.0 Consensus size: 90
1812259 TAGATTGCTT
1812269 AGTAAATTTATTCAGTTGCTACCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCAGTTGCTACCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1812334 GTCTTTTTGTTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTTGTCTTTTGGTTGA
* * * * *
1812361 AGTAAATTTATTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCAGTTGCTACCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1812426 ATTTGTCTTT-TTTTTGTCTTTTGGTTGA
62 ATTTGTCTTTGTTTTTGTCTTTTGGTTGA
1812454 A
1 A
1812455 AGTTTGAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
92 32 0.38
93 19 0.22
94 6 0.07
95 2 0.02
96 26 0.31
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (90 bp):
AGTAAATTTATTCAGTTGCTACCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTGTTTTTGTCTTTTGGTTGA
Found at i:1812752 original size:21 final size:21
Alignment explanation
Indices: 1812728--1812794 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1812718 TCATTCCTCG
1812728 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1812749 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1812770 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1812791 AGAG
1 AGAG
1812795 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1812752 original size:42 final size:42
Alignment explanation
Indices: 1812676--1812794 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1812666 GACTCTCCTG
* * * * * * *
1812676 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1812718 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1812760 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1812795 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1814160 original size:14 final size:14
Alignment explanation
Indices: 1814141--1814176 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1814131 ATTGTTTAAT
1814141 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1814155 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1814169 TGATTTGT
1 TGATTTGT
1814177 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1814307 original size:19 final size:19
Alignment explanation
Indices: 1814283--1814398 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
1814273 AAAAAGTACT
*
1814283 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1814302 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
1814316 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1814335 ATCGCAACGCG-AAT----
1 ATCGCAACGCGAAATGAAA
* *
1814349 TTCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1814368 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
1814387 ATCGCAACGCGA
1 ATCGCAACGCGA
1814399 TTTTCATTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
14 19 0.24
15 4 0.05
16 2 0.03
17 2 0.03
18 4 0.05
19 47 0.59
20 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1814377 original size:33 final size:32
Alignment explanation
Indices: 1814283--1814381 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 32
1814273 AAAAAGTACT
*
1814283 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1814316 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
*
1814348 TTTCGCAATGCGAAATGAAAATCGCAACGCGAA
1 -ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1814381 A
1 A
1814382 CTAAAATCGC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 1 0.02
33 61 0.98
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAA
Found at i:1814441 original size:33 final size:32
Alignment explanation
Indices: 1814395--1814513 Score: 168
Period size: 33 Copynumber: 3.6 Consensus size: 32
1814385 AAATCGCAAC
1814395 GCGATTTTCATTTCGCATTGCGATTCCCTCGTT
1 GCGATTTTCATTTCGCATTGCGATT-CCTCGTT
* * *
1814428 GTGATTTTTATTTCGCATTGCGAAATT-CGCGTT
1 GCGATTTTCATTTCGCATTGCG--ATTCCTCGTT
1814461 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTC-CTCGTT
1814494 GCGATTTTCATTTCGCATTG
1 GCGATTTTCATTTCGCATTG
1814514 TGATAGTAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
31 3 0.04
33 70 0.92
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (32 bp):
GCGATTTTCATTTCGCATTGCGATTCCTCGTT
Found at i:1816836 original size:12 final size:12
Alignment explanation
Indices: 1816807--1816844 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1816797 TCTTCGGGGA
1816807 CTTTTTCTTCTTT
1 CTTTTTCTTC-TT
*
1816820 TTTTTTCTTCTT
1 CTTTTTCTTCTT
