Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007761.1 Hibiscus syriacus cultivar Beakdansim tig00110030_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: 1497221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:962763 original size:138 final size:138
Alignment explanation
Indices: 962606--962869 Score: 393
Period size: 138 Copynumber: 1.9 Consensus size: 138
962596 GTGTTTCAAG
* * ** * * * *
962606 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTTTTTCAAG
1 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
962671 GGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTA
962736 GTTCCAAA
131 GTTCCAAA
* * *
962744 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
962809 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
66 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
962870 TTTATTTCAA
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 111 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (138 bp):
AGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTA
GTTCCAAA
Found at i:962905 original size:101 final size:102
Alignment explanation
Indices: 962694--962951 Score: 331
Period size: 101 Copynumber: 2.5 Consensus size: 102
962684 AGAGAGACGA
* * ** *
962694 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAA
* * *
962759 GGAGACAAAATTTGTTTCAAATAAAACATATTCAAAT
66 AGAGACAAAATTTATTTCAAAGAAAACATATTCAAAT
* *
962796 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAA
* * * *
962860 AGAGACAAAATTTATTTCAAGGGAAATATTTTC-AAT
66 AGAGACAAAATTTATTTCAAAGAAAACATATTCAAAT
** * *
962896 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAA
962952 TGTTTTCAAT
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
100 5 0.04
101 78 0.57
102 53 0.39
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (102 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAA
AGAGACAAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:962974 original size:66 final size:66
Alignment explanation
Indices: 962836--963018 Score: 305
Period size: 66 Copynumber: 2.8 Consensus size: 66
962826 AGACAAAATT
* ** *
962836 TGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA-TTTATTTCAAGGGAAATATTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATATTTTCAATGTTT
962900 A
66 A
*
962901 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATATTTTCAATGTTT
962966 A
66 A
*
962967 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAT
963019 TATCTCAAGC
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 31 0.28
66 80 0.72
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATATTTTCAATGTTT
A
Found at i:963025 original size:37 final size:38
Alignment explanation
Indices: 962958--963032 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
962948 GAAATGTTTT
* * *
962958 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
* *
962996 CAATATTT-TGTTTCAAGGGAAATTATCTCAAGCGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
963033 TAAAATCTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (38 bp):
CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
Found at i:964764 original size:11 final size:12
Alignment explanation
Indices: 964704--964765 Score: 74
Period size: 13 Copynumber: 5.0 Consensus size: 12
964694 TTTTCTTCAA
964704 TTTTC-CTTTGTT
1 TTTTCTCTTT-TT
964716 TTTTCTCTTTTT
1 TTTTCTCTTTTT
964728 ATTTTCTCTTTGTT
1 -TTTTCTCTTT-TT
964742 TTTT-TCTCTTTT
1 TTTTCTCT-TTTT
964754 TTTTCTCTTTTT
1 TTTTCTCTTTTT
964766 GTTCTGATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
12 20 0.44
13 23 0.51
14 2 0.04
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:964768 original size:27 final size:27
Alignment explanation
Indices: 964703--964763 Score: 94
Period size: 25 Copynumber: 2.4 Consensus size: 27
964693 TTTTTCTTCA
964703 ATTTTC-CTTTG-TTTTTTCTCTTTTT
1 ATTTTCTCTTTGTTTTTTTCTCTTTTT
964728 ATTTTCTCTTTGTTTTTTTCTC-TTTT
1 ATTTTCTCTTTGTTTTTTTCTCTTTTT
964754 -TTTTCTCTTT
1 ATTTTCTCTTT
964764 TTGTTCTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 16 0.47
26 9 0.26
27 9 0.26
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (27 bp):
ATTTTCTCTTTGTTTTTTTCTCTTTTT
Found at i:966748 original size:17 final size:18
Alignment explanation
Indices: 966708--966748 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
966698 CTTTTAAATG
966708 ATGAAAATGATGAAAAAA
1 ATGAAAATGATGAAAAAA
966726 AT-AAAA-GA-GAACAAAA
1 ATGAAAATGATGAA-AAAA
966742 ATGAAAA
1 ATGAAAA
966749 AGGTTAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 8 0.38
18 2 0.10
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (18 bp):
ATGAAAATGATGAAAAAA
Found at i:967897 original size:26 final size:25
Alignment explanation
Indices: 967832--967896 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
967822 GCAAACGTGA
967832 GAATAATAAATAAAACAAGAAAAAAT
1 GAATAA-AAATAAAACAAGAAAAAAT
*
967858 GAA-AAATAACAAAACAAGTAAAAAAT
1 GAATAAA-AATAAAACAAG-AAAAAAT
967884 -AATAAAAATAAAA
1 GAATAAAAATAAAA
967897 ATGTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 20 0.59
26 13 0.38
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.14
Consensus pattern (25 bp):
GAATAAAAATAAAACAAGAAAAAAT
Found at i:968174 original size:2 final size:2
Alignment explanation
Indices: 968167--968193 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
968157 AGAATATTAA
968167 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
968194 AACGTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:968269 original size:2 final size:2
Alignment explanation
Indices: 968257--968304 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
968247 TTAATACATC
* *
968257 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
968297 TA TA TA TA
1 TA TA TA TA
968305 AAAATAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:968314 original size:22 final size:22
Alignment explanation
Indices: 968274--968338 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
968264 ATATATATAT
*
968274 ATATATATATATAAT-ATATAAG
1 ATATATATA-AAAATAATATAAG
*
968296 ATATATATAAAAATAATATAAT
1 ATATATATAAAAATAATATAAG
* *
968318 ATAAATA-AAAAAGGAATATAA
1 ATATATATAAAAA-TAATATAA
968339 TAAATAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.24
22 28 0.76
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
ATATATATAAAAATAATATAAG
Found at i:968319 original size:20 final size:21
Alignment explanation
Indices: 968268--968328 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
968258 ATACATATAT
* *
968268 ATATATATATATATATATAAT-
1 ATATAGATATATATA-AAAATA
968289 ATATAAGATATATATAAAAATA
1 ATAT-AGATATATATAAAAATA
*
968311 ATATA-ATATAAATAAAAA
1 ATATAGATATATATAAAAA
968329 AGGAATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 12 0.34
21 9 0.26
22 14 0.40
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATAGATATATATAAAAATA
Found at i:972032 original size:2 final size:2
Alignment explanation
Indices: 972025--972057 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
972015 AGTTATGAGA
972025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
972058 ACAAGCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:972581 original size:39 final size:39
Alignment explanation
Indices: 972527--972604 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
972517 AGTCGAGAGT
972527 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
972566 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
972605 ATTTCAGTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26
Consensus pattern (39 bp):
TACAGTGGTCCTATGGGACATAGTGGTCCTTCGGGACAA
Found at i:972603 original size:18 final size:18
Alignment explanation
Indices: 972530--972595 Score: 89
Period size: 18 Copynumber: 3.5 Consensus size: 18
972520 CGAGAGTTAC
972530 AGTGGTCCTATGGGACAT
1 AGTGGTCCTATGGGACAT
972548 AGTGGTCCT-TCGGGACAAT
1 AGTGGTCCTAT-GGGAC-AT
972567 ACAGTGGTCCTATGGGACAT
1 --AGTGGTCCTATGGGACAT
972587 AGTGGTCCT
1 AGTGGTCCT
972596 TCGGGACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.02
18 23 0.53
19 2 0.05
20 2 0.05
21 14 0.33
22 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTATGGGACAT
Found at i:972879 original size:18 final size:18
Alignment explanation
Indices: 972858--972911 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
972848 TACATGATCG
972858 TGATAGAGATCATGATAA
1 TGATAGAGATCATGATAA
** **
972876 TGATATTGATGTTGATAA
1 TGATAGAGATCATGATAA
972894 TGATAGAGATCATGATAA
1 TGATAGAGATCATGATAA
972912 AGATGTTTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (18 bp):
TGATAGAGATCATGATAA
Found at i:972905 original size:36 final size:36
Alignment explanation
Indices: 972858--972932 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
972848 TACATGATCG
*
972858 TGATAGAGATCATGATAATGAT-ATTGATGTTGATAA
1 TGATAGAGATCATGATAAAGATGATTG-TGTTGATAA
*
972894 TGATAGAGATCATGATAAAGATGTTTGTGTTGATAA
1 TGATAGAGATCATGATAAAGATGATTGTGTTGATAA
972930 TGA
1 TGA
972933 GGGTATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 33 0.92
37 3 0.08
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (36 bp):
TGATAGAGATCATGATAAAGATGATTGTGTTGATAA
Found at i:977834 original size:18 final size:18
Alignment explanation
Indices: 977811--977845 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
977801 CGAGGGTTAC
*
977811 AGTGGTCCTACGGGACAT
1 AGTGGTCATACGGGACAT
*
977829 AGTGGTCATTCGGGACA
