Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008314.1 Hibiscus syriacus cultivar Beakdansim tig00111008_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: 2414839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1653124 original size:18 final size:17
Alignment explanation
Indices: 1653092--1653133 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
1653082 AATTGAATTT
*
1653092 CAATTCATGACAGATTC
1 CAATTCCTGACAGATTC
1653109 CAATTCCTGAACAGATTC
1 CAATTCCTG-ACAGATTC
1653127 CAATTCC
1 CAATTCC
1653134 CTTAGAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (17 bp):
CAATTCCTGACAGATTC
Found at i:1657118 original size:36 final size:36
Alignment explanation
Indices: 1657050--1657251 Score: 184
Period size: 36 Copynumber: 5.5 Consensus size: 36
1657040 TGAAAATACG
* *
1657050 TATATAATATATATGGTTTTTAAAACACTTTTAAAAAC
1 TATATAATATATAT-ATTTTAAAAACA-TTTTAAAAAC
* *
1657088 TATATATTATATATATTTTCAAAACATTTTAAAATA-
1 TATATAATATATATATTTTAAAAACATTTTAAAA-AC
1657124 TATATAATATATA-ATTTTTGAAAAACATTTTAAAAA-
1 TATATAATATATATA-TTTT-AAAAACATTTTAAAAAC
*
1657160 TATATAATATATA-ATTTTTGAAAAACATTTTGAAAAC
1 TATATAATATATATA-TTTT-AAAAACATTTTAAAAAC
* * * *
1657197 -ATATAATATATA-ATTTTTAGAGCATTTTTGAAAAC
1 TATATAATATATATATTTTAAAAACA-TTTTAAAAAC
1657232 T-TATATATAATATATATTTT
1 TATATA-AT-ATATATATTTT
1657252 TTTTAAAATA
Statistics
Matches: 146, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
34 4 0.03
35 19 0.13
36 75 0.51
37 30 0.21
38 18 0.12
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATAATATATATATTTTAAAAACATTTTAAAAAC
Found at i:1657134 original size:72 final size:73
Alignment explanation
Indices: 1657050--1657251 Score: 225
Period size: 72 Copynumber: 2.8 Consensus size: 73
1657040 TGAAAATACG
* *
1657050 TATATAATATATATGGTTTTTAAAACACTTTTAAAAACTATATATTATATATATTTT-CAAAACA
1 TATATAATATATA--ATTTTTAAAACACTTTTAAAAACTATATATTATATATATTTTGAAAAACA
1657114 TTTTAAAATA
64 TTTTAAAATA
*
1657124 TATATAATATATAATTTTTGAAAA-ACATTTTAAAAA-TATATAATATATA-ATTTTTGAAAAAC
1 TATATAATATATAATTTTT-AAAACAC-TTTTAAAAACTATATATTATATATA-TTTTGAAAAAC
*
1657186 ATTTTGAAA-A
63 ATTTTAAAATA
* * * * * *
1657196 CATATAATATATAATTTTTAGAGCATTTTTGAAAACTTATATATAATATATATTTT
1 TATATAATATATAATTTTTAAAACACTTTTAAAAAC-TATATATTATATATATTTT
1657252 TTTTAAAATA
Statistics
Matches: 109, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
71 11 0.10
72 43 0.39
73 41 0.38
74 14 0.13
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (73 bp):
TATATAATATATAATTTTTAAAACACTTTTAAAAACTATATATTATATATATTTTGAAAAACATT
TTAAAATA
Found at i:1657285 original size:32 final size:31
Alignment explanation
Indices: 1657242--1657343 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 31
1657232 TTATATATAA
* * *
1657242 TATATATTTTTTTTAAAATATTTTTAAAAAAT
1 TATATAATTTTTTAAAAACATTTTT-AAAAAT
*
1657274 TATATAATTTTTAAAAGAACATTTTTAAAAAT
1 TATATAATTTTTTAAA-AACATTTTTAAAAAT
* *
1657306 TAT-TAGTTTTTTGAAAAACATTTTTGAAAATT
1 TATATAATTTTTT-AAAAACATTTTT-AAAAAT
1657338 TATATA
1 TATATA
1657344 TAGTATATAG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
31 16 0.27
32 33 0.56
33 10 0.17
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (31 bp):
TATATAATTTTTTAAAAACATTTTTAAAAAT
Found at i:1657412 original size:13 final size:13
Alignment explanation
Indices: 1657394--1657419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1657384 ATATTATATA
1657394 GTTTTTATTTATT
1 GTTTTTATTTATT
1657407 GTTTTTATTTATT
1 GTTTTTATTTATT
1657420 ATTATTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTATTTATT
Found at i:1658934 original size:29 final size:27
Alignment explanation
Indices: 1658894--1658956 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
1658884 TCTTTTCCTC
* *
1658894 TTTTTTCTTTTGTATTTATT-TTGATTTA
1 TTTTTT-TTTT-TGTTTATTATTGAATTA
1658922 TTTTTTTTATTTGTTTATTATTGAATTA
1 TTTTTTTT-TTTGTTTATTATTGAATTA
*
1658950 TCTTTTT
1 TTTTTTT
1658957 AACATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.75
Consensus pattern (27 bp):
TTTTTTTTTTTGTTTATTATTGAATTA
Found at i:1660732 original size:18 final size:19
Alignment explanation
Indices: 1660711--1660756 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1660701 TATTTAGACA
1660711 TTTTGCATTTT-TTATTTT
1 TTTTGCATTTTGTTATTTT
1660729 TTTTGCATTTTGTTATTTT
1 TTTTGCATTTTGTTATTTT
*
1660748 CTTTGCATT
1 TTTTGCATT
1660757 CACATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.72
Consensus pattern (19 bp):
TTTTGCATTTTGTTATTTT
Found at i:1664322 original size:84 final size:83
Alignment explanation
Indices: 1664149--1664910 Score: 790
Period size: 84 Copynumber: 9.2 Consensus size: 83
1664139 TTTAAAACAA
* * * * *
1664149 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTA
* * *
1664214 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
*
1664233 ATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACT
*
1664298 ACGCTCAGCTCCAAGGCAT
65 ACGCTCAGCTCCAAGGCAC
* * * * * * *
1664317 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACT
1664382 ACGCTCAGCT-CAACGGCAC
65 ACGCTCAGCTCCAA-GGCAC
* * ** *
1664401 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTA
1664463 CGCTCAGCT-CAACGGCAC
66 CGCTCAGCTCCAA-GGCAC
* * * ** * *
1664481 ATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCA--AAAGACCACCAAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTA
* * *
1664544 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* *
1664563 ATCATTCGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACT
*
1664628 ACGCTCAGCTCCAAGGCAT
65 ACGCTCAGCTCCAAGGCAC
* * * * * * *
1664647 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-GCCACCAAAGACCTTCGAGTTCGACT
*
1664712 ACGCTCAGCT-CAACGGTAC
65 ACGCTCAGCTCCAA-GGCAC
* * * ** *
1664731 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTA
* * *
1664793 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* * * * *** *
1664812 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACT
*
1664877 ACGCTCAACTCCAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
*
1664896 ATCATTTACAGCATA
1 ATCATTTGCAGCATA
1664911 GCTCAAGGTA
Statistics
Matches: 567, Mismatches: 93, Indels: 36
0.81 0.13 0.05
Matches are distributed among these distances:
80 97 0.17
81 62 0.11
82 43 0.08
83 9 0.02
84 277 0.49
85 79 0.14
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (83 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCAC
Found at i:1664801 original size:330 final size:333
Alignment explanation
Indices: 1664149--1664863 Score: 1175
Period size: 330 Copynumber: 2.2 Consensus size: 333
1664139 TTTAAAACAA
* * * ** *
1664149 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCACAAAAGACCACCAAGTTCGATTA
* *
1664214 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACCA
66 CACTCAGCTTCGAGGGCACATCATTCGCAGCATAACTTAAGCCGAGAAAGGTTATCTGCCAACCA
*
1664279 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAG
131 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAG
1664344 AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCATTTG
196 AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCATTTG
*
1664409 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGC-TC
261 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
1664473 AACGGCAC
326 AACGGCAC
* * * *
1664481 ATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTG-C-CAAAAGACCACCAAGTTCGATTA
1 ATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCACAAAAGACCACCAAGTTCGATTA
*
1664544 CACTCAGCTTCGAGGGCACATCATTCGCAGCATAACTTAAGCCGAGAAGGGTTATCTGCCAACCA
66 CACTCAGCTTCGAGGGCACATCATTCGCAGCATAACTTAAGCCGAGAAAGGTTATCTGCCAACCA
1664609 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAG
131 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAG
* *
1664674 AAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGTACATCATTTG
196 AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCATTTG
*
1664739 CAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
261 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
* *
1664804 GAGGGCAC
326 AACGGCAC
* * * * *
1664812 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACC
1 ATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCA-CAAAAGACC
1664864 TTTGAGTTCG
Statistics
Matches: 350, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
330 268 0.77
331 40 0.11
332 33 0.09
334 9 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (333 bp):
ATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGTCACAAAAGACCACCAAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTCGCAGCATAACTTAAGCCGAGAAAGGTTATCTGCCAACCA
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAG
AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCATTTG
CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
AACGGCAC
Found at i:1664863 original size:249 final size:247
Alignment explanation
Indices: 1664149--1664910 Score: 933
Period size: 249 Copynumber: 3.1 Consensus size: 247
1664139 TTTAAAACAA
* * *
1664149 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGGCA-CAAAGACCTTCGAGTTCGATTA
* * * * *
1664214 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACCA
65 CGCTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTG----CCA
** * * * * ** * *
1664279 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTA
125 AAGACCACCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGCCTA
* * *
1664343 GAAGGGTTGTCTGCCAA-CAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCAC
190 GAAGGGTTATCT-ACAACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCAC
* * * **
1664401 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-GC-CAAAGACCCCCGAGTTCGATTAC
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGGCACAAAGACCTTCGAGTTCGATTAC
*
1664464 GCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAAAAGAC
66 GCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCC-AAAGAC
* * *