1816832 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1816844 C
1 C
1816845 AGGATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1817053 original size:24 final size:24
Alignment explanation
Indices: 1817019--1817072 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1817009 CTGAAACATC
*
1817019 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1817043 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1817067 ATCAAA
1 ATCAAA
1817073 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1817979 original size:20 final size:20
Alignment explanation
Indices: 1817890--1817981 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1817880 TGCGAATTTG
* *
1817890 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
1817910 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
1817930 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
1817951 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
1817971 GAAAATCGCAA
1 GAAAATCGCAA
1817982 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:1818220 original size:20 final size:20
Alignment explanation
Indices: 1818195--1818262 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1818185 CAACGGGGAA
1818195 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1818215 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
1818235 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1818255 ATCACAAC
1 ATCGCAAC
1818263 TAGAAAATCG
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 5 0.14
20 25 0.71
21 5 0.14
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1818311 original size:19 final size:18
Alignment explanation
Indices: 1818289--1818356 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
1818279 GAAATGAAAA
1818289 TTGCATTGCGATTTTC--
1 TTGCATTGCGATTTTCAT
*
1818305 -T-CGTTGCGATTTTCAT
1 TTGCATTGCGATTTTCAT
1818321 TTCGCATTGCGATTTTCAT
1 TT-GCATTGCGATTTTCAT
1818340 TTCGCATTGCGATTTTC
1 TT-GCATTGCGATTTTC
1818357 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
17 1 0.02
19 31 0.69
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGCATTGCGATTTTCAT
Found at i:1818313 original size:14 final size:16
Alignment explanation
Indices: 1818293--1818366 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1818283 TGAAAATTGC
1818293 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1818308 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1818325 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1818344 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1818360 -TTGCGAT
1 ATTGCGAT
1818367 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1819957 original size:41 final size:42
Alignment explanation
Indices: 1819912--1820003 Score: 134
Period size: 41 Copynumber: 2.2 Consensus size: 42
1819902 CCTCTTCAAC
*
1819912 GATGACAGTGGCCTCTTGAACG-GTGG-GGGGAACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGG-ACTCTTGAGG
*
1819953 GATGACAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
1819995 AATGACAGG
1 GATGACAGG
1820004 TGAGTCGGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 21 0.46
42 21 0.46
43 4 0.09
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1819970 original size:21 final size:21
Alignment explanation
Indices: 1819938--1820003 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1819928 TGAACGGTGG
1819938 GGGGAACTCTTGAGGGATGACA
1 GGGG-ACTCTTGAGGGATGACA
* ** *
1819960 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGACA
*
1819981 GGGGACTCTTGAGGAATGACA
1 GGGGACTCTTGAGGGATGACA
1820002 GG
1 GG
1820004 TGAGTCGGGC
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
20 2 0.06
21 25 0.76
22 6 0.18
ACGTcount: A:0.24, C:0.15, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGACA
Found at i:1820001 original size:42 final size:41
Alignment explanation
Indices: 1819913--1820003 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 41
1819903 CTCTTCAACG
* *
1819913 ATGACAGTGGCCTCTTGAACGGTGGGGGGAACTCTTGAGGG
1 ATGACAGGGGCCTCTTGAACGGTGGGGGGAACTCTTGAGGA
*
1819954 ATGACAGGGGCCTCTTGAACGATTGGAGGGG-ACTCTTGAGGA
1 ATGACAGGGGCCTCTTGAACG-GTGG-GGGGAACTCTTGAGGA
1819996 ATGACAGG
1 ATGACAGG
1820004 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 20 0.44
42 21 0.47
43 4 0.09
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.21
Consensus pattern (41 bp):