1 AGTGGTCATACGGGACA
977846 AATTTCAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCATACGGGACAT
Found at i:978111 original size:18 final size:18
Alignment explanation
Indices: 978088--978155 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
978078 AATGTTAATA
*
978088 CATGATAGTGATATAGAT
1 CATGATAATGATATAGAT
*
978106 CATGATAATGATATTGAT
1 CATGATAATGATATAGAT
** *
978124 GTTGATAATGATAGAGAT
1 CATGATAATGATATAGAT
*
978142 CATGATAAAGATAT
1 CATGATAATGATAT
978156 TTGTGTTGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (18 bp):
CATGATAATGATATAGAT
Found at i:978142 original size:36 final size:36
Alignment explanation
Indices: 978090--978168 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
978080 TGTTAATACA
* * *
978090 TGATAGTGATATAGATCATGATAATGATA-TTGATGT
1 TGATAATGATAGAGATCATGATAAAGATATTTG-TGT
978126 TGATAATGATAGAGATCATGATAAAGATATTTGTGT
1 TGATAATGATAGAGATCATGATAAAGATATTTGTGT
978162 TGATAAT
1 TGATAAT
978169 TAGAGTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
36 36 0.92
37 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (36 bp):
TGATAATGATAGAGATCATGATAAAGATATTTGTGT
Found at i:980809 original size:35 final size:35
Alignment explanation
Indices: 980752--980831 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
980742 TAATATGTAC
*
980752 TACTATATACTAAACTACTTAATATGAAGACTATA
1 TACTATATACTAAACTACTTAATATGAAAACTATA
* * *
980787 TACTATATATTATACTATTTAATATGAAAACTATA
1 TACTATATACTAAACTACTTAATATGAAAACTATA
980822 TACTATATAC
1 TACTATATAC
980832 GTACTATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (35 bp):
TACTATATACTAAACTACTTAATATGAAAACTATA
Found at i:981900 original size:12 final size:13
Alignment explanation
Indices: 981885--981917 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
981875 TTCTTTTGTT
981885 TTCTCTT-TCTTC
1 TTCTCTTCTCTTC
981897 TTCTCTTTCTCTTC
1 TTCTC-TTCTCTTC
981911 TTCTCTT
1 TTCTCTT
981918 ATTTATTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 4 0.21
14 10 0.53
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTCTTCTCTTC
Found at i:987592 original size:27 final size:27
Alignment explanation
Indices: 987531--987651 Score: 106
Period size: 27 Copynumber: 4.6 Consensus size: 27
987521 TATTTATAAG
* * * *
987531 AATTAAAAGAAATAAAGATTTAAAGGCG
1 AATTAAAAGGAATAAACATTAAAAGG-A
*
987559 AA-TAAAAGGAATAAACATTAAAAAGA
1 AATTAAAAGGAATAAACATTAAAAGGA
* * *
987585 AATCAAAAGGAA-AAATATT-ATAGGA
1 AATTAAAAGGAATAAACATTAAAAGGA
* * *
987610 AGTTAAAAAGAATAAAGATTAAAAGGA
1 AATTAAAAGGAATAAACATTAAAAGGA
987637 AATTAAAA-GAATAAA
1 AATTAAAAGGAATAAA
987652 AAATTAAATA
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
25 13 0.17
26 21 0.28
27 39 0.52
28 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.15, T:0.19
Consensus pattern (27 bp):
AATTAAAAGGAATAAACATTAAAAGGA
Found at i:987666 original size:26 final size:25
Alignment explanation
Indices: 987561--987659 Score: 74
Period size: 26 Copynumber: 3.8 Consensus size: 25
987551 TAAAGGCGAA
*
987561 TAAAAGGAATAAACATTAAAAAGAAAT
1 TAAAA-GAATAAAAATT-AAAAGAAAT
* * * * *
987588 CAAAAGGAA-AAATATTATAGGAAGT
1 TAAAA-GAATAAAAATTAAAAGAAAT
*
987613 TAAAAAGAATAAAGATTAAAAGGAAAT
1 T-AAAAGAATAAAAATTAAAA-GAAAT
987640 TAAAAGAATAAAAAATTAAA
1 TAAAAGAAT-AAAAATTAAA
987660 TAAAATTGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
25 9 0.16
26 26 0.46
27 22 0.39
ACGTcount: A:0.66, C:0.02, G:0.13, T:0.19
Consensus pattern (25 bp):
TAAAAGAATAAAAATTAAAAGAAAT
Found at i:998675 original size:17 final size:19
Alignment explanation
Indices: 998647--998686 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
998637 ATTCCACCAA
*
998647 TTTTCCTCTTTT-ATTTAT
1 TTTTCCTCTTTTCATTCAT
998665 TTTTCCT-TTTTCATTCAT
1 TTTTCCTCTTTTCATTCAT
998683 TTTT
1 TTTT
998687 TTTTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTCCTCTTTTCATTCAT
Found at i:1000250 original size:35 final size:35
Alignment explanation
Indices: 1000190--1000258 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
1000180 ATTACAATAT
*
1000190 ATTAAACTACTTAATATGAAGACTATATACTATAA
1 ATTAAACTACTTAATATGAAAACTATATACTATAA
* * *
1000225 ATTATACTATTTAATTTGAAAACTATATACTATA
1 ATTAAACTACTTAATATGAAAACTATATACTATA
1000259 TACATACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (35 bp):
ATTAAACTACTTAATATGAAAACTATATACTATAA
Found at i:1000365 original size:10 final size:10
Alignment explanation
Indices: 1000350--1000374 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1000340 GATTAAGCAT
1000350 TTTAGTTGCA
1 TTTAGTTGCA
1000360 TTTAGTTGCA
1 TTTAGTTGCA
1000370 TTTAG
1 TTTAG
1000375 GACATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:1001769 original size:55 final size:55
Alignment explanation
Indices: 1001689--1002182 Score: 643
Period size: 55 Copynumber: 9.0 Consensus size: 55
1001679 ATTACCAAAT
* * * * *
1001689 GGCACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
1 GGCACTGTGTGTG-TAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
1001746 GACACTGTATGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTACG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
1001801 GGCATTGTGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
1001856 GGCACTGTGTGTGAAAAACCAATAAATTCGTAATAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* ** *
1001911 GGCACTGTGTGTGCAAAACTAAGAAATTTGTAAGAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
1001966 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
1002021 GGCACTGTATGTGTAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATG
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * * *
1002076 GGCTCTGTGTATG-CAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
1002130 GGCACTGTGTGTG--CAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
1 GGCACTGTGTGTGTAAAAC-TAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1002183 CGAAACTAAG
Statistics
Matches: 388, Mismatches: 48, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
53 3 0.01
54 80 0.21
55 291 0.75
56 4 0.01
57 10 0.03
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (55 bp):
GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:1002002 original size:165 final size:165
Alignment explanation
Indices: 1001689--1002178 Score: 709
Period size: 165 Copynumber: 3.0 Consensus size: 165
1001679 ATTACCAAAT
* * * * *
1001689 GGCACTTTGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGACACTGT
1 GGCACTGTGTGTG-AAAAA-CTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGT
* * * * * *
1001754 ATGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTACGGGCATTGTGTGTGAAAAA
64 GTGTGCAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAA
1001819 CTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
129 CTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
* * *
1001856 GGCACTGTGTGTGAAAAACCAATAAATTCGTAATAAGTTTATGAATTTCCGTATGGGCACTGTGT
1 GGCACTGTGTGTGAAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
** *
1001921 GTGCAAAACTAAGAAATTTGTAAGAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAAAACT
66 GTGCAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACT
1001986 AAGAAATTCATAATAAGTTTATGAATTTCCATATG
131 AAGAAATTCATAATAAGTTTATGAATTTCCATATG
* * *
1002021 GGCACTGTATGTGTAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCTCTGTGT
1 GGCACTGTGTGTGAAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
* *
1002086 ATGC-AAACTAAGAAATTCATAATG-AGTTTATGAATTTCTGTATTGGCACTGTGTGTGC--AAC
66 GTGCAAAACTAAGAAATTCATAA-GAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAAC
*
1002147 TTAAGAAATTCATAATGAGTTTATGAATTTCC
130 -TAAGAAATTCATAATAAGTTTATGAATTTCC
1002179 GTATCGAAAC
Statistics
Matches: 292, Mismatches: 29, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
162 3 0.01
163 30 0.10
164 48 0.16
165 194 0.66
166 5 0.02
167 12 0.04
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (165 bp):
GGCACTGTGTGTGAAAAACTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATGGGCACTGTGT
GTGCAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACT
AAGAAATTCATAATAAGTTTATGAATTTCCATATG
Found at i:1004768 original size:21 final size:21
Alignment explanation
Indices: 1004748--1004786 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1004738 CACTACAAGA
*
1004748 ATTT-ATGGCATCGACAAAAG
1 ATTTCATGGCATCAACAAAAG
*
1004768 ATTTCATGGCTTCAACAAA
1 ATTTCATGGCATCAACAAA
1004787 GACCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (21 bp):
ATTTCATGGCATCAACAAAAG
Found at i:1007306 original size:23 final size:23
Alignment explanation
Indices: 1007273--1007335 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
1007263 CAGCTCGTAT
1007273 AAATGCACCAAAGTGCCGTGTAG
1 AAATGCACCAAAGTGCCGTGTAG
*
1007296 AATTGCACCAAAGTGCCGTGTAG
1 AAATGCACCAAAGTGCCGTGTAG
1007319 AAATGCACCAAAGTGCC
1 AAATGCACCAAAGTGCC
1007336 ATACAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCGTGTAG
Found at i:1008029 original size:19 final size:18
Alignment explanation
Indices: 1007985--1008029 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1007975 CACTATCCTA
* *
1007985 AATTTATACATATCATTT
1 AATTTATACATAACATAT
*
1008003 AATCTATACTATAACATAT
1 AATTTATAC-ATAACATAT
1008022 AATTTATA
1 AATTTATA
1008030 TCACTTATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTATACATAACATAT
Found at i:1008585 original size:31 final size:31
Alignment explanation