1664529 CACCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTCGCAGCATAACTTAAGCCGAGAAGG
130 CACCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGCCTAGAAGG
* * *
1664594 GTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
195 GTTATCT-ACAACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * * *
1664647 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGGC-AC-AAAGACCTTCGAGTTCGATT
* * *
1664712 ACGCTCAGCTCAACGGTACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
64 ACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCCAAAGA
* * * *
1664777 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
129 CCACCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGCCTAGAAG
** *
1664842 GGTTATCTATGACCAAAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGCAC
194 GGTTATCTACAACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
1664896 ATCATTTACAGCATA
1 ATCATTTGCAGCATA
1664911 GCTCAAGGTA
Statistics
Matches: 442, Mismatches: 59, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
244 2 0.00
245 24 0.05
246 109 0.25
247 6 0.01
248 47 0.11
249 148 0.33
250 72 0.16
251 1 0.00
252 33 0.07
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (247 bp):
ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGGCACAAAGACCTTCGAGTTCGATTAC
GCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTGCCAAAGACC
ACCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGCCTAGAAGGG
TTATCTACAACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
Found at i:1665629 original size:75 final size:74
Alignment explanation
Indices: 1665534--1665768 Score: 246
Period size: 75 Copynumber: 3.1 Consensus size: 74
1665524 TGAAAATACG
* *
1665534 TATATAATATATATGGTTTTTAAAACACTTTTAAAAACTATATATTATATATATATTTTCAAAAC
1 TATATAATATATA--ATTTTTAAAACACTTTTAAAAACTATATATTATATATAT-TTTTAAAAAC
1665599 ATTTTTAAAAAA
63 ATTTTTAAAAAA
*
1665611 TATATAATATATAATTTTTGAAAA-ACATTTTAAAAA-TATATAATATATA-ATTTTTGAAAAAC
1 TATATAATATATAATTTTT-AAAACAC-TTTTAAAAACTATATATTATATATATTTTT-AAAAAC
*
1665673 A-TTTT-GAAAA
63 ATTTTTAAAAAA
* * * * * * *
1665683 CATATAATATATAATTTTTAGAGCATTTTTGAAAACTTATATATAATATATAATTTTTTTAAAAC
1 TATATAATATATAATTTTTAAAACACTTTTAAAAAC-TATATATTATATAT-A-TTTTTAAAAAC
1665748 ATTTTTAAAAAA
63 ATTTTTAAAAAA
1665760 TTATATAAT
1 -TATATAAT
1665769 TTTTAAAAGA
Statistics
Matches: 132, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
71 10 0.08
72 23 0.17
73 19 0.14
74 8 0.06
75 26 0.20
76 22 0.17
77 17 0.13
78 7 0.05
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (74 bp):
TATATAATATATAATTTTTAAAACACTTTTAAAAACTATATATTATATATATTTTTAAAAACATT
TTTAAAAAA
Found at i:1665646 original size:36 final size:36
Alignment explanation
Indices: 1665534--1665850 Score: 241
Period size: 36 Copynumber: 8.7 Consensus size: 36
1665524 TGAAAATACG
* *
1665534 TATATAATATAT-ATGGTTTTTAAAACACTTTTAAAAA
1 TATATAATATATAAT--TTTTAAAAACATTTTTAAAAA
* *
1665571 CTATATATTATATATATATTTTCAAAACATTTTTAAAAAA
1 -TATATAATATATA-AT-TTTTAAAAACATTTTT-AAAAA
1665611 TATATAATATATAATTTTTGAAAAACA-TTTTAAAAA
1 TATATAATATATAATTTTT-AAAAACATTTTTAAAAA
*
1665647 TATATAATATATAATTTTTGAAAAACA-TTTTGAAAA
1 TATATAATATATAATTTTT-AAAAACATTTTTAAAAA
* * *
1665683 CATATAATATATAATTTTT-AGAGCATTTTTGAAAACTTA
1 TATATAATATATAATTTTTAAAAACATTTTT-AAAA---A
*
1665722 TATATAATATATAATTTTTTTAAAACATTTTT-AAAA
1 TATATAATATATAA-TTTTTAAAAACATTTTTAAAAA
1665758 -A-AT--TATATAATTTTTAAAAGAACATTTTTAAAAA
1 TATATAATATATAATTTTT-AAA-AACATTTTTAAAAA
*
1665792 T-TAT--TAGT-T--TTTTGAAAAACATTTTTGAAAATGTA
1 TATATAATA-TATAATTTTTAAAAACATTTTT-AAAA---A
* *
1665827 TATATAGTATATAGTTTTTAAAAA
1 TATATAATATATAATTTTTAAAAA
1665851 AATAAACAGT
Statistics
Matches: 235, Mismatches: 17, Indels: 52
0.77 0.06 0.17
Matches are distributed among these distances:
31 14 0.06
32 16 0.07
33 13 0.06
34 10 0.04
35 12 0.05
36 66 0.28
37 9 0.04
38 22 0.09
39 43 0.18
40 21 0.09
41 9 0.04
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (36 bp):
TATATAATATATAATTTTTAAAAACATTTTTAAAAA
Found at i:1665770 original size:32 final size:31
Alignment explanation
Indices: 1665729--1665830 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 31
1665719 TTATATATAA
*
1665729 TATATAATTTTTTTAAAACATTTTTAAAAAAT
1 TATATAATTTTTTAAAAACATTTTT-AAAAAT
*
1665761 TATATAATTTTTAAAAGAACATTTTTAAAAAT
1 TATATAATTTTTTAAA-AACATTTTTAAAAAT
* *
1665793 TAT-TAGTTTTTTGAAAAACATTTTTGAAAAT
1 TATATAATTTTTT-AAAAACATTTTTAAAAAT
1665824 GTATATA
1 -TATATA
1665831 TAGTATATAG
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
31 21 0.34
32 29 0.48
33 11 0.18
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (31 bp):
TATATAATTTTTTAAAAACATTTTTAAAAAT
Found at i:1665899 original size:13 final size:13
Alignment explanation
Indices: 1665881--1665906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1665871 ATATTATATA
1665881 GTTTTTATTTATT
1 GTTTTTATTTATT
1665894 GTTTTTATTTATT
1 GTTTTTATTTATT
1665907 ATTATTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTATTTATT
Found at i:1667198 original size:15 final size:15
Alignment explanation
Indices: 1667162--1667197 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1667152 TACTATTTTC
1667162 TTTTTTTCATTATCA
1 TTTTTTTCATTATCA
*
1667177 TTTTTTTCTTTAT-A
1 TTTTTTTCATTATCA
1667191 TTTTTTT
1 TTTTTTT
1667198 TAAAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTCATTATCA
Found at i:1667280 original size:12 final size:13
Alignment explanation
Indices: 1667211--1667277 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 13
1667201 AAAAATCCAA
1667211 TTTTTATTTATCATT
1 TTTTTATTT-T-ATT
*
1667226 TTTTTCTATTTA-T
1 TTTTTAT-TTTATT
1667239 TTTTTATTTTATT
1 TTTTTATTTTATT
1667252 TTTAAGCTTATTTTATT
1 TTT----TTATTTTATT
1667269 TTTTTATTT
1 TTTTTATTT
1667278 ATTCTTTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
12 4 0.09
13 17 0.39
14 1 0.02
15 7 0.16
16 2 0.05
17 13 0.30
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:1668039 original size:14 final size:14
Alignment explanation
Indices: 1668007--1668042 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1667997 AGATTTTTAC
*
1668007 GCAGAGATTTATTT
1 GCAGGGATTTATTT
1668021 GCAGGGATTTATTT
1 GCAGGGATTTATTT
1668035 GCAGGGAT
1 GCAGGGAT
1668043 CACTCCCCAT
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:0.25, C:0.08, G:0.31, T:0.36
Consensus pattern (14 bp):
GCAGGGATTTATTT
Found at i:1672856 original size:18 final size:18
Alignment explanation
Indices: 1672812--1672877 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
1672802 GAACACCCTC
*
1672812 AAAATTTTATATTCTATAT
1 AAAATTTTATTTTCTAT-T
***
1672831 ATTTTTTTATTTTCTATT
1 AAAATTTTATTTTCTATT
* *
1672849 GAAATTTTATTTTTCTTTT
1 AAAATTTTA-TTTTCTATT
1672868 AAAATTTTAT
1 AAAATTTTAT
1672878 AAGTTCGTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
18 7 0.19
19 29 0.81
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (18 bp):
AAAATTTTATTTTCTATT
Found at i:1672876 original size:19 final size:19
Alignment explanation
Indices: 1672835--1672877 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1672825 CTATATATTT
*
1672835 TTTTA-TTTTCTATTGAAA
1 TTTTATTTTTCTATTAAAA
*
1672853 TTTTATTTTTCTTTTAAAA
1 TTTTATTTTTCTATTAAAA
1672872 TTTTAT
1 TTTTAT
1672878 AAGTTCGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATTTTTCTATTAAAA
Found at i:1678824 original size:2 final size:2
Alignment explanation
Indices: 1678817--1678858 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1678807 ATAAAATCTT
1678817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1678859 AAGAAGGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1693812 original size:19 final size:19
Alignment explanation
Indices: 1693788--1693826 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1693778 TCGAATGCAT
1693788 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1693807 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1693826 T
1 T
1693827 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1693928 original size:64 final size:63
Alignment explanation
Indices: 1693725--1693934 Score: 226
Period size: 65 Copynumber: 3.3 Consensus size: 63
1693715 TATTCAAAGG
* * * * *
1693725 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAATTAATT-GAACATCGAATGCATT
1 CATGCACCGATGCA-CAATCCATGCATCGATGCATC-AGGTATT-TTTCAAACATCGAATGCATT
*
1693789 C
63 T
** * *
1693790 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAATATTTTCAAAACATCGAATGCATT
1 CATGCACCGATGCACAATCCATGCATCGATGCA-TCAGGTAT-TTTTC-AAACATCGAATGCATT
1693854 T
63 T
* *
1693855 GATGCATCGATGCACAATCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACAATCCATGCATCGATGCATCAGG-TATTTTTCAAACATCGAATGCATTT
*
1693919 CATGCATCGATGCACA
1 CATGCACCGATGCACA
1693935 CTTGGTGCAC
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 66 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACAATCCATGCATCGATGCATCAGGTATTTTTCAAACATCGAATGCATTT
Found at i:1693949 original size:64 final size:64
Alignment explanation
Indices: 1693725--1693954 Score: 234
Period size: 64 Copynumber: 3.6 Consensus size: 64
1693715 TATTCAAAGG
* * * *
1693725 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
1693787 TTC
62 TTT
* * *
1693790 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* * **
1693855 GATGCATCGATGCACAATCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
1693919 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1693955 AGTGTTCCAA
Statistics
Matches: 141, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
63 6 0.04
64 70 0.50
65 65 0.46
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1701367 original size:21 final size:21
Alignment explanation
Indices: 1701325--1701368 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1701315 ACCCCGGGAG
*
1701325 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1701346 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1701367 CT
1 CT