ATGACAGGGGCCTCTTGAACGGTGGGGGGAACTCTTGAGGA
Found at i:1820417 original size:20 final size:20
Alignment explanation
Indices: 1820392--1820437 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1820382 TCACTTCGCA
1820392 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
1820412 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
1820432 TTGCGA
1 TTGCGA
1820438 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1820995 original size:18 final size:18
Alignment explanation
Indices: 1820972--1821019 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1820962 CGGGTCGATC
1820972 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1820990 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1821008 AGGTGATGGCTC
1 AGGTGATGGCTC
1821020 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1822386 original size:20 final size:20
Alignment explanation
Indices: 1822338--1822396 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1822328 AATAGTTTCT
* *
1822338 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1822358 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
1822378 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
1822397 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1822677 original size:22 final size:22
Alignment explanation
Indices: 1822650--1822693 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1822640 GATGGAGATA
1822650 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1822672 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1822694 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1822911 original size:20 final size:20
Alignment explanation
Indices: 1822886--1822972 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
1822876 GTATTATCTC
*
1822886 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
1822906 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
* *
1822926 GTTGTGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
* * *
1822946 GTTGCGATAGTCAGTACCGC
1 GTTGCGAAAGTCAGTATCGA
1822966 GTTGCGA
1 GTTGCGA
1822973 TTTTCCAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:1823007 original size:21 final size:20
Alignment explanation
Indices: 1822983--1823035 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1822973 TTTTCCAAAT
1822983 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
1823004 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
*
1823025 TCACATTGCGA
1 TCGCATTGCGA
1823036 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1823772 original size:182 final size:182
Alignment explanation
Indices: 1823201--1823850 Score: 876
Period size: 183 Copynumber: 3.6 Consensus size: 182
1823191 TATTTTCTCT
* * * * * *
1823201 TTTA-GAATTTAAAAGAAAATAAGTTATAGCGCTTATAAAGTGTCGATACTTTAAAAAAATATAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTT-AAAAAATGTAT
* *
1823265 CGATCCATAATAATATAACAGGTAAAAAAAGGACAAAACAAGTCTAAAAAATGACAAAACTGGTA
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACAGGTCTAAAAAATGACAAAACTGGTA
* *
1823330 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAATATCGACAA
130 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* *
1823383 TTTATGAATTTAAAAGAGAAGAAATTATAGCGCCTAAAACGTGTCGACACTTTAAAAAGATGTAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAA-ATGTAT
* *
1823448 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACATGTCTAAAAAATGACAAAACCGGTA
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACAGGTCTAAAAAATGACAAAACTGGTA
1823513 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
130 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * *
1823566 TTTCTGAATTTAAAAGATAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTTAAAAAATGTAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACAC-TTTAAAAAATGTAT
** * * * * *
1823631 TAATCCATAACAATATAACAAGTAAAAATATGACAAAA-ACGGTCT-CAAAATGACAAAACTAGT
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACA-GGTCTAAAAAATGACAAAACTGGT
* *** * *
1823694 AAAAGGATACTAAATATATTGAAATTGTCAATAATTTAATATAAGTATCGACAC
129 AAAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * * *
1823748 TTTATGAATTTAAAAGAGAAGAAG-TATAACGCCTACAAAGTGACGACACTTTATGAAAATGTAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTA-AAAAATGTAT
* * * * *
1823812 CGATCTATAACAATATAATATGTAAAAATATGACAAAAC
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAAC
1823851 CGGTAAAACG
Statistics
Matches: 417, Mismatches: 45, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
180 4 0.01
181 63 0.15
182 95 0.23
183 247 0.59
184 8 0.02
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (182 bp):
TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAAATGTATC
GATCCATAACAATATAACAGGTAAAAAAAGGACAAAACAGGTCTAAAAAATGACAAAACTGGTAA
AACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
Found at i:1823883 original size:161 final size:162
Alignment explanation
Indices: 1823680--1824016 Score: 428
Period size: 161 Copynumber: 2.1 Consensus size: 162
1823670 CGGTCTCAAA
** * *
1823680 ATGACAAAACTAGTAAAAGGATACTAAATATATTGAAATTGTCAATAATTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAACGATACTAAATATATTGAAATTGTCAATAATTTAATATAAATATCGA
* *
1823745 CACTTTATGAATTTAAAAGAGAAG-AAGTATAACGCCTACAAAGTGACGACAC-TTTATGAAAAT
66 CACTTTATGAATTTAAAAGAGAAGAAAGTATAACGCCTAAAAAGTGACGACACTTTTA-AAAAAT
* * *
1823808 GTATCGATCTATAACAATATAATATGTAAAAAT
130 ATATCGATCTATAACAATATAACAGGTAAAAAT
* * * * *
1823841 ATGACAAAACCGGTAAAACGTTAC-AAGATATGTTGCAATTGTCGATAATTTAATATAAATATTG
1 ATGACAAAACCGGTAAAACGATACTAA-ATATATTGAAATTGTCAATAATTTAATATAAATATCG
* * * * * *
1823905 ACACTTTCTGAATTTAAAAGAGAAGAAATTATAGCGTCTAAAAAGTGTCGATACTTTTAAAAAAT
65 ACACTTTATGAATTTAAAAGAGAAGAAAGTATAACGCCTAAAAAGTGACGACACTTTTAAAAAAT
* *
1823970 ATATCGATTTATAATAATATAACAGGTAAAAAT
130 ATATCGATCTATAACAATATAACAGGTAAAAAT
*
1824003 ATGACAAAATCGGT
1 ATGACAAAACCGGT
1824017 CTCAAAATGA
Statistics
Matches: 150, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
160 2 0.01
161 76 0.51
162 68 0.45
163 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (162 bp):
ATGACAAAACCGGTAAAACGATACTAAATATATTGAAATTGTCAATAATTTAATATAAATATCGA
CACTTTATGAATTTAAAAGAGAAGAAAGTATAACGCCTAAAAAGTGACGACACTTTTAAAAAATA
TATCGATCTATAACAATATAACAGGTAAAAAT
Found at i:1825083 original size:36 final size:36
Alignment explanation
Indices: 1825029--1825164 Score: 211
Period size: 36 Copynumber: 3.8 Consensus size: 36
1825019 GCTGCTGTTG
* *
1825029 GCGTTTCCCAA-CGAGAGGCTGCTGCAGTTGCGGTCA
1 GCGTCTCCCAACCG-GAGGCTGCTGCAGTTGCGGTTA
*
1825065 GCGTCTCCCAACCGGAGGCTGCTGCAGTTGAGGTTA
1 GCGTCTCCCAACCGGAGGCTGCTGCAGTTGCGGTTA
* *
1825101 TCGTCTCCCAACTGGAGGCTGCTGCAGTTGCGGTTA
1 GCGTCTCCCAACCGGAGGCTGCTGCAGTTGCGGTTA
1825137 GCGTCTCCCAACCGGAGGCTGCTGCAGT
1 GCGTCTCCCAACCGGAGGCTGCTGCAGT
1825165 GGGCGTTCGG
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 89 0.98
37 2 0.02
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.23
Consensus pattern (36 bp):
GCGTCTCCCAACCGGAGGCTGCTGCAGTTGCGGTTA
Found at i:1825846 original size:155 final size:152
Alignment explanation
Indices: 1825529--1825841 Score: 466
Period size: 155 Copynumber: 2.0 Consensus size: 152
1825519 ACTCAAATGT
* * *
1825529 CAAATTAAGTCGAATCCAAGTCAAAAACAAATACCCATTTACAATTATTTACTCATTACCACAAC
1 CAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTACAACTATTTACCCATTACCACAAC
*
1825594 CCATATGCATTACATCCAATACTTTACATGTCACCAAATGACCCAAACCATCTTACAAAGTCAAA
66 CCATATACATTACATCCAATACTTTACATGTCACCAAATGACCCAAACCATCTTACAAAGTCAAA
1825659 CTCATAGCCCATTTTTAACCCAA
131 CTCATAGCCCATTTTTAACCC-A
*
1825682 GTCAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTGCAACTATTTACCCATTACCACA
1 --CAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTACAACTATTTACCCATTACCACA
* *
1825747 ACCCATATACATTACATCCGATACTTTACATGTCACCCATGACCAAATGACTC-AACCATCTTAC
64 ACCCATATACATTACATCCAATACTTTACATGT----C---ACCAAATGACCCAAACCATCTTAC
1825811 AAAGTCAAACTCATAGCCCATTTTTAACCCA
122 AAAGTCAAACTCATAGCCCATTTTTAACCCA
1825842 ATTAAACCCA
Statistics
Matches: 144, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
155 90 0.62
159 1 0.01
160 1 0.01
161 41 0.28
162 11 0.08
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.26
Consensus pattern (152 bp):
CAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTACAACTATTTACCCATTACCACAAC
CCATATACATTACATCCAATACTTTACATGTCACCAAATGACCCAAACCATCTTACAAAGTCAAA
CTCATAGCCCATTTTTAACCCA
Found at i:1826260 original size:14 final size:15
Alignment explanation
Indices: 1826241--1826276 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1826231 ATTAAATTTT
*
1826241 AAAAAATGTT-ATAG
1 AAAAAATGTTAAAAG
1826255 AAAAAATGTTAAAAG
1 AAAAAATGTTAAAAG
1826270 AAAAAAT
1 AAAAAAT