Indices: 1008549--1008608 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1008539 AACTTAAAAG
* *
1008549 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1008580 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1008609 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1009109 original size:28 final size:28
Alignment explanation
Indices: 1009078--1009189 Score: 134
Period size: 28 Copynumber: 4.3 Consensus size: 28
1009068 TATATGATAT
1009078 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATTAA
*
1009107 AAAATTAATAT-T-TAAT-T--TATTTA
1 AAAATTAATATCTATAATATAATATTAA
1009130 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
*
1009158 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
1009182 AAAATTAA
1 AAAATTAA
1009190 AATTAAATTA
Statistics
Matches: 75, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
23 16 0.21
24 13 0.17
25 8 0.11
26 9 0.12
27 2 0.03
28 21 0.28
29 6 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:1009115 original size:14 final size:14
Alignment explanation
Indices: 1009098--1009169 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
1009088 ATCTATAATA
1009098 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
1009112 TAATATT---TAAT
1 TAATATTAAAAAAT
*
1009123 T--TATTTAAAAAT
1 TAATATTAAAAAAT
* *
1009135 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
1009149 TAATATTAAAAAAT
1 TAATATTAAAAAAT
1009163 TAATATT
1 TAATATT
1009170 TAATTTATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
9 4 0.09
11 4 0.09
12 4 0.09
13 5 0.11
14 23 0.52
15 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:1009117 original size:19 final size:20
Alignment explanation
Indices: 1009093--1009140 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
1009083 TAAATATCTA
1009093 TAATATAA-TATTAAAAAAT
1 TAATATAATTATTAAAAAAT
*
1009112 TAATATTTAATTTATTTAAAAAT
1 TAATA--TAA-TTATTAAAAAAT
1009135 TAATAT
1 TAATAT
1009141 CTATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 5 0.21
21 4 0.17
23 15 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATAATTATTAAAAAAT
Found at i:1009184 original size:51 final size:52
Alignment explanation
Indices: 1009078--1009189 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 52
1009068 TATATGATAT
1009078 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-A
1 AAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1009130 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1009182 AAAATTAA
1 AAAATTAA
1009190 AATTAAATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 44 0.75
52 15 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (52 bp):
AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
Found at i:1009186 original size:24 final size:24
Alignment explanation
Indices: 1009103--1009198 Score: 122
Period size: 24 Copynumber: 3.9 Consensus size: 24
1009093 TAATATAATA
1009103 TTAAAAAATTAATATTTAATTTAT
1 TTAAAAAATTAATATTTAATTTAT
*
1009127 TT-AAAAATTAATATCTATAATATAAT
1 TTAAAAAATTAATAT-T-TAAT-TTAT
1009153 ATTAAAAAATTAATATTTAATTTAT
1 -TTAAAAAATTAATATTTAATTTAT
* *
1009178 TTAAAAAATTAAAATTAAATT
1 TTAAAAAATTAATATTTAATT
1009199 AAAATTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 12 0.19
24 22 0.35
25 7 0.11
26 7 0.11
27 3 0.05
28 12 0.19
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAAAAATTAATATTTAATTTAT
Found at i:1009193 original size:6 final size:6
Alignment explanation
Indices: 1009182--1009230 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
1009172 ATTTATTTAA
* *
1009182 AAAATT AAAATT -AAATT AAAATT AAAA-T CAAA-T ATAATAT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT-T AAAATT
1009228 AAA
1 AAA
1009231 TATAAAACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 12 0.33
6 19 0.53
7 5 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:1009202 original size:17 final size:17
Alignment explanation
Indices: 1009182--1009237 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
1009172 ATTTATTTAA
1009182 AAAATTAAAATTAAATT
1 AAAATTAAAATTAAATT
*
1009199 AAAATTAAAATCAAA-T
1 AAAATTAAAATTAAATT
*
1009215 ATAATATAAAATTAAATAT
1 AAAAT-TAAAATTAAAT-T
1009234 AAAA
1 AAAA
1009238 CCTCATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 5 0.16
17 23 0.72
19 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTAAAATTAAATT
Found at i:1009208 original size:24 final size:25
Alignment explanation
Indices: 1009078--1009208 Score: 97
Period size: 28 Copynumber: 5.1 Consensus size: 25
1009068 TATATGATAT
*
1009078 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATAT-TA-AAT-TAAAATTAA
* * *
1009107 AAAATTAATATTTAATT--TATTTA
1 AAAATTAATATTAAATTAAAATTAA
*
1009130 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATAT-TA-AAT-TAAAATTAA
* * *
1009158 AAAATTAATATTTAATT-TATTTAA
1 AAAATTAATATTAAATTAAAATTAA
*
1009182 AAAATTAAAATTAAATTAAAATTAA
1 AAAATTAATATTAAATTAAAATTAA
1009207 AA
1 AA
1009209 TCAAATATAA
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
23 16 0.19
24 20 0.24
25 12 0.14
26 7 0.08
27 2 0.02
28 21 0.25
29 6 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATTAATATTAAATTAAAATTAA
Found at i:1009226 original size:12 final size:11
Alignment explanation
Indices: 1009158--1009237 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
1009148 ATAATATTAA
1009158 AAAATTAATAT
1 AAAATTAATAT
** * *
1009169 TTAATTTATTT
1 AAAATTAATAT
1009180 AAAA--AAT-T
1 AAAATTAATAT
1009188 AAAATTAA-ATT
1 AAAATTAATA-T
*
1009199 AAAATTAAAAT
1 AAAATTAATAT
*
1009210 CAAATATAATAT
1 AAAAT-TAATAT
1009222 AAAATTAAATAT
1 AAAATT-AATAT
1009234 AAAA
1 AAAA
1009238 CCTCATTGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
8 5 0.10
9 2 0.04
10 2 0.04
11 24 0.46
12 19 0.37
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:1013480 original size:23 final size:23
Alignment explanation
Indices: 1013426--1013489 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1013416 CAGCTTGTAT
*
1013426 AAATGCACCGAAGTACCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
1013449 AATTACACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
1013472 AAATGCACCAAAGTGCCA
1 AAATGCACCGAAGTGCCA
1013490 TACAAAATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1027595 original size:20 final size:20
Alignment explanation
Indices: 1027556--1027594 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1027546 CACTGCAAGA
1027556 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
1027576 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
1027595 GGCCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1030240 original size:112 final size:112
Alignment explanation
Indices: 1030041--1030266 Score: 380
Period size: 112 Copynumber: 2.0 Consensus size: 112
1030031 TTTAGGTCTT
*
1030041 CTACTACAGCAAAATCAGTAATTCATGTTCAATGAAGAATGTCACAATGTATTCATGGACCTGAA
1 CTACTACAGCAAAATCAGCAATTCATGTTCAATGAAGAATGTCACAATGTATTCATGGACCTGAA
* * *
1030106 TAAAAACTTGCTTCAACTCCAATTGTTGTTCCACTTGACTGGGATGC
66 TAAAAACTTGCTTCAACACCAATTGTTGTTCCACTTAACTGGGACGC
* *
1030153 CTACTGCAGTAAAATCAGCAATTCATGTTCAATGAAGAATGTCACAATGTATTCATGGACCTGAA
1 CTACTACAGCAAAATCAGCAATTCATGTTCAATGAAGAATGTCACAATGTATTCATGGACCTGAA
* *
1030218 TAAAAACTTGCTTCAGCACCAATTGTTTTTCCACTTAACTGGGACGC
66 TAAAAACTTGCTTCAACACCAATTGTTGTTCCACTTAACTGGGACGC
1030265 CT
1 CT
1030267 CTTTCGAGCT
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (112 bp):
CTACTACAGCAAAATCAGCAATTCATGTTCAATGAAGAATGTCACAATGTATTCATGGACCTGAA
TAAAAACTTGCTTCAACACCAATTGTTGTTCCACTTAACTGGGACGC
Found at i:1035100 original size:19 final size:19
Alignment explanation
Indices: 1035076--1035116 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1035066 CCTAAATATT
*
1035076 TATACCTTCGTTTGGTGCA
1 TATACCTTCGTTTAGTGCA
1035095 TATACCTTCGTTTAGTGCA
1 TATACCTTCGTTTAGTGCA
1035114 TAT
1 TAT
1035117 GTTGTGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (19 bp):
TATACCTTCGTTTAGTGCA
Found at i:1042525 original size:43 final size:43
Alignment explanation
Indices: 1042458--1042936 Score: 611
Period size: 43 Copynumber: 11.0 Consensus size: 43
1042448 AATCCCCAGG
*
1042458 TTCCCCAGGTTCCTTTGCCGTGTGCAAGGGTAAGCCTTACAGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * *
1042501 TTCCCCAAGTTCCTTTGCTTTGTGCATGGGTAAGCCTTA-AGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
1042543 TTCCTCAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
1042586 TTCCCCCAAGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGT
1 TT-CCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * * * * *
1042630 TTCCTCAGGTTCATTTGTTGTGTGGAAAGGTAAGCCTTATAGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
1042673 TTCCCAAGGTTCCTTTACTGTGTGCAAGGGTAAGCCTTACAGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
1042716 TTCCCCTAGGTTCCTTTGCTGTGTGCAATGGTAAGCCTTACAGT
1 TTCCCC-AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * * *
1042760 TTCCACAGGTTCCTTTTCTATGTGCAAGGGTAAGCCTTACATT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
1042803 TTCCCCAAGGTTCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTT
1 TTCCCC-AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-T
* * *
1042848 TTCCCCAGGTTCCTTTGTTGTGTGAAAGGGTAAGACCTTACCGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGT
* * * * * *
1042892 TT-CCCAGGCTCTTTTACTATGTGAAAGGGTAAGACCTTACCGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGT
1042935 TT
1 TT
1042937 TTGCATGCTC
Statistics
Matches: 382, Mismatches: 48, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
42 37 0.10
43 191 0.50
44 140 0.37
45 14 0.04
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (43 bp):
TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
Found at i:1042674 original size:87 final size:86
Alignment explanation
Indices: 1042458--1042936 Score: 599
Period size: 87 Copynumber: 5.5 Consensus size: 86
1042448 AATCCCCAGG
*
1042458 TTCCCCAGGTTCCTTTGCCGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGCTT-T
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTG-TTGT
*
1042522 GTGCATGGGTAAGCCTTA-AGT
65 GTGCAAGGGTAAGCCTTACAGT
* *
1042543 TTCCTCAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAAGTTCCTTTGTTGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAAGTTCCTTTGTTGT
1042608 GTGCAAGGGTAAGCCTTACAGT
65 GTGCAAGGGTAAGCCTTACAGT
* * * * * * **
1042630 TTCCTCAGGTTCATTTGTTGTGTGGAAAGGTAAGCCTTATAGTTT-CCCAAGGTTCCTTTACTGT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAA-GTTCCTTTGTTGT
1042694 GTGCAAGGGTAAGCCTTACAGT
65 GTGCAAGGGTAAGCCTTACAGT
* * * *
1042716 TTCCCCTAGGTTCCTTTGCTGTGTGCAATGGTAAGCCTTACAGTTTCCACAGGTTCCTTT-TCTA
1 TTCCCC-AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGT-TG
*
1042780 TGTGCAAGGGTAAGCCTTACATT
64 TGTGCAAGGGTAAGCCTTACAGT
* *
1042803 TTCCCCAAGGTTCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGTTG
1 TTCCCC-AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAAGTTCCTTTGTTG
* *
1042868 TGTGAAAGGGTAAGACCTTACCGT
64 TGTGCAAGGGTAAG-CCTTACAGT
* * * * * *
1042892 TT-CCCAGGCTCTTTTACTATGTGAAAGGGTAAGACCTTACCGTTT
1 TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTT
1042937 TTGCATGCTC
Statistics
Matches: 346, Mismatches: 37, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
85 49 0.14
86 71 0.21
87 173 0.50
88 43 0.12
89 10 0.03
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (86 bp):
TTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTTCCTTTGTTGTG
TGCAAGGGTAAGCCTTACAGT
Found at i:1044161 original size:46 final size:45
Alignment explanation
Indices: 1044039--1044176 Score: 206
Period size: 45 Copynumber: 3.0 Consensus size: 45
1044029 ATCGGTACTA
* *
1044039 CTTTTGTTATTTTTAAATAAAACTATCCT-TGACTAGTTGTTGGGC
1 CTTTTGTTATTTTTAAATAAAACTA-GCTGTGACTAGCTGTTGGGC
* *
1044084 CTTTTGTTATTTTTAAATAAAACTAGTTGTGACTAGGTGTTGGGC
1 CTTTTGTTATTTTTAAATAAAACTAGCTGTGACTAGCTGTTGGGC
*
1044129 CTTTTGTTTTTTTTTAAATAAAACTAGCTGTGACTAGCTGTTGGGC
1 CTTTTG-TTATTTTTAAATAAAACTAGCTGTGACTAGCTGTTGGGC
1044175 CT
1 CT
1044177 GATGGTATCA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 46 0.54
46 38 0.45
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (45 bp):
CTTTTGTTATTTTTAAATAAAACTAGCTGTGACTAGCTGTTGGGC
Found at i:1044296 original size:20 final size:20
Alignment explanation
Indices: 1044271--1044319 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1044261 TGTTGGTAGT
1044271 ATCGATACTACCTAGTGAGG
1 ATCGATACTACCTAGTGAGG
* *
1044291 ATCGATACTTCTTAGTGAGG
1 ATCGATACTACCTAGTGAGG
*
1044311 ATCAATACT
1 ATCGATACT
1044320 TCTCATACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
ATCGATACTACCTAGTGAGG
Found at i:1044558 original size:16 final size:14
Alignment explanation
Indices: 1044537--1044657 Score: 62
Period size: 13 Copynumber: 8.9 Consensus size: 14
1044527 ATAGTTCAAC
1044537 ATATACTTTAATACTT
1 ATATACTTT-ATA-TT
1044553 ATATACTTTATATT
1 ATATACTTTATATT
* *
1044567 ATATACATATACACTT
1 ATATAC-TTTATA-TT
*
1044583 -TAGT-CTTTATAAT
1 ATA-TACTTTATATT
1044596 -TATACTTTATA-T
1 ATATACTTTATATT
* *
1044608 ATATA--ATATACT
1 ATATACTTTATATT
1044620 -TATACTTTATATT
1 ATATACTTTATATT
* *
1044633 AT-TA-TATATGTAT
1 ATATACTTTATAT-T
1044646 ATATACTTTATA
1 ATATACTTTATA
1044658 CTAAAACTAT
Statistics
Matches: 81, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
11 8 0.10
12 8 0.10
13 24 0.30
14 15 0.19
15 14 0.17
16 12 0.15
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATACTTTATATT
Found at i:1044572 original size:22 final size:22
Alignment explanation
Indices: 1044547--1044634 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 22
1044537 ATATACTTTA
*
1044547 ATACTTATATACTTTATATTAT
1 ATACATATATACTTTATATTAT
* *
1044569 ATACATATACACTTTAGTCTT-T
1 ATACATATATACTTTA-TATTAT
1044591 ATA-AT-TATACTTTATA-TAT
1 ATACATATATACTTTATATTAT
*
1044610 ATAATATACTTATACTTTATATTAT
1 AT-ACATA--TATACTTTATATTAT
1044635 TATATATGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 9 0.17
21 4 0.08
22 18 0.34
23 3 0.06
24 11 0.21
25 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (22 bp):
ATACATATATACTTTATATTAT
Found at i:1044657 original size:27 final size:24
Alignment explanation
Indices: 1044595--1044640 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1044585 GTCTTTATAA
1044595 TTATACTTTATATATATAATATAC
1 TTATACTTTATATATATAATATAC
*
1044619 TTATACTTTATAT-TATTATATA
1 TTATACTTTATATATATAATATA
1044641 TGTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATACTTTATATATATAATATAC
Found at i:1048986 original size:122 final size:121
Alignment explanation
Indices: 1048761--1048986 Score: 262
Period size: 122 Copynumber: 1.9 Consensus size: 121
1048751 TTTGGTCCAT
* *
1048761 GATTTCCTATTCCTTTAATTCCACATTCATTTTAAGTCAACATTTTACAAAATTTGAACCACATA
1 GATTTCCTATTCCTTAAATTCCACATTCATTTTAAGT-AACATTTTACAAAATTTAAACCACATA
* * *
1048826 CTCCTAAACCATCATAGAATACATATGTACTTTTAATTCAGTCCCTCAATTTTGCAC
65 CTCCCAAACCATCATAGAATACATAAGTACTTTCAATTCAGTCCCTCAATTTTGCAC
* * * *
1048883 GATTTCCATATTTCTTAAATT-CATCCTTCATTTTAAGT-ACGTTTTGACCAAATTTAAACCACA
1 GATTTCC-TATTCCTTAAATTCCA-CATTCATTTTAAGTAACATTTT-ACAAAATTTAAACCACA
* **
1048946 TGCTCCCCTACCA-CTATAGAATACATAAGTAAC-TTCAATTC
63 TACTCCCAAACCATC-ATAGAATACATAAGT-ACTTTCAATTC
1048987 TATTATTTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
121 7 0.08
122 54 0.62
123 26 0.30
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (121 bp):
GATTTCCTATTCCTTAAATTCCACATTCATTTTAAGTAACATTTTACAAAATTTAAACCACATAC
TCCCAAACCATCATAGAATACATAAGTACTTTCAATTCAGTCCCTCAATTTTGCAC
Found at i:1049742 original size:25 final size:27
Alignment explanation
Indices: 1049668--1049753 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 27
1049658 TAATTCGGTT
*
1049668 AATTTTCGAATTAACAAAAAAAAATTTAA
1 AATTTTCTAATT--CAAAAAAAAATTTAA
* * *
1049697 AATTTTCTAATTTATATAAAAA-TT-A
1 AATTTTCTAATTCAAAAAAAAATTTAA
* *
1049722 AATTTTTTAATTCAAAAAAAAAGTTTAT
1 AATTTTCTAATTCAAAAAAAAA-TTTAA
1049750 AATT
1 AATT
1049754 AATTTAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
25 19 0.42
26 2 0.04
27 9 0.20
28 4 0.09
29 11 0.24
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
AATTTTCTAATTCAAAAAAAAATTTAA
Found at i:1049947 original size:186 final size:186
Alignment explanation
Indices: 1049723--1050098 Score: 619
Period size: 186 Copynumber: 2.0 Consensus size: 186
1049713 TAAAAATTAA
* *
1049723 ATTTTTTAATTCAAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATT
1 ATTTTTTAATTCAAAAAAAAAGTTCACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
*
1049788 TCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTGTT
66 TCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATT
* * * *
1049853 AATTGAGTTTTAAATGGTTTGGGCTTAGCTCATATGTTATATATAATATATATAAT
131 AATTGAGTTTTAAATAGTTTGGGCTGACCCCATATGTTATATATAATATATATAAT
*
1049909 ATTTTTTAATT-AAGAAAAACAGTTCACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 ATTTTTTAATTCAA-AAAAAAAGTTCACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
* * *
1049973 TTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
65 TTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
* *
1050038 TAATTGGGTTTTAAATAGTTTGGGCTGACCCCATATGTTATATATAATATATTTAAT
130 TAATTGAGTTTTAAATAGTTTGGGCTGACCCCATATGTTATATATAATATATATAAT
1050095 ATTT
1 ATTT
1050099 AAAATTTAAT
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
185 2 0.01
186 174 0.99
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (186 bp):
ATTTTTTAATTCAAAAAAAAAGTTCACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
TCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATT
AATTGAGTTTTAAATAGTTTGGGCTGACCCCATATGTTATATATAATATATATAAT
Found at i:1050154 original size:27 final size:27
Alignment explanation
Indices: 1050124--1050176 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1050114 TTAATTAAAC
*
1050124 GAATTCGAACCGAATTAACTGTTAACT
1 GAATTCGAACCGAATTAACCGTTAACT
1050151 GAATTCGAACCGAATTAACCGTTAAC
1 GAATTCGAACCGAATTAACCGTTAAC
1050177 CGAACTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (27 bp):
GAATTCGAACCGAATTAACCGTTAACT
Found at i:1053114 original size:2 final size:2
Alignment explanation
Indices: 1053107--1053141 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1053097 GTTAGTGATT
1053107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1053142 TAAAATATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1053170 original size:24 final size:23
Alignment explanation
Indices: 1053130--1053206 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 23
1053120 ATATATATAT
*
1053130 ATATATATATATTAAAATATAGTTA
1 ATATA-ATAT-TTAAAATATAATTA
* *
1053155 ATATAATATTTAAAAAAATAATAA
1 ATATAATATTT-AAAATATAATTA
1053179 AT-TCAATATTTTAAAATA-AATTTA
1 ATAT-AATA-TTTAAAATATAA-TTA
1053203 ATAT
1 ATAT