1701369 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1702433 original size:19 final size:19
Alignment explanation
Indices: 1702409--1702447 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1702399 TCGAATGCAT
1702409 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1702428 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1702447 T
1 T
1702448 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1702549 original size:64 final size:63
Alignment explanation
Indices: 1702346--1702555 Score: 226
Period size: 65 Copynumber: 3.3 Consensus size: 63
1702336 TATTCAAAGG
* * * * *
1702346 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAATTAATT-GAACATCGAATGCATT
1 CATGCACCGATGCA-CAATCCATGCATCGATGCATC-AGGTATT-TTTCAAACATCGAATGCATT
*
1702410 C
63 T
** * *
1702411 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAATATTTTCAAAACATCGAATGCATT
1 CATGCACCGATGCACAATCCATGCATCGATGCA-TCAGGTAT-TTTTC-AAACATCGAATGCATT
1702475 T
63 T
* *
1702476 GATGCATCGATGCACAATCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACAATCCATGCATCGATGCATCAGG-TATTTTTCAAACATCGAATGCATTT
*
1702540 CATGCATCGATGCACA
1 CATGCACCGATGCACA
1702556 CTTGGTGCAC
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 66 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACAATCCATGCATCGATGCATCAGGTATTTTTCAAACATCGAATGCATTT
Found at i:1702570 original size:64 final size:64
Alignment explanation
Indices: 1702346--1702575 Score: 234
Period size: 64 Copynumber: 3.6 Consensus size: 64
1702336 TATTCAAAGG
* * * *
1702346 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
1702408 TTC
62 TTT
* * *
1702411 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* * **
1702476 GATGCATCGATGCACAATCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
1702540 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1702576 AGTGTTCCAA
Statistics
Matches: 141, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
63 6 0.04
64 70 0.50
65 65 0.46
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1709191 original size:108 final size:106
Alignment explanation
Indices: 1709042--1709365 Score: 298
Period size: 108 Copynumber: 3.0 Consensus size: 106
1709032 CATATATATC
* ** * *
1709042 TATATTATATAGTTTGCAAATGGTTTTTGAAAATATATATA-TATATA-TAATATA-ATTTTGAA
1 TATATTATATAGTTTTCAAAACGTTTTTGAAAACATATATATTATATATTAA-AAACATTTTG-A
* *
1709104 AACATTTATATATTATATAGTTTTCTAAAACGTTTTTG-AAA-ATAAA
64 AA-A--TATATAATATATAGTTTT-TAAAAC-ATTTTGAAAACATAAA
* * *
1709150 TATAATATATAGTTTTCAAAACATTTTTGAAAACATGTATATTATATAGTTTAAAAACATTTTGA
1 TATATTATATAGTTTTCAAAACGTTTTTGAAAACATATATATTATATA--TTAAAAACATTTTGA
**
1709215 AAATATATAATATATAGTTTTTAAAACATTTTGAAAACATTTA
64 AAATATATAATATATAGTTTTTAAAACATTTTGAAAACATAAA
* * * * *
1709258 TATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAAATATAATATATAGTTTTTAAAACATTT
1 TATATTATATAG-TTTTCAAAACGTTTTTGAAAA-CATATAT-AT-TATA-TATTAAAAACA-TT
* *
1709323 TTGAATATATATATTATATAGTTTTTAAAACATTTTAGAAAAC
60 TTGAAAATATATAATATATAGTTTTTAAAACATTTT-GAAAAC
1709366 TATGTAATTT
Statistics
Matches: 180, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
106 5 0.03
107 9 0.05
108 65 0.36
109 25 0.14
110 5 0.03
111 15 0.08
112 49 0.27
113 7 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (106 bp):
TATATTATATAGTTTTCAAAACGTTTTTGAAAACATATATATTATATATTAAAAACATTTTGAAA
ATATATAATATATAGTTTTTAAAACATTTTGAAAACATAAA
Found at i:1709254 original size:146 final size:148
Alignment explanation
Indices: 1709096--1709373 Score: 456
Period size: 146 Copynumber: 1.9 Consensus size: 148
1709086 ATATAATATA
1709096 ATTTTGAAAACATTTATATATTATATAGTTTTCTAAAACGTTTTTGAAAAT-AAATATAATATAT
1 ATTTTGAAAACATTTATATATTATATAGTTTTCTAAAACGTTTTTGAAAATAAAATATAATATAT
*
1709160 AGTTTTCAAAACATTTTTGAAAACATGTATATTATATAG-TTTAAAAACATTTT-GAAAA-TATA
66 AGTTTTCAAAACATTTTTG--AACATATATATTATATAGTTTTAAAAACATTTTAGAAAACTATA
1709222 TAATATATAGTTTTTAAAAC
129 TAATATATAGTTTTTAAAAC
*
1709242 ATTTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAAATATAATATAT
1 ATTTTGAAAACATTTATATATTATATAGTTTTCTAAAACGTTTTTGAAAATAAAATATAATATAT
* * * *
1709307 AGTTTTTAAAACATTTTTGAATATATATATTATATAGTTTTTAAAACATTTTAGAAAACTATGTA
66 AGTTTTCAAAACATTTTTGAACATATATATTATATAGTTTTAAAAACATTTTAGAAAACTATATA
1709372 AT
131 AT
1709374 TTTGAAAATA
Statistics
Matches: 122, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
145 16 0.13
146 63 0.52
147 36 0.30
148 7 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (148 bp):
ATTTTGAAAACATTTATATATTATATAGTTTTCTAAAACGTTTTTGAAAATAAAATATAATATAT
AGTTTTCAAAACATTTTTGAACATATATATTATATAGTTTTAAAAACATTTTAGAAAACTATATA
ATATATAGTTTTTAAAAC
Found at i:1709428 original size:34 final size:36
Alignment explanation
Indices: 1709370--1709447 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
1709360 GAAAACTATG
*
1709370 TAATTTTGAAAATATTTTTTAAAAATATATAATATA
1 TAATTTTGAAAATAGTTTTTAAAAATATATAATATA
*
1709406 TAATTTT-AAAAT-GTTTTTAAAAATATATATTATA
1 TAATTTTGAAAATAGTTTTTAAAAATATATAATATA
1709440 TAGATTTT
1 TA-ATTTT
1709448 TGGAAAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
34 22 0.56
35 10 0.26
36 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (36 bp):
TAATTTTGAAAATAGTTTTTAAAAATATATAATATA
Found at i:1710738 original size:27 final size:26
Alignment explanation
Indices: 1710698--1710780 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 26
1710688 CTTATATATA
1710698 TATATATATTTTAT-TTATTTCTTTATT
1 TATATATATTTTATATTATTT-TTTA-T
*
1710725 TTTATATATTTTATGATT-TTTTTTAT
1 TATATATATTTTAT-ATTATTTTTTAT
*
1710751 TATATATATTCTATATTATTTTTTAAT
1 TATATATATTTTATATTATTTTTT-AT
1710778 TAT
1 TAT
1710781 TTTCTACTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.06
26 19 0.39
27 22 0.45
28 3 0.06
29 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (26 bp):
TATATATATTTTATATTATTTTTTAT
Found at i:1710983 original size:6 final size:6
Alignment explanation
Indices: 1710967--1710997 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1710957 TCAAATCGGG
*
1710967 TAATTT AAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT T
1710998 CGCAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TAATTT
Found at i:1712695 original size:19 final size:19
Alignment explanation
Indices: 1712671--1712716 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1712661 ATTTAGACAT
1712671 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1712690 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1712709 TTTGCATT
1 TTTGCATT
1712717 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:1716343 original size:84 final size:82
Alignment explanation
Indices: 1716076--1717014 Score: 929
Period size: 84 Copynumber: 11.4 Consensus size: 82
1716066 CTTAAGACAA
* * *
1716076 CATTTGCAGCAT-GACTTAAGTTGAGAAGTGTTATCTACCAACCAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAG-CTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTA
* *
1716140 CATTCAACTACAAGGCACAT
64 CACTCAGCT-CAAGGCACAT
* * *
1716160 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
* *
1716222 CTCAGCTTTGAGGGCACAT
66 CTCAGC--TCAAGGCACAT
* * * * * * * *
1716241 CATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAATAAAAGACCTTTGAGTTTGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
*
1716306 GCTCAGCTCAATGGCACAT
65 ACTCAGCTCAA-GGCACAT
* ** * *
1716325 CATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG-C--CAAAGACCCCCGAGTTTGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
* * *
1716387 CTCAGCTTTGAGGGCACGT
66 CTCAGC--TCAAGGCACAT
* * * * * *
1716406 CATTTGCAGTATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
*
1716471 TCTCAGCTCAACGGCACAT
65 ACTCAGCTCAA-GGCACAT
* ** *
1716490 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
* *
1716552 CTCAGCTTCGAGGGCACGT
66 CTCAGC-TC-AAGGCACAT
*
1716571 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
1716636 ACTCAGCTCCAAGGCACAT
65 ACTCAGCT-CAAGGCACAT
* * ** *
1716655 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATG-C--CAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
* *
1716717 CTCAGCTTCGAGGGCACGT
66 CTCAGC-TC-AAGGCACAT
*
1716736 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
1716801 ACTCAGCTCCAAGGCACAT
65 ACTCAGCT-CAAGGCACAT
* * ** * * *
1716820 CATTTGCAGCACAACTTAAGTCTTGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
*
1716885 GCTCAGCTCCAAGGCACAT
65 ACTCAGCT-CAAGGCACAT
* * ** *
1716904 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
* * *
1716966 CTCAACTTCGAGGTCATAT
66 CTCAGC-TCAAGG-CACAT
* * * * *
1716985 CATTTACAACATAGCTCAAGGCAAGAAGGG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGG
1717015 CTATTGGTCA
Statistics
Matches: 708, Mismatches: 115, Indels: 67
0.80 0.13 0.08
Matches are distributed among these distances:
80 129 0.18
81 193 0.27
82 8 0.01
83 10 0.01
84 263 0.37
85 105 0.15
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (82 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACA
CTCAGCTCAAGGCACAT
Found at i:1716362 original size:165 final size:165
Alignment explanation
Indices: 1716076--1717018 Score: 1243
Period size: 165 Copynumber: 5.7 Consensus size: 165
1716066 CTTAAGACAA
* * * * *
1716076 CATTTGCAGCATGACTTAAGTTGAGAAGTGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
* * *
1716141 ATTCAACTACAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
1716206 CTCGAGTTCGATTACACTCAGCTTTGAGGGCACAT
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
* * * * * * *
1716241 CATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAATAAAAGACCTTTGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
* *
1716306 GCTCAGCT-CAATGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGAC
66 ACTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
1716370 CCCCGAGTTTGATTACACTCAGCTTTGAGGGCACGT
130 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
* * * * *
1716406 CATTTGCAGTATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