1826277 AAAATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (15 bp):
AAAAAATGTTAAAAG
Found at i:1826598 original size:18 final size:18
Alignment explanation
Indices: 1826576--1826618 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1826566 GTTATTTTTA
*
1826576 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
1826594 GAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1826612 AAATAAA
1 AAATAAA
1826619 TAATCTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1828171 original size:8 final size:9
Alignment explanation
Indices: 1828151--1828179 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1828141 TTTAAAATGC
1828151 TTTTAACAT
1 TTTTAACAT
1828160 TTTTAACAT
1 TTTTAACAT
1828169 TTTTAACAT
1 TTTTAACAT
1828178 TT
1 TT
1828180 CTCCCCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAACAT
Found at i:1828790 original size:18 final size:18
Alignment explanation
Indices: 1828769--1828807 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1828759 GCATTTGATA
*
1828769 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
1828787 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
1828805 CTC
1 CTC
1828808 GTGCTGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:1830437 original size:23 final size:23
Alignment explanation
Indices: 1830386--1830469 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1830376 TAGAACCTCC
* *
1830386 AGGGGGTATCGATTCCCC--TAC
1 AGGGGGAATCGATTCCCCTTTAA
*
1830407 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGATTCCCCTTTAA
* *
1830430 AGGGGGAATCGATTTCCCTTCAA
1 AGGGGGAATCGATTCCCCTTTAA
* *
1830453 GGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
1830470 TCTACACCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.31
23 36 0.69
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCCTTTAA
Found at i:1834180 original size:21 final size:21
Alignment explanation
Indices: 1834130--1834181 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1834120 GAAGCTTTAA
*
1834130 GATCATCAATTTTCTTTTGAT
1 GATCATCATTTTTCTTTTGAT
1834151 GATCATCATTTTTCTTTTGAT
1 GATCATCATTTTTCTTTTGAT
1834172 GATCATCATT
1 GATCATCATT
1834182 GAGCTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (21 bp):
GATCATCATTTTTCTTTTGAT
Found at i:1834188 original size:21 final size:21
Alignment explanation
Indices: 1834143--1834188 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1834133 CATCAATTTT
***
1834143 CTTTTGATGATCATCATTTTT
1 CTTTTGATGATCATCATTGAG
1834164 CTTTTGATGATCATCATTGAG
1 CTTTTGATGATCATCATTGAG
1834185 CTTT
1 CTTT
1834189 GAAAGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (21 bp):
CTTTTGATGATCATCATTGAG
Found at i:1837782 original size:270 final size:269
Alignment explanation
Indices: 1837334--1837938 Score: 889
Period size: 270 Copynumber: 2.2 Consensus size: 269
1837324 CGATCCATTG
** *
1837334 GGTATGATATCCTTC-TTCATGAAGTTGAAATTGT-GAGTGGCTCATTCGTTGTGAAGTTGAGCT
1 GGTATGATATCCTTCGTTC-TGAAGTCAAAATCGTAG-GTGGCTCATTCGTTGTGAAGTTGAGCT
* * *
1837397 TTGAACTGAAAAATCCTGAGCACGATATCATTCTTCATGAAGTTGAAATCGGGCTCAAAGCATTG
64 TTGAACTAAAAAATCCTAAGCACGATATCATTCTTCATGAAGTTGAAACCGGGCTCAAAGCATTG
* * *
1837462 GAAAGTCGCTCCTGGATCGTCTTCTAGCCCAATACACTTCGTCGTGAAGCTGAAATTTGACCTGA
129 GAAAGTCACTCCTGGATCGTATTCTAGCCCAATACACTTCGTCGTGAAGCTGAAATTTAACCTGA
*
1837527 AGACTTTGGTATGAAACT-GGTTTTTCATTGTTGTGTTACAGATGACTCATTCGTCGTGAAGTTG
194 AGACCTTGGTATGAAA-TAGGTTTTTCATTGTTGTGTTACAGATGACTCATTCGTCGTGAAG-TG
*
1837591 -GGTAAATCTTTT
257 AGCTAAATCTTTT
*
1837603 GGTATGGTATCCTTCGTTCTGAAGTCAAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTT
1 GGTATGATATCCTTCGTTCTGAAGTCAAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTT
1837668 GAACTAAAAAAATCCTAAGCACGATATTC-TT-TGTCATGAAGTTGAAACCGGGCTCAAAGCATT
66 GAACT-AAAAAATCCTAAGCACGATA-TCATTCT-TCATGAAGTTGAAACCGGGCTCAAAGCATT
* * * *
1837731 GGAAAGTCACTCCTGGATCGTATTCTAGCCCAATATACTTCTTTGTGAAGCTGAACTTTAACCTG
128 GGAAAGTCACTCCTGGATCGTATTCTAGCCCAATACACTTCGTCGTGAAGCTGAAATTTAACCTG
1837796 AAGACCTTGGTATGAAATAGGTTTTTCATTGTTGTGTTACAGATGACTCATTCGTCGTGAAGTGA
193 AAGACCTTGGTATGAAATAGGTTTTTCATTGTTGTGTTACAGATGACTCATTCGTCGTGAAGTGA
*
1837861 GCTCAATCTTTT
258 GCTAAATCTTTT
** * * * *
1837873 GGTTACAATATCCTTCGTTGTGAAGTCAAAATCGTAGGTGGCTCATTTGTTGTGAAATTAAGCTT
1 GG-TATGATATCCTTCGTTCTGAAGTCAAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTT
1837938 T
65 T
1837939 AAATTGGATA
Statistics
Matches: 304, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
269 64 0.21
270 182 0.60
271 58 0.19
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (269 bp):
GGTATGATATCCTTCGTTCTGAAGTCAAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTT
GAACTAAAAAATCCTAAGCACGATATCATTCTTCATGAAGTTGAAACCGGGCTCAAAGCATTGGA
AAGTCACTCCTGGATCGTATTCTAGCCCAATACACTTCGTCGTGAAGCTGAAATTTAACCTGAAG
ACCTTGGTATGAAATAGGTTTTTCATTGTTGTGTTACAGATGACTCATTCGTCGTGAAGTGAGCT
AAATCTTTT
Found at i:1838142 original size:123 final size:123
Alignment explanation
Indices: 1837911--1838152 Score: 279
Period size: 123 Copynumber: 2.0 Consensus size: 123
1837901 AAATCGTAGG
* *
1837911 TGGCTCATTTGTTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
1 TGGCTCATTCGCTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
* * * * * ** *
1837976 CTCGTAAATTGAATCACTTTGAGATTAGTATCTTTTGTTGTGAATTTGAAATTGTGGA
66 CTCGAAAATTGAATCACTCTGAGATTAATACCATTTGCCGTGAAGTTGAAATTGTGGA
* * * * *
1838034 TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAGTTGAAATCCAAT
1 TGGCTCATTCGCTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
* * ** * *
1838099 CTTGAAAATTGCATTGGCTCT-AGTTTAATACCATTTGCCGTGAAGTTGACATTG
66 CTCGAAAATTG-AATCACTCTGAGATTAATACCATTTGCCGTGAAGTTGAAATTG
1838153 ACTCTAACAA
Statistics
Matches: 97, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
123 92 0.95
124 5 0.05
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (123 bp):
TGGCTCATTCGCTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
CTCGAAAATTGAATCACTCTGAGATTAATACCATTTGCCGTGAAGTTGAAATTGTGGA
Found at i:1845323 original size:14 final size:13
Alignment explanation
Indices: 1845306--1845370 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
1845296 ATTAAATTTC
1845306 ATAAAATAAAAATA
1 ATAAAATAAAAA-A
1845320 ATAAAATATAAAAA
1 ATAAAATA-AAAAA
*** *
1845334 A-ATGTTAAAACA
1 ATAAAATAAAAAA
1845346 A-AAAATAGAAAAA
1 ATAAAATA-AAAAA
1845359 ATAAAATAAAAA
1 ATAAAATAAAAA
1845371 GTGGGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
12 8 0.20
13 12 0.30
14 16 0.40
15 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (13 bp):
ATAAAATAAAAAA
Found at i:1845587 original size:18 final size:18
Alignment explanation
Indices: 1845566--1845608 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1845556 GTTGTTTTTA
*
1845566 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1845584 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1845602 AAATAAA
1 AAATAAA
1845609 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1847126 original size:24 final size:24
Alignment explanation
Indices: 1847098--1847177 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
1847088 AAAACTACTG
1847098 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
*
1847122 CGTAGAATATGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
* *
1847146 CATAG-ATTTGTC-CTGAAG-GACCA
1 CGTAGAATTTG-CACCGAAGTG-CCA
1847169 CGTAGAATT
1 CGTAGAATT
1847178 GTCTCGAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 16 0.33
24 31 0.65
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGCACCGAAGTGCCA
Found at i:1847169 original size:23 final size:23
Alignment explanation
Indices: 1847143--1847200 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1847133 CACCGAAGTG
*
1847143 CCACATAGATTTGTC-CTGAAGGA
1 CCACATAGAATTGTCTC-GAAGGA
* *
1847166 CCACGTAGAATTGTCTCGAATGA
1 CCACATAGAATTGTCTCGAAGGA
*
1847189 CCACATAAAATT
1 CCACATAGAATT
1847201 ATTCCGACGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (23 bp):
CCACATAGAATTGTCTCGAAGGA
Found at i:1848388 original size:18 final size:17
Alignment explanation
Indices: 1848362--1848395 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1848352 TAAAATTTTC
1848362 TCACCATGAAAATGGAGT
1 TCACCATG-AAATGGAGT
*
1848380 TCACGATGAAATGGAG
1 TCACCATGAAATGGAG
1848396 AAAAGAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (17 bp):
TCACCATGAAATGGAGT
Found at i:1854015 original size:23 final size:23
Alignment explanation
Indices: 1853989--1854039 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1853979 AAGTGCCACA
* * *
1853989 TAGATTTATCCCGAAGGATCGTG
1 TAGAATTATCCCGAAGGACCGCG
*
1854012 TAGAATTGTCCCGAAGGACCGCG
1 TAGAATTATCCCGAAGGACCGCG
1854035 TAGAA
1 TAGAA