1053207 GTATAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
23 5 0.12
24 28 0.67
25 9 0.21
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATATAATATTTAAAATATAATTA
Found at i:1059289 original size:23 final size:23
Alignment explanation
Indices: 1059236--1059290 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
1059226 ATATGTAATA
*
1059236 TATGTATATGAATATAACTATGT
1 TATGTATATGAATATAACTATAT
1059259 TATGGTATATGAA-ATAAGC-ATCAT
1 TAT-GTATATGAATATAA-CTAT-AT
1059283 TATGTATA
1 TATGTATA
1059291 AAGATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (23 bp):
TATGTATATGAATATAACTATAT
Found at i:1062088 original size:23 final size:23
Alignment explanation
Indices: 1062057--1062115 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1062047 CTTTCCTTGG
* *
1062057 CTTTGCTTCTTTTTTTTTTAATT
1 CTTTTCTTCTTTTTTTTCTAATT
*
1062080 CTTTTCTTCTTGTTTTTCTAATT
1 CTTTTCTTCTTTTTTTTCTAATT
1062103 -TTTTCTTCTTTTT
1 CTTTTCTTCTTTTT
1062116 GTCTTTGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (23 bp):
CTTTTCTTCTTTTTTTTCTAATT
Found at i:1062481 original size:22 final size:22
Alignment explanation
Indices: 1062456--1062497 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1062446 AGAATTAAGT
1062456 GGATGATGAAGGTCTTGATGGA
1 GGATGATGAAGGTCTTGATGGA
* * *
1062478 GGATGTTGATGGTGTTGATG
1 GGATGATGAAGGTCTTGATG
1062498 TTGAAATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.02, G:0.43, T:0.33
Consensus pattern (22 bp):
GGATGATGAAGGTCTTGATGGA
Found at i:1064597 original size:18 final size:19
Alignment explanation
Indices: 1064561--1064598 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1064551 TATTCATAAG
1064561 GTATCGATACCTGAAGGGTA
1 GTATCGATACC-GAAGGGTA
1064581 GTATCGATACC-AAGGGTA
1 GTATCGATACCGAAGGGTA
1064599 CCGATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GTATCGATACCGAAGGGTA
Found at i:1065363 original size:22 final size:23
Alignment explanation
Indices: 1065338--1065380 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1065328 AATCGAGGGT
* *
1065338 TACAT-AGGTCTTTTGGGACATA
1 TACATGAGGTCCTTCGGGACATA
1065360 TACATGAGGTCCTTCGGGACA
1 TACATGAGGTCCTTCGGGACA
1065381 AGTTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
TACATGAGGTCCTTCGGGACATA
Found at i:1073335 original size:19 final size:20
Alignment explanation
Indices: 1073312--1073354 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1073302 AAAGAAGAAA
* * *
1073312 AAAAAAAGAAATGCCCACAT
1 AAAACAAGAAATACACACAT
1073332 AAAATCAAGAAATACACACAT
1 AAAA-CAAGAAATACACACAT
1073353 AA
1 AA
1073355 GTATTAAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.63, C:0.19, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAACAAGAAATACACACAT
Found at i:1075010 original size:24 final size:24
Alignment explanation
Indices: 1074983--1075030 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1074973 CTTCTCCACC
1074983 GAACAGTCCACGTTTCTACCAGCT
1 GAACAGTCCACGTTTCTACCAGCT
1075007 GAACAGTCCACGTTTCTACCAGCT
1 GAACAGTCCACGTTTCTACCAGCT
1075031 CCCTCAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (24 bp):
GAACAGTCCACGTTTCTACCAGCT
Found at i:1075789 original size:18 final size:19
Alignment explanation
Indices: 1075753--1075790 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1075743 CACGGAATGT
1075753 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
1075773 AAGATTACCAG-GGAATAA
1 AAGATTACCAGAGGAATAA
1075791 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:1075803 original size:15 final size:16
Alignment explanation
Indices: 1075752--1075796 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
1075742 TCACGGAATG
1075752 TAAGATTACCAGTAGGAA
1 TAAGATTACCAG--GGAA
1075770 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
1075788 TAAGATTAC
1 TAAGATTAC
1075797 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 6 0.24
20 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:1078457 original size:12 final size:12
Alignment explanation
Indices: 1078440--1078469 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1078430 AGGTAAACAT
1078440 GGATACTTTGAA
1 GGATACTTTGAA
1078452 GGATACTTTGAA
1 GGATACTTTGAA
1078464 GGATAC
1 GGATAC
1078470 GGTCAAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (12 bp):
GGATACTTTGAA
Found at i:1079760 original size:18 final size:18
Alignment explanation
Indices: 1079737--1079771 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1079727 CAAGACTTAA
*
1079737 TTTTAATGGTTTAAAATT
1 TTTTAAGGGTTTAAAATT
1079755 TTTTAAGGGTTTAAAAT
1 TTTTAAGGGTTTAAAAT
1079772 ACAATTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
TTTTAAGGGTTTAAAATT
Found at i:1082392 original size:24 final size:24
Alignment explanation
Indices: 1082365--1082413 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1082355 TGCATGACAT
*
1082365 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGCTTTATACATCA
1082389 TGTACATAGATGCTTTATACATCA
1 TGTACATAGATGCTTTATACATCA
1082413 T
1 T
1082414 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (24 bp):
TGTACATAGATGCTTTATACATCA
Found at i:1083150 original size:42 final size:42
Alignment explanation
Indices: 1083091--1083176 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
1083081 TTCTTGTTGC
1083091 TTTGTTAACTATTTTGGAAATAATTGTAATAGCTAAACTAAA
1 TTTGTTAACTATTTTGGAAATAATTGTAATAGCTAAACTAAA
*
1083133 TTTGTTAACTATTTTGGAAATAATTGTAATGGCTAAACTAAA
1 TTTGTTAACTATTTTGGAAATAATTGTAATAGCTAAACTAAA
1083175 TT
1 TT
1083177 GTTTTACTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTGTTAACTATTTTGGAAATAATTGTAATAGCTAAACTAAA
Found at i:1083159 original size:22 final size:22
Alignment explanation
Indices: 1083092--1083159 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1083082 TCTTGTTGCT
1083092 TTGTTAACTATTTTGGAAATAA
1 TTGTTAACTATTTTGGAAATAA
**
1083114 TTG-TAA-TA-GCT--AAACTAAA
1 TTGTTAACTATTTTGGAAA-T-AA
1083133 TTTGTTAACTATTTTGGAAATAA
1 -TTGTTAACTATTTTGGAAATAA
1083156 TTGT
1 TTGT
1083160 AATGGCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 3 0.09
18 1 0.03
19 3 0.09
20 5 0.15
21 6 0.18
22 9 0.26
23 3 0.09
24 1 0.03
25 3 0.09
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (22 bp):
TTGTTAACTATTTTGGAAATAA
Found at i:1086375 original size:57 final size:57
Alignment explanation
Indices: 1086277--1086478 Score: 291
Period size: 57 Copynumber: 3.5 Consensus size: 57
1086267 TGACATTGAT
* * *
1086277 TGTGCAAAAAGTTAAGAAATTCATAATTAGTTTAT-ATATTTCTGTATGGGCACTTTG
1 TGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGA-ATTTCTGTATGGGCACTTTG
* * **
1086334 TGTGCAAAAAGCTAAGAAATTTATACTAAGTGTATGAATTTCCATATGGGCACTTTG
1 TGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCTGTATGGGCACTTTG
**
1086391 TGTGCAAAAAGCTAAGAAATTCATACCAAGTGTATGAATTT-TCGTATGGGCACTTTG
1 TGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCT-GTATGGGCACTTTG
1086448 TGTGCAAAAAGCTAAGAAATTCATAATAAGT
1 TGTGCAAAAAGCTAAGAAATTCATAATAAGT
1086479 AGGTAAATTC
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
57 129 0.99
58 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (57 bp):
TGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCTGTATGGGCACTTTG
Found at i:1086511 original size:114 final size:113
Alignment explanation
Indices: 1086279--1086511 Score: 283
Period size: 114 Copynumber: 2.0 Consensus size: 113
1086269 ACATTGATTG
* ** *
1086279 TGCAAAAAGTTAAGAAATTCATAATTAGTTTATATATTTCTGTATGGGCACTTTGTGTGCAAAAA
1 TGCAAAAAGCTAAGAAATTCATAACAAGTGTATATATTTCTGTATGGGCACTTTGTGTGCAAAAA
* * * ** *
1086344 GCTAAGAAATTTATACTAAGTGTATGAATTTCCATATGGGCACTTTGTG
66 GCTAAGAAATTCATAATAAGTGTA-GAATTCCCATATGGGCACTGGGTA
*
1086393 TGCAAAAAGCTAAGAAATTCATACCAAGTGTATGA-ATTT-TCGTATGGGCACTTTGTGTGCAAA
1 TGCAAAAAGCTAAGAAATTCATAACAAGTGTAT-ATATTTCT-GTATGGGCACTTTGTGTGCAAA
* *
1086456 AAGCTAAGAAATTCATAATAAGTAGGTA-AATTCCCATATTGGCAGTGGGTA
64 AAGCTAAGAAATTCATAATAAGT--GTAGAATTCCCATATGGGCACTGGGTA
1086507 TGCAA
1 TGCAA
1086512 CCCACGTAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
113 1 0.01
114 97 0.95
115 1 0.01
116 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (113 bp):
TGCAAAAAGCTAAGAAATTCATAACAAGTGTATATATTTCTGTATGGGCACTTTGTGTGCAAAAA
GCTAAGAAATTCATAATAAGTGTAGAATTCCCATATGGGCACTGGGTA
Found at i:1088574 original size:23 final size:23
Alignment explanation
Indices: 1088541--1088587 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1088531 AGAAGCTAGC
1088541 AAGGCTCAACTCAGCGTGTGGCG
1 AAGGCTCAACTCAGCGTGTGGCG
* *
1088564 AAGGCTTAACTCCGCGTGTGGCG
1 AAGGCTCAACTCAGCGTGTGGCG
1088587 A
1 A
1088588 CACAAGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (23 bp):
AAGGCTCAACTCAGCGTGTGGCG
Found at i:1088860 original size:37 final size:37
Alignment explanation
Indices: 1088810--1088892 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
1088800 GAGATAAAAT
*
1088810 CTTCGAGATTTGGCTATCACTTAGTTGTTTGCTTAAC
1 CTTCGAGAGTTGGCTATCACTTAGTTGTTTGCTTAAC
*
1088847 CTTCGAGAGTTGGCTATCACTTAGTTGTTTGCTTAAT
1 CTTCGAGAGTTGGCTATCACTTAGTTGTTTGCTTAAC
*
1088884 GTTCGAGAG
1 CTTCGAGAG
1088893 AGTTAAGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (37 bp):
CTTCGAGAGTTGGCTATCACTTAGTTGTTTGCTTAAC
Found at i:1097025 original size:23 final size:23
Alignment explanation
Indices: 1096992--1097055 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1096982 TAGCTCATAT