*
1716471 TCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 ACTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
1716535 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
130 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
*
1716571 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
*
1716636 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACC
66 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1716701 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
*
1716736 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
* * ** * *
1716801 ACTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTTGAAGGGTTGTCTGCCAACAAAA
66 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAA
*** * * * *
1716866 GACCTTTGAGTTCGATTACGCTCAGC-TCCAAGGCACAT
127 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
* * * ** *
1716904 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
* * * * * * * * *
1716965 ACTCAACTTCGAGGTCATATCATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
66 ACTCAGCTCCAAGG-CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
1717019 TGGTCAATAA
Statistics
Matches: 701, Mismatches: 70, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
164 33 0.05
165 594 0.85
166 4 0.01
167 1 0.00
168 44 0.06
169 25 0.04
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (165 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
Found at i:1716861 original size:249 final size:249
Alignment explanation
Indices: 1716076--1716989 Score: 1128
Period size: 249 Copynumber: 3.7 Consensus size: 249
1716066 CTTAAGACAA
* * * *
1716076 CATTTGCAGCATGACTTAAGTTGAGAAGTGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
1716141 ATTCAACTACAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * *
1716206 CTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCACAACTTAAGTCTAGAAGGG
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* ** * * *
1716271 TTGTCTGCCAATAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAATGGCACAT
196 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACAT
* * ** * *
1716325 CATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG----CCAAAGACCCCCGAGTTTGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
** * * * * * * *
1716386 ACTCAGCTTTGAGGGCACGTCATTTGCAGTATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAA
66 ACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AA
*** * * * * * *
1716451 AGACCTTTGAGTTTGACTACTCTCAGC-TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
126 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAG
* ** * * * *
1716515 AAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACGT
191 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACAT
1716571 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
1716636 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACC
66 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
1716701 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACGTCATTTGCAGCATAACTTAAGTCGAGAAGGG
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
1716766 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
196 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* ** * * * *
1716820 CATTTGCAGCACAACTTAAGTCTTGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
1716885 GCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
1716950 CCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTT
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1716990 ACAACATAGC
Statistics
Matches: 556, Mismatches: 93, Indels: 32
0.82 0.14 0.05
Matches are distributed among these distances:
245 71 0.13
246 127 0.23
247 2 0.00
248 1 0.00
249 276 0.50
250 79 0.14
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (249 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
Found at i:1717643 original size:43 final size:44
Alignment explanation
Indices: 1717596--1717701 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 44
1717586 GCAAATGGTT
1717596 TTTGAAAATATATATATATATATAATATA-ATTTTGAAAACATA
1 TTTGAAAATATATATATATATATAATATAGATTTTGAAAACATA
* * * * *
1717639 TTTGAAAACAT-T-TATATAT-T-ATATAGTTTTTTAAAACGTT
1 TTTGAAAATATATATATATATATAATATAGATTTTGAAAACATA
*
1717679 TTTGAAAATAAATATA-ATATATA
1 TTTGAAAATATATATATATATATA
1717702 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
39 5 0.10
40 20 0.39
41 12 0.24
42 4 0.08
43 10 0.20
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (44 bp):
TTTGAAAATATATATATATATATAATATAGATTTTGAAAACATA
Found at i:1717897 original size:146 final size:145
Alignment explanation
Indices: 1717613--1717914 Score: 475
Period size: 146 Copynumber: 2.1 Consensus size: 145
1717603 ATATATATAT
1717613 ATATATAATATAATTTTGAAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGT
1 ATATATAATATAATTTTGAAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGT
* *
1717678 TTTTGAAAATAAATATAATATATAGTTTTCAAAACATTTTTGAAAACATGTATATTATATAGTTT
66 TTTTGAAAATAAATAAAATATATAGTTTTCAAAACATTTTT-AAAACATATATATTATATAGTTT
1717743 AAAAACATTTT-GAAA
130 AAAAACATTTTAGAAA
*
1717758 ATATATAATATATAGTTTTTAAAACAT-TTTGAAAACATTTATATATTATATAGTTTTTTAAAAC
1 ATATATAATATA-A-TTTTGAAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAAC
* *
1717822 GTTTTTGAAAATAAAATAAAATATATAGTTTTTAAAACATTTTT-AAATATATATATTATATAGT
64 GTTTTTGAAAAT-AAATAAAATATATAGTTTTCAAAACATTTTTAAAACATATATATTATATAG-
*
1717886 TTTTAAAACATTTTAGAAA
127 TTTAAAAACATTTTAGAAA
1717905 ACTATATAAT
1 A-TATATAAT
1717915 TTTGAAAATA
Statistics
Matches: 145, Mismatches: 6, Indels: 9
0.91 0.04 0.06
Matches are distributed among these distances:
145 29 0.20
146 63 0.43
147 45 0.31
148 8 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (145 bp):
ATATATAATATAATTTTGAAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGT
TTTTGAAAATAAATAAAATATATAGTTTTCAAAACATTTTTAAAACATATATATTATATAGTTTA
AAAACATTTTAGAAA
Found at i:1717922 original size:29 final size:29
Alignment explanation
Indices: 1717878--1717943 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
1717868 ATATATATAT
* * *
1717878 TATATAGTTTTTAAAACATTTTAGAAAAC
1 TATATAATTTTGAAAACATTTTAGAAAAA
* **
1717907 TATATAATTTTGAAAATATTTTTTAAAAA
1 TATATAATTTTGAAAACATTTTAGAAAAA
1717936 TATATAAT
1 TATATAAT
1717944 ATATAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAATTTTGAAAACATTTTAGAAAAA
Found at i:1717929 original size:64 final size:63
Alignment explanation
Indices: 1717839--1717975 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
1717829 AAAATAAAAT
* * * * *
1717839 AAAATATATAGTTTTTAAAACA-TTTTTAAATATATATATTATATAGTTTTTAAAACATTTTAG
1 AAAATATATAATTTTGAAAACATTTTTTAAAAATATATAATATATA-ATTTTAAAACATTTTAG
* **
1717902 AAAACTATATAATTTTGAAAATATTTTTTAAAAATATATAATATATAATTTTAAAATGTTTTTA-
1 AAAA-TATATAATTTTGAAAACATTTTTTAAAAATATATAATATATAATTTTAAAA-CATTTTAG
1717966 AAAATATATA
1 AAAATATATA
1717976 TTATATAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
63 10 0.16
64 27 0.43
65 26 0.41
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (63 bp):
AAAATATATAATTTTGAAAACATTTTTTAAAAATATATAATATATAATTTTAAAACATTTTAG
Found at i:1717947 original size:36 final size:35
Alignment explanation
Indices: 1717907--1717999 Score: 125
Period size: 34 Copynumber: 2.6 Consensus size: 35
1717897 TTTAGAAAAC
*
1717907 TATATAATTTTGAAAATATTTTTTAAAAATATATAA
1 TATATAATTTTGAAAAT-GTTTTTAAAAATATATAA
*
1717943 TATATAATTTT-AAAATGTTTTTAAAAATATATAT
1 TATATAATTTTGAAAATGTTTTTAAAAATATATAA
1717977 TATATAGATATTTAGAAAATGTT
1 TATATA-AT-TTT-GAAAATGTT
1718000 CTTTTGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
34 22 0.43
35 7 0.14
36 14 0.27
38 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATAATTTTGAAAATGTTTTTAAAAATATATAA
Found at i:1718047 original size:18 final size:18
Alignment explanation
Indices: 1718024--1718075 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
1718014 TATTTACCTT
*
1718024 TTTATTTTTTATTTTTTA
1 TTTATTTTTTATTTCTTA
*
1718042 TTTA-TTTTTATTACTTA
1 TTTATTTTTTATTTCTTA
1718059 TTT-TTATTTTATTTCTT
1 TTTATT-TTTTATTTCTT
1718076 TTGTTTCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATTTTTTATTTCTTA
Found at i:1718049 original size:24 final size:23
Alignment explanation
Indices: 1718012--1718072 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
1718002 TTTGTTTTAA
**
1718012 TTTATTTACCTTTTTATTTTTTATTT
1 TTTATTTA--TTTTTATTACTTA-TT
1718038 TTTATTTATTTTTATTACTTATT
1 TTTATTTATTTTTATTACTTATT
1718061 TTTATTTTATTT
1 TTTA-TTTATTT
1718073 CTTTTGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 6 0.19
24 18 0.56
26 8 0.25
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTATTTTTATTACTTATT
Found at i:1718061 original size:13 final size:13
Alignment explanation
Indices: 1718022--1718066 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1718012 TTTATTTACC
*
1718022 TTTTTATTTTTTA
1 TTTTTATTATTTA
1718035 -TTTT-TTATTTA
1 TTTTTATTATTTA
*
1718046 TTTTTATTACTTA
1 TTTTTATTATTTA
1718059 TTTTTATT
1 TTTTTATT
1718067 TTATTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.21
12 8 0.29
13 14 0.50
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:1719279 original size:30 final size:28
Alignment explanation
Indices: 1719244--1719329 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 28
1719234 ACTACTCTTA
1719244 TATATATATATATATTTATTTATTTATTTT
1 TATATATATATATATTT-TTTA-TTATTTT
* * *
1719274 TATATAT-TTTATGATTTTTTTATTATATA
1 TATATATATATAT-A-TTTTTTATTATTTT
*
1719303 TAT-TCTATAT-TATTTTTTAATTATTTT
1 TATATATATATATATTTTTT-ATTATTTT
1719330 CTACTTCCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
26 6 0.13
27 7 0.16
28 3 0.07
29 14 0.31
30 12 0.27
31 3 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (28 bp):
TATATATATATATATTTTTTATTATTTT
Found at i:1724634 original size:22 final size:20
Alignment explanation
Indices: 1724584--1724635 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1724574 TTTTCGTTTT