1854040 CCTTTGACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (23 bp):
TAGAATTATCCCGAAGGACCGCG
Found at i:1855543 original size:17 final size:19
Alignment explanation
Indices: 1855516--1855563 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1855506 ATTTTGAAAC
1855516 ATCGAATGCACT-TGA-TGT
1 ATCG-ATGCACTCTGAGTGT
*
1855534 ATCGATGCACTCTTAGTGT
1 ATCGATGCACTCTGAGTGT
*
1855553 ACCGATGCACT
1 ATCGATGCACT
1855564 AAGGGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (19 bp):
ATCGATGCACTCTGAGTGT
Found at i:1857511 original size:21 final size:21
Alignment explanation
Indices: 1857486--1857525 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1857476 ATAAGACTAT
1857486 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
1857507 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1857526 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:1861263 original size:24 final size:24
Alignment explanation
Indices: 1861236--1861316 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1861226 ACACTTAACA
1861236 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
1861260 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
1861282 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
1861304 GTGCATCGATGCA
1 GTGCATCGATGCA
1861317 CGGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:1862632 original size:21 final size:21
Alignment explanation
Indices: 1862590--1862633 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1862580 ACTCCGGGAG
* *
1862590 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1862611 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1862632 CT
1 CT
1862634 CCTCCGGTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1863871 original size:17 final size:19
Alignment explanation
Indices: 1863843--1863891 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1863833 TATTTTGAAA
1863843 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1863861 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1863880 CACCGATGCACT
1 CATCGATGCACT
1863892 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1866342 original size:5 final size:5
Alignment explanation
Indices: 1866332--1866375 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
1866322 TATTTAATTC
* * *
1866332 TTTAG TTTAG TTTAG TTTAG TTTAG TTTTG TTTAT TTTAT TTTA
1 TTTAG TTTAG TTTAG TTTAG TTTAG TTTAG TTTAG TTTAG TTTA
1866376 TTCTTTTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (5 bp):
TTTAG
Found at i:1871414 original size:20 final size:22
Alignment explanation
Indices: 1871369--1871426 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
1871359 GCATGAGTAG
1871369 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1871393 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
* *
1871413 TGTACCGATGCACT
1 TGCATCGATGCACT
1871427 TCAATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 2 0.06
24 13 0.41
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1873039 original size:23 final size:24
Alignment explanation
Indices: 1872980--1873040 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
1872970 ACATCGTAAA
1872980 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTACGGTGCAATTTCTACG
* * * *
1873003 CGGAACTTCAGTGCAATTT-TACG
1 TGGCACTACGGTGCAATTTCTACG
*
1873026 TGGCACTCCGGTGCA
1 TGGCACTACGGTGCA
1873041 TTTATATAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (24 bp):
TGGCACTACGGTGCAATTTCTACG
Found at i:1875364 original size:20 final size:22
Alignment explanation
Indices: 1875319--1875380 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
1875309 GCATGAGTAG
1875319 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1875343 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
* *
1875363 TGTACCGATGCACT-TTAA
1 TGCATCGATGCACTGTTAA
1875381 TGGGAAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1880256 original size:20 final size:22
Alignment explanation
Indices: 1880211--1880268 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
1880201 GCATGAGTAG
1880211 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1880235 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
* *
1880255 TGTACCGATGCACT
1 TGCATCGATGCACT
1880269 TCAATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 2 0.06
24 13 0.41
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Done.