1096992 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
** * **
1097015 ATTTGCACCGAAATGCCGGGTAG
1 AAATGCACCGAAGTGCCACGTAG
1097038 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1097056 TATAAGATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1104511 original size:34 final size:34
Alignment explanation
Indices: 1104473--1104540 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1104463 TGAAATTCAT
* *
1104473 AGGTATCGATACCTGCCTGTG-TGTATCGATACAC
1 AGGTATCGATACATCCCTG-GATGTATCGATACAC
*
1104507 AGGTATCGGTACATCCCTGGATGTATCGATACAC
1 AGGTATCGATACATCCCTGGATGTATCGATACAC
1104541 CATGAAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (34 bp):
AGGTATCGATACATCCCTGGATGTATCGATACAC
Found at i:1108470 original size:2 final size:2
Alignment explanation
Indices: 1108463--1108503 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1108453 ACTTTAATGT
*
1108463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1108504 GCTTGCATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1108592 original size:2 final size:2
Alignment explanation
Indices: 1108585--1108614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1108575 TATTTAAGTA
1108585 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
1108615 TGATATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1113875 original size:30 final size:30
Alignment explanation
Indices: 1113835--1114044 Score: 165
Period size: 30 Copynumber: 6.8 Consensus size: 30
1113825 GGCACAAGTT
* *
1113835 TGCTAAGAAATGAATAAAGTGAATGATACA
1 TGCTATGAAATAAATAAAGTGAATGATACA
* * *
1113865 -GTCTATGAAATAAAAAAAAAAGTGAGTGGTACA
1 TG-CTATGAAAT---AAATAAAGTGAATGATACA
* * **
1113898 TGCTATGAAATAAATAAAATGAAAGGCACAA
1 TGCTATGAAATAAATAAAGTGAATGATAC-A
1113929 GTTTGCT-TGAAATAAATAAAGTGAATGATACA
1 ---TGCTATGAAATAAATAAAGTGAATGATACA
* *
1113961 TGCTATGAAATAAAAAGAAGTGAGTGGA-ACA
1 TGCTATGAAATAAATA-AAGTGAAT-GATACA
* * * *
1113992 TGCTATGAAATAAATGAATTTAATGGTACA
1 TGCTATGAAATAAATAAAGTGAATGATACA
*
1114022 TGCTATGAAATGAATAAAGTGAA
1 TGCTATGAAATAAATAAAGTGAA
1114045 AGGAACATGT
Statistics
Matches: 141, Mismatches: 26, Indels: 26
0.73 0.13 0.13
Matches are distributed among these distances:
29 6 0.04
30 58 0.41
31 25 0.18
32 3 0.02
33 44 0.31
34 5 0.04
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.25
Consensus pattern (30 bp):
TGCTATGAAATAAATAAAGTGAATGATACA
Found at i:1113887 original size:33 final size:33
Alignment explanation
Indices: 1113850--1114005 Score: 102
Period size: 33 Copynumber: 4.9 Consensus size: 33
1113840 AGAAATGAAT
1113850 AAAGTGAATGATACA-GTCTATGAAATAAAAAAA
1 AAAGTGAATGATACATG-CTATGAAATAAAAAAA
* *
1113883 AAAGTGAGTGGTACATGCTATGAAATAAATAAAA
1 AAAGTGAATGATACATGCTATGAAATAAA-AAAA
* * *
1113917 TGAAAG-GCACAAG-T--TTGCT-TGAAAT---AAAT
1 --AAAGTG-A-ATGATACATGCTATGAAATAAAAAAA
1113946 AAAGTGAATGATACATGCTATGAAAT--AAAAA
1 AAAGTGAATGATACATGCTATGAAATAAAAAAA
* *
1113977 GAAGTGAGTGGA-ACATGCTATGAAATAAA
1 AAAGTGAAT-GATACATGCTATGAAATAAA
1114006 TGAATTTAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
26 2 0.02
27 6 0.06
28 1 0.01
29 7 0.07
30 6 0.06
31 24 0.25
32 2 0.02
33 32 0.33
34 9 0.09
35 1 0.01
36 6 0.06
37 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (33 bp):
AAAGTGAATGATACATGCTATGAAATAAAAAAA
Found at i:1113973 original size:26 final size:27
Alignment explanation
Indices: 1113942--1114010 Score: 70
Period size: 31 Copynumber: 2.4 Consensus size: 27
1113932 TGCTTGAAAT
1113942 AAATAAAGTGAATGA-T-ACATGCTATG
1 AAATAAA-TGAATGAGTGACATGCTATG
*
1113968 AAATAAAAAGAAGTGAGTGGAACATGCTATG
1 AAAT-AAATGAA-TGAGT-G-ACATGCTATG
1113999 AAATAAATGAAT
1 AAATAAATGAAT
1114011 TTAATGGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
26 7 0.20
27 6 0.17
28 1 0.03
29 1 0.03
30 6 0.17
31 14 0.40
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (27 bp):
AAATAAATGAATGAGTGACATGCTATG
Found at i:1114053 original size:30 final size:30
Alignment explanation
Indices: 1113803--1114053 Score: 150
Period size: 30 Copynumber: 8.0 Consensus size: 30
1113793 TTACATTGGC
* *
1113803 CTATGAAATAAATAAAATGAAAGGCACAAGTTTG
1 CTATGAAATAAATAAAGTGAAAGGAAC-A---TG
* * *
1113837 CTAAGAAATGAATAAAGTG-AATGATACA-G
1 CTATGAAATAAATAAAGTGAAAGGA-ACATG
* ** *
1113866 TCTATGAAATAAAAAAAAAAGTGAGTGGTACATG
1 -CTATGAAAT---AAATAAAGTGAAAGGAACATG
* *
1113900 CTATGAAATAAATAAAATGAAAGGCACAAGTTTG
1 CTATGAAATAAATAAAGTGAAAGGAAC-A---TG
*
1113934 CT-TGAAATAAATAAAGTG-AATGATACATG
1 CTATGAAATAAATAAAGTGAAAGGA-ACATG
* **
1113963 CTATGAAATAAAAAGAAGTGAGTGGAACATG
1 CTATGAAATAAATA-AAGTGAAAGGAACATG
* * * * *
1113994 CTATGAAATAAATGAATTTAATGGTACATG
1 CTATGAAATAAATAAAGTGAAAGGAACATG
*
1114024 CTATGAAATGAATAAAGTGAAAGGAACATG
1 CTATGAAATAAATAAAGTGAAAGGAACATG
1114054 TCTGATATGA
Statistics
Matches: 166, Mismatches: 36, Indels: 34
0.70 0.15 0.14
Matches are distributed among these distances:
29 5 0.03
30 67 0.40
31 23 0.14
32 6 0.04
33 41 0.25
34 24 0.14
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATGAAATAAATAAAGTGAAAGGAACATG
Found at i:1117984 original size:29 final size:29
Alignment explanation
Indices: 1117929--1117984 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1117919 AAATTGTTGA
* *
1117929 TTAGTGACCAAAATAAAAATTTTGAAAGT
1 TTAGTGACCAAAATAAAAACTTAGAAAGT
* * *
1117958 TTAGTGGCCAAAGTATAAACTTAGAAA
1 TTAGTGACCAAAATAAAAACTTAGAAA
1117985 AGTTCAAGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (29 bp):
TTAGTGACCAAAATAAAAACTTAGAAAGT
Found at i:1119249 original size:30 final size:30
Alignment explanation
Indices: 1119177--1119444 Score: 229
Period size: 30 Copynumber: 8.7 Consensus size: 30
1119167 TTTACAATGG
* *
1119177 GCTATGAAATAAATAAAATGAAAGGCACAAGTTT
1 GCTATGAAATAAATAAAATGAATGGTAC-A---T
* * *
1119211 GCTATGAAATGAATAAAGTGAATGATACAT
1 GCTATGAAATAAATAAAATGAATGGTACAT
*
1119241 GC-ATTGAAATAAA-AAAATGAGTGGTACAT
1 GCTA-TGAAATAAATAAAATGAATGGTACAT
* *
1119270 GCTAAGAAATAAA-AAAATGAGTGGTACAT
1 GCTATGAAATAAATAAAATGAATGGTACAT
*
1119299 GCTATGAAATAAATAAAATGGAA-GGCACAAATTT
1 GCTATGAAATAAATAAAAT-GAATGGTAC--A--T
* * * *
1119333 GTTATGAAATGAATAAAGTGAATGATACAT
1 GCTATGAAATAAATAAAATGAATGGTACAT
* * *
1119363 GTTATGAAATAAAAAAAATGAGTGGTACAT
1 GCTATGAAATAAATAAAATGAATGGTACAT
* * *
1119393 GCTATGAAATAAATGAAGTTAATGGTACAT
1 GCTATGAAATAAATAAAATGAATGGTACAT
* *
1119423 GCTATGAAATGAATAAAGTGAA
1 GCTATGAAATAAATAAAATGAA
1119445 AGGCACGGGT
Statistics
Matches: 193, Mismatches: 32, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
29 52 0.27
30 90 0.47
31 2 0.01
32 2 0.01
33 4 0.02
34 43 0.22
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (30 bp):
GCTATGAAATAAATAAAATGAATGGTACAT
Found at i:1119463 original size:64 final size:61
Alignment explanation
Indices: 1119177--1119466 Score: 221
Period size: 64 Copynumber: 4.7 Consensus size: 61
1119167 TTTACAATGG
* * *
1119177 GCTATGAAATAAATAAAATGAAAGGCACAAGTTTGCTATGAAATGAATAAAGTGAATGATACAT
1 GCTATGAAATAAATAAAATGAAAGGCAC---TTTGATATGAAATAAATAAAGTGAATGGTACAT
** * * * * * *
1119241 GC-ATTGAAATAAA-AAAATGAGTGGTAC-ATGCTAAGAAATAAA-AAAATGAGTGGTACAT
1 GCTA-TGAAATAAATAAAATGAAAGGCACTTTGATATGAAATAAATAAAGTGAATGGTACAT
* * * *
1119299 GCTATGAAATAAATAAAATGGAAGGCACAAATTTGTTATGAAATGAATAAAGTGAATGATACAT
1 GCTATGAAATAAATAAAATGAAAGGCAC---TTTGATATGAAATAAATAAAGTGAATGGTACAT
* * ** * * * * *
1119363 GTTATGAAATAAAAAAAATGAGTGGTAC-ATGCTATGAAATAAATGAAGTTAATGGTACAT
1 GCTATGAAATAAATAAAATGAAAGGCACTTTGATATGAAATAAATAAAGTGAATGGTACAT
* *
1119423 GCTATGAAATGAATAAAGTGAAAGGCACGGGTTTGATATGAAAT
1 GCTATGAAATAAATAAAATGAAAGGCAC---TTTGATATGAAAT
1119467 GGAAATGTGC
Statistics
Matches: 173, Mismatches: 41, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
58 24 0.14
59 23 0.13
60 47 0.27
63 23 0.13
64 56 0.32
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (61 bp):
GCTATGAAATAAATAAAATGAAAGGCACTTTGATATGAAATAAATAAAGTGAATGGTACAT
Found at i:1119466 original size:94 final size:91
Alignment explanation
Indices: 1119266--1119446 Score: 215
Period size: 94 Copynumber: 2.0 Consensus size: 91
1119256 AATGAGTGGT
* *
1119266 ACATGCTAAGAAATAAAAAAATGAGTGGTACATGCTATGAAATAAATAAAATGGAAGGCACAAAT
1 ACATGATATGAAATAAAAAAATGAGTGGTACATGCTATGAAATAAATAAAATGGAAGGCAC-AA-
* * *
1119331 TTGTTATGAAATGAATAAAGTGAATGAT
64 TTGCTATGAAATGAATAAAGTGAAAGAC
* * * * *
1119359 ACATGTTATGAAATAAAAAAAATGAGTGGTACATGCTATGAAATAAATGAAGT-TAATGGTAC-A
1 ACATGATATGAAAT-AAAAAAATGAGTGGTACATGCTATGAAATAAATAAAATGGAA-GGCACAA
1119422 -TGCTATGAAATGAATAAAGTGAAAG
64 TTGCTATGAAATGAATAAAGTGAAAG
1119447 GCACGGGTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
90 23 0.29
92 1 0.01
93 14 0.18
94 40 0.51
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (91 bp):
ACATGATATGAAATAAAAAAATGAGTGGTACATGCTATGAAATAAATAAAATGGAAGGCACAATT
GCTATGAAATGAATAAAGTGAAAGAC
Found at i:1121745 original size:28 final size:28
Alignment explanation
Indices: 1121652--1121745 Score: 66
Period size: 30 Copynumber: 3.2 Consensus size: 28
1121642 CCTTCTTTTC
1121652 CCATCCTTTTTACTTTTCATTAACTCCT
1 CCATCCTTTTTACTTTTCATTAACTCCT
* ** * *
1121680 CCA-CACAATCATATCATTTT-TTTATATTCTCT
1 CCATC-C-TTTTTA-C-TTTTCATTA-ACTC-CT
1121712 CTCATCCTTTTTACTTTTCATTAACTCCT
1 C-CATCCTTTTTACTTTTCATTAACTCCT
1121741 CCATC
1 CCATC
1121746 ACATCTCTCC
Statistics
Matches: 47, Mismatches: 10, Indels: 18
0.63 0.13 0.24
Matches are distributed among these distances:
27 1 0.02
28 8 0.17