1724584 AATATTTAT-TTATAAAATA
1 AATATTTATATTATAAAATA
* * *
1724603 AAAATCTATAATTGTAAAATTA
1 AATATTTAT-ATTATAAAA-TA
1724625 AATATTTATAT
1 AATATTTATAT
1724636 ATAGTTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 7 0.28
21 9 0.36
22 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AATATTTATATTATAAAATA
Found at i:1727054 original size:27 final size:27
Alignment explanation
Indices: 1727004--1727056 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1726994 GAATAAATAA
*
1727004 ATAAATTTAAATATTTAGATTTTGTTT
1 ATAAATTTAAATATTTAGACTTTGTTT
*
1727031 ATAAGATTTGAATATTTA-ACTTTGTT
1 ATAA-ATTTAAATATTTAGACTTTGTT
1727057 ATTTGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (27 bp):
ATAAATTTAAATATTTAGACTTTGTTT
Found at i:1731334 original size:2 final size:2
Alignment explanation
Indices: 1731327--1731394 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1731317 AAGAATGTAA
1731327 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
1731369 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
1731395 CTTATTTGGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1740388 original size:1 final size:1
Alignment explanation
Indices: 1740382--1740408 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1740372 CTGAAACCGC
1740382 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1740409 CAGGTGATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1741717 original size:2 final size:2
Alignment explanation
Indices: 1741710--1741743 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1741700 TATACATTAC
1741710 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
1741744 CTTCATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1751191 original size:25 final size:25
Alignment explanation
Indices: 1751163--1751213 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1751153 AACCTAATCT
1751163 ATAGCACTCTGCAAATCCAGCTCAG
1 ATAGCACTCTGCAAATCCAGCTCAG
1751188 ATAGCACTCTGCAAATCCAGCTCAG
1 ATAGCACTCTGCAAATCCAGCTCAG
1751213 A
1 A
1751214 AGCCTTGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (25 bp):
ATAGCACTCTGCAAATCCAGCTCAG
Found at i:1752728 original size:161 final size:161
Alignment explanation
Indices: 1752456--1752959 Score: 972
Period size: 161 Copynumber: 3.1 Consensus size: 161
1752446 AGATTTTCAA
*
1752456 GTTCGAGATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
1 GTTCGATATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
*
1752521 CTAAAGCAATCCCCACCTGTAGTTGAGTCGATTCTTTTAAGAAATGAACTAATGATCATCTATAC
66 CTAAAGCAATCCCCACCTGTAGTTGAGTCAATTCTTTTAAGAAATGAACTAATGATCATCTATAC
1752586 TATTACTACACCAACTCTTAATTTTAACCAT
131 TATTACTACACCAACTCTTAATTTTAACCAT
1752617 GTTCGATATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
1 GTTCGATATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
1752682 CTAAAGCAATCCCCACCTGTAGTTGAGTCAATTCTTTTAAGAAATGAACTAATGATCATCTATAC
66 CTAAAGCAATCCCCACCTGTAGTTGAGTCAATTCTTTTAAGAAATGAACTAATGATCATCTATAC
1752747 TATTACTACACCAACTCTTAATTTTAACCAT
131 TATTACTACACCAACTCTTAATTTTAACCAT
1752778 GTTCGATATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
1 GTTCGATATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
1752843 CTAAAGCAATCCCCACCTGTAGTTGAGTCAATTCTTTTAAGAAATGAACTAATGATCATCTATAC
66 CTAAAGCAATCCCCACCTGTAGTTGAGTCAATTCTTTTAAGAAATGAACTAATGATCATCTATAC
1752908 TATTACTACACCAACTCTTAATTTTAACCAT
131 TATTACTACACCAACTCTTAATTTTAACCAT
**
1752939 GTTCGATATCATCCTCAATAT
1 GTTCGATATCATTTTCAATAT
1752960 TTTCCATCTC
Statistics
Matches: 339, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 339 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (161 bp):
GTTCGATATCATTTTCAATATCATTTCAGTAAACATTAAGGCATCTAAAAAGCCAATGCAAGTAG
CTAAAGCAATCCCCACCTGTAGTTGAGTCAATTCTTTTAAGAAATGAACTAATGATCATCTATAC
TATTACTACACCAACTCTTAATTTTAACCAT
Found at i:1753625 original size:6 final size:6
Alignment explanation
Indices: 1753616--1753648 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1753606 TTTTTGTTTA
1753616 TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCT
1 TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCT
1753649 TTCAATCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCTCAC
Found at i:1761616 original size:17 final size:18
Alignment explanation
Indices: 1761594--1761632 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1761584 ATATTATATA
1761594 AATTTAGTT-ATAATTTT
1 AATTTAGTTAATAATTTT
1761611 AATTTAGTTAAATAATTTT
1 AATTTAGTT-AATAATTTT
1761630 AAT
1 AAT
1761633 CTTCAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
AATTTAGTTAATAATTTT
Found at i:1763908 original size:10 final size:10
Alignment explanation
Indices: 1763908--1763942 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1763898 CATAACCGAA
*
1763908 CGAACATAAA
1 CGAACATAAC
*
1763918 CGAATATAAC
1 CGAACATAAC
1763928 CGAACATAAC
1 CGAACATAAC
1763938 CGAAC
1 CGAAC
1763943 GAACATAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (10 bp):
CGAACATAAC
Found at i:1763908 original size:20 final size:22
Alignment explanation
Indices: 1763885--1763942 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
1763875 ATAAATGAAT
*
1763885 GAACATAAATGAACATAACCGAAC
1 GAACATAAACGAACATAACC--AC
*
1763909 GAACATAAACGAATATAA-C-C
1 GAACATAAACGAACATAACCAC
*
1763929 GAACATAACCGAAC
1 GAACATAAACGAAC
1763943 GAACATAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
23 1 0.03
24 16 0.53
ACGTcount: A:0.53, C:0.22, G:0.12, T:0.12
Consensus pattern (22 bp):
GAACATAAACGAACATAACCAC
Found at i:1763912 original size:14 final size:14
Alignment explanation
Indices: 1763895--1763957 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 14
1763885 GAACATAAAT
1763895 GAACATAACCGAAC
1 GAACATAACCGAAC
*
1763909 GAACATAAACGAATATAACC
1 GAACATAACCG-----AA-C
1763929 GAACATAACCGAAC
1 GAACATAACCGAAC
*
1763943 GAACATAACCAAAC
1 GAACATAACCGAAC
1763957 G
1 G
1763958 TTCACGAACG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 25 0.62
15 2 0.05
19 2 0.05
20 11 0.28
ACGTcount: A:0.52, C:0.25, G:0.13, T:0.10
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:1763912 original size:24 final size:24
Alignment explanation
Indices: 1763885--1763932 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1763875 ATAAATGAAT
*
1763885 GAACATAAATGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1763909 GAACATAAACGAATATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
1763933 ATAACCGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1768425 original size:50 final size:50
Alignment explanation
Indices: 1768350--1768463 Score: 192
Period size: 50 Copynumber: 2.3 Consensus size: 50
1768340 GATTAACCGA
*
1768350 CAACACTGACTTATGCATGTATAAGTTAGTCATTTCATTTACTAAACTAT
1 CAACACTGACTTACGCATGTATAAGTTAGTCATTTCATTTACTAAACTAT
* *
1768400 CAACACTAACTTACGCCTGTATAAGTTAGTCATTTCATTTACTAAACTAT
1 CAACACTGACTTACGCATGTATAAGTTAGTCATTTCATTTACTAAACTAT
*
1768450 CATCACTGACTTAC
1 CAACACTGACTTAC
1768464 ACTGGTATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (50 bp):
CAACACTGACTTACGCATGTATAAGTTAGTCATTTCATTTACTAAACTAT
Found at i:1779670 original size:17 final size:17
Alignment explanation
Indices: 1779658--1779692 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1779648 TTATATTTAT
1779658 TTATATAAAATATAATA
1 TTATATAAAATATAATA
*
1779675 TTATATAAAAAATAATA
1 TTATATAAAATATAATA
1779692 T
1 T
1779693 CGTGGCCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATATAAAATATAATA
Found at i:1783942 original size:37 final size:37
Alignment explanation
Indices: 1783895--1783968 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1783885 GATGCAATAG
* *
1783895 ACATCTACACTTCCTTCTGATTAATTCACATCAATCA
1 ACATCAACACTTCCTTCTGATTAATGCACATCAATCA
*
1783932 ACATCAACACTTCCTTCTGATTACTGCACATCAATCA
1 ACATCAACACTTCCTTCTGATTAATGCACATCAATCA
1783969 GGGTGTATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (37 bp):
ACATCAACACTTCCTTCTGATTAATGCACATCAATCA
Found at i:1792363 original size:21 final size:21
Alignment explanation
Indices: 1792327--1792379 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1792317 CAGATTTGTT
*
1792327 TTATATAAT-ATT-ATTTTTA
1 TTATCTAATGATTAATTTTTA
1792346 TTAT-TAAATGATTAATTTTTA
1 TTATCT-AATGATTAATTTTTA
1792367 TTATCTAATGATT
1 TTATCTAATGATT
1792380 TAAAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 3 0.10
21 18 0.60
22 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (21 bp):
TTATCTAATGATTAATTTTTA
Found at i:1792686 original size:14 final size:14
Alignment explanation
Indices: 1792661--1792700 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1792651 GGAGGGAGAA
1792661 TGTTTA-GATTTAG
1 TGTTTAGGATTTAG
1792674 TGTTTAGGATTTAG
1 TGTTTAGGATTTAG
*
1792688 TGTTTAGGGTTTA
1 TGTTTAGGATTTA
1792701 AATTTTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.53
Consensus pattern (14 bp):
TGTTTAGGATTTAG
Found at i:1793145 original size:282 final size:282
Alignment explanation
Indices: 1792739--1793264 Score: 874
Period size: 282 Copynumber: 1.9 Consensus size: 282
1792729 AACTAAATAT
* **
1792739 TTTAGGGTTTAGGGTTTGCAAAATCAATAATTACTGATATTATTTGTTGTATATTGATTTTGGAA
1 TTTAGGGTTTAGGATTCACAAAATCAATAATTACTGATATTATTTGTTGTATATTGATTTTGGAA
* * ** *
1792804 GCCTAAACCCTAAAATATTTTGGTTGTTGCTGAAAACCTTTATAAGTTCATGGTATGTTGAGGGC
66 GCCTAAACCCTAAAATATTTTGATTATTGCTGAAAACCTTTATAAACTCATGATATGTTGAGGGC
1792869 AATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTGTTTTTTATAAGA
131 AATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTGTTTTTTATAAGA
*
1792934 AAAAATTGATTAGAGGGAGAATGGTTAGGATTTAGTGTTTAAGGTTTAGCGTTTAGAGTTTTCAA
196 AAAAATTGATTAGAGGGAGAATGGTTAGGATTTAGGGTTTAAGGTTTAGCGTTTAGAGTTTTCAA
1792999 CAATAACCAAAATATTTTAGGG
261 CAATAACCAAAATATTTTAGGG
* * *
1793021 TTTAGGGTTTAGGATTCACAAAATCAATAGTTCCTTATATTATTTGTTGTATATTGATTTTGGAA
1 TTTAGGGTTTAGGATTCACAAAATCAATAATTACTGATATTATTTGTTGTATATTGATTTTGGAA