29 6 0.13
30 11 0.23
31 11 0.23
32 6 0.13
33 3 0.06
34 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (28 bp):
CCATCCTTTTTACTTTTCATTAACTCCT
Found at i:1130415 original size:20 final size:19
Alignment explanation
Indices: 1130390--1130443 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1130380 GCGAAATAAA
1130390 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1130410 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1130430 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1130444 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1130518 original size:20 final size:20
Alignment explanation
Indices: 1130493--1130545 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1130483 GATTTTCCAT
*
1130493 AATCGCAACGCGAATAT-TAA
1 AATCGCAACGCGAACATAT-A
1130513 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
*
1130533 AATTGCAACGCGA
1 AATCGCAACGCGA
1130546 TTATGATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:1130598 original size:20 final size:20
Alignment explanation
Indices: 1130566--1130784 Score: 233
Period size: 20 Copynumber: 10.8 Consensus size: 20
1130556 CGTAACGAGT
*
1130566 ATCCGTAAAATCGCAACGCGT
1 ATCCGT-AAATCGCAACGCGA
1130587 ATCCGTAAATCGCAACGAC-A
1 ATCCGTAAATCGCAACG-CGA
* *
1130607 ATACGTAAAATCGCAACGCGT
1 ATCCGT-AAATCGCAACGCGA
**
1130628 ATCCGTAAATCGCAACTAGA
1 ATCCGTAAATCGCAACGCGA
* *
1130648 ATACGTAAATCGCAACGCGT
1 ATCCGTAAATCGCAACGCGA
* *
1130668 ATCTGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGCGA
* * *
1130688 ATACGTAAATCGCAATGCGT
1 ATCCGTAAATCGCAACGCGA
* *
1130708 ATCCGTAAATCGCAATGTGA
1 ATCCGTAAATCGCAACGCGA
* *
1130728 ATACGTAAATCGCAATGCGA
1 ATCCGTAAATCGCAACGCGA
* *
1130748 ATACGTAAATCGCAATGCGA
1 ATCCGTAAATCGCAACGCGA
*
1130768 ATCTGTAAATCGCAACG
1 ATCCGTAAATCGCAACG
1130785 AGATTCTGAC
Statistics
Matches: 167, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
20 144 0.86
21 23 0.14
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGCGA
Found at i:1130669 original size:40 final size:40
Alignment explanation
Indices: 1130573--1130784 Score: 277
Period size: 40 Copynumber: 5.3 Consensus size: 40
1130563 AGTATCCGTA
* *
1130573 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGT
1130613 AAAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGT
1 -AAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGT
* *
1130654 AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGT
* *
1130694 AAATCGCAATGCGTATCCGTAAATCGCAA-TGTGAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACT-AGAATACGT
* * * *
1130734 AAATCGCAATGCGAATACGTAAATCGCAA-TGCGAAT-CTGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACT-AGAATAC-GT
1130774 AAATCGCAACG
1 AAATCGCAACG
1130785 AGATTCTGAC
Statistics
Matches: 157, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.01
40 118 0.75
41 38 0.24
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACTAGAATACGT
Found at i:1131666 original size:24 final size:24
Alignment explanation
Indices: 1131639--1131692 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1131629 GTATTCGAAA
1131639 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1131663 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1131687 TTTGAT
1 TTTGAT
1131693 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1134151 original size:20 final size:20
Alignment explanation
Indices: 1134108--1134156 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1134098 GATATTCATT
* * *
1134108 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCAGAAA
*
1134128 TGACTATCGCAACGCATAAA
1 TGACTATCGCAACGCAGAAA
1134148 TGACTATCG
1 TGACTATCG
1134157 TAATGAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TGACTATCGCAACGCAGAAA
Found at i:1134190 original size:19 final size:19
Alignment explanation
Indices: 1134166--1134207 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1134156 GTAATGAGAG
1134166 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1134185 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1134204 AATC
1 AATC
1134208 ACAACGAGTT
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:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1134476 original size:20 final size:20
Alignment explanation
Indices: 1134451--1134505 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1134441 AGACATTCAT
*
1134451 TTGACTATCACAATGCGGAA
1 TTGACTATCGCAATGCGGAA
* *
1134471 TTGACTATCGCAACGTGGAA
1 TTGACTATCGCAATGCGGAA
*
1134491 ATGACTATCGCAATG
1 TTGACTATCGCAATG
1134506 AGAGAATCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (20 bp):
TTGACTATCGCAATGCGGAA
Found at i:1134521 original size:344 final size:344
Alignment explanation
Indices: 1133887--1134536 Score: 1201
Period size: 344 Copynumber: 1.9 Consensus size: 344
1133877 GCCATCACAA
*
1133887 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAACCGGCTTCACCTTT
1 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
* *
1133952 TGGGACTGTTAACTTAGGTGATTTTTAAATGTAAACGTTGTATTATGTGTATATTATGTGTGAAC
66 TGGGACTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
1134017 TTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTATGATAAGTTCAG
131 TTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTATGATAAGTTCAG
* * *
1134082 TTGTTATCACTTATTAGATATTCATTTGACTATCGCAATGCGGAATTGACTATCGCAACGCATAA
196 TTGTTATCACTTATTAGACATTCATTTGACTATCACAATGCGGAATTGACTATCGCAACGCAGAA
* *
1134147 ATGACTATCGTAATGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCACAA
261 ATGACTATCGCAATGAGAGAATCACAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCACAA
1134212 CGAGTTCGCATTGCGATTT
326 CGAGTTCGCATTGCGATTT
1134231 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
1 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
1134296 TGGGACTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
66 TGGGACTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
*
1134361 TTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCAG
131 TTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTATGATAAGTTCAG
**
1134426 TTGTTATCACTTATTAGACATTCATTTGACTATCACAATGCGGAATTGACTATCGCAACGTGGAA
196 TTGTTATCACTTATTAGACATTCATTTGACTATCACAATGCGGAATTGACTATCGCAACGCAGAA
1134491 ATGACTATCGCAATGAGAGAATCACAATGCGAAATGAAAATCGCAA
261 ATGACTATCGCAATGAGAGAATCACAATGCGAAATGAAAATCGCAA
1134537 CGAGTGAATC
Statistics
Matches: 295, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
344 295 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (344 bp):
TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
TGGGACTATTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
TTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTATGATAAGTTCAG
TTGTTATCACTTATTAGACATTCATTTGACTATCACAATGCGGAATTGACTATCGCAACGCAGAA
ATGACTATCGCAATGAGAGAATCACAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCACAA
CGAGTTCGCATTGCGATTT
Found at i:1134565 original size:34 final size:33
Alignment explanation
Indices: 1134488--1134572 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
1134478 TCGCAACGTG
** *
1134488 GAAATGACTATCGCAATGAGAGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
* *
1134521 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
1134554 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
1134573 CGAAACTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.63
34 17 0.37
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:1134603 original size:19 final size:19
Alignment explanation
Indices: 1134581--1134725 Score: 192
Period size: 19 Copynumber: 7.8 Consensus size: 19
1134571 CGCGAAACTA
*
1134581 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
1134600 ATTTTTGTATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
1134618 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1134634 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1134653 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1134672 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1134691 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
1134710 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
1134726 AGTCTGTTTT
Statistics
Matches: 112, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
14 6 0.05
16 6 0.05
17 3 0.03
18 4 0.04
19 73 0.65
20 20 0.18
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:1134846 original size:14 final size:14
Alignment explanation
Indices: 1134827--1134863 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1134817 CATCAATTAA
1134827 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1134841 ACAAATCATCTTTT
1 ACAAATCAACATTT
1134855 ACAAATCAA
1 ACAAATCAA
1134864 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1136202 original size:20 final size:20
Alignment explanation
Indices: 1136177--1136366 Score: 211
Period size: 20 Copynumber: 9.4 Consensus size: 20
1136167 TAAAAATCGT
*
1136177 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATACGC
*
1136197 GTTGCGATTTTACGTATA-GTC
1 GTTGCGA-TTTACGGATACG-C
1136218 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
1136238 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
* *
1136258 ATTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* * * * *
1136278 ATTGAGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
*
1136298 GTTGCGATTTACGGATACGT
1 GTTGCGATTTACGGATACGC
1136318 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1136338 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACGC
1136359 GTTGCGAT
1 GTTGCGAT
1136367 AGTCAGAATC
Statistics
Matches: 142, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
20 106 0.75
21 36 0.25
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1136263 original size:40 final size:40
Alignment explanation
Indices: 1136177--1136366 Score: 245
Period size: 40 Copynumber: 4.7 Consensus size: 40
1136167 TAAAAATCGT
* *
1136177 GTTGCGATTTATGGATACGCGTTGCGATTTTACGTATAGTC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATACTC
* *
1136218 GTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATACTC
* * * * *
1136258 ATTGCGATTTACAGATACGCATTGAGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATACTC
* * *
1136298 GTTGCGATTTACGGATACGTGTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATACTC
*
1136338 GTTGCGATTTTACGGATACTCGTTGCGAT
1 GTTGCGA-TTTACGGATACGCGTTGCGAT
1136367 AGTCAGAATC
Statistics
Matches: 131, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
40 87 0.66
41 44 0.34
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGTATACTC
Found at i:1138796 original size:38 final size:38
Alignment explanation
Indices: 1138740--1138816 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
1138730 CCCTTCAATT
1138740 TCTAAGTTGCTATTTGTGAATAAAACCATGGGATCTAA
1 TCTAAGTTGCTATTTGTGAATAAAACCATGGGATCTAA
*
1138778 TCTATGTTGCT-TTCTGTGAATAAAACCATGGGATCTAA
1 TCTAAGTTGCTATT-TGTGAATAAAACCATGGGATCTAA
1138816 T
1 T
1138817 GGACCAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (38 bp):
TCTAAGTTGCTATTTGTGAATAAAACCATGGGATCTAA
Found at i:1139079 original size:60 final size:60
Alignment explanation
Indices: 1138993--1139109 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
1138983 GCAAAAATGG
* * * *
1138993 TCCCCCAACTATAGGATATTCCTTTGTTGAGTCCCCCAACTATTAAAAGTTATAAAATAT
1 TCCCCCAACTATAGAATATTCCTTTGTTGAGTCCCCCAACTAGTAAAAATTACAAAATAT
* * *
1139053 TCCCCCAACTATAGAATGTTGCTTTGTTGAGTCCCTCAACTAGTAAAAATTACAAAA
1 TCCCCCAACTATAGAATATTCCTTTGTTGAGTCCCCCAACTAGTAAAAATTACAAAA
1139110 ATGGTCACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (60 bp):
TCCCCCAACTATAGAATATTCCTTTGTTGAGTCCCCCAACTAGTAAAAATTACAAAATAT
Found at i:1139385 original size:60 final size:59
Alignment explanation
Indices: 1139321--1139442 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 59
1139311 AACACAATGA
* * *
1139321 ATAGTCAGGTGACCATTTTGTAATTTTTAATAGTCAAGGGACTCAACAAAGCAATATCCT
1 ATAGTCAGGGGACCATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAA-AAATATCCT
* * ** *
1139381 ATAGTCGGGGGACCATTTTGTAACTTTTAATATTCGGGGGACTCAATAAAAAATATCCT
1 ATAGTCAGGGGACCATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAAAATATCCT
1139440 ATA
1 ATA
1139443 ATTGAGGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
59 11 0.20
60 43 0.80
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (59 bp):
ATAGTCAGGGGACCATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAAAATATCCT
Found at i:1139738 original size:35 final size:35
Alignment explanation
Indices: 1139691--1139776 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1139681 AAAACAATCA
* * *
1139691 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
1139726 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
1139761 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
1139777 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1139770 original size:21 final size:21
Alignment explanation
Indices: 1139745--1139787 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1139735 TTCTAAACCC
1139745 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1139766 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1139787 T
1 T
1139788 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:1139934 original size:17 final size:17
Alignment explanation
Indices: 1139908--1139940 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1139898 TATTAATGTA
1139908 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
1139926 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
1139941 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:1140628 original size:126 final size:126
Alignment explanation
Indices: 1140403--1140646 Score: 407
Period size: 126 Copynumber: 1.9 Consensus size: 126
1140393 AATTTTCTTC
* * *
1140403 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTAAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTAAGAT
*
1140468 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATA
* * * * *
1140529 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTAAGAT
1140594 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
1140647 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (126 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTAAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATA
Found at i:1141237 original size:12 final size:12
Alignment explanation
Indices: 1141216--1141246 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1141206 GTGACCATTA
*
1141216 CTATACTTTATC
1 CTATATTTTATC
1141228 CTATATTTTATC
1 CTATATTTTATC
1141240 CTATATT
1 CTATATT
1141247 CTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (12 bp):
CTATATTTTATC
Found at i:1146757 original size:6 final size:6
Alignment explanation
Indices: 1146746--1146822 Score: 86
Period size: 6 Copynumber: 12.8 Consensus size: 6
1146736 ATCAGCATTT
* *
1146746 ATATAC ATATAC ATATAC ATATAG ATATAC ATATAC ATACATAC ATATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT--ATAC ATATAC
* *
1146796 ATATA- A-ATAC ATATAT ATATAT ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
1146823 TAATGAGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.05
5 2 0.03
6 52 0.83
8 6 0.10
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:1146813 original size:4 final size:4
Alignment explanation
Indices: 1146745--1146824 Score: 70
Period size: 4 Copynumber: 20.0 Consensus size: 4
1146735 AATCAGCATT
* * * * * * * *
1146745 TATA TACA TATA CATA TACA TATA GATA TACA TATA CATA CATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
1146793 TATA TATA AATA CATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA
1146825 ATGAGAAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (4 bp):
TATA
Found at i:1147723 original size:60 final size:60
Alignment explanation
Indices: 1147609--1147726 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
1147599 GATCAAATTG
* * * *
1147609 TAACTATTAATAGTCGGAGGACTTAACAATGCATTGTCCTATAGTCGGTGGACCATTTTA
1 TAACTATTAATAGTCAGAGGACTCAACAATGCATTGTCATATAGTCGGTAGACCATTTTA
*
1147669 TAACTTTTAATAGTCTAGA-GACTCAACAGA-GCATTGTCATATAGTCGAG-AGACCATTT
1 TAACTATTAATAGTC-AGAGGACTCAACA-ATGCATTGTCATATAGTCG-GTAGACCATTT
1147727 GTGTACTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (60 bp):
TAACTATTAATAGTCAGAGGACTCAACAATGCATTGTCATATAGTCGGTAGACCATTTTA
Found at i:1150066 original size:2 final size:2
Alignment explanation
Indices: 1150059--1150114 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1150049 ATCTTAATTA
1150059 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
1150101 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1150115 TAAAATCAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1151688 original size:24 final size:24
Alignment explanation
Indices: 1151661--1151715 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1151651 AAAATCTAGG
* *
1151661 TCAGAAATCAGAATTGAATTCAGA
1 TCAGAAATCAGAATAGAATTCAAA
**
1151685 TCAGGTATCAGAATAGAATTCAAA
1 TCAGAAATCAGAATAGAATTCAAA
1151709 TCA-AAAT
1 TCAGAAAT
1151716 TTAGATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (24 bp):
TCAGAAATCAGAATAGAATTCAAA
Found at i:1154768 original size:60 final size:59
Alignment explanation
Indices: 1154639--1154771 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 59
1154629 CATATGTTCA
* * * * * * *
1154639 TAAACTATAACCCTTATTTTAAATTTGTCTTTAAACTTTTAAATATTGTAATTTCATCC
1 TAAACTATGACCCTTATTTTAAACTAGTCCTTAAAATTTTAAACATTCTAATTTCATCC
* * *
1154698 TCAAAATATGACTCTTATTTTAAACTAGTCCTTAAAATTTTGAACATTCTAATTTCATCCC
1 T-AAACTATGACCCTTATTTTAAACTAGTCCTTAAAATTTTAAACATTCTAATTTCAT-CC
1154759 TAAACTATGACCC
1 TAAACTATGACCC
1154772 CTTTCTAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 1 0.02
60 56 0.93
61 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (59 bp):
TAAACTATGACCCTTATTTTAAACTAGTCCTTAAAATTTTAAACATTCTAATTTCATCC
Found at i:1154825 original size:12 final size:12
Alignment explanation
Indices: 1154805--1154840 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1154795 TTTAAATATT
*
1154805 CCAATTTCATCC
1 CCAAATTCATCC
1154817 CCAAATTCATCC
1 CCAAATTCATCC
1154829 CCAAATTCATCC
1 CCAAATTCATCC
1154841 AAATATGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.28
Consensus pattern (12 bp):
CCAAATTCATCC
Found at i:1158354 original size:20 final size:21
Alignment explanation
Indices: 1158331--1158384 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1158321 GAAAATTTTG
1158331 AAATTTTTTTAAAAATA-AAA
1 AAATTTTTTTAAAAATATAAA
* ** *
1158351 AAATATTAGTAAAATTATAAA
1 AAATTTTTTTAAAAATATAAA
1158372 AAATTGTTTTTAA
1 AAATT-TTTTTAA
1158385 CTATAAAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
20 13 0.52
21 7 0.28
22 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
AAATTTTTTTAAAAATATAAA
Done.