1793086 -CCTTAAACCCTAAAATATTTTGATTATTGCTGAAAACCTTTATAAACTCATGATATGTTGAGGG
66 GCC-TAAACCCTAAAATATTTTGATTATTGCTGAAAACCTTTATAAACTCATGATATGTTGAGGG
* *
1793150 CAATGAAGGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACATATTTGTTTTTTATAAG
130 CAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTGTTTTTTATAAG
* * * *
1793215 AAGAAATTGATTGGAGGGAGAATGGTTAGGGTTTAGGGTTTAGGGTTTAG
195 AAAAAATTGATTAGAGGGAGAATGGTTAGGATTTAGGGTTTAAGGTTTAG
1793265 GGTTCACAAA
Statistics
Matches: 225, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
281 2 0.01
282 223 0.99
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (282 bp):
TTTAGGGTTTAGGATTCACAAAATCAATAATTACTGATATTATTTGTTGTATATTGATTTTGGAA
GCCTAAACCCTAAAATATTTTGATTATTGCTGAAAACCTTTATAAACTCATGATATGTTGAGGGC
AATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTGTTTTTTATAAGA
AAAAATTGATTAGAGGGAGAATGGTTAGGATTTAGGGTTTAAGGTTTAGCGTTTAGAGTTTTCAA
CAATAACCAAAATATTTTAGGG
Found at i:1793252 original size:7 final size:7
Alignment explanation
Indices: 1793240--1793268 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1793230 GGGAGAATGG
1793240 TTAGGGT
1 TTAGGGT
1793247 TTAGGGT
1 TTAGGGT
1793254 TTAGGGT
1 TTAGGGT
1793261 TTAGGGT
1 TTAGGGT
1793268 T
1 T
1793269 CACAAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:1793364 original size:7 final size:7
Alignment explanation
Indices: 1793352--1793381 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1793342 TTGTTGCTAA
1793352 AAACCCT
1 AAACCCT
1793359 AAACCCT
1 AAACCCT
1793366 AAACCCT
1 AAACCCT
*
1793373 AAATCCT
1 AAACCCT
1793380 AA
1 AA
1793382 TCATTCTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:1793684 original size:32 final size:34
Alignment explanation
Indices: 1793648--1793720 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
1793638 AACATATATC
*
1793648 AATAATATAAAAA-ATAT-TAATGTTAAT-ATAAT
1 AATAATATAAAAACATATATAAT-TTAATAATAAA
* *
1793680 AATAAAATAAAAACATATATCATTTAATAATAAA
1 AATAATATAAAAACATATATAATTTAATAATAAA
1793714 AATAATA
1 AATAATA
1793721 CTCTATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 12 0.35
33 9 0.26
34 13 0.38
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (34 bp):
AATAATATAAAAACATATATAATTTAATAATAAA
Found at i:1794572 original size:19 final size:17
Alignment explanation
Indices: 1794544--1794582 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
1794534 TAATAATTGA
*
1794544 ATTATCTTATCATTTTTAT
1 ATTATATTAT-ATTTTT-T
1794563 ATTATATTATATTTTTT
1 ATTATATTATATTTTTT
1794580 ATT
1 ATT
1794583 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATATTATATTTTTT
Found at i:1795637 original size:15 final size:15
Alignment explanation
Indices: 1795614--1795645 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1795604 TTCTCAGGTA
*
1795614 TCTCTCTTTTCATCT
1 TCTCCCTTTTCATCT
1795629 TCTCCCTTTTCATCT
1 TCTCCCTTTTCATCT
1795644 TC
1 TC
1795646 CTTGACCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTCCCTTTTCATCT
Found at i:1795696 original size:28 final size:26
Alignment explanation
Indices: 1795634--1795696 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
1795624 CATCTTCTCC
1795634 CTTTTCATCTTCCTTGACCTCCTTTT
1 CTTTTCATCTTCCTTGACCTCCTTTT
*
1795660 CTTGATTCATCTTTCTTGACCTCCATTTT
1 CTT--TTCATCTTCCTTGACCTCC-TTTT
1795689 CATTTTCA
1 C-TTTTCA
1795697 CCGACGAGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
28 22 0.69
29 5 0.16
30 2 0.06
ACGTcount: A:0.13, C:0.30, G:0.05, T:0.52
Consensus pattern (26 bp):
CTTTTCATCTTCCTTGACCTCCTTTT
Found at i:1797645 original size:17 final size:17
Alignment explanation
Indices: 1797623--1797661 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1797613 TAATATTATT
1797623 TAAAATACAAATT-TTTA
1 TAAAATA-AAATTATTTA
*
1797640 TAAAATATAATTATTTA
1 TAAAATAAAATTATTTA
1797657 TAAAA
1 TAAAA
1797662 AATGAACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATAAAATTATTTA
Found at i:1800929 original size:3 final size:3
Alignment explanation
Indices: 1800923--1800973 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1800913 TGTTGTACCC
1800923 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1800971 TAA
1 TAA
1800974 CCATTGTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1801609 original size:12 final size:13
Alignment explanation
Indices: 1801571--1801636 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 13
1801561 AAAATATATG
*
1801571 TTATATATTAATA
1 TTATATAATAATA
1801584 -TATAT-AT-ATA
1 TTATATAATAATA
1801594 -TATATAATAA-A
1 TTATATAATAATA
*
1801605 TTATATAAGAATA
1 TTATATAATAATA
1801618 TTATA-AATAATA
1 TTATATAATAATA
1801630 TTA-ATAA
1 TTATATAA
1801637 AAATTTCAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
10 8 0.18
11 5 0.11
12 26 0.58
13 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TTATATAATAATA
Found at i:1802114 original size:16 final size:17
Alignment explanation
Indices: 1802093--1802136 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
1802083 ATTCTAAATC
1802093 ATATATAAAATTTTT-T
1 ATATATAAAATTTTTAT
*
1802109 ATATATACTAATTTTTAT
1 ATATATA-AAATTTTTAT
1802127 ATTATATAAA
1 A-TATATAAA
1802137 TAGTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 3 0.13
19 6 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATAAAATTTTTAT
Found at i:1808457 original size:393 final size:393
Alignment explanation
Indices: 1807732--1808497 Score: 1498
Period size: 393 Copynumber: 1.9 Consensus size: 393
1807722 CCACTAATGT
*
1807732 TCGGTTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACCTCTGATAGTGAAGTGCCTGACAA
1 TCGGTTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACCTCTGACAGTGAAGTGCCTGACAA
1807797 TACCTTCCTCTTCACAGACTTTCAGAAATGGATCATTTTTGTACTCTCCACCATTGTCTGTACGG
66 TACCTTCCTCTTCACAGACTTTCAGAAATGGATCATTTTTGTACTCTCCACCATTGTCTGTACGG
1807862 AGACGTTTGATTTTTCTGCCTGTTTGAGTCTCCATCATCTTTTTCCATTTAAGGAAAAATCCTAG
131 AGACGTTTGATTTTTCTGCCTGTTTGAGTCTCCATCATCTTTTTCCATTTAAGGAAAAATCCTAG
1807927 CACCTCATCCTTTGTCTTCATTGGATACACCCAAACTCTCCAGAAAAAATCATCAACAAAGGTGA
196 CACCTCATCCTTTGTCTTCATTGGATACACCCAAACTCTCCAGAAAAAATCATCAACAAAGGTGA
1807992 CATAATAGTGTGTTCCTCCCAATGAAGTTATCTTGGAAGGCCCCCATACATCTGAATGAACATAA
261 CATAATAGTGTGTTCCTCCCAATGAAGTTATCTTGGAAGGCCCCCATACATCTGAATGAACATAA
1808057 TCCAAAATACCTTTAGTATCATGGATTGA-TGTTCCAAATTTCACCTTCTAGGCAGTTAAACCAT
326 TCCAAAATACCTTTAGTATCATGGATT-ACTGTTCCAAATTTCACCTTCTAGGCAGTTAAACCAT
1808121 ATTA
390 ATTA
1808125 TCGGTTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACCTCTGACAGTGAAGTGCCTGACAA
1 TCGGTTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACCTCTGACAGTGAAGTGCCTGACAA
1808190 TACCTTCCTCTTCACAGACTTTCAGAAATGGATCATTTTTGTACTCTCCACCATTGTCTGTACGG
66 TACCTTCCTCTTCACAGACTTTCAGAAATGGATCATTTTTGTACTCTCCACCATTGTCTGTACGG
*
1808255 AGACGTTTGATTTTTCTGCTTGTTTGAGTCTCCATCATCTTTTTCCATTTAAGGAAAAATCCTAG
131 AGACGTTTGATTTTTCTGCCTGTTTGAGTCTCCATCATCTTTTTCCATTTAAGGAAAAATCCTAG
1808320 CACCTCATCCTTTGTCTTCATTGGATACACCCAAACTCTCCAGAAAAAATCATCAACAAAGGTGA
196 CACCTCATCCTTTGTCTTCATTGGATACACCCAAACTCTCCAGAAAAAATCATCAACAAAGGTGA
1808385 CATAATAGTGTGTTCCTCCCAATGAAGTTATCTTGGAAGGCCCCCATACATCTGAATGAACATAA
261 CATAATAGTGTGTTCCTCCCAATGAAGTTATCTTGGAAGGCCCCCATACATCTGAATGAACATAA
1808450 TCCAAAATACCTTTAGTATCATGGATTACTGTTCCAAATTTCACCTTC
326 TCCAAAATACCTTTAGTATCATGGATTACTGTTCCAAATTTCACCTTC
1808498 GTCTTCTTCC
Statistics
Matches: 370, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
392 1 0.00
393 369 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (393 bp):
TCGGTTCATACGCTCTGCCACCCCATTCTGTTGTGGTGTACCTCTGACAGTGAAGTGCCTGACAA
TACCTTCCTCTTCACAGACTTTCAGAAATGGATCATTTTTGTACTCTCCACCATTGTCTGTACGG
AGACGTTTGATTTTTCTGCCTGTTTGAGTCTCCATCATCTTTTTCCATTTAAGGAAAAATCCTAG
CACCTCATCCTTTGTCTTCATTGGATACACCCAAACTCTCCAGAAAAAATCATCAACAAAGGTGA
CATAATAGTGTGTTCCTCCCAATGAAGTTATCTTGGAAGGCCCCCATACATCTGAATGAACATAA
TCCAAAATACCTTTAGTATCATGGATTACTGTTCCAAATTTCACCTTCTAGGCAGTTAAACCATA
TTA
Found at i:1812008 original size:17 final size:17
Alignment explanation
Indices: 1811986--1812019 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1811976 TTTTTAATTG
1811986 TCACGTAGTACTTCCGT
1 TCACGTAGTACTTCCGT
1812003 TCACGTAGTACTTCCGT
1 TCACGTAGTACTTCCGT
1812020 AAAGGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (17 bp):
TCACGTAGTACTTCCGT
Found at i:1830413 original size:14 final size:14
Alignment explanation
Indices: 1830394--1830423 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1830384 CTAAAATTTT
*
1830394 AAATAAAATATATA
1 AAATAAAATAAATA
1830408 AAATAAAATAAATA
1 AAATAAAATAAATA
1830422 AA
1 AA
1830424 TTTATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:1831926 original size:37 final size:37
Alignment explanation
Indices: 1831850--1831926 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
1831840 TTTTTATATT
*
1831850 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
*
1831887 TTTAATTTT-TAAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAA-AAAATTATATAAATATTAT-CAA
1831924 TTT
1 TTT
1831927 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 18 0.50
37 18 0.50
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1832108 original size:20 final size:20
Alignment explanation
Indices: 1832072--1832109 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1832062 ATCCTATTTC
**
1832072 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTACATTCTCA
1832092 CTGATAATCTTACATTCT
1 CTGATAATCTTACATTCT
1832110 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (20 bp):
CTGATAATCTTACATTCTCA
Found at i:1832750 original size:30 final size:28
Alignment explanation
Indices: 1832707--1832780 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
1832697 TTTTATTTTT
* * *
1832707 ATTTTTAGATTATATAATTTAGATTATTAA
1 ATTTTAAGTTTATATAATTT--ATTATGAA
* *
1832737 ATTTTATGTTTATATTATTTATTATGAA
1 ATTTTAAGTTTATATAATTTATTATGAA
*
1832765 ATTTTAAGTTTTTATA
1 ATTTTAAGTTTATATA
1832781 TAGGTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
28 20 0.56
30 16 0.44
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (28 bp):
ATTTTAAGTTTATATAATTTATTATGAA
Found at i:1833378 original size:2 final size:2
Alignment explanation
Indices: 1833368--1833426 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1833358 TTAAAAAAGT
1833368 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1833409 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1833427 CATGAGTATT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1834575 original size:22 final size:22
Alignment explanation
Indices: 1834550--1834602 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1834540 AATAGTATTA
* *
1834550 TGAACAGTAATGAACAGTTCTG
1 TGAACAGTAATGAACAATACTG
1834572 TGAACAGTAATGAACAATACTG
1 TGAACAGTAATGAACAATACTG
1834594 TGAACAGTA
1 TGAACAGTA
1834603 TCGATGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (22 bp):
TGAACAGTAATGAACAATACTG
Found at i:1835309 original size:32 final size:31
Alignment explanation
Indices: 1835255--1835388 Score: 202
Period size: 32 Copynumber: 4.3 Consensus size: 31
1835245 GTTCCTAAGA
* *
1835255 ACATAGGTAA-CTATCCATATGTCCGGAAAG
1 ACATAGGTAATCTGTCCATATGTCCCGAAAG
1835285 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAA-TCTGTCCATATGTCCCGAAAG
1835317 ACATAGGTAATCCTGTCCATATGTCCCGAAAG
1 ACATAGGTAAT-CTGTCCATATGTCCCGAAAG
1835349 ACATAGGTAATAC--TCCATATGTCCCGAAAG
1 ACATAGGTAAT-CTGTCCATATGTCCCGAAAG
1835379 ACATAGGTAA
1 ACATAGGTAA
1835389 CCTTCGACTC
Statistics
Matches: 98, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
30 37 0.38
31 1 0.01
32 60 0.61
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
ACATAGGTAATCTGTCCATATGTCCCGAAAG
Found at i:1835325 original size:62 final size:60
Alignment explanation
Indices: 1835255--1835389 Score: 207
Period size: 62 Copynumber: 2.2 Consensus size: 60
1835245 GTTCCTAAGA
* *
1835255 ACATAGGTAACTATCCATATGTCCGGAAAGACATAGGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAACTATCCATATGTCCCGAAAGACATAGGTAATAC--TCCATATGTCCCGAAAG
*
1835317 ACATAGGTAATCCTGTCCATATGTCCCGAAAGACATAGGTAATACTCCATATGTCCCGAAAG
1 ACATAGGTAA--CTATCCATATGTCCCGAAAGACATAGGTAATACTCCATATGTCCCGAAAG
1835379 ACATAGGTAAC
1 ACATAGGTAAC
1835390 CTTCGACTCT
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
60 1 0.01
62 37 0.54
64 30 0.44
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (60 bp):
ACATAGGTAACTATCCATATGTCCCGAAAGACATAGGTAATACTCCATATGTCCCGAAAG
Found at i:1836786 original size:3 final size:3
Alignment explanation
Indices: 1836778--1836813 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
1836768 TCTCACGTAT
1836778 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TGAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GA
1836814 TATTTATGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:1837271 original size:2 final size:2
Alignment explanation
Indices: 1837264--1837290 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1837254 TAAAAATAAT
1837264 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1837291 TGGCTAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1838953 original size:2 final size:2
Alignment explanation
Indices: 1838946--1838982 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1838936 TTTAAATTGT
1838946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1838983 TTTAAAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1839955 original size:23 final size:23
Alignment explanation
Indices: 1839912--1839955 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1839902 TAAATCCCAC
* **
1839912 ATTATTTAAATATTATTTTTTTA
1 ATTATTTAAATATAAACTTTTTA
1839935 ATTATTTAAATATAAACTTTT
1 ATTATTTAAATATAAACTTTT
1839956 AAACATGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTATTTAAATATAAACTTTTTA
Found at i:1843120 original size:14 final size:14
Alignment explanation
Indices: 1843101--1843131 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1843091 ATTATGTACC
1843101 AAACTGCACTTTTT
1 AAACTGCACTTTTT
*
1843115 AAACTGTACTTTTT
1 AAACTGCACTTTTT
1843129 AAA
1 AAA
1843132 ATACTACAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (14 bp):
AAACTGCACTTTTT
Found at i:1844156 original size:17 final size:17
Alignment explanation
Indices: 1844134--1844172 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1844124 TGAATCAAAT
1844134 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1844151 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1844168 -AATTA
1 TAATTA
1844173 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1844529 original size:54 final size:54
Alignment explanation
Indices: 1844447--1844562 Score: 223
Period size: 54 Copynumber: 2.1 Consensus size: 54
1844437 ATTTTACTAA
1844447 ATGTGTTCGATCTAAAATTTTATTTGTACATACTTCATATAAAAAAATTAATAT
1 ATGTGTTCGATCTAAAATTTTATTTGTACATACTTCATATAAAAAAATTAATAT
1844501 ATGTGTTCGATCTAAAATTTTATTTGTACATACTTCATATAAAAAAATTAATAT
1 ATGTGTTCGATCTAAAATTTTATTTGTACATACTTCATATAAAAAAATTAATAT
*
1844555 ATATGTTC
1 ATGTGTTC
1844563 ACCTTAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (54 bp):
ATGTGTTCGATCTAAAATTTTATTTGTACATACTTCATATAAAAAAATTAATAT
Found at i:1844543 original size:27 final size:27
Alignment explanation
Indices: 1844459--1844544 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
1844449 GTGTTCGATC
1844459 TAAAATTTTATTTGTACATACTTCATA
1 TAAAATTTTATTTGTACATACTTCATA
** ** * ** *
1844486 TAAAA--AAATTAATATATGTGTTCGATC
1 TAAAATTTTATTTGTACAT-ACTTC-ATA
1844513 TAAAATTTTATTTGTACATACTTCATA
1 TAAAATTTTATTTGTACATACTTCATA
1844540 TAAAA
1 TAAAA
1844545 AAATTAATAT
Statistics
Matches: 39, Mismatches: 16, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
25 7 0.18
26 3 0.08
27 19 0.49
28 3 0.08
29 7 0.18
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (27 bp):
TAAAATTTTATTTGTACATACTTCATA
Found at i:1844776 original size:15 final size:15
Alignment explanation
Indices: 1844751--1844790 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1844741 TTAATTTCCG
*
1844751 TTAACTCCCTTTTGT
1 TTAAGTCCCTTTTGT
*
1844766 TTACGTCCCTTTTGT
1 TTAAGTCCCTTTTGT
1844781 TTAAGTCCCT
1 TTAAGTCCCT
1844791 AACATGGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.12, C:0.28, G:0.10, T:0.50
Consensus pattern (15 bp):
TTAAGTCCCTTTTGT
Found at i:1844875 original size:31 final size:31
Alignment explanation
Indices: 1844837--1844896 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1844827 CGACTGAAGA
*
1844837 ACTAAAATCAAGCAGATCGATAACATTAGAG
1 ACTAAAATCAAACAGATCGATAACATTAGAG
* *
1844868 ACTAAAATCAAACATATCGATAACGTTAG
1 ACTAAAATCAAACAGATCGATAACATTAG
1844897 GTACCGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (31 bp):
ACTAAAATCAAACAGATCGATAACATTAGAG
Found at i:1846790 original size:45 final size:44
Alignment explanation
Indices: 1846725--1846810 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
1846715 CTAAAAATAT
*
1846725 TTTTTTATATTAGGACATATAAAGTGATAACATAAATTTTTTATA
1 TTTTTTATATTAGGACATATAAAGTAATAACAT-AATTTTTTATA
* * * *
1846770 TTTTTTATGTTTGGATATATAAATTAATAACATAATTTTTT
1 TTTTTTATATTAGGACATATAAAGTAATAACATAATTTTTT
1846811 CGTATGAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 8 0.22
45 28 0.78
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (44 bp):
TTTTTTATATTAGGACATATAAAGTAATAACATAATTTTTTATA
Found at i:1846987 original size:60 final size:60
Alignment explanation
Indices: 1846877--1846989 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
1846867 TACATGGTGA
* *
1846877 TGTTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGGTCTATTGACTATAGGATGT
1 TGTTTTGTTGAGTCTCCCAACTATTAAAAGTTACAAAATGGTCTACTGACTATAGGATGT
1846937 TGTTTTGTTGAGTC-CTCCAACTATTAAAAGTTACAAAATGGTC-ACCTGACTAT
1 TGTTTTGTTGAGTCTC-CCAACTATTAAAAGTTACAAAATGGTCTA-CTGACTAT
1846990 TCATATGTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
59 2 0.04
60 47 0.96
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (60 bp):
TGTTTTGTTGAGTCTCCCAACTATTAAAAGTTACAAAATGGTCTACTGACTATAGGATGT
Found at i:1849713 original size:13 final size:14
Alignment explanation
Indices: 1849695--1849728 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1849685 TATACGCTCT
*
1849695 CCCTAACTTAA-AA
1 CCCTAAATTAATAA
1849708 CCCTAAATTAATAA
1 CCCTAAATTAATAA
1849722 CCCTAAA
1 CCCTAAA
1849729 CCTTAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAATTAATAA
Found at i:1850767 original size:27 final size:28
Alignment explanation
Indices: 1850730--1850795 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
1850720 TCTAATTCAA
1850730 ATATTCGGGTCGGG-TTTTTTAAGTGTG
1 ATATTCGGGTCGGGTTTTTTTAAGTGTG
*
1850757 ATATTCAGGTCGGGTTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTTTTTTTAAGTGTG
1850785 ATATTCGGGTC
1 ATATTCGGGTC
1850796 AGGTCGGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.17, C:0.09, G:0.30, T:0.44
Consensus pattern (28 bp):
ATATTCGGGTCGGGTTTTTTTAAGTGTG
Found at i:1860535 original size:39 final size:40
Alignment explanation
Indices: 1860492--1860579 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 40
1860482 AGCTAAATAT
*
1860492 GAAGACTCCACGACTACATGACGTCTTCAGGC-AATTGAA
1 GAAGACTACACGACTACATGACGTCTTCAGGCAAATTGAA
** *
1860531 GAAGACTACACGACTGTATGTCGTCTTCAGGCAAATTGAA
1 GAAGACTACACGACTACATGACGTCTTCAGGCAAATTGAA
1860571 -AAGACTACA
1 GAAGACTACA
1860580 GGAGTGTACG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 37 0.84
40 7 0.16
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (40 bp):
GAAGACTACACGACTACATGACGTCTTCAGGCAAATTGAA
Found at i:1860595 original size:39 final size:39
Alignment explanation
Indices: 1860513--1860599 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
1860503 GACTACATGA
* *
1860513 CGTCTTCAGGCAATTGAAGAAGACTACACGACTGTATGT
1 CGTCTTCAGGCAATTGAAGAAGACTACACGACTGTACGG
* *
1860552 CGTCTTCAGGCAAATTGAA-AAGACTACAGGAGTGTACGG
1 CGTCTTCAGGC-AATTGAAGAAGACTACACGACTGTACGG
1860591 CGTCTTCAG
1 CGTCTTCAG
1860600 ATCAATAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 36 0.84
40 7 0.16
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (39 bp):
CGTCTTCAGGCAATTGAAGAAGACTACACGACTGTACGG
Found at i:1869012 original size:18 final size:18
Alignment explanation
Indices: 1868989--1869079 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 18
1868979 GTTCAGTATT
1868989 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
1869007 TGTCCCAAAGGACTATTGA
1 TGTCCCGAAGGACCACT-A
* *
1869026 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
1869045 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
1869063 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1869080 GTATATCCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
18 47 0.77
19 2 0.03
20 12 0.20
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1869204 original size:23 final size:22
Alignment explanation
Indices: 1869176--1869237 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
1869166 ATCACTGCTA
1869176 TCATTTCTCATATAGCACATAAT
1 TCATTTCTCATATA-CACATAAT
*
1869199 TCA-TT-TCATATACACATGAT
1 TCATTTCTCATATACACATAAT
*
1869219 TC-TTT-TCAATATTCACATA
1 TCATTTCTC-ATATACACATA
1869238 CCTGTATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.38
21 16 0.47
22 2 0.06
23 3 0.09
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (22 bp):
TCATTTCTCATATACACATAAT
Found at i:1869220 original size:20 final size:20
Alignment explanation
Indices: 1869183--1869237 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1869173 CTATCATTTC
1869183 TCATATAGCACATAATTCATT
1 TCATATA-CACATAATTCATT
* *
1869204 TCATATACACATGATTCTTT
1 TCATATACACATAATTCATT
*
1869224 TCAATATTCACATA
1 TC-ATATACACATA
1869238 CCTGTATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (20 bp):
TCATATACACATAATTCATT
Found at i:1869664 original size:24 final size:22
Alignment explanation
Indices: 1869602--1869664 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
1869592 AATGAGGGTA
1869602 TGCATCGATGCACTC-T-ACAG
1 TGCATCGATGCACTCTTAACAG
* * *
1869622 TGTATCGATGCATTCCTTAACGGG
1 TGCATCGATGCACT-CTTAAC-AG
1869646 TGCATCGATGCACTACTTA
1 TGCATCGATGCACT-CTTA
1869665 TGCATCGGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 12 0.36
21 1 0.03
22 1 0.03
23 2 0.06
24 17 0.52
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCACTCTTAACAG
Found at i:1869711 original size:63 final size:63
Alignment explanation
Indices: 1869643--1869764 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 63
1869633 ATTCCTTAAC
*
1869643 GGGTGCATCGATGCACTACTTATGCATCGGTGCA-TGAATCACATTCGATGTTTGTATTTAATG
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACT-AATCACATTCGATGTTTGTATTTAATG
* * ** *
1869706 GGGTGCATCGATGCACTCCTTATGCATTGATGCACTAATGGCATTCGATGTTTTTATTT
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTT
1869765 TATCAGAGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 51 0.98
64 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (63 bp):
GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTTAATG
Found at i:1876185 original size:27 final size:27
Alignment explanation
Indices: 1876151--1876259 Score: 200
Period size: 27 Copynumber: 4.0 Consensus size: 27
1876141 TGGGTACCAA
1876151 TGTTTAATTGGCTAACATATAACCATT
1 TGTTTAATTGGCTAACATATAACCATT
*
1876178 TGTTTAATTGGCTAATATATAACCATT
1 TGTTTAATTGGCTAACATATAACCATT
*
1876205 TGTTTAATTGGCTAATATATAACCATT
1 TGTTTAATTGGCTAACATATAACCATT
1876232 TGTTTAATTGGCTAACATATAACCATT
1 TGTTTAATTGGCTAACATATAACCATT
1876259 T
1 T
1876260 AAAGAACCTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (27 bp):
TGTTTAATTGGCTAACATATAACCATT
Found at i:1877108 original size:63 final size:63
Alignment explanation
Indices: 1877007--1877132 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
1876997 CCCCACTTCC
* *
1877007 CAAGAAGTATAATCAATTATTTTAATTTGGGTGCTTTAATAGTTCTCCTTTAACTCATTATTT
1 CAAGAAGTATAATCAATTATTTTAATTTGGGTGATTTAATAGCTCTCCTTTAACTCATTATTT
* * *
1877070 CAAGAAGTATTATCAATTATTTTAATTTGGGTGATTTAATAGCTCTCCTTTAATTTATTATTT
1 CAAGAAGTATAATCAATTATTTTAATTTGGGTGATTTAATAGCTCTCCTTTAACTCATTATTT
1877133 GCATATTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (63 bp):
CAAGAAGTATAATCAATTATTTTAATTTGGGTGATTTAATAGCTCTCCTTTAACTCATTATTT
Found at i:1883045 original size:20 final size:21
Alignment explanation
Indices: 1883020--1883071 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1883010 TTTTCCCAAT
*
1883020 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1883040 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1883061 TCGCAATGCGA
1 TCGCAATGCGA
1883072 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1883084 original size:41 final size:41
Alignment explanation
Indices: 1883057--1883134 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1883047 GCGAATTGGG
* * *
1883057 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
1883098 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
1883135 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:1883085 original size:20 final size:20
Alignment explanation
Indices: 1883060--1883154 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1883050 AATTGGGAAA
*
1883060 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1883080 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1883101 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1883121 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1883141 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1883155 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1883372 original size:22 final size:22
Alignment explanation
Indices: 1883344--1883387 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1883334 CACTCTCTCA
1883344 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
1883366 CCCATCTTCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1883388 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1883676 original size:20 final size:20
Alignment explanation
Indices: 1883651--1883688 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1883641 CGATTCTCTC
1883651 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1883671 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1883689 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1885028 original size:18 final size:18
Alignment explanation
Indices: 1885007--1885051 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1884997 TCCACTTCGG
*
1885007 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1885025 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1885043 GAGCCATCA
1 GAGCCATCA
1885052 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1885549 original size:20 final size:20
Alignment explanation
Indices: 1885524--1885569 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1885514 TAGTTTACTT
1885524 TCGCAACAC-GAAAATGACTA
1 TCGCAACACGGAAAATG-CTA
* *
1885544 TCGCAACGCGGAAATTGCTA
1 TCGCAACACGGAAAATGCTA
1885564 TCGCAA
1 TCGCAA
1885570 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
TCGCAACACGGAAAATGCTA
Found at i:1885585 original size:19 final size:19
Alignment explanation
Indices: 1885563--1885604 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1885553 GGAAATTGCT
1885563 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1885582 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1885601 ATCG
1 ATCG
1885605 TCTTTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1885701 original size:19 final size:19
Alignment explanation
Indices: 1885645--1885760 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 19
1885635 AGTTGTACAT
1885645 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1885663 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
1885677 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
1885696 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
**
1885716 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
1885735 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
1885755 TTGCGA
1 TTGCGA
1885761 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 9 0.11
19 26 0.33
20 29 0.37
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1887764 original size:19 final size:19
Alignment explanation
Indices: 1887742--1887809 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1887732 ATCGCAACGA
1887742 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1887761 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1887780 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1887794 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1887810 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1887885 original size:20 final size:20
Alignment explanation
Indices: 1887828--1887885 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1887818 TCGCATTGCG
* *
1887828 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1887848 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1887868 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1887886 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1888996 original size:24 final size:24
Alignment explanation
Indices: 1888945--1888998 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1888935 GTATTCGAAA
* *
1888945 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATATTGGTCAATACACAGAC
* *
1888969 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACAGAC
1888993 TTTGAT
1 TTTGAT
1888999 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:1889190 original size:12 final size:12
Alignment explanation
Indices: 1889173--1889197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1889163 ATATAATCCT
1889173 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1889185 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1889197 G
1 G
1889198 